Merge branch 'develop' into 10889_bump_PG17_FlyWay10 IQSS#10889

.github/PULL_REQUEST_TEMPLATE.md

@@ -2,7 +2,7 @@
 
 **Which issue(s) this PR closes**:
 
-Closes #
+- Closes #
 
 **Special notes for your reviewer**:
 

.github/workflows/guides_build_sphinx.yml

@@ -11,6 +11,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
-    - uses: OdumInstitute/sphinx-action@master
+    - uses: uncch-rdmc/sphinx-action@master
       with:
         docs-folder: "doc/sphinx-guides/"

doc/release-notes/10379-MetricsBugsFixes.md

@@ -0,0 +1,10 @@
+
+### Metrics API Bug fixes
+
+Two bugs in the Metrics API have been fixed:
+
+- The /datasets and /datasets/byMonth endpoints could report incorrect values if/when they have been called using the dataLocation parameter (which allows getting metrics for local, remote (harvested), or all datasets) as the metrics cache was not storing different values for these cases. 
+
+- Metrics endpoints who's calculation relied on finding the latest published datasetversion were incorrect if/when the minor version number was > 9. 
+
+When deploying the new release, the [/api/admin/clearMetricsCache](https://guides.dataverse.org/en/latest/api/native-api.html#metrics) API should be called to remove old cached values that may be incorrect.

doc/release-notes/10697-improve-permission-indexing.md

@@ -0,0 +1,7 @@
+### Reindexing after a role assignment is less memory intensive
+
+Adding/removing a user from a role on a collection, particularly the root collection, could lead to a significant increase in memory use resulting in Dataverse itself failing with an out-of-memory condition. Such changes now consume much less memory.
+
+If you have experienced out-of-memory failures in Dataverse in the past that could have been caused by this problem, you may wish to run a [reindex in place](https://guides.dataverse.org/en/latest/admin/solr-search-index.html#reindex-in-place) to update any out-of-date information.
+
+For more information, see #10697 and #10698.

doc/release-notes/10708 - MDC Citation and DOI parsing improvements.md

@@ -0,0 +1,3 @@
+MDC Citation retrieval with the PID settings has been fixed.
+DOI parsing in Dataverse is case insensitive, improving interaction with services that may change the case.
+Warnings related to managed/excluded PID lists for PID providers have been reduced

doc/release-notes/10886-update-to-conditions-to-display-image_url.md

@@ -0,0 +1,8 @@
+Search API (/api/search) responses for Datafiles include image_url for the thumbnail if each of the following are true:
+1. The DataFile is not Harvested
+2. A Thumbnail is available for the Datafile
+3. If the Datafile is Restricted then the caller must have Download File Permission for the Datafile
+4. The Datafile is NOT actively embargoed
+5. The Datafile's retention period has NOT expired
+
+See also #10875 and #10886.

doc/release-notes/10914-users-token-api-credentials.md

@@ -0,0 +1,3 @@
+Extended the users/token GET endpoint to support any auth mechanism for retrieving the token information.
+
+Previously, this endpoint only accepted an API token to retrieve its information. Now, it accepts any authentication mechanism and returns the associated API token information.

doc/release-notes/10919-minor-DataCiteXML-bugfix.md

@@ -0,0 +1 @@
+A minor bug fix was made to avoid sending a useless ", null" in the DataCiteXML sent to DataCite and in the DataCite export when a dataset has a metadata entry for "Software Name" and no entry for "Software Version". The bug fix will update datasets upon publication. Anyone with existing published datasets with this problem can be fixed by [pushing updated metadata to DataCite for affected datasets](https://guides.dataverse.org/en/6.4/admin/dataverses-datasets.html#update-metadata-for-a-published-dataset-at-the-pid-provider) and [re-exporting the dataset metadata](https://guides.dataverse.org/en/6.4/admin/metadataexport.html#batch-exports-through-the-api) or by following steps 9 and 10 in the v6.4 release notes to update and re-export all datasets.

doc/release-notes/10939-i18n-docker.md

@@ -0,0 +1,5 @@
+## Multiple Language in Docker
+
+Configuration and documentation has been added to explain how to set up multiple languages (e.g. English and French) in the tutorial for setting up Dataverse in Docker.
+
+See also #10939

doc/release-notes/10947-unpublished-files-appearing-in-search-results-for-anon-user.md

@@ -0,0 +1,11 @@
+## Unpublished file bug fix
+
+A bug fix was made that gets the major version of a Dataset when all major versions were deaccessioned. This fixes the incorrect showing of the files as "Unpublished" in the search list even when they are published.
+This fix affects the indexing, meaning these datasets must be re-indexed once Dataverse is updated. This can be manually done by calling the index API for each affected Dataset.
+
+Example:
+```shell
+curl http://localhost:8080/api/admin/index/dataset?persistentId=doi:10.7910/DVN/6X4ZZL
+```
+
+See also #10947 and #10974.

doc/sphinx-guides/source/admin/metadatacustomization.rst

@@ -579,7 +579,7 @@ In general, the external vocabulary support mechanism may be a better choice for
 The specifics of the user interface for entering/selecting a vocabulary term and how that term is then displayed are managed by third-party Javascripts. The initial Javascripts that have been created provide auto-completion, displaying a list of choices that match what the user has typed so far, but other interfaces, such as displaying a tree of options for a hierarchical vocabulary, are possible. 
 Similarly, existing scripts do relatively simple things for displaying a term - showing the term's name in the appropriate language and providing a link to an external URL with more information, but more sophisticated displays are possible.
 
-Scripts supporting use of vocabularies from services supporting the SKOMOS protocol (see https://skosmos.org), retrieving ORCIDs (from https://orcid.org), services based on Ontoportal product (see https://ontoportal.org/), and using ROR (https://ror.org/) are available https://github.com/gdcc/dataverse-external-vocab-support. (Custom scripts can also be used and community members are encouraged to share new scripts through the dataverse-external-vocab-support repository.)
+Scripts supporting use of vocabularies from services supporting the SKOSMOS protocol (see https://skosmos.org), retrieving ORCIDs (from https://orcid.org), services based on Ontoportal product (see https://ontoportal.org/), and using ROR (https://ror.org/) are available https://github.com/gdcc/dataverse-external-vocab-support. (Custom scripts can also be used and community members are encouraged to share new scripts through the dataverse-external-vocab-support repository.)
 
 Configuration involves specifying which fields are to be mapped, to which Solr field they should be indexed, whether free-text entries are allowed, which vocabulary(ies) should be used, what languages those vocabulary(ies) are available in, and several service protocol and service instance specific parameters, including the ability to send HTTP headers on calls to the service.
 These are all defined in the :ref:`:CVocConf <:CVocConf>` setting as a JSON array. Details about the required elements as well as example JSON arrays are available at https://github.com/gdcc/dataverse-external-vocab-support, along with an example metadata block that can be used for testing.

doc/sphinx-guides/source/container/running/demo.rst

@@ -137,6 +137,23 @@ In the example below of configuring :ref:`:FooterCopyright` we use the default u
 
 One you make this change it should be visible in the copyright in the bottom left of every page.
 
+Multiple Languages
+++++++++++++++++++
+
+Generally speaking, you'll want to follow :ref:`i18n` in the Installation Guide to set up multiple languages such as English and French.
+
+To set up the toggle between English and French, we'll use a slight variation on the command in the instructions above, adding the unblock key we created above:
+
+``curl "http://localhost:8080/api/admin/settings/:Languages?unblock-key=unblockme" -X PUT -d '[{"locale":"en","title":"English"},{"locale":"fr","title":"Français"}]'``
+
+Similarly, when loading the "languages.zip" file, we'll add the unblock key:
+
+``curl "http://localhost:8080/api/admin/datasetfield/loadpropertyfiles?unblock-key=unblockme" -X POST --upload-file /tmp/languages/languages.zip -H "Content-Type: application/zip"``
+
+Stop and start the Dataverse container in order for the language toggle to work.
+
+Note that ``dataverse.lang.directory=/dv/lang`` has already been configured for you in the ``compose.yml`` file. The step where you loaded "languages.zip" should have populated the ``/dv/lang`` directory with files ending in ".properties".
+
 Next Steps
 ----------
 

doc/sphinx-guides/source/developers/version-control.rst

@@ -291,16 +291,16 @@ By default, when a pull request is made from a fork, "Allow edits from maintaine
 
 This is a nice feature of GitHub because it means that the core dev team for the Dataverse Project can make small (or even large) changes to a pull request from a contributor to help the pull request along on its way to QA and being merged.
 
-GitHub documents how to make changes to a fork at https://help.github.com/articles/committing-changes-to-a-pull-request-branch-created-from-a-fork/ but as of this writing the steps involve making a new clone of the repo. This works but you might find it more convenient to add a "remote" to your existing clone. The example below uses the fork at https://github.com/OdumInstitute/dataverse and the branch ``4709-postgresql_96`` but the technique can be applied to any fork and branch:
+GitHub documents how to make changes to a fork at https://help.github.com/articles/committing-changes-to-a-pull-request-branch-created-from-a-fork/ but as of this writing the steps involve making a new clone of the repo. This works but you might find it more convenient to add a "remote" to your existing clone. The example below uses the fork at https://github.com/uncch-rdmc/dataverse and the branch ``4709-postgresql_96`` but the technique can be applied to any fork and branch:
 
 .. code-block:: bash
 
-        git remote add OdumInstitute [email protected]:OdumInstitute/dataverse.git
-        git fetch OdumInstitute
+        git remote add uncch-rdmc [email protected]:uncch-rdmc/dataverse.git
+        git fetch uncch-rdmc
         git checkout 4709-postgresql_96
         vim path/to/file.txt
         git commit
-        git push OdumInstitute 4709-postgresql_96
+        git push uncch-rdmc 4709-postgresql_96
 
 .. _develop-into-develop:
 

doc/sphinx-guides/source/installation/config.rst

@@ -1783,7 +1783,7 @@ Now that you have a "languages.zip" file, you can load it into your Dataverse in
 
 ``curl http://localhost:8080/api/admin/datasetfield/loadpropertyfiles -X POST --upload-file /tmp/languages/languages.zip -H "Content-Type: application/zip"``
 
-Click on the languages using the drop down in the header to try them out.
+Stop and start Payara and then click on the languages using the drop down in the header to try them out.
 
 .. _help-translate:
 

doc/sphinx-guides/source/qa/testing-infrastructure.md

@@ -31,6 +31,8 @@ To build and test a PR, we use a job called `IQSS_Dataverse_Internal` on <https:
 
 1. If for some reason it didn't deploy, check the server.log file. It may just be a caching issue so try un-deploying, deleting cache, restarting, and re-deploying on the server (`su - dataverse` then `/usr/local/payara6/bin/asadmin list-applications; /usr/local/payara6/bin/asadmin undeploy dataverse-6.1; /usr/local/payara6/bin/asadmin deploy /tmp/dataverse-6.1.war`)
 
+1. When a Jenkins job fails after a release, it might be due to the version number in the `pom.xml` file not being updated in the pull request (PR). To verify this, open the relevant GitHub issue, navigate to the PR branch, and go to `dataverse > modules > dataverse-parent > pom.xml`. Look for the version number, typically shown as `<revision>6.3</revision>`, and ensure it matches the current Dataverse build version. If it doesn't match, ask the developer to update the branch with the latest from the "develop" branch.
+
 1. If that didn't work, you may have run into a Flyway DB script collision error but that should be indicated by the server.log. See {doc}`/developers/sql-upgrade-scripts` in the Developer Guide. In the case of a collision, ask the developer to rename the script.
 
 1.	Assuming the above steps worked, and they should 99% of the time, test away! Note: be sure to `tail -F server.log` in a terminal window while you are doing any testing. This way you can spot problems that may not appear in the UI and have easier access to any stack traces for easier reporting.

doc/sphinx-guides/source/style/text.rst

@@ -9,4 +9,4 @@ Here we describe the guidelines that help us provide helpful, clear and consiste
 Metadata Text Guidelines
 ========================
 
-These guidelines are maintained in `a Google Doc <https://docs.google.com/document/d/1uRk_dAZlaCS91YFbqE6L9Jwhwum7mOadkJ59XUx40Sg>`__ as we expect to make frequent changes to them. We welcome comments in the Google Doc.
+These guidelines are maintained in `a Google Doc <https://docs.google.com/document/d/1tY5t3gjrIgAGoRxVMWQSCh46fnbSmnFDLQ7aLkNLhJ8/>`__ as we expect to make frequent changes to them. We welcome comments in the Google Doc.

docker-compose-dev.yml

@@ -57,6 +57,7 @@ services:
         -Ddataverse.pid.fake.label=FakeDOIProvider
         -Ddataverse.pid.fake.authority=10.5072
         -Ddataverse.pid.fake.shoulder=FK2/
+        -Ddataverse.lang.directory=/dv/lang
     ports:
       - "8080:8080" # HTTP (Dataverse Application)
       - "4949:4848" # HTTPS (Payara Admin Console)

docker/compose/demo/compose.yml

@@ -26,6 +26,7 @@ services:
         -Ddataverse.pid.fake.label=FakeDOIProvider
         -Ddataverse.pid.fake.authority=10.5072
         -Ddataverse.pid.fake.shoulder=FK2/
+        -Ddataverse.lang.directory=/dv/lang
     ports:
       - "8080:8080" # HTTP (Dataverse Application)
       - "4848:4848" # HTTP (Payara Admin Console)

pom.xml

@@ -30,7 +30,7 @@
         <flyway.version>10.19.0</flyway.version>
         <jhove.version>1.20.1</jhove.version>
         <poi.version>5.2.1</poi.version>
-        <tika.version>2.4.1</tika.version>
+        <tika.version>2.9.1</tika.version>
         <netcdf.version>5.5.3</netcdf.version>
 
         <openapi.infoTitle>Dataverse API</openapi.infoTitle>
@@ -68,6 +68,17 @@
                     </exclusion>
                 </exclusions>
             </dependency>
+            <!-- Dependency for Apache Abdera and Apache Tika. Tika needs newer version. -->
+            <dependency>
+                <groupId>org.apache.james</groupId>
+                <artifactId>apache-mime4j-core</artifactId>
+                <version>0.8.10</version>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.james</groupId>
+                <artifactId>apache-mime4j-dom</artifactId>
+                <version>0.8.7</version>
+            </dependency>
         </dependencies>
     </dependencyManagement>
     <!-- Declare any DIRECT dependencies here.
@@ -558,7 +569,7 @@
         <dependency>
             <groupId>org.xmlunit</groupId>
             <artifactId>xmlunit-core</artifactId>
-            <version>2.9.1</version>
+            <version>2.10.0</version>
         </dependency>
         <dependency>
           <groupId>com.google.cloud</groupId>
@@ -620,7 +631,7 @@
         <dependency>
             <groupId>org.xmlunit</groupId>
             <artifactId>xmlunit-assertj3</artifactId>
-            <version>2.8.2</version>
+            <version>2.10.0</version>
             <scope>test</scope>
         </dependency>
         <dependency>

src/main/java/edu/harvard/iq/dataverse/Dataset.java

@@ -483,8 +483,17 @@ public Date getMostRecentMajorVersionReleaseDate() {
         if (this.isHarvested()) {
             return getVersions().get(0).getReleaseTime();
         } else {
+            Long majorVersion = null;
             for (DatasetVersion version : this.getVersions()) {
-                if (version.isReleased() && version.getMinorVersionNumber().equals((long) 0)) {
+                if (version.isReleased()) {
+                    if (version.getMinorVersionNumber().equals((long) 0)) {
+                        return version.getReleaseTime();
+                    } else if (majorVersion == null) {
+                        majorVersion = version.getVersionNumber();
+                    }
+                } else if (version.isDeaccessioned() && majorVersion != null
+                        && majorVersion.longValue() == version.getVersionNumber().longValue()
+                        && version.getMinorVersionNumber().equals((long) 0)) {
                     return version.getReleaseTime();
                 }
             }