Merge branch 'release-3.2.x' into TASK-5964

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OrganizationsCommandExecutor.java

@@ -12,6 +12,7 @@
 import org.opencb.opencga.app.cli.main.options.OrganizationsCommandOptions;
 import org.opencb.opencga.catalog.exceptions.CatalogAuthenticationException;
 import org.opencb.opencga.catalog.utils.ParamUtils.AddRemoveAction;
+import org.opencb.opencga.catalog.utils.ParamUtils.BasicUpdateAction;
 import org.opencb.opencga.catalog.utils.ParamUtils.UpdateAction;
 import org.opencb.opencga.client.exceptions.ClientException;
 import org.opencb.opencga.core.common.JacksonUtils;
@@ -214,6 +215,7 @@ private RestResponse<Note> updateNotes() throws Exception {
         ObjectMap queryParams = new ObjectMap();
         queryParams.putIfNotEmpty("include", commandOptions.include);
         queryParams.putIfNotEmpty("exclude", commandOptions.exclude);
+        queryParams.putIfNotNull("tagsAction", commandOptions.tagsAction);
         queryParams.putIfNotNull("includeResult", commandOptions.includeResult);
 
 

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/StudiesCommandExecutor.java

@@ -448,6 +448,7 @@ private RestResponse<Note> updateNotes() throws Exception {
         ObjectMap queryParams = new ObjectMap();
         queryParams.putIfNotEmpty("include", commandOptions.include);
         queryParams.putIfNotEmpty("exclude", commandOptions.exclude);
+        queryParams.putIfNotNull("tagsAction", commandOptions.tagsAction);
         queryParams.putIfNotNull("includeResult", commandOptions.includeResult);
 
 

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/OrganizationsCommandOptions.java

@@ -214,6 +214,9 @@ public class UpdateNotesCommandOptions {
         @Parameter(names = {"--id"}, description = "Note unique identifier.", required = true, arity = 1)
         public String id; 
 
+        @Parameter(names = {"--tags-action"}, description = "Action to be performed if the array of tags is being updated.", required = false, arity = 1)
+        public String tagsAction = "ADD"; 
+
         @Parameter(names = {"--include-result"}, description = "Flag indicating to include the created or updated document result in the response", required = false, help = true, arity = 0)
         public boolean includeResult = false; 
 

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/StudiesCommandOptions.java

@@ -505,6 +505,9 @@ public class UpdateNotesCommandOptions {
         @Parameter(names = {"--id"}, description = "Note unique identifier.", required = true, arity = 1)
         public String id; 
 
+        @Parameter(names = {"--tags-action"}, description = "Action to be performed if the array of tags is being updated.", required = false, arity = 1)
+        public String tagsAction = "ADD"; 
+
         @Parameter(names = {"--include-result"}, description = "Flag indicating to include the created or updated document result in the response", required = false, help = true, arity = 0)
         public boolean includeResult = false; 
 

opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/NoteMongoDBAdaptor.java

@@ -234,7 +234,7 @@ private UpdateDocument parseAndValidateUpdateParams(Document note, ObjectMap par
                     filterStringListParams(parameters, document.getSet(), tagsParams);
                     break;
                 case REMOVE:
-                    filterStringListParams(parameters, document.getPull(), tagsParams);
+                    filterStringListParams(parameters, document.getPullAll(), tagsParams);
                     break;
                 case ADD:
                     filterStringListParams(parameters, document.getAddToSet(), tagsParams);

opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/NoteManager.java

@@ -302,8 +302,7 @@ private OpenCGAResult<Note> update(long noteUid, NoteUpdateParams noteUpdatePara
         // Write who's performing the update
         updateMap.put(NoteDBAdaptor.QueryParams.USER_ID.key(), tokenPayload.getUserId());
 
-        OpenCGAResult<Note> update = catalogDBAdaptorFactory.getCatalogNoteDBAdaptor(organizationId).update(noteUid, updateMap,
-                QueryOptions.empty());
+        OpenCGAResult<Note> update = catalogDBAdaptorFactory.getCatalogNoteDBAdaptor(organizationId).update(noteUid, updateMap, options);
         if (options.getBoolean(ParamConstants.INCLUDE_RESULT_PARAM)) {
             // Fetch updated note
             OpenCGAResult<Note> result = catalogDBAdaptorFactory.getCatalogNoteDBAdaptor(organizationId).get(noteUid, options);

opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/NoteManagerTest.java

@@ -7,6 +7,9 @@
 import org.opencb.opencga.catalog.db.api.NoteDBAdaptor;
 import org.opencb.opencga.catalog.exceptions.CatalogAuthorizationException;
 import org.opencb.opencga.catalog.exceptions.CatalogException;
+import org.opencb.opencga.catalog.utils.Constants;
+import org.opencb.opencga.catalog.utils.ParamUtils;
+import org.opencb.opencga.core.api.ParamConstants;
 import org.opencb.opencga.core.models.notes.Note;
 import org.opencb.opencga.core.models.notes.NoteCreateParams;
 import org.opencb.opencga.core.models.notes.NoteUpdateParams;
@@ -16,6 +19,8 @@
 import org.opencb.opencga.core.testclassification.duration.MediumTests;
 
 import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Map;
 
 import static org.junit.Assert.*;
 
@@ -190,6 +195,45 @@ public void updateStudyNoteTest() throws CatalogException {
         catalogManager.getNotesManager().updateStudyNote(studyFqn, note.getId(), noteUpdateParams, INCLUDE_RESULT, normalToken1);
     }
 
+    @Test
+    public void noteTagsUpdateTest() throws CatalogException {
+        NoteCreateParams noteCreateParams = new NoteCreateParams()
+                .setId("note1")
+                .setVisibility(Note.Visibility.PRIVATE)
+                .setValueType(Note.Type.STRING)
+                .setTags(Arrays.asList("tag1", "tag2"))
+                .setValue("hello");
+        Note note = catalogManager.getNotesManager().createStudyNote(studyFqn, noteCreateParams, INCLUDE_RESULT, ownerToken).first();
+        assertEquals(2, note.getTags().size());
+        assertArrayEquals(Arrays.asList("tag1", "tag2").toArray(), note.getTags().toArray());
+
+        QueryOptions queryOptions = new QueryOptions();
+        Map<String, Object> actionMap = new HashMap<>();
+        actionMap.put(NoteDBAdaptor.QueryParams.TAGS.key(), ParamUtils.BasicUpdateAction.ADD);
+        queryOptions.put(Constants.ACTIONS, actionMap);
+        queryOptions.put(ParamConstants.INCLUDE_RESULT_PARAM, true);
+        NoteUpdateParams updateParams = new NoteUpdateParams().setTags(Arrays.asList("tag3", "tag1"));
+        note = catalogManager.getNotesManager().updateStudyNote(studyFqn, note.getId(), updateParams, queryOptions, ownerToken).first();
+        assertEquals(3, note.getTags().size());
+        assertArrayEquals(Arrays.asList("tag1", "tag2", "tag3").toArray(), note.getTags().toArray());
+
+        // Remove tag1 and tag2
+        actionMap.put(NoteDBAdaptor.QueryParams.TAGS.key(), ParamUtils.BasicUpdateAction.REMOVE);
+        queryOptions.put(Constants.ACTIONS, actionMap);
+        updateParams = new NoteUpdateParams().setTags(Arrays.asList("tag1", "tag2"));
+        note = catalogManager.getNotesManager().updateStudyNote(studyFqn, note.getId(), updateParams, queryOptions, ownerToken).first();
+        assertEquals(1, note.getTags().size());
+        assertArrayEquals(Arrays.asList("tag3").toArray(), note.getTags().toArray());
+
+        // Set new list of tags
+        actionMap.put(NoteDBAdaptor.QueryParams.TAGS.key(), ParamUtils.BasicUpdateAction.SET);
+        queryOptions.put(Constants.ACTIONS, actionMap);
+        updateParams = new NoteUpdateParams().setTags(Arrays.asList("tag4", "tag5"));
+        note = catalogManager.getNotesManager().updateStudyNote(studyFqn, note.getId(), updateParams, queryOptions, ownerToken).first();
+        assertEquals(2, note.getTags().size());
+        assertArrayEquals(Arrays.asList("tag4", "tag5").toArray(), note.getTags().toArray());
+    }
+
     @Test
     public void getStudyNoteTest() throws CatalogException {
         NoteCreateParams noteCreateParams1 = new NoteCreateParams()

opencga-client/src/main/R/R/Organization-methods.R

@@ -23,7 +23,7 @@
 #' | createNotes | /{apiVersion}/organizations/notes/create | include, exclude, includeResult, body[*] |
 #' | searchNotes | /{apiVersion}/organizations/notes/search | include, exclude, creationDate, modificationDate, id, scope, visibility, uuid, userId, tags, version |
 #' | deleteNotes | /{apiVersion}/organizations/notes/{id}/delete | id[*], includeResult |
-#' | updateNotes | /{apiVersion}/organizations/notes/{id}/update | include, exclude, id[*], includeResult, body[*] |
+#' | updateNotes | /{apiVersion}/organizations/notes/{id}/update | include, exclude, id[*], tagsAction, includeResult, body[*] |
 #' | userUpdateStatus | /{apiVersion}/organizations/user/{user}/status/update | include, exclude, user[*], organization, includeResult, body[*] |
 #' | updateUser | /{apiVersion}/organizations/user/{user}/update | include, exclude, user[*], organization, includeResult, body[*] |
 #' | updateConfiguration | /{apiVersion}/organizations/{organization}/configuration/update | include, exclude, organization[*], includeResult, authenticationOriginsAction, body[*] |
@@ -85,6 +85,7 @@ setMethod("organizationClient", "OpencgaR", function(OpencgaR, id, organization,
         #' @param include Fields included in the response, whole JSON path must be provided.
         #' @param exclude Fields excluded in the response, whole JSON path must be provided.
         #' @param id Note unique identifier.
+        #' @param tagsAction Action to be performed if the array of tags is being updated. Allowed values: ['ADD SET REMOVE']
         #' @param includeResult Flag indicating to include the created or updated document result in the response.
         #' @param data JSON containing the Note fields to be updated.
         updateNotes=fetchOpenCGA(object=OpencgaR, category="organizations", categoryId=NULL, subcategory="notes",

opencga-client/src/main/R/R/Study-methods.R

@@ -31,7 +31,7 @@
 #' | createNotes | /{apiVersion}/studies/{study}/notes/create | include, exclude, study[*], includeResult, body[*] |
 #' | searchNotes | /{apiVersion}/studies/{study}/notes/search | include, exclude, study[*], creationDate, modificationDate, id, uuid, userId, tags, visibility, version |
 #' | deleteNotes | /{apiVersion}/studies/{study}/notes/{id}/delete | study[*], id[*], includeResult |
-#' | updateNotes | /{apiVersion}/studies/{study}/notes/{id}/update | include, exclude, study[*], id[*], includeResult, body[*] |
+#' | updateNotes | /{apiVersion}/studies/{study}/notes/{id}/update | include, exclude, study[*], id[*], tagsAction, includeResult, body[*] |
 #' | permissionRules | /{apiVersion}/studies/{study}/permissionRules | study[*], entity[*] |
 #' | updatePermissionRules | /{apiVersion}/studies/{study}/permissionRules/update | study[*], entity[*], action, body[*] |
 #' | runTemplates | /{apiVersion}/studies/{study}/templates/run | study[*], jobId, jobDependsOn, jobDescription, jobTags, jobScheduledStartTime, jobPriority, jobDryRun, body[*] |
@@ -191,6 +191,7 @@ setMethod("studyClient", "OpencgaR", function(OpencgaR, group, id, members, stud
         #' @param exclude Fields excluded in the response, whole JSON path must be provided.
         #' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
         #' @param id Note unique identifier.
+        #' @param tagsAction Action to be performed if the array of tags is being updated. Allowed values: ['ADD SET REMOVE']
         #' @param includeResult Flag indicating to include the created or updated document result in the response.
         #' @param data JSON containing the Note fields to be updated.
         updateNotes=fetchOpenCGA(object=OpencgaR, category="studies", categoryId=study, subcategory="notes",

opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/OrganizationClient.java

@@ -128,6 +128,7 @@ public RestResponse<Note> deleteNotes(String id, ObjectMap params) throws Client
      * @param params Map containing any of the following optional parameters.
      *       include: Fields included in the response, whole JSON path must be provided.
      *       exclude: Fields excluded in the response, whole JSON path must be provided.
+     *       tagsAction: Action to be performed if the array of tags is being updated.
      *       includeResult: Flag indicating to include the created or updated document result in the response.
      * @return a RestResponse object.
      * @throws ClientException ClientException if there is any server error.

opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java

@@ -288,6 +288,7 @@ public RestResponse<Note> deleteNotes(String study, String id, ObjectMap params)
      * @param params Map containing any of the following optional parameters.
      *       include: Fields included in the response, whole JSON path must be provided.
      *       exclude: Fields excluded in the response, whole JSON path must be provided.
+     *       tagsAction: Action to be performed if the array of tags is being updated.
      *       includeResult: Flag indicating to include the created or updated document result in the response.
      * @return a RestResponse object.
      * @throws ClientException ClientException if there is any server error.

opencga-client/src/main/javascript/Organization.js

@@ -97,6 +97,8 @@ export default class Organization extends OpenCGAParentClass {
     * @param {Object} [params] - The Object containing the following optional parameters:
     * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided.
     * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided.
+    * @param {"ADD SET REMOVE"} [params.tagsAction = "ADD"] - Action to be performed if the array of tags is being updated. The default
+    *     value is ADD.
     * @param {Boolean} [params.includeResult = "false"] - Flag indicating to include the created or updated document result in the response.
     *     The default value is false.
     * @returns {Promise} Promise object in the form of RestResponse instance.

opencga-client/src/main/javascript/Study.js

@@ -219,6 +219,8 @@ export default class Study extends OpenCGAParentClass {
     * @param {Object} [params] - The Object containing the following optional parameters:
     * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided.
     * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided.
+    * @param {"ADD SET REMOVE"} [params.tagsAction = "ADD"] - Action to be performed if the array of tags is being updated. The default
+    *     value is ADD.
     * @param {Boolean} [params.includeResult = "false"] - Flag indicating to include the created or updated document result in the response.
     *     The default value is false.
     * @returns {Promise} Promise object in the form of RestResponse instance.

opencga-client/src/main/python/pyopencga/rest_clients/organization_client.py

@@ -104,6 +104,8 @@ def update_notes(self, id, data=None, **options):
             must be provided.
         :param str exclude: Fields excluded in the response, whole JSON path
             must be provided.
+        :param str tags_action: Action to be performed if the array of tags is
+            being updated. Allowed values: ['ADD SET REMOVE']
         :param bool include_result: Flag indicating to include the created or
             updated document result in the response.
         """

opencga-client/src/main/python/pyopencga/rest_clients/study_client.py

@@ -270,6 +270,8 @@ def update_notes(self, study, id, data=None, **options):
             must be provided.
         :param str exclude: Fields excluded in the response, whole JSON path
             must be provided.
+        :param str tags_action: Action to be performed if the array of tags is
+            being updated. Allowed values: ['ADD SET REMOVE']
         :param bool include_result: Flag indicating to include the created or
             updated document result in the response.
         """

opencga-server/src/main/java/org/opencb/opencga/server/rest/OrganizationWSServer.java

@@ -17,6 +17,7 @@
 package org.opencb.opencga.server.rest;
 
 import org.opencb.commons.datastore.core.QueryOptions;
+import org.opencb.opencga.catalog.db.api.NoteDBAdaptor;
 import org.opencb.opencga.catalog.db.api.OrganizationDBAdaptor;
 import org.opencb.opencga.catalog.utils.Constants;
 import org.opencb.opencga.catalog.utils.ParamUtils;
@@ -204,9 +205,17 @@ public Response createNote(
     })
     public Response updateNote(
             @ApiParam(value = FieldConstants.NOTES_ID_DESCRIPTION) @PathParam(FieldConstants.NOTES_ID_PARAM) String noteId,
+            @ApiParam(value = "Action to be performed if the array of tags is being updated.", allowableValues = "ADD,REMOVE,SET", defaultValue = "ADD")
+                @QueryParam("tagsAction") ParamUtils.BasicUpdateAction tagsAction,
             @ApiParam(value = ParamConstants.INCLUDE_RESULT_DESCRIPTION, defaultValue = "false") @QueryParam(ParamConstants.INCLUDE_RESULT_PARAM) boolean includeResult,
             @ApiParam(value = "JSON containing the Note fields to be updated.", required = true) NoteUpdateParams parameters) {
         try {
+            if (tagsAction == null) {
+                tagsAction = ParamUtils.BasicUpdateAction.ADD;
+            }
+            Map<String, Object> actionMap = new HashMap<>();
+            actionMap.put(NoteDBAdaptor.QueryParams.TAGS.key(), tagsAction);
+            queryOptions.put(Constants.ACTIONS, actionMap);
             OpenCGAResult<Note> result = catalogManager.getNotesManager().updateOrganizationNote(noteId, parameters, queryOptions, token);
             return createOkResponse(result);
         } catch (Exception e) {

opencga-server/src/main/java/org/opencb/opencga/server/rest/StudyWSServer.java

@@ -23,6 +23,7 @@
 import org.opencb.commons.datastore.core.DataResult;
 import org.opencb.commons.datastore.core.QueryOptions;
 import org.opencb.opencga.analysis.templates.TemplateRunner;
+import org.opencb.opencga.catalog.db.api.NoteDBAdaptor;
 import org.opencb.opencga.catalog.db.api.StudyDBAdaptor;
 import org.opencb.opencga.catalog.managers.StudyManager;
 import org.opencb.opencga.catalog.utils.Constants;
@@ -46,7 +47,9 @@
 import javax.ws.rs.core.*;
 import java.io.IOException;
 import java.io.InputStream;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 
 import static org.opencb.opencga.core.api.ParamConstants.JOB_DEPENDS_ON;
 
@@ -613,9 +616,17 @@ public Response createNote(
     public Response updateNote(
             @ApiParam(value = ParamConstants.STUDY_DESCRIPTION) @PathParam(ParamConstants.STUDY_PARAM) String studyStr,
             @ApiParam(value = FieldConstants.NOTES_ID_DESCRIPTION) @PathParam(FieldConstants.NOTES_ID_PARAM) String noteId,
+            @ApiParam(value = "Action to be performed if the array of tags is being updated.", allowableValues = "ADD,REMOVE,SET", defaultValue = "ADD")
+                @QueryParam("tagsAction") ParamUtils.BasicUpdateAction tagsAction,
             @ApiParam(value = ParamConstants.INCLUDE_RESULT_DESCRIPTION, defaultValue = "false") @QueryParam(ParamConstants.INCLUDE_RESULT_PARAM) boolean includeResult,
             @ApiParam(value = "JSON containing the Note fields to be updated.", required = true) NoteUpdateParams parameters) {
         try {
+            if (tagsAction == null) {
+                tagsAction = ParamUtils.BasicUpdateAction.ADD;
+            }
+            Map<String, Object> actionMap = new HashMap<>();
+            actionMap.put(NoteDBAdaptor.QueryParams.TAGS.key(), tagsAction);
+            queryOptions.put(Constants.ACTIONS, actionMap);
             OpenCGAResult<Note> result = catalogManager.getNotesManager().updateStudyNote(studyStr, noteId, parameters, queryOptions, token);
             return createOkResponse(result);
         } catch (Exception e) {

opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/search/solr/SolrQueryParser.java

@@ -492,7 +492,7 @@ private String parseGenomicFilter(Query query) {
         // Consequence types (cts)
         String ctLogicalOperator = " OR ";
         if (StringUtils.isNotEmpty(query.getString(ANNOT_CONSEQUENCE_TYPE.key(), ""))) {
-            consequenceTypes = Arrays.asList(query.getString(ANNOT_CONSEQUENCE_TYPE.key()).split("[,;]"));
+            consequenceTypes = parseConsequenceTypes(Arrays.asList(query.getString(ANNOT_CONSEQUENCE_TYPE.key()).split("[,;]")));
             if (query.getString(ANNOT_CONSEQUENCE_TYPE.key()).contains(";")) {
                 ctLogicalOperator = " AND ";
                 // TODO This must be removed as soon as we have the Query procesing in use