Merge branch 'TASK-6445' into TASK-7100

src/core/clients/opencga/api/Admin.js

@@ -37,7 +37,7 @@ export default class Admin extends OpenCGAParentClass {
     /** Group by operation
     * @param {String} fields - Comma separated list of fields by which to group by.
     * @param {"AUDIT NOTE ORGANIZATION USER PROJECT STUDY FILE SAMPLE JOB INDIVIDUAL COHORT DISEASE_PANEL FAMILY CLINICAL_ANALYSIS
-    *     INTERPRETATION VARIANT ALIGNMENT CLINICAL EXPRESSION RGA FUNCTIONAL"} entity - Entity to be grouped by.
+    *     INTERPRETATION VARIANT ALIGNMENT CLINICAL EXPRESSION RGA WORKFLOW FUNCTIONAL"} entity - Entity to be grouped by.
     * @param {Object} [params] - The Object containing the following optional parameters:
     * @param {Boolean} [params.count] - Count the number of elements matching the group.
     * @param {Number} [params.limit = "50"] - Maximum number of documents (groups) to be returned. The default value is 50.

src/core/clients/opencga/api/Job.js

@@ -13,11 +13,11 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  * WARNING: AUTOGENERATED CODE
- *
+ * 
  * This code was generated by a tool.
- *
+ * 
  * Manual changes to this file may cause unexpected behavior in your application.
- * Manual changes to this file will be overwritten if the code is regenerated.
+ * Manual changes to this file will be overwritten if the code is regenerated. 
  *
 **/
 
@@ -66,6 +66,12 @@ export default class Job extends OpenCGAParentClass {
     * @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.
     * @param {String} [params.toolType] - Tool type executed by the job [OPERATION, ANALYSIS].
+    * @param {String} [params.tool.externalExecutor.id] - Id of the external executor. This field is only applicable for jobs executed by an
+    *     external executor.
+    * @param {String} [params.parentId] - Job id that generated this job (if any).
+    * @param {Boolean} [params.dryRun] - Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will validate
+    *     that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
+    * @param {Boolean} [params.internal.killJobRequested] - Flag indicating that the user requested to kill the job.
     * @param {String} [params.userId] - User that created the job.
     * @param {String} [params.priority] - Priority of the job.
     * @param {String} [params.status] - Filter by status.
@@ -120,6 +126,12 @@ export default class Job extends OpenCGAParentClass {
     * @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.
     * @param {String} [params.toolType] - Tool type executed by the job [OPERATION, ANALYSIS].
+    * @param {String} [params.tool.externalExecutor.id] - Id of the external executor. This field is only applicable for jobs executed by an
+    *     external executor.
+    * @param {String} [params.parentId] - Job id that generated this job (if any).
+    * @param {Boolean} [params.dryRun] - Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will validate
+    *     that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
+    * @param {Boolean} [params.internal.killJobRequested] - Flag indicating that the user requested to kill the job.
     * @param {String} [params.userId] - User that created the job.
     * @param {String} [params.priority] - Priority of the job.
     * @param {String} [params.status] - Filter by status.
@@ -141,6 +153,44 @@ export default class Job extends OpenCGAParentClass {
         return this._get("jobs", null, null, null, "search", params);
     }
 
+    /** Execute an analysis from a custom binary.
+    * @param {Object} data - body.
+    * @param {Object} [params] - The Object containing the following optional parameters:
+    * @param {String} [params.study] - Study [[organization@]project:]study where study and project can be either the ID or UUID.
+    * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not
+    *     provided.
+    * @param {String} [params.jobDescription] - Job description.
+    * @param {String} [params.jobDependsOn] - Comma separated list of existing job IDs the job will depend on.
+    * @param {String} [params.jobTags] - Job tags.
+    * @param {String} [params.jobScheduledStartTime] - Time when the job is scheduled to start.
+    * @param {String} [params.jobPriority] - Priority of the job.
+    * @param {Boolean} [params.jobDryRun] - Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will
+    *     validate that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
+    * @returns {Promise} Promise object in the form of RestResponse instance.
+    */
+    buildTool(data, params) {
+        return this._post("jobs", null, "tool", null, "build", data, params);
+    }
+
+    /** Execute an analysis from a custom binary.
+    * @param {Object} data - NextFlow run parameters.
+    * @param {Object} [params] - The Object containing the following optional parameters:
+    * @param {String} [params.study] - Study [[organization@]project:]study where study and project can be either the ID or UUID.
+    * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not
+    *     provided.
+    * @param {String} [params.jobDescription] - Job description.
+    * @param {String} [params.jobDependsOn] - Comma separated list of existing job IDs the job will depend on.
+    * @param {String} [params.jobTags] - Job tags.
+    * @param {String} [params.jobScheduledStartTime] - Time when the job is scheduled to start.
+    * @param {String} [params.jobPriority] - Priority of the job.
+    * @param {Boolean} [params.jobDryRun] - Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will
+    *     validate that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
+    * @returns {Promise} Promise object in the form of RestResponse instance.
+    */
+    runTool(data, params) {
+        return this._post("jobs", null, "tool", null, "run", data, params);
+    }
+
     /** Provide a summary of the running jobs
     * @param {Object} [params] - The Object containing the following optional parameters:
     * @param {Number} [params.limit = "20"] - Maximum number of jobs to be returned. The default value is 20.
@@ -241,4 +291,4 @@ export default class Job extends OpenCGAParentClass {
         return this._get("jobs", job, "log", null, "tail", params);
     }
 
-}
+}

src/core/clients/opencga/api/Organization.js

@@ -13,11 +13,11 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  * WARNING: AUTOGENERATED CODE
- *
+ * 
  * This code was generated by a tool.
- *
+ * 
  * Manual changes to this file may cause unexpected behavior in your application.
- * Manual changes to this file will be overwritten if the code is regenerated.
+ * Manual changes to this file will be overwritten if the code is regenerated. 
  *
 **/
 
@@ -180,4 +180,4 @@ export default class Organization extends OpenCGAParentClass {
         return this._post("organizations", organization, null, null, "update", data, params);
     }
 
-}
+}

src/core/clients/opencga/api/Study.js

@@ -13,11 +13,11 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  * WARNING: AUTOGENERATED CODE
- *
+ * 
  * This code was generated by a tool.
- *
+ * 
  * Manual changes to this file may cause unexpected behavior in your application.
- * Manual changes to this file will be overwritten if the code is regenerated.
+ * Manual changes to this file will be overwritten if the code is regenerated. 
  *
 **/
 
@@ -119,7 +119,7 @@ export default class Study extends OpenCGAParentClass {
     * @param {String} [params.userId] - User ID.
     * @param {String} [params.action] - Action performed by the user.
     * @param {"AUDIT NOTE ORGANIZATION USER PROJECT STUDY FILE SAMPLE JOB INDIVIDUAL COHORT DISEASE_PANEL FAMILY CLINICAL_ANALYSIS
-    *     INTERPRETATION VARIANT ALIGNMENT CLINICAL EXPRESSION RGA FUNCTIONAL"} [params.resource] - Resource involved.
+    *     INTERPRETATION VARIANT ALIGNMENT CLINICAL EXPRESSION RGA WORKFLOW FUNCTIONAL"} [params.resource] - Resource involved.
     * @param {String} [params.resourceId] - Resource ID.
     * @param {String} [params.resourceUuid] - resource UUID.
     * @param {"SUCCESS ERROR"} [params.status] - Filter by status.
@@ -342,4 +342,4 @@ export default class Study extends OpenCGAParentClass {
         return this._post("studies", study, "variableSets", variableSet, "variables/update", data, params);
     }
 
-}
+}

src/core/clients/opencga/api/Variant.js

@@ -444,6 +444,25 @@ export default class Variant extends OpenCGAParentClass {
         return this._post("analysis", null, "variant/knockout", null, "run", data, params);
     }
 
+    /** BCFtools liftover plugin maps coordinates from assembly 37 to 38.
+    * @param {Object} data - BCFtools +liftover plugin params.
+    * @param {Object} [params] - The Object containing the following optional parameters:
+    * @param {String} [params.study] - study.
+    * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not
+    *     provided.
+    * @param {String} [params.jobDescription] - Job description.
+    * @param {String} [params.jobDependsOn] - Comma separated list of existing job IDs the job will depend on.
+    * @param {String} [params.jobTags] - Job tags.
+    * @param {String} [params.jobScheduledStartTime] - Time when the job is scheduled to start.
+    * @param {String} [params.jobPriority] - Priority of the job.
+    * @param {Boolean} [params.jobDryRun] - Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will
+    *     validate that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
+    * @returns {Promise} Promise object in the form of RestResponse instance.
+    */
+    runLiftover(data, params) {
+        return this._post("analysis", null, "variant/liftover", null, "run", data, params);
+    }
+
     /** Run mendelian error analysis to infer uniparental disomy regions.
     * @param {Object} data - Mendelian error analysis params.
     * @param {Object} [params] - The Object containing the following optional parameters:

src/core/clients/opencga/api/VariantOperation.js

@@ -488,6 +488,16 @@ export default class VariantOperation extends OpenCGAParentClass {
         return this._delete("operation", null, "variant/secondaryIndex", null, "delete", params);
     }
 
+    /** Execute Variant Setup to allow using the variant engine. This setup is necessary before starting any variant operation.
+    * @param {Object} [data] - Variant setup params.
+    * @param {Object} [params] - The Object containing the following optional parameters:
+    * @param {String} [params.study] - Study [[organization@]project:]study where study and project can be either the ID or UUID.
+    * @returns {Promise} Promise object in the form of RestResponse instance.
+    */
+    setupVariant(data, params) {
+        return this._post("operation", null, "variant", null, "setup", data, params);
+    }
+
     /** Deletes the VariantStats of a cohort/s from the database
     * @param {Object} data - Variant stats delete params.
     * @param {Object} [params] - The Object containing the following optional parameters: