diff --git a/cypress/e2e/iva/variant-interpreter-grid-cancer-cnv.cy.js b/cypress/e2e/iva/variant-interpreter-grid-cancer-cnv.cy.js index 981229dfaa..d719156266 100644 --- a/cypress/e2e/iva/variant-interpreter-grid-cancer-cnv.cy.js +++ b/cypress/e2e/iva/variant-interpreter-grid-cancer-cnv.cy.js @@ -168,11 +168,9 @@ context("Variant Interpreter Grid Cancer CNV", () => { it("should display Cohort Stats (Population Frequencies) tooltip", () => { cy.get("tbody tr:first > td") - .eq(10) - .within(() => { - cy.get("a") - .trigger("mouseover"); - }); + .eq(13) + .find("a") + .trigger("mouseover"); cy.get(".qtip-content") .should("be.visible"); }); diff --git a/cypress/e2e/iva/variant-interpreter-grid-cancer.cy.js b/cypress/e2e/iva/variant-interpreter-grid-cancer.cy.js index de196e0fe9..ba7159e103 100644 --- a/cypress/e2e/iva/variant-interpreter-grid-cancer.cy.js +++ b/cypress/e2e/iva/variant-interpreter-grid-cancer.cy.js @@ -208,23 +208,20 @@ context("Variant Interpreter Grid Cancer", () => { }); }); - it("should display cohort stats (population frequencies) tooltip", () => { + it("should display cohort stats tooltip", () => { cy.get("tbody tr:first > td") - .eq(10) - .within(() => { - cy.get("a").trigger("mouseover"); - }); + .eq(13) + .find("a") + .trigger("mouseover"); cy.get(".qtip-content") .should("be.visible"); }); - it("should reference population frequencies tooltip", () => { + it("should display reference population frequencies tooltip", () => { cy.get("tbody tr:first > td") - .eq(11) - .within(() => { - cy.get("a") - .trigger("mouseover"); - }); + .eq(14) + .find("a") + .trigger("mouseover"); cy.get(".qtip-content") .should("be.visible"); }); diff --git a/cypress/e2e/iva/variant-interpreter-grid-germline.cy.js b/cypress/e2e/iva/variant-interpreter-grid-germline.cy.js index e2b4ff34ee..210841ffad 100644 --- a/cypress/e2e/iva/variant-interpreter-grid-germline.cy.js +++ b/cypress/e2e/iva/variant-interpreter-grid-germline.cy.js @@ -168,51 +168,23 @@ context("Variant Interpreter Grid Germiline", () => { }); }); - it("should display cohort stats (Population Frequencies) tooltip", () => { + it("should display cohort stats tooltip", () => { cy.get("tbody tr:first > td") - .eq(9) - .within(() => { - cy.get("a") - .trigger("mouseover"); - }); + .eq(12) + .find("a") + .trigger("mouseover"); cy.get(".qtip-content") .should("be.visible"); }); it("should display reference population frequencies tooltip", () => { cy.get("tbody tr:first > td") - .eq(10) - .within(() => { - cy.get("a") - .trigger("mouseover"); - }); - cy.get(".qtip-content") - .should("be.visible"); - }); - - it("should display ACMG Prediction (Classification) tooltip", () => { - cy.get("tbody tr:first > td") - .eq(16) - .within(() => { - cy.get("a") - .trigger("mouseover"); - }); - cy.get(".qtip-content") - .should("be.visible"); - }); - - it("should display OMIM Prediction (Classification) tooltip", () => { - UtilsTest.changePage(browserInterpreterGrid,2); - - cy.get("tbody tr:nth-child(6) > td:nth-child(15)") - .within(() => { - cy.get("a") - .trigger("mouseover"); - }); + .eq(13) + .find("a") + .trigger("mouseover"); cy.get(".qtip-content") .should("be.visible"); }); - }); context("Helpers", () => { diff --git a/src/core/bioinfo/bioinfo-utils.js b/src/core/bioinfo/bioinfo-utils.js index 49f4144c20..11bc1e66a6 100644 --- a/src/core/bioinfo/bioinfo-utils.js +++ b/src/core/bioinfo/bioinfo-utils.js @@ -262,7 +262,7 @@ export default class BioinfoUtils { case "GO": return this.getGeneOntologyLink(ontologyTermId); case "OMIM": - return this.getOmimLink(id); + return this.getOmimOntologyLink(id); case "ORPHA": return this.getOrphanetLink(id); case "MONDO": @@ -293,16 +293,24 @@ export default class BioinfoUtils { return `https://hpo.jax.org/app/browse/term/${hpoTerm}`; } + // static getOmimLink(omimEntry) { + // return `https://www.omim.org/entry/${omimEntry}`; + // } + static getSequenceOntologyLink(soTerm) { return `http://www.sequenceontology.org/browser/current_svn/term/${soTerm}`; } - static getOmimLink(soTerm) { - return `https://omim.org/entry/${soTerm}"`; + static getOmimOntologyLink(soTerm) { + return `https://www.omim.org/entry/${soTerm}"`; } static getOrphanetLink(orphaId) { return `https://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=${orphaId}`; } + static getPharmGKBLink(pharmGKBId) { + return `https://www.pharmgkb.org/chemical/${pharmGKBId}`; + } + } diff --git a/src/core/clients/opencga/api/Admin.js b/src/core/clients/opencga/api/Admin.js index 5997bed882..3f6204d416 100644 --- a/src/core/clients/opencga/api/Admin.js +++ b/src/core/clients/opencga/api/Admin.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-06 * * 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. @@ -34,8 +36,8 @@ export default class Admin extends OpenCGAParentClass { /** Group by operation * @param {String} fields - Comma separated list of fields by which to group by. - * @param {"AUDIT 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. + * @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. * @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. @@ -107,7 +109,6 @@ export default class Admin extends OpenCGAParentClass { * value is false. * @param {String} [params.organization] - Organization id. * @param {String} [params.user] - User ID. - * @param {String} [params.account] - Account type [GUEST, FULL, ADMINISTRATOR]. * @param {String} [params.authenticationId] - Authentication origin ID. * @returns {Promise} Promise object in the form of RestResponse instance. */ diff --git a/src/core/clients/opencga/api/Alignment.js b/src/core/clients/opencga/api/Alignment.js index 9173d6738d..fc30217787 100644 --- a/src/core/clients/opencga/api/Alignment.js +++ b/src/core/clients/opencga/api/Alignment.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-06 * * 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. @@ -41,6 +43,10 @@ export default class Alignment extends OpenCGAParentClass { * @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. */ runBwa(data, params) { @@ -56,6 +62,10 @@ export default class Alignment extends OpenCGAParentClass { * @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. */ runCoverageIndex(data, params) { @@ -71,6 +81,10 @@ export default class Alignment extends OpenCGAParentClass { * @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. */ coverageQcGeneCoverageStatsRun(data, params) { @@ -136,6 +150,10 @@ export default class Alignment extends OpenCGAParentClass { * @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. */ runDeeptools(data, params) { @@ -151,6 +169,10 @@ export default class Alignment extends OpenCGAParentClass { * @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. */ runFastqc(data, params) { @@ -166,6 +188,10 @@ export default class Alignment extends OpenCGAParentClass { * @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. */ runIndex(data, params) { @@ -182,6 +208,10 @@ export default class Alignment extends OpenCGAParentClass { * @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. */ runPicard(data, params) { @@ -198,6 +228,10 @@ export default class Alignment extends OpenCGAParentClass { * @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. */ runQc(data, params) { @@ -244,6 +278,10 @@ export default class Alignment extends OpenCGAParentClass { * @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. */ runSamtools(data, params) { diff --git a/src/core/clients/opencga/api/ClinicalAnalysis.js b/src/core/clients/opencga/api/ClinicalAnalysis.js index 2d47cced78..931d5fe01c 100644 --- a/src/core/clients/opencga/api/ClinicalAnalysis.js +++ b/src/core/clients/opencga/api/ClinicalAnalysis.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-06 * * 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. @@ -116,6 +118,7 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * @param {String} [params.dueDate] - Clinical Analysis due date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {String} [params.qualityControlSummary] - Clinical Analysis quality control summary. * @param {String} [params.release] - Release when it was created. + * @param {Number} [params.snapshot] - Snapshot value (Latest version of the entry in the specified release). * @param {String} [params.status] - Filter by status. * @param {String} [params.internalStatus] - Filter by internal status. * @param {String} [params.annotation] - Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit @@ -134,6 +137,7 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * @param {String} [params.id] - Comma separated list of Interpretation IDs up to a maximum of 100. 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.uuid] - Comma separated list of Interpretation UUIDs up to a maximum of 100. + * @param {String} [params.name] - Comma separated list of Interpretation names up to a maximum of 100. * @param {String} [params.clinicalAnalysisId] - Clinical Analysis id. * @param {String} [params.analystId] - Analyst ID. * @param {String} [params.methodName] - Interpretation method name. Also admits basic regular expressions using the operator '~', i.e. @@ -164,6 +168,7 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * @param {String} [params.id] - Comma separated list of Interpretation IDs up to a maximum of 100. 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.uuid] - Comma separated list of Interpretation UUIDs up to a maximum of 100. + * @param {String} [params.name] - Comma separated list of Interpretation names up to a maximum of 100. * @param {String} [params.clinicalAnalysisId] - Clinical Analysis id. * @param {String} [params.analystId] - Analyst ID. * @param {String} [params.methodName] - Interpretation method name. Also admits basic regular expressions using the operator '~', i.e. @@ -207,6 +212,10 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * @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) { @@ -214,7 +223,7 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { } /** Run exomiser interpretation analysis - * @param {Object} data - Exomizer interpretation analysis params. + * @param {Object} data - Exomiser 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 @@ -222,6 +231,10 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * @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. */ runInterpreterExomiser(data, params) { @@ -237,6 +250,10 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * @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) { @@ -252,6 +269,10 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * @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) { @@ -267,6 +288,10 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * @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. */ runInterpreterZetta(data, params) { @@ -282,6 +307,10 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * @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. */ load(data, params) { @@ -399,6 +428,10 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * @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 {Boolean} [params.auxiliarIndex = "false"] - Index auxiliar collection to improve performance assuming RGA is completely * indexed. The default value is false. * @returns {Promise} Promise object in the form of RestResponse instance. @@ -577,6 +610,7 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * @param {String} [params.dueDate] - Clinical Analysis due date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {String} [params.qualityControlSummary] - Clinical Analysis quality control summary. * @param {String} [params.release] - Release when it was created. + * @param {Number} [params.snapshot] - Snapshot value (Latest version of the entry in the specified release). * @param {String} [params.status] - Filter by status. * @param {String} [params.internalStatus] - Filter by internal status. * @param {String} [params.annotation] - Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit @@ -600,8 +634,7 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * but also increase execution time. * @param {String} [params.savedFilter] - Use a saved filter at User level. * @param {String} [params.includeInterpretation] - Interpretation ID to include the fields related to this interpretation. - * @param {String} [params.id] - List of IDs, these can be rs IDs (dbSNP) or variants in the format chrom:start:ref:alt, e.g. - * rs116600158,19:7177679:C:T. + * @param {String} [params.id] - List of variant IDs in the format chrom:start:ref:alt, e.g. 19:7177679:C:T. * @param {String} [params.region] - List of regions, these can be just a single chromosome name or regions in the format chr:start-end, * e.g.: 2,3:100000-200000. * @param {String} [params.type] - List of types, accepted values are SNV, MNV, INDEL, SV, COPY_NUMBER, COPY_NUMBER_LOSS, @@ -653,7 +686,7 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * @param {String} [params.ct] - List of SO consequence types, e.g. missense_variant,stop_lost or SO:0001583,SO:0001578. Accepts aliases * 'loss_of_function' and 'protein_altering'. * @param {String} [params.xref] - List of any external reference, these can be genes, proteins or variants. Accepted IDs include HGNC, - * Ensembl genes, dbSNP, ClinVar, HPO, Cosmic, ... + * Ensembl genes, dbSNP, ClinVar, HPO, Cosmic, HGVS ... * @param {String} [params.biotype] - List of biotypes, e.g. protein_coding. * @param {String} [params.proteinSubstitution] - Protein substitution scores include SIFT and PolyPhen. You can query using the score * {protein_score}[<|>|<=|>=]{number} or the description {protein_score}[~=|=]{description} e.g. polyphen>0.1,sift=tolerant. @@ -774,6 +807,8 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. * @param {Boolean} [params.flattenAnnotations = "false"] - Flatten the annotations?. The default value is false. * @param {String} [params.study] - Study [[organization@]project:]study where study and project can be either the ID or UUID. + * @param {String} [params.version] - Comma separated list of clinical versions. 'all' to get all the clinical versions. Not supported if + * multiple clinical ids are provided. * @param {Boolean} [params.deleted = "false"] - Boolean to retrieve deleted entries. The default value is false. * @returns {Promise} Promise object in the form of RestResponse instance. */ @@ -805,7 +840,7 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * @returns {Promise} Promise object in the form of RestResponse instance. */ clearInterpretation(clinicalAnalysis, interpretations, params) { - return this._post("analysis/clinical", clinicalAnalysis, "interpretation", interpretations, "clear", params); + return this._post("analysis/clinical", clinicalAnalysis, "interpretation", interpretations, "clear", null, params); } /** Delete interpretation @@ -830,7 +865,7 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * @returns {Promise} Promise object in the form of RestResponse instance. */ revertInterpretation(clinicalAnalysis, interpretation, version, params) { - return this._post("analysis/clinical", clinicalAnalysis, "interpretation", interpretation, "revert", {version, ...params}); + return this._post("analysis/clinical", clinicalAnalysis, "interpretation", interpretation, "revert", null, {version, ...params}); } /** Update interpretation fields diff --git a/src/core/clients/opencga/api/Cohort.js b/src/core/clients/opencga/api/Cohort.js index 237d874af6..dcd44092cc 100644 --- a/src/core/clients/opencga/api/Cohort.js +++ b/src/core/clients/opencga/api/Cohort.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-06 * * 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. diff --git a/src/core/clients/opencga/api/DiseasePanel.js b/src/core/clients/opencga/api/DiseasePanel.js index 44b47ec7d9..1aca2e4ef5 100644 --- a/src/core/clients/opencga/api/DiseasePanel.js +++ b/src/core/clients/opencga/api/DiseasePanel.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-06 * * 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. @@ -107,6 +109,10 @@ export default class DiseasePanel extends OpenCGAParentClass { * @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) { diff --git a/src/core/clients/opencga/api/Family.js b/src/core/clients/opencga/api/Family.js index 028113d98b..55a5ac0caf 100644 --- a/src/core/clients/opencga/api/Family.js +++ b/src/core/clients/opencga/api/Family.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-06 * * 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. diff --git a/src/core/clients/opencga/api/File.js b/src/core/clients/opencga/api/File.js index 4419c507e8..cfedee4d93 100644 --- a/src/core/clients/opencga/api/File.js +++ b/src/core/clients/opencga/api/File.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-06 * * 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. @@ -129,6 +131,10 @@ export default class File extends OpenCGAParentClass { * @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.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. */ @@ -164,6 +170,10 @@ export default class File extends OpenCGAParentClass { * @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. */ runLink(data, params) { @@ -179,6 +189,10 @@ export default class File extends OpenCGAParentClass { * @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. */ runPostlink(data, params) { @@ -252,7 +266,7 @@ export default class File extends OpenCGAParentClass { * @returns {Promise} Promise object in the form of RestResponse instance. */ upload(params) { - return this._post("files", null, null, null, "upload", params); + return this._post("files", null, null, null, "upload", null, params); } /** Return the acl defined for the file or folder. If member is provided, it will only return the acl for the member. @@ -389,6 +403,19 @@ export default class File extends OpenCGAParentClass { return this._get("files", file, null, null, "image", params); } + /** Move file to a different path + * @param {String} file - File id, UUID or name. + * @param {Object} data - Parameters to modify. + * @param {Object} [params] - The Object containing the following optional parameters: + * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. + * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. + * @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. + */ + move(file, data, params) { + return this._post("files", file, null, null, "move", data, params); + } + /** Refresh metadata from the selected file or folder. Return updated files. * @param {String} file - File id, name or path. Paths must be separated by : instead of /. * @param {Object} [params] - The Object containing the following optional parameters: diff --git a/src/core/clients/opencga/api/GA4GH.js b/src/core/clients/opencga/api/GA4GH.js index b06055721c..222eaa7c67 100644 --- a/src/core/clients/opencga/api/GA4GH.js +++ b/src/core/clients/opencga/api/GA4GH.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-06 * * 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. @@ -37,7 +39,7 @@ export default class GA4GH extends OpenCGAParentClass { * @returns {Promise} Promise object in the form of RestResponse instance. */ searchReads() { - return this._post("ga4gh", null, "reads", null, "search"); + return this._post("ga4gh", null, "reads", null, "search", null); } /** Fetch alignment files using HTSget protocol @@ -76,7 +78,7 @@ export default class GA4GH extends OpenCGAParentClass { * @returns {Promise} Promise object in the form of RestResponse instance. */ searchVariants() { - return this._post("ga4gh", null, "variants", null, "search"); + return this._post("ga4gh", null, "variants", null, "search", null); } } \ No newline at end of file diff --git a/src/core/clients/opencga/api/Individual.js b/src/core/clients/opencga/api/Individual.js index a3307d522d..fb33520e6d 100644 --- a/src/core/clients/opencga/api/Individual.js +++ b/src/core/clients/opencga/api/Individual.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-06 * * 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. diff --git a/src/core/clients/opencga/api/Job.js b/src/core/clients/opencga/api/Job.js index b83184040e..ffc0b066fd 100644 --- a/src/core/clients/opencga/api/Job.js +++ b/src/core/clients/opencga/api/Job.js @@ -1,21 +1,23 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 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 + * + * 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. * WARNING: AUTOGENERATED CODE - * + * * This code was generated by a tool. - * Autogenerated on: 2024-03-06 - * + * * 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. * **/ @@ -93,6 +95,7 @@ export default class Job extends OpenCGAParentClass { * @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.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. */ @@ -203,6 +206,16 @@ export default class Job extends OpenCGAParentClass { return this._post("jobs", jobs, null, null, "update", data, params); } + /** Send a signal to kill a pending or running job + * @param {String} job - Job ID or UUID. + * @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. + */ + kill(job, params) { + return this._post("jobs", job, null, null, "kill", null, params); + } + /** Show the first lines of a log file (up to a limit) * @param {String} job - Job ID or UUID. * @param {Object} [params] - The Object containing the following optional parameters: @@ -228,4 +241,4 @@ export default class Job extends OpenCGAParentClass { return this._get("jobs", job, "log", null, "tail", params); } -} \ No newline at end of file +} diff --git a/src/core/clients/opencga/api/Meta.js b/src/core/clients/opencga/api/Meta.js index 7028dd5ea7..0a536de0c0 100644 --- a/src/core/clients/opencga/api/Meta.js +++ b/src/core/clients/opencga/api/Meta.