-
-
-
-
-
-
-
-
-
+
+
@@ -163,7 +156,7 @@
-
+
@@ -200,7 +193,7 @@
-
+
@@ -208,9 +201,9 @@
-
+
-
+
@@ -218,10 +211,10 @@
-
+
-
+
@@ -658,7 +651,8 @@
+ RESTRICTION: the glob-like pattern in the name attribute must have a "*"
+ only at the start or the end. -->
@@ -666,19 +660,23 @@
-
+
+
+
+
+
+
+
-
-
-
-
+
+
@@ -724,43 +722,6 @@
field first in an ascending sort and last in a descending sort.
-->
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-
-
-
-
-
-
- 7.3.0
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- ${solr.data.dir:}
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- ${solr.lock.type:native}
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- ${solr.ulog.dir:}
- ${solr.ulog.numVersionBuckets:65536}
-
-
-
-
- ${solr.autoCommit.maxTime:15000}
- false
-
-
-
-
-
- ${solr.autoSoftCommit.maxTime:-1}
-
-
-
-
-
-
-
-
-
-
-
-
-
- 1024
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- true
-
-
-
-
-
- 20
-
-
- 200
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- false
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- explicit
- 10
- edismax
- 0.075
-
- dvName^400
- authorName^180
- dvSubject^190
- dvDescription^180
- dvAffiliation^170
- title^130
- subject^120
- keyword^110
- topicClassValue^100
- dsDescriptionValue^90
- authorAffiliation^80
- publicationCitation^60
- producerName^50
- fileName^30
- fileDescription^30
- variableLabel^20
- variableName^10
- _text_^1.0
-
-
- dvName^200
- authorName^100
- dvSubject^100
- dvDescription^100
- dvAffiliation^100
- title^75
- subject^75
- keyword^75
- topicClassValue^75
- dsDescriptionValue^75
- authorAffiliation^75
- publicationCitation^75
- producerName^75
-
-
-
- isHarvested:false^25000
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- explicit
- json
- true
-
-
-
-
-
-
-
- explicit
-
-
-
-
-
- _text_
-
-
-
-
-
-
- true
- ignored_
- _text_
-
-
-
-
-
-
-
-
- text_general
-
-
-
-
-
- default
- _text_
- solr.DirectSolrSpellChecker
-
- internal
-
- 0.5
-
- 2
-
- 1
-
- 5
-
- 4
-
- 0.01
-
-
-
-
-
-
-
-
-
-
-
- default
- on
- true
- 10
- 5
- 5
- true
- true
- 10
- 5
-
-
- spellcheck
-
-
-
-
-
-
-
-
-
- true
-
-
- tvComponent
-
-
-
-
-
-
-
-
-
-
-
- true
- false
-
-
- terms
-
-
-
-
-
-
-
- string
-
-
-
-
-
- explicit
-
-
- elevator
-
-
-
-
-
-
-
-
-
-
- 100
-
-
-
-
-
-
-
- 70
-
- 0.5
-
- [-\w ,/\n\"']{20,200}
-
-
-
-
-
-
- ]]>
- ]]>
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- ,,
- ,,
- ,,
- ,,
- ,]]>
- ]]>
-
-
-
-
-
- 10
- .,!?
-
-
-
-
-
-
- WORD
-
-
- en
- US
-
-
-
-
-
-
-
-
-
-
-
-
-
- [^\w-\.]
- _
-
-
-
-
-
-
- yyyy-MM-dd'T'HH:mm:ss.SSSZ
- yyyy-MM-dd'T'HH:mm:ss,SSSZ
- yyyy-MM-dd'T'HH:mm:ss.SSS
- yyyy-MM-dd'T'HH:mm:ss,SSS
- yyyy-MM-dd'T'HH:mm:ssZ
- yyyy-MM-dd'T'HH:mm:ss
- yyyy-MM-dd'T'HH:mmZ
- yyyy-MM-dd'T'HH:mm
- yyyy-MM-dd HH:mm:ss.SSSZ
- yyyy-MM-dd HH:mm:ss,SSSZ
- yyyy-MM-dd HH:mm:ss.SSS
- yyyy-MM-dd HH:mm:ss,SSS
- yyyy-MM-dd HH:mm:ssZ
- yyyy-MM-dd HH:mm:ss
- yyyy-MM-dd HH:mmZ
- yyyy-MM-dd HH:mm
- yyyy-MM-dd
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- text/plain; charset=UTF-8
-
-
-
-
- ${velocity.template.base.dir:}
- ${velocity.solr.resource.loader.enabled:true}
- ${velocity.params.resource.loader.enabled:false}
-
-
-
-
- 5
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+ 9.7
+
+
+
+
+
+
+
+
+
+
+ ${solr.data.dir:}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ${solr.lock.type:native}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ${solr.ulog.dir:}
+ ${solr.ulog.numVersionBuckets:65536}
+
+
+
+
+ ${solr.autoCommit.maxTime:15000}
+ false
+
+
+
+
+
+ ${solr.autoSoftCommit.maxTime:-1}
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ${solr.max.booleanClauses:1024}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ true
+
+
+
+
+
+ 20
+
+
+ 200
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ false
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ explicit
+ 10
+
+ edismax
+ 0.075
+
+ dvName^400
+ authorName^180
+ dvSubject^190
+ dvDescription^180
+ dvAffiliation^170
+ title^130
+ subject^120
+ keyword^110
+ topicClassValue^100
+ dsDescriptionValue^90
+ authorAffiliation^80
+ publicationCitation^60
+ producerName^50
+ fileName^30
+ fileDescription^30
+ variableLabel^20
+ variableName^10
+ _text_^1.0
+
+
+ dvName^200
+ authorName^100
+ dvSubject^100
+ dvDescription^100
+ dvAffiliation^100
+ title^75
+ subject^75
+ keyword^75
+ topicClassValue^75
+ dsDescriptionValue^75
+ authorAffiliation^75
+ publicationCitation^75
+ producerName^75
+
+
+
+ isHarvested:false^25000
+
+
+
+
+
+
+
+ explicit
+ json
+ true
+
+
+
+
+
+
+ _text_
+
+
+
+
+
+
+ text_general
+
+
+
+
+
+ default
+ _text_
+ solr.DirectSolrSpellChecker
+
+ internal
+
+ 0.5
+
+ 2
+
+ 1
+
+ 5
+
+ 4
+
+ 0.01
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 100
+
+
+
+
+
+
+
+ 70
+
+ 0.5
+
+ [-\w ,/\n\"']{20,200}
+
+
+
+
+
+
+ ]]>
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ,,
+ ,,
+ ,,
+ ,,
+ ,]]>
+ ]]>
+
+
+
+
+
+ 10
+ .,!?
+
+
+
+
+
+
+ WORD
+
+
+ en
+ US
+
+
+
+
+
+
+
+
+
+
+
+
+ [^\w-\.]
+ _
+
+
+
+
+
+
+ yyyy-MM-dd['T'[HH:mm[:ss[.SSS]][z
+ yyyy-MM-dd['T'[HH:mm[:ss[,SSS]][z
+ yyyy-MM-dd HH:mm[:ss[.SSS]][z
+ yyyy-MM-dd HH:mm[:ss[,SSS]][z
+ [EEE, ]dd MMM yyyy HH:mm[:ss] z
+ EEEE, dd-MMM-yy HH:mm:ss z
+ EEE MMM ppd HH:mm:ss [z ]yyyy
+
+
+
+
+ java.lang.String
+ text_general
+
+ *_str
+ 256
+
+
+ true
+
+
+ java.lang.Boolean
+ booleans
+
+
+ java.util.Date
+ pdates
+
+
+ java.lang.Long
+ java.lang.Integer
+ plongs
+
+
+ java.lang.Number
+ pdoubles
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/conf/solr/8.11.1/update-fields.sh b/conf/solr/9.3.0/update-fields.sh
similarity index 100%
rename from conf/solr/8.11.1/update-fields.sh
rename to conf/solr/9.3.0/update-fields.sh
diff --git a/conf/vagrant/etc/shibboleth/attribute-map.xml b/conf/vagrant/etc/shibboleth/attribute-map.xml
deleted file mode 100644
index f6386b620f5..00000000000
--- a/conf/vagrant/etc/shibboleth/attribute-map.xml
+++ /dev/null
@@ -1,141 +0,0 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/conf/vagrant/etc/shibboleth/dataverse-idp-metadata.xml b/conf/vagrant/etc/shibboleth/dataverse-idp-metadata.xml
deleted file mode 100644
index 67225b5e670..00000000000
--- a/conf/vagrant/etc/shibboleth/dataverse-idp-metadata.xml
+++ /dev/null
@@ -1,298 +0,0 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- testshib.org
-
- TestShib Test IdP
- TestShib IdP. Use this as a source of attributes
- for your test SP.
- https://www.testshib.org/images/testshib-transp.png
-
-
-
-
-
-
-
- MIIEDjCCAvagAwIBAgIBADANBgkqhkiG9w0BAQUFADBnMQswCQYDVQQGEwJVUzEV
- MBMGA1UECBMMUGVubnN5bHZhbmlhMRMwEQYDVQQHEwpQaXR0c2J1cmdoMREwDwYD
- VQQKEwhUZXN0U2hpYjEZMBcGA1UEAxMQaWRwLnRlc3RzaGliLm9yZzAeFw0wNjA4
- MzAyMTEyMjVaFw0xNjA4MjcyMTEyMjVaMGcxCzAJBgNVBAYTAlVTMRUwEwYDVQQI
- EwxQZW5uc3lsdmFuaWExEzARBgNVBAcTClBpdHRzYnVyZ2gxETAPBgNVBAoTCFRl
- c3RTaGliMRkwFwYDVQQDExBpZHAudGVzdHNoaWIub3JnMIIBIjANBgkqhkiG9w0B
- AQEFAAOCAQ8AMIIBCgKCAQEArYkCGuTmJp9eAOSGHwRJo1SNatB5ZOKqDM9ysg7C
- yVTDClcpu93gSP10nH4gkCZOlnESNgttg0r+MqL8tfJC6ybddEFB3YBo8PZajKSe
- 3OQ01Ow3yT4I+Wdg1tsTpSge9gEz7SrC07EkYmHuPtd71CHiUaCWDv+xVfUQX0aT
- NPFmDixzUjoYzbGDrtAyCqA8f9CN2txIfJnpHE6q6CmKcoLADS4UrNPlhHSzd614
- kR/JYiks0K4kbRqCQF0Dv0P5Di+rEfefC6glV8ysC8dB5/9nb0yh/ojRuJGmgMWH
- gWk6h0ihjihqiu4jACovUZ7vVOCgSE5Ipn7OIwqd93zp2wIDAQABo4HEMIHBMB0G
- A1UdDgQWBBSsBQ869nh83KqZr5jArr4/7b+QazCBkQYDVR0jBIGJMIGGgBSsBQ86
- 9nh83KqZr5jArr4/7b+Qa6FrpGkwZzELMAkGA1UEBhMCVVMxFTATBgNVBAgTDFBl
- bm5zeWx2YW5pYTETMBEGA1UEBxMKUGl0dHNidXJnaDERMA8GA1UEChMIVGVzdFNo
- aWIxGTAXBgNVBAMTEGlkcC50ZXN0c2hpYi5vcmeCAQAwDAYDVR0TBAUwAwEB/zAN
- BgkqhkiG9w0BAQUFAAOCAQEAjR29PhrCbk8qLN5MFfSVk98t3CT9jHZoYxd8QMRL
- I4j7iYQxXiGJTT1FXs1nd4Rha9un+LqTfeMMYqISdDDI6tv8iNpkOAvZZUosVkUo
- 93pv1T0RPz35hcHHYq2yee59HJOco2bFlcsH8JBXRSRrJ3Q7Eut+z9uo80JdGNJ4
- /SJy5UorZ8KazGj16lfJhOBXldgrhppQBb0Nq6HKHguqmwRfJ+WkxemZXzhediAj
- Geka8nz8JjwxpUjAiSWYKLtJhGEaTqCYxCCX2Dw+dOTqUzHOZ7WKv4JXPK5G/Uhr
- 8K/qhmFT2nIQi538n6rVYLeWj8Bbnl+ev0peYzxFyF5sQA==
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- urn:mace:shibboleth:1.0:nameIdentifier
- urn:oasis:names:tc:SAML:2.0:nameid-format:transient
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- MIIEDjCCAvagAwIBAgIBADANBgkqhkiG9w0BAQUFADBnMQswCQYDVQQGEwJVUzEV
- MBMGA1UECBMMUGVubnN5bHZhbmlhMRMwEQYDVQQHEwpQaXR0c2J1cmdoMREwDwYD
- VQQKEwhUZXN0U2hpYjEZMBcGA1UEAxMQaWRwLnRlc3RzaGliLm9yZzAeFw0wNjA4
- MzAyMTEyMjVaFw0xNjA4MjcyMTEyMjVaMGcxCzAJBgNVBAYTAlVTMRUwEwYDVQQI
- EwxQZW5uc3lsdmFuaWExEzARBgNVBAcTClBpdHRzYnVyZ2gxETAPBgNVBAoTCFRl
- c3RTaGliMRkwFwYDVQQDExBpZHAudGVzdHNoaWIub3JnMIIBIjANBgkqhkiG9w0B
- AQEFAAOCAQ8AMIIBCgKCAQEArYkCGuTmJp9eAOSGHwRJo1SNatB5ZOKqDM9ysg7C
- yVTDClcpu93gSP10nH4gkCZOlnESNgttg0r+MqL8tfJC6ybddEFB3YBo8PZajKSe
- 3OQ01Ow3yT4I+Wdg1tsTpSge9gEz7SrC07EkYmHuPtd71CHiUaCWDv+xVfUQX0aT
- NPFmDixzUjoYzbGDrtAyCqA8f9CN2txIfJnpHE6q6CmKcoLADS4UrNPlhHSzd614
- kR/JYiks0K4kbRqCQF0Dv0P5Di+rEfefC6glV8ysC8dB5/9nb0yh/ojRuJGmgMWH
- gWk6h0ihjihqiu4jACovUZ7vVOCgSE5Ipn7OIwqd93zp2wIDAQABo4HEMIHBMB0G
- A1UdDgQWBBSsBQ869nh83KqZr5jArr4/7b+QazCBkQYDVR0jBIGJMIGGgBSsBQ86
- 9nh83KqZr5jArr4/7b+Qa6FrpGkwZzELMAkGA1UEBhMCVVMxFTATBgNVBAgTDFBl
- bm5zeWx2YW5pYTETMBEGA1UEBxMKUGl0dHNidXJnaDERMA8GA1UEChMIVGVzdFNo
- aWIxGTAXBgNVBAMTEGlkcC50ZXN0c2hpYi5vcmeCAQAwDAYDVR0TBAUwAwEB/zAN
- BgkqhkiG9w0BAQUFAAOCAQEAjR29PhrCbk8qLN5MFfSVk98t3CT9jHZoYxd8QMRL
- I4j7iYQxXiGJTT1FXs1nd4Rha9un+LqTfeMMYqISdDDI6tv8iNpkOAvZZUosVkUo
- 93pv1T0RPz35hcHHYq2yee59HJOco2bFlcsH8JBXRSRrJ3Q7Eut+z9uo80JdGNJ4
- /SJy5UorZ8KazGj16lfJhOBXldgrhppQBb0Nq6HKHguqmwRfJ+WkxemZXzhediAj
- Geka8nz8JjwxpUjAiSWYKLtJhGEaTqCYxCCX2Dw+dOTqUzHOZ7WKv4JXPK5G/Uhr
- 8K/qhmFT2nIQi538n6rVYLeWj8Bbnl+ev0peYzxFyF5sQA==
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- urn:mace:shibboleth:1.0:nameIdentifier
- urn:oasis:names:tc:SAML:2.0:nameid-format:transient
-
-
-
-
- TestShib Two Identity Provider
- TestShib Two
- http://www.testshib.org/testshib-two/
-
-
- Nate
- Klingenstein
- ndk@internet2.edu
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- TestShib Test SP
- TestShib SP. Log into this to test your machine.
- Once logged in check that all attributes that you expected have been
- released.
- https://www.testshib.org/images/testshib-transp.png
-
-
-
-
-
-
-
- MIIEPjCCAyagAwIBAgIBADANBgkqhkiG9w0BAQUFADB3MQswCQYDVQQGEwJVUzEV
- MBMGA1UECBMMUGVubnN5bHZhbmlhMRMwEQYDVQQHEwpQaXR0c2J1cmdoMSIwIAYD
- VQQKExlUZXN0U2hpYiBTZXJ2aWNlIFByb3ZpZGVyMRgwFgYDVQQDEw9zcC50ZXN0
- c2hpYi5vcmcwHhcNMDYwODMwMjEyNDM5WhcNMTYwODI3MjEyNDM5WjB3MQswCQYD
- VQQGEwJVUzEVMBMGA1UECBMMUGVubnN5bHZhbmlhMRMwEQYDVQQHEwpQaXR0c2J1
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- Ew9zcC50ZXN0c2hpYi5vcmcwggEiMA0GCSqGSIb3DQEBAQUAA4IBDwAwggEKAoIB
- AQDJyR6ZP6MXkQ9z6RRziT0AuCabDd3x1m7nLO9ZRPbr0v1LsU+nnC363jO8nGEq
- sqkgiZ/bSsO5lvjEt4ehff57ERio2Qk9cYw8XCgmYccVXKH9M+QVO1MQwErNobWb
- AjiVkuhWcwLWQwTDBowfKXI87SA7KR7sFUymNx5z1aoRvk3GM++tiPY6u4shy8c7
- vpWbVfisfTfvef/y+galxjPUQYHmegu7vCbjYP3On0V7/Ivzr+r2aPhp8egxt00Q
- XpilNai12LBYV3Nv/lMsUzBeB7+CdXRVjZOHGuQ8mGqEbsj8MBXvcxIKbcpeK5Zi
- JCVXPfarzuriM1G5y5QkKW+LAgMBAAGjgdQwgdEwHQYDVR0OBBYEFKB6wPDxwYrY
- StNjU5P4b4AjBVQVMIGhBgNVHSMEgZkwgZaAFKB6wPDxwYrYStNjU5P4b4AjBVQV
- oXukeTB3MQswCQYDVQQGEwJVUzEVMBMGA1UECBMMUGVubnN5bHZhbmlhMRMwEQYD
- VQQHEwpQaXR0c2J1cmdoMSIwIAYDVQQKExlUZXN0U2hpYiBTZXJ2aWNlIFByb3Zp
- ZGVyMRgwFgYDVQQDEw9zcC50ZXN0c2hpYi5vcmeCAQAwDAYDVR0TBAUwAwEB/zAN
- BgkqhkiG9w0BAQUFAAOCAQEAc06Kgt7ZP6g2TIZgMbFxg6vKwvDL0+2dzF11Onpl
- 5sbtkPaNIcj24lQ4vajCrrGKdzHXo9m54BzrdRJ7xDYtw0dbu37l1IZVmiZr12eE
- Iay/5YMU+aWP1z70h867ZQ7/7Y4HW345rdiS6EW663oH732wSYNt9kr7/0Uer3KD
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- Inh+vYSYngQB2sx9LGkR9KHaMKNIGCDehk93Xla4pWJx1w==
-
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- urn:oasis:names:tc:SAML:2.0:nameid-format:transient
- urn:mace:shibboleth:1.0:nameIdentifier
-
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- TestShib Two Service Provider
- TestShib Two
- http://www.testshib.org/testshib-two/
-
-
- Nate
- Klingenstein
- ndk@internet2.edu
-
-
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-
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-
diff --git a/conf/vagrant/etc/shibboleth/shibboleth2.xml b/conf/vagrant/etc/shibboleth/shibboleth2.xml
deleted file mode 100644
index 946e73bdf6a..00000000000
--- a/conf/vagrant/etc/shibboleth/shibboleth2.xml
+++ /dev/null
@@ -1,85 +0,0 @@
-
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diff --git a/conf/vagrant/etc/yum.repos.d/epel-apache-maven.repo b/conf/vagrant/etc/yum.repos.d/epel-apache-maven.repo
deleted file mode 100644
index 1e0f8200040..00000000000
--- a/conf/vagrant/etc/yum.repos.d/epel-apache-maven.repo
+++ /dev/null
@@ -1,15 +0,0 @@
-# Place this file in your /etc/yum.repos.d/ directory
-
-[epel-apache-maven]
-name=maven from apache foundation.
-baseurl=http://repos.fedorapeople.org/repos/dchen/apache-maven/epel-$releasever/$basearch/
-enabled=1
-skip_if_unavailable=1
-gpgcheck=0
-
-[epel-apache-maven-source]
-name=maven from apache foundation. - Source
-baseurl=http://repos.fedorapeople.org/repos/dchen/apache-maven/epel-$releasever/SRPMS
-enabled=0
-skip_if_unavailable=1
-gpgcheck=0
diff --git a/conf/vagrant/etc/yum.repos.d/shibboleth.repo b/conf/vagrant/etc/yum.repos.d/shibboleth.repo
deleted file mode 100644
index adf42185d8a..00000000000
--- a/conf/vagrant/etc/yum.repos.d/shibboleth.repo
+++ /dev/null
@@ -1,9 +0,0 @@
-[shibboleth]
-name=Shibboleth (rockylinux8)
-# Please report any problems to https://shibboleth.atlassian.net/jira
-type=rpm-md
-mirrorlist=https://shibboleth.net/cgi-bin/mirrorlist.cgi/rockylinux8
-gpgcheck=1
-gpgkey=https://shibboleth.net/downloads/service-provider/RPMS/repomd.xml.key
- https://shibboleth.net/downloads/service-provider/RPMS/cantor.repomd.xml.key
-enabled=1
diff --git a/conf/vagrant/var/lib/pgsql/data/pg_hba.conf b/conf/vagrant/var/lib/pgsql/data/pg_hba.conf
deleted file mode 100644
index e3244686066..00000000000
--- a/conf/vagrant/var/lib/pgsql/data/pg_hba.conf
+++ /dev/null
@@ -1,74 +0,0 @@
-# PostgreSQL Client Authentication Configuration File
-# ===================================================
-#
-# Refer to the "Client Authentication" section in the
-# PostgreSQL documentation for a complete description
-# of this file. A short synopsis follows.
-#
-# This file controls: which hosts are allowed to connect, how clients
-# are authenticated, which PostgreSQL user names they can use, which
-# databases they can access. Records take one of these forms:
-#
-# local DATABASE USER METHOD [OPTIONS]
-# host DATABASE USER CIDR-ADDRESS METHOD [OPTIONS]
-# hostssl DATABASE USER CIDR-ADDRESS METHOD [OPTIONS]
-# hostnossl DATABASE USER CIDR-ADDRESS METHOD [OPTIONS]
-#
-# (The uppercase items must be replaced by actual values.)
-#
-# The first field is the connection type: "local" is a Unix-domain socket,
-# "host" is either a plain or SSL-encrypted TCP/IP socket, "hostssl" is an
-# SSL-encrypted TCP/IP socket, and "hostnossl" is a plain TCP/IP socket.
-#
-# DATABASE can be "all", "sameuser", "samerole", a database name, or
-# a comma-separated list thereof.
-#
-# USER can be "all", a user name, a group name prefixed with "+", or
-# a comma-separated list thereof. In both the DATABASE and USER fields
-# you can also write a file name prefixed with "@" to include names from
-# a separate file.
-#
-# CIDR-ADDRESS specifies the set of hosts the record matches.
-# It is made up of an IP address and a CIDR mask that is an integer
-# (between 0 and 32 (IPv4) or 128 (IPv6) inclusive) that specifies
-# the number of significant bits in the mask. Alternatively, you can write
-# an IP address and netmask in separate columns to specify the set of hosts.
-#
-# METHOD can be "trust", "reject", "md5", "password", "gss", "sspi", "krb5",
-# "ident", "pam", "ldap" or "cert". Note that "password" sends passwords
-# in clear text; "md5" is preferred since it sends encrypted passwords.
-#
-# OPTIONS are a set of options for the authentication in the format
-# NAME=VALUE. The available options depend on the different authentication
-# methods - refer to the "Client Authentication" section in the documentation
-# for a list of which options are available for which authentication methods.
-#
-# Database and user names containing spaces, commas, quotes and other special
-# characters must be quoted. Quoting one of the keywords "all", "sameuser" or
-# "samerole" makes the name lose its special character, and just match a
-# database or username with that name.
-#
-# This file is read on server startup and when the postmaster receives
-# a SIGHUP signal. If you edit the file on a running system, you have
-# to SIGHUP the postmaster for the changes to take effect. You can use
-# "pg_ctl reload" to do that.
-
-# Put your actual configuration here
-# ----------------------------------
-#
-# If you want to allow non-local connections, you need to add more
-# "host" records. In that case you will also need to make PostgreSQL listen
-# on a non-local interface via the listen_addresses configuration parameter,
-# or via the -i or -h command line switches.
-#
-
-
-
-# TYPE DATABASE USER CIDR-ADDRESS METHOD
-
-# "local" is for Unix domain socket connections only
-local all all trust
-# IPv4 local connections:
-host all all 127.0.0.1/32 trust
-# IPv6 local connections:
-host all all ::1/128 trust
diff --git a/conf/vagrant/var/www/dataverse/error-documents/503.html b/conf/vagrant/var/www/dataverse/error-documents/503.html
deleted file mode 100644
index 95a7dea4107..00000000000
--- a/conf/vagrant/var/www/dataverse/error-documents/503.html
+++ /dev/null
@@ -1 +0,0 @@
-Custom "site is unavailable" 503 page.
diff --git a/doc/release-notes/6.0-release-notes.md b/doc/release-notes/6.0-release-notes.md
new file mode 100644
index 00000000000..df916216f5b
--- /dev/null
+++ b/doc/release-notes/6.0-release-notes.md
@@ -0,0 +1,300 @@
+# Dataverse 6.0
+
+This is a platform upgrade release. Payara, Solr, and Java have been upgraded. No features have been added to the Dataverse software itself. Only a handful of bugs were fixed.
+
+Thank you to all of the community members who contributed code, suggestions, bug reports, and other assistance across the project!
+
+## Release Highlights (Major Upgrades, Breaking Changes)
+
+This release contains major upgrades to core components. Detailed upgrade instructions can be found below.
+
+### Runtime
+
+- The required Java version has been increased from version 11 to 17.
+ - See PR #9764 for details.
+- Payara application server has been upgraded to version 6.2023.8.
+ - This is a required update.
+ - Please note that Payara Community 5 has reached [end of life](https://www.payara.fish/products/payara-platform-product-lifecycle/)
+ - See PR #9685 and PR #9795 for details.
+- Solr has been upgraded to version 9.3.0.
+ - See PR #9787 for details.
+- PostgreSQL 13 remains the tested and supported version.
+ - That said, the installer and Flyway have been upgraded to support PostgreSQL 14 and 15. See the [PostgreSQL](https://guides.dataverse.org/en/6.0/installation/prerequisites.html#postgresql) section of the Installation Guide and PR #9877 for details.
+
+### Development
+
+- Removal of Vagrant and Docker All In One (docker-aio), deprecated in Dataverse v5.14. See PR #9838 and PR #9685 for details.
+- All tests have been migrated to use JUnit 5 exclusively from now on. See PR #9796 for details.
+
+## Installation
+
+If this is a new installation, please follow our [Installation Guide](https://guides.dataverse.org/en/latest/installation/). Please don't be shy about [asking for help](https://guides.dataverse.org/en/latest/installation/intro.html#getting-help) if you need it!
+
+Once you are in production, we would be delighted to update our [map of Dataverse installations](https://dataverse.org/installations) around the world to include yours! Please [create an issue](https://github.com/IQSS/dataverse-installations/issues) or email us at support@dataverse.org to join the club!
+
+You are also very welcome to join the [Global Dataverse Community Consortium](https://dataversecommunity.global) (GDCC).
+
+## Upgrade Instructions
+
+Upgrading requires a maintenance window and downtime. Please plan ahead, create backups of your database, etc.
+
+These instructions assume that you've already upgraded through all the 5.x releases and are now running Dataverse 5.14.
+
+### Upgrade from Java 11 to Java 17
+
+Java 17 is now required for Dataverse. Solr can run under Java 11 or Java 17 but the latter is recommended. In preparation for the Java upgrade, stop both Dataverse/Payara and Solr.
+
+1. Undeploy Dataverse, if deployed, using the unprivileged service account.
+
+ `sudo -u dataverse /usr/local/payara5/bin/asadmin list-applications`
+
+ `sudo -u dataverse /usr/local/payara5/bin/asadmin undeploy dataverse-5.14`
+
+1. Stop Payara 5.
+
+ `sudo -u dataverse /usr/local/payara5/bin/asadmin stop-domain`
+
+1. Stop Solr 8.
+
+ `sudo systemctl stop solr.service`
+
+1. Install Java 17.
+
+ Assuming you are using RHEL or a derivative such as Rocky Linux:
+
+ `sudo yum install java-17-openjdk`
+
+1. Set Java 17 as the default.
+
+ Assuming you are using RHEL or a derivative such as Rocky Linux:
+
+ `sudo alternatives --config java`
+
+1. Test that Java 17 is the default.
+
+ `java -version`
+
+### Upgrade from Payara 5 to Payara 6
+
+If you are running Payara as a non-root user (and you should be!), **remember not to execute the commands below as root**. Use `sudo` to change to that user first. For example, `sudo -i -u dataverse` if `dataverse` is your dedicated application user.
+
+1. Download Payara 6.2023.8.
+
+ `curl -L -O https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2023.8/payara-6.2023.8.zip`
+
+1. Unzip it to /usr/local (or your preferred location).
+
+ `sudo unzip payara-6.2023.8.zip -d /usr/local/`
+
+1. Change ownership of the unzipped Payara to your "service" user ("dataverse" by default).
+
+ `sudo chown -R dataverse /usr/local/payara6`
+
+1. Undeploy Dataverse, if deployed, using the unprivileged service account.
+
+ `sudo -u dataverse /usr/local/payara5/bin/asadmin list-applications`
+
+ `sudo -u dataverse /usr/local/payara5/bin/asadmin undeploy dataverse-5.14`
+
+1. Stop Payara 5, if running.
+
+ `sudo -u dataverse /usr/local/payara5/bin/asadmin stop-domain`
+
+1. Copy Dataverse-related lines from Payara 5 to Payara 6 domain.xml.
+
+ `sudo -u dataverse cp /usr/local/payara6/glassfish/domains/domain1/config/domain.xml /usr/local/payara6/glassfish/domains/domain1/config/domain.xml.orig`
+
+ `sudo egrep 'dataverse|doi' /usr/local/payara5/glassfish/domains/domain1/config/domain.xml > lines.txt`
+
+ `sudo vi /usr/local/payara6/glassfish/domains/domain1/config/domain.xml`
+
+ The lines will appear in two sections, examples shown below (but your content will vary).
+
+ Section 1: system properties (under ``)
+
+ ```
+
+
+
+
+
+ ```
+
+ Note: if you used the Dataverse installer, you won't have a `dataverse.db.password` property. See "Create password aliases" below.
+
+ Section 2: JVM options (under ``, the one under ``, not under ``)
+
+ ```
+ -Ddataverse.files.directory=/usr/local/dvn/data
+ -Ddataverse.files.file.type=file
+ -Ddataverse.files.file.label=file
+ -Ddataverse.files.file.directory=/usr/local/dvn/data
+ -Ddataverse.rserve.host=localhost
+ -Ddataverse.rserve.port=6311
+ -Ddataverse.rserve.user=rserve
+ -Ddataverse.rserve.password=rserve
+ -Ddataverse.auth.password-reset-timeout-in-minutes=60
+ -Ddataverse.timerServer=true
+ -Ddataverse.fqdn=dev1.dataverse.org
+ -Ddataverse.siteUrl=https://dev1.dataverse.org
+ -Ddataverse.files.storage-driver-id=file
+ -Ddoi.username=testaccount
+ -Ddoi.password=notmypassword
+ -Ddoi.baseurlstring=https://mds.test.datacite.org/
+ -Ddoi.dataciterestapiurlstring=https://api.test.datacite.org
+ ```
+
+1. Check the `Xmx` setting in `domain.xml`.
+
+ Under `/usr/local/payara6/glassfish/domains/domain1/config/domain.xml`, check the `Xmx` setting under ``, where you put the JVM options, not the one under ``. Note that there are two such settings, and you want to adjust the one in the stanza with Dataverse options. This sets the JVM heap size; a good rule of thumb is half of your system's total RAM. You may specify the value in MB (`8192m`) or GB (`8g`).
+
+1. Copy `jhove.conf` and `jhoveConfig.xsd` from Payara 5, edit and change `payara5` to `payara6`.
+
+ `sudo cp /usr/local/payara5/glassfish/domains/domain1/config/jhove* /usr/local/payara6/glassfish/domains/domain1/config/`
+
+ `sudo chown dataverse /usr/local/payara6/glassfish/domains/domain1/config/jhove*`
+
+ `sudo -u dataverse vi /usr/local/payara6/glassfish/domains/domain1/config/jhove.conf`
+
+1. Copy logos from Payara 5 to Payara 6.
+
+ These logos are for collections (dataverses).
+
+ `sudo -u dataverse cp -r /usr/local/payara5/glassfish/domains/domain1/docroot/logos /usr/local/payara6/glassfish/domains/domain1/docroot`
+
+1. If you are using Make Data Count (MDC), edit :MDCLogPath.
+
+ Your `:MDCLogPath` database setting might be pointing to a Payara 5 directory such as `/usr/local/payara5/glassfish/domains/domain1/logs`. If so, edit this to be Payara 6. You'll probably want to copy your logs over as well.
+
+1. Update systemd unit file (or other init system) from `/usr/local/payara5` to `/usr/local/payara6`, if applicable.
+
+1. Start Payara.
+
+ `sudo -u dataverse /usr/local/payara6/bin/asadmin start-domain`
+
+1. Create a Java mail resource, replacing "localhost" for mailhost with your mail relay server, and replacing "localhost" for fromaddress with the FQDN of your Dataverse server.
+
+ `sudo -u dataverse /usr/local/payara6/bin/asadmin create-javamail-resource --mailhost "localhost" --mailuser "dataversenotify" --fromaddress "do-not-reply@localhost" mail/notifyMailSession`
+
+1. Create password aliases for your database, rserve and datacite jvm-options, if you're using them.
+
+ `echo "AS_ADMIN_ALIASPASSWORD=yourDBpassword" > /tmp/dataverse.db.password.txt`
+
+ `sudo -u dataverse /usr/local/payara6/bin/asadmin create-password-alias --passwordfile /tmp/dataverse.db.password.txt`
+
+ When you are prompted "Enter the value for the aliasname operand", enter `dataverse.db.password`
+
+ You should see "Command create-password-alias executed successfully."
+
+ You'll want to perform similar commands for `rserve_password_alias` and `doi_password_alias` if you're using Rserve and/or DataCite.
+
+1. Enable workaround for FISH-7722.
+
+ The following workaround is for https://github.com/payara/Payara/issues/6337
+
+ `sudo -u dataverse /usr/local/payara6/bin/asadmin create-jvm-options --add-opens=java.base/java.io=ALL-UNNAMED`
+
+1. Create the network listener on port 8009.
+
+ `sudo -u dataverse /usr/local/payara6/bin/asadmin create-network-listener --protocol http-listener-1 --listenerport 8009 --jkenabled true jk-connector`
+
+1. Deploy the Dataverse 6.0 war file.
+
+ `sudo -u dataverse /usr/local/payara6/bin/asadmin deploy /path/to/dataverse-6.0.war`
+
+1. Check that you get a version number from Dataverse.
+
+ This is just a sanity check that Dataverse has been deployed properly.
+
+ `curl http://localhost:8080/api/info/version`
+
+1. Perform one final Payara restart to ensure that timers are initialized properly.
+
+ `sudo -u dataverse /usr/local/payara6/bin/asadmin stop-domain`
+
+ `sudo -u dataverse /usr/local/payara6/bin/asadmin start-domain`
+
+### Upgrade from Solr 8 to 9
+
+Solr has been upgraded to Solr 9. You must install Solr fresh and reindex. You cannot use your old `schema.xml` because the format has changed.
+
+The instructions below are copied from https://guides.dataverse.org/en/6.0/installation/prerequisites.html#installing-solr and tweaked a bit for an upgrade scenario.
+
+We assume that you already have a user called "solr" (from the instructions above), added during your initial installation of Solr. We also assume that you have already stopped Solr 8 as explained in the instructions above about upgrading Java.
+
+1. Become the "solr" user and then download and configure Solr.
+
+ `su - solr`
+
+ `cd /usr/local/solr`
+
+ `wget https://archive.apache.org/dist/solr/solr/9.3.0/solr-9.3.0.tgz`
+
+ `tar xvzf solr-9.3.0.tgz`
+
+ `cd solr-9.3.0`
+
+ `cp -r server/solr/configsets/_default server/solr/collection1`
+
+1. Unzip "dvinstall.zip" from this release. Unzip it into /tmp. Then copy the following files into place.
+
+ `cp /tmp/dvinstall/schema*.xml /usr/local/solr/solr-9.3.0/server/solr/collection1/conf`
+
+ `cp /tmp/dvinstall/solrconfig.xml /usr/local/solr/solr-9.3.0/server/solr/collection1/conf`
+
+1. A Dataverse installation requires a change to the jetty.xml file that ships with Solr.
+
+ Edit `/usr/local/solr/solr-9.3.0/server/etc/jetty.xml`, increasing `requestHeaderSize` from `8192` to `102400`
+
+1. Tell Solr to create the core "collection1" on startup.
+
+ `echo "name=collection1" > /usr/local/solr/solr-9.3.0/server/solr/collection1/core.properties`
+
+1. Update your init script.
+
+ Your init script may be located at `/etc/systemd/system/solr.service`, for example. Update the path to Solr to be `/usr/local/solr/solr-9.3.0`.
+
+1. Start Solr using your init script and check collection1.
+
+ The collection1 check below should print out fields Dataverse uses like "dsDescription".
+
+ `systemctl start solr.service`
+
+ `curl http://localhost:8983/solr/collection1/schema/fields`
+
+1. Reindex Solr.
+
+ For details, see https://guides.dataverse.org/en/6.0/admin/solr-search-index.html but here is the reindex command:
+
+ `curl http://localhost:8080/api/admin/index`
+
+1. If you have custom metadata blocks installed, you must update your Solr `schema.xml` to include your custom fields.
+
+ For details, please see https://guides.dataverse.org/en/6.0/admin/metadatacustomization.html#updating-the-solr-schema
+
+ At a high level you will be copying custom fields from the output of http://localhost:8080/api/admin/index/solr/schema or using a script to automate this.
+
+## Potential Archiver Incompatibilities with Payara 6
+
+The [Google Cloud and DuraCloud archivers](https://guides.dataverse.org/en/5.14/installation/config.html#bagit-export) may not work in Dataverse 6.0.
+
+This is due to the archivers' dependence on libraries that include classes in `javax.* packages` that are no longer available. If these classes are actually used when the archivers run, the archivers would fail. As these two archivers require additional setup, they have not been tested in 6.0. Community members using these archivers or considering their use are encouraged to test them with 6.0 and report any errors and/or provide fixes for them that can be included in future releases.
+
+## Bug Fix for Dataset Templates with Custom Terms of Use
+
+A bug was fixed for the following scenario:
+
+- Create a template with custom terms.
+- Set that template as the default.
+- Try to create a dataset.
+- A 500 error appears before the form to create dataset is even shown.
+
+For more details, see issue #9825 and PR #9892
+
+## Complete List of Changes
+
+For the complete list of code changes in this release, see the [6.0 Milestone](https://github.com/IQSS/dataverse/milestone/109?closed=1) in GitHub.
+
+## Getting Help
+
+For help with upgrading, installing, or general questions please post to the [Dataverse Community Google Group](https://groups.google.com/forum/#!forum/dataverse-community) or email support@dataverse.org.
diff --git a/doc/shib/shib.md b/doc/shib/shib.md
index 2c178a93f35..9cff6d827e7 100644
--- a/doc/shib/shib.md
+++ b/doc/shib/shib.md
@@ -82,11 +82,7 @@ Run `service httpd restart`.
## Update/verify files under /etc/shibboleth
-For /etc/shibboleth/shibboleth2.xml use the version from https://github.com/IQSS/dataverse/blob/master/conf/vagrant/etc/shibboleth/shibboleth2.xml but replace "pdurbin.pagekite.me" with the "shibtest.dataverse.org".
-
-Put https://github.com/IQSS/dataverse/blob/master/conf/vagrant/etc/shibboleth/dataverse-idp-metadata.xml at /etc/shibboleth/dataverse-idp-metadata.xml
-
-Put https://github.com/IQSS/dataverse/blob/master/conf/vagrant/etc/shibboleth/attribute-map.xml at
+Get files from the Installation Guide.
After making these changes, run `service shibd restart` and `service httpd restart`.
diff --git a/doc/sphinx-guides/source/_static/admin/counter-processor-config.yaml b/doc/sphinx-guides/source/_static/admin/counter-processor-config.yaml
index 4f338905751..26144544d9e 100644
--- a/doc/sphinx-guides/source/_static/admin/counter-processor-config.yaml
+++ b/doc/sphinx-guides/source/_static/admin/counter-processor-config.yaml
@@ -1,8 +1,8 @@
# currently no other option but to have daily logs and have year-month-day format in the name with
# 4-digit year and 2-digit month and day
-# /usr/local/payara5/glassfish/domains/domain1/logs/counter_2019-01-11.log
+# /usr/local/payara6/glassfish/domains/domain1/logs/counter_2019-01-11.log
#log_name_pattern: sample_logs/counter_(yyyy-mm-dd).log
-log_name_pattern: /usr/local/payara5/glassfish/domains/domain1/logs/mdc/counter_(yyyy-mm-dd).log
+log_name_pattern: /usr/local/payara6/glassfish/domains/domain1/logs/mdc/counter_(yyyy-mm-dd).log
# path_types regular expressions allow matching to classify page urls as either an investigation or request
# based on specific URL structure for your system.
diff --git a/scripts/vagrant/counter-processor-config.yaml b/doc/sphinx-guides/source/_static/developers/counter-processor-config.yaml
similarity index 100%
rename from scripts/vagrant/counter-processor-config.yaml
rename to doc/sphinx-guides/source/_static/developers/counter-processor-config.yaml
diff --git a/doc/sphinx-guides/source/_static/installation/files/etc/init.d/payara.init.root b/doc/sphinx-guides/source/_static/installation/files/etc/init.d/payara.init.root
index 1de94331523..b9ef9960318 100755
--- a/doc/sphinx-guides/source/_static/installation/files/etc/init.d/payara.init.root
+++ b/doc/sphinx-guides/source/_static/installation/files/etc/init.d/payara.init.root
@@ -4,7 +4,7 @@
set -e
-ASADMIN=/usr/local/payara5/bin/asadmin
+ASADMIN=/usr/local/payara6/bin/asadmin
case "$1" in
start)
diff --git a/doc/sphinx-guides/source/_static/installation/files/etc/init.d/payara.init.service b/doc/sphinx-guides/source/_static/installation/files/etc/init.d/payara.init.service
index 7c457e615d8..19bb190e740 100755
--- a/doc/sphinx-guides/source/_static/installation/files/etc/init.d/payara.init.service
+++ b/doc/sphinx-guides/source/_static/installation/files/etc/init.d/payara.init.service
@@ -3,7 +3,7 @@
# description: Payara App Server
set -e
-ASADMIN=/usr/local/payara5/bin/asadmin
+ASADMIN=/usr/local/payara6/bin/asadmin
APP_SERVER_USER=dataverse
case "$1" in
diff --git a/doc/sphinx-guides/source/_static/installation/files/etc/init.d/solr b/doc/sphinx-guides/source/_static/installation/files/etc/init.d/solr
index 7ca04cdff3f..9cf8902eb14 100755
--- a/doc/sphinx-guides/source/_static/installation/files/etc/init.d/solr
+++ b/doc/sphinx-guides/source/_static/installation/files/etc/init.d/solr
@@ -5,7 +5,7 @@
# chkconfig: 35 92 08
# description: Starts and stops Apache Solr
-SOLR_DIR="/usr/local/solr/solr-8.11.1"
+SOLR_DIR="/usr/local/solr/solr-9.3.0"
SOLR_COMMAND="bin/solr"
SOLR_ARGS="-m 1g -j jetty.host=127.0.0.1"
SOLR_USER=solr
diff --git a/doc/sphinx-guides/source/_static/installation/files/etc/systemd/payara.service b/doc/sphinx-guides/source/_static/installation/files/etc/systemd/payara.service
index c8c82f6d6b2..c8efcb9c6f9 100644
--- a/doc/sphinx-guides/source/_static/installation/files/etc/systemd/payara.service
+++ b/doc/sphinx-guides/source/_static/installation/files/etc/systemd/payara.service
@@ -4,9 +4,9 @@ After = syslog.target network.target
[Service]
Type = forking
-ExecStart = /usr/bin/java -jar /usr/local/payara5/glassfish/lib/client/appserver-cli.jar start-domain
-ExecStop = /usr/bin/java -jar /usr/local/payara5/glassfish/lib/client/appserver-cli.jar stop-domain
-ExecReload = /usr/bin/java -jar /usr/local/payara5/glassfish/lib/client/appserver-cli.jar restart-domain
+ExecStart = /usr/bin/java -jar /usr/local/payara6/glassfish/lib/client/appserver-cli.jar start-domain
+ExecStop = /usr/bin/java -jar /usr/local/payara6/glassfish/lib/client/appserver-cli.jar stop-domain
+ExecReload = /usr/bin/java -jar /usr/local/payara6/glassfish/lib/client/appserver-cli.jar restart-domain
User=dataverse
LimitNOFILE=32768
Environment="LANG=en_US.UTF-8"
diff --git a/doc/sphinx-guides/source/_static/installation/files/etc/systemd/solr.service b/doc/sphinx-guides/source/_static/installation/files/etc/systemd/solr.service
index d89ee108377..0b8a8528490 100644
--- a/doc/sphinx-guides/source/_static/installation/files/etc/systemd/solr.service
+++ b/doc/sphinx-guides/source/_static/installation/files/etc/systemd/solr.service
@@ -5,9 +5,9 @@ After = syslog.target network.target remote-fs.target nss-lookup.target
[Service]
User = solr
Type = forking
-WorkingDirectory = /usr/local/solr/solr-8.11.1
-ExecStart = /usr/local/solr/solr-8.11.1/bin/solr start -m 1g -j "jetty.host=127.0.0.1"
-ExecStop = /usr/local/solr/solr-8.11.1/bin/solr stop
+WorkingDirectory = /usr/local/solr/solr-9.3.0
+ExecStart = /usr/local/solr/solr-9.3.0/bin/solr start -m 1g -j "jetty.host=127.0.0.1"
+ExecStop = /usr/local/solr/solr-9.3.0/bin/solr stop
LimitNOFILE=65000
LimitNPROC=65000
Restart=on-failure
diff --git a/doc/sphinx-guides/source/_static/installation/files/usr/local/payara5/glassfish/domains/domain1/config/logging.properties b/doc/sphinx-guides/source/_static/installation/files/usr/local/payara5/glassfish/domains/domain1/config/logging.properties
deleted file mode 100644
index 4054c794452..00000000000
--- a/doc/sphinx-guides/source/_static/installation/files/usr/local/payara5/glassfish/domains/domain1/config/logging.properties
+++ /dev/null
@@ -1,166 +0,0 @@
-#
-# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
-#
-# Copyright (c) 2013 Oracle and/or its affiliates. All rights reserved.
-#
-# The contents of this file are subject to the terms of either the GNU
-# General Public License Version 2 only ("GPL") or the Common Development
-# and Distribution License("CDDL") (collectively, the "License"). You
-# may not use this file except in compliance with the License. You can
-# obtain a copy of the License at
-# https://glassfish.dev.java.net/public/CDDL+GPL_1_1.html
-# or packager/legal/LICENSE.txt. See the License for the specific
-# language governing permissions and limitations under the License.
-#
-# When distributing the software, include this License Header Notice in each
-# file and include the License file at packager/legal/LICENSE.txt.
-#
-# GPL Classpath Exception:
-# Oracle designates this particular file as subject to the "Classpath"
-# exception as provided by Oracle in the GPL Version 2 section of the License
-# file that accompanied this code.
-#
-# Modifications:
-# If applicable, add the following below the License Header, with the fields
-# enclosed by brackets [] replaced by your own identifying information:
-# "Portions Copyright [year] [name of copyright owner]"
-#
-# Contributor(s):
-# If you wish your version of this file to be governed by only the CDDL or
-# only the GPL Version 2, indicate your decision by adding "[Contributor]
-# elects to include this software in this distribution under the [CDDL or GPL
-# Version 2] license." If you don't indicate a single choice of license, a
-# recipient has the option to distribute your version of this file under
-# either the CDDL, the GPL Version 2 or to extend the choice of license to
-# its licensees as provided above. However, if you add GPL Version 2 code
-# and therefore, elected the GPL Version 2 license, then the option applies
-# only if the new code is made subject to such option by the copyright
-# holder.
-#
-# Portions Copyright [2016-2021] [Payara Foundation and/or its affiliates]
-
-#GlassFish logging.properties list
-#Update June 13 2012
-
-#All attributes details
-handlers=java.util.logging.ConsoleHandler
-handlerServices=com.sun.enterprise.server.logging.GFFileHandler,com.sun.enterprise.server.logging.SyslogHandler
-java.util.logging.ConsoleHandler.formatter=com.sun.enterprise.server.logging.UniformLogFormatter
-java.util.logging.FileHandler.count=1
-java.util.logging.FileHandler.formatter=java.util.logging.XMLFormatter
-java.util.logging.FileHandler.limit=50000
-java.util.logging.FileHandler.pattern=%h/java%u.log
-com.sun.enterprise.server.logging.GFFileHandler.compressOnRotation=false
-com.sun.enterprise.server.logging.GFFileHandler.excludeFields=
-com.sun.enterprise.server.logging.GFFileHandler.file=${com.sun.aas.instanceRoot}/logs/server.log
-com.sun.enterprise.server.logging.GFFileHandler.flushFrequency=1
-com.sun.enterprise.server.logging.GFFileHandler.formatter=com.sun.enterprise.server.logging.ODLLogFormatter
-com.sun.enterprise.server.logging.GFFileHandler.level=ALL
-com.sun.enterprise.server.logging.GFFileHandler.logStandardStreams=true
-com.sun.enterprise.server.logging.GFFileHandler.logtoConsole=false
-com.sun.enterprise.server.logging.GFFileHandler.logtoFile=true
-com.sun.enterprise.server.logging.GFFileHandler.maxHistoryFiles=0
-com.sun.enterprise.server.logging.GFFileHandler.multiLineMode=true
-com.sun.enterprise.server.logging.GFFileHandler.retainErrorsStasticsForHours=0
-com.sun.enterprise.server.logging.GFFileHandler.rotationLimitInBytes=2000000
-com.sun.enterprise.server.logging.GFFileHandler.rotationOnDateChange=false
-com.sun.enterprise.server.logging.GFFileHandler.rotationTimelimitInMinutes=0
-com.sun.enterprise.server.logging.SyslogHandler.level=ALL
-com.sun.enterprise.server.logging.SyslogHandler.useSystemLogging=false
-log4j.logger.org.hibernate.validator.util.Version=warn
-com.sun.enterprise.server.logging.UniformLogFormatter.ansiColor=true
-
-#Payara Notification logging properties
-fish.payara.enterprise.server.logging.PayaraNotificationFileHandler.compressOnRotation=false
-fish.payara.enterprise.server.logging.PayaraNotificationFileHandler.file=${com.sun.aas.instanceRoot}/logs/notification.log
-fish.payara.enterprise.server.logging.PayaraNotificationFileHandler.formatter=com.sun.enterprise.server.logging.ODLLogFormatter
-fish.payara.enterprise.server.logging.PayaraNotificationFileHandler.logtoFile=true
-fish.payara.enterprise.server.logging.PayaraNotificationFileHandler.maxHistoryFiles=0
-fish.payara.enterprise.server.logging.PayaraNotificationFileHandler.rotationLimitInBytes=2000000
-fish.payara.enterprise.server.logging.PayaraNotificationFileHandler.rotationOnDateChange=false
-fish.payara.enterprise.server.logging.PayaraNotificationFileHandler.rotationTimelimitInMinutes=0
-fish.payara.deprecated.jsonlogformatter.underscoreprefix=false
-
-#All log level details
-
-.level=INFO
-ShoalLogger.level=CONFIG
-com.hazelcast.level=WARNING
-java.util.logging.ConsoleHandler.level=FINEST
-javax.enterprise.resource.corba.level=INFO
-javax.enterprise.resource.javamail.level=INFO
-javax.enterprise.resource.jdo.level=INFO
-javax.enterprise.resource.jms.level=INFO
-javax.enterprise.resource.jta.level=INFO
-javax.enterprise.resource.resourceadapter.level=INFO
-javax.enterprise.resource.sqltrace.level=FINE
-javax.enterprise.resource.webcontainer.jsf.application.level=INFO
-javax.enterprise.resource.webcontainer.jsf.config.level=INFO
-javax.enterprise.resource.webcontainer.jsf.context.level=INFO
-javax.enterprise.resource.webcontainer.jsf.facelets.level=INFO
-javax.enterprise.resource.webcontainer.jsf.lifecycle.level=INFO
-javax.enterprise.resource.webcontainer.jsf.managedbean.level=INFO
-javax.enterprise.resource.webcontainer.jsf.renderkit.level=INFO
-javax.enterprise.resource.webcontainer.jsf.resource.level=INFO
-javax.enterprise.resource.webcontainer.jsf.taglib.level=INFO
-javax.enterprise.resource.webcontainer.jsf.timing.level=INFO
-javax.enterprise.system.container.cmp.level=INFO
-javax.enterprise.system.container.ejb.level=INFO
-javax.enterprise.system.container.ejb.mdb.level=INFO
-javax.enterprise.system.container.web.level=INFO
-javax.enterprise.system.core.classloading.level=INFO
-javax.enterprise.system.core.config.level=INFO
-javax.enterprise.system.core.level=INFO
-javax.enterprise.system.core.security.level=INFO
-javax.enterprise.system.core.selfmanagement.level=INFO
-javax.enterprise.system.core.transaction.level=INFO
-javax.enterprise.system.level=INFO
-javax.enterprise.system.ssl.security.level=INFO
-javax.enterprise.system.tools.admin.level=INFO
-javax.enterprise.system.tools.backup.level=INFO
-javax.enterprise.system.tools.deployment.common.level=WARNING
-javax.enterprise.system.tools.deployment.dol.level=WARNING
-javax.enterprise.system.tools.deployment.level=INFO
-javax.enterprise.system.util.level=INFO
-javax.enterprise.system.webservices.registry.level=INFO
-javax.enterprise.system.webservices.rpc.level=INFO
-javax.enterprise.system.webservices.saaj.level=INFO
-javax.level=INFO
-javax.mail.level=INFO
-javax.org.glassfish.persistence.level=INFO
-org.apache.catalina.level=INFO
-org.apache.coyote.level=INFO
-org.apache.jasper.level=INFO
-org.eclipse.persistence.session.level=INFO
-org.glassfish.admingui.level=INFO
-org.glassfish.naming.level=INFO
-org.jvnet.hk2.osgiadapter.level=INFO
-
-javax.enterprise.resource.corba.level=INFO
-javax.enterprise.resource.jta.level=INFO
-javax.enterprise.system.webservices.saaj.level=INFO
-javax.enterprise.system.container.ejb.level=INFO
-javax.enterprise.system.container.ejb.mdb.level=INFO
-javax.enterprise.resource.javamail.level=INFO
-javax.enterprise.system.webservices.rpc.level=INFO
-javax.enterprise.system.container.web.level=INFO
-javax.enterprise.resource.jms.level=INFO
-javax.enterprise.system.webservices.registry.level=INFO
-javax.enterprise.resource.webcontainer.jsf.application.level=INFO
-javax.enterprise.resource.webcontainer.jsf.resource.level=INFO
-javax.enterprise.resource.webcontainer.jsf.config.level=INFO
-javax.enterprise.resource.webcontainer.jsf.context.level=INFO
-javax.enterprise.resource.webcontainer.jsf.facelets.level=INFO
-javax.enterprise.resource.webcontainer.jsf.lifecycle.level=INFO
-javax.enterprise.resource.webcontainer.jsf.managedbean.level=INFO
-javax.enterprise.resource.webcontainer.jsf.renderkit.level=INFO
-javax.enterprise.resource.webcontainer.jsf.taglib.level=INFO
-javax.enterprise.resource.webcontainer.jsf.timing.level=INFO
-javax.org.glassfish.persistence.level=INFO
-javax.enterprise.system.tools.backup.level=INFO
-javax.mail.level=INFO
-org.glassfish.admingui.level=INFO
-org.glassfish.naming.level=INFO
-org.eclipse.persistence.session.level=INFO
-javax.enterprise.system.tools.deployment.dol.level=WARNING
-javax.enterprise.system.tools.deployment.common.level=WARNING
diff --git a/doc/sphinx-guides/source/_static/util/clear_timer.sh b/doc/sphinx-guides/source/_static/util/clear_timer.sh
index 1d9966e4e07..641b2695084 100755
--- a/doc/sphinx-guides/source/_static/util/clear_timer.sh
+++ b/doc/sphinx-guides/source/_static/util/clear_timer.sh
@@ -8,7 +8,7 @@
# if you'd like to avoid that.
# directory where Payara is installed
-PAYARA_DIR=/usr/local/payara5
+PAYARA_DIR=/usr/local/payara6
# directory within Payara (defaults)
DV_DIR=${PAYARA_DIR}/glassfish/domains/domain1
diff --git a/doc/sphinx-guides/source/_static/util/counter_daily.sh b/doc/sphinx-guides/source/_static/util/counter_daily.sh
index a12439d9cf8..674972b18f2 100644
--- a/doc/sphinx-guides/source/_static/util/counter_daily.sh
+++ b/doc/sphinx-guides/source/_static/util/counter_daily.sh
@@ -1,7 +1,7 @@
#! /bin/bash
COUNTER_PROCESSOR_DIRECTORY="/usr/local/counter-processor-0.1.04"
-MDC_LOG_DIRECTORY="/usr/local/payara5/glassfish/domains/domain1/logs/mdc"
+MDC_LOG_DIRECTORY="/usr/local/payara6/glassfish/domains/domain1/logs/mdc"
# counter_daily.sh
diff --git a/doc/sphinx-guides/source/admin/harvestclients.rst b/doc/sphinx-guides/source/admin/harvestclients.rst
index da922459f46..59fc4dc2c64 100644
--- a/doc/sphinx-guides/source/admin/harvestclients.rst
+++ b/doc/sphinx-guides/source/admin/harvestclients.rst
@@ -35,8 +35,8 @@ For example:
.. code-block:: bash
- sudo touch /usr/local/payara5/glassfish/domains/domain1/logs/stopharvest_bigarchive.70916
- sudo chown dataverse /usr/local/payara5/glassfish/domains/domain1/logs/stopharvest_bigarchive.70916
+ sudo touch /usr/local/payara6/glassfish/domains/domain1/logs/stopharvest_bigarchive.70916
+ sudo chown dataverse /usr/local/payara6/glassfish/domains/domain1/logs/stopharvest_bigarchive.70916
Note: If the application server is stopped and restarted, any running harvesting jobs will be killed but may remain marked as in progress in the database. We thus recommend using the mechanism here to stop ongoing harvests prior to a server restart.
@@ -44,6 +44,6 @@ Note: If the application server is stopped and restarted, any running harvesting
What if a Run Fails?
~~~~~~~~~~~~~~~~~~~~
-Each harvesting client run logs a separate file per run to the app server's default logging directory (``/usr/local/payara5/glassfish/domains/domain1/logs/`` unless you've changed it). Look for filenames in the format ``harvest_TARGET_YYYY_MM_DD_timestamp.log`` to get a better idea of what's going wrong.
+Each harvesting client run logs a separate file per run to the app server's default logging directory (``/usr/local/payara6/glassfish/domains/domain1/logs/`` unless you've changed it). Look for filenames in the format ``harvest_TARGET_YYYY_MM_DD_timestamp.log`` to get a better idea of what's going wrong.
Note that you'll want to run a minimum of Dataverse Software 4.6, optimally 4.18 or beyond, for the best OAI-PMH interoperability.
diff --git a/doc/sphinx-guides/source/admin/make-data-count.rst b/doc/sphinx-guides/source/admin/make-data-count.rst
index ec6ff9a685b..fe32af6649a 100644
--- a/doc/sphinx-guides/source/admin/make-data-count.rst
+++ b/doc/sphinx-guides/source/admin/make-data-count.rst
@@ -72,10 +72,9 @@ Enable or Disable Display of Make Data Count Metrics
By default, when MDC logging is enabled (when ``:MDCLogPath`` is set), your Dataverse installation will display MDC metrics instead of it's internal (legacy) metrics. You can avoid this (e.g. to collect MDC metrics for some period of time before starting to display them) by setting ``:DisplayMDCMetrics`` to false.
+The following discussion assumes ``:MDCLogPath`` has been set to ``/usr/local/payara6/glassfish/domains/domain1/logs/mdc``
You can also decide to display MDC metrics along with Dataverse's traditional download counts from the time before MDC was enabled. To do this, set the :ref:`:MDCStartDate` to when you started MDC logging.
-The following discussion assumes ``:MDCLogPath`` has been set to ``/usr/local/payara5/glassfish/domains/domain1/logs/mdc``
-
Configure Counter Processor
~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -104,7 +103,7 @@ Soon we will be setting up a cron job to run nightly but we start with a single
* If you are running Counter Processor for the first time in the middle of a month, you will need create blank log files for the previous days. e.g.:
- * ``cd /usr/local/payara5/glassfish/domains/domain1/logs/mdc``
+ * ``cd /usr/local/payara6/glassfish/domains/domain1/logs/mdc``
* ``touch counter_2019-02-01.log``
diff --git a/doc/sphinx-guides/source/admin/metadatacustomization.rst b/doc/sphinx-guides/source/admin/metadatacustomization.rst
index cac051ddb59..4f737bd730b 100644
--- a/doc/sphinx-guides/source/admin/metadatacustomization.rst
+++ b/doc/sphinx-guides/source/admin/metadatacustomization.rst
@@ -413,13 +413,10 @@ Setting Up a Dev Environment for Testing
You have several options for setting up a dev environment for testing metadata block changes:
-- Vagrant: See the :doc:`/developers/tools` section of the Developer Guide.
-- docker-aio: See https://github.com/IQSS/dataverse/tree/develop/conf/docker-aio
+- Docker: See :doc:`/container/index`.
- AWS deployment: See the :doc:`/developers/deployment` section of the Developer Guide.
- Full dev environment: See the :doc:`/developers/dev-environment` section of the Developer Guide.
-To get a clean environment in Vagrant, you'll be running ``vagrant destroy``. In Docker, you'll use ``docker rm``. For a full dev environment or AWS installation, you might find ``rebuild`` and related scripts at ``scripts/deploy/phoenix.dataverse.org`` useful.
-
Editing TSV files
~~~~~~~~~~~~~~~~~
@@ -516,7 +513,7 @@ the Solr schema configuration, including any enabled metadata schemas:
``curl "http://localhost:8080/api/admin/index/solr/schema"``
-You can use :download:`update-fields.sh <../../../../conf/solr/8.11.1/update-fields.sh>` to easily add these to the
+You can use :download:`update-fields.sh <../../../../conf/solr/9.3.0/update-fields.sh>` to easily add these to the
Solr schema you installed for your Dataverse installation.
The script needs a target XML file containing your Solr schema. (See the :doc:`/installation/prerequisites/` section of
@@ -540,7 +537,7 @@ from some place else than your Dataverse installation).
Please note that reconfigurations of your Solr index might require a re-index. Usually release notes indicate
a necessary re-index, but for your custom metadata you will need to keep track on your own.
-Please note also that if you are going to make a pull request updating ``conf/solr/8.11.1/schema.xml`` with fields you have
+Please note also that if you are going to make a pull request updating ``conf/solr/9.3.0/schema.xml`` with fields you have
added, you should first load all the custom metadata blocks in ``scripts/api/data/metadatablocks`` (including ones you
don't care about) to create a complete list of fields. (This might change in the future.)
diff --git a/doc/sphinx-guides/source/admin/troubleshooting.rst b/doc/sphinx-guides/source/admin/troubleshooting.rst
index 9f085ba90cd..acbdcaae17e 100644
--- a/doc/sphinx-guides/source/admin/troubleshooting.rst
+++ b/doc/sphinx-guides/source/admin/troubleshooting.rst
@@ -53,15 +53,13 @@ Long-Running Ingest Jobs Have Exhausted System Resources
Ingest is both CPU- and memory-intensive, and depending on your system resources and the size and format of tabular data files uploaded, may render your Dataverse installation unresponsive or nearly inoperable. It is possible to cancel these jobs by purging the ingest queue.
-``/usr/local/payara5/mq/bin/imqcmd -u admin query dst -t q -n DataverseIngest`` will query the DataverseIngest destination. The password, unless you have changed it, matches the username.
+``/usr/local/payara6/mq/bin/imqcmd -u admin query dst -t q -n DataverseIngest`` will query the DataverseIngest destination. The password, unless you have changed it, matches the username.
-``/usr/local/payara5/mq/bin/imqcmd -u admin purge dst -t q -n DataverseIngest`` will purge the DataverseIngest queue, and prompt for your confirmation.
+``/usr/local/payara6/mq/bin/imqcmd -u admin purge dst -t q -n DataverseIngest`` will purge the DataverseIngest queue, and prompt for your confirmation.
Finally, list destinations to verify that the purge was successful:
-``/usr/local/payara5/mq/bin/imqcmd -u admin list dst``
-
-If you are still running Glassfish, substitute glassfish4 for payara5 above. If you have installed your Dataverse installation in some other location, adjust the above paths accordingly.
+``/usr/local/payara6/mq/bin/imqcmd -u admin list dst``
.. _troubleshooting-payara:
@@ -73,7 +71,7 @@ Payara
Finding the Payara Log File
~~~~~~~~~~~~~~~~~~~~~~~~~~~
-``/usr/local/payara5/glassfish/domains/domain1/logs/server.log`` is the main place to look when you encounter problems (assuming you installed Payara in the default directory). Hopefully an error message has been logged. If there's a stack trace, it may be of interest to developers, especially they can trace line numbers back to a tagged version or commit. Send more of the stack trace (the entire file if possible) to developers who can help (see "Getting Help", below) and be sure to say which version of the Dataverse Software you have installed.
+``/usr/local/payara6/glassfish/domains/domain1/logs/server.log`` is the main place to look when you encounter problems (assuming you installed Payara in the default directory). Hopefully an error message has been logged. If there's a stack trace, it may be of interest to developers, especially they can trace line numbers back to a tagged version or commit. Send more of the stack trace (the entire file if possible) to developers who can help (see "Getting Help", below) and be sure to say which version of the Dataverse Software you have installed.
.. _increase-payara-logging:
diff --git a/doc/sphinx-guides/source/api/getting-started.rst b/doc/sphinx-guides/source/api/getting-started.rst
index 544f0921bd7..a6f6c259a25 100644
--- a/doc/sphinx-guides/source/api/getting-started.rst
+++ b/doc/sphinx-guides/source/api/getting-started.rst
@@ -11,7 +11,7 @@ Servers You Can Test With
Rather than using a production Dataverse installation, API users are welcome to use http://demo.dataverse.org for testing. You can email support@dataverse.org if you have any trouble with this server.
-If you would rather have full control over your own test server, deployments to AWS, Docker, Vagrant, and more are covered in the :doc:`/developers/index` and the :doc:`/installation/index`.
+If you would rather have full control over your own test server, deployments to AWS, Docker, and more are covered in the :doc:`/developers/index` and the :doc:`/installation/index`.
Getting an API Token
--------------------
diff --git a/doc/sphinx-guides/source/conf.py b/doc/sphinx-guides/source/conf.py
index 2c2ddf1bdf6..7ff17eb45ed 100755
--- a/doc/sphinx-guides/source/conf.py
+++ b/doc/sphinx-guides/source/conf.py
@@ -66,9 +66,9 @@
# built documents.
#
# The short X.Y version.
-version = '5.14'
+version = '6.0'
# The full version, including alpha/beta/rc tags.
-release = '5.14'
+release = '6.0'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
diff --git a/doc/sphinx-guides/source/container/base-image.rst b/doc/sphinx-guides/source/container/base-image.rst
index ed06314ef0e..1a47a8fc413 100644
--- a/doc/sphinx-guides/source/container/base-image.rst
+++ b/doc/sphinx-guides/source/container/base-image.rst
@@ -41,7 +41,7 @@ Image Contents
The base image provides:
-- `Eclipse Temurin JRE using Java 11 `_
+- `Eclipse Temurin JRE using Java 17 `_
- `Payara Community Application Server `_
- CLI tools necessary to run Dataverse (i. e. ``curl`` or ``jq`` - see also :doc:`../installation/prerequisites` in Installation Guide)
- Linux tools for analysis, monitoring and so on
diff --git a/doc/sphinx-guides/source/container/dev-usage.rst b/doc/sphinx-guides/source/container/dev-usage.rst
index 3fbe55766d5..04c7eba7913 100644
--- a/doc/sphinx-guides/source/container/dev-usage.rst
+++ b/doc/sphinx-guides/source/container/dev-usage.rst
@@ -9,17 +9,7 @@ Please note! This Docker setup is not for production!
Quickstart
----------
-First, install Java 11 and Maven.
-
-After cloning the repo, try this:
-
-``mvn -Pct clean package docker:run``
-
-After some time you should be able to log in:
-
-- url: http://localhost:8080
-- username: dataverseAdmin
-- password: admin1
+See :ref:`container-dev-quickstart`.
Intro
-----
@@ -172,7 +162,7 @@ restart the application container:
Using ``docker container inspect dev_dataverse | grep Image`` you can verify the changed checksums.
-Using A Debugger
+Using a Debugger
----------------
The :doc:`base-image` enables usage of the `Java Debugging Wire Protocol `_
@@ -183,3 +173,8 @@ There are a lot of tutorials how to connect your IDE's debugger to a remote endp
as the endpoint. Here are links to the most common IDEs docs on remote debugging:
`Eclipse `_,
`IntelliJ `_
+
+Building Your Own Base Image
+----------------------------
+
+If you find yourself tasked with upgrading Payara, you will need to create your own base image before running the :ref:`container-dev-quickstart`. For instructions, see :doc:`base-image`.
diff --git a/doc/sphinx-guides/source/developers/big-data-support.rst b/doc/sphinx-guides/source/developers/big-data-support.rst
index b238a7623eb..04885571a01 100644
--- a/doc/sphinx-guides/source/developers/big-data-support.rst
+++ b/doc/sphinx-guides/source/developers/big-data-support.rst
@@ -173,6 +173,8 @@ See also :ref:`Globus settings <:GlobusBasicToken>`.
Data Capture Module (DCM)
-------------------------
+Please note: The DCM feature is deprecated.
+
Data Capture Module (DCM) is an experimental component that allows users to upload large datasets via rsync over ssh.
DCM was developed and tested using Glassfish but these docs have been updated with references to Payara.
@@ -209,7 +211,7 @@ The JSON that a DCM sends to your Dataverse installation on successful checksum
:language: json
- ``status`` - The valid strings to send are ``validation passed`` and ``validation failed``.
-- ``uploadFolder`` - This is the directory on disk where your Dataverse installation should attempt to find the files that a DCM has moved into place. There should always be a ``files.sha`` file and a least one data file. ``files.sha`` is a manifest of all the data files and their checksums. The ``uploadFolder`` directory is inside the directory where data is stored for the dataset and may have the same name as the "identifier" of the persistent id (DOI or Handle). For example, you would send ``"uploadFolder": "DNXV2H"`` in the JSON file when the absolute path to this directory is ``/usr/local/payara5/glassfish/domains/domain1/files/10.5072/FK2/DNXV2H/DNXV2H``.
+- ``uploadFolder`` - This is the directory on disk where your Dataverse installation should attempt to find the files that a DCM has moved into place. There should always be a ``files.sha`` file and a least one data file. ``files.sha`` is a manifest of all the data files and their checksums. The ``uploadFolder`` directory is inside the directory where data is stored for the dataset and may have the same name as the "identifier" of the persistent id (DOI or Handle). For example, you would send ``"uploadFolder": "DNXV2H"`` in the JSON file when the absolute path to this directory is ``/usr/local/payara6/glassfish/domains/domain1/files/10.5072/FK2/DNXV2H/DNXV2H``.
- ``totalSize`` - Your Dataverse installation will use this value to represent the total size in bytes of all the files in the "package" that's created. If 360 data files and one ``files.sha`` manifest file are in the ``uploadFolder``, this value is the sum of the 360 data files.
@@ -231,9 +233,9 @@ Add Dataverse Installation settings to use mock (same as using DCM, noted above)
At this point you should be able to download a placeholder rsync script. Your Dataverse installation is then waiting for news from the DCM about if checksum validation has succeeded or not. First, you have to put files in place, which is usually the job of the DCM. You should substitute "X1METO" for the "identifier" of the dataset you create. You must also use the proper path for where you store files in your dev environment.
-- ``mkdir /usr/local/payara5/glassfish/domains/domain1/files/10.5072/FK2/X1METO``
-- ``mkdir /usr/local/payara5/glassfish/domains/domain1/files/10.5072/FK2/X1METO/X1METO``
-- ``cd /usr/local/payara5/glassfish/domains/domain1/files/10.5072/FK2/X1METO/X1METO``
+- ``mkdir /usr/local/payara6/glassfish/domains/domain1/files/10.5072/FK2/X1METO``
+- ``mkdir /usr/local/payara6/glassfish/domains/domain1/files/10.5072/FK2/X1METO/X1METO``
+- ``cd /usr/local/payara6/glassfish/domains/domain1/files/10.5072/FK2/X1METO/X1METO``
- ``echo "hello" > file1.txt``
- ``shasum file1.txt > files.sha``
@@ -248,104 +250,11 @@ The following low level command should only be used when troubleshooting the "im
``curl -H "X-Dataverse-key: $API_TOKEN" -X POST "$DV_BASE_URL/api/batch/jobs/import/datasets/files/$DATASET_DB_ID?uploadFolder=$UPLOAD_FOLDER&totalSize=$TOTAL_SIZE"``
-Steps to set up a DCM via Docker for Development
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-If you need a fully operating DCM client for development purposes, these steps will guide you to setting one up. This includes steps to set up the DCM on S3 variant.
-
-Docker Image Set-up
-^^^^^^^^^^^^^^^^^^^
-
-See https://github.com/IQSS/dataverse/blob/develop/conf/docker-dcm/readme.md
-
-- Install docker if you do not have it
-
-Optional steps for setting up the S3 Docker DCM Variant
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-- Before: the default bucket for DCM to hold files in S3 is named test-dcm. It is coded into `post_upload_s3.bash` (line 30). Change to a different bucket if needed.
-- Also Note: With the new support for multiple file store in the Dataverse Software, DCM requires a store with id="s3" and DCM will only work with this store.
-
- - Add AWS bucket info to dcmsrv
- - Add AWS credentials to ``~/.aws/credentials``
-
- - ``[default]``
- - ``aws_access_key_id =``
- - ``aws_secret_access_key =``
-
-- Dataverse installation configuration (on dvsrv):
-
- - Set S3 as the storage driver
-
- - ``cd /opt/payara5/bin/``
- - ``./asadmin delete-jvm-options "\-Ddataverse.files.storage-driver-id=file"``
- - ``./asadmin create-jvm-options "\-Ddataverse.files.storage-driver-id=s3"``
- - ``./asadmin create-jvm-options "\-Ddataverse.files.s3.type=s3"``
- - ``./asadmin create-jvm-options "\-Ddataverse.files.s3.label=s3"``
-
-
- - Add AWS bucket info to your Dataverse installation
- - Add AWS credentials to ``~/.aws/credentials``
-
- - ``[default]``
- - ``aws_access_key_id =``
- - ``aws_secret_access_key =``
-
- - Also: set region in ``~/.aws/config`` to create a region file. Add these contents:
-
- - ``[default]``
- - ``region = us-east-1``
-
- - Add the S3 bucket names to your Dataverse installation
-
- - S3 bucket for your Dataverse installation
-
- - ``/usr/local/payara5/glassfish/bin/asadmin create-jvm-options "-Ddataverse.files.s3.bucket-name=iqsstestdcmbucket"``
-
- - S3 bucket for DCM (as your Dataverse installation needs to do the copy over)
-
- - ``/usr/local/payara5/glassfish/bin/asadmin create-jvm-options "-Ddataverse.files.dcm-s3-bucket-name=test-dcm"``
-
- - Set download method to be HTTP, as DCM downloads through S3 are over this protocol ``curl -X PUT "http://localhost:8080/api/admin/settings/:DownloadMethods" -d "native/http"``
-
-Using the DCM Docker Containers
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-For using these commands, you will need to connect to the shell prompt inside various containers (e.g. ``docker exec -it dvsrv /bin/bash``)
-
-- Create a dataset and download rsync upload script
-
- - connect to client container: ``docker exec -it dcm_client bash``
- - create dataset: ``cd /mnt ; ./create.bash`` ; this will echo the database ID to stdout
- - download transfer script: ``./get_transfer.bash $database_id_from_create_script``
- - execute the transfer script: ``bash ./upload-${database_id_from-create_script}.bash`` , and follow instructions from script.
-
-- Run script
-
- - e.g. ``bash ./upload-3.bash`` (``3`` being the database id from earlier commands in this example).
-
-- Manually run post upload script on dcmsrv
-
- - for posix implementation: ``docker exec -it dcmsrv /opt/dcm/scn/post_upload.bash``
- - for S3 implementation: ``docker exec -it dcmsrv /opt/dcm/scn/post_upload_s3.bash``
-
-Additional DCM docker development tips
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-- You can completely blow away all the docker images with these commands (including non DCM ones!)
- - ``docker-compose -f docmer-compose.yml down -v``
-
-- There are a few logs to tail
-
- - dvsrv : ``tail -n 2000 -f /opt/payara5/glassfish/domains/domain1/logs/server.log``
- - dcmsrv : ``tail -n 2000 -f /var/log/lighttpd/breakage.log``
- - dcmsrv : ``tail -n 2000 -f /var/log/lighttpd/access.log``
-
-- You may have to restart the app server domain occasionally to deal with memory filling up. If deployment is getting reallllllly slow, its a good time.
-
Repository Storage Abstraction Layer (RSAL)
-------------------------------------------
+Please note: The RSAL feature is deprecated.
+
Steps to set up a DCM via Docker for Development
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/doc/sphinx-guides/source/developers/classic-dev-env.rst b/doc/sphinx-guides/source/developers/classic-dev-env.rst
new file mode 100755
index 00000000000..062a1bb36f3
--- /dev/null
+++ b/doc/sphinx-guides/source/developers/classic-dev-env.rst
@@ -0,0 +1,266 @@
+=======================
+Classic Dev Environment
+=======================
+
+These are the old instructions we used for Dataverse 4 and 5. They should still work but these days we favor running Dataverse in Docker as described in :doc:`dev-environment`.
+
+These instructions are purposefully opinionated and terse to help you get your development environment up and running as quickly as possible! Please note that familiarity with running commands from the terminal is assumed.
+
+.. contents:: |toctitle|
+ :local:
+
+Quick Start (Docker)
+--------------------
+
+The quickest way to get Dataverse running is in Docker as explained in :doc:`../container/dev-usage` section of the Container Guide.
+
+
+Classic Dev Environment
+-----------------------
+
+Since before Docker existed, we have encouraged installing Dataverse and all its dependencies directly on your development machine, as described below. This can be thought of as the "classic" development environment for Dataverse.
+
+However, in 2023 we decided that we'd like to encourage all developers to start using Docker instead and opened https://github.com/IQSS/dataverse/issues/9616 to indicate that we plan to rewrite this page to recommend the use of Docker.
+
+There's nothing wrong with the classic instructions below and we don't plan to simply delete them. They are a valid alternative to running Dataverse in Docker. We will likely move them to another page.
+
+Set Up Dependencies
+-------------------
+
+Supported Operating Systems
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Mac OS X or Linux is required because the setup scripts assume the presence of standard Unix utilities.
+
+Windows is gaining support through Docker as described in the :doc:`windows` section.
+
+Install Java
+~~~~~~~~~~~~
+
+The Dataverse Software requires Java 11.
+
+We suggest downloading OpenJDK from https://adoptopenjdk.net
+
+On Linux, you are welcome to use the OpenJDK available from package managers.
+
+Install Netbeans or Maven
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+NetBeans IDE is recommended, and can be downloaded from http://netbeans.org . Developers may use any editor or IDE. We recommend NetBeans because it is free, works cross platform, has good support for Jakarta EE projects, and includes a required build tool, Maven.
+
+Below we describe how to build the Dataverse Software war file with Netbeans but if you prefer to use only Maven, you can find installation instructions in the :doc:`tools` section.
+
+Install Homebrew (Mac Only)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+On Mac, install Homebrew to simplify the steps below: https://brew.sh
+
+Clone the Dataverse Software Git Repo
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Fork https://github.com/IQSS/dataverse and then clone your fork like this:
+
+``git clone git@github.com:[YOUR GITHUB USERNAME]/dataverse.git``
+
+Build the Dataverse Software War File
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+If you installed Netbeans, follow these steps:
+
+- Launch Netbeans and click "File" and then "Open Project". Navigate to where you put the Dataverse Software code and double-click "Dataverse" to open the project.
+- If you see "resolve project problems," go ahead and let Netbeans try to resolve them. This will probably including downloading dependencies, which can take a while.
+- Allow Netbeans to install nb-javac (required for Java 8 and below).
+- Select "Dataverse" under Projects and click "Run" in the menu and then "Build Project (Dataverse)". Check back for "BUILD SUCCESS" at the end.
+
+If you installed Maven instead of Netbeans, run ``mvn package``. Check for "BUILD SUCCESS" at the end.
+
+NOTE: Do you use a locale different than ``en_US.UTF-8`` on your development machine? Are you in a different timezone
+than Harvard (Eastern Time)? You might experience issues while running tests that were written with these settings
+in mind. The Maven ``pom.xml`` tries to handle this for you by setting the locale to ``en_US.UTF-8`` and timezone
+``UTC``, but more, not yet discovered building or testing problems might lurk in the shadows.
+
+Install jq
+~~~~~~~~~~
+
+On Mac, run this command:
+
+``brew install jq``
+
+On Linux, install ``jq`` from your package manager or download a binary from http://stedolan.github.io/jq/
+
+Install Payara
+~~~~~~~~~~~~~~
+
+Payara 6.2023.8 or higher is required.
+
+To install Payara, run the following commands:
+
+``cd /usr/local``
+
+``sudo curl -O -L https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2023.8/payara-6.2023.8.zip``
+
+``sudo unzip payara-6.2023.8.zip``
+
+``sudo chown -R $USER /usr/local/payara6``
+
+If nexus.payara.fish is ever down for maintenance, Payara distributions are also available from https://repo1.maven.org/maven2/fish/payara/distributions/payara/
+
+Install Service Dependencies Directly on localhost
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Install PostgreSQL
+^^^^^^^^^^^^^^^^^^
+
+The Dataverse Software has been tested with PostgreSQL versions up to 13. PostgreSQL version 10+ is required.
+
+On Mac, go to https://www.postgresql.org/download/macosx/ and choose "Interactive installer by EDB" option. Note that version 13.5 is used in the command line examples below, but the process should be similar for other versions. When prompted to set a password for the "database superuser (postgres)" just enter "password".
+
+After installation is complete, make a backup of the ``pg_hba.conf`` file like this:
+
+``sudo cp /Library/PostgreSQL/13/data/pg_hba.conf /Library/PostgreSQL/13/data/pg_hba.conf.orig``
+
+Then edit ``pg_hba.conf`` with an editor such as vi:
+
+``sudo vi /Library/PostgreSQL/13/data/pg_hba.conf``
+
+In the "METHOD" column, change all instances of "scram-sha-256" (or whatever is in that column) to "trust". This will make it so PostgreSQL doesn't require a password.
+
+In the Finder, click "Applications" then "PostgreSQL 13" and launch the "Reload Configuration" app. Click "OK" after you see "server signaled".
+
+Next, to confirm the edit worked, launch the "pgAdmin" application from the same folder. Under "Browser", expand "Servers" and double click "PostgreSQL 13". When you are prompted for a password, leave it blank and click "OK". If you have successfully edited "pg_hba.conf", you can get in without a password.
+
+On Linux, you should just install PostgreSQL using your favorite package manager, such as ``yum``. (Consult the PostgreSQL section of :doc:`/installation/prerequisites` in the main Installation guide for more info and command line examples). Find ``pg_hba.conf`` and set the authentication method to "trust" and restart PostgreSQL.
+
+Install Solr
+^^^^^^^^^^^^
+
+`Solr `_ 9.3.0 is required.
+
+To install Solr, execute the following commands:
+
+``sudo mkdir /usr/local/solr``
+
+``sudo chown $USER /usr/local/solr``
+
+``cd /usr/local/solr``
+
+``curl -O http://archive.apache.org/dist/solr/solr/9.3.0/solr-9.3.0.tgz``
+
+``tar xvfz solr-9.3.0.tgz``
+
+``cd solr-9.3.0/server/solr``
+
+``cp -r configsets/_default collection1``
+
+``curl -O https://raw.githubusercontent.com/IQSS/dataverse/develop/conf/solr/9.3.0/schema.xml``
+
+``curl -O https://raw.githubusercontent.com/IQSS/dataverse/develop/conf/solr/9.3.0/schema_dv_mdb_fields.xml``
+
+``mv schema*.xml collection1/conf``
+
+``curl -O https://raw.githubusercontent.com/IQSS/dataverse/develop/conf/solr/9.3.0/solrconfig.xml``
+
+``mv solrconfig.xml collection1/conf/solrconfig.xml``
+
+``cd /usr/local/solr/solr-9.3.0``
+
+(Please note that the extra jetty argument below is a security measure to limit connections to Solr to only your computer. For extra security, run a firewall.)
+
+``bin/solr start -j "-Djetty.host=127.0.0.1"``
+
+``bin/solr create_core -c collection1 -d server/solr/collection1/conf``
+
+Install Service Dependencies Using Docker Compose
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+To avoid having to install service dependencies like PostgreSQL or Solr directly on your localhost, there is the alternative of using the ``docker-compose-dev.yml`` file available in the repository root. For this option you need to have Docker and Docker Compose installed on your machine.
+
+The ``docker-compose-dev.yml`` can be configured to only run the service dependencies necessary to support a Dataverse installation running directly on localhost. In addition to PostgreSQL and Solr, it also runs a SMTP server.
+
+Before running the Docker Compose file, you need to update the value of the ``DATAVERSE_DB_USER`` environment variable to ``postgres``. The variable can be found inside the ``.env`` file in the repository root. This step is required as the Dataverse installation script expects that database user.
+
+To run the Docker Compose file, go to the Dataverse repository root, then run:
+
+``docker-compose -f docker-compose-dev.yml up -d --scale dev_dataverse=0``
+
+Note that this command omits the Dataverse container defined in the Docker Compose file, since Dataverse is going to be installed directly on localhost in the next section.
+
+The command runs the containers in detached mode, but if you want to run them attached and thus view container logs in real time, remove the ``-d`` option from the command.
+
+Data volumes of each dependency will be persisted inside the ``docker-dev-volumes`` folder, inside the repository root.
+
+If you want to stop the containers, then run (for detached mode only, otherwise use ``Ctrl + C``):
+
+``docker-compose -f docker-compose-dev.yml stop``
+
+If you want to remove the containers, then run:
+
+``docker-compose -f docker-compose-dev.yml down``
+
+If you want to run a single container (the mail server, for example) then run:
+
+``docker-compose -f docker-compose-dev.yml up dev_smtp``
+
+For a fresh installation, and before running the Software Installer Script, it is recommended to delete the docker-dev-env folder to avoid installation problems due to existing data in the containers.
+
+Run the Dataverse Software Installer Script
+-------------------------------------------
+
+Navigate to the directory where you cloned the Dataverse Software git repo change directories to the ``scripts/installer`` directory like this:
+
+``cd scripts/installer``
+
+Create a Python virtual environment, activate it, then install dependencies:
+
+``python3 -m venv venv``
+
+``source venv/bin/activate``
+
+``pip install psycopg2-binary``
+
+The installer will try to connect to the SMTP server you tell it to use. If you haven't used the Docker Compose option for setting up the dependencies, or you don't have a mail server handy, you can run ``nc -l 25`` in another terminal and choose "localhost" (the default) to get past this check.
+
+Finally, run the installer (see also :download:`README_python.txt <../../../../scripts/installer/README_python.txt>` if necessary):
+
+``python3 install.py``
+
+Verify the Dataverse Software is Running
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+After the script has finished, you should be able to log into your Dataverse installation with the following credentials:
+
+- http://localhost:8080
+- username: dataverseAdmin
+- password: admin
+
+Configure Your Development Environment for Publishing
+-----------------------------------------------------
+
+Run the following command:
+
+``curl http://localhost:8080/api/admin/settings/:DoiProvider -X PUT -d FAKE``
+
+This will disable DOI registration by using a fake (in-code) DOI provider. Please note that this feature is only available in Dataverse Software 4.10+ and that at present, the UI will give no indication that the DOIs thus minted are fake.
+
+Developers may also wish to consider using :ref:`PermaLinks `
+
+Configure Your Development Environment for GUI Edits
+----------------------------------------------------
+
+Out of the box, a JSF setting is configured for production use and prevents edits to the GUI (xhtml files) from being visible unless you do a full deployment.
+
+It is recommended that you run the following command so that simply saving the xhtml file in Netbeans is enough for the change to show up.
+
+``asadmin create-system-properties "dataverse.jsf.refresh-period=1"``
+
+For more on JSF settings like this, see :ref:`jsf-config`.
+
+Next Steps
+----------
+
+If you can log in to the Dataverse installation, great! If not, please see the :doc:`troubleshooting` section. For further assistance, please see "Getting Help" in the :doc:`intro` section.
+
+You're almost ready to start hacking on code. Now that the installer script has you up and running, you need to continue on to the :doc:`tips` section to get set up to deploy code from your IDE or the command line.
+
+----
+
+Previous: :doc:`intro` | Next: :doc:`tips`
diff --git a/doc/sphinx-guides/source/developers/containers.rst b/doc/sphinx-guides/source/developers/containers.rst
index b42f7f5a2e2..175b178b455 100755
--- a/doc/sphinx-guides/source/developers/containers.rst
+++ b/doc/sphinx-guides/source/developers/containers.rst
@@ -25,11 +25,6 @@ The primary community-lead projects (which the core team is drawing inspiration
- https://github.com/IQSS/dataverse-docker
- https://github.com/IQSS/dataverse-kubernetes (especially the https://github.com/EOSC-synergy/dataverse-kubernetes fork)
-Deprecated Projects
--------------------
-
-The :doc:`testing` section mentions using docker-aio for integration tests. We do not plan to keep this project alive.
-
Using Containers for Reproducible Research
------------------------------------------
diff --git a/doc/sphinx-guides/source/developers/debugging.rst b/doc/sphinx-guides/source/developers/debugging.rst
index 2088afe5521..50e8901b1ff 100644
--- a/doc/sphinx-guides/source/developers/debugging.rst
+++ b/doc/sphinx-guides/source/developers/debugging.rst
@@ -20,8 +20,8 @@ during development without recompiling. Changing the options will require at lea
how you get these options in. (Variable substitution only happens during deployment and when using system properties
or environment variables, you'll need to pass these into the domain, which usually will require an app server restart.)
-Please note that since Payara 5.2021.1 supporting MicroProfile Config 2.0, you can
-`use profiles `_
+Please note you can use
+`MicroProfile Config `_
to maintain your settings more easily for different environments.
.. list-table::
diff --git a/doc/sphinx-guides/source/developers/dependencies.rst b/doc/sphinx-guides/source/developers/dependencies.rst
index 65edfa3ffac..0208c49f90a 100644
--- a/doc/sphinx-guides/source/developers/dependencies.rst
+++ b/doc/sphinx-guides/source/developers/dependencies.rst
@@ -344,8 +344,7 @@ Repositories
------------
Maven receives all dependencies from *repositories*. These can be public like `Maven Central `_
-and others, but you can also use a private repository on premises or in the cloud. Last but not least, you can use
-local repositories, which can live next to your application code (see ``local_lib`` dir within the Dataverse Software codebase).
+and others, but you can also use a private repository on premises or in the cloud.
Repositories are defined within the Dataverse Software POM like this:
@@ -364,11 +363,6 @@ Repositories are defined within the Dataverse Software POM like this:
http://repository.primefaces.org
default
-
- dvn.private
- Local repository for hosting jars not available from network repositories.
- file://${project.basedir}/local_lib
-
You can also add repositories to your local Maven settings, see `docs `_.
diff --git a/doc/sphinx-guides/source/developers/dev-environment.rst b/doc/sphinx-guides/source/developers/dev-environment.rst
index b3f7fb1c1af..1301994cc82 100755
--- a/doc/sphinx-guides/source/developers/dev-environment.rst
+++ b/doc/sphinx-guides/source/developers/dev-environment.rst
@@ -2,263 +2,81 @@
Development Environment
=======================
-These instructions are purposefully opinionated and terse to help you get your development environment up and running as quickly as possible! Please note that familiarity with running commands from the terminal is assumed.
+These instructions are oriented around Docker but the "classic" instructions we used for Dataverse 4 and 5 are still available at :doc:`classic-dev-env`.
.. contents:: |toctitle|
:local:
-Quick Start (Docker)
---------------------
+.. _container-dev-quickstart:
-The quickest way to get Dataverse running is in Docker as explained in :doc:`../container/dev-usage` section of the Container Guide.
-
-
-Classic Dev Environment
------------------------
-
-Since before Docker existed, we have encouraged installing Dataverse and all its dependencies directly on your development machine, as described below. This can be thought of as the "classic" development environment for Dataverse.
+Quickstart
+----------
-However, in 2023 we decided that we'd like to encourage all developers to start using Docker instead and opened https://github.com/IQSS/dataverse/issues/9616 to indicate that we plan to rewrite this page to recommend the use of Docker.
+First, install Java 17, Maven, and Docker.
-There's nothing wrong with the classic instructions below and we don't plan to simply delete them. They are a valid alternative to running Dataverse in Docker. We will likely move them to another page.
+After cloning the `dataverse repo `_, run this:
-Set Up Dependencies
--------------------
+``mvn -Pct clean package docker:run``
-Supported Operating Systems
-~~~~~~~~~~~~~~~~~~~~~~~~~~~
+After some time you should be able to log in:
-Mac OS X or Linux is required because the setup scripts assume the presence of standard Unix utilities.
+- url: http://localhost:8080
+- username: dataverseAdmin
+- password: admin1
-Windows is gaining support through Docker as described in the :doc:`windows` section.
+Detailed Steps
+--------------
Install Java
~~~~~~~~~~~~
-The Dataverse Software requires Java 11.
+The Dataverse Software requires Java 17.
-We suggest downloading OpenJDK from https://adoptopenjdk.net
+On Mac and Windows, we suggest downloading OpenJDK from https://adoptium.net (formerly `AdoptOpenJDK `_) or `SDKMAN `_.
On Linux, you are welcome to use the OpenJDK available from package managers.
-Install Netbeans or Maven
-~~~~~~~~~~~~~~~~~~~~~~~~~
+Install Maven
+~~~~~~~~~~~~~
-NetBeans IDE is recommended, and can be downloaded from http://netbeans.org . Developers may use any editor or IDE. We recommend NetBeans because it is free, works cross platform, has good support for Jakarta EE projects, and includes a required build tool, Maven.
+Follow instructions at https://maven.apache.org
-Below we describe how to build the Dataverse Software war file with Netbeans but if you prefer to use only Maven, you can find installation instructions in the :doc:`tools` section.
+Install and Start Docker
+~~~~~~~~~~~~~~~~~~~~~~~~
-Install Homebrew (Mac Only)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Follow instructions at https://www.docker.com
-On Mac, install Homebrew to simplify the steps below: https://brew.sh
+Be sure to start Docker.
-Clone the Dataverse Software Git Repo
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Git Clone Repo
+~~~~~~~~~~~~~~
Fork https://github.com/IQSS/dataverse and then clone your fork like this:
``git clone git@github.com:[YOUR GITHUB USERNAME]/dataverse.git``
-Build the Dataverse Software War File
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-If you installed Netbeans, follow these steps:
-
-- Launch Netbeans and click "File" and then "Open Project". Navigate to where you put the Dataverse Software code and double-click "Dataverse" to open the project.
-- If you see "resolve project problems," go ahead and let Netbeans try to resolve them. This will probably including downloading dependencies, which can take a while.
-- Allow Netbeans to install nb-javac (required for Java 8 and below).
-- Select "Dataverse" under Projects and click "Run" in the menu and then "Build Project (Dataverse)". Check back for "BUILD SUCCESS" at the end.
-
-If you installed Maven instead of Netbeans, run ``mvn package``. Check for "BUILD SUCCESS" at the end.
-
-NOTE: Do you use a locale different than ``en_US.UTF-8`` on your development machine? Are you in a different timezone
-than Harvard (Eastern Time)? You might experience issues while running tests that were written with these settings
-in mind. The Maven ``pom.xml`` tries to handle this for you by setting the locale to ``en_US.UTF-8`` and timezone
-``UTC``, but more, not yet discovered building or testing problems might lurk in the shadows.
-
-Install jq
-~~~~~~~~~~
-
-On Mac, run this command:
-
-``brew install jq``
-
-On Linux, install ``jq`` from your package manager or download a binary from http://stedolan.github.io/jq/
-
-Install Payara
-~~~~~~~~~~~~~~
-
-Payara 5.2022.3 or higher is required.
-
-To install Payara, run the following commands:
-
-``cd /usr/local``
-
-``sudo curl -O -L https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/5.2022.3/payara-5.2022.3.zip``
-
-``sudo unzip payara-5.2022.3.zip``
-
-``sudo chown -R $USER /usr/local/payara5``
-
-If nexus.payara.fish is ever down for maintenance, Payara distributions are also available from https://repo1.maven.org/maven2/fish/payara/distributions/payara/
-
-Install Service Dependencies Directly on localhost
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Install PostgreSQL
-^^^^^^^^^^^^^^^^^^
-
-The Dataverse Software has been tested with PostgreSQL versions up to 13. PostgreSQL version 10+ is required.
-
-On Mac, go to https://www.postgresql.org/download/macosx/ and choose "Interactive installer by EDB" option. Note that version 13.5 is used in the command line examples below, but the process should be similar for other versions. When prompted to set a password for the "database superuser (postgres)" just enter "password".
-
-After installation is complete, make a backup of the ``pg_hba.conf`` file like this:
-
-``sudo cp /Library/PostgreSQL/13/data/pg_hba.conf /Library/PostgreSQL/13/data/pg_hba.conf.orig``
-
-Then edit ``pg_hba.conf`` with an editor such as vi:
-
-``sudo vi /Library/PostgreSQL/13/data/pg_hba.conf``
-
-In the "METHOD" column, change all instances of "scram-sha-256" (or whatever is in that column) to "trust". This will make it so PostgreSQL doesn't require a password.
-
-In the Finder, click "Applications" then "PostgreSQL 13" and launch the "Reload Configuration" app. Click "OK" after you see "server signaled".
-
-Next, to confirm the edit worked, launch the "pgAdmin" application from the same folder. Under "Browser", expand "Servers" and double click "PostgreSQL 13". When you are prompted for a password, leave it blank and click "OK". If you have successfully edited "pg_hba.conf", you can get in without a password.
-
-On Linux, you should just install PostgreSQL using your favorite package manager, such as ``yum``. (Consult the PostgreSQL section of :doc:`/installation/prerequisites` in the main Installation guide for more info and command line examples). Find ``pg_hba.conf`` and set the authentication method to "trust" and restart PostgreSQL.
-
-Install Solr
-^^^^^^^^^^^^
-
-`Solr `_ 8.11.1 is required.
-
-To install Solr, execute the following commands:
-
-``sudo mkdir /usr/local/solr``
-
-``sudo chown $USER /usr/local/solr``
-
-``cd /usr/local/solr``
-
-``curl -O http://archive.apache.org/dist/lucene/solr/8.11.1/solr-8.11.1.tgz``
-
-``tar xvfz solr-8.11.1.tgz``
-
-``cd solr-8.11.1/server/solr``
-
-``cp -r configsets/_default collection1``
+Build and Run
+~~~~~~~~~~~~~
-``curl -O https://raw.githubusercontent.com/IQSS/dataverse/develop/conf/solr/8.11.1/schema.xml``
+Change into the ``dataverse`` directory you just cloned and run the following command:
-``curl -O https://raw.githubusercontent.com/IQSS/dataverse/develop/conf/solr/8.11.1/schema_dv_mdb_fields.xml``
+``mvn -Pct clean package docker:run``
-``mv schema*.xml collection1/conf``
+Verify
+~~~~~~
-``curl -O https://raw.githubusercontent.com/IQSS/dataverse/develop/conf/solr/8.11.1/solrconfig.xml``
+After some time you should be able to log in:
-``mv solrconfig.xml collection1/conf/solrconfig.xml``
-
-``cd /usr/local/solr/solr-8.11.1``
-
-(Please note that the extra jetty argument below is a security measure to limit connections to Solr to only your computer. For extra security, run a firewall.)
-
-``bin/solr start -j "-Djetty.host=127.0.0.1"``
-
-``bin/solr create_core -c collection1 -d server/solr/collection1/conf``
-
-Install Service Dependencies Using Docker Compose
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-To avoid having to install service dependencies like PostgreSQL or Solr directly on your localhost, there is the alternative of using the ``docker-compose-dev.yml`` file available in the repository root. For this option you need to have Docker and Docker Compose installed on your machine.
-
-The ``docker-compose-dev.yml`` can be configured to only run the service dependencies necessary to support a Dataverse installation running directly on localhost. In addition to PostgreSQL and Solr, it also runs a SMTP server.
-
-Before running the Docker Compose file, you need to update the value of the ``DATAVERSE_DB_USER`` environment variable to ``postgres``. The variable can be found inside the ``.env`` file in the repository root. This step is required as the Dataverse installation script expects that database user.
-
-To run the Docker Compose file, go to the Dataverse repository root, then run:
-
-``docker-compose -f docker-compose-dev.yml up -d --scale dev_dataverse=0``
-
-Note that this command omits the Dataverse container defined in the Docker Compose file, since Dataverse is going to be installed directly on localhost in the next section.
-
-The command runs the containers in detached mode, but if you want to run them attached and thus view container logs in real time, remove the ``-d`` option from the command.
-
-Data volumes of each dependency will be persisted inside the ``docker-dev-volumes`` folder, inside the repository root.
-
-If you want to stop the containers, then run (for detached mode only, otherwise use ``Ctrl + C``):
-
-``docker-compose -f docker-compose-dev.yml stop``
-
-If you want to remove the containers, then run:
-
-``docker-compose -f docker-compose-dev.yml down``
-
-If you want to run a single container (the mail server, for example) then run:
-
-``docker-compose -f docker-compose-dev.yml up dev_smtp``
-
-For a fresh installation, and before running the Software Installer Script, it is recommended to delete the docker-dev-env folder to avoid installation problems due to existing data in the containers.
-
-Run the Dataverse Software Installer Script
--------------------------------------------
-
-Navigate to the directory where you cloned the Dataverse Software git repo change directories to the ``scripts/installer`` directory like this:
-
-``cd scripts/installer``
-
-Create a Python virtual environment, activate it, then install dependencies:
-
-``python3 -m venv venv``
-
-``source venv/bin/activate``
-
-``pip install psycopg2-binary``
-
-The installer will try to connect to the SMTP server you tell it to use. If you haven't used the Docker Compose option for setting up the dependencies, or you don't have a mail server handy, you can run ``nc -l 25`` in another terminal and choose "localhost" (the default) to get past this check.
-
-Finally, run the installer (see also :download:`README_python.txt <../../../../scripts/installer/README_python.txt>` if necessary):
-
-``python3 install.py``
-
-Verify the Dataverse Software is Running
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-After the script has finished, you should be able to log into your Dataverse installation with the following credentials:
-
-- http://localhost:8080
+- url: http://localhost:8080
- username: dataverseAdmin
-- password: admin
-
-Configure Your Development Environment for Publishing
------------------------------------------------------
-
-Run the following command:
-
-``curl http://localhost:8080/api/admin/settings/:DoiProvider -X PUT -d FAKE``
-
-This will disable DOI registration by using a fake (in-code) DOI provider. Please note that this feature is only available in Dataverse Software 4.10+ and that at present, the UI will give no indication that the DOIs thus minted are fake.
-
-Developers may also wish to consider using :ref:`PermaLinks `
-
-Configure Your Development Environment for GUI Edits
-----------------------------------------------------
-
-Out of the box, a JSF setting is configured for production use and prevents edits to the GUI (xhtml files) from being visible unless you do a full deployment.
-
-It is recommended that you run the following command so that simply saving the xhtml file in Netbeans is enough for the change to show up.
-
-``asadmin create-system-properties "dataverse.jsf.refresh-period=1"``
-
-For more on JSF settings like this, see :ref:`jsf-config`.
-
-Next Steps
-----------
+- password: admin1
-If you can log in to the Dataverse installation, great! If not, please see the :doc:`troubleshooting` section. For further assistance, please see "Getting Help" in the :doc:`intro` section.
+More Information
+----------------
-You're almost ready to start hacking on code. Now that the installer script has you up and running, you need to continue on to the :doc:`tips` section to get set up to deploy code from your IDE or the command line.
+See also the :doc:`/container/dev-usage` section of the Container Guide.
-----
+Getting Help
+------------
-Previous: :doc:`intro` | Next: :doc:`tips`
+Please feel free to reach out at https://chat.dataverse.org or https://groups.google.com/g/dataverse-dev if you have any difficulty setting up a dev environment!
diff --git a/doc/sphinx-guides/source/developers/index.rst b/doc/sphinx-guides/source/developers/index.rst
index d70b682fcda..3ac9e955ea2 100755
--- a/doc/sphinx-guides/source/developers/index.rst
+++ b/doc/sphinx-guides/source/developers/index.rst
@@ -27,6 +27,7 @@ Developer Guide
deployment
containers
making-releases
+ making-library-releases
metadataexport
tools
unf/index
@@ -41,4 +42,5 @@ Developer Guide
dataset-migration-api
workflows
fontcustom
+ classic-dev-env
diff --git a/doc/sphinx-guides/source/developers/intro.rst b/doc/sphinx-guides/source/developers/intro.rst
index 7f4e8c1ba34..4a64c407fc1 100755
--- a/doc/sphinx-guides/source/developers/intro.rst
+++ b/doc/sphinx-guides/source/developers/intro.rst
@@ -52,7 +52,9 @@ Related Guides
If you are a developer who wants to make use of the Dataverse Software APIs, please see the :doc:`/api/index`. If you have front-end UI questions, please see the :doc:`/style/index`.
-If you are a sysadmin who likes to code, you may be interested in hacking on installation scripts mentioned in the :doc:`/installation/index`. We validate the installation scripts with :doc:`/developers/tools` such as `Vagrant `_ and Docker (see the :doc:`containers` section).
+If you are a sysadmin who likes to code, you may be interested in hacking on installation scripts mentioned in the :doc:`/installation/index`.
+
+If you are a Docker enthusiasts, please check out the :doc:`/container/index`.
Related Projects
----------------
diff --git a/doc/sphinx-guides/source/developers/make-data-count.rst b/doc/sphinx-guides/source/developers/make-data-count.rst
index a3c0d10dc5e..8eaa5c0d7f8 100644
--- a/doc/sphinx-guides/source/developers/make-data-count.rst
+++ b/doc/sphinx-guides/source/developers/make-data-count.rst
@@ -30,15 +30,13 @@ Full Setup
The recommended way to work on the Make Data Count feature is to spin up an EC2 instance that has both the Dataverse Software and Counter Processor installed. Go to the :doc:`deployment` page for details on how to spin up an EC2 instance and make sure that your Ansible file is configured to install Counter Processor before running the "create" script.
-(Alternatively, you can try installing Counter Processor in Vagrant. :download:`setup-counter-processor.sh <../../../../scripts/vagrant/setup-counter-processor.sh>` might help you get it installed.)
-
After you have spun to your EC2 instance, set ``:MDCLogPath`` so that the Dataverse installation creates a log for Counter Processor to operate on. For more on this database setting, see the :doc:`/installation/config` section of the Installation Guide.
Next you need to have the Dataverse installation add some entries to the log that Counter Processor will operate on. To do this, click on some published datasets and download some files.
-Next you should run Counter Processor to convert the log into a SUSHI report, which is in JSON format. Before running Counter Processor, you need to put a configuration file into place. As a starting point use :download:`counter-processor-config.yaml <../../../../scripts/vagrant/counter-processor-config.yaml>` and edit the file, paying particular attention to the following settings:
+Next you should run Counter Processor to convert the log into a SUSHI report, which is in JSON format. Before running Counter Processor, you need to put a configuration file into place. As a starting point use :download:`counter-processor-config.yaml <../_static/developers/counter-processor-config.yaml>` and edit the file, paying particular attention to the following settings:
-- ``log_name_pattern`` You might want something like ``/usr/local/payara5/glassfish/domains/domain1/logs/counter_(yyyy-mm-dd).log``
+- ``log_name_pattern`` You might want something like ``/usr/local/payara6/glassfish/domains/domain1/logs/counter_(yyyy-mm-dd).log``
- ``year_month`` You should probably set this to the current month.
- ``output_file`` This needs to be a directory that the "dataverse" Unix user can read but that the "counter" user can write to. In dev, you can probably get away with "/tmp" as the directory.
- ``platform`` Out of the box from Counter Processor this is set to ``Dash`` but this should be changed to match the name of your Dataverse installation. Examples are "Harvard Dataverse Repository" for Harvard University or "LibraData" for the University of Virginia.
diff --git a/doc/sphinx-guides/source/developers/making-library-releases.rst b/doc/sphinx-guides/source/developers/making-library-releases.rst
new file mode 100755
index 00000000000..63b6eeb1c2a
--- /dev/null
+++ b/doc/sphinx-guides/source/developers/making-library-releases.rst
@@ -0,0 +1,93 @@
+=======================
+Making Library Releases
+=======================
+
+.. contents:: |toctitle|
+ :local:
+
+Introduction
+------------
+
+Note: See :doc:`making-releases` for Dataverse itself.
+
+We release Java libraries to Maven Central that are used by Dataverse (and perhaps `other `_ `software `_!):
+
+- https://central.sonatype.com/namespace/org.dataverse
+- https://central.sonatype.com/namespace/io.gdcc
+
+We release JavaScript/TypeScript libraries to npm:
+
+- https://www.npmjs.com/package/@iqss/dataverse-design-system
+
+Maven Central (Java)
+--------------------
+
+From the perspective of the Maven Central, we are both `producers `_ because we publish/release libraries there and `consumers `_ because we pull down those libraries (and many others) when we build Dataverse.
+
+Releasing Existing Libraries to Maven Central
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+If you need to release an existing library, all the setup should be done already. The steps below assume that GitHub Actions are in place to do the heavy lifting for you, such as signing artifacts with GPG.
+
+Releasing a Snapshot Version to Maven Central
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+`Snapshot `_ releases are published automatically through GitHub Actions (e.g. through a `snapshot workflow `_ for the SWORD library) every time a pull request is merged (or the default branch, typically ``main``, is otherwise updated).
+
+That is to say, to make a snapshot release, you only need to get one or more commits into the default branch.
+
+Releasing a Release (Non-Snapshot) Version to Maven Central
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+From a pom.xml it may not be apparent that snapshots like ``6.0-SNAPSHOT`` might be changing under your feet. Browsing the snapshot repository (e.g. our `UNF 6.0-SNAPSHOT `_), may reveal versions changing over time. To finalize the code and stop it from changing, we publish/release what Maven calls a "`release version `_". This will remove ``-SNAPSHOT`` from the version (through an ``mvn`` command).
+
+Non-snapshot releases (`release `_ versions) are published automatically through GitHub Actions (e.g. through a `release workflow `_), kicked off locally by an ``mvn`` command that invokes the `Maven Release Plugin `_.
+
+First, run a clean:
+
+``mvn release:clean``
+
+Then run a prepare:
+
+``mvn release:prepare``
+
+The prepare step is interactive. You will be prompted for the following information:
+
+- the release version (e.g. `2.0.0 `_)
+- the git tag to create and push (e.g. `sword2-server-2.0.0 `_)
+- the next development (snapshot) version (e.g. `2.0.1-SNAPSHOT `_)
+
+These examples from the SWORD library. Below is what to expect from the interactive session. In many cases, you can just hit enter to accept the defaults.
+
+.. code-block:: bash
+
+ [INFO] 5/17 prepare:map-release-versions
+ What is the release version for "SWORD v2 Common Server Library (forked)"? (sword2-server) 2.0.0: :
+ [INFO] 6/17 prepare:input-variables
+ What is the SCM release tag or label for "SWORD v2 Common Server Library (forked)"? (sword2-server) sword2-server-2.0.0: :
+ [INFO] 7/17 prepare:map-development-versions
+ What is the new development version for "SWORD v2 Common Server Library (forked)"? (sword2-server) 2.0.1-SNAPSHOT: :
+ [INFO] 8/17 prepare:rewrite-poms-for-release
+
+It can take some time for the jar to be visible on Maven Central. You can start by looking on the repo1 server, like this: https://repo1.maven.org/maven2/io/gdcc/sword2-server/2.0.0/
+
+Don't bother putting the new version in a pom.xml until you see it on repo1.
+
+Note that the next snapshot release should be available as well, like this: https://s01.oss.sonatype.org/content/groups/staging/io/gdcc/sword2-server/2.0.1-SNAPSHOT/
+
+Releasing a New Library to Maven Central
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+At a high level:
+
+- Use an existing pom.xml as a starting point.
+- Use existing GitHub Actions workflows as a starting point.
+- Create secrets in the new library's GitHub repo used by the workflow.
+- If you need an entire new namespace, look at previous issues such as https://issues.sonatype.org/browse/OSSRH-94575 and https://issues.sonatype.org/browse/OSSRH-94577
+
+npm (JavaScript/TypeScript)
+---------------------------
+
+Currently, publishing `@iqss/dataverse-design-system `_ to npm done manually. We plan to automate this as part of https://github.com/IQSS/dataverse-frontend/issues/140
+
+https://www.npmjs.com/package/js-dataverse is the previous 1.0 version of js-dataverse. No 1.x releases are planned. We plan to publish 2.0 (used by the new frontend) as discussed in https://github.com/IQSS/dataverse-frontend/issues/13
\ No newline at end of file
diff --git a/doc/sphinx-guides/source/developers/making-releases.rst b/doc/sphinx-guides/source/developers/making-releases.rst
index a2575bb5f50..23c4773a06e 100755
--- a/doc/sphinx-guides/source/developers/making-releases.rst
+++ b/doc/sphinx-guides/source/developers/making-releases.rst
@@ -8,6 +8,8 @@ Making Releases
Introduction
------------
+Note: See :doc:`making-library-releases` for how to publish our libraries to Maven Central.
+
See :doc:`version-control` for background on our branching strategy.
The steps below describe making both regular releases and hotfix releases.
diff --git a/doc/sphinx-guides/source/developers/testing.rst b/doc/sphinx-guides/source/developers/testing.rst
index c228d8e20ca..acaeccf4f23 100755
--- a/doc/sphinx-guides/source/developers/testing.rst
+++ b/doc/sphinx-guides/source/developers/testing.rst
@@ -47,12 +47,14 @@ Writing Unit Tests with JUnit
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
We are aware that there are newer testing tools such as TestNG, but we use `JUnit `_ because it's tried and true.
-We support both (legacy) JUnit 4.x tests (forming the majority of our tests) and
-newer JUnit 5 based testing.
+We support JUnit 5 based testing and require new tests written with it.
+(Since Dataverse 6.0, we migrated all of our tests formerly based on JUnit 4.)
-NOTE: When adding new tests, you should give JUnit 5 a go instead of adding more dependencies to JUnit 4.x.
-
-If writing tests is new to you, poke around existing unit tests which all end in ``Test.java`` and live under ``src/test``. Each test is annotated with ``@Test`` and should have at least one assertion which specifies the expected result. In Netbeans, you can run all the tests in it by clicking "Run" -> "Test File". From the test file, you should be able to navigate to the code that's being tested by right-clicking on the file and clicking "Navigate" -> "Go to Test/Tested class". Likewise, from the code, you should be able to use the same "Navigate" menu to go to the tests.
+If writing tests is new to you, poke around existing unit tests which all end in ``Test.java`` and live under ``src/test``.
+Each test is annotated with ``@Test`` and should have at least one assertion which specifies the expected result.
+In Netbeans, you can run all the tests in it by clicking "Run" -> "Test File".
+From the test file, you should be able to navigate to the code that's being tested by right-clicking on the file and clicking "Navigate" -> "Go to Test/Tested class".
+Likewise, from the code, you should be able to use the same "Navigate" menu to go to the tests.
NOTE: Please remember when writing tests checking possibly localized outputs to check against ``en_US.UTF-8`` and ``UTC``
l10n strings!
@@ -62,22 +64,24 @@ Refactoring Code to Make It Unit-Testable
Existing code is not necessarily written in a way that lends itself to easy testing. Generally speaking, it is difficult to write unit tests for both JSF "backing" beans (which end in ``Page.java``) and "service" beans (which end in ``Service.java``) because they require the database to be running in order to test them. If service beans can be exercised via API they can be tested with integration tests (described below) but a good technique for making the logic testable it to move code to "util beans" (which end in ``Util.java``) that operate on Plain Old Java Objects (POJOs). ``PrivateUrlUtil.java`` is a good example of moving logic from ``PrivateUrlServiceBean.java`` to a "util" bean to make the code testable.
-Parameterized Tests and JUnit Theories
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Parameterized Tests
+^^^^^^^^^^^^^^^^^^^
+
Often times you will want to test a method multiple times with similar values.
In order to avoid test bloat (writing a test for every data combination),
JUnit offers Data-driven unit tests. This allows a test to be run for each set
of defined data values.
-JUnit 4 uses ``Parameterized.class`` and ``Theories.class``. For reference, take a look at issue https://github.com/IQSS/dataverse/issues/5619.
-
-JUnit 5 doesn't offer theories (see `jqwik `_ for this), but
-greatly extended parameterized testing. Some guidance how to write those:
+JUnit 5 offers great parameterized testing. Some guidance how to write those:
- https://junit.org/junit5/docs/current/user-guide/#writing-tests-parameterized-tests
- https://www.baeldung.com/parameterized-tests-junit-5
- https://blog.codefx.org/libraries/junit-5-parameterized-tests/
-- See also some examples in our codebase.
+- See also many examples in our codebase.
+
+Note that JUnit 5 also offers support for custom test parameter resolvers. This enables keeping tests cleaner,
+as preparation might happen within some extension and the test code is more focused on the actual testing.
+See https://junit.org/junit5/docs/current/user-guide/#extensions-parameter-resolution for more information.
JUnit 5 Test Helper Extensions
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -116,11 +120,14 @@ In addition, there is a writeup on "The Testable Command" at https://github.com/
Running Non-Essential (Excluded) Unit Tests
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-You should be aware that some unit tests have been deemed "non-essential" and have been annotated with ``@Category(NonEssentialTests.class)`` and are excluded from the "dev" Maven profile, which is the default profile. All unit tests (that have not been annotated with ``@Ignore``), including these non-essential tests, are run from continuous integration systems such as Jenkins and GitHub Actions with the following ``mvn`` command that invokes a non-default profile:
+You should be aware that some unit tests have been deemed "non-essential" and have been annotated with ``@Tag(Tags.NOT_ESSENTIAL_UNITTESTS)`` and are excluded from the "dev" Maven profile, which is the default profile.
+All unit tests (that have not been annotated with ``@Disable``), including these non-essential tests, are run from continuous integration systems such as Jenkins and GitHub Actions with the following ``mvn`` command that invokes a non-default profile:
``mvn test -P all-unit-tests``
-Generally speaking, unit tests have been flagged as non-essential because they are slow or because they require an Internet connection. You should not feel obligated to run these tests continuously but you can use the ``mvn`` command above to run them. To iterate on the unit test in Netbeans and execute it with "Run -> Test File", you must temporarily comment out the annotation flagging the test as non-essential.
+Generally speaking, unit tests have been flagged as non-essential because they are slow or because they require an Internet connection.
+You should not feel obligated to run these tests continuously but you can use the ``mvn`` command above to run them.
+To iterate on the unit test in Netbeans and execute it with "Run -> Test File", you must temporarily comment out the annotation flagging the test as non-essential.
Integration Tests
-----------------
@@ -173,12 +180,7 @@ Finally, run the script:
Running the full API test suite using Docker
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-.. note::
- Sunsetting of this module is imminent.** There is no schedule yet, but expect it to go away.
- Please let the `Dataverse Containerization Working Group `_ know if you are a user and
- what should be preserved.
-
-To run the full suite of integration tests on your laptop, we recommend using the "all in one" Docker configuration described in ``conf/docker-aio/readme.md`` in the root of the repo.
+To run the full suite of integration tests on your laptop, running Dataverse and its dependencies in Docker, as explained in the :doc:`/container/dev-usage` section of the Container Guide.
Alternatively, you can run tests against the app server running on your laptop by following the "getting set up" steps below.
@@ -308,9 +310,9 @@ To run these tests, simply call out to Maven:
Measuring Coverage of Integration Tests
---------------------------------------
-Measuring the code coverage of integration tests with Jacoco requires several steps. In order to make these steps clear we'll use "/usr/local/payara5" as the Payara directory and "dataverse" as the Payara Unix user.
+Measuring the code coverage of integration tests with Jacoco requires several steps. In order to make these steps clear we'll use "/usr/local/payara6" as the Payara directory and "dataverse" as the Payara Unix user.
-Please note that this was tested under Glassfish 4 but it is hoped that the same steps will work with Payara 5.
+Please note that this was tested under Glassfish 4 but it is hoped that the same steps will work with Payara.
Add jacocoagent.jar to Payara
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -329,9 +331,9 @@ Note that we are running the following commands as the user "dataverse". In shor
cd local/jacoco-0.8.1
wget https://github.com/jacoco/jacoco/releases/download/v0.8.1/jacoco-0.8.1.zip
unzip jacoco-0.8.1.zip
- /usr/local/payara5/bin/asadmin stop-domain
- cp /home/dataverse/local/jacoco-0.8.1/lib/jacocoagent.jar /usr/local/payara5/glassfish/lib
- /usr/local/payara5/bin/asadmin start-domain
+ /usr/local/payara6/bin/asadmin stop-domain
+ cp /home/dataverse/local/jacoco-0.8.1/lib/jacocoagent.jar /usr/local/payara6/glassfish/lib
+ /usr/local/payara6/bin/asadmin start-domain
Add jacococli.jar to the WAR File
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -354,21 +356,21 @@ Run this as the "dataverse" user.
.. code-block:: bash
- /usr/local/payara5/bin/asadmin deploy dataverse-jacoco.war
+ /usr/local/payara6/bin/asadmin deploy dataverse-jacoco.war
-Note that after deployment the file "/usr/local/payara5/glassfish/domains/domain1/config/jacoco.exec" exists and is empty.
+Note that after deployment the file "/usr/local/payara6/glassfish/domains/domain1/config/jacoco.exec" exists and is empty.
Run Integration Tests
~~~~~~~~~~~~~~~~~~~~~
Note that even though you see "docker-aio" in the command below, we assume you are not necessarily running the test suite within Docker. (Some day we'll probably move this script to another directory.) For this reason, we pass the URL with the normal port (8080) that app servers run on to the ``run-test-suite.sh`` script.
-Note that "/usr/local/payara5/glassfish/domains/domain1/config/jacoco.exec" will become non-empty after you stop and start Payara. You must stop and start Payara before every run of the integration test suite.
+Note that "/usr/local/payara6/glassfish/domains/domain1/config/jacoco.exec" will become non-empty after you stop and start Payara. You must stop and start Payara before every run of the integration test suite.
.. code-block:: bash
- /usr/local/payara5/bin/asadmin stop-domain
- /usr/local/payara5/bin/asadmin start-domain
+ /usr/local/payara6/bin/asadmin stop-domain
+ /usr/local/payara6/bin/asadmin start-domain
git clone https://github.com/IQSS/dataverse.git
cd dataverse
conf/docker-aio/run-test-suite.sh http://localhost:8080
@@ -383,7 +385,7 @@ Run these commands as the "dataverse" user. The ``cd dataverse`` means that you
.. code-block:: bash
cd dataverse
- java -jar /home/dataverse/local/jacoco-0.8.1/lib/jacococli.jar report --classfiles target/classes --sourcefiles src/main/java --html target/coverage-it/ /usr/local/payara5/glassfish/domains/domain1/config/jacoco.exec
+ java -jar /home/dataverse/local/jacoco-0.8.1/lib/jacococli.jar report --classfiles target/classes --sourcefiles src/main/java --html target/coverage-it/ /usr/local/payara6/glassfish/domains/domain1/config/jacoco.exec
Read Code Coverage Report
~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -504,7 +506,6 @@ Browser-Based Testing
Installation Testing
~~~~~~~~~~~~~~~~~~~~
-- Run `vagrant up` on a server to test the installer
- Work with @donsizemore to automate testing of https://github.com/GlobalDataverseCommunityConsortium/dataverse-ansible
Future Work on Load/Performance Testing
diff --git a/doc/sphinx-guides/source/developers/tips.rst b/doc/sphinx-guides/source/developers/tips.rst
index bf75a05f84e..e1ee40cafa5 100755
--- a/doc/sphinx-guides/source/developers/tips.rst
+++ b/doc/sphinx-guides/source/developers/tips.rst
@@ -19,20 +19,20 @@ Undeploy the war File from the Dataverse Software Installation Script
Because the initial deployment of the war file was done outside of Netbeans by the Dataverse Software installation script, it's a good idea to undeploy that war file to give Netbeans a clean slate to work with.
-Assuming you installed Payara in ``/usr/local/payara5``, run the following ``asadmin`` command to see the version of the Dataverse Software that the Dataverse Software installation script deployed:
+Assuming you installed Payara in ``/usr/local/payara6``, run the following ``asadmin`` command to see the version of the Dataverse Software that the Dataverse Software installation script deployed:
-``/usr/local/payara5/bin/asadmin list-applications``
+``/usr/local/payara6/bin/asadmin list-applications``
You will probably see something like ``dataverse-5.0 `` as the output. To undeploy, use whichever version you see like this:
-``/usr/local/payara5/bin/asadmin undeploy dataverse-5.0``
+``/usr/local/payara6/bin/asadmin undeploy dataverse-5.0``
Now that Payara doesn't have anything deployed, we can proceed with getting Netbeans set up to deploy the code.
Add Payara as a Server in Netbeans
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-Launch Netbeans and click "Tools" and then "Servers". Click "Add Server" and select "Payara Server" and set the installation location to ``/usr/local/payara5``. The defaults are fine so you can click "Next" and "Finish".
+Launch Netbeans and click "Tools" and then "Servers". Click "Add Server" and select "Payara Server" and set the installation location to ``/usr/local/payara6``. The defaults are fine so you can click "Next" and "Finish".
Please note that if you are on a Mac, Netbeans may be unable to start Payara due to proxy settings in Netbeans. Go to the "General" tab in Netbeans preferences and click "Test connection" to see if you are affected. If you get a green checkmark, you're all set. If you get a red exclamation mark, change "Proxy Settings" to "No Proxy" and retest. A more complicated answer having to do with changing network settings is available at https://discussions.apple.com/thread/7680039?answerId=30715103022#30715103022 and the bug is also described at https://netbeans.org/bugzilla/show_bug.cgi?id=268076
@@ -117,7 +117,7 @@ Deploying With ``asadmin``
Sometimes you want to deploy code without using Netbeans or from the command line on a server you have ssh'ed into.
-For the ``asadmin`` commands below, we assume you have already changed directories to ``/usr/local/payara5/glassfish/bin`` or wherever you have installed Payara.
+For the ``asadmin`` commands below, we assume you have already changed directories to ``/usr/local/payara6/glassfish/bin`` or wherever you have installed Payara.
There are four steps to this process:
diff --git a/doc/sphinx-guides/source/developers/tools.rst b/doc/sphinx-guides/source/developers/tools.rst
index cbd27d6e8d2..a21becd14cf 100755
--- a/doc/sphinx-guides/source/developers/tools.rst
+++ b/doc/sphinx-guides/source/developers/tools.rst
@@ -25,21 +25,6 @@ Maven
With Maven installed you can run ``mvn package`` and ``mvn test`` from the command line. It can be downloaded from https://maven.apache.org
-.. _vagrant:
-
-Vagrant
-+++++++
-
-Vagrant allows you to spin up a virtual machine running the Dataverse Software on your development workstation. You'll need to install Vagrant from https://www.vagrantup.com and VirtualBox from https://www.virtualbox.org.
-
-We assume you have already cloned the repo from https://github.com/IQSS/dataverse as explained in the :doc:`/developers/dev-environment` section.
-
-From the root of the git repo (where the ``Vagrantfile`` is), run ``vagrant up`` and eventually you should be able to reach a Dataverse installation at http://localhost:8888 (the ``forwarded_port`` indicated in the ``Vagrantfile``).
-
-Please note that running ``vagrant up`` for the first time should run the ``downloads/download.sh`` script for you to download required software such as an app server, Solr, etc. However, these dependencies change over time so it's a place to look if ``vagrant up`` was working but later fails.
-
-On Windows if you see an error like ``/usr/bin/perl^M: bad interpreter`` you might need to run ``dos2unix`` on the installation scripts.
-
PlantUML
++++++++
diff --git a/doc/sphinx-guides/source/installation/advanced.rst b/doc/sphinx-guides/source/installation/advanced.rst
index a842d566595..87f2a4fd0ab 100644
--- a/doc/sphinx-guides/source/installation/advanced.rst
+++ b/doc/sphinx-guides/source/installation/advanced.rst
@@ -13,8 +13,8 @@ Multiple App Servers
You should be conscious of the following when running multiple app servers.
- Only one app server can be the dedicated timer server, as explained in the :doc:`/admin/timers` section of the Admin Guide.
-- When users upload a logo or footer for their Dataverse collection using the "theme" feature described in the :doc:`/user/dataverse-management` section of the User Guide, these logos are stored only on the app server the user happened to be on when uploading the logo. By default these logos and footers are written to the directory ``/usr/local/payara5/glassfish/domains/domain1/docroot/logos``.
-- When a sitemap is created by an app server it is written to the filesystem of just that app server. By default the sitemap is written to the directory ``/usr/local/payara5/glassfish/domains/domain1/docroot/sitemap``.
+- When users upload a logo or footer for their Dataverse collection using the "theme" feature described in the :doc:`/user/dataverse-management` section of the User Guide, these logos are stored only on the app server the user happened to be on when uploading the logo. By default these logos and footers are written to the directory ``/usr/local/payara6/glassfish/domains/domain1/docroot/logos``.
+- When a sitemap is created by an app server it is written to the filesystem of just that app server. By default the sitemap is written to the directory ``/usr/local/payara6/glassfish/domains/domain1/docroot/sitemap``.
- If Make Data Count is used, its raw logs must be copied from each app server to single instance of Counter Processor. See also :ref:`:MDCLogPath` section in the Configuration section of this guide and the :doc:`/admin/make-data-count` section of the Admin Guide.
- Dataset draft version logging occurs separately on each app server. See :ref:`edit-draft-versions-logging` section in Monitoring of the Admin Guide for details.
- Password aliases (``dataverse.db.password``, etc.) are stored per app server.
diff --git a/doc/sphinx-guides/source/installation/config.rst b/doc/sphinx-guides/source/installation/config.rst
index 8493702406b..f9fe74afc7c 100644
--- a/doc/sphinx-guides/source/installation/config.rst
+++ b/doc/sphinx-guides/source/installation/config.rst
@@ -501,7 +501,7 @@ Logging & Slow Performance
File Storage: Using a Local Filesystem and/or Swift and/or Object Stores and/or Trusted Remote Stores
-----------------------------------------------------------------------------------------------------
-By default, a Dataverse installation stores all data files (files uploaded by end users) on the filesystem at ``/usr/local/payara5/glassfish/domains/domain1/files``. This path can vary based on answers you gave to the installer (see the :ref:`dataverse-installer` section of the Installation Guide) or afterward by reconfiguring the ``dataverse.files.\.directory`` JVM option described below.
+By default, a Dataverse installation stores all data files (files uploaded by end users) on the filesystem at ``/usr/local/payara6/glassfish/domains/domain1/files``. This path can vary based on answers you gave to the installer (see the :ref:`dataverse-installer` section of the Installation Guide) or afterward by reconfiguring the ``dataverse.files.\.directory`` JVM option described below.
A Dataverse installation can alternately store files in a Swift or S3-compatible object store, and can now be configured to support multiple stores at once. With a multi-store configuration, the location for new files can be controlled on a per-Dataverse collection basis.
@@ -975,7 +975,7 @@ All of these processes are triggered after finishing transfers over the wire and
Before being moved there,
- JSF Web UI uploads are stored at :ref:`${dataverse.files.uploads} `, defaulting to
- ``/usr/local/payara5/glassfish/domains/domain1/uploads`` folder in a standard installation. This place is
+ ``/usr/local/payara6/glassfish/domains/domain1/uploads`` folder in a standard installation. This place is
configurable and might be set to a separate disk volume where stale uploads are purged periodically.
- API uploads are stored at the system's temporary files location indicated by the Java system property
``java.io.tmpdir``, defaulting to ``/tmp`` on Linux. If this location is backed by a `tmpfs `_
@@ -1053,7 +1053,7 @@ Custom Navbar Logo
The Dataverse Software allows you to replace the default Dataverse Project icon and name branding in the navbar with your own custom logo. Note that this logo is separate from the logo used in the theme of the root Dataverse collection (see :ref:`theme`).
-The custom logo image file is expected to be small enough to fit comfortably in the navbar, no more than 50 pixels in height and 160 pixels in width. Create a ``navbar`` directory in your Payara ``logos`` directory and place your custom logo there. By default, your logo image file will be located at ``/usr/local/payara5/glassfish/domains/domain1/docroot/logos/navbar/logo.png``.
+The custom logo image file is expected to be small enough to fit comfortably in the navbar, no more than 50 pixels in height and 160 pixels in width. Create a ``navbar`` directory in your Payara ``logos`` directory and place your custom logo there. By default, your logo image file will be located at ``/usr/local/payara6/glassfish/domains/domain1/docroot/logos/navbar/logo.png``.
Given this location for the custom logo image file, run this curl command to add it to your settings:
@@ -1518,7 +1518,7 @@ The Google Cloud Archiver also requires a key file that must be renamed to 'goog
For example:
-``cp /usr/local/payara5/glassfish/domains/domain1/files/googlecloudkey.json``
+``cp /usr/local/payara6/glassfish/domains/domain1/files/googlecloudkey.json``
.. _S3 Archiver Configuration:
@@ -1634,7 +1634,7 @@ You have a couple of options for putting an updated robots.txt file into product
For more of an explanation of ``ProxyPassMatch`` see the :doc:`shibboleth` section.
-If you are not fronting Payara with Apache you'll need to prevent Payara from serving the robots.txt file embedded in the war file by overwriting robots.txt after the war file has been deployed. The downside of this technique is that you will have to remember to overwrite robots.txt in the "exploded" war file each time you deploy the war file, which probably means each time you upgrade to a new version of the Dataverse Software. Furthermore, since the version of the Dataverse Software is always incrementing and the version can be part of the file path, you will need to be conscious of where on disk you need to replace the file. For example, for Dataverse Software 4.6.1 the path to robots.txt may be ``/usr/local/payara5/glassfish/domains/domain1/applications/dataverse-4.6.1/robots.txt`` with the version number ``4.6.1`` as part of the path.
+If you are not fronting Payara with Apache you'll need to prevent Payara from serving the robots.txt file embedded in the war file by overwriting robots.txt after the war file has been deployed. The downside of this technique is that you will have to remember to overwrite robots.txt in the "exploded" war file each time you deploy the war file, which probably means each time you upgrade to a new version of the Dataverse Software. Furthermore, since the version of the Dataverse Software is always incrementing and the version can be part of the file path, you will need to be conscious of where on disk you need to replace the file. For example, for Dataverse Software 4.6.1 the path to robots.txt may be ``/usr/local/payara6/glassfish/domains/domain1/applications/dataverse-4.6.1/robots.txt`` with the version number ``4.6.1`` as part of the path.
Creating a Sitemap and Submitting it to Search Engines
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -1647,7 +1647,7 @@ Create or update your sitemap by adding the following curl command to cron to ru
This will create or update a file in the following location unless you have customized your installation directory for Payara:
-``/usr/local/payara5/glassfish/domains/domain1/docroot/sitemap/sitemap.xml``
+``/usr/local/payara6/glassfish/domains/domain1/docroot/sitemap/sitemap.xml``
On Dataverse installation with many datasets, the creation or updating of the sitemap can take a while. You can check Payara's server.log file for "BEGIN updateSiteMap" and "END updateSiteMap" lines to know when the process started and stopped and any errors in between.
@@ -1690,7 +1690,7 @@ When changing values these values with ``asadmin``, you'll need to delete the ol
``./asadmin create-jvm-options "-Ddataverse.fqdn=dataverse.example.com"``
-It's also possible to change these values by stopping Payara, editing ``payara5/glassfish/domains/domain1/config/domain.xml``, and restarting Payara.
+It's also possible to change these values by stopping Payara, editing ``payara6/glassfish/domains/domain1/config/domain.xml``, and restarting Payara.
.. _dataverse.fqdn:
@@ -1786,7 +1786,7 @@ Configure a folder to store the incoming file stream during uploads (before tran
Please also see :ref:`temporary-file-storage` for more details.
You can use an absolute path or a relative, which is relative to the application server domain directory.
-Defaults to ``./uploads``, which resolves to ``/usr/local/payara5/glassfish/domains/domain1/uploads`` in a default
+Defaults to ``./uploads``, which resolves to ``/usr/local/payara6/glassfish/domains/domain1/uploads`` in a default
installation.
Can also be set via *MicroProfile Config API* sources, e.g. the environment variable ``DATAVERSE_FILES_UPLOADS``.
@@ -3485,7 +3485,7 @@ Sets how long a cached metrics result is used before re-running the query for a
Sets the path where the raw Make Data Count logs are stored before being processed. If not set, no logs will be created for Make Data Count. See also the :doc:`/admin/make-data-count` section of the Admin Guide.
-``curl -X PUT -d '/usr/local/payara5/glassfish/domains/domain1/logs' http://localhost:8080/api/admin/settings/:MDCLogPath``
+``curl -X PUT -d '/usr/local/payara6/glassfish/domains/domain1/logs' http://localhost:8080/api/admin/settings/:MDCLogPath``
.. _:DisplayMDCMetrics:
diff --git a/doc/sphinx-guides/source/installation/installation-main.rst b/doc/sphinx-guides/source/installation/installation-main.rst
index 8559d6ce194..021a97415e3 100755
--- a/doc/sphinx-guides/source/installation/installation-main.rst
+++ b/doc/sphinx-guides/source/installation/installation-main.rst
@@ -28,8 +28,8 @@ Unpack the zip file - this will create the directory ``dvinstall``.
Just make sure the user running the installer has write permission to:
-- /usr/local/payara5/glassfish/lib
-- /usr/local/payara5/glassfish/domains/domain1
+- /usr/local/payara6/glassfish/lib
+- /usr/local/payara6/glassfish/domains/domain1
- the current working directory of the installer (it currently writes its logfile there), and
- your jvm-option specified files.dir
@@ -47,7 +47,7 @@ Follow the instructions in the text file.
The script will prompt you for some configuration values. If this is a test/evaluation installation, it may be possible to accept the default values provided for most of the settings:
- Internet Address of your host: localhost
-- Payara Directory: /usr/local/payara5
+- Payara Directory: /usr/local/payara6
- Payara User: current user running the installer script
- Administrator email address for this Dataverse installation: (none)
- SMTP (mail) server to relay notification messages: localhost
@@ -98,7 +98,7 @@ The supplied site URL will be saved under the JVM option :ref:`dataverse.siteUrl
**IMPORTANT:** Please note, that "out of the box" the installer will configure the Dataverse installation to leave unrestricted access to the administration APIs from (and only from) localhost. Please consider the security implications of this arrangement (anyone with shell access to the server can potentially mess with your Dataverse installation). An alternative solution would be to block open access to these sensitive API endpoints completely; and to only allow requests supplying a pre-defined "unblock token" (password). If you prefer that as a solution, please consult the supplied script ``post-install-api-block.sh`` for examples on how to set it up. See also "Securing Your Installation" under the :doc:`config` section.
-The Dataverse Software uses JHOVE_ to help identify the file format (CSV, PNG, etc.) for files that users have uploaded. The installer places files called ``jhove.conf`` and ``jhoveConfig.xsd`` into the directory ``/usr/local/payara5/glassfish/domains/domain1/config`` by default and makes adjustments to the jhove.conf file based on the directory into which you chose to install Payara.
+The Dataverse Software uses JHOVE_ to help identify the file format (CSV, PNG, etc.) for files that users have uploaded. The installer places files called ``jhove.conf`` and ``jhoveConfig.xsd`` into the directory ``/usr/local/payara6/glassfish/domains/domain1/config`` by default and makes adjustments to the jhove.conf file based on the directory into which you chose to install Payara.
.. _JHOVE: http://jhove.openpreservation.org
@@ -249,7 +249,7 @@ Deleting Uploaded Files
The path below will depend on the value for ``dataverse.files.directory`` as described in the :doc:`config` section:
-``rm -rf /usr/local/payara5/glassfish/domains/domain1/files``
+``rm -rf /usr/local/payara6/glassfish/domains/domain1/files``
Rerun Installer
^^^^^^^^^^^^^^^
diff --git a/doc/sphinx-guides/source/installation/intro.rst b/doc/sphinx-guides/source/installation/intro.rst
index 2251af7b81b..67fc774bdbd 100644
--- a/doc/sphinx-guides/source/installation/intro.rst
+++ b/doc/sphinx-guides/source/installation/intro.rst
@@ -48,7 +48,7 @@ If you've encountered a problem installing Dataverse and are ready to ask for he
- Operating system (usually a Linux distribution) and version.
- Output from the installer (STDOUT, STDERR).
- The ``scripts/api/setup-all.*.log`` files left behind by the installer.
-- The ``server.log`` file from Payara (by default at ``/usr/local/payara5/glassfish/domains/domain1/logs/server.log``).
+- The ``server.log`` file from Payara (by default at ``/usr/local/payara6/glassfish/domains/domain1/logs/server.log``).
Improving this Guide
--------------------
diff --git a/doc/sphinx-guides/source/installation/prerequisites.rst b/doc/sphinx-guides/source/installation/prerequisites.rst
index d95aa78bb26..1847f1b8f63 100644
--- a/doc/sphinx-guides/source/installation/prerequisites.rst
+++ b/doc/sphinx-guides/source/installation/prerequisites.rst
@@ -19,7 +19,7 @@ We assume you plan to run your Dataverse installation on Linux and we recommend
Java
----
-The Dataverse Software requires Java SE 11 (or higher).
+The Dataverse Software requires Java SE 17 (or higher).
Installing Java
===============
@@ -30,11 +30,11 @@ The Oracle JDK can be downloaded from http://www.oracle.com/technetwork/java/jav
On a RHEL/derivative, install OpenJDK (devel version) using yum::
- # sudo yum install java-11-openjdk
+ # sudo yum install java-17-openjdk
-If you have multiple versions of Java installed, Java 11 should be the default when ``java`` is invoked from the command line. You can test this by running ``java -version``.
+If you have multiple versions of Java installed, Java 17 should be the default when ``java`` is invoked from the command line. You can test this by running ``java -version``.
-On RHEL/derivative you can make Java 11 the default with the ``alternatives`` command, having it prompt you to select the version of Java from a list::
+On RHEL/derivative you can make Java 17 the default with the ``alternatives`` command, having it prompt you to select the version of Java from a list::
# alternatives --config java
@@ -44,7 +44,7 @@ On RHEL/derivative you can make Java 11 the default with the ``alternatives`` co
Payara
------
-Payara 5.2022.3 is recommended. Newer versions might work fine, regular updates are recommended.
+Payara 6.2023.8 is recommended. Newer versions might work fine. Regular updates are recommended.
Installing Payara
=================
@@ -53,11 +53,11 @@ Installing Payara
# useradd dataverse
-- Download and install Payara (installed in ``/usr/local/payara5`` in the example commands below)::
+- Download and install Payara (installed in ``/usr/local/payara6`` in the example commands below)::
- # wget https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/5.2022.3/payara-5.2022.3.zip
- # unzip payara-5.2022.3.zip
- # mv payara5 /usr/local
+ # wget https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2023.8/payara-6.2023.8.zip
+ # unzip payara-6.2023.8.zip
+ # mv payara6 /usr/local
If nexus.payara.fish is ever down for maintenance, Payara distributions are also available from https://repo1.maven.org/maven2/fish/payara/distributions/payara/
@@ -65,15 +65,15 @@ If you intend to install and run Payara under a service account (and we hope you
- Set service account permissions::
- # chown -R root:root /usr/local/payara5
- # chown dataverse /usr/local/payara5/glassfish/lib
- # chown -R dataverse:dataverse /usr/local/payara5/glassfish/domains/domain1
+ # chown -R root:root /usr/local/payara6
+ # chown dataverse /usr/local/payara6/glassfish/lib
+ # chown -R dataverse:dataverse /usr/local/payara6/glassfish/domains/domain1
After installation, you may chown the lib/ directory back to root; the installer only needs write access to copy the JDBC driver into that directory.
- Change from ``-client`` to ``-server`` under ``-client``::
- # vim /usr/local/payara5/glassfish/domains/domain1/config/domain.xml
+ # vim /usr/local/payara6/glassfish/domains/domain1/config/domain.xml
This recommendation comes from http://www.c2b2.co.uk/middleware-blog/glassfish-4-performance-tuning-monitoring-and-troubleshooting.php among other places.
@@ -97,10 +97,14 @@ Also note that Payara may utilize more than the default number of file descripto
PostgreSQL
----------
+PostgreSQL 13 is recommended because it's the version we test against. Version 10 or higher is required because that's what's `supported by Flyway `_, which we use for database migrations.
+
+You are welcome to experiment with newer versions of PostgreSQL, but please note that as of PostgreSQL 15, permissions have been restricted on the ``public`` schema (`release notes `_, `EDB blog post `_, `Crunchy Data blog post `_). The Dataverse installer has been updated to restore the old permissions, but this may not be a long term solution.
+
Installing PostgreSQL
=====================
-The application has been tested with PostgreSQL versions up to 13 and version 10+ is required. We recommend installing the latest version that is available for your OS distribution. *For example*, to install PostgreSQL 13 under RHEL7/derivative::
+*For example*, to install PostgreSQL 13 under RHEL7/derivative::
# yum install -y https://download.postgresql.org/pub/repos/yum/reporpms/EL-7-x86_64/pgdg-redhat-repo-latest.noarch.rpm
# yum makecache fast
@@ -154,12 +158,12 @@ Configuring Database Access for the Dataverse Installation (and the Dataverse So
Solr
----
-The Dataverse Software search index is powered by Solr.
+The Dataverse software search index is powered by Solr.
Supported Versions
==================
-The Dataverse Software has been tested with Solr version 8.11.1. Future releases in the 8.x series are likely to be compatible; however, this cannot be confirmed until they are officially tested. Major releases above 8.x (e.g. 9.x) are not supported.
+The Dataverse software has been tested with Solr version 9.3.0. Future releases in the 9.x series are likely to be compatible. Please get in touch (:ref:`support`) if you are having trouble with a newer version.
Installing Solr
===============
@@ -174,19 +178,19 @@ Become the ``solr`` user and then download and configure Solr::
su - solr
cd /usr/local/solr
- wget https://archive.apache.org/dist/lucene/solr/8.11.1/solr-8.11.1.tgz
- tar xvzf solr-8.11.1.tgz
- cd solr-8.11.1
+ wget https://archive.apache.org/dist/solr/solr/9.3.0/solr-9.3.0.tgz
+ tar xvzf solr-9.3.0.tgz
+ cd solr-9.3.0
cp -r server/solr/configsets/_default server/solr/collection1
You should already have a "dvinstall.zip" file that you downloaded from https://github.com/IQSS/dataverse/releases . Unzip it into ``/tmp``. Then copy the files into place::
- cp /tmp/dvinstall/schema*.xml /usr/local/solr/solr-8.11.1/server/solr/collection1/conf
- cp /tmp/dvinstall/solrconfig.xml /usr/local/solr/solr-8.11.1/server/solr/collection1/conf
+ cp /tmp/dvinstall/schema*.xml /usr/local/solr/solr-9.3.0/server/solr/collection1/conf
+ cp /tmp/dvinstall/solrconfig.xml /usr/local/solr/solr-9.3.0/server/solr/collection1/conf
Note: The Dataverse Project team has customized Solr to boost results that come from certain indexed elements inside the Dataverse installation, for example prioritizing results from Dataverse collections over Datasets. If you would like to remove this, edit your ``solrconfig.xml`` and remove the ```` element and its contents. If you have ideas about how this boosting could be improved, feel free to contact us through our Google Group https://groups.google.com/forum/#!forum/dataverse-dev .
-A Dataverse installation requires a change to the ``jetty.xml`` file that ships with Solr. Edit ``/usr/local/solr/solr-8.11.1/server/etc/jetty.xml`` , increasing ``requestHeaderSize`` from ``8192`` to ``102400``
+A Dataverse installation requires a change to the ``jetty.xml`` file that ships with Solr. Edit ``/usr/local/solr/solr-9.3.0/server/etc/jetty.xml`` , increasing ``requestHeaderSize`` from ``8192`` to ``102400``
Solr will warn about needing to increase the number of file descriptors and max processes in a production environment but will still run with defaults. We have increased these values to the recommended levels by adding ulimit -n 65000 to the init script, and the following to ``/etc/security/limits.conf``::
@@ -205,7 +209,7 @@ Solr launches asynchronously and attempts to use the ``lsof`` binary to watch fo
Finally, you need to tell Solr to create the core "collection1" on startup::
- echo "name=collection1" > /usr/local/solr/solr-8.11.1/server/solr/collection1/core.properties
+ echo "name=collection1" > /usr/local/solr/solr-9.3.0/server/solr/collection1/core.properties
Solr Init Script
================
diff --git a/doc/sphinx-guides/source/versions.rst b/doc/sphinx-guides/source/versions.rst
index d5ffb2acb66..2000a2097f0 100755
--- a/doc/sphinx-guides/source/versions.rst
+++ b/doc/sphinx-guides/source/versions.rst
@@ -7,7 +7,8 @@ Dataverse Software Documentation Versions
This list provides a way to refer to the documentation for previous and future versions of the Dataverse Software. In order to learn more about the updates delivered from one version to another, visit the `Releases `__ page in our GitHub repo.
- pre-release `HTML (not final!) `__ and `PDF (experimental!) `__ built from the :doc:`develop ` branch :doc:`(how to contribute!) `
-- 5.14
+- 6.0
+- `5.14 `__
- `5.13 `__
- `5.12.1 `__
- `5.12 `__
diff --git a/downloads/.gitignore b/downloads/.gitignore
deleted file mode 100644
index 1b51bf4def7..00000000000
--- a/downloads/.gitignore
+++ /dev/null
@@ -1,4 +0,0 @@
-payara-5.201.zip
-solr-7.3.0.tgz
-weld-osgi-bundle-2.2.10.Final-glassfish4.jar
-schemaSpy_5.0.0.jar
diff --git a/downloads/download.sh b/downloads/download.sh
deleted file mode 100755
index 7b9de0397cb..00000000000
--- a/downloads/download.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/bin/sh
-curl -L -O https://s3-eu-west-1.amazonaws.com/payara.fish/Payara+Downloads/5.2022.3/payara-5.2022.3.zip
-curl -L -O https://archive.apache.org/dist/lucene/solr/8.11.1/solr-8.11.1.tgz
-curl -L -O https://search.maven.org/remotecontent?filepath=org/jboss/weld/weld-osgi-bundle/2.2.10.Final/weld-osgi-bundle-2.2.10.Final-glassfish4.jar
-curl -s -L http://sourceforge.net/projects/schemaspy/files/schemaspy/SchemaSpy%205.0.0/schemaSpy_5.0.0.jar/download > schemaSpy_5.0.0.jar
diff --git a/downloads/stata-13-test-files/Stata14TestFile.dta b/downloads/stata-13-test-files/Stata14TestFile.dta
deleted file mode 100644
index 6f1c31dc798..00000000000
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diff --git a/local_lib/com/apicatalog/titanium-json-ld/1.3.0-SNAPSHOT/titanium-json-ld-1.3.0-SNAPSHOT.jar b/local_lib/com/apicatalog/titanium-json-ld/1.3.0-SNAPSHOT/titanium-json-ld-1.3.0-SNAPSHOT.jar
deleted file mode 100644
index ee499ae4b76..00000000000
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diff --git a/local_lib/edu/harvard/iq/dvn/unf5/5.0/unf5-5.0.jar b/local_lib/edu/harvard/iq/dvn/unf5/5.0/unf5-5.0.jar
deleted file mode 100644
index dc41f94046f..00000000000
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diff --git a/local_lib/edu/harvard/iq/dvn/unf5/5.0/unf5-5.0.jar.md5 b/local_lib/edu/harvard/iq/dvn/unf5/5.0/unf5-5.0.jar.md5
deleted file mode 100644
index 7018ea4e822..00000000000
--- a/local_lib/edu/harvard/iq/dvn/unf5/5.0/unf5-5.0.jar.md5
+++ /dev/null
@@ -1 +0,0 @@
-eeef5c0dc201d1105b9529a51fa8cdab
diff --git a/local_lib/edu/harvard/iq/dvn/unf5/5.0/unf5-5.0.jar.sha1 b/local_lib/edu/harvard/iq/dvn/unf5/5.0/unf5-5.0.jar.sha1
deleted file mode 100644
index 97f192f3732..00000000000
--- a/local_lib/edu/harvard/iq/dvn/unf5/5.0/unf5-5.0.jar.sha1
+++ /dev/null
@@ -1 +0,0 @@
-1fa716d318920fd59fc63f77965d113decf97355
diff --git a/local_lib/edu/harvard/iq/dvn/unf5/5.0/unf5-5.0.pom b/local_lib/edu/harvard/iq/dvn/unf5/5.0/unf5-5.0.pom
deleted file mode 100644
index ea2e4c03f9f..00000000000
--- a/local_lib/edu/harvard/iq/dvn/unf5/5.0/unf5-5.0.pom
+++ /dev/null
@@ -1,8 +0,0 @@
-
-
- 4.0.0
- edu.harvard.iq.dvn
- unf5
- 5.0
-
diff --git a/local_lib/edu/harvard/iq/dvn/unf5/5.0/unf5-5.0.pom.md5 b/local_lib/edu/harvard/iq/dvn/unf5/5.0/unf5-5.0.pom.md5
deleted file mode 100644
index a88cf2a1c02..00000000000
--- a/local_lib/edu/harvard/iq/dvn/unf5/5.0/unf5-5.0.pom.md5
+++ /dev/null
@@ -1 +0,0 @@
-2df5dac09375e1e7fcd66c705d9ca2ef
diff --git a/local_lib/edu/harvard/iq/dvn/unf5/5.0/unf5-5.0.pom.sha1 b/local_lib/edu/harvard/iq/dvn/unf5/5.0/unf5-5.0.pom.sha1
deleted file mode 100644
index 967b977b79e..00000000000
--- a/local_lib/edu/harvard/iq/dvn/unf5/5.0/unf5-5.0.pom.sha1
+++ /dev/null
@@ -1 +0,0 @@
-431cd55e2e9379677d14e402dd3c474bb7be4ac9
diff --git a/local_lib/net/handle/handle/8.1.1/handle-8.1.1.jar b/local_lib/net/handle/handle/8.1.1/handle-8.1.1.jar
deleted file mode 100644
index 1f8e1c3eb12..00000000000
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diff --git a/local_lib/net/handle/handle/8.1.1/handle-8.1.1.pom b/local_lib/net/handle/handle/8.1.1/handle-8.1.1.pom
deleted file mode 100644
index e3c09349172..00000000000
--- a/local_lib/net/handle/handle/8.1.1/handle-8.1.1.pom
+++ /dev/null
@@ -1,9 +0,0 @@
-
-
- 4.0.0
- net.handle
- handle
- 8.1.1
- POM was created from install:install-file
-
diff --git a/local_lib/nom/tam/fits/fits/2012-10-25-generated/fits-2012-10-25-generated.jar b/local_lib/nom/tam/fits/fits/2012-10-25-generated/fits-2012-10-25-generated.jar
deleted file mode 100644
index b3bddd62c24..00000000000
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diff --git a/local_lib/nom/tam/fits/fits/2012-10-25-generated/fits-2012-10-25-generated.jar.md5 b/local_lib/nom/tam/fits/fits/2012-10-25-generated/fits-2012-10-25-generated.jar.md5
deleted file mode 100644
index 576062f55a1..00000000000
--- a/local_lib/nom/tam/fits/fits/2012-10-25-generated/fits-2012-10-25-generated.jar.md5
+++ /dev/null
@@ -1 +0,0 @@
-b0abb2fee242c479f305f47352600bbf
diff --git a/local_lib/nom/tam/fits/fits/2012-10-25-generated/fits-2012-10-25-generated.jar.sha1 b/local_lib/nom/tam/fits/fits/2012-10-25-generated/fits-2012-10-25-generated.jar.sha1
deleted file mode 100644
index e81e8450ef0..00000000000
--- a/local_lib/nom/tam/fits/fits/2012-10-25-generated/fits-2012-10-25-generated.jar.sha1
+++ /dev/null
@@ -1 +0,0 @@
-9643e138cb5ed2684838e4b4faa118adfb2ecb4b
diff --git a/local_lib/nom/tam/fits/fits/2012-10-25-generated/fits-2012-10-25-generated.pom b/local_lib/nom/tam/fits/fits/2012-10-25-generated/fits-2012-10-25-generated.pom
deleted file mode 100644
index b57cd67278b..00000000000
--- a/local_lib/nom/tam/fits/fits/2012-10-25-generated/fits-2012-10-25-generated.pom
+++ /dev/null
@@ -1,8 +0,0 @@
-
-
- 4.0.0
- nom.tam.fits
- fits
- 2012-10-25-generated
-
diff --git a/local_lib/nom/tam/fits/fits/2012-10-25-generated/fits-2012-10-25-generated.pom.md5 b/local_lib/nom/tam/fits/fits/2012-10-25-generated/fits-2012-10-25-generated.pom.md5
deleted file mode 100644
index 777b4df3325..00000000000
--- a/local_lib/nom/tam/fits/fits/2012-10-25-generated/fits-2012-10-25-generated.pom.md5
+++ /dev/null
@@ -1 +0,0 @@
-23ca47c46df791f220a87cfef3b2190c
diff --git a/local_lib/nom/tam/fits/fits/2012-10-25-generated/fits-2012-10-25-generated.pom.sha1 b/local_lib/nom/tam/fits/fits/2012-10-25-generated/fits-2012-10-25-generated.pom.sha1
deleted file mode 100644
index b5f41fd1a69..00000000000
--- a/local_lib/nom/tam/fits/fits/2012-10-25-generated/fits-2012-10-25-generated.pom.sha1
+++ /dev/null
@@ -1 +0,0 @@
-c1ec9dfbbc72dc4623d309d772b804e47284ee27
diff --git a/local_lib/nom/tam/fits/fits/maven-metadata.xml b/local_lib/nom/tam/fits/fits/maven-metadata.xml
deleted file mode 100644
index 4fc3254df3f..00000000000
--- a/local_lib/nom/tam/fits/fits/maven-metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-
-
- nom.tam.fits
- fits
-
- 2012-10-25-generated
-
- 2012-10-25-generated
-
- 20130925190525
-
-
diff --git a/local_lib/nom/tam/fits/fits/maven-metadata.xml.md5 b/local_lib/nom/tam/fits/fits/maven-metadata.xml.md5
deleted file mode 100644
index b6d7e4a726f..00000000000
--- a/local_lib/nom/tam/fits/fits/maven-metadata.xml.md5
+++ /dev/null
@@ -1 +0,0 @@
-545c78160393b4c80e40377f2a7cf406
\ No newline at end of file
diff --git a/local_lib/nom/tam/fits/fits/maven-metadata.xml.sha1 b/local_lib/nom/tam/fits/fits/maven-metadata.xml.sha1
deleted file mode 100644
index 188cf8ae044..00000000000
--- a/local_lib/nom/tam/fits/fits/maven-metadata.xml.sha1
+++ /dev/null
@@ -1 +0,0 @@
-9cf56b8ef3f2bacdc669c2c7cdcd7cd50ed38dbb
\ No newline at end of file
diff --git a/local_lib/org/dataverse/unf/6.0/unf-6.0.jar b/local_lib/org/dataverse/unf/6.0/unf-6.0.jar
deleted file mode 100644
index d2738e2dadd..00000000000
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diff --git a/local_lib/org/dataverse/unf/6.0/unf-6.0.jar.md5 b/local_lib/org/dataverse/unf/6.0/unf-6.0.jar.md5
deleted file mode 100644
index 04ca3e73ce8..00000000000
--- a/local_lib/org/dataverse/unf/6.0/unf-6.0.jar.md5
+++ /dev/null
@@ -1 +0,0 @@
-bd9b84a9ad737a81a2699ab81541a901
diff --git a/local_lib/org/dataverse/unf/6.0/unf-6.0.jar.sha1 b/local_lib/org/dataverse/unf/6.0/unf-6.0.jar.sha1
deleted file mode 100644
index a48cef32570..00000000000
--- a/local_lib/org/dataverse/unf/6.0/unf-6.0.jar.sha1
+++ /dev/null
@@ -1 +0,0 @@
-4cad279c362e4c5c17a2058dc2c8f2fc97c76bf8
diff --git a/local_lib/org/dataverse/unf/6.0/unf-6.0.pom b/local_lib/org/dataverse/unf/6.0/unf-6.0.pom
deleted file mode 100644
index 06f1508723f..00000000000
--- a/local_lib/org/dataverse/unf/6.0/unf-6.0.pom
+++ /dev/null
@@ -1,8 +0,0 @@
-
-
- 4.0.0
- org.dataverse
- unf
- 6.0
-
diff --git a/local_lib/org/dataverse/unf/6.0/unf-6.0.pom.md5 b/local_lib/org/dataverse/unf/6.0/unf-6.0.pom.md5
deleted file mode 100644
index 138bc9c95f6..00000000000
--- a/local_lib/org/dataverse/unf/6.0/unf-6.0.pom.md5
+++ /dev/null
@@ -1 +0,0 @@
-230c5b1f5ae71bb2fe80ef9e7209f681
diff --git a/local_lib/org/dataverse/unf/6.0/unf-6.0.pom.sha1 b/local_lib/org/dataverse/unf/6.0/unf-6.0.pom.sha1
deleted file mode 100644
index 689e8045418..00000000000
--- a/local_lib/org/dataverse/unf/6.0/unf-6.0.pom.sha1
+++ /dev/null
@@ -1 +0,0 @@
-286b819f2fc7432a94b5940c6171be1589f66a37
diff --git a/modules/container-base/src/main/docker/Dockerfile b/modules/container-base/src/main/docker/Dockerfile
index bbd02a14328..97aa4cd2792 100644
--- a/modules/container-base/src/main/docker/Dockerfile
+++ b/modules/container-base/src/main/docker/Dockerfile
@@ -164,6 +164,8 @@ RUN <org.apache.jasper.servlet.JspServlet#org.apache.jasper.servlet.JspServlet\n \n development\n false\n \n \n genStrAsCharArray\n true\n #' "${DOMAIN_DIR}/config/default-web.xml"
+ sed -i 's#org.glassfish.wasp.servlet.JspServlet#org.glassfish.wasp.servlet.JspServlet\n \n development\n false\n \n \n genStrAsCharArray\n true\n #' "${DOMAIN_DIR}/config/default-web.xml"
# Cleanup old CA certificates to avoid unnecessary log clutter during startup
${SCRIPT_DIR}/removeExpiredCaCerts.sh
# Delete generated files
diff --git a/modules/container-base/src/main/docker/scripts/removeExpiredCaCerts.sh b/modules/container-base/src/main/docker/scripts/removeExpiredCaCerts.sh
index 205a9eda5d7..c019c09130e 100644
--- a/modules/container-base/src/main/docker/scripts/removeExpiredCaCerts.sh
+++ b/modules/container-base/src/main/docker/scripts/removeExpiredCaCerts.sh
@@ -8,6 +8,14 @@
set -euo pipefail
KEYSTORE="${DOMAIN_DIR}/config/cacerts.jks"
+if [ ! -r "${KEYSTORE}" ]; then
+ KEYSTORE="${DOMAIN_DIR}/config/cacerts.p12"
+ if [ ! -r "${KEYSTORE}" ]; then
+ echo "Could not find CA certs keystore"
+ exit 1
+ fi
+fi
+
keytool -list -v -keystore "${KEYSTORE}" -storepass changeit 2>/dev/null | \
grep -i 'alias\|until' > aliases.txt
diff --git a/modules/container-configbaker/Dockerfile b/modules/container-configbaker/Dockerfile
index cbda948db14..564216b3572 100644
--- a/modules/container-configbaker/Dockerfile
+++ b/modules/container-configbaker/Dockerfile
@@ -33,6 +33,7 @@ RUN chmod +x ${SCRIPT_DIR}/*.sh ${BOOTSTRAP_DIR}/*/*.sh
# Copy the Solr config bits
COPY --from=solr /opt/solr/server/solr/configsets/_default ${SOLR_TEMPLATE}/
COPY maven/solr/*.xml ${SOLR_TEMPLATE}/conf/
+RUN rm ${SOLR_TEMPLATE}/conf/managed-schema.xml
# Copy the data from scripts/api that provide the common base setup you'd get from the installer.
# ".dockerignore" will take care of taking only the bare necessities
diff --git a/modules/container-configbaker/assembly.xml b/modules/container-configbaker/assembly.xml
index f5b309175ed..3285eef510a 100644
--- a/modules/container-configbaker/assembly.xml
+++ b/modules/container-configbaker/assembly.xml
@@ -8,7 +8,7 @@
- conf/solr/8.11.1
+ conf/solr/9.3.0
solr
@@ -43,4 +43,4 @@
-
\ No newline at end of file
+
diff --git a/modules/dataverse-parent/pom.xml b/modules/dataverse-parent/pom.xml
index 05f7874d31c..c45d59e4f5f 100644
--- a/modules/dataverse-parent/pom.xml
+++ b/modules/dataverse-parent/pom.xml
@@ -131,9 +131,9 @@
- 5.14
+ 6.0
- 11
+ 17
UTF-8
-Xdoclint:none
@@ -148,9 +148,9 @@
-Duser.timezone=${project.timezone} -Dfile.encoding=${project.build.sourceEncoding} -Duser.language=${project.language} -Duser.region=${project.region}
- 5.2022.3
- 42.5.1
- 8.11.1
+ 6.2023.8
+ 42.6.0
+ 9.3.0
1.12.290
0.177.0
@@ -165,16 +165,14 @@
4.4.14
- 5.0.0
+ 5.1.0
1.15.0
2.10.1
-
- 4.13.1
- 5.7.0
- ${junit.jupiter.version}
- 2.28.2
+
+ 5.10.0
+ 5.4.0
9.3
@@ -193,6 +191,7 @@
3.2.1
3.4.1
1.3.0
+ 3.3.0
3.1.2
1.6.13
@@ -255,6 +254,11 @@
maven-failsafe-plugin
${maven-failsafe-plugin.version}
+
+ org.apache.maven.plugins
+ maven-enforcer-plugin
+ ${maven-enforcer-plugin.version}
+
org.apache.maven.plugins
maven-checkstyle-plugin
@@ -314,6 +318,47 @@
+
+
+ org.apache.maven.plugins
+ maven-enforcer-plugin
+
+
+ no-junit4
+ generate-test-resources
+
+ enforce
+
+
+
+
+
+ junit:junit:*:*:test
+ org.junit:junit:*:*:test
+ org.junit.vintage:*:*:*:test
+
+
+
+
+
+
+ general-reqs
+
+ enforce
+
+ initialize
+
+
+
+
+ [${target.java.version}.0,)
+
+
+
+
+
+
+
oss-sonatype
oss-sonatype
+
+ https://oss.sonatype.org/content/repositories/snapshots/
+
+
+ true
+
+
+
+ s01-oss-sonatype
+ s01-oss-sonatype
https://s01.oss.sonatype.org/content/repositories/snapshots/
@@ -385,7 +435,7 @@
true
- -->
+
@@ -393,11 +443,9 @@
ct
- 5.2022.5
+
diff --git a/modules/dataverse-spi/pom.xml b/modules/dataverse-spi/pom.xml
index 6235d309e89..b00053fe5e0 100644
--- a/modules/dataverse-spi/pom.xml
+++ b/modules/dataverse-spi/pom.xml
@@ -13,7 +13,7 @@
io.gdcc
dataverse-spi
- 1.0.0${project.version.suffix}
+ 2.0.0${project.version.suffix}
jar
Dataverse SPI Plugin API
diff --git a/modules/dataverse-spi/src/main/java/io/gdcc/spi/export/ExportDataProvider.java b/modules/dataverse-spi/src/main/java/io/gdcc/spi/export/ExportDataProvider.java
index 228992c8288..d039ac39e8f 100644
--- a/modules/dataverse-spi/src/main/java/io/gdcc/spi/export/ExportDataProvider.java
+++ b/modules/dataverse-spi/src/main/java/io/gdcc/spi/export/ExportDataProvider.java
@@ -3,8 +3,8 @@
import java.io.InputStream;
import java.util.Optional;
-import javax.json.JsonArray;
-import javax.json.JsonObject;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonObject;
/**
* Provides all the metadata Dataverse has about a given dataset that can then
diff --git a/modules/dataverse-spi/src/main/java/io/gdcc/spi/export/XMLExporter.java b/modules/dataverse-spi/src/main/java/io/gdcc/spi/export/XMLExporter.java
index 9afe7ba1cfd..3c3fa35c69d 100644
--- a/modules/dataverse-spi/src/main/java/io/gdcc/spi/export/XMLExporter.java
+++ b/modules/dataverse-spi/src/main/java/io/gdcc/spi/export/XMLExporter.java
@@ -1,6 +1,6 @@
package io.gdcc.spi.export;
-import javax.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.MediaType;
/**
* XML Exporter is an extension of the base Exporter interface that adds the
diff --git a/pom.xml b/pom.xml
index 96f598af0f5..7ba22d2a076 100644
--- a/pom.xml
+++ b/pom.xml
@@ -26,7 +26,7 @@
war
1.2.18.4
- 8.5.10
+ 9.21.2
1.20.1
0.8.7
5.2.1
@@ -96,7 +96,7 @@
io.gdcc
sword2-server
- 1.2.1
+ 2.0.0
@@ -119,7 +119,7 @@
com.apicatalog
titanium-json-ld
- 1.3.0-SNAPSHOT
+ 1.3.2
com.google.code.gson
@@ -160,12 +160,20 @@
flyway-core
${flyway.version}
+
+
+ org.eclipse.persistence
+ org.eclipse.persistence.jpa
+ provided
+
com.google.guava
guava
- 29.0-jre
+ 32.1.2-jre
jar
+
+
org.eclipse.microprofile.config
microprofile-config-api
@@ -174,13 +182,14 @@
jakarta.platform
jakarta.jakartaee-api
- ${jakartaee-api.version}
provided
-
+
+
+
- org.glassfish
- jakarta.json
+ org.eclipse.angus
+ angus-activation
provided
@@ -188,12 +197,20 @@
fish.payara.api
payara-api
provided
+
+ ${payara.version}
+
+
+
- com.sun.mail
- jakarta.mail
+ org.eclipse.parsson
+ jakarta.json
provided
+
+
org.glassfish
jakarta.faces
@@ -203,6 +220,7 @@
org.primefaces
primefaces
11.0.0
+ jakarta
org.primefaces.themes
@@ -212,9 +230,10 @@
org.omnifaces
omnifaces
- 3.8
+ 4.0-M13
+
jakarta.validation
jakarta.validation-api
@@ -225,9 +244,12 @@
hibernate-validator
provided
+
+
+
- org.glassfish
- jakarta.el
+ org.glassfish.expressly
+ expressly
provided
@@ -261,29 +283,23 @@
org.apache.solr
solr-solrj
- 8.11.1
+ 9.3.0
colt
colt
1.2.0
-
+
- nom.tam.fits
- fits
- 2012-10-25-generated
+ gov.nasa.gsfc.heasarc
+ nom-tam-fits
+ 1.12.0
net.handle
- handle
- 8.1.1
-
-
-
- edu.harvard.iq.dvn
- unf5
- 5.0
+ handle-client
+ 9.3.1
@@ -343,18 +359,24 @@
org.ocpsoft.rewrite
rewrite-servlet
- 3.5.0.Final
+ 6.0.0-SNAPSHOT
org.ocpsoft.rewrite
rewrite-config-prettyfaces
- 3.5.0.Final
+ 6.0.0-SNAPSHOT
edu.ucsb.nceas
ezid
1.0.0
jar
+
+
+ junit
+ junit
+
+
org.jsoup
@@ -394,7 +416,7 @@
oauth2-oidc-sdk
10.7.1
-
+
io.gdcc
xoai-data-provider
@@ -415,15 +437,13 @@
- org.glassfish.jersey.containers
- jersey-container-servlet
- 2.23.2
+ org.glassfish.jersey.core
+ jersey-server
org.glassfish.jersey.media
jersey-media-multipart
- 2.23.2
com.mashape.unirest
@@ -513,7 +533,7 @@
io.gdcc
dataverse-spi
- 1.0.0
+ 2.0.0
@@ -522,18 +542,6 @@
${junit.jupiter.version}
test
-
- junit
- junit
- ${junit.version}
- test
-
-
- org.junit.vintage
- junit-vintage-engine
- ${junit.vintage.version}
- test
-
org.hamcrest
hamcrest-library
@@ -553,9 +561,9 @@
test
- com.jayway.restassured
+ io.rest-assured
rest-assured
- 2.4.0
+ 5.3.1
test
@@ -574,6 +582,12 @@
org.testcontainers
testcontainers
test
+
+
+ junit
+ junit
+
+
org.testcontainers
@@ -761,7 +775,7 @@
true
- edu.harvard.iq.dataverse.NonEssentialTests
+ not-essential-unittests
diff --git a/scripts/dev/dev-rebuild.sh b/scripts/dev/dev-rebuild.sh
index 71857b14068..9eae195b135 100755
--- a/scripts/dev/dev-rebuild.sh
+++ b/scripts/dev/dev-rebuild.sh
@@ -1,8 +1,9 @@
#!/bin/sh
-PAYARA_DIR=/usr/local/payara5
+PAYARA_DIR=/usr/local/payara6
ASADMIN=$PAYARA_DIR/glassfish/bin/asadmin
DB_NAME=dvndb
DB_USER=dvnapp
+export PGPASSWORD=secret
echo "Checking if there is a war file to undeploy..."
LIST_APP=$($ASADMIN list-applications -t)
@@ -23,7 +24,7 @@ echo "Deleting ALL DATA FILES uploaded to Dataverse..."
rm -rf $PAYARA_DIR/glassfish/domains/domain1/files
echo "Terminating database sessions so we can drop the database..."
-psql -U postgres -c "
+psql -h localhost -U postgres -c "
SELECT pg_terminate_backend(pg_stat_activity.pid)
FROM pg_stat_activity
WHERE pg_stat_activity.datname = '$DB_NAME'
@@ -31,14 +32,14 @@ WHERE pg_stat_activity.datname = '$DB_NAME'
" template1
echo "Dropping the database..."
-psql -U $DB_USER -c "DROP DATABASE \"$DB_NAME\"" template1
+psql -h localhost -U $DB_USER -c "DROP DATABASE \"$DB_NAME\"" template1
echo $?
echo "Clearing out data from Solr..."
-curl http://localhost:8983/solr/collection1/update/json?commit=true -H "Content-type: application/json" -X POST -d "{\"delete\": { \"query\":\"*:*\"}}"
+curl "http://localhost:8983/solr/collection1/update/json?commit=true" -H "Content-type: application/json" -X POST -d "{\"delete\": { \"query\":\"*:*\"}}"
echo "Creating a new database..."
-psql -U $DB_USER -c "CREATE DATABASE \"$DB_NAME\" WITH OWNER = \"$DB_USER\"" template1
+psql -h localhost -U $DB_USER -c "CREATE DATABASE \"$DB_NAME\" WITH OWNER = \"$DB_USER\"" template1
echo $?
echo "Starting app server..."
@@ -53,7 +54,7 @@ cd scripts/api
cd ../..
echo "Creating SQL sequence..."
-psql -U $DB_USER $DB_NAME -f doc/sphinx-guides/source/_static/util/createsequence.sql
+psql -h localhost -U $DB_USER $DB_NAME -f doc/sphinx-guides/source/_static/util/createsequence.sql
echo "Setting DOI provider to \"FAKE\"..."
curl http://localhost:8080/api/admin/settings/:DoiProvider -X PUT -d FAKE
diff --git a/scripts/installer/Makefile b/scripts/installer/Makefile
index d40d4d792ea..399bc65168a 100644
--- a/scripts/installer/Makefile
+++ b/scripts/installer/Makefile
@@ -7,7 +7,6 @@ JHOVE_SCHEMA=${INSTALLER_ZIP_DIR}/jhoveConfig.xsd
SOLR_SCHEMA=${INSTALLER_ZIP_DIR}/schema.xml ${INSTALLER_ZIP_DIR}/update-fields.sh
SOLR_CONFIG=${INSTALLER_ZIP_DIR}/solrconfig.xml
PYTHON_FILES=${INSTALLER_ZIP_DIR}/README_python.txt ${INSTALLER_ZIP_DIR}/installConfig.py ${INSTALLER_ZIP_DIR}/installUtils.py ${INSTALLER_ZIP_DIR}/install.py ${INSTALLER_ZIP_DIR}/installAppServer.py ${INSTALLER_ZIP_DIR}/requirements.txt ${INSTALLER_ZIP_DIR}/default.config ${INSTALLER_ZIP_DIR}/interactive.config
-INSTALL_SCRIPT=${INSTALLER_ZIP_DIR}/install
installer: dvinstall.zip
@@ -56,13 +55,13 @@ ${JHOVE_SCHEMA}: ../../conf/jhove/jhoveConfig.xsd ${INSTALLER_ZIP_DIR}
@echo copying jhove schema file
/bin/cp ../../conf/jhove/jhoveConfig.xsd ${INSTALLER_ZIP_DIR}
-${SOLR_SCHEMA}: ../../conf/solr/8.11.1/schema.xml ../../conf/solr/8.11.1/update-fields.sh ${INSTALLER_ZIP_DIR}
+${SOLR_SCHEMA}: ../../conf/solr/9.3.0/schema.xml ../../conf/solr/9.3.0/update-fields.sh ${INSTALLER_ZIP_DIR}
@echo copying Solr schema file
- /bin/cp ../../conf/solr/8.11.1/schema.xml ../../conf/solr/8.11.1/update-fields.sh ${INSTALLER_ZIP_DIR}
+ /bin/cp ../../conf/solr/9.3.0/schema.xml ../../conf/solr/9.3.0/update-fields.sh ${INSTALLER_ZIP_DIR}
-${SOLR_CONFIG}: ../../conf/solr/8.11.1/solrconfig.xml ${INSTALLER_ZIP_DIR}
+${SOLR_CONFIG}: ../../conf/solr/9.3.0/solrconfig.xml ${INSTALLER_ZIP_DIR}
@echo copying Solr config file
- /bin/cp ../../conf/solr/8.11.1/solrconfig.xml ${INSTALLER_ZIP_DIR}
+ /bin/cp ../../conf/solr/9.3.0/solrconfig.xml ${INSTALLER_ZIP_DIR}
${PYTHON_FILES}: README_python.txt install.py installConfig.py installAppServer.py installUtils.py requirements.txt default.config interactive.config ${INSTALLER_ZIP_DIR}
@echo copying Python installer files
diff --git a/scripts/installer/README.txt b/scripts/installer/README.txt
index 350a17fc00c..c3ed8211082 100644
--- a/scripts/installer/README.txt
+++ b/scripts/installer/README.txt
@@ -1,42 +1 @@
-The installer script (install) can be run either by a developer (inside the source tree), or by an end-user installing the Dataverse. The latter will obtain the script as part of the distribution bundle; and they will be running it inside the unzipped bundle directory.
-
-In the former (developer) case, the installer will be looking for the files it needs in the other directories in the source tree.
-For example, the war file (once built) can be found in ../../target/. The name of the war file will be dataverse-{VERSION}.war, where
-{VERSION} is the version number of the Dataverse, obtained from the pom file (../../pom.xml). For example, as of writing this README.txt (July 2015) the war file is ../../target/dataverse-4.1.war/
-
-When building a distribution archive, the Makefile will pile all the files that the installer needs in one directory (./dvinstall here) and then zip it up. We upload the resulting zip bundle on github as the actual software release. This way the end user only gets the files they actually need to install the Dataverse app. So they can do so without pulling the entire source tree.
-
-
-The installer script itself (the perl script ./install) knows to look for all these files in 2 places (for example, it will look for the war file in ../../target/; if it's not there, it'll assume this is a distribution bundle and look for it as ./dataverse.war)
-
-Here's the list of the files that the installer needs:
-
-the war file:
-target/dataverse-{VERSION}.war
-
-and also:
-
-from scripts/installer (this directory):
-
-install
-glassfish-setup.sh
-
-from scripts/api:
-
-setup-all.sh
-setup-builtin-roles.sh
-setup-datasetfields.sh
-setup-dvs.sh
-setup-identity-providers.sh
-setup-users.sh
-data (the entire directory with all its contents)
-
-from conf/jhove:
-
-jhove.conf
-
-SOLR schema and config files, from conf/solr/8.11.1:
-
-schema.xml
-schema_dv_mdb_fields.xml
-solrconfig.xml
+See README_python.txt
diff --git a/scripts/installer/as-setup.sh b/scripts/installer/as-setup.sh
index 49ebce059d2..fc5b378cff5 100755
--- a/scripts/installer/as-setup.sh
+++ b/scripts/installer/as-setup.sh
@@ -56,15 +56,15 @@ function preliminary_setup()
# avoid OutOfMemoryError: PermGen per http://eugenedvorkin.com/java-lang-outofmemoryerror-permgen-space-error-during-deployment-to-glassfish/
#./asadmin $ASADMIN_OPTS list-jvm-options
- # Note that these JVM options are different for Payara5 and Glassfish4:
+ # Note that these JVM options are different for Payara and Glassfish4:
# old Glassfish4 options: (commented out)
#./asadmin $ASADMIN_OPTS delete-jvm-options "-XX\:MaxPermSize=192m"
#./asadmin $ASADMIN_OPTS create-jvm-options "-XX\:MaxPermSize=512m"
#./asadmin $ASADMIN_OPTS create-jvm-options "-XX\:PermSize=256m"
- # payara5 ships with the "-server" option already in domain.xml, so no need:
+ # Payara ships with the "-server" option already in domain.xml, so no need:
#./asadmin $ASADMIN_OPTS delete-jvm-options -client
- # new Payara5 options: (thanks to donsizemore@unc.edu)
+ # new Payara options: (thanks to donsizemore@unc.edu)
./asadmin $ASADMIN_OPTS create-jvm-options "-XX\:MaxMetaspaceSize=512m"
./asadmin $ASADMIN_OPTS create-jvm-options "-XX\:MetaspaceSize=256m"
./asadmin $ASADMIN_OPTS create-jvm-options "-Dfish.payara.classloading.delegate=false"
@@ -116,6 +116,9 @@ function preliminary_setup()
./asadmin $ASADMIN_OPTS create-jvm-options "-Ddataverse.timerServer=true"
+ # Workaround for FISH-7722: Failed to deploy war with @Stateless https://github.com/payara/Payara/issues/6337
+ ./asadmin $ASADMIN_OPTS create-jvm-options --add-opens=java.base/java.io=ALL-UNNAMED
+
# enable comet support
./asadmin $ASADMIN_OPTS set server-config.network-config.protocols.protocol.http-listener-1.http.comet-support-enabled="true"
@@ -155,18 +158,18 @@ function final_setup(){
if [ "$DOCKER_BUILD" = "true" ]
then
- FILES_DIR="/usr/local/payara5/glassfish/domains/domain1/files"
+ FILES_DIR="/usr/local/payara6/glassfish/domains/domain1/files"
RSERVE_HOST="localhost"
RSERVE_PORT="6311"
RSERVE_USER="rserve"
RSERVE_PASS="rserve"
HOST_ADDRESS="localhost\:8080"
- pushd /usr/local/payara5/glassfish/bin/
+ pushd /usr/local/payara6/glassfish/bin/
./asadmin start-domain domain1
preliminary_setup
- chmod -R 777 /usr/local/payara5/
- rm -rf /usr/local/payara5/glassfish/domains/domain1/generated
- rm -rf /usr/local/payara5/glassfish/domains/domain1/applications
+ chmod -R 777 /usr/local/payara6/
+ rm -rf /usr/local/payara6/glassfish/domains/domain1/generated
+ rm -rf /usr/local/payara6/glassfish/domains/domain1/applications
popd
exit 0
fi
@@ -276,7 +279,7 @@ if [ ! -d "$DOMAIN_DIR" ]
exit 2
fi
-echo "Setting up your app. server (Payara5) to support Dataverse"
+echo "Setting up your app. server (Payara) to support Dataverse"
echo "Payara directory: "$GLASSFISH_ROOT
echo "Domain directory: "$DOMAIN_DIR
diff --git a/scripts/installer/default.config b/scripts/installer/default.config
index 312dd2cb2d8..8647cd02416 100644
--- a/scripts/installer/default.config
+++ b/scripts/installer/default.config
@@ -1,7 +1,7 @@
[glassfish]
HOST_DNS_ADDRESS = localhost
GLASSFISH_USER = dataverse
-GLASSFISH_DIRECTORY = /usr/local/payara5
+GLASSFISH_DIRECTORY = /usr/local/payara6
GLASSFISH_ADMIN_USER = admin
GLASSFISH_ADMIN_PASSWORD = secret
GLASSFISH_HEAP = 2048
diff --git a/scripts/installer/install b/scripts/installer/install
deleted file mode 100755
index 2208f014606..00000000000
--- a/scripts/installer/install
+++ /dev/null
@@ -1,1538 +0,0 @@
-#!/usr/bin/perl
-
-use strict;
-use warnings;
-use Getopt::Long;
-use Socket;
-use File::Copy;
-
-# command line options:
-
-my $verbose;
-my $postgresonly;
-my $hostname;
-my $gfuser;
-my $gfdir;
-my $mailserver;
-my $noninteractive;
-my $skipdatabasesetup;
-my $force;
-my $nogfpasswd;
-my $admin_email;
-
-my ($rez) = GetOptions(
- #"length=i" => \$length, # numeric
- #"file=s" => \$data, # string
- "verbose" => \$verbose,
- "pg_only" => \$postgresonly,
- "skip_db_setup" => \$skipdatabasesetup,
- "hostname=s" => \$hostname,
- "gfuser=s" => \$gfuser,
- "gfdir=s" => \$gfdir,
- "mailserver=s" => \$mailserver,
- "y|yes" => \$noninteractive,
- "f|force" => \$force,
- "nogfpasswd" => \$nogfpasswd,
- "admin_email=s" => \$admin_email,
-);
-
-# openshift/docker-specific - name of the "pod" executing the installer:
-my $pod_name = "";
-if (exists($ENV{'MY_POD_NAME'}))
-{
- $pod_name = $ENV{'MY_POD_NAME'};
-}
-
-my $jq_exec_path = "";
-my $psql_exec_path = "";
-my $cwd;
-my $WARFILE_LOCATION = "dataverse.war";
-
-
-my @CONFIG_VARIABLES;
-
-if ($postgresonly)
-{
- @CONFIG_VARIABLES =
- ( 'POSTGRES_SERVER', 'POSTGRES_PORT', 'POSTGRES_DATABASE', 'POSTGRES_USER', 'POSTGRES_PASSWORD', 'POSTGRES_ADMIN_PASSWORD' );
-
-}
-else
-{
-
- @CONFIG_VARIABLES = (
- 'HOST_DNS_ADDRESS',
- 'GLASSFISH_USER',
- 'GLASSFISH_DIRECTORY',
- 'ADMIN_EMAIL',
- 'MAIL_SERVER',
-
- 'POSTGRES_SERVER',
- 'POSTGRES_PORT',
- 'POSTGRES_ADMIN_PASSWORD',
- 'POSTGRES_DATABASE',
- 'POSTGRES_USER',
- 'POSTGRES_PASSWORD',
-
- 'SOLR_LOCATION',
-
- 'RSERVE_HOST',
- 'RSERVE_PORT',
- 'RSERVE_USER',
- 'RSERVE_PASSWORD',
-
- 'DOI_USERNAME',
- 'DOI_PASSWORD',
- 'DOI_BASEURL',
- 'DOI_DATACITERESTAPIURL'
-
- );
-}
-
-my %CONFIG_DEFAULTS;
-
-&read_config_defaults("default.config");
-
-my %CONFIG_PROMPTS;
-my %CONFIG_COMMENTS;
-
-&read_interactive_config_values("interactive.config");
-
-my $API_URL = "http://localhost:8080/api";
-
-# jodbc.postgresql.org recommends 4.2 for Java 8.
-# updated drivers may be obtained from
-# https://jdbc.postgresql.org/download.html
-my $postgres_jdbc = "postgresql-42.2.12.jar";
-
-# 0. A few preliminary checks:
-
-# 0a. OS:
-
-my $uname_out = `uname -a`;
-
-my @uname_tokens = split( " ", $uname_out );
-
-my $WORKING_OS;
-if ( $uname_tokens[0] eq "Darwin" ) {
- print "\nThis appears to be a MacOS X system; good.\n";
- # TODO: check the OS version
-
- $WORKING_OS = "MacOSX";
-}
-elsif ( $uname_tokens[0] eq "Linux" ) {
- if ( -f "/etc/redhat-release" ) {
- print "\nThis appears to be a RedHat system; good.\n";
- $WORKING_OS = "RedHat";
- # TODO: check the distro version
- }
- else {
- print "\nThis appears to be a non-RedHat Linux system;\n";
- print "this installation *may* succeed; but we're not making any promises!\n";
- $WORKING_OS = "Linux";
- }
-} else {
- print "\nWARNING: This appears to be neither a Linux or MacOS X system!\n";
- print "This installer script will most likely fail. Please refer to the\n";
- print "DVN Installers Guide for more information.\n\n";
-
- $WORKING_OS = "Unknown";
-
- unless ($noninteractive) {
- exit 0;
- }
-
- print "(Normally we would stop right there; but since the \"--yes\" option was specified, we'll attempt to continue)\n\n";
-
-}
-
-
-# 0b. host name:
-
-if ($hostname) {
- $CONFIG_DEFAULTS{'HOST_DNS_ADDRESS'} = $hostname;
-} else {
- my $hostname_from_cmdline = `hostname`;
- chop $hostname_from_cmdline;
-
- $CONFIG_DEFAULTS{'HOST_DNS_ADDRESS'} = $hostname_from_cmdline;
-}
-
-# 0c. check if there is the default.config file with the pre-set configuration values:
-
-# read default configuration values from tab separated file "default.config" if it exists
-# moved after the $hostname_from_cmdline section to avoid excessively complicating the logic
-# of command line argument, automatic selection, or config file.
-#
-# NOTE: if the file contain any Postgres configuration (for example: "POSTGRES_USER dvnApp")
-# but an environmental variable with the same name exists - THE ENV. VAR WILL WIN! (don't ask)
-# (actually this is to accommodate the openshift docker deployment scenario)
-
-sub trim { my $s = shift; $s =~ s/^\s+|\s+$//g; return $s };
-
-#my $config_default_file = "default.config";
-#
-#if ( -e $config_default_file )
-#{
-# print("loading default configuration values from $config_default_file\n");
-# open( my $inp_cfg, $config_default_file );
-# while( my $ln = <$inp_cfg> )
-# {
-# my @xs = split('\t', $ln );
-# if ( 2 == @xs )
-# {
-# my $k = $xs[0];
-# my $v = trim($xs[1]);
-## if (defined $ENV{$k} && ($k eq "POSTGRES_USER" || $k eq "POSTGRES_PASSWORD")) {
-## $v = $ENV{$k};
-## }
-## if (defined $ENV{'POSTGRESQL_ADMIN_PASSWORD'} && $k eq "POSTGRES_ADMIN_PASSWORD") {
-## $v = $ENV{'POSTGRESQL_ADMIN_PASSWORD'};
-## }
-# $CONFIG_DEFAULTS{$k}=$v;
-# }
-# }
-#}
-#else
-#{
-# print("using hard-coded default configuration values (no $config_default_file available)\n");
-#}
-
-# 0d. current OS user. (the first one we find wins)
-
-my $current_user = $ENV{LOGNAME} || $ENV{USER} || getpwuid($<);
-
-# if the username was specified on the command-line, it takes precendence:
-if ($gfuser) {
- print "Using CLI-specified user $gfuser.\n";
- $CONFIG_DEFAULTS{'GLASSFISH_USER'} = $gfuser;
-}
-
-
-if (!$CONFIG_DEFAULTS{'GLASSFISH_USER'} || !$noninteractive) {
- $CONFIG_DEFAULTS{'GLASSFISH_USER'} = $current_user;
- print "using $current_user.\n";
-}
-
-
-# prefer that we not install as root.
-unless ( $< != 0 ) {
- print "####################################################################\n";
- print " It is recommended that this script not be run as root.\n";
- print " Consider creating the service account \"dataverse\", giving it ownership\n";
- print " on the glassfish/domains/domain1/ and glassfish/lib/ directories,\n";
- print " along with the JVM-specified files.dir location, and designate\n";
- print " that account to launch and run the Application Server (Payara),\n";
- print " AND use that user account to run this installer.\n";
- print "####################################################################\n";
-
- unless ($noninteractive)
- {
- print "\nPress any key to continue, or ctrl-C to exit the installer...\n\n";
- system "stty cbreak /dev/tty 2>&1";
- unless ($noninteractive) {
- my $key = getc(STDIN);
- }
- system "stty -cbreak /dev/tty 2>&1";
- print "\n";
- }
-}
-
-# ensure $gfuser exists or bail
-my $gfidcmd="id $CONFIG_DEFAULTS{'GLASSFISH_USER'} > /dev/null";
-my $gfreturncode=system($gfidcmd);
-if ($gfreturncode != 0) {
- die "Couldn't find user $gfuser. Please ensure the account exists and is readable by the user running this installer.\n";
-}
-
-# 0e. the following 2 options can also be specified on the command line, and
-# also take precedence over the default values that are hard-coded and/or
-# provided in the default.config file:
-
-if ($mailserver) {
- $CONFIG_DEFAULTS{'MAIL_SERVER'} = $mailserver;
-}
-
-if ($gfdir) {
- $CONFIG_DEFAULTS{'GLASSFISH_DIRECTORY'} = $gfdir;
-}
-
-# 1. CHECK FOR SOME MANDATORY COMPONENTS (WAR FILE, ETC.)
-# since we can't do anything without these things in place, better check for
-# them before we go into the interactive config mode.
-# (skip if this is a database-only setup)
-
-unless ($postgresonly)
-{
-# 1a. war file:
- print "\nChecking if the application .war file is available... ";
-
-# if this installer section is running out of the installer zip bundle directory,
-# the war file will be sitting right here, named "dataverse.war":
-
- $WARFILE_LOCATION = "dataverse.war";
-
-# but if it's not here, this is probably a personal development
-# setup, so their build should be up in their source tree:
-
- unless ( -f $WARFILE_LOCATION ) {
- my $DATAVERSE_VERSION = "";
- my $DATAVERSE_POM_FILE = "../../modules/dataverse-parent/pom.xml";
- if ( -f $DATAVERSE_POM_FILE )
- {
- open DPF, $DATAVERSE_POM_FILE;
- my $pom_line;
- while ($pom_line=)
- {
- chop $pom_line;
- if ($pom_line =~/^[ \t]*([0-9\.]+)<\/revision>/)
- {
- $DATAVERSE_VERSION=$1;
- last;
- }
- }
- close DPF;
-
- if ($DATAVERSE_VERSION ne "") {
- $WARFILE_LOCATION = "../../target/dataverse-" . $DATAVERSE_VERSION . ".war";
- }
- }
- }
-
-# But, if the war file cannot be found in either of the 2
-# places - we'll just have to give up:
-
- unless ( -f $WARFILE_LOCATION ) {
- print "\nWARNING: Can't find the project .war file!\n";
- print "\tAre you running the installer in the right directory?\n";
- print "\tHave you built the war file?\n";
- print "\t(if not, build the project and run the installer again)\n";
-
- exit 0;
- }
- print " Yes, it is!\n";
-
-
-# 1b. check and remember the working dir:
- chomp( $cwd = `pwd` );
-
-# 1d. jq executable:
-
- my $sys_path = $ENV{'PATH'};
- my @sys_path_dirs = split( ":", $sys_path );
-
- if ( $pod_name ne "start-glassfish") # Why is that again?
- {
- for my $sys_path_dir (@sys_path_dirs) {
- if ( -x $sys_path_dir . "/jq" ) {
- $jq_exec_path = $sys_path_dir;
- last;
- }
- }
- if ( $jq_exec_path eq "" ) {
- print STDERR "\nERROR: I haven't been able to find the jq command in your PATH! Please install it from http://stedolan.github.io/jq/\n";
- exit 1;
-
- }
- }
-
-}
-
-
-# 2. INTERACTIVE CONFIG SECTION:
-
-print "\nWelcome to the Dataverse installer.\n";
-unless ($postgresonly) {
- print "You will be guided through the process of setting up a NEW\n";
- print "instance of the dataverse application\n";
-}
-else {
- print "You will be guided through the process of configuring your\n";
- print "PostgreSQL database for use by the Dataverse application.\n";
-}
-
-my $yesno;
-
-unless ($noninteractive)
-{
- print "\nATTENTION: As of Dataverse v.4.19, we are offering a new, experimental \n";
- print "version of the installer script, implemented in Python. It will eventually \n";
- print "replace this script (implemented in Perl). Consult the file README_python.txt \n";
- print "for more information on how to run it. \n";
-
- print "\nWould you like to exit and use the new installer instead? [y/n] ";
- $yesno = <>;
- chop $yesno;
-
- while ( $yesno ne "y" && $yesno ne "n" ) {
- print "Please enter 'y' or 'n'!\n";
- print "(or ctrl-C to exit the installer)\n";
- $yesno = <>;
- chop $yesno;
- }
-
- exit 0 if $yesno eq "y";
-}
-
-ENTERCONFIG:
-
-print "\n";
-print "Please enter the following configuration values:\n";
-print "(hit [RETURN] to accept the default value)\n";
-print "\n";
-
-for my $ENTRY (@CONFIG_VARIABLES)
-{
- my $config_prompt = $CONFIG_PROMPTS{$ENTRY};
- my $config_comment = $CONFIG_COMMENTS{$ENTRY};
-
- if ( $config_comment eq '' )
- {
- print $config_prompt . ": ";
- print "[" . $CONFIG_DEFAULTS{$ENTRY} . "] ";
- }
- else
- {
- print $config_prompt . $config_comment;
- print "[" . $CONFIG_DEFAULTS{$ENTRY} . "] ";
- }
-
- my $user_entry = "";
-
- # ($noninteractive means the installer is being run in the non-interactive mode; it will use
- # the default values specified so far, without prompting the user for alternative values)\
- unless ($noninteractive)
- {
- $user_entry = <>;
- chop $user_entry;
-
- if ( $user_entry ne "" ) {
- $CONFIG_DEFAULTS{$ENTRY} = $user_entry;
- }
-
- # for some values, we'll try to do some validation right here, in real time:
-
- if ($ENTRY eq 'ADMIN_EMAIL')
- {
- $user_entry = $CONFIG_DEFAULTS{$ENTRY};
- my $attempts = 0;
- while ($user_entry !~/[A-Za-z0-9._%+-]+@[A-Za-z0-9.-]+\.[A-Za-z]{2,4}/)
- {
- $attempts++;
- print "Please enter a valid email address: ";
- $user_entry = <>;
- chop $user_entry;
- }
-
- if ($attempts)
- {
- print "OK, looks legit.\n";
- $CONFIG_DEFAULTS{$ENTRY} = $user_entry;
- }
- }
- elsif ($ENTRY eq 'GLASSFISH_DIRECTORY')
- {
- # CHECK IF GLASSFISH DIR LOOKS OK:
- print "\nChecking your Glassfish installation...";
-
- my $g_dir = $CONFIG_DEFAULTS{'GLASSFISH_DIRECTORY'};
-
-
- unless ( -d $g_dir . "/glassfish/domains/domain1" )
- {
- while ( !( -d $g_dir . "/glassfish/domains/domain1" ) )
- {
- print "\nInvalid Glassfish directory " . $g_dir . "!\n";
- print "Enter the root directory of your Glassfish installation:\n";
- print "(Or ctrl-C to exit the installer): ";
-
- $g_dir = <>;
- chop $g_dir;
- }
- }
-
- # verify that we can write in the Glassfish directory
- # (now that we are no longer requiring to run the installer as root)
-
- my @g_testdirs = ( "/glassfish/domains/domain1",
- "/glassfish/domains/domain1/config",
- "/glassfish/lib");
-
- for my $test_dir (@g_testdirs)
- {
- if (!(-w ($g_dir . $test_dir)))
- {
- print "\n";
- die("ERROR: " . $g_dir . $test_dir . " not writable to the user running the installer! Check permissions on Payara5 hierarchy.\n");
- }
- }
-
-
-
- print "$g_dir looks OK!\n";
- $CONFIG_DEFAULTS{'GLASSFISH_DIRECTORY'} = $g_dir;
-
- }
- elsif ($ENTRY eq 'MAIL_SERVER')
- {
- my $smtp_server = "";
- while (! &validate_smtp_server() )
- {
- print "Enter a valid SMTP (mail) server:\n";
- print "(Or ctrl-C to exit the installer): ";
-
- $smtp_server = <>;
- chop $smtp_server;
-
- $CONFIG_DEFAULTS{'MAIL_SERVER'} = $smtp_server unless $smtp_server eq '';
- }
-
- print "\nOK, we were able to establish connection to the SMTP server you have specified.\n";
- print "Please note that you *may* need to configure some extra settings before your \n";
- print "Dataverse can send email. Please consult the \"Mail Host Configuration & Authentication\"\n";
- print "section of the installation guide (http://guides.dataverse.org/en/latest/installation/installation-main.html)\n";
- print "for more information.\n";
- }
- }
-
- print "\n";
-}
-
-# 2b. CONFIRM VALUES ENTERED:
-
-print "\nOK, please confirm what you've entered:\n\n";
-
-for my $ENTRY (@CONFIG_VARIABLES) {
- print $CONFIG_PROMPTS{$ENTRY} . ": " . $CONFIG_DEFAULTS{$ENTRY} . "\n";
-}
-
-if ($noninteractive) {
- $yesno = "y";
-}
-else {
- print "\nIs this correct? [y/n] ";
- $yesno = <>;
- chop $yesno;
-}
-
-while ( $yesno ne "y" && $yesno ne "n" ) {
- print "Please enter 'y' or 'n'!\n";
- print "(or ctrl-C to exit the installer)\n";
- $yesno = <>;
- chop $yesno;
-}
-
-if ( $yesno eq "n" ) {
- goto ENTERCONFIG;
-}
-
-# 3. SET UP POSTGRES USER AND DATABASE
-
-unless($pod_name eq "start-glassfish" || $pod_name eq "dataverse-glassfish-0" || $skipdatabasesetup) {
- &setup_postgres();
-# (there's no return code - if anything goes wrong, the method will exit the script, with some diagnostic messages for the user)
- print "\nOK, done.\n";
-
- if ($postgresonly)
- {
- exit 0;
- }
-}
-
-# 5. CONFIGURE PAYARA
-
-my $glassfish_dir = $CONFIG_DEFAULTS{'GLASSFISH_DIRECTORY'};
-
-my $done = &setup_appserver();
-
-# Check if the App is running:
-
-unless ((
- my $exit_code =
- system( $glassfish_dir . "/bin/asadmin list-applications | grep -q '^dataverse'" )
- ) == 0 )
-{
- # If the "asadmin list-applications" has failed, it may only mean that an earlier
- # "asadmin login" had failed, and asadmin is now failing to run without the user
- # supplying the username and password. (And the fact that we are trying to pile the
- # output to grep prevents it from providing the prompts).
- # So before we give up, we'll try an alternative:
-
- unless ((
- my $exit_code_2 =
- system( "curl http://localhost:8080/robots.txt | grep -q '^User-agent'" )
- ) == 0 )
- {
- print STDERR "It appears that the Dataverse application is not running...\n";
- print STDERR "Even though the \"asadmin deploy\" command had succeeded earlier.\n\n";
- print STDERR "Aborting - sorry...\n\n";
-
- exit 1;
- }
-}
-
-
-print "\nOK, the Dataverse application appears to be running...\n\n";
-
-# Run the additional setup scripts, that populate the metadata block field values, create users
-# and dataverses, etc.
-
-unless ( -d "data" && -f "setup-datasetfields.sh" && -f "setup-users.sh" && -f "setup-dvs.sh" && -f "setup-all.sh" ) {
- chdir("../api");
-}
-
-unless ( -d "data" && -f "setup-datasetfields.sh" && -f "setup-users.sh" && -f "setup-dvs.sh" && -f "setup-builtin-roles.sh" && -f "setup-all.sh" ) {
- print "\nERROR: Can't find the metadata and user/dataverse setup scripts!\n";
- print "\tAre you running the installer in the right directory?\n";
- exit 1;
-}
-
-# if there's an admin_email set from arguments, replace the value in `dv-root.json` (called by `setup-all.sh`)
-if ($admin_email)
-{
- print "setting contact email for root dataverse to: $admin_email\n";
- set_root_contact_email( $admin_email );
-}
-else
-{
- print "using default contact email for root dataverse\n";
-}
-
-for my $script ( "setup-all.sh" ) {
- # (there's only 1 setup script to run now - it runs all the other required scripts)
- print "Executing post-deployment setup script " . $script . "... ";
-
- my $my_hostname = $CONFIG_DEFAULTS{'HOST_DNS_ADDRESS'};
-
- # We used to filter the supplied scripts, replacing "localhost" and the port, in
- # case they are running Dataverse on a different port... Now we are simply requiring
- # that the port 8080 is still configured in domain.xml when they are running the
- # installer:
- my $run_script;
- #if ( $my_hostname ne "localhost" ) {
- # system( "sed 's/localhost:8080/$my_hostname/g' < " . $script . " > tmpscript.sh; chmod +x tmpscript.sh" );
- # $run_script = "tmpscript.sh";
- #}
- #else {
- $run_script = $script;
- #}
-
- unless ( my $exit_code = system( "./" . $run_script . " > $run_script.$$.log 2>&1") == 0 )
- {
- print "\nERROR executing script " . $script . "!\n";
- exit 1;
- }
- print "done!\n";
-}
-
-# SOME ADDITIONAL SETTINGS THAT ARE NOT TAKEN CARE OF BY THE setup-all SCRIPT
-# NEED TO BE CONFIGURED HERE:
-
-print "Making additional configuration changes...\n\n";
-
-
-# a. Configure the Admin email in the Dataverse settings:
-
-print "Executing " . "curl -X PUT -d " . $CONFIG_DEFAULTS{'ADMIN_EMAIL'} . " " . $API_URL . "/admin/settings/:SystemEmail" . "\n";
-
-my $exit_code = system("curl -X PUT -d " . $CONFIG_DEFAULTS{'ADMIN_EMAIL'} . " " . $API_URL . "/admin/settings/:SystemEmail");
-if ( $exit_code )
-{
- print "WARNING: failed to configure the admin email in the Dataverse settings!\n\n";
-}
-else
-{
- print "OK.\n\n";
-}
-
-# b. If this installation is going to be using a remote SOLR search engine service, configure its location in the settings:
-
-if ($CONFIG_DEFAULTS{'SOLR_LOCATION'} ne 'LOCAL')
-{
- print "Executing " . "curl -X PUT -d " . $CONFIG_DEFAULTS{'SOLR_LOCATION'} . " " . $API_URL . "/admin/settings/:SolrHostColonPort" . "\n";
- my $exit_code = system("curl -X PUT -d " . $CONFIG_DEFAULTS{'SOLR_LOCATION'} . " " . $API_URL . "/admin/settings/:SolrHostColonPort");
- if ( $exit_code )
- {
- print "WARNING: failed to configure the location of the remote SOLR service!\n\n";
- }
- else
- {
- print "OK.\n\n";
- }
-}
-
-
-
-chdir($cwd);
-
-print "\n\nYou should now have a running Dataverse instance at\n";
-print " http://" . $CONFIG_DEFAULTS{'HOST_DNS_ADDRESS'} . ":8080\n\n\n";
-
-if ($WARFILE_LOCATION =~/([0-9]\.[0-9]\.[0-9])\.war$/)
-{
- my $version = $1;
- print "If this is a personal development installation, we recommend that you undeploy the currently-running copy \n";
- print "of the application, with the following asadmin command:\n\n";
- print "\t" . $CONFIG_DEFAULTS{'GLASSFISH_DIRECTORY'} . '/bin/asadmin undeploy dataverse-' . $version . "\n\n";
- print "before attempting to deploy from your development environment in NetBeans.\n\n";
-}
-
-
-print "\nYour Dataverse has been configured to use DataCite, to register DOI global identifiers in the \n";
-print "test name space \"10.5072\" with the \"shoulder\" \"FK2\"\n";
-print "However, you have to contact DataCite (support\@datacite.org) and request a test account, before you \n";
-print "can publish datasets. Once you receive the account name and password, add them to your domain.xml,\n";
-print "as the following two JVM options:\n";
-print "\t-Ddoi.username=...\n";
-print "\t-Ddoi.password=...\n";
-print "and restart payara5\n";
-print "If this is a production Dataverse and you are planning to register datasets as \n";
-print "\"real\", non-test DOIs or Handles, consult the \"Persistent Identifiers and Publishing Datasets\"\n";
-print "section of the Installataion guide, on how to configure your Dataverse with the proper registration\n";
-print "credentials.\n\n";
-
-
-
-# (going to skip the Rserve check; it's no longer a required, or even a recommended component)
-
-exit 0;
-
-# 9. FINALLY, CHECK IF RSERVE IS RUNNING:
-print "\n\nFinally, checking if Rserve is running and accessible...\n";
-
-unless ( $CONFIG_DEFAULTS{'RSERVE_PORT'} =~ /^[0-9][0-9]*$/ ) {
- print $CONFIG_DEFAULTS{'RSERVE_HOST'} . " does not look like a valid port number,\n";
- print "defaulting to 6311.\n\n";
-
- $CONFIG_DEFAULTS{'RSERVE_PORT'} = 6311;
-}
-
-my ( $rserve_iaddr, $rserve_paddr, $rserve_proto );
-
-unless ( $rserve_iaddr = inet_aton( $CONFIG_DEFAULTS{'RSERVE_HOST'} ) ) {
- print STDERR "Could not look up $CONFIG_DEFAULTS{'RSERVE_HOST'},\n";
- print STDERR "the host you specified as your R server.\n";
- print STDERR "\nDVN can function without a working R server, but\n";
- print STDERR "much of the functionality concerning running statistics\n";
- print STDERR "and analysis on quantitative data will not be available.\n";
- print STDERR "Please consult the Installers guide for more info.\n";
-
- exit 0;
-}
-
-$rserve_paddr = sockaddr_in( $CONFIG_DEFAULTS{'RSERVE_PORT'}, $rserve_iaddr );
-$rserve_proto = getprotobyname('tcp');
-
-unless ( socket( SOCK, PF_INET, SOCK_STREAM, $rserve_proto )
- && connect( SOCK, $rserve_paddr ) )
-{
- print STDERR "Could not establish connection to $CONFIG_DEFAULTS{'RSERVE_HOST'}\n";
- print STDERR "on port $CONFIG_DEFAULTS{'RSERVE_PORT'}, the address you provided\n";
- print STDERR "for your R server.\n";
- print STDERR "DVN can function without a working R server, but\n";
- print STDERR "much of the functionality concerning running statistics\n";
- print STDERR "and analysis on quantitative data will not be available.\n";
- print STDERR "Please consult the \"Installing R\" section in the Installers guide\n";
- print STDERR "for more info.\n";
-
- exit 0;
-
-}
-
-close(SOCK);
-print "\nOK!\n";
-
-# 5. CONFIGURE PAYARA
-sub setup_appserver {
- my $success = 1;
- my $failure = 0;
-
- my $glassfish_dir = $CONFIG_DEFAULTS{'GLASSFISH_DIRECTORY'};
-
- print "\nProceeding with the app. server (Payara5) setup.\n";
-
-# 5a. DETERMINE HOW MUCH MEMORY TO GIVE TO GLASSFISH AS HEAP:
-
- my $gf_heap_default = "2048m";
- my $sys_mem_total = 0;
-
- if ( -e "/proc/meminfo" && open MEMINFO, "/proc/meminfo" ) {
- # Linux
-
- while ( my $mline = ) {
- if ( $mline =~ /MemTotal:[ \t]*([0-9]*) kB/ ) {
- $sys_mem_total = $1;
- }
- }
-
- close MEMINFO;
-
-# TODO: Figure out how to determine the amount of memory when running in Docker
-# because we're wondering if Dataverse can run in the free OpenShift Online
-# offering that only gives you 1 GB of memory. Obviously, if this is someone's
-# first impression of Dataverse, we want to to run well! What if you try to
-# ingest a large file or perform other memory-intensive operations? For more
-# context, see https://github.com/IQSS/dataverse/issues/4040#issuecomment-331282286
- if ( -e "/sys/fs/cgroup/memory/memory.limit_in_bytes" && open CGROUPMEM, "/sys/fs/cgroup/memory/memory.limit_in_bytes" ) {
- print "INFO: This system has the CGROUP file /sys/fs/cgroup/memory/memory.limit_in_bytes\n";
- while ( my $limitline = ) {
- ### TODO: NO, WE ARE NOT NECESSARILY IN DOCKER!
- ###print "We must be running in Docker! Fancy!\n";
- # The goal of this cgroup check is for
- # "Setting the heap limit for Glassfish/Payara to 750MB"
- # to change to some other value, based on memory available.
- print "INFO: /sys/fs/cgroup/memory/memory.limit_in_bytes: $limitline\n";
- my $limit_in_kb = $limitline / 1024;
- print "INFO: CGROUP limit_in_kb = $limit_in_kb [ignoring]\n";
- # In openshift.json, notice how PostgreSQL and Solr have
- # resources.limits.memory set to "256Mi".
- # If you try to give the Dataverse/Glassfish container twice
- # as much memory (512 MB) and allow $sys_mem_total to
- # be set below, you should see the following:
- # "Setting the heap limit for Glassfish to 192MB."
- # FIXME: dataverse.war will not deploy with only 512 MB of memory.
- # Again, the goal is 1 GB total (512MB + 256MB + 256MB) for
- # Glassfish, PostgreSQL, and Solr to fit in the free OpenShift tier.
- #print "setting sys_mem_total to: $limit_in_kb\n";
- #$sys_mem_total = $limit_in_kb;
- }
- close CGROUPMEM;
- }
- }
- elsif ( -x "/usr/sbin/sysctl" )
- {
- # MacOS X, probably...
-
- $sys_mem_total = `/usr/sbin/sysctl -n hw.memsize`;
- chop $sys_mem_total;
- if ( $sys_mem_total > 0 ) {
- $sys_mem_total = int( $sys_mem_total / 1024 );
- # size in kb
- }
- }
-
- if ( $sys_mem_total > 0 ) {
- # setting the default heap size limit to 3/8 of the available
- # amount of memory:
- $gf_heap_default = ( int( $sys_mem_total / ( 8 / 3 * 1024 ) ) );
-
- print "\nSetting the heap limit for Payara5 to " . $gf_heap_default . "MB. \n";
- print "You may need to adjust this setting to better suit \n";
- print "your system.\n\n";
-
- #$gf_heap_default .= "m";
-
- }
- else
- {
- print "\nCould not determine the amount of memory on your system.\n";
- print "Setting the heap limit for Payara5 to 2GB. You may need \n";
- print "to adjust the value to better suit your system.\n\n";
- }
-
- push @CONFIG_VARIABLES, "DEF_MEM_SIZE";
- $CONFIG_DEFAULTS{"DEF_MEM_SIZE"} = $gf_heap_default;
-
-# TODO:
-# is the below still the case with Payara5?
-# if the system has more than 4GB of memory (I believe), glassfish must
-# be run with the 64 bit flag set explicitly (at least that was the case
-# with the MacOS glassfish build...). Verify, and if still the case,
-# add a check.
-
- print "\n*********************\n";
- print "PLEASE NOTE, SOME OF THE ASADMIN COMMANDS ARE GOING TO FAIL,\n";
- print "FOR EXAMPLE, IF A CONFIGURATION SETTING THAT WE ARE TRYING\n";
- print "TO CREATE ALREADY EXISTS; OR IF A JVM OPTION THAT WE ARE\n";
- print "DELETING DOESN'T. THESE \"FAILURES\" ARE NORMAL!\n";
- print "*********************\n\n";
- print "When/if asadmin asks you to \"Enter admin user name\",\n";
- print "it should be safe to hit return and accept the default\n";
- print "(which is \"admin\").\n";
-
- print "\nPress any key to continue...\n\n";
-
- unless ($noninteractive)
- {
- system "stty cbreak /dev/tty 2>&1";
- unless ($noninteractive) {
- my $key = getc(STDIN);
- }
- system "stty -cbreak /dev/tty 2>&1";
- }
-
- print "\n";
-
-# 5b. start domain, if not running:
-
- my $javacheck = `java -version`;
- my $exitcode = $?;
- unless ( $exitcode == 0 ) {
- print STDERR "$javacheck\n" if $javacheck;
- print STDERR "Do you have java installed?\n";
- exit 1;
- }
- my $DOMAIN = "domain1";
- my $DOMAIN_DOWN =
- `$CONFIG_DEFAULTS{'GLASSFISH_DIRECTORY'}/bin/asadmin list-domains | grep "$DOMAIN " | grep "not running"`;
- print STDERR $DOMAIN_DOWN . "\n";
- if ($DOMAIN_DOWN) {
- print "Trying to start domain up...\n";
- if ( $current_user eq $CONFIG_DEFAULTS{'GLASSFISH_USER'} ){
- system( $CONFIG_DEFAULTS{'GLASSFISH_DIRECTORY'} . "/bin/asadmin start-domain domain1" );
- }
- else
- {
- system( "sudo -u $CONFIG_DEFAULTS{'GLASSFISH_USER'} " . $CONFIG_DEFAULTS{'GLASSFISH_DIRECTORY'} . "/bin/asadmin start-domain domain1" );
- }
- # TODO: (?) - retest that the domain is running now?
- }
- else
- {
- print "domain appears to be up...\n";
- }
-
-# 5c. create asadmin login, so that the user doesn't have to enter
-# the username and password for every asadmin command, if
-# access to :4848 is password-protected:
-
- system( $glassfish_dir. "/bin/asadmin login" );
-
-# 5d. configure glassfish using ASADMIN commands:
-
- $success = &run_asadmin_script();
-
-# CHECK EXIT STATUS, BARF IF SETUP SCRIPT FAILED:
-
- unless ($success) {
- print "\nERROR! Failed to configure Payara5 domain!\n";
- print "(see the error messages above - if any)\n";
- print "Aborting...\n";
-
- exit 1;
- }
-
-# 5e. Additional config files:
-
- my $JHOVE_CONFIG = "jhove.conf";
- my $JHOVE_CONF_SCHEMA = "jhoveConfig.xsd";
-
-
- my $JHOVE_CONFIG_DIST = $JHOVE_CONFIG;
- my $JHOVE_CONF_SCHEMA_DIST = $JHOVE_CONF_SCHEMA;
-
-# (if the installer is being run NOT as part of a distribution zipped bundle, but
-# from inside the source tree - adjust the locations of the jhove config files:
-
- unless ( -f $JHOVE_CONFIG ) {
- $JHOVE_CONFIG_DIST = "../../conf/jhove/jhove.conf";
- $JHOVE_CONF_SCHEMA_DIST = "../../conf/jhove/jhoveConfig.xsd";
- }
-
-# but if we can't find the files in either location, it must mean
-# that they are not running the script in the correct directory - so
-# nothing else left for us to do but give up:
-
- unless ( -f $JHOVE_CONFIG_DIST && -f $JHOVE_CONF_SCHEMA_DIST ) {
- print "\nERROR! JHOVE configuration files not found in the config dir!\n";
- print "(are you running the installer in the right directory?\n";
- print "Aborting...\n";
- exit 1;
- }
-
- print "\nCopying additional configuration files... ";
-
- #system( "/bin/cp -f " . $JHOVE_CONF_SCHEMA_DIST . " " . $glassfish_dir . "/glassfish/domains/domain1/config" );
- my $jhove_success = copy ($JHOVE_CONF_SCHEMA_DIST, $glassfish_dir . "/glassfish/domains/domain1/config");
- unless ($jhove_success)
- {
- print "\n*********************\n";
- print "ERROR: failed to copy jhove config file into " . $glassfish_dir . "/glassfish/domains/domain1/config - do you have write permission in that directory?";
- exit 1;
- }
-
-# The JHOVE conf file has an absolute PATH of the JHOVE config schema file (uh, yeah...)
-# - so it may need to be readjusted here:
-
- if ( $glassfish_dir ne "/usr/local/payara5" )
- {
- system( "sed 's:/usr/local/payara5:$glassfish_dir:g' < " . $JHOVE_CONFIG_DIST . " > " . $glassfish_dir . "/glassfish/domains/domain1/config/" . $JHOVE_CONFIG);
- }
- else
- {
- system( "/bin/cp -f " . $JHOVE_CONFIG_DIST . " " . $glassfish_dir . "/glassfish/domains/domain1/config" );
- }
-
- print "done!\n";
-
-# 5f. check if payara is running:
-# TODO.
-
-# 5g. DEPLOY THE APPLICATION:
-
- print "\nAttempting to deploy the application.\n";
- print "Command line: " . $glassfish_dir . "/bin/asadmin deploy " . $WARFILE_LOCATION . "\n";
- unless ((
- my $exit_code =
- system( $glassfish_dir . "/bin/asadmin deploy " . $WARFILE_LOCATION )
- ) == 0 )
- {
- print STDERR "Failed to deploy the application! WAR file: " . $WARFILE_LOCATION . ".\n";
- print STDERR "(exit code: " . $exit_code . ")\n";
- print STDERR "Aborting.\n";
- exit 1;
- }
-
-
- print "Finished configuring Payara and deploying the dataverse application. \n";
-
-
- return $success;
-}
-
-sub run_asadmin_script {
- my $success = 1;
- my $failure = 0;
-
- # We are going to run a standalone shell script with a bunch of asadmin
- # commands to set up all the Payara components for the application.
- # All the parameters must be passed to that script as environmental
- # variables:
-
- $ENV{'GLASSFISH_ROOT'} = $CONFIG_DEFAULTS{'GLASSFISH_DIRECTORY'};
- $ENV{'GLASSFISH_DOMAIN'} = "domain1";
- $ENV{'ASADMIN_OPTS'} = "";
- $ENV{'MEM_HEAP_SIZE'} = $CONFIG_DEFAULTS{'DEF_MEM_SIZE'};
-
- $ENV{'DB_PORT'} = $CONFIG_DEFAULTS{'POSTGRES_PORT'};
- $ENV{'DB_HOST'} = $CONFIG_DEFAULTS{'POSTGRES_SERVER'};
- $ENV{'DB_NAME'} = $CONFIG_DEFAULTS{'POSTGRES_DATABASE'};
- $ENV{'DB_USER'} = $CONFIG_DEFAULTS{'POSTGRES_USER'};
- $ENV{'DB_PASS'} = $CONFIG_DEFAULTS{'POSTGRES_PASSWORD'};
-
- $ENV{'RSERVE_HOST'} = $CONFIG_DEFAULTS{'RSERVE_HOST'};
- $ENV{'RSERVE_PORT'} = $CONFIG_DEFAULTS{'RSERVE_PORT'};
- $ENV{'RSERVE_USER'} = $CONFIG_DEFAULTS{'RSERVE_USER'};
- $ENV{'RSERVE_PASS'} = $CONFIG_DEFAULTS{'RSERVE_PASSWORD'};
- $ENV{'DOI_BASEURL'} = $CONFIG_DEFAULTS{'DOI_BASEURL'};
- $ENV{'DOI_USERNAME'} = $CONFIG_DEFAULTS{'DOI_USERNAME'};
- $ENV{'DOI_PASSWORD'} = $CONFIG_DEFAULTS{'DOI_PASSWORD'};
- $ENV{'DOI_DATACITERESTAPIURL'} = $CONFIG_DEFAULTS{'DOI_DATACITERESTAPIURL'};
-
- $ENV{'HOST_ADDRESS'} = $CONFIG_DEFAULTS{'HOST_DNS_ADDRESS'};
-
- my ($mail_server_host, $mail_server_port) = split (":", $CONFIG_DEFAULTS{'MAIL_SERVER'});
-
- $ENV{'SMTP_SERVER'} = $mail_server_host;
-
- if ($mail_server_port)
- {
- $ENV{'SMTP_SERVER_PORT'} = $mail_server_port;
- }
-
- $ENV{'FILES_DIR'} =
- $CONFIG_DEFAULTS{'GLASSFISH_DIRECTORY'} . "/glassfish/domains/" . $ENV{'GLASSFISH_DOMAIN'} . "/files";
-
- system("./as-setup.sh");
-
- if ($?) {
- return $failure;
- }
- return $success;
-}
-
-sub create_pg_hash {
- my $pg_username = shift @_;
- my $pg_password = shift @_;
-
- my $encode_line = $pg_password . $pg_username;
-
- # for Redhat:
-
- ##print STDERR "executing /bin/echo -n $encode_line | md5sum\n";
-
- my $hash;
- if ( $WORKING_OS eq "MacOSX" ) {
- $hash = `/bin/echo -n $encode_line | md5`;
- }
- else {
- $hash = `/bin/echo -n $encode_line | md5sum`;
- }
-
- chop $hash;
-
- $hash =~ s/ \-$//;
-
- if ( ( length($hash) != 32 ) || ( $hash !~ /^[0-9a-f]*$/ ) ) {
- print STDERR "Failed to generate a MD5-encrypted password hash for the Postgres database.\n";
- exit 1;
- }
-
- return $hash;
-}
-
-sub validate_smtp_server {
- my ( $mail_server_iaddr, $mail_server__paddr, $mail_server_proto, $mail_server_status );
-
- $mail_server_status = 1;
-
- my $userentry = $CONFIG_DEFAULTS{'MAIL_SERVER'};
- my ($testserver, $testport) = split (":", $userentry);
-
- unless ( $mail_server_iaddr = inet_aton( $testserver ) ) {
- print STDERR "Could not look up $testserver,\n";
- print STDERR "the host you specified as your mail server\n";
- $mail_server_status = 0;
- }
-
- if ($mail_server_status) {
- $testport = 25 unless $testport;
- my $mail_server_paddr = sockaddr_in( $testport, $mail_server_iaddr );
- $mail_server_proto = getprotobyname('tcp');
-
- unless ( socket( SOCK, PF_INET, SOCK_STREAM, $mail_server_proto )
- && connect( SOCK, $mail_server_paddr ) )
- {
- print STDERR "Could not establish connection to $CONFIG_DEFAULTS{'MAIL_SERVER'},\n";
- print STDERR "the address you provided for your Mail server.\n";
- print STDERR "Please select a valid mail server, and try again.\n\n";
-
- $mail_server_status = 0;
- }
-
- close(SOCK);
- }
-
- return $mail_server_status;
-}
-
-# support function for set_root_contact_email
-sub search_replace_file
-{
- my ($infile, $pattern, $replacement, $outfile) = @_;
- open (my $inp, $infile);
- local $/ = undef;
- my $txt = <$inp>;
- close $inp;
- $txt =~s/$pattern/$replacement/g;
- open (my $opf, '>:encoding(UTF-8)', $outfile);
- print $opf $txt;
- close $opf;
- return;
-}
-# set the email address for the default `dataverseAdmin` account
-sub set_root_contact_email
-{
- my ($contact_email) = @_;
- my $config_json = "data/user-admin.json";
- search_replace_file($config_json,"\"email\":\"dataverse\@mailinator.com\"","\"email\":\"$contact_email\"",$config_json);
- return;
-}
-
-
-sub setup_postgres {
- my $pg_local_connection = 0;
- my $pg_major_version = 0;
- my $pg_minor_version = 0;
-
-
-# We'll need to do a few things as the Postgres admin user;
-# We'll assume the name of the admin user is "postgres".
- my $POSTGRES_ADMIN_USER = "postgres";
-
-
-
-##Handling container env
-
- if ($pod_name eq "start-glassfish")
- {
- # When we are in this openshift "start-glassfish" pod, we get all the
- # Postgres configuration from the environmental variables.
- print "Init container starting \n";
- $CONFIG_DEFAULTS{'POSTGRES_SERVER'} = $ENV{"POSTGRES_SERVER"} . "." . $ENV{"POSTGRES_SERVICE_HOST"};
- $CONFIG_DEFAULTS{'POSTGRES_DATABASE'} = $ENV{"POSTGRES_DATABASE"};
- $CONFIG_DEFAULTS{'POSTGRES_USER'} = $ENV{"POSTGRES_USER"};
- $CONFIG_DEFAULTS{'POSTGRES_ADMIN_PASSWORD'} = $ENV{"POSTGRES_ADMIN_PASSWORD"};
- # there was a weird case of the postgres admin password option spelled differently in openshift.json
- # - as "POSTGRESQL_ADMIN_PASSWORD"; I'm going to change it in openshift.json - but I'm leaving this
- # next line here, just in case: (L.A. -- Sept. 2018)
- $CONFIG_DEFAULTS{'POSTGRES_ADMIN_PASSWORD'} = $ENV{'POSTGRESQL_ADMIN_PASSWORD'};
- $CONFIG_DEFAULTS{'POSTGRES_PASSWORD'} = $ENV{"POSTGRES_PASSWORD"};
- }
-
- if ( $CONFIG_DEFAULTS{'POSTGRES_SERVER'} eq 'localhost' || $CONFIG_DEFAULTS{'POSTGRES_SERVER'} eq '127.0.0.1' )
- {
- $pg_local_connection = 1;
- }
-# elsif ($postgresonly)
-# {
-# print "In the --pg_only mode the script can only be run LOCALLY,\n";
-# print "i.e., on the server where PostgresQL is running, with the\n";
-# print "Postgres server address as localhost - \"127.0.0.1\".\n";
-# exit 1;
-# }
-
-#If it is executing in a container, proceed easy with this all-in-one block
-
-
-
-
-# 3b. LOCATE THE psql EXECUTABLE:
-
- if ( $pod_name eq "start-glassfish"){
- $psql_exec_path = "/usr/bin"
- }
- else
- {
- my $sys_path = $ENV{'PATH'};
- my @sys_path_dirs = split( ":", $sys_path );
-
- for my $sys_path_dir (@sys_path_dirs) {
-
- if ( -x $sys_path_dir . "/psql" ) {
- $psql_exec_path = $sys_path_dir;
-
- last;
- }
- }
- }
-
- my $psql_major_version = 0;
- my $psql_minor_version = 0;
-
-# 3c. IF PSQL WAS FOUND IN THE PATH, CHECK ITS VERSION:
-
- unless ( $psql_exec_path eq "" ) {
- open( PSQLOUT, $psql_exec_path . "/psql --version|" );
-
- my $psql_version_line = ;
- chop $psql_version_line;
- close PSQLOUT;
-
- my ( $postgresName, $postgresNameLong, $postgresVersion ) = split( " ", $psql_version_line );
-
- unless ( $postgresName eq "psql" && $postgresVersion =~ /^[0-9][0-9\.]*$/ ) {
- print STDERR "\nWARNING: Unexpected output from psql command!\n";
- }
- else
- {
- my (@psql_version_tokens) = split( '\.', $postgresVersion );
-
- print "\n\nFound Postgres psql command, version $postgresVersion.\n\n";
-
- $psql_major_version = $psql_version_tokens[0];
- $psql_minor_version = $psql_version_tokens[1];
-
- $pg_major_version = $psql_major_version;
- $pg_minor_version = $psql_minor_version;
-
- }
- }
-
-# a frequent problem with MacOSX is that the copy of psql found in the PATH
-# belongs to the older version of PostgresQL supplied with the OS, which happens
-# to be incompatible with the newer builds from the Postgres project; which are
-# recommended to be used with Dataverse. So if this is a MacOSX box, we'll
-# check what other versions of PG are available, and select the highest version
-# we can find:
-
- if ( $WORKING_OS eq "MacOSX" ) {
- my $macos_pg_major_version = 0;
- my $macos_pg_minor_version = 0;
-
- for $macos_pg_minor_version ( "9", "8", "7", "6", "5", "4", "3", "2", "1", "0" ) {
- if ( -x "/Library/PostgreSQL/9." . $macos_pg_minor_version . "/bin/psql" ) {
- $macos_pg_major_version = 9;
- if ( ( $macos_pg_major_version > $psql_major_version )
- || ( $macos_pg_minor_version >= $psql_minor_version ) )
- {
- $psql_exec_path = "/Library/PostgreSQL/9." . $macos_pg_minor_version . "/bin";
- $pg_major_version = $macos_pg_major_version;
- $pg_minor_version = $macos_pg_minor_version;
- }
- last;
- }
- }
- }
-
- my $psql_admin_exec = "";
-
- if ( $psql_exec_path eq "" )
- {
- if ( $pg_local_connection || $noninteractive)
- {
- print STDERR "\nERROR: I haven't been able to find the psql command in your PATH!\n";
- print STDERR "Please make sure PostgresQL is properly installed; if necessary, add\n";
- print STDERR "the location of psql to the PATH, then try again.\n\n";
-
- exit 1;
- }
- else
- {
- print "WARNING: I haven't been able to find the psql command in your PATH!\n";
- print "But since we are configuring a Dataverse instance to use a remote Postgres server,\n";
- print "we can still set up the database by running a setup script on that remote server\n";
- print "(see below for instructions).\n";
-
- }
- } else {
-
- print "(Using psql version " . $pg_major_version . "." . $pg_minor_version . ": " . $psql_exec_path . "/psql)\n";
-
-
- $psql_admin_exec = "PGPASSWORD=" . $CONFIG_DEFAULTS{'POSTGRES_ADMIN_PASSWORD'} . "; export PGPASSWORD; " . $psql_exec_path;
- $psql_exec_path = "PGPASSWORD=" . $CONFIG_DEFAULTS{'POSTGRES_PASSWORD'} . "; export PGPASSWORD; " . $psql_exec_path;
-
- print "Checking if we can talk to Postgres as the admin user...\n";
- }
-
-# 3d. CHECK IF WE CAN TALK TO POSTGRES AS THE ADMIN:
-
- if ($psql_exec_path eq "" || system( $psql_admin_exec . "/psql -h " . $CONFIG_DEFAULTS{'POSTGRES_SERVER'} . " -p " . $CONFIG_DEFAULTS{'POSTGRES_PORT'} . " -U " . $POSTGRES_ADMIN_USER . " -d postgres -c 'SELECT * FROM pg_roles' > /dev/null 2>&1" ) )
- {
- # No, we can't. :(
- if ($pg_local_connection || $noninteractive)
- {
- # If Postgres is running locally, this is a fatal condition.
- # We'll give them some (potentially) helpful pointers and exit.
-
- print "(Tried executing: " . $psql_admin_exec . "/psql -h " . $CONFIG_DEFAULTS{'POSTGRES_SERVER'} . " -p " . $CONFIG_DEFAULTS{'POSTGRES_PORT'} . " -U " . $POSTGRES_ADMIN_USER . " -d postgres -c 'SELECT * FROM pg_roles' > /dev/null 2>&1) \n";
- print "Nope, I haven't been able to connect to the local instance of PostgresQL as the admin user.\n";
- print "\nIs postgresql running? \n";
- print " On a RedHat-like system, you can check the status of the daemon with\n\n";
- print " service postgresql start\n\n";
- print " On MacOSX, use Applications -> PostgresQL -> Start Server.\n";
- print " (or, if there's no \"Start Server\" item in your PostgresQL folder, \n";
- print " simply restart your MacOSX system!)\n";
- print "\nAlso, please make sure that the daemon is listening to network connections!\n";
- print " - at least on the localhost interface. (See \"Installing Postgres\" section\n";
- print " of the installation manual).\n";
- print "\nFinally, did you supply the correct admin password?\n";
- print " Don't know the admin password for your Postgres installation?\n";
- print " - then simply set the access level to \"trust\" temporarily (for localhost only!)\n";
- print " in your pg_hba.conf file. Again, please consult the \n";
- print " installation manual).\n";
- exit 1;
- }
- else
- {
- # If we are configuring the Dataverse instance to use a Postgres server
- # running on a remote host, it is possible to configure the database
- # without opening remote access for the admin user. They will simply
- # have to run this script in the "postgres-only" mode on that server, locally,
- # then resume the installation here:
- print "(Tried executing: " . $psql_admin_exec . "/psql -h " . $CONFIG_DEFAULTS{'POSTGRES_SERVER'} . " -p " . $CONFIG_DEFAULTS{'POSTGRES_PORT'} . " -U " . $POSTGRES_ADMIN_USER . " -d postgres -c 'SELECT * FROM pg_roles' > /dev/null 2>&1)\n\n";
- print "Haven't been able to connect to the remote Postgres server as the admin user.\n";
- print "(Or you simply don't have psql installed on this server)\n";
- print "It IS possible to configure a database for your Dataverse on a remote server,\n";
- print "without having admin access to that remote Postgres installation.\n\n";
- print "In order to do that, please copy the installer (the entire package) to the server\n";
- print "where PostgresQL is running and run the installer with the \"--pg_only\" option:\n\n";
- print " ./install --pg_only\n\n";
-
- print "Press any key to continue the installation process once that has been\n";
- print "done. Or press ctrl-C to exit the installer.\n\n";
-
- system "stty cbreak /dev/tty 2>&1";
- my $key = getc(STDIN);
- system "stty -cbreak /dev/tty 2>&1";
- print "\n";
- }
- }
- else
- {
- print "Yes, we can!\n";
-
- # ok, we can proceed with configuring things...
-
- print "\nConfiguring Postgres Database:\n";
-
- # 4c. CHECK IF THIS DB ALREADY EXISTS:
-
- my $psql_command_dbcheck =
- $psql_admin_exec . "/psql -h " . $CONFIG_DEFAULTS{'POSTGRES_SERVER'} . " -p " . $CONFIG_DEFAULTS{'POSTGRES_PORT'} . " -U " . $POSTGRES_ADMIN_USER . " -c '' -d " . $CONFIG_DEFAULTS{'POSTGRES_DATABASE'} . ">/dev/null 2>&1";
-
- if ( ( my $exitcode = system($psql_command_dbcheck) ) == 0 )
- {
- if ($force)
- {
- print "WARNING! Database "
- . $CONFIG_DEFAULTS{'POSTGRES_DATABASE'}
- . " already exists but --force given... continuing.\n";
- }
- else
- {
- print "WARNING! Database " . $CONFIG_DEFAULTS{'POSTGRES_DATABASE'} . " already exists!\n";
-
- if ($noninteractive)
- {
- exit 1;
- }
- else
- {
- print "\nPress any key to continue, or ctrl-C to exit the installer...\n\n";
-
- system "stty cbreak /dev/tty 2>&1";
- my $key = getc(STDIN);
- system "stty -cbreak /dev/tty 2>&1";
- print "\n";
-
- }
- }
- }
-
- # 3e. CHECK IF THIS USER ALREADY EXISTS:
-
- my $psql_command_rolecheck =
- $psql_exec_path . "/psql -h " . $CONFIG_DEFAULTS{'POSTGRES_SERVER'} . " -c '' -d postgres " . $CONFIG_DEFAULTS{'POSTGRES_USER'} . " >/dev/null 2>&1";
- my $exitcode;
-
- if ( ( $exitcode = system($psql_command_rolecheck) ) == 0 )
- {
- print "User (role) " . $CONFIG_DEFAULTS{'POSTGRES_USER'} . " already exists;\n";
- print "Proceeding.";
- }
- else
- {
- # 3f. CREATE DVN DB USER:
-
- print "\nCreating Postgres user (role) for the DVN:\n";
-
- open TMPCMD, ">/tmp/pgcmd.$$.tmp";
-
- # with md5-encrypted password:
- my $pg_password_md5 =
- &create_pg_hash( $CONFIG_DEFAULTS{'POSTGRES_USER'}, $CONFIG_DEFAULTS{'POSTGRES_PASSWORD'} );
- my $sql_command =
- "CREATE ROLE \""
- . $CONFIG_DEFAULTS{'POSTGRES_USER'}
- . "\" PASSWORD 'md5"
- . $pg_password_md5
- . "' NOSUPERUSER CREATEDB CREATEROLE INHERIT LOGIN";
-
- print TMPCMD $sql_command;
- close TMPCMD;
-
- my $psql_commandline = $psql_admin_exec . "/psql -h " . $CONFIG_DEFAULTS{'POSTGRES_SERVER'} . " -p " . $CONFIG_DEFAULTS{'POSTGRES_PORT'} . " -U " . $POSTGRES_ADMIN_USER . " -d postgres -f /tmp/pgcmd.$$.tmp >/dev/null 2>&1";
-
- my $out = qx($psql_commandline 2>&1);
- $exitcode = $?;
- unless ( $exitcode == 0 )
- {
- print STDERR "Could not create the DVN Postgres user role!\n";
- print STDERR "(SQL: " . $sql_command . ")\n";
- print STDERR "(psql exit code: " . $exitcode . ")\n";
- print STDERR "(STDERR and STDOUT was: " . $out . ")\n";
- exit 1;
- }
-
- unlink "/tmp/pgcmd.$$.tmp";
- print "done.\n";
- }
-
- # 3g. CREATE DVN DB:
-
- print "\nCreating Postgres database:\n";
-
- my $psql_command =
- $psql_admin_exec
- . "/createdb -h " . $CONFIG_DEFAULTS{'POSTGRES_SERVER'} . " -p " . $CONFIG_DEFAULTS{'POSTGRES_PORT'} . " -U " . $POSTGRES_ADMIN_USER ." "
- . $CONFIG_DEFAULTS{'POSTGRES_DATABASE'} . " --owner="
- . $CONFIG_DEFAULTS{'POSTGRES_USER'};
-
- my $out = qx($psql_command 2>&1);
- $exitcode = $?;
- unless ( $exitcode == 0 )
- {
- print STDERR "Could not create Postgres database for the Dataverse app!\n";
- print STDERR "(command: " . $psql_command . ")\n";
- print STDERR "(psql exit code: " . $exitcode . ")\n";
- print STDERR "(STDOUT and STDERR: " . $out . ")\n";
- if ($force)
- {
- print STDERR "\ncalled with --force, continuing\n";
- }
- else
- {
- print STDERR "\naborting the installation (sorry!)\n\n";
- exit 1;
- }
- }
- }
-
-# Whether the user and the database were created locally or remotely, we'll now
-# verify that we can talk to that database, with the credentials of the database
-# user that we want the Dataverse application to be using:
-
- if ( $psql_exec_path ne "" && system( $psql_exec_path . "/psql -h " . $CONFIG_DEFAULTS{'POSTGRES_SERVER'} . " -p " . $CONFIG_DEFAULTS{'POSTGRES_PORT'} . " -U " . $CONFIG_DEFAULTS{'POSTGRES_USER'} . " -d " . $CONFIG_DEFAULTS{'POSTGRES_DATABASE'} . " -c 'SELECT * FROM pg_roles' > /dev/null 2>&1" ) )
- {
- print STDERR "Oops, haven't been able to connect to the database " . $CONFIG_DEFAULTS{'POSTGRES_DATABASE'} . ",\n";
- print STDERR "running on " . $CONFIG_DEFAULTS{'POSTGRES_SERVER'} . ", as user " . $CONFIG_DEFAULTS{'POSTGRES_USER'} . ".\n\n";
- print STDERR "Aborting the installation (sorry!)\n";
- exit 1;
- }
-}
-
-sub read_config_defaults {
- my $config_file = shift @_;
-
- unless ( -f $config_file )
- {
- print STDERR "Can't find the config file " . $config_file . "!\n";
- exit 1;
- }
-
- open CF, $config_file || die "Can't open config file " . $config_file . " for reading.\n";
-
- while ()
- {
- chop;
-
- if ( $_ =~/^[A-Z]/ && $_ =~/ *= */ )
- {
- my ($name, $value) = split(/ *= */, $_, 2);
- $CONFIG_DEFAULTS{$name} = $value;
- }
- }
- close CF;
-}
-
-sub read_interactive_config_values {
- my $config_file = shift @_;
-
- unless ( -f $config_file )
- {
- print STDERR "Can't find the config file " . $config_file . "!\n";
- exit 1;
- }
-
- open CF, $config_file || die "Can't open config file " . $config_file . " for reading.\n";
-
- my $mode = "";
-
- while ()
- {
- chop;
-
- if ( $_ eq "[prompts]" || $_ eq "[comments]" )
- {
- $mode = $_;
- }
-
- if ( $_ =~/^[A-Z]/ && $_ =~/ *= */ )
- {
- my ($name, $value) = split(/ *= */, $_, 2);
-
- if ( $mode eq "[prompts]" )
- {
- $CONFIG_PROMPTS{$name} = $value;
- }
- elsif ( $mode eq "[comments]" )
- {
- $value =~s/\\n/\n/g;
- $CONFIG_COMMENTS{$name} = $value;
- }
- }
- }
- close CF;
-}
diff --git a/scripts/installer/install.py b/scripts/installer/install.py
index 5acb4d760a4..3aedbd8c6ad 100644
--- a/scripts/installer/install.py
+++ b/scripts/installer/install.py
@@ -252,8 +252,8 @@
# 1d. check java version
java_version = subprocess.check_output(["java", "-version"], stderr=subprocess.STDOUT).decode()
print("Found java version "+java_version)
- if not re.search('(1.8|11)', java_version):
- sys.exit("Dataverse requires OpenJDK 1.8 or 11. Please make sure it's in your PATH, and try again.")
+ if not re.search('(17)', java_version):
+ sys.exit("Dataverse requires OpenJDK 17. Please make sure it's in your PATH, and try again.")
# 1e. check if the setup scripts - setup-all.sh, are available as well, maybe?
# @todo (?)
@@ -314,7 +314,7 @@
gfDir = config.get('glassfish', 'GLASSFISH_DIRECTORY')
while not test_appserver_directory(gfDir):
print("\nInvalid Payara directory!")
- gfDir = read_user_input("Enter the root directory of your Payara5 installation:\n(Or ctrl-C to exit the installer): ")
+ gfDir = read_user_input("Enter the root directory of your Payara installation:\n(Or ctrl-C to exit the installer): ")
config.set('glassfish', 'GLASSFISH_DIRECTORY', gfDir)
elif option == "mail_server":
mailServer = config.get('system', 'MAIL_SERVER')
@@ -380,12 +380,13 @@
print("Can't connect to PostgresQL as the admin user.\n")
sys.exit("Is the server running, have you adjusted pg_hba.conf, etc?")
- # 3b. get the Postgres version (do we need it still?)
+ # 3b. get the Postgres version for new permissions model in versions 15+
try:
- pg_full_version = conn.server_version
- print("PostgresQL version: "+str(pg_full_version))
+ pg_full_version = str(conn.server_version)
+ pg_major_version = pg_full_version[0:2]
+ print("PostgreSQL version: "+pg_major_version)
except:
- print("Warning: Couldn't determine PostgresQL version.")
+ print("Warning: Couldn't determine PostgreSQL version.")
conn.close()
# 3c. create role:
@@ -410,7 +411,9 @@
else:
sys.exit("Couldn't create database or database already exists.\n")
- conn_cmd = "GRANT ALL PRIVILEGES on DATABASE "+pgDb+" to "+pgUser+";"
+ # 3e. set permissions:
+
+ conn_cmd = "GRANT CREATE PRIVILEGES on DATABASE "+pgDb+" to "+pgUser+";"
try:
cur.execute(conn_cmd)
except:
@@ -418,6 +421,19 @@
cur.close()
conn.close()
+ if int(pg_major_version) >= 15:
+ conn_cmd = "GRANT ALL ON SCHEMA public TO "+pgUser+";"
+ print("PostgreSQL 15 or higher detected. Running " + conn_cmd)
+ try:
+ cur.execute(conn_cmd)
+ except:
+ if force:
+ print("WARNING: failed to grant permissions on schema public - continuing, since the --force option was specified")
+ else:
+ sys.exit("Couldn't grant privileges on schema public to "+pgUser)
+ cur.close()
+ conn.close()
+
print("Database and role created!")
if pgOnly:
print("postgres-only setup complete.")
@@ -511,12 +527,12 @@
try:
copy2(jhoveConfigSchemaDist, gfConfigDir)
# The JHOVE conf file has an absolute PATH of the JHOVE config schema file (uh, yeah...)
- # and may need to be adjusted, if Payara is installed anywhere other than /usr/local/payara5:
- if gfDir == "/usr/local/payara5":
+ # and may need to be adjusted, if Payara is installed anywhere other than /usr/local/payara6:
+ if gfDir == "/usr/local/payara6":
copy2(jhoveConfigDist, gfConfigDir)
else:
- # use sed to replace /usr/local/payara5 in the distribution copy with the real gfDir:
- sedCommand = "sed 's:/usr/local/payara5:"+gfDir+":g' < " + jhoveConfigDist + " > " + gfConfigDir + "/" + jhoveConfig
+ # use sed to replace /usr/local/payara6 in the distribution copy with the real gfDir:
+ sedCommand = "sed 's:/usr/local/payara6:"+gfDir+":g' < " + jhoveConfigDist + " > " + gfConfigDir + "/" + jhoveConfig
subprocess.call(sedCommand, shell=True)
print("done.")
diff --git a/scripts/installer/installAppServer.py b/scripts/installer/installAppServer.py
index 8b719ac09d1..698f5ba9a58 100644
--- a/scripts/installer/installAppServer.py
+++ b/scripts/installer/installAppServer.py
@@ -3,7 +3,7 @@
def runAsadminScript(config):
# We are going to run a standalone shell script with a bunch of asadmin
- # commands to set up all the app. server (payara5) components for the application.
+ # commands to set up all the app. server (payara6) components for the application.
# All the parameters must be passed to that script as environmental
# variables:
os.environ['GLASSFISH_DOMAIN'] = "domain1";
diff --git a/scripts/installer/installUtils.py b/scripts/installer/installUtils.py
index 7cc368de5f8..ff5e6eb708d 100644
--- a/scripts/installer/installUtils.py
+++ b/scripts/installer/installUtils.py
@@ -57,7 +57,7 @@ def test_appserver_directory(directory):
#print("version: major: "+str(major_version)+", minor: "+str(minor_version))
- if major_version != 5 or minor_version < 201:
+ if major_version != 6 or minor_version < 2023:
return False
return True
diff --git a/scripts/installer/interactive.config b/scripts/installer/interactive.config
index 86ea926fe5d..ef8110c554f 100644
--- a/scripts/installer/interactive.config
+++ b/scripts/installer/interactive.config
@@ -26,7 +26,7 @@ DOI_BASEURL = Datacite URL
DOI_DATACITERESTAPIURL = Datacite REST API URL
[comments]
HOST_DNS_ADDRESS = :(enter numeric IP address, if FQDN is unavailable)
-GLASSFISH_USER = :This user will be running the App. Server (Payara5) service on your system.\n - If this is a dev. environment, this should be your own username; \n - In production, we suggest you create the account "dataverse", or use any other unprivileged user account\n:
+GLASSFISH_USER = :This user will be running the App. Server (Payara) service on your system.\n - If this is a dev. environment, this should be your own username; \n - In production, we suggest you create the account "dataverse", or use any other unprivileged user account\n:
GLASSFISH_DIRECTORY =
GLASSFISH_REQUEST_TIMEOUT = :\n Defaults to 1800 seconds (30 minutes)
ADMIN_EMAIL = :\n(please enter a valid email address!)
diff --git a/scripts/tests/ec2-memory-benchmark/ec2-memory-benchmark-remote.sh b/scripts/tests/ec2-memory-benchmark/ec2-memory-benchmark-remote.sh
index 0cfdd20c272..367aa214563 100755
--- a/scripts/tests/ec2-memory-benchmark/ec2-memory-benchmark-remote.sh
+++ b/scripts/tests/ec2-memory-benchmark/ec2-memory-benchmark-remote.sh
@@ -5,7 +5,7 @@ then
EC2_HTTP_LOCATION=""
fi
-DATAVERSE_APP_DIR=/usr/local/payara5/glassfish/domains/domain1/applications/dataverse; export DATAVERSE_APP_DIR
+DATAVERSE_APP_DIR=/usr/local/payara6/glassfish/domains/domain1/applications/dataverse; export DATAVERSE_APP_DIR
# restart app server
diff --git a/scripts/vagrant/install-dataverse.sh b/scripts/vagrant/install-dataverse.sh
deleted file mode 100644
index c9873f7d3ec..00000000000
--- a/scripts/vagrant/install-dataverse.sh
+++ /dev/null
@@ -1,31 +0,0 @@
-#!/usr/bin/env bash
-
-if [ ! -z "$1" ]; then
- MAILSERVER=$1
- MAILSERVER_ARG="--mailserver $MAILSERVER"
-fi
-WAR=/dataverse/target/dataverse*.war
-if [ ! -f $WAR ]; then
- echo "no war file found... building"
- #echo "Installing nss on CentOS 6 to avoid java.security.KeyException while building war file: https://github.com/IQSS/dataverse/issues/2744"
- #yum install -y nss
- su $SUDO_USER -s /bin/sh -c "cd /dataverse && source /etc/profile.d/maven.sh && mvn -q package"
-fi
-cd /dataverse/scripts/installer
-
-# move any pre-existing `default.config` file out of the way to avoid overwriting
-pid=$$
-if [ -e default.config ]; then
- cp default.config tmp-${pid}-default.config
-fi
-
-# Switch to newer Python-based installer
-python3 ./install.py --noninteractive --config_file="default.config"
-
-if [ -e tmp-${pid}-default.config ]; then # if we moved it out, move it back
- mv -f tmp-${pid}-default.config default.config
-fi
-
-echo "If "vagrant up" was successful (check output above) Dataverse is running on port 8080 of the Linux machine running within Vagrant, but this port has been forwarded to port 8088 of the computer you ran "vagrant up" on. For this reason you should go to http://localhost:8088 to see the Dataverse app running."
-
-echo "Please also note that the installation script has now started Payara, but has not set up an autostart mechanism for it.\nTherefore, the next time this VM is started, Payara must be started manually.\nSee https://guides.dataverse.org/en/latest/installation/prerequisites.html#launching-payara-on-system-boot for details."
diff --git a/scripts/vagrant/rpmbuild.sh b/scripts/vagrant/rpmbuild.sh
deleted file mode 100755
index f10830afb5b..00000000000
--- a/scripts/vagrant/rpmbuild.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/sh
-rpm -Uvh http://dl.fedoraproject.org/pub/epel/7/x86_64/e/epel-release-7-7.noarch.rpm
-yum install -y rpm-build httpd-devel libapreq2-devel R-devel
diff --git a/scripts/vagrant/setup-counter-processor.sh b/scripts/vagrant/setup-counter-processor.sh
deleted file mode 100755
index a418e8d6251..00000000000
--- a/scripts/vagrant/setup-counter-processor.sh
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/bin/bash
-echo "Setting up counter-processor"
-echo "Installing dependencies"
-yum -y install unzip vim-enhanced
-yum install -y https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
-# EPEL provides Python 3.6.6, new enough (3.6.4 in .python-version)
-yum -y install python36 jq
-# "ensurepip" tip from https://stackoverflow.com/questions/50408941/recommended-way-to-install-pip3-on-centos7/52518512#52518512
-python3.6 -m ensurepip
-# FIXME: actually use this dedicated "counter" user.
-COUNTER_USER=counter
-echo "Ensuring Unix user '$COUNTER_USER' exists"
-useradd $COUNTER_USER || :
-COMMIT='7974dad259465ba196ef639f48dea007cae8f9ac'
-UNZIPPED_DIR="counter-processor-$COMMIT"
-if [ ! -e $UNZIPPED_DIR ]; then
- ZIP_FILE="${COMMIT}.zip"
- echo "Downloading and unzipping $ZIP_FILE"
- wget https://github.com/CDLUC3/counter-processor/archive/$ZIP_FILE
- unzip $ZIP_FILE
-fi
-cd $UNZIPPED_DIR
-echo "Installation of the GeoLite2 country database for counter-processor can no longer be automated. See the Installation Guide for the manual installation process."
-pip3 install -r requirements.txt
-# For now, parsing sample_logs/counter_2018-05-08.log
-for i in `echo {00..31}`; do
- # avoid errors like: No such file or directory: 'sample_logs/counter_2018-05-01.log'
- touch sample_logs/counter_2018-05-$i.log
-done
-#LOG_GLOB="sample_logs/counter_2018-05-*.log"
-#START_DATE="2018-05-08"
-#END_DATE="2018-05-09"
-CONFIG_FILE=/dataverse/scripts/vagrant/counter-processor-config.yaml python3.6 main.py
diff --git a/scripts/vagrant/setup-solr.sh b/scripts/vagrant/setup-solr.sh
deleted file mode 100755
index 70d3fc632a7..00000000000
--- a/scripts/vagrant/setup-solr.sh
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/bin/bash
-echo "Setting up Solr"
-dnf install -qy lsof
-SOLR_USER=solr
-SOLR_HOME=/usr/local/solr
-mkdir $SOLR_HOME
-chown $SOLR_USER:$SOLR_USER $SOLR_HOME
-su $SOLR_USER -s /bin/sh -c "cp /dataverse/downloads/solr-8.11.1.tgz $SOLR_HOME"
-su $SOLR_USER -s /bin/sh -c "cd $SOLR_HOME && tar xfz solr-8.11.1.tgz"
-su $SOLR_USER -s /bin/sh -c "cd $SOLR_HOME/solr-8.11.1/server/solr && cp -r configsets/_default . && mv _default collection1"
-su $SOLR_USER -s /bin/sh -c "cp /dataverse/conf/solr/8.11.1/schema*.xml $SOLR_HOME/solr-8.11.1/server/solr/collection1/conf/"
-su $SOLR_USER -s /bin/sh -c "cp /dataverse/conf/solr/8.11.1/solrconfig.xml $SOLR_HOME/solr-8.11.1/server/solr/collection1/conf/solrconfig.xml"
-su $SOLR_USER -s /bin/sh -c "cd $SOLR_HOME/solr-8.11.1 && bin/solr start && bin/solr create_core -c collection1 -d server/solr/collection1/conf/"
-cp /dataverse/doc/sphinx-guides/source/_static/installation/files/etc/init.d/solr /etc/init.d/solr
-chmod 755 /etc/init.d/solr
-/etc/init.d/solr stop
-/etc/init.d/solr start
-chkconfig solr on
diff --git a/scripts/vagrant/setup.sh b/scripts/vagrant/setup.sh
deleted file mode 100644
index 0af4afb22af..00000000000
--- a/scripts/vagrant/setup.sh
+++ /dev/null
@@ -1,96 +0,0 @@
-#!/bin/bash
-echo "Installing dependencies for Dataverse"
-
-# wget seems to be missing in box 'bento/centos-8.2'
-dnf install -qy wget
-
-# python3 and psycopg2 for the Dataverse installer
-dnf install -qy python3 python3-psycopg2
-
-# JQ
-echo "Installing jq for the setup scripts"
-dnf install -qy epel-release
-dnf install -qy jq
-
-echo "Adding Shibboleth yum repo"
-cp /dataverse/conf/vagrant/etc/yum.repos.d/shibboleth.repo /etc/yum.repos.d
-# Uncomment this (and other shib stuff below) if you want
-# to use Vagrant (and maybe PageKite) to test Shibboleth.
-#yum install -y shibboleth shibboleth-embedded-ds
-
-# java configuration et alia
-dnf install -qy java-11-openjdk-devel httpd mod_ssl unzip
-alternatives --set java /usr/lib/jvm/jre-11-openjdk/bin/java
-java -version
-
-# maven included in centos8 requires 1.8.0 - download binary instead
-wget -q https://archive.apache.org/dist/maven/maven-3/3.8.2/binaries/apache-maven-3.8.2-bin.tar.gz
-tar xfz apache-maven-3.8.2-bin.tar.gz
-mkdir /opt/maven
-mv apache-maven-3.8.2/* /opt/maven/
-echo "export JAVA_HOME=/usr/lib/jvm/jre-openjdk" > /etc/profile.d/maven.sh
-echo "export M2_HOME=/opt/maven" >> /etc/profile.d/maven.sh
-echo "export MAVEN_HOME=/opt/maven" >> /etc/profile.d/maven.sh
-echo "export PATH=/opt/maven/bin:${PATH}" >> /etc/profile.d/maven.sh
-chmod 0755 /etc/profile.d/maven.sh
-
-# disable centos8 postgresql module and install postgresql13-server
-dnf -qy module disable postgresql
-dnf install -qy https://download.postgresql.org/pub/repos/yum/reporpms/EL-8-x86_64/pgdg-redhat-repo-latest.noarch.rpm
-dnf install -qy postgresql13-server
-/usr/pgsql-13/bin/postgresql-13-setup initdb
-/usr/bin/systemctl stop postgresql-13
-cp /dataverse/conf/vagrant/var/lib/pgsql/data/pg_hba.conf /var/lib/pgsql/13/data/pg_hba.conf
-/usr/bin/systemctl start postgresql-13
-/usr/bin/systemctl enable postgresql-13
-
-PAYARA_USER=dataverse
-echo "Ensuring Unix user '$PAYARA_USER' exists"
-useradd $PAYARA_USER || :
-SOLR_USER=solr
-echo "Ensuring Unix user '$SOLR_USER' exists"
-useradd $SOLR_USER || :
-DOWNLOAD_DIR='/dataverse/downloads'
-PAYARA_ZIP="$DOWNLOAD_DIR/payara-5.2022.3.zip"
-SOLR_TGZ="$DOWNLOAD_DIR/solr-8.11.1.tgz"
-if [ ! -f $PAYARA_ZIP ] || [ ! -f $SOLR_TGZ ]; then
- echo "Couldn't find $PAYARA_ZIP or $SOLR_TGZ! Running download script...."
- cd $DOWNLOAD_DIR && ./download.sh && cd
- echo "Done running download script."
-fi
-PAYARA_USER_HOME=~dataverse
-PAYARA_ROOT=/usr/local/payara5
-if [ ! -d $PAYARA_ROOT ]; then
- echo "Copying $PAYARA_ZIP to $PAYARA_USER_HOME and unzipping"
- su $PAYARA_USER -s /bin/sh -c "cp $PAYARA_ZIP $PAYARA_USER_HOME"
- su $PAYARA_USER -s /bin/sh -c "cd $PAYARA_USER_HOME && unzip -q $PAYARA_ZIP"
- # default.config defaults to /usr/local/payara5 so let's go with that
- rsync -a $PAYARA_USER_HOME/payara5/ $PAYARA_ROOT/
-else
- echo "$PAYARA_ROOT already exists"
-fi
-
-#service shibd start
-/usr/bin/systemctl stop httpd
-cp /dataverse/conf/httpd/conf.d/dataverse.conf /etc/httpd/conf.d/dataverse.conf
-mkdir -p /var/www/dataverse/error-documents
-cp /dataverse/conf/vagrant/var/www/dataverse/error-documents/503.html /var/www/dataverse/error-documents
-/usr/bin/systemctl start httpd
-#curl -k --sslv3 https://pdurbin.pagekite.me/Shibboleth.sso/Metadata > /tmp/pdurbin.pagekite.me
-#cp -a /etc/shibboleth/shibboleth2.xml /etc/shibboleth/shibboleth2.xml.orig
-#cp -a /etc/shibboleth/attribute-map.xml /etc/shibboleth/attribute-map.xml.orig
-# need more attributes, such as sn, givenName, mail
-#cp /dataverse/conf/vagrant/etc/shibboleth/attribute-map.xml /etc/shibboleth/attribute-map.xml
-# FIXME: automate this?
-#curl 'https://www.testshib.org/cgi-bin/sp2config.cgi?dist=Others&hostname=pdurbin.pagekite.me' > /etc/shibboleth/shibboleth2.xml
-#cp /dataverse/conf/vagrant/etc/shibboleth/shibboleth2.xml /etc/shibboleth/shibboleth2.xml
-#service shibd restart
-#curl -k --sslv3 https://pdurbin.pagekite.me/Shibboleth.sso/Metadata > /downloads/pdurbin.pagekite.me
-#service httpd restart
-
-echo "#########################################################################################"
-echo "# This is a Vagrant test box, so we're disabling firewalld. #
-echo "# Re-enable it with $ sudo systemctl enable firewalld && sudo systemctl start firewalld #"
-echo "#########################################################################################"
-systemctl disable firewalld
-systemctl stop firewalld
diff --git a/src/main/java/edu/harvard/iq/dataverse/AbstractGlobalIdServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/AbstractGlobalIdServiceBean.java
index 2a3f2d50364..f1bfc3e290b 100644
--- a/src/main/java/edu/harvard/iq/dataverse/AbstractGlobalIdServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/AbstractGlobalIdServiceBean.java
@@ -3,8 +3,8 @@
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
import edu.harvard.iq.dataverse.util.SystemConfig;
import java.io.InputStream;
-import javax.ejb.EJB;
-import javax.inject.Inject;
+import jakarta.ejb.EJB;
+import jakarta.inject.Inject;
import java.util.*;
import java.util.logging.Level;
import java.util.logging.Logger;
@@ -222,6 +222,11 @@ public GlobalId parsePersistentId(String fullIdentifierString) {
if(!isConfigured()) {
return null;
}
+ // Occasionally, the protocol separator character ':' comes in still
+ // URL-encoded as %3A (usually as a result of the URL having been
+ // encoded twice):
+ fullIdentifierString = fullIdentifierString.replace("%3A", ":");
+
int index1 = fullIdentifierString.indexOf(':');
if (index1 > 0) { // ':' found with one or more characters before it
String protocol = fullIdentifierString.substring(0, index1);
diff --git a/src/main/java/edu/harvard/iq/dataverse/AlternativePersistentIdentifier.java b/src/main/java/edu/harvard/iq/dataverse/AlternativePersistentIdentifier.java
index 6fc7262925a..db3c6029a78 100644
--- a/src/main/java/edu/harvard/iq/dataverse/AlternativePersistentIdentifier.java
+++ b/src/main/java/edu/harvard/iq/dataverse/AlternativePersistentIdentifier.java
@@ -3,14 +3,14 @@
import java.io.Serializable;
import java.util.Date;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Temporal;
-import javax.persistence.TemporalType;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Temporal;
+import jakarta.persistence.TemporalType;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/ApiTokenPage.java b/src/main/java/edu/harvard/iq/dataverse/ApiTokenPage.java
index 4838847e400..16ff4d266d8 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ApiTokenPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ApiTokenPage.java
@@ -5,14 +5,14 @@
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
import edu.harvard.iq.dataverse.util.BundleUtil;
import edu.harvard.iq.dataverse.api.Util;
-import java.sql.Timestamp;
+
import java.util.ArrayList;
import java.util.List;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
/**
* @todo Rename this to ApiTokenFragment? The separate page is being taken out
diff --git a/src/main/java/edu/harvard/iq/dataverse/AuxiliaryFile.java b/src/main/java/edu/harvard/iq/dataverse/AuxiliaryFile.java
index 344032ef5e3..d03ebbc6f7b 100644
--- a/src/main/java/edu/harvard/iq/dataverse/AuxiliaryFile.java
+++ b/src/main/java/edu/harvard/iq/dataverse/AuxiliaryFile.java
@@ -4,16 +4,16 @@
import edu.harvard.iq.dataverse.util.BundleUtil;
import java.io.Serializable;
import java.util.MissingResourceException;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.NamedNativeQueries;
-import javax.persistence.NamedNativeQuery;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.NamedNativeQueries;
+import jakarta.persistence.NamedNativeQuery;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/AuxiliaryFileServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/AuxiliaryFileServiceBean.java
index 05f3e209632..8c96f98ce39 100644
--- a/src/main/java/edu/harvard/iq/dataverse/AuxiliaryFileServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/AuxiliaryFileServiceBean.java
@@ -14,19 +14,19 @@
import java.util.ArrayList;
import java.util.List;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
-import javax.persistence.PersistenceContext;
-import javax.persistence.Query;
-import javax.persistence.TypedQuery;
-import javax.ws.rs.ClientErrorException;
-import javax.ws.rs.InternalServerErrorException;
-import javax.ws.rs.ServerErrorException;
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.core.Response;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.Query;
+import jakarta.persistence.TypedQuery;
+import jakarta.ws.rs.ClientErrorException;
+import jakarta.ws.rs.InternalServerErrorException;
+import jakarta.ws.rs.ServerErrorException;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.Response;
import org.apache.tika.Tika;
diff --git a/src/main/java/edu/harvard/iq/dataverse/BannerMessage.java b/src/main/java/edu/harvard/iq/dataverse/BannerMessage.java
index 4f465168580..214e26965fa 100644
--- a/src/main/java/edu/harvard/iq/dataverse/BannerMessage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/BannerMessage.java
@@ -4,13 +4,13 @@
import edu.harvard.iq.dataverse.util.BundleUtil;
import java.io.Serializable;
import java.util.Collection;
-import javax.persistence.CascadeType;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.OneToMany;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.OneToMany;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/BannerMessageServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/BannerMessageServiceBean.java
index 91b4128c545..0e757998d58 100644
--- a/src/main/java/edu/harvard/iq/dataverse/BannerMessageServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/BannerMessageServiceBean.java
@@ -10,10 +10,10 @@
import java.util.Date;
import java.util.List;
import java.util.logging.Logger;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/BannerMessageText.java b/src/main/java/edu/harvard/iq/dataverse/BannerMessageText.java
index dbae9a6dc27..ea2dd1b41fc 100644
--- a/src/main/java/edu/harvard/iq/dataverse/BannerMessageText.java
+++ b/src/main/java/edu/harvard/iq/dataverse/BannerMessageText.java
@@ -6,13 +6,13 @@
package edu.harvard.iq.dataverse;
import java.io.Serializable;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/CitationServlet.java b/src/main/java/edu/harvard/iq/dataverse/CitationServlet.java
index f6b4e3dc99a..68c8d49ad7e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/CitationServlet.java
+++ b/src/main/java/edu/harvard/iq/dataverse/CitationServlet.java
@@ -6,14 +6,14 @@
package edu.harvard.iq.dataverse;
import edu.harvard.iq.dataverse.pidproviders.PidUtil;
-import edu.harvard.iq.dataverse.util.StringUtil;
+
import java.io.IOException;
-import java.io.PrintWriter;
-import javax.ejb.EJB;
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServlet;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+
+import jakarta.ejb.EJB;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.http.HttpServlet;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/ConfigureFragmentBean.java b/src/main/java/edu/harvard/iq/dataverse/ConfigureFragmentBean.java
index d51a73fd2dc..bf509c33995 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ConfigureFragmentBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ConfigureFragmentBean.java
@@ -16,10 +16,10 @@
import java.sql.Timestamp;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
import java.util.Date;
diff --git a/src/main/java/edu/harvard/iq/dataverse/ControlledVocabAlternate.java b/src/main/java/edu/harvard/iq/dataverse/ControlledVocabAlternate.java
index 5d5d9597746..9542cfe3f71 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ControlledVocabAlternate.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ControlledVocabAlternate.java
@@ -7,15 +7,15 @@
import java.io.Serializable;
import java.util.Objects;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Table;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/ControlledVocabularyValue.java b/src/main/java/edu/harvard/iq/dataverse/ControlledVocabularyValue.java
index 181d939f4a1..5dcce98a90f 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ControlledVocabularyValue.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ControlledVocabularyValue.java
@@ -17,16 +17,16 @@
import java.util.Objects;
import java.util.logging.Logger;
import java.util.MissingResourceException;
-import javax.persistence.CascadeType;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.ManyToOne;
-import javax.persistence.OneToMany;
-import javax.persistence.Table;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.OneToMany;
+import jakarta.persistence.Table;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/ControlledVocabularyValueConverter.java b/src/main/java/edu/harvard/iq/dataverse/ControlledVocabularyValueConverter.java
index 1d530e136ba..eadc13721b3 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ControlledVocabularyValueConverter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ControlledVocabularyValueConverter.java
@@ -5,13 +5,13 @@
*/
package edu.harvard.iq.dataverse;
-import javax.ejb.EJB;
-import javax.enterprise.inject.spi.CDI;
+import jakarta.ejb.EJB;
+import jakarta.enterprise.inject.spi.CDI;
-import javax.faces.component.UIComponent;
-import javax.faces.context.FacesContext;
-import javax.faces.convert.Converter;
-import javax.faces.convert.FacesConverter;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.convert.Converter;
+import jakarta.faces.convert.FacesConverter;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/ControlledVocabularyValueServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/ControlledVocabularyValueServiceBean.java
index 0e9501414d0..4255c3b2dbc 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ControlledVocabularyValueServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ControlledVocabularyValueServiceBean.java
@@ -6,11 +6,11 @@
package edu.harvard.iq.dataverse;
import java.util.List;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.persistence.TypedQuery;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.TypedQuery;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/CustomQuestion.java b/src/main/java/edu/harvard/iq/dataverse/CustomQuestion.java
index 64723fff79a..2cb6f27c3e4 100644
--- a/src/main/java/edu/harvard/iq/dataverse/CustomQuestion.java
+++ b/src/main/java/edu/harvard/iq/dataverse/CustomQuestion.java
@@ -1,7 +1,7 @@
package edu.harvard.iq.dataverse;
import java.io.Serializable;
import java.util.List;
-import javax.persistence.*;
+import jakarta.persistence.*;
import org.hibernate.validator.constraints.NotBlank;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/CustomQuestionResponse.java b/src/main/java/edu/harvard/iq/dataverse/CustomQuestionResponse.java
index 32af06014a7..f19ee3c3fc7 100644
--- a/src/main/java/edu/harvard/iq/dataverse/CustomQuestionResponse.java
+++ b/src/main/java/edu/harvard/iq/dataverse/CustomQuestionResponse.java
@@ -7,8 +7,8 @@
import java.io.Serializable;
import java.util.List;
-import javax.faces.model.SelectItem;
-import javax.persistence.*;
+import jakarta.faces.model.SelectItem;
+import jakarta.persistence.*;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/CustomQuestionValue.java b/src/main/java/edu/harvard/iq/dataverse/CustomQuestionValue.java
index a5329c8b96d..f3a6b83b53f 100644
--- a/src/main/java/edu/harvard/iq/dataverse/CustomQuestionValue.java
+++ b/src/main/java/edu/harvard/iq/dataverse/CustomQuestionValue.java
@@ -1,7 +1,7 @@
package edu.harvard.iq.dataverse;
import java.io.Serializable;
-import javax.persistence.*;
+import jakarta.persistence.*;
import org.hibernate.validator.constraints.NotBlank;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/CustomizationFilesServlet.java b/src/main/java/edu/harvard/iq/dataverse/CustomizationFilesServlet.java
index 713d365ba0f..9dd524127d7 100644
--- a/src/main/java/edu/harvard/iq/dataverse/CustomizationFilesServlet.java
+++ b/src/main/java/edu/harvard/iq/dataverse/CustomizationFilesServlet.java
@@ -14,13 +14,13 @@
import java.io.PrintWriter;
import java.nio.file.Path;
import java.nio.file.Paths;
-import javax.servlet.ServletException;
-import javax.servlet.annotation.WebServlet;
-import javax.servlet.http.HttpServlet;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.annotation.WebServlet;
+import jakarta.servlet.http.HttpServlet;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
-import javax.ejb.EJB;
+import jakarta.ejb.EJB;
import org.apache.commons.io.IOUtils;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterCache.java b/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterCache.java
index 7ccd4adb78f..7c75b1a4da6 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterCache.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterCache.java
@@ -7,14 +7,14 @@
import java.io.Serializable;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Lob;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Lob;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
import org.hibernate.validator.constraints.NotBlank;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterService.java b/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterService.java
index b748897dafe..9ecc4a3ecc9 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterService.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterService.java
@@ -18,11 +18,11 @@
import java.util.Map;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.persistence.TypedQuery;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.TypedQuery;
import edu.harvard.iq.dataverse.settings.JvmSettings;
import org.apache.commons.text.StringEscapeUtils;
diff --git a/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteServiceBean.java
index fa0a745d80f..48786b41824 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteServiceBean.java
@@ -3,7 +3,6 @@
import java.io.IOException;
import java.net.HttpURLConnection;
import java.net.URL;
-import java.util.ArrayList;
import java.util.Base64;
import java.util.HashMap;
import java.util.List;
@@ -11,8 +10,8 @@
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
import edu.harvard.iq.dataverse.settings.JvmSettings;
import org.apache.commons.httpclient.HttpException;
diff --git a/src/main/java/edu/harvard/iq/dataverse/DOIEZIdServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DOIEZIdServiceBean.java
index d9b0fde15da..86b74b72f30 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DOIEZIdServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DOIEZIdServiceBean.java
@@ -7,7 +7,7 @@
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.Stateless;
+import jakarta.ejb.Stateless;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/DashboardPage.java b/src/main/java/edu/harvard/iq/dataverse/DashboardPage.java
index 99c7951c96e..c37c3f52bc7 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DashboardPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DashboardPage.java
@@ -5,23 +5,21 @@
*/
package edu.harvard.iq.dataverse;
-import edu.harvard.iq.dataverse.authorization.AuthenticationServiceBean;
import edu.harvard.iq.dataverse.harvest.client.HarvestingClient;
import edu.harvard.iq.dataverse.harvest.client.HarvestingClientServiceBean;
import edu.harvard.iq.dataverse.harvest.server.OAISet;
import edu.harvard.iq.dataverse.harvest.server.OAISetServiceBean;
-import static edu.harvard.iq.dataverse.util.JsfHelper.JH;
import edu.harvard.iq.dataverse.util.BundleUtil;
import edu.harvard.iq.dataverse.util.SystemConfig;
import java.util.List;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.faces.application.FacesMessage;
-import javax.faces.context.FacesContext;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataCitation.java b/src/main/java/edu/harvard/iq/dataverse/DataCitation.java
index 30e03046822..9b4b89db44f 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataCitation.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataCitation.java
@@ -14,7 +14,6 @@
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.io.Writer;
-import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Date;
@@ -27,7 +26,7 @@
import java.util.regex.Pattern;
import java.util.stream.Collectors;
-import javax.ejb.EJBException;
+import jakarta.ejb.EJBException;
import javax.xml.stream.XMLOutputFactory;
import javax.xml.stream.XMLStreamException;
import javax.xml.stream.XMLStreamWriter;
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataFile.java b/src/main/java/edu/harvard/iq/dataverse/DataFile.java
index 4e323496188..0f83ae3c5c8 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataFile.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataFile.java
@@ -29,10 +29,10 @@
import java.util.Set;
import java.util.logging.Logger;
import java.util.stream.Collectors;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.persistence.*;
-import javax.validation.constraints.Pattern;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.persistence.*;
+import jakarta.validation.constraints.Pattern;
import org.hibernate.validator.constraints.NotBlank;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataFileCategory.java b/src/main/java/edu/harvard/iq/dataverse/DataFileCategory.java
index f569a69b13a..f5abe9ac78a 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataFileCategory.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataFileCategory.java
@@ -10,16 +10,16 @@
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Collection;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToMany;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToMany;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Table;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataFileCategoryServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DataFileCategoryServiceBean.java
index 3fa4691a6dd..29dcb22c3ec 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataFileCategoryServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataFileCategoryServiceBean.java
@@ -3,8 +3,8 @@
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
import edu.harvard.iq.dataverse.util.BundleUtil;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataFileConverter.java b/src/main/java/edu/harvard/iq/dataverse/DataFileConverter.java
index 18531f5203d..701e826f12e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataFileConverter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataFileConverter.java
@@ -1,13 +1,13 @@
package edu.harvard.iq.dataverse;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.enterprise.inject.spi.CDI;
+import jakarta.ejb.EJB;
+import jakarta.enterprise.inject.spi.CDI;
-import javax.faces.component.UIComponent;
-import javax.faces.context.FacesContext;
-import javax.faces.convert.Converter;
-import javax.faces.convert.FacesConverter;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.convert.Converter;
+import jakarta.faces.convert.FacesConverter;
@FacesConverter("dataFileConverter")
public class DataFileConverter implements Converter {
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataFileServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DataFileServiceBean.java
index c30bfce368a..98ee3351458 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataFileServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataFileServiceBean.java
@@ -21,16 +21,16 @@
import java.util.UUID;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.ejb.TransactionAttribute;
-import javax.ejb.TransactionAttributeType;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
-import javax.persistence.PersistenceContext;
-import javax.persistence.Query;
-import javax.persistence.TypedQuery;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.ejb.TransactionAttribute;
+import jakarta.ejb.TransactionAttributeType;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.Query;
+import jakarta.persistence.TypedQuery;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataFileTag.java b/src/main/java/edu/harvard/iq/dataverse/DataFileTag.java
index 275d47cf1de..f4f66d3c874 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataFileTag.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataFileTag.java
@@ -11,15 +11,15 @@
import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Table;
import org.apache.commons.lang3.StringUtils;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataTable.java b/src/main/java/edu/harvard/iq/dataverse/DataTable.java
index 614e7394583..a17d8c65138 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataTable.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataTable.java
@@ -7,26 +7,23 @@
package edu.harvard.iq.dataverse;
import java.io.Serializable;
-import java.util.ArrayList;
import java.util.List;
-import javax.persistence.CascadeType;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.OneToMany;
-import javax.validation.constraints.Size;
-import javax.persistence.OrderBy;
-import org.hibernate.validator.constraints.NotBlank;
-import org.hibernate.validator.constraints.URL;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.OneToMany;
+import jakarta.validation.constraints.Size;
+import jakarta.persistence.OrderBy;
import edu.harvard.iq.dataverse.datavariable.DataVariable;
import java.util.Objects;
-import javax.persistence.Column;
-import javax.persistence.Index;
-import javax.persistence.Table;
+import jakarta.persistence.Column;
+import jakarta.persistence.Index;
+import jakarta.persistence.Table;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataTagsAPITestingBean.java b/src/main/java/edu/harvard/iq/dataverse/DataTagsAPITestingBean.java
index 2f987dde82b..713c86190fc 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataTagsAPITestingBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataTagsAPITestingBean.java
@@ -5,11 +5,11 @@
import java.io.Serializable;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.enterprise.context.SessionScoped;
-import javax.faces.context.FacesContext;
-import javax.inject.Named;
-import javax.json.JsonObject;
+import jakarta.ejb.EJB;
+import jakarta.enterprise.context.SessionScoped;
+import jakarta.faces.context.FacesContext;
+import jakarta.inject.Named;
+import jakarta.json.JsonObject;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataTagsContainer.java b/src/main/java/edu/harvard/iq/dataverse/DataTagsContainer.java
index 5cf9c623bde..eeda70c1f17 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataTagsContainer.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataTagsContainer.java
@@ -1,7 +1,7 @@
package edu.harvard.iq.dataverse;
-import javax.ejb.Stateless;
-import javax.json.JsonObject;
+import jakarta.ejb.Stateless;
+import jakarta.json.JsonObject;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/Dataset.java b/src/main/java/edu/harvard/iq/dataverse/Dataset.java
index f9c839a0fff..620e66c6c54 100644
--- a/src/main/java/edu/harvard/iq/dataverse/Dataset.java
+++ b/src/main/java/edu/harvard/iq/dataverse/Dataset.java
@@ -17,22 +17,22 @@
import java.util.List;
import java.util.Objects;
import java.util.Set;
-import javax.persistence.CascadeType;
-import javax.persistence.Entity;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.NamedStoredProcedureQuery;
-import javax.persistence.OneToMany;
-import javax.persistence.OneToOne;
-import javax.persistence.OrderBy;
-import javax.persistence.ParameterMode;
-import javax.persistence.StoredProcedureParameter;
-import javax.persistence.Table;
-import javax.persistence.Temporal;
-import javax.persistence.TemporalType;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Entity;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.NamedStoredProcedureQuery;
+import jakarta.persistence.OneToMany;
+import jakarta.persistence.OneToOne;
+import jakarta.persistence.OrderBy;
+import jakarta.persistence.ParameterMode;
+import jakarta.persistence.StoredProcedureParameter;
+import jakarta.persistence.Table;
+import jakarta.persistence.Temporal;
+import jakarta.persistence.TemporalType;
import edu.harvard.iq.dataverse.settings.JvmSettings;
import edu.harvard.iq.dataverse.util.StringUtil;
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetConverter.java b/src/main/java/edu/harvard/iq/dataverse/DatasetConverter.java
index 2d19cf5fe06..b779e084250 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetConverter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetConverter.java
@@ -6,12 +6,12 @@
package edu.harvard.iq.dataverse;
-import javax.ejb.EJB;
-import javax.enterprise.inject.spi.CDI;
-import javax.faces.component.UIComponent;
-import javax.faces.context.FacesContext;
-import javax.faces.convert.Converter;
-import javax.faces.convert.FacesConverter;
+import jakarta.ejb.EJB;
+import jakarta.enterprise.inject.spi.CDI;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.convert.Converter;
+import jakarta.faces.convert.FacesConverter;
@FacesConverter("datasetConverter")
public class DatasetConverter implements Converter {
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetDistributor.java b/src/main/java/edu/harvard/iq/dataverse/DatasetDistributor.java
index 00936b9365a..3252b7f0367 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetDistributor.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetDistributor.java
@@ -7,7 +7,7 @@
package edu.harvard.iq.dataverse;
import java.util.Comparator;
-import javax.persistence.Version;
+import jakarta.persistence.Version;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetField.java b/src/main/java/edu/harvard/iq/dataverse/DatasetField.java
index 31d08f84c02..c836a20893f 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetField.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetField.java
@@ -19,20 +19,20 @@
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
-import javax.persistence.CascadeType;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.JoinTable;
-import javax.persistence.ManyToMany;
-import javax.persistence.ManyToOne;
-import javax.persistence.OneToMany;
-import javax.persistence.OrderBy;
-import javax.persistence.Table;
-import javax.persistence.Transient;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.JoinTable;
+import jakarta.persistence.ManyToMany;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.OneToMany;
+import jakarta.persistence.OrderBy;
+import jakarta.persistence.Table;
+import jakarta.persistence.Transient;
import org.apache.commons.lang3.StringUtils;
@Entity
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetFieldCompoundValue.java b/src/main/java/edu/harvard/iq/dataverse/DatasetFieldCompoundValue.java
index 5d83f1e4f8d..c679cd7edad 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetFieldCompoundValue.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetFieldCompoundValue.java
@@ -14,17 +14,17 @@
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
-import javax.persistence.CascadeType;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.ManyToOne;
-import javax.persistence.OneToMany;
-import javax.persistence.OrderBy;
-import javax.persistence.Table;
-import javax.persistence.Transient;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.OneToMany;
+import jakarta.persistence.OrderBy;
+import jakarta.persistence.Table;
+import jakarta.persistence.Transient;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.tuple.ImmutablePair;
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetFieldConstant.java b/src/main/java/edu/harvard/iq/dataverse/DatasetFieldConstant.java
index e57a2a1538d..1621b80df55 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetFieldConstant.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetFieldConstant.java
@@ -6,8 +6,8 @@
package edu.harvard.iq.dataverse;
-import javax.enterprise.context.Dependent;
-import javax.inject.Named;
+import jakarta.enterprise.context.Dependent;
+import jakarta.inject.Named;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetFieldDefaultValue.java b/src/main/java/edu/harvard/iq/dataverse/DatasetFieldDefaultValue.java
index bad482dbca9..7746099818e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetFieldDefaultValue.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetFieldDefaultValue.java
@@ -8,18 +8,18 @@
import java.io.Serializable;
import java.util.Collection;
-import javax.persistence.CascadeType;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.OneToMany;
-import javax.persistence.OrderBy;
-import javax.persistence.Table;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.OneToMany;
+import jakarta.persistence.OrderBy;
+import jakarta.persistence.Table;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetFieldServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DatasetFieldServiceBean.java
index 89f8c11d076..620d4bf3e09 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetFieldServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetFieldServiceBean.java
@@ -17,24 +17,24 @@
import java.util.Set;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.json.Json;
-import javax.json.JsonArray;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonException;
-import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
-import javax.json.JsonReader;
-import javax.json.JsonString;
-import javax.json.JsonValue;
-import javax.json.JsonValue.ValueType;
-import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
-import javax.persistence.NonUniqueResultException;
-import javax.persistence.PersistenceContext;
-import javax.persistence.TypedQuery;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.json.Json;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonException;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.json.JsonReader;
+import jakarta.json.JsonString;
+import jakarta.json.JsonValue;
+import jakarta.json.JsonValue.ValueType;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.NonUniqueResultException;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.TypedQuery;
import org.apache.commons.codec.digest.DigestUtils;
import org.apache.commons.httpclient.HttpException;
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetFieldType.java b/src/main/java/edu/harvard/iq/dataverse/DatasetFieldType.java
index df126514308..824b486a42d 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetFieldType.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetFieldType.java
@@ -13,8 +13,8 @@
import java.util.Set;
import java.util.TreeMap;
import java.util.MissingResourceException;
-import javax.faces.model.SelectItem;
-import javax.persistence.*;
+import jakarta.faces.model.SelectItem;
+import jakarta.persistence.*;
/**
* Defines the meaning and constraints of a metadata field and its values.
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetFieldValidator.java b/src/main/java/edu/harvard/iq/dataverse/DatasetFieldValidator.java
index 3ded24d7a59..6d3fda2812d 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetFieldValidator.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetFieldValidator.java
@@ -5,11 +5,11 @@
*/
package edu.harvard.iq.dataverse;
-import javax.validation.ConstraintValidator;
-import javax.validation.ConstraintValidatorContext;
+import jakarta.validation.ConstraintValidator;
+import jakarta.validation.ConstraintValidatorContext;
import edu.harvard.iq.dataverse.util.BundleUtil;
-import java.util.Collections;
+
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetFieldValue.java b/src/main/java/edu/harvard/iq/dataverse/DatasetFieldValue.java
index 2447a6478fd..1064187ccd6 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetFieldValue.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetFieldValue.java
@@ -10,17 +10,17 @@
import edu.harvard.iq.dataverse.util.MarkupChecker;
import java.io.Serializable;
import java.util.Comparator;
-import java.util.ResourceBundle;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-import javax.persistence.Transient;
+
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Table;
+import jakarta.persistence.Transient;
import org.apache.commons.lang3.StringUtils;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetFieldValueValidator.java b/src/main/java/edu/harvard/iq/dataverse/DatasetFieldValueValidator.java
index 132955859ff..b6c21014f04 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetFieldValueValidator.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetFieldValueValidator.java
@@ -13,14 +13,13 @@
import java.util.GregorianCalendar;
import java.util.logging.Logger;
import java.util.regex.Pattern;
-import javax.validation.ConstraintValidator;
-import javax.validation.ConstraintValidatorContext;
+import jakarta.validation.ConstraintValidator;
+import jakarta.validation.ConstraintValidatorContext;
import edu.harvard.iq.dataverse.util.BundleUtil;
import edu.harvard.iq.dataverse.validation.EMailValidator;
import edu.harvard.iq.dataverse.validation.URLValidator;
import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.validator.routines.UrlValidator;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetLinkingDataverse.java b/src/main/java/edu/harvard/iq/dataverse/DatasetLinkingDataverse.java
index 8f8e9b103c1..dec07a09643 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetLinkingDataverse.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetLinkingDataverse.java
@@ -2,19 +2,19 @@
import java.io.Serializable;
import java.util.Date;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.OneToOne;
-import javax.persistence.Table;
-import javax.persistence.Temporal;
-import javax.persistence.TemporalType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.OneToOne;
+import jakarta.persistence.Table;
+import jakarta.persistence.Temporal;
+import jakarta.persistence.TemporalType;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetLinkingServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DatasetLinkingServiceBean.java
index 3789efcd443..39c82bfa3f1 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetLinkingServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetLinkingServiceBean.java
@@ -8,12 +8,13 @@
import java.util.ArrayList;
import java.util.List;
import java.util.logging.Logger;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.persistence.Query;
-import javax.persistence.TypedQuery;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.Query;
+import jakarta.persistence.TypedQuery;
/**
*
@@ -63,7 +64,7 @@ public DatasetLinkingDataverse findDatasetLinkingDataverse(Long datasetId, Long
.setParameter("datasetId", datasetId)
.setParameter("linkingDataverseId", linkingDataverseId)
.getSingleResult();
- } catch (javax.persistence.NoResultException e) {
+ } catch (NoResultException e) {
logger.fine("no datasetLinkingDataverse found for datasetId " + datasetId + " and linkingDataverseId " + linkingDataverseId);
return null;
}
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetLock.java b/src/main/java/edu/harvard/iq/dataverse/DatasetLock.java
index 7b857545c20..cc0078ecbc5 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetLock.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetLock.java
@@ -20,25 +20,24 @@
package edu.harvard.iq.dataverse;
-import static edu.harvard.iq.dataverse.DatasetLock.Reason.Workflow;
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
import java.util.Date;
import java.io.Serializable;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-import javax.persistence.Temporal;
-import javax.persistence.TemporalType;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.EnumType;
+import jakarta.persistence.Enumerated;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Table;
+import jakarta.persistence.Temporal;
+import jakarta.persistence.TemporalType;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java
index 393c6cfad16..d20175b6e1a 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java
@@ -58,7 +58,6 @@
import edu.harvard.iq.dataverse.util.StringUtil;
import edu.harvard.iq.dataverse.util.SystemConfig;
-import edu.harvard.iq.dataverse.util.URLTokenUtil;
import edu.harvard.iq.dataverse.util.WebloaderUtil;
import edu.harvard.iq.dataverse.validation.URLValidator;
import edu.harvard.iq.dataverse.workflows.WorkflowComment;
@@ -84,27 +83,27 @@
import java.util.logging.Logger;
import java.util.stream.Collectors;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.faces.application.FacesMessage;
-import javax.faces.context.FacesContext;
-import javax.faces.event.ActionEvent;
-import javax.faces.event.ValueChangeEvent;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.event.ActionEvent;
+import jakarta.faces.event.ValueChangeEvent;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
import org.apache.commons.lang3.StringUtils;
import org.primefaces.event.FileUploadEvent;
import org.primefaces.model.file.UploadedFile;
-import javax.validation.ConstraintViolation;
+import jakarta.validation.ConstraintViolation;
import org.apache.commons.httpclient.HttpClient;
//import org.primefaces.context.RequestContext;
import java.util.Arrays;
import java.util.HashSet;
-import javax.faces.model.SelectItem;
-import javax.faces.validator.ValidatorException;
+import jakarta.faces.model.SelectItem;
+import jakarta.faces.validator.ValidatorException;
import java.util.logging.Level;
import edu.harvard.iq.dataverse.engine.command.exception.IllegalCommandException;
@@ -125,12 +124,12 @@
import edu.harvard.iq.dataverse.makedatacount.MakeDataCountLoggingServiceBean;
import edu.harvard.iq.dataverse.makedatacount.MakeDataCountLoggingServiceBean.MakeDataCountEntry;
import java.util.Collections;
-import javax.faces.component.UIComponent;
-import javax.faces.component.UIInput;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.component.UIInput;
-import javax.faces.event.AjaxBehaviorEvent;
-import javax.servlet.ServletOutputStream;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.faces.event.AjaxBehaviorEvent;
+import jakarta.servlet.ServletOutputStream;
+import jakarta.servlet.http.HttpServletResponse;
import org.apache.commons.text.StringEscapeUtils;
import org.apache.commons.lang3.mutable.MutableBoolean;
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetRelMaterial.java b/src/main/java/edu/harvard/iq/dataverse/DatasetRelMaterial.java
index f432e4f5bbf..53ea62f566a 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetRelMaterial.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetRelMaterial.java
@@ -6,14 +6,14 @@
package edu.harvard.iq.dataverse;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Version;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Version;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java
index c93236f347b..52eb5868c35 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java
@@ -31,22 +31,21 @@
import java.util.logging.FileHandler;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.Asynchronous;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.ejb.Stateless;
-import javax.ejb.TransactionAttribute;
-import javax.ejb.TransactionAttributeType;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.LockModeType;
-import javax.persistence.NoResultException;
-import javax.persistence.PersistenceContext;
-import javax.persistence.Query;
-import javax.persistence.StoredProcedureQuery;
-import javax.persistence.TypedQuery;
-import org.apache.commons.lang3.RandomStringUtils;
-import org.ocpsoft.common.util.Strings;
+import jakarta.ejb.Asynchronous;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.ejb.Stateless;
+import jakarta.ejb.TransactionAttribute;
+import jakarta.ejb.TransactionAttributeType;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.LockModeType;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.Query;
+import jakarta.persistence.StoredProcedureQuery;
+import jakarta.persistence.TypedQuery;
+import org.apache.commons.lang3.StringUtils;
/**
*
@@ -119,7 +118,7 @@ public Dataset find(Object pk) {
public Dataset findDeep(Object pk) {
return (Dataset) em.createNamedQuery("Dataset.findById")
.setParameter("id", pk)
- // Optimization hints: retrieve all data in one query; this prevents point queries when iterating over the files
+ // Optimization hints: retrieve all data in one query; this prevents point queries when iterating over the files
.setHint("eclipselink.left-join-fetch", "o.files.ingestRequest")
.setHint("eclipselink.left-join-fetch", "o.files.thumbnailForDataset")
.setHint("eclipselink.left-join-fetch", "o.files.dataTables")
@@ -331,7 +330,7 @@ public Dataset findByGlobalId(String globalId) {
* in the dataset components, a ConstraintViolationException will be thrown,
* which can be further parsed to detect the specific offending values.
* @param id the id of the dataset
- * @throws javax.validation.ConstraintViolationException
+ * @throws ConstraintViolationException
*/
@TransactionAttribute(TransactionAttributeType.REQUIRES_NEW)
@@ -399,7 +398,7 @@ public DatasetVersionUser getDatasetVersionUser(DatasetVersion version, User use
query.setParameter("userId", au.getId());
try {
return query.getSingleResult();
- } catch (javax.persistence.NoResultException e) {
+ } catch (NoResultException e) {
return null;
}
}
@@ -514,7 +513,7 @@ public List listLocks(DatasetLock.Reason lockType, AuthenticatedUse
}
try {
return query.getResultList();
- } catch (javax.persistence.NoResultException e) {
+ } catch (NoResultException e) {
return null;
}
}
@@ -595,7 +594,7 @@ public Map getArchiveDescriptionsForHarvestedDatasets(Set da
return null;
}
- String datasetIdStr = Strings.join(datasetIds, ", ");
+ String datasetIdStr = StringUtils.join(datasetIds, ", ");
String qstr = "SELECT d.id, h.archiveDescription FROM harvestingClient h, dataset d WHERE d.harvestingClient_id = h.id AND d.id IN (" + datasetIdStr + ")";
List searchResults;
@@ -771,11 +770,11 @@ public void reExportDatasetAsync(Dataset dataset) {
public void exportDataset(Dataset dataset, boolean forceReExport) {
if (dataset != null) {
- // Note that the logic for handling a dataset is similar to what is implemented in exportAllDatasets,
+ // Note that the logic for handling a dataset is similar to what is implemented in exportAllDatasets,
// but when only one dataset is exported we do not log in a separate export logging file
if (dataset.isReleased() && dataset.getReleasedVersion() != null && !dataset.isDeaccessioned()) {
- // can't trust dataset.getPublicationDate(), no.
+ // can't trust dataset.getPublicationDate(), no.
Date publicationDate = dataset.getReleasedVersion().getReleaseTime(); // we know this dataset has a non-null released version! Maybe not - SEK 8/19 (We do now! :)
if (forceReExport || (publicationDate != null
&& (dataset.getLastExportTime() == null
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetTopicClass.java b/src/main/java/edu/harvard/iq/dataverse/DatasetTopicClass.java
index f253e1810a1..91a4ff3cf5a 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetTopicClass.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetTopicClass.java
@@ -6,8 +6,8 @@
package edu.harvard.iq.dataverse;
-import javax.persistence.Column;
-import javax.persistence.Version;
+import jakarta.persistence.Column;
+import jakarta.persistence.Version;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetVersion.java b/src/main/java/edu/harvard/iq/dataverse/DatasetVersion.java
index 9d5c27ae9fd..93f45bd288e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetVersion.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetVersion.java
@@ -25,37 +25,37 @@
import java.util.logging.Logger;
import java.util.stream.Collectors;
-import javax.json.Json;
-import javax.json.JsonArray;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
-import javax.persistence.CascadeType;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.OneToMany;
-import javax.persistence.OneToOne;
-import javax.persistence.OrderBy;
-import javax.persistence.Table;
-import javax.persistence.Temporal;
-import javax.persistence.TemporalType;
-import javax.persistence.Transient;
-import javax.persistence.UniqueConstraint;
-import javax.persistence.Version;
-import javax.validation.ConstraintViolation;
-import javax.validation.Validation;
-import javax.validation.Validator;
-import javax.validation.constraints.Size;
+import jakarta.json.Json;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.EnumType;
+import jakarta.persistence.Enumerated;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.OneToMany;
+import jakarta.persistence.OneToOne;
+import jakarta.persistence.OrderBy;
+import jakarta.persistence.Table;
+import jakarta.persistence.Temporal;
+import jakarta.persistence.TemporalType;
+import jakarta.persistence.Transient;
+import jakarta.persistence.UniqueConstraint;
+import jakarta.persistence.Version;
+import jakarta.validation.ConstraintViolation;
+import jakarta.validation.Validation;
+import jakarta.validation.Validator;
+import jakarta.validation.constraints.Size;
import org.apache.commons.lang3.StringUtils;
/**
@@ -1814,7 +1814,7 @@ public String getPublicationDateAsString() {
// So something will need to be modified to accommodate this. -- L.A.
/**
* We call the export format "Schema.org JSON-LD" and extensive Javadoc can
- * be found in {@link SchemaDotOrgExporter}.
+ * be found in {@link edu.harvard.iq.dataverse.export.SchemaDotOrgExporter}.
*/
public String getJsonLd() {
// We show published datasets only for "datePublished" field below.
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetVersionConverter.java b/src/main/java/edu/harvard/iq/dataverse/DatasetVersionConverter.java
index 98f0d707bdc..b670fb18afc 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetVersionConverter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetVersionConverter.java
@@ -5,12 +5,12 @@
*/
package edu.harvard.iq.dataverse;
-import javax.ejb.EJB;
-import javax.enterprise.inject.spi.CDI;
-import javax.faces.component.UIComponent;
-import javax.faces.context.FacesContext;
-import javax.faces.convert.Converter;
-import javax.faces.convert.FacesConverter;
+import jakarta.ejb.EJB;
+import jakarta.enterprise.inject.spi.CDI;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.convert.Converter;
+import jakarta.faces.convert.FacesConverter;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetVersionNoteValidator.java b/src/main/java/edu/harvard/iq/dataverse/DatasetVersionNoteValidator.java
index c086fed3b10..a5ea487a68f 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetVersionNoteValidator.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetVersionNoteValidator.java
@@ -6,8 +6,8 @@
package edu.harvard.iq.dataverse;
import edu.harvard.iq.dataverse.util.BundleUtil;
-import javax.validation.ConstraintValidator;
-import javax.validation.ConstraintValidatorContext;
+import jakarta.validation.ConstraintValidator;
+import jakarta.validation.ConstraintValidatorContext;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetVersionServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DatasetVersionServiceBean.java
index 607c46d3662..28243c37eee 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetVersionServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetVersionServiceBean.java
@@ -13,7 +13,7 @@
import edu.harvard.iq.dataverse.util.BundleUtil;
import edu.harvard.iq.dataverse.util.MarkupChecker;
import edu.harvard.iq.dataverse.util.SystemConfig;
-import java.io.IOException;
+
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Arrays;
@@ -22,22 +22,21 @@
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
-import java.util.concurrent.Future;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.json.Json;
-import javax.json.JsonObjectBuilder;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.persistence.Query;
-import javax.persistence.TypedQuery;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.json.Json;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.Query;
+import jakarta.persistence.TypedQuery;
import org.apache.commons.lang3.StringUtils;
-import org.apache.solr.client.solrj.SolrServerException;
-
+
/**
*
* @author skraffmiller
@@ -196,7 +195,7 @@ public DatasetVersion findByFriendlyVersionNumber(Long datasetId, String friendl
query.setParameter("majorVersionNumber", majorVersionNumber);
query.setParameter("minorVersionNumber", minorVersionNumber);
foundDatasetVersion = (DatasetVersion) query.getSingleResult();
- } catch (javax.persistence.NoResultException e) {
+ } catch (NoResultException e) {
logger.warning("no ds version found: " + datasetId + " " + friendlyVersionNumber);
// DO nothing, just return null.
}
@@ -224,7 +223,7 @@ public DatasetVersion findByFriendlyVersionNumber(Long datasetId, String friendl
}
}
return retVal;
- } catch (javax.persistence.NoResultException e) {
+ } catch (NoResultException e) {
logger.warning("no ds version found: " + datasetId + " " + friendlyVersionNumber);
// DO nothing, just return null.
}
@@ -451,7 +450,7 @@ private DatasetVersion getDatasetVersionByQuery(String queryString){
msg("Found: " + ds);
return ds;
- } catch (javax.persistence.NoResultException e) {
+ } catch (NoResultException e) {
msg("DatasetVersion not found: " + queryString);
logger.log(Level.FINE, "DatasetVersion not found: {0}", queryString);
return null;
@@ -1217,7 +1216,7 @@ public List getUnarchivedDatasetVersions(){
try {
List dsl = em.createNamedQuery("DatasetVersion.findUnarchivedReleasedVersion", DatasetVersion.class).getResultList();
return dsl;
- } catch (javax.persistence.NoResultException e) {
+ } catch (NoResultException e) {
logger.log(Level.FINE, "No unarchived DatasetVersions found: {0}");
return null;
} catch (EJBException e) {
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetVersionUI.java b/src/main/java/edu/harvard/iq/dataverse/DatasetVersionUI.java
index 6e9f9c17f7a..55b98c178bb 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetVersionUI.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetVersionUI.java
@@ -6,6 +6,7 @@
package edu.harvard.iq.dataverse;
import edu.harvard.iq.dataverse.util.MarkupChecker;
+
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Calendar;
@@ -14,12 +15,12 @@
import java.util.Date;
import java.util.List;
import java.util.TreeMap;
-import javax.ejb.EJB;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.json.JsonObject;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
+
+import jakarta.ejb.EJB;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetVersionUser.java b/src/main/java/edu/harvard/iq/dataverse/DatasetVersionUser.java
index eda62a080f8..e56fad71253 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetVersionUser.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetVersionUser.java
@@ -4,20 +4,20 @@
import edu.harvard.iq.dataverse.authorization.users.User;
import java.io.Serializable;
import java.sql.Timestamp;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
-import javax.persistence.JoinColumn;
+import jakarta.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.Table;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.Table;
/**
* Records the last time a {@link User} handled a {@link DatasetVersion}.
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetWidgetsPage.java b/src/main/java/edu/harvard/iq/dataverse/DatasetWidgetsPage.java
index 9c47a58811a..1dd42903118 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetWidgetsPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetWidgetsPage.java
@@ -14,10 +14,10 @@
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
import org.primefaces.event.FileUploadEvent;
import org.primefaces.model.file.UploadedFile;
diff --git a/src/main/java/edu/harvard/iq/dataverse/Dataverse.java b/src/main/java/edu/harvard/iq/dataverse/Dataverse.java
index 50d5ae09548..682c1dc6744 100644
--- a/src/main/java/edu/harvard/iq/dataverse/Dataverse.java
+++ b/src/main/java/edu/harvard/iq/dataverse/Dataverse.java
@@ -2,7 +2,6 @@
import edu.harvard.iq.dataverse.harvest.client.HarvestingClient;
import edu.harvard.iq.dataverse.authorization.DataverseRole;
-import edu.harvard.iq.dataverse.dataaccess.DataAccess;
import edu.harvard.iq.dataverse.search.savedsearch.SavedSearch;
import edu.harvard.iq.dataverse.util.BundleUtil;
import edu.harvard.iq.dataverse.util.SystemConfig;
@@ -13,29 +12,28 @@
import java.util.List;
import java.util.Objects;
import java.util.Set;
-import javax.persistence.CascadeType;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
-import javax.persistence.FetchType;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.JoinTable;
-import javax.persistence.ManyToMany;
-import javax.persistence.ManyToOne;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.OneToMany;
-import javax.persistence.OneToOne;
-import javax.persistence.OrderBy;
-import javax.persistence.Table;
-import javax.persistence.Transient;
-import javax.validation.constraints.NotNull;
-import javax.validation.constraints.Pattern;
-import javax.validation.constraints.Size;
-
-import org.apache.commons.lang3.StringUtils;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.EnumType;
+import jakarta.persistence.Enumerated;
+import jakarta.persistence.FetchType;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.JoinTable;
+import jakarta.persistence.ManyToMany;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.OneToMany;
+import jakarta.persistence.OneToOne;
+import jakarta.persistence.OrderBy;
+import jakarta.persistence.Table;
+import jakarta.persistence.Transient;
+import jakarta.validation.constraints.NotNull;
+import jakarta.validation.constraints.Pattern;
+import jakarta.validation.constraints.Size;
+
import org.hibernate.validator.constraints.NotBlank;
import org.hibernate.validator.constraints.NotEmpty;
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataverseContact.java b/src/main/java/edu/harvard/iq/dataverse/DataverseContact.java
index 46021ddbc9b..d77767985eb 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataverseContact.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataverseContact.java
@@ -7,15 +7,15 @@
import java.io.Serializable;
import java.util.Objects;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Table;
import edu.harvard.iq.dataverse.validation.ValidateEmail;
import org.hibernate.validator.constraints.NotBlank;
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataverseConverter.java b/src/main/java/edu/harvard/iq/dataverse/DataverseConverter.java
index 7d09c300dde..d802117043b 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataverseConverter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataverseConverter.java
@@ -6,12 +6,12 @@
package edu.harvard.iq.dataverse;
-import javax.ejb.EJB;
-import javax.enterprise.inject.spi.CDI;
-import javax.faces.component.UIComponent;
-import javax.faces.context.FacesContext;
-import javax.faces.convert.Converter;
-import javax.faces.convert.FacesConverter;
+import jakarta.ejb.EJB;
+import jakarta.enterprise.inject.spi.CDI;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.convert.Converter;
+import jakarta.faces.convert.FacesConverter;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataverseFacet.java b/src/main/java/edu/harvard/iq/dataverse/DataverseFacet.java
index bfd465b8f54..768c2308e50 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataverseFacet.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataverseFacet.java
@@ -8,16 +8,16 @@
import java.io.Serializable;
import java.util.Objects;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.Table;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.Table;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataverseFacetServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DataverseFacetServiceBean.java
index 67bf6a820e2..5c77989f6d6 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataverseFacetServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataverseFacetServiceBean.java
@@ -2,11 +2,11 @@
import edu.harvard.iq.dataverse.util.LruCache;
import java.util.List;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataverseFeaturedDataverse.java b/src/main/java/edu/harvard/iq/dataverse/DataverseFeaturedDataverse.java
index 662ee74c3bf..39ad6ca9520 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataverseFeaturedDataverse.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataverseFeaturedDataverse.java
@@ -2,16 +2,16 @@
import java.io.Serializable;
import java.util.Objects;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.Table;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.Table;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataverseFieldTypeInputLevel.java b/src/main/java/edu/harvard/iq/dataverse/DataverseFieldTypeInputLevel.java
index 92b1ff7c2cf..c4749be0cb3 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataverseFieldTypeInputLevel.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataverseFieldTypeInputLevel.java
@@ -6,17 +6,17 @@
package edu.harvard.iq.dataverse;
import java.io.Serializable;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.Table;
-import javax.persistence.UniqueConstraint;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.Table;
+import jakarta.persistence.UniqueConstraint;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataverseFieldTypeInputLevelServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DataverseFieldTypeInputLevelServiceBean.java
index 42a1290fdbd..66c700f59ce 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataverseFieldTypeInputLevelServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataverseFieldTypeInputLevelServiceBean.java
@@ -7,13 +7,13 @@
import edu.harvard.iq.dataverse.util.LruCache;
import java.util.List;
-import java.util.logging.Logger;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
-import javax.persistence.PersistenceContext;
-import javax.persistence.Query;
+
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.Query;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataverseHeaderFragment.java b/src/main/java/edu/harvard/iq/dataverse/DataverseHeaderFragment.java
index 1e1353a11fc..389b85c19d9 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataverseHeaderFragment.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataverseHeaderFragment.java
@@ -19,11 +19,11 @@
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.faces.context.FacesContext;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
import org.apache.commons.lang3.StringUtils;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataverseLinkingDataverse.java b/src/main/java/edu/harvard/iq/dataverse/DataverseLinkingDataverse.java
index 788308dce1e..3030922ea5e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataverseLinkingDataverse.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataverseLinkingDataverse.java
@@ -7,18 +7,18 @@
import java.io.Serializable;
import java.util.Date;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.OneToOne;
-import javax.persistence.Table;
-import javax.persistence.Temporal;
-import javax.persistence.TemporalType;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.OneToOne;
+import jakarta.persistence.Table;
+import jakarta.persistence.Temporal;
+import jakarta.persistence.TemporalType;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataverseLinkingServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DataverseLinkingServiceBean.java
index c823deddb64..834ff96e392 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataverseLinkingServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataverseLinkingServiceBean.java
@@ -8,13 +8,13 @@
import java.util.ArrayList;
import java.util.List;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.persistence.Query;
-import javax.persistence.TypedQuery;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.Query;
+import jakarta.persistence.TypedQuery;
/**
*
@@ -66,7 +66,7 @@ public DataverseLinkingDataverse findDataverseLinkingDataverse(Long dataverseId,
.setParameter("dataverseId", dataverseId)
.setParameter("linkingDataverseId", linkingDataverseId)
.getSingleResult();
- } catch (javax.persistence.NoResultException e) {
+ } catch (jakarta.persistence.NoResultException e) {
logger.fine("No DataverseLinkingDataverse found for dataverseId " + dataverseId + " and linkedDataverseId " + linkingDataverseId);
return null;
}
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataverseMetadataBlockFacet.java b/src/main/java/edu/harvard/iq/dataverse/DataverseMetadataBlockFacet.java
index a2659b81974..c93144b2e97 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataverseMetadataBlockFacet.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataverseMetadataBlockFacet.java
@@ -1,13 +1,13 @@
package edu.harvard.iq.dataverse;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Table;
import java.io.Serializable;
import java.util.Objects;
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataversePage.java b/src/main/java/edu/harvard/iq/dataverse/DataversePage.java
index b48ff725e1e..daf33f444d9 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataversePage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataversePage.java
@@ -28,27 +28,26 @@
import static edu.harvard.iq.dataverse.util.JsfHelper.JH;
import edu.harvard.iq.dataverse.util.SystemConfig;
import java.util.List;
-import javax.ejb.EJB;
-import javax.faces.application.FacesMessage;
-import javax.faces.context.FacesContext;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
-import java.util.HashSet;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.faces.component.UIComponent;
-import javax.faces.component.UIInput;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.component.UIInput;
import org.primefaces.model.DualListModel;
-import javax.ejb.EJBException;
-import javax.faces.event.ValueChangeEvent;
-import javax.faces.model.SelectItem;
+import jakarta.ejb.EJBException;
+import jakarta.faces.event.ValueChangeEvent;
+import jakarta.faces.model.SelectItem;
import org.apache.commons.text.StringEscapeUtils;
import org.apache.commons.lang3.StringUtils;
import org.primefaces.PrimeFaces;
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataverseRequestServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DataverseRequestServiceBean.java
index e193b535412..58a3837dbf9 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataverseRequestServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataverseRequestServiceBean.java
@@ -1,11 +1,11 @@
package edu.harvard.iq.dataverse;
import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
-import javax.annotation.PostConstruct;
-import javax.enterprise.context.RequestScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
-import javax.servlet.http.HttpServletRequest;
+import jakarta.annotation.PostConstruct;
+import jakarta.enterprise.context.RequestScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
+import jakarta.servlet.http.HttpServletRequest;
/**
* The service bean to go to when one needs the current {@link DataverseRequest}.
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataverseRoleServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DataverseRoleServiceBean.java
index b83593f5b6e..78d5eaf3414 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataverseRoleServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataverseRoleServiceBean.java
@@ -17,13 +17,13 @@
import java.util.Set;
import java.util.logging.Logger;
import java.util.stream.Collectors;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.persistence.TypedQuery;
-//import javax.validation.constraints.NotNull;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.TypedQuery;
+//import jakarta.validation.constraints.NotNull;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataverseServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DataverseServiceBean.java
index e092f209acd..7194a1ef31e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataverseServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataverseServiceBean.java
@@ -30,18 +30,18 @@
import java.util.Map;
import java.util.logging.Logger;
import java.util.Properties;
-import java.util.concurrent.Future;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Inject;
-import javax.inject.Named;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
-import javax.persistence.NonUniqueResultException;
-import javax.persistence.PersistenceContext;
-import javax.persistence.TypedQuery;
+
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.NonUniqueResultException;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.TypedQuery;
import org.apache.solr.client.solrj.SolrServerException;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataverseSession.java b/src/main/java/edu/harvard/iq/dataverse/DataverseSession.java
index c6016939c08..e8d76e1825e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataverseSession.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataverseSession.java
@@ -18,13 +18,13 @@
import java.util.List;
import java.util.Locale;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.enterprise.context.SessionScoped;
-import javax.faces.context.FacesContext;
-import javax.inject.Inject;
-import javax.inject.Named;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpSession;
+import jakarta.ejb.EJB;
+import jakarta.enterprise.context.SessionScoped;
+import jakarta.faces.context.FacesContext;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpSession;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataverseTheme.java b/src/main/java/edu/harvard/iq/dataverse/DataverseTheme.java
index 0c6341db485..539669328a7 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataverseTheme.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataverseTheme.java
@@ -8,16 +8,16 @@
import java.io.Serializable;
import java.util.Objects;
-import javax.persistence.Entity;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.OneToOne;
-import javax.persistence.Table;
+import jakarta.persistence.Entity;
+import jakarta.persistence.EnumType;
+import jakarta.persistence.Enumerated;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.OneToOne;
+import jakarta.persistence.Table;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/DefaultValueSet.java b/src/main/java/edu/harvard/iq/dataverse/DefaultValueSet.java
index ad48f15fc54..a2dc785c470 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DefaultValueSet.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DefaultValueSet.java
@@ -8,13 +8,13 @@
import java.io.Serializable;
import java.util.List;
-import javax.persistence.CascadeType;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.OneToMany;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.OneToMany;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/DvObject.java b/src/main/java/edu/harvard/iq/dataverse/DvObject.java
index e3013b8cf51..9e7f3f3fe96 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DvObject.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DvObject.java
@@ -5,14 +5,13 @@
import java.sql.Timestamp;
import java.text.SimpleDateFormat;
-import java.util.Arrays;
import java.util.Date;
import java.util.List;
import java.util.Objects;
import java.util.Set;
import java.util.logging.Logger;
-import javax.persistence.*;
+import jakarta.persistence.*;
/**
* Base of the object hierarchy for "anything that can be inside a dataverse".
diff --git a/src/main/java/edu/harvard/iq/dataverse/DvObjectContainer.java b/src/main/java/edu/harvard/iq/dataverse/DvObjectContainer.java
index 6ff01ef3ea8..a322a25103e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DvObjectContainer.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DvObjectContainer.java
@@ -2,8 +2,7 @@
import edu.harvard.iq.dataverse.dataaccess.DataAccess;
import edu.harvard.iq.dataverse.util.SystemConfig;
-import java.util.Locale;
-import javax.persistence.MappedSuperclass;
+import jakarta.persistence.MappedSuperclass;
import org.apache.commons.lang3.StringUtils;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/DvObjectServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DvObjectServiceBean.java
index c9127af7c2b..d4219c36149 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DvObjectServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DvObjectServiceBean.java
@@ -12,19 +12,18 @@
import java.util.Set;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.Stateless;
-import javax.ejb.TransactionAttribute;
-import static javax.ejb.TransactionAttributeType.REQUIRES_NEW;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
-import javax.persistence.NonUniqueResultException;
-import javax.persistence.PersistenceContext;
-import javax.persistence.Query;
-import javax.persistence.StoredProcedureQuery;
+import jakarta.ejb.Stateless;
+import jakarta.ejb.TransactionAttribute;
+import static jakarta.ejb.TransactionAttributeType.REQUIRES_NEW;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.NonUniqueResultException;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.Query;
+import jakarta.persistence.StoredProcedureQuery;
import org.apache.commons.lang3.StringUtils;
-import org.ocpsoft.common.util.Strings;
/**
* Your goto bean for everything {@link DvObject}, that's not tied to any
@@ -134,7 +133,7 @@ private DvObject runFindByGlobalId(Query query, GlobalId gid, DvObject.DType dty
query.setParameter("authority", gid.getAuthority());
query.setParameter("dtype", dtype.getDType());
foundDvObject = (DvObject) query.getSingleResult();
- } catch (javax.persistence.NoResultException e) {
+ } catch (NoResultException e) {
// (set to .info, this can fill the log file with thousands of
// these messages during a large harvest run)
logger.fine("no dvObject found: " + gid.asString());
@@ -155,7 +154,7 @@ private Long runFindIdByGlobalId(Query query, GlobalId gid, DvObject.DType dtype
query.setParameter("authority", gid.getAuthority());
query.setParameter("dtype", dtype.getDType());
foundDvObject = (Long) query.getSingleResult();
- } catch (javax.persistence.NoResultException e) {
+ } catch (NoResultException e) {
// (set to .info, this can fill the log file with thousands of
// these messages during a large harvest run)
logger.fine("no dvObject found: " + gid.asString());
@@ -323,7 +322,7 @@ public Map getObjectPathsByIds(Set objectIds){
return null;
}
- String datasetIdStr = Strings.join(objectIds, ", ");
+ String datasetIdStr = StringUtils.join(objectIds, ", ");
String qstr = "WITH RECURSIVE path_elements AS ((" +
" SELECT id, owner_id FROM dvobject WHERE id in (" + datasetIdStr + "))" +
diff --git a/src/main/java/edu/harvard/iq/dataverse/EditDataFilesPageHelper.java b/src/main/java/edu/harvard/iq/dataverse/EditDataFilesPageHelper.java
index 1bf6bee82eb..883baeedef4 100644
--- a/src/main/java/edu/harvard/iq/dataverse/EditDataFilesPageHelper.java
+++ b/src/main/java/edu/harvard/iq/dataverse/EditDataFilesPageHelper.java
@@ -4,8 +4,8 @@
import edu.harvard.iq.dataverse.util.file.CreateDataFileResult;
import org.apache.commons.text.StringEscapeUtils;
-import javax.ejb.Stateless;
-import javax.inject.Inject;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Inject;
import java.util.Arrays;
import java.util.List;
import java.util.Optional;
diff --git a/src/main/java/edu/harvard/iq/dataverse/EditDatafilesPage.java b/src/main/java/edu/harvard/iq/dataverse/EditDatafilesPage.java
index 1c033b37872..02a148f8cc5 100644
--- a/src/main/java/edu/harvard/iq/dataverse/EditDatafilesPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/EditDatafilesPage.java
@@ -39,7 +39,6 @@
import edu.harvard.iq.dataverse.util.FileUtil;
import edu.harvard.iq.dataverse.util.JsfHelper;
import edu.harvard.iq.dataverse.util.SystemConfig;
-import edu.harvard.iq.dataverse.util.URLTokenUtil;
import edu.harvard.iq.dataverse.util.WebloaderUtil;
import edu.harvard.iq.dataverse.util.BundleUtil;
import edu.harvard.iq.dataverse.util.EjbUtil;
@@ -58,23 +57,23 @@
import java.util.Map;
import java.util.Optional;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.faces.application.FacesMessage;
-import javax.faces.context.FacesContext;
-import javax.faces.event.ActionEvent;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.event.ActionEvent;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
import edu.harvard.iq.dataverse.util.file.CreateDataFileResult;
import org.primefaces.event.FileUploadEvent;
import org.primefaces.model.file.UploadedFile;
-import javax.json.Json;
-import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
-import javax.json.JsonArray;
-import javax.json.JsonReader;
+import jakarta.json.Json;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonReader;
import org.apache.commons.httpclient.HttpClient;
import org.apache.commons.io.IOUtils;
import org.apache.commons.httpclient.methods.GetMethod;
@@ -82,10 +81,10 @@
import java.util.Collection;
import java.util.Set;
import java.util.logging.Level;
-import javax.faces.event.AjaxBehaviorEvent;
-import javax.faces.event.FacesEvent;
-import javax.servlet.ServletOutputStream;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.faces.event.AjaxBehaviorEvent;
+import jakarta.faces.event.FacesEvent;
+import jakarta.servlet.ServletOutputStream;
+import jakarta.servlet.http.HttpServletResponse;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.mutable.MutableBoolean;
import org.primefaces.PrimeFaces;
diff --git a/src/main/java/edu/harvard/iq/dataverse/EjbDataverseEngine.java b/src/main/java/edu/harvard/iq/dataverse/EjbDataverseEngine.java
index 7185887ecc3..bad8903c091 100644
--- a/src/main/java/edu/harvard/iq/dataverse/EjbDataverseEngine.java
+++ b/src/main/java/edu/harvard/iq/dataverse/EjbDataverseEngine.java
@@ -24,11 +24,10 @@
import edu.harvard.iq.dataverse.search.IndexServiceBean;
import edu.harvard.iq.dataverse.search.SearchServiceBean;
import java.util.Map;
-import java.util.Map.Entry;
import java.util.Set;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
import edu.harvard.iq.dataverse.search.SolrIndexServiceBean;
import edu.harvard.iq.dataverse.search.savedsearch.SavedSearchServiceBean;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
@@ -41,16 +40,16 @@
import java.util.Stack;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.annotation.Resource;
-import javax.ejb.EJBContext;
-import javax.ejb.EJBException;
-import javax.ejb.TransactionAttribute;
-import static javax.ejb.TransactionAttributeType.REQUIRES_NEW;
-import static javax.ejb.TransactionAttributeType.SUPPORTS;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.validation.ConstraintViolation;
-import javax.validation.ConstraintViolationException;
+import jakarta.annotation.Resource;
+import jakarta.ejb.EJBContext;
+import jakarta.ejb.EJBException;
+import jakarta.ejb.TransactionAttribute;
+import static jakarta.ejb.TransactionAttributeType.REQUIRES_NEW;
+import static jakarta.ejb.TransactionAttributeType.SUPPORTS;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.validation.ConstraintViolation;
+import jakarta.validation.ConstraintViolationException;
/**
* An EJB capable of executing {@link Command}s in a JEE environment.
diff --git a/src/main/java/edu/harvard/iq/dataverse/EjbDataverseEngineInner.java b/src/main/java/edu/harvard/iq/dataverse/EjbDataverseEngineInner.java
index d8339dce856..891fe91dc66 100644
--- a/src/main/java/edu/harvard/iq/dataverse/EjbDataverseEngineInner.java
+++ b/src/main/java/edu/harvard/iq/dataverse/EjbDataverseEngineInner.java
@@ -4,13 +4,13 @@
import edu.harvard.iq.dataverse.engine.command.Command;
import edu.harvard.iq.dataverse.engine.command.CommandContext;
import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
-import javax.annotation.Resource;
-import javax.ejb.EJBContext;
-import javax.ejb.Stateless;
-import javax.ejb.TransactionAttribute;
-import static javax.ejb.TransactionAttributeType.REQUIRED;
+import jakarta.annotation.Resource;
+import jakarta.ejb.EJBContext;
+import jakarta.ejb.Stateless;
+import jakarta.ejb.TransactionAttribute;
+import static jakarta.ejb.TransactionAttributeType.REQUIRED;
-import javax.inject.Named;
+import jakarta.inject.Named;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/Embargo.java b/src/main/java/edu/harvard/iq/dataverse/Embargo.java
index eac83edd296..29959b9f2d4 100644
--- a/src/main/java/edu/harvard/iq/dataverse/Embargo.java
+++ b/src/main/java/edu/harvard/iq/dataverse/Embargo.java
@@ -1,7 +1,7 @@
package edu.harvard.iq.dataverse;
-import javax.persistence.*;
+import jakarta.persistence.*;
import edu.harvard.iq.dataverse.util.BundleUtil;
diff --git a/src/main/java/edu/harvard/iq/dataverse/EmbargoServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/EmbargoServiceBean.java
index afbeab404c7..d0a8d214959 100644
--- a/src/main/java/edu/harvard/iq/dataverse/EmbargoServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/EmbargoServiceBean.java
@@ -3,12 +3,12 @@
import edu.harvard.iq.dataverse.actionlogging.ActionLogRecord;
import edu.harvard.iq.dataverse.actionlogging.ActionLogServiceBean;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.persistence.Query;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.Query;
import java.util.List;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/ExternalVocabularyValue.java b/src/main/java/edu/harvard/iq/dataverse/ExternalVocabularyValue.java
index 3618da79630..7ebfa0302ac 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ExternalVocabularyValue.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ExternalVocabularyValue.java
@@ -9,13 +9,13 @@
import java.io.Serializable;
import java.sql.Timestamp;
import java.util.Objects;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.Table;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.Table;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/FacetConverter.java b/src/main/java/edu/harvard/iq/dataverse/FacetConverter.java
index 75ef62200bf..fd41315dbc0 100644
--- a/src/main/java/edu/harvard/iq/dataverse/FacetConverter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/FacetConverter.java
@@ -5,13 +5,13 @@
*/
package edu.harvard.iq.dataverse;
-import javax.ejb.EJB;
-import javax.enterprise.inject.spi.CDI;
+import jakarta.ejb.EJB;
+import jakarta.enterprise.inject.spi.CDI;
-import javax.faces.component.UIComponent;
-import javax.faces.context.FacesContext;
-import javax.faces.convert.Converter;
-import javax.faces.convert.FacesConverter;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.convert.Converter;
+import jakarta.faces.convert.FacesConverter;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/FeaturedDataverseServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/FeaturedDataverseServiceBean.java
index e7362587c36..d4d701cb02f 100644
--- a/src/main/java/edu/harvard/iq/dataverse/FeaturedDataverseServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/FeaturedDataverseServiceBean.java
@@ -9,11 +9,11 @@
import java.util.ArrayList;
import java.util.List;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/FileAccessRequest.java b/src/main/java/edu/harvard/iq/dataverse/FileAccessRequest.java
index 76c5df4409a..6f68815c2ca 100644
--- a/src/main/java/edu/harvard/iq/dataverse/FileAccessRequest.java
+++ b/src/main/java/edu/harvard/iq/dataverse/FileAccessRequest.java
@@ -2,16 +2,16 @@
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
-import javax.persistence.Column;
-import javax.persistence.Embeddable;
-import javax.persistence.EmbeddedId;
-import javax.persistence.Entity;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.MapsId;
-import javax.persistence.Table;
-import javax.persistence.Temporal;
-import javax.persistence.TemporalType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Embeddable;
+import jakarta.persistence.EmbeddedId;
+import jakarta.persistence.Entity;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.MapsId;
+import jakarta.persistence.Table;
+import jakarta.persistence.Temporal;
+import jakarta.persistence.TemporalType;
import java.io.Serializable;
import java.util.Date;
diff --git a/src/main/java/edu/harvard/iq/dataverse/FileDirectoryNameValidator.java b/src/main/java/edu/harvard/iq/dataverse/FileDirectoryNameValidator.java
index e0c2b83ab65..84c033afcaf 100644
--- a/src/main/java/edu/harvard/iq/dataverse/FileDirectoryNameValidator.java
+++ b/src/main/java/edu/harvard/iq/dataverse/FileDirectoryNameValidator.java
@@ -7,8 +7,8 @@
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import javax.validation.ConstraintValidator;
-import javax.validation.ConstraintValidatorContext;
+import jakarta.validation.ConstraintValidator;
+import jakarta.validation.ConstraintValidatorContext;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/FileDownload.java b/src/main/java/edu/harvard/iq/dataverse/FileDownload.java
index fad03d2a0a1..a79281f71f0 100644
--- a/src/main/java/edu/harvard/iq/dataverse/FileDownload.java
+++ b/src/main/java/edu/harvard/iq/dataverse/FileDownload.java
@@ -6,18 +6,18 @@
package edu.harvard.iq.dataverse;
import java.io.Serializable;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Temporal;
-import javax.persistence.TemporalType;
-import javax.persistence.Transient;
-import javax.persistence.CascadeType;
-import javax.persistence.OneToOne;
-import javax.persistence.MapsId;
-import javax.persistence.FetchType;
-import javax.persistence.JoinColumn;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Temporal;
+import jakarta.persistence.TemporalType;
+import jakarta.persistence.Transient;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.OneToOne;
+import jakarta.persistence.MapsId;
+import jakarta.persistence.FetchType;
+import jakarta.persistence.JoinColumn;
import java.util.Date;
diff --git a/src/main/java/edu/harvard/iq/dataverse/FileDownloadHelper.java b/src/main/java/edu/harvard/iq/dataverse/FileDownloadHelper.java
index 850efc2f1ae..c4b4978e0f8 100644
--- a/src/main/java/edu/harvard/iq/dataverse/FileDownloadHelper.java
+++ b/src/main/java/edu/harvard/iq/dataverse/FileDownloadHelper.java
@@ -18,10 +18,10 @@
import java.util.List;
import java.util.Map;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
import org.primefaces.PrimeFaces;
//import org.primefaces.context.RequestContext;
diff --git a/src/main/java/edu/harvard/iq/dataverse/FileDownloadServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/FileDownloadServiceBean.java
index a90489be29a..e2b07717358 100644
--- a/src/main/java/edu/harvard/iq/dataverse/FileDownloadServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/FileDownloadServiceBean.java
@@ -18,7 +18,6 @@
import edu.harvard.iq.dataverse.privateurl.PrivateUrl;
import edu.harvard.iq.dataverse.privateurl.PrivateUrlServiceBean;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
-import edu.harvard.iq.dataverse.util.BundleUtil;
import edu.harvard.iq.dataverse.util.FileUtil;
import edu.harvard.iq.dataverse.util.StringUtil;
import java.io.IOException;
@@ -29,16 +28,16 @@
import java.util.List;
import java.util.UUID;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.faces.context.FacesContext;
-import javax.inject.Inject;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.persistence.Query;
-import javax.servlet.ServletOutputStream;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.faces.context.FacesContext;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.Query;
+import jakarta.servlet.ServletOutputStream;
+import jakarta.servlet.http.HttpServletResponse;
import org.primefaces.PrimeFaces;
//import org.primefaces.context.RequestContext;
diff --git a/src/main/java/edu/harvard/iq/dataverse/FileMetadata.java b/src/main/java/edu/harvard/iq/dataverse/FileMetadata.java
index 01131bdca01..461c8b14e46 100644
--- a/src/main/java/edu/harvard/iq/dataverse/FileMetadata.java
+++ b/src/main/java/edu/harvard/iq/dataverse/FileMetadata.java
@@ -22,24 +22,24 @@
import java.util.Map;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.CascadeType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.JoinTable;
-import javax.persistence.ManyToMany;
-import javax.persistence.ManyToOne;
-import javax.persistence.OneToMany;
-import javax.persistence.OrderBy;
-import javax.persistence.Table;
-import javax.persistence.Transient;
-import javax.persistence.Version;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.JoinTable;
+import jakarta.persistence.ManyToMany;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.OneToMany;
+import jakarta.persistence.OrderBy;
+import jakarta.persistence.Table;
+import jakarta.persistence.Transient;
+import jakarta.persistence.Version;
import edu.harvard.iq.dataverse.datavariable.CategoryMetadata;
import edu.harvard.iq.dataverse.datavariable.DataVariable;
@@ -49,12 +49,12 @@
import edu.harvard.iq.dataverse.util.StringUtil;
import java.util.HashSet;
import java.util.Set;
-import javax.validation.ConstraintViolation;
-import javax.validation.Validation;
-import javax.validation.Validator;
-import javax.validation.ValidatorFactory;
+import jakarta.validation.ConstraintViolation;
+import jakarta.validation.Validation;
+import jakarta.validation.Validator;
+import jakarta.validation.ValidatorFactory;
import org.hibernate.validator.constraints.NotBlank;
-import javax.validation.constraints.Pattern;
+import jakarta.validation.constraints.Pattern;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/FilePage.java b/src/main/java/edu/harvard/iq/dataverse/FilePage.java
index bee5ce20339..49c904c3ac3 100644
--- a/src/main/java/edu/harvard/iq/dataverse/FilePage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/FilePage.java
@@ -30,8 +30,6 @@
import edu.harvard.iq.dataverse.externaltools.ExternalToolServiceBean;
import edu.harvard.iq.dataverse.makedatacount.MakeDataCountLoggingServiceBean;
import edu.harvard.iq.dataverse.makedatacount.MakeDataCountLoggingServiceBean.MakeDataCountEntry;
-import edu.harvard.iq.dataverse.makedatacount.MakeDataCountUtil;
-import edu.harvard.iq.dataverse.privateurl.PrivateUrl;
import edu.harvard.iq.dataverse.privateurl.PrivateUrlServiceBean;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
import edu.harvard.iq.dataverse.util.BundleUtil;
@@ -39,9 +37,8 @@
import edu.harvard.iq.dataverse.util.JsfHelper;
import static edu.harvard.iq.dataverse.util.JsfHelper.JH;
import edu.harvard.iq.dataverse.util.SystemConfig;
-import edu.harvard.iq.dataverse.util.json.JsonUtil;
+
import java.io.IOException;
-import java.time.format.DateTimeFormatter;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
@@ -49,19 +46,19 @@
import java.util.List;
import java.util.Set;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.faces.application.FacesMessage;
-import javax.faces.component.UIComponent;
-import javax.faces.context.FacesContext;
-import javax.faces.validator.ValidatorException;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
-import javax.json.JsonArray;
-import javax.json.JsonObject;
-import javax.json.JsonValue;
-import javax.validation.ConstraintViolation;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.validator.ValidatorException;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonValue;
+import jakarta.validation.ConstraintViolation;
import org.primefaces.PrimeFaces;
import org.primefaces.component.tabview.TabView;
@@ -1249,4 +1246,13 @@ public boolean isHasPublicStore() {
return settingsWrapper.isTrueForKey(SettingsServiceBean.Key.PublicInstall, StorageIO.isPublicStore(DataAccess.getStorageDriverFromIdentifier(file.getStorageIdentifier())));
}
+ /**
+ * This method only exists because in file-edit-button-fragment.xhtml we
+ * call bean.editFileMetadata() and we need both FilePage (this bean) and
+ * DatasetPage to have the method defined to prevent errors in server.log.
+ */
+ public String editFileMetadata(){
+ return "";
+ }
+
}
diff --git a/src/main/java/edu/harvard/iq/dataverse/FileUploadRenderer.java b/src/main/java/edu/harvard/iq/dataverse/FileUploadRenderer.java
index 5e73ef65f25..ce3b0d65875 100644
--- a/src/main/java/edu/harvard/iq/dataverse/FileUploadRenderer.java
+++ b/src/main/java/edu/harvard/iq/dataverse/FileUploadRenderer.java
@@ -6,8 +6,8 @@
package edu.harvard.iq.dataverse;
-import javax.faces.component.UIComponent;
-import javax.faces.context.FacesContext;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.context.FacesContext;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/ForeignMetadataFieldMapping.java b/src/main/java/edu/harvard/iq/dataverse/ForeignMetadataFieldMapping.java
index 40d219d2638..db83ab953a1 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ForeignMetadataFieldMapping.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ForeignMetadataFieldMapping.java
@@ -3,13 +3,8 @@
package edu.harvard.iq.dataverse;
import java.io.Serializable;
-import javax.persistence.*;
+import jakarta.persistence.*;
import java.util.Collection;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeMap;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/ForeignMetadataFormatMapping.java b/src/main/java/edu/harvard/iq/dataverse/ForeignMetadataFormatMapping.java
index 0fac75257c8..eb7b97b1a84 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ForeignMetadataFormatMapping.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ForeignMetadataFormatMapping.java
@@ -7,18 +7,18 @@
package edu.harvard.iq.dataverse;
import java.io.Serializable;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
import java.util.List;
-import javax.persistence.CascadeType;
-import javax.persistence.Column;
-import javax.persistence.Index;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.OneToMany;
-import javax.persistence.Table;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Index;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.OneToMany;
+import jakarta.persistence.Table;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/Guestbook.java b/src/main/java/edu/harvard/iq/dataverse/Guestbook.java
index 18913bfd5bf..2ef23d1f925 100644
--- a/src/main/java/edu/harvard/iq/dataverse/Guestbook.java
+++ b/src/main/java/edu/harvard/iq/dataverse/Guestbook.java
@@ -3,27 +3,25 @@
import edu.harvard.iq.dataverse.util.BundleUtil;
import java.io.Serializable;
-import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Date;
-import javax.persistence.CascadeType;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.OneToMany;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.OneToMany;
import java.util.List;
import java.util.Objects;
-import javax.persistence.Column;
-import javax.persistence.ManyToOne;
-import javax.persistence.OrderBy;
-import javax.persistence.Temporal;
-import javax.persistence.TemporalType;
-import javax.persistence.Transient;
+import jakarta.persistence.Column;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.OrderBy;
+import jakarta.persistence.Temporal;
+import jakarta.persistence.TemporalType;
+import jakarta.persistence.Transient;
import edu.harvard.iq.dataverse.util.DateUtil;
-import org.apache.commons.text.StringEscapeUtils;
import org.hibernate.validator.constraints.NotBlank;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/GuestbookPage.java b/src/main/java/edu/harvard/iq/dataverse/GuestbookPage.java
index 7cbb69e5c1d..9fb584a9133 100644
--- a/src/main/java/edu/harvard/iq/dataverse/GuestbookPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/GuestbookPage.java
@@ -17,13 +17,13 @@
import java.util.Iterator;
import java.util.List;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.faces.application.FacesMessage;
-import javax.faces.context.FacesContext;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
import org.apache.commons.lang3.StringUtils;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/GuestbookResponse.java b/src/main/java/edu/harvard/iq/dataverse/GuestbookResponse.java
index 69404482fce..0057fbeddab 100644
--- a/src/main/java/edu/harvard/iq/dataverse/GuestbookResponse.java
+++ b/src/main/java/edu/harvard/iq/dataverse/GuestbookResponse.java
@@ -13,8 +13,8 @@
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
-import javax.persistence.*;
-import javax.validation.constraints.Size;
+import jakarta.persistence.*;
+import jakarta.validation.constraints.Size;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/GuestbookResponseServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/GuestbookResponseServiceBean.java
index 2f795a4da74..bd598d2dca0 100644
--- a/src/main/java/edu/harvard/iq/dataverse/GuestbookResponseServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/GuestbookResponseServiceBean.java
@@ -21,17 +21,17 @@
import java.util.List;
import java.util.Map;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.ejb.TransactionAttribute;
-import javax.ejb.TransactionAttributeType;
-import javax.faces.model.SelectItem;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.persistence.Query;
-import javax.persistence.StoredProcedureQuery;
-import javax.persistence.TypedQuery;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.ejb.TransactionAttribute;
+import jakarta.ejb.TransactionAttributeType;
+import jakarta.faces.model.SelectItem;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.Query;
+import jakarta.persistence.StoredProcedureQuery;
+import jakarta.persistence.TypedQuery;
import org.apache.commons.text.StringEscapeUtils;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/GuestbookResponsesPage.java b/src/main/java/edu/harvard/iq/dataverse/GuestbookResponsesPage.java
index 23aac4a24a3..c53df93def8 100644
--- a/src/main/java/edu/harvard/iq/dataverse/GuestbookResponsesPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/GuestbookResponsesPage.java
@@ -6,20 +6,19 @@
package edu.harvard.iq.dataverse;
import edu.harvard.iq.dataverse.engine.command.impl.UpdateDataverseCommand;
-import static edu.harvard.iq.dataverse.util.JsfHelper.JH;
import edu.harvard.iq.dataverse.util.BundleUtil;
import edu.harvard.iq.dataverse.util.SystemConfig;
import java.util.List;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.faces.application.FacesMessage;
-import javax.faces.context.FacesContext;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
-import javax.servlet.ServletOutputStream;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.ejb.EJB;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
+import jakarta.servlet.ServletOutputStream;
+import jakarta.servlet.http.HttpServletResponse;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/GuestbookServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/GuestbookServiceBean.java
index 5394ddc652a..fcd4e91d455 100644
--- a/src/main/java/edu/harvard/iq/dataverse/GuestbookServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/GuestbookServiceBean.java
@@ -5,12 +5,11 @@
*/
package edu.harvard.iq.dataverse;
-import java.util.List;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.persistence.Query;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.Query;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/HandlenetServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/HandlenetServiceBean.java
index d2149a3072a..4942db9e7ec 100644
--- a/src/main/java/edu/harvard/iq/dataverse/HandlenetServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/HandlenetServiceBean.java
@@ -29,8 +29,8 @@
import java.util.*;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
import java.security.PrivateKey;
/* Handlenet imports: */
diff --git a/src/main/java/edu/harvard/iq/dataverse/HarvestingClientsPage.java b/src/main/java/edu/harvard/iq/dataverse/HarvestingClientsPage.java
index 5be7578f7f8..f008db1403f 100644
--- a/src/main/java/edu/harvard/iq/dataverse/HarvestingClientsPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/HarvestingClientsPage.java
@@ -27,17 +27,17 @@
import java.util.logging.Level;
import java.util.logging.Logger;
import java.util.regex.Pattern;
-import javax.ejb.EJB;
-import javax.faces.application.FacesMessage;
-import javax.faces.component.UIComponent;
-import javax.faces.component.UIInput;
-import javax.faces.context.FacesContext;
-import javax.faces.event.ActionEvent;
-import javax.faces.model.SelectItem;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
-import javax.servlet.http.HttpServletRequest;
+import jakarta.ejb.EJB;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.component.UIInput;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.event.ActionEvent;
+import jakarta.faces.model.SelectItem;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
+import jakarta.servlet.http.HttpServletRequest;
import org.apache.commons.lang3.StringUtils;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/HarvestingDataverseConfig.java b/src/main/java/edu/harvard/iq/dataverse/HarvestingDataverseConfig.java
index 28df6e19e65..6709b978c47 100644
--- a/src/main/java/edu/harvard/iq/dataverse/HarvestingDataverseConfig.java
+++ b/src/main/java/edu/harvard/iq/dataverse/HarvestingDataverseConfig.java
@@ -6,16 +6,16 @@
package edu.harvard.iq.dataverse;
import java.io.Serializable;
-import javax.persistence.CascadeType;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.OneToOne;
-import javax.persistence.Table;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.OneToOne;
+import jakarta.persistence.Table;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/HarvestingSetsPage.java b/src/main/java/edu/harvard/iq/dataverse/HarvestingSetsPage.java
index 432683a5797..6dbba34920b 100644
--- a/src/main/java/edu/harvard/iq/dataverse/HarvestingSetsPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/HarvestingSetsPage.java
@@ -6,11 +6,6 @@
package edu.harvard.iq.dataverse;
import edu.harvard.iq.dataverse.authorization.AuthenticationServiceBean;
-import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
-import edu.harvard.iq.dataverse.engine.command.impl.CreateHarvestingClientCommand;
-import edu.harvard.iq.dataverse.engine.command.impl.UpdateHarvestingClientCommand;
-import edu.harvard.iq.dataverse.harvest.client.HarvestingClient;
-import edu.harvard.iq.dataverse.harvest.client.HarvestingClientServiceBean;
import edu.harvard.iq.dataverse.harvest.server.OAIRecord;
import edu.harvard.iq.dataverse.harvest.server.OAIRecordServiceBean;
import edu.harvard.iq.dataverse.harvest.server.OAISet;
@@ -26,15 +21,15 @@
import java.util.logging.Level;
import java.util.logging.Logger;
import java.util.regex.Pattern;
-import javax.ejb.EJB;
-import javax.faces.application.FacesMessage;
-import javax.faces.component.UIComponent;
-import javax.faces.component.UIInput;
-import javax.faces.context.FacesContext;
-import javax.faces.event.ActionEvent;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.component.UIInput;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.event.ActionEvent;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
import org.apache.commons.lang3.StringUtils;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/HomepageServlet.java b/src/main/java/edu/harvard/iq/dataverse/HomepageServlet.java
index ef9b3267db4..e1864194436 100644
--- a/src/main/java/edu/harvard/iq/dataverse/HomepageServlet.java
+++ b/src/main/java/edu/harvard/iq/dataverse/HomepageServlet.java
@@ -7,12 +7,12 @@
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
import java.io.IOException;
-import javax.ejb.EJB;
-import javax.servlet.RequestDispatcher;
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServlet;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.ejb.EJB;
+import jakarta.servlet.RequestDispatcher;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.http.HttpServlet;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/LinkValidator.java b/src/main/java/edu/harvard/iq/dataverse/LinkValidator.java
index 2ecfc55f67e..7d540f0a425 100644
--- a/src/main/java/edu/harvard/iq/dataverse/LinkValidator.java
+++ b/src/main/java/edu/harvard/iq/dataverse/LinkValidator.java
@@ -5,13 +5,13 @@
*/
package edu.harvard.iq.dataverse;
-import javax.faces.application.FacesMessage;
-import javax.faces.component.UIComponent;
-import javax.faces.component.UIInput;
-import javax.faces.context.FacesContext;
-import javax.faces.validator.FacesValidator;
-import javax.faces.validator.Validator;
-import javax.faces.validator.ValidatorException;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.component.UIInput;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.validator.FacesValidator;
+import jakarta.faces.validator.Validator;
+import jakarta.faces.validator.ValidatorException;
import edu.harvard.iq.dataverse.util.BundleUtil;
@FacesValidator(value = "linkValidator")
diff --git a/src/main/java/edu/harvard/iq/dataverse/LoginPage.java b/src/main/java/edu/harvard/iq/dataverse/LoginPage.java
index 2420ce08550..16d2cc53cb9 100644
--- a/src/main/java/edu/harvard/iq/dataverse/LoginPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/LoginPage.java
@@ -9,30 +9,27 @@
import edu.harvard.iq.dataverse.authorization.exceptions.AuthenticationFailedException;
import edu.harvard.iq.dataverse.authorization.providers.builtin.BuiltinAuthenticationProvider;
import edu.harvard.iq.dataverse.authorization.providers.builtin.BuiltinUserServiceBean;
-import edu.harvard.iq.dataverse.authorization.providers.shib.ShibAuthenticationProvider;
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
import edu.harvard.iq.dataverse.util.BundleUtil;
import edu.harvard.iq.dataverse.util.JsfHelper;
-import edu.harvard.iq.dataverse.util.SessionUtil;
-import static edu.harvard.iq.dataverse.util.JsfHelper.JH;
import edu.harvard.iq.dataverse.util.SystemConfig;
import java.io.UnsupportedEncodingException;
import java.net.URLDecoder;
import java.util.*;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.faces.application.FacesMessage;
-import javax.faces.component.UIComponent;
-import javax.faces.context.FacesContext;
-import javax.faces.event.AjaxBehaviorEvent;
-import javax.faces.validator.ValidatorException;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
-import javax.servlet.http.HttpServletRequest;
+import jakarta.ejb.EJB;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.event.AjaxBehaviorEvent;
+import jakarta.faces.validator.ValidatorException;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
+import jakarta.servlet.http.HttpServletRequest;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/MailServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/MailServiceBean.java
index bc7b34ee8b7..f17732df7b6 100644
--- a/src/main/java/edu/harvard/iq/dataverse/MailServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/MailServiceBean.java
@@ -5,7 +5,6 @@
*/
package edu.harvard.iq.dataverse;
-import com.sun.mail.smtp.SMTPSendFailedException;
import edu.harvard.iq.dataverse.authorization.groups.Group;
import edu.harvard.iq.dataverse.authorization.groups.GroupServiceBean;
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
@@ -24,25 +23,23 @@
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
-import java.util.Properties;
-import java.util.Map;
-import java.util.HashMap;
import java.util.List;
import java.util.Set;
import java.util.logging.Logger;
-import javax.annotation.Resource;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.mail.Address;
-import javax.mail.Message;
-import javax.mail.MessagingException;
-import javax.mail.Session;
-import javax.mail.Transport;
-import javax.mail.internet.AddressException;
-import javax.mail.internet.InternetAddress;
-import javax.mail.internet.MimeMessage;
+import jakarta.annotation.Resource;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.mail.Address;
+import jakarta.mail.Message;
+import jakarta.mail.MessagingException;
+import jakarta.mail.Session;
+import jakarta.mail.Transport;
+import jakarta.mail.internet.AddressException;
+import jakarta.mail.internet.InternetAddress;
+import jakarta.mail.internet.MimeMessage;
import edu.harvard.iq.dataverse.validation.EMailValidator;
+import jakarta.json.JsonObject;
import org.apache.commons.lang3.StringUtils;
/**
@@ -124,9 +121,9 @@ public boolean sendSystemEmail(String to, String subject, String messageText, bo
try {
Transport.send(msg, recipients);
sent = true;
- } catch (SMTPSendFailedException ssfe) {
+ } catch (MessagingException ssfe) {
logger.warning("Failed to send mail to: " + to);
- logger.warning("SMTPSendFailedException Message: " + ssfe);
+ logger.warning("MessagingException Message: " + ssfe);
}
} else {
logger.fine("Skipping sending mail to " + to + ", because the \"no-reply\" address not set (" + Key.SystemEmail + " setting).");
@@ -616,7 +613,7 @@ public String getMessageTextBasedOnNotification(UserNotification userNotificatio
case DATASETMENTIONED:
String additionalInfo = userNotification.getAdditionalInfo();
dataset = (Dataset) targetObject;
- javax.json.JsonObject citingResource = null;
+ JsonObject citingResource = null;
citingResource = JsonUtil.getJsonObject(additionalInfo);
diff --git a/src/main/java/edu/harvard/iq/dataverse/ManageFilePermissionsPage.java b/src/main/java/edu/harvard/iq/dataverse/ManageFilePermissionsPage.java
index fd309790026..1b4af29c915 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ManageFilePermissionsPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ManageFilePermissionsPage.java
@@ -12,7 +12,6 @@
import edu.harvard.iq.dataverse.authorization.Permission;
import edu.harvard.iq.dataverse.authorization.RoleAssignee;
import edu.harvard.iq.dataverse.authorization.RoleAssigneeDisplayInfo;
-import edu.harvard.iq.dataverse.authorization.groups.Group;
import edu.harvard.iq.dataverse.authorization.groups.GroupServiceBean;
import edu.harvard.iq.dataverse.authorization.groups.impl.explicit.ExplicitGroupServiceBean;
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
@@ -28,14 +27,14 @@
import java.util.*;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.faces.application.FacesMessage;
-import javax.faces.event.ActionEvent;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
+import jakarta.ejb.EJB;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.event.ActionEvent;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
import org.apache.commons.lang3.ObjectUtils;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/ManageGroupsPage.java b/src/main/java/edu/harvard/iq/dataverse/ManageGroupsPage.java
index 8513ca33b47..583e195ab0d 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ManageGroupsPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ManageGroupsPage.java
@@ -22,17 +22,17 @@
import java.util.logging.Level;
import java.util.logging.Logger;
import java.util.regex.Pattern;
-import javax.ejb.EJB;
-import javax.faces.application.FacesMessage;
-import javax.faces.component.UIComponent;
-import javax.faces.component.UIInput;
-import javax.faces.context.FacesContext;
-import javax.faces.event.ActionEvent;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
+import jakarta.ejb.EJB;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.component.UIInput;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.event.ActionEvent;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
import org.apache.commons.lang3.StringUtils;
diff --git a/src/main/java/edu/harvard/iq/dataverse/ManageGuestbooksPage.java b/src/main/java/edu/harvard/iq/dataverse/ManageGuestbooksPage.java
index 7db0ecc0767..cc89cfd9d56 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ManageGuestbooksPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ManageGuestbooksPage.java
@@ -11,17 +11,19 @@
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.faces.application.FacesMessage;
-import javax.faces.context.FacesContext;
-import javax.faces.event.ActionEvent;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.servlet.ServletOutputStream;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.ejb.EJB;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.event.AbortProcessingException;
+import jakarta.faces.event.ActionEvent;
+import jakarta.faces.event.AjaxBehaviorEvent;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.servlet.ServletOutputStream;
+import jakarta.servlet.http.HttpServletResponse;
/**
*
@@ -325,7 +327,7 @@ public void setDisplayDownloadAll(boolean displayDownloadAll) {
this.displayDownloadAll = displayDownloadAll;
}
- public String updateGuestbooksRoot(javax.faces.event.AjaxBehaviorEvent event) throws javax.faces.event.AbortProcessingException {
+ public String updateGuestbooksRoot(AjaxBehaviorEvent event) throws AbortProcessingException {
try {
dataverse = engineService.submit(
new UpdateDataverseGuestbookRootCommand(!isInheritGuestbooksValue(),
diff --git a/src/main/java/edu/harvard/iq/dataverse/ManagePermissionsPage.java b/src/main/java/edu/harvard/iq/dataverse/ManagePermissionsPage.java
index e71e04bc42f..bf78b9d088f 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ManagePermissionsPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ManagePermissionsPage.java
@@ -29,18 +29,17 @@
import java.util.Date;
import java.util.LinkedList;
import java.util.List;
-import java.util.ResourceBundle;
import java.util.Set;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.faces.application.FacesMessage;
-import javax.faces.event.ActionEvent;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
+import jakarta.ejb.EJB;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.event.ActionEvent;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
import org.apache.commons.text.StringEscapeUtils;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/ManageTemplatesPage.java b/src/main/java/edu/harvard/iq/dataverse/ManageTemplatesPage.java
index 37ee7948a14..98369a2eab3 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ManageTemplatesPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ManageTemplatesPage.java
@@ -14,15 +14,17 @@
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.faces.application.FacesMessage;
-import javax.faces.event.ActionEvent;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
+import jakarta.ejb.EJB;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.event.ActionEvent;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
import edu.harvard.iq.dataverse.util.BundleUtil;
+import jakarta.faces.event.AbortProcessingException;
+import jakarta.faces.event.AjaxBehaviorEvent;
/**
*
* @author skraffmiller
@@ -237,7 +239,7 @@ public void viewSelectedTemplate(Template selectedTemplate) {
tempPage.setTemplate(selectedTemplate);
}
- public String updateTemplatesRoot(javax.faces.event.AjaxBehaviorEvent event) throws javax.faces.event.AbortProcessingException {
+ public String updateTemplatesRoot(AjaxBehaviorEvent event) throws AbortProcessingException {
try {
if (dataverse.getOwner() != null) {
if (isInheritTemplatesValue() && dataverse.getDefaultTemplate() == null && dataverse.getOwner().getDefaultTemplate() != null) {
diff --git a/src/main/java/edu/harvard/iq/dataverse/MetadataBlock.java b/src/main/java/edu/harvard/iq/dataverse/MetadataBlock.java
index 33e75efffb5..0fd7c2efbc7 100644
--- a/src/main/java/edu/harvard/iq/dataverse/MetadataBlock.java
+++ b/src/main/java/edu/harvard/iq/dataverse/MetadataBlock.java
@@ -8,21 +8,21 @@
import java.util.List;
import java.util.MissingResourceException;
import java.util.Objects;
-import javax.persistence.CascadeType;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.OneToMany;
-import javax.persistence.OneToOne;
-import javax.persistence.OrderBy;
-import javax.persistence.Table;
-import javax.persistence.Transient;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.OneToMany;
+import jakarta.persistence.OneToOne;
+import jakarta.persistence.OrderBy;
+import jakarta.persistence.Table;
+import jakarta.persistence.Transient;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/MetadataBlockConverter.java b/src/main/java/edu/harvard/iq/dataverse/MetadataBlockConverter.java
index c5bd48ae785..49c50e82efb 100644
--- a/src/main/java/edu/harvard/iq/dataverse/MetadataBlockConverter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/MetadataBlockConverter.java
@@ -5,13 +5,13 @@
*/
package edu.harvard.iq.dataverse;
-import javax.ejb.EJB;
-import javax.enterprise.inject.spi.CDI;
+import jakarta.ejb.EJB;
+import jakarta.enterprise.inject.spi.CDI;
-import javax.faces.component.UIComponent;
-import javax.faces.context.FacesContext;
-import javax.faces.convert.Converter;
-import javax.faces.convert.FacesConverter;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.convert.Converter;
+import jakarta.faces.convert.FacesConverter;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/MetadataBlockServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/MetadataBlockServiceBean.java
index f34637dbfaf..bb6daa264ba 100644
--- a/src/main/java/edu/harvard/iq/dataverse/MetadataBlockServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/MetadataBlockServiceBean.java
@@ -1,11 +1,11 @@
package edu.harvard.iq.dataverse;
import java.util.List;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
-import javax.persistence.PersistenceContext;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.PersistenceContext;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/Metric.java b/src/main/java/edu/harvard/iq/dataverse/Metric.java
index 5526604f77c..0e71ab44db4 100644
--- a/src/main/java/edu/harvard/iq/dataverse/Metric.java
+++ b/src/main/java/edu/harvard/iq/dataverse/Metric.java
@@ -5,21 +5,20 @@
*/
package edu.harvard.iq.dataverse;
-import java.io.IOException;
import java.io.Serializable;
import java.sql.Timestamp;
import java.util.Date;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-import javax.persistence.Temporal;
-import javax.persistence.TemporalType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Table;
+import jakarta.persistence.Temporal;
+import jakarta.persistence.TemporalType;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/NavigationWrapper.java b/src/main/java/edu/harvard/iq/dataverse/NavigationWrapper.java
index 37a11396f37..832d7ec19ef 100644
--- a/src/main/java/edu/harvard/iq/dataverse/NavigationWrapper.java
+++ b/src/main/java/edu/harvard/iq/dataverse/NavigationWrapper.java
@@ -14,12 +14,12 @@
import java.util.Map;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.faces.context.FacesContext;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
import org.apache.commons.lang3.StringUtils;
/**
@@ -96,7 +96,8 @@ private String sendError(int errorCode) {
try {
context.getExternalContext().responseSendError(errorCode,null);
} catch (IOException ex) {
- Logger.getLogger(PermissionsWrapper.class.getName()).log(Level.SEVERE, null, ex);
+ //Logger.getLogger(PermissionsWrapper.class.getName()).log(Level.SEVERE, null, ex);
+ Logger.getLogger(NavigationWrapper.class.getName()).fine("Caught exception in sendError(): "+ex.getMessage());
}
context.responseComplete();
return "";
diff --git a/src/main/java/edu/harvard/iq/dataverse/PackagePopupFragmentBean.java b/src/main/java/edu/harvard/iq/dataverse/PackagePopupFragmentBean.java
index fac2abeddb8..0c5218fb927 100644
--- a/src/main/java/edu/harvard/iq/dataverse/PackagePopupFragmentBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/PackagePopupFragmentBean.java
@@ -6,8 +6,8 @@
package edu.harvard.iq.dataverse;
-import javax.faces.view.ViewScoped;
-import javax.inject.Named;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Named;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/PermissionServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/PermissionServiceBean.java
index 8c0a0bf90b0..a1de33a764e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/PermissionServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/PermissionServiceBean.java
@@ -1,6 +1,5 @@
package edu.harvard.iq.dataverse;
-import edu.harvard.iq.dataverse.DatasetLock.Reason;
import edu.harvard.iq.dataverse.authorization.AuthenticationServiceBean;
import edu.harvard.iq.dataverse.authorization.DataverseRole;
import edu.harvard.iq.dataverse.authorization.providers.builtin.BuiltinUserServiceBean;
@@ -17,14 +16,14 @@
import java.util.Map;
import java.util.Set;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
import java.util.HashSet;
import java.util.List;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
import static edu.harvard.iq.dataverse.engine.command.CommandHelper.CH;
import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
import edu.harvard.iq.dataverse.engine.command.exception.IllegalCommandException;
@@ -41,7 +40,7 @@
import java.util.logging.Level;
import java.util.stream.Collectors;
import static java.util.stream.Collectors.toList;
-import javax.persistence.Query;
+import jakarta.persistence.Query;
/**
* Your one-stop-shop for deciding which user can do what action on which
diff --git a/src/main/java/edu/harvard/iq/dataverse/PermissionsWrapper.java b/src/main/java/edu/harvard/iq/dataverse/PermissionsWrapper.java
index 4ee45fc85a1..5ce9edb3a9e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/PermissionsWrapper.java
+++ b/src/main/java/edu/harvard/iq/dataverse/PermissionsWrapper.java
@@ -14,10 +14,10 @@
import java.util.HashMap;
import java.util.Map;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/RoleAssigneeConverter.java b/src/main/java/edu/harvard/iq/dataverse/RoleAssigneeConverter.java
index a5e4cebbd95..0d863f47324 100644
--- a/src/main/java/edu/harvard/iq/dataverse/RoleAssigneeConverter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/RoleAssigneeConverter.java
@@ -7,13 +7,13 @@
package edu.harvard.iq.dataverse;
import edu.harvard.iq.dataverse.authorization.RoleAssignee;
-import javax.ejb.EJB;
-import javax.enterprise.inject.spi.CDI;
+import jakarta.ejb.EJB;
+import jakarta.enterprise.inject.spi.CDI;
-import javax.faces.component.UIComponent;
-import javax.faces.context.FacesContext;
-import javax.faces.convert.Converter;
-import javax.faces.convert.FacesConverter;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.convert.Converter;
+import jakarta.faces.convert.FacesConverter;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/RoleAssigneeServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/RoleAssigneeServiceBean.java
index c6f2b7f28a5..059d5a8ffd3 100644
--- a/src/main/java/edu/harvard/iq/dataverse/RoleAssigneeServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/RoleAssigneeServiceBean.java
@@ -21,12 +21,12 @@
import java.util.TreeMap;
import java.util.logging.Logger;
import java.util.stream.Collectors;
-import javax.annotation.PostConstruct;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
+import jakarta.annotation.PostConstruct;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
import org.apache.commons.lang3.StringUtils;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/RoleAssignment.java b/src/main/java/edu/harvard/iq/dataverse/RoleAssignment.java
index f053a449da4..df004fe1357 100644
--- a/src/main/java/edu/harvard/iq/dataverse/RoleAssignment.java
+++ b/src/main/java/edu/harvard/iq/dataverse/RoleAssignment.java
@@ -3,19 +3,19 @@
import edu.harvard.iq.dataverse.authorization.DataverseRole;
import edu.harvard.iq.dataverse.authorization.RoleAssignee;
import java.util.Objects;
-import javax.persistence.CascadeType;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.Table;
-import javax.persistence.UniqueConstraint;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.Table;
+import jakarta.persistence.UniqueConstraint;
/**
* A role of a user in a Dataverse. A User may have many roles in a given Dataverse.
diff --git a/src/main/java/edu/harvard/iq/dataverse/RolePermissionFragment.java b/src/main/java/edu/harvard/iq/dataverse/RolePermissionFragment.java
index dd3044d3749..1bd337452c2 100644
--- a/src/main/java/edu/harvard/iq/dataverse/RolePermissionFragment.java
+++ b/src/main/java/edu/harvard/iq/dataverse/RolePermissionFragment.java
@@ -26,16 +26,18 @@
import java.util.Set;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.faces.application.FacesMessage;
-import javax.faces.event.ActionEvent;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
+import jakarta.ejb.EJB;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.event.ActionEvent;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
import edu.harvard.iq.dataverse.util.BundleUtil;
+import jakarta.faces.event.AbortProcessingException;
+import jakarta.faces.event.AjaxBehaviorEvent;
import org.apache.commons.text.StringEscapeUtils;
import org.apache.commons.lang3.StringUtils;
@@ -92,7 +94,7 @@ public void setInheritAssignments(boolean inheritAssignments) {
this.inheritAssignments = inheritAssignments;
}
- public void updatePermissionRoot(javax.faces.event.AjaxBehaviorEvent event) throws javax.faces.event.AbortProcessingException {
+ public void updatePermissionRoot(AjaxBehaviorEvent event) throws AbortProcessingException {
try {
dvObject = commandEngine.submit(
new UpdatePermissionRootCommand(!inheritAssignments,
diff --git a/src/main/java/edu/harvard/iq/dataverse/S3PackageImporter.java b/src/main/java/edu/harvard/iq/dataverse/S3PackageImporter.java
index a099f5f3939..71318a0184a 100644
--- a/src/main/java/edu/harvard/iq/dataverse/S3PackageImporter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/S3PackageImporter.java
@@ -17,9 +17,6 @@
import com.amazonaws.services.s3.model.S3Object;
import com.amazonaws.services.s3.model.S3ObjectSummary;
import edu.harvard.iq.dataverse.api.AbstractApiBean;
-import edu.harvard.iq.dataverse.batch.jobs.importer.filesystem.FileRecordWriter;
-import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
-import edu.harvard.iq.dataverse.engine.command.exception.IllegalCommandException;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
import edu.harvard.iq.dataverse.util.FileUtil;
import java.io.BufferedReader;
@@ -31,9 +28,9 @@
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
/**
* This class is for importing files added to s3 outside of dataverse.
diff --git a/src/main/java/edu/harvard/iq/dataverse/SendFeedbackDialog.java b/src/main/java/edu/harvard/iq/dataverse/SendFeedbackDialog.java
index 13a7cc51357..6be768321c4 100644
--- a/src/main/java/edu/harvard/iq/dataverse/SendFeedbackDialog.java
+++ b/src/main/java/edu/harvard/iq/dataverse/SendFeedbackDialog.java
@@ -11,16 +11,16 @@
import java.util.Optional;
import java.util.Random;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.faces.application.FacesMessage;
-import javax.faces.component.UIComponent;
-import javax.faces.context.FacesContext;
-import javax.faces.event.ActionEvent;
-import javax.faces.validator.ValidatorException;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
-import javax.mail.internet.InternetAddress;
+import jakarta.ejb.EJB;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.event.ActionEvent;
+import jakarta.faces.validator.ValidatorException;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
+import jakarta.mail.internet.InternetAddress;
import org.apache.commons.validator.routines.EmailValidator;
@ViewScoped
diff --git a/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java b/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java
index 14b429f3219..307301049f0 100644
--- a/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java
+++ b/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java
@@ -27,17 +27,16 @@
import java.util.logging.Logger;
import java.util.Set;
-import javax.ejb.EJB;
-import javax.faces.application.FacesMessage;
-import javax.faces.component.UIComponent;
-import javax.faces.component.UIInput;
-import javax.faces.context.FacesContext;
-import javax.faces.validator.ValidatorException;
-import javax.faces.view.ViewScoped;
-import javax.inject.Named;
-import javax.json.Json;
-import javax.json.JsonObject;
-import javax.mail.internet.InternetAddress;
+import jakarta.ejb.EJB;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.component.UIInput;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.validator.ValidatorException;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Named;
+import jakarta.json.JsonObject;
+import jakarta.mail.internet.InternetAddress;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/Shib.java b/src/main/java/edu/harvard/iq/dataverse/Shib.java
index 0f0e20aba94..bee1182e248 100644
--- a/src/main/java/edu/harvard/iq/dataverse/Shib.java
+++ b/src/main/java/edu/harvard/iq/dataverse/Shib.java
@@ -25,15 +25,15 @@
import java.util.Date;
import java.util.List;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.faces.application.FacesMessage;
-import javax.faces.context.ExternalContext;
-import javax.faces.context.FacesContext;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
-import javax.servlet.http.HttpServletRequest;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.context.ExternalContext;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
+import jakarta.servlet.http.HttpServletRequest;
@ViewScoped
@Named("Shib")
diff --git a/src/main/java/edu/harvard/iq/dataverse/SuperUserPage.java b/src/main/java/edu/harvard/iq/dataverse/SuperUserPage.java
index cd6d53fd8a8..adf2e7d3010 100644
--- a/src/main/java/edu/harvard/iq/dataverse/SuperUserPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/SuperUserPage.java
@@ -6,11 +6,11 @@
import java.util.concurrent.CancellationException;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.Future;
-import javax.ejb.EJB;
-import javax.enterprise.context.SessionScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
-import javax.json.JsonObjectBuilder;
+import jakarta.ejb.EJB;
+import jakarta.enterprise.context.SessionScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
+import jakarta.json.JsonObjectBuilder;
@SessionScoped
@Named("SuperUserPage")
diff --git a/src/main/java/edu/harvard/iq/dataverse/Template.java b/src/main/java/edu/harvard/iq/dataverse/Template.java
index cc1190d36d9..05c6df51197 100644
--- a/src/main/java/edu/harvard/iq/dataverse/Template.java
+++ b/src/main/java/edu/harvard/iq/dataverse/Template.java
@@ -12,31 +12,31 @@
import java.util.TreeMap;
import java.util.stream.Collectors;
-import javax.json.Json;
-import javax.json.JsonObjectBuilder;
-import javax.json.JsonString;
-import javax.persistence.CascadeType;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.OneToMany;
-import javax.persistence.OneToOne;
-import javax.persistence.Table;
-import javax.persistence.Temporal;
-import javax.persistence.TemporalType;
-import javax.persistence.Transient;
-import javax.validation.constraints.Size;
+import jakarta.json.Json;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.json.JsonString;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.OneToMany;
+import jakarta.persistence.OneToOne;
+import jakarta.persistence.Table;
+import jakarta.persistence.Temporal;
+import jakarta.persistence.TemporalType;
+import jakarta.persistence.Transient;
+import jakarta.validation.constraints.Size;
import edu.harvard.iq.dataverse.util.DateUtil;
import edu.harvard.iq.dataverse.util.json.JsonUtil;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
import org.hibernate.validator.constraints.NotBlank;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/TemplateConverter.java b/src/main/java/edu/harvard/iq/dataverse/TemplateConverter.java
index 98b24f84801..1d855e029ce 100644
--- a/src/main/java/edu/harvard/iq/dataverse/TemplateConverter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/TemplateConverter.java
@@ -6,12 +6,12 @@
package edu.harvard.iq.dataverse;
-import javax.ejb.EJB;
-import javax.enterprise.inject.spi.CDI;
-import javax.faces.component.UIComponent;
-import javax.faces.context.FacesContext;
-import javax.faces.convert.Converter;
-import javax.faces.convert.FacesConverter;
+import jakarta.ejb.EJB;
+import jakarta.enterprise.inject.spi.CDI;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.convert.Converter;
+import jakarta.faces.convert.FacesConverter;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/TemplatePage.java b/src/main/java/edu/harvard/iq/dataverse/TemplatePage.java
index 56898943467..fff520fd259 100644
--- a/src/main/java/edu/harvard/iq/dataverse/TemplatePage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/TemplatePage.java
@@ -15,12 +15,12 @@
import java.util.Date;
import java.util.List;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.faces.application.FacesMessage;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/TemplateServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/TemplateServiceBean.java
index f2ac8779d2d..46382fc2588 100644
--- a/src/main/java/edu/harvard/iq/dataverse/TemplateServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/TemplateServiceBean.java
@@ -2,14 +2,13 @@
import edu.harvard.iq.dataverse.search.IndexServiceBean;
import java.util.List;
-import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.persistence.TypedQuery;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.TypedQuery;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/TermsOfUseAndAccess.java b/src/main/java/edu/harvard/iq/dataverse/TermsOfUseAndAccess.java
index a8616283332..ee865770dbe 100644
--- a/src/main/java/edu/harvard/iq/dataverse/TermsOfUseAndAccess.java
+++ b/src/main/java/edu/harvard/iq/dataverse/TermsOfUseAndAccess.java
@@ -6,15 +6,15 @@
package edu.harvard.iq.dataverse;
import java.io.Serializable;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.OneToOne;
-import javax.persistence.Transient;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.OneToOne;
+import jakarta.persistence.Transient;
import edu.harvard.iq.dataverse.license.License;
diff --git a/src/main/java/edu/harvard/iq/dataverse/TermsOfUseAndAccessValidator.java b/src/main/java/edu/harvard/iq/dataverse/TermsOfUseAndAccessValidator.java
index 2cf78db0f03..ca38a305d63 100644
--- a/src/main/java/edu/harvard/iq/dataverse/TermsOfUseAndAccessValidator.java
+++ b/src/main/java/edu/harvard/iq/dataverse/TermsOfUseAndAccessValidator.java
@@ -6,8 +6,8 @@
package edu.harvard.iq.dataverse;
import edu.harvard.iq.dataverse.util.BundleUtil;
-import javax.validation.ConstraintValidator;
-import javax.validation.ConstraintValidatorContext;
+import jakarta.validation.ConstraintValidator;
+import jakarta.validation.ConstraintValidatorContext;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/ThemeWidgetFragment.java b/src/main/java/edu/harvard/iq/dataverse/ThemeWidgetFragment.java
index e270d3842f6..9a62a99722a 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ThemeWidgetFragment.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ThemeWidgetFragment.java
@@ -18,16 +18,16 @@
import java.nio.file.StandardCopyOption;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.annotation.PreDestroy;
-import javax.ejb.EJB;
-import javax.faces.application.FacesMessage;
-import javax.faces.component.UIComponent;
-import javax.faces.component.html.HtmlInputText;
-import javax.faces.context.FacesContext;
-import javax.faces.validator.ValidatorException;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.annotation.PreDestroy;
+import jakarta.ejb.EJB;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.component.html.HtmlInputText;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.validator.ValidatorException;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
import org.apache.commons.lang3.StringUtils;
import org.primefaces.PrimeFaces;
diff --git a/src/main/java/edu/harvard/iq/dataverse/ThumbnailServiceWrapper.java b/src/main/java/edu/harvard/iq/dataverse/ThumbnailServiceWrapper.java
index 6c8db8c124b..319ae06eefb 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ThumbnailServiceWrapper.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ThumbnailServiceWrapper.java
@@ -8,24 +8,21 @@
import edu.harvard.iq.dataverse.dataaccess.DataAccess;
import edu.harvard.iq.dataverse.dataaccess.StorageIO;
import edu.harvard.iq.dataverse.dataaccess.ImageThumbConverter;
-import edu.harvard.iq.dataverse.dataset.DatasetUtil;
+
import static edu.harvard.iq.dataverse.dataset.DatasetUtil.datasetLogoThumbnail;
import edu.harvard.iq.dataverse.search.SolrSearchResult;
import edu.harvard.iq.dataverse.util.FileUtil;
-import java.io.File;
+
import java.io.IOException;
import java.io.InputStream;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
import java.util.Base64;
import java.util.HashMap;
import java.util.Map;
-import javax.ejb.EJB;
-import javax.enterprise.context.RequestScoped;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.enterprise.context.RequestScoped;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
import org.apache.commons.io.IOUtils;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/UserBannerMessage.java b/src/main/java/edu/harvard/iq/dataverse/UserBannerMessage.java
index 7bd4f2d898f..888669ee615 100644
--- a/src/main/java/edu/harvard/iq/dataverse/UserBannerMessage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/UserBannerMessage.java
@@ -4,15 +4,15 @@
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
import java.io.Serializable;
import java.util.Date;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.OneToOne;
-import javax.persistence.Temporal;
-import javax.persistence.TemporalType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.OneToOne;
+import jakarta.persistence.Temporal;
+import jakarta.persistence.TemporalType;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/UserNotification.java b/src/main/java/edu/harvard/iq/dataverse/UserNotification.java
index b68a1b9d13e..a87404b69a7 100644
--- a/src/main/java/edu/harvard/iq/dataverse/UserNotification.java
+++ b/src/main/java/edu/harvard/iq/dataverse/UserNotification.java
@@ -12,17 +12,17 @@
import java.util.Collections;
import java.util.HashSet;
import java.util.stream.Collectors;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.Enumerated;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-import javax.persistence.Transient;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.Enumerated;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Table;
+import jakarta.persistence.Transient;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/UserNotificationServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/UserNotificationServiceBean.java
index 947ee3ce989..a2a71ff8b40 100644
--- a/src/main/java/edu/harvard/iq/dataverse/UserNotificationServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/UserNotificationServiceBean.java
@@ -14,16 +14,16 @@
import java.sql.Timestamp;
import java.util.List;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.ejb.TransactionAttribute;
-import javax.ejb.TransactionAttributeType;
-import javax.inject.Inject;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.persistence.Query;
-import javax.persistence.TypedQuery;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.ejb.TransactionAttribute;
+import jakarta.ejb.TransactionAttributeType;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.Query;
+import jakarta.persistence.TypedQuery;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/UserServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/UserServiceBean.java
index 2d8ecf64f76..93892376edc 100644
--- a/src/main/java/edu/harvard/iq/dataverse/UserServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/UserServiceBean.java
@@ -12,16 +12,15 @@
import java.util.Date;
import java.util.logging.Logger;
import java.util.stream.Collectors;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.ejb.TransactionAttribute;
-import javax.ejb.TransactionAttributeType;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.persistence.Query;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.ejb.TransactionAttribute;
+import jakarta.ejb.TransactionAttributeType;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.Query;
import org.apache.commons.lang3.StringUtils;
-import org.ocpsoft.common.util.Strings;
@Stateless
@Named
@@ -190,7 +189,7 @@ private HashMap> retrieveRolesForUsers(List userO
// Add '@' to each identifier and delimit the list by ","
// -------------------------------------------------
String identifierListString = userIdentifierList.stream()
- .filter(x -> !Strings.isNullOrEmpty(x))
+ .filter(x -> x != null && !x.isEmpty())
.map(x -> "'@" + x + "'")
.collect(Collectors.joining(", "));
diff --git a/src/main/java/edu/harvard/iq/dataverse/ValidateDataFileDirectoryName.java b/src/main/java/edu/harvard/iq/dataverse/ValidateDataFileDirectoryName.java
index 94e33d6220a..9e8ce42491d 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ValidateDataFileDirectoryName.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ValidateDataFileDirectoryName.java
@@ -10,8 +10,8 @@
import java.lang.annotation.Retention;
import static java.lang.annotation.RetentionPolicy.RUNTIME;
import java.lang.annotation.Target;
-import javax.validation.Constraint;
-import javax.validation.Payload;
+import jakarta.validation.Constraint;
+import jakarta.validation.Payload;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/ValidateDatasetFieldType.java b/src/main/java/edu/harvard/iq/dataverse/ValidateDatasetFieldType.java
index ae7b4a1eaef..f36a1d9541e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ValidateDatasetFieldType.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ValidateDatasetFieldType.java
@@ -13,8 +13,8 @@
import java.lang.annotation.Retention;
import java.lang.annotation.Target;
-import javax.validation.Constraint;
-import javax.validation.Payload;
+import jakarta.validation.Constraint;
+import jakarta.validation.Payload;
@Target({TYPE, ANNOTATION_TYPE})
@Retention(RUNTIME)
diff --git a/src/main/java/edu/harvard/iq/dataverse/ValidateTermsOfUseAndAccess.java b/src/main/java/edu/harvard/iq/dataverse/ValidateTermsOfUseAndAccess.java
index 8717d10fc8d..f55e93af674 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ValidateTermsOfUseAndAccess.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ValidateTermsOfUseAndAccess.java
@@ -10,8 +10,8 @@
import java.lang.annotation.Retention;
import static java.lang.annotation.RetentionPolicy.RUNTIME;
import java.lang.annotation.Target;
-import javax.validation.Constraint;
-import javax.validation.Payload;
+import jakarta.validation.Constraint;
+import jakarta.validation.Payload;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/ValidateVersionNote.java b/src/main/java/edu/harvard/iq/dataverse/ValidateVersionNote.java
index 405a7feb52f..c8d64d4a642 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ValidateVersionNote.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ValidateVersionNote.java
@@ -11,8 +11,8 @@
import java.lang.annotation.Retention;
import static java.lang.annotation.RetentionPolicy.RUNTIME;
import java.lang.annotation.Target;
-import javax.validation.Constraint;
-import javax.validation.Payload;
+import jakarta.validation.Constraint;
+import jakarta.validation.Payload;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/WidgetWrapper.java b/src/main/java/edu/harvard/iq/dataverse/WidgetWrapper.java
index 743d8f2d092..a8ea5fabde4 100644
--- a/src/main/java/edu/harvard/iq/dataverse/WidgetWrapper.java
+++ b/src/main/java/edu/harvard/iq/dataverse/WidgetWrapper.java
@@ -5,10 +5,10 @@
*/
package edu.harvard.iq.dataverse;
-import javax.faces.context.FacesContext;
-import javax.faces.view.ViewScoped;
-import javax.inject.Named;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Named;
+import jakarta.servlet.http.HttpServletResponse;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/actionlogging/ActionLogRecord.java b/src/main/java/edu/harvard/iq/dataverse/actionlogging/ActionLogRecord.java
index 31a9ad25e5b..6743c3f2143 100644
--- a/src/main/java/edu/harvard/iq/dataverse/actionlogging/ActionLogRecord.java
+++ b/src/main/java/edu/harvard/iq/dataverse/actionlogging/ActionLogRecord.java
@@ -3,16 +3,16 @@
import java.util.Date;
import java.util.Objects;
import java.util.UUID;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.PrePersist;
-import javax.persistence.Table;
-import javax.persistence.Temporal;
-import javax.persistence.TemporalType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.EnumType;
+import jakarta.persistence.Enumerated;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.PrePersist;
+import jakarta.persistence.Table;
+import jakarta.persistence.Temporal;
+import jakarta.persistence.TemporalType;
/**
* Logs a single action in the action log.
diff --git a/src/main/java/edu/harvard/iq/dataverse/actionlogging/ActionLogServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/actionlogging/ActionLogServiceBean.java
index ba19fdd9eeb..2d16f52bb09 100644
--- a/src/main/java/edu/harvard/iq/dataverse/actionlogging/ActionLogServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/actionlogging/ActionLogServiceBean.java
@@ -1,11 +1,11 @@
package edu.harvard.iq.dataverse.actionlogging;
import java.util.Date;
-import javax.ejb.Stateless;
-import javax.ejb.TransactionAttribute;
-import javax.ejb.TransactionAttributeType;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
+import jakarta.ejb.Stateless;
+import jakarta.ejb.TransactionAttribute;
+import jakarta.ejb.TransactionAttributeType;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
/**
* A service bean that persists {@link ActionLogRecord}s to the DB.
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/AbstractApiBean.java b/src/main/java/edu/harvard/iq/dataverse/api/AbstractApiBean.java
index 6b3e27becb7..5a4c9ab9058 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/AbstractApiBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/AbstractApiBean.java
@@ -57,24 +57,24 @@
import java.util.concurrent.Callable;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.json.Json;
-import javax.json.JsonArray;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
-import javax.json.JsonReader;
-import javax.json.JsonValue;
-import javax.json.JsonValue.ValueType;
-import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
-import javax.persistence.PersistenceContext;
-import javax.servlet.http.HttpServletRequest;
-import javax.ws.rs.container.ContainerRequestContext;
-import javax.ws.rs.core.*;
-import javax.ws.rs.core.Response.ResponseBuilder;
-import javax.ws.rs.core.Response.Status;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.json.Json;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.json.JsonReader;
+import jakarta.json.JsonValue;
+import jakarta.json.JsonValue.ValueType;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.PersistenceContext;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.ws.rs.container.ContainerRequestContext;
+import jakarta.ws.rs.core.*;
+import jakarta.ws.rs.core.Response.ResponseBuilder;
+import jakarta.ws.rs.core.Response.Status;
import static org.apache.commons.lang3.StringUtils.isNumeric;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Access.java b/src/main/java/edu/harvard/iq/dataverse/api/Access.java
index 02441a9ee11..0341f8c1127 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/Access.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/Access.java
@@ -31,7 +31,7 @@
import edu.harvard.iq.dataverse.RoleAssignment;
import edu.harvard.iq.dataverse.UserNotification;
import edu.harvard.iq.dataverse.UserNotificationServiceBean;
-import static edu.harvard.iq.dataverse.api.AbstractApiBean.error;
+
import static edu.harvard.iq.dataverse.api.Datasets.handleVersion;
import edu.harvard.iq.dataverse.api.auth.AuthRequired;
@@ -73,7 +73,7 @@
import edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder;
import java.util.logging.Logger;
-import javax.ejb.EJB;
+import jakarta.ejb.EJB;
import java.io.InputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
@@ -88,47 +88,46 @@
import java.util.List;
import java.util.Properties;
import java.util.logging.Level;
-import javax.inject.Inject;
-import javax.json.Json;
+import jakarta.inject.Inject;
+import jakarta.json.Json;
import java.net.URI;
-import javax.json.JsonArrayBuilder;
-import javax.persistence.TypedQuery;
-
-import javax.ws.rs.GET;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.Produces;
-
-import javax.ws.rs.container.ContainerRequestContext;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.HttpHeaders;
-import javax.ws.rs.core.UriInfo;
-
-
-import javax.servlet.http.HttpServletResponse;
-import javax.ws.rs.BadRequestException;
-import javax.ws.rs.Consumes;
-import javax.ws.rs.DELETE;
-import javax.ws.rs.ForbiddenException;
-import javax.ws.rs.NotFoundException;
-import javax.ws.rs.POST;
-import javax.ws.rs.PUT;
-import javax.ws.rs.QueryParam;
-import javax.ws.rs.ServiceUnavailableException;
-import javax.ws.rs.WebApplicationException;
-import javax.ws.rs.core.Response;
-import static javax.ws.rs.core.Response.Status.BAD_REQUEST;
-import javax.ws.rs.core.StreamingOutput;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.persistence.TypedQuery;
+
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.Produces;
+
+import jakarta.ws.rs.container.ContainerRequestContext;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.HttpHeaders;
+import jakarta.ws.rs.core.UriInfo;
+
+
+import jakarta.servlet.http.HttpServletResponse;
+import jakarta.ws.rs.BadRequestException;
+import jakarta.ws.rs.Consumes;
+import jakarta.ws.rs.DELETE;
+import jakarta.ws.rs.ForbiddenException;
+import jakarta.ws.rs.NotFoundException;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.PUT;
+import jakarta.ws.rs.QueryParam;
+import jakarta.ws.rs.ServiceUnavailableException;
+import jakarta.ws.rs.WebApplicationException;
+import jakarta.ws.rs.core.Response;
+import static jakarta.ws.rs.core.Response.Status.BAD_REQUEST;
+import jakarta.ws.rs.core.StreamingOutput;
import static edu.harvard.iq.dataverse.util.json.JsonPrinter.json;
import java.net.URISyntaxException;
-import java.util.stream.Collectors;
-import java.util.stream.Stream;
-import javax.json.JsonObjectBuilder;
-import javax.ws.rs.RedirectionException;
-import javax.ws.rs.ServerErrorException;
-import javax.ws.rs.core.MediaType;
-import static javax.ws.rs.core.Response.Status.FORBIDDEN;
-import static javax.ws.rs.core.Response.Status.UNAUTHORIZED;
+
+import jakarta.json.JsonObjectBuilder;
+import jakarta.ws.rs.RedirectionException;
+import jakarta.ws.rs.ServerErrorException;
+import jakarta.ws.rs.core.MediaType;
+import static jakarta.ws.rs.core.Response.Status.FORBIDDEN;
+import static jakarta.ws.rs.core.Response.Status.UNAUTHORIZED;
import org.glassfish.jersey.media.multipart.FormDataBodyPart;
import org.glassfish.jersey.media.multipart.FormDataParam;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Admin.java b/src/main/java/edu/harvard/iq/dataverse/api/Admin.java
index 2e98388b4b6..fd3b9a89e54 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/Admin.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/Admin.java
@@ -18,7 +18,6 @@
import edu.harvard.iq.dataverse.settings.JvmSettings;
import edu.harvard.iq.dataverse.validation.EMailValidator;
import edu.harvard.iq.dataverse.EjbDataverseEngine;
-import edu.harvard.iq.dataverse.GlobalId;
import edu.harvard.iq.dataverse.HandlenetServiceBean;
import edu.harvard.iq.dataverse.Template;
import edu.harvard.iq.dataverse.TemplateServiceBean;
@@ -48,19 +47,19 @@
import edu.harvard.iq.dataverse.engine.command.impl.AbstractSubmitToArchiveCommand;
import edu.harvard.iq.dataverse.engine.command.impl.PublishDataverseCommand;
import edu.harvard.iq.dataverse.settings.Setting;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObjectBuilder;
-import javax.ws.rs.Consumes;
-import javax.ws.rs.DELETE;
-import javax.ws.rs.GET;
-import javax.ws.rs.POST;
-import javax.ws.rs.PUT;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.container.ContainerRequestContext;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.Response;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.ws.rs.Consumes;
+import jakarta.ws.rs.DELETE;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.PUT;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.container.ContainerRequestContext;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.Response;
import static edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder.jsonObjectBuilder;
import java.io.InputStream;
@@ -69,14 +68,14 @@
import java.util.Map.Entry;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.json.JsonObject;
-import javax.json.JsonReader;
-import javax.validation.ConstraintViolation;
-import javax.validation.ConstraintViolationException;
-import javax.ws.rs.Produces;
-import javax.ws.rs.core.Response.Status;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonReader;
+import jakarta.validation.ConstraintViolation;
+import jakarta.validation.ConstraintViolationException;
+import jakarta.ws.rs.Produces;
+import jakarta.ws.rs.core.Response.Status;
import org.apache.commons.io.IOUtils;
@@ -117,12 +116,12 @@
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
-import javax.inject.Inject;
-import javax.json.JsonArray;
-import javax.persistence.Query;
-import javax.ws.rs.QueryParam;
-import javax.ws.rs.WebApplicationException;
-import javax.ws.rs.core.StreamingOutput;
+import jakarta.inject.Inject;
+import jakarta.json.JsonArray;
+import jakarta.persistence.Query;
+import jakarta.ws.rs.QueryParam;
+import jakarta.ws.rs.WebApplicationException;
+import jakarta.ws.rs.core.StreamingOutput;
/**
* Where the secure, setup API calls live.
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/ApiBlockingFilter.java b/src/main/java/edu/harvard/iq/dataverse/api/ApiBlockingFilter.java
index 6bf852d25f7..0e5b8226310 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/ApiBlockingFilter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/ApiBlockingFilter.java
@@ -10,21 +10,22 @@
import java.util.TreeSet;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.servlet.FilterChain;
-import javax.servlet.FilterConfig;
-import javax.servlet.ServletException;
-import javax.servlet.ServletRequest;
-import javax.servlet.ServletResponse;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.ejb.EJB;
+import jakarta.servlet.Filter;
+import jakarta.servlet.FilterChain;
+import jakarta.servlet.FilterConfig;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.ServletRequest;
+import jakarta.servlet.ServletResponse;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
/**
* A web filter to block API administration calls.
* @author michael
*/
-public class ApiBlockingFilter implements javax.servlet.Filter {
+public class ApiBlockingFilter implements Filter {
public static final String UNBLOCK_KEY_QUERYPARAM = "unblock-key";
interface BlockPolicy {
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/ApiConfiguration.java b/src/main/java/edu/harvard/iq/dataverse/api/ApiConfiguration.java
index f9ba088a4e9..d076ab8f973 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/ApiConfiguration.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/ApiConfiguration.java
@@ -1,6 +1,6 @@
package edu.harvard.iq.dataverse.api;
-import javax.ws.rs.ApplicationPath;
+import jakarta.ws.rs.ApplicationPath;
import edu.harvard.iq.dataverse.api.auth.AuthFilter;
import org.glassfish.jersey.media.multipart.MultiPartFeature;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/ApiRouter.java b/src/main/java/edu/harvard/iq/dataverse/api/ApiRouter.java
index 691afeaef20..193e1059415 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/ApiRouter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/ApiRouter.java
@@ -1,21 +1,22 @@
package edu.harvard.iq.dataverse.api;
+import jakarta.servlet.Filter;
import java.io.IOException;
import java.util.logging.Logger;
-import javax.servlet.FilterChain;
-import javax.servlet.FilterConfig;
-import javax.servlet.RequestDispatcher;
-import javax.servlet.ServletException;
-import javax.servlet.ServletRequest;
-import javax.servlet.ServletResponse;
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.FilterChain;
+import jakarta.servlet.FilterConfig;
+import jakarta.servlet.RequestDispatcher;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.ServletRequest;
+import jakarta.servlet.ServletResponse;
+import jakarta.servlet.http.HttpServletRequest;
/**
* Routes API calls that don't have a version number to the latest API version
*
* @author michael
*/
-public class ApiRouter implements javax.servlet.Filter {
+public class ApiRouter implements Filter {
private static final Logger logger = Logger.getLogger(ApiRouter.class.getName());
@Override
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/BatchImport.java b/src/main/java/edu/harvard/iq/dataverse/api/BatchImport.java
index bf9ce2adc5a..a2d06bff93e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/BatchImport.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/BatchImport.java
@@ -15,16 +15,16 @@
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
import java.io.IOException;
import java.io.PrintWriter;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.json.JsonObjectBuilder;
-import javax.ws.rs.GET;
-import javax.ws.rs.POST;
-import javax.ws.rs.Path;
-import javax.ws.rs.QueryParam;
-import javax.ws.rs.container.ContainerRequestContext;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.Response;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.QueryParam;
+import jakarta.ws.rs.container.ContainerRequestContext;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.Response;
@Stateless
@Path("batch")
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/BatchServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/api/BatchServiceBean.java
index 8fe58298481..daddc447117 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/BatchServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/BatchServiceBean.java
@@ -14,12 +14,12 @@
import java.util.Date;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.Asynchronous;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObjectBuilder;
+import jakarta.ejb.Asynchronous;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObjectBuilder;
/**
* EJB for kicking off big batch jobs asynchronously from the REST API (BatchImport.java)
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/BuiltinUsers.java b/src/main/java/edu/harvard/iq/dataverse/api/BuiltinUsers.java
index 9262cc6ef46..50862bc0d35 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/BuiltinUsers.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/BuiltinUsers.java
@@ -13,25 +13,22 @@
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
import java.sql.Timestamp;
-import java.util.Calendar;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.json.Json;
-import javax.json.JsonObjectBuilder;
-import javax.ws.rs.GET;
-import javax.ws.rs.POST;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.QueryParam;
-import javax.ws.rs.core.Response;
-import javax.ws.rs.core.Response.Status;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.json.Json;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.QueryParam;
+import jakarta.ws.rs.core.Response;
+import jakarta.ws.rs.core.Response.Status;
import java.util.Date;
import static edu.harvard.iq.dataverse.util.json.JsonPrinter.json;
import static edu.harvard.iq.dataverse.util.json.JsonPrinter.json;
-import static edu.harvard.iq.dataverse.util.json.JsonPrinter.json;
-import static edu.harvard.iq.dataverse.util.json.JsonPrinter.json;
/**
* REST API bean for managing {@link BuiltinUser}s.
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/BundleDownloadInstanceWriter.java b/src/main/java/edu/harvard/iq/dataverse/api/BundleDownloadInstanceWriter.java
index 7edb0ac838c..35f19375902 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/BundleDownloadInstanceWriter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/BundleDownloadInstanceWriter.java
@@ -12,14 +12,14 @@
import java.io.OutputStream;
import java.io.IOException;
-import javax.ws.rs.InternalServerErrorException;
-import javax.ws.rs.NotFoundException;
-import javax.ws.rs.WebApplicationException;
-
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.core.MultivaluedMap;
-import javax.ws.rs.ext.MessageBodyWriter;
-import javax.ws.rs.ext.Provider;
+import jakarta.ws.rs.InternalServerErrorException;
+import jakarta.ws.rs.NotFoundException;
+import jakarta.ws.rs.WebApplicationException;
+
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.MultivaluedMap;
+import jakarta.ws.rs.ext.MessageBodyWriter;
+import jakarta.ws.rs.ext.Provider;
import edu.harvard.iq.dataverse.DataFile;
import edu.harvard.iq.dataverse.dataaccess.*;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/DataTagsAPI.java b/src/main/java/edu/harvard/iq/dataverse/api/DataTagsAPI.java
index 063033d4747..d7c8bd827d1 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/DataTagsAPI.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/DataTagsAPI.java
@@ -5,18 +5,18 @@
import java.util.Map;
import java.util.concurrent.ConcurrentHashMap;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.json.JsonObject;
-import javax.ws.rs.GET;
-import javax.ws.rs.POST;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.client.Client;
-import javax.ws.rs.client.ClientBuilder;
-import javax.ws.rs.client.WebTarget;
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.core.Response;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.json.JsonObject;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.client.Client;
+import jakarta.ws.rs.client.ClientBuilder;
+import jakarta.ws.rs.client.WebTarget;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.Response;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/DatasetFieldServiceApi.java b/src/main/java/edu/harvard/iq/dataverse/api/DatasetFieldServiceApi.java
index 4ec728a8159..00b7dfa6e36 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/DatasetFieldServiceApi.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/DatasetFieldServiceApi.java
@@ -20,18 +20,18 @@
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.validation.ConstraintViolation;
-import javax.validation.ConstraintViolationException;
-import javax.ws.rs.Consumes;
-import javax.ws.rs.GET;
-import javax.ws.rs.POST;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.core.Response;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.validation.ConstraintViolation;
+import jakarta.validation.ConstraintViolationException;
+import jakarta.ws.rs.Consumes;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.core.Response;
import edu.harvard.iq.dataverse.util.BundleUtil;
import edu.harvard.iq.dataverse.util.ConstraintViolationUtil;
@@ -41,9 +41,9 @@
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.persistence.NoResultException;
-import javax.persistence.TypedQuery;
-import javax.ws.rs.core.Response.Status;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.TypedQuery;
+import jakarta.ws.rs.core.Response.Status;
import java.io.BufferedInputStream;
import java.io.FileOutputStream;
@@ -207,7 +207,7 @@ public Response showControlledVocabularyForSubject() {
@GET
@Path("loadNAControlledVocabularyValue")
public Response loadNAControlledVocabularyValue() {
- // the find will throw a javax.persistence.NoResultException if no values are in db
+ // the find will throw a NoResultException if no values are in db
// datasetFieldService.findNAControlledVocabularyValue();
TypedQuery naValueFinder = em.createQuery("SELECT OBJECT(o) FROM ControlledVocabularyValue AS o WHERE o.datasetFieldType is null AND o.strValue = :strvalue", ControlledVocabularyValue.class);
naValueFinder.setParameter("strvalue", DatasetField.NA_VALUE);
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java
index dcd7eacf50b..dbea63cb1c8 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java
@@ -63,9 +63,7 @@
import edu.harvard.iq.dataverse.externaltools.ExternalToolHandler;
import edu.harvard.iq.dataverse.ingest.IngestServiceBean;
import edu.harvard.iq.dataverse.privateurl.PrivateUrl;
-import edu.harvard.iq.dataverse.api.AbstractApiBean.WrappedResponse;
import edu.harvard.iq.dataverse.api.dto.RoleAssignmentDTO;
-import edu.harvard.iq.dataverse.batch.util.LoggingUtil;
import edu.harvard.iq.dataverse.dataaccess.DataAccess;
import edu.harvard.iq.dataverse.dataaccess.ImageThumbConverter;
import edu.harvard.iq.dataverse.dataaccess.S3AccessIO;
@@ -85,7 +83,6 @@
import edu.harvard.iq.dataverse.makedatacount.MakeDataCountUtil;
import edu.harvard.iq.dataverse.privateurl.PrivateUrlServiceBean;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
-import edu.harvard.iq.dataverse.settings.SettingsServiceBean.Key;
import edu.harvard.iq.dataverse.util.ArchiverUtil;
import edu.harvard.iq.dataverse.util.BundleUtil;
import edu.harvard.iq.dataverse.util.EjbUtil;
@@ -96,7 +93,6 @@
import edu.harvard.iq.dataverse.util.json.JSONLDUtil;
import edu.harvard.iq.dataverse.util.json.JsonLDTerm;
import edu.harvard.iq.dataverse.util.json.JsonParseException;
-import edu.harvard.iq.dataverse.util.json.JsonPrinter;
import edu.harvard.iq.dataverse.util.SignpostingResources;
import edu.harvard.iq.dataverse.util.json.JsonUtil;
import edu.harvard.iq.dataverse.search.IndexServiceBean;
@@ -131,32 +127,31 @@
import java.util.regex.Pattern;
import java.util.stream.Collectors;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.inject.Inject;
-import javax.json.*;
-import javax.json.stream.JsonParsingException;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-import javax.ws.rs.BadRequestException;
-import javax.ws.rs.Consumes;
-import javax.ws.rs.DELETE;
-import javax.ws.rs.DefaultValue;
-import javax.ws.rs.GET;
-import javax.ws.rs.NotAcceptableException;
-import javax.ws.rs.POST;
-import javax.ws.rs.PUT;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.Produces;
-import javax.ws.rs.QueryParam;
-import javax.ws.rs.container.ContainerRequestContext;
-import javax.ws.rs.core.*;
-import javax.ws.rs.core.Response.Status;
-import static javax.ws.rs.core.Response.Status.BAD_REQUEST;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.inject.Inject;
+import jakarta.json.*;
+import jakarta.json.stream.JsonParsingException;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
+import jakarta.ws.rs.BadRequestException;
+import jakarta.ws.rs.Consumes;
+import jakarta.ws.rs.DELETE;
+import jakarta.ws.rs.DefaultValue;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.NotAcceptableException;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.PUT;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.Produces;
+import jakarta.ws.rs.QueryParam;
+import jakarta.ws.rs.container.ContainerRequestContext;
+import jakarta.ws.rs.core.*;
+import jakarta.ws.rs.core.Response.Status;
+import static jakarta.ws.rs.core.Response.Status.BAD_REQUEST;
import org.apache.commons.lang3.StringUtils;
-import org.apache.solr.client.solrj.SolrServerException;
import org.glassfish.jersey.media.multipart.FormDataBodyPart;
import org.glassfish.jersey.media.multipart.FormDataContentDisposition;
import org.glassfish.jersey.media.multipart.FormDataParam;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Dataverses.java b/src/main/java/edu/harvard/iq/dataverse/api/Dataverses.java
index 5214e3fbdcb..a60775cbd38 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/Dataverses.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/Dataverses.java
@@ -2,8 +2,6 @@
import edu.harvard.iq.dataverse.DataFile;
import edu.harvard.iq.dataverse.Dataset;
-import edu.harvard.iq.dataverse.DatasetAuthor;
-import edu.harvard.iq.dataverse.DatasetField;
import edu.harvard.iq.dataverse.DatasetFieldType;
import edu.harvard.iq.dataverse.DatasetVersion;
import edu.harvard.iq.dataverse.Dataverse;
@@ -22,9 +20,7 @@
import edu.harvard.iq.dataverse.GuestbookServiceBean;
import edu.harvard.iq.dataverse.MetadataBlock;
import edu.harvard.iq.dataverse.RoleAssignment;
-import edu.harvard.iq.dataverse.DatasetFieldType.FieldType;
-import static edu.harvard.iq.dataverse.api.AbstractApiBean.error;
import edu.harvard.iq.dataverse.api.dto.ExplicitGroupDTO;
import edu.harvard.iq.dataverse.api.dto.RoleAssignmentDTO;
import edu.harvard.iq.dataverse.api.dto.RoleDTO;
@@ -36,7 +32,6 @@
import edu.harvard.iq.dataverse.authorization.groups.impl.explicit.ExplicitGroupProvider;
import edu.harvard.iq.dataverse.authorization.groups.impl.explicit.ExplicitGroupServiceBean;
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
-import edu.harvard.iq.dataverse.authorization.users.PrivateUrlUser;
import edu.harvard.iq.dataverse.authorization.users.User;
import edu.harvard.iq.dataverse.dataverse.DataverseUtil;
import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
@@ -91,33 +86,33 @@
import java.util.TreeSet;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.ejb.Stateless;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonNumber;
-import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
-import javax.json.JsonString;
-import javax.json.JsonValue;
-import javax.json.JsonValue.ValueType;
-import javax.json.stream.JsonParsingException;
-import javax.validation.ConstraintViolationException;
-import javax.ws.rs.BadRequestException;
-import javax.ws.rs.Consumes;
-import javax.ws.rs.DELETE;
-import javax.ws.rs.GET;
-import javax.ws.rs.POST;
-import javax.ws.rs.PUT;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.Produces;
-import javax.ws.rs.QueryParam;
-import javax.ws.rs.container.ContainerRequestContext;
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.core.Response;
-import javax.ws.rs.core.Response.Status;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.ejb.Stateless;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonNumber;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.json.JsonString;
+import jakarta.json.JsonValue;
+import jakarta.json.JsonValue.ValueType;
+import jakarta.json.stream.JsonParsingException;
+import jakarta.validation.ConstraintViolationException;
+import jakarta.ws.rs.BadRequestException;
+import jakarta.ws.rs.Consumes;
+import jakarta.ws.rs.DELETE;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.PUT;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.Produces;
+import jakarta.ws.rs.QueryParam;
+import jakarta.ws.rs.container.ContainerRequestContext;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.Response;
+import jakarta.ws.rs.core.Response.Status;
import static edu.harvard.iq.dataverse.util.json.JsonPrinter.toJsonArray;
import static edu.harvard.iq.dataverse.util.json.JsonPrinter.json;
import java.io.IOException;
@@ -129,11 +124,11 @@
import java.util.Map;
import java.util.Optional;
import java.util.stream.Collectors;
-import javax.servlet.http.HttpServletResponse;
-import javax.validation.constraints.NotNull;
-import javax.ws.rs.WebApplicationException;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.StreamingOutput;
+import jakarta.servlet.http.HttpServletResponse;
+import jakarta.validation.constraints.NotNull;
+import jakarta.ws.rs.WebApplicationException;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.StreamingOutput;
import javax.xml.stream.XMLStreamException;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/DownloadInstance.java b/src/main/java/edu/harvard/iq/dataverse/api/DownloadInstance.java
index c9eb3638b90..e9f869ad8b9 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/DownloadInstance.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/DownloadInstance.java
@@ -14,9 +14,9 @@
import java.util.logging.Logger;
import edu.harvard.iq.dataverse.dataaccess.OptionalAccessService;
-import javax.faces.context.FacesContext;
-import javax.ws.rs.core.HttpHeaders;
-import javax.ws.rs.core.UriInfo;
+import jakarta.faces.context.FacesContext;
+import jakarta.ws.rs.core.HttpHeaders;
+import jakarta.ws.rs.core.UriInfo;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/DownloadInstanceWriter.java b/src/main/java/edu/harvard/iq/dataverse/api/DownloadInstanceWriter.java
index 2410da04072..af681234e82 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/DownloadInstanceWriter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/DownloadInstanceWriter.java
@@ -12,14 +12,14 @@
import java.io.OutputStream;
import java.io.IOException;
-import javax.ws.rs.WebApplicationException;
+import jakarta.ws.rs.WebApplicationException;
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.core.MultivaluedMap;
-import javax.ws.rs.core.Response;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.MultivaluedMap;
+import jakarta.ws.rs.core.Response;
-import javax.ws.rs.ext.MessageBodyWriter;
-import javax.ws.rs.ext.Provider;
+import jakarta.ws.rs.ext.MessageBodyWriter;
+import jakarta.ws.rs.ext.Provider;
import edu.harvard.iq.dataverse.DataFile;
import edu.harvard.iq.dataverse.dataaccess.*;
@@ -43,12 +43,12 @@
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.inject.Inject;
-import javax.ws.rs.ClientErrorException;
-import javax.ws.rs.NotFoundException;
-import javax.ws.rs.RedirectionException;
-import javax.ws.rs.ServiceUnavailableException;
-import javax.ws.rs.core.HttpHeaders;
+import jakarta.inject.Inject;
+import jakarta.ws.rs.ClientErrorException;
+import jakarta.ws.rs.NotFoundException;
+import jakarta.ws.rs.RedirectionException;
+import jakarta.ws.rs.ServiceUnavailableException;
+import jakarta.ws.rs.core.HttpHeaders;
import org.apache.tika.mime.MimeType;
import org.apache.tika.mime.MimeTypeException;
import org.apache.tika.mime.MimeTypes;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/EditDDI.java b/src/main/java/edu/harvard/iq/dataverse/api/EditDDI.java
index 3960fe4e996..1b74ab5479e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/EditDDI.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/EditDDI.java
@@ -2,9 +2,7 @@
import edu.harvard.iq.dataverse.api.auth.AuthRequired;
import edu.harvard.iq.dataverse.authorization.Permission;
-import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
import edu.harvard.iq.dataverse.authorization.users.User;
-import edu.harvard.iq.dataverse.batch.util.LoggingUtil;
import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
import edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetVersionCommand;
@@ -28,28 +26,25 @@
import edu.harvard.iq.dataverse.datavariable.VariableCategory;
import edu.harvard.iq.dataverse.datavariable.VariableMetadataDDIParser;
import edu.harvard.iq.dataverse.search.IndexServiceBean;
-import org.apache.solr.client.solrj.SolrServerException;
-
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.ejb.Stateless;
-import javax.inject.Inject;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.ws.rs.container.ContainerRequestContext;
-import javax.ws.rs.core.Response;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.Path;
-import javax.ws.rs.PUT;
-import javax.ws.rs.Consumes;
-import javax.ws.rs.PathParam;
+
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Inject;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.ws.rs.container.ContainerRequestContext;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.Response;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PUT;
+import jakarta.ws.rs.Consumes;
+import jakarta.ws.rs.PathParam;
import javax.xml.stream.XMLStreamException;
import javax.xml.stream.XMLInputFactory;
import javax.xml.stream.XMLStreamReader;
-import java.io.IOException;
import java.io.InputStream;
-import java.util.concurrent.Future;
import java.util.logging.Level;
import java.util.logging.Logger;
import java.util.List;
@@ -57,11 +52,9 @@
import java.util.Map;
import java.util.HashMap;
import java.util.Collection;
-import java.util.Date;
-import java.sql.Timestamp;
-import javax.validation.ConstraintViolationException;
+import jakarta.validation.ConstraintViolationException;
@Stateless
@Path("edit")
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/ExternalTools.java b/src/main/java/edu/harvard/iq/dataverse/api/ExternalTools.java
index e53b54482b8..1feac1141bb 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/ExternalTools.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/ExternalTools.java
@@ -4,15 +4,15 @@
import edu.harvard.iq.dataverse.externaltools.ExternalTool;
import edu.harvard.iq.dataverse.externaltools.ExternalToolServiceBean;
import java.util.logging.Logger;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.ws.rs.DELETE;
-import javax.ws.rs.GET;
-import javax.ws.rs.POST;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.core.Response;
-import static javax.ws.rs.core.Response.Status.BAD_REQUEST;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.ws.rs.DELETE;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.core.Response;
+import static jakarta.ws.rs.core.Response.Status.BAD_REQUEST;
@Path("admin/externalTools")
public class ExternalTools extends AbstractApiBean {
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/FeedbackApi.java b/src/main/java/edu/harvard/iq/dataverse/api/FeedbackApi.java
index 53829cf09cc..8a178f8da62 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/FeedbackApi.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/FeedbackApi.java
@@ -11,17 +11,17 @@
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
import edu.harvard.iq.dataverse.util.MailUtil;
-import javax.ejb.EJB;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonNumber;
-import javax.json.JsonObject;
-import javax.mail.internet.AddressException;
-import javax.mail.internet.InternetAddress;
-import javax.ws.rs.POST;
-import javax.ws.rs.Path;
-import javax.ws.rs.core.Response;
-import javax.ws.rs.core.Response.Status;
+import jakarta.ejb.EJB;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonNumber;
+import jakarta.json.JsonObject;
+import jakarta.mail.internet.AddressException;
+import jakarta.mail.internet.InternetAddress;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.core.Response;
+import jakarta.ws.rs.core.Response.Status;
@Path("admin/feedback")
public class FeedbackApi extends AbstractApiBean {
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Files.java b/src/main/java/edu/harvard/iq/dataverse/api/Files.java
index f6eda085c95..3324523afbc 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/Files.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/Files.java
@@ -55,26 +55,26 @@
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.inject.Inject;
-import javax.json.Json;
-import javax.servlet.http.HttpServletResponse;
-import javax.ws.rs.Consumes;
-import javax.ws.rs.DELETE;
-import javax.ws.rs.GET;
-import javax.ws.rs.POST;
-import javax.ws.rs.PUT;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.QueryParam;
-import javax.ws.rs.container.ContainerRequestContext;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.HttpHeaders;
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.core.Response;
-import static javax.ws.rs.core.Response.Status.BAD_REQUEST;
-import javax.ws.rs.core.UriInfo;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.inject.Inject;
+import jakarta.json.Json;
+import jakarta.servlet.http.HttpServletResponse;
+import jakarta.ws.rs.Consumes;
+import jakarta.ws.rs.DELETE;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.PUT;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.QueryParam;
+import jakarta.ws.rs.container.ContainerRequestContext;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.HttpHeaders;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.Response;
+import static jakarta.ws.rs.core.Response.Status.BAD_REQUEST;
+import jakarta.ws.rs.core.UriInfo;
import org.glassfish.jersey.media.multipart.FormDataBodyPart;
import org.glassfish.jersey.media.multipart.FormDataContentDisposition;
import org.glassfish.jersey.media.multipart.FormDataParam;
@@ -448,7 +448,7 @@ public Response updateFileMetadata(@Context ContainerRequestContext crc, @FormDa
return error(Response.Status.BAD_REQUEST, "An error has occurred attempting to update the requested DataFile. It is not part of the current version of the Dataset.");
}
- javax.json.JsonObject jsonObject = JsonUtil.getJsonObject(jsonData);
+ jakarta.json.JsonObject jsonObject = JsonUtil.getJsonObject(jsonData);
String incomingLabel = jsonObject.getString("label", null);
String incomingDirectoryLabel = jsonObject.getString("directoryLabel", null);
String existingLabel = df.getFileMetadata().getLabel();
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Groups.java b/src/main/java/edu/harvard/iq/dataverse/api/Groups.java
index 5a587efadf3..d56a787c7ff 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/Groups.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/Groups.java
@@ -9,26 +9,26 @@
import edu.harvard.iq.dataverse.util.json.JsonParseException;
import edu.harvard.iq.dataverse.util.json.JsonParser;
-import javax.ejb.Stateless;
-import javax.interceptor.Interceptors;
-import javax.ws.rs.GET;
-import javax.ws.rs.Path;
-import javax.ws.rs.core.Response;
+import jakarta.ejb.Stateless;
+import jakarta.interceptor.Interceptors;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.core.Response;
import static edu.harvard.iq.dataverse.util.json.JsonPrinter.*;
import java.util.Optional;
import java.util.logging.Level;
import java.util.logging.Logger;
import java.util.regex.Pattern;
-import javax.annotation.PostConstruct;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObject;
-import javax.json.JsonString;
-import javax.ws.rs.DELETE;
-import javax.ws.rs.POST;
-import javax.ws.rs.PUT;
-import javax.ws.rs.PathParam;
+import jakarta.annotation.PostConstruct;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonString;
+import jakarta.ws.rs.DELETE;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.PUT;
+import jakarta.ws.rs.PathParam;
import static org.apache.commons.lang3.StringUtils.isNumeric;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/HarvestingClients.java b/src/main/java/edu/harvard/iq/dataverse/api/HarvestingClients.java
index e739b1520a0..d7eec9f5757 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/HarvestingClients.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/HarvestingClients.java
@@ -1,7 +1,6 @@
package edu.harvard.iq.dataverse.api;
import edu.harvard.iq.dataverse.Dataverse;
-import edu.harvard.iq.dataverse.DataverseServiceBean;
import edu.harvard.iq.dataverse.api.auth.AuthRequired;
import edu.harvard.iq.dataverse.harvest.client.HarvestingClient;
@@ -17,27 +16,27 @@
import edu.harvard.iq.dataverse.util.StringUtil;
import edu.harvard.iq.dataverse.util.json.JsonParseException;
import edu.harvard.iq.dataverse.util.json.JsonPrinter;
-import javax.json.JsonObjectBuilder;
+import jakarta.json.JsonObjectBuilder;
import static edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder.jsonObjectBuilder;
import java.io.IOException;
import java.io.StringReader;
import java.util.ArrayList;
import java.util.List;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObject;
-import javax.ws.rs.DELETE;
-import javax.ws.rs.GET;
-import javax.ws.rs.POST;
-import javax.ws.rs.PUT;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.QueryParam;
-import javax.ws.rs.container.ContainerRequestContext;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.Response;
+import jakarta.ejb.EJB;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObject;
+import jakarta.ws.rs.DELETE;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.PUT;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.QueryParam;
+import jakarta.ws.rs.container.ContainerRequestContext;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.Response;
@Path("harvest/clients")
public class HarvestingClients extends AbstractApiBean {
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/HarvestingServer.java b/src/main/java/edu/harvard/iq/dataverse/api/HarvestingServer.java
index f5e3e669083..308b910c425 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/HarvestingServer.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/HarvestingServer.java
@@ -11,29 +11,29 @@
import edu.harvard.iq.dataverse.harvest.server.OAISetServiceBean;
import edu.harvard.iq.dataverse.util.BundleUtil;
import edu.harvard.iq.dataverse.util.json.JsonParseException;
-import javax.json.JsonObjectBuilder;
+import jakarta.json.JsonObjectBuilder;
import static edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder.jsonObjectBuilder;
import java.io.IOException;
import java.io.StringReader;
import java.util.List;
import java.util.logging.Logger;
import java.util.regex.Pattern;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.json.Json;
-import javax.json.JsonReader;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObject;
-import javax.ws.rs.DELETE;
-import javax.ws.rs.GET;
-import javax.ws.rs.POST;
-import javax.ws.rs.PUT;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.QueryParam;
-import javax.ws.rs.container.ContainerRequestContext;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.Response;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.json.Json;
+import jakarta.json.JsonReader;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObject;
+import jakarta.ws.rs.DELETE;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.PUT;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.QueryParam;
+import jakarta.ws.rs.container.ContainerRequestContext;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.Response;
import org.apache.commons.lang3.StringUtils;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Index.java b/src/main/java/edu/harvard/iq/dataverse/api/Index.java
index 1361de8fbf7..4910c460b6a 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/Index.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/Index.java
@@ -47,26 +47,24 @@
import java.util.Set;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.Future;
-import java.util.concurrent.TimeUnit;
-import java.util.concurrent.TimeoutException;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
-import javax.validation.ConstraintViolation;
-import javax.validation.ConstraintViolationException;
-import javax.ws.rs.DELETE;
-import javax.ws.rs.GET;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.QueryParam;
-import javax.ws.rs.container.ContainerRequestContext;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.Response;
-import javax.ws.rs.core.Response.Status;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.validation.ConstraintViolation;
+import jakarta.validation.ConstraintViolationException;
+import jakarta.ws.rs.DELETE;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.QueryParam;
+import jakarta.ws.rs.container.ContainerRequestContext;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.Response;
+import jakarta.ws.rs.core.Response.Status;
import org.apache.solr.client.solrj.SolrServerException;
@Path("admin/index")
@@ -199,7 +197,7 @@ private Response indexAllOrSubset(Long numPartitionsSelected, Long partitionIdTo
}
}
}
- if (sb.toString().equals("javax.ejb.EJBException: Transaction aborted javax.transaction.RollbackException java.lang.IllegalStateException ")) {
+ if (sb.toString().contains("java.lang.IllegalStateException ")) {
return ok("indexing went as well as can be expected... got java.lang.IllegalStateException but some indexing may have happened anyway");
} else {
return error(Status.INTERNAL_SERVER_ERROR, sb.toString());
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Info.java b/src/main/java/edu/harvard/iq/dataverse/api/Info.java
index cfee582f69d..3349c34dfcc 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/Info.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/Info.java
@@ -4,14 +4,14 @@
import edu.harvard.iq.dataverse.settings.JvmSettings;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
import edu.harvard.iq.dataverse.util.SystemConfig;
-import javax.ejb.EJB;
-import javax.json.Json;
-import javax.json.JsonValue;
-import javax.ws.rs.GET;
-import javax.ws.rs.Path;
-import javax.ws.rs.container.ContainerRequestContext;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.Response;
+import jakarta.ejb.EJB;
+import jakarta.json.Json;
+import jakarta.json.JsonValue;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.container.ContainerRequestContext;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.Response;
@Path("info")
public class Info extends AbstractApiBean {
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/LDNInbox.java b/src/main/java/edu/harvard/iq/dataverse/api/LDNInbox.java
index 3b725468161..05d12f1083c 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/LDNInbox.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/LDNInbox.java
@@ -28,20 +28,20 @@
import java.sql.Timestamp;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.json.Json;
-import javax.json.JsonObject;
-import javax.json.JsonValue;
-import javax.json.JsonWriter;
-import javax.servlet.http.HttpServletRequest;
-import javax.ws.rs.BadRequestException;
-import javax.ws.rs.ServiceUnavailableException;
-import javax.ws.rs.Consumes;
-import javax.ws.rs.ForbiddenException;
-import javax.ws.rs.POST;
-import javax.ws.rs.Path;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.Response;
+import jakarta.ejb.EJB;
+import jakarta.json.Json;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonValue;
+import jakarta.json.JsonWriter;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.ws.rs.BadRequestException;
+import jakarta.ws.rs.ServiceUnavailableException;
+import jakarta.ws.rs.Consumes;
+import jakarta.ws.rs.ForbiddenException;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.Response;
@Path("inbox")
public class LDNInbox extends AbstractApiBean {
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Licenses.java b/src/main/java/edu/harvard/iq/dataverse/api/Licenses.java
index a9d7eb8024c..ab50ebbf2e4 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/Licenses.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/Licenses.java
@@ -2,20 +2,20 @@
import edu.harvard.iq.dataverse.actionlogging.ActionLogRecord;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.ws.rs.DELETE;
-import javax.ws.rs.GET;
-import javax.ws.rs.POST;
-import javax.ws.rs.PUT;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.container.ContainerRequestContext;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.Response;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.ws.rs.DELETE;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.PUT;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.container.ContainerRequestContext;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.Response;
import java.util.logging.Logger;
-import javax.ejb.Stateless;
-import javax.ws.rs.core.Response.Status;
+import jakarta.ejb.Stateless;
+import jakarta.ws.rs.core.Response.Status;
import edu.harvard.iq.dataverse.api.auth.AuthRequired;
import edu.harvard.iq.dataverse.authorization.users.User;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Logout.java b/src/main/java/edu/harvard/iq/dataverse/api/Logout.java
index d6d8d5cdc44..e8d8be04459 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/Logout.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/Logout.java
@@ -4,10 +4,10 @@
import edu.harvard.iq.dataverse.DataverseSession;
import edu.harvard.iq.dataverse.settings.FeatureFlags;
-import javax.inject.Inject;
-import javax.ws.rs.POST;
-import javax.ws.rs.Path;
-import javax.ws.rs.core.Response;
+import jakarta.inject.Inject;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.core.Response;
@Path("logout")
public class Logout extends AbstractApiBean {
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Mail.java b/src/main/java/edu/harvard/iq/dataverse/api/Mail.java
index 3b5050b480b..5fac2f30c89 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/Mail.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/Mail.java
@@ -2,10 +2,10 @@
import edu.harvard.iq.dataverse.MailServiceBean;
import edu.harvard.iq.dataverse.actionlogging.ActionLogRecord;
-import javax.ejb.EJB;
-import javax.ws.rs.GET;
-import javax.ws.rs.Path;
-import javax.ws.rs.core.Response;
+import jakarta.ejb.EJB;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.core.Response;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/MakeDataCountApi.java b/src/main/java/edu/harvard/iq/dataverse/api/MakeDataCountApi.java
index 0193c7774f1..6b48dbf8415 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/MakeDataCountApi.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/MakeDataCountApi.java
@@ -18,19 +18,19 @@
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.json.Json;
-import javax.json.JsonArray;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
-import javax.json.JsonValue;
-import javax.ws.rs.POST;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.QueryParam;
-import javax.ws.rs.core.Response;
-import javax.ws.rs.core.Response.Status;
+import jakarta.ejb.EJB;
+import jakarta.json.Json;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.json.JsonValue;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.QueryParam;
+import jakarta.ws.rs.core.Response;
+import jakarta.ws.rs.core.Response.Status;
/**
* Note that there are makeDataCount endpoints in Datasets.java as well.
