catalog: add method to remove user from all groups in one go, #TASK-7192

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_1_0/UserBanMigration.java

@@ -38,6 +38,7 @@ protected void run() throws Exception {
                     );
                 });
 
+        // Patch 2. Organization 'configuration.defaultUserExpirationDate' field was not set for existing organizations
         MongoCollection<Document> orgCollection = getMongoCollection(OrganizationMongoDBAdaptorFactory.ORGANIZATION_COLLECTION);
         orgCollection.updateMany(Filters.exists("configuration.defaultUserExpirationDate", false),
                 Updates.set("configuration.defaultUserExpirationDate", Constants.DEFAULT_USER_EXPIRATION_DATE));

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_2_1/MoveUserAccountToInternalMigration.java

@@ -1,14 +1,17 @@
 package org.opencb.opencga.app.migrations.v3.v3_2_1;
 
+import com.mongodb.client.MongoCollection;
 import com.mongodb.client.model.Filters;
 import com.mongodb.client.model.Projections;
 import com.mongodb.client.model.UpdateOneModel;
+import com.mongodb.client.model.Updates;
 import org.bson.Document;
 import org.bson.conversions.Bson;
 import org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor;
 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.catalog.utils.Constants;
 
 import java.util.Arrays;
 
@@ -46,5 +49,14 @@ protected void run() throws Exception {
 
                     bulk.add(new UpdateOneModel<>(Filters.eq("_id", document.get("_id")), updateDocument.toFinalUpdateDocument()));
                 });
+
+        // Due to patch 2 from TASK-6013, default user expirationDate for some users was not set.
+        MongoCollection<Document> userCollection = getMongoCollection(OrganizationMongoDBAdaptorFactory.USER_COLLECTION);
+        userCollection.updateMany(
+                Filters.or(
+                        Filters.eq("internal.account.expirationDate", null),
+                        Filters.eq("internal.account.expirationDate", "")
+                ),
+                Updates.set("internal.account.expirationDate", Constants.DEFAULT_USER_EXPIRATION_DATE));
     }
 }

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

@@ -252,6 +252,8 @@ OpenCGAResult<Group> setUsersToGroup(long studyId, String groupId, List<String>
 
     OpenCGAResult<Group> removeUsersFromAllGroups(long studyId, List<String> users) throws CatalogException;
 
+    OpenCGAResult<Group> removeUsersFromAllGroups(List<String> users) throws CatalogException;
+
     /**
      * Delete a group.
      *

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

@@ -418,13 +418,13 @@ private void fixFederationClientForRemoval(ObjectMap parameters) {
         }
         List<Document> federationParamList = new LinkedList<>();
         for (Object federationClient : parameters.getAsList(QueryParams.FEDERATION_CLIENTS.key())) {
-            if (federationClient instanceof FederationServerParams) {
-                federationParamList.add(new Document("id", ((FederationServerParams) federationClient).getId()));
+            if (federationClient instanceof FederationClientParams) {
+                federationParamList.add(new Document("id", ((FederationClientParams) federationClient).getId()));
             } else {
                 federationParamList.add(new Document("id", ((Map) federationClient).get("id")));
             }
         }
-        parameters.putNested(QueryParams.FEDERATION_CLIENTS.key(), federationParamList, false);
+        parameters.put(QueryParams.FEDERATION_CLIENTS.key(), federationParamList, false);
     }
 
     private void fixFederationServerForRemoval(ObjectMap parameters) {
@@ -433,13 +433,13 @@ private void fixFederationServerForRemoval(ObjectMap parameters) {
         }
         List<Document> federationParamList = new LinkedList<>();
         for (Object federationServer : parameters.getAsList(QueryParams.FEDERATION_SERVERS.key())) {
-            if (federationServer instanceof FederationClientParams) {
-                federationParamList.add(new Document("id", ((FederationClientParams) federationServer).getId()));
+            if (federationServer instanceof FederationServerParams) {
+                federationParamList.add(new Document("id", ((FederationServerParams) federationServer).getId()));
             } else {
                 federationParamList.add(new Document("id", ((Map) federationServer).get("id")));
             }
         }
-        parameters.putNested(QueryParams.FEDERATION_SERVERS.key(), federationParamList, false);
+        parameters.put(QueryParams.FEDERATION_SERVERS.key(), federationParamList, false);
     }
 
     private void fixAuthOriginsForRemoval(ObjectMap parameters) {

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

@@ -492,7 +492,7 @@ OpenCGAResult<Group> removeUsersFromAdminsGroup(ClientSession clientSession, Lis
 
     @Override
     public OpenCGAResult<Group> removeUsersFromAllGroups(long studyId, List<String> users) throws CatalogException {
-        if (users == null || users.size() == 0) {
+        if (CollectionUtils.isEmpty(users)) {
             throw new CatalogDBException("Unable to remove users from groups. List of users is empty");
         }
 
@@ -507,7 +507,7 @@ public OpenCGAResult<Group> removeUsersFromAllGroups(long studyId, List<String>
                 Bson pull = Updates.pullAll("groups.$.userIds", users);
 
                 // Pull those users while they are still there
-                DataResult update;
+                DataResult<?> update;
                 do {
                     update = studyCollection.update(clientSession, query, pull, null);
                 } while (update.getNumUpdated() > 0);
@@ -520,6 +520,36 @@ public OpenCGAResult<Group> removeUsersFromAllGroups(long studyId, List<String>
         }
     }
 
+    @Override
+    public OpenCGAResult<Group> removeUsersFromAllGroups(List<String> users) throws CatalogException {
+        if (CollectionUtils.isEmpty(users)) {
+            throw new CatalogDBException("Unable to remove users from groups. List of users is empty");
+        }
+
+        try {
+            return runTransaction(clientSession -> {
+                long tmpStartTime = startQuery();
+                logger.debug("Removing list of users '{}' from all groups from all studies", users);
+
+                Document query = new Document()
+                        .append(QueryParams.GROUP_USER_IDS.key(), new Document("$in", users));
+                Bson pull = Updates.pullAll("groups.$.userIds", users);
+
+                QueryOptions multi = new QueryOptions(MongoDBCollection.MULTI, true);
+                // Pull those users while they are still there
+                DataResult<?> update;
+                do {
+                    update = studyCollection.update(clientSession, query, pull, multi);
+                } while (update.getNumUpdated() > 0);
+
+                return endWrite(tmpStartTime, -1, -1, null);
+            });
+        } catch (Exception e) {
+            logger.error("Could not remove users from all groups from all studies. {}", e.getMessage());
+            throw e;
+        }
+    }
+
     @Override
     public OpenCGAResult<Group> deleteGroup(long studyId, String groupId) throws CatalogDBException {
         Bson queryBson = new Document()