Merge branch 'develop' into TASK-6442

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

@@ -19,6 +19,7 @@
 import org.opencb.opencga.core.config.Optimizations;
 import org.opencb.opencga.core.models.notes.Note;
 import org.opencb.opencga.core.models.notes.NoteCreateParams;
+import org.opencb.opencga.core.models.notes.NoteType;
 import org.opencb.opencga.core.models.notes.NoteUpdateParams;
 import org.opencb.opencga.core.models.organizations.Organization;
 import org.opencb.opencga.core.models.organizations.OrganizationConfiguration;
@@ -164,6 +165,7 @@ private RestResponse<Note> createNotes() throws Exception {
         } else {
             ObjectMap beanParams = new ObjectMap();
             putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotNull(beanParams, "type", commandOptions.type, true);
             putNestedIfNotNull(beanParams, "tags", commandOptions.tags, true);
             putNestedIfNotNull(beanParams, "visibility", commandOptions.visibility, true);
             putNestedIfNotNull(beanParams, "valueType", commandOptions.valueType, true);
@@ -186,6 +188,7 @@ private RestResponse<Note> searchNotes() throws Exception {
         queryParams.putIfNotEmpty("creationDate", commandOptions.creationDate);
         queryParams.putIfNotEmpty("modificationDate", commandOptions.modificationDate);
         queryParams.putIfNotEmpty("id", commandOptions.id);
+        queryParams.putIfNotEmpty("type", commandOptions.type);
         queryParams.putIfNotEmpty("scope", commandOptions.scope);
         queryParams.putIfNotEmpty("visibility", commandOptions.visibility);
         queryParams.putIfNotEmpty("uuid", commandOptions.uuid);
@@ -230,6 +233,7 @@ private RestResponse<Note> updateNotes() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), NoteUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
+            putNestedIfNotNull(beanParams, "type", commandOptions.type, true);
             putNestedIfNotNull(beanParams, "tags", commandOptions.tags, true);
             putNestedIfNotNull(beanParams, "visibility", commandOptions.visibility, true);
 

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

@@ -33,6 +33,7 @@
 import org.opencb.opencga.core.models.job.Job;
 import org.opencb.opencga.core.models.notes.Note;
 import org.opencb.opencga.core.models.notes.NoteCreateParams;
+import org.opencb.opencga.core.models.notes.NoteType;
 import org.opencb.opencga.core.models.notes.NoteUpdateParams;
 import org.opencb.opencga.core.models.study.CustomGroup;
 import org.opencb.opencga.core.models.study.Group;
@@ -398,6 +399,7 @@ private RestResponse<Note> createNotes() throws Exception {
         } else {
             ObjectMap beanParams = new ObjectMap();
             putNestedIfNotEmpty(beanParams, "id", commandOptions.id, true);
+            putNestedIfNotNull(beanParams, "type", commandOptions.type, true);
             putNestedIfNotNull(beanParams, "tags", commandOptions.tags, true);
             putNestedIfNotNull(beanParams, "visibility", commandOptions.visibility, true);
             putNestedIfNotNull(beanParams, "valueType", commandOptions.valueType, true);
@@ -420,6 +422,7 @@ private RestResponse<Note> searchNotes() throws Exception {
         queryParams.putIfNotEmpty("creationDate", commandOptions.creationDate);
         queryParams.putIfNotEmpty("modificationDate", commandOptions.modificationDate);
         queryParams.putIfNotEmpty("id", commandOptions.id);
+        queryParams.putIfNotEmpty("type", commandOptions.type);
         queryParams.putIfNotEmpty("uuid", commandOptions.uuid);
         queryParams.putIfNotEmpty("userId", commandOptions.userId);
         queryParams.putIfNotEmpty("tags", commandOptions.tags);
@@ -463,6 +466,7 @@ private RestResponse<Note> updateNotes() throws Exception {
                     .readValue(new java.io.File(commandOptions.jsonFile), NoteUpdateParams.class);
         } else {
             ObjectMap beanParams = new ObjectMap();
+            putNestedIfNotNull(beanParams, "type", commandOptions.type, true);
             putNestedIfNotNull(beanParams, "tags", commandOptions.tags, true);
             putNestedIfNotNull(beanParams, "visibility", commandOptions.visibility, true);
 

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

@@ -127,6 +127,9 @@ public class CreateNotesCommandOptions {
         @Parameter(names = {"--id"}, description = "The body web service id parameter", required = false, arity = 1)
         public String id;
 
+        @Parameter(names = {"--type"}, description = "Enum param allowed values: VARIANT, GENE, TRANSCRIPT, PROTEIN, JOB, FILE, SAMPLE, INDIVIDUAL, FAMILY, COHORT, DISEASE_PANEL, CLINICAL_ANALYSIS, WORKFLOW, ORGANIZATION, OTHER, UNKNOWN", required = false, arity = 1)
+        public String type;
+
         @Parameter(names = {"--tags"}, description = "The body web service tags parameter", required = false, arity = 1)
         public String tags;
 
@@ -159,6 +162,9 @@ public class SearchNotesCommandOptions {
         @Parameter(names = {"--id"}, description = "Note unique identifier.", required = false, arity = 1)
         public String id; 
 
+        @Parameter(names = {"--type"}, description = "Note type.", required = false, arity = 1)
+        public String type; 
+
         @Parameter(names = {"--scope"}, description = "Scope of the Note.", required = false, arity = 1)
         public String scope; 
 
@@ -220,6 +226,9 @@ public class UpdateNotesCommandOptions {
         @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; 
 
+        @Parameter(names = {"--type"}, description = "Enum param allowed values: VARIANT, GENE, TRANSCRIPT, PROTEIN, JOB, FILE, SAMPLE, INDIVIDUAL, FAMILY, COHORT, DISEASE_PANEL, CLINICAL_ANALYSIS, WORKFLOW, ORGANIZATION, OTHER, UNKNOWN", required = false, arity = 1)
+        public String type;
+
         @Parameter(names = {"--tags"}, description = "The body web service tags parameter", required = false, arity = 1)
         public String tags;
 

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

@@ -412,6 +412,9 @@ public class CreateNotesCommandOptions {
         @Parameter(names = {"--id"}, description = "The body web service id parameter", required = false, arity = 1)
         public String id;
 
+        @Parameter(names = {"--type"}, description = "Enum param allowed values: VARIANT, GENE, TRANSCRIPT, PROTEIN, JOB, FILE, SAMPLE, INDIVIDUAL, FAMILY, COHORT, DISEASE_PANEL, CLINICAL_ANALYSIS, WORKFLOW, ORGANIZATION, OTHER, UNKNOWN", required = false, arity = 1)
+        public String type;
+
         @Parameter(names = {"--tags"}, description = "The body web service tags parameter", required = false, arity = 1)
         public String tags;
 
@@ -447,6 +450,9 @@ public class SearchNotesCommandOptions {
         @Parameter(names = {"--id"}, description = "Note unique identifier.", required = false, arity = 1)
         public String id; 
 
+        @Parameter(names = {"--type"}, description = "Note type.", required = false, arity = 1)
+        public String type; 
+
         @Parameter(names = {"--uuid"}, description = "Unique 32-character identifier assigned automatically by OpenCGA.", required = false, arity = 1)
         public String uuid; 
 
@@ -511,6 +517,9 @@ public class UpdateNotesCommandOptions {
         @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; 
 
+        @Parameter(names = {"--type"}, description = "Enum param allowed values: VARIANT, GENE, TRANSCRIPT, PROTEIN, JOB, FILE, SAMPLE, INDIVIDUAL, FAMILY, COHORT, DISEASE_PANEL, CLINICAL_ANALYSIS, WORKFLOW, ORGANIZATION, OTHER, UNKNOWN", required = false, arity = 1)
+        public String type;
+
         @Parameter(names = {"--tags"}, description = "The body web service tags parameter", required = false, arity = 1)
         public String tags;
 

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v4/v4_0_0/catalog/AddNewNoteTypeMigration.java

@@ -0,0 +1,43 @@
+package org.opencb.opencga.app.migrations.v4.v4_0_0.catalog;
+
+import com.mongodb.client.MongoCollection;
+import com.mongodb.client.model.Filters;
+import com.mongodb.client.model.Updates;
+import org.bson.Document;
+import org.bson.conversions.Bson;
+import org.opencb.opencga.catalog.db.mongodb.OrganizationMongoDBAdaptorFactory;
+import org.opencb.opencga.catalog.migration.Migration;
+import org.opencb.opencga.catalog.migration.MigrationTool;
+import org.opencb.opencga.core.api.ParamConstants;
+import org.opencb.opencga.core.models.notes.NoteType;
+
+import java.util.Arrays;
+
+@Migration(id = "addNewNoteType__task_7046",
+        description = "Add new Note type #7046", version = "4.0.0",
+        language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20241030)
+public class AddNewNoteTypeMigration extends MigrationTool {
+
+    @Override
+    protected void run() throws Exception {
+        NoteType type = NoteType.UNKNOWN;
+        if (ParamConstants.ADMIN_ORGANIZATION.equals(organizationId)) {
+            type = NoteType.ORGANIZATION;
+        }
+        MongoCollection<Document> collection = getMongoCollection(OrganizationMongoDBAdaptorFactory.NOTE_COLLECTION);
+        Bson query = Filters.exists("type", false);
+        Bson update = Updates.set("type", type);
+        logger.info("Setting all notes from organization '{}' to type '{}'", organizationId, type);
+        collection.updateMany(query, update);
+
+        // Drop old index
+        Document oldIndex = new Document()
+                .append("id", 1)
+                .append("studyUid", 1)
+                .append("version", 1);
+        dropIndex(Arrays.asList(OrganizationMongoDBAdaptorFactory.NOTE_COLLECTION, OrganizationMongoDBAdaptorFactory.NOTE_ARCHIVE_COLLECTION),
+                oldIndex);
+        // Generate new indexes
+        catalogManager.installIndexes(organizationId, token);
+    }
+}

opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/api/NoteDBAdaptor.java

@@ -32,6 +32,7 @@ enum QueryParams implements QueryParam {
         UUID("uuid", STRING, ""),
         SCOPE("scope", STRING, ""),
         STUDY("study", STRING, ""),
+        TYPE("type", STRING, ""),
         TAGS("tags", TEXT_ARRAY, ""),
         USER_ID("userId", STRING, ""),
         VISIBILITY("visibility", STRING, ""),

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

@@ -38,6 +38,7 @@
 import org.opencb.opencga.core.config.Configuration;
 import org.opencb.opencga.core.models.notes.Note;
 import org.opencb.opencga.core.models.notes.NoteCreateParams;
+import org.opencb.opencga.core.models.notes.NoteType;
 import org.opencb.opencga.core.models.organizations.Organization;
 import org.opencb.opencga.core.models.organizations.OrganizationSummary;
 import org.opencb.opencga.core.response.OpenCGAResult;
@@ -278,7 +279,7 @@ public OpenCGAResult<Organization> createOrganization(Organization organization,
 
             OrganizationSummary organizationSummary = new OrganizationSummary(organization.getId(),
                     organizationDBAdaptorFactory.getMongoDataStore().getDatabaseName(), OrganizationTag.ACTIVE.name(), null);
-            NoteCreateParams noteCreateParams = new NoteCreateParams(ORGANIZATION_PREFIX + organization.getId(),
+            NoteCreateParams noteCreateParams = new NoteCreateParams(ORGANIZATION_PREFIX + organization.getId(), NoteType.ORGANIZATION,
                     Collections.singletonList(OrganizationTag.ACTIVE.name()), Note.Visibility.PRIVATE, Note.Type.OBJECT, null);
             try {
                 String orgSummaryString = JacksonUtils.getDefaultObjectMapper().writeValueAsString(organizationSummary);

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

@@ -208,7 +208,7 @@ private UpdateDocument parseAndValidateUpdateParams(Document note, ObjectMap par
 //            document.getSet().put(PRIVATE_MODIFICATION_DATE, date);
 //        }
 
-        final String[] acceptedStringParams = {QueryParams.USER_ID.key(), QueryParams.VISIBILITY.key()};
+        final String[] acceptedStringParams = {QueryParams.USER_ID.key(), QueryParams.VISIBILITY.key(), QueryParams.TYPE.key()};
         filterStringParams(parameters, document.getSet(), acceptedStringParams);
 
         Object value = parameters.get(QueryParams.VALUE.key());
@@ -399,6 +399,7 @@ private Bson parseQuery(Query query) throws CatalogDBException {
                         break;
                     case ID:
                     case UUID:
+                    case TYPE:
                     case SCOPE:
                     case USER_ID:
                     case TAGS:

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

@@ -24,6 +24,7 @@
 import org.opencb.opencga.core.models.common.Enums;
 import org.opencb.opencga.core.models.notes.Note;
 import org.opencb.opencga.core.models.notes.NoteCreateParams;
+import org.opencb.opencga.core.models.notes.NoteType;
 import org.opencb.opencga.core.models.notes.NoteUpdateParams;
 import org.opencb.opencga.core.models.study.Study;
 import org.opencb.opencga.core.response.OpenCGAResult;
@@ -396,6 +397,7 @@ public static void validateNewNote(Note note, String userId) throws CatalogParam
         ParamUtils.checkObj(note.getValueType(), NoteDBAdaptor.QueryParams.VALUE_TYPE.key());
         ParamUtils.checkObj(note.getValue(), NoteDBAdaptor.QueryParams.VALUE.key());
 
+        note.setType(ParamUtils.defaultObject(note.getType(), NoteType.UNKNOWN));
         note.setTags(CollectionUtils.isNotEmpty(note.getTags()) ? note.getTags() : Collections.emptyList());
         note.setUserId(userId);
 

opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationManager.java

@@ -213,6 +213,9 @@ public void runMigration(String organizationId, String version, Collection<Migra
         for (Class<? extends MigrationTool> migration : runnableMigrations) {
             run(organizationId, migration, appHomePath, params, token);
         }
+
+        // 5. Execute install indexes just in case there are new indexes
+        catalogManager.installIndexes(organizationId, token);
     }
 
     public List<Class<? extends MigrationTool>> getPendingMigrations(String organizationId, String version, String token)

opencga-catalog/src/main/resources/catalog-indexes.txt

@@ -1,7 +1,8 @@
-{"collections": ["note", "note_archive"], "fields": {"id": 1, "studyUid": 1, "version": 1}, "options": {"unique": true}}
+{"collections": ["note", "note_archive"], "fields": {"id": 1, "studyUid": 1, "type": 1, "version": 1}, "options": {"unique": true}}
 {"collections": ["note", "note_archive"], "fields": {"uid": 1, "version": 1}, "options": {"unique": true}}
 {"collections": ["note", "note_archive"], "fields": {"uuid": 1, "version": 1}, "options": {"unique": true}}
 {"collections": ["note", "note_archive"], "fields": {"scope": 1, "studyUid": 1}, "options": {}}
+{"collections": ["note", "note_archive"], "fields": {"type": 1, "studyUid": 1}, "options": {}}
 {"collections": ["note", "note_archive"], "fields": {"studyUid": 1}, "options": {}}
 {"collections": ["note", "note_archive"], "fields": {"visibility": 1, "studyUid": 1}, "options": {}}
 {"collections": ["note", "note_archive"], "fields": {"userId": 1, "studyUid": 1}, "options": {}}

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

@@ -12,6 +12,7 @@
 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.NoteType;
 import org.opencb.opencga.core.models.notes.NoteUpdateParams;
 import org.opencb.opencga.core.models.organizations.Organization;
 import org.opencb.opencga.core.models.study.Study;
@@ -37,11 +38,14 @@ public void createOrganizationNoteTest() throws CatalogException {
         Note note = catalogManager.getNotesManager().createOrganizationNote(noteCreateParams, INCLUDE_RESULT, ownerToken).first();
         assertEquals(noteCreateParams.getId(), note.getId());
         assertEquals(orgOwnerUserId, note.getUserId());
+        assertEquals(NoteType.UNKNOWN, note.getType());
 
         noteCreateParams.setId("note2");
+        noteCreateParams.setType(NoteType.FAMILY);
         note = catalogManager.getNotesManager().createOrganizationNote(noteCreateParams, INCLUDE_RESULT, orgAdminToken1).first();
         assertEquals(noteCreateParams.getId(), note.getId());
         assertEquals(orgAdminUserId1, note.getUserId());
+        assertEquals(NoteType.FAMILY, note.getType());
 
         thrown.expect(CatalogAuthorizationException.class);
         thrown.expectMessage("denied");
@@ -59,10 +63,12 @@ public void updateOrganizationNoteTest() throws CatalogException {
         assertEquals(1, note.getVersion());
 
         NoteUpdateParams noteUpdateParams = new NoteUpdateParams()
-                .setTags(Arrays.asList("tag1", "tag2"));
+                .setTags(Arrays.asList("tag1", "tag2"))
+                .setType(NoteType.GENE);
         note = catalogManager.getNotesManager().updateOrganizationNote(note.getId(), noteUpdateParams, INCLUDE_RESULT, ownerToken).first();
         assertEquals(2, note.getVersion());
         assertEquals(orgOwnerUserId, note.getUserId());
+        assertEquals(NoteType.GENE, note.getType());
         assertEquals(2, note.getTags().size());
         assertArrayEquals(noteUpdateParams.getTags().toArray(), note.getTags().toArray());
 

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

@@ -21,7 +21,7 @@
 #' | -- | :-- | --: |
 #' | create | /{apiVersion}/organizations/create | include, exclude, includeResult, body[*] |
 #' | 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 |
+#' | searchNotes | /{apiVersion}/organizations/notes/search | include, exclude, creationDate, modificationDate, id, type, scope, visibility, uuid, userId, tags, version |
 #' | deleteNotes | /{apiVersion}/organizations/notes/{id}/delete | id[*], includeResult |
 #' | 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[*] |
@@ -64,6 +64,7 @@ setMethod("organizationClient", "OpencgaR", function(OpencgaR, id, organization,
         #' @param creationDate Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
         #' @param modificationDate Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
         #' @param id Note unique identifier.
+        #' @param type Note type.
         #' @param scope Scope of the Note.
         #' @param visibility Visibility of the Note.
         #' @param uuid Unique 32-character identifier assigned automatically by OpenCGA.

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

@@ -29,7 +29,7 @@
 #' | updateGroups | /{apiVersion}/studies/{study}/groups/update | study[*], action, body[*] |
 #' | updateGroupsUsers | /{apiVersion}/studies/{study}/groups/{group}/users/update | study[*], group[*], action, body[*] |
 #' | 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 |
+#' | searchNotes | /{apiVersion}/studies/{study}/notes/search | include, exclude, study[*], creationDate, modificationDate, id, type, 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[*], tagsAction, includeResult, body[*] |
 #' | permissionRules | /{apiVersion}/studies/{study}/permissionRules | study[*], entity[*] |
@@ -169,6 +169,7 @@ setMethod("studyClient", "OpencgaR", function(OpencgaR, group, id, members, stud
         #' @param creationDate Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
         #' @param modificationDate Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
         #' @param id Note unique identifier.
+        #' @param type Note type.
         #' @param uuid Unique 32-character identifier assigned automatically by OpenCGA.
         #' @param userId User that wrote that Note.
         #' @param tags Note tags.