Merge remote-tracking branch 'IQSS/develop' into FakeFilePIDs

.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/10904-edit-dataverse-collection-endpoint.md

@@ -0,0 +1 @@
+Adds a new endpoint (`PUT /api/dataverses/<identifier>`) for updating an existing Dataverse collection using a JSON file following the same structure as the one used in the API for the creation.

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doc/release-notes/10947-unpublished-files-appearing-in-search-results-for-anon-user.md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+## Unpublished file bug fix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 This fixes the incorrect showing of the files as "Unpublished" in the search list even when they are published.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/api/native-api.rst

@@ -74,6 +74,58 @@ The request JSON supports an optional ``metadataBlocks`` object, with the follow
 
 To obtain an example of how these objects are included in the JSON file, download :download:`dataverse-complete-optional-params.json <../_static/api/dataverse-complete-optional-params.json>` file and modify it to suit your needs.
 
+.. _update-dataverse-api:
+
+Update a Dataverse Collection
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Updates an existing Dataverse collection using a JSON file following the same structure as the one used in the API for the creation. (see :ref:`create-dataverse-api`).
+
+The steps for updating a Dataverse collection are:
+
+- Prepare a JSON file containing the fields for the properties you want to update. You do not need to include all the properties, only the ones you want to update.
+- Execute a curl command or equivalent.
+
+As an example, you can download :download:`dataverse-complete.json <../_static/api/dataverse-complete.json>` file and modify it to suit your needs. The controlled vocabulary for ``dataverseType`` is the following:
+
+- ``DEPARTMENT``
+- ``JOURNALS``
+- ``LABORATORY``
+- ``ORGANIZATIONS_INSTITUTIONS``
+- ``RESEARCHERS``
+- ``RESEARCH_GROUP``
+- ``RESEARCH_PROJECTS``
+- ``TEACHING_COURSES``
+- ``UNCATEGORIZED``
+
+The curl command below assumes you are using the name "dataverse-complete.json" and that this file is in your current working directory.
+
+Next you need to figure out the alias or database id of the Dataverse collection you want to update.
+
+.. code-block:: bash
+
+  export API_TOKEN=xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx
+  export SERVER_URL=https://demo.dataverse.org
+  export DV_ALIAS=dvAlias
+
+  curl -H "X-Dataverse-key:$API_TOKEN" -X PUT "$SERVER_URL/api/dataverses/$DV_ALIAS" --upload-file dataverse-complete.json
+
+The fully expanded example above (without environment variables) looks like this:
+
+.. code-block:: bash
+
+  curl -H "X-Dataverse-key:xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx" -X PUT "https://demo.dataverse.org/api/dataverses/dvAlias" --upload-file dataverse-complete.json
+
+You should expect an HTTP 200 response and JSON beginning with "status":"OK" followed by a representation of the updated Dataverse collection.
+
+Same as in :ref:`create-dataverse-api`, the request JSON supports an optional ``metadataBlocks`` object, with the following supported sub-objects:
+
+- ``metadataBlockNames``: The names of the metadata blocks you want to add to the Dataverse collection.
+- ``inputLevels``: The names of the fields in each metadata block for which you want to add a custom configuration regarding their inclusion or requirement when creating and editing datasets in the new Dataverse collection. Note that if the corresponding metadata blocks names are not specified in the ``metadataBlockNames``` field, they will be added automatically to the Dataverse collection.
+- ``facetIds``: The names of the fields to use as facets for browsing datasets and collections in the new Dataverse collection. Note that the order of the facets is defined by their order in the provided JSON array.
+
+To obtain an example of how these objects are included in the JSON file, download :download:`dataverse-complete-optional-params.json <../_static/api/dataverse-complete-optional-params.json>` file and modify it to suit your needs.
+
 .. _view-dataverse:
 
 View a Dataverse Collection

doc/sphinx-guides/source/container/dev-usage.rst

@@ -140,6 +140,56 @@ Alternatives:
 - If you used Docker Compose for running, you may use ``docker compose -f docker-compose-dev.yml logs <service name>``.
   Options are the same.
 
+Accessing Harvesting Log Files
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+\1. Open a terminal and access the Dataverse container.
+
+Run the following command to access the Dataverse container (assuming your container is named dataverse-1):
+
+.. code-block::
+
+  docker exec -it dataverse-1 bash
+
+This command opens an interactive shell within the dataverse-1 container.
+
+\2. Navigate to the log files directory.
+
+Once inside the container, navigate to the directory where Dataverse logs are stored:
+
+.. code-block::
+
+  cd /opt/payara/appserver/glassfish/domains/domain1/logs
+
+This directory contains various log files, including those relevant to harvesting.
+
+\3. Create a directory for copying files.
+
+Create a directory where you'll copy the files you want to access on your local machine:
+
+.. code-block::
+
+  mkdir /dv/filesToCopy
+
+This will create a new folder named filesToCopy inside /dv.
+
+\4. Copy the files to the new directory.
+
+Copy all files from the current directory to the newly created filesToCopy directory:
+
+.. code-block::
+
+  cp * /dv/filesToCopy
+
+This command copies all files in the logs directory to /dv/filesToCopy.
+
+\5. Access the files on your local machine.
+
+On your local machine, the copied files should appear in the following directory:
+
+.. code-block::
+
+  docker-dev-volumes/app/data/filesToCopy
 
 Redeploying
 -----------

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:
 

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();
                 }
             }

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

@@ -891,6 +891,10 @@ public List<DatasetFieldType> findAllDisplayedOnCreateInMetadataBlock(MetadataBl
     }
 
     public List<DatasetFieldType> findAllInMetadataBlockAndDataverse(MetadataBlock metadataBlock, Dataverse dataverse, boolean onlyDisplayedOnCreate) {
+        if (!dataverse.isMetadataBlockRoot() && dataverse.getOwner() != null) {
+            return findAllInMetadataBlockAndDataverse(metadataBlock, dataverse.getOwner(), onlyDisplayedOnCreate);
+        }
+
         CriteriaBuilder criteriaBuilder = em.getCriteriaBuilder();
         CriteriaQuery<DatasetFieldType> criteriaQuery = criteriaBuilder.createQuery(DatasetFieldType.class);