server: remove non-working admin jwt update service, #TASK-7922

Author: pfurio

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

@@ -46,7 +46,6 @@ public class AdminCliOptionsParser extends CliOptionsParser {
     private final ToolsCommandOptions toolsCommandOptions;
     private final ServerCommandOptions serverCommandOptions;
     private final PanelCommandOptions panelCommandOptions;
-    private final AdminCliOptionsParser.MetaCommandOptions metaCommandOptions;
     private final MigrationCommandOptions migrationCommandOptions;
     private final StorageCommandOptions storageCommandOptions;
 
@@ -110,11 +109,6 @@ public AdminCliOptionsParser() {
         panelSubCommands.addCommand("panelapp", panelCommandOptions.panelAppCommandOptions);
         panelSubCommands.addCommand("cancer-gene-census", panelCommandOptions.cancerGeneCensusCommandOptions);
 
-        this.metaCommandOptions = new AdminCliOptionsParser.MetaCommandOptions();
-        this.jCommander.addCommand("meta", this.metaCommandOptions);
-        JCommander metaSubCommands = this.jCommander.getCommands().get("meta");
-        metaSubCommands.addCommand("update", this.metaCommandOptions.metaKeyCommandOptions);
-
         this.migrationCommandOptions = new MigrationCommandOptions(jCommander, commonCommandOptions);
         this.jCommander.addCommand("migration", this.migrationCommandOptions);
         JCommander migrationSubCommands = this.jCommander.getCommands().get("migration");
@@ -323,17 +317,6 @@ public ServerCommandOptions() {
         }
     }
 
-    @Parameters( commandNames = {"meta"}, commandDescription = "Manage Meta data")
-    public class MetaCommandOptions extends AdminCliOptionsParser.CommandOptions {
-
-        public MetaKeyCommandOptions metaKeyCommandOptions;
-        public AdminCommonCommandOptions commonOptions = AdminCliOptionsParser.this.commonCommandOptions;
-
-        public MetaCommandOptions() {
-            this.metaKeyCommandOptions = new MetaKeyCommandOptions();
-        }
-    }
-
     /**
      * Auxiliary class for Database connection.
      */
@@ -862,10 +845,6 @@ public ServerCommandOptions getServerCommandOptions() {
         return serverCommandOptions;
     }
 
-    public AdminCliOptionsParser.MetaCommandOptions getMetaCommandOptions() {
-        return this.metaCommandOptions;
-    }
-
     public PanelCommandOptions getPanelCommandOptions() {
         return panelCommandOptions;
     }

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

@@ -105,9 +105,6 @@ public static void main(String[] args) {
                         case "server":
                             commandExecutor = new ServerCommandExecutor(cliOptionsParser.getServerCommandOptions());
                             break;
-                        case "meta":
-                            commandExecutor = new MetaCommandExecutor(cliOptionsParser.getMetaCommandOptions());
-                            break;
                         case "panel":
                             commandExecutor = new PanelCommandExecutor(cliOptionsParser.getPanelCommandOptions());
                             break;

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

@@ -54,7 +54,7 @@ public abstract class OpenCgaCompleter implements Completer {
             .map(Candidate::new)
             .collect(toList());
 
-    private List<Candidate> adminList = asList( "audit-group-by","catalog-install","catalog-jwt","organizations-list","resource-fetch","users-create","users-import","users-permissions","users-search","users-sync","update-groups-users")
+    private List<Candidate> adminList = asList( "audit-group-by","catalog-install","organizations-list","resource-fetch","users-create","users-import","users-permissions","users-search","users-sync","update-groups-users")
             .stream()
             .map(Candidate::new)
             .collect(toList());

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

@@ -179,7 +179,6 @@ public OpencgaCliOptionsParser() {
         JCommander adminSubCommands = jCommander.getCommands().get("admin");
         adminSubCommands.addCommand("audit-group-by", adminCommandOptions.groupByAuditCommandOptions);
         adminSubCommands.addCommand("catalog-install", adminCommandOptions.installCatalogCommandOptions);
-        adminSubCommands.addCommand("catalog-jwt", adminCommandOptions.jwtCatalogCommandOptions);
         adminSubCommands.addCommand("organizations-list", adminCommandOptions.listOrganizationsCommandOptions);
         adminSubCommands.addCommand("resource-fetch", adminCommandOptions.fetchResourceCommandOptions);
         adminSubCommands.addCommand("users-create", adminCommandOptions.createUsersCommandOptions);

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

@@ -17,7 +17,6 @@
 import org.opencb.opencga.core.models.Acl;
 import org.opencb.opencga.core.models.admin.DeprecatedGroupSyncParams;
 import org.opencb.opencga.core.models.admin.InstallationParams;
-import org.opencb.opencga.core.models.admin.JWTParams;
 import org.opencb.opencga.core.models.admin.UserImportParams;
 import org.opencb.opencga.core.models.admin.UserUpdateGroup;
 import org.opencb.opencga.core.models.common.Enums.Resource;
@@ -70,9 +69,6 @@ public void execute() throws Exception {
             case "catalog-install":
                 queryResponse = installCatalog();
                 break;
-            case "catalog-jwt":
-                queryResponse = jwtCatalog();
-                break;
             case "organizations-list":
                 queryResponse = listOrganizations();
                 break;
@@ -149,35 +145,6 @@ private RestResponse<ObjectMap> installCatalog() throws Exception {
         return openCGAClient.getAdminClient().installCatalog(installationParams);
     }
 
