Merge pull request IQSS#10172 from ErykKul/10116_incomplete_matadata_…

…label_setting 10116 incomplete matadata label setting
uncch-rdmc · May 14, 2024 · da3dd95 · da3dd95
2 parents ae78c04 + c40838c
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diff --git a/doc/release-notes/10116-incomplete-metadata-label-setting.md b/doc/release-notes/10116-incomplete-metadata-label-setting.md
@@ -0,0 +1 @@
+Bug fixed for the ``incomplete metadata`` label being shown for published dataset with incomplete metadata in certain scenarios. This label will now be shown for draft versions of such datasets and published datasets that the user can edit. This label can also be made invisible for published datasets (regardless of edit rights) with the new option ``dataverse.ui.show-validity-label-when-published`` set to `false`.
diff --git a/doc/sphinx-guides/source/installation/config.rst b/doc/sphinx-guides/source/installation/config.rst
@@ -2945,6 +2945,24 @@ Defaults to ``false``.
 Can also be set via any `supported MicroProfile Config API source`_, e.g. the environment variable
 ``DATAVERSE_API_ALLOW_INCOMPLETE_METADATA``. Will accept ``[tT][rR][uU][eE]|1|[oO][nN]`` as "true" expressions.
 
+.. _dataverse.ui.show-validity-label-when-published:
+
+dataverse.ui.show-validity-label-when-published
++++++++++++++++++++++++++++++++++++++++++++++++
+
+Even when you do not allow incomplete metadata to be saved in dataverse, some metadata may end up being incomplete, e.g., after making a metadata field mandatory. Datasets where that field is
+not filled out, become incomplete, and therefore can be labeled with the ``incomplete metadata`` label. By default, this label is only shown for draft datasets and published datasets that the
+user can edit. This option can be disabled by setting it to ``false`` where only draft datasets with incomplete metadata will have that label. When disabled, all published dataset will not have
+that label. Note that you need to reindex the datasets after changing the metadata definitions. Reindexing will update the labels and other dataset information according to the new situation.
+
+When enabled (by default), published datasets with incomplete metadata will have an ``incomplete metadata`` label attached to them, but only for the datasets that the user can edit.
+You can list these datasets, for example, with the validity of metadata filter shown in "My Data" page that can be turned on by enabling the :ref:`dataverse.ui.show-validity-filter` option.
+
+Defaults to ``true``.
+
+Can also be set via any `supported MicroProfile Config API source`_, e.g. the environment variable
+``DATAVERSE_API_SHOW_LABEL_FOR_INCOMPLETE_WHEN_PUBLISHED``. Will accept ``[tT][rR][uU][eE]|1|[oO][nN]`` as "true" expressions.
+
 .. _dataverse.signposting.level1-author-limit:
 
 dataverse.signposting.level1-author-limit
@@ -3142,6 +3160,8 @@ Defaults to ``false``.
 Can also be set via any `supported MicroProfile Config API source`_, e.g. the environment variable
 ``DATAVERSE_UI_ALLOW_REVIEW_FOR_INCOMPLETE``. Will accept ``[tT][rR][uU][eE]|1|[oO][nN]`` as "true" expressions.
 
+.. _dataverse.ui.show-validity-filter:
+
 dataverse.ui.show-validity-filter
 +++++++++++++++++++++++++++++++++
 

diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java
@@ -2296,13 +2296,11 @@ private void displayPublishMessage(){
 
     public boolean isValid() {
         if (valid == null) {
-            DatasetVersion version = dataset.getLatestVersion();
-            if (!version.isDraft()) {
+            if (workingVersion.isDraft() || (canUpdateDataset() && JvmSettings.UI_SHOW_VALIDITY_LABEL_WHEN_PUBLISHED.lookupOptional(Boolean.class).orElse(true))) {
+                valid = workingVersion.isValid();
+            } else {
                 valid = true;
             }
-            DatasetVersion newVersion = version.cloneDatasetVersion();
-            newVersion.setDatasetFields(newVersion.initDatasetFields());
-            valid = newVersion.isValid();
         }
         return valid;
     }

diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetVersion.java b/src/main/java/edu/harvard/iq/dataverse/DatasetVersion.java
@@ -1728,7 +1728,36 @@ public List<ConstraintViolation<DatasetField>> validateRequired() {
     }
 
     public boolean isValid() {
-        return validate().isEmpty();
+        // first clone to leave the original untouched
+        final DatasetVersion newVersion = this.cloneDatasetVersion();
+        // initDatasetFields
+        newVersion.setDatasetFields(newVersion.initDatasetFields());
+        // remove special "N/A" values and empty values
+        newVersion.removeEmptyValues();
+        // check validity of present fields and detect missing mandatory fields
+        return newVersion.validate().isEmpty();
+    }
+
+    private void removeEmptyValues() {
+        if (this.getDatasetFields() != null) {
+            for (DatasetField dsf : this.getDatasetFields()) {
+                removeEmptyValues(dsf);
+            }
+        }
+    }
+
+    private void removeEmptyValues(DatasetField dsf) {
+        if (dsf.getDatasetFieldType().isPrimitive()) { // primitive
+            final Iterator<DatasetFieldValue> i = dsf.getDatasetFieldValues().iterator();
+            while (i.hasNext()) {
+                final String v = i.next().getValue();
+                if (StringUtils.isBlank(v) || DatasetField.NA_VALUE.equals(v)) {
+                    i.remove();
+                }
+            }
+        } else {
+            dsf.getDatasetFieldCompoundValues().forEach(cv -> cv.getChildDatasetFields().forEach(v -> removeEmptyValues(v)));
+        }
     }
 
     public Set<ConstraintViolation> validate() {

diff --git a/src/main/java/edu/harvard/iq/dataverse/FilePage.java b/src/main/java/edu/harvard/iq/dataverse/FilePage.java
@@ -34,6 +34,7 @@
 import edu.harvard.iq.dataverse.makedatacount.MakeDataCountLoggingServiceBean;
 import edu.harvard.iq.dataverse.makedatacount.MakeDataCountLoggingServiceBean.MakeDataCountEntry;
 import edu.harvard.iq.dataverse.privateurl.PrivateUrlServiceBean;
+import edu.harvard.iq.dataverse.settings.JvmSettings;
 import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
 import edu.harvard.iq.dataverse.util.BundleUtil;
 import edu.harvard.iq.dataverse.util.FileUtil;
@@ -314,13 +315,18 @@ private void displayPublishMessage(){
         }               
     }
 
+    Boolean valid = null;
+
     public boolean isValid() {
-        if (!fileMetadata.getDatasetVersion().isDraft()) {
-            return true;
+        if (valid == null) {
+            final DatasetVersion workingVersion = fileMetadata.getDatasetVersion();
+            if (workingVersion.isDraft() || (canUpdateDataset() && JvmSettings.UI_SHOW_VALIDITY_LABEL_WHEN_PUBLISHED.lookupOptional(Boolean.class).orElse(true))) {
+                valid = workingVersion.isValid();
+            } else {
+                valid = true;
+            }
         }
-        DatasetVersion newVersion = fileMetadata.getDatasetVersion().cloneDatasetVersion();
-        newVersion.setDatasetFields(newVersion.initDatasetFields());
-        return newVersion.isValid();
+        return valid;
     }
 
     private boolean canViewUnpublishedDataset() {

diff --git a/src/main/java/edu/harvard/iq/dataverse/mydata/DataRetrieverAPI.java b/src/main/java/edu/harvard/iq/dataverse/mydata/DataRetrieverAPI.java
@@ -3,6 +3,7 @@
  */
 package edu.harvard.iq.dataverse.mydata;
 
+import edu.harvard.iq.dataverse.DatasetServiceBean;
 import edu.harvard.iq.dataverse.DataverseRoleServiceBean;
 import edu.harvard.iq.dataverse.DataverseServiceBean;
 import edu.harvard.iq.dataverse.DataverseSession;
@@ -63,7 +64,7 @@ public class DataRetrieverAPI extends AbstractApiBean {
     private static final String retrieveDataPartialAPIPath = "retrieve";
 
     @Inject
-    DataverseSession session;    
+    DataverseSession session;
 
     @EJB
     DataverseRoleServiceBean dataverseRoleService;
@@ -81,6 +82,8 @@ public class DataRetrieverAPI extends AbstractApiBean {
     //MyDataQueryHelperServiceBean myDataQueryHelperServiceBean;
     @EJB
     GroupServiceBean groupService;
+    @EJB
+    DatasetServiceBean datasetService;
 
     private List<DataverseRole> roleList;
     private DataverseRolePermissionHelper rolePermissionHelper;
@@ -491,7 +494,8 @@ private JsonArrayBuilder formatSolrDocs(SolrQueryResponse solrResponse, RoleTagR
             // -------------------------------------------
             // (a) Get core card data from solr
             // -------------------------------------------
-            myDataCardInfo = doc.getJsonForMyData();
+
+            myDataCardInfo = doc.getJsonForMyData(isValid(doc));
 
             if (doc.getEntity() != null && !doc.getEntity().isInstanceofDataFile()){
                 String parentAlias = dataverseService.getParentAliasString(doc);
@@ -514,4 +518,8 @@ private JsonArrayBuilder formatSolrDocs(SolrQueryResponse solrResponse, RoleTagR
         return jsonSolrDocsArrayBuilder;
 
