Merge branch 'develop' into multi-license

.github/workflows/reviewdog_checkstyle.yml

@@ -0,0 +1,21 @@
+name: Maven CheckStyle Task
+on:
+   pull_request:
+       paths:
+           - "**.java"
+
+jobs:
+    checkstyle_job:
+        runs-on: ubuntu-latest
+        name: Checkstyle job
+        steps:
+            - name: Checkout
+              uses: actions/checkout@v2
+            - name: Run check style
+              uses: nikitasavinov/checkstyle-action@master
+              with:
+                  fail_on_error: true
+                  reporter: github-pr-review
+                  checkstyle_config: checkstyle.xml
+                  github_token: ${{ secrets.GITHUB_TOKEN }}
+

conf/docker-aio/run-test-suite.sh

@@ -6,6 +6,8 @@ if [ -z "$dvurl" ]; then
 	dvurl="http://localhost:8084"
 fi
 
+integrationtests=$(<../../tests/integration-tests.txt)
+
 # Please note the "dataverse.test.baseurl" is set to run for "all-in-one" Docker environment.
 # TODO: Rather than hard-coding the list of "IT" classes here, add a profile to pom.xml.
-source maven/maven.sh && mvn test -Dtest=DataversesIT,DatasetsIT,SwordIT,AdminIT,BuiltinUsersIT,UsersIT,UtilIT,ConfirmEmailIT,FileMetadataIT,FilesIT,SearchIT,InReviewWorkflowIT,HarvestingServerIT,MoveIT,MakeDataCountApiIT,FileTypeDetectionIT,EditDDIIT,ExternalToolsIT,AccessIT,DuplicateFilesIT,DownloadFilesIT,LinkIT,DeleteUsersIT,DeactivateUsersIT,AuxiliaryFilesIT -Ddataverse.test.baseurl=$dvurl
+mvn test -Dtest=$integrationtests -Ddataverse.test.baseurl=$dvurl

doc/release-notes/5.0-release-notes.md

@@ -313,7 +313,7 @@ The instructions below describe the upgrade procedure based on moving an existin
 
 1. Update Astrophysics Metadata Block (if used)
 
-   `wget https://github.com/IQSS/dataverse/releases/download/5.0/astrophysics.tsv`
+   `wget https://github.com/IQSS/dataverse/releases/download/v5.0/astrophysics.tsv`
    `curl http://localhost:8080/api/admin/datasetfield/load -X POST --data-binary @astrophysics.tsv -H "Content-type: text/tab-separated-values"` 
 
 2. (Recommended) Run ReExportall to update JSON Exports  

doc/release-notes/5.5-release-notes.md

@@ -16,7 +16,7 @@ Users trying to download a zip file larger than the Dataverse installation's :Zi
 
 ### Guidelines on Depositing Code
 
-The Software Metadata Working Group has created guidelines on depositing research code in a Dataverse installation. Learn more in the [Dataset Management section](https://guides.dataverse.org/en/latest/dataset-management) of the Dataverse Guides.
+The Software Metadata Working Group has created guidelines on depositing research code in a Dataverse installation. Learn more in the [Dataset Management section](https://guides.dataverse.org/en/latest/user/dataset-management.html#research-code) of the Dataverse Guides.
 
 ### New Metrics API
 

doc/sphinx-guides/source/api/native-api.rst

@@ -825,14 +825,20 @@ through the Dataverse application.
 
 For example, if you have a dataset version with 2 files, one with the folder named "subfolder":
 
+|image1|
+
 .. |image1| image:: ./img/dataset_page_files_view.png
 
 or, as viewed as a tree on the dataset page:
 
+|image2|
+
 .. |image2| image:: ./img/dataset_page_tree_view.png
 
 The output of the API for the top-level folder (``/api/datasets/{dataset}/dirindex/``) will be as follows:
 
+|image3|
+
 .. |image3| image:: ./img/index_view_top.png
 
 with the underlying html source:
@@ -851,6 +857,8 @@ with the underlying html source:
 
 The ``/dirindex/?folder=subfolder`` link above will produce the following view:
 
+|image4|
+
 .. |image4| image:: ./img/index_view_subfolder.png
 
 with the html source as follows:

doc/sphinx-guides/source/developers/dev-environment.rst

@@ -139,8 +139,6 @@ To install Solr, execute the following commands:
 
 ``curl -O https://raw.githubusercontent.com/IQSS/dataverse/develop/conf/solr/8.8.1/schema_dv_mdb_fields.xml``
 
-``curl -O https://raw.githubusercontent.com/IQSS/dataverse/develop/conf/solr/8.8.1/schema_dv_mdb_copies.xml``
-
 ``mv schema*.xml collection1/conf``
 
 ``curl -O https://raw.githubusercontent.com/IQSS/dataverse/develop/conf/solr/8.8.1/solrconfig.xml``

doc/sphinx-guides/source/developers/testing.rst

@@ -246,7 +246,7 @@ Once installed, you may run commands with ``mvn [options] [<goal(s)>] [<phase(s)
 
   ``mvn test -Dtest=FileMetadataIT -Ddataverse.test.baseurl='http://localhost:8080'``
 
-To see the full list of tests used by the Docker option mentioned above, see :download:`run-test-suite.sh <../../../../conf/docker-aio/run-test-suite.sh>`.
+If you are adding a new test class, be sure to add it to :download:`tests/integration-tests.txt <../../../../tests/integration-tests.txt>` so that our automated testing knows about it.
 
 
 Writing and Using a Testcontainers Test
@@ -438,13 +438,6 @@ How to Run the Phoenix Tests
 - Log into Jenkins and click "Build Now" at https://build.hmdc.harvard.edu:8443/job/phoenix.dataverse.org-build-develop/
 - Wait for all three chained Jenkins jobs to complete and note if they passed or failed. If you see a failure, open a GitHub issue or at least get the attention of some developers.
 
-List of Tests Run Against the Phoenix Server
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-We haven't thought much about a good way to publicly list the "IT" classes that are executed against the phoenix server. (Currently your best bet is to look at the ``Executing Maven`` line at the top of the "Full Log" of "Console Output" of ``phoenix.dataverse.org-apitest-develop`` Jenkins job mentioned above.) We endeavor to keep the list of tests in the "all-in-one" Docker environment described above in sync with the list of tests configured in Jenkins. That is to say, refer to :download:`run-test-suite.sh <../../../../conf/docker-aio/run-test-suite.sh>` mentioned in ``conf/docker-aio/readme.md`` for the current list of IT tests that are expected to pass. Here's a dump of that file:
-
-.. literalinclude:: ../../../../conf/docker-aio/run-test-suite.sh
-
 Accessibility Testing
 ---------------------
 

scripts/installer/Makefile

@@ -4,7 +4,7 @@ GLASSFISH_SETUP_SCRIPT=${INSTALLER_ZIP_DIR}/as-setup.sh
 API_SCRIPTS=${INSTALLER_ZIP_DIR}/setup-datasetfields.sh ${INSTALLER_ZIP_DIR}/setup-users.sh ${INSTALLER_ZIP_DIR}/setup-builtin-roles.sh ${INSTALLER_ZIP_DIR}/setup-dvs.sh ${INSTALLER_ZIP_DIR}/data ${INSTALLER_ZIP_DIR}/setup-identity-providers.sh  ${INSTALLER_ZIP_DIR}/setup-all.sh ${INSTALLER_ZIP_DIR}/post-install-api-block.sh
 JHOVE_CONFIG=${INSTALLER_ZIP_DIR}/jhove.conf
 JHOVE_SCHEMA=${INSTALLER_ZIP_DIR}/jhoveConfig.xsd
-SOLR_SCHEMA=${INSTALLER_ZIP_DIR}/schema.xml ${INSTALLER_ZIP_DIR}/schema_dv_mdb_fields.xml ${INSTALLER_ZIP_DIR}/schema_dv_mdb_copies.xml ${INSTALLER_ZIP_DIR}/updateSchemaMDB.sh
+SOLR_SCHEMA=${INSTALLER_ZIP_DIR}/schema.xml ${INSTALLER_ZIP_DIR}/schema_dv_mdb_fields.xml ${INSTALLER_ZIP_DIR}/updateSchemaMDB.sh
 SOLR_CONFIG=${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
@@ -56,7 +56,7 @@ ${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/8.8.1/schema.xml ../../conf/solr/8.8.1/schema_dv_mdb_fields.xml ../../conf/solr/8.8.1/schema_dv_mdb_copies.xml ../../conf/solr/8.8.1/updateSchemaMDB.sh ${INSTALLER_ZIP_DIR}
+${SOLR_SCHEMA}:		../../conf/solr/8.8.1/schema.xml ../../conf/solr/8.8.1/schema_dv_mdb_fields.xml ../../conf/solr/8.8.1/updateSchemaMDB.sh ${INSTALLER_ZIP_DIR}
 	@echo copying Solr schema file
 	/bin/cp ../../conf/solr/8.8.1/schema*.xml ../../conf/solr/8.8.1/updateSchemaMDB.sh ${INSTALLER_ZIP_DIR}
 

scripts/installer/README.txt

@@ -38,6 +38,5 @@ jhove.conf
 SOLR schema and config files, from conf/solr/8.8.1: 
 
 schema.xml
-schema_dv_cmb_copies.xml
-schema_dv_cmb_fields.xml
+schema_dv_mdb_fields.xml
 solrconfig.xml

src/main/java/edu/harvard/iq/dataverse/api/Admin.java

@@ -384,9 +384,8 @@ private Response deleteAuthenticatedUser(AuthenticatedUser au) {
         authSvc.removeAuthentictedUserItems(au);
 
         authSvc.deleteAuthenticatedUser(au.getId());
-        return ok("AuthenticatedUser " + au.getIdentifier() + " deleted. ");
-
-    }  
+        return ok("AuthenticatedUser " + au.getIdentifier() + " deleted.");
+    }
 
     @POST
     @Path("authenticatedUsers/{identifier}/deactivate")

src/main/java/edu/harvard/iq/dataverse/api/Datasets.java

@@ -501,7 +501,7 @@ public Response getFileAccessFolderView(@PathParam("id") String datasetId, @Quer
 
         String indexFileName = folderName.equals("") ? ".index.html"
                 : ".index-" + folderName.replace('/', '_') + ".html";
-        response.setHeader("Content-disposition", "attachment; filename=\"" + indexFileName + "\"");
+        response.setHeader("Content-disposition", "filename=\"" + indexFileName + "\"");
 
 
         return Response.ok()

src/test/java/edu/harvard/iq/dataverse/api/AdminIT.java

@@ -74,9 +74,7 @@ public void testListAuthenticatedUsers() throws Exception {
 
         Response deleteSuperuser = UtilIT.deleteUser(superuserUsername);
         assertEquals(200, deleteSuperuser.getStatusCode());
-
     }
-
 
     @Test
     public void testFilterAuthenticatedUsersForbidden() throws Exception {

tests/integration-tests.txt

@@ -0,0 +1 @@
+DataversesIT,DatasetsIT,SwordIT,AdminIT,BuiltinUsersIT,UsersIT,UtilIT,ConfirmEmailIT,FileMetadataIT,FilesIT,SearchIT,InReviewWorkflowIT,HarvestingServerIT,MoveIT,MakeDataCountApiIT,FileTypeDetectionIT,EditDDIIT,ExternalToolsIT,AccessIT,DuplicateFilesIT,DownloadFilesIT,LinkIT,DeleteUsersIT,DeactivateUsersIT,AuxiliaryFilesIT