diff --git a/doc/release-notes/10117-guestbook-question-size-limit-raised.md b/doc/release-notes/10117-guestbook-question-size-limit-raised.md deleted file mode 100644 index ab5e84d78fe..00000000000 --- a/doc/release-notes/10117-guestbook-question-size-limit-raised.md +++ /dev/null @@ -1 +0,0 @@ -Custom questions in Guestbooks can now be more than 255 characters and the bug causing a silent failure when questions were longer than this limit has been fixed. \ No newline at end of file diff --git a/doc/release-notes/10379-MetricsBugsFixes.md b/doc/release-notes/10379-MetricsBugsFixes.md deleted file mode 100644 index 0ebc6d99f0b..00000000000 --- a/doc/release-notes/10379-MetricsBugsFixes.md +++ /dev/null @@ -1,10 +0,0 @@ - -### 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. \ No newline at end of file diff --git a/doc/release-notes/10661-guestbook-email-bug-fix.md b/doc/release-notes/10661-guestbook-email-bug-fix.md deleted file mode 100644 index 05e70c9762a..00000000000 --- a/doc/release-notes/10661-guestbook-email-bug-fix.md +++ /dev/null @@ -1,4 +0,0 @@ - -### Guestbook Email Validation Bug fix - -Guestbook UI Form: Email address is now checked for valid email format diff --git a/doc/release-notes/10688_whitespace_trimming.md b/doc/release-notes/10688_whitespace_trimming.md deleted file mode 100644 index 52904c00fbf..00000000000 --- a/doc/release-notes/10688_whitespace_trimming.md +++ /dev/null @@ -1,6 +0,0 @@ -### Added whitespace trimming to uploaded custom metadata TSV files - -When loading custom metadata blocks using the `api/admin/datasetfield/load` API, whitespace can be introduced into field names. -This change trims whitespace at the beginning and end of all values read into the API before persisting them. - -For more information, see #10688. diff --git a/doc/release-notes/10697-improve-permission-indexing.md b/doc/release-notes/10697-improve-permission-indexing.md deleted file mode 100644 index b232b1c4d3c..00000000000 --- a/doc/release-notes/10697-improve-permission-indexing.md +++ /dev/null @@ -1,7 +0,0 @@ -### 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. diff --git a/doc/release-notes/10708 - MDC Citation and DOI parsing improvements.md b/doc/release-notes/10708 - MDC Citation and DOI parsing improvements.md deleted file mode 100644 index 86c1bb14d32..00000000000 --- a/doc/release-notes/10708 - MDC Citation and DOI parsing improvements.md +++ /dev/null @@ -1,3 +0,0 @@ -MDC Citation retrieval with the PID settings has been fixed. -PID parsing in Dataverse is now case insensitive, improving interaction with services that may change the case of PIDs. -Warnings related to managed/excluded PID lists for PID providers have been reduced diff --git a/doc/release-notes/10742-newest-oldest-sort-order-backwards.md b/doc/release-notes/10742-newest-oldest-sort-order-backwards.md deleted file mode 100644 index 0afaf45449d..00000000000 --- a/doc/release-notes/10742-newest-oldest-sort-order-backwards.md +++ /dev/null @@ -1,3 +0,0 @@ -## Minor bug fix to UI to fix the order of the files on the Dataset Files page when ordering by Date - -A fix was made to the ui to fix the ordering 'Newest' and 'Oldest' which were reversed diff --git a/doc/release-notes/10772-fix-importDDI-otherId.md b/doc/release-notes/10772-fix-importDDI-otherId.md deleted file mode 100644 index d5a9018b2b2..00000000000 --- a/doc/release-notes/10772-fix-importDDI-otherId.md +++ /dev/null @@ -1,2 +0,0 @@ -Bug Fix : -This PR fixes the `edu.harvard.iq.dataverse.util.json.JsonParseException: incorrect multiple for field otherId` error when DDI harvested data contains multiple ortherId. \ No newline at end of file diff --git a/doc/release-notes/10793-optimisticlockexception handling.md b/doc/release-notes/10793-optimisticlockexception handling.md deleted file mode 100644 index 3312063be8f..00000000000 --- a/doc/release-notes/10793-optimisticlockexception handling.md +++ /dev/null @@ -1,2 +0,0 @@ -Improvements have been made in handling the errors when a dataset has been edited in one window and an attempt is made to -edit/publish it in another. diff --git a/doc/release-notes/10814-Differencing improvement.md b/doc/release-notes/10814-Differencing improvement.md deleted file mode 100644 index 49bbdae3e1b..00000000000 --- a/doc/release-notes/10814-Differencing improvement.md +++ /dev/null @@ -1,3 +0,0 @@ -### More Scalable Dataset Version Differencing - -Differencing between dataset versions, which is done during dataset edit operations and to populate the dataset page versions table has been made signficantly more scalable. diff --git a/doc/release-notes/10837-exclude-others-ns-harvesting-oai-dc.md b/doc/release-notes/10837-exclude-others-ns-harvesting-oai-dc.md deleted file mode 100644 index c1826bfaed5..00000000000 --- a/doc/release-notes/10837-exclude-others-ns-harvesting-oai-dc.md +++ /dev/null @@ -1,3 +0,0 @@ -Some repository extend the "oai_dc" metadata prefix with specific namespaces. In this case, harvesting of these datasets is not possible, as an XML parsing error is raised. - -The PR [#10837](https://github.com/IQSS/dataverse/pull/10837) allows the harvesting of these datasets by excluding tags with namespaces that are not "dc:", and harvest only metadata with the "dc" namespace. diff --git a/doc/release-notes/10857-add-expiration-date-to-recreate-token-api.md b/doc/release-notes/10857-add-expiration-date-to-recreate-token-api.md deleted file mode 100644 index b450867c630..00000000000 --- a/doc/release-notes/10857-add-expiration-date-to-recreate-token-api.md +++ /dev/null @@ -1 +0,0 @@ -An optional query parameter called 'returnExpiration' has been added to the 'users/token/recreate' endpoint, which, if set to true, returns the expiration time in the response message. diff --git a/doc/release-notes/10886-update-to-conditions-to-display-image_url.md b/doc/release-notes/10886-update-to-conditions-to-display-image_url.md deleted file mode 100644 index 6dfe8eb9f2d..00000000000 --- a/doc/release-notes/10886-update-to-conditions-to-display-image_url.md +++ /dev/null @@ -1,8 +0,0 @@ -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. diff --git a/doc/release-notes/10888-add-api-for-comparing-dataset-versions.md b/doc/release-notes/10888-add-api-for-comparing-dataset-versions.md deleted file mode 100644 index b82441ee11a..00000000000 --- a/doc/release-notes/10888-add-api-for-comparing-dataset-versions.md +++ /dev/null @@ -1,21 +0,0 @@ -The following API have been added: - -/api/datasets/{persistentId}/versions/{versionId0}/compare/{versionId1} - -This API lists the changes between 2 dataset versions. The Json response shows the changes per field within the Metadata block and the Terms Of Access. Also listed are the files that have been added or removed. Files that have been modified will also display the new file data plus the fields that have been modified. -When compare includes an unpublished/draft version the api token must be associated with a user having view unpublished privileges -An error will be returned if VERSION0 was not created before VERSION1 - -Example of Metadata Block field change: -```json -{ - "blockName": "Life Sciences Metadata", - "changed": [ - { - "fieldName": "Design Type", - "oldValue": "", - "newValue": "Parallel Group Design; Nested Case Control Design" - } - ] -} -``` diff --git a/doc/release-notes/10889_bump_PG17_FlyWay10.md b/doc/release-notes/10889_bump_PG17_FlyWay10.md deleted file mode 100644 index 932c06fbc3d..00000000000 --- a/doc/release-notes/10889_bump_PG17_FlyWay10.md +++ /dev/null @@ -1,7 +0,0 @@ -This release bumps both the Postgres JDBC driver and Flyway versions. This should better support Postgres version 17, and as of version 10 Flyway no longer requires a paid subscription to support older versions of Postgres. - -While we don't encourage the use of older Postgres versions, this flexibility may benefit some of our long-standing installations in their upgrade paths. Postgres 13 remains the version used with automated testing. - -As part of this update, the containerized development environment now uses Postgres 17 instead of 16. Developers must delete their data (`rm -rf docker-dev-volumes`) and start with an empty database. They can rerun the quickstart in the dev guide. - -The Docker compose file used for [evaluations or demos](https://dataverse-guide--10912.org.readthedocs.build/en/10912/container/running/demo.html) has been upgraded from Postgres 13 to 17. diff --git a/doc/release-notes/10901deaccessioned file edit fix.md b/doc/release-notes/10901deaccessioned file edit fix.md deleted file mode 100644 index db12b1fc978..00000000000 --- a/doc/release-notes/10901deaccessioned file edit fix.md +++ /dev/null @@ -1 +0,0 @@ -When a dataset was deaccessioned and was the only previous version it will cause an error when trying to update the files. \ No newline at end of file diff --git a/doc/release-notes/10904-edit-dataverse-collection-endpoint.md b/doc/release-notes/10904-edit-dataverse-collection-endpoint.md deleted file mode 100644 index b9256941eea..00000000000 --- a/doc/release-notes/10904-edit-dataverse-collection-endpoint.md +++ /dev/null @@ -1 +0,0 @@ -Adds a new endpoint (`PUT /api/dataverses/`) for updating an existing Dataverse collection using a JSON file following the same structure as the one used in the API for the creation. diff --git a/doc/release-notes/10914-users-token-api-credentials.md b/doc/release-notes/10914-users-token-api-credentials.md deleted file mode 100644 index 888214481f6..00000000000 --- a/doc/release-notes/10914-users-token-api-credentials.md +++ /dev/null @@ -1,3 +0,0 @@ -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. diff --git a/doc/release-notes/10919-minor-DataCiteXML-bugfix.md b/doc/release-notes/10919-minor-DataCiteXML-bugfix.md deleted file mode 100644 index 4fa0c1142b1..00000000000 --- a/doc/release-notes/10919-minor-DataCiteXML-bugfix.md +++ /dev/null @@ -1 +0,0 @@ -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. diff --git a/doc/release-notes/10939-i18n-docker.md b/doc/release-notes/10939-i18n-docker.md deleted file mode 100644 index d9887b684db..00000000000 --- a/doc/release-notes/10939-i18n-docker.md +++ /dev/null @@ -1,5 +0,0 @@ -## 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 diff --git a/doc/release-notes/10947-unpublished-files-appearing-in-search-results-for-anon-user.md b/doc/release-notes/10947-unpublished-files-appearing-in-search-results-for-anon-user.md deleted file mode 100644 index 66ea04b124f..00000000000 --- a/doc/release-notes/10947-unpublished-files-appearing-in-search-results-for-anon-user.md +++ /dev/null @@ -1,11 +0,0 @@ -## 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. diff --git