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-06 * * 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. diff --git a/src/core/clients/opencga/api/Organization.js b/src/core/clients/opencga/api/Organization.js index 3884dc598d..37cbe70cb8 100644 --- a/src/core/clients/opencga/api/Organization.js +++ b/src/core/clients/opencga/api/Organization.js @@ -1,21 +1,23 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 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 + * + * 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. * WARNING: AUTOGENERATED CODE - * + * * This code was generated by a tool. - * Autogenerated on: 2024-03-06 - * + * * 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. * **/ @@ -45,6 +47,112 @@ export default class Organization extends OpenCGAParentClass { return this._post("organizations", null, null, null, "create", data, params); } + /** Create a new note + * @param {Object} data - JSON containing the Note to be added. + * @param {Object} [params] - The Object containing the following optional parameters: + * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. + * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. + * @param {Boolean} [params.includeResult = "false"] - Flag indicating to include the created or updated document result in the response. + * The default value is false. + * @returns {Promise} Promise object in the form of RestResponse instance. + */ + createNotes(data, params) { + return this._post("organizations", null, "notes", null, "create", data, params); + } + + /** Search for notes of scope ORGANIZATION + * @param {Object} [params] - The Object containing the following optional parameters: + * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. + * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. + * @param {String} [params.creationDate] - Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. + * @param {String} [params.modificationDate] - Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. + * @param {String} [params.id] - Note unique identifier. + * @param {String} [params.scope] - Scope of the Note. + * @param {String} [params.visibility] - Visibility of the Note. + * @param {String} [params.uuid] - Unique 32-character identifier assigned automatically by OpenCGA. + * @param {String} [params.userId] - User that wrote that Note. + * @param {String} [params.tags] - Note tags. + * @param {String} [params.version] - Autoincremental version assigned to the registered entry. By default, updates does not create new + * versions. To enable versioning, users must set the `incVersion` flag from the /update web service when updating the document. + * @returns {Promise} Promise object in the form of RestResponse instance. + */ + searchNotes(params) { + return this._get("organizations", null, "notes", null, "search", params); + } + + /** Delete note + * @param {String} id - Note unique identifier. + * @param {Object} [params] - The Object containing the following optional parameters: + * @param {Boolean} [params.includeResult = "false"] - Flag indicating to include the created or updated document result in the response. + * The default value is false. + * @returns {Promise} Promise object in the form of RestResponse instance. + */ + deleteNotes(id, params) { + return this._delete("organizations", null, "notes", id, "delete", params); + } + + /** Update a note + * @param {String} id - Note unique identifier. + * @param {Object} data - JSON containing the Note fields to be updated. + * @param {Object} [params] - The Object containing the following optional parameters: + * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. + * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. + * @param {"ADD SET REMOVE"} [params.tagsAction = "ADD"] - Action to be performed if the array of tags is being updated. The default + * value is ADD. + * @param {Boolean} [params.includeResult = "false"] - Flag indicating to include the created or updated document result in the response. + * The default value is false. + * @returns {Promise} Promise object in the form of RestResponse instance. + */ + updateNotes(id, data, params) { + return this._post("organizations", null, "notes", id, "update", data, params); + } + + /** Update the user status + * @param {String} user - User ID. + * @param {Object} data - JSON containing the User fields to be updated. + * @param {Object} [params] - The Object containing the following optional parameters: + * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. + * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. + * @param {String} [params.organization] - Organization id. + * @param {Boolean} [params.includeResult = "false"] - Flag indicating to include the created or updated document result in the response. + * The default value is false. + * @returns {Promise} Promise object in the form of RestResponse instance. + */ + userUpdateStatus(user, data, params) { + return this._post("organizations/user", user, "status", null, "update", data, params); + } + + /** Update the user information + * @param {String} user - User ID. + * @param {Object} data - JSON containing the User fields to be updated. + * @param {Object} [params] - The Object containing the following optional parameters: + * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. + * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. + * @param {String} [params.organization] - Organization id. + * @param {Boolean} [params.includeResult = "false"] - Flag indicating to include the created or updated document result in the response. + * The default value is false. + * @returns {Promise} Promise object in the form of RestResponse instance. + */ + updateUser(user, data, params) { + return this._post("organizations", null, "user", user, "update", data, params); + } + + /** Update the Organization configuration attributes + * @param {String} organization - Organization id. + * @param {Object} data - JSON containing the params to be updated. + * @param {Object} [params] - The Object containing the following optional parameters: + * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. + * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. + * @param {Boolean} [params.includeResult = "false"] - Flag indicating to include the created or updated document result in the response. + * The default value is false. + * @param {"ADD SET REMOVE REPLACE"} [params.authenticationOriginsAction = "ADD"] - Action to be performed if the array of + * authenticationOrigins is being updated. The default value is ADD. + * @returns {Promise} Promise object in the form of RestResponse instance. + */ + updateConfiguration(organization, data, params) { + return this._post("organizations", organization, "configuration", null, "update", data, params); + } + /** Return the organization information * @param {String} organization - Organization id. * @param {Object} [params] - The Object containing the following optional parameters: @@ -72,4 +180,4 @@ export default class Organization extends OpenCGAParentClass { return this._post("organizations", organization, null, null, "update", data, params); } -} \ No newline at end of file +} diff --git a/src/core/clients/opencga/api/Project.js b/src/core/clients/opencga/api/Project.js index 3767afc6bc..041fa7ed69 100644 --- a/src/core/clients/opencga/api/Project.js +++ b/src/core/clients/opencga/api/Project.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-06 * * 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. @@ -83,7 +85,7 @@ export default class Project extends OpenCGAParentClass { * @returns {Promise} Promise object in the form of RestResponse instance. */ incRelease(project) { - return this._post("projects", project, null, null, "incRelease"); + return this._post("projects", project, null, null, "incRelease", null); } /** Fetch all the studies contained in the project diff --git a/src/core/clients/opencga/api/Sample.js b/src/core/clients/opencga/api/Sample.js index 1d4f379fa3..48edf930fc 100644 --- a/src/core/clients/opencga/api/Sample.js +++ b/src/core/clients/opencga/api/Sample.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-06 * * 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. diff --git a/src/core/clients/opencga/api/Study.js b/src/core/clients/opencga/api/Study.js index b170fbf1c1..c638ea47b8 100644 --- a/src/core/clients/opencga/api/Study.js +++ b/src/core/clients/opencga/api/Study.js @@ -1,21 +1,23 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 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 + * + * 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. * WARNING: AUTOGENERATED CODE - * + * * This code was generated by a tool. - * Autogenerated on: 2024-03-06 - * + * * 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. * **/ @@ -116,8 +118,8 @@ export default class Study extends OpenCGAParentClass { * @param {String} [params.operationId] - Audit operation UUID. * @param {String} [params.userId] - User ID. * @param {String} [params.action] - Action performed by the user. - * @param {"AUDIT 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. + * @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. * @param {String} [params.resourceId] - Resource ID. * @param {String} [params.resourceUuid] - resource UUID. * @param {"SUCCESS ERROR"} [params.status] - Filter by status. @@ -164,6 +166,69 @@ export default class Study extends OpenCGAParentClass { return this._post("studies", study, "groups", group, "users/update", data, params); } + /** Create a new note + * @param {String} study - Study [[organization@]project:]study where study and project can be either the ID or UUID. + * @param {Object} data - JSON containing the Note to be added. + * @param {Object} [params] - The Object containing the following optional parameters: + * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. + * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. + * @param {Boolean} [params.includeResult = "false"] - Flag indicating to include the created or updated document result in the response. + * The default value is false. + * @returns {Promise} Promise object in the form of RestResponse instance. + */ + createNotes(study, data, params) { + return this._post("studies", study, "notes", null, "create", data, params); + } + + /** Search for notes of scope 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: + * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. + * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. + * @param {String} [params.creationDate] - Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. + * @param {String} [params.modificationDate] - Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. + * @param {String} [params.id] - Note unique identifier. + * @param {String} [params.uuid] - Unique 32-character identifier assigned automatically by OpenCGA. + * @param {String} [params.userId] - User that wrote that Note. + * @param {String} [params.tags] - Note tags. + * @param {String} [params.visibility] - Visibility of the Note. + * @param {String} [params.version] - Autoincremental version assigned to the registered entry. By default, updates does not create new + * versions. To enable versioning, users must set the `incVersion` flag from the /update web service when updating the document. + * @returns {Promise} Promise object in the form of RestResponse instance. + */ + searchNotes(study, params) { + return this._get("studies", study, "notes", null, "search", params); + } + + /** Delete note + * @param {String} study - Study [[organization@]project:]study where study and project can be either the ID or UUID. + * @param {String} id - Note unique identifier. + * @param {Object} [params] - The Object containing the following optional parameters: + * @param {Boolean} [params.includeResult = "false"] - Flag indicating to include the created or updated document result in the response. + * The default value is false. + * @returns {Promise} Promise object in the form of RestResponse instance. + */ + deleteNotes(study, id, params) { + return this._delete("studies", study, "notes", id, "delete", params); + } + + /** Update a note + * @param {String} study - Study [[organization@]project:]study where study and project can be either the ID or UUID. + * @param {String} id - Note unique identifier. + * @param {Object} data - JSON containing the Note fields to be updated. + * @param {Object} [params] - The Object containing the following optional parameters: + * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. + * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. + * @param {"ADD SET REMOVE"} [params.tagsAction = "ADD"] - Action to be performed if the array of tags is being updated. The default + * value is ADD. + * @param {Boolean} [params.includeResult = "false"] - Flag indicating to include the created or updated document result in the response. + * The default value is false. + * @returns {Promise} Promise object in the form of RestResponse instance. + */ + updateNotes(study, id, data, params) { + return this._post("studies", study, "notes", id, "update", data, params); + } + /** Fetch permission rules * @param {String} study - Study [[organization@]project:]study where study and project can be either the ID or UUID. * @param {"SAMPLES FILES COHORTS INDIVIDUALS FAMILIES JOBS CLINICAL_ANALYSES DISEASE_PANELS"} entity - Entity where the permission rules @@ -199,6 +264,10 @@ export default class Study extends OpenCGAParentClass { * @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. */ runTemplates(study, data, params) { @@ -212,11 +281,11 @@ export default class Study extends OpenCGAParentClass { * @returns {Promise} Promise object in the form of RestResponse instance. */ uploadTemplates(study, params) { - return this._post("studies", study, "templates", null, "upload", params); + return this._post("studies", study, "templates", null, "upload", null, params); } /** Delete template - * @param {String} [study] - Study [[organization@]project:]study where study and project can be either the ID or UUID. + * @param {String} study - Study [[organization@]project:]study where study and project can be either the ID or UUID. * @param {String} templateId - Template id. * @returns {Promise} Promise object in the form of RestResponse instance. */ @@ -273,4 +342,4 @@ export default class Study extends OpenCGAParentClass { return this._post("studies", study, "variableSets", variableSet, "variables/update", data, params); } -} \ No newline at end of file +} diff --git a/src/core/clients/opencga/api/User.js b/src/core/clients/opencga/api/User.js index c5c7544c65..32b28182c7 100644 --- a/src/core/clients/opencga/api/User.js +++ b/src/core/clients/opencga/api/User.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-06 * * 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. @@ -37,7 +39,7 @@ export default class User extends OpenCGAParentClass { * @returns {Promise} Promise object in the form of RestResponse instance. */ anonymous(organization) { - return this._post("users", null, null, null, "anonymous", organization); + return this._post("users", null, null, null, "anonymous", null, organization); } /** Create a new user @@ -64,6 +66,24 @@ export default class User extends OpenCGAParentClass { return this._post("users", null, null, null, "password", data); } + /** User search method + * @param {Object} [params] - The Object containing the following optional parameters: + * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. + * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. + * @param {Number} [params.limit] - Number of results to be returned. + * @param {Number} [params.skip] - Number of results to skip. + * @param {Boolean} [params.count = "false"] - Get the total number of results matching the query. Deactivated by default. The default + * value is false. + * @param {String} [params.organization] - Organization id. + * @param {String} [params.id] - Comma separated list user IDs up to a maximum of 100. 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.authenticationId] - Authentication origin ID. + * @returns {Promise} Promise object in the form of RestResponse instance. + */ + search(params) { + return this._get("users", null, null, null, "search", params); + } + /** Return the user information including its projects and studies * @param {String} users - Comma separated list of user IDs. * @param {Object} [params] - The Object containing the following optional parameters: diff --git a/src/core/clients/opencga/api/Variant.js b/src/core/clients/opencga/api/Variant.js index 98d42a16fd..7d8b01966d 100644 --- a/src/core/clients/opencga/api/Variant.js +++ b/src/core/clients/opencga/api/Variant.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-06 * * 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. @@ -57,7 +59,7 @@ export default class Variant extends OpenCGAParentClass { * @param {String} [params.ct] - List of SO consequence types, e.g. missense_variant,stop_lost or SO:0001583,SO:0001578. Accepts aliases * 'loss_of_function' and 'protein_altering'. * @param {String} [params.xref] - List of any external reference, these can be genes, proteins or variants. Accepted IDs include HGNC, - * Ensembl genes, dbSNP, ClinVar, HPO, Cosmic, ... + * Ensembl genes, dbSNP, ClinVar, HPO, Cosmic, HGVS ... * @param {String} [params.biotype] - List of biotypes, e.g. protein_coding. * @param {String} [params.proteinSubstitution] - Protein substitution scores include SIFT and PolyPhen. You can query using the score * {protein_score}[<|>|<=|>=]{number} or the description {protein_score}[~=|=]{description} e.g. polyphen>0.1,sift=tolerant. @@ -103,8 +105,7 @@ export default class Variant extends OpenCGAParentClass { /** Query variant annotations from any saved versions * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.id] - List of IDs, these can be rs IDs (dbSNP) or variants in the format chrom:start:ref:alt, e.g. - * rs116600158,19:7177679:C:T. + * @param {String} [params.id] - List of variant IDs in the format chrom:start:ref:alt, e.g. 19:7177679:C:T. * @param {String} [params.region] - List of regions, these can be just a single chromosome name or regions in the format chr:start-end, * e.g.: 2,3:100000-200000. * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. @@ -159,6 +160,10 @@ export default class Variant extends OpenCGAParentClass { * @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. */ runCohortStats(data, params) { @@ -174,6 +179,10 @@ export default class Variant extends OpenCGAParentClass { * @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. */ runExomiser(data, params) { @@ -192,6 +201,10 @@ export default class Variant extends OpenCGAParentClass { * @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. */ runExport(data, params) { @@ -223,6 +236,10 @@ export default class Variant extends OpenCGAParentClass { * @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. */ runFamilyQc(data, params) { @@ -236,6 +253,10 @@ export default class Variant extends OpenCGAParentClass { * @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.study] - Study [[organization@]project:]study where study and project can be either the ID or UUID. * @param {String} [params.file] - Files to remove. * @param {Boolean} [params.resume] - Resume a previously failed indexation. @@ -254,6 +275,10 @@ export default class Variant extends OpenCGAParentClass { * @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. */ runGatk(data, params) { @@ -271,6 +296,10 @@ export default class Variant extends OpenCGAParentClass { * @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. */ runGenomePlot(data, params) { @@ -286,6 +315,10 @@ export default class Variant extends OpenCGAParentClass { * @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. */ runGwas(data, params) { @@ -301,6 +334,10 @@ export default class Variant extends OpenCGAParentClass { * @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. */ runHrDetect(data, params) { @@ -316,6 +353,10 @@ export default class Variant extends OpenCGAParentClass { * @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. */ runIndex(data, params) { @@ -331,6 +372,10 @@ export default class Variant extends OpenCGAParentClass { * @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. */ runIndividualQc(data, params) { @@ -346,6 +391,10 @@ export default class Variant extends OpenCGAParentClass { * @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. */ runInferredSex(data, params) { @@ -385,6 +434,10 @@ export default class Variant extends OpenCGAParentClass { * @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. */ runKnockout(data, params) { @@ -400,6 +453,10 @@ export default class Variant extends OpenCGAParentClass { * @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. */ runMendelianError(data, params) { @@ -485,6 +542,10 @@ export default class Variant extends OpenCGAParentClass { * @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. */ runMutationalSignature(data, params) { @@ -500,6 +561,10 @@ export default class Variant extends OpenCGAParentClass { * @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. */ runPlink(data, params) { @@ -519,8 +584,7 @@ export default class Variant extends OpenCGAParentClass { * @param {Number} [params.approximateCountSamplingSize] - Sampling size to get the approximate count. Larger values increase accuracy * but also increase execution time. * @param {String} [params.savedFilter] - Use a saved filter at User level. - * @param {String} [params.id] - List of IDs, these can be rs IDs (dbSNP) or variants in the format chrom:start:ref:alt, e.g. - * rs116600158,19:7177679:C:T. + * @param {String} [params.id] - List of variant IDs in the format chrom:start:ref:alt, e.g. 19:7177679:C:T. * @param {String} [params.region] - List of regions, these can be just a single chromosome name or regions in the format chr:start-end, * e.g.: 2,3:100000-200000. * @param {String} [params.type] - List of types, accepted values are SNV, MNV, INDEL, SV, COPY_NUMBER, COPY_NUMBER_LOSS, @@ -595,7 +659,7 @@ export default class Variant extends OpenCGAParentClass { * @param {String} [params.ct] - List of SO consequence types, e.g. missense_variant,stop_lost or SO:0001583,SO:0001578. Accepts aliases * 'loss_of_function' and 'protein_altering'. * @param {String} [params.xref] - List of any external reference, these can be genes, proteins or variants. Accepted IDs include HGNC, - * Ensembl genes, dbSNP, ClinVar, HPO, Cosmic, ... + * Ensembl genes, dbSNP, ClinVar, HPO, Cosmic, HGVS ... * @param {String} [params.biotype] - List of biotypes, e.g. protein_coding. * @param {String} [params.proteinSubstitution] - Protein substitution scores include SIFT and PolyPhen. You can query using the score * {protein_score}[<|>|<=|>=]{number} or the description {protein_score}[~=|=]{description} e.g. polyphen>0.1,sift=tolerant. @@ -648,6 +712,10 @@ export default class Variant extends OpenCGAParentClass { * @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. */ runRelatedness(data, params) { @@ -663,6 +731,10 @@ export default class Variant extends OpenCGAParentClass { * @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. */ runRvtests(data, params) { @@ -733,6 +805,10 @@ export default class Variant extends OpenCGAParentClass { * @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. */ runSampleEligibility(data, params) { @@ -751,6 +827,10 @@ export default class Variant extends OpenCGAParentClass { * @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. */ runSampleQc(data, params) { @@ -779,6 +859,10 @@ export default class Variant extends OpenCGAParentClass { * @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. */ runSample(data, params) { @@ -826,6 +910,10 @@ export default class Variant extends OpenCGAParentClass { * @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. */ runSampleStats(data, params) { @@ -842,6 +930,10 @@ export default class Variant extends OpenCGAParentClass { * @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. */ runStatsExport(data, params) { @@ -857,6 +949,10 @@ export default class Variant extends OpenCGAParentClass { * @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. */ runStats(data, params) { diff --git a/src/core/clients/opencga/api/VariantOperation.js b/src/core/clients/opencga/api/VariantOperation.js index 9ceb02dd57..0d79024c49 100644 --- a/src/core/clients/opencga/api/VariantOperation.js +++ b/src/core/clients/opencga/api/VariantOperation.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-06 * * 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. @@ -52,6 +54,10 @@ export default class VariantOperation extends OpenCGAParentClass { * @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.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. */ @@ -66,6 +72,10 @@ export default class VariantOperation extends OpenCGAParentClass { * @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 [organization@]project where project can be either the ID or the alias. * @param {String} [params.annotationId] - Annotation identifier. * @returns {Promise} Promise object in the form of RestResponse instance. @@ -82,6 +92,10 @@ export default class VariantOperation extends OpenCGAParentClass { * @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 [organization@]project where project can be either the ID or the alias. * @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. @@ -98,6 +112,10 @@ export default class VariantOperation extends OpenCGAParentClass { * @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 [organization@]project where project can be either the ID or the alias. * @returns {Promise} Promise object in the form of RestResponse instance. */ @@ -124,6 +142,10 @@ export default class VariantOperation extends OpenCGAParentClass { * @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.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. */ @@ -139,6 +161,10 @@ export default class VariantOperation extends OpenCGAParentClass { * @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.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. */ @@ -154,6 +180,10 @@ export default class VariantOperation extends OpenCGAParentClass { * @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.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. */ @@ -169,6 +199,10 @@ export default class VariantOperation extends OpenCGAParentClass { * @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.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. */ @@ -184,6 +218,10 @@ export default class VariantOperation extends OpenCGAParentClass { * @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.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. */ @@ -199,6 +237,10 @@ export default class VariantOperation extends OpenCGAParentClass { * @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. */ @@ -214,6 +256,10 @@ export default class VariantOperation extends OpenCGAParentClass { * @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. */ repairVariantMetadata(data, params) { @@ -228,6 +274,10 @@ export default class VariantOperation extends OpenCGAParentClass { * @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.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. */ @@ -243,6 +293,10 @@ export default class VariantOperation extends OpenCGAParentClass { * @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. */ pruneVariant(data, params) { @@ -257,6 +311,10 @@ export default class VariantOperation extends OpenCGAParentClass { * @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.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. */ @@ -272,6 +330,10 @@ export default class VariantOperation extends OpenCGAParentClass { * @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.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. */ @@ -297,6 +359,10 @@ export default class VariantOperation extends OpenCGAParentClass { * @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.study] - Study [[organization@]project:]study where study and project can be either the ID or UUID. * @param {String} [params.name] - Unique name of the score within the study. * @param {Boolean} [params.resume] - Resume a previously failed remove. @@ -322,6 +388,10 @@ export default class VariantOperation extends OpenCGAParentClass { * @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.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. */ @@ -337,6 +407,10 @@ export default class VariantOperation extends OpenCGAParentClass { * @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 [organization@]project where project can be either the ID or the alias. * @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. @@ -353,6 +427,10 @@ export default class VariantOperation extends OpenCGAParentClass { * @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.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. */ @@ -379,6 +457,10 @@ export default class VariantOperation extends OpenCGAParentClass { * @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 [organization@]project where project can be either the ID or the alias. * @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. @@ -394,6 +476,10 @@ export default class VariantOperation extends OpenCGAParentClass { * @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.study] - Study [[organization@]project:]study where study and project can be either the ID or UUID. * @param {String} [params.samples] - Samples to remove. Needs to provide all the samples in the secondary index. * @returns {Promise} Promise object in the form of RestResponse instance. @@ -411,6 +497,10 @@ export default class VariantOperation extends OpenCGAParentClass { * @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. */ deleteVariantStats(data, params) { @@ -426,6 +516,10 @@ export default class VariantOperation extends OpenCGAParentClass { * @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. */ indexVariantStats(data, params) { @@ -440,6 +534,10 @@ export default class VariantOperation extends OpenCGAParentClass { * @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.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. */ diff --git a/src/core/clients/opencga/opencga-catalog-utils.js b/src/core/clients/opencga/opencga-catalog-utils.js index 171143d871..745d55275e 100644 --- a/src/core/clients/opencga/opencga-catalog-utils.js +++ b/src/core/clients/opencga/opencga-catalog-utils.js @@ -89,23 +89,49 @@ export default class OpencgaCatalogUtils { return false; } + // Check if the provided user is admin in the organization + static isOrganizationAdmin(organization, userId) { + if (!organization || !userId) { + return false; + } + // 1. Check if user is the organization admin + if (organization?.owner === userId) { + return true; + } else { + // Check if user is an admin of the organization + if (organization?.admins?.includes?.(userId)) { + return true; + } + } + // Other case, user is not admin of the organization + return false; + } + // Check if the user has the right the permissions in the study. static isAdmin(study, userLogged) { if (!study || !userLogged) { console.error(`No valid parameters, study: ${study}, user: ${userLogged}`); return false; } - // Check if user is the Study owner - const studyOwner = study.fqn.split("@")[0]; - if (userLogged === studyOwner) { + const admins = study.groups.find(group => group.id === "@admins"); + return !!admins.userIds.includes(userLogged); + } + + // Check if the provided user is admin in the organization + static isOrganizationAdmin(organization, userId) { + if (!organization || !userId) { + return false; + } + // 1. Check if user is the organization admin + if (organization?.owner === userId) { return true; } else { - // Check if user is a Study admin, belongs to @admins group - const admins = study.groups.find(group => group.id === "@admins"); - if (admins.userIds.includes(userLogged)) { + // Check if user is an admin of the organization + if (organization?.admins?.includes?.(userId)) { return true; } } + // Other case, user is not admin of the organization return false; } diff --git a/src/core/clients/opencga/opencga-client.js b/src/core/clients/opencga/opencga-client.js index c94b0e2083..bb7cd4c831 100644 --- a/src/core/clients/opencga/opencga-client.js +++ b/src/core/clients/opencga/opencga-client.js @@ -220,7 +220,7 @@ export class OpenCGAClient { if (!this.clients.has("organization")) { this.clients.set("organization", new Organization(this._config)); } - return this.clients.get("organizaton"); + return this.clients.get("organization"); } /* @@ -399,9 +399,13 @@ export class OpenCGAClient { console.error(e); } - + // Save projects session.projects = session.user.projects; + // Fetch organization info + const organizationResponse = await this.organization() + .info(session.user.organization); + session.organization = organizationResponse.responses[0].results[0]; // Fetch authorised Projects and Studies console.log("Fetching projects and studies"); diff --git a/src/core/clients/opencga/opencga-parent-class.js b/src/core/clients/opencga/opencga-parent-class.js index 14e74f6eec..bf24d279eb 100644 --- a/src/core/clients/opencga/opencga-parent-class.js +++ b/src/core/clients/opencga/opencga-parent-class.js @@ -33,11 +33,14 @@ export default class OpenCGAParentClass { _options.token = sid; } } - + // CAUTION Vero 2024-05-10: We believe this bit of code is useless. Temporarily commented out. + // In users endpoint, we cannot find GET method where the path param {user/users} should be autocompleted. + // When needed, they should be explicitly set. // If category == users and userId is not given, we try to set it - if (category1 === "users" && (ids1 === undefined || ids1 === null || ids1 === "")) { - ids1 = this._getUserId(); - } + // if (category1 === "users" && (ids1 === undefined || ids1 === null || ids1 === "")) { + // ids1 = this._getUserId(); + // } + let url = this._createRestUrl(host, version, category1, ids1, category2, ids2, action); // if (method === "GET") { url = this._addQueryParams(url, _params); @@ -58,13 +61,6 @@ export default class OpenCGAParentClass { } _post(category1, ids1, category2, ids2, action, body, params = {}, options = {}) { - // Clear and Revert actions do not need a body, but needs a params - if (category2 === "interpretation" && (action === "clear" || action === "revert")) { - // eslint-disable-next-line no-param-reassign - params = body; - // eslint-disable-next-line no-param-reassign - body = {}; - } const host = this._config.host; const version = this._config.version; // const rpc = this._config.mode; diff --git a/src/core/utils-new.js b/src/core/utils-new.js index 9215532b05..1e3b20d637 100644 --- a/src/core/utils-new.js +++ b/src/core/utils-new.js @@ -265,7 +265,7 @@ export default class UtilsNew { } static initTooltip(scope) { - $("a[tooltip-title], span[tooltip-title]", scope).each(function () { + $("a[tooltip-title], span[tooltip-title], table[tooltip-title], td[tooltip-title]", scope).each(function () { $(this).qtip({ content: { title: $(this).attr("tooltip-title"), @@ -304,32 +304,10 @@ export default class UtilsNew { return document.createRange().createContextualFragment(`${html}`); } - static jobStatusFormatter(status, appendDescription = false) { - const description = appendDescription && status.description ? `
${status.description}` : ""; - // FIXME remove this backward-compatibility check in next v2.3 - const statusId = status.id || status.name; - switch (statusId) { - case "PENDING": - case "QUEUED": - return ` ${statusId}${description}`; - case "RUNNING": - return ` ${statusId}${description}`; - case "DONE": - return ` ${statusId}${description}`; - case "ERROR": - return ` ${statusId}${description}`; - case "UNKNOWN": - return ` ${statusId}${description}`; - case "ABORTED": - return ` ${statusId}${description}`; - case "DELETED": - return ` ${statusId}${description}`; - } - return "-"; - } - // Capitalizes the first letter of a string and lowercase the rest. - static capitalize = ([first, ...rest]) => first.toUpperCase() + rest.join("").toLowerCase(); + static capitalize([first, ...rest]) { + return first.toUpperCase() + rest.join("").toLowerCase(); + } /* * This function creates a table (rows and columns) a given Object or array of Objects using the fields provided. @@ -1099,4 +1077,14 @@ export default class UtilsNew { .filter(item => !!item); } + // Group elements in array by the value in the given key + static groupBy(array, key) { + return array.reduce((result, currentValue) => { + const objectValue = UtilsNew.getObjectValue(currentValue, key); + // eslint-disable-next-line no-param-reassign + (result[objectValue] = result[objectValue] || []).push(currentValue); + return result; + }, {}); + } + } diff --git a/src/sites/iva/conf/browsers.settings.js b/src/sites/iva/conf/browsers.settings.js index 8ed956c77c..8b995e5d82 100644 --- a/src/sites/iva/conf/browsers.settings.js +++ b/src/sites/iva/conf/browsers.settings.js @@ -293,7 +293,7 @@ const CATALOG_SETTINGS = { }, // merge criterium: uses this array as filter for internal 1D array. // It is supported either details[] or hiddenDetails[]. - details: ["annotationSummary", "annotationConsType", "annotationPropFreq", "annotationClinical", "cohortStats", "samples", "beacon", "json-view"] + details: ["annotationSummary", "annotationConsType", "annotationPropFreq", "annotationClinical", "annotationPharmacogenomics", "cohortStats", "samples", "beacon", "json-view"] // hiddenDetails: ["json-view"] }, DISEASE_PANEL_BROWSER: { diff --git a/src/sites/iva/conf/config.js b/src/sites/iva/conf/config.js index c47814fff3..82dcb03b17 100644 --- a/src/sites/iva/conf/config.js +++ b/src/sites/iva/conf/config.js @@ -141,6 +141,11 @@ const CATALOG_NAVBAR_MENU = { name: "Cohort Browser", visibility: "public" }, + { + id: "note-browser", + name: "Note Browser", + visibility: "public", + }, { separator: true, visibility: "public" @@ -757,9 +762,18 @@ const SUITE = {
` }, menu: [ + { + id: "organization-admin", + name: "Organizations Admin", + fa_icon: "fas fa-file-invoice", + icon: "img/tools/icons/variant_browser.svg", + description: "", + visibility: "public", + featured: true, + }, { id: "study-admin", - name: "Study admin", + name: "Study Admin", fa_icon: "fas fa-file-invoice", icon: "img/tools/icons/variant_browser.svg", description: "", @@ -777,7 +791,7 @@ const SUITE = { // }, { id: "study-admin-iva", - name: "IVA configuration", + name: "IVA Configuration", fa_icon: "fas fa-file-invoice", icon: "img/tools/icons/variant_browser.svg", description: "", @@ -793,24 +807,33 @@ const SUITE = { // visibility: "public", // featured: false, // }, + // { + // id: "study-variant-admin", + // name: "Study Variant Admin", + // fa_icon: "fas fa-file-invoice", + // icon: "img/tools/icons/variant_browser.svg", + // description: "", + // visibility: "public", + // featured: true, + // }, { - id: "study-variant-admin", - name: "Study Variant Admin", - fa_icon: "fas fa-file-invoice", - icon: "img/tools/icons/variant_browser.svg", - description: "", - visibility: "public", - featured: true, - }, - { - id: "projects-admin", - name: "Project Manager", + id: "operations-admin", + name: "Operations Admin", fa_icon: "fas fa-file-invoice", icon: "img/tools/icons/variant_browser.svg", description: "", visibility: "public", featured: true, }, + // { + // id: "projects-admin", + // name: "Project Manager", + // fa_icon: "fas fa-file-invoice", + // icon: "img/tools/icons/variant_browser.svg", + // description: "", + // visibility: "public", + // featured: true, + // }, ], fileExplorer: { visibility: "private" diff --git a/src/sites/iva/conf/opencga-variant-browser.settings.js b/src/sites/iva/conf/opencga-variant-browser.settings.js index cd44032a00..d65c80ccf1 100644 --- a/src/sites/iva/conf/opencga-variant-browser.settings.js +++ b/src/sites/iva/conf/opencga-variant-browser.settings.js @@ -88,6 +88,6 @@ const OPENCGA_VARIANT_BROWSER_SETTINGS = { }, // merge criterium: uses this array as filter for internal 1D array. // It is supported either details[] or hiddenDetails[]. - details: ["annotationSummary", "annotationConsType", "annotationPropFreq", "annotationClinical", "cohortStats", "samples", "beacon", "json-view"] + details: ["annotationSummary", "annotationConsType", "annotationPropFreq", "annotationClinical", "annotationPharmacogenomics", "cohortStats", "samples", "beacon", "json-view"] // hiddenDetails: ["json-view"] }; diff --git a/src/sites/iva/iva-app.js b/src/sites/iva/iva-app.js index bd6d64bacb..a25a0aea52 100644 --- a/src/sites/iva/iva-app.js +++ b/src/sites/iva/iva-app.js @@ -22,10 +22,8 @@ import {html, LitElement, nothing} from "lit"; import "./getting-started.js"; import "./iva-settings.js"; -// @dev[jsorolla] import {OpenCGAClient} from "../../core/clients/opencga/opencga-client.js"; import {CellBaseClient} from "../../core/clients/cellbase/cellbase-client.js"; -import {ReactomeClient} from "../../core/clients/reactome/reactome-client.js"; import UtilsNew from "../../core/utils-new.js"; import NotificationUtils from "../../webcomponents/commons/utils/notification-utils.js"; @@ -38,7 +36,6 @@ import "../../webcomponents/variant/variant-beacon.js"; import "../../webcomponents/opencga/opencga-gene-view.js"; import "../../webcomponents/opencga/opencga-transcript-view.js"; import "../../webcomponents/opencga/opencga-protein-view.js"; -// import "../../webcomponents/user/opencga-projects.js"; import "../../webcomponents/sample/sample-browser.js"; import "../../webcomponents/sample/sample-view.js"; import "../../webcomponents/sample/sample-variant-stats-browser.js"; @@ -47,7 +44,6 @@ import "../../webcomponents/sample/sample-update.js"; import "../../webcomponents/disease-panel/disease-panel-browser.js"; import "../../webcomponents/disease-panel/disease-panel-update.js"; import "../../webcomponents/file/file-browser.js"; -// import "../../webcomponents/file/file-update.js"; import "../../webcomponents/family/family-browser.js"; import "../../webcomponents/family/family-update.js"; import "../../webcomponents/individual/individual-browser.js"; @@ -81,15 +77,16 @@ import "../../webcomponents/clinical/clinical-analysis-create.js"; import "../../webcomponents/file/file-manager.js"; import "../../webcomponents/job/job-monitor.js"; import "../../webcomponents/loading-spinner.js"; +import "../../webcomponents/organization/admin/organization-admin.js"; import "../../webcomponents/project/projects-admin.js"; import "../../webcomponents/study/admin/study-admin.js"; import "../../webcomponents/study/admin/study-admin-iva.js"; import "../../webcomponents/study/admin/catalog-admin.js"; import "../../webcomponents/study/admin/variant/study-variant-admin.js"; -import "../../webcomponents/user/user-login.js"; +import "../../webcomponents/study/admin/variant/operations-admin.js"; import "../../webcomponents/user/user-profile.js"; -// import "../../webcomponents/user/user-password-reset.js"; import "../../webcomponents/api/rest-api.js"; +import "../../webcomponents/note/note-browser.js"; import "../../webcomponents/commons/layouts/custom-footer.js"; import "../../webcomponents/commons/layouts/custom-navbar.js"; @@ -99,6 +96,7 @@ import "../../webcomponents/commons/layouts/custom-welcome.js"; import "../../webcomponents/commons/layouts/custom-landing.js"; import "../../webcomponents/clinical/rga/rga-browser.js"; + import OpencgaCatalogUtils from "../../core/clients/opencga/opencga-catalog-utils"; import ExtensionsManager from "../../webcomponents/extensions-manager.js"; @@ -158,7 +156,6 @@ class IvaApp extends LitElement { const components = [ "home", "gettingstarted", - "login", "aboutzetta", // "reset-password", "settings", @@ -229,15 +226,19 @@ class IvaApp extends LitElement { "diseasePanelUpdate", "clinicalAnalysis", // Admin + "organization-admin", "study-admin", "study-admin-iva", // "catalog-admin", + "operations-admin", "study-variant-admin", "opencga-admin", "variants-admin", - "projects-admin", + // "projects-admin", // REST-API "rest-api", + // note + "note-browser", ]; // Add custom tools @@ -823,39 +824,6 @@ class IvaApp extends LitElement { // this.hashFragmentListener(); } - // renderHashFragments(tool) { - // console.log(`Update hash fragment URL with tool: '${tool ? `#${tool}` : this.tool}'`); - // - // // Keep global 'tool' param updated. - // if (tool && this.tool !== `#${tool}`) { - // this.tool = `#${tool}`; - // } - // - // // Build hash fragment URL as: #tool/projectId/studyId - // let newHashFragmentUrl = tool ? `#${tool}` : this.tool; - // if (this.opencgaSession?.project) { - // newHashFragmentUrl += "/" + this.opencgaSession.project.id; - // if (this.opencgaSession.study) { - // newHashFragmentUrl += "/" + this.opencgaSession.study.id; - // } - // } - // - // if (window.location.hash === newHashFragmentUrl) { // || newHashFragmentUrl === "#interpreter" - // this.hashFragmentListener(); - // } else { - // window.location.hash = newHashFragmentUrl; - // } - // } - - route(e) { - this.tool = e.detail.hash; - if (e.detail?.resource) { - this.queries = {...this.queries, [e.detail.resource]: e.detail?.query}; - } - // this.renderHashFragments(); - this.hashFragmentListener(); - } - hashFragmentListener() { console.log("hashFragmentListener - Hide all enabled elements"); @@ -984,14 +952,14 @@ class IvaApp extends LitElement { } changeActiveStudy(studyFqn) { - if (this.opencgaSession.study.fqn === studyFqn) { + if (this.opencgaSession?.study?.fqn === studyFqn) { console.log("New selected study is already the current active study!"); return; } // Change active study let studyFound = false; - for (const project of this.opencgaSession.projects) { + for (const project of (this.opencgaSession?.projects || [])) { const studyIndex = project.studies.findIndex(s => s.fqn === studyFqn); if (studyIndex >= 0) { this.opencgaSession.project = project; @@ -1171,6 +1139,10 @@ class IvaApp extends LitElement { // } onSessionUpdateRequest() { + NotificationUtils.dispatch(this, NotificationUtils.NOTIFY_SUCCESS, { + title: "Refresh Session: Session Update Request", + message: "Session updated correctly", + }); this._createOpenCGASession(); } @@ -1249,8 +1221,7 @@ class IvaApp extends LitElement { + @login="${this.onLogin}"> `; } @@ -1290,11 +1261,9 @@ class IvaApp extends LitElement { @changeTool="${e => this.changeTool(e.detail.value)}" @changeApp="${e => this.onChangeApp(e.detail.event, e.detail.toggle)}" @studySelect="${ e => this.onStudySelect(e.detail.event, e.detail.study)}" - @jobSelected="${e => this.onJobSelected(e)}" - @route="${this.route}"> + @jobSelected="${e => this.onJobSelected(e)}"> - + ${ this.isCreatingSession ? html`
- ${this.config.enabledComponents.home && !this.isCreatingSession ? html` -
- - -
- ` : nothing} - - - ${this.config.enabledComponents.customPage ? this.renderCustomPage() : nothing} + ${!this.isCreatingSession ? html` + ${this.config.enabledComponents.home ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents.terms ? html` -
- -
- ` : nothing} + + ${this.config.enabledComponents.customPage ? this.renderCustomPage() : nothing} - ${this.config.enabledComponents.contact ? html` -
- -
- ` : nothing} + ${this.config.enabledComponents.terms ? html` +
+ +
+ ` : nothing} - ${this.config.enabledComponents.faq ? html` -
- -
- ` : nothing} + ${this.config.enabledComponents.contact ? html` +
+ +
+ ` : nothing} - ${this.config.enabledComponents.gettingstarted ? html` -
- -
- ` : nothing} + ${this.config.enabledComponents.faq ? html` +
+ +
+ ` : nothing} - ${this.config.enabledComponents?.aboutzetta ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents.gettingstarted ? html` +
+ +
+ ` : nothing} - ${this.config.enabledComponents.login ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents?.aboutzetta ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["variant-browser"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents["variant-browser"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["clinicalAnalysisPortal"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents["clinicalAnalysisPortal"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["rga"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents["rga"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["rd-interpreter"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents["rd-interpreter"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["cancer-interpreter"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents["cancer-interpreter"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents.beacon ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents.beacon ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents.genomeBrowser ? html` -
- Not available yet... -
- ` : nothing} + ${this.config.enabledComponents.genomeBrowser ? html` +
+ Not available yet... +
+ ` : nothing} - ${this.config.enabledComponents.sample ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents.sample ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents.panel ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents.panel ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents.file ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents.file ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["disease-panel"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents["disease-panel"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["diseasePanelUpdate"] ? html` -
- + - -
- ` : nothing} + }> + +
+ ` : nothing} - - ${this.config.enabledComponents["sample-view"] ? html` -
- - -
- ` : nothing} + + ${this.config.enabledComponents["sample-view"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["fileUpdate"] ? html` - ${this.fileId} ` }" icon="fas fa-vial icon-padding"> -
- ${this.fileId} ` }" icon="fas fa-vial icon-padding"> +
+ - -
- ` : nothing} + }> + +
+ ` : nothing} - ${this.config.enabledComponents["sampleUpdate"] ? html` - ${this.sampleId} ` }" icon="fas fa-vial icon-padding"> -
- ${this.sampleId} ` }" icon="fas fa-vial icon-padding"> +
+ - -
- ` : nothing} + }> + +
+ ` : nothing} - ${this.config.enabledComponents["individualUpdate"] ? html` - ${this.individualId} ` }" icon="fas fa-vial icon-padding"> -
- ${this.individualId} ` }" icon="fas fa-vial icon-padding"> +
+ - -
- ` : nothing} + }> + +
+ ` : nothing} - ${this.config.enabledComponents["familyUpdate"] ? html` - ${this.familyId} ` }" icon="fas fa-vial icon-padding"> -
- ${this.familyId} ` }" icon="fas fa-vial icon-padding"> +
+ - -
- ` : nothing} - - ${this.config.enabledComponents.gene ? html` -
- - -
- ` : nothing} + }> + +
+ ` : nothing} - ${this.config.enabledComponents.transcript ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents.gene ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents.protein ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents.transcript ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents.individual ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents.protein ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents.family ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents.individual ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents.cohort ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents.family ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents.clinicalAnalysis ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents.cohort ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents.job ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents.clinicalAnalysis ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["cat-browser"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents.job ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["cat-analysis"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents["note-browser"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["cat-clinical"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents["cat-browser"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["cat-tools"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents["cat-analysis"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["cat-catalog"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents["cat-clinical"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["cat-alignment"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents["cat-tools"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["cat-ga4gh"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents["cat-catalog"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["sampleVariantStatsBrowser"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents["cat-alignment"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["sampleCancerVariantStatsBrowser"] ? html` -
- -
- ` : nothing} + ${this.config.enabledComponents["cat-ga4gh"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["sample-variant-stats"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents["sampleVariantStatsBrowser"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["cohort-variant-stats"] ? html` -
- -
- ` : nothing} + ${this.config.enabledComponents["sampleCancerVariantStatsBrowser"] ? html` +
+ +
+ ` : nothing} - ${this.config.enabledComponents["eligibility"] ? html` -
- -
- ` : nothing} + ${this.config.enabledComponents["sample-variant-stats"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["sample-eligibility"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents["cohort-variant-stats"] ? html` +
+ +
+ ` : nothing} - ${this.config.enabledComponents["knockout"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents["eligibility"] ? html` +
+ +
+ ` : nothing} - ${this.config.enabledComponents["inferred-sex"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents["sample-eligibility"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["individual-relatedness"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents["knockout"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["mendelian-error"] ? html` -
- -
- ` : nothing} + ${this.config.enabledComponents["inferred-sex"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["sample-qc"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents["individual-relatedness"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["individual-qc"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents["mendelian-error"] ? html` +
+ +
+ ` : nothing} - ${this.config.enabledComponents["family-qc"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents["sample-qc"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["plink"] ? html` -
- -
- ` : nothing} + ${this.config.enabledComponents["individual-qc"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["gatk"] ? html` -
- -
- ` : nothing} + ${this.config.enabledComponents["family-qc"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["variant-export"] ? html` -
- -
- ` : nothing} + ${this.config.enabledComponents["plink"] ? html` +
+ +
+ ` : nothing} - ${this.config.enabledComponents["variant-stats-exporter"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents["gatk"] ? html` +
+ +
+ ` : nothing} - ${this.config.enabledComponents["mutational-signature"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents["variant-export"] ? html` +
+ +
+ ` : nothing} - ${this.config.enabledComponents["gwas"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents["variant-stats-exporter"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["rd-tiering"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents["mutational-signature"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["clinical-analysis-create"] ? html` - -
- - -
- ` : nothing} + ${this.config.enabledComponents["gwas"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents.account ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents["rd-tiering"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["file-manager"] ? html` -
- -
- ` : nothing} + ${this.config.enabledComponents["clinical-analysis-create"] ? html` + +
+ + +
+ ` : nothing} - ${this.config.enabledComponents.settings ? html` -
- -
- ` : nothing} + ${this.config.enabledComponents.account ? html` +
+ + +
+ ` : nothing} + ${this.config.enabledComponents["file-manager"] ? html` +
+ +
+ ` : nothing} - ${this.config.enabledComponents["interpreter"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents.settings ? html` +
+ +
+ ` : nothing} - - ${this.config.enabledComponents["alignment-index"] ? html` -
- -
- ` : nothing} + ${this.config.enabledComponents["interpreter"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["coverage-index"] ? html` -
- -
- ` : nothing} + + ${this.config.enabledComponents["alignment-index"] ? html` +
+ +
+ ` : nothing} - ${this.config.enabledComponents["alignment-stats"] ? html` -
- -
- ` : nothing} + ${this.config.enabledComponents["coverage-index"] ? html` +
+ +
+ ` : nothing} - ${this.config.enabledComponents["job-view"] ? html` - -
- - -
- ` : nothing} + ${this.config.enabledComponents["alignment-stats"] ? html` +
+ +
+ ` : nothing} - - ${this.config.enabledComponents["projects-admin"] ? html` - -
- - -
- ` : nothing} + ${this.config.enabledComponents["job-view"] ? html` + +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["catalog-admin"] ? html` -
- - -
- ` : nothing} + + ${this.config.enabledComponents["organization-admin"] ? html` + +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["opencga-admin"] ? html` - -
- - -
- ` : nothing} + ${this.config.enabledComponents["catalog-admin"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["study-admin"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents["projects-admin"] ? html` + +
+ + +
+ ` : nothing} - - - ${this.config.enabledComponents["study-admin-iva"] ? html` -
- - -
- ` : nothing} + ${this.config.enabledComponents["study-admin"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["study-variant-admin"] ? html` -
- - -
- ` : nothing} + + + ${this.config.enabledComponents["study-admin-iva"] ? html` +
+ + +
+ ` : nothing} - ${this.config.enabledComponents["rest-api"] ? html` - -
- -
- ` : nothing} + ${this.config.enabledComponents["operations-admin"] ? html` +
+ + +
+ ` : nothing} - ${ExtensionsManager.getTools().map(tool => html` - ${this.config.enabledComponents[tool.id] ? html` + ${this.config.enabledComponents["rest-api"] ? html` +
- ${tool.render(this.opencgaSession)} +
` : nothing} - `)} + + ${ExtensionsManager.getTools().map(tool => html` + ${this.config.enabledComponents[tool.id] ? html` +
+ ${tool.render(this.opencgaSession)} +
+ ` : nothing} + `)} + ` : nothing}
{ result = UtilsNew.objectClone(response.responses[0].results); }) @@ -405,7 +408,8 @@ export default class OpencgaRestInput extends LitElement { #postEndpoint(url, isForm) { // Add Study - url += "study=" + encodeURIComponent(this.opencgaSession.study.fqn); + // Fixme: not all endpoints require study. E.g. POST /users/password/ + url += "study=" + encodeURIComponent(this.opencgaSession?.study?.fqn); // Replace PATH params this.endpoint.parameters @@ -431,7 +435,7 @@ export default class OpencgaRestInput extends LitElement { const _options = { sid: this.opencgaSession.opencgaClient._config.token, token: this.opencgaSession.opencgaClient._config.token, - data: isForm ? this.formatBody(this.data?.body) : JSON.parse(this.dataJson?.body), + data: isForm ? this.formatBody(this.data?.body) : JSON.parse(this.dataJson?.body || "{}"), method: "POST", }; diff --git a/src/webcomponents/api/rest-utils.js b/src/webcomponents/api/rest-utils.js index 288717b7da..5d300398f8 100644 --- a/src/webcomponents/api/rest-utils.js +++ b/src/webcomponents/api/rest-utils.js @@ -1,7 +1,8 @@ // ******************************************************************** // 0. Functions for checking if the param is: enum | primitive | object // ******************************************************************** -import UtilsNew from "../../core/utils-new"; +import UtilsNew from "../../core/utils-new.js"; +import CatalogUtils from "../../core/clients/opencga/opencga-catalog-utils.js"; export default { @@ -39,7 +40,7 @@ export default { }, isAdministrator(opencgaSession) { - return opencgaSession?.user?.account?.type === "ADMINISTRATOR" || opencgaSession?.user.id === "OPENCGA"; + return opencgaSession?.user?.id?.toUpperCase() === "OPENCGA" || CatalogUtils.isOrganizationAdmin(opencgaSession?.organization, opencgaSession?.user?.id); }, sortArray(elements) { diff --git a/src/webcomponents/clinical/analysis/rd-tiering-analysis.js b/src/webcomponents/clinical/analysis/rd-tiering-analysis.js index c92ee9adbd..4ac8966af2 100644 --- a/src/webcomponents/clinical/analysis/rd-tiering-analysis.js +++ b/src/webcomponents/clinical/analysis/rd-tiering-analysis.js @@ -20,7 +20,6 @@ import UtilsNew from "../../../core/utils-new.js"; import "../../commons/forms/data-form.js"; import "../../commons/filters/catalog-search-autocomplete.js"; - export default class RdTieringAnalysis extends LitElement { constructor() { @@ -161,7 +160,7 @@ export default class RdTieringAnalysis extends LitElement { display: { render: (panels, dataFormFilterChange) => { // Get whether disease panels can be modified or are fixed - const casePanelLock = !!this.clinicalAnalysis; + const casePanelLock = !!this.clinicalAnalysis?.panelLocked; // Get the list of disease panels for the dropdown let diseasePanels = []; if (casePanelLock) { diff --git a/src/webcomponents/clinical/clinical-analysis-browser.js b/src/webcomponents/clinical/clinical-analysis-browser.js index c12512e229..fc25fcadc3 100644 --- a/src/webcomponents/clinical/clinical-analysis-browser.js +++ b/src/webcomponents/clinical/clinical-analysis-browser.js @@ -14,7 +14,7 @@ * limitations under the License. */ -import {LitElement, html} from "lit"; +import {LitElement, html, nothing} from "lit"; import UtilsNew from "../../core/utils-new.js"; import OpencgaCatalogUtils from "../../core/clients/opencga/opencga-catalog-utils.js"; import NotificationUtils from "../commons/utils/notification-utils.js"; @@ -141,16 +141,18 @@ export default class ClinicalAnalysisBrowser extends LitElement { .query="${params.executedQuery}" .active="${params.active}" @selectanalysis="${params.onSelectClinicalAnalysis}" - @selectrow="${e => params.onClickRow(e, "clinicalAnalysis")}" - @rowUpdate="${e => params.onComponentUpdate(e, "clinicalAnalysis")}" - @clinicalAnalysisUpdate="${e => params.onComponentUpdate(e, "clinicalAnalysis")}" + @selectrow="${e => params.onClickRow(e)}" + @rowUpdate="${e => params.onComponentUpdate(e)}" + @clinicalAnalysisUpdate="${e => params.onComponentUpdate(e)}" @settingsUpdate="${() => this.onSettingsUpdate()}"> - - + ${params?.detail ? html` + + + ` : nothing} `, }, { diff --git a/src/webcomponents/clinical/clinical-analysis-create.js b/src/webcomponents/clinical/clinical-analysis-create.js index bd7dc66d52..38dd40ad98 100644 --- a/src/webcomponents/clinical/clinical-analysis-create.js +++ b/src/webcomponents/clinical/clinical-analysis-create.js @@ -108,7 +108,7 @@ export default class ClinicalAnalysisCreate extends LitElement { // id: this.opencgaSession?.user?.id // }, comments: [], - panelLock: false, + panelLocked: false, samples: [], }; } @@ -358,7 +358,35 @@ export default class ClinicalAnalysisCreate extends LitElement { delete data.dueDate; } - this.opencgaSession.opencgaClient.clinical().create(data, {study: this.opencgaSession.study.fqn, createDefaultInterpretation: true}) + this.opencgaSession.opencgaClient.clinical() + .create(data, { + study: this.opencgaSession.study.fqn, + includeResult: true + }) + .then(response => { + const interpretationId = response?.responses?.[0]?.results?.[0]?.interpretation?.id; + const interpretationData = { + method: { + name: "iva-default", + version: this.opencgaSession?.about?.Version || "-", + dependencies: [ + { + name: "OpenCGA", + version: this.opencgaSession?.about?.Version || "-", + }, + { + name: "Cellbase", + version: this.opencgaSession.project?.cellbase?.version || "-", + }, + ], + }, + }; + return this.opencgaSession.opencgaClient.clinical() + .updateInterpretation(data.id, interpretationId, interpretationData, { + study: this.opencgaSession.study.fqn, + methodsAction: "SET", + }); + }) .then(() => { NotificationUtils.dispatch(this, NotificationUtils.NOTIFY_SUCCESS, { title: "Clinical analysis created", @@ -478,7 +506,7 @@ export default class ClinicalAnalysisCreate extends LitElement { }, { title: "Disease Panel Lock", - field: "panelLock", + field: "panelLocked", type: "toggle-switch", display: { helpMessage: "You must select at least one of the Clinical Analysis panels to enable Disease Panel Lock.", @@ -502,7 +530,7 @@ export default class ClinicalAnalysisCreate extends LitElement { return html` diff --git a/src/webcomponents/clinical/clinical-analysis-grid.js b/src/webcomponents/clinical/clinical-analysis-grid.js index f0f4977dfc..bd670c9114 100644 --- a/src/webcomponents/clinical/clinical-analysis-grid.js +++ b/src/webcomponents/clinical/clinical-analysis-grid.js @@ -22,7 +22,7 @@ import CatalogGridFormatter from "../commons/catalog-grid-formatter.js"; import "../commons/opencb-grid-toolbar.js"; import LitUtils from "../commons/utils/lit-utils.js"; import NotificationUtils from "../commons/utils/notification-utils.js"; -import ModalUtils from "../commons/modal/modal-utils"; +import ModalUtils from "../commons/modal/modal-utils.js"; export default class ClinicalAnalysisGrid extends LitElement { @@ -337,22 +337,21 @@ export default class ClinicalAnalysisGrid extends LitElement { ${currentPriorityText} - ${isEditable ? `