app: generate new clients and cli, #TASK-4917

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

@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2023-04-18 OpenCB
+* Copyright 2015-2023-08-30 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
@@ -70,7 +70,7 @@ public abstract class OpenCgaCompleter implements Completer {
             .map(Candidate::new)
             .collect(toList());
 
-    private List<Candidate> adminList = asList( "audit-group-by","catalog-index-stats","catalog-install","catalog-jwt","users-create","users-import","users-search","users-sync")
+    private List<Candidate> adminList = asList( "audit-group-by","catalog-index-stats","catalog-install","catalog-jwt","users-create","users-import","users-search","users-sync","update-groups-users")
             .stream()
             .map(Candidate::new)
             .collect(toList());

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

@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2023-04-18 OpenCB
+* Copyright 2015-2023-08-30 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
@@ -188,6 +188,7 @@ public OpencgaCliOptionsParser() {
         adminSubCommands.addCommand("users-import", adminCommandOptions.importUsersCommandOptions);
         adminSubCommands.addCommand("users-search", adminCommandOptions.searchUsersCommandOptions);
         adminSubCommands.addCommand("users-sync", adminCommandOptions.syncUsersCommandOptions);
+        adminSubCommands.addCommand("update-groups-users", adminCommandOptions.usersUpdateGroupsCommandOptions);
 
         individualsCommandOptions = new IndividualsCommandOptions(commonCommandOptions, jCommander);
         jCommander.addCommand("individuals", individualsCommandOptions);

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

@@ -19,11 +19,13 @@
 import org.opencb.opencga.app.cli.main.options.AdminCommandOptions;
 
 import java.util.Map;
+import org.opencb.opencga.catalog.utils.ParamUtils.AddRemoveAction;
 import org.opencb.opencga.core.models.admin.GroupSyncParams;
 import org.opencb.opencga.core.models.admin.InstallationParams;
 import org.opencb.opencga.core.models.admin.JWTParams;
 import org.opencb.opencga.core.models.admin.UserCreateParams;
 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;
 import org.opencb.opencga.core.models.sample.Sample;
 import org.opencb.opencga.core.models.study.Group;
@@ -87,6 +89,9 @@ public void execute() throws Exception {
             case "users-sync":
                 queryResponse = syncUsers();
                 break;
+            case "update-groups-users":
+                queryResponse = usersUpdateGroups();
+                break;
             default:
                 logger.error("Subcommand not valid");
                 break;
@@ -288,4 +293,35 @@ private RestResponse<Group> syncUsers() throws Exception {
         }
         return openCGAClient.getAdminClient().syncUsers(groupSyncParams);
     }
+
+    private RestResponse<Group> usersUpdateGroups() throws Exception {
+        logger.debug("Executing usersUpdateGroups in Admin command line");
+
+        AdminCommandOptions.UsersUpdateGroupsCommandOptions commandOptions = adminCommandOptions.usersUpdateGroupsCommandOptions;
+
+        ObjectMap queryParams = new ObjectMap();
+        queryParams.putIfNotNull("action", commandOptions.action);
+
+
+        UserUpdateGroup userUpdateGroup = null;
+        if (commandOptions.jsonDataModel) {
+            userUpdateGroup = new UserUpdateGroup();
+            RestResponse<Group> res = new RestResponse<>();
+            res.setType(QueryType.VOID);
+            PrintUtils.println(getObjectAsJSON(userUpdateGroup));
+            return res;
+        } else if (commandOptions.jsonFile != null) {
+            userUpdateGroup = JacksonUtils.getDefaultObjectMapper()
+                    .readValue(new java.io.File(commandOptions.jsonFile), UserUpdateGroup.class);
+        } else {
+            ObjectMap beanParams = new ObjectMap();
+            putNestedIfNotNull(beanParams, "studyIds",commandOptions.studyIds, true);
+            putNestedIfNotNull(beanParams, "groupIds",commandOptions.groupIds, true);
+
+            userUpdateGroup = JacksonUtils.getDefaultObjectMapper().copy()
+                    .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true)
+                    .readValue(beanParams.toJson(), UserUpdateGroup.class);
+        }
+        return openCGAClient.getAdminClient().usersUpdateGroups(commandOptions.user, userUpdateGroup, queryParams);
+    }
 }

