core: add priority and jobPriority params, #TASK-6089

opencb · Jul 3, 2024 · 83ef3aa · 83ef3aa
1 parent bbfe0f9
commit 83ef3aa
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Showing 17 changed files with 105 additions and 104 deletions.
diff --git a/...a-app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomJobsCommandExecutor.java b/...a-app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomJobsCommandExecutor.java
@@ -48,7 +48,7 @@ public RestResponse<JobTop> top(CustomJobsCommandOptions.TopCommandOptions c) th
         query.putIfNotEmpty(ParamConstants.JOB_TOOL_ID_PARAM, c.toolId);
         query.putIfNotEmpty(ParamConstants.INTERNAL_STATUS_PARAM, c.internalStatus);
         query.putIfNotEmpty(ParamConstants.JOB_USER_PARAM, c.userId);
-        query.putIfNotEmpty(ParamConstants.JOB_PRIORITY_PARAM, c.jobPriority);
+        query.putIfNotEmpty(ParamConstants.JOB_PRIORITY_PARAM, c.priority);
         query.putAll(c.commonOptions.params);
 
         new JobsTopManager(openCGAClient, query, c.iterations, c.jobsLimit, c.delay, c.plain, c.columns).run();

diff --git a/...ga-app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomJobsCommandOptions.java b/...ga-app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomJobsCommandOptions.java
@@ -64,8 +64,8 @@ public class TopCommandOptions {
         @Parameter(names = {"--user-id"}, description = ParamConstants.JOB_USER_DESCRIPTION, arity = 1)
         public String userId;
 
-        @Parameter(names = {"--job-priority"}, description = ParamConstants.JOB_PRIORITY_DESCRIPTION, arity = 1)
-        public String jobPriority;
+        @Parameter(names = {"--priority"}, description = ParamConstants.JOB_PRIORITY_DESCRIPTION, arity = 1)
+        public String priority;
 
         @Parameter(names = {"--internal-status"}, description = ParamConstants.JOB_STATUS_DESCRIPTION, arity = 1)
         public String internalStatus;

diff --git a/...app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomStudiesCommandOptions.java b/...app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomStudiesCommandOptions.java
@@ -54,25 +54,25 @@ public class RunTemplatesCommandOptions {
         @Parameter(names = {"--resume"}, description = "Resume study metadata ingestion.", arity = 0)
         public boolean resume;
 
-        @Parameter(names = {"--jobId"}, description = "Job id.", arity = 1)
+        @Parameter(names = {"--job-id", "--jobId"}, description = "Job id.", arity = 1)
         public String jobId;
 
-        @Parameter(names = {"--jobDependsOn"}, description = "Job depends on.", arity = 1)
+        @Parameter(names = {"--job-depends-on", "--jobDependsOn"}, description = "Job depends on.", arity = 1)
         public String jobDependsOn;
 
-        @Parameter(names = {"--jobDescription"}, description = "Job description.", arity = 1)
+        @Parameter(names = {"--job-description", "--jobDescription"}, description = "Job description.", arity = 1)
         public String jobDescription;
 
-        @Parameter(names = {"--jobTags"}, description = "Job tags.", arity = 1)
+        @Parameter(names = {"--job-tags", "--jobTags"}, description = "Job tags.", arity = 1)
         public String jobTags;
 
-        @Parameter(names = {"--jobScheduledStartTime"}, description = "Job scheduled start time.", arity = 1)
+        @Parameter(names = {"--job-scheduled-start-time"}, description = "Job scheduled start time.", arity = 1)
         public String jobScheduledStartTime;
 
-        @Parameter(names = {"--jobPriority"}, description = "Job priority.", arity = 1)
+        @Parameter(names = {"--job-priority"}, description = "Job priority.", arity = 1)
         public String jobPriority;
 
-        @Parameter(names = {"--jobDryRun"}, description = "Job dry-run mode.", arity = 1)
+        @Parameter(names = {"--job-dry-run"}, description = "Job dry-run mode.", arity = 1)
         public Boolean jobDryRun;
     }
 }
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/JobsCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/JobsCommandExecutor.java
@@ -210,7 +210,7 @@ private RestResponse<Object> distinct() throws Exception {
         queryParams.putIfNotEmpty("toolId", commandOptions.toolId);
         queryParams.putIfNotEmpty("toolType", commandOptions.toolType);
         queryParams.putIfNotEmpty("userId", commandOptions.userId);
-        queryParams.putIfNotEmpty("jobPriority", commandOptions.jobPriority);
+        queryParams.putIfNotEmpty("priority", commandOptions.priority);
         queryParams.putIfNotEmpty("status", commandOptions.status);
         queryParams.putIfNotEmpty("internalStatus", commandOptions.internalStatus);
         queryParams.putIfNotEmpty("creationDate", commandOptions.creationDate);
@@ -286,7 +286,7 @@ private RestResponse<Job> search() throws Exception {
         queryParams.putIfNotEmpty("toolId", commandOptions.toolId);
         queryParams.putIfNotEmpty("toolType", commandOptions.toolType);
         queryParams.putIfNotEmpty("userId", commandOptions.userId);
-        queryParams.putIfNotEmpty("jobPriority", commandOptions.jobPriority);
+        queryParams.putIfNotEmpty("priority", commandOptions.priority);
         queryParams.putIfNotEmpty("status", commandOptions.status);
         queryParams.putIfNotEmpty("internalStatus", commandOptions.internalStatus);
         queryParams.putIfNotEmpty("creationDate", commandOptions.creationDate);
@@ -313,7 +313,7 @@ private RestResponse<JobTop> top() throws Exception {
         queryParams.putIfNotNull("limit", commandOptions.limit);
         queryParams.putIfNotEmpty("study", commandOptions.study);
         queryParams.putIfNotEmpty("internalStatus", commandOptions.internalStatus);
-        queryParams.putIfNotEmpty("jobPriority", commandOptions.jobPriority);
+        queryParams.putIfNotEmpty("priority", commandOptions.priority);
         queryParams.putIfNotEmpty("userId", commandOptions.userId);
         queryParams.putIfNotEmpty("toolId", commandOptions.toolId);
         if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {

diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/JobsCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/JobsCommandOptions.java
@@ -194,8 +194,8 @@ public class DistinctCommandOptions {
         @Parameter(names = {"--user-id"}, description = "User that created the job", required = false, arity = 1)
         public String userId; 
 
-        @Parameter(names = {"--job-priority"}, description = "Priority of the job", required = false, arity = 1)
-        public String jobPriority; 
+        @Parameter(names = {"--priority"}, description = "Priority of the job", required = false, arity = 1)
+        public String priority; 
 
         @Parameter(names = {"--status"}, description = "Filter by status", required = false, arity = 1)
         public String status; 
@@ -318,8 +318,8 @@ public class SearchCommandOptions {
         @Parameter(names = {"--user-id"}, description = "User that created the job", required = false, arity = 1)
         public String userId; 
 
-        @Parameter(names = {"--job-priority"}, description = "Priority of the job", required = false, arity = 1)
-        public String jobPriority; 
+        @Parameter(names = {"--priority"}, description = "Priority of the job", required = false, arity = 1)
+        public String priority; 
 
         @Parameter(names = {"--status"}, description = "Filter by status", required = false, arity = 1)
         public String status; 

diff --git a/opencga-client/src/main/R/R/Job-methods.R b/opencga-client/src/main/R/R/Job-methods.R
@@ -21,10 +21,10 @@
 #' | -- | :-- | --: |
 #' | updateAcl | /{apiVersion}/jobs/acl/{members}/update | members[*], action[*], body[*] |
 #' | create | /{apiVersion}/jobs/create | study, body[*] |
-#' | distinct | /{apiVersion}/jobs/distinct | study, otherStudies, id, uuid, toolId, toolType, userId, jobPriority, status, internalStatus, creationDate, modificationDate, visited, tags, input, output, acl, release, deleted, field[*] |
+#' | distinct | /{apiVersion}/jobs/distinct | study, otherStudies, id, uuid, toolId, toolType, userId, priority, status, internalStatus, creationDate, modificationDate, visited, tags, input, output, acl, release, deleted, field[*] |
 #' | retry | /{apiVersion}/jobs/retry | jobId, jobDescription, jobDependsOn, jobTags, study, body[*] |
-#' | search | /{apiVersion}/jobs/search | include, exclude, limit, skip, count, study, otherStudies, id, uuid, toolId, toolType, userId, jobPriority, status, internalStatus, creationDate, modificationDate, visited, tags, input, output, acl, release, deleted |
-#' | top | /{apiVersion}/jobs/top | limit, study, internalStatus, jobPriority, userId, toolId |
+#' | search | /{apiVersion}/jobs/search | include, exclude, limit, skip, count, study, otherStudies, id, uuid, toolId, toolType, userId, priority, status, internalStatus, creationDate, modificationDate, visited, tags, input, output, acl, release, deleted |
+#' | top | /{apiVersion}/jobs/top | limit, study, internalStatus, priority, userId, toolId |
 #' | acl | /{apiVersion}/jobs/{jobs}/acl | jobs[*], member, silent |
 #' | delete | /{apiVersion}/jobs/{jobs}/delete | study, jobs[*] |
 #' | info | /{apiVersion}/jobs/{jobs}/info | include, exclude, jobs[*], study, deleted |
@@ -67,7 +67,7 @@ setMethod("jobClient", "OpencgaR", function(OpencgaR, job, jobs, members, endpoi
         #' @param toolId Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
         #' @param toolType Tool type executed by the job [OPERATION, ANALYSIS].
         #' @param userId User that created the job.
-        #' @param jobPriority Priority of the job.
+        #' @param priority Priority of the job.
         #' @param status Filter by status.
         #' @param internalStatus Filter by internal status.
         #' @param creationDate Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
@@ -108,7 +108,7 @@ setMethod("jobClient", "OpencgaR", function(OpencgaR, job, jobs, members, endpoi
         #' @param toolId Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
         #' @param toolType Tool type executed by the job [OPERATION, ANALYSIS].
         #' @param userId User that created the job.
-        #' @param jobPriority Priority of the job.
+        #' @param priority Priority of the job.
         #' @param status Filter by status.
         #' @param internalStatus Filter by internal status.
         #' @param creationDate Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
@@ -128,7 +128,7 @@ setMethod("jobClient", "OpencgaR", function(OpencgaR, job, jobs, members, endpoi
         #' @param limit Maximum number of jobs to be returned.
         #' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
         #' @param internalStatus Filter by internal status.
-        #' @param jobPriority Priority of the job.
+        #' @param priority Priority of the job.
         #' @param userId User that created the job.
         #' @param toolId Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
         top=fetchOpenCGA(object=OpencgaR, category="jobs", categoryId=NULL, subcategory=NULL, subcategoryId=NULL,

diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java
@@ -94,7 +94,7 @@ public RestResponse<Job> create(JobCreateParams data, ObjectMap params) throws C
      *            '~value' for case sensitive, '~/value/i' for case insensitive search.
      *       toolType: Tool type executed by the job [OPERATION, ANALYSIS].
      *       userId: User that created the job.
-     *       jobPriority: Priority of the job.
+     *       priority: Priority of the job.
      *       status: Filter by status.
      *       internalStatus: Filter by internal status.
      *       creationDate: Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
@@ -152,7 +152,7 @@ public RestResponse<Job> retry(JobRetryParams data, ObjectMap params) throws Cli
      *            '~value' for case sensitive, '~/value/i' for case insensitive search.
      *       toolType: Tool type executed by the job [OPERATION, ANALYSIS].
      *       userId: User that created the job.
-     *       jobPriority: Priority of the job.
+     *       priority: Priority of the job.
      *       status: Filter by status.
      *       internalStatus: Filter by internal status.
      *       creationDate: Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
@@ -180,7 +180,7 @@ public RestResponse<Job> search(ObjectMap params) throws ClientException {
      *       limit: Maximum number of jobs to be returned.
      *       study: Study [[organization@]project:]study where study and project can be either the ID or UUID.
      *       internalStatus: Filter by internal status.
-     *       jobPriority: Priority of the job.
+     *       priority: Priority of the job.
      *       userId: User that created the job.
      *       toolId: Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g.
      *            '~value' for case sensitive, '~/value/i' for case insensitive search.

diff --git a/opencga-client/src/main/javascript/Job.js b/opencga-client/src/main/javascript/Job.js
@@ -67,7 +67,7 @@ export default class Job extends OpenCGAParentClass {
     *     '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
     * @param {String} [params.toolType] - Tool type executed by the job [OPERATION, ANALYSIS].
     * @param {String} [params.userId] - User that created the job.
-    * @param {String} [params.jobPriority] - Priority of the job.
+    * @param {String} [params.priority] - Priority of the job.
     * @param {String} [params.status] - Filter by status.
     * @param {String} [params.internalStatus] - Filter by internal status.
     * @param {String} [params.creationDate] - Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
@@ -120,7 +120,7 @@ export default class Job extends OpenCGAParentClass {
     *     '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
     * @param {String} [params.toolType] - Tool type executed by the job [OPERATION, ANALYSIS].
     * @param {String} [params.userId] - User that created the job.
-    * @param {String} [params.jobPriority] - Priority of the job.
+    * @param {String} [params.priority] - Priority of the job.
     * @param {String} [params.status] - Filter by status.
     * @param {String} [params.internalStatus] - Filter by internal status.
     * @param {String} [params.creationDate] - Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
@@ -145,7 +145,7 @@ export default class Job extends OpenCGAParentClass {
     * @param {Number} [params.limit = "20"] - Maximum number of jobs to be returned. The default value is 20.
     * @param {String} [params.study] - Study [[organization@]project:]study where study and project can be either the ID or UUID.
     * @param {String} [params.internalStatus] - Filter by internal status.
-    * @param {String} [params.jobPriority] - Priority of the job.
+    * @param {String} [params.priority] - Priority of the job.
     * @param {String} [params.userId] - User that created the job.
     * @param {String} [params.toolId] - Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e.
     *     '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.

diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py
@@ -71,7 +71,7 @@ def distinct(self, field, **options):
         :param str tool_type: Tool type executed by the job [OPERATION,
             ANALYSIS].
         :param str user_id: User that created the job.
-        :param str job_priority: Priority of the job.
+        :param str priority: Priority of the job.
         :param str status: Filter by status.
         :param str internal_status: Filter by internal status.
         :param str creation_date: Creation date. Format: yyyyMMddHHmmss.
@@ -142,7 +142,7 @@ def search(self, **options):
         :param str tool_type: Tool type executed by the job [OPERATION,
             ANALYSIS].
         :param str user_id: User that created the job.
-        :param str job_priority: Priority of the job.
+        :param str priority: Priority of the job.
         :param str status: Filter by status.
         :param str internal_status: Filter by internal status.
         :param str creation_date: Creation date. Format: yyyyMMddHHmmss.
@@ -173,7 +173,7 @@ def top(self, **options):
         :param str study: Study [[organization@]project:]study where study and
             project can be either the ID or UUID.
         :param str internal_status: Filter by internal status.
-        :param str job_priority: Priority of the job.
+        :param str priority: Priority of the job.
         :param str user_id: User that created the job.
         :param str tool_id: Tool ID executed by the job. Also admits basic
             regular expressions using the operator '~', i.e. '~{perl-regex}'

diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java b/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java
@@ -559,7 +559,8 @@ public class ParamConstants {
     public static final String JOB_TOOL_TYPE_DESCRIPTION = "Tool type executed by the job [OPERATION, ANALYSIS]";
     public static final String JOB_USER_PARAM = "userId";
     public static final String JOB_USER_DESCRIPTION = "User that created the job";
-    public static final String JOB_PRIORITY_PARAM = "jobPriority";
+    public static final String JOB_PRIORITY_PARAM = "priority";
+    public static final String SUBMIT_JOB_PRIORITY_PARAM = "jobPriority";
     public static final String JOB_PRIORITY_DESCRIPTION = "Priority of the job";
     public static final String JOB_INTERNAL_STATUS_PARAM = INTERNAL_STATUS_PARAM;
     public static final String JOB_INTERNAL_STATUS_DESCRIPTION = INTERNAL_STATUS_DESCRIPTION;

diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/rest/FileWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/server/rest/FileWSServer.java
@@ -99,7 +99,7 @@ public Response downloadAndRegister(
             @ApiParam(value = ParamConstants.JOB_DEPENDS_ON_DESCRIPTION) @QueryParam(JOB_DEPENDS_ON) String dependsOn,
             @ApiParam(value = ParamConstants.JOB_TAGS_DESCRIPTION) @QueryParam(ParamConstants.JOB_TAGS) String jobTags,
             @ApiParam(value = ParamConstants.JOB_SCHEDULED_START_TIME_DESCRIPTION) @QueryParam(ParamConstants.JOB_SCHEDULED_START_TIME) String scheduledStartTime,
-            @ApiParam(value = ParamConstants.JOB_PRIORITY_DESCRIPTION) @QueryParam(ParamConstants.JOB_PRIORITY_PARAM) String jobPriority,
+            @ApiParam(value = ParamConstants.JOB_PRIORITY_DESCRIPTION) @QueryParam(ParamConstants.SUBMIT_JOB_PRIORITY_PARAM) String jobPriority,
             @ApiParam(value = ParamConstants.JOB_DRY_RUN_DESCRIPTION) @QueryParam(ParamConstants.JOB_DRY_RUN) Boolean dryRun,
             @ApiParam(value = ParamConstants.STUDY_DESCRIPTION) @QueryParam(ParamConstants.STUDY_PARAM) String studyStr,
             @ApiParam(name = "body", value = "Fetch parameters", required = true) FileFetch fetchParams) {
@@ -713,7 +713,7 @@ public Response postlink(
             @ApiParam(value = ParamConstants.JOB_DESCRIPTION_DESCRIPTION) @QueryParam(ParamConstants.JOB_DESCRIPTION) String jobDescription,
             @ApiParam(value = ParamConstants.JOB_TAGS_DESCRIPTION) @QueryParam(ParamConstants.JOB_TAGS) String jobTags,
             @ApiParam(value = ParamConstants.JOB_SCHEDULED_START_TIME_DESCRIPTION) @QueryParam(ParamConstants.JOB_SCHEDULED_START_TIME) String scheduledStartTime,
-            @ApiParam(value = ParamConstants.JOB_PRIORITY_DESCRIPTION) @QueryParam(ParamConstants.JOB_PRIORITY_PARAM) String jobPriority,
+            @ApiParam(value = ParamConstants.JOB_PRIORITY_DESCRIPTION) @QueryParam(ParamConstants.SUBMIT_JOB_PRIORITY_PARAM) String jobPriority,
             @ApiParam(value = ParamConstants.JOB_DRY_RUN_DESCRIPTION) @QueryParam(ParamConstants.JOB_DRY_RUN) Boolean dryRun,
             @ApiParam(name = "body", value = "File parameters", required = true) PostLinkToolParams params) {
         return submitJob(PostLinkSampleAssociation.ID, studyStr, params, jobId, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun);
@@ -729,7 +729,7 @@ public Response linkAsync(
             @ApiParam(value = ParamConstants.JOB_DESCRIPTION_DESCRIPTION) @QueryParam(ParamConstants.JOB_DESCRIPTION) String jobDescription,
             @ApiParam(value = ParamConstants.JOB_TAGS_DESCRIPTION) @QueryParam(ParamConstants.JOB_TAGS) String jobTags,
             @ApiParam(value = ParamConstants.JOB_SCHEDULED_START_TIME_DESCRIPTION) @QueryParam(ParamConstants.JOB_SCHEDULED_START_TIME) String scheduledStartTime,
-            @ApiParam(value = ParamConstants.JOB_PRIORITY_DESCRIPTION) @QueryParam(ParamConstants.JOB_PRIORITY_PARAM) String jobPriority,
+            @ApiParam(value = ParamConstants.JOB_PRIORITY_DESCRIPTION) @QueryParam(ParamConstants.SUBMIT_JOB_PRIORITY_PARAM) String jobPriority,
             @ApiParam(value = ParamConstants.JOB_DRY_RUN_DESCRIPTION) @QueryParam(ParamConstants.JOB_DRY_RUN) Boolean dryRun,
             @ApiParam(name = "body", value = "File parameters", required = true) FileLinkToolParams params) {
         return submitJob(FileLinkTask.ID, studyStr, params, jobId, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun);