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* initial semantic API endpoint * merge new fields with existing ones * differences from IQSS/develop that break compilation * Add jsonld lib to compact to local context * use expand/compact, refactor, add :startmigration endpoint * try fix for parse error * log value * return dataset * manage versionState, add debug output * move debug ore generation after configuring dataset * set versionstate, simplify, move terms init outside loop * parse version number * fix toStrings * debug null pointer in DataverseFieldTypeInputLevel * add support for fields with their own formal URI * allow non-published to support debugging and future use * refactor, use expanded version directly * add modification time * expanded has array with 1 val - handle it * log compound values to start * compact with no context for decontextualize * handle appending and compound fields * sort compound field children by display order * parse date/time correctly * Revert "sort compound field children by display order" This reverts commit 8596ac8. * typo * now use Uri instead of label when matching terms * set dsfield of dsfvalue * additional debug, always set display order * generate URIs for child types to match current ore maps * allow oremap to work w/o modified date for debug * null check on date itself * fix compound value iteration don't replace existing value - always add a new value, but, if not appending, clear the list of values to start * fix ttype map for terms with no uri - use title not name as is done currently in generating the ORE map * handle date format variations, including DV internal ones see note in Dataverses - using Date() versus Timestamp() causes a difference in precision and, perhaps surprisingly, a difference in the response from version.getLastUpdateTime().toString() in creating the OREmap. * and the format in current published bags * initial endpoint to release a migrated dataset * create metadataOnOrig field * add metadataOnOrig to solr * use Finalize Publication command Curate is for cases with an existing published version and migrated datasets only have 1 version Also - don't want to go through Publish command since it creates new version numbers, etc. * add debug, allow more details in 400 responses * fix date-time issue * typos * create transfer bag type with orig files handle no checksums on orig files * missing tab * add type param * add semantic metadata api call only * remove OREMap parameter * fix error handling FWIW: We have an error handler for the edu.harvard.iq.dataverse.util.json.JsonParseException class but not for javax.json.stream.JsonParsingException which was getting caught by the Throwable handler and returned as a 500 error with json message {} * append to current terms * add replace param * handle append on terms - fix cut/paste errors * fix logic * specify default * make replace still append for multiple val fields * add migrating switch * expose uri in datasetField api * track defined namespaces and avoid having contexts with specific entries for terms that are in a namespace already * define equals, avoid duplicates in list * replace string with const * constant for CC0_URI * GET/DELETE endpoints * 7130-handle missing contact name * Fix multiple description logic for info file * put is always for :draft version * don't cast to String[] * add more logging * handle unpublished versions * add method that can return JsonObjectBuilder which can be used with existing AbstractApiBean.ok() * log details on failure * multiple updates/fixes, added logging * fix terms retrieval * date test fixes for locale * Java 11 update and test fixes inc. for different exception mesg * update pom for v11 and running tests under 11 * fix for edu.harvard.iq.dataverse.api.AdminIT test fail in Java 11 The DV code tested in testLoadMetadataBlock_ErrorHandling assumed it could parse the message of an ArrayOutOfBounds exception as an it to determine the column that fails. This message is now a String. Rather than parse it (and fail if it changes), I modified the code so that the length of the values array is visible in the catch and can be sent directly (the first out of bounds index is if/when the index is values.length). * flyway script adding the new constraint (IQSS#7451) * A diagnostics script, to check and fix any duplicated harvested storageidentifiers, and re-check the local ones for any new dupes, just in case. (IQSS#7451) * A pre-release text for the new diagnostics script (will discuss the approach in the PR/dv-tech) (IQSS#7451) * Arming the script bomb... (IQSS#7451) * switched to a conditional