     }
+
+    private boolean isValid(SolrSearchResult result) {
+        return result.isValid(x -> true);
+    }
 }        
diff --git a/src/main/java/edu/harvard/iq/dataverse/mydata/MyDataFilterParams.java b/src/main/java/edu/harvard/iq/dataverse/mydata/MyDataFilterParams.java
@@ -292,7 +292,7 @@ public String getSolrFragmentForPublicationStatus(){
     }
 
     public String getSolrFragmentForDatasetValidity(){
-        if ((this.datasetValidities == null) || (this.datasetValidities.isEmpty())){
+        if ((this.datasetValidities == null) || (this.datasetValidities.isEmpty()) || (this.datasetValidities.size() > 1)){
             return "";
         }
 

diff --git a/src/main/java/edu/harvard/iq/dataverse/search/IndexServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/search/IndexServiceBean.java
@@ -835,16 +835,7 @@ public SolrInputDocuments toSolrDocs(IndexableDataset indexableDataset, Set<Long
         solrInputDocument.addField(SearchFields.DATASET_PERSISTENT_ID, dataset.getGlobalId().toString());
         solrInputDocument.addField(SearchFields.PERSISTENT_URL, dataset.getPersistentURL());
         solrInputDocument.addField(SearchFields.TYPE, "datasets");
-
-        boolean valid;
-        if (!indexableDataset.getDatasetVersion().isDraft()) {
-            valid = true;
-        } else {
-            DatasetVersion version = indexableDataset.getDatasetVersion().cloneDatasetVersion();
-            version.setDatasetFields(version.initDatasetFields());
-            valid = version.isValid();
-        }
-        solrInputDocument.addField(SearchFields.DATASET_VALID, valid);
+        solrInputDocument.addField(SearchFields.DATASET_VALID, indexableDataset.getDatasetVersion().isValid());
 
         final Dataverse dataverse = dataset.getDataverseContext();
         final String dvIndexableCategoryName = dataverse.getIndexableCategoryName();

diff --git a/src/main/java/edu/harvard/iq/dataverse/search/SearchIncludeFragment.java b/src/main/java/edu/harvard/iq/dataverse/search/SearchIncludeFragment.java
@@ -355,8 +355,7 @@ The real issue here (https://github.com/IQSS/dataverse/issues/7304) is caused
              * https://github.com/IQSS/dataverse/issues/84
              */
             int numRows = 10;
-            HttpServletRequest httpServletRequest = (HttpServletRequest) FacesContext.getCurrentInstance().getExternalContext().getRequest();
-            DataverseRequest dataverseRequest = new DataverseRequest(session.getUser(), httpServletRequest);
+            DataverseRequest dataverseRequest = getDataverseRequest();
             List<Dataverse> dataverses = new ArrayList<>();
             dataverses.add(dataverse);
             solrQueryResponse = searchService.search(dataverseRequest, dataverses, queryToPassToSolr, filterQueriesFinal, sortField, sortOrder.toString(), paginationStart, onlyDataRelatedToMe, numRows, false, null, null, !isFacetsDisabled(), true);
@@ -1489,9 +1488,14 @@ public boolean isRetentionExpired(SolrSearchResult result) {
             return false;
         }
     }
+
+    private DataverseRequest getDataverseRequest() {
+        final HttpServletRequest httpServletRequest = (HttpServletRequest) FacesContext.getCurrentInstance().getExternalContext().getRequest();
+        return new DataverseRequest(session.getUser(), httpServletRequest);
+    }
 
     public boolean isValid(SolrSearchResult result) {
-        return result.isValid();
+        return result.isValid(x -> permissionsWrapper.canUpdateDataset(getDataverseRequest(), datasetService.find(x.getEntityId())));
     }
 
     public enum SortOrder {

diff --git a/src/main/java/edu/harvard/iq/dataverse/search/SolrSearchResult.java b/src/main/java/edu/harvard/iq/dataverse/search/SolrSearchResult.java
@@ -7,6 +7,7 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.function.Predicate;
 import java.util.logging.Logger;
 
 import edu.harvard.iq.dataverse.*;
@@ -19,6 +20,7 @@
 
 import edu.harvard.iq.dataverse.api.Util;
 import edu.harvard.iq.dataverse.dataset.DatasetThumbnail;
+import edu.harvard.iq.dataverse.settings.JvmSettings;
 import edu.harvard.iq.dataverse.util.DateUtil;
 import edu.harvard.iq.dataverse.util.json.JsonPrinter;
 import edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder;
@@ -402,15 +404,15 @@ public JsonArrayBuilder getRelevance() {
 	 *
 	 * @return
 	 */
-	public JsonObjectBuilder getJsonForMyData() {
+	public JsonObjectBuilder getJsonForMyData(boolean isValid) {
 
 		JsonObjectBuilder myDataJson = json(true, true, true);// boolean showRelevance, boolean showEntityIds, boolean showApiUrls)
 
 		myDataJson.add("publication_statuses", this.getPublicationStatusesAsJSON())
 				.add("is_draft_state", this.isDraftState()).add("is_in_review_state", this.isInReviewState())
 				.add("is_unpublished_state", this.isUnpublishedState()).add("is_published", this.isPublishedState())
 				.add("is_deaccesioned", this.isDeaccessionedState())
-				.add("is_valid", this.isValid())
+				.add("is_valid", isValid)
 				.add("date_to_display_on_card", getDateToDisplayOnCard());
 
 		// Add is_deaccessioned attribute, even though MyData currently screens any deaccessioned info out
@@ -1256,7 +1258,19 @@ public void setDatasetValid(Boolean datasetValid) {
 		this.datasetValid = datasetValid == null || Boolean.valueOf(datasetValid);
 	}
 
-	public boolean isValid() {
-		return datasetValid;
+	public boolean isValid(Predicate<SolrSearchResult> canUpdateDataset) {
+        if (this.datasetValid) {
+            return true;
+        }
+        if (!this.getType().equals("datasets")) {
+            return true;
+        }
+        if (this.isDraftState()) {
+            return false;
+        }
+        if (!JvmSettings.UI_SHOW_VALIDITY_LABEL_WHEN_PUBLISHED.lookupOptional(Boolean.class).orElse(true)) {
+            return true;
+        }
+		return !canUpdateDataset.test(this);
     }
 }
diff --git a/src/main/java/edu/harvard/iq/dataverse/settings/JvmSettings.java b/src/main/java/edu/harvard/iq/dataverse/settings/JvmSettings.java
@@ -230,6 +230,7 @@ public enum JvmSettings {
     SCOPE_UI(PREFIX, "ui"),
     UI_ALLOW_REVIEW_INCOMPLETE(SCOPE_UI, "allow-review-for-incomplete"),
     UI_SHOW_VALIDITY_FILTER(SCOPE_UI, "show-validity-filter"),
+    UI_SHOW_VALIDITY_LABEL_WHEN_PUBLISHED(SCOPE_UI, "show-validity-label-when-published"),
 
     // NetCDF SETTINGS
     SCOPE_NETCDF(PREFIX, "netcdf"),

diff --git a/src/main/webapp/file.xhtml b/src/main/webapp/file.xhtml
@@ -77,7 +77,7 @@
                                         <h:outputText value="#{bundle['dataset.versionUI.unpublished']}" styleClass="label label-warning" rendered="#{!FilePage.fileMetadata.datasetVersion.dataset.released}"/>
                                         <h:outputText value="#{bundle['dataset.versionUI.deaccessioned']}" styleClass="label label-danger" rendered="#{FilePage.fileMetadata.datasetVersion.deaccessioned}"/>
                                         <h:outputText value="#{FilePage.fileMetadata.datasetVersion.externalStatusLabel}" styleClass="label label-info" rendered="#{FilePage.fileMetadata.datasetVersion.externalStatusLabel!=null  and FilePage.canPublishDataset()}"/>
-                                        <h:outputText value="#{bundle['incomplete']}" styleClass="label label-danger" rendered="#{FilePage.fileMetadata.datasetVersion.draft and !FilePage.fileMetadata.datasetVersion.valid}"/>
+                                        <h:outputText value="#{bundle['incomplete']}" styleClass="label label-danger" rendered="#{!FilePage.valid}"/>
                                         <!-- DATASET VERSION NUMBER -->
                                         <h:outputText styleClass="label label-default" rendered="#{FilePage.fileMetadata.datasetVersion.released and !(FilePage.fileMetadata.datasetVersion.draft or FilePage.fileMetadata.datasetVersion.inReview)}"
                                                       value="#{bundle['file.DatasetVersion']} #{FilePage.fileMetadata.datasetVersion.versionNumber}.#{FilePage.fileMetadata.datasetVersion.minorVersionNumber}"/>
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Bug fixed for the ``incomplete metadata`` label being shown for published dataset with incomplete metadata in certain scenarios. This label will now be shown for draft versions of such datasets and published datasets that the user can edit. This label can also be made invisible for published datasets (regardless of edit rights) with the new option ``dataverse.ui.show-validity-label-when-published`` set to `false`.