a/doc/release-notes/10969-order-subfields-version-difference.md b/doc/release-notes/10969-order-subfields-version-difference.md deleted file mode 100644 index 3f245ebe069..00000000000 --- a/doc/release-notes/10969-order-subfields-version-difference.md +++ /dev/null @@ -1,2 +0,0 @@ -Bug Fix: -In order to facilitate the comparison between the draft version and the published version of a dataset, a sort on subfields has been added (#10969) \ No newline at end of file diff --git a/doc/release-notes/10977-globus-filesize-lookup.md b/doc/release-notes/10977-globus-filesize-lookup.md deleted file mode 100644 index 49fd10d9ffe..00000000000 --- a/doc/release-notes/10977-globus-filesize-lookup.md +++ /dev/null @@ -1,6 +0,0 @@ -## A new Globus optimization setting - -An optimization has been added for the Globus upload workflow, with a corresponding new database setting: `:GlobusBatchLookupSize` - - -See the [Database Settings](https://guides.dataverse.org/en/6.5/installation/config.html#GlobusBatchLookupSize) section of the Guides for more information. \ No newline at end of file diff --git a/doc/release-notes/11012-get-dataverse-api-ext.md b/doc/release-notes/11012-get-dataverse-api-ext.md deleted file mode 100644 index 641aa373174..00000000000 --- a/doc/release-notes/11012-get-dataverse-api-ext.md +++ /dev/null @@ -1 +0,0 @@ -The JSON payload of the getDataverse endpoint has been extended to include properties isMetadataBlockRoot and isFacetRoot. diff --git a/doc/release-notes/11018-update-dataverse-endpoint-update.md b/doc/release-notes/11018-update-dataverse-endpoint-update.md deleted file mode 100644 index c2d9cf64af3..00000000000 --- a/doc/release-notes/11018-update-dataverse-endpoint-update.md +++ /dev/null @@ -1,8 +0,0 @@ -The updateDataverse API endpoint has been updated to support an "inherit from parent" configuration for metadata blocks, facets, and input levels. - -When it comes to omitting any of these fields in the request JSON: - -- Omitting ``facetIds`` or ``metadataBlockNames`` causes the Dataverse collection to inherit the corresponding configuration from its parent. -- Omitting ``inputLevels`` removes any existing custom input levels in the Dataverse collection. - -Previously, not setting these fields meant keeping the existing ones in the Dataverse. diff --git a/doc/release-notes/11049-oai-identifiers-as-pids.md b/doc/release-notes/11049-oai-identifiers-as-pids.md deleted file mode 100644 index 8b53a461a70..00000000000 --- a/doc/release-notes/11049-oai-identifiers-as-pids.md +++ /dev/null @@ -1,5 +0,0 @@ -## When harvesting, Dataverse can now use the identifier from the OAI-PMH record header as the persistent id for the harvested dataset. - -This will allow harvesting from sources that do not include a persistent id in their oai_dc metadata records, but use valid dois or handles as the OAI-PMH record header identifiers. - -It is also possible to optionally configure a harvesting client to use this OAI-PMH identifier as the **preferred** choice for the persistent id. See the [Harvesting Clients API](https://guides.dataverse.org/en/6.5/api/native-api.html#create-a-harvesting-client) section of the Guides, #11049 and #10982 for more information. \ No newline at end of file diff --git a/doc/release-notes/220-harvard-edu-audit-files.md b/doc/release-notes/220-harvard-edu-audit-files.md deleted file mode 100644 index fc857e3a02b..00000000000 --- a/doc/release-notes/220-harvard-edu-audit-files.md +++ /dev/null @@ -1,16 +0,0 @@ -### New API to Audit Datafiles across the database - -This is a superuser only API endpoint to audit Datasets with DataFiles where the physical files are missing or the file metadata is missing. -The Datasets scanned can be limited by optional firstId and lastId query parameters, or a given CSV list of Dataset Identifiers. -Once the audit report is generated, a superuser can either delete the missing file(s) from the Dataset or contact the author to re-upload the missing file(s). - -The JSON response includes: -- List of files in each DataFile where the file exists in the database but the physical file is not in the file store. -- List of DataFiles where the FileMetadata is missing. -- Other failures found when trying to process the Datasets - -curl -H "X-Dataverse-key:$API_TOKEN" "http://localhost:8080/api/admin/datafiles/auditFiles" -curl -H "X-Dataverse-key:$API_TOKEN" "http://localhost:8080/api/admin/datafiles/auditFiles?firstId=0&lastId=1000" -curl -H "X-Dataverse-key:$API_TOKEN" "http://localhost:8080/api/admin/datafiles/auditFiles?datasetIdentifierList=doi:10.5072/FK2/RVNT9Q,doi:10.5072/FK2/RVNT9Q" - -For more information, see [the docs](https://dataverse-guide--11016.org.readthedocs.build/en/11016/api/native-api.html#datafile-audit), #11016, and [#220](https://github.com/IQSS/dataverse.harvard.edu/issues/220) diff --git a/doc/release-notes/6.5-release-notes.md b/doc/release-notes/6.5-release-notes.md new file mode 100644 index 00000000000..2e27f4419bd --- /dev/null +++ b/doc/release-notes/6.5-release-notes.md @@ -0,0 +1,391 @@ +# Dataverse 6.5 + +Please note: To read these instructions in full, please go to https://github.com/IQSS/dataverse/releases/tag/v6.5 rather than the [list of releases](https://github.com/IQSS/dataverse/releases), which will cut them off. + +This release brings new features, enhancements, and bug fixes to Dataverse. Thank