TASK-5716 - Renaming a file is not reflected on the list of files contained by samples

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

@@ -136,7 +136,7 @@ private void status() throws CatalogException, JsonProcessingException {
             if (catalogManager.existsCatalogDB()) {
                 result.put("installed", true);
 
-                MongoDBAdaptorFactory factory = new MongoDBAdaptorFactory(configuration);
+                MongoDBAdaptorFactory factory = new MongoDBAdaptorFactory(configuration, catalogManager.getIoManagerFactory());
                 MongoDBCollection metaCollection = factory.getMongoDBCollectionMap().get(MongoDBAdaptorFactory.METADATA_COLLECTION);
                 Document metaDocument = metaCollection.find(new Document(), QueryOptions.empty()).first();
 

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

@@ -58,12 +58,16 @@ OpenCGAResult update(Query query, ObjectMap parameters, List<VariableSet> variab
     /**
      * Add the variable to all the possible annotations from the variableSetId using the default value.
      *
+     * @param studyUid      Study uid.
      * @param variableSetId variable set id to identify the annotations that will add a new annotation.
-     * @param variable new variable that will be added.
+     * @param variable      new variable that will be added.
      * @return a OpenCGAResult object.
      * @throws CatalogDBException if the variable could not be added to an existing annotationSet.
+     * @throws CatalogParameterException if there is any unexpected parameter.
+     * @throws CatalogAuthorizationException if the operation is not authorized.
      */
-    OpenCGAResult addVariableToAnnotations(long variableSetId, Variable variable) throws CatalogDBException;
+    OpenCGAResult addVariableToAnnotations(long studyUid, long variableSetId, Variable variable)
+            throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException;
 
 //    /**
 //     * This method will rename the id of all the annotations corresponding to the variableSetId changing oldName per newName.
@@ -80,21 +84,25 @@ OpenCGAResult update(Query query, ObjectMap parameters, List<VariableSet> variab
     /**
      * Remove the annotation with annotationName from the annotation set.
      *
-     * @param variableSetId variable set id for which the annotationSets have to delete the annotation.
+     * @param studyUid       Study uid.
+     * @param variableSetId  variable set id for which the annotationSets have to delete the annotation.
      * @param annotationName Annotation name.
      * @return a OpenCGAResult object.
      * @throws CatalogDBException when there is an error in the database.
+     * @throws CatalogParameterException if there is any unexpected parameter.
+     * @throws CatalogAuthorizationException if the operation is not authorized.
      */
-    OpenCGAResult removeAnnotationField(long variableSetId, String annotationName) throws CatalogDBException;
+    OpenCGAResult removeAnnotationField(long studyUid, long variableSetId, String annotationName)
+            throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException;
 
     /**
      * Makes a groupBy to obtain the different values that every annotation has and the total number of each.
      *
      *
-     * @param studyId study id.
+     * @param studyUid study uid.
      * @param variableSetId variable set id for which the group by will be done.
      * @return a list of Feature count with every different value.
      * @throws CatalogDBException when there is an error in the database.
      */
-    OpenCGAResult<VariableSummary> getAnnotationSummary(long studyId, long variableSetId) throws CatalogDBException;
+    OpenCGAResult<VariableSummary> getAnnotationSummary(long studyUid, long variableSetId) throws CatalogDBException;
 }

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

@@ -25,9 +25,7 @@
 import org.opencb.opencga.catalog.exceptions.CatalogParameterException;
 import org.opencb.opencga.core.response.OpenCGAResult;
 
-import java.util.ArrayList;
 import java.util.List;
-import java.util.Objects;
 import java.util.function.Consumer;
 
 /**
@@ -61,19 +59,6 @@ default OpenCGAResult<T> stats() {
     OpenCGAResult<T> get(Query query, QueryOptions options)
             throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException;
 
-    OpenCGAResult nativeGet(Query query, QueryOptions options)
-            throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException;
-
-    default List<OpenCGAResult> nativeGet(List<Query> queries, QueryOptions options)
-            throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
-        Objects.requireNonNull(queries);
-        List<OpenCGAResult> queryResults = new ArrayList<>(queries.size());
-        for (Query query : queries) {
-            queryResults.add(nativeGet(query, options));
-        }
-        return queryResults;
-    }
-
     OpenCGAResult<T> update(long id, ObjectMap parameters, QueryOptions queryOptions)
             throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException;
 

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

@@ -287,32 +287,6 @@ OpenCGAResult<File> get(long fileId, QueryOptions options)
     OpenCGAResult<File> getAllInStudy(long studyId, QueryOptions options)
             throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException;
 
-    /***
-     * Retrieves all the files present in the folder.
-     *
-     * @param studyId Study id where the files will be extracted from.
-     * @param path Directory where the files will be extracted from.
-     * @param options Options to filter the file output.
-     * @return A OpenCGAResult object containing the files present in the folder of the given study.
-     * @throws CatalogDBException when the study or the path does not exist.
-     */
-    OpenCGAResult<File> getAllFilesInFolder(long studyId, String path, QueryOptions options) throws CatalogDBException;
-
-    /***
-     * Renames the file.
-     *
-     * @param fileId Id of the file to be renamed.
-     * @param filePath New file or directory name (containing the full path).
-     * @param fileUri New file uri (containing the full path).
-     * @param options Options to filter the file output.
-     * @return A OpenCGAResult object.
-     * @throws CatalogDBException when the filePath already exists.
-     * @throws CatalogParameterException if there is any formatting error.
-     * @throws CatalogAuthorizationException if the user is not authorised to perform the query.
-     */
-    OpenCGAResult rename(long fileId, String filePath, String fileUri, QueryOptions options)
-            throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException;
-
     /**
      * Removes the mark of the permission rule (if existed) from all the entries from the study to notify that permission rule would need to
      * be applied.

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

@@ -186,20 +186,9 @@ default List<OpenCGAResult<Project>> get(List<Query> queries, QueryOptions optio
         return queryResults;
     }
 
-    OpenCGAResult nativeGet(Query query, QueryOptions options) throws CatalogDBException;
-
     OpenCGAResult nativeGet(Query query, QueryOptions options, String user)
             throws CatalogDBException, CatalogAuthorizationException;
 
-    default List<OpenCGAResult> nativeGet(List<Query> queries, QueryOptions options) throws CatalogDBException {
-        Objects.requireNonNull(queries);
-        List<OpenCGAResult> queryResults = new ArrayList<>(queries.size());
-        for (Query query : queries) {
-            queryResults.add(nativeGet(query, options));
-        }
-        return queryResults;
-    }
-
     OpenCGAResult<Project> update(long id, ObjectMap parameters, QueryOptions queryOptions)
             throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException;
 

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

@@ -82,20 +82,9 @@ default List<OpenCGAResult<Study>> get(List<Query> queries, QueryOptions options
         return queryResults;
     }
 
-    OpenCGAResult nativeGet(Query query, QueryOptions options) throws CatalogDBException;
-
     OpenCGAResult nativeGet(Query query, QueryOptions options, String user)
             throws CatalogDBException, CatalogAuthorizationException;
 
-    default List<OpenCGAResult> nativeGet(List<Query> queries, QueryOptions options) throws CatalogDBException {
-        Objects.requireNonNull(queries);
-        List<OpenCGAResult> queryResults = new ArrayList<>(queries.size());
-        for (Query query : queries) {
-            queryResults.add(nativeGet(query, options));
-        }
-        return queryResults;
-    }
-
     OpenCGAResult<Study> update(long id, ObjectMap parameters, QueryOptions queryOptions)
             throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException;
 
@@ -395,14 +384,14 @@ default void checkVariableSetExists(String variableSetId, long studyId) throws C
 
     OpenCGAResult<VariableSet> createVariableSet(long studyId, VariableSet variableSet) throws CatalogDBException;
 
-    OpenCGAResult<VariableSet> addFieldToVariableSet(long variableSetId, Variable variable, String user)
-            throws CatalogDBException, CatalogAuthorizationException;
+    OpenCGAResult<VariableSet> addFieldToVariableSet(long studyUid, long variableSetId, Variable variable, String user)
+            throws CatalogDBException, CatalogAuthorizationException, CatalogParameterException;
 
     OpenCGAResult<VariableSet> renameFieldVariableSet(long variableSetId, String oldName, String newName, String user)
             throws CatalogDBException, CatalogAuthorizationException;
 
-    OpenCGAResult<VariableSet> removeFieldFromVariableSet(long variableSetId, String name, String user)
-            throws CatalogDBException, CatalogAuthorizationException;
+    OpenCGAResult<VariableSet> removeFieldFromVariableSet(long studyUid, long variableSetId, String name, String user)
+            throws CatalogDBException, CatalogAuthorizationException, CatalogParameterException;
 
     OpenCGAResult<VariableSet> getVariableSet(long variableSetUid, QueryOptions options) throws CatalogDBException;