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

@@ -41,6 +41,7 @@ public class AdminCommandOptions {
         public ImportUsersCommandOptions importUsersCommandOptions;
         public SearchUsersCommandOptions searchUsersCommandOptions;
         public SyncUsersCommandOptions syncUsersCommandOptions;
+        public UsersUpdateGroupsCommandOptions usersUpdateGroupsCommandOptions;
 
 
     public AdminCommandOptions(CommonCommandOptions commonCommandOptions, JCommander jCommander) {
@@ -55,6 +56,7 @@ public AdminCommandOptions(CommonCommandOptions commonCommandOptions, JCommander
         this.importUsersCommandOptions = new ImportUsersCommandOptions();
         this.searchUsersCommandOptions = new SearchUsersCommandOptions();
         this.syncUsersCommandOptions = new SyncUsersCommandOptions();
+        this.usersUpdateGroupsCommandOptions = new UsersUpdateGroupsCommandOptions();
 
     }
 
@@ -278,4 +280,30 @@ public class SyncUsersCommandOptions {
 
     }
 
+    @Parameters(commandNames = {"update-groups-users"}, commandDescription ="Add or remove users from existing groups")
+    public class UsersUpdateGroupsCommandOptions {
+
+        @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 = {"--user", "-u"}, description = "User ID", required = true, arity = 1)
+        public String user; 
+
+        @Parameter(names = {"--action"}, description = "Action to be performed: ADD or REMOVE user to/from groups", required = false, arity = 1)
+        public String action = "ADD"; 
+
+        @Parameter(names = {"--study-ids"}, description = "The body web service studyIds parameter", required = false, arity = 1)
+        public String studyIds;
+
+        @Parameter(names = {"--group-ids"}, description = "The body web service groupIds parameter", required = false, arity = 1)
+        public String groupIds;
+
+    }
+
 }

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

@@ -925,8 +925,8 @@ public class RunGwasCommandOptions {
         @Parameter(names = {"--phenotype"}, description = "The body web service phenotype parameter", required = false, arity = 1)
         public String phenotype;
 
-        @Parameter(names = {"--index"}, description = "The body web service index parameter", required = false, arity = 1)
-        public Boolean index;
+        @Parameter(names = {"--index"}, description = "The body web service index parameter", required = false, help = true, arity = 0)
+        public boolean index = false;
 
         @Parameter(names = {"--index-score-id"}, description = "The body web service indexScoreId parameter", required = false, arity = 1)
         public String indexScoreId;

opencga-client/src/main/R/R/Admin-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-04-18
+#    Autogenerated on: 2023-08-30
 #    
 #    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.
@@ -28,14 +28,15 @@
 #' | importUsers | /{apiVersion}/admin/users/import | body[*] |
 #' | searchUsers | /{apiVersion}/admin/users/search | include, exclude, limit, skip, count, user, account, authenticationId |
 #' | syncUsers | /{apiVersion}/admin/users/sync | body[*] |
+#' | usersUpdateGroups | /{apiVersion}/admin/users/{user}/groups/update | user[*], action, body[*] |
 #'
 #' @md
 #' @seealso \url{http://docs.opencb.org/display/opencga/Using+OpenCGA} and the RESTful API documentation
 #' \url{http://bioinfo.hpc.cam.ac.uk/opencga-prod/webservices/}
 #' [*]: Required parameter
 #' @export
 
-setMethod("adminClient", "OpencgaR", function(OpencgaR, endpointName, params=NULL, ...) {
+setMethod("adminClient", "OpencgaR", function(OpencgaR, user, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/admin/audit/groupBy:
@@ -100,5 +101,13 @@ setMethod("adminClient", "OpencgaR", function(OpencgaR, endpointName, params=NUL
         #' @param data JSON containing the parameters.
         syncUsers=fetchOpenCGA(object=OpencgaR, category="admin", categoryId=NULL, subcategory="users",
                 subcategoryId=NULL, action="sync", params=params, httpMethod="POST", as.queryParam=NULL, ...),
+
+        #' @section Endpoint /{apiVersion}/admin/users/{user}/groups/update:
+        #' Add or remove users from existing groups.
+        #' @param user User ID.
+        #' @param action Action to be performed: ADD or REMOVE user to/from groups. Allowed values: ['ADD REMOVE']
+        #' @param data JSON containing the parameters.
+        usersUpdateGroups=fetchOpenCGA(object=OpencgaR, category="admin/users", categoryId=user, subcategory="groups",
+                subcategoryId=NULL, action="update", params=params, httpMethod="POST", as.queryParam=NULL, ...),
     )
 })

opencga-client/src/main/R/R/Alignment-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-04-18
+#    Autogenerated on: 2023-08-30
 #    
 #    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.

opencga-client/src/main/R/R/AllGenerics.R

@@ -1,6 +1,6 @@
 # ##############################################################################
 ## UserClient
-setGeneric("userClient", function(OpencgaR, filterId, users, user, endpointName, params=NULL, ...)
+setGeneric("userClient", function(OpencgaR, user, filterId, users, endpointName, params=NULL, ...)
     standardGeneric("userClient"))
 
 # ##############################################################################
@@ -10,17 +10,17 @@ setGeneric("projectClient", function(OpencgaR, projects, project, endpointName,
 
 # ##############################################################################
 ## StudyClient
-setGeneric("studyClient", function(OpencgaR, members, templateId, studies, variableSet, group, study, endpointName, params=NULL, ...)
+setGeneric("studyClient", function(OpencgaR, members, variableSet, studies, group, study, templateId, endpointName, params=NULL, ...)
     standardGeneric("studyClient"))
 
 # ##############################################################################
 ## FileClient
-setGeneric("fileClient", function(OpencgaR, folder, file, members, files, annotationSet, endpointName, params=NULL, ...)
+setGeneric("fileClient", function(OpencgaR, files, members, file, annotationSet, folder, endpointName, params=NULL, ...)
     standardGeneric("fileClient"))
 
 # ##############################################################################
 ## JobClient
-setGeneric("jobClient", function(OpencgaR, members, jobs, job, endpointName, params=NULL, ...)
+setGeneric("jobClient", function(OpencgaR, members, job, jobs, endpointName, params=NULL, ...)
     standardGeneric("jobClient"))
 
 # ##############################################################################
@@ -30,17 +30,17 @@ setGeneric("sampleClient", function(OpencgaR, members, sample, samples, annotati
 
 # ##############################################################################
 ## IndividualClient
-setGeneric("individualClient", function(OpencgaR, members, individual, annotationSet, individuals, endpointName, params=NULL, ...)
+setGeneric("individualClient", function(OpencgaR, members, individuals, annotationSet, individual, endpointName, params=NULL, ...)
     standardGeneric("individualClient"))
 
 # ##############################################################################
 ## FamilyClient
-setGeneric("familyClient", function(OpencgaR, members, families, family, annotationSet, endpointName, params=NULL, ...)
+setGeneric("familyClient", function(OpencgaR, members, family, annotationSet, families, endpointName, params=NULL, ...)
     standardGeneric("familyClient"))
 
 # ##############################################################################
 ## CohortClient
-setGeneric("cohortClient", function(OpencgaR, members, cohort, annotationSet, cohorts, endpointName, params=NULL, ...)
+setGeneric("cohortClient", function(OpencgaR, members, annotationSet, cohort, cohorts, endpointName, params=NULL, ...)
     standardGeneric("cohortClient"))
 
 # ##############################################################################
@@ -60,7 +60,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...)
 
 # ##############################################################################
 ## ClinicalClient
-setGeneric("clinicalClient", function(OpencgaR, clinicalAnalysis, members, interpretation, clinicalAnalyses, interpretations, endpointName, params=NULL, ...)
+setGeneric("clinicalClient", function(OpencgaR, interpretations, members, interpretation, clinicalAnalysis, clinicalAnalyses, endpointName, params=NULL, ...)
     standardGeneric("clinicalClient"))
 
 # ##############################################################################
@@ -80,6 +80,6 @@ setGeneric("ga4ghClient", function(OpencgaR, file, study, endpointName, params=N
 
 # ##############################################################################
 ## AdminClient
-setGeneric("adminClient", function(OpencgaR, endpointName, params=NULL, ...)
+setGeneric("adminClient", function(OpencgaR, user, endpointName, params=NULL, ...)
     standardGeneric("adminClient"))
 

opencga-client/src/main/R/R/Clinical-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-04-18
+#    Autogenerated on: 2023-08-30
 #    
 #    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.
@@ -58,7 +58,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("clinicalClient", "OpencgaR", function(OpencgaR, clinicalAnalysis, members, interpretation, clinicalAnalyses, interpretations, endpointName, params=NULL, ...) {
+setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretations, members, interpretation, clinicalAnalysis, clinicalAnalyses, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update:

opencga-client/src/main/R/R/Cohort-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-04-18
+#    Autogenerated on: 2023-08-30
 #    
 #    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.
@@ -39,7 +39,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("cohortClient", "OpencgaR", function(OpencgaR, members, cohort, annotationSet, cohorts, endpointName, params=NULL, ...) {
+setMethod("cohortClient", "OpencgaR", function(OpencgaR, members, annotationSet, cohort, cohorts, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/cohorts/acl/{members}/update:

opencga-client/src/main/R/R/Family-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-04-18
+#    Autogenerated on: 2023-08-30
 #    
 #    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.
@@ -38,7 +38,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("familyClient", "OpencgaR", function(OpencgaR, members, families, family, annotationSet, endpointName, params=NULL, ...) {
+setMethod("familyClient", "OpencgaR", function(OpencgaR, members, family, annotationSet, families, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/families/acl/{members}/update:

opencga-client/src/main/R/R/File-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-04-18
+#    Autogenerated on: 2023-08-30
 #    
 #    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.
@@ -54,7 +54,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("fileClient", "OpencgaR", function(OpencgaR, folder, file, members, files, annotationSet, endpointName, params=NULL, ...) {
+setMethod("fileClient", "OpencgaR", function(OpencgaR, files, members, file, annotationSet, folder, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/files/acl/{members}/update:

opencga-client/src/main/R/R/GA4GH-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-04-18
+#    Autogenerated on: 2023-08-30
 #    
 #    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.

opencga-client/src/main/R/R/Individual-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-04-18
+#    Autogenerated on: 2023-08-30
 #    
 #    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.
@@ -39,7 +39,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("individualClient", "OpencgaR", function(OpencgaR, members, individual, annotationSet, individuals, endpointName, params=NULL, ...) {
+setMethod("individualClient", "OpencgaR", function(OpencgaR, members, individuals, annotationSet, individual, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/individuals/acl/{members}/update:

opencga-client/src/main/R/R/Job-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-04-18
+#    Autogenerated on: 2023-08-30
 #    
 #    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.
@@ -40,7 +40,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("jobClient", "OpencgaR", function(OpencgaR, members, jobs, job, endpointName, params=NULL, ...) {
+setMethod("jobClient", "OpencgaR", function(OpencgaR, members, job, jobs, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/jobs/acl/{members}/update:

opencga-client/src/main/R/R/Meta-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-04-18
+#    Autogenerated on: 2023-08-30
 #    
 #    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.