you to all of the community members who contributed code, suggestions, bug reports, and other assistance across the project! + +## Release Highlights + +Highlights for Dataverse 6.5 include: + +- new API endpoints, including editing of collections, Search API file counts, listing of exporters, comparing dataset versions, and auditing data files +- UX improvements, especially Preview URLs +- increased harvesting flexibility +- performance gains +- a [security vulnerability](https://github.com/IQSS/dataverse-security/issues/98) addressed +- many bug fixes +- and more! Please see below. + +## Features Added + +### Private URL Renamed to Preview URL and Improved + +The name of the URL that may be used by dataset administrators to share a draft version of a dataset has been changed from Private URL to Preview URL. + +Also, additional information about the creation of Preview URLs has been added to the popup accessed via edit menu of the Dataset Page. + +Users of the Anonymous Preview URL will no longer be able to see the name of the Dataverse that the dataset is in but will be able to see the name of the repository. + +Any Private URLs created in previous versions of Dataverse will continue to work. + +The old "privateUrl" API endpoints for the creation and deletion of Preview (formerly Private) URLs have been deprecated. They will continue to work but please switch to the "previewUrl" equivalents that have been [documented](https://guides.dataverse.org/en/6.5/api/native-api.html#create-a-preview-url-for-a-dataset) in the API Guide. + +See also #8184, #8185, #10950, #10961, and #11085. + +### Showing Differences Between Dataset Versions is More Scalable + +Showing differences between dataset versions, which is done during dataset edit operations and to populate the dataset page versions table, has been made significantly more scalable. See #10814 and #10818. + +### Version Differences Details Sorting Added + +In order to facilitate the comparison between the draft version and the published version of a dataset, a sort on subfields has been added. See #10969. + +### Reindexing After a Role Assignment is Less Memory Intensive + +Adding or 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. A Solr reindexing step is included in the upgrade instructions below. See also #10697 and #10698. + +### Longer Custom Questions in Guestbooks + +Custom questions in Guestbooks can now be more than 255 characters and the bug causing a silent failure when questions were longer than this limit has been fixed. See also #9492, #10117, #10118. + +### PostgreSQL and Flyway Updates + +This release bumps the version of PostgreSQL and Flyway used in containers as well as the PostgreSQL JDBC driver used all installations, including classic (non-Docker) installations. PostgreSQL and its driver have been bumped to version 17. Flyway has been bumped to version 10. + +PostgreSQL 13 remains the version used with automated testing, leading us to continue to [recommend](https://guides.dataverse.org/en/6.5/installation/prerequisites.html#postgresql) that version for classic installations. + +As of Flyway 10, supporting older versions of PostgreSQL no longer requires a paid subscription. While we don't encourage the use of older PostgreSQL versions, this flexibility may benefit some of our long-standing installations in their upgrade paths. + +As part of this update, the containerized development environment now uses Postgres 17 instead of 16. Developers must delete their data (`rm -rf docker-dev-volumes`) and start with an empty database (rerun the [quickstart](https://guides.dataverse.org/en/6.5/developers/dev-environment.html#quickstart) in the dev guide), as [explained](https://groups.google.com/g/dataverse-dev/c/ffoNj5UXyzU/m/nE5oGY_sAQAJ) on the dev mailing list. + +The Docker compose file used for [evaluations or demos](https://guides.dataverse.org/en/6.4/container/running/demo.html) has been upgraded from Postgres 13 to 17. + +See also #10889 and #10912. + +### Harvesting "oai_dc" Metadata Prefix When Extended With Specific Namespaces + +Some data repositories extend the "oai_dc" metadata prefix with specific namespaces. In this case, harvesting of these datasets into Dataverse was not possible because an XML parsing error was raised. + +Harvesting of these datasets has been fixed by excluding tags with namespaces that are not "dc:". That is, only harvesting metadata with the "dc" namespace. See #10837. + +### Harvested Dataset PID from Record Header + +When harvesting, Dataverse can now use the identifier from the OAI-PMH record header as the persistent id for the harvested dataset. + +This will allow harvesting from sources that do not include a persistent id in their oai_dc metadata records, but use valid DOIs or handles as the OAI-PMH record header identifiers. + +It is also possible to optionally configure a harvesting client to use this OAI-PMH identifier as the **preferred** choice for the persistent id. See the [Harvesting Clients API](https://guides.dataverse.org/en/6.5/api/native-api.html#create-a-harvesting-client) section of the Guides, #11049 and #10982 for more information. + +### Harvested Datasets Can Have Multiple "otherId" Values + +When harvesting using the DDI format, datasets can now have multiple "otherId" values. See #10772. + +### Multiple Languages in Docker + +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 [the tutorial](https://guides.dataverse.org/en/6.5/container/running/demo.html#multiple-languages), #10939, and #10940. + +### GlobusBatchLookupSize + +An optimization has been added for the Globus upload workflow, with a corresponding new database setting: `:GlobusBatchLookupSize` + +See the [Database Settings](https://guides.dataverse.org/en/6.5/installation/config.html#GlobusBatchLookupSize) section of the guides, #10977, and #11040 for more information. + +## Bugs Fixed + +### Relation Type (Related Publication) and DataCite + +The subfield "Relation Type" was added to the field "Related Publication" in Dataverse 6.4 (#10632) but couldn't be used without workarounds described in an [announcement](https://groups.google.com/g/dataverse-community/c/zlRGJtu3x4g/m/GtVZ26uaBQAJ) about the problem. The bug has been fixed and workarounds are no longer required. See #10926 and the announcement above. + +### Sort Order for Files + +"Newest" and "Oldest" were reversed when sorting files on the dataset landing page. This has been fixed. See #10742 and #11000. + +### Guestbook Email Validation + +In the Guestbook UI form, the email address is now checked for validity. See #10661 and #11022. + +### Updating Files Now Possible When Latest and Only Dataset Version is Deaccessioned + +When a dataset was deaccessioned, and was the only previous version, it would cause an error when trying to update the files. This has been fixed. See #9351 and #10901. + +### My Data Filter by Username Feature Restored + +The superuser-only feature of filtering by a username on the My Data page was not working. Entering a username in the "Results for Username" field now returns data for the desired user. See also #7239 and #10980. + +### Better Handling of Parallel Edit/Publish Errors + +Improvements have been made in handling the errors when a dataset has been edited in one browser window and an attempt is made to edit or publish it in another. (This practice is discouraged, by the way.) See #10793 and #10794. + +### Facets Filter Labels Now Translated Above Search Results + +On the main page, it's possible to filter results using search facets. If internationalization (i18n) has been enabled in the Dataverse installation, allowing pages to be displayed in several languages, the facets were correctly translated in the filter column at the left. However, they were not being translated above the search results, remaining in the default language, English. This has been fixed. See #9408 and #10158. + +### Unpublished File Bug Fix Related to Deaccessioning + +A bug fix was made related to retrieval of 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. In the upgrade instructions below, there is a step to reindex Solr. See also #10947 and #10974. + +### Minor DataCiteXML Fix (Useless Null) + +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/6.5/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/6.5/admin/metadataexport.html#batch-exports-through-the-api). See "Pushing updated metadata to DataCite" in the upgrade instructions below. See also #10919. + +### PIDs and Make Data Count Citation Retrieval + +Make Data Count (MDC) citation retrieval with the PID settings has been fixed. PID parsing in Dataverse is now case insensitive, improving interaction with services that may change the case of PIDs. Warnings related to managed/excluded PID lists for PID providers have been reduced. See #10708. + +### Quirk in Overview Display When Using External Controlled Variables + +This bugfix corrects an issue when there are duplicated entries on the metadata page. It is fixed by correcting an IF-clause in metadataFragment.xhtml. See #11005 and #11034. + +### Globus "missing properties" Logging Fixed + +In previous releases, logging would show Globus-related strings were missing from properties files. This has been fixed. See #11030. + +## API Updates + +### Editing Collections + +A new endpoint (`PUT /api/dataverses/`) for updating an existing collection (dataverse) has been added. It uses the same JSON structure as the one used for collection creation. See also [the docs](https://guides.dataverse.org/en/6.5/api/native-api.html#update-a-dataverse-collection), #10904, and #10925. + +### fileCount Added to Search API + +A new search field called `fileCount` can be searched to discover the number of files per dataset. The upgrade instructions below explain how to update your Solr `schema.xml` file to add the new field and reindex Solr. See also #8941 and #10598. + +### List Dataset Metadata Exporters + +A list of available dataset metadata exporters can now be retrieved programmatically via API. See [the docs](https://guides.dataverse.org/en/6.5/api/native-api.html#get-export-formats) and #10739. + +### Comparing Dataset Versions + +An API has been added to compare dataset versions. See [the docs](https://guides.dataverse.org/en/6.5/api/native-api.html#compare-versions-of-a-dataset), #10888, and #10945. + +### Audit Data Files + +A superuser-only API endpoint has been added to audit datasets with data files where the physical files are missing or the file metadata is missing. See [the docs](https://guides.dataverse.org/en/6.5/api/native-api.html#datafile-audit), #11016, and [#220](https://github.com/IQSS/dataverse.harvard.edu/issues/220). + +### Update Collection API Inheritance + +The update collection (dataverse) API endpoint has been updated to support an "inherit from parent" configuration for metadata blocks, facets, and input levels. + +Previously, not setting these fields meant using a copy of the settings from the parent collection, which could get out of sync. See also [the docs](https://guides.dataverse.org/en/6.5/api/native-api.html#update-a-dataverse-collection), #11018, and #11026. + +### isMetadataBlockRoot and isFacetRoot + +The JSON payload of the "get collection" endpoint has been extended to include properties isMetadataBlockRoot and isFacetRoot. See also [the docs](https://guides.dataverse.org/en/6.5/api/native-api.html#view-a-dataverse-collection), #11012, and #11013. + +### Whitespace Trimming When Loading Metadata Block TSV Files + +When loading custom metadata blocks using the `api/admin/datasetfield/load` API endpoint, whitespace can be introduced into field names. Whitespace is now trimmed from the beginning and end of all values read into the API before persisting them. See #10688 and #10696. + +### Image URLs from the Search API + +As of 6.4 (#10855) `image_url` is being returned from the Search API. The logic has been updated to only show the image if each of the following are true: + +1. The data file is not harvested +2. A thumbnail is available for the data file +3. If the data file is restricted, then the caller must have DownloadFile permission for the data file +4. The data file is NOT actively embargoed +5. The data file's retention period has NOT expired + +See also #10875 and #10886. + +### Metrics API Bug Fixes + +Two bugs in the Metrics API have been fixed: + +- The /datasets and /datasets/byMonth endpoints could report incorrect values if or 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 whose calculation relied on finding the latest published dataset version were incorrect if/when the minor version number was > 9. + +The upgrade instructions below include a step for clearing the metrics cache. + +See also #10379 and #10865. + +### API Tokens + +An optional query parameter called "returnExpiration" has been added to the `/api/users/token/recreate` endpoint, which, if set to true, returns the expiration time in the response. See [the docs](https://guides.dataverse.org/en/6.5/api/native-api.html#recreate-a-token), #10857 and #10858. + +The `/api/users/token` endpoint has been extended 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. See #10914 and #10924. + +## Settings Added + +- `:GlobusBatchLookupSize` + +## Backward Incompatible Changes + +Generally speaking, see the [API Changelog](https://guides.dataverse.org/en/latest/api/changelog.html) for a list of backward-incompatible API changes. + +### List Collections Linked to a Dataset + +The API endpoint that returns a list of collections that a dataset has been linked to has been improved to provide a more structured JSON response. See [the docs](https://guides.dataverse.org/en/6.5/admin/dataverses-datasets.html#list-collections-that-are-linked-from-a-dataset), #9650, and #9665. + +## Complete List of Changes + +For the complete list of code changes in this release, see the [6.5 milestone](https://github.com/IQSS/dataverse/issues?q=milestone%3A6.5+is%3Aclosed) in GitHub. + +## Getting Help + +For help with upgrading, installing, or general questions please post to the [Dataverse Community Google Group](https://groups.google.com/g/dataverse-community) or email support@dataverse.org. + +## Installation + +If this is a new installation, please follow our [Installation Guide](https://guides.dataverse.org/en/latest/installation/). Please don't be shy about [asking for help](https://guides.dataverse.org/en/latest/installation/intro.html#getting-help) if you need it! + +Once you are in production, we would be delighted to update our [map of Dataverse installations](https://dataverse.org/installations) around the world to include yours! Please [create an issue](https://github.com/IQSS/dataverse-installations/issues) or email us at support@dataverse.org to join the club! + +You are also very welcome to join the [Global Dataverse Community Consortium](https://www.gdcc.io/) (GDCC). + + +## Upgrade Instructions + +Upgrading requires a maintenance window and downtime. Please plan accordingly, create backups of your database, etc. + +These instructions assume that you've already upgraded through all the 5.x releases and are now running Dataverse 6.4. + +0\. These instructions assume that you are upgrading from the immediate previous version. If you are running an earlier version, the only supported way to upgrade is to progress through the upgrades to all the releases in between before attempting the upgrade to this version. + +If you are running Payara as a non-root user (and you should be!), **remember not to execute the commands below as root**. By default, Payara runs as the `dataverse` user. In the commands below, we use sudo to run the commands as a non-root user. + +Also, we assume that Payara 6 is installed in `/usr/local/payara6`. If not, adjust as needed. + +```shell +export PAYARA=/usr/local/payara6 +``` + +(or `setenv PAYARA /usr/local/payara6` if you are using a `csh`-like shell) + +1\. List deployed applications + +```shell +$PAYARA/bin/asadmin list-applications +``` + +2\. Undeploy the previous version (should match "list-applications" above) + +```shell +$PAYARA/bin/asadmin undeploy dataverse-6.4 +``` + +3\. Stop and start Payara + +```shell +sudo service payara stop +sudo service payara start +``` + +4\. Download and deploy this version + +```shell +wget https://github.com/IQSS/dataverse/releases/download/v6.5/dataverse-6.5.war +$PAYARA/bin/asadmin deploy dataverse-6.5.war +``` + +Note: if you have any trouble deploying, stop Payara, remove the following directories, start Payara, and try to deploy again. + +```shell +sudo service payara stop +sudo rm -rf $PAYARA/glassfish/domains/domain1/generated +sudo rm -rf $PAYARA/glassfish/domains/domain1/osgi-cache +sudo rm -rf $PAYARA/glassfish/domains/domain1/lib/databases +``` + +5\. For installations with internationalization: + +Please remember to update translations via [Dataverse language packs](https://github.com/GlobalDataverseCommunityConsortium/dataverse-language-packs). + +6\. Restart Payara + +```shell +sudo service payara stop +sudo service payara start +``` +7\. Update Solr schema.xml file. Start with the standard v6.5 schema.xml, then, if your installation uses any custom or experimental metadata blocks, update it to include the extra fields (step 7a). + +Run the commands below as a non-root user. + +Stop Solr (usually `sudo service solr stop`, depending on Solr installation/OS, see the [Installation Guide](https://guides.dataverse.org/en/6.5/installation/prerequisites.html#solr-init-script)). + +```shell +sudo service solr stop +``` + +Replace schema.xml + +Please note that the path to Solr may differ from the example below. + +```shell +wget https://raw.githubusercontent.com/IQSS/dataverse/v6.5/conf/solr/schema.xml +sudo cp schema.xml /usr/local/solr/solr-9.4.1/server/solr/collection1/conf +``` + +Start Solr (but if you use any custom metadata blocks, perform the next step, 7a first). + +```shell +sudo service solr start +``` + +7a\. For installations with custom or experimental metadata blocks: + +Before starting Solr, update the `schema.xml` file to include all the extra metadata fields that your installation uses. + +We do this by collecting the output of Dataverse's Solr schema API endpoint (`/api/admin/index/solr/schema`) and piping it to the `update-fields.sh` script which updates the `schema.xml` file supplied as an argument. + +The example below assumes the default installation location of Solr, but you can modify the commands as needed. + +```shell +wget https://raw.githubusercontent.com/IQSS/dataverse/v6.5/conf/solr/update-fields.sh +chmod +x update-fields.sh +curl "http://localhost:8080/api/admin/index/solr/schema" | sudo ./update-fields.sh /usr/local/solr/solr-9.4.1/server/solr/collection1/conf/schema.xml +``` + +Now start Solr. + + +```shell +sudo service solr start +``` + +8\. Reindex Solr + +Below is the simplest way to reindex Solr: + +```shell +curl http://localhost:8080/api/admin/index +``` + +The API above rebuilds the existing index. If you want to be absolutely sure that your index is up-to-date and consistent, you may consider wiping it clean and reindexing everything from scratch (see [the guides](https://guides.dataverse.org/en/latest/admin/solr-search-index.html)). Just note that, depending on the size of your database, a full reindex may take a while and the users will be seeing incomplete search results during that window. + +9\. Run reExportAll to update dataset metadata exports + +Below is the simple way to reexport all dataset metadata. For more advanced usage, please see [the guides](http://guides.dataverse.org/en/6.4/admin/metadataexport.html#batch-exports-through-the-api). + +```shell +curl http://localhost:8080/api/admin/metadata/reExportAll +``` + +10\. Clear metrics cache + +Run the [clearMetricsCache](https://guides.dataverse.org/en/6.5/api/native-api.html#metrics) API endpoint to remove old cached values that may be incorrect. + +```shell +curl -X DELETE http://localhost:8080/api/admin/clearMetricsCache +``` + +11\. Pushing updated metadata to DataCite + +(If you don't use DataCite, you can skip this. Also, if you aren't affected by the "useless null" bug described above, you can skip this.) + +Entries at DataCite for published datasets can be updated by a superuser using an API call (newly [documented](https://guides.dataverse.org/en/6.5/admin/dataverses-datasets.html#update-metadata-for-all-published-datasets-at-the-pid-provider)): + +`curl -X POST -H 'X-Dataverse-key:' http://localhost:8080/api/datasets/modifyRegistrationPIDMetadataAll` + +This will loop through all published datasets (and released files with PIDs). As long as the loop completes, the call will return a 200/OK response. Any PIDs for which the update fails can be found using the following command: + +`grep 'Failure for id' server.log` + +Failures may occur if PIDs were never registered, or if they were never made findable. Any such cases can be fixed manually in DataCite Fabrica or using the [Reserve a PID](https://guides.dataverse.org/en/6.4/api/native-api.html#reserve-a-pid) API call and the newly documented `/api/datasets//modifyRegistration` call respectively. See https://guides.dataverse.org/en/6.4/admin/dataverses-datasets.html#send-dataset-metadata-to-pid-provider. Please reach out with any questions. + +PIDs can also be updated by a superuser on a per-dataset basis using + +`curl -X POST -H 'X-Dataverse-key:' http://localhost:8080/api/datasets//modifyRegistrationMetadata` diff --git a/doc/release-notes/7239-mydata-results-by-username.md b/doc/release-notes/7239-mydata-results-by-username.md deleted file mode 100644 index fa1ce56d89e..00000000000 --- a/doc/release-notes/7239-mydata-results-by-username.md +++ /dev/null @@ -1,3 +0,0 @@ -## Fix My Data filter results by username for Administrators - -The filtering for the username on the MyData page was not working. This is only available for superusers. This fixes the "Results for Username" field to return the data for the desired user. See also #7239 and #10980. diff --git a/doc/release-notes/8184-rename-private-url.md b/doc/release-notes/8184-rename-private-url.md deleted file mode 100644 index 7acb03fd735..00000000000 --- a/doc/release-notes/8184-rename-private-url.md +++ /dev/null @@ -1,11 +0,0 @@ -###Private URL renamed Preview URL - -With this release the name of the URL that may be used by dataset administrators to share a draft version of a dataset has been changed from Private URL to Preview URL. - -Also, additional information about the creation of Preview URLs has been added to the popup accessed via edit menu of the Dataset Page. - -Any Private URLs created in previous versions of Dataverse will continue to work. - -The old "privateUrl" API endpoints for the creation and deletion of Preview (formerly Private) URLs have been deprecated. They will continue to work but please switch to the "previewUrl" equivalents that have been [documented](https://dataverse-guide--10961.org.readthedocs.build/en/10961/api/native-api.html#create-a-preview-url-for-a-dataset) in the API Guide. - -See also #8184, #8185, #10950, and #10961. diff --git a/doc/release-notes/8941-adding-fileCount-in-solr.md b/doc/release-notes/8941-adding-fileCount-in-solr.md deleted file mode 100644 index 164b91e6123..00000000000 --- a/doc/release-notes/8941-adding-fileCount-in-solr.md +++ /dev/null @@ -1,15 +0,0 @@ -## Release Highlights - -### Adding fileCount as SOLR field - -A new search field called `fileCount` can be searched to discover the number of files per dataset. (#10598) - -## Upgrade Instructions - -1. Update your Solr `schema.xml` to include the new field. -For details, please see https://guides.dataverse.org/en/latest/admin/metadatacustomization.html#updating-the-solr-schema - -2. Reindex Solr. -Once the schema.xml is updated, Solr must be restarted and a reindex initiated. -For details, see https://guides.dataverse.org/en/latest/admin/solr-search-index.html but here is the reindex command: -`curl http://localhost:8080/api/admin/index` diff --git a/doc/release-notes/9408-fix-facets-labels-not-translated-in-result-block.md b/doc/release-notes/9408-fix-facets-labels-not-translated-in-result-block.md deleted file mode 100644 index 344859e2dbd..00000000000 --- a/doc/release-notes/9408-fix-facets-labels-not-translated-in-result-block.md +++ /dev/null @@ -1,7 +0,0 @@ -## Fix facets filter labels not translated in result block - -On the main page, it's possible to filter results using search facets. If internationalization (i18n) has been activated in the Dataverse installation, allowing pages to be displayed in several languages, the facets are translated in the filter column. However, they aren't translated in the search results and remain in the default language, English. - -This version of Dataverse fix this, and includes internationalization in the facets visible in the search results section. - -For more information, see issue [#9408](https://github.com/IQSS/dataverse/issues/9408) and pull request [#10158](https://github.com/IQSS/dataverse/pull/10158) diff --git a/doc/release-notes/9650-5-improve-list-linked-dataverses-API.md b/doc/release-notes/9650-5-improve-list-linked-dataverses-API.md deleted file mode 100644 index 8c79955891b..00000000000 --- a/doc/release-notes/9650-5-improve-list-linked-dataverses-API.md +++ /dev/null @@ -1,5 +0,0 @@ -The following API have been added: - -/api/datasets/{datasetId}/links - -It lists the linked dataverses to a dataset. It can be executed only by administrators. \ No newline at end of file diff --git a/doc/release-notes/expose-export-formats.md b/doc/release-notes/expose-export-formats.md deleted file mode 100644 index a21906d7bbb..00000000000 --- a/doc/release-notes/expose-export-formats.md +++ /dev/null @@ -1,2 +0,0 @@ -# New API method for listing the available exporters -Found at `/api/info/exportFormats`, produces an object with available format names as keys, and as values an object with various info about the exporter. See also #10739. \ No newline at end of file diff --git a/src/main/webapp/metadataFragment.xhtml b/src/main/webapp/metadataFragment.xhtml index 723f95148cd..f8367ce01f8 100755 --- a/src/main/webapp/metadataFragment.xhtml +++ b/src/main/webapp/metadataFragment.xhtml @@ -130,7 +130,7 @@ - + v1files1 = with(v1.body().asString()).param("fileToFind", "cc0.png") @@ -2290,7 +2289,6 @@ public void testDeleteFile() { Response postv1draft2 = UtilIT.getDatasetVersion(datasetPid, DS_VERSION_DRAFT, apiToken); postv1draft2.prettyPrint(); postv1draft2.then().assertThat() - .body("data.files[0].dataFile.filename", equalTo("orcid_16x16.png")) .statusCode(OK.getStatusCode()); Map v1files2 = with(postv1draft2.body().asString()).param("fileToFind", "orcid_16x16.png")