constraint. (IQSS#7451) * Update PRE-RELEASE-INFO.txt * update StringUtils package * Do not count thumbnails and prep downloads, when redirecting to S3 (similarly to how these downloads are treated when done internally, without redirecting to the remote bucket, in line 457). IQSS#7924 * Implement usage of user supplied handle for authentication. This is an optional parameter. * Fix mising ";" coding error. * move metadataOnOrig out of citation block which makes it optional * IQSS#7431 remove XML prolog from the individual records of OAI-PMH ListRecords response * IQSS#7431 adding integration tests * Bump httpclient from 4.5.5 to 4.5.13 Bumps httpclient from 4.5.5 to 4.5.13. --- updated-dependencies: - dependency-name: org.apache.httpcomponents:httpclient dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * More forceful language in the "pre-release note" about the dvobject constraint being enforced on existing databases in the next release. (IQSS#7451) * renamed the flyway script for the dvobject constraint (since it didn't make it into 5.5) (IQSS#7451) * Better check HandleAuthHandle for default value of null. If unequal to null then use it. * Change "string" to "String" with uppercase first character * build(ci): atempt to fix coveralls report. IQSS#7977 * Change parameter "HandleAuthHandle" so it start with a lower case character when it is being assigned. * Update 5.3-release-notes.md Removed incorrect statement: (If you are using a PostgreSQL server on `localhost:5432`, you can omit `dataverse.db.host` and `dataverse.db.port`.) * sync with migration api branch (tests, docs, bug fixes) * rename SQL update script IQSS#7451 * prevent page from blowing up if no remind msg in bundle IQSS#7975 * get "create dataset" working again IQSS#7986 * remove TODO IQSS#7986 Per comment from Jim: "This works and doesn't break the anonymized access functionality as I thought it might." * add anonymized access methods * fix test * Update doc/release-notes/6497-semantic-api.md Co-authored-by: Philip Durbin <philipdurbin@gmail.com> * Update doc/sphinx-guides/source/developers/dataset-semantic-metadata-api.rst Co-authored-by: Philip Durbin <philipdurbin@gmail.com> * add create example, remove solr schema copies file * removed debug logging * missing header * Added an extra clause for some IQSS-specific harvested identifiers. Extremely unlikely to be encountered anywhere else; but need to be included to be able to QA on a copy of the prod. db. Plus some extr diagnostics. (IQSS#7451) * IQSS#7893 link Rserve documentation to necessary files in Dataverse repo * IQSS#7893 remove redundant script mention per feedback from Leonid * Adding -H + API token to curl commands Without ``-H`` and the API token in these curl commands, the native API rejects the user's requests on the ground that they are a 'guest'. * remove metadataOnOrig per review * IQSS#7893 use fixedwidthplain text instead, clone master instead of develop * fixes the small formatting issue with the link (IQSS#7893) * Update doc/sphinx-guides/source/api/native-api.rst Co-authored-by: Philip Durbin <philip_durbin@harvard.edu> * Update doc/sphinx-guides/source/api/native-api.rst Co-authored-by: Philip Durbin <philip_durbin@harvard.edu> * Update doc/sphinx-guides/source/api/native-api.rst Co-authored-by: Philip Durbin <philip_durbin@harvard.edu> * Update doc/sphinx-guides/source/api/native-api.rst Co-authored-by: Philip Durbin <philip_durbin@harvard.edu> * Update documentation to be more consise about the handle and give a better example. * IQSS#7936 append deaccessionDialog.reasons with periods for proper display * add missing create method (in migrate PR) * No "@id" npe fix * avoid npe in logging * only require "@id" when migrating * fix logging in create case * WIP * Temporary conflict solution * Added marker comments where code must be revised/fixed later '// TODO: FIX FOR MULTI-LICENSE' Co-authored-by: qqmyers <qqmyers@hotmail.com> Co-authored-by: Leonid Andreev <leonid@hmdc.harvard.edu> Co-authored-by: Gustavo Durand <scolapasta+github@gmail.com> Co-authored-by: Robert Verkerk <robert.verkerk@surfsara.nl> Co-authored-by: pkiraly <pkiraly@gwdg.de> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Oliver Bertuch <o.bertuch@fz-juelich.de> Co-authored-by: Kevin Condon <kcondon@hmdc.harvard.edu> Co-authored-by: Philip Durbin <philip_durbin@harvard.edu> Co-authored-by: Philip Durbin <philipdurbin@gmail.com> Co-authored-by: Don Sizemore <don.sizemore@gmail.com> Co-authored-by: Benjamin Peuch <benjamin.peuch@gmail.com> Co-authored-by: Jan van Mansum <janvanmansum@users.noreply.github.com>
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