catalog: add new type field in Note data model, #TASK-7046

opencb · Oct 7, 2024 · 0f94256 · 0f94256
1 parent 3b7a8df
commit 0f94256
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Showing 11 changed files with 77 additions and 11 deletions.
diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/api/NoteDBAdaptor.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/api/NoteDBAdaptor.java
@@ -31,6 +31,7 @@ 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, ""),

diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/NoteMongoDBAdaptor.java b/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:

diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationManager.java
@@ -210,6 +210,9 @@ 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)

diff --git a/opencga-catalog/src/main/resources/catalog-indexes.txt b/opencga-catalog/src/main/resources/catalog-indexes.txt
@@ -2,6 +2,7 @@
 {"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": {}}

diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/api/FieldConstants.java b/opencga-core/src/main/java/org/opencb/opencga/core/api/FieldConstants.java
@@ -54,6 +54,7 @@ public class FieldConstants {
     public static final String NOTES_ID_DESCRIPTION = "Note unique identifier.";
     public static final String NOTES_SCOPE_DESCRIPTION = "Scope of the Note.";
     public static final String NOTES_STUDY_DESCRIPTION = "Study FQN if the Note scope is STUDY.";
+    public static final String NOTES_TYPE_DESCRIPTION = "Note type.";
     public static final String NOTES_TAGS_DESCRIPTION = "Note tags.";
     public static final String NOTES_USER_ID_DESCRIPTION = "User that wrote that Note.";
     public static final String NOTES_VISIBILITY_DESCRIPTION = "Visibility of the Note.";
@@ -62,6 +63,7 @@ public class FieldConstants {
 
     public static final String NOTES_ID_PARAM = "id";
     public static final String NOTES_SCOPE_PARAM = "scope";
+    public static final String NOTES_TYPE_PARAM = "type";
     public static final String NOTES_STUDY_PARAM = "study";
     public static final String NOTES_TAGS_PARAM = "tags";
     public static final String NOTES_USER_ID_PARAM = "userId";

diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/models/notes/Note.java b/opencga-core/src/main/java/org/opencb/opencga/core/models/notes/Note.java
@@ -26,6 +26,9 @@ public class Note extends PrivateStudyUid {
     @DataField(id = "study", indexed = true, immutable = true, description = FieldConstants.NOTES_STUDY_DESCRIPTION)
     private String study;
 
+    @DataField(id = "type", indexed = true, description = FieldConstants.NOTES_TYPE_DESCRIPTION)
+    private NoteType type;
+
     @DataField(id = "tags", indexed = true, description = FieldConstants.NOTES_TAGS_DESCRIPTION)
     private List<String> tags;
 
@@ -73,12 +76,13 @@ public enum Type {
     public Note() {
     }
 
-    public Note(String id, String uuid, Scope scope, String study, List<String> tags, String userId, Visibility visibility, int version,
-                String creationDate, String modificationDate, Type valueType, Object value) {
+    public Note(String id, String uuid, Scope scope, String study, NoteType type, List<String> tags, String userId, Visibility visibility,
+                int version, String creationDate, String modificationDate, Type valueType, Object value) {
         this.id = id;
         this.uuid = uuid;
         this.scope = scope;
         this.study = study;
+        this.type = type;
         this.tags = tags;
         this.userId = userId;
         this.visibility = visibility;
@@ -91,11 +95,12 @@ public Note(String id, String uuid, Scope scope, String study, List<String> tags
 
     @Override
     public String toString() {
-        final StringBuilder sb = new StringBuilder("Notes{");
+        final StringBuilder sb = new StringBuilder("Note{");
         sb.append("id='").append(id).append('\'');
         sb.append(", uuid='").append(uuid).append('\'');
         sb.append(", scope=").append(scope);
         sb.append(", study='").append(study).append('\'');
+        sb.append(", type=").append(type);
         sb.append(", tags=").append(tags);
         sb.append(", userId='").append(userId).append('\'');
         sb.append(", visibility=").append(visibility);
@@ -144,6 +149,15 @@ public Note setStudy(String study) {
         return this;
     }
 
+    public NoteType getType() {
+        return type;
+    }
+
+    public Note setType(NoteType type) {
+        this.type = type;
+        return this;
+    }
+
     public List<String> getTags() {
         return tags;
     }

diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/models/notes/NoteCreateParams.java b/opencga-core/src/main/java/org/opencb/opencga/core/models/notes/NoteCreateParams.java
@@ -8,6 +8,7 @@
 public class NoteCreateParams {
 
     private String id;
+    private NoteType type;
     private List<String> tags;
     private Note.Visibility visibility;
     private Note.Type valueType;
@@ -16,8 +17,9 @@ public class NoteCreateParams {
     public NoteCreateParams() {
     }
 
-    public NoteCreateParams(String id, List<String> tags, Note.Visibility visibility, Note.Type valueType, Object value) {
+    public NoteCreateParams(String id, NoteType type, List<String> tags, Note.Visibility visibility, Note.Type valueType, Object value) {
         this.id = id;
+        this.type = type;
         this.tags = tags;
         this.visibility = visibility;
         this.valueType = valueType;
@@ -26,8 +28,9 @@ public NoteCreateParams(String id, List<String> tags, Note.Visibility visibility
 
     @Override
     public String toString() {
-        final StringBuilder sb = new StringBuilder("NotesCreateParams{");
+        final StringBuilder sb = new StringBuilder("NoteCreateParams{");
         sb.append("id='").append(id).append('\'');
+        sb.append(", type=").append(type);
         sb.append(", tags=").append(tags);
         sb.append(", visibility=").append(visibility);
         sb.append(", valueType=").append(valueType);
@@ -37,8 +40,8 @@ public String toString() {
     }
 
     public Note toNote(Note.Scope scope, String userId) {
-        return new Note(id, null, scope, null, tags != null ? tags : Collections.emptyList(), userId, visibility, 1, TimeUtils.getTime(),
-                TimeUtils.getTime(), valueType, value != null ? value : Collections.emptyMap());
+        return new Note(id, null, scope, null, type, tags != null ? tags : Collections.emptyList(), userId, visibility, 1,
+                TimeUtils.getTime(), TimeUtils.getTime(), valueType, value != null ? value : Collections.emptyMap());
     }
 
     public String getId() {
@@ -50,6 +53,15 @@ public NoteCreateParams setId(String id) {
         return this;
     }
 
+    public NoteType getType() {
+        return type;
+    }
+
+    public NoteCreateParams setType(NoteType type) {
+        this.type = type;
+        return this;
+    }
+
     public List<String> getTags() {
         return tags;
     }

diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/models/notes/NoteType.java b/opencga-core/src/main/java/org/opencb/opencga/core/models/notes/NoteType.java
@@ -0,0 +1,18 @@
+package org.opencb.opencga.core.models.notes;
+
+public enum NoteType {
+    VARIANT,
+    GENE,
+    TRANSCRIPT,
+    PROTEIN,
+    JOB,
+    FILE,
+    SAMPLE,
+    INDIVIDUAL,
+    FAMILY,
+    COHORT,
+    DISEASE_PANEL,
+    CLINICAL_ANALYSIS,
+    WORKFLOW,
+    OTHER
+}
diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/models/notes/NoteUpdateParams.java b/opencga-core/src/main/java/org/opencb/opencga/core/models/notes/NoteUpdateParams.java
@@ -10,14 +10,16 @@
 
 public class NoteUpdateParams {
 
+    private NoteType type;
     private List<String> tags;
     private Note.Visibility visibility;
     private Object value;
 
     public NoteUpdateParams() {
     }
 
-    public NoteUpdateParams(List<String> tags, Note.Visibility visibility, Object value) {
+    public NoteUpdateParams(NoteType type, List<String> tags, Note.Visibility visibility, Object value) {
+        this.type = type;
         this.tags = tags;
         this.visibility = visibility;
         this.value = value;
@@ -30,14 +32,24 @@ public ObjectMap getUpdateMap() throws JsonProcessingException {
 
     @Override
     public String toString() {
-        final StringBuilder sb = new StringBuilder("NotesUpdateParams{");
-        sb.append("tags=").append(tags);
+        final StringBuilder sb = new StringBuilder("NoteUpdateParams{");
+        sb.append("type=").append(type);
+        sb.append(", tags=").append(tags);
         sb.append(", visibility=").append(visibility);
         sb.append(", value=").append(value);
         sb.append('}');
         return sb.toString();
     }
 
+    public NoteType getType() {
+        return type;
+    }
+
+    public NoteUpdateParams setType(NoteType type) {
+        this.type = type;
+        return this;
+    }
+
     public List<String> getTags() {
         return tags;
     }

diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/rest/OrganizationWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/server/rest/OrganizationWSServer.java
@@ -160,6 +160,7 @@ public Response noteSearch(
             @ApiParam(value = ParamConstants.CREATION_DATE_DESCRIPTION) @QueryParam(ParamConstants.CREATION_DATE_PARAM) String creationDate,
             @ApiParam(value = ParamConstants.MODIFICATION_DATE_DESCRIPTION) @QueryParam(ParamConstants.MODIFICATION_DATE_PARAM) String modificationDate,
             @ApiParam(value = FieldConstants.NOTES_ID_DESCRIPTION) @QueryParam(FieldConstants.NOTES_ID_PARAM) String noteId,
+            @ApiParam(value = FieldConstants.NOTES_TYPE_DESCRIPTION) @QueryParam(FieldConstants.NOTES_TYPE_PARAM) String type,
             @ApiParam(value = FieldConstants.NOTES_SCOPE_DESCRIPTION) @QueryParam(FieldConstants.NOTES_SCOPE_PARAM) String scope,
             @ApiParam(value = FieldConstants.NOTES_VISIBILITY_DESCRIPTION) @QueryParam(FieldConstants.NOTES_VISIBILITY_PARAM) String visibility,
             @ApiParam(value = FieldConstants.GENERIC_UUID_DESCRIPTION) @QueryParam("uuid") String uuid,

diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/rest/StudyWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/server/rest/StudyWSServer.java
@@ -568,6 +568,7 @@ public Response noteSearch(
             @ApiParam(value = ParamConstants.CREATION_DATE_DESCRIPTION) @QueryParam(ParamConstants.CREATION_DATE_PARAM) String creationDate,
             @ApiParam(value = ParamConstants.MODIFICATION_DATE_DESCRIPTION) @QueryParam(ParamConstants.MODIFICATION_DATE_PARAM) String modificationDate,
             @ApiParam(value = FieldConstants.NOTES_ID_DESCRIPTION) @QueryParam(FieldConstants.NOTES_ID_PARAM) String noteId,
+            @ApiParam(value = FieldConstants.NOTES_TYPE_DESCRIPTION) @QueryParam(FieldConstants.NOTES_TYPE_PARAM) String type,
             @ApiParam(value = FieldConstants.GENERIC_UUID_DESCRIPTION) @QueryParam("uuid") String uuid,
             @ApiParam(value = FieldConstants.NOTES_USER_ID_DESCRIPTION) @QueryParam(FieldConstants.NOTES_USER_ID_PARAM) String userId,
             @ApiParam(value = FieldConstants.NOTES_TAGS_DESCRIPTION) @QueryParam(FieldConstants.NOTES_TAGS_PARAM) String tags,