-    private RestResponse<ObjectMap> jwtCatalog() throws Exception {
-        logger.debug("Executing jwtCatalog in Admin command line");
-
-        AdminCommandOptions.JwtCatalogCommandOptions commandOptions = adminCommandOptions.jwtCatalogCommandOptions;
-
-        ObjectMap queryParams = new ObjectMap();
-        queryParams.putIfNotEmpty("organization", commandOptions.organization);
-
-
-        JWTParams jWTParams = null;
-        if (commandOptions.jsonDataModel) {
-            RestResponse<ObjectMap> res = new RestResponse<>();
-            res.setType(QueryType.VOID);
-            PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/catalog/jwt"));
-            return res;
-        } else if (commandOptions.jsonFile != null) {
-            jWTParams = JacksonUtils.getDefaultObjectMapper()
-                    .readValue(new java.io.File(commandOptions.jsonFile), JWTParams.class);
-        } else {
-            ObjectMap beanParams = new ObjectMap();
-            putNestedIfNotEmpty(beanParams, "secretKey", commandOptions.secretKey, true);
-
-            jWTParams = JacksonUtils.getDefaultObjectMapper().copy()
-                    .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
-                    .readValue(beanParams.toJson(), JWTParams.class);
-        }
-        return openCGAClient.getAdminClient().jwtCatalog(jWTParams, queryParams);
-    }
-
     private RestResponse<String> listOrganizations() throws Exception {
         logger.debug("Executing listOrganizations in Admin command line");
 

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

@@ -35,7 +35,6 @@ public class AdminCommandOptions {
 
         public GroupByAuditCommandOptions groupByAuditCommandOptions;
         public InstallCatalogCommandOptions installCatalogCommandOptions;
-        public JwtCatalogCommandOptions jwtCatalogCommandOptions;
         public ListOrganizationsCommandOptions listOrganizationsCommandOptions;
         public FetchResourceCommandOptions fetchResourceCommandOptions;
         public CreateUsersCommandOptions createUsersCommandOptions;
@@ -52,7 +51,6 @@ public AdminCommandOptions(CommonCommandOptions commonCommandOptions, JCommander
         this.commonCommandOptions = commonCommandOptions;
         this.groupByAuditCommandOptions = new GroupByAuditCommandOptions();
         this.installCatalogCommandOptions = new InstallCatalogCommandOptions();
-        this.jwtCatalogCommandOptions = new JwtCatalogCommandOptions();
         this.listOrganizationsCommandOptions = new ListOrganizationsCommandOptions();
         this.fetchResourceCommandOptions = new FetchResourceCommandOptions();
         this.createUsersCommandOptions = new CreateUsersCommandOptions();
@@ -119,26 +117,6 @@ public class InstallCatalogCommandOptions {
 
     }
 
-    @Parameters(commandNames = {"catalog-jwt"}, commandDescription ="Change JWT secret key")
-    public class JwtCatalogCommandOptions {
-    
-        @ParametersDelegate
-        public CommonCommandOptions commonOptions = commonCommandOptions;
-    
-        @Parameter(names = {"--json-file"}, description = "File with the body data in JSON format. Note, that using this parameter will ignore all the other parameters.", required = false, arity = 1)
-        public String jsonFile;
-    
-        @Parameter(names = {"--json-data-model"}, description = "Show example of file structure for body data.", help = true, arity = 0)
-        public Boolean jsonDataModel = false;
-    
-        @Parameter(names = {"--organization"}, description = "Organization id", required = false, arity = 1)
-        public String organization; 
-    
-        @Parameter(names = {"--secret-key"}, description = "The body web service secretKey parameter", required = false, arity = 1)
-        public String secretKey;
-    
-    }
-
     @Parameters(commandNames = {"organizations-list"}, commandDescription ="List current Organizations")
     public class ListOrganizationsCommandOptions {
 

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

@@ -79,8 +79,6 @@ default String getCatalogDatabase(String prefix, String organization) {
 
     MigrationDBAdaptor getMigrationDBAdaptor(String organization) throws CatalogDBException;
 
-    MetaDBAdaptor getCatalogMetaDBAdaptor(String organization) throws CatalogDBException;
-
     OpenCGAResult<Organization> createOrganization(Organization organization, QueryOptions options, String userId) throws CatalogException;
 
     void deleteOrganization(Organization organization) throws CatalogDBException;

opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/DBAdaptorFactory.java

@@ -258,11 +258,6 @@ public MigrationDBAdaptor getMigrationDBAdaptor(String organizationId) throws Ca
         return getOrganizationMongoDBAdaptorFactory(organizationId).getMigrationDBAdaptor();
     }
 
-    @Override
-    public MetaDBAdaptor getCatalogMetaDBAdaptor(String organizationId) throws CatalogDBException {
-        return getOrganizationMongoDBAdaptorFactory(organizationId).getCatalogMetaDBAdaptor();
-    }
-
     @Override
     public OpenCGAResult<Organization> createOrganization(Organization organization, QueryOptions options, String userId)
             throws CatalogException {

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

@@ -435,10 +435,6 @@ public MigrationMongoDBAdaptor getMigrationDBAdaptor() {
         return migrationDBAdaptor;
     }
 
-    public MetaMongoDBAdaptor getCatalogMetaDBAdaptor() {
-        return null;
-    }
-
     public NoteMongoDBAdaptor getCatalogNotesDBAdaptor() {
         return notesDBAdaptor;
     }