Merge remote-tracking branch 'IQSS/develop' into DANS_Performance2

doc/release-notes/10901deaccessioned file edit fix.md

@@ -0,0 +1 @@
+When a dataset was deaccessioned and was the only previous version it will cause an error when trying to update the files. 

doc/release-notes/9408-fix-facets-labels-not-translated-in-result-block.md

@@ -0,0 +1,7 @@
+## 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)

doc/release-notes/9650-5-improve-list-linked-dataverses-API.md

@@ -0,0 +1,5 @@
+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.

doc/sphinx-guides/source/admin/dataverses-datasets.rst

@@ -129,15 +129,21 @@ Lists the link(s) created between a dataset and a Dataverse collection (see the
 
     curl -H "X-Dataverse-key: $API_TOKEN" http://$SERVER/api/datasets/$linked-dataset-id/links
 
-It returns a list in the following format:
+It returns a list in the following format (new format as of v6.4):
 
 .. code-block:: json
 
   {
     "status": "OK",
     "data": {
-      "dataverses that link to dataset id 56782": [
-        "crc990 (id 18802)"
+      "id": 5,
+      "identifier": "FK2/OTCWMM",
+      "linked-dataverses": [
+        {
+          "id": 2,
+          "alias": "dataverse1",
+          "displayName": "Lab experiments 2023 June"
+        }
       ]
     }
   }

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

@@ -12,7 +12,7 @@ v6.4
 
 - **/api/datasets/$dataset-id/modifyRegistration**: Changed from GET to POST
 - **/api/datasets/modifyRegistrationPIDMetadataAll**: Changed from GET to POST
-
+- **/api/datasets/{identifier}/links**: The GET endpoint returns a list of Dataverses linked to the given Dataset. The format of the response has changes for v6.4 making it backward incompatible.
 
 v6.3
 ----

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

@@ -333,15 +333,20 @@ public DatasetVersion getLatestVersion() {
         return getVersions().get(0);
     }
 
-    public DatasetVersion getLatestVersionForCopy() {
+    public DatasetVersion getLatestVersionForCopy(boolean includeDeaccessioned) {
         for (DatasetVersion testDsv : getVersions()) {
-            if (testDsv.isReleased() || testDsv.isArchived()) {
+            if (testDsv.isReleased() || testDsv.isArchived() 
+                || (testDsv.isDeaccessioned() && includeDeaccessioned)) {
                 return testDsv;
             }
         }
         return getVersions().get(0);
     }
 
+    public DatasetVersion getLatestVersionForCopy(){
+        return getLatestVersionForCopy(false);
+    }
+
     public List<DatasetVersion> getVersions() {
         return versions;
     }

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

@@ -2077,10 +2077,16 @@ public Response getLinks(@Context ContainerRequestContext crc, @PathParam("id")
             List<Dataverse> dvsThatLinkToThisDatasetId = dataverseSvc.findDataversesThatLinkToThisDatasetId(datasetId);
             JsonArrayBuilder dataversesThatLinkToThisDatasetIdBuilder = Json.createArrayBuilder();
             for (Dataverse dataverse : dvsThatLinkToThisDatasetId) {
-                dataversesThatLinkToThisDatasetIdBuilder.add(dataverse.getAlias() + " (id " + dataverse.getId() + ")");
+                JsonObjectBuilder datasetBuilder = Json.createObjectBuilder();
+                datasetBuilder.add("id", dataverse.getId());
+                datasetBuilder.add("alias", dataverse.getAlias());
+                datasetBuilder.add("displayName", dataverse.getDisplayName());
+                dataversesThatLinkToThisDatasetIdBuilder.add(datasetBuilder.build());
             }
             JsonObjectBuilder response = Json.createObjectBuilder();
-            response.add("dataverses that link to dataset id " + datasetId, dataversesThatLinkToThisDatasetIdBuilder);
+            response.add("id", datasetId);
+            response.add("identifier", dataset.getIdentifier());
+            response.add("linked-dataverses", dataversesThatLinkToThisDatasetIdBuilder);
             return ok(response);
         } catch (WrappedResponse wr) {
             return wr.getResponse();

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

@@ -343,10 +343,10 @@ public Response deleteFileInDataset(@Context ContainerRequestContext crc, @PathP
             DataFile dataFile = findDataFileOrDie(fileIdOrPersistentId);
             FileMetadata fileToDelete = dataFile.getLatestFileMetadata();
             Dataset dataset = dataFile.getOwner();
-            DatasetVersion v = dataset.getOrCreateEditVersion();
+            dataset.getOrCreateEditVersion();
             deletePhysicalFile = !dataFile.isReleased();
 
-            UpdateDatasetVersionCommand update_cmd = new UpdateDatasetVersionCommand(dataset, dvRequest,  Arrays.asList(fileToDelete), v);
+            UpdateDatasetVersionCommand update_cmd = new UpdateDatasetVersionCommand(dataset, dvRequest,  Arrays.asList(fileToDelete));
             update_cmd.setValidateLenient(true);
 
             try {

src/main/java/edu/harvard/iq/dataverse/engine/command/impl/UpdateDatasetVersionCommand.java

@@ -126,7 +126,7 @@ public Dataset execute(CommandContext ctxt) throws CommandException {
         DatasetVersion latestVersion = theDataset.getLatestVersion();
         if(persistedVersion==null) {
             Long id = latestVersion.getId();
-            persistedVersion = ctxt.datasetVersion().find(id!=null ? id: getDataset().getLatestVersionForCopy().getId());
+            persistedVersion = ctxt.datasetVersion().find(id!=null ? id: getDataset().getLatestVersionForCopy(true).getId());
         }
         //Get or create (currently only when called with fmVarMet != null) a new edit version
         DatasetVersion editVersion = theDataset.getOrCreateEditVersion(fmVarMet);

src/main/java/edu/harvard/iq/dataverse/search/SearchIncludeFragment.java

@@ -34,6 +34,7 @@
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.MissingResourceException;
 import java.util.Optional;
 import java.util.Set;
 import java.util.logging.Logger;
@@ -1231,40 +1232,33 @@ public String getTypeFromFilterQuery(String filterQuery) {
     }
 
     public List<String> getFriendlyNamesFromFilterQuery(String filterQuery) {
-
-
-        if ((filterQuery == null)||
-            (datasetfieldFriendlyNamesBySolrField == null)||
-            (staticSolrFieldFriendlyNamesBySolrField==null)){
+
+        if ((filterQuery == null) ||
+                (datasetfieldFriendlyNamesBySolrField == null) ||
+                (staticSolrFieldFriendlyNamesBySolrField == null)) {
             return null;
         }
-        
-        if(!filterQuery.contains(":")) {
+
+        if (!filterQuery.contains(":")) {
             return null;
         }
-        
+
         int index = filterQuery.indexOf(":");
         String key = filterQuery.substring(0,index);
         String value = filterQuery.substring(index+1);
 
-        List<String> friendlyNames = new ArrayList<>();
+        // friendlyNames get 2 entries : key and value
+        List<String> friendlyNames = new ArrayList<>(2);
 
+        // Get dataset field friendly name from default ressource bundle file
         String datasetfieldFriendyName = datasetfieldFriendlyNamesBySolrField.get(key);
         if (datasetfieldFriendyName != null) {
             friendlyNames.add(datasetfieldFriendyName);
         } else {
+            // Get non dataset field friendly name from "staticSearchFields" ressource bundle file
             String nonDatasetSolrField = staticSolrFieldFriendlyNamesBySolrField.get(key);
             if (nonDatasetSolrField != null) {
                 friendlyNames.add(nonDatasetSolrField);
-            } else if (key.equals(SearchFields.PUBLICATION_STATUS)) {
-                /**
-                 * @todo Refactor this quick fix for
-                 * https://github.com/IQSS/dataverse/issues/618 . We really need
-                 * to get rid of all the reflection that's happening with
-                 * solrQueryResponse.getStaticSolrFieldFriendlyNamesBySolrField()
-                 * and
-                 */
-                friendlyNames.add("Publication Status");
             } else {
                 // meh. better than nuthin'
                 friendlyNames.add(key);
@@ -1276,9 +1270,13 @@ public List<String> getFriendlyNamesFromFilterQuery(String filterQuery) {
         String valueWithoutQuotes = noTrailingQuote;
 