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Meta.java b/src/main/java/edu/harvard/iq/dataverse/api/Meta.java
index 1ca97f2ec69..a38840ba50d 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/Meta.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/Meta.java
@@ -15,19 +15,19 @@
import edu.harvard.iq.dataverse.export.DDIExportServiceBean;
import java.util.logging.Logger;
-import javax.ejb.EJB;
+import jakarta.ejb.EJB;
import java.io.ByteArrayOutputStream;
-import javax.ws.rs.GET;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.QueryParam;
-import javax.ws.rs.Produces;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.HttpHeaders;
-import javax.servlet.http.HttpServletResponse;
-import javax.ws.rs.NotFoundException;
-import javax.ws.rs.ServiceUnavailableException;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.QueryParam;
+import jakarta.ws.rs.Produces;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.HttpHeaders;
+import jakarta.servlet.http.HttpServletResponse;
+import jakarta.ws.rs.NotFoundException;
+import jakarta.ws.rs.ServiceUnavailableException;
/*
Custom API exceptions [NOT YET IMPLEMENTED]
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Metadata.java b/src/main/java/edu/harvard/iq/dataverse/api/Metadata.java
index b0d82b69d1b..bd937878286 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/Metadata.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/Metadata.java
@@ -8,22 +8,17 @@
import edu.harvard.iq.dataverse.Dataset;
import edu.harvard.iq.dataverse.DatasetServiceBean;
-import java.io.IOException;
-import java.util.concurrent.Future;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObjectBuilder;
-import javax.ws.rs.*;
-import javax.ws.rs.core.Response;
+import jakarta.ejb.EJB;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.ws.rs.*;
-import javax.ws.rs.core.Response;
+import jakarta.ws.rs.core.Response;
-import edu.harvard.iq.dataverse.DatasetVersion;
import edu.harvard.iq.dataverse.harvest.server.OAISetServiceBean;
import edu.harvard.iq.dataverse.harvest.server.OAISet;
-import org.apache.solr.client.solrj.SolrServerException;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/MetadataBlocks.java b/src/main/java/edu/harvard/iq/dataverse/api/MetadataBlocks.java
index b3e1dad13af..448fb48e389 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/MetadataBlocks.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/MetadataBlocks.java
@@ -1,12 +1,12 @@
package edu.harvard.iq.dataverse.api;
import edu.harvard.iq.dataverse.MetadataBlock;
-import javax.ws.rs.GET;
-import javax.ws.rs.Path;
-import javax.ws.rs.Produces;
-import javax.ws.rs.core.Response;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.Produces;
+import jakarta.ws.rs.core.Response;
import static edu.harvard.iq.dataverse.util.json.JsonPrinter.brief;
-import javax.ws.rs.PathParam;
+import jakarta.ws.rs.PathParam;
import static edu.harvard.iq.dataverse.util.json.JsonPrinter.json;
import static edu.harvard.iq.dataverse.util.json.JsonPrinter.toJsonArray;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Metrics.java b/src/main/java/edu/harvard/iq/dataverse/api/Metrics.java
index e966fd200d5..7bb2570334b 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/Metrics.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/Metrics.java
@@ -12,22 +12,22 @@
import java.util.List;
import java.util.logging.Logger;
-import javax.json.JsonArray;
-import javax.json.JsonObject;
-import javax.ws.rs.GET;
-import javax.ws.rs.NotFoundException;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.Produces;
-import javax.ws.rs.QueryParam;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.core.Request;
-import javax.ws.rs.core.Response;
-
-import static javax.ws.rs.core.Response.Status.BAD_REQUEST;
-import javax.ws.rs.core.UriInfo;
-import javax.ws.rs.core.Variant;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonObject;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.NotFoundException;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.Produces;
+import jakarta.ws.rs.QueryParam;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.Request;
+import jakarta.ws.rs.core.Response;
+
+import static jakarta.ws.rs.core.Response.Status.BAD_REQUEST;
+import jakarta.ws.rs.core.UriInfo;
+import jakarta.ws.rs.core.Variant;
/**
* API endpoints for various metrics.
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Notifications.java b/src/main/java/edu/harvard/iq/dataverse/api/Notifications.java
index 006a95d85a5..37c894d3071 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/Notifications.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/Notifications.java
@@ -11,19 +11,19 @@
import java.util.Optional;
import java.util.Set;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObjectBuilder;
-import javax.ws.rs.DELETE;
-import javax.ws.rs.GET;
-import javax.ws.rs.PUT;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.container.ContainerRequestContext;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.Response;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.ws.rs.DELETE;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.PUT;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.container.ContainerRequestContext;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.Response;
import edu.harvard.iq.dataverse.util.MailUtil;
import edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Pids.java b/src/main/java/edu/harvard/iq/dataverse/api/Pids.java
index 2e6e97f7ced..534e42fd505 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/Pids.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/Pids.java
@@ -10,24 +10,24 @@
import edu.harvard.iq.dataverse.settings.JvmSettings;
import edu.harvard.iq.dataverse.util.BundleUtil;
import java.util.Arrays;
-import javax.ejb.Stateless;
-import javax.json.Json;
-import javax.json.JsonArray;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObjectBuilder;
-import javax.ws.rs.DELETE;
-import javax.ws.rs.GET;
-import javax.ws.rs.InternalServerErrorException;
-import javax.ws.rs.NotFoundException;
-import javax.ws.rs.POST;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.Produces;
-import javax.ws.rs.QueryParam;
-import javax.ws.rs.container.ContainerRequestContext;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.core.Response;
+import jakarta.ejb.Stateless;
+import jakarta.json.Json;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.ws.rs.DELETE;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.InternalServerErrorException;
+import jakarta.ws.rs.NotFoundException;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.Produces;
+import jakarta.ws.rs.QueryParam;
+import jakarta.ws.rs.container.ContainerRequestContext;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.Response;
/**
* PIDs are Persistent IDentifiers such as DOIs or Handles.
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Prov.java b/src/main/java/edu/harvard/iq/dataverse/api/Prov.java
index f0f18f781f1..37b4792920f 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/Prov.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/Prov.java
@@ -15,23 +15,23 @@
import java.io.StringReader;
import java.util.HashMap;
import java.util.logging.Logger;
-import javax.inject.Inject;
-import javax.json.Json;
-import javax.json.JsonException;
-import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
-import javax.ws.rs.Consumes;
-import javax.ws.rs.DELETE;
-import javax.ws.rs.GET;
-import javax.ws.rs.POST;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.QueryParam;
-import javax.ws.rs.container.ContainerRequestContext;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.Response;
-import static javax.ws.rs.core.Response.Status.BAD_REQUEST;
-import static javax.ws.rs.core.Response.Status.FORBIDDEN;
+import jakarta.inject.Inject;
+import jakarta.json.Json;
+import jakarta.json.JsonException;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.ws.rs.Consumes;
+import jakarta.ws.rs.DELETE;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.QueryParam;
+import jakarta.ws.rs.container.ContainerRequestContext;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.Response;
+import static jakarta.ws.rs.core.Response.Status.BAD_REQUEST;
+import static jakarta.ws.rs.core.Response.Status.FORBIDDEN;
@Path("files")
public class Prov extends AbstractApiBean {
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Roles.java b/src/main/java/edu/harvard/iq/dataverse/api/Roles.java
index b7f9e4821e5..8812f95dea1 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/Roles.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/Roles.java
@@ -1,29 +1,26 @@
package edu.harvard.iq.dataverse.api;
-import static edu.harvard.iq.dataverse.api.AbstractApiBean.error;
-
import edu.harvard.iq.dataverse.api.auth.AuthRequired;
import edu.harvard.iq.dataverse.api.dto.RoleDTO;
import edu.harvard.iq.dataverse.authorization.DataverseRole;
import edu.harvard.iq.dataverse.authorization.Permission;
-import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
import edu.harvard.iq.dataverse.authorization.users.User;
-import javax.ws.rs.GET;
-import javax.ws.rs.POST;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
import static edu.harvard.iq.dataverse.util.json.JsonPrinter.*;
import edu.harvard.iq.dataverse.engine.command.impl.CreateRoleCommand;
import edu.harvard.iq.dataverse.engine.command.impl.DeleteRoleCommand;
import edu.harvard.iq.dataverse.util.BundleUtil;
import java.util.Arrays;
import java.util.List;
-import javax.ejb.Stateless;
-import javax.ws.rs.DELETE;
-import javax.ws.rs.QueryParam;
-import javax.ws.rs.container.ContainerRequestContext;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.Response;
+import jakarta.ejb.Stateless;
+import jakarta.ws.rs.DELETE;
+import jakarta.ws.rs.QueryParam;
+import jakarta.ws.rs.container.ContainerRequestContext;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.Response;
/**
* Util API for managing roles. Might not make it to the production version.
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/SavedSearches.java b/src/main/java/edu/harvard/iq/dataverse/api/SavedSearches.java
index 7ead0d23711..5d0365d022e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/SavedSearches.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/SavedSearches.java
@@ -11,23 +11,23 @@
import java.util.ArrayList;
import java.util.List;
import java.util.logging.Logger;
-import javax.ejb.EJBException;
-import javax.json.Json;
-import javax.json.JsonArray;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
-import javax.ws.rs.DELETE;
-import javax.ws.rs.GET;
-import javax.ws.rs.POST;
-import javax.ws.rs.PUT;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.QueryParam;
-import javax.ws.rs.core.Response;
-import static javax.ws.rs.core.Response.Status.BAD_REQUEST;
-import static javax.ws.rs.core.Response.Status.INTERNAL_SERVER_ERROR;
-import static javax.ws.rs.core.Response.Status.NOT_FOUND;
+import jakarta.ejb.EJBException;
+import jakarta.json.Json;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.ws.rs.DELETE;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.PUT;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.QueryParam;
+import jakarta.ws.rs.core.Response;
+import static jakarta.ws.rs.core.Response.Status.BAD_REQUEST;
+import static jakarta.ws.rs.core.Response.Status.INTERNAL_SERVER_ERROR;
+import static jakarta.ws.rs.core.Response.Status.NOT_FOUND;
@Path("admin/savedsearches")
public class SavedSearches extends AbstractApiBean {
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Search.java b/src/main/java/edu/harvard/iq/dataverse/api/Search.java
index d3c9d0a4cc6..c760534ca7b 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/Search.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/Search.java
@@ -24,19 +24,18 @@
import java.util.Arrays;
import java.util.List;
import java.util.Map;
-import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObjectBuilder;
-import javax.servlet.http.HttpServletResponse;
-import javax.ws.rs.GET;
-import javax.ws.rs.Path;
-import javax.ws.rs.QueryParam;
-import javax.ws.rs.container.ContainerRequestContext;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.Response;
+import jakarta.ejb.EJB;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.servlet.http.HttpServletResponse;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.QueryParam;
+import jakarta.ws.rs.container.ContainerRequestContext;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.Response;
import org.apache.commons.lang3.StringUtils;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/SiteMap.java b/src/main/java/edu/harvard/iq/dataverse/api/SiteMap.java
index 787c3380e5b..37d6a2aa3fe 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/SiteMap.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/SiteMap.java
@@ -2,13 +2,13 @@
import edu.harvard.iq.dataverse.sitemap.SiteMapServiceBean;
import edu.harvard.iq.dataverse.sitemap.SiteMapUtil;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.ws.rs.POST;
-import javax.ws.rs.Path;
-import javax.ws.rs.Produces;
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.core.Response;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.Produces;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.Response;
@Stateless
@Path("admin/sitemap")
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/StorageSites.java b/src/main/java/edu/harvard/iq/dataverse/api/StorageSites.java
index 54adeecd9f9..2915328428e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/StorageSites.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/StorageSites.java
@@ -3,16 +3,16 @@
import edu.harvard.iq.dataverse.locality.StorageSite;
import edu.harvard.iq.dataverse.locality.StorageSiteUtil;
import java.util.List;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObject;
-import javax.ws.rs.DELETE;
-import javax.ws.rs.GET;
-import javax.ws.rs.POST;
-import javax.ws.rs.PUT;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.core.Response;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObject;
+import jakarta.ws.rs.DELETE;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.PUT;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.core.Response;
@Path("admin/storageSites")
public class StorageSites extends AbstractApiBean {
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/TestApi.java b/src/main/java/edu/harvard/iq/dataverse/api/TestApi.java
index 42caa95b9f5..87be1f14e05 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/TestApi.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/TestApi.java
@@ -2,20 +2,19 @@
import edu.harvard.iq.dataverse.DataFile;
import edu.harvard.iq.dataverse.Dataset;
-import static edu.harvard.iq.dataverse.api.AbstractApiBean.error;
import edu.harvard.iq.dataverse.authorization.users.ApiToken;
import edu.harvard.iq.dataverse.externaltools.ExternalTool;
import edu.harvard.iq.dataverse.externaltools.ExternalToolHandler;
import java.util.List;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObjectBuilder;
-import javax.ws.rs.GET;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.QueryParam;
-import javax.ws.rs.core.Response;
-import static javax.ws.rs.core.Response.Status.BAD_REQUEST;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.QueryParam;
+import jakarta.ws.rs.core.Response;
+import static jakarta.ws.rs.core.Response.Status.BAD_REQUEST;
@Path("admin/test")
public class TestApi extends AbstractApiBean {
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/TestIngest.java b/src/main/java/edu/harvard/iq/dataverse/api/TestIngest.java
index 15c3b34f6af..05ba150df8e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/TestIngest.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/TestIngest.java
@@ -18,22 +18,22 @@
import edu.harvard.iq.dataverse.util.StringUtil;
import java.io.BufferedInputStream;
import java.util.logging.Logger;
-import javax.ejb.EJB;
+import jakarta.ejb.EJB;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.nio.file.Paths;
import java.nio.file.StandardCopyOption;
-import javax.ws.rs.GET;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.Produces;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.HttpHeaders;
-import javax.ws.rs.core.UriInfo;
-import javax.servlet.http.HttpServletResponse;
-import javax.ws.rs.QueryParam;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.Produces;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.HttpHeaders;
+import jakarta.ws.rs.core.UriInfo;
+import jakarta.servlet.http.HttpServletResponse;
+import jakarta.ws.rs.QueryParam;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Users.java b/src/main/java/edu/harvard/iq/dataverse/api/Users.java
index 14bf25c91b2..791fc7aa774 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/Users.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/Users.java
@@ -5,8 +5,6 @@
*/
package edu.harvard.iq.dataverse.api;
-import static edu.harvard.iq.dataverse.api.AbstractApiBean.error;
-
import edu.harvard.iq.dataverse.api.auth.AuthRequired;
import edu.harvard.iq.dataverse.authorization.users.ApiToken;
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
@@ -15,32 +13,30 @@
import edu.harvard.iq.dataverse.engine.command.impl.GetUserTracesCommand;
import edu.harvard.iq.dataverse.engine.command.impl.MergeInAccountCommand;
import edu.harvard.iq.dataverse.engine.command.impl.RevokeAllRolesCommand;
-import edu.harvard.iq.dataverse.metrics.MetricsUtil;
import edu.harvard.iq.dataverse.util.FileUtil;
import static edu.harvard.iq.dataverse.util.json.JsonPrinter.json;
-import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.Stateless;
-import javax.json.JsonArray;
-import javax.json.JsonObjectBuilder;
-import javax.ws.rs.BadRequestException;
-import javax.ws.rs.DELETE;
-import javax.ws.rs.GET;
-import javax.ws.rs.POST;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.Produces;
-import javax.ws.rs.container.ContainerRequestContext;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.core.Request;
-import javax.ws.rs.core.Response;
-import javax.ws.rs.core.Variant;
+import jakarta.ejb.Stateless;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.ws.rs.BadRequestException;
+import jakarta.ws.rs.DELETE;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.Produces;
+import jakarta.ws.rs.container.ContainerRequestContext;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.Request;
+import jakarta.ws.rs.core.Response;
+import jakarta.ws.rs.core.Variant;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Util.java b/src/main/java/edu/harvard/iq/dataverse/api/Util.java
index 82adedc709f..25855769a38 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/Util.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/Util.java
@@ -7,9 +7,9 @@
import java.util.TimeZone;
import java.util.TreeSet;
import java.util.stream.Collectors;
-import javax.json.Json;
-import javax.json.JsonArray;
-import javax.json.JsonReader;
+import jakarta.json.Json;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonReader;
public class Util {
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Workflows.java b/src/main/java/edu/harvard/iq/dataverse/api/Workflows.java
index 4269a0215bf..4eadcedf71a 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/Workflows.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/Workflows.java
@@ -8,11 +8,11 @@
import java.util.Arrays;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ws.rs.POST;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.core.Response;
+import jakarta.ejb.EJB;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.core.Response;
/**
* API Endpoint for external systems to report the results of workflow step
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/WorkflowsAdmin.java b/src/main/java/edu/harvard/iq/dataverse/api/WorkflowsAdmin.java
index 4babe6875e2..8d5024c1c14 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/WorkflowsAdmin.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/WorkflowsAdmin.java
@@ -11,18 +11,18 @@
import edu.harvard.iq.dataverse.workflow.WorkflowServiceBean;
import java.util.Arrays;
import java.util.Optional;
-import javax.ejb.EJB;
-import javax.json.Json;
-import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
-import javax.json.JsonValue;
-import javax.ws.rs.DELETE;
-import javax.ws.rs.GET;
-import javax.ws.rs.POST;
-import javax.ws.rs.PUT;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.core.Response;
+import jakarta.ejb.EJB;
+import jakarta.json.Json;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.json.JsonValue;
+import jakarta.ws.rs.DELETE;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.PUT;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.core.Response;
/**
* API Endpoint for managing workflows.
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/auth/ApiKeyAuthMechanism.java b/src/main/java/edu/harvard/iq/dataverse/api/auth/ApiKeyAuthMechanism.java
index 60b75757f3c..0dd8a28baca 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/auth/ApiKeyAuthMechanism.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/auth/ApiKeyAuthMechanism.java
@@ -7,8 +7,8 @@
import edu.harvard.iq.dataverse.authorization.users.User;
import edu.harvard.iq.dataverse.privateurl.PrivateUrlServiceBean;
-import javax.inject.Inject;
-import javax.ws.rs.container.ContainerRequestContext;
+import jakarta.inject.Inject;
+import jakarta.ws.rs.container.ContainerRequestContext;
import java.util.logging.Logger;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/auth/AuthFilter.java b/src/main/java/edu/harvard/iq/dataverse/api/auth/AuthFilter.java
index dea9c571d22..34a72d718f0 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/auth/AuthFilter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/auth/AuthFilter.java
@@ -3,12 +3,12 @@
import edu.harvard.iq.dataverse.api.ApiConstants;
import edu.harvard.iq.dataverse.authorization.users.User;
-import javax.annotation.Priority;
-import javax.inject.Inject;
-import javax.ws.rs.Priorities;
-import javax.ws.rs.container.ContainerRequestContext;
-import javax.ws.rs.container.ContainerRequestFilter;
-import javax.ws.rs.ext.Provider;
+import jakarta.annotation.Priority;
+import jakarta.inject.Inject;
+import jakarta.ws.rs.Priorities;
+import jakarta.ws.rs.container.ContainerRequestContext;
+import jakarta.ws.rs.container.ContainerRequestFilter;
+import jakarta.ws.rs.ext.Provider;
import java.io.IOException;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/auth/AuthMechanism.java b/src/main/java/edu/harvard/iq/dataverse/api/auth/AuthMechanism.java
index e9bf1f39361..bd34acbf702 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/auth/AuthMechanism.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/auth/AuthMechanism.java
@@ -2,7 +2,7 @@
import edu.harvard.iq.dataverse.authorization.users.User;
-import javax.ws.rs.container.ContainerRequestContext;
+import jakarta.ws.rs.container.ContainerRequestContext;
/**
* @author Guillermo Portas
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/auth/AuthRequired.java b/src/main/java/edu/harvard/iq/dataverse/api/auth/AuthRequired.java
index 4deacc7f66e..bf0d785eeb3 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/auth/AuthRequired.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/auth/AuthRequired.java
@@ -1,6 +1,6 @@
package edu.harvard.iq.dataverse.api.auth;
-import javax.ws.rs.NameBinding;
+import jakarta.ws.rs.NameBinding;
import java.lang.annotation.ElementType;
import java.lang.annotation.Retention;
import java.lang.annotation.Target;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/auth/BearerTokenAuthMechanism.java b/src/main/java/edu/harvard/iq/dataverse/api/auth/BearerTokenAuthMechanism.java
index c4b03728179..b5a48427fa5 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/auth/BearerTokenAuthMechanism.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/auth/BearerTokenAuthMechanism.java
@@ -11,9 +11,9 @@
import edu.harvard.iq.dataverse.authorization.users.User;
import edu.harvard.iq.dataverse.settings.FeatureFlags;
-import javax.inject.Inject;
-import javax.ws.rs.container.ContainerRequestContext;
-import javax.ws.rs.core.HttpHeaders;
+import jakarta.inject.Inject;
+import jakarta.ws.rs.container.ContainerRequestContext;
+import jakarta.ws.rs.core.HttpHeaders;
import java.io.IOException;
import java.util.List;
import java.util.Optional;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/auth/CompoundAuthMechanism.java b/src/main/java/edu/harvard/iq/dataverse/api/auth/CompoundAuthMechanism.java
index 59384ff0336..801e2752b9e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/auth/CompoundAuthMechanism.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/auth/CompoundAuthMechanism.java
@@ -3,8 +3,8 @@
import edu.harvard.iq.dataverse.authorization.users.GuestUser;
import edu.harvard.iq.dataverse.authorization.users.User;
-import javax.inject.Inject;
-import javax.ws.rs.container.ContainerRequestContext;
+import jakarta.inject.Inject;
+import jakarta.ws.rs.container.ContainerRequestContext;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/auth/SessionCookieAuthMechanism.java b/src/main/java/edu/harvard/iq/dataverse/api/auth/SessionCookieAuthMechanism.java
index 53aec9235a4..c1471c3f5b3 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/auth/SessionCookieAuthMechanism.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/auth/SessionCookieAuthMechanism.java
@@ -4,8 +4,8 @@
import edu.harvard.iq.dataverse.authorization.users.User;
import edu.harvard.iq.dataverse.settings.FeatureFlags;
-import javax.inject.Inject;
-import javax.ws.rs.container.ContainerRequestContext;
+import jakarta.inject.Inject;
+import jakarta.ws.rs.container.ContainerRequestContext;
public class SessionCookieAuthMechanism implements AuthMechanism {
@Inject
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/auth/SignedUrlAuthMechanism.java b/src/main/java/edu/harvard/iq/dataverse/api/auth/SignedUrlAuthMechanism.java
index caa58dfddf3..f8572144236 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/auth/SignedUrlAuthMechanism.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/auth/SignedUrlAuthMechanism.java
@@ -7,9 +7,9 @@
import edu.harvard.iq.dataverse.settings.JvmSettings;
import edu.harvard.iq.dataverse.util.UrlSignerUtil;
-import javax.inject.Inject;
-import javax.ws.rs.container.ContainerRequestContext;
-import javax.ws.rs.core.UriInfo;
+import jakarta.inject.Inject;
+import jakarta.ws.rs.container.ContainerRequestContext;
+import jakarta.ws.rs.core.UriInfo;
import java.net.URLDecoder;
import java.nio.charset.StandardCharsets;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/auth/WorkflowKeyAuthMechanism.java b/src/main/java/edu/harvard/iq/dataverse/api/auth/WorkflowKeyAuthMechanism.java
index e673e14e677..bbd67713e85 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/auth/WorkflowKeyAuthMechanism.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/auth/WorkflowKeyAuthMechanism.java
@@ -4,8 +4,8 @@
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
import edu.harvard.iq.dataverse.authorization.users.User;
-import javax.inject.Inject;
-import javax.ws.rs.container.ContainerRequestContext;
+import jakarta.inject.Inject;
+import jakarta.ws.rs.container.ContainerRequestContext;
/**
* @author Guillermo Portas
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/auth/WrappedAuthErrorResponse.java b/src/main/java/edu/harvard/iq/dataverse/api/auth/WrappedAuthErrorResponse.java
index 18eafde6ede..40431557261 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/auth/WrappedAuthErrorResponse.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/auth/WrappedAuthErrorResponse.java
@@ -3,8 +3,8 @@
import edu.harvard.iq.dataverse.api.ApiConstants;
import edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder;
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.core.Response;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.Response;
public class WrappedAuthErrorResponse extends Exception {
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/batchjob/BatchJobResource.java b/src/main/java/edu/harvard/iq/dataverse/api/batchjob/BatchJobResource.java
index 37c29f20efe..09a60b1b700 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/batchjob/BatchJobResource.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/batchjob/BatchJobResource.java
@@ -4,17 +4,17 @@
import edu.harvard.iq.dataverse.api.AbstractApiBean;
import edu.harvard.iq.dataverse.batch.entities.JobExecutionEntity;
-import javax.batch.operations.JobOperator;
-import javax.batch.runtime.BatchRuntime;
-import javax.batch.runtime.JobExecution;
-import javax.batch.runtime.JobInstance;
-import javax.ejb.Stateless;
-import javax.ws.rs.GET;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.Produces;
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.core.Response;
+import jakarta.batch.operations.JobOperator;
+import jakarta.batch.runtime.BatchRuntime;
+import jakarta.batch.runtime.JobExecution;
+import jakarta.batch.runtime.JobInstance;
+import jakarta.ejb.Stateless;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.Produces;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.Response;
import java.util.ArrayList;
import java.util.List;
import java.util.Set;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/batchjob/FileRecordJobResource.java b/src/main/java/edu/harvard/iq/dataverse/api/batchjob/FileRecordJobResource.java
index 8695c7dcab7..b7a6b7cfafd 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/batchjob/FileRecordJobResource.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/batchjob/FileRecordJobResource.java
@@ -6,21 +6,21 @@
import edu.harvard.iq.dataverse.api.auth.AuthRequired;
import edu.harvard.iq.dataverse.batch.jobs.importer.ImportMode;
import edu.harvard.iq.dataverse.engine.command.impl.ImportFromFileSystemCommand;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.ws.rs.DefaultValue;
-import javax.ws.rs.POST;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.Produces;
-import javax.ws.rs.QueryParam;
-import javax.ws.rs.container.ContainerRequestContext;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.core.Response;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.ws.rs.DefaultValue;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.Produces;
+import jakarta.ws.rs.QueryParam;
+import jakarta.ws.rs.container.ContainerRequestContext;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.Response;
import java.util.logging.Logger;
-import javax.json.Json;
-import javax.json.JsonObject;
+import jakarta.json.Json;
+import jakarta.json.JsonObject;
@Stateless
@Path("batch/jobs")
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionDepositManagerImpl.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionDepositManagerImpl.java
index 6543d771ebe..5bc50903be8 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionDepositManagerImpl.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionDepositManagerImpl.java
@@ -18,12 +18,12 @@
import edu.harvard.iq.dataverse.util.ConstraintViolationUtil;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.inject.Inject;
-import javax.servlet.http.HttpServletRequest;
-import javax.validation.ConstraintViolation;
-import javax.validation.ConstraintViolationException;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.inject.Inject;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.validation.ConstraintViolation;
+import jakarta.validation.ConstraintViolationException;
import org.apache.abdera.parser.ParseException;
import org.swordapp.server.AuthCredentials;
import org.swordapp.server.CollectionDepositManager;
@@ -174,7 +174,9 @@ public DepositReceipt createNew(String collectionUri, Deposit deposit, AuthCrede
// curl --insecure --data-binary "@multipart.dat" -H 'Content-Type: multipart/related; boundary="===============0670350989=="' -H "MIME-Version: 1.0" https://sword:sword@localhost:8181/dvn/api/data-deposit/v1/swordv2/collection/dataverse/sword/hdl:1902.1/12345
// but...
// "Yeah, multipart is critically broken across all implementations" -- http://www.mail-archive.com/sword-app-tech@lists.sourceforge.net/msg00327.html
- throw new UnsupportedOperationException("Not yet implemented");
+ //
+ // OB 2022-03-24 -> sword2-server v2.0 library drops support for multipart/related.
+ throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Multipart/related RFC2387 type posts are not supported. Please POST an Atom entry instead.");
} else {
throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "expected deposit types are isEntryOnly, isBinaryOnly, and isMultiPart");
}
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionListManagerImpl.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionListManagerImpl.java
index c7ed00a23d0..084136f2b5d 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionListManagerImpl.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionListManagerImpl.java
@@ -11,9 +11,9 @@
import edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetVersionCommand;
import java.util.List;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.inject.Inject;
-import javax.servlet.http.HttpServletRequest;
+import jakarta.ejb.EJB;
+import jakarta.inject.Inject;
+import jakarta.servlet.http.HttpServletRequest;
import javax.xml.namespace.QName;
import org.apache.abdera.Abdera;
import org.apache.abdera.i18n.iri.IRI;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ContainerManagerImpl.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ContainerManagerImpl.java
index b605f3717a8..4d4d1d08b51 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ContainerManagerImpl.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ContainerManagerImpl.java
@@ -25,12 +25,12 @@
import java.util.List;
import java.util.Map;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.inject.Inject;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.servlet.http.HttpServletRequest;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.inject.Inject;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.servlet.http.HttpServletRequest;
import org.apache.abdera.parser.ParseException;
import org.swordapp.server.AuthCredentials;
import org.swordapp.server.ContainerManager;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/MediaResourceManagerImpl.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/MediaResourceManagerImpl.java
index 482e35df781..93b7dc96563 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/MediaResourceManagerImpl.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/MediaResourceManagerImpl.java
@@ -9,9 +9,6 @@
import edu.harvard.iq.dataverse.EjbDataverseEngine;
import edu.harvard.iq.dataverse.PermissionServiceBean;
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
-import edu.harvard.iq.dataverse.dataaccess.StorageIO;
-import edu.harvard.iq.dataverse.datacapturemodule.DataCaptureModuleUtil;
-import edu.harvard.iq.dataverse.datasetutility.FileExceedsMaxSizeException;
import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
import edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetVersionCommand;
@@ -29,12 +26,12 @@
import java.util.Map;
import java.util.Set;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.inject.Inject;
-import javax.servlet.http.HttpServletRequest;
-import javax.validation.ConstraintViolation;
-import javax.validation.ConstraintViolationException;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.inject.Inject;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.validation.ConstraintViolation;
+import jakarta.validation.ConstraintViolationException;
import edu.harvard.iq.dataverse.util.file.CreateDataFileResult;
import org.swordapp.server.AuthCredentials;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2CollectionServlet.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2CollectionServlet.java
index a761afd1324..c509a8d6f52 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2CollectionServlet.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2CollectionServlet.java
@@ -2,10 +2,10 @@
import java.io.IOException;
import java.util.concurrent.locks.ReentrantLock;
-import javax.inject.Inject;
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.inject.Inject;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
import org.swordapp.server.CollectionAPI;
import org.swordapp.server.servlets.SwordServlet;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2ContainerServlet.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2ContainerServlet.java
index 441186cc63f..53dce24c0fe 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2ContainerServlet.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2ContainerServlet.java
@@ -2,10 +2,10 @@
import java.io.IOException;
import java.util.concurrent.locks.ReentrantLock;
-import javax.inject.Inject;
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.inject.Inject;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
import org.swordapp.server.ContainerAPI;
import org.swordapp.server.ContainerManager;
import org.swordapp.server.StatementManager;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2MediaResourceServlet.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2MediaResourceServlet.java
index c455a6fd26a..245ab6ab23b 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2MediaResourceServlet.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2MediaResourceServlet.java
@@ -2,10 +2,10 @@
import java.io.IOException;
import java.util.concurrent.locks.ReentrantLock;
-import javax.inject.Inject;
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.inject.Inject;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
import org.swordapp.server.MediaResourceAPI;
import org.swordapp.server.servlets.SwordServlet;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2ServiceDocumentServlet.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2ServiceDocumentServlet.java
index 37db76d3c9c..eab005d87fa 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2ServiceDocumentServlet.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2ServiceDocumentServlet.java
@@ -1,10 +1,10 @@
package edu.harvard.iq.dataverse.api.datadeposit;
import java.io.IOException;
-import javax.inject.Inject;
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.inject.Inject;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
import org.swordapp.server.ServiceDocumentAPI;
import org.swordapp.server.servlets.SwordServlet;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2StatementServlet.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2StatementServlet.java
index ed1202d8c77..4bcc9c6afe8 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2StatementServlet.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SWORDv2StatementServlet.java
@@ -1,10 +1,10 @@
package edu.harvard.iq.dataverse.api.datadeposit;
import java.io.IOException;
-import javax.inject.Inject;
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.inject.Inject;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
import org.swordapp.server.StatementAPI;
import org.swordapp.server.StatementManager;
import org.swordapp.server.servlets.SwordServlet;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ServiceDocumentManagerImpl.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ServiceDocumentManagerImpl.java
index 049b20f605b..134d54aef88 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ServiceDocumentManagerImpl.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/ServiceDocumentManagerImpl.java
@@ -8,8 +8,8 @@
import edu.harvard.iq.dataverse.util.SystemConfig;
import java.util.List;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.inject.Inject;
+import jakarta.ejb.EJB;
+import jakarta.inject.Inject;
import org.apache.commons.lang3.StringUtils;
import org.swordapp.server.AuthCredentials;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/StatementManagerImpl.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/StatementManagerImpl.java
index 05864fb2da0..95763e0eafb 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/StatementManagerImpl.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/StatementManagerImpl.java
@@ -17,9 +17,9 @@
import java.util.Optional;
import java.util.logging.Logger;
import static java.util.stream.Collectors.joining;
-import javax.ejb.EJB;
-import javax.inject.Inject;
-import javax.servlet.http.HttpServletRequest;
+import jakarta.ejb.EJB;
+import jakarta.inject.Inject;
+import jakarta.servlet.http.HttpServletRequest;
import org.apache.abdera.i18n.iri.IRI;
import org.apache.abdera.i18n.iri.IRISyntaxException;
import org.apache.abdera.model.AtomDate;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SwordConfigurationImpl.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SwordConfigurationImpl.java
index 1e506c6a0b1..a5564e9fbdb 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SwordConfigurationImpl.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SwordConfigurationImpl.java
@@ -6,7 +6,7 @@
import java.util.Arrays;
import java.util.List;
import java.util.logging.Logger;
-import javax.ejb.EJB;
+import jakarta.ejb.EJB;
import org.swordapp.server.SwordConfiguration;
public class SwordConfigurationImpl implements SwordConfiguration {
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SwordFilter.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SwordFilter.java
new file mode 100644
index 00000000000..aa7e028a4ba
--- /dev/null
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SwordFilter.java
@@ -0,0 +1,49 @@
+package edu.harvard.iq.dataverse.api.datadeposit;
+
+import jakarta.servlet.Filter;
+import jakarta.servlet.FilterChain;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.ServletRequest;
+import jakarta.servlet.ServletResponse;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequestWrapper;
+import java.io.IOException;
+
+public class SwordFilter implements Filter {
+
+ @Override
+ public void doFilter(ServletRequest request, ServletResponse response, FilterChain chain) throws IOException, ServletException {
+ HttpServletRequest req = (HttpServletRequest) request;
+ MutateHeaders requestWrapper = new MutateHeaders(req);
+ chain.doFilter(requestWrapper, response);
+ }
+
+ /**
+ * We are mutating headers because Payara 6 is more strict than Paraya 5 and
+ * wants "attachment; filename=" instead of just "filename=". In order to
+ * not break backward compatibility, we add "attachment; " for our (SWORD)
+ * API users. (This only seem to affect our SWORD API.) That is, the can
+ * continue to send '-H "Content-Disposition: filename=example.zip"' as
+ * we've documented for years.
+ */
+ public class MutateHeaders extends HttpServletRequestWrapper {
+
+ public MutateHeaders(HttpServletRequest request) {
+ super(request);
+ }
+
+ // inspired by https://stackoverflow.com/questions/2811769/adding-an-http-header-to-the-request-in-a-servlet-filter/2811841#2811841
+ @Override
+ public String getHeader(String name) {
+ String header = super.getHeader(name);
+ if ("Content-Disposition".equalsIgnoreCase(name)) {
+ if (header.startsWith("filename=")) {
+ header = header.replaceFirst("filename=", "attachment; filename=");
+ }
+ }
+ return (header != null) ? header : super.getParameter(name);
+ }
+
+ }
+
+}
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SwordServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SwordServiceBean.java
index 2e093dbcf36..22b6ee05e48 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SwordServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/SwordServiceBean.java
@@ -19,10 +19,10 @@
import java.util.List;
import java.util.Map;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
import org.apache.commons.lang3.StringUtils;
import org.swordapp.server.SwordEntry;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/errorhandlers/ConstraintViolationExceptionHandler.java b/src/main/java/edu/harvard/iq/dataverse/api/errorhandlers/ConstraintViolationExceptionHandler.java
index 4cbf31d1d2c..bb57059a99a 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/errorhandlers/ConstraintViolationExceptionHandler.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/errorhandlers/ConstraintViolationExceptionHandler.java
@@ -1,17 +1,15 @@
package edu.harvard.iq.dataverse.api.errorhandlers;
-import edu.harvard.iq.dataverse.util.json.JsonPrinter;
-
-import javax.json.Json;
-import javax.json.JsonArray;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObject;
-import javax.validation.ConstraintViolation;
-import javax.validation.ConstraintViolationException;
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.core.Response;
-import javax.ws.rs.ext.ExceptionMapper;
-import javax.ws.rs.ext.Provider;
+import jakarta.json.Json;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObject;
+import jakarta.validation.ConstraintViolation;
+import jakarta.validation.ConstraintViolationException;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.Response;
+import jakarta.ws.rs.ext.ExceptionMapper;
+import jakarta.ws.rs.ext.Provider;
import java.util.List;
import java.util.stream.Collectors;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/errorhandlers/JsonParseExceptionHandler.java b/src/main/java/edu/harvard/iq/dataverse/api/errorhandlers/JsonParseExceptionHandler.java
index 286272d9de3..2f974a1c5be 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/errorhandlers/JsonParseExceptionHandler.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/errorhandlers/JsonParseExceptionHandler.java
@@ -2,17 +2,14 @@
import edu.harvard.iq.dataverse.util.json.JsonParseException;
-import javax.json.Json;
-import javax.servlet.http.HttpServletRequest;
-import javax.ws.rs.BadRequestException;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.core.Response;
-import javax.ws.rs.ext.ExceptionMapper;
-import javax.ws.rs.ext.Provider;
-import java.util.UUID;
-import java.util.logging.Level;
-import java.util.logging.Logger;
+import jakarta.json.Json;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.ws.rs.BadRequestException;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.Response;
+import jakarta.ws.rs.ext.ExceptionMapper;
+import jakarta.ws.rs.ext.Provider;
/**
* Make a failing JSON parsing request appear to be a BadRequest (error code 400)
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/errorhandlers/ThrowableHandler.java b/src/main/java/edu/harvard/iq/dataverse/api/errorhandlers/ThrowableHandler.java
index 4064ee21474..8e43a1876bf 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/errorhandlers/ThrowableHandler.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/errorhandlers/ThrowableHandler.java
@@ -2,11 +2,11 @@
import edu.harvard.iq.dataverse.api.util.JsonResponseBuilder;
-import javax.servlet.http.HttpServletRequest;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.Response;
-import javax.ws.rs.ext.ExceptionMapper;
-import javax.ws.rs.ext.Provider;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.Response;
+import jakarta.ws.rs.ext.ExceptionMapper;
+import jakarta.ws.rs.ext.Provider;
import java.util.Optional;
import java.util.logging.Level;
import java.util.logging.Logger;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/errorhandlers/WebApplicationExceptionHandler.java b/src/main/java/edu/harvard/iq/dataverse/api/errorhandlers/WebApplicationExceptionHandler.java
index 5f28bfd0afc..e67e91e63c9 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/errorhandlers/WebApplicationExceptionHandler.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/errorhandlers/WebApplicationExceptionHandler.java
@@ -8,12 +8,12 @@
import edu.harvard.iq.dataverse.api.util.JsonResponseBuilder;
import edu.harvard.iq.dataverse.util.BundleUtil;
-import javax.servlet.http.HttpServletRequest;
-import javax.ws.rs.WebApplicationException;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.Response;
-import javax.ws.rs.ext.ExceptionMapper;
-import javax.ws.rs.ext.Provider;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.ws.rs.WebApplicationException;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.Response;
+import jakarta.ws.rs.ext.ExceptionMapper;
+import jakarta.ws.rs.ext.Provider;
import java.util.Optional;
import java.util.logging.Level;
import java.util.logging.Logger;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/imports/CustomFieldMap.java b/src/main/java/edu/harvard/iq/dataverse/api/imports/CustomFieldMap.java
index fc96215cef0..2bea36a6047 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/imports/CustomFieldMap.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/imports/CustomFieldMap.java
@@ -7,14 +7,14 @@
package edu.harvard.iq.dataverse.api.imports;
import java.io.Serializable;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.Table;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.Table;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/imports/CustomFieldServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/api/imports/CustomFieldServiceBean.java
index e7b8e71495b..240baeefcff 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/imports/CustomFieldServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/imports/CustomFieldServiceBean.java
@@ -5,9 +5,9 @@
*/
package edu.harvard.iq.dataverse.api.imports;
-import javax.ejb.Stateless;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
+import jakarta.ejb.Stateless;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/imports/ImportDDIServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/api/imports/ImportDDIServiceBean.java
index 39b9ddbcf5f..8f7934dd528 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/imports/ImportDDIServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/imports/ImportDDIServiceBean.java
@@ -22,15 +22,14 @@
import java.util.Map;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.ejb.Stateless;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.ejb.Stateless;
import javax.xml.stream.XMLStreamConstants;
import javax.xml.stream.XMLStreamException;
import javax.xml.stream.XMLStreamReader;
import javax.xml.stream.XMLInputFactory;
-import edu.harvard.iq.dataverse.util.json.ControlledVocabularyException;
import org.apache.commons.lang3.StringUtils;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/imports/ImportGenericServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/api/imports/ImportGenericServiceBean.java
index 57d7714ba77..f7a6cf54dd5 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/imports/ImportGenericServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/imports/ImportGenericServiceBean.java
@@ -11,7 +11,6 @@
import edu.harvard.iq.dataverse.DatasetVersion;
import edu.harvard.iq.dataverse.ForeignMetadataFieldMapping;
import edu.harvard.iq.dataverse.ForeignMetadataFormatMapping;
-import edu.harvard.iq.dataverse.GlobalId;
import edu.harvard.iq.dataverse.HandlenetServiceBean;
import edu.harvard.iq.dataverse.MetadataBlockServiceBean;
import edu.harvard.iq.dataverse.api.dto.*;
@@ -32,19 +31,19 @@
import java.util.Map;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.json.Json;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.json.Json;
import javax.xml.stream.XMLStreamConstants;
import javax.xml.stream.XMLStreamException;
import javax.xml.stream.XMLStreamReader;
-import javax.json.JsonObject;
-import javax.json.JsonReader;
-import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
-import javax.persistence.PersistenceContext;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonReader;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.PersistenceContext;
import javax.xml.stream.XMLInputFactory;
import net.handle.hdllib.HandleException;
import net.handle.hdllib.HandleResolver;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/imports/ImportServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/api/imports/ImportServiceBean.java
index cb6cef6ded5..bcb67b180c8 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/imports/ImportServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/imports/ImportServiceBean.java
@@ -51,23 +51,23 @@
import java.util.logging.Level;
import java.util.logging.LogRecord;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.ejb.Stateless;
-import javax.ejb.TransactionAttribute;
-import javax.ejb.TransactionAttributeType;
-import static javax.ejb.TransactionAttributeType.REQUIRES_NEW;
-import javax.json.Json;
-import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
-import javax.json.JsonReader;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.validation.ConstraintViolation;
-import javax.validation.ConstraintViolationException;
-import javax.validation.Validation;
-import javax.validation.Validator;
-import javax.validation.ValidatorFactory;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.ejb.Stateless;
+import jakarta.ejb.TransactionAttribute;
+import jakarta.ejb.TransactionAttributeType;
+import static jakarta.ejb.TransactionAttributeType.REQUIRES_NEW;
+import jakarta.json.Json;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.json.JsonReader;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.validation.ConstraintViolation;
+import jakarta.validation.ConstraintViolationException;
+import jakarta.validation.Validation;
+import jakarta.validation.Validator;
+import jakarta.validation.ValidatorFactory;
import javax.xml.stream.XMLStreamException;
import org.apache.commons.lang3.StringUtils;
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/util/JsonResponseBuilder.java b/src/main/java/edu/harvard/iq/dataverse/api/util/JsonResponseBuilder.java
index aef17d1ab34..71a010b7e6d 100644
--- a/src/main/java/edu/harvard/iq/dataverse/api/util/JsonResponseBuilder.java
+++ b/src/main/java/edu/harvard/iq/dataverse/api/util/JsonResponseBuilder.java
@@ -2,14 +2,14 @@
import edu.harvard.iq.dataverse.api.ApiBlockingFilter;
-import javax.json.Json;
-import javax.json.JsonValue;
-import javax.json.JsonObjectBuilder;
-import javax.servlet.ServletResponse;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.core.Response;
+import jakarta.json.Json;
+import jakarta.json.JsonValue;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.servlet.ServletResponse;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.Response;
import org.apache.commons.lang3.exception.ExceptionUtils;
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/AuthFilter.java b/src/main/java/edu/harvard/iq/dataverse/authorization/AuthFilter.java
index 15d1cb07a11..a2cf3082ae7 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/AuthFilter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/AuthFilter.java
@@ -8,14 +8,14 @@
import java.util.logging.Level;
import java.util.logging.Logger;
import java.util.logging.SimpleFormatter;
-import javax.inject.Inject;
-import javax.servlet.Filter;
-import javax.servlet.FilterChain;
-import javax.servlet.FilterConfig;
-import javax.servlet.ServletException;
-import javax.servlet.ServletRequest;
-import javax.servlet.ServletResponse;
-import javax.servlet.http.HttpServletRequest;
+import jakarta.inject.Inject;
+import jakarta.servlet.Filter;
+import jakarta.servlet.FilterChain;
+import jakarta.servlet.FilterConfig;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.ServletRequest;
+import jakarta.servlet.ServletResponse;
+import jakarta.servlet.http.HttpServletRequest;
public class AuthFilter implements Filter {
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/AuthTestDataServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/authorization/AuthTestDataServiceBean.java
index 3715900733c..9cee3ec67c7 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/AuthTestDataServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/AuthTestDataServiceBean.java
@@ -15,7 +15,7 @@
import java.util.HashMap;
import java.util.Map;
import java.util.logging.Logger;
-import javax.ejb.Stateless;
+import jakarta.ejb.Stateless;
import org.apache.commons.lang3.StringUtils;
@Stateless
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/AuthenticatedUserLookup.java b/src/main/java/edu/harvard/iq/dataverse/authorization/AuthenticatedUserLookup.java
index 94a773bc977..3291dd2efbf 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/AuthenticatedUserLookup.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/AuthenticatedUserLookup.java
@@ -2,17 +2,17 @@
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
import java.io.Serializable;
-import javax.persistence.CascadeType;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.OneToOne;
-import javax.persistence.Table;
-import javax.persistence.UniqueConstraint;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.OneToOne;
+import jakarta.persistence.Table;
+import jakarta.persistence.UniqueConstraint;
/**
* A somewhat glorified key-value pair, persisted in the database.
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/AuthenticationProvidersRegistrationServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/authorization/AuthenticationProvidersRegistrationServiceBean.java
index 6289865baf0..a93d01527a0 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/AuthenticationProvidersRegistrationServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/AuthenticationProvidersRegistrationServiceBean.java
@@ -22,15 +22,15 @@
import java.util.Map;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.annotation.PostConstruct;
-import javax.ejb.EJB;
-import javax.ejb.Lock;
-import static javax.ejb.LockType.READ;
-import static javax.ejb.LockType.WRITE;
-import javax.ejb.Singleton;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
+import jakarta.annotation.PostConstruct;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Lock;
+import static jakarta.ejb.LockType.READ;
+import static jakarta.ejb.LockType.WRITE;
+import jakarta.ejb.Singleton;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/AuthenticationServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/authorization/AuthenticationServiceBean.java
index 9bf53116efa..106a83a4ad1 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/AuthenticationServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/AuthenticationServiceBean.java
@@ -6,31 +6,23 @@
import edu.harvard.iq.dataverse.RoleAssigneeServiceBean;
import edu.harvard.iq.dataverse.UserNotificationServiceBean;
import edu.harvard.iq.dataverse.UserServiceBean;
-import edu.harvard.iq.dataverse.authorization.providers.oauth2.oidc.OIDCAuthenticationProviderFactory;
import edu.harvard.iq.dataverse.search.IndexServiceBean;
import edu.harvard.iq.dataverse.actionlogging.ActionLogRecord;
import edu.harvard.iq.dataverse.actionlogging.ActionLogServiceBean;
import edu.harvard.iq.dataverse.authorization.exceptions.AuthenticationFailedException;
-import edu.harvard.iq.dataverse.authorization.exceptions.AuthenticationProviderFactoryNotFoundException;
-import edu.harvard.iq.dataverse.authorization.exceptions.AuthorizationSetupException;
import edu.harvard.iq.dataverse.authorization.groups.impl.explicit.ExplicitGroup;
import edu.harvard.iq.dataverse.authorization.groups.impl.explicit.ExplicitGroupServiceBean;
import edu.harvard.iq.dataverse.authorization.providers.AuthenticationProviderFactory;
-import edu.harvard.iq.dataverse.authorization.providers.AuthenticationProviderRow;
import edu.harvard.iq.dataverse.authorization.providers.builtin.BuiltinAuthenticationProvider;
-import edu.harvard.iq.dataverse.authorization.providers.builtin.BuiltinAuthenticationProviderFactory;
import edu.harvard.iq.dataverse.authorization.providers.builtin.BuiltinUser;
import edu.harvard.iq.dataverse.authorization.providers.builtin.BuiltinUserServiceBean;
import edu.harvard.iq.dataverse.authorization.providers.builtin.PasswordEncryption;
import edu.harvard.iq.dataverse.authorization.providers.oauth2.AbstractOAuth2AuthenticationProvider;
-import edu.harvard.iq.dataverse.authorization.providers.oauth2.OAuth2AuthenticationProviderFactory;
import edu.harvard.iq.dataverse.authorization.providers.shib.ShibAuthenticationProvider;
-import edu.harvard.iq.dataverse.authorization.providers.shib.ShibAuthenticationProviderFactory;
import edu.harvard.iq.dataverse.authorization.users.ApiToken;
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
import edu.harvard.iq.dataverse.confirmemail.ConfirmEmailData;
import edu.harvard.iq.dataverse.confirmemail.ConfirmEmailServiceBean;
-import edu.harvard.iq.dataverse.engine.command.impl.RevokeAllRolesCommand;
import edu.harvard.iq.dataverse.passwordreset.PasswordResetData;
import edu.harvard.iq.dataverse.passwordreset.PasswordResetServiceBean;
import edu.harvard.iq.dataverse.search.savedsearch.SavedSearchServiceBean;
@@ -44,7 +36,6 @@
import java.util.Calendar;
import java.util.Collection;
import java.util.Date;
-import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
@@ -53,21 +44,21 @@
import java.util.logging.Level;
import java.util.logging.Logger;
import java.util.stream.Collectors;
-import javax.annotation.PostConstruct;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
-import javax.persistence.NonUniqueResultException;
-import javax.persistence.PersistenceContext;
-import javax.persistence.Query;
-import javax.persistence.TypedQuery;
-import javax.validation.ConstraintViolation;
-import javax.validation.Validation;
-import javax.validation.Validator;
-import javax.validation.ValidatorFactory;
+import jakarta.annotation.PostConstruct;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.NonUniqueResultException;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.Query;
+import jakarta.persistence.TypedQuery;
+import jakarta.validation.ConstraintViolation;
+import jakarta.validation.Validation;
+import jakarta.validation.Validator;
+import jakarta.validation.ValidatorFactory;
/**
* AuthenticationService is for general authentication-related operations.
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/DataverseRole.java b/src/main/java/edu/harvard/iq/dataverse/authorization/DataverseRole.java
index 12ddf817221..ff1a5546f38 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/DataverseRole.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/DataverseRole.java
@@ -11,19 +11,19 @@
import java.util.MissingResourceException;
import java.util.Objects;
import java.util.Set;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.Table;
-import javax.validation.constraints.Pattern;
-import javax.validation.constraints.Size;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.Table;
+import jakarta.validation.constraints.Pattern;
+import jakarta.validation.constraints.Size;
/**
* A role is an annotated set of permissions. A role belongs
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/DataverseRolePermissionHelper.java b/src/main/java/edu/harvard/iq/dataverse/authorization/DataverseRolePermissionHelper.java
index 4e6b54a8d49..966247bce2e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/DataverseRolePermissionHelper.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/DataverseRolePermissionHelper.java
@@ -4,21 +4,17 @@
import edu.harvard.iq.dataverse.DataFile;
import edu.harvard.iq.dataverse.Dataset;
import edu.harvard.iq.dataverse.Dataverse;
-import edu.harvard.iq.dataverse.DataverseRoleServiceBean;
-import edu.harvard.iq.dataverse.authorization.DataverseRole;
-import java.sql.Array;
-import java.util.AbstractMap;
+
import java.util.ArrayList;
import java.util.HashMap;
-import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
import org.apache.commons.lang3.StringUtils;
/*
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/groups/GroupServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/authorization/groups/GroupServiceBean.java
index 66293a4f781..a746eee0a60 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/groups/GroupServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/groups/GroupServiceBean.java
@@ -26,11 +26,11 @@
import java.util.logging.Logger;
import static java.util.stream.Collectors.toSet;
import java.util.stream.Stream;
-import javax.annotation.PostConstruct;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.annotation.PostConstruct;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/PersistedGlobalGroup.java b/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/PersistedGlobalGroup.java
index 52785d5c7e2..1ef3b01d752 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/PersistedGlobalGroup.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/PersistedGlobalGroup.java
@@ -3,14 +3,14 @@
import edu.harvard.iq.dataverse.authorization.groups.Group;
import edu.harvard.iq.dataverse.authorization.RoleAssigneeDisplayInfo;
import java.io.Serializable;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.Table;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.Table;
/**
* Convenience base class for implementing groups that apply to the entire Dataverse
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/explicit/ExplicitGroup.java b/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/explicit/ExplicitGroup.java
index 43705a2240e..2723561d8b4 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/explicit/ExplicitGroup.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/explicit/ExplicitGroup.java
@@ -13,24 +13,24 @@
import java.util.Objects;
import java.util.Set;
import java.util.TreeSet;
-import javax.persistence.Column;
-import javax.persistence.ElementCollection;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.JoinTable;
-import javax.persistence.ManyToMany;
-import javax.persistence.ManyToOne;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.PostLoad;
-import javax.persistence.PrePersist;
-import javax.persistence.Table;
-import javax.persistence.Transient;
-import javax.validation.constraints.Pattern;
+import jakarta.persistence.Column;
+import jakarta.persistence.ElementCollection;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.JoinTable;
+import jakarta.persistence.ManyToMany;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.PostLoad;
+import jakarta.persistence.PrePersist;
+import jakarta.persistence.Table;
+import jakarta.persistence.Transient;
+import jakarta.validation.constraints.Pattern;
import org.hibernate.validator.constraints.NotBlank;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/explicit/ExplicitGroupServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/explicit/ExplicitGroupServiceBean.java
index b7c1b46b3a7..a688fac0e34 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/explicit/ExplicitGroupServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/explicit/ExplicitGroupServiceBean.java
@@ -10,17 +10,16 @@
import java.util.List;
import java.util.Set;
import java.util.TreeSet;
-import java.util.logging.Level;
import java.util.logging.Logger;
import java.util.stream.Collectors;
import static java.util.stream.Collectors.joining;
-import javax.annotation.PostConstruct;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
-import javax.persistence.PersistenceContext;
+import jakarta.annotation.PostConstruct;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.PersistenceContext;
/**
* A bean providing the {@link ExplicitGroupProvider}s with container services,
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/ipaddress/IpGroup.java b/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/ipaddress/IpGroup.java
index a3231557898..038fbbfc6e0 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/ipaddress/IpGroup.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/ipaddress/IpGroup.java
@@ -12,12 +12,12 @@
import java.util.HashSet;
import java.util.Objects;
import java.util.Set;
-import javax.persistence.CascadeType;
-import javax.persistence.Entity;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.OneToMany;
-import javax.persistence.Transient;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Entity;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.OneToMany;
+import jakarta.persistence.Transient;
@NamedQueries({
@NamedQuery(name="IpGroup.findAll",
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/ipaddress/IpGroupsServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/ipaddress/IpGroupsServiceBean.java
index c03cf26e11e..15282045b3a 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/ipaddress/IpGroupsServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/ipaddress/IpGroupsServiceBean.java
@@ -10,12 +10,12 @@
import java.util.List;
import java.util.Set;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
-import javax.persistence.PersistenceContext;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.PersistenceContext;
/**
* Provides CRUD tools to efficiently manage IP groups in a Java EE container.
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/ipaddress/ip/IPv4Range.java b/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/ipaddress/ip/IPv4Range.java
index 3ecd7689e1c..8694b7d455b 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/ipaddress/ip/IPv4Range.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/ipaddress/ip/IPv4Range.java
@@ -1,13 +1,13 @@
package edu.harvard.iq.dataverse.authorization.groups.impl.ipaddress.ip;
import java.math.BigInteger;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.Table;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.Table;
/**
* A range of IPv4 addresses. In order to make SQL querying efficient, the actual fields
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/ipaddress/ip/IPv6Range.java b/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/ipaddress/ip/IPv6Range.java
index d1301d550c7..379c64a88cf 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/ipaddress/ip/IPv6Range.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/ipaddress/ip/IPv6Range.java
@@ -1,13 +1,13 @@
package edu.harvard.iq.dataverse.authorization.groups.impl.ipaddress.ip;
import java.io.Serializable;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.Table;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.Table;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/ipaddress/ip/IpAddressRange.java b/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/ipaddress/ip/IpAddressRange.java
index b71dbcd0eba..fc21397898f 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/ipaddress/ip/IpAddressRange.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/ipaddress/ip/IpAddressRange.java
@@ -2,8 +2,8 @@
import edu.harvard.iq.dataverse.authorization.groups.impl.ipaddress.IpGroup;
import java.util.Objects;
-import javax.persistence.ManyToOne;
-import javax.persistence.MappedSuperclass;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.MappedSuperclass;
/**
* A range of {@link IpAddress}es. Abstract class - to instantiate, you need to
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/maildomain/MailDomainGroup.java b/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/maildomain/MailDomainGroup.java
index def11c57076..15b2fd1810c 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/maildomain/MailDomainGroup.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/maildomain/MailDomainGroup.java
@@ -6,11 +6,11 @@
import java.util.Arrays;
import java.util.List;
import java.util.Objects;
-import javax.persistence.Entity;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.Transient;
-import javax.validation.constraints.NotEmpty;
+import jakarta.persistence.Entity;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.Transient;
+import jakarta.validation.constraints.NotEmpty;
;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/maildomain/MailDomainGroupServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/maildomain/MailDomainGroupServiceBean.java
index 58e72b7b575..b1b1e883705 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/maildomain/MailDomainGroupServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/maildomain/MailDomainGroupServiceBean.java
@@ -9,14 +9,14 @@
import java.util.logging.Logger;
import java.util.regex.Pattern;
import java.util.stream.Collectors;
-import javax.annotation.PostConstruct;
-import javax.ejb.*;
-import javax.inject.Inject;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
-import javax.persistence.PersistenceContext;
-import javax.ws.rs.NotFoundException;
+import jakarta.annotation.PostConstruct;
+import jakarta.ejb.*;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.PersistenceContext;
+import jakarta.ws.rs.NotFoundException;
/**
* A bean providing the {@link MailDomainGroupProvider}s with container services, such as database connectivity.
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/shib/ShibGroup.java b/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/shib/ShibGroup.java
index 79fda0ca7d7..30850f0fb20 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/shib/ShibGroup.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/shib/ShibGroup.java
@@ -1,17 +1,16 @@
package edu.harvard.iq.dataverse.authorization.groups.impl.shib;
-import edu.harvard.iq.dataverse.authorization.RoleAssignee;
import edu.harvard.iq.dataverse.authorization.RoleAssigneeDisplayInfo;
import edu.harvard.iq.dataverse.authorization.groups.Group;
import edu.harvard.iq.dataverse.authorization.groups.GroupProvider;
import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
import java.io.Serializable;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Transient;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Transient;
/**
* Persistence for Shibboleth groups.
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/shib/ShibGroupServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/shib/ShibGroupServiceBean.java
index c15e56ee7e0..7a7844b7c1e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/shib/ShibGroupServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/groups/impl/shib/ShibGroupServiceBean.java
@@ -11,14 +11,14 @@
import java.util.List;
import java.util.Set;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
-import javax.persistence.NonUniqueResultException;
-import javax.persistence.PersistenceContext;
-import javax.persistence.TypedQuery;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.NonUniqueResultException;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.TypedQuery;
/**
* @todo Consider merging this bean into the newer and more generic
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/AuthenticationProviderRow.java b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/AuthenticationProviderRow.java
index 6b9c545b7f9..2f37c777877 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/AuthenticationProviderRow.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/AuthenticationProviderRow.java
@@ -2,13 +2,13 @@
import edu.harvard.iq.dataverse.authorization.AuthenticationProvider;
import java.util.Objects;
-import javax.persistence.Entity;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.Lob;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.Table;
+import jakarta.persistence.Entity;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.Lob;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.Table;
/**
* Database-storable form of an {@code AuthenticationProvider}.
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/builtin/BuiltinUser.java b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/builtin/BuiltinUser.java
index c2510b8b043..2ce36997ea9 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/builtin/BuiltinUser.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/builtin/BuiltinUser.java
@@ -5,20 +5,20 @@
import edu.harvard.iq.dataverse.passwordreset.PasswordResetData;
import java.io.Serializable;
-import javax.persistence.CascadeType;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.OneToOne;
-import javax.persistence.Table;
-import javax.persistence.Transient;
-import javax.validation.constraints.NotBlank;
-import javax.validation.constraints.Size;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.OneToOne;
+import jakarta.persistence.Table;
+import jakarta.persistence.Transient;
+import jakarta.validation.constraints.NotBlank;
+import jakarta.validation.constraints.Size;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/builtin/BuiltinUserServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/builtin/BuiltinUserServiceBean.java
index c39c7cb2985..ffbc5d7a027 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/builtin/BuiltinUserServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/builtin/BuiltinUserServiceBean.java
@@ -9,17 +9,17 @@
import java.util.Set;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
-import javax.persistence.NonUniqueResultException;
-import javax.persistence.PersistenceContext;
-import javax.validation.ConstraintViolation;
-import javax.validation.Validation;
-import javax.validation.Validator;
-import javax.validation.ValidatorFactory;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.NonUniqueResultException;
+import jakarta.persistence.PersistenceContext;
+import jakarta.validation.ConstraintViolation;
+import jakarta.validation.Validation;
+import jakarta.validation.Validator;
+import jakarta.validation.ValidatorFactory;
/**
*
@@ -88,7 +88,7 @@ public BuiltinUser findByUserName(String userName) {
return em.createNamedQuery("BuiltinUser.findByUserName", BuiltinUser.class)
.setParameter("userName", userName)
.getSingleResult();
- } catch (javax.persistence.NoResultException e) {
+ } catch (NoResultException e) {
return null;
} catch (NonUniqueResultException ex) {
logger.log(Level.WARNING, "multiple accounts found for username {0}", userName);
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/builtin/DataverseUserPage.java b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/builtin/DataverseUserPage.java
index 5c0f3a49f76..dc4644dfccd 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/builtin/DataverseUserPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/builtin/DataverseUserPage.java
@@ -51,15 +51,15 @@
import java.util.logging.Level;
import java.util.logging.Logger;
import java.util.stream.Collectors;
-import javax.ejb.EJB;
-import javax.faces.application.FacesMessage;
-import javax.faces.component.UIComponent;
-import javax.faces.component.UIInput;
-import javax.faces.context.FacesContext;
-import javax.faces.event.ActionEvent;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.component.UIInput;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.event.ActionEvent;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
import org.apache.commons.lang3.StringUtils;
import org.hibernate.validator.constraints.NotBlank;
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/AbstractOAuth2AuthenticationProvider.java b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/AbstractOAuth2AuthenticationProvider.java
index 01139cd2e27..48efe1e2592 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/AbstractOAuth2AuthenticationProvider.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/AbstractOAuth2AuthenticationProvider.java
@@ -14,7 +14,7 @@
import edu.harvard.iq.dataverse.authorization.AuthenticationProviderDisplayInfo;
import edu.harvard.iq.dataverse.util.BundleUtil;
-import javax.validation.constraints.NotNull;
+import jakarta.validation.constraints.NotNull;
import java.io.IOException;
import java.util.*;
import java.util.concurrent.ExecutionException;
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/OAuth2FirstLoginPage.java b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/OAuth2FirstLoginPage.java
index 54ba3ec6a05..821e8a5ea6c 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/OAuth2FirstLoginPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/OAuth2FirstLoginPage.java
@@ -30,14 +30,14 @@
import java.util.Map;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.enterprise.context.SessionScoped;
-import javax.faces.application.FacesMessage;
-import javax.faces.component.UIComponent;
-import javax.faces.component.UIInput;
-import javax.faces.context.FacesContext;
-import javax.inject.Named;
-import javax.inject.Inject;
+import jakarta.ejb.EJB;
+import jakarta.enterprise.context.SessionScoped;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.component.UIInput;
+import jakarta.faces.context.FacesContext;
+import jakarta.inject.Named;
+import jakarta.inject.Inject;
import org.hibernate.validator.constraints.NotBlank;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/OAuth2LoginBackingBean.java b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/OAuth2LoginBackingBean.java
index c5be41a014a..99df2375a79 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/OAuth2LoginBackingBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/OAuth2LoginBackingBean.java
@@ -20,12 +20,12 @@
import java.util.logging.Level;
import java.util.logging.Logger;
import static java.util.stream.Collectors.toList;
-import javax.ejb.EJB;
-import javax.inject.Named;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.servlet.http.HttpServletRequest;
-import javax.validation.constraints.NotNull;
+import jakarta.ejb.EJB;
+import jakarta.inject.Named;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.validation.constraints.NotNull;
import static edu.harvard.iq.dataverse.util.StringUtil.toOption;
import edu.harvard.iq.dataverse.util.SystemConfig;
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/OAuth2TokenData.java b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/OAuth2TokenData.java
index a5ee5ddf537..59f659ff297 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/OAuth2TokenData.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/OAuth2TokenData.java
@@ -4,14 +4,14 @@
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
import java.io.Serializable;
import java.sql.Timestamp;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.ManyToOne;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
/**
* Token data for a given user, received from an OAuth2 system. Contains the
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/OAuth2TokenDataServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/OAuth2TokenDataServiceBean.java
index d8f1fa7600b..b1dcb6df8cc 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/OAuth2TokenDataServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/OAuth2TokenDataServiceBean.java
@@ -2,10 +2,10 @@
import java.util.List;
import java.util.Optional;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
/**
* CRUD for {@link OAuth2TokenData}.
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/impl/GitHubOAuth2AP.java b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/impl/GitHubOAuth2AP.java
index 62f3cc382e2..8829a25336b 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/impl/GitHubOAuth2AP.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/impl/GitHubOAuth2AP.java
@@ -9,9 +9,9 @@
import edu.harvard.iq.dataverse.util.BundleUtil;
import java.io.StringReader;
import java.util.Collections;
-import javax.json.Json;
-import javax.json.JsonObject;
-import javax.json.JsonReader;
+import jakarta.json.Json;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonReader;
/**
* IDP adaptor for GitHub.com
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/impl/GoogleOAuth2AP.java b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/impl/GoogleOAuth2AP.java
index 1fa5470d551..a864ecb810a 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/impl/GoogleOAuth2AP.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/impl/GoogleOAuth2AP.java
@@ -8,9 +8,9 @@
import java.io.StringReader;
import java.util.Arrays;
import java.util.UUID;
-import javax.json.Json;
-import javax.json.JsonObject;
-import javax.json.JsonReader;
+import jakarta.json.Json;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonReader;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/impl/MicrosoftOAuth2AP.java b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/impl/MicrosoftOAuth2AP.java
index da260a9fb0e..bd3caccc220 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/impl/MicrosoftOAuth2AP.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/impl/MicrosoftOAuth2AP.java
@@ -8,9 +8,9 @@
import java.util.Collections;
import java.util.logging.Logger;
import java.io.StringReader;
-import javax.json.Json;
-import javax.json.JsonObject;
-import javax.json.JsonReader;
+import jakarta.json.Json;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonReader;
import edu.harvard.iq.dataverse.authorization.AuthenticatedUserDisplayInfo;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/impl/OrcidOAuth2AP.java b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/impl/OrcidOAuth2AP.java
index 02177ee0032..089ca40e164 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/impl/OrcidOAuth2AP.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/impl/OrcidOAuth2AP.java
@@ -23,10 +23,10 @@
import static java.util.stream.Collectors.joining;
import java.util.stream.IntStream;
import java.util.stream.Stream;
-import javax.json.Json;
-import javax.json.JsonObject;
-import javax.json.JsonReader;
-import javax.validation.constraints.NotNull;
+import jakarta.json.Json;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonReader;
+import jakarta.validation.constraints.NotNull;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/shib/ShibServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/shib/ShibServiceBean.java
index 3e986a15689..0921b2c6683 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/shib/ShibServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/shib/ShibServiceBean.java
@@ -4,17 +4,11 @@
import com.google.gson.JsonElement;
import com.google.gson.JsonParser;
import edu.harvard.iq.dataverse.authorization.AuthTestDataServiceBean;
-import edu.harvard.iq.dataverse.authorization.AuthenticationRequest;
-import edu.harvard.iq.dataverse.authorization.AuthenticationResponse;
import edu.harvard.iq.dataverse.authorization.AuthenticationServiceBean;
-import edu.harvard.iq.dataverse.authorization.exceptions.AuthenticationFailedException;
-import edu.harvard.iq.dataverse.authorization.providers.builtin.BuiltinAuthenticationProvider;
import edu.harvard.iq.dataverse.authorization.providers.builtin.BuiltinUser;
import edu.harvard.iq.dataverse.authorization.providers.builtin.BuiltinUserServiceBean;
-import edu.harvard.iq.dataverse.authorization.providers.builtin.PasswordEncryption;
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
-import edu.harvard.iq.dataverse.util.BundleUtil;
import edu.harvard.iq.dataverse.util.SystemConfig;
import java.io.IOException;
import java.io.InputStream;
@@ -25,11 +19,11 @@
import java.util.Map;
import java.util.UUID;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.servlet.http.HttpServletRequest;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.servlet.http.HttpServletRequest;
@Named
@Stateless
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/shib/ShibUtil.java b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/shib/ShibUtil.java
index f8b30710656..fff135e0dec 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/shib/ShibUtil.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/shib/ShibUtil.java
@@ -12,7 +12,7 @@
import java.util.Map;
import java.util.UUID;
import java.util.logging.Logger;
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
public class ShibUtil {
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/users/ApiToken.java b/src/main/java/edu/harvard/iq/dataverse/authorization/users/ApiToken.java
index fc7ed8a9060..0de7d7754a1 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/users/ApiToken.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/users/ApiToken.java
@@ -2,18 +2,18 @@
import java.io.Serializable;
import java.sql.Timestamp;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.Table;
-import javax.validation.constraints.NotNull;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.Table;
+import jakarta.validation.constraints.NotNull;
@Entity
@NamedQueries({
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/users/AuthenticatedUser.java b/src/main/java/edu/harvard/iq/dataverse/authorization/users/AuthenticatedUser.java
index 9fdfce2f1a7..89429b912f6 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/users/AuthenticatedUser.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/users/AuthenticatedUser.java
@@ -23,22 +23,22 @@
import java.util.Objects;
import java.util.Set;
-import javax.json.Json;
-import javax.json.JsonObjectBuilder;
-import javax.persistence.CascadeType;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.OneToMany;
-import javax.persistence.OneToOne;
-import javax.persistence.PostLoad;
-import javax.persistence.PrePersist;
-import javax.persistence.Transient;
-import javax.validation.constraints.NotNull;
+import jakarta.json.Json;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.OneToMany;
+import jakarta.persistence.OneToOne;
+import jakarta.persistence.PostLoad;
+import jakarta.persistence.PrePersist;
+import jakarta.persistence.Transient;
+import jakarta.validation.constraints.NotNull;
import org.hibernate.validator.constraints.NotBlank;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/batch/entities/JobExecutionEntity.java b/src/main/java/edu/harvard/iq/dataverse/batch/entities/JobExecutionEntity.java
index be2167fa4d5..debece131d3 100644
--- a/src/main/java/edu/harvard/iq/dataverse/batch/entities/JobExecutionEntity.java
+++ b/src/main/java/edu/harvard/iq/dataverse/batch/entities/JobExecutionEntity.java
@@ -1,10 +1,10 @@
package edu.harvard.iq.dataverse.batch.entities;
-import javax.batch.operations.JobOperator;
-import javax.batch.runtime.BatchRuntime;
-import javax.batch.runtime.BatchStatus;
-import javax.batch.runtime.JobExecution;
-import javax.batch.runtime.StepExecution;
+import jakarta.batch.operations.JobOperator;
+import jakarta.batch.runtime.BatchRuntime;
+import jakarta.batch.runtime.BatchStatus;
+import jakarta.batch.runtime.JobExecution;
+import jakarta.batch.runtime.StepExecution;
import java.util.ArrayList;
import java.util.Date;
import java.util.LinkedHashMap;
diff --git a/src/main/java/edu/harvard/iq/dataverse/batch/entities/StepExecutionEntity.java b/src/main/java/edu/harvard/iq/dataverse/batch/entities/StepExecutionEntity.java
index 65ed3f32e1b..ba20386ed07 100644
--- a/src/main/java/edu/harvard/iq/dataverse/batch/entities/StepExecutionEntity.java
+++ b/src/main/java/edu/harvard/iq/dataverse/batch/entities/StepExecutionEntity.java
@@ -1,8 +1,8 @@
package edu.harvard.iq.dataverse.batch.entities;
-import javax.batch.runtime.BatchStatus;
-import javax.batch.runtime.Metric;
-import javax.batch.runtime.StepExecution;
+import jakarta.batch.runtime.BatchStatus;
+import jakarta.batch.runtime.Metric;
+import jakarta.batch.runtime.StepExecution;
import java.util.Date;
import java.util.HashMap;
import java.util.Map;
diff --git a/src/main/java/edu/harvard/iq/dataverse/batch/jobs/importer/filesystem/FileRecordJobListener.java b/src/main/java/edu/harvard/iq/dataverse/batch/jobs/importer/filesystem/FileRecordJobListener.java
index a5ba9a00bd2..593a5cbfdc3 100644
--- a/src/main/java/edu/harvard/iq/dataverse/batch/jobs/importer/filesystem/FileRecordJobListener.java
+++ b/src/main/java/edu/harvard/iq/dataverse/batch/jobs/importer/filesystem/FileRecordJobListener.java
@@ -40,22 +40,22 @@
import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
import edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetVersionCommand;
-import javax.batch.api.BatchProperty;
-import javax.batch.api.chunk.listener.ItemReadListener;
-import javax.batch.api.listener.JobListener;
-import javax.batch.api.listener.StepListener;
-import javax.batch.operations.JobOperator;
-import javax.batch.runtime.BatchRuntime;
-import javax.batch.runtime.BatchStatus;
-import javax.batch.runtime.JobExecution;
-import javax.batch.runtime.StepExecution;
-import javax.batch.runtime.context.JobContext;
-import javax.batch.runtime.context.StepContext;
-import javax.ejb.EJB;
-import javax.enterprise.context.Dependent;
-import javax.inject.Inject;
-import javax.inject.Named;
-import javax.servlet.http.HttpServletRequest;
+import jakarta.batch.api.BatchProperty;
+import jakarta.batch.api.chunk.listener.ItemReadListener;
+import jakarta.batch.api.listener.JobListener;
+import jakarta.batch.api.listener.StepListener;
+import jakarta.batch.operations.JobOperator;
+import jakarta.batch.runtime.BatchRuntime;
+import jakarta.batch.runtime.BatchStatus;
+import jakarta.batch.runtime.JobExecution;
+import jakarta.batch.runtime.StepExecution;
+import jakarta.batch.runtime.context.JobContext;
+import jakarta.batch.runtime.context.StepContext;
+import jakarta.ejb.EJB;
+import jakarta.enterprise.context.Dependent;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
+import jakarta.servlet.http.HttpServletRequest;
import edu.harvard.iq.dataverse.settings.JvmSettings;
import org.apache.commons.io.IOUtils;
@@ -74,8 +74,8 @@
import java.util.logging.Handler;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.batch.operations.JobSecurityException;
-import javax.batch.operations.NoSuchJobExecutionException;
+import jakarta.batch.operations.JobSecurityException;
+import jakarta.batch.operations.NoSuchJobExecutionException;
@Named
@Dependent
diff --git a/src/main/java/edu/harvard/iq/dataverse/batch/jobs/importer/filesystem/FileRecordProcessor.java b/src/main/java/edu/harvard/iq/dataverse/batch/jobs/importer/filesystem/FileRecordProcessor.java
index af7caf32a7c..e5db80b9aa6 100644
--- a/src/main/java/edu/harvard/iq/dataverse/batch/jobs/importer/filesystem/FileRecordProcessor.java
+++ b/src/main/java/edu/harvard/iq/dataverse/batch/jobs/importer/filesystem/FileRecordProcessor.java
@@ -25,15 +25,15 @@
import edu.harvard.iq.dataverse.DatasetServiceBean;
import edu.harvard.iq.dataverse.DatasetVersion;
-import javax.annotation.PostConstruct;
-import javax.batch.api.chunk.ItemProcessor;
-import javax.batch.operations.JobOperator;
-import javax.batch.runtime.BatchRuntime;
-import javax.batch.runtime.context.JobContext;
-import javax.ejb.EJB;
-import javax.enterprise.context.Dependent;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.annotation.PostConstruct;
+import jakarta.batch.api.chunk.ItemProcessor;
+import jakarta.batch.operations.JobOperator;
+import jakarta.batch.runtime.BatchRuntime;
+import jakarta.batch.runtime.context.JobContext;
+import jakarta.ejb.EJB;
+import jakarta.enterprise.context.Dependent;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
import java.io.File;
import java.util.Properties;
import java.util.logging.Level;
diff --git a/src/main/java/edu/harvard/iq/dataverse/batch/jobs/importer/filesystem/FileRecordReader.java b/src/main/java/edu/harvard/iq/dataverse/batch/jobs/importer/filesystem/FileRecordReader.java
index a4f8ffd2378..fb702c21df2 100644
--- a/src/main/java/edu/harvard/iq/dataverse/batch/jobs/importer/filesystem/FileRecordReader.java
+++ b/src/main/java/edu/harvard/iq/dataverse/batch/jobs/importer/filesystem/FileRecordReader.java
@@ -28,17 +28,17 @@
import org.apache.commons.io.filefilter.NotFileFilter;
import org.apache.commons.io.filefilter.WildcardFileFilter;
-import javax.annotation.PostConstruct;
-import javax.batch.api.BatchProperty;
-import javax.batch.api.chunk.AbstractItemReader;
-import javax.batch.operations.JobOperator;
-import javax.batch.runtime.BatchRuntime;
-import javax.batch.runtime.context.JobContext;
-import javax.batch.runtime.context.StepContext;
-import javax.ejb.EJB;
-import javax.enterprise.context.Dependent;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.annotation.PostConstruct;
+import jakarta.batch.api.BatchProperty;
+import jakarta.batch.api.chunk.AbstractItemReader;
+import jakarta.batch.operations.JobOperator;
+import jakarta.batch.runtime.BatchRuntime;
+import jakarta.batch.runtime.context.JobContext;
+import jakarta.batch.runtime.context.StepContext;
+import jakarta.ejb.EJB;
+import jakarta.enterprise.context.Dependent;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
import java.io.File;
import java.io.FileFilter;
import java.io.Serializable;
diff --git a/src/main/java/edu/harvard/iq/dataverse/batch/jobs/importer/filesystem/FileRecordWriter.java b/src/main/java/edu/harvard/iq/dataverse/batch/jobs/importer/filesystem/FileRecordWriter.java
index 195ed57bd43..ba34a3d1ed1 100644
--- a/src/main/java/edu/harvard/iq/dataverse/batch/jobs/importer/filesystem/FileRecordWriter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/batch/jobs/importer/filesystem/FileRecordWriter.java
@@ -36,17 +36,17 @@
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
import edu.harvard.iq.dataverse.util.FileUtil;
-import javax.annotation.PostConstruct;
-import javax.batch.api.BatchProperty;
-import javax.batch.api.chunk.AbstractItemWriter;
-import javax.batch.operations.JobOperator;
-import javax.batch.runtime.BatchRuntime;
-import javax.batch.runtime.context.JobContext;
-import javax.batch.runtime.context.StepContext;
-import javax.ejb.EJB;
-import javax.enterprise.context.Dependent;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.annotation.PostConstruct;
+import jakarta.batch.api.BatchProperty;
+import jakarta.batch.api.chunk.AbstractItemWriter;
+import jakarta.batch.operations.JobOperator;
+import jakarta.batch.runtime.BatchRuntime;
+import jakarta.batch.runtime.context.JobContext;
+import jakarta.batch.runtime.context.StepContext;
+import jakarta.ejb.EJB;
+import jakarta.enterprise.context.Dependent;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
import java.io.File;
import java.io.Serializable;
import java.sql.Timestamp;
@@ -57,7 +57,7 @@
import java.util.Properties;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
import edu.harvard.iq.dataverse.GlobalIdServiceBean;
@Named
diff --git a/src/main/java/edu/harvard/iq/dataverse/batch/util/LoggingUtil.java b/src/main/java/edu/harvard/iq/dataverse/batch/util/LoggingUtil.java
index a2f76ca953d..19d1112ba54 100644
--- a/src/main/java/edu/harvard/iq/dataverse/batch/util/LoggingUtil.java
+++ b/src/main/java/edu/harvard/iq/dataverse/batch/util/LoggingUtil.java
@@ -25,7 +25,7 @@
import edu.harvard.iq.dataverse.engine.command.Command;
import org.apache.commons.io.FileUtils;
-import javax.batch.runtime.JobExecution;
+import jakarta.batch.runtime.JobExecution;
import java.io.File;
import java.io.IOException;
import java.text.SimpleDateFormat;
diff --git a/src/main/java/edu/harvard/iq/dataverse/branding/BrandingUtil.java b/src/main/java/edu/harvard/iq/dataverse/branding/BrandingUtil.java
index 3cb071fe03f..c230229abf9 100644
--- a/src/main/java/edu/harvard/iq/dataverse/branding/BrandingUtil.java
+++ b/src/main/java/edu/harvard/iq/dataverse/branding/BrandingUtil.java
@@ -6,7 +6,7 @@
import java.util.Arrays;
import java.util.logging.Logger;
-import javax.mail.internet.InternetAddress;
+import jakarta.mail.internet.InternetAddress;
public class BrandingUtil {
diff --git a/src/main/java/edu/harvard/iq/dataverse/branding/BrandingUtilHelper.java b/src/main/java/edu/harvard/iq/dataverse/branding/BrandingUtilHelper.java
index 274970f8b8e..7729ab4763e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/branding/BrandingUtilHelper.java
+++ b/src/main/java/edu/harvard/iq/dataverse/branding/BrandingUtilHelper.java
@@ -1,9 +1,9 @@
package edu.harvard.iq.dataverse.branding;
-import javax.annotation.PostConstruct;
-import javax.ejb.EJB;
-import javax.ejb.Singleton;
-import javax.ejb.Startup;
+import jakarta.annotation.PostConstruct;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Singleton;
+import jakarta.ejb.Startup;
import edu.harvard.iq.dataverse.DataverseServiceBean;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
diff --git a/src/main/java/edu/harvard/iq/dataverse/confirmemail/ConfirmEmailData.java b/src/main/java/edu/harvard/iq/dataverse/confirmemail/ConfirmEmailData.java
index c05750c13e6..0ad9ab59f4b 100644
--- a/src/main/java/edu/harvard/iq/dataverse/confirmemail/ConfirmEmailData.java
+++ b/src/main/java/edu/harvard/iq/dataverse/confirmemail/ConfirmEmailData.java
@@ -5,17 +5,17 @@
import java.sql.Timestamp;
import java.util.Date;
import java.util.UUID;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.OneToOne;
-import javax.persistence.Table;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.OneToOne;
+import jakarta.persistence.Table;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/confirmemail/ConfirmEmailPage.java b/src/main/java/edu/harvard/iq/dataverse/confirmemail/ConfirmEmailPage.java
index 07aea0d5011..b76e3db1379 100644
--- a/src/main/java/edu/harvard/iq/dataverse/confirmemail/ConfirmEmailPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/confirmemail/ConfirmEmailPage.java
@@ -7,10 +7,10 @@
import edu.harvard.iq.dataverse.util.JsfHelper;
import java.util.Arrays;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/confirmemail/ConfirmEmailServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/confirmemail/ConfirmEmailServiceBean.java
index e1053c3a93f..a54fd6bb0c1 100644
--- a/src/main/java/edu/harvard/iq/dataverse/confirmemail/ConfirmEmailServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/confirmemail/ConfirmEmailServiceBean.java
@@ -1,6 +1,5 @@
package edu.harvard.iq.dataverse.confirmemail;
-import edu.harvard.iq.dataverse.Dataverse;
import edu.harvard.iq.dataverse.DataverseServiceBean;
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
import edu.harvard.iq.dataverse.authorization.AuthenticationServiceBean;
@@ -16,13 +15,13 @@
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
-import javax.persistence.NonUniqueResultException;
-import javax.persistence.PersistenceContext;
-import javax.persistence.TypedQuery;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.NonUniqueResultException;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.TypedQuery;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/dashboard/DashboardDatamovePage.java b/src/main/java/edu/harvard/iq/dataverse/dashboard/DashboardDatamovePage.java
index 54e3114a0ae..6fc80312bf5 100644
--- a/src/main/java/edu/harvard/iq/dataverse/dashboard/DashboardDatamovePage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/dashboard/DashboardDatamovePage.java
@@ -8,7 +8,6 @@
import edu.harvard.iq.dataverse.EjbDataverseEngine;
import edu.harvard.iq.dataverse.PermissionsWrapper;
import edu.harvard.iq.dataverse.SettingsWrapper;
-import edu.harvard.iq.dataverse.authorization.groups.impl.ipaddress.ip.IpAddress;
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
@@ -22,16 +21,16 @@
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.faces.application.FacesMessage;
-import javax.faces.component.UIInput;
-import javax.faces.context.FacesContext;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.servlet.http.HttpServletRequest;
+import jakarta.ejb.EJB;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.component.UIInput;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.servlet.http.HttpServletRequest;
@ViewScoped
@Named("DashboardDatamovePage")
diff --git a/src/main/java/edu/harvard/iq/dataverse/dashboard/DashboardUsersPage.java b/src/main/java/edu/harvard/iq/dataverse/dashboard/DashboardUsersPage.java
index 5b5a21e21bf..477e4c0fdd6 100644
--- a/src/main/java/edu/harvard/iq/dataverse/dashboard/DashboardUsersPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/dashboard/DashboardUsersPage.java
@@ -24,10 +24,10 @@
import java.util.Map;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
@ViewScoped
@Named("DashboardUsersPage")
diff --git a/src/main/java/edu/harvard/iq/dataverse/dataaccess/FileAccessIO.java b/src/main/java/edu/harvard/iq/dataverse/dataaccess/FileAccessIO.java
index 8ee3f0cf53c..d95df1567bd 100644
--- a/src/main/java/edu/harvard/iq/dataverse/dataaccess/FileAccessIO.java
+++ b/src/main/java/edu/harvard/iq/dataverse/dataaccess/FileAccessIO.java
@@ -565,21 +565,26 @@ private String getDatasetDirectory() throws IOException {
if (isDirectAccess()) {
throw new IOException("No DvObject defined in the Data Access Object");
}
-
- Path datasetDirectoryPath=null;
+ String authorityForFS = null;
+ String identifierForFS = null;
if (dvObject instanceof Dataset) {
- datasetDirectoryPath = Paths.get(this.getDataset().getAuthorityForFileStorage(), this.getDataset().getIdentifierForFileStorage());
+ authorityForFS = this.getDataset().getAuthorityForFileStorage();
+ identifierForFS = this.getDataset().getIdentifierForFileStorage();
} else if (dvObject instanceof DataFile) {
- datasetDirectoryPath = Paths.get(this.getDataFile().getOwner().getAuthorityForFileStorage(), this.getDataFile().getOwner().getIdentifierForFileStorage());
+ authorityForFS = this.getDataFile().getOwner().getAuthorityForFileStorage();
+ identifierForFS = this.getDataFile().getOwner().getIdentifierForFileStorage();
} else if (dvObject instanceof Dataverse) {
throw new IOException("FileAccessIO: Dataverses are not a supported dvObject");
}
-
- if (datasetDirectoryPath == null) {
+
+ if (authorityForFS == null || identifierForFS == null) {
throw new IOException("Could not determine the filesystem directory of the parent dataset.");
}
- String datasetDirectory = Paths.get(getFilesRootDirectory(), datasetDirectoryPath.toString()).toString();
+
+ // Determine the final directory tree. As of JDK 16, the first component of the path MUST be non-null
+ // (we check for that via the setting), but also the others make no sense if they are null.
+ String datasetDirectory = Paths.get(getFilesRootDirectory(), authorityForFS, identifierForFS).toString();
if (dvObject.getStorageIdentifier() == null || dvObject.getStorageIdentifier().isEmpty()) {
throw new IOException("Data Access: No local storage identifier defined for this datafile.");
diff --git a/src/main/java/edu/harvard/iq/dataverse/dataaccess/S3AccessIO.java b/src/main/java/edu/harvard/iq/dataverse/dataaccess/S3AccessIO.java
index f6bca84941e..822ada0b83e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/dataaccess/S3AccessIO.java
+++ b/src/main/java/edu/harvard/iq/dataverse/dataaccess/S3AccessIO.java
@@ -69,9 +69,9 @@
import org.eclipse.microprofile.config.Config;
import org.eclipse.microprofile.config.ConfigProvider;
-import javax.json.Json;
-import javax.json.JsonObjectBuilder;
-import javax.validation.constraints.NotNull;
+import jakarta.json.Json;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.validation.constraints.NotNull;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/datacapturemodule/DataCaptureModuleServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/datacapturemodule/DataCaptureModuleServiceBean.java
index c33b4e0fc71..bf5d4a0d6ab 100644
--- a/src/main/java/edu/harvard/iq/dataverse/datacapturemodule/DataCaptureModuleServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/datacapturemodule/DataCaptureModuleServiceBean.java
@@ -6,8 +6,8 @@
import com.mashape.unirest.http.Unirest;
import com.mashape.unirest.http.exceptions.UnirestException;
import java.io.Serializable;
-import javax.ejb.Stateless;
-import javax.inject.Named;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
/**
* This class contains all the methods that have external runtime dependencies
diff --git a/src/main/java/edu/harvard/iq/dataverse/datacapturemodule/DataCaptureModuleUtil.java b/src/main/java/edu/harvard/iq/dataverse/datacapturemodule/DataCaptureModuleUtil.java
index 1aa384d205e..460e4727afc 100644
--- a/src/main/java/edu/harvard/iq/dataverse/datacapturemodule/DataCaptureModuleUtil.java
+++ b/src/main/java/edu/harvard/iq/dataverse/datacapturemodule/DataCaptureModuleUtil.java
@@ -8,9 +8,9 @@
import edu.harvard.iq.dataverse.util.SystemConfig;
import java.util.Arrays;
import java.util.logging.Logger;
-import javax.json.Json;
-import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
+import jakarta.json.Json;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonObjectBuilder;
public class DataCaptureModuleUtil {
diff --git a/src/main/java/edu/harvard/iq/dataverse/datasetutility/AddReplaceFileHelper.java b/src/main/java/edu/harvard/iq/dataverse/datasetutility/AddReplaceFileHelper.java
index 4c2510b6ccb..98d5afc47e6 100644
--- a/src/main/java/edu/harvard/iq/dataverse/datasetutility/AddReplaceFileHelper.java
+++ b/src/main/java/edu/harvard/iq/dataverse/datasetutility/AddReplaceFileHelper.java
@@ -17,7 +17,6 @@
import edu.harvard.iq.dataverse.PermissionServiceBean;
import edu.harvard.iq.dataverse.api.ApiConstants;
import edu.harvard.iq.dataverse.api.Util;
-import edu.harvard.iq.dataverse.api.Files;
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
import edu.harvard.iq.dataverse.authorization.users.User;
import edu.harvard.iq.dataverse.dataaccess.DataAccess;
@@ -48,23 +47,22 @@
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.Asynchronous;
-import javax.ejb.EJBException;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonNumber;
-import javax.json.JsonObject;
-import javax.json.JsonArray;
-import javax.json.JsonObjectBuilder;
-import javax.validation.ConstraintViolation;
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.core.Response;
+import jakarta.ejb.Asynchronous;
+import jakarta.ejb.EJBException;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonNumber;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.validation.ConstraintViolation;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.Response;
import edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder;
import org.apache.commons.io.IOUtils;
-import org.ocpsoft.common.util.Strings;
-import static javax.ws.rs.core.Response.Status.BAD_REQUEST;
+import static jakarta.ws.rs.core.Response.Status.BAD_REQUEST;
/**
* Methods to add or replace a single file.
@@ -1217,7 +1215,7 @@ private boolean step_030_createNewFilesViaIngest(){
initialFileList = result.getDataFiles();
} catch (IOException ex) {
- if (!Strings.isNullOrEmpty(ex.getMessage())) {
+ if (ex.getMessage() != null && !ex.getMessage().isEmpty()) {
this.addErrorSevere(getBundleErr("ingest_create_file_err") + " " + ex.getMessage());
} else {
this.addErrorSevere(getBundleErr("ingest_create_file_err"));
@@ -2152,7 +2150,7 @@ public Response addFiles(String jsonData, Dataset dataset, User authUser) {
}
}
- catch ( javax.json.stream.JsonParsingException ex) {
+ catch ( jakarta.json.stream.JsonParsingException ex) {
ex.printStackTrace();
return error(BAD_REQUEST, "Json Parsing Exception :" + ex.getMessage());
}
@@ -2321,7 +2319,7 @@ public Response replaceFiles(String jsonData, Dataset ds, User authUser) {
}
}
- catch ( javax.json.stream.JsonParsingException ex) {
+ catch ( jakarta.json.stream.JsonParsingException ex) {
ex.printStackTrace();
return error(BAD_REQUEST, "Json Parsing Exception :" + ex.getMessage());
}
diff --git a/src/main/java/edu/harvard/iq/dataverse/datavariable/CategoryMetadata.java b/src/main/java/edu/harvard/iq/dataverse/datavariable/CategoryMetadata.java
index 5e03899b790..a9b1694d842 100644
--- a/src/main/java/edu/harvard/iq/dataverse/datavariable/CategoryMetadata.java
+++ b/src/main/java/edu/harvard/iq/dataverse/datavariable/CategoryMetadata.java
@@ -1,13 +1,13 @@
package edu.harvard.iq.dataverse.datavariable;
-import javax.persistence.Index;
-import javax.persistence.Entity;
-import javax.persistence.Table;
-import javax.persistence.GenerationType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.Id;
-import javax.persistence.ManyToOne;
-import javax.persistence.JoinColumn;
+import jakarta.persistence.Index;
+import jakarta.persistence.Entity;
+import jakarta.persistence.Table;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.Id;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.JoinColumn;
@Entity
@Table(indexes = {@Index(columnList="category_id"), @Index(columnList="variablemetadata_id")})
diff --git a/src/main/java/edu/harvard/iq/dataverse/datavariable/DataVariable.java b/src/main/java/edu/harvard/iq/dataverse/datavariable/DataVariable.java
index 6462f690cac..b2e9441a163 100644
--- a/src/main/java/edu/harvard/iq/dataverse/datavariable/DataVariable.java
+++ b/src/main/java/edu/harvard/iq/dataverse/datavariable/DataVariable.java
@@ -8,22 +8,22 @@
import java.io.Serializable;
import java.util.Collection;
-import javax.persistence.CascadeType;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.OneToMany;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.OneToMany;
import org.hibernate.validator.constraints.NotBlank;
import edu.harvard.iq.dataverse.DataTable;
import java.util.ArrayList;
import java.util.List;
-import javax.persistence.Column;
-import javax.persistence.Index;
-import javax.persistence.OrderBy;
-import javax.persistence.Table;
+import jakarta.persistence.Column;
+import jakarta.persistence.Index;
+import jakarta.persistence.OrderBy;
+import jakarta.persistence.Table;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/datavariable/SummaryStatistic.java b/src/main/java/edu/harvard/iq/dataverse/datavariable/SummaryStatistic.java
index bf81aff3e2b..6896ef360ce 100644
--- a/src/main/java/edu/harvard/iq/dataverse/datavariable/SummaryStatistic.java
+++ b/src/main/java/edu/harvard/iq/dataverse/datavariable/SummaryStatistic.java
@@ -7,14 +7,14 @@
package edu.harvard.iq.dataverse.datavariable;
import java.io.Serializable;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Table;
/*
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/datavariable/VarGroup.java b/src/main/java/edu/harvard/iq/dataverse/datavariable/VarGroup.java
index 242110e333f..b52c76930d7 100644
--- a/src/main/java/edu/harvard/iq/dataverse/datavariable/VarGroup.java
+++ b/src/main/java/edu/harvard/iq/dataverse/datavariable/VarGroup.java
@@ -1,14 +1,14 @@
package edu.harvard.iq.dataverse.datavariable;
-import javax.persistence.Entity;
-import javax.persistence.Table;
-import javax.persistence.Index;
-import javax.persistence.Id;
-import javax.persistence.ManyToOne;
-import javax.persistence.JoinColumn;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.Table;
+import jakarta.persistence.Index;
+import jakarta.persistence.Id;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Column;
import java.util.HashSet;
import java.util.Set;
diff --git a/src/main/java/edu/harvard/iq/dataverse/datavariable/VariableCategory.java b/src/main/java/edu/harvard/iq/dataverse/datavariable/VariableCategory.java
index 6a3e702a561..5ccef82b5d1 100644
--- a/src/main/java/edu/harvard/iq/dataverse/datavariable/VariableCategory.java
+++ b/src/main/java/edu/harvard/iq/dataverse/datavariable/VariableCategory.java
@@ -8,16 +8,16 @@
import java.io.Serializable;
import java.util.List;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
import edu.harvard.iq.dataverse.util.AlphaNumericComparator;
-import javax.persistence.Index;
-import javax.persistence.Table;
+import jakarta.persistence.Index;
+import jakarta.persistence.Table;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/datavariable/VariableMetadata.java b/src/main/java/edu/harvard/iq/dataverse/datavariable/VariableMetadata.java
index c18355c9979..29e821c28a4 100644
--- a/src/main/java/edu/harvard/iq/dataverse/datavariable/VariableMetadata.java
+++ b/src/main/java/edu/harvard/iq/dataverse/datavariable/VariableMetadata.java
@@ -2,18 +2,18 @@
import java.io.Serializable;
-import javax.persistence.Entity;
-import javax.persistence.Table;
-import javax.persistence.Index;
-import javax.persistence.UniqueConstraint;
-import javax.persistence.Id;
-import javax.persistence.ManyToOne;
-import javax.persistence.JoinColumn;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Column;
-import javax.persistence.OneToMany;
-import javax.persistence.CascadeType;
+import jakarta.persistence.Entity;
+import jakarta.persistence.Table;
+import jakarta.persistence.Index;
+import jakarta.persistence.UniqueConstraint;
+import jakarta.persistence.Id;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Column;
+import jakarta.persistence.OneToMany;
+import jakarta.persistence.CascadeType;
import java.util.Collection;
import java.util.ArrayList;
diff --git a/src/main/java/edu/harvard/iq/dataverse/datavariable/VariableRange.java b/src/main/java/edu/harvard/iq/dataverse/datavariable/VariableRange.java
index 17098e6af54..eb04eac846b 100644
--- a/src/main/java/edu/harvard/iq/dataverse/datavariable/VariableRange.java
+++ b/src/main/java/edu/harvard/iq/dataverse/datavariable/VariableRange.java
@@ -7,14 +7,14 @@
package edu.harvard.iq.dataverse.datavariable;
import java.io.Serializable;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Table;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/datavariable/VariableRangeItem.java b/src/main/java/edu/harvard/iq/dataverse/datavariable/VariableRangeItem.java
index 81db4225515..d5f99f7e016 100644
--- a/src/main/java/edu/harvard/iq/dataverse/datavariable/VariableRangeItem.java
+++ b/src/main/java/edu/harvard/iq/dataverse/datavariable/VariableRangeItem.java
@@ -8,14 +8,14 @@
import java.io.Serializable;
import java.math.BigDecimal;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Table;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/datavariable/VariableServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/datavariable/VariableServiceBean.java
index 8287d1c7041..9fb4a3fd34c 100644
--- a/src/main/java/edu/harvard/iq/dataverse/datavariable/VariableServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/datavariable/VariableServiceBean.java
@@ -7,12 +7,12 @@
package edu.harvard.iq.dataverse.datavariable;
import java.util.List;
-import java.util.logging.Logger;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.persistence.TypedQuery;
+
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.TypedQuery;
/**
*
@@ -105,7 +105,7 @@ public VariableFormatType findVariableFormatTypeByName(String name) {
VariableFormatType type = null;
try {
type = (VariableFormatType)query.getSingleResult();
- } catch (javax.persistence.NoResultException e) {
+ } catch (jakarta.persistence.NoResultException e) {
// DO nothing, just return null.
}
return type;
@@ -116,7 +116,7 @@ public VariableIntervalType findVariableIntervalTypeByName(String name) {
VariableIntervalType type = null;
try {
type=(VariableIntervalType)em.createQuery(query).getSingleResult();
- } catch (javax.persistence.NoResultException e) {
+ } catch (jakarta.persistence.NoResultException e) {
// DO nothing, just return null.
}
return type;
@@ -127,7 +127,7 @@ public SummaryStatisticType findSummaryStatisticTypeByName(String name) {
SummaryStatisticType type = null;
try {
type = (SummaryStatisticType) em.createQuery(query).getSingleResult();
- } catch (javax.persistence.NoResultException e) {
+ } catch (jakarta.persistence.NoResultException e) {
// DO nothing, just return null.
}
return type;
diff --git a/src/main/java/edu/harvard/iq/dataverse/dataverse/DataverseUtil.java b/src/main/java/edu/harvard/iq/dataverse/dataverse/DataverseUtil.java
index 52a9501aefb..7964c56835e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/dataverse/DataverseUtil.java
+++ b/src/main/java/edu/harvard/iq/dataverse/dataverse/DataverseUtil.java
@@ -16,7 +16,7 @@
import java.util.Map;
import java.util.logging.Logger;
-import javax.ws.rs.BadRequestException;
+import jakarta.ws.rs.BadRequestException;
import opennlp.tools.util.StringUtil;
import org.apache.commons.io.FileUtils;
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/CommandContext.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/CommandContext.java
index ef5b9dba407..55a375acb6c 100644
--- a/src/main/java/edu/harvard/iq/dataverse/engine/command/CommandContext.java
+++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/CommandContext.java
@@ -42,7 +42,7 @@
import edu.harvard.iq.dataverse.util.SystemConfig;
import edu.harvard.iq.dataverse.workflow.WorkflowServiceBean;
import java.util.Stack;
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
/**
* An interface for accessing Dataverse's resources, user info etc. Used by the
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/DataverseRequest.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/DataverseRequest.java
index 05be37802f0..d792b616a0c 100644
--- a/src/main/java/edu/harvard/iq/dataverse/engine/command/DataverseRequest.java
+++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/DataverseRequest.java
@@ -1,7 +1,6 @@
package edu.harvard.iq.dataverse.engine.command;
import edu.harvard.iq.dataverse.api.AbstractApiBean;
-import edu.harvard.iq.dataverse.api.batchjob.FileRecordJobResource;
import edu.harvard.iq.dataverse.authorization.groups.impl.ipaddress.ip.IpAddress;
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
import edu.harvard.iq.dataverse.authorization.users.User;
@@ -11,7 +10,7 @@
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/AbstractDatasetCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/AbstractDatasetCommand.java
index 36fe3ea7bc1..6061461306d 100644
--- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/AbstractDatasetCommand.java
+++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/AbstractDatasetCommand.java
@@ -14,7 +14,6 @@
import edu.harvard.iq.dataverse.engine.command.exception.CommandExecutionException;
import edu.harvard.iq.dataverse.engine.command.exception.IllegalCommandException;
import edu.harvard.iq.dataverse.util.BundleUtil;
-import edu.harvard.iq.dataverse.util.json.JsonUtil;
import java.sql.Timestamp;
import java.util.Date;
@@ -23,14 +22,10 @@
import java.util.logging.Logger;
import static java.util.stream.Collectors.joining;
-import javax.json.JsonObject;
-import javax.servlet.http.HttpServletRequest;
-import javax.validation.ConstraintViolation;
+import jakarta.validation.ConstraintViolation;
import edu.harvard.iq.dataverse.GlobalIdServiceBean;
import edu.harvard.iq.dataverse.MetadataBlock;
-import edu.harvard.iq.dataverse.MetadataBlockServiceBean;
import edu.harvard.iq.dataverse.TermsOfUseAndAccess;
-import edu.harvard.iq.dataverse.pidproviders.FakePidProviderServiceBean;
import edu.harvard.iq.dataverse.settings.JvmSettings;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/AddRoleAssigneesToExplicitGroupCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/AddRoleAssigneesToExplicitGroupCommand.java
index 8ba1d181609..59c5d970b09 100644
--- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/AddRoleAssigneesToExplicitGroupCommand.java
+++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/AddRoleAssigneesToExplicitGroupCommand.java
@@ -16,7 +16,7 @@
import java.util.Set;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJBException;
+import jakarta.ejb.EJBException;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/ChangeUserIdentifierCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/ChangeUserIdentifierCommand.java
index 4a5998aea00..94aff3e3f5d 100644
--- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/ChangeUserIdentifierCommand.java
+++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/ChangeUserIdentifierCommand.java
@@ -18,11 +18,11 @@
import edu.harvard.iq.dataverse.engine.command.exception.IllegalCommandException;
import java.util.List;
import java.util.Set;
-import javax.validation.ConstraintViolation;
-import javax.validation.Validation;
-import javax.validation.Validator;
-import javax.validation.ValidatorFactory;
-import javax.ws.rs.core.Response;
+import jakarta.validation.ConstraintViolation;
+import jakarta.validation.Validation;
+import jakarta.validation.Validator;
+import jakarta.validation.ValidatorFactory;
+import jakarta.ws.rs.core.Response;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/CreateRoleCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/CreateRoleCommand.java
index cb9b0a3c774..8cffcd3d821 100644
--- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/CreateRoleCommand.java
+++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/CreateRoleCommand.java
@@ -1,7 +1,6 @@
package edu.harvard.iq.dataverse.engine.command.impl;
import edu.harvard.iq.dataverse.Dataverse;
-import edu.harvard.iq.dataverse.api.AbstractApiBean;
import edu.harvard.iq.dataverse.authorization.DataverseRole;
import edu.harvard.iq.dataverse.authorization.Permission;
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
@@ -13,7 +12,7 @@
import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
import edu.harvard.iq.dataverse.engine.command.exception.IllegalCommandException;
import edu.harvard.iq.dataverse.util.BundleUtil;
-import javax.persistence.NoResultException;
+import jakarta.persistence.NoResultException;
/**
* Create a new role in a dataverse.
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/CreateSavedSearchCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/CreateSavedSearchCommand.java
index 147e1870566..7a549a51dd5 100644
--- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/CreateSavedSearchCommand.java
+++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/CreateSavedSearchCommand.java
@@ -12,7 +12,7 @@
import edu.harvard.iq.dataverse.search.savedsearch.SavedSearchServiceBean;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.json.JsonObjectBuilder;
+import jakarta.json.JsonObjectBuilder;
@RequiredPermissions(Permission.PublishDataverse)
public class CreateSavedSearchCommand extends AbstractCommand {
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DRSSubmitToArchiveCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DRSSubmitToArchiveCommand.java
index f23033f09fa..594d4fe25ba 100644
--- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DRSSubmitToArchiveCommand.java
+++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DRSSubmitToArchiveCommand.java
@@ -34,10 +34,10 @@
import java.util.Set;
import java.util.logging.Logger;
-import javax.json.Json;
-import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
-import javax.json.JsonValue;
+import jakarta.json.Json;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.json.JsonValue;
import javax.net.ssl.SSLContext;
import org.apache.commons.codec.digest.DigestUtils;
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DuraCloudSubmitToArchiveCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DuraCloudSubmitToArchiveCommand.java
index 2ca73af3b3c..d6d7b49d172 100644
--- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DuraCloudSubmitToArchiveCommand.java
+++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DuraCloudSubmitToArchiveCommand.java
@@ -21,8 +21,8 @@
import java.util.Map;
import java.util.logging.Logger;
-import javax.json.Json;
-import javax.json.JsonObjectBuilder;
+import jakarta.json.Json;
+import jakarta.json.JsonObjectBuilder;
import org.apache.commons.codec.binary.Hex;
import org.duracloud.client.ContentStore;
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/FinalizeDatasetPublicationCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/FinalizeDatasetPublicationCommand.java
index 253c761f0c3..f5e70209744 100644
--- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/FinalizeDatasetPublicationCommand.java
+++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/FinalizeDatasetPublicationCommand.java
@@ -37,8 +37,8 @@
import java.util.concurrent.Future;
import org.apache.solr.client.solrj.SolrServerException;
-import javax.ejb.EJB;
-import javax.inject.Inject;
+import jakarta.ejb.EJB;
+import jakarta.inject.Inject;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/GetProvJsonCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/GetProvJsonCommand.java
index 23f08aadd3e..2de2adff099 100644
--- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/GetProvJsonCommand.java
+++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/GetProvJsonCommand.java
@@ -12,9 +12,9 @@
import java.io.IOException;
import java.io.InputStream;
import java.util.logging.Logger;
-import javax.json.Json;
-import javax.json.JsonObject;
-import javax.json.JsonReader;
+import jakarta.json.Json;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonReader;
@RequiredPermissions(Permission.EditDataset)
public class GetProvJsonCommand extends AbstractCommand {
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/GetUserTracesCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/GetUserTracesCommand.java
index f3324ba6f2e..e41d70d9804 100644
--- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/GetUserTracesCommand.java
+++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/GetUserTracesCommand.java
@@ -17,14 +17,14 @@
import edu.harvard.iq.dataverse.engine.command.exception.PermissionException;
import edu.harvard.iq.dataverse.search.savedsearch.SavedSearch;
import edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder;
-import java.math.BigDecimal;
+
import java.util.List;
import java.util.Set;
import java.util.logging.Logger;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObjectBuilder;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObjectBuilder;
// Superuser-only enforced below.
@RequiredPermissions({})
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/GoogleCloudSubmitToArchiveCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/GoogleCloudSubmitToArchiveCommand.java
index da2701a41e7..512987866d4 100644
--- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/GoogleCloudSubmitToArchiveCommand.java
+++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/GoogleCloudSubmitToArchiveCommand.java
@@ -19,8 +19,8 @@
import edu.harvard.iq.dataverse.workflow.step.WorkflowStepResult;
import org.apache.commons.codec.binary.Hex;
-import javax.json.Json;
-import javax.json.JsonObjectBuilder;
+import jakarta.json.Json;
+import jakarta.json.JsonObjectBuilder;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/ImportFromFileSystemCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/ImportFromFileSystemCommand.java
index 5f31ea756eb..c03c77d42fd 100644
--- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/ImportFromFileSystemCommand.java
+++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/ImportFromFileSystemCommand.java
@@ -14,12 +14,12 @@
import edu.harvard.iq.dataverse.engine.command.exception.IllegalCommandException;
import edu.harvard.iq.dataverse.settings.JvmSettings;
-import javax.batch.operations.JobOperator;
-import javax.batch.operations.JobSecurityException;
-import javax.batch.operations.JobStartException;
-import javax.batch.runtime.BatchRuntime;
-import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
+import jakarta.batch.operations.JobOperator;
+import jakarta.batch.operations.JobSecurityException;
+import jakarta.batch.operations.JobStartException;
+import jakarta.batch.runtime.BatchRuntime;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonObjectBuilder;
import java.io.File;
import java.util.Properties;
import java.util.logging.Level;
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/LinkDataverseCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/LinkDataverseCommand.java
index 1c63a1a3c4f..55fe96556a5 100644
--- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/LinkDataverseCommand.java
+++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/LinkDataverseCommand.java
@@ -23,8 +23,8 @@
import java.util.Arrays;
import java.util.Collections;
import java.util.Date;
-import java.util.concurrent.Future;
-import javax.ws.rs.core.Response;
+
+import jakarta.ws.rs.core.Response;
import org.apache.solr.client.solrj.SolrServerException;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/LocalSubmitToArchiveCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/LocalSubmitToArchiveCommand.java
index c7e91b2967b..d2f061b6e70 100644
--- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/LocalSubmitToArchiveCommand.java
+++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/LocalSubmitToArchiveCommand.java
@@ -17,8 +17,8 @@
import java.util.Map;
import java.util.logging.Logger;
-import javax.json.Json;
-import javax.json.JsonObjectBuilder;
+import jakarta.json.Json;
+import jakarta.json.JsonObjectBuilder;
import java.io.File;
import java.io.FileOutputStream;
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/RedetectFileTypeCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/RedetectFileTypeCommand.java
index bdb6ceffd6d..b9346a43af8 100644
--- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/RedetectFileTypeCommand.java
+++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/RedetectFileTypeCommand.java
@@ -20,7 +20,7 @@
import java.nio.channels.FileChannel;
import java.nio.channels.ReadableByteChannel;
import java.util.logging.Logger;
-import javax.ejb.EJBException;
+import jakarta.ejb.EJBException;
@RequiredPermissions(Permission.EditDataset)
public class RedetectFileTypeCommand extends AbstractCommand {
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/S3SubmitToArchiveCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/S3SubmitToArchiveCommand.java
index f24d956e9d7..f02edd54b86 100644
--- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/S3SubmitToArchiveCommand.java
+++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/S3SubmitToArchiveCommand.java
@@ -20,9 +20,9 @@
import java.util.Map;
import java.util.logging.Logger;
-import javax.json.Json;
-import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
+import jakarta.json.Json;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonObjectBuilder;
import org.eclipse.microprofile.config.Config;
import org.eclipse.microprofile.config.ConfigProvider;
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/UningestFileCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/UningestFileCommand.java
index 29180f65e36..f2b89746160 100644
--- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/UningestFileCommand.java
+++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/UningestFileCommand.java
@@ -22,11 +22,11 @@
import edu.harvard.iq.dataverse.engine.command.exception.IllegalCommandException;
import edu.harvard.iq.dataverse.engine.command.exception.PermissionException;
import edu.harvard.iq.dataverse.util.FileUtil;
-import edu.harvard.iq.dataverse.util.StringUtil;
+
import java.io.IOException;
import java.util.Collections;
import java.util.logging.Logger;
-import javax.persistence.Query;
+import jakarta.persistence.Query;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/UpdateDatasetVersionCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/UpdateDatasetVersionCommand.java
index 5f4ac24c1d9..7591bebe796 100644
--- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/UpdateDatasetVersionCommand.java
+++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/UpdateDatasetVersionCommand.java
@@ -17,7 +17,7 @@
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.validation.ConstraintViolationException;
+import jakarta.validation.ConstraintViolationException;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/UpdateDataverseCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/UpdateDataverseCommand.java
index 218b0ea89d9..56c76f04c05 100644
--- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/UpdateDataverseCommand.java
+++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/UpdateDataverseCommand.java
@@ -6,7 +6,7 @@
import edu.harvard.iq.dataverse.Dataverse.DataverseType;
import edu.harvard.iq.dataverse.DataverseFieldTypeInputLevel;
import edu.harvard.iq.dataverse.authorization.Permission;
-import edu.harvard.iq.dataverse.batch.util.LoggingUtil;
+
import static edu.harvard.iq.dataverse.dataverse.DataverseUtil.validateDataverseMetadataExternally;
import edu.harvard.iq.dataverse.engine.command.AbstractCommand;
import edu.harvard.iq.dataverse.engine.command.CommandContext;
@@ -14,14 +14,11 @@
import edu.harvard.iq.dataverse.engine.command.RequiredPermissions;
import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
import edu.harvard.iq.dataverse.engine.command.exception.IllegalCommandException;
-import edu.harvard.iq.dataverse.search.IndexResponse;
-import java.io.IOException;
+
import java.util.ArrayList;
import java.util.List;
-import java.util.concurrent.Future;
import java.util.logging.Logger;
-import javax.persistence.TypedQuery;
-import org.apache.solr.client.solrj.SolrServerException;
+import jakarta.persistence.TypedQuery;
/**
* Update an existing dataverse.
diff --git a/src/main/java/edu/harvard/iq/dataverse/export/DCTermsExporter.java b/src/main/java/edu/harvard/iq/dataverse/export/DCTermsExporter.java
index 8df17e71ae6..f82c0d9ad3d 100644
--- a/src/main/java/edu/harvard/iq/dataverse/export/DCTermsExporter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/export/DCTermsExporter.java
@@ -12,7 +12,7 @@
import java.util.Locale;
import java.util.Optional;
-import javax.json.JsonObject;
+import jakarta.json.JsonObject;
import javax.xml.stream.XMLStreamException;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/export/DDIExportServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/export/DDIExportServiceBean.java
index 59ff539af37..5119b4b96c7 100644
--- a/src/main/java/edu/harvard/iq/dataverse/export/DDIExportServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/export/DDIExportServiceBean.java
@@ -33,14 +33,14 @@
import java.util.logging.Logger;
import java.util.logging.Level;
import java.io.OutputStream;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.ejb.TransactionAttribute;
-import javax.ejb.TransactionAttributeType;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.ejb.TransactionAttribute;
+import jakarta.ejb.TransactionAttributeType;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
import javax.xml.stream.XMLStreamWriter;
import javax.xml.stream.XMLStreamException;
import javax.xml.stream.XMLOutputFactory;
diff --git a/src/main/java/edu/harvard/iq/dataverse/export/DDIExporter.java b/src/main/java/edu/harvard/iq/dataverse/export/DDIExporter.java
index 66a9ea6c665..d48ce3a537d 100644
--- a/src/main/java/edu/harvard/iq/dataverse/export/DDIExporter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/export/DDIExporter.java
@@ -2,7 +2,6 @@
package edu.harvard.iq.dataverse.export;
import com.google.auto.service.AutoService;
-import edu.harvard.iq.dataverse.DatasetVersion;
import edu.harvard.iq.dataverse.export.ddi.DdiExportUtil;
import io.gdcc.spi.export.ExportDataProvider;
import io.gdcc.spi.export.ExportException;
@@ -13,7 +12,7 @@
import java.util.Locale;
import java.util.Optional;
-import javax.json.JsonObject;
+import jakarta.json.JsonObject;
import javax.xml.stream.XMLStreamException;
import javax.xml.stream.XMLStreamWriter;
import javax.xml.stream.XMLOutputFactory;
diff --git a/src/main/java/edu/harvard/iq/dataverse/export/DublinCoreExporter.java b/src/main/java/edu/harvard/iq/dataverse/export/DublinCoreExporter.java
index 04b7892d737..0fa32dd4bfa 100644
--- a/src/main/java/edu/harvard/iq/dataverse/export/DublinCoreExporter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/export/DublinCoreExporter.java
@@ -2,7 +2,6 @@
package edu.harvard.iq.dataverse.export;
import com.google.auto.service.AutoService;
-import edu.harvard.iq.dataverse.DatasetVersion;
import edu.harvard.iq.dataverse.export.dublincore.DublinCoreExportUtil;
import io.gdcc.spi.export.ExportDataProvider;
import io.gdcc.spi.export.ExportException;
@@ -13,7 +12,7 @@
import java.util.Locale;
import java.util.Optional;
-import javax.json.JsonObject;
+import jakarta.json.JsonObject;
import javax.xml.stream.XMLStreamException;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/export/ExportService.java b/src/main/java/edu/harvard/iq/dataverse/export/ExportService.java
index eed84a19a66..8342e7df92a 100644
--- a/src/main/java/edu/harvard/iq/dataverse/export/ExportService.java
+++ b/src/main/java/edu/harvard/iq/dataverse/export/ExportService.java
@@ -9,7 +9,6 @@
import static edu.harvard.iq.dataverse.dataaccess.DataAccess.getStorageIO;
import edu.harvard.iq.dataverse.dataaccess.DataAccessOption;
import edu.harvard.iq.dataverse.dataaccess.StorageIO;
-import io.gdcc.spi.export.ExportDataProvider;
import io.gdcc.spi.export.ExportException;
import io.gdcc.spi.export.Exporter;
import io.gdcc.spi.export.XMLExporter;
@@ -47,7 +46,7 @@
import java.util.Set;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.MediaType;
import org.apache.commons.io.IOUtils;
diff --git a/src/main/java/edu/harvard/iq/dataverse/export/HtmlCodeBookExporter.java b/src/main/java/edu/harvard/iq/dataverse/export/HtmlCodeBookExporter.java
index 1b449060b17..9d0b107299e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/export/HtmlCodeBookExporter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/export/HtmlCodeBookExporter.java
@@ -1,23 +1,18 @@
package edu.harvard.iq.dataverse.export;
import com.google.auto.service.AutoService;
-import edu.harvard.iq.dataverse.Dataset;
-import edu.harvard.iq.dataverse.DatasetVersion;
import edu.harvard.iq.dataverse.export.ddi.DdiExportUtil;
import io.gdcc.spi.export.ExportDataProvider;
import io.gdcc.spi.export.ExportException;
import io.gdcc.spi.export.Exporter;
import edu.harvard.iq.dataverse.util.BundleUtil;
-import javax.json.JsonObject;
-import javax.ws.rs.core.MediaType;
+import jakarta.json.JsonObject;
+import jakarta.ws.rs.core.MediaType;
import javax.xml.stream.XMLStreamException;
-import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
-import java.nio.file.Path;
-import java.nio.file.Paths;
import java.util.Locale;
import java.util.Optional;
diff --git a/src/main/java/edu/harvard/iq/dataverse/export/InternalExportDataProvider.java b/src/main/java/edu/harvard/iq/dataverse/export/InternalExportDataProvider.java
index 7c76c4972a8..a7967f6ccb6 100644
--- a/src/main/java/edu/harvard/iq/dataverse/export/InternalExportDataProvider.java
+++ b/src/main/java/edu/harvard/iq/dataverse/export/InternalExportDataProvider.java
@@ -3,11 +3,11 @@
import java.io.InputStream;
import java.util.Optional;
-import javax.json.Json;
-import javax.json.JsonArray;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
+import jakarta.json.Json;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonObjectBuilder;
import edu.harvard.iq.dataverse.DOIDataCiteRegisterService;
import edu.harvard.iq.dataverse.DataCitation;
diff --git a/src/main/java/edu/harvard/iq/dataverse/export/JSONExporter.java b/src/main/java/edu/harvard/iq/dataverse/export/JSONExporter.java
index 30347017071..a54e61c7c1e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/export/JSONExporter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/export/JSONExporter.java
@@ -2,7 +2,6 @@
package edu.harvard.iq.dataverse.export;
import com.google.auto.service.AutoService;
-import edu.harvard.iq.dataverse.DatasetVersion;
import io.gdcc.spi.export.ExportDataProvider;
import io.gdcc.spi.export.ExportException;
import io.gdcc.spi.export.Exporter;
@@ -11,8 +10,8 @@
import java.util.Locale;
import java.util.Optional;
-import javax.json.JsonObject;
-import javax.ws.rs.core.MediaType;
+import jakarta.json.JsonObject;
+import jakarta.ws.rs.core.MediaType;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/export/OAI_DDIExporter.java b/src/main/java/edu/harvard/iq/dataverse/export/OAI_DDIExporter.java
index de97a88d1fa..0b4121c6025 100644
--- a/src/main/java/edu/harvard/iq/dataverse/export/OAI_DDIExporter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/export/OAI_DDIExporter.java
@@ -2,7 +2,6 @@
package edu.harvard.iq.dataverse.export;
import com.google.auto.service.AutoService;
-import edu.harvard.iq.dataverse.DatasetVersion;
import edu.harvard.iq.dataverse.export.ddi.DdiExportUtil;
import io.gdcc.spi.export.ExportDataProvider;
import io.gdcc.spi.export.ExportException;
@@ -13,7 +12,7 @@
import java.util.Locale;
import java.util.Optional;
-import javax.json.JsonObject;
+import jakarta.json.JsonObject;
import javax.xml.stream.XMLStreamException;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/export/OAI_OREExporter.java b/src/main/java/edu/harvard/iq/dataverse/export/OAI_OREExporter.java
index 06fee32e220..feec4403570 100644
--- a/src/main/java/edu/harvard/iq/dataverse/export/OAI_OREExporter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/export/OAI_OREExporter.java
@@ -1,21 +1,18 @@
package edu.harvard.iq.dataverse.export;
import com.google.auto.service.AutoService;
-import edu.harvard.iq.dataverse.DatasetVersion;
import io.gdcc.spi.export.ExportDataProvider;
import io.gdcc.spi.export.ExportException;
import io.gdcc.spi.export.Exporter;
-import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
import edu.harvard.iq.dataverse.util.BundleUtil;
-import edu.harvard.iq.dataverse.util.bagit.OREMap;
+
import java.io.OutputStream;
import java.util.Locale;
import java.util.Optional;
-import java.util.ResourceBundle;
import java.util.logging.Logger;
-import javax.json.JsonObject;
-import javax.ws.rs.core.MediaType;
+import jakarta.json.JsonObject;
+import jakarta.ws.rs.core.MediaType;
@AutoService(Exporter.class)
public class OAI_OREExporter implements Exporter {
diff --git a/src/main/java/edu/harvard/iq/dataverse/export/OpenAireExporter.java b/src/main/java/edu/harvard/iq/dataverse/export/OpenAireExporter.java
index 03b8ebfa76f..8bd4ae6a042 100644
--- a/src/main/java/edu/harvard/iq/dataverse/export/OpenAireExporter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/export/OpenAireExporter.java
@@ -3,12 +3,11 @@
import java.io.OutputStream;
import java.util.Locale;
-import javax.json.JsonObject;
+import jakarta.json.JsonObject;
import javax.xml.stream.XMLStreamException;
import com.google.auto.service.AutoService;
-import edu.harvard.iq.dataverse.DatasetVersion;
import edu.harvard.iq.dataverse.export.openaire.OpenAireExportUtil;
import io.gdcc.spi.export.ExportDataProvider;
import io.gdcc.spi.export.ExportException;
diff --git a/src/main/java/edu/harvard/iq/dataverse/export/SchemaDotOrgExporter.java b/src/main/java/edu/harvard/iq/dataverse/export/SchemaDotOrgExporter.java
index f3be1e83d2d..5428715b905 100644
--- a/src/main/java/edu/harvard/iq/dataverse/export/SchemaDotOrgExporter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/export/SchemaDotOrgExporter.java
@@ -9,7 +9,7 @@
import java.io.OutputStream;
import java.util.Locale;
import java.util.logging.Logger;
-import javax.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.MediaType;
/**
* Schema.org JSON-LD is used by Google Dataset Search and other services to
diff --git a/src/main/java/edu/harvard/iq/dataverse/export/ddi/DdiExportUtil.java b/src/main/java/edu/harvard/iq/dataverse/export/ddi/DdiExportUtil.java
index 846267e0a2c..24449e8010a 100644
--- a/src/main/java/edu/harvard/iq/dataverse/export/ddi/DdiExportUtil.java
+++ b/src/main/java/edu/harvard/iq/dataverse/export/ddi/DdiExportUtil.java
@@ -3,26 +3,13 @@
import com.google.gson.Gson;
import edu.harvard.iq.dataverse.ControlledVocabularyValue;
-import edu.harvard.iq.dataverse.DataFile;
-import edu.harvard.iq.dataverse.DataTable;
import edu.harvard.iq.dataverse.DatasetFieldConstant;
-import edu.harvard.iq.dataverse.DatasetVersion;
import edu.harvard.iq.dataverse.DvObjectContainer;
-import edu.harvard.iq.dataverse.FileMetadata;
-import edu.harvard.iq.dataverse.GlobalId;
import edu.harvard.iq.dataverse.api.dto.DatasetDTO;
import edu.harvard.iq.dataverse.api.dto.DatasetVersionDTO;
import edu.harvard.iq.dataverse.api.dto.FieldDTO;
import edu.harvard.iq.dataverse.api.dto.FileDTO;
import edu.harvard.iq.dataverse.api.dto.MetadataBlockDTO;
-import edu.harvard.iq.dataverse.datavariable.VariableMetadata;
-import edu.harvard.iq.dataverse.datavariable.DataVariable;
-import edu.harvard.iq.dataverse.datavariable.VariableServiceBean;
-import edu.harvard.iq.dataverse.datavariable.VariableRange;
-import edu.harvard.iq.dataverse.datavariable.SummaryStatistic;
-import edu.harvard.iq.dataverse.datavariable.VariableCategory;
-import edu.harvard.iq.dataverse.datavariable.VarGroup;
-import edu.harvard.iq.dataverse.datavariable.CategoryMetadata;
import static edu.harvard.iq.dataverse.export.DDIExportServiceBean.LEVEL_FILE;
import static edu.harvard.iq.dataverse.export.DDIExportServiceBean.NOTE_SUBJECT_TAG;
@@ -34,43 +21,36 @@
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
-import edu.harvard.iq.dataverse.util.BundleUtil;
-import edu.harvard.iq.dataverse.util.FileUtil;
import edu.harvard.iq.dataverse.util.SystemConfig;
-import edu.harvard.iq.dataverse.util.json.JsonPrinter;
import edu.harvard.iq.dataverse.util.json.JsonUtil;
import edu.harvard.iq.dataverse.util.xml.XmlPrinter;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.nio.file.Files;
-import java.nio.file.Path;
import java.nio.file.Paths;
import java.time.LocalDate;
import java.util.*;
import java.util.Map.Entry;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.json.Json;
-import javax.json.JsonArray;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObject;
-import javax.json.JsonString;
-import javax.json.JsonValue;
+import jakarta.ejb.EJB;
+import jakarta.json.Json;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonString;
+import jakarta.json.JsonValue;
import javax.xml.stream.XMLOutputFactory;
import javax.xml.stream.XMLStreamException;
import javax.xml.stream.XMLStreamWriter;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.FactoryConfigurationError;
import javax.xml.parsers.ParserConfigurationException;
import org.xml.sax.SAXException;
-import org.xml.sax.SAXParseException;
import org.w3c.dom.Document;
import org.apache.commons.lang3.StringUtils;
-import org.w3c.dom.DOMException;
// For write operation
import javax.xml.transform.Transformer;
@@ -80,9 +60,7 @@
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamSource;
import javax.xml.transform.stream.StreamResult;
-import java.io.File;
import java.io.InputStream;
-import java.io.InputStreamReader;
public class DdiExportUtil {
diff --git a/src/main/java/edu/harvard/iq/dataverse/export/ddi/DdiExportUtilHelper.java b/src/main/java/edu/harvard/iq/dataverse/export/ddi/DdiExportUtilHelper.java
index 149c6791a7e..d0cd8a4cae7 100644
--- a/src/main/java/edu/harvard/iq/dataverse/export/ddi/DdiExportUtilHelper.java
+++ b/src/main/java/edu/harvard/iq/dataverse/export/ddi/DdiExportUtilHelper.java
@@ -1,9 +1,9 @@
package edu.harvard.iq.dataverse.export.ddi;
-import javax.annotation.PostConstruct;
-import javax.ejb.EJB;
-import javax.ejb.Singleton;
-import javax.ejb.Startup;
+import jakarta.annotation.PostConstruct;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Singleton;
+import jakarta.ejb.Startup;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
diff --git a/src/main/java/edu/harvard/iq/dataverse/export/dublincore/DublinCoreExportUtil.java b/src/main/java/edu/harvard/iq/dataverse/export/dublincore/DublinCoreExportUtil.java
index 238cea78fb5..6b7cb844f3e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/export/dublincore/DublinCoreExportUtil.java
+++ b/src/main/java/edu/harvard/iq/dataverse/export/dublincore/DublinCoreExportUtil.java
@@ -14,18 +14,16 @@
import edu.harvard.iq.dataverse.api.dto.LicenseDTO;
import edu.harvard.iq.dataverse.api.dto.MetadataBlockDTO;
import edu.harvard.iq.dataverse.export.ddi.DdiExportUtil;
-import edu.harvard.iq.dataverse.license.License;
import edu.harvard.iq.dataverse.pidproviders.PidUtil;
import edu.harvard.iq.dataverse.util.json.JsonUtil;
-import java.io.ByteArrayOutputStream;
+
import java.io.OutputStream;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
-import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.json.JsonObject;
+import jakarta.json.JsonObject;
import javax.xml.stream.XMLOutputFactory;
import javax.xml.stream.XMLStreamException;
import javax.xml.stream.XMLStreamWriter;
diff --git a/src/main/java/edu/harvard/iq/dataverse/export/openaire/OpenAireExportUtil.java b/src/main/java/edu/harvard/iq/dataverse/export/openaire/OpenAireExportUtil.java
index 6e1e61ebd06..f7e75ca03fa 100644
--- a/src/main/java/edu/harvard/iq/dataverse/export/openaire/OpenAireExportUtil.java
+++ b/src/main/java/edu/harvard/iq/dataverse/export/openaire/OpenAireExportUtil.java
@@ -8,7 +8,7 @@
import java.util.Set;
import java.util.logging.Logger;
-import javax.json.JsonObject;
+import jakarta.json.JsonObject;
import javax.xml.stream.XMLOutputFactory;
import javax.xml.stream.XMLStreamException;
import javax.xml.stream.XMLStreamWriter;
@@ -21,7 +21,6 @@
import edu.harvard.iq.dataverse.DatasetFieldConstant;
import edu.harvard.iq.dataverse.GlobalId;
import edu.harvard.iq.dataverse.HandlenetServiceBean;
-import edu.harvard.iq.dataverse.TermsOfUseAndAccess;
import edu.harvard.iq.dataverse.api.dto.DatasetDTO;
import edu.harvard.iq.dataverse.api.dto.DatasetVersionDTO;
import edu.harvard.iq.dataverse.api.dto.FieldDTO;
@@ -31,8 +30,8 @@
import edu.harvard.iq.dataverse.util.json.JsonUtil;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import javax.mail.internet.AddressException;
-import javax.mail.internet.InternetAddress;
+import jakarta.mail.internet.AddressException;
+import jakarta.mail.internet.InternetAddress;
public class OpenAireExportUtil {
diff --git a/src/main/java/edu/harvard/iq/dataverse/externaltools/ExternalTool.java b/src/main/java/edu/harvard/iq/dataverse/externaltools/ExternalTool.java
index bea6cebc1d7..7f1f46c06cb 100644
--- a/src/main/java/edu/harvard/iq/dataverse/externaltools/ExternalTool.java
+++ b/src/main/java/edu/harvard/iq/dataverse/externaltools/ExternalTool.java
@@ -6,20 +6,20 @@
import java.io.Serializable;
import java.util.Arrays;
import java.util.List;
-import java.util.logging.Logger;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObjectBuilder;
-import javax.persistence.CascadeType;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.OneToMany;
+
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.EnumType;
+import jakarta.persistence.Enumerated;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.OneToMany;
/**
* A specification or definition for how an external tool is intended to
diff --git a/src/main/java/edu/harvard/iq/dataverse/externaltools/ExternalToolHandler.java b/src/main/java/edu/harvard/iq/dataverse/externaltools/ExternalToolHandler.java
index dac046373ba..a52679deebc 100644
--- a/src/main/java/edu/harvard/iq/dataverse/externaltools/ExternalToolHandler.java
+++ b/src/main/java/edu/harvard/iq/dataverse/externaltools/ExternalToolHandler.java
@@ -22,15 +22,15 @@
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.json.Json;
-import javax.json.JsonArray;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonNumber;
-import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
-import javax.json.JsonString;
-import javax.json.JsonValue;
-import javax.ws.rs.HttpMethod;
+import jakarta.json.Json;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonNumber;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.json.JsonString;
+import jakarta.json.JsonValue;
+import jakarta.ws.rs.HttpMethod;
import org.apache.commons.codec.binary.StringUtils;
diff --git a/src/main/java/edu/harvard/iq/dataverse/externaltools/ExternalToolServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/externaltools/ExternalToolServiceBean.java
index 5ecf5cd755c..e13843eadfa 100644
--- a/src/main/java/edu/harvard/iq/dataverse/externaltools/ExternalToolServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/externaltools/ExternalToolServiceBean.java
@@ -6,34 +6,31 @@
import edu.harvard.iq.dataverse.DataFileServiceBean;
import edu.harvard.iq.dataverse.authorization.users.ApiToken;
import edu.harvard.iq.dataverse.externaltools.ExternalTool.Type;
-import edu.harvard.iq.dataverse.util.URLTokenUtil;
import edu.harvard.iq.dataverse.util.URLTokenUtil.ReservedWord;
import edu.harvard.iq.dataverse.util.json.JsonUtil;
import edu.harvard.iq.dataverse.externaltools.ExternalTool.Scope;
-import java.io.StringReader;
import java.util.ArrayList;
import java.util.List;
import java.util.Set;
import java.util.logging.Logger;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.json.Json;
-import javax.json.JsonArray;
-import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
-import javax.json.JsonReader;
-import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
-import javax.persistence.NonUniqueResultException;
-import javax.persistence.PersistenceContext;
-import javax.persistence.TypedQuery;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.json.Json;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.json.JsonReader;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.NonUniqueResultException;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.TypedQuery;
import static edu.harvard.iq.dataverse.externaltools.ExternalTool.*;
-import java.util.stream.Collectors;
-import java.util.stream.Stream;
-import javax.ejb.EJB;
-import javax.json.JsonValue;
+
+import jakarta.ejb.EJB;
+import jakarta.json.JsonValue;
@Stateless
@Named
diff --git a/src/main/java/edu/harvard/iq/dataverse/externaltools/ExternalToolType.java b/src/main/java/edu/harvard/iq/dataverse/externaltools/ExternalToolType.java
index 3564d1871b5..fb4c0f5dc5d 100644
--- a/src/main/java/edu/harvard/iq/dataverse/externaltools/ExternalToolType.java
+++ b/src/main/java/edu/harvard/iq/dataverse/externaltools/ExternalToolType.java
@@ -1,18 +1,18 @@
package edu.harvard.iq.dataverse.externaltools;
import java.io.Serializable;
-import javax.persistence.CascadeType;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.EnumType;
+import jakarta.persistence.Enumerated;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Table;
@Entity
@Table(indexes = {
diff --git a/src/main/java/edu/harvard/iq/dataverse/feedback/Feedback.java b/src/main/java/edu/harvard/iq/dataverse/feedback/Feedback.java
index c9acb491aa2..c1162eb8db6 100644
--- a/src/main/java/edu/harvard/iq/dataverse/feedback/Feedback.java
+++ b/src/main/java/edu/harvard/iq/dataverse/feedback/Feedback.java
@@ -1,7 +1,7 @@
package edu.harvard.iq.dataverse.feedback;
-import javax.json.Json;
-import javax.json.JsonObjectBuilder;
+import jakarta.json.Json;
+import jakarta.json.JsonObjectBuilder;
import edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder;
diff --git a/src/main/java/edu/harvard/iq/dataverse/feedback/FeedbackUtil.java b/src/main/java/edu/harvard/iq/dataverse/feedback/FeedbackUtil.java
index 750a3923806..6ae0e165141 100644
--- a/src/main/java/edu/harvard/iq/dataverse/feedback/FeedbackUtil.java
+++ b/src/main/java/edu/harvard/iq/dataverse/feedback/FeedbackUtil.java
@@ -17,8 +17,8 @@
import java.util.List;
import java.util.logging.Logger;
-import javax.json.JsonObject;
-import javax.mail.internet.InternetAddress;
+import jakarta.json.JsonObject;
+import jakarta.mail.internet.InternetAddress;
public class FeedbackUtil {
diff --git a/src/main/java/edu/harvard/iq/dataverse/flyway/StartupFlywayMigrator.java b/src/main/java/edu/harvard/iq/dataverse/flyway/StartupFlywayMigrator.java
index 71b53bd43f2..39bc46216ca 100644
--- a/src/main/java/edu/harvard/iq/dataverse/flyway/StartupFlywayMigrator.java
+++ b/src/main/java/edu/harvard/iq/dataverse/flyway/StartupFlywayMigrator.java
@@ -2,12 +2,12 @@
import org.flywaydb.core.Flyway;
-import javax.annotation.PostConstruct;
-import javax.annotation.Resource;
-import javax.ejb.Singleton;
-import javax.ejb.Startup;
-import javax.ejb.TransactionManagement;
-import javax.ejb.TransactionManagementType;
+import jakarta.annotation.PostConstruct;
+import jakarta.annotation.Resource;
+import jakarta.ejb.Singleton;
+import jakarta.ejb.Startup;
+import jakarta.ejb.TransactionManagement;
+import jakarta.ejb.TransactionManagementType;
import javax.sql.DataSource;
@Startup
diff --git a/src/main/java/edu/harvard/iq/dataverse/globus/GlobusServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/globus/GlobusServiceBean.java
index 9d80c5cc280..d2613422be9 100644
--- a/src/main/java/edu/harvard/iq/dataverse/globus/GlobusServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/globus/GlobusServiceBean.java
@@ -4,19 +4,19 @@
import com.google.gson.GsonBuilder;
import edu.harvard.iq.dataverse.*;
-import javax.ejb.Asynchronous;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.ejb.TransactionAttribute;
-import javax.ejb.TransactionAttributeType;
-import javax.inject.Inject;
-import javax.inject.Named;
-import javax.json.Json;
-import javax.json.JsonArray;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObject;
-import javax.json.JsonPatch;
-import javax.servlet.http.HttpServletRequest;
+import jakarta.ejb.Asynchronous;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.ejb.TransactionAttribute;
+import jakarta.ejb.TransactionAttributeType;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
+import jakarta.json.Json;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonPatch;
+import jakarta.servlet.http.HttpServletRequest;
import static edu.harvard.iq.dataverse.util.json.JsonPrinter.json;
import static edu.harvard.iq.dataverse.util.json.JsonPrinter.toJsonArray;
diff --git a/src/main/java/edu/harvard/iq/dataverse/harvest/client/ClientHarvestRun.java b/src/main/java/edu/harvard/iq/dataverse/harvest/client/ClientHarvestRun.java
index 50d06807a13..ba6f5c3dec2 100644
--- a/src/main/java/edu/harvard/iq/dataverse/harvest/client/ClientHarvestRun.java
+++ b/src/main/java/edu/harvard/iq/dataverse/harvest/client/ClientHarvestRun.java
@@ -7,14 +7,14 @@
import java.io.Serializable;
import java.util.Date;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Temporal;
-import javax.persistence.TemporalType;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Temporal;
+import jakarta.persistence.TemporalType;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvesterServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvesterServiceBean.java
index 40bd45ecb30..20884e3360c 100644
--- a/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvesterServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvesterServiceBean.java
@@ -21,13 +21,13 @@
import java.util.logging.FileHandler;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.annotation.Resource;
-import javax.ejb.Asynchronous;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.ejb.Stateless;
-import javax.ejb.Timer;
-import javax.inject.Named;
+import jakarta.annotation.Resource;
+import jakarta.ejb.Asynchronous;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.ejb.Stateless;
+import jakarta.ejb.Timer;
+import jakarta.inject.Named;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.TransformerException;
import org.apache.commons.lang3.mutable.MutableBoolean;
@@ -51,8 +51,8 @@
import java.nio.file.Files;
import java.nio.file.Paths;
import java.nio.file.Path;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
/**
*
@@ -69,7 +69,7 @@ public class HarvesterServiceBean {
@EJB
DatasetServiceBean datasetService;
@Resource
- javax.ejb.TimerService timerService;
+ jakarta.ejb.TimerService timerService;
@EJB
DataverseTimerServiceBean dataverseTimerService;
@EJB
@@ -148,12 +148,12 @@ public void doHarvest(DataverseRequest dataverseRequest, Long harvestingClientId
String logTimestamp = logFormatter.format(new Date());
Logger hdLogger = Logger.getLogger("edu.harvard.iq.dataverse.harvest.client.HarvesterServiceBean." + harvestingClientConfig.getName() + logTimestamp);
- String logFileName = "../logs" + File.separator + "harvest_" + harvestingClientConfig.getName() + "_" + logTimestamp + ".log";
+ String logFileName = System.getProperty("com.sun.aas.instanceRoot") + File.separator + "logs" + File.separator + "harvest_" + harvestingClientConfig.getName() + "_" + logTimestamp + ".log";
FileHandler fileHandler = new FileHandler(logFileName);
hdLogger.setUseParentHandlers(false);
hdLogger.addHandler(fileHandler);
- PrintWriter importCleanupLog = new PrintWriter(new FileWriter( "../logs/harvest_cleanup_" + harvestingClientConfig.getName() + "_" + logTimestamp+".txt"));
+ PrintWriter importCleanupLog = new PrintWriter(new FileWriter(System.getProperty("com.sun.aas.instanceRoot") + File.separator + "logs/harvest_cleanup_" + harvestingClientConfig.getName() + "_" + logTimestamp + ".txt"));
List harvestedDatasetIds = new ArrayList<>();
diff --git a/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvestingClient.java b/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvestingClient.java
index d27ddc41b7f..40db55f2a0c 100644
--- a/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvestingClient.java
+++ b/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvestingClient.java
@@ -17,25 +17,25 @@
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
-import javax.persistence.CascadeType;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.OneToMany;
-import javax.persistence.OneToOne;
-import javax.persistence.OrderBy;
-import javax.persistence.Table;
-import javax.persistence.Temporal;
-import javax.persistence.TemporalType;
-import javax.validation.constraints.Pattern;
-import javax.validation.constraints.Size;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.OneToMany;
+import jakarta.persistence.OneToOne;
+import jakarta.persistence.OrderBy;
+import jakarta.persistence.Table;
+import jakarta.persistence.Temporal;
+import jakarta.persistence.TemporalType;
+import jakarta.validation.constraints.Pattern;
+import jakarta.validation.constraints.Size;
import org.hibernate.validator.constraints.NotBlank;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvestingClientServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvestingClientServiceBean.java
index 13cc44ce919..7ec6d75a41c 100644
--- a/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvestingClientServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvestingClientServiceBean.java
@@ -5,25 +5,23 @@
import edu.harvard.iq.dataverse.DataverseRequestServiceBean;
import edu.harvard.iq.dataverse.DataverseServiceBean;
import edu.harvard.iq.dataverse.EjbDataverseEngine;
-import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
-import edu.harvard.iq.dataverse.engine.command.impl.DeleteHarvestingClientCommand;
import edu.harvard.iq.dataverse.search.IndexServiceBean;
import edu.harvard.iq.dataverse.timer.DataverseTimerServiceBean;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.logging.Logger;
-import javax.ejb.Asynchronous;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.ejb.TransactionAttribute;
-import javax.ejb.TransactionAttributeType;
-import javax.inject.Inject;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
-import javax.persistence.NonUniqueResultException;
-import javax.persistence.PersistenceContext;
+import jakarta.ejb.Asynchronous;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.ejb.TransactionAttribute;
+import jakarta.ejb.TransactionAttributeType;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.NonUniqueResultException;
+import jakarta.persistence.PersistenceContext;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/harvest/server/OAIRecord.java b/src/main/java/edu/harvard/iq/dataverse/harvest/server/OAIRecord.java
index 49e40e786ea..94753d8594d 100644
--- a/src/main/java/edu/harvard/iq/dataverse/harvest/server/OAIRecord.java
+++ b/src/main/java/edu/harvard/iq/dataverse/harvest/server/OAIRecord.java
@@ -21,12 +21,12 @@
import java.io.Serializable;
import java.util.Date;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Temporal;
-import javax.persistence.TemporalType;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Temporal;
+import jakarta.persistence.TemporalType;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/harvest/server/OAIRecordServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/harvest/server/OAIRecordServiceBean.java
index e73dbb9fc07..1b4a7bc7db0 100644
--- a/src/main/java/edu/harvard/iq/dataverse/harvest/server/OAIRecordServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/harvest/server/OAIRecordServiceBean.java
@@ -13,27 +13,22 @@
import edu.harvard.iq.dataverse.search.IndexServiceBean;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
import java.time.Instant;
-import java.io.File;
-import java.io.IOException;
-import java.sql.Timestamp;
-import java.text.SimpleDateFormat;
import java.util.Collection;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import java.util.logging.FileHandler;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.ejb.TransactionAttribute;
-import static javax.ejb.TransactionAttributeType.REQUIRES_NEW;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.persistence.TypedQuery;
-import javax.persistence.TemporalType;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.ejb.TransactionAttribute;
+import static jakarta.ejb.TransactionAttributeType.REQUIRES_NEW;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.TypedQuery;
+import jakarta.persistence.TemporalType;
/**
*
@@ -265,7 +260,7 @@ public OAIRecord findOAIRecordBySetNameandGlobalId(String setName, String global
try {
oaiRecord = (OAIRecord) query.setMaxResults(1).getSingleResult();
- } catch (javax.persistence.NoResultException e) {
+ } catch (jakarta.persistence.NoResultException e) {
// Do nothing, just return null.
}
logger.fine("returning oai record.");
diff --git a/src/main/java/edu/harvard/iq/dataverse/harvest/server/OAISet.java b/src/main/java/edu/harvard/iq/dataverse/harvest/server/OAISet.java
index 038bb66de32..8d6b04effef 100644
--- a/src/main/java/edu/harvard/iq/dataverse/harvest/server/OAISet.java
+++ b/src/main/java/edu/harvard/iq/dataverse/harvest/server/OAISet.java
@@ -20,16 +20,16 @@
package edu.harvard.iq.dataverse.harvest.server;
import java.io.Serializable;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.OneToOne;
-import javax.persistence.Version;
-import javax.validation.constraints.Pattern;
-import javax.validation.constraints.Size;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.OneToOne;
+import jakarta.persistence.Version;
+import jakarta.validation.constraints.Pattern;
+import jakarta.validation.constraints.Size;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/harvest/server/OAISetServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/harvest/server/OAISetServiceBean.java
index 6b28c8808a0..2bd666401c7 100644
--- a/src/main/java/edu/harvard/iq/dataverse/harvest/server/OAISetServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/harvest/server/OAISetServiceBean.java
@@ -17,19 +17,17 @@
import java.util.logging.FileHandler;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.Asynchronous;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.ejb.TransactionAttribute;
-import javax.ejb.TransactionAttributeType;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import org.apache.solr.client.solrj.SolrClient;
+import jakarta.ejb.Asynchronous;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.ejb.TransactionAttribute;
+import jakarta.ejb.TransactionAttributeType;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
import org.apache.solr.client.solrj.SolrQuery;
import org.apache.solr.client.solrj.SolrServerException;
-import org.apache.solr.client.solrj.impl.HttpSolrClient;
-import org.apache.solr.client.solrj.impl.HttpSolrClient.RemoteSolrException;
+import org.apache.solr.client.solrj.impl.BaseHttpSolrClient.RemoteSolrException;
import org.apache.solr.client.solrj.response.QueryResponse;
import org.apache.solr.common.SolrDocument;
import org.apache.solr.common.SolrDocumentList;
diff --git a/src/main/java/edu/harvard/iq/dataverse/harvest/server/web/servlet/OAIServlet.java b/src/main/java/edu/harvard/iq/dataverse/harvest/server/web/servlet/OAIServlet.java
index 9cf1629abfc..96a19acc0e8 100644
--- a/src/main/java/edu/harvard/iq/dataverse/harvest/server/web/servlet/OAIServlet.java
+++ b/src/main/java/edu/harvard/iq/dataverse/harvest/server/web/servlet/OAIServlet.java
@@ -38,17 +38,16 @@
import java.io.IOException;
-import java.time.Instant;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.inject.Inject;
+import jakarta.ejb.EJB;
+import jakarta.inject.Inject;
import org.eclipse.microprofile.config.inject.ConfigProperty;
-import javax.mail.internet.InternetAddress;
-import javax.servlet.ServletConfig;
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServlet;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.mail.internet.InternetAddress;
+import jakarta.servlet.ServletConfig;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.http.HttpServlet;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
import javax.xml.stream.XMLStreamException;
import org.eclipse.microprofile.config.Config;
import org.eclipse.microprofile.config.ConfigProvider;
diff --git a/src/main/java/edu/harvard/iq/dataverse/ingest/IngestMessageBean.java b/src/main/java/edu/harvard/iq/dataverse/ingest/IngestMessageBean.java
index 77ec6701bc6..f56fe608a52 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ingest/IngestMessageBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ingest/IngestMessageBean.java
@@ -29,15 +29,15 @@
import java.time.Instant;
import java.util.Iterator;
import java.util.logging.Logger;
-import javax.ejb.ActivationConfigProperty;
-import javax.ejb.EJB;
-import javax.ejb.MessageDriven;
-import javax.ejb.TransactionAttribute;
-import javax.ejb.TransactionAttributeType;
-import javax.jms.JMSException;
-import javax.jms.Message;
-import javax.jms.MessageListener;
-import javax.jms.ObjectMessage;
+import jakarta.ejb.ActivationConfigProperty;
+import jakarta.ejb.EJB;
+import jakarta.ejb.MessageDriven;
+import jakarta.ejb.TransactionAttribute;
+import jakarta.ejb.TransactionAttributeType;
+import jakarta.jms.JMSException;
+import jakarta.jms.Message;
+import jakarta.jms.MessageListener;
+import jakarta.jms.ObjectMessage;
/**
*
* This is an experimental, JMS-based implementation of asynchronous
@@ -49,7 +49,7 @@
mappedName = "java:app/jms/queue/ingest",
activationConfig = {
@ActivationConfigProperty(propertyName = "acknowledgeMode", propertyValue = "Auto-acknowledge"),
- @ActivationConfigProperty(propertyName = "destinationType", propertyValue = "javax.jms.Queue")
+ @ActivationConfigProperty(propertyName = "destinationType", propertyValue = "jakarta.jms.Queue")
}
)
diff --git a/src/main/java/edu/harvard/iq/dataverse/ingest/IngestQueueProducer.java b/src/main/java/edu/harvard/iq/dataverse/ingest/IngestQueueProducer.java
index 1ba63207208..0fed25e5c88 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ingest/IngestQueueProducer.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ingest/IngestQueueProducer.java
@@ -1,19 +1,19 @@
package edu.harvard.iq.dataverse.ingest;
-import javax.annotation.Resource;
+import jakarta.annotation.Resource;
// https://www.baeldung.com/jee-cdi-vs-ejb-singleton
-import javax.inject.Singleton;
-import javax.enterprise.inject.Produces;
-import javax.jms.JMSConnectionFactoryDefinition;
-import javax.jms.JMSDestinationDefinition;
-import javax.jms.Queue;
-import javax.jms.QueueConnectionFactory;
+import jakarta.inject.Singleton;
+import jakarta.enterprise.inject.Produces;
+import jakarta.jms.JMSConnectionFactoryDefinition;
+import jakarta.jms.JMSDestinationDefinition;
+import jakarta.jms.Queue;
+import jakarta.jms.QueueConnectionFactory;
@JMSConnectionFactoryDefinition(
description = "Dataverse Ingest Queue Factory",
name = "java:app/jms/factory/ingest",
resourceAdapter = "jmsra",
- interfaceName = "javax.jms.QueueConnectionFactory",
+ interfaceName = "jakarta.jms.QueueConnectionFactory",
maxPoolSize = 250,
minPoolSize = 1,
properties = {
@@ -25,7 +25,7 @@
description = "Dataverse Ingest Queue",
name = "java:app/jms/queue/ingest",
resourceAdapter = "jmsra",
- interfaceName="javax.jms.Queue",
+ interfaceName="jakarta.jms.Queue",
destinationName = "DataverseIngest"
)
@Singleton
diff --git a/src/main/java/edu/harvard/iq/dataverse/ingest/IngestReport.java b/src/main/java/edu/harvard/iq/dataverse/ingest/IngestReport.java
index 31208abf839..a1a8bde77f4 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ingest/IngestReport.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ingest/IngestReport.java
@@ -9,17 +9,17 @@
import edu.harvard.iq.dataverse.DataFile;
import java.io.Serializable;
import java.util.Date;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.Lob;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-import javax.persistence.Temporal;
-import javax.persistence.TemporalType;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.Lob;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Table;
+import jakarta.persistence.Temporal;
+import jakarta.persistence.TemporalType;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/ingest/IngestRequest.java b/src/main/java/edu/harvard/iq/dataverse/ingest/IngestRequest.java
index 024e90325c3..a5d6a1af75c 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ingest/IngestRequest.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ingest/IngestRequest.java
@@ -7,16 +7,16 @@
import edu.harvard.iq.dataverse.DataFile;
import java.io.Serializable;
-import javax.persistence.CascadeType;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.OneToOne;
-import javax.persistence.Table;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.OneToOne;
+import jakarta.persistence.Table;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/ingest/IngestServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/ingest/IngestServiceBean.java
index c1e82042898..40dc3d6fdd6 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ingest/IngestServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ingest/IngestServiceBean.java
@@ -107,20 +107,20 @@
import java.util.logging.Logger;
import java.util.Hashtable;
import java.util.Optional;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.jms.Queue;
-import javax.jms.QueueConnectionFactory;
-import javax.annotation.Resource;
-import javax.ejb.Asynchronous;
-import javax.jms.JMSException;
-import javax.jms.QueueConnection;
-import javax.jms.QueueSender;
-import javax.jms.QueueSession;
-import javax.jms.Message;
-import javax.faces.application.FacesMessage;
-import javax.ws.rs.core.MediaType;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.jms.Queue;
+import jakarta.jms.QueueConnectionFactory;
+import jakarta.annotation.Resource;
+import jakarta.ejb.Asynchronous;
+import jakarta.jms.JMSException;
+import jakarta.jms.QueueConnection;
+import jakarta.jms.QueueSender;
+import jakarta.jms.QueueSession;
+import jakarta.jms.Message;
+import jakarta.faces.application.FacesMessage;
+import jakarta.ws.rs.core.MediaType;
import ucar.nc2.NetcdfFile;
import ucar.nc2.NetcdfFiles;
diff --git a/src/main/java/edu/harvard/iq/dataverse/ingest/IngestServiceShapefileHelper.java b/src/main/java/edu/harvard/iq/dataverse/ingest/IngestServiceShapefileHelper.java
index 9ea2cd0343f..8c5dad237b1 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ingest/IngestServiceShapefileHelper.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ingest/IngestServiceShapefileHelper.java
@@ -16,7 +16,7 @@
import java.io.IOException;
import java.util.List;
import java.util.logging.Logger;
-//import javax.ejb.EJB;
+//import jakarta.ejb.EJB;
/**
* Used by the IngestServiceBean to redistribute a zipped Shapefile*
diff --git a/src/main/java/edu/harvard/iq/dataverse/ingest/IngestUtil.java b/src/main/java/edu/harvard/iq/dataverse/ingest/IngestUtil.java
index 368824680c0..3d30f7e6ec3 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ingest/IngestUtil.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ingest/IngestUtil.java
@@ -20,15 +20,12 @@
package edu.harvard.iq.dataverse.ingest;
import edu.harvard.iq.dataverse.DataFile;
-import edu.harvard.iq.dataverse.Dataset;
import edu.harvard.iq.dataverse.DatasetVersion;
import edu.harvard.iq.dataverse.FileMetadata;
import edu.harvard.iq.dataverse.util.FileUtil;
import java.io.File;
-import java.io.FileWriter;
import java.io.IOException;
-import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
@@ -36,9 +33,9 @@
import java.util.List;
import java.util.Set;
import java.util.logging.Logger;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObjectBuilder;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObjectBuilder;
import org.dataverse.unf.UNFUtil;
import org.dataverse.unf.UnfException;
diff --git a/src/main/java/edu/harvard/iq/dataverse/ingest/tabulardata/impl/plugins/rdata/RDATAFileReader.java b/src/main/java/edu/harvard/iq/dataverse/ingest/tabulardata/impl/plugins/rdata/RDATAFileReader.java
index 6d17a5bd553..eb1353fd792 100644
--- a/src/main/java/edu/harvard/iq/dataverse/ingest/tabulardata/impl/plugins/rdata/RDATAFileReader.java
+++ b/src/main/java/edu/harvard/iq/dataverse/ingest/tabulardata/impl/plugins/rdata/RDATAFileReader.java
@@ -21,14 +21,12 @@
import java.io.*;
-import java.io.FileReader;
import java.io.InputStreamReader;
import java.text.*;
import java.util.logging.*;
import java.util.*;
-import java.security.NoSuchAlgorithmException;
-import javax.inject.Inject;
+import jakarta.inject.Inject;
// Rosuda Wrappers and Methods for R-calls to Rserve
import edu.harvard.iq.dataverse.settings.JvmSettings;
@@ -43,18 +41,14 @@
import edu.harvard.iq.dataverse.datavariable.DataVariable;
import edu.harvard.iq.dataverse.datavariable.VariableCategory;
-import edu.harvard.iq.dataverse.ingest.plugin.spi.*;
import edu.harvard.iq.dataverse.ingest.tabulardata.TabularDataFileReader;
import edu.harvard.iq.dataverse.ingest.tabulardata.spi.TabularDataFileReaderSpi;
import edu.harvard.iq.dataverse.ingest.tabulardata.TabularDataIngest;
import edu.harvard.iq.dataverse.rserve.*;
-import javax.naming.Context;
-import javax.naming.InitialContext;
-import javax.naming.NamingException;
import org.apache.commons.lang3.RandomStringUtils;
-import org.apache.commons.lang3.ArrayUtils;
+
/**
* Dataverse 4.0 implementation of TabularDataFileReader for the
* RData Binary Format.
