diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomJobsCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomJobsCommandExecutor.java index 1a224f9892..dffedddcab 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomJobsCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomJobsCommandExecutor.java @@ -48,7 +48,7 @@ public RestResponse 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/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomJobsCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomJobsCommandOptions.java index 85eb3e7b5d..2b1b600471 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomJobsCommandOptions.java +++ b/opencga-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/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomStudiesCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomStudiesCommandOptions.java index 4aa8090ac6..74ff7b9ce3 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomStudiesCommandOptions.java +++ b/opencga-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; } } \ No newline at end of file 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 index 3fcec35d52..ed13685ebe 100644 --- 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 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 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 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 index cedda5e101..7efaf88172 100644 --- 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 index 4f3b365035..860bcea33d 100644 --- 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 index 0562a53fcb..a32f67ec78 100644 --- 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 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 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 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 index 0e899d6f41..5135fcf87f 100644 --- 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 index 43958cd5a5..9c71a3d6c6 100644 --- 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 index d866988560..c616de1565 100644 --- 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 index 342bc7bc87..01be67e5a1 100644 --- 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); diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/rest/PanelWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/server/rest/PanelWSServer.java index f25fce1beb..7d36dec438 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/rest/PanelWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/rest/PanelWSServer.java @@ -83,7 +83,7 @@ public Response importPanel( @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 = "Panel parameters") PanelImportParams params) { return submitJob(PanelImportTask.ID, studyStr, params, jobId, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/rest/StudyWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/server/rest/StudyWSServer.java index 2f82db118d..f6cc3fe888 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/rest/StudyWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/rest/StudyWSServer.java @@ -548,7 +548,7 @@ public Response executeTemplate( @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(value = TemplateParams.DESCRIPTION, required = true) TemplateParams params) { return submitJob(TemplateRunner.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/rest/analysis/AlignmentWebService.java b/opencga-server/src/main/java/org/opencb/opencga/server/rest/analysis/AlignmentWebService.java index a966e1f938..277f289a6b 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/rest/analysis/AlignmentWebService.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/rest/analysis/AlignmentWebService.java @@ -84,7 +84,7 @@ public Response indexRun( @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(value = AlignmentIndexParams.DESCRIPTION, required = true) AlignmentIndexParams params) { return submitJob(AlignmentIndexOperation.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -181,7 +181,7 @@ public Response coverageRun( @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(value = CoverageIndexParams.DESCRIPTION, required = true) CoverageIndexParams params) { @@ -393,7 +393,7 @@ public Response geneCoverageStatsRun( @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(value = AlignmentGeneCoverageStatsParams.DESCRIPTION, required = true) AlignmentGeneCoverageStatsParams params) { @@ -414,7 +414,7 @@ public Response qcRun( @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(value = AlignmentQcParams.DESCRIPTION, required = true) AlignmentQcParams params) { @@ -435,7 +435,7 @@ public Response bwaRun( @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(value = BwaWrapperParams.DESCRIPTION, required = true) BwaWrapperParams params) { return submitJob(BwaWrapperAnalysis.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -451,7 +451,7 @@ public Response samtoolsRun( @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(value = SamtoolsWrapperParams.DESCRIPTION, required = true) SamtoolsWrapperParams params) { return submitJob(SamtoolsWrapperAnalysis.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -467,7 +467,7 @@ public Response deeptoolsRun( @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(value = DeeptoolsWrapperParams.DESCRIPTION, required = true) DeeptoolsWrapperParams params) { return submitJob(DeeptoolsWrapperAnalysis.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -483,7 +483,7 @@ public Response fastqcRun( @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(value = FastqcWrapperParams.DESCRIPTION, required = true) FastqcWrapperParams params) { return submitJob(FastqcWrapperAnalysis.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -499,7 +499,7 @@ public Response picardRun( @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(value = PicardWrapperParams.DESCRIPTION, required = true) PicardWrapperParams params) { return submitJob(PicardWrapperAnalysis.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/rest/analysis/ClinicalWebService.java b/opencga-server/src/main/java/org/opencb/opencga/server/rest/analysis/ClinicalWebService.java index bd2db9505e..f893c1f598 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/rest/analysis/ClinicalWebService.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/rest/analysis/ClinicalWebService.java @@ -171,7 +171,7 @@ public Response load( @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 = ClinicalAnalysisLoadParams.DESCRIPTION, required = true) ClinicalAnalysisLoadParams params) { try { @@ -1165,7 +1165,7 @@ public Response rgaIndexRun( @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.INDEX_AUXILIAR_COLLECTION_DESCRIPTION, defaultValue = "false") @QueryParam(ParamConstants.INDEX_AUXILIAR_COLLECTION) boolean indexAuxiliarColl, @@ -1299,7 +1299,7 @@ public Response interpretationTieringRun( @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 = TieringInterpretationAnalysisParams.DESCRIPTION, required = true) TieringInterpretationAnalysisParams params) { return submitJob(TieringInterpretationAnalysis.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -1316,7 +1316,7 @@ public Response interpretationExomiserRun( @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 = ExomiserInterpretationAnalysisParams.DESCRIPTION, required = true) ExomiserInterpretationAnalysisParams params) { return submitJob(ExomiserInterpretationAnalysis.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -1332,7 +1332,7 @@ public Response interpretationTeamRun( @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 = TeamInterpretationAnalysisParams.DESCRIPTION, required = true) TeamInterpretationAnalysisParams params) { return submitJob(TeamInterpretationAnalysis.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -1348,7 +1348,7 @@ public Response interpretationZettaRun( @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 = ZettaInterpretationAnalysisParams.DESCRIPTION, required = true) ZettaInterpretationAnalysisParams params) { return submitJob(ZettaInterpretationAnalysis.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -1364,7 +1364,7 @@ public Response interpretationCancerTieringRun( @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 = CancerTieringInterpretationAnalysisParams.DESCRIPTION, required = true) CancerTieringInterpretationAnalysisParams params) { return submitJob(CancerTieringInterpretationAnalysis.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/rest/analysis/VariantWebService.java b/opencga-server/src/main/java/org/opencb/opencga/server/rest/analysis/VariantWebService.java index 364f3dc834..be6ec91c91 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/rest/analysis/VariantWebService.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/rest/analysis/VariantWebService.java @@ -187,7 +187,7 @@ public Response variantFileIndex( @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(value = VariantIndexParams.DESCRIPTION, required = true) VariantIndexParams params) { return submitJob(VariantIndexOperationTool.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -203,7 +203,7 @@ public Response variantFileDelete( @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 study, @ApiParam(value = "Files to remove") @QueryParam("file") String file, @@ -405,7 +405,7 @@ public Response export( @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 = VariantExportParams.DESCRIPTION, required = true) VariantExportParams params) { return submitJob(VariantExportTool.ID, project, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -451,7 +451,7 @@ public Response statsRun( @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 = VariantStatsAnalysisParams.DESCRIPTION, required = true) VariantStatsAnalysisParams params) { return submitJob(VariantStatsAnalysis.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -468,7 +468,7 @@ public Response statsExport( @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 = VariantStatsExportParams.DESCRIPTION, required = true) VariantStatsExportParams params) { return submitJob("variant-stats-export", project, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -574,7 +574,7 @@ public Response sampleRun( @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 = SampleVariantFilterParams.DESCRIPTION, required = true) SampleVariantFilterParams params) { return submitJob(SampleVariantFilterAnalysis.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -590,7 +590,7 @@ public Response sampleEligibility( @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 = SampleEligibilityAnalysisParams.DESCRIPTION, required = true) SampleEligibilityAnalysisParams params) { return submitJob(SampleEligibilityAnalysis.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -606,7 +606,7 @@ public Response exomiserRun( @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(value = ExomiserWrapperParams.DESCRIPTION, required = true) ExomiserWrapperParams params) { return submitJob(ExomiserWrapperAnalysis.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -704,7 +704,7 @@ public Response sampleStatsRun( @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 = SampleVariantStatsAnalysisParams.DESCRIPTION, required = true) SampleVariantStatsAnalysisParams params) { return submitJob(SampleVariantStatsAnalysis.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -756,7 +756,7 @@ public Response cohortStatsRun( @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 = CohortVariantStatsAnalysisParams.DESCRIPTION, required = true) CohortVariantStatsAnalysisParams params) { return submitJob(CohortVariantStatsAnalysis.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -932,7 +932,7 @@ public Response gwasRun( @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 = GwasAnalysisParams.DESCRIPTION, required = true) GwasAnalysisParams params) { return submitJob(GwasAnalysis.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -962,7 +962,7 @@ public Response mutationalSignatureRun( @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 = MutationalSignatureAnalysisParams.DESCRIPTION, required = true) MutationalSignatureAnalysisParams params) { return submitJob(MutationalSignatureAnalysis.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -1080,7 +1080,7 @@ public Response hrDetectRun( @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 = HRDetectAnalysisParams.DESCRIPTION, required = true) HRDetectAnalysisParams params) { return submitJob(HRDetectAnalysis.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -1096,7 +1096,7 @@ public Response mendelianErrorRun( @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 = MendelianErrorAnalysisParams.DESCRIPTION, required = true) MendelianErrorAnalysisParams params) { return submitJob(MendelianErrorAnalysis.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -1112,7 +1112,7 @@ public Response inferredSexRun( @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 = InferredSexAnalysisParams.DESCRIPTION, required = true) InferredSexAnalysisParams params) { return run(() -> { @@ -1134,7 +1134,7 @@ public Response relatednessRun( @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 = RelatednessAnalysisParams.DESCRIPTION, required = true) RelatednessAnalysisParams params) { return submitJob(RelatednessAnalysis.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -1150,7 +1150,7 @@ public Response familyQcRun( @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 = FamilyQcAnalysisParams.DESCRIPTION, required = true) FamilyQcAnalysisParams params) { return submitJob(FamilyQcAnalysis.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -1166,7 +1166,7 @@ public Response individualQcRun( @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 = IndividualQcAnalysisParams.DESCRIPTION, required = true) IndividualQcAnalysisParams params) { return run(() -> { @@ -1189,7 +1189,7 @@ public Response sampleQcRun( @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 = SampleQcAnalysisParams.DESCRIPTION, required = true) SampleQcAnalysisParams params) { @@ -1206,7 +1206,7 @@ public Response plinkRun( @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 = PlinkWrapperParams.DESCRIPTION, required = true) PlinkWrapperParams params) { return submitJob(PlinkWrapperAnalysis.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -1222,7 +1222,7 @@ public Response rvtestsRun( @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 = RvtestsWrapperParams.DESCRIPTION, required = true) RvtestsWrapperParams params) { return submitJob(RvtestsWrapperAnalysis.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -1238,7 +1238,7 @@ public Response gatkRun( @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 = GatkWrapperParams.DESCRIPTION, required = true) GatkWrapperParams params) { return submitJob(GatkWrapperAnalysis.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -1254,7 +1254,7 @@ public Response knockoutRun( @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 = KnockoutAnalysisParams.DESCRIPTION, required = true) KnockoutAnalysisParams params) { return submitJob(KnockoutAnalysis.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -1298,7 +1298,7 @@ public Response genomePlotRun( @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 = GenomePlotAnalysisParams.DESCRIPTION, required = true) GenomePlotAnalysisParams params) { // To be sure: do not update quality control sample diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/rest/operations/VariantOperationWebService.java b/opencga-server/src/main/java/org/opencb/opencga/server/rest/operations/VariantOperationWebService.java index 460493c89c..a2143f4509 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/rest/operations/VariantOperationWebService.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/rest/operations/VariantOperationWebService.java @@ -110,7 +110,7 @@ public Response variantIndex( @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 study, @ApiParam(value = VariantIndexParams.DESCRIPTION) VariantIndexParams params) { @@ -126,7 +126,7 @@ public Response variantDelete( @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 study, @ApiParam(value = VariantFileDeleteParams.DESCRIPTION) VariantFileDeleteParams params) { @@ -142,7 +142,7 @@ public Response variantStudyDelete( @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 study, @ApiParam(value = VariantStudyDeleteParams.DESCRIPTION) VariantStudyDeleteParams params) { @@ -158,7 +158,7 @@ public Response variantIndexLauncher( @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 study, @ApiParam(value = VariantFileIndexJobLauncherParams.DESCRIPTION) VariantFileIndexJobLauncherParams params) { @@ -174,7 +174,7 @@ public Response variantMetadataSynchronize( @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 study, @ApiParam(value = VariantStorageMetadataSynchronizeParams.DESCRIPTION) VariantStorageMetadataSynchronizeParams params) { @@ -190,7 +190,7 @@ public Response variantMetadataRepair( @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 = VariantStorageMetadataRepairToolParams.DESCRIPTION) VariantStorageMetadataRepairToolParams params) { return submitJobAdmin(VariantStorageMetadataRepairTool.ID, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -206,7 +206,7 @@ public Response statsIndex( @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 = VariantStatsAnalysisParams.DESCRIPTION, required = true) VariantStatsIndexParams params) { return submitJob(VariantStatsIndexOperationTool.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -222,7 +222,7 @@ public Response statsDelete( @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 = VariantStatsDeleteParams.DESCRIPTION, required = true) VariantStatsDeleteParams params) { return submitJob(VariantStatsDeleteOperationTool.ID, study, params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun); @@ -239,7 +239,7 @@ public Response secondaryIndex( @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 = VariantCatalogQueryUtils.PROJECT_DESC) @QueryParam(ParamConstants.PROJECT_PARAM) String project, @ApiParam(value = ParamConstants.STUDY_DESCRIPTION) @QueryParam(ParamConstants.STUDY_PARAM) String study, @@ -256,7 +256,7 @@ public Response variantSecondaryAnnotationIndex( @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 = VariantCatalogQueryUtils.PROJECT_DESC) @QueryParam(ParamConstants.PROJECT_PARAM) String project, @ApiParam(value = ParamConstants.STUDY_DESCRIPTION) @QueryParam(ParamConstants.STUDY_PARAM) String study, @@ -273,7 +273,7 @@ public Response secondaryIndex( @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 study, @ApiParam(value = "Samples to remove. Needs to provide all the samples in the secondary index.") @QueryParam("samples") String samples) { @@ -292,7 +292,7 @@ public Response annotation( @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.PROJECT_DESCRIPTION) @QueryParam(ParamConstants.PROJECT_PARAM) String project, @ApiParam(value = ParamConstants.STUDY_DESCRIPTION) @QueryParam(ParamConstants.STUDY_PARAM) String study, @@ -309,7 +309,7 @@ public Response annotationDelete( @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 = VariantCatalogQueryUtils.PROJECT_DESC) @QueryParam(ParamConstants.PROJECT_PARAM) String project, @ApiParam(value = "Annotation identifier") @QueryParam("annotationId") String annotationId @@ -330,7 +330,7 @@ public Response annotationSave( @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 = VariantCatalogQueryUtils.PROJECT_DESC) @QueryParam(ParamConstants.PROJECT_PARAM) String project, @ApiParam(value = VariantAnnotationSaveParams.DESCRIPTION) VariantAnnotationSaveParams params) { @@ -347,7 +347,7 @@ public Response scoreIndex( @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 study, @ApiParam(value = VariantScoreIndexParams.DESCRIPTION) VariantScoreIndexParams params) { @@ -363,7 +363,7 @@ public Response scoreDelete( @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 study, @ApiParam(value = "Unique name of the score within the study") @QueryParam("name") String name, @@ -409,7 +409,7 @@ public Response sampleGenotypeIndex( @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 study, @ApiParam(value = VariantSecondarySampleIndexParams.DESCRIPTION) VariantSecondarySampleIndexParams params) { @@ -426,7 +426,7 @@ public Response sampleIndex( @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 study, @ApiParam(value = VariantSecondarySampleIndexParams.DESCRIPTION) VariantSecondarySampleIndexParams params) { @@ -442,7 +442,7 @@ public Response variantSecondarySampleIndex( @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 study, @ApiParam(value = VariantSecondarySampleIndexParams.DESCRIPTION) VariantSecondarySampleIndexParams params) { @@ -458,7 +458,7 @@ public Response variantSampleDelete( @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 study, @ApiParam(value = VariantSampleDeleteParams.DESCRIPTION) VariantSampleDeleteParams params) { @@ -475,7 +475,7 @@ public Response familyGenotypeIndex( @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 study, @ApiParam(value = VariantFamilyIndexParams.DESCRIPTION) VariantFamilyIndexParams params) { @@ -492,7 +492,7 @@ public Response familyIndex( @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 study, @ApiParam(value = VariantFamilyIndexParams.DESCRIPTION) VariantFamilyIndexParams params) { @@ -508,7 +508,7 @@ public Response aggregateFamily( @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 study, @ApiParam(value = VariantAggregateFamilyParams.DESCRIPTION) VariantAggregateFamilyParams params) { @@ -524,7 +524,7 @@ public Response aggregate( @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 study, @ApiParam(value = VariantAggregateParams.DESCRIPTION) VariantAggregateParams params) { @@ -540,7 +540,7 @@ public Response julie( @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.PROJECT_PARAM) @QueryParam(ParamConstants.PROJECT_PARAM) String project, @ApiParam(value = JulieParams.DESCRIPTION, required = true) JulieParams params) { @@ -556,7 +556,7 @@ public Response variantPrune( @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 = VariantPruneParams.DESCRIPTION) VariantPruneParams params) { return submitOperationToProject(VariantPruneOperationTool.ID, params.getProject(), params, jobName, jobDescription, dependsOn, jobTags, scheduledStartTime, jobPriority, dryRun);