TASK-7413 - Implement notifications system

opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantStorageManager.java

@@ -1080,7 +1080,7 @@ protected VariantStorageEngine getVariantStorageEngineByProject(String project,
     private VariantStorageEngine getVariantStorageEngineByDatastore(DataStore dataStore, String alias, String projectFqnStr, String token) throws StorageEngineException, CatalogException {
         VariantStorageEngine variantStorageEngine = storageEngineFactory
                 .getVariantStorageEngine(dataStore.getStorageEngine(), dataStore.getDbName(), alias);
-        CatalogFqn projectFqn = CatalogFqn.fromProjectFqn(projectFqnStr);
+        CatalogFqn projectFqn = CatalogFqn.extractFqnFromProjectFqn(projectFqnStr);
         variantStorageEngine.getOptions().put("catalog.organization", projectFqn.getOrganizationId());
         variantStorageEngine.getOptions().put("catalog.project", projectFqn.getProjectId());
         setCellbaseConfiguration(variantStorageEngine, projectFqnStr, token);

opencga-app/app/misc/clients/r_client_generator.py

@@ -13,6 +13,7 @@ def __init__(self, server_url, output_dir):
         self.categories = {
         	'Federations': 'Federation',
         	'Organizations': 'Organization',
+        	'Notifications': 'Notification',
             'Users': 'User',
             'Projects': 'Project',
             'Studies': 'Study',

opencga-app/app/misc/clients/rest_client_generator.py

@@ -38,6 +38,7 @@ def __init__(self, rest_api_file, output_dir):
         self.categories = {
         	'Federations': 'Federation',
             'Organizations': 'Organization',
+            'Notifications': 'Notification',
             'Users': 'User',
             'Projects': 'Project',
             'Studies': 'Study',

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

@@ -81,7 +81,6 @@ public AdminCliOptionsParser() {
         usersSubCommands.addCommand("import", usersCommandOptions.importCommandOptions);
         usersSubCommands.addCommand("sync", usersCommandOptions.syncCommandOptions);
         usersSubCommands.addCommand("delete", usersCommandOptions.deleteUserCommandOptions);
-        usersSubCommands.addCommand("quota", usersCommandOptions.quotaUserCommandOptions);
         usersSubCommands.addCommand("stats", usersCommandOptions.statsUserCommandOptions);
 
         auditCommandOptions = new AuditCommandOptions();
@@ -238,7 +237,6 @@ public class UsersCommandOptions extends CommandOptions {
         public SyncCommandOptions syncCommandOptions;
         public DeleteUserCommandOptions deleteUserCommandOptions;
         public StatsUserCommandOptions statsUserCommandOptions;
-        public QuotaUserCommandOptions quotaUserCommandOptions;
 
         public AdminCommonCommandOptions commonOptions = AdminCliOptionsParser.this.commonCommandOptions;
 
@@ -248,7 +246,6 @@ public UsersCommandOptions() {
             this.syncCommandOptions = new SyncCommandOptions();
             this.deleteUserCommandOptions = new DeleteUserCommandOptions();
             this.statsUserCommandOptions = new StatsUserCommandOptions();
-            this.quotaUserCommandOptions = new QuotaUserCommandOptions();
         }
     }
 
@@ -656,21 +653,6 @@ public class DeleteUserCommandOptions extends CatalogDatabaseCommandOptions {
 
     }
 
-
-    @Parameters(commandNames = {"quota"}, commandDescription = "Set a new disk quota for an user")
-    public class QuotaUserCommandOptions extends CatalogDatabaseCommandOptions {
-
-        @ParametersDelegate
-        public AdminCommonCommandOptions commonOptions = AdminCliOptionsParser.this.commonCommandOptions;
-
-
-        @Parameter(names = {"-u", "--user-id"}, description = "User id to get stats from", required = true, arity = 1)
-        public String userId;
-
-        @Parameter(names = {"--quota"}, description = "Disk quota in GB", required = true, arity = 1)
-        public long quota;
-    }
-
     @Parameters(commandNames = {"stats"}, commandDescription = "Print summary stats for an user")
     public class StatsUserCommandOptions extends CatalogDatabaseCommandOptions {
 
@@ -683,7 +665,6 @@ public class StatsUserCommandOptions extends CatalogDatabaseCommandOptions {
 
     }
 
-
     /*
      * TOOL SUB-COMMANDS
      */

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

@@ -20,11 +20,9 @@
 import org.apache.commons.lang3.StringUtils;
 import org.opencb.commons.datastore.core.DataResult;
 import org.opencb.commons.datastore.core.Event;
-import org.opencb.commons.datastore.core.ObjectMap;
 import org.opencb.commons.datastore.core.QueryOptions;
 import org.opencb.commons.utils.ListUtils;
 import org.opencb.opencga.app.cli.admin.AdminCliOptionsParser;
-import org.opencb.opencga.catalog.db.api.UserDBAdaptor;
 import org.opencb.opencga.catalog.exceptions.CatalogException;
 import org.opencb.opencga.catalog.managers.CatalogManager;
 import org.opencb.opencga.core.models.user.User;
@@ -63,9 +61,6 @@ public void execute() throws Exception {
             case "delete":
                 delete();
                 break;
-            case "quota":
-                setQuota();
-                break;
             default:
                 logger.error("Subcommand not valid");
                 break;
@@ -189,20 +184,4 @@ private void delete() throws CatalogException, IOException {
         }
     }
 
-    private void setQuota() throws CatalogException {
-        setCatalogDatabaseCredentials(usersCommandOptions.quotaUserCommandOptions.databaseHost,
-                usersCommandOptions.quotaUserCommandOptions.prefix, usersCommandOptions.quotaUserCommandOptions.databaseUser,
-                usersCommandOptions.quotaUserCommandOptions.databasePassword,
-                usersCommandOptions.quotaUserCommandOptions.commonOptions.adminPassword);
-
-        try (CatalogManager catalogManager = new CatalogManager(configuration)) {
-            catalogManager.getUserManager().loginAsAdmin(usersCommandOptions.quotaUserCommandOptions.commonOptions.adminPassword);
-
-            User user = catalogManager.getUserManager().update(usersCommandOptions.quotaUserCommandOptions.userId, new ObjectMap
-                    (UserDBAdaptor.QueryParams.QUOTA.key(), usersCommandOptions.quotaUserCommandOptions.quota * 1073741824), null, null).first();
-
-            System.out.println("The disk quota has been properly updated: " + user.toString());
-        }
-    }
-
 }

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java

@@ -24,7 +24,7 @@
 
 public abstract class OpenCgaCompleter implements Completer {
 
-    protected List<Candidate> commands = asList("login","logout","help","use","variant","projects","panels","clinical","jobs","admin","workflows","individuals","families","users","samples","alignments","meta","organizations","studies","files","operations","cohorts")
+    protected List<Candidate> commands = asList("login","logout","help","use","variant","projects","panels","clinical","jobs","admin","workflows","individuals","families","users","samples","alignments","meta","organizations","studies","files","operations","notifications","cohorts")
             .stream()
             .map(Candidate::new)
             .collect(toList());
@@ -114,6 +114,11 @@ public abstract class OpenCgaCompleter implements Completer {
             .map(Candidate::new)
             .collect(toList());
 
+    private List<Candidate> notificationsList = asList( "aggregationstats","create","search","info","visit")
+            .stream()
+            .map(Candidate::new)
+            .collect(toList());
+
     private List<Candidate> cohortsList = asList( "acl-update","aggregationstats","annotation-sets-load","create","distinct","generate","search","acl","delete","info","update","annotation-sets-annotations-update")
             .stream()
             .map(Candidate::new)
@@ -144,6 +149,7 @@ public void complete(LineReader lineReader, ParsedLine parsedLine, List<Candidat
         mapCandidates.put( "studies", studiesList);
         mapCandidates.put( "files", filesList);
         mapCandidates.put( "operations", operationsList);
+        mapCandidates.put( "notifications", notificationsList);
         mapCandidates.put( "cohorts", cohortsList);
          candidates.addAll(checkCandidates(mapCandidates,command)); 
      }

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java

@@ -35,6 +35,7 @@ public class OpencgaCliOptionsParser extends CustomCliOptionsParser {
     private final StudiesCommandOptions studiesCommandOptions;
     private final FilesCommandOptions filesCommandOptions;
     private final OperationsVariantStorageCommandOptions operationsVariantStorageCommandOptions;
+    private final NotificationsCommandOptions notificationsCommandOptions;
     private final CohortsCommandOptions cohortsCommandOptions;
 
     enum OutputFormat {IDS, ID_CSV, NAME_ID_MAP, ID_LIST, RAW, PRETTY_JSON, PLAIN_JSON}
@@ -397,6 +398,15 @@ public OpencgaCliOptionsParser() {
         operationsVariantStorageSubCommands.addCommand("variant-stats-index", operationsVariantStorageCommandOptions.indexVariantStatsCommandOptions);
         operationsVariantStorageSubCommands.addCommand("variant-study-delete", operationsVariantStorageCommandOptions.deleteVariantStudyCommandOptions);
 
+        notificationsCommandOptions = new NotificationsCommandOptions(commonCommandOptions, jCommander);
+        jCommander.addCommand("notifications", notificationsCommandOptions);
+        JCommander notificationsSubCommands = jCommander.getCommands().get("notifications");
+        notificationsSubCommands.addCommand("aggregationstats", notificationsCommandOptions.aggregationStatsCommandOptions);
+        notificationsSubCommands.addCommand("create", notificationsCommandOptions.createCommandOptions);
+        notificationsSubCommands.addCommand("search", notificationsCommandOptions.searchCommandOptions);
+        notificationsSubCommands.addCommand("info", notificationsCommandOptions.infoCommandOptions);
+        notificationsSubCommands.addCommand("visit", notificationsCommandOptions.visitCommandOptions);
+
         cohortsCommandOptions = new CohortsCommandOptions(commonCommandOptions, jCommander);
         jCommander.addCommand("cohorts", cohortsCommandOptions);
         JCommander cohortsSubCommands = jCommander.getCommands().get("cohorts");
@@ -499,6 +509,11 @@ public OperationsVariantStorageCommandOptions getOperationsVariantStorageCommand
     }
 
 
+    public NotificationsCommandOptions getNotificationsCommandOptions() {
+        return notificationsCommandOptions;
+    }
+
+
     public CohortsCommandOptions getCohortsCommandOptions() {
         return cohortsCommandOptions;
     }

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

@@ -13,6 +13,9 @@ public static OpencgaCommandExecutor getOpencgaCommandExecutor(OpencgaCliOptions
             case "organizations":
                 commandExecutor = new OrganizationsCommandExecutor(cliOptionsParser.getOrganizationsCommandOptions());
                 break;
+            case "notifications":
+                commandExecutor = new NotificationsCommandExecutor(cliOptionsParser.getNotificationsCommandOptions());
+                break;
             case "users":
                 commandExecutor = new UsersCommandExecutor(cliOptionsParser.getUsersCommandOptions());
                 break;

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

@@ -0,0 +1,184 @@
+package org.opencb.opencga.app.cli.main.executors;
+
+import com.fasterxml.jackson.databind.DeserializationFeature;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import java.util.HashMap;
+import java.util.List;
+import org.opencb.commons.datastore.core.FacetField;
+import org.opencb.commons.datastore.core.ObjectMap;
+import org.opencb.commons.utils.PrintUtils;
+import org.opencb.opencga.app.cli.main.*;
+import org.opencb.opencga.app.cli.main.executors.OpencgaCommandExecutor;
+import org.opencb.opencga.app.cli.main.options.NotificationsCommandOptions;
+import org.opencb.opencga.catalog.exceptions.CatalogAuthenticationException;
+import org.opencb.opencga.core.common.JacksonUtils;
+import org.opencb.opencga.core.exceptions.ClientException;
+import org.opencb.opencga.core.models.notification.Notification;
+import org.opencb.opencga.core.models.notification.NotificationCreateParams;
+import org.opencb.opencga.core.models.notification.NotificationLevel;
+import org.opencb.opencga.core.models.notification.NotificationScope;
+import org.opencb.opencga.core.response.QueryType;
+import org.opencb.opencga.core.response.RestResponse;
+
+
+/*
+* WARNING: AUTOGENERATED CODE
+*
+* This code was generated by a tool.
+*
+* Manual changes to this file may cause unexpected behavior in your application.
+* Manual changes to this file will be overwritten if the code is regenerated.
+*  
+*/
+/**
+ * This class contains methods for the Notifications command line.
+ *    PATH: /{apiVersion}/notifications
+ */
+public class NotificationsCommandExecutor extends OpencgaCommandExecutor {
+
+    public String categoryName = "notifications";
+    public NotificationsCommandOptions notificationsCommandOptions;
+
+    public NotificationsCommandExecutor(NotificationsCommandOptions notificationsCommandOptions) throws CatalogAuthenticationException {
+        super(notificationsCommandOptions.commonCommandOptions);
+        this.notificationsCommandOptions = notificationsCommandOptions;
+    }
+
+    @Override
+    public void execute() throws Exception {
+
+        logger.debug("Executing Notifications command line");
+
+        String subCommandString = getParsedSubCommand(notificationsCommandOptions.jCommander);
+
+        RestResponse queryResponse = null;
+
+        switch (subCommandString) {
+            case "aggregationstats":
+                queryResponse = aggregationStats();
+                break;
+            case "create":
+                queryResponse = create();
+                break;
+            case "search":
+                queryResponse = search();
+                break;
+            case "info":
+                queryResponse = info();
+                break;
+            case "visit":
+                queryResponse = visit();
+                break;
+            default:
+                logger.error("Subcommand not valid");
+                break;
+        }
+
+        createOutput(queryResponse);
+
+    }
+
+    private RestResponse<FacetField> aggregationStats() throws Exception {
+        logger.debug("Executing aggregationStats in Notifications command line");
+
+        NotificationsCommandOptions.AggregationStatsCommandOptions commandOptions = notificationsCommandOptions.aggregationStatsCommandOptions;
+
+        ObjectMap queryParams = new ObjectMap();
+        queryParams.putIfNotEmpty("organization", commandOptions.organization);
+        queryParams.putIfNotEmpty("uuid", commandOptions.uuid);
+        queryParams.putIfNotEmpty("type", commandOptions.type);
+        queryParams.putIfNotEmpty("scope", commandOptions.scope);
+        queryParams.putIfNotEmpty("fqn", commandOptions.fqn);
+        queryParams.putIfNotEmpty("sender", commandOptions.sender);
+        queryParams.putIfNotEmpty("target", commandOptions.target);
+        queryParams.putIfNotEmpty("receiver", commandOptions.receiver);
+        queryParams.putIfNotEmpty("internalStatus", commandOptions.internalStatus);
+        queryParams.putIfNotNull("visited", commandOptions.visited);
+        queryParams.putIfNotEmpty("creationDate", commandOptions.creationDate);
+        queryParams.putIfNotEmpty("modificationDate", commandOptions.modificationDate);
+        queryParams.putIfNotEmpty("field", commandOptions.field);
+
+        return openCGAClient.getNotificationClient().aggregationStats(queryParams);
+    }
+
+    private RestResponse<Notification> create() throws Exception {
+        logger.debug("Executing create in Notifications command line");
+
+        NotificationsCommandOptions.CreateCommandOptions commandOptions = notificationsCommandOptions.createCommandOptions;
+
+        NotificationCreateParams notificationCreateParams = null;
+        if (commandOptions.jsonDataModel) {
+            RestResponse<Notification> res = new RestResponse<>();
+            res.setType(QueryType.VOID);
+            PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/notifications/create"));
+            return res;
+        } else if (commandOptions.jsonFile != null) {
+            notificationCreateParams = JacksonUtils.getDefaultObjectMapper()
+                    .readValue(new java.io.File(commandOptions.jsonFile), NotificationCreateParams.class);
+        } else {
+            ObjectMap beanParams = new ObjectMap();
+            putNestedIfNotEmpty(beanParams, "subject", commandOptions.subject, true);
+            putNestedIfNotEmpty(beanParams, "content", commandOptions.content, true);
+            putNestedIfNotNull(beanParams, "level", commandOptions.level, true);
+            putNestedIfNotNull(beanParams, "scope", commandOptions.scope, true);
+            putNestedIfNotEmpty(beanParams, "fqn", commandOptions.fqn, true);
+            putNestedIfNotNull(beanParams, "targets", commandOptions.targets, true);
+
+            notificationCreateParams = JacksonUtils.getDefaultObjectMapper().copy()
+                    .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
+                    .readValue(beanParams.toJson(), NotificationCreateParams.class);
+        }
+        return openCGAClient.getNotificationClient().create(notificationCreateParams);
+    }
+
+    private RestResponse<Notification> search() throws Exception {
+        logger.debug("Executing search in Notifications command line");
+
+        NotificationsCommandOptions.SearchCommandOptions commandOptions = notificationsCommandOptions.searchCommandOptions;
+
+        ObjectMap queryParams = new ObjectMap();
+        queryParams.putIfNotEmpty("include", commandOptions.include);
+        queryParams.putIfNotEmpty("exclude", commandOptions.exclude);
+        queryParams.putIfNotNull("limit", commandOptions.limit);
+        queryParams.putIfNotNull("skip", commandOptions.skip);
+        queryParams.putIfNotNull("count", commandOptions.count);
+        queryParams.putIfNotEmpty("organization", commandOptions.organization);
+        queryParams.putIfNotEmpty("uuid", commandOptions.uuid);
+        queryParams.putIfNotEmpty("type", commandOptions.type);
+        queryParams.putIfNotEmpty("scope", commandOptions.scope);
+        queryParams.putIfNotEmpty("fqn", commandOptions.fqn);
+        queryParams.putIfNotEmpty("sender", commandOptions.sender);
+        queryParams.putIfNotEmpty("target", commandOptions.target);
+        queryParams.putIfNotEmpty("receiver", commandOptions.receiver);
+        queryParams.putIfNotEmpty("internalStatus", commandOptions.internalStatus);
+        queryParams.putIfNotNull("visited", commandOptions.visited);
+        queryParams.putIfNotEmpty("creationDate", commandOptions.creationDate);
+        queryParams.putIfNotEmpty("modificationDate", commandOptions.modificationDate);
+
+        return openCGAClient.getNotificationClient().search(queryParams);
+    }
+
+    private RestResponse<Notification> info() throws Exception {
+        logger.debug("Executing info in Notifications command line");
+
+        NotificationsCommandOptions.InfoCommandOptions commandOptions = notificationsCommandOptions.infoCommandOptions;
+
+        ObjectMap queryParams = new ObjectMap();
+        queryParams.putIfNotEmpty("include", commandOptions.include);
+        queryParams.putIfNotEmpty("exclude", commandOptions.exclude);
+        queryParams.putIfNotEmpty("organization", commandOptions.organization);
+
+        return openCGAClient.getNotificationClient().info(commandOptions.notification, queryParams);
+    }
+
+    private RestResponse<Notification> visit() throws Exception {
+        logger.debug("Executing visit in Notifications command line");
+
+        NotificationsCommandOptions.VisitCommandOptions commandOptions = notificationsCommandOptions.visitCommandOptions;
+
+        ObjectMap queryParams = new ObjectMap();
+        queryParams.putIfNotEmpty("organization", commandOptions.organization);
+
+        return openCGAClient.getNotificationClient().visit(commandOptions.notification, queryParams);
+    }
+}