diff --git a/src/main/java/edu/harvard/iq/dataverse/license/License.java b/src/main/java/edu/harvard/iq/dataverse/license/License.java
index c6e2cdbc2e5..fe19073ab8d 100644
--- a/src/main/java/edu/harvard/iq/dataverse/license/License.java
+++ b/src/main/java/edu/harvard/iq/dataverse/license/License.java
@@ -1,15 +1,15 @@
package edu.harvard.iq.dataverse.license;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.OneToMany;
-import javax.persistence.Table;
-import javax.persistence.UniqueConstraint;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.OneToMany;
+import jakarta.persistence.Table;
+import jakarta.persistence.UniqueConstraint;
import edu.harvard.iq.dataverse.TermsOfUseAndAccess;
diff --git a/src/main/java/edu/harvard/iq/dataverse/license/LicenseConverter.java b/src/main/java/edu/harvard/iq/dataverse/license/LicenseConverter.java
index 4f874132128..26b7ca63a29 100644
--- a/src/main/java/edu/harvard/iq/dataverse/license/LicenseConverter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/license/LicenseConverter.java
@@ -6,11 +6,11 @@
package edu.harvard.iq.dataverse.license;
-import javax.enterprise.inject.spi.CDI;
-import javax.faces.component.UIComponent;
-import javax.faces.context.FacesContext;
-import javax.faces.convert.Converter;
-import javax.faces.convert.FacesConverter;
+import jakarta.enterprise.inject.spi.CDI;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.convert.Converter;
+import jakarta.faces.convert.FacesConverter;
@FacesConverter("licenseConverter")
public class LicenseConverter implements Converter {
diff --git a/src/main/java/edu/harvard/iq/dataverse/license/LicenseServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/license/LicenseServiceBean.java
index 9704e4b92dc..93f4958038c 100644
--- a/src/main/java/edu/harvard/iq/dataverse/license/LicenseServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/license/LicenseServiceBean.java
@@ -5,13 +5,13 @@
import edu.harvard.iq.dataverse.api.AbstractApiBean.WrappedResponse;
import static edu.harvard.iq.dataverse.dataset.DatasetUtil.getLocalizedLicenseName;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
-import javax.persistence.PersistenceContext;
-import javax.persistence.PersistenceException;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.PersistenceException;
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;
diff --git a/src/main/java/edu/harvard/iq/dataverse/locality/DvObjectStorageLocation.java b/src/main/java/edu/harvard/iq/dataverse/locality/DvObjectStorageLocation.java
index 33486128e7b..5844c8b6ab9 100644
--- a/src/main/java/edu/harvard/iq/dataverse/locality/DvObjectStorageLocation.java
+++ b/src/main/java/edu/harvard/iq/dataverse/locality/DvObjectStorageLocation.java
@@ -2,11 +2,11 @@
import edu.harvard.iq.dataverse.DvObject;
import java.io.Serializable;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.OneToOne;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.OneToOne;
/**
* Future use, maybe. Once we're happy with the design we'll enable it as an
diff --git a/src/main/java/edu/harvard/iq/dataverse/locality/StorageSite.java b/src/main/java/edu/harvard/iq/dataverse/locality/StorageSite.java
index d873b9f8989..c074cb5918f 100644
--- a/src/main/java/edu/harvard/iq/dataverse/locality/StorageSite.java
+++ b/src/main/java/edu/harvard/iq/dataverse/locality/StorageSite.java
@@ -2,13 +2,13 @@
import java.io.Serializable;
import java.util.Objects;
-import javax.json.Json;
-import javax.json.JsonObjectBuilder;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
+import jakarta.json.Json;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
@Entity
public class StorageSite implements Serializable {
diff --git a/src/main/java/edu/harvard/iq/dataverse/locality/StorageSiteServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/locality/StorageSiteServiceBean.java
index c7057ab9318..781e896e9a7 100644
--- a/src/main/java/edu/harvard/iq/dataverse/locality/StorageSiteServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/locality/StorageSiteServiceBean.java
@@ -2,12 +2,12 @@
import java.util.List;
import java.util.logging.Logger;
-import javax.ejb.Stateless;
-import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
-import javax.persistence.NonUniqueResultException;
-import javax.persistence.PersistenceContext;
-import javax.persistence.TypedQuery;
+import jakarta.ejb.Stateless;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.NonUniqueResultException;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.TypedQuery;
@Stateless
public class StorageSiteServiceBean {
diff --git a/src/main/java/edu/harvard/iq/dataverse/locality/StorageSiteUtil.java b/src/main/java/edu/harvard/iq/dataverse/locality/StorageSiteUtil.java
index ebc2bb0f19f..6ff0f7ca379 100644
--- a/src/main/java/edu/harvard/iq/dataverse/locality/StorageSiteUtil.java
+++ b/src/main/java/edu/harvard/iq/dataverse/locality/StorageSiteUtil.java
@@ -2,7 +2,7 @@
import edu.harvard.iq.dataverse.util.SystemConfig;
import java.util.List;
-import javax.json.JsonObject;
+import jakarta.json.JsonObject;
public class StorageSiteUtil {
diff --git a/src/main/java/edu/harvard/iq/dataverse/makedatacount/DatasetExternalCitations.java b/src/main/java/edu/harvard/iq/dataverse/makedatacount/DatasetExternalCitations.java
index 3c1c0bc0c68..469f3abe9da 100644
--- a/src/main/java/edu/harvard/iq/dataverse/makedatacount/DatasetExternalCitations.java
+++ b/src/main/java/edu/harvard/iq/dataverse/makedatacount/DatasetExternalCitations.java
@@ -7,14 +7,14 @@
import edu.harvard.iq.dataverse.Dataset;
import java.io.Serializable;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.validation.constraints.NotNull;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.validation.constraints.NotNull;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/makedatacount/DatasetExternalCitationsServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/makedatacount/DatasetExternalCitationsServiceBean.java
index c05fc9b1a4e..50c24274bb2 100644
--- a/src/main/java/edu/harvard/iq/dataverse/makedatacount/DatasetExternalCitationsServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/makedatacount/DatasetExternalCitationsServiceBean.java
@@ -10,16 +10,16 @@
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.json.JsonArray;
-import javax.json.JsonObject;
-import javax.json.JsonValue;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.persistence.Query;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonValue;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.Query;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/makedatacount/DatasetMetrics.java b/src/main/java/edu/harvard/iq/dataverse/makedatacount/DatasetMetrics.java
index fe0565c3ff8..ac3dff356eb 100644
--- a/src/main/java/edu/harvard/iq/dataverse/makedatacount/DatasetMetrics.java
+++ b/src/main/java/edu/harvard/iq/dataverse/makedatacount/DatasetMetrics.java
@@ -3,15 +3,15 @@
import edu.harvard.iq.dataverse.Dataset;
import java.io.Serializable;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Transient;
-import javax.validation.constraints.NotNull;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Transient;
+import jakarta.validation.constraints.NotNull;
/**
* Cached versions of views, downloads, and citations to show in the UI and API.
diff --git a/src/main/java/edu/harvard/iq/dataverse/makedatacount/DatasetMetricsServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/makedatacount/DatasetMetricsServiceBean.java
index 39afdf318ad..0925c164bf4 100644
--- a/src/main/java/edu/harvard/iq/dataverse/makedatacount/DatasetMetricsServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/makedatacount/DatasetMetricsServiceBean.java
@@ -5,26 +5,23 @@
import edu.harvard.iq.dataverse.DatasetServiceBean;
import java.io.StringReader;
import java.math.BigDecimal;
-import java.sql.Timestamp;
import java.util.ArrayList;
-import java.util.Date;
import java.util.List;
import java.util.ListIterator;
import java.util.Set;
-import java.util.concurrent.Future;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.json.Json;
-import javax.json.JsonArray;
-import javax.json.JsonObject;
-import javax.json.JsonReader;
-import javax.json.JsonValue;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.persistence.Query;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.json.Json;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonReader;
+import jakarta.json.JsonValue;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.Query;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/makedatacount/MakeDataCountLoggingServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/makedatacount/MakeDataCountLoggingServiceBean.java
index e1a635a9d6c..5edf2fde0c3 100644
--- a/src/main/java/edu/harvard/iq/dataverse/makedatacount/MakeDataCountLoggingServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/makedatacount/MakeDataCountLoggingServiceBean.java
@@ -16,14 +16,14 @@
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.TimeZone;
-import javax.ejb.EJB;
-import javax.enterprise.context.RequestScoped;
-import javax.faces.context.FacesContext;
-import javax.inject.Named;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpSession;
-import javax.ws.rs.core.HttpHeaders;
-import javax.ws.rs.core.UriInfo;
+import jakarta.ejb.EJB;
+import jakarta.enterprise.context.RequestScoped;
+import jakarta.faces.context.FacesContext;
+import jakarta.inject.Named;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpSession;
+import jakarta.ws.rs.core.HttpHeaders;
+import jakarta.ws.rs.core.UriInfo;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/makedatacount/MakeDataCountUtil.java b/src/main/java/edu/harvard/iq/dataverse/makedatacount/MakeDataCountUtil.java
index f3d45642083..8f32750f090 100644
--- a/src/main/java/edu/harvard/iq/dataverse/makedatacount/MakeDataCountUtil.java
+++ b/src/main/java/edu/harvard/iq/dataverse/makedatacount/MakeDataCountUtil.java
@@ -1,17 +1,16 @@
package edu.harvard.iq.dataverse.makedatacount;
import java.util.ArrayList;
-import java.util.Arrays;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.stream.Collectors;
import java.util.stream.Stream;
-import javax.json.JsonArray;
-import javax.json.JsonObject;
-import javax.json.JsonValue;
-import javax.persistence.Transient;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonValue;
+import jakarta.persistence.Transient;
/**
* See doc/sphinx-guides/source/admin/make-data-count.rst for user facing docs
diff --git a/src/main/java/edu/harvard/iq/dataverse/metadataimport/ForeignMetadataImportServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/metadataimport/ForeignMetadataImportServiceBean.java
index 88af8478a8f..33f8277919a 100644
--- a/src/main/java/edu/harvard/iq/dataverse/metadataimport/ForeignMetadataImportServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/metadataimport/ForeignMetadataImportServiceBean.java
@@ -2,7 +2,6 @@
package edu.harvard.iq.dataverse.metadataimport;
-import edu.harvard.iq.dataverse.ControlledVocabularyValue;
import edu.harvard.iq.dataverse.DatasetVersion;
import edu.harvard.iq.dataverse.DatasetField;
import edu.harvard.iq.dataverse.DatasetFieldCompoundValue;
@@ -17,13 +16,13 @@
import java.io.IOException;
import java.util.logging.Logger;
import java.io.StringReader;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
-import javax.persistence.PersistenceContext;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.PersistenceContext;
import javax.xml.stream.XMLStreamConstants;
import javax.xml.stream.XMLStreamException;
import javax.xml.stream.XMLStreamReader;
diff --git a/src/main/java/edu/harvard/iq/dataverse/metrics/MetricsServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/metrics/MetricsServiceBean.java
index ff5ffee8f85..065b42e5afe 100644
--- a/src/main/java/edu/harvard/iq/dataverse/metrics/MetricsServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/metrics/MetricsServiceBean.java
@@ -3,7 +3,6 @@
import edu.harvard.iq.dataverse.DatasetVersion;
import edu.harvard.iq.dataverse.Dataverse;
import edu.harvard.iq.dataverse.Metric;
-import edu.harvard.iq.dataverse.makedatacount.DatasetMetrics;
import edu.harvard.iq.dataverse.makedatacount.MakeDataCountUtil.MetricType;
import static edu.harvard.iq.dataverse.metrics.MetricsUtil.*;
@@ -23,19 +22,19 @@
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.json.Json;
-import javax.json.JsonArray;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
-import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
-import javax.persistence.NonUniqueResultException;
-import javax.persistence.PersistenceContext;
-import javax.persistence.Query;
-import javax.ws.rs.core.UriInfo;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.json.Json;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.NonUniqueResultException;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.Query;
+import jakarta.ws.rs.core.UriInfo;
@Stateless
public class MetricsServiceBean implements Serializable {
@@ -383,7 +382,7 @@ public JsonArray filesByType(Dataverse d) {
jab.add(stats);
}
- } catch (javax.persistence.NoResultException nr) {
+ } catch (NoResultException nr) {
// do nothing
}
return jab.build();
@@ -519,7 +518,7 @@ public JsonArray fileDownloads(String yyyymm, Dataverse d, boolean uniqueCounts)
job.add(MetricsUtil.COUNT, (long) result[2]);
jab.add(job);
}
- } catch (javax.persistence.NoResultException nr) {
+ } catch (NoResultException nr) {
// do nothing
}
return jab.build();
@@ -558,7 +557,7 @@ public JsonArray uniqueDatasetDownloads(String yyyymm, Dataverse d) {
jab.add(job);
}
- } catch (javax.persistence.NoResultException nr) {
+ } catch (NoResultException nr) {
// do nothing
}
return jab.build();
@@ -718,7 +717,7 @@ public Metric getMetric(String name, String dataLocation, String dayString, Data
Metric metric = null;
try {
metric = (Metric) query.getSingleResult();
- } catch (javax.persistence.NoResultException nr) {
+ } catch (NoResultException nr) {
// do nothing
logger.fine("No result");
} catch (NonUniqueResultException nur) {
diff --git a/src/main/java/edu/harvard/iq/dataverse/metrics/MetricsUtil.java b/src/main/java/edu/harvard/iq/dataverse/metrics/MetricsUtil.java
index 72d8f5402bb..74bb53e1191 100644
--- a/src/main/java/edu/harvard/iq/dataverse/metrics/MetricsUtil.java
+++ b/src/main/java/edu/harvard/iq/dataverse/metrics/MetricsUtil.java
@@ -6,21 +6,19 @@
import java.time.LocalDate;
import java.time.YearMonth;
import java.time.format.DateTimeFormatter;
-import java.time.format.DateTimeFormatterBuilder;
import java.time.format.DateTimeParseException;
-import java.time.temporal.ChronoField;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.logging.Logger;
-import javax.json.Json;
-import javax.json.JsonArray;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
-import javax.json.JsonReader;
-import javax.ws.rs.BadRequestException;
+import jakarta.json.Json;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.json.JsonReader;
+import jakarta.ws.rs.BadRequestException;
public class MetricsUtil {
diff --git a/src/main/java/edu/harvard/iq/dataverse/mydata/DataRetrieverAPI.java b/src/main/java/edu/harvard/iq/dataverse/mydata/DataRetrieverAPI.java
index d244021d01a..e9898031343 100644
--- a/src/main/java/edu/harvard/iq/dataverse/mydata/DataRetrieverAPI.java
+++ b/src/main/java/edu/harvard/iq/dataverse/mydata/DataRetrieverAPI.java
@@ -25,25 +25,23 @@
import edu.harvard.iq.dataverse.search.SearchException;
import edu.harvard.iq.dataverse.search.SearchFields;
import edu.harvard.iq.dataverse.search.SortBy;
-import java.math.BigDecimal;
-import java.util.Arrays;
+
import java.util.List;
import java.util.Map;
-import java.util.Random;
import java.util.logging.Logger;
import java.util.Locale;
-import javax.ejb.EJB;
-import javax.inject.Inject;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObjectBuilder;
-import javax.ws.rs.GET;
-import javax.ws.rs.Path;
-import javax.ws.rs.Produces;
-import javax.ws.rs.QueryParam;
-import javax.ws.rs.DefaultValue;
-import javax.ws.rs.container.ContainerRequestContext;
-import javax.ws.rs.core.Context;
+import jakarta.ejb.EJB;
+import jakarta.inject.Inject;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.Produces;
+import jakarta.ws.rs.QueryParam;
+import jakarta.ws.rs.DefaultValue;
+import jakarta.ws.rs.container.ContainerRequestContext;
+import jakarta.ws.rs.core.Context;
import edu.harvard.iq.dataverse.util.BundleUtil;
import org.apache.commons.lang3.StringUtils;
diff --git a/src/main/java/edu/harvard/iq/dataverse/mydata/MyDataFilterParams.java b/src/main/java/edu/harvard/iq/dataverse/mydata/MyDataFilterParams.java
index c378034f951..2ab248fcc0b 100644
--- a/src/main/java/edu/harvard/iq/dataverse/mydata/MyDataFilterParams.java
+++ b/src/main/java/edu/harvard/iq/dataverse/mydata/MyDataFilterParams.java
@@ -17,9 +17,9 @@
import java.util.HashMap;
import java.util.List;
import java.util.logging.Logger;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObjectBuilder;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObjectBuilder;
import org.apache.commons.lang3.StringUtils;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/mydata/MyDataFinder.java b/src/main/java/edu/harvard/iq/dataverse/mydata/MyDataFinder.java
index 6acdfd9cdde..917884f3549 100644
--- a/src/main/java/edu/harvard/iq/dataverse/mydata/MyDataFinder.java
+++ b/src/main/java/edu/harvard/iq/dataverse/mydata/MyDataFinder.java
@@ -18,9 +18,9 @@
import java.util.Map;
import java.util.Set;
import java.util.logging.Logger;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObjectBuilder;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObjectBuilder;
import org.apache.commons.lang3.StringUtils;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/mydata/MyDataPage.java b/src/main/java/edu/harvard/iq/dataverse/mydata/MyDataPage.java
index 2567f8b2774..3ae64d9d760 100644
--- a/src/main/java/edu/harvard/iq/dataverse/mydata/MyDataPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/mydata/MyDataPage.java
@@ -18,12 +18,12 @@
import java.util.Arrays;
import java.util.List;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.faces.context.FacesContext;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
-import javax.servlet.http.HttpServletRequest;
+import jakarta.ejb.EJB;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
+import jakarta.servlet.http.HttpServletRequest;
/*
* To change this license header, choose License Headers in Project Properties.
diff --git a/src/main/java/edu/harvard/iq/dataverse/mydata/Pager.java b/src/main/java/edu/harvard/iq/dataverse/mydata/Pager.java
index 4bf13e04284..096974b9d72 100644
--- a/src/main/java/edu/harvard/iq/dataverse/mydata/Pager.java
+++ b/src/main/java/edu/harvard/iq/dataverse/mydata/Pager.java
@@ -15,9 +15,9 @@
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObjectBuilder;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObjectBuilder;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/mydata/RolePermissionHelperPage.java b/src/main/java/edu/harvard/iq/dataverse/mydata/RolePermissionHelperPage.java
index 4c596d1bb84..dcb76f42acb 100644
--- a/src/main/java/edu/harvard/iq/dataverse/mydata/RolePermissionHelperPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/mydata/RolePermissionHelperPage.java
@@ -3,16 +3,15 @@
import edu.harvard.iq.dataverse.DatasetPage;
import edu.harvard.iq.dataverse.DataverseRoleServiceBean;
import edu.harvard.iq.dataverse.DataverseSession;
-import edu.harvard.iq.dataverse.DvObject;
import edu.harvard.iq.dataverse.RoleAssigneeServiceBean;
import edu.harvard.iq.dataverse.authorization.DataverseRole;
import edu.harvard.iq.dataverse.authorization.DataverseRolePermissionHelper;
import java.util.List;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
/*
* To change this license header, choose License Headers in Project Properties.
diff --git a/src/main/java/edu/harvard/iq/dataverse/mydata/RoleTagRetriever.java b/src/main/java/edu/harvard/iq/dataverse/mydata/RoleTagRetriever.java
index cf7380a9a9b..e328a50e962 100644
--- a/src/main/java/edu/harvard/iq/dataverse/mydata/RoleTagRetriever.java
+++ b/src/main/java/edu/harvard/iq/dataverse/mydata/RoleTagRetriever.java
@@ -23,9 +23,8 @@
import java.util.Set;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import org.apache.commons.lang3.StringUtils;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
/**
* Input: dvObject id, parent Id, and dvObject type (from Solr)
diff --git a/src/main/java/edu/harvard/iq/dataverse/passwordreset/PasswordResetData.java b/src/main/java/edu/harvard/iq/dataverse/passwordreset/PasswordResetData.java
index a3150161c52..c078860ad8e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/passwordreset/PasswordResetData.java
+++ b/src/main/java/edu/harvard/iq/dataverse/passwordreset/PasswordResetData.java
@@ -6,19 +6,19 @@
import java.sql.Timestamp;
import java.util.Date;
import java.util.UUID;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.OneToOne;
-import javax.persistence.Table;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.EnumType;
+import jakarta.persistence.Enumerated;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.OneToOne;
+import jakarta.persistence.Table;
@Table(indexes = {@Index(columnList="token")
, @Index(columnList="builtinuser_id")})
diff --git a/src/main/java/edu/harvard/iq/dataverse/passwordreset/PasswordResetPage.java b/src/main/java/edu/harvard/iq/dataverse/passwordreset/PasswordResetPage.java
index b9eabf45159..b19721d56bb 100644
--- a/src/main/java/edu/harvard/iq/dataverse/passwordreset/PasswordResetPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/passwordreset/PasswordResetPage.java
@@ -16,19 +16,19 @@
import edu.harvard.iq.dataverse.util.SystemConfig;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.faces.application.FacesMessage;
-import javax.faces.context.FacesContext;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
import edu.harvard.iq.dataverse.validation.PasswordValidatorServiceBean;
import java.util.Arrays;
import java.util.Date;
import java.util.List;
-import javax.faces.component.UIComponent;
-import javax.faces.component.UIInput;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.component.UIInput;
import org.apache.commons.lang3.StringUtils;
import org.hibernate.validator.constraints.NotBlank;
diff --git a/src/main/java/edu/harvard/iq/dataverse/passwordreset/PasswordResetServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/passwordreset/PasswordResetServiceBean.java
index c8db23985d8..5d1c167d2a5 100644
--- a/src/main/java/edu/harvard/iq/dataverse/passwordreset/PasswordResetServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/passwordreset/PasswordResetServiceBean.java
@@ -10,18 +10,17 @@
import edu.harvard.iq.dataverse.util.SystemConfig;
import java.text.MessageFormat;
-import java.util.Date;
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
-import javax.persistence.NonUniqueResultException;
-import javax.persistence.PersistenceContext;
-import javax.persistence.TypedQuery;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.NonUniqueResultException;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.TypedQuery;
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
@Stateless
diff --git a/src/main/java/edu/harvard/iq/dataverse/pidproviders/FakePidProviderServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/pidproviders/FakePidProviderServiceBean.java
index 54d64710511..3bd9d9dd022 100644
--- a/src/main/java/edu/harvard/iq/dataverse/pidproviders/FakePidProviderServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/pidproviders/FakePidProviderServiceBean.java
@@ -3,13 +3,13 @@
import edu.harvard.iq.dataverse.DOIServiceBean;
import edu.harvard.iq.dataverse.DvObject;
import edu.harvard.iq.dataverse.GlobalId;
-import java.util.ArrayList;
+
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.logging.Logger;
-import javax.ejb.Stateless;
+import jakarta.ejb.Stateless;
@Stateless
public class FakePidProviderServiceBean extends DOIServiceBean {
diff --git a/src/main/java/edu/harvard/iq/dataverse/pidproviders/PermaLinkPidProviderServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/pidproviders/PermaLinkPidProviderServiceBean.java
index f387188b690..d145a7ec106 100644
--- a/src/main/java/edu/harvard/iq/dataverse/pidproviders/PermaLinkPidProviderServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/pidproviders/PermaLinkPidProviderServiceBean.java
@@ -4,21 +4,17 @@
import edu.harvard.iq.dataverse.DvObject;
import edu.harvard.iq.dataverse.GlobalId;
import edu.harvard.iq.dataverse.GlobalIdServiceBean;
-import edu.harvard.iq.dataverse.engine.command.impl.CreateNewDatasetCommand;
import edu.harvard.iq.dataverse.settings.JvmSettings;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean.Key;
import edu.harvard.iq.dataverse.util.SystemConfig;
-import java.lang.StackWalker.StackFrame;
-import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.logging.Logger;
-import java.util.stream.Stream;
-import javax.annotation.PostConstruct;
-import javax.ejb.Stateless;
+import jakarta.annotation.PostConstruct;
+import jakarta.ejb.Stateless;
/**
* PermaLink provider
diff --git a/src/main/java/edu/harvard/iq/dataverse/pidproviders/PidHelper.java b/src/main/java/edu/harvard/iq/dataverse/pidproviders/PidHelper.java
index 478f5d6c2c4..5bc855a9593 100644
--- a/src/main/java/edu/harvard/iq/dataverse/pidproviders/PidHelper.java
+++ b/src/main/java/edu/harvard/iq/dataverse/pidproviders/PidHelper.java
@@ -1,10 +1,10 @@
package edu.harvard.iq.dataverse.pidproviders;
import java.util.Arrays;
-import javax.annotation.PostConstruct;
-import javax.ejb.EJB;
-import javax.ejb.Singleton;
-import javax.ejb.Startup;
+import jakarta.annotation.PostConstruct;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Singleton;
+import jakarta.ejb.Startup;
import edu.harvard.iq.dataverse.DOIDataCiteServiceBean;
import edu.harvard.iq.dataverse.DOIEZIdServiceBean;
diff --git a/src/main/java/edu/harvard/iq/dataverse/pidproviders/PidUtil.java b/src/main/java/edu/harvard/iq/dataverse/pidproviders/PidUtil.java
index 4db7d099a47..78305648f67 100644
--- a/src/main/java/edu/harvard/iq/dataverse/pidproviders/PidUtil.java
+++ b/src/main/java/edu/harvard/iq/dataverse/pidproviders/PidUtil.java
@@ -16,13 +16,13 @@
import java.util.Map;
import java.util.logging.Logger;
-import javax.json.Json;
-import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
-import javax.ws.rs.BadRequestException;
-import javax.ws.rs.InternalServerErrorException;
-import javax.ws.rs.NotFoundException;
-import javax.ws.rs.ServiceUnavailableException;
+import jakarta.json.Json;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.ws.rs.BadRequestException;
+import jakarta.ws.rs.InternalServerErrorException;
+import jakarta.ws.rs.NotFoundException;
+import jakarta.ws.rs.ServiceUnavailableException;
public class PidUtil {
diff --git a/src/main/java/edu/harvard/iq/dataverse/pidproviders/UnmanagedDOIServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/pidproviders/UnmanagedDOIServiceBean.java
index 20f1051763f..f7e9372cc9b 100644
--- a/src/main/java/edu/harvard/iq/dataverse/pidproviders/UnmanagedDOIServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/pidproviders/UnmanagedDOIServiceBean.java
@@ -1,13 +1,12 @@
package edu.harvard.iq.dataverse.pidproviders;
import java.io.IOException;
-import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.logging.Logger;
-import javax.annotation.PostConstruct;
-import javax.ejb.Stateless;
+import jakarta.annotation.PostConstruct;
+import jakarta.ejb.Stateless;
import org.apache.commons.httpclient.HttpException;
import org.apache.commons.lang3.NotImplementedException;
diff --git a/src/main/java/edu/harvard/iq/dataverse/pidproviders/UnmanagedHandlenetServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/pidproviders/UnmanagedHandlenetServiceBean.java
index 8847a99bd20..c856c5363e0 100644
--- a/src/main/java/edu/harvard/iq/dataverse/pidproviders/UnmanagedHandlenetServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/pidproviders/UnmanagedHandlenetServiceBean.java
@@ -7,7 +7,7 @@
import java.util.*;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.Stateless;
+import jakarta.ejb.Stateless;
import org.apache.commons.lang3.NotImplementedException;
/** This class is just used to parse Handles that are not managed by any account configured in Dataverse
diff --git a/src/main/java/edu/harvard/iq/dataverse/privateurl/PrivateUrlPage.java b/src/main/java/edu/harvard/iq/dataverse/privateurl/PrivateUrlPage.java
index b0658f10b34..9af4bb6af9e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/privateurl/PrivateUrlPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/privateurl/PrivateUrlPage.java
@@ -4,10 +4,10 @@
import edu.harvard.iq.dataverse.authorization.users.PrivateUrlUser;
import java.io.Serializable;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
/**
* Backing bean for JSF page. Sets session to {@link PrivateUrlUser}.
diff --git a/src/main/java/edu/harvard/iq/dataverse/privateurl/PrivateUrlServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/privateurl/PrivateUrlServiceBean.java
index 8eb0dfe4ebd..9e5879106e4 100644
--- a/src/main/java/edu/harvard/iq/dataverse/privateurl/PrivateUrlServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/privateurl/PrivateUrlServiceBean.java
@@ -8,14 +8,14 @@
import edu.harvard.iq.dataverse.util.SystemConfig;
import java.io.Serializable;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
-import javax.persistence.NonUniqueResultException;
-import javax.persistence.PersistenceContext;
-import javax.persistence.TypedQuery;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.NonUniqueResultException;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.TypedQuery;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/provenance/ProvEntityFileDataConverter.java b/src/main/java/edu/harvard/iq/dataverse/provenance/ProvEntityFileDataConverter.java
index 65b97b80eea..ba5aba1b69b 100644
--- a/src/main/java/edu/harvard/iq/dataverse/provenance/ProvEntityFileDataConverter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/provenance/ProvEntityFileDataConverter.java
@@ -1,11 +1,11 @@
package edu.harvard.iq.dataverse.provenance;
-import javax.enterprise.inject.spi.CDI;
-import javax.faces.component.UIComponent;
-import javax.faces.context.FacesContext;
-import javax.faces.convert.Converter;
-import javax.faces.convert.FacesConverter;
-import javax.inject.Inject;
+import jakarta.enterprise.inject.spi.CDI;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.convert.Converter;
+import jakarta.faces.convert.FacesConverter;
+import jakarta.inject.Inject;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/provenance/ProvInvestigator.java b/src/main/java/edu/harvard/iq/dataverse/provenance/ProvInvestigator.java
index a17e77f2a9e..c2eecb90d9e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/provenance/ProvInvestigator.java
+++ b/src/main/java/edu/harvard/iq/dataverse/provenance/ProvInvestigator.java
@@ -5,12 +5,12 @@
import com.google.gson.GsonBuilder;
import com.google.gson.JsonElement;
import com.google.gson.JsonParser;
-import edu.harvard.iq.dataverse.api.AbstractApiBean;
+
import java.util.HashMap;
import java.util.Map;
import java.util.Set;
import java.util.logging.Logger;
-import javax.json.JsonObject;
+import jakarta.json.JsonObject;
import org.everit.json.schema.Schema;
import org.everit.json.schema.ValidationException;
import org.everit.json.schema.loader.SchemaLoader;
diff --git a/src/main/java/edu/harvard/iq/dataverse/provenance/ProvPopupFragmentBean.java b/src/main/java/edu/harvard/iq/dataverse/provenance/ProvPopupFragmentBean.java
index a4b7cdf8d4e..6e8a512902a 100644
--- a/src/main/java/edu/harvard/iq/dataverse/provenance/ProvPopupFragmentBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/provenance/ProvPopupFragmentBean.java
@@ -24,19 +24,19 @@
import java.util.HashMap;
import java.util.Map;
import java.util.logging.Level;
-import javax.ejb.EJB;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
import org.apache.commons.io.IOUtils;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
-import javax.faces.application.FacesMessage;
-import javax.faces.context.ExternalContext;
-import javax.faces.context.FacesContext;
-import javax.json.JsonObject;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.context.ExternalContext;
+import jakarta.faces.context.FacesContext;
+import jakarta.json.JsonObject;
import org.primefaces.model.file.UploadedFile;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/repositorystorageabstractionlayer/RepositoryStorageAbstractionLayerPage.java b/src/main/java/edu/harvard/iq/dataverse/repositorystorageabstractionlayer/RepositoryStorageAbstractionLayerPage.java
index 4d89a2842cd..c252d2e3330 100644
--- a/src/main/java/edu/harvard/iq/dataverse/repositorystorageabstractionlayer/RepositoryStorageAbstractionLayerPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/repositorystorageabstractionlayer/RepositoryStorageAbstractionLayerPage.java
@@ -6,10 +6,10 @@
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
import java.util.List;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.json.JsonArray;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.json.JsonArray;
@Stateless
@Named
diff --git a/src/main/java/edu/harvard/iq/dataverse/repositorystorageabstractionlayer/RepositoryStorageAbstractionLayerUtil.java b/src/main/java/edu/harvard/iq/dataverse/repositorystorageabstractionlayer/RepositoryStorageAbstractionLayerUtil.java
index ee52254d6f5..8501fba3ce0 100644
--- a/src/main/java/edu/harvard/iq/dataverse/repositorystorageabstractionlayer/RepositoryStorageAbstractionLayerUtil.java
+++ b/src/main/java/edu/harvard/iq/dataverse/repositorystorageabstractionlayer/RepositoryStorageAbstractionLayerUtil.java
@@ -3,15 +3,15 @@
import edu.harvard.iq.dataverse.Dataset;
import edu.harvard.iq.dataverse.locality.StorageSite;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
-import edu.harvard.iq.dataverse.util.SystemConfig;
+
import java.io.File;
import java.util.ArrayList;
import java.util.List;
import java.util.logging.Logger;
-import javax.json.Json;
-import javax.json.JsonArray;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObject;
+import jakarta.json.Json;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObject;
public class RepositoryStorageAbstractionLayerUtil {
diff --git a/src/main/java/edu/harvard/iq/dataverse/search/AdvancedSearchPage.java b/src/main/java/edu/harvard/iq/dataverse/search/AdvancedSearchPage.java
index ef37569ac54..bc92959a5ac 100644
--- a/src/main/java/edu/harvard/iq/dataverse/search/AdvancedSearchPage.java
+++ b/src/main/java/edu/harvard/iq/dataverse/search/AdvancedSearchPage.java
@@ -14,20 +14,16 @@
import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
import java.util.ArrayList;
-import java.util.Arrays;
import java.util.Collection;
import java.util.HashMap;
-import java.util.HashSet;
import java.util.List;
import java.util.Map;
-import java.util.Set;
-import java.util.StringTokenizer;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.faces.view.ViewScoped;
-import javax.inject.Inject;
-import javax.inject.Named;
-import javax.json.JsonObject;
+import jakarta.ejb.EJB;
+import jakarta.faces.view.ViewScoped;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
+import jakarta.json.JsonObject;
import org.apache.commons.lang3.StringUtils;
diff --git a/src/main/java/edu/harvard/iq/dataverse/search/FacetLabel.java b/src/main/java/edu/harvard/iq/dataverse/search/FacetLabel.java
index f8bd0ea5a10..f97c1641479 100644
--- a/src/main/java/edu/harvard/iq/dataverse/search/FacetLabel.java
+++ b/src/main/java/edu/harvard/iq/dataverse/search/FacetLabel.java
@@ -1,6 +1,6 @@
package edu.harvard.iq.dataverse.search;
-import javax.inject.Named;
+import jakarta.inject.Named;
@Named
public class FacetLabel implements Comparable{
diff --git a/src/main/java/edu/harvard/iq/dataverse/search/Highlight.java b/src/main/java/edu/harvard/iq/dataverse/search/Highlight.java
index 98a882c13ca..d40d8c362af 100644
--- a/src/main/java/edu/harvard/iq/dataverse/search/Highlight.java
+++ b/src/main/java/edu/harvard/iq/dataverse/search/Highlight.java
@@ -1,7 +1,7 @@
package edu.harvard.iq.dataverse.search;
import java.util.List;
-import javax.inject.Named;
+import jakarta.inject.Named;
@Named
public class Highlight {
diff --git a/src/main/java/edu/harvard/iq/dataverse/search/IndexAsync.java b/src/main/java/edu/harvard/iq/dataverse/search/IndexAsync.java
index a04ae934259..c9cf1cd9dc7 100644
--- a/src/main/java/edu/harvard/iq/dataverse/search/IndexAsync.java
+++ b/src/main/java/edu/harvard/iq/dataverse/search/IndexAsync.java
@@ -5,9 +5,9 @@
import java.util.Collection;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.Asynchronous;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
+import jakarta.ejb.Asynchronous;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
@Stateless
public class IndexAsync {
diff --git a/src/main/java/edu/harvard/iq/dataverse/search/IndexBatchServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/search/IndexBatchServiceBean.java
index 932f58d875d..0eeb681514c 100644
--- a/src/main/java/edu/harvard/iq/dataverse/search/IndexBatchServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/search/IndexBatchServiceBean.java
@@ -1,30 +1,27 @@
package edu.harvard.iq.dataverse.search;
-import edu.harvard.iq.dataverse.Dataset;
import edu.harvard.iq.dataverse.DatasetServiceBean;
import edu.harvard.iq.dataverse.Dataverse;
import edu.harvard.iq.dataverse.DataverseServiceBean;
import edu.harvard.iq.dataverse.DvObjectServiceBean;
import edu.harvard.iq.dataverse.util.SystemConfig;
import java.io.IOException;
-import java.sql.Timestamp;
import java.util.ArrayList;
-import java.util.Date;
import java.util.List;
import java.util.concurrent.Future;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.AsyncResult;
-import javax.ejb.Asynchronous;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
+import jakarta.ejb.AsyncResult;
+import jakarta.ejb.Asynchronous;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
import org.apache.solr.client.solrj.SolrServerException;
@Named
diff --git a/src/main/java/edu/harvard/iq/dataverse/search/IndexServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/search/IndexServiceBean.java
index 669125090b8..d6d0be7a17b 100644
--- a/src/main/java/edu/harvard/iq/dataverse/search/IndexServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/search/IndexServiceBean.java
@@ -41,7 +41,6 @@
import java.io.IOException;
import java.io.InputStream;
import java.sql.Timestamp;
-import java.text.NumberFormat;
import java.text.SimpleDateFormat;
import java.time.LocalDate;
import java.util.ArrayList;
@@ -54,26 +53,25 @@
import java.util.List;
import java.util.Locale;
import java.util.Map;
-import java.util.Optional;
import java.util.Set;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.Future;
import java.util.function.Function;
import java.util.logging.Logger;
import java.util.stream.Collectors;
-import javax.annotation.PostConstruct;
-import javax.annotation.PreDestroy;
-import javax.ejb.AsyncResult;
-import javax.ejb.Asynchronous;
-import javax.ejb.EJB;
-import javax.ejb.EJBException;
-import javax.ejb.Stateless;
-import javax.ejb.TransactionAttribute;
-import static javax.ejb.TransactionAttributeType.REQUIRES_NEW;
-import javax.inject.Named;
-import javax.json.JsonObject;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
+import jakarta.annotation.PostConstruct;
+import jakarta.annotation.PreDestroy;
+import jakarta.ejb.AsyncResult;
+import jakarta.ejb.Asynchronous;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBException;
+import jakarta.ejb.Stateless;
+import jakarta.ejb.TransactionAttribute;
+import static jakarta.ejb.TransactionAttributeType.REQUIRES_NEW;
+import jakarta.inject.Named;
+import jakarta.json.JsonObject;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
diff --git a/src/main/java/edu/harvard/iq/dataverse/search/SearchFilesServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/search/SearchFilesServiceBean.java
index 2bf8807e301..8caee7d16b4 100644
--- a/src/main/java/edu/harvard/iq/dataverse/search/SearchFilesServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/search/SearchFilesServiceBean.java
@@ -7,11 +7,11 @@
import java.util.ArrayList;
import java.util.List;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.faces.context.FacesContext;
-import javax.inject.Named;
-import javax.servlet.http.HttpServletRequest;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.faces.context.FacesContext;
+import jakarta.inject.Named;
+import jakarta.servlet.http.HttpServletRequest;
@Named
@Stateless
diff --git a/src/main/java/edu/harvard/iq/dataverse/search/SearchIncludeFragment.java b/src/main/java/edu/harvard/iq/dataverse/search/SearchIncludeFragment.java
index bfe397cf48c..2ce06541afa 100644
--- a/src/main/java/edu/harvard/iq/dataverse/search/SearchIncludeFragment.java
+++ b/src/main/java/edu/harvard/iq/dataverse/search/SearchIncludeFragment.java
@@ -8,8 +8,6 @@
import edu.harvard.iq.dataverse.DatasetFieldType;
import edu.harvard.iq.dataverse.DatasetFieldType.FieldType;
import edu.harvard.iq.dataverse.DatasetServiceBean;
-import edu.harvard.iq.dataverse.DatasetVersion;
-import edu.harvard.iq.dataverse.DatasetVersion.VersionState;
import edu.harvard.iq.dataverse.DatasetVersionServiceBean;
import edu.harvard.iq.dataverse.Dataverse;
import edu.harvard.iq.dataverse.DataverseFacet;
@@ -37,12 +35,12 @@
import java.util.Optional;
import java.util.Set;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.enterprise.context.RequestScoped;
-import javax.faces.context.FacesContext;
-import javax.inject.Inject;
-import javax.inject.Named;
-import javax.servlet.http.HttpServletRequest;
+import jakarta.ejb.EJB;
+import jakarta.enterprise.context.RequestScoped;
+import jakarta.faces.context.FacesContext;
+import jakarta.inject.Inject;
+import jakarta.inject.Named;
+import jakarta.servlet.http.HttpServletRequest;
import org.apache.commons.lang3.StringUtils;
@@ -215,7 +213,7 @@ public String searchRedirect(String dataverseRedirectPage, Dataverse dataverseIn
qParam = "&q=" + query;
}
- return widgetWrapper.wrapURL(dataverseRedirectPage + "?faces-redirect=true&q=" + qParam + optionalDataverseScope);
+ return widgetWrapper.wrapURL(dataverseRedirectPage + "?faces-redirect=true" + qParam + optionalDataverseScope);
}
diff --git a/src/main/java/edu/harvard/iq/dataverse/search/SearchPermissionsServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/search/SearchPermissionsServiceBean.java
index e96164d442d..0dd2153f75b 100644
--- a/src/main/java/edu/harvard/iq/dataverse/search/SearchPermissionsServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/search/SearchPermissionsServiceBean.java
@@ -22,9 +22,9 @@
import java.util.Map;
import java.util.Set;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
/**
* Determine whether items should be searchable.
diff --git a/src/main/java/edu/harvard/iq/dataverse/search/SearchServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/search/SearchServiceBean.java
index 9ac4b2406e8..44976d232c2 100644
--- a/src/main/java/edu/harvard/iq/dataverse/search/SearchServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/search/SearchServiceBean.java
@@ -20,7 +20,6 @@
import edu.harvard.iq.dataverse.util.SystemConfig;
import java.io.IOException;
import java.lang.reflect.Field;
-import java.net.URL;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Calendar;
@@ -36,16 +35,16 @@
import java.util.MissingResourceException;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.EJBTransactionRolledbackException;
-import javax.ejb.Stateless;
-import javax.ejb.TransactionRolledbackLocalException;
-import javax.inject.Named;
-import javax.persistence.NoResultException;
+import jakarta.ejb.EJB;
+import jakarta.ejb.EJBTransactionRolledbackException;
+import jakarta.ejb.Stateless;
+import jakarta.ejb.TransactionRolledbackLocalException;
+import jakarta.inject.Named;
+import jakarta.persistence.NoResultException;
import org.apache.solr.client.solrj.SolrQuery;
import org.apache.solr.client.solrj.SolrQuery.SortClause;
import org.apache.solr.client.solrj.SolrServerException;
-import org.apache.solr.client.solrj.impl.HttpSolrClient.RemoteSolrException;
+import org.apache.solr.client.solrj.impl.BaseHttpSolrClient.RemoteSolrException;
import org.apache.solr.client.solrj.response.FacetField;
import org.apache.solr.client.solrj.response.QueryResponse;
import org.apache.solr.client.solrj.response.RangeFacet;
diff --git a/src/main/java/edu/harvard/iq/dataverse/search/SolrClientService.java b/src/main/java/edu/harvard/iq/dataverse/search/SolrClientService.java
index 0dc2fe08b54..b36130de7c8 100644
--- a/src/main/java/edu/harvard/iq/dataverse/search/SolrClientService.java
+++ b/src/main/java/edu/harvard/iq/dataverse/search/SolrClientService.java
@@ -10,11 +10,11 @@
import org.apache.solr.client.solrj.SolrClient;
import org.apache.solr.client.solrj.impl.HttpSolrClient;
-import javax.annotation.PostConstruct;
-import javax.annotation.PreDestroy;
-import javax.ejb.EJB;
-import javax.ejb.Singleton;
-import javax.inject.Named;
+import jakarta.annotation.PostConstruct;
+import jakarta.annotation.PreDestroy;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Singleton;
+import jakarta.inject.Named;
import java.io.IOException;
import java.util.logging.Logger;
diff --git a/src/main/java/edu/harvard/iq/dataverse/search/SolrIndexServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/search/SolrIndexServiceBean.java
index 5856004ce53..04021eb75b6 100644
--- a/src/main/java/edu/harvard/iq/dataverse/search/SolrIndexServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/search/SolrIndexServiceBean.java
@@ -20,11 +20,11 @@
import java.util.Set;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.json.Json;
-import javax.json.JsonObjectBuilder;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.json.Json;
+import jakarta.json.JsonObjectBuilder;
import org.apache.solr.client.solrj.SolrServerException;
import org.apache.solr.client.solrj.response.UpdateResponse;
import org.apache.solr.common.SolrInputDocument;
diff --git a/src/main/java/edu/harvard/iq/dataverse/search/SolrQueryResponse.java b/src/main/java/edu/harvard/iq/dataverse/search/SolrQueryResponse.java
index b499b80961e..893099ff08d 100644
--- a/src/main/java/edu/harvard/iq/dataverse/search/SolrQueryResponse.java
+++ b/src/main/java/edu/harvard/iq/dataverse/search/SolrQueryResponse.java
@@ -5,8 +5,8 @@
import java.util.List;
import java.util.Map;
import java.util.logging.Logger;
-import javax.json.Json;
-import javax.json.JsonObjectBuilder;
+import jakarta.json.Json;
+import jakarta.json.JsonObjectBuilder;
import org.apache.solr.client.solrj.SolrQuery;
import org.apache.solr.client.solrj.response.FacetField;
diff --git a/src/main/java/edu/harvard/iq/dataverse/search/SolrSearchResult.java b/src/main/java/edu/harvard/iq/dataverse/search/SolrSearchResult.java
index b58c22b64c9..6ad7f9dbbf6 100644
--- a/src/main/java/edu/harvard/iq/dataverse/search/SolrSearchResult.java
+++ b/src/main/java/edu/harvard/iq/dataverse/search/SolrSearchResult.java
@@ -9,10 +9,10 @@
import java.util.Map;
import java.util.logging.Logger;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonObjectBuilder;
import org.apache.commons.collections4.CollectionUtils;
diff --git a/src/main/java/edu/harvard/iq/dataverse/search/savedsearch/SavedSearch.java b/src/main/java/edu/harvard/iq/dataverse/search/savedsearch/SavedSearch.java
index 66bb63ed596..ff4a2e4aa96 100644
--- a/src/main/java/edu/harvard/iq/dataverse/search/savedsearch/SavedSearch.java
+++ b/src/main/java/edu/harvard/iq/dataverse/search/savedsearch/SavedSearch.java
@@ -5,16 +5,16 @@
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
-import javax.persistence.CascadeType;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.OneToMany;
-import javax.persistence.Table;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.OneToMany;
+import jakarta.persistence.Table;
@Entity
@Table(indexes = {@Index(columnList="definitionpoint_id")
diff --git a/src/main/java/edu/harvard/iq/dataverse/search/savedsearch/SavedSearchFilterQuery.java b/src/main/java/edu/harvard/iq/dataverse/search/savedsearch/SavedSearchFilterQuery.java
index f884a9529c9..7f51f9c8728 100644
--- a/src/main/java/edu/harvard/iq/dataverse/search/savedsearch/SavedSearchFilterQuery.java
+++ b/src/main/java/edu/harvard/iq/dataverse/search/savedsearch/SavedSearchFilterQuery.java
@@ -1,16 +1,16 @@
package edu.harvard.iq.dataverse.search.savedsearch;
import java.io.Serializable;
-import javax.persistence.CascadeType;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Table;
@Entity
@Table(indexes = {@Index(columnList="savedsearch_id")})
diff --git a/src/main/java/edu/harvard/iq/dataverse/search/savedsearch/SavedSearchServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/search/savedsearch/SavedSearchServiceBean.java
index 587e054dc4a..7fc2bdf79a3 100644
--- a/src/main/java/edu/harvard/iq/dataverse/search/savedsearch/SavedSearchServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/search/savedsearch/SavedSearchServiceBean.java
@@ -21,24 +21,23 @@
import edu.harvard.iq.dataverse.search.SortBy;
import edu.harvard.iq.dataverse.util.SystemConfig;
import java.util.ArrayList;
-import java.util.Collections;
import java.util.Date;
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.EJB;
-import javax.ejb.Schedule;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObjectBuilder;
-import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
-import javax.persistence.NonUniqueResultException;
-import javax.persistence.PersistenceContext;
-import javax.persistence.TypedQuery;
-import javax.servlet.http.HttpServletRequest;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Schedule;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.NoResultException;
+import jakarta.persistence.NonUniqueResultException;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.TypedQuery;
+import jakarta.servlet.http.HttpServletRequest;
@Stateless
@Named
diff --git a/src/main/java/edu/harvard/iq/dataverse/settings/Setting.java b/src/main/java/edu/harvard/iq/dataverse/settings/Setting.java
index 160ed693eee..b1910a2fbb5 100644
--- a/src/main/java/edu/harvard/iq/dataverse/settings/Setting.java
+++ b/src/main/java/edu/harvard/iq/dataverse/settings/Setting.java
@@ -2,13 +2,13 @@
import java.io.Serializable;
import java.util.Objects;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.Id;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.Id;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
/**
* A single value in the config of dataverse.
diff --git a/src/main/java/edu/harvard/iq/dataverse/settings/SettingsServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/settings/SettingsServiceBean.java
index ead0ac3bd39..2826df74ed1 100644
--- a/src/main/java/edu/harvard/iq/dataverse/settings/SettingsServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/settings/SettingsServiceBean.java
@@ -5,16 +5,16 @@
import edu.harvard.iq.dataverse.api.ApiBlockingFilter;
import edu.harvard.iq.dataverse.util.StringUtil;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.json.Json;
-import javax.json.JsonArray;
-import javax.json.JsonObject;
-import javax.json.JsonReader;
-import javax.json.JsonValue;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.json.Json;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonReader;
+import jakarta.json.JsonValue;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
import org.json.JSONArray;
import org.json.JSONException;
diff --git a/src/main/java/edu/harvard/iq/dataverse/sitemap/SiteMapServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/sitemap/SiteMapServiceBean.java
index 14db98e540e..a51acd1f54f 100644
--- a/src/main/java/edu/harvard/iq/dataverse/sitemap/SiteMapServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/sitemap/SiteMapServiceBean.java
@@ -3,8 +3,8 @@
import edu.harvard.iq.dataverse.Dataset;
import edu.harvard.iq.dataverse.Dataverse;
import java.util.List;
-import javax.ejb.Asynchronous;
-import javax.ejb.Stateless;
+import jakarta.ejb.Asynchronous;
+import jakarta.ejb.Stateless;
@Stateless
public class SiteMapServiceBean {
diff --git a/src/main/java/edu/harvard/iq/dataverse/timer/DataverseTimerServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/timer/DataverseTimerServiceBean.java
index b132bff9429..6eb3a8df0bc 100644
--- a/src/main/java/edu/harvard/iq/dataverse/timer/DataverseTimerServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/timer/DataverseTimerServiceBean.java
@@ -25,17 +25,17 @@
import java.util.Iterator;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.annotation.PostConstruct;
-import javax.annotation.Resource;
-import javax.ejb.EJB;
-import javax.ejb.Singleton;
-import javax.ejb.Startup;
-import javax.ejb.Timeout;
-import javax.ejb.Timer;
-import javax.ejb.TimerConfig;
-import javax.ejb.TransactionAttribute;
-import javax.ejb.TransactionAttributeType;
-import javax.servlet.http.HttpServletRequest;
+import jakarta.annotation.PostConstruct;
+import jakarta.annotation.Resource;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Singleton;
+import jakarta.ejb.Startup;
+import jakarta.ejb.Timeout;
+import jakarta.ejb.Timer;
+import jakarta.ejb.TimerConfig;
+import jakarta.ejb.TransactionAttribute;
+import jakarta.ejb.TransactionAttributeType;
+import jakarta.servlet.http.HttpServletRequest;
/**
@@ -55,7 +55,7 @@ public class DataverseTimerServiceBean implements Serializable {
private static final Logger logger = Logger.getLogger("edu.harvard.iq.dataverse.timer.DataverseTimerServiceBean");
@Resource
- javax.ejb.TimerService timerService;
+ jakarta.ejb.TimerService timerService;
@EJB
HarvesterServiceBean harvesterService;
@EJB
@@ -109,7 +109,7 @@ public void createTimer(Date initialExpiration, long intervalDuration, Serializa
*/
@Timeout
@TransactionAttribute(TransactionAttributeType.NOT_SUPPORTED)
- public void handleTimeout(javax.ejb.Timer timer) {
+ public void handleTimeout(jakarta.ejb.Timer timer) {
// We have to put all the code in a try/catch block because
// if an exception is thrown from this method, Glassfish will automatically
// call the method a second time. (The minimum number of re-tries for a Timer method is 1)
diff --git a/src/main/java/edu/harvard/iq/dataverse/userdata/UserListResult.java b/src/main/java/edu/harvard/iq/dataverse/userdata/UserListResult.java
index 07937638607..5e7f532d2ac 100644
--- a/src/main/java/edu/harvard/iq/dataverse/userdata/UserListResult.java
+++ b/src/main/java/edu/harvard/iq/dataverse/userdata/UserListResult.java
@@ -7,14 +7,13 @@
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
import edu.harvard.iq.dataverse.mydata.Pager;
-import edu.harvard.iq.dataverse.util.BundleUtil;
+
import java.util.ArrayList;
import java.util.List;
-import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObjectBuilder;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObjectBuilder;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/BundleUtil.java b/src/main/java/edu/harvard/iq/dataverse/util/BundleUtil.java
index 26694c0ac6c..922e6ff5d28 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/BundleUtil.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/BundleUtil.java
@@ -12,7 +12,7 @@
import java.util.logging.Logger;
import java.util.Map;
import java.util.HashMap;
-import javax.faces.context.FacesContext;
+import jakarta.faces.context.FacesContext;
public class BundleUtil {
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/ClockUtil.java b/src/main/java/edu/harvard/iq/dataverse/util/ClockUtil.java
index 9c1c89430d5..d51f70229a9 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/ClockUtil.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/ClockUtil.java
@@ -1,8 +1,8 @@
package edu.harvard.iq.dataverse.util;
-import javax.enterprise.inject.Produces;
-import javax.inject.Qualifier;
-import javax.inject.Singleton;
+import jakarta.enterprise.inject.Produces;
+import jakarta.inject.Qualifier;
+import jakarta.inject.Singleton;
import java.lang.annotation.ElementType;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/ConstraintViolationUtil.java b/src/main/java/edu/harvard/iq/dataverse/util/ConstraintViolationUtil.java
index d2e59fac9f5..1910fde6489 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/ConstraintViolationUtil.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/ConstraintViolationUtil.java
@@ -5,8 +5,8 @@
*/
package edu.harvard.iq.dataverse.util;
-import javax.validation.ConstraintViolation;
-import javax.validation.ConstraintViolationException;
+import jakarta.validation.ConstraintViolation;
+import jakarta.validation.ConstraintViolationException;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
index 800c05ae6dc..62cd318706f 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
@@ -1,12 +1,12 @@
package edu.harvard.iq.dataverse.util;
-import javax.annotation.Resource;
-import javax.annotation.sql.DataSourceDefinition;
-import javax.enterprise.inject.Produces;
-import javax.inject.Singleton;
+import jakarta.annotation.Resource;
+import jakarta.annotation.sql.DataSourceDefinition;
+import jakarta.enterprise.inject.Produces;
+import jakarta.inject.Singleton;
import javax.sql.DataSource;
-// Find docs here: https://javaee.github.io/javaee-spec/javadocs/javax/annotation/sql/DataSourceDefinition.html
+// Find docs here: https://jakarta.ee/specifications/annotations/2.1/apidocs/jakarta.annotation/jakarta/annotation/sql/datasourcedefinition
@Singleton
@DataSourceDefinition(
name = "java:app/jdbc/dataverse",
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/DatasetFieldWalker.java b/src/main/java/edu/harvard/iq/dataverse/util/DatasetFieldWalker.java
index df97998d9e8..25032860d11 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/DatasetFieldWalker.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/DatasetFieldWalker.java
@@ -3,7 +3,6 @@
import edu.harvard.iq.dataverse.ControlledVocabularyValue;
import edu.harvard.iq.dataverse.DatasetField;
import edu.harvard.iq.dataverse.DatasetFieldCompoundValue;
-import edu.harvard.iq.dataverse.DatasetFieldServiceBean;
import edu.harvard.iq.dataverse.DatasetFieldType;
import edu.harvard.iq.dataverse.DatasetFieldValue;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
@@ -12,12 +11,10 @@
import java.util.Comparator;
import java.util.List;
import java.util.Map;
-import java.util.SortedSet;
-import java.util.TreeSet;
import java.util.logging.Logger;
-import javax.json.Json;
-import javax.json.JsonObject;
+import jakarta.json.Json;
+import jakarta.json.JsonObject;
/**
* A means of iterating over {@link DatasetField}s, or a collection of them.
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/EjbUtil.java b/src/main/java/edu/harvard/iq/dataverse/util/EjbUtil.java
index cf337b0a020..fd8c8fa4a9c 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/EjbUtil.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/EjbUtil.java
@@ -1,6 +1,6 @@
package edu.harvard.iq.dataverse.util;
-import javax.ejb.EJBException;
+import jakarta.ejb.EJBException;
public class EjbUtil {
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/FileUtil.java b/src/main/java/edu/harvard/iq/dataverse/util/FileUtil.java
index 7137db9ca78..5f7643b3115 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/FileUtil.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/FileUtil.java
@@ -64,8 +64,6 @@
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
-import java.nio.channels.FileChannel;
-import java.nio.channels.WritableByteChannel;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
@@ -87,11 +85,11 @@
import java.util.UUID;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.activation.MimetypesFileTypeMap;
-import javax.ejb.EJBException;
-import javax.enterprise.inject.spi.CDI;
-import javax.json.JsonArray;
-import javax.json.JsonObject;
+import jakarta.activation.MimetypesFileTypeMap;
+import jakarta.ejb.EJBException;
+import jakarta.enterprise.inject.spi.CDI;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonObject;
import javax.xml.stream.XMLStreamConstants;
import javax.xml.stream.XMLStreamException;
import javax.xml.stream.XMLStreamReader;
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/JsfHelper.java b/src/main/java/edu/harvard/iq/dataverse/util/JsfHelper.java
index 5b87b18573b..b02ac63cacd 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/JsfHelper.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/JsfHelper.java
@@ -1,11 +1,9 @@
package edu.harvard.iq.dataverse.util;
-import java.util.Locale;
-import java.util.ResourceBundle;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.faces.application.FacesMessage;
-import javax.faces.context.FacesContext;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.context.FacesContext;
/**
* Utility class for common JSF tasks.
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/MailUtil.java b/src/main/java/edu/harvard/iq/dataverse/util/MailUtil.java
index 72980c3451a..dcb6e078df6 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/MailUtil.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/MailUtil.java
@@ -8,8 +8,8 @@
import java.util.Arrays;
import java.util.List;
import java.util.logging.Logger;
-import javax.mail.internet.AddressException;
-import javax.mail.internet.InternetAddress;
+import jakarta.mail.internet.AddressException;
+import jakarta.mail.internet.InternetAddress;
public class MailUtil {
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/PersonOrOrgUtil.java b/src/main/java/edu/harvard/iq/dataverse/util/PersonOrOrgUtil.java
index 431013771c5..f68957ad060 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/PersonOrOrgUtil.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/PersonOrOrgUtil.java
@@ -4,10 +4,10 @@
import java.util.List;
import java.util.logging.Logger;
-import javax.json.JsonArray;
-import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
-import javax.json.JsonString;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.json.JsonString;
import edu.harvard.iq.dataverse.util.json.JsonUtil;
import edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder;
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/RequiredCheckboxValidator.java b/src/main/java/edu/harvard/iq/dataverse/util/RequiredCheckboxValidator.java
index 0221d45e4b0..fdac50ee58a 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/RequiredCheckboxValidator.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/RequiredCheckboxValidator.java
@@ -1,12 +1,12 @@
package edu.harvard.iq.dataverse.util;
import java.text.MessageFormat;
-import javax.faces.application.FacesMessage;
-import javax.faces.component.UIComponent;
-import javax.faces.component.UIInput;
-import javax.faces.context.FacesContext;
-import javax.faces.validator.Validator;
-import javax.faces.validator.ValidatorException;
+import jakarta.faces.application.FacesMessage;
+import jakarta.faces.component.UIComponent;
+import jakarta.faces.component.UIInput;
+import jakarta.faces.context.FacesContext;
+import jakarta.faces.validator.Validator;
+import jakarta.faces.validator.ValidatorException;
/**
* from http://balusc.blogspot.com/2008/09/validate-required-checkbox.html via
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/SessionUtil.java b/src/main/java/edu/harvard/iq/dataverse/util/SessionUtil.java
index 0539ea40cb8..effa1980d70 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/SessionUtil.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/SessionUtil.java
@@ -4,8 +4,8 @@
import java.util.HashMap;
import java.util.Map.Entry;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpSession;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpSession;
public class SessionUtil {
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/SignpostingResources.java b/src/main/java/edu/harvard/iq/dataverse/util/SignpostingResources.java
index 54be3a8765f..2c9b7167059 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/SignpostingResources.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/SignpostingResources.java
@@ -16,9 +16,9 @@ Two configurable options allow changing the limit for the number of authors or d
import edu.harvard.iq.dataverse.*;
import edu.harvard.iq.dataverse.dataset.DatasetUtil;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObjectBuilder;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObjectBuilder;
import java.util.ArrayList;
import java.util.LinkedList;
import java.util.List;
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/SystemConfig.java b/src/main/java/edu/harvard/iq/dataverse/util/SystemConfig.java
index b9459e748bf..4fed3a05976 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/SystemConfig.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/SystemConfig.java
@@ -13,15 +13,15 @@
import edu.harvard.iq.dataverse.validation.PasswordValidatorUtil;
import org.passay.CharacterRule;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Named;
-import javax.json.Json;
-import javax.json.JsonArray;
-import javax.json.JsonObject;
-import javax.json.JsonReader;
-import javax.json.JsonString;
-import javax.json.JsonValue;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
+import jakarta.json.Json;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonReader;
+import jakarta.json.JsonString;
+import jakarta.json.JsonValue;
import java.io.StringReader;
import java.net.InetAddress;
import java.net.UnknownHostException;
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/URLTokenUtil.java b/src/main/java/edu/harvard/iq/dataverse/util/URLTokenUtil.java
index 4acf2d544e8..4ae76a7b8db 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/URLTokenUtil.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/URLTokenUtil.java
@@ -5,8 +5,8 @@
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import javax.json.Json;
-import javax.json.JsonValue;
+import jakarta.json.Json;
+import jakarta.json.JsonValue;
import edu.harvard.iq.dataverse.DataFile;
import edu.harvard.iq.dataverse.Dataset;
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/WebloaderUtil.java b/src/main/java/edu/harvard/iq/dataverse/util/WebloaderUtil.java
index c2d9bf67236..acbdc6aa3c6 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/WebloaderUtil.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/WebloaderUtil.java
@@ -1,22 +1,12 @@
package edu.harvard.iq.dataverse.util;
-import java.util.Date;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.Locale;
-import java.util.Map.Entry;
import java.util.logging.Logger;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpSession;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpSession;
import edu.harvard.iq.dataverse.Dataset;
-import edu.harvard.iq.dataverse.DatasetPage;
-import edu.harvard.iq.dataverse.authorization.AuthenticationServiceBean;
import edu.harvard.iq.dataverse.authorization.users.ApiToken;
-import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
-import edu.harvard.iq.dataverse.authorization.users.User;
-import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
public class WebloaderUtil {
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/bagit/BagGenerator.java b/src/main/java/edu/harvard/iq/dataverse/util/bagit/BagGenerator.java
index 8061b6e339e..baba1a0cb43 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/bagit/BagGenerator.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/bagit/BagGenerator.java
@@ -110,7 +110,7 @@ public class BagGenerator {
private String apiKey = null;
- private javax.json.JsonObject oremapObject;
+ private jakarta.json.JsonObject oremapObject;
private JsonObject aggregation;
private String dataciteXml;
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/bagit/OREMap.java b/src/main/java/edu/harvard/iq/dataverse/util/bagit/OREMap.java
index c9e71296d0f..b3995b5957e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/bagit/OREMap.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/bagit/OREMap.java
@@ -30,12 +30,12 @@
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.json.Json;
-import javax.json.JsonArray;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
-import javax.json.JsonValue;
+import jakarta.json.Json;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.json.JsonValue;
import org.apache.commons.lang3.exception.ExceptionUtils;
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/bagit/OREMapHelper.java b/src/main/java/edu/harvard/iq/dataverse/util/bagit/OREMapHelper.java
index 6cd7f0928dc..4d63edac268 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/bagit/OREMapHelper.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/bagit/OREMapHelper.java
@@ -3,10 +3,10 @@
import edu.harvard.iq.dataverse.DatasetFieldServiceBean;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
-import javax.annotation.PostConstruct;
-import javax.ejb.EJB;
-import javax.ejb.Singleton;
-import javax.ejb.Startup;
+import jakarta.annotation.PostConstruct;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Singleton;
+import jakarta.ejb.Startup;
/**
* This is a small helper bean
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/file/BagItFileHandlerFactory.java b/src/main/java/edu/harvard/iq/dataverse/util/file/BagItFileHandlerFactory.java
index 53c80037223..4b0263030dc 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/file/BagItFileHandlerFactory.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/file/BagItFileHandlerFactory.java
@@ -7,10 +7,10 @@
import edu.harvard.iq.dataverse.util.bagit.data.FileDataProviderFactory;
import edu.harvard.iq.dataverse.util.bagit.data.FileUtilWrapper;
-import javax.annotation.PostConstruct;
-import javax.ejb.EJB;
-import javax.enterprise.context.SessionScoped;
-import javax.inject.Named;
+import jakarta.annotation.PostConstruct;
+import jakarta.ejb.EJB;
+import jakarta.enterprise.context.SessionScoped;
+import jakarta.inject.Named;
import java.io.Serializable;
import java.util.Optional;
import java.util.logging.Logger;
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/json/BriefJsonPrinter.java b/src/main/java/edu/harvard/iq/dataverse/util/json/BriefJsonPrinter.java
index ee0a882a10d..3fcaf6b11ff 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/json/BriefJsonPrinter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/json/BriefJsonPrinter.java
@@ -1,11 +1,10 @@
package edu.harvard.iq.dataverse.util.json;
import edu.harvard.iq.dataverse.DatasetVersion;
-import edu.harvard.iq.dataverse.authorization.providers.builtin.BuiltinUser;
import edu.harvard.iq.dataverse.MetadataBlock;
import static edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder.jsonObjectBuilder;
import edu.harvard.iq.dataverse.workflow.Workflow;
-import javax.json.JsonObjectBuilder;
+import jakarta.json.JsonObjectBuilder;
/**
* A Json printer that prints minimal data on objects. Useful when embedding
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/json/JSONLDUtil.java b/src/main/java/edu/harvard/iq/dataverse/util/json/JSONLDUtil.java
index 0fd9705031d..113a6128364 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/json/JSONLDUtil.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/json/JSONLDUtil.java
@@ -18,17 +18,17 @@
import java.util.logging.Logger;
-import javax.json.Json;
-import javax.json.JsonArray;
-import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
-import javax.json.JsonString;
-import javax.json.JsonValue;
-import javax.json.JsonWriter;
-import javax.json.JsonWriterFactory;
-import javax.json.JsonValue.ValueType;
-import javax.json.stream.JsonGenerator;
-import javax.ws.rs.BadRequestException;
+import jakarta.json.Json;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.json.JsonString;
+import jakarta.json.JsonValue;
+import jakarta.json.JsonWriter;
+import jakarta.json.JsonWriterFactory;
+import jakarta.json.JsonValue.ValueType;
+import jakarta.json.stream.JsonGenerator;
+import jakarta.ws.rs.BadRequestException;
import edu.harvard.iq.dataverse.ControlledVocabularyValue;
import edu.harvard.iq.dataverse.Dataset;
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonParser.java b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonParser.java
index 59290449988..febb785cd95 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonParser.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonParser.java
@@ -50,13 +50,13 @@
import java.util.Set;
import java.util.logging.Logger;
import java.util.stream.Collectors;
-import javax.json.Json;
-import javax.json.JsonArray;
-import javax.json.JsonObject;
-import javax.json.JsonReader;
-import javax.json.JsonString;
-import javax.json.JsonValue;
-import javax.json.JsonValue.ValueType;
+import jakarta.json.Json;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonReader;
+import jakarta.json.JsonString;
+import jakarta.json.JsonValue;
+import jakarta.json.JsonValue.ValueType;
/**
* Parses JSON objects into domain objects.
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java
index 5080ae524c7..b6026998bb7 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java
@@ -17,7 +17,6 @@
import edu.harvard.iq.dataverse.DataverseContact;
import edu.harvard.iq.dataverse.DataverseFacet;
import edu.harvard.iq.dataverse.DataverseTheme;
-import edu.harvard.iq.dataverse.api.Datasets;
import edu.harvard.iq.dataverse.authorization.DataverseRole;
import edu.harvard.iq.dataverse.authorization.groups.impl.maildomain.MailDomainGroup;
import edu.harvard.iq.dataverse.authorization.providers.builtin.BuiltinUser;
@@ -55,12 +54,10 @@
import edu.harvard.iq.dataverse.workflow.step.WorkflowStepData;
import java.util.*;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObjectBuilder;
-import javax.json.JsonValue;
-
-import org.apache.commons.collections4.CollectionUtils;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.json.JsonValue;
import java.util.function.BiConsumer;
import java.util.function.BinaryOperator;
@@ -71,10 +68,10 @@
import java.util.stream.Collectors;
import static java.util.stream.Collectors.toList;
-import javax.ejb.EJB;
-import javax.ejb.Singleton;
-import javax.json.JsonArray;
-import javax.json.JsonObject;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Singleton;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonObject;
/**
* Convert objects to Json.
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinterHelper.java b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinterHelper.java
index 1c7dce24680..55f9ecb5ce8 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinterHelper.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinterHelper.java
@@ -3,10 +3,10 @@
import edu.harvard.iq.dataverse.DatasetFieldServiceBean;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
-import javax.annotation.PostConstruct;
-import javax.ejb.EJB;
-import javax.ejb.Singleton;
-import javax.ejb.Startup;
+import jakarta.annotation.PostConstruct;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Singleton;
+import jakarta.ejb.Startup;
/**
* This is a small helper bean
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonUtil.java b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonUtil.java
index d02099eddb5..09d02854bab 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonUtil.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonUtil.java
@@ -9,11 +9,11 @@
import java.util.HashMap;
import java.util.Map;
import java.util.logging.Logger;
-import javax.json.Json;
-import javax.json.JsonArray;
-import javax.json.JsonWriter;
-import javax.json.JsonWriterFactory;
-import javax.json.stream.JsonGenerator;
+import jakarta.json.Json;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonWriter;
+import jakarta.json.JsonWriterFactory;
+import jakarta.json.stream.JsonGenerator;
public class JsonUtil {
@@ -47,7 +47,7 @@ public static String prettyPrint(JsonArray jsonArray) {
return stringWriter.toString();
}
- public static String prettyPrint(javax.json.JsonObject jsonObject) {
+ public static String prettyPrint(jakarta.json.JsonObject jsonObject) {
Map config = new HashMap<>();
config.put(JsonGenerator.PRETTY_PRINTING, true);
JsonWriterFactory jsonWriterFactory = Json.createWriterFactory(config);
@@ -58,13 +58,13 @@ public static String prettyPrint(javax.json.JsonObject jsonObject) {
return stringWriter.toString();
}
- public static javax.json.JsonObject getJsonObject(String serializedJson) {
+ public static jakarta.json.JsonObject getJsonObject(String serializedJson) {
try (StringReader rdr = new StringReader(serializedJson)) {
return Json.createReader(rdr).readObject();
}
}
- public static javax.json.JsonArray getJsonArray(String serializedJson) {
+ public static jakarta.json.JsonArray getJsonArray(String serializedJson) {
try (StringReader rdr = new StringReader(serializedJson)) {
return Json.createReader(rdr).readArray();
}
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/json/NullSafeJsonBuilder.java b/src/main/java/edu/harvard/iq/dataverse/util/json/NullSafeJsonBuilder.java
index 59a23a43452..ef8ab39122f 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/json/NullSafeJsonBuilder.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/json/NullSafeJsonBuilder.java
@@ -5,11 +5,11 @@
import java.math.BigDecimal;
import java.math.BigInteger;
import java.sql.Timestamp;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
-import javax.json.JsonValue;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.json.JsonValue;
/**
* A JSON builder that drops any null values. If we didn't drop'em,
diff --git a/src/main/java/edu/harvard/iq/dataverse/validation/EMailValidator.java b/src/main/java/edu/harvard/iq/dataverse/validation/EMailValidator.java
index 5050aad5bf7..624e49623f2 100644
--- a/src/main/java/edu/harvard/iq/dataverse/validation/EMailValidator.java
+++ b/src/main/java/edu/harvard/iq/dataverse/validation/EMailValidator.java
@@ -1,7 +1,7 @@
package edu.harvard.iq.dataverse.validation;
-import javax.validation.ConstraintValidator;
-import javax.validation.ConstraintValidatorContext;
+import jakarta.validation.ConstraintValidator;
+import jakarta.validation.ConstraintValidatorContext;
import org.apache.commons.validator.routines.EmailValidator;
diff --git a/src/main/java/edu/harvard/iq/dataverse/validation/PasswordValidatorServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/validation/PasswordValidatorServiceBean.java
index c32e6728358..41e7f1b8b22 100644
--- a/src/main/java/edu/harvard/iq/dataverse/validation/PasswordValidatorServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/validation/PasswordValidatorServiceBean.java
@@ -18,9 +18,9 @@
import java.util.logging.Logger;
import java.util.regex.Pattern;
import java.util.stream.Collectors;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.inject.Named;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.inject.Named;
import org.passay.CharacterCharacteristicsRule;
import org.passay.CharacterRule;
import org.passay.DictionaryRule;
diff --git a/src/main/java/edu/harvard/iq/dataverse/validation/URLValidator.java b/src/main/java/edu/harvard/iq/dataverse/validation/URLValidator.java
index 846ae48783a..285f34d3f8c 100644
--- a/src/main/java/edu/harvard/iq/dataverse/validation/URLValidator.java
+++ b/src/main/java/edu/harvard/iq/dataverse/validation/URLValidator.java
@@ -1,7 +1,6 @@
package edu.harvard.iq.dataverse.validation;
-import edu.harvard.iq.dataverse.util.BundleUtil;
-import javax.validation.ConstraintValidator;
-import javax.validation.ConstraintValidatorContext;
+import jakarta.validation.ConstraintValidator;
+import jakarta.validation.ConstraintValidatorContext;
import org.apache.commons.validator.routines.UrlValidator;
/**
diff --git a/src/main/java/edu/harvard/iq/dataverse/validation/ValidateEmail.java b/src/main/java/edu/harvard/iq/dataverse/validation/ValidateEmail.java
index 310dc950858..6ec677bd7a8 100644
--- a/src/main/java/edu/harvard/iq/dataverse/validation/ValidateEmail.java
+++ b/src/main/java/edu/harvard/iq/dataverse/validation/ValidateEmail.java
@@ -11,8 +11,8 @@
import java.lang.annotation.Retention;
import java.lang.annotation.Target;
-import javax.validation.Constraint;
-import javax.validation.Payload;
+import jakarta.validation.Constraint;
+import jakarta.validation.Payload;
/**
*
* @author skraffmi
diff --git a/src/main/java/edu/harvard/iq/dataverse/validation/ValidateURL.java b/src/main/java/edu/harvard/iq/dataverse/validation/ValidateURL.java
index 5aaab0c2e8e..3834b119598 100644
--- a/src/main/java/edu/harvard/iq/dataverse/validation/ValidateURL.java
+++ b/src/main/java/edu/harvard/iq/dataverse/validation/ValidateURL.java
@@ -6,8 +6,8 @@
import java.lang.annotation.Retention;
import static java.lang.annotation.RetentionPolicy.RUNTIME;
import java.lang.annotation.Target;
-import javax.validation.Constraint;
-import javax.validation.Payload;
+import jakarta.validation.Constraint;
+import jakarta.validation.Payload;
@Target({FIELD})
@Retention(RUNTIME)
diff --git a/src/main/java/edu/harvard/iq/dataverse/validation/ValidateUserName.java b/src/main/java/edu/harvard/iq/dataverse/validation/ValidateUserName.java
index 0583b70df49..6307edd073a 100644
--- a/src/main/java/edu/harvard/iq/dataverse/validation/ValidateUserName.java
+++ b/src/main/java/edu/harvard/iq/dataverse/validation/ValidateUserName.java
@@ -10,11 +10,11 @@
import java.lang.annotation.Retention;
import static java.lang.annotation.RetentionPolicy.RUNTIME;
import java.lang.annotation.Target;
-import javax.validation.Constraint;
-import javax.validation.Payload;
-import javax.validation.constraints.NotBlank;
-import javax.validation.constraints.Size;
-import javax.validation.constraints.Pattern;
+import jakarta.validation.Constraint;
+import jakarta.validation.Payload;
+import jakarta.validation.constraints.NotBlank;
+import jakarta.validation.constraints.Size;
+import jakarta.validation.constraints.Pattern;
/**
*
diff --git a/src/main/java/edu/harvard/iq/dataverse/workflow/PendingWorkflowInvocation.java b/src/main/java/edu/harvard/iq/dataverse/workflow/PendingWorkflowInvocation.java
index 577e0f756de..94fefa9bc13 100644
--- a/src/main/java/edu/harvard/iq/dataverse/workflow/PendingWorkflowInvocation.java
+++ b/src/main/java/edu/harvard/iq/dataverse/workflow/PendingWorkflowInvocation.java
@@ -9,14 +9,14 @@
import java.io.Serializable;
import java.util.HashMap;
import java.util.Map;
-import javax.persistence.ElementCollection;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.Id;
-import javax.persistence.ManyToOne;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.OneToOne;
+import jakarta.persistence.ElementCollection;
+import jakarta.persistence.Entity;
+import jakarta.persistence.FetchType;
+import jakarta.persistence.Id;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.OneToOne;
/**
* A workflow whose current step waits for an external system to complete a
diff --git a/src/main/java/edu/harvard/iq/dataverse/workflow/Workflow.java b/src/main/java/edu/harvard/iq/dataverse/workflow/Workflow.java
index 6c73ed0e64b..bd32c517bc6 100644
--- a/src/main/java/edu/harvard/iq/dataverse/workflow/Workflow.java
+++ b/src/main/java/edu/harvard/iq/dataverse/workflow/Workflow.java
@@ -6,16 +6,16 @@
import java.util.List;
import java.util.Map;
import java.util.Objects;
-import javax.persistence.CascadeType;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.OneToMany;
-import javax.persistence.OrderColumn;
+import jakarta.persistence.CascadeType;
+import jakarta.persistence.Entity;
+import jakarta.persistence.FetchType;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+import jakarta.persistence.OneToMany;
+import jakarta.persistence.OrderColumn;
/**
* A list of steps that can be executed with a given context.
diff --git a/src/main/java/edu/harvard/iq/dataverse/workflow/WorkflowServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/workflow/WorkflowServiceBean.java
index cf78c4f8cdf..47f24c9b8bd 100644
--- a/src/main/java/edu/harvard/iq/dataverse/workflow/WorkflowServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/workflow/WorkflowServiceBean.java
@@ -6,7 +6,6 @@
import edu.harvard.iq.dataverse.EjbDataverseEngine;
import edu.harvard.iq.dataverse.RoleAssigneeServiceBean;
import edu.harvard.iq.dataverse.UserNotification;
-import edu.harvard.iq.dataverse.UserNotification.Type;
import edu.harvard.iq.dataverse.UserNotificationServiceBean;
import edu.harvard.iq.dataverse.authorization.users.ApiToken;
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
@@ -33,15 +32,15 @@
import java.util.Optional;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.ejb.Asynchronous;
-import javax.ejb.EJB;
-import javax.ejb.Stateless;
-import javax.ejb.TransactionAttribute;
-import javax.ejb.TransactionAttributeType;
-import javax.inject.Inject;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.persistence.TypedQuery;
+import jakarta.ejb.Asynchronous;
+import jakarta.ejb.EJB;
+import jakarta.ejb.Stateless;
+import jakarta.ejb.TransactionAttribute;
+import jakarta.ejb.TransactionAttributeType;
+import jakarta.inject.Inject;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.TypedQuery;
/**
* Service bean for managing and executing {@link Workflow}s
diff --git a/src/main/java/edu/harvard/iq/dataverse/workflow/internalspi/ArchivalSubmissionWorkflowStep.java b/src/main/java/edu/harvard/iq/dataverse/workflow/internalspi/ArchivalSubmissionWorkflowStep.java
index 105af6a00d8..b0567bff107 100644
--- a/src/main/java/edu/harvard/iq/dataverse/workflow/internalspi/ArchivalSubmissionWorkflowStep.java
+++ b/src/main/java/edu/harvard/iq/dataverse/workflow/internalspi/ArchivalSubmissionWorkflowStep.java
@@ -1,6 +1,5 @@
package edu.harvard.iq.dataverse.workflow.internalspi;
-import edu.harvard.iq.dataverse.DatasetVersion;
import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
import edu.harvard.iq.dataverse.engine.command.impl.AbstractSubmitToArchiveCommand;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
@@ -10,13 +9,12 @@
import edu.harvard.iq.dataverse.workflow.step.WorkflowStep;
import edu.harvard.iq.dataverse.workflow.step.WorkflowStepResult;
-import java.lang.reflect.Constructor;
import java.util.HashMap;
import java.util.Map;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
/**
* A step that submits a BagIT bag of the newly published dataset version via a
diff --git a/src/main/java/edu/harvard/iq/dataverse/workflow/internalspi/AuthorizedExternalStep.java b/src/main/java/edu/harvard/iq/dataverse/workflow/internalspi/AuthorizedExternalStep.java
index bbe200aaeb3..ee770d4057e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/workflow/internalspi/AuthorizedExternalStep.java
+++ b/src/main/java/edu/harvard/iq/dataverse/workflow/internalspi/AuthorizedExternalStep.java
@@ -6,23 +6,18 @@
import edu.harvard.iq.dataverse.workflow.WorkflowContext.TriggerType;
import edu.harvard.iq.dataverse.workflow.step.Failure;
import edu.harvard.iq.dataverse.workflow.step.Pending;
-import edu.harvard.iq.dataverse.workflow.step.Success;
import edu.harvard.iq.dataverse.workflow.step.WorkflowStep;
import edu.harvard.iq.dataverse.workflow.step.WorkflowStepResult;
import edu.harvard.iq.dataverse.workflows.WorkflowUtil;
-import static edu.harvard.iq.dataverse.workflow.step.WorkflowStepResult.OK;
-
-import java.io.StringReader;
import java.nio.charset.StandardCharsets;
import java.util.HashMap;
import java.util.Map;
import java.util.logging.Level;
import java.util.logging.Logger;
-import java.util.regex.Pattern;
-import javax.json.Json;
-import javax.json.JsonObject;
+import jakarta.json.Json;
+import jakarta.json.JsonObject;
import org.apache.commons.httpclient.HttpClient;
import org.apache.commons.httpclient.HttpMethodBase;
diff --git a/src/main/java/edu/harvard/iq/dataverse/workflow/internalspi/LDNAnnounceDatasetVersionStep.java b/src/main/java/edu/harvard/iq/dataverse/workflow/internalspi/LDNAnnounceDatasetVersionStep.java
index 13024f9f68f..124eea801d9 100644
--- a/src/main/java/edu/harvard/iq/dataverse/workflow/internalspi/LDNAnnounceDatasetVersionStep.java
+++ b/src/main/java/edu/harvard/iq/dataverse/workflow/internalspi/LDNAnnounceDatasetVersionStep.java
@@ -27,12 +27,12 @@
import java.util.UUID;
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.json.Json;
-import javax.json.JsonArray;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObject;
-import javax.json.JsonObjectBuilder;
-import javax.json.JsonValue;
+import jakarta.json.Json;
+import jakarta.json.JsonArray;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObject;
+import jakarta.json.JsonObjectBuilder;
+import jakarta.json.JsonValue;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpPost;
diff --git a/src/main/java/edu/harvard/iq/dataverse/workflow/step/WorkflowStepData.java b/src/main/java/edu/harvard/iq/dataverse/workflow/step/WorkflowStepData.java
index a06531a2666..07bcf247533 100644
--- a/src/main/java/edu/harvard/iq/dataverse/workflow/step/WorkflowStepData.java
+++ b/src/main/java/edu/harvard/iq/dataverse/workflow/step/WorkflowStepData.java
@@ -3,14 +3,14 @@
import edu.harvard.iq.dataverse.workflow.Workflow;
import java.io.Serializable;
import java.util.Map;
-import javax.persistence.Column;
-import javax.persistence.ElementCollection;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.ManyToOne;
+import jakarta.persistence.Column;
+import jakarta.persistence.ElementCollection;
+import jakarta.persistence.Entity;
+import jakarta.persistence.FetchType;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.ManyToOne;
/**
* A database row describing a step in a workflow. Actual steps can be instantiated
diff --git a/src/main/java/edu/harvard/iq/dataverse/workflows/WorkflowComment.java b/src/main/java/edu/harvard/iq/dataverse/workflows/WorkflowComment.java
index d03afcaa91a..7cfa226d7ba 100644
--- a/src/main/java/edu/harvard/iq/dataverse/workflows/WorkflowComment.java
+++ b/src/main/java/edu/harvard/iq/dataverse/workflows/WorkflowComment.java
@@ -5,14 +5,14 @@
import java.io.Serializable;
import java.sql.Timestamp;
import java.util.Date;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.EnumType;
+import jakarta.persistence.Enumerated;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.JoinColumn;
@Entity
public class WorkflowComment implements Serializable {
diff --git a/src/main/java/edu/harvard/iq/dataverse/workflows/WorkflowUtil.java b/src/main/java/edu/harvard/iq/dataverse/workflows/WorkflowUtil.java
index e6e6bfd23c8..456b829ba61 100644
--- a/src/main/java/edu/harvard/iq/dataverse/workflows/WorkflowUtil.java
+++ b/src/main/java/edu/harvard/iq/dataverse/workflows/WorkflowUtil.java
@@ -8,12 +8,11 @@
import java.util.logging.Level;
import java.util.logging.Logger;
-import javax.json.Json;
-import javax.json.JsonArrayBuilder;
-import javax.json.JsonObject;
+import jakarta.json.Json;
+import jakarta.json.JsonArrayBuilder;
+import jakarta.json.JsonObject;
import edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder;
-import edu.harvard.iq.dataverse.workflow.internalspi.PauseWithMessageStep;
import edu.harvard.iq.dataverse.workflow.step.Failure;
import edu.harvard.iq.dataverse.workflow.step.Success;
import edu.harvard.iq.dataverse.workflow.step.WorkflowStepResult;
diff --git a/src/main/resources/META-INF/batch-jobs/FileSystemImportJob.xml b/src/main/resources/META-INF/batch-jobs/FileSystemImportJob.xml
index 167fbdbec5d..0294f15e967 100644
--- a/src/main/resources/META-INF/batch-jobs/FileSystemImportJob.xml
+++ b/src/main/resources/META-INF/batch-jobs/FileSystemImportJob.xml
@@ -34,14 +34,14 @@
-
+
-
+
diff --git a/src/main/resources/META-INF/persistence.xml b/src/main/resources/META-INF/persistence.xml
index 45552f36939..e6224dcdf01 100644
--- a/src/main/resources/META-INF/persistence.xml
+++ b/src/main/resources/META-INF/persistence.xml
@@ -1,11 +1,11 @@
-
+
-
org.eclipse.persistence.jpa.PersistenceProvider
java:app/jdbc/dataverse
-
+
+
+
+
+ 
+