Merge pull request #1050 from opencb/TASK-7983

TASK-7983 - Fix the clinical interpretation analysis tool

Author: jmjuanes

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

@@ -134,7 +134,7 @@ export default class Admin extends OpenCGAParentClass {
         return this._get("admin", null, "users", null, "search", params);
     }
 
-    /** Synchronise a group of users from an authentication origin with a group in a study from catalog
+    /** [DEPRECATED] Moved to /users/sync
     * @param {Object} data - JSON containing the parameters.
     * @param {Object} [params] - The Object containing the following optional parameters:
     * @param {String} [params.organization] - Organization id.

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

@@ -273,25 +273,6 @@ export default class ClinicalAnalysis extends OpenCGAParentClass {
         return this._get("analysis", null, "clinical/interpretation", interpretations, "info", params);
     }
 
-    /** Run cancer tiering interpretation analysis
-    * @param {Object} data - Cancer tiering interpretation analysis 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.
-    * @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.
-    */
-    runInterpreterCancerTiering(data, params) {
-        return this._post("analysis", null, "clinical/interpreter/cancerTiering", null, "run", data, params);
-    }
-
     /** Run exomiser interpretation analysis
     * @param {Object} data - Exomiser interpretation analysis params.
     * @param {Object} [params] - The Object containing the following optional parameters:
@@ -311,46 +292,8 @@ export default class ClinicalAnalysis extends OpenCGAParentClass {
         return this._post("analysis", null, "clinical/interpreter/exomiser", null, "run", data, params);
     }
 
-    /** Run TEAM interpretation analysis
-    * @param {Object} data - TEAM interpretation analysis 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.
-    * @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.
-    */
-    runInterpreterTeam(data, params) {
-        return this._post("analysis", null, "clinical/interpreter/team", null, "run", data, params);
-    }
-
-    /** Run tiering interpretation analysis
-    * @param {Object} data - Tiering interpretation analysis 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.
-    * @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.
-    */
-    runInterpreterTiering(data, params) {
-        return this._post("analysis", null, "clinical/interpreter/tiering", null, "run", data, params);
-    }
-
-    /** Run Zetta interpretation analysis
-    * @param {Object} data - Zetta interpretation analysis params.
+    /** Run clinical interpretation analysis for rare diseases
+    * @param {Object} data - Parameters to execute the rare disease interpretation analysis.
     * @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
@@ -364,8 +307,8 @@ export default class ClinicalAnalysis extends OpenCGAParentClass {
     *     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.
     */
-    runInterpreterZetta(data, params) {
-        return this._post("analysis", null, "clinical/interpreter/zetta", null, "run", data, params);
+    runInterpreterRd(data, params) {
+        return this._post("analysis", null, "clinical/interpreter/rd", null, "run", data, params);
     }
 
     /** Load clinical analyses from a file

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

@@ -145,15 +145,6 @@ export default class DiseasePanel extends OpenCGAParentClass {
     * @param {Object} [data] - Panel 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.jobDependsOn] - Comma separated list of existing job IDs the job will depend on.
-    * @param {String} [params.jobDescription] - Job description.
-    * @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.
     */
     importPanels(data, params) {

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

@@ -305,8 +305,8 @@ export default class File extends OpenCGAParentClass {
     *     JSON AVRO PARQUET PDF IMAGE PLAIN BINARY NONE UNKNOWN"} [params.fileFormat] - [DEPRECATED] File format.
     * @param {"MICROARRAY_EXPRESSION_ONECHANNEL_AGILENT MICROARRAY_EXPRESSION_ONECHANNEL_AFFYMETRIX MICROARRAY_EXPRESSION_ONECHANNEL_GENEPIX
     *     MICROARRAY_EXPRESSION_TWOCHANNELS_AGILENT MICROARRAY_EXPRESSION_TWOCHANNELS_GENEPIX DATAMATRIX_EXPRESSION IDLIST IDLIST_RANKED
-    *     ANNOTATION_GENEVSANNOTATION OTHER_NEWICK OTHER_BLAST OTHER_INTERACTION OTHER_GENOTYPE OTHER_PLINK OTHER_VCF OTHER_PED VCF4 VARIANT
-    *     ALIGNMENT COVERAGE SEQUENCE PEDIGREE REFERENCE_GENOME NONE UNKNOWN"} [params.bioformat] - File bioformat.
+    *     ANNOTATION_GENEVSANNOTATION OTHER_NEWICK OTHER_BLAST OTHER_INTERACTION OTHER_GENOTYPE OTHER_PLINK OTHER_VCF OTHER_PED VCF4 CVDB
+    *     VARIANT ALIGNMENT COVERAGE SEQUENCE PEDIGREE REFERENCE_GENOME NONE UNKNOWN"} [params.bioformat] - File bioformat.
     * @param {String} [params.checksum] - Expected MD5 file checksum.
     * @param {Boolean} [params.resource] - Boolean field indicating whether the file is a resource or not.
     * @param {String} [params.study] - Study [[organization@]project:]study where study and project can be either the ID or UUID.

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

@@ -69,12 +69,13 @@ export default class Meta extends OpenCGAParentClass {
     }
 
     /** Opencga openapi json
+    * @param {String} url - Opencga host with environment.
     * @param {Object} [params] - The Object containing the following optional parameters:
-    * @param {String} [params.token] - List of categories to get API from.
+    * @param {String} [params.study] - Opencga study to be default in queries.
     * @returns {Promise} Promise object in the form of RestResponse instance.
     */
-    openapi(params) {
-        return this._get("meta", null, null, null, "openapi", params);
+    openapi(url, params) {
+        return this._get("meta", null, null, null, "openapi", {url, ...params});
     }
 
     /** Ping Opencga webservices.

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

@@ -142,6 +142,15 @@ export default class Study extends OpenCGAParentClass {
         return this._get("studies", study, null, null, "groups", params);
     }
 
+    /** Associate a remote group from an authentication origin with a local group in a study
+    * @param {String} study - Study [[organization@]project:]study where study and project can be either the ID or UUID.
+    * @param {Object} data - JSON containing the parameters.
+    * @returns {Promise} Promise object in the form of RestResponse instance.
+    */
+    syncGroups(study, data) {
+        return this._post("studies", study, "groups", null, "sync", data);
+    }
+
     /** Add or remove a group
     * @param {String} study - Study [[organization@]project:]study where study and project can be either the ID or UUID.
     * @param {Object} data - JSON containing the parameters.
@@ -308,6 +317,15 @@ export default class Study extends OpenCGAParentClass {
         return this._post("studies", study, null, null, "update", data, params);
     }
 
+    /** Synchronize all users from the remote groups of a given authentication origin
+    * @param {String} study - Study [[organization@]project:]study where study and project can be either the ID or UUID.
+    * @param {String} authenticationOriginId - Authentication origin ID.
+    * @returns {Promise} Promise object in the form of RestResponse instance.
+    */
+    syncUsers(study, authenticationOriginId) {
+        return this._post("studies", study, "users", null, "sync", null, authenticationOriginId);
+    }
+
     /** Fetch variableSets from a study
     * @param {String} study - Study [[organization@]project:]study where study and project can be either the ID or UUID.
     * @param {Object} [params] - The Object containing the following optional parameters:

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

@@ -84,6 +84,25 @@ export default class VariantOperation extends OpenCGAParentClass {
         return this._delete("operation", null, "variant/annotation", null, "delete", params);
     }
 
+    /** Install a variant annotation extension and configure the project to use it
+    * @param {Object} [data] - Parameters to configure a variant annotation extension.
+    * @param {Object} [params] - The Object containing the following optional parameters:
+    * @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.
+    * @param {String} [params.project] - project.
+    * @returns {Promise} Promise object in the form of RestResponse instance.
+    */
+    variantAnnotationExtensionConfigure(data, params) {
+        return this._post("operation", null, "variant/annotation/extension", null, "configure", data, params);
+    }
+
     /** Create and load variant annotations into the database
     * @param {Object} [data] - Variant annotation index params.
     * @param {Object} [params] - The Object containing the following optional parameters:

src/webcomponents/clinical/analysis/rd-interpreter-analysis.js

@@ -0,0 +1,164 @@
+/*
+ * Copyright 2015-2016 OpenCB
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+import {LitElement, html} from "lit";
+import AnalysisUtils from "../../commons/analysis/analysis-utils.js";
+import UtilsNew from "../../../core/utils-new.js";
+import "../../commons/forms/data-form.js";
+import "../../commons/filters/catalog-search-autocomplete.js";
+
+export default class RdInterpreterAnalysis extends LitElement {
+
+    constructor() {
+        super();
+
+        this.#init();
+    }
+
+    createRenderRoot() {
+        return this;
+    }
+
+    static get properties() {
+        return {
+            toolParams: {
+                type: Object,
+            },
+            opencgaSession: {
+                type: Object,
+            },
+            displayConfig: {
+                type: Object,
+            },
+        };
+    }
+
+    #init() {
+        this.ANALYSIS_TOOL = "rd-interpreter";
+        this.ANALYSIS_TITLE = "RD Interpreter";
+        this.ANALYSIS_DESCRIPTION = "Executes an RD Interpreter analysis job";
+        this.DEFAULT_TOOLPARAMS = {};
+
+        this._toolParams = UtilsNew.objectClone(this.DEFAULT_TOOLPARAMS);
+        this._config = this.getDefaultConfig();
+    }
+
+    update(changedProperties) {
+        if (changedProperties.has("toolParams")) {
+            this._toolParams = {
+                ...UtilsNew.objectClone(this.DEFAULT_TOOLPARAMS),
+                ...this.toolParams,
+            };
+        }
+
+        if(changedProperties.has("displayConfig") || changedProperties.has("toolParams")) {
+            this._config = this.getDefaultConfig();
+        }
+
+        super.update(changedProperties);
+    }
+
+    check() {
+        return null;
+    }
+
+    onFieldChange() {
+        this._toolParams = {...this._toolParams};
+        this.requestUpdate();
+    }
+
+    onSubmit() {
+        const toolParams = {
+            clinicalAnalysisId: this._toolParams.clinicalAnalysisId || "",
+        };
+
+        AnalysisUtils.submit(
+            this.ANALYSIS_TITLE,
+            this.opencgaSession.opencgaClient.clinical()
+                .runInterpreterRd(toolParams, {
+                    study: this.opencgaSession.study.fqn,
+                    ...AnalysisUtils.fillJobParams(this._toolParams, this.ANALYSIS_TOOL),
+                }),
+            this,
+        );
+    }
+
+    onClear() {
+        this._toolParams = {
+            ...UtilsNew.objectClone(this.DEFAULT_TOOLPARAMS),
+            ...this.toolParams,
+        };
+        this._config = this.getDefaultConfig();
+        this.requestUpdate();
+    }
+
+    render() {
+        return html`
+            <data-form
+                .data="${this._toolParams}"
+                .config="${this._config}"
+                @fieldChange="${event => this.onFieldChange(event)}"
+                @clear="${event => this.onClear(event)}"
+                @submit="${event => this.onSubmit(event)}">
+            </data-form>
+        `;
+    }
+
+    getDefaultConfig() {
+        const params = [
+            {
+                title: "Input Parameters",
+                elements: [
+                    {
+                        title: "Clinical Analysis ID",
+                        field: "clinicalAnalysisId",
+                        type: "custom",
+                        display: {
+                            render: (clinicalAnalysisId, onFieldChange) => html`
+                                <catalog-search-autocomplete
+                                    .value="${clinicalAnalysisId}"
+                                    .resource="${"CLINICAL_ANALYSIS"}"
+                                    .opencgaSession="${this.opencgaSession}"
+                                    .config="${{
+                                        multiple: false,
+                                        disabled: !!this.toolParams?.clinicalAnalysisId,
+                                    }}"
+                                    @filterChange="${event => onFieldChange(event.detail.value)}">
+                                </catalog-search-autocomplete>
+                            `,
+                        },
+                    },
+                ],
+            },
+        ];
+
+        return AnalysisUtils.getAnalysisConfiguration(
+            this.ANALYSIS_TOOL,
+            this.ANALYSIS_TITLE,
+            this.ANALYSIS_DESCRIPTION,
+            params,
+            this.check(),
+            {
+                display: {
+                    ...this.displayConfig,
+                },
+            },
+        );
+    }
+
+}
+
+customElements.define("rd-interpreter-analysis", RdInterpreterAnalysis);