Merge branch 'develop' into 10517-dataset-types #10517

We bumped our db migration script to .2

Conflicts:
src/main/resources/db/migration/V6.3.0.1.sql
src/test/java/edu/harvard/iq/dataverse/api/UtilIT.java

Author: pdurbin

.github/ISSUE_TEMPLATE/bug_report.md

@@ -14,7 +14,7 @@ Thank you for contributing to the Dataverse Project through the creation of a bu
 WARNING: If this is a security issue it should be reported privately to [email protected]
 
 More information on bug issues and contributions can be found in the "Contributing to Dataverse" page:
-https://github.com/IQSS/dataverse/blob/develop/CONTRIBUTING.md#bug-reportsissues
+https://guides.dataverse.org/en/latest/contributor/index.html
 
 Please fill out as much of the template as you can.
 Start below this comment section.
@@ -44,7 +44,6 @@ Start below this comment section.
 **Any related open or closed issues to this bug report?**
 
 
-
 **Screenshots:**
 
 No matter the issue, screenshots are always welcome.
@@ -53,3 +52,7 @@ To add a screenshot, please use one of the following formats and/or methods desc
 
 * https://help.github.com/en/articles/file-attachments-on-issues-and-pull-requests
 *
+
+
+**Are you thinking about creating a pull request for this issue?**
+Help is always welcome, is this bug something you or your organization plan to fix?

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,7 +1,7 @@
 ---
 name: Feature request
 about: Suggest an idea or new feature for the Dataverse software!
-title: 'Feature Request/Idea:'
+title: 'Feature Request:'
 labels: 'Type: Feature'
 assignees: ''
 
@@ -11,7 +11,7 @@ assignees: ''
 Thank you for contributing to the Dataverse Project through the creation of a feature request!
 
 More information on ideas/feature requests and contributions can be found in the "Contributing to Dataverse" page:
-https://github.com/IQSS/dataverse/blob/develop/CONTRIBUTING.md#ideasfeature-requests
+https://guides.dataverse.org/en/latest/contributor/index.html
 
 Please fill out as much of the template as you can.
 Start below this comment section.
@@ -34,3 +34,6 @@ Start below this comment section.
 
 
 **Any open or closed issues related to this feature request?**
+
+**Are you thinking about creating a pull request for this feature?**  
+Help is always welcome, is this feature something you or your organization plan to implement?

.github/ISSUE_TEMPLATE/idea_proposal.md

@@ -0,0 +1,40 @@
+---
+name: Idea proposal
+about: Propose a new idea for discussion to improve the Dataverse software!
+title: 'Suggestion:'
+labels: 'Type: Suggestion'
+assignees: ''
+
+---
+
+<!--
+Thank you for contributing to the Dataverse Project through the creation of a feature request!
+
+More information on ideas/feature requests and contributions can be found in the "Contributing to Dataverse" page:
+https://guides.dataverse.org/en/latest/contributor/index.html
+
+Please fill out as much of the template as you can.
+Start below this comment section.
+-->
+
+**Overview of the Suggestion**
+
+
+**What kind of user is the suggestion intended for?**
+(Example users roles: API User, Curator, Depositor, Guest, Superuser, Sysadmin)
+
+
+**What inspired this idea?**
+
+
+**What existing behavior do you want changed?**
+
+
+**Any brand new behavior do you want to add to Dataverse?**
+
+
+**Any open or closed issues related to this suggestion?**
+
+
+**Are you thinking about creating a pull request for this issue?**
+Help is always welcome, is this idea something you or your organization plan to implement?

doc/release-notes/10508-base-image-fixes.md

@@ -0,0 +1,12 @@
+# Security and Compatibility Fixes to the Container Base Image
+
+- Switch "wait-for" to "wait4x", aligned with the Configbaker Image
+- Update "jattach" to v2.2
+- Install AMD64 / ARM64 versions of tools as necessary
+- Run base image as unprivileged user by default instead of `root` - this was an oversight from OpenShift changes
+- Linux User, Payara Admin and Domain Master passwords:
+  - Print hints about default, public knowledge passwords in place for
+  - Enable replacing these passwords at container boot time
+- Enable building with updates Temurin JRE image based on Ubuntu 24.04 LTS
+- Fix entrypoint script troubles with pre- and postboot script files
+- Unify location of files at CONFIG_DIR=/opt/payara/config, avoid writing to other places

doc/release-notes/10633-add-dataverse-api-extension.md

@@ -0,0 +1 @@
+The addDataverse (/api/dataverses/{identifier}) API endpoint has been extended to allow adding metadata blocks, input levels and facet ids at creation time, as the Dataverse page in create mode does in JSF.

doc/release-notes/8796-fix-license-display-indexing.md

@@ -0,0 +1 @@
+When datasets have neither a license nor custom terms of use the display will indicate this. Also, these datasets will no longer be indexed as having custom terms. 

doc/release-notes/8945-ignore-shapefiles-under-hidden-directories-in-zip.md

@@ -0,0 +1,5 @@
+### Shapefile Handling will now ignore files under a hidden directory within the zip file
+
+Directories that are hidden will be ignored when determining if a zip file contains Shapefile files.
+
+For more information, see #8945.

doc/release-notes/9081-CC0-waiver-turned-into-custom-license.md

@@ -0,0 +1,6 @@
+In an earlier Dataverse release, Datasets with only 'CC0 Waiver' in termsofuse field were converted to 'Custom License' instead of CC0 1.0 licenses during an automated process. A new process was added to correct this. Only Datasets with no terms other than the one create by the previous process will be modified.
+- The existing 'Terms of Use' must be equal to 'This dataset is made available under a Creative Commons CC0 license with the following additional/modified terms and conditions: CC0 Waiver'
+- The following terms fields must be empty: Confidentiality Declaration, Special Permissions, Restrictions, Citation Requirements, Depositor Requirements, Conditions, and Disclaimer.
+- The License ID must not be assigned.
+
+This process will set the License ID to that of the CC0 1.0 license and remove the contents of termsofuse field.

doc/release-notes/api-blocking-filter-json.md

@@ -0,0 +1,3 @@
+* When any `ApiBlockingFilter` policy applies to a request, the JSON in the body of the error response is now valid JSON.
+  In case an API client did any special processing to allow it to parse the body, that is no longer necessary.
+  The status code of such responses has not changed.

doc/sphinx-guides/source/_static/api/dataverse-complete-optional-params.json

@@ -0,0 +1,65 @@
+{
+  "name": "Scientific Research",
+  "alias": "science",
+  "dataverseContacts": [
+    {
+      "contactEmail": "[email protected]"
+    },
+    {
+      "contactEmail": "[email protected]"
+    }
+  ],
+  "affiliation": "Scientific Research University",
+  "description": "We do all the science.",
+  "dataverseType": "LABORATORY",
+  "metadataBlocks": {
+    "metadataBlockNames": [
+      "citation", "geospatial"
+    ],
+    "inputLevels": [
+      {
+        "datasetFieldTypeName": "geographicCoverage",
+        "include": true,
+        "required": true
+      },
+      {
+        "datasetFieldTypeName": "country",
+        "include": true,
+        "required": true
+      },
+      {
+        "datasetFieldTypeName": "geographicUnit",
+        "include": false,
+        "required": false
+      },
+      {
+        "datasetFieldTypeName": "geographicBoundingBox",
+        "include": false,
+        "required": false
+      },
+      {
+        "datasetFieldTypeName": "westLongitude",
+        "include": false,
+        "required": false
+      },
+      {
+        "datasetFieldTypeName": "eastLongitude",
+        "include": false,
+        "required": false
+      },
+      {
+        "datasetFieldTypeName": "northLatitude",
+        "include": false,
+        "required": false
+      },
+      {
+        "datasetFieldTypeName": "southLatitude",
+        "include": false,
+        "required": false
+      }
+    ],
+    "facetIds": [
+      "authorName", "authorAffiliation"
+    ]
+  }
+}

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

@@ -66,6 +66,14 @@ The fully expanded example above (without environment variables) looks like this
 
 You should expect an HTTP 200 response and JSON beginning with "status":"OK" followed by a representation of the newly-created Dataverse collection.
 
+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
@@ -258,6 +266,25 @@ The fully expanded example above (without environment variables) looks like this
 
   curl -H "X-Dataverse-key:xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx" "https://demo.dataverse.org/api/dataverses/root/metadatablockfacets"
 
+List Field Type Input Levels Configured for a Dataverse Collection
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+|CORS| List the dataverse field type input levels configured for a given Dataverse collection ``id``:
+
+.. code-block:: bash
+
+  export API_TOKEN=xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx
+  export SERVER_URL=https://demo.dataverse.org
+  export ID=root
+
+  curl -H "X-Dataverse-key:$API_TOKEN" "$SERVER_URL/api/dataverses/$ID/inputLevels"
+
+The fully expanded example above (without environment variables) looks like this:
+
+.. code-block:: bash
+
+  curl -H "X-Dataverse-key:xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx" "https://demo.dataverse.org/api/dataverses/root/inputLevels"
+
 Set Metadata Block Facets for a Dataverse Collection
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

doc/sphinx-guides/source/container/base-image.rst

@@ -46,7 +46,7 @@ The base image provides:
 - 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
 - `Jattach <https://github.com/apangin/jattach>`__ (attach to running JVM)
-- `wait-for <https://github.com/eficode/wait-for>`__ (tool to "wait for" a service to be available)
+- `wait4x <https://github.com/atkrad/wait4x>`__ (tool to "wait for" a service to be available)
 - `dumb-init <https://github.com/Yelp/dumb-init>`__ (see :ref:`below <base-entrypoint>` for details)
 
 This image is created as a "multi-arch image", see :ref:`below <base-multiarch>`.
@@ -85,7 +85,7 @@ Some additional notes, using Maven parameters to change the build and use ...:
     (See also `Docker Hub search example <https://hub.docker.com/_/eclipse-temurin/tags?page=1&name=11-jre>`_)
 - ... a different Java Distribution: add ``-Djava.image="name:tag"`` with precise reference to an
   image available local or remote.
-- ... a different UID/GID for the ``payara`` user/group: add ``-Dbase.image.uid=1234`` (or ``.gid``)
+- ... a different UID/GID for the ``payara`` user/group (default ``1000:1000``): add ``-Dbase.image.uid=1234`` (or ``.gid``)
 
 Automated Builds & Publishing
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -151,12 +151,12 @@ provides. These are mostly based on environment variables (very common with cont
       - [preboot]_
       - Abs. path
       - Provide path to file with ``asadmin`` commands to run **before** boot of application server.
-        See also `Pre/postboot script docs`_.
+        See also `Pre/postboot script docs`_. Must be writeable by Payara Linux user!
     * - ``POSTBOOT_COMMANDS``
       - [postboot]_
       - Abs. path
       - Provide path to file with ``asadmin`` commands to run **after** boot of application server.
-        See also `Pre/postboot script docs`_.
+        See also `Pre/postboot script docs`_. Must be writeable by Payara Linux user!
     * - ``JVM_ARGS``
       - (empty)
       - String
@@ -231,6 +231,18 @@ provides. These are mostly based on environment variables (very common with cont
       - See :ref:`:ApplicationServerSettings` ``http.request-timeout-seconds``.
 
         *Note:* can also be set using any other `MicroProfile Config Sources`_ available via ``dataverse.http.timeout``.
+    * - ``PAYARA_ADMIN_PASSWORD``
+      - ``admin``
+      - String
+      - Set to secret string to change `Payara Admin Console`_ Adminstrator User ("admin") password.
+    * - ``LINUX_PASSWORD``
+      - ``payara``
+      - String
+      - Set to secret string to change the Payara Linux User ("payara", default UID=1000) password.
+    * - ``DOMAIN_PASSWORD``
+      - ``changeit``
+      - String
+      - Set to secret string to change the `Domain Master Password`_.
 
 
 .. [preboot] ``${CONFIG_DIR}/pre-boot-commands.asadmin``
@@ -374,3 +386,5 @@ from `run-java-sh recommendations`_.
 .. _Pre/postboot script docs: https://docs.payara.fish/community/docs/Technical%20Documentation/Payara%20Micro%20Documentation/Payara%20Micro%20Configuration%20and%20Management/Micro%20Management/Asadmin%20Commands/Pre%20and%20Post%20Boot%20Commands.html
 .. _MicroProfile Config Sources: https://docs.payara.fish/community/docs/Technical%20Documentation/MicroProfile/Config/Overview.html
 .. _run-java-sh recommendations: https://github.com/fabric8io-images/run-java-sh/blob/master/TUNING.md#recommandations
+.. _Domain Master Password: https://docs.payara.fish/community/docs/Technical%20Documentation/Payara%20Server%20Documentation/Security%20Guide/Administering%20System%20Security.html#to-change-the-master-password
+.. _Payara Admin Console: https://docs.payara.fish/community/docs/Technical%20Documentation/Payara%20Server%20Documentation/General%20Administration/Overview.html#administration-console

doc/sphinx-guides/source/developers/making-releases.rst

@@ -8,12 +8,12 @@ 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.
+This document is about releasing the main Dataverse app (https://github.com/IQSS/dataverse). See :doc:`making-library-releases` for how to release our various libraries. Other projects have their own release documentation.
 
 The steps below describe making both regular releases and hotfix releases.
 
+Below you'll see branches like "develop" and "master" mentioned. For more on our branching strategy, see :doc:`version-control`.
+
 .. _write-release-notes:
 
 Write Release Notes
@@ -24,10 +24,10 @@ Developers express the need for an addition to release notes by creating a "rele
 The task at or near release time is to collect these snippets into a single file.
 
 - Create an issue in GitHub to track the work of creating release notes for the upcoming release.
-- Create a branch, add a .md file for the release (ex. 5.10.1 Release Notes) in ``/doc/release-notes`` and write the release notes, making sure to pull content from the release note snippets mentioned above.
-- Delete the release note snippets as the content is added to the main release notes file.
-- Include instructions to describe the steps required to upgrade the application from the previous version. These must be customized for release numbers and special circumstances such as changes to metadata blocks and infrastructure.
-- Take the release notes .md through the regular Code Review and QA process.
+- Create a branch, add a .md file for the release (ex. 5.10.1 Release Notes) in ``/doc/release-notes`` and write the release notes, making sure to pull content from the release note snippets mentioned above. Snippets may not include any issue number or pull request number in the text so be sure copy the number from the filename of the snippet into the final release note.
+- Delete (``git rm``) the release note snippets as the content is added to the main release notes file.
+- Include instructions describing the steps required to upgrade the application from the previous version. These must be customized for release numbers and special circumstances such as changes to metadata blocks and infrastructure.
+- Take the release notes .md through the regular Code Review and QA process. That is, make a pull request.
 
 Create a GitHub Issue and Branch for the Release
 ------------------------------------------------
@@ -70,6 +70,13 @@ Once important tests have passed (compile, unit tests, etc.), merge the pull req
 
 If this is a hotfix release, skip this whole "merge develop to master" step (the "develop" branch is not involved until later).
 
+Add Milestone to Pull Requests and Issues
+-----------------------------------------
+
+Often someone is making sure that the proper milestone (e.g. 5.10.1) is being applied to pull requests and issues, but sometimes this falls between the cracks.
+
+Check for merged pull requests that have no milestone by going to https://github.com/IQSS/dataverse/pulls and entering `is:pr is:merged no:milestone <https://github.com/IQSS/dataverse/pulls?q=is%3Apr+is%3Amerged+no%3Amilestone>`_ as a query. If you find any, add the milestone to the pull request and any issues it closes. This includes the "merge develop into master" pull request above.
+
 (Optional) Test Docker Images
 -----------------------------
 
@@ -106,7 +113,7 @@ Create a Draft Release on GitHub
 Go to https://github.com/IQSS/dataverse/releases/new to start creating a draft release.
 
 - Under "Choose a tag" you will be creating a new tag. Have it start with a "v" such as ``v5.10.1``. Click "Create new tag on publish".
-- Under "Target" go to "Recent Commits" and select the merge commit from when you merged ``develop`` into ``master`` above. This commit will appear in ``/api/info/version`` from a running installation.
+- Under "Target", choose "master". This commit will appear in ``/api/info/version`` from a running installation.
 - Under "Release title" use the same name as the tag such as ``v5.10.1``.
 - In the description, copy and paste the content from the release notes .md file created in the "Write Release Notes" steps above.
 - Click "Save draft" because we do not want to publish the release yet.
@@ -153,6 +160,7 @@ ssh into the dataverse-internal server and do the following:
 - ``mkdir target``
 - ``cp /tmp/dataverse-5.10.1.war target``
 - ``cd scripts/installer``
+- ``make clean``
 - ``make``
 
 A zip file called ``dvinstall.zip`` should be produced.
@@ -175,7 +183,7 @@ Upload the following artifacts to the draft release you created:
 Deploy on Demo
 --------------
 
-Now that you have the release ready to go, give it one final test by deploying it on https://demo.dataverse.org . Note that this is also an opportunity to re-test the upgrade checklist as described in the release note. 
+Now that you have the release ready to go, consider giving it one final test by deploying it on https://demo.dataverse.org. Note that this is also an opportunity to re-test the upgrade checklist as described in the release note.
 
 Publish the Release
 -------------------
@@ -194,7 +202,7 @@ ssh into the guides server and update the symlink to point to the latest release
   cd /var/www/html/en
   ln -s 5.10.1 latest
 
-
+This step could be done before publishing the release if you'd like to double check that links in the release notes work.
 
 Close Milestone on GitHub and Create a New One
 ----------------------------------------------