         if (key.equals(SearchFields.METADATA_TYPES) && getDataverse() != null && getDataverse().getMetadataBlockFacets() != null) {
-            Optional<String> friendlyName = getDataverse().getMetadataBlockFacets().stream().filter(block -> block.getMetadataBlock().getName().equals(valueWithoutQuotes)).findFirst().map(block -> block.getMetadataBlock().getLocaleDisplayFacet());
+            Optional<String> friendlyName = getDataverse().getMetadataBlockFacets()
+                    .stream()
+                    .filter(block -> block.getMetadataBlock().getName().equals(valueWithoutQuotes))
+                    .findFirst()
+                    .map(block -> block.getMetadataBlock().getLocaleDisplayFacet());
             logger.fine(String.format("action=getFriendlyNamesFromFilterQuery key=%s value=%s friendlyName=%s", key, value, friendlyName));
-            if(friendlyName.isPresent()) {
+            if (friendlyName.isPresent()) {
                 friendlyNames.add(friendlyName.get());
                 return friendlyNames;
             }
@@ -1290,7 +1288,15 @@ public List<String> getFriendlyNamesFromFilterQuery(String filterQuery) {
             }
         }
 
-        friendlyNames.add(valueWithoutQuotes);
+        // Get value friendly name from default ressource bundle file
+        String valueFriendlyName;
+        try {
+            valueFriendlyName = BundleUtil.getStringFromPropertyFile(noTrailingQuote, "Bundle");
+        } catch (MissingResourceException e) {
+            valueFriendlyName = noTrailingQuote;
+        }
+
+        friendlyNames.add(valueFriendlyName);
         return friendlyNames;
     }
 

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

@@ -667,6 +667,60 @@ public void testCreatePublishDestroyDataset() {
         deleteDatasetResponse.prettyPrint();
         assertEquals(200, deleteDatasetResponse.getStatusCode());
 
+        // Start of test of deleting a file from a deaccessioned version.
+
+        // Create Dataset for deaccession test.
+        Response deaccessionTestDataset = UtilIT.createRandomDatasetViaNativeApi(dataverseAlias, apiToken);
+        deaccessionTestDataset.prettyPrint();
+        deaccessionTestDataset.then().assertThat().statusCode(CREATED.getStatusCode());
+        Integer deaccessionTestDatasetId = UtilIT.getDatasetIdFromResponse(deaccessionTestDataset);
+
+        // File upload for deaccession test.
+        String pathToFile = "src/main/webapp/resources/images/dataverseproject.png";   
+        Response uploadResponse = UtilIT.uploadFileViaNative(deaccessionTestDatasetId.toString(), pathToFile, apiToken);
+        uploadResponse.prettyPrint();
+        uploadResponse.then().assertThat().statusCode(OK.getStatusCode());
+        Integer deaccessionTestFileId = JsonPath.from(uploadResponse.body().asString()).getInt("data.files[0].dataFile.id");
+
+        // Publish Dataset for deaccession test.
+        Response deaccessionTestPublishResponse = UtilIT.publishDatasetViaNativeApi(deaccessionTestDatasetId, "major", apiToken);
+        deaccessionTestPublishResponse.prettyPrint();
+
+        // Deaccession Dataset for deaccession test.
+        Response deaccessionTestDatasetResponse = UtilIT.deaccessionDataset(deaccessionTestDatasetId, DS_VERSION_LATEST_PUBLISHED, "Test deaccession reason.", null, apiToken);
+        deaccessionTestDatasetResponse.prettyPrint();
+        deaccessionTestDatasetResponse.then().assertThat().statusCode(OK.getStatusCode());
+
+        // Version check for deaccession test - Deaccessioned.
+        Response deaccessionTestVersions = UtilIT.getDatasetVersions(deaccessionTestDatasetId.toString(), apiToken);
+        deaccessionTestVersions.prettyPrint();
+        deaccessionTestVersions.then().assertThat()
+                .body("data[0].latestVersionPublishingState", equalTo("DEACCESSIONED"))
+                .statusCode(OK.getStatusCode());
+
+        // File deletion / Draft creation due diligence check for deaccession test.
+        Response deaccessionTestDeleteFile =  UtilIT.deleteFileInDataset(deaccessionTestFileId, apiToken);
+        deaccessionTestDeleteFile.prettyPrint();
+        deaccessionTestDeleteFile
+                .then().assertThat()
+                .statusCode(OK.getStatusCode());
+
+        // Version check for deaccession test - Draft.
+        deaccessionTestVersions = UtilIT.getDatasetVersions(deaccessionTestDatasetId.toString(), apiToken);
+        deaccessionTestVersions.prettyPrint();
+        deaccessionTestVersions.then().assertThat()
+                .body("data[0].latestVersionPublishingState", equalTo("DRAFT"))
+                .statusCode(OK.getStatusCode());
+
+        // Deleting Dataset for deaccession test.
+        Response deaccessionTestDelete = UtilIT.destroyDataset(deaccessionTestDatasetId, apiToken);
+        deaccessionTestDelete.prettyPrint();
+        deaccessionTestDelete.then()
+                .assertThat()
+                .statusCode(OK.getStatusCode());
+
+        //  End of deaccession test.
+
         Response deleteDataverseResponse = UtilIT.deleteDataverse(dataverseAlias, apiToken);
         deleteDataverseResponse.prettyPrint();
         assertEquals(200, deleteDataverseResponse.getStatusCode());
@@ -2963,6 +3017,34 @@ public void testLinkingDatasets() {
         linkDataset.then().assertThat()
                 .statusCode(OK.getStatusCode());
 
+        // Link another to test the list of linked datasets
+        Response createDataverse3 = UtilIT.createRandomDataverse(apiToken);
+        createDataverse3.prettyPrint();
+        createDataverse3.then().assertThat()
+                .statusCode(CREATED.getStatusCode());
+        String dataverse3Alias = UtilIT.getAliasFromResponse(createDataverse3);
+        Integer dataverse3Id = UtilIT.getDatasetIdFromResponse(createDataverse3);
+        linkDataset = UtilIT.linkDataset(datasetPid, dataverse3Alias, superuserApiToken);
+        linkDataset.prettyPrint();
+        linkDataset.then().assertThat()
+                .statusCode(OK.getStatusCode());
+        // get the list in Json format
+        Response linkDatasetsResponse = UtilIT.getDatasetLinks(datasetPid, superuserApiToken);
+        linkDatasetsResponse.prettyPrint();
+        linkDatasetsResponse.then().assertThat()
+                .statusCode(OK.getStatusCode());
+        JsonObject linkDatasets = Json.createReader(new StringReader(linkDatasetsResponse.asString())).readObject();
+        JsonArray lst = linkDatasets.getJsonObject("data").getJsonArray("linked-dataverses");
+        List<Integer> ids = List.of(dataverse2Id, dataverse3Id);
+        List<Integer> uniqueids = new ArrayList<>();
+        assertEquals(ids.size(), lst.size());
+        for (int i = 0; i < lst.size(); i++) {
+            int id = lst.getJsonObject(i).getInt("id");
+            assertTrue(ids.contains(id));
+            assertFalse(uniqueids.contains(id));
+            uniqueids.add(id);
+        }
+
 //Experimental code for trying to trick test into thinking the dataset has been harvested
 /*
 createDataset = UtilIT.createRandomDatasetViaNativeApi(dataverse1Alias, apiToken);

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

@@ -278,8 +278,8 @@ public void testMoveLinkedDataset() {
                 .body("message", equalTo("Use the query parameter forceMove=true to complete the move. This dataset is linked to the new host dataverse or one of its parents. This move would remove the link to this dataset. "));
 
         JsonObject linksBeforeData = Json.createReader(new StringReader(getLinksBefore.asString())).readObject();
-        assertEquals("OK", linksBeforeData.getString("status"));
-        assertEquals(dataverse2Alias + " (id " + dataverse2Id + ")", linksBeforeData.getJsonObject("data").getJsonArray("dataverses that link to dataset id " + datasetId).getString(0));
+        assertEquals(datasetId, linksBeforeData.getJsonObject("data").getInt("id"));
+        assertEquals(dataverse2Id, linksBeforeData.getJsonObject("data").getJsonArray("linked-dataverses").get(0).asJsonObject().getInt("id"));
 
         boolean forceMove = true;
         Response forceMoveLinkedDataset = UtilIT.moveDataset(datasetId.toString(), dataverse2Alias, forceMove, superuserApiToken);
@@ -308,8 +308,7 @@ public void testMoveLinkedDataset() {
 
         JsonObject linksAfterData = Json.createReader(new StringReader(getLinksAfter.asString())).readObject();
         assertEquals("OK", linksAfterData.getString("status"));
-        assertEquals(0, linksAfterData.getJsonObject("data").getJsonArray("dataverses that link to dataset id " + datasetId).size());
-
+        assertEquals(0, linksAfterData.getJsonObject("data").getJsonArray("linked-dataverses").size());
     }
 
     @Test