From fc11c583c589346256f63a53491f262363c611f7 Mon Sep 17 00:00:00 2001 From: =?utf8?q?Daniel=20Kuty=C5=82a?= Date: Wed, 12 May 2021 23:48:42 +0200 Subject: [PATCH] 17595: Added new workflow MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit Arvados-DCO-1.1-Signed-off-by: Daniel Kutyła --- .../fixtures/workflow_with_array_fields.yaml | 116 ++---------------- cypress/integration/favorites.spec.js | 6 +- 2 files changed, 13 insertions(+), 109 deletions(-) diff --git a/cypress/fixtures/workflow_with_array_fields.yaml b/cypress/fixtures/workflow_with_array_fields.yaml index c5d5f66f..fc71cf86 100644 --- a/cypress/fixtures/workflow_with_array_fields.yaml +++ b/cypress/fixtures/workflow_with_array_fields.yaml @@ -4,119 +4,23 @@ --- "$graph": -- "$namespaces": - arv: http://arvados.org/cwl# - class: ExpressionTool - doc: get the gct and vcf files, add other files - expression: | - $\{ - var fileArray = []; - - // get files from collection - for (var j = 0; j < inputs.collectionArray.length; j++) { - for (var i = 0; i < inputs.collectionArray[j].listing.length; i++) { - var matchedName = inputs.collectionArray[j].listing[i].basename.match(/^(.+)(.gct|.vcf|.vcf.gz|.gct.tsv|.vcf.tsv)$/); - if (matchedName) { - var nameString = inputs.collectionArray[j].listing[i].basename.split(".")[0] - fileArray.push(inputs.collectionArray[j].listing[i]) - } - } - } - - // get any other files from the input file array - for (var i = 0; i < inputs.additionalFileArray.length; i++) { - fileArray.push(inputs.additionalFileArray[i]) - } - - - return { - "collectedArray": fileArray, - "nameString": nameString - } - - } - id: "#collectFiles.cwl" - inputs: - - id: "#collectFiles.cwl/additionalFileArray" - type: - items: File - type: array - - id: "#collectFiles.cwl/collectionArray" - type: - items: Directory - type: array - outputs: - - id: "#collectFiles.cwl/collectedArray" - type: - items: File - type: array - - id: "#collectFiles.cwl/nameString" - type: string - requirements: - - class: InlineJavascriptRequirement - class: Workflow - doc: A workflow to collect .gct and .vcf files files and store them