Merge branch 'develop' into 9507-show-linked-collections

doc/release-notes/9412-markdown-previewer.md

@@ -0,0 +1 @@
+There is now a Markdown (.md) previewer: https://dataverse-guide--9986.org.readthedocs.build/en/9986/user/dataset-management.html#file-previews

doc/sphinx-guides/source/_static/admin/dataverse-external-tools.tsv

@@ -2,6 +2,6 @@ Tool	Type	Scope	Description
 Data Explorer	explore	file	"A GUI which lists the variables in a tabular data file allowing searching, charting and cross tabulation analysis. See the README.md file at https://github.com/scholarsportal/dataverse-data-explorer-v2 for the instructions on adding Data Explorer to your Dataverse."
 Whole Tale	explore	dataset	"A platform for the creation of reproducible research packages that allows users to launch containerized interactive analysis environments based on popular tools such as Jupyter and RStudio. Using this integration, Dataverse users can launch Jupyter and RStudio environments to analyze published datasets. For more information, see the `Whole Tale User Guide <https://wholetale.readthedocs.io/en/stable/users_guide/integration.html>`_."
 Binder	explore	dataset	Binder allows you to spin up custom computing environments in the cloud (including Jupyter notebooks) with the files from your dataset. `Installation instructions <https://github.com/data-exp-lab/girder_ythub/issues/10>`_ are in the Data Exploration Lab girder_ythub project.
-File Previewers	explore	file	"A set of tools that display the content of files - including audio, html, `Hypothes.is <https://hypothes.is/>`_ annotations, images, PDF, text, video, tabular data, spreadsheets, GeoJSON, zip, and NcML files - allowing them to be viewed without downloading the file. The previewers can be run directly from github.io, so the only required step is using the Dataverse API to register the ones you want to use. Documentation, including how to optionally brand the previewers, and an invitation to contribute through github are in the README.md file. Initial development was led by the Qualitative Data Repository and the spreasdheet previewer was added by the Social Sciences and Humanities Open Cloud (SSHOC) project. https://github.com/gdcc/dataverse-previewers"
+File Previewers	explore	file	"A set of tools that display the content of files - including audio, html, `Hypothes.is <https://hypothes.is/>`_ annotations, images, PDF, Markdown, text, video, tabular data, spreadsheets, GeoJSON, zip, and NcML files - allowing them to be viewed without downloading the file. The previewers can be run directly from github.io, so the only required step is using the Dataverse API to register the ones you want to use. Documentation, including how to optionally brand the previewers, and an invitation to contribute through github are in the README.md file. Initial development was led by the Qualitative Data Repository and the spreasdheet previewer was added by the Social Sciences and Humanities Open Cloud (SSHOC) project. https://github.com/gdcc/dataverse-previewers"
 Data Curation Tool	configure	file	"A GUI for curating data by adding labels, groups, weights and other details to assist with informed reuse. See the README.md file at https://github.com/scholarsportal/Dataverse-Data-Curation-Tool for the installation instructions."
 Ask the Data	query	file	Ask the Data is an experimental tool that allows you ask natural language questions about the data contained in Dataverse tables (tabular data). See the README.md file at https://github.com/IQSS/askdataverse/tree/main/askthedata for the instructions on adding Ask the Data to your Dataverse installation. 

doc/sphinx-guides/source/user/dataset-management.rst

@@ -200,6 +200,7 @@ Previewers are available for the following file types:
 
 - Text
 - PDF
+- Markdown
 - Tabular (CSV, Excel, etc., see :doc:`tabulardataingest/index`)
 - Code (R, etc.)
 - Images (PNG, GIF, JPG)

docker-compose-dev.yml

@@ -18,6 +18,7 @@ services:
       - DATAVERSE_AUTH_OIDC_CLIENT_ID=test
       - DATAVERSE_AUTH_OIDC_CLIENT_SECRET=94XHrfNRwXsjqTqApRrwWmhDLDHpIYV8
       - DATAVERSE_AUTH_OIDC_AUTH_SERVER_URL=http://keycloak.mydomain.com:8090/realms/test
+      - DATAVERSE_JSF_REFRESH_PERIOD=1
     ports:
       - "8080:8080" # HTTP (Dataverse Application)
       - "4848:4848" # HTTP (Payara Admin Console)
@@ -31,6 +32,9 @@ services:
     volumes:
       - ./docker-dev-volumes/app/data:/dv
       - ./docker-dev-volumes/app/secrets:/secrets
+      # Uncomment for changes to xhtml to be deployed immediately (if supported your IDE or toolchain).
+      # Replace 6.0 with the current version.
+      # - ./target/dataverse-6.0:/opt/payara/deployments/dataverse
     tmpfs:
       - /dumps:mode=770,size=2052M,uid=1000,gid=1000
       - /tmp:mode=770,size=2052M,uid=1000,gid=1000

modules/container-configbaker/Dockerfile

@@ -26,18 +26,19 @@ RUN true && \
   # Make our working directories
   mkdir -p ${SCRIPT_DIR} ${SECRETS_DIR} ${SOLR_TEMPLATE}
 
-# Get in the scripts and make them executable (just in case...)
+# Get in the scripts 
 COPY maven/scripts maven/solr/update-fields.sh ${SCRIPT_DIR}/
+# 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
+COPY maven/setup ${SCRIPT_DIR}/bootstrap/base/
+# Make the scripts executable
 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
-COPY maven/setup ${SCRIPT_DIR}/bootstrap/base/
 
 # Set the entrypoint to tini (as a process supervisor)
 ENTRYPOINT ["/usr/bin/dumb-init", "--"]

modules/dataverse-parent/pom.xml

@@ -429,6 +429,7 @@
             <url>https://artifacts.unidata.ucar.edu/repository/unidata-all/</url>
         </repository>
         <!-- Uncomment when using snapshot releases from Maven Central -->
+        <!--
         <repository>
             <id>oss-sonatype</id>
             <name>oss-sonatype</name>
@@ -449,7 +450,7 @@
                 <enabled>true</enabled>
             </snapshots>
         </repository>
-        <!-- -->
+        -->
     </repositories>
 
     <profiles>

pom.xml

@@ -373,12 +373,12 @@
         <dependency>
             <groupId>org.ocpsoft.rewrite</groupId>
             <artifactId>rewrite-servlet</artifactId>
-            <version>6.0.0-SNAPSHOT</version>
+            <version>10.0.0.Final</version>
         </dependency>
         <dependency>
             <groupId>org.ocpsoft.rewrite</groupId>
             <artifactId>rewrite-config-prettyfaces</artifactId>
-            <version>6.0.0-SNAPSHOT</version>
+            <version>10.0.0.Final</version>
         </dependency>
         <dependency>
             <groupId>edu.ucsb.nceas</groupId>

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

@@ -113,7 +113,7 @@ public int hashCode() {
 
     @Override
     public boolean equals(Object object) {
-        if (!(object instanceof DatasetField)) {
+        if (!(object instanceof DatasetFieldDefaultValue)) {
             return false;
         }
         DatasetFieldDefaultValue other = (DatasetFieldDefaultValue) object;

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

@@ -99,7 +99,7 @@ public int hashCode() {
 
     @Override
     public boolean equals(Object object) {
-        if (!(object instanceof DatasetFieldType)) {
+        if (!(object instanceof DataverseContact)) {
             return false;
         }
         DataverseContact other = (DataverseContact) object;

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

@@ -93,7 +93,7 @@ public int hashCode() {
 
     @Override
     public boolean equals(Object object) {
-        if (!(object instanceof DatasetFieldType)) {
+        if (!(object instanceof DataverseFacet)) {
             return false;
         }
         DataverseFacet other = (DataverseFacet) object;

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

@@ -85,7 +85,7 @@ public int hashCode() {
 
     @Override
     public boolean equals(Object object) {
-        if (!(object instanceof DatasetFieldType)) {
+        if (!(object instanceof DataverseFeaturedDataverse)) {
             return false;
         }
         DataverseFeaturedDataverse other = (DataverseFeaturedDataverse) object;

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

@@ -181,7 +181,7 @@ public int hashCode() {
 
     @Override
     public boolean equals(Object object) {
-        if (!(object instanceof DatasetFieldType)) {
+        if (!(object instanceof DataverseTheme)) {
             return false;
         }
         DataverseTheme other = (DataverseTheme) object;

src/test/java/edu/harvard/iq/dataverse/DatasetFieldDefaultValueTest.java

@@ -0,0 +1,47 @@
+package edu.harvard.iq.dataverse;
+
+import org.junit.jupiter.api.Test;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+
+import org.junit.jupiter.api.BeforeEach;
+
+public class DatasetFieldDefaultValueTest {
+    private DatasetFieldDefaultValue dataverseContact;
+
+    @BeforeEach
+    public void before() {
+        this.dataverseContact = new DatasetFieldDefaultValue();
+        this.dataverseContact.setId(1L);
+    }
+
+    @Test
+    public void testEqualsWithNull() {
+        assertFalse(this.dataverseContact.equals(null));
+    }
+
+    @Test
+    public void testEqualsWithDifferentClass() {
+        DatasetField datasetField = new DatasetField();
+
+        assertFalse(this.dataverseContact.equals(datasetField));
+    }
+
+    @Test
+    public void testEqualsWithSameClassSameId() {
+        DatasetFieldDefaultValue dataverseContact1 = new DatasetFieldDefaultValue();
+        dataverseContact1.setId(1L);
+
+        assertTrue(this.dataverseContact.equals(dataverseContact1));
+    }
+
+    @Test
+    public void testEqualsWithSameClassDifferentId() {
+        DatasetFieldDefaultValue dataverseContact1 = new DatasetFieldDefaultValue();
+        dataverseContact1.setId(2L);
+
+        assertFalse(this.dataverseContact.equals(dataverseContact1));
+    }
+}

src/test/java/edu/harvard/iq/dataverse/DataverseContactTest.java

@@ -0,0 +1,47 @@
+package edu.harvard.iq.dataverse;
+
+import org.junit.jupiter.api.Test;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+
+import org.junit.jupiter.api.BeforeEach;
+
+public class DataverseContactTest {
+    private DataverseContact dataverseContact;
+
+    @BeforeEach
+    public void before() {
+        this.dataverseContact = new DataverseContact();
+        this.dataverseContact.setId(1L);
+    }
+
+    @Test
+    public void testEqualsWithNull() {
+        assertFalse(this.dataverseContact.equals(null));
+    }
+
+    @Test
+    public void testEqualsWithDifferentClass() {
+        DatasetFieldType datasetFieldType = new DatasetFieldType();
+
+        assertFalse(this.dataverseContact.equals(datasetFieldType));
+    }
+
+    @Test
+    public void testEqualsWithSameClassSameId() {
+        DataverseContact dataverseContact1 = new DataverseContact();
+        dataverseContact1.setId(1L);
+
+        assertTrue(this.dataverseContact.equals(dataverseContact1));
+    }
+
+    @Test
+    public void testEqualsWithSameClassDifferentId() {
+        DataverseContact dataverseContact1 = new DataverseContact();
+        dataverseContact1.setId(2L);
+
+        assertFalse(this.dataverseContact.equals(dataverseContact1));
+    }
+}

src/test/java/edu/harvard/iq/dataverse/DataverseFacetTest.java

@@ -0,0 +1,47 @@
+package edu.harvard.iq.dataverse;
+
+import org.junit.jupiter.api.Test;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+
+import org.junit.jupiter.api.BeforeEach;
+
+public class DataverseFacetTest {
+    private DataverseFacet dataverseFacet;
+
+    @BeforeEach
+    public void before() {
+        this.dataverseFacet = new DataverseFacet();
+        this.dataverseFacet.setId(1L);
+    }
+
+    @Test
+    public void testEqualsWithNull() {
+        assertFalse(this.dataverseFacet.equals(null));
+    }
+
+    @Test
+    public void testEqualsWithDifferentClass() {
+        DatasetFieldType datasetFieldType = new DatasetFieldType();
+
+        assertFalse(this.dataverseFacet.equals(datasetFieldType));
+    }
+
+    @Test
+    public void testEqualsWithSameClassSameId() {
+        DataverseFacet dataverseFacet1 = new DataverseFacet();
+        dataverseFacet1.setId(1L);
+
+        assertTrue(this.dataverseFacet.equals(dataverseFacet1));
+    }
+
+    @Test
+    public void testEqualsWithSameClassDifferentId() {
+        DataverseFacet dataverseFacet1 = new DataverseFacet();
+        dataverseFacet1.setId(2L);
+
+        assertFalse(this.dataverseFacet.equals(dataverseFacet1));
+    }
+}

src/test/java/edu/harvard/iq/dataverse/DataverseFeaturedDataverseTest.java

@@ -0,0 +1,47 @@
+package edu.harvard.iq.dataverse;
+
+import org.junit.jupiter.api.Test;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+
+import org.junit.jupiter.api.BeforeEach;
+
+public class DataverseFeaturedDataverseTest {
+    private DataverseFeaturedDataverse dataverseFeaturedDataverse;
+
+    @BeforeEach
+    public void before() {
+        this.dataverseFeaturedDataverse = new DataverseFeaturedDataverse();
+        this.dataverseFeaturedDataverse.setId(1L);
+    }
+
+    @Test
+    public void testEqualsWithNull() {
+        assertFalse(this.dataverseFeaturedDataverse.equals(null));
+    }
+
+    @Test
+    public void testEqualsWithDifferentClass() {
+        DatasetFieldType datasetFieldType = new DatasetFieldType();
+
+        assertFalse(this.dataverseFeaturedDataverse.equals(datasetFieldType));
+    }
+
+    @Test
+    public void testEqualsWithSameClassSameId() {
+        DataverseFeaturedDataverse dataverseFeaturedDataverse1 = new DataverseFeaturedDataverse();
+        dataverseFeaturedDataverse1.setId(1L);
+
+        assertTrue(this.dataverseFeaturedDataverse.equals(dataverseFeaturedDataverse1));
+    }
+
+    @Test
+    public void testEqualsWithSameClassDifferentId() {
+        DataverseFeaturedDataverse dataverseFeaturedDataverse1 = new DataverseFeaturedDataverse();
+        dataverseFeaturedDataverse1.setId(2L);
+
+        assertFalse(this.dataverseFeaturedDataverse.equals(dataverseFeaturedDataverse1));
+    }
+}

src/test/java/edu/harvard/iq/dataverse/DataverseThemeTest.java

@@ -0,0 +1,47 @@
+package edu.harvard.iq.dataverse;
+
+import org.junit.jupiter.api.Test;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+
+import org.junit.jupiter.api.BeforeEach;
+
+public class DataverseThemeTest {
+    private DataverseTheme dataverseTheme;
+
+    @BeforeEach
+    public void before() {
+        this.dataverseTheme = new DataverseTheme();
+        this.dataverseTheme.setId(1L);
+    }
+
+    @Test
+    public void testEqualsWithNull() {
+        assertFalse(this.dataverseTheme.equals(null));
+    }
+
+    @Test
+    public void testEqualsWithDifferentClass() {
+        DatasetFieldType datasetFieldType = new DatasetFieldType();
+
+        assertFalse(this.dataverseTheme.equals(datasetFieldType));
+    }
+
+    @Test
+    public void testEqualsWithSameClassSameId() {
+        DataverseTheme dataverseTheme1 = new DataverseTheme();
+        dataverseTheme1.setId(1L);
+
+        assertTrue(this.dataverseTheme.equals(dataverseTheme1));
+    }
+
+    @Test
+    public void testEqualsWithSameClassDifferentId() {
+        DataverseTheme dataverseTheme1 = new DataverseTheme();
+        dataverseTheme1.setId(2L);
+
+        assertFalse(this.dataverseTheme.equals(dataverseTheme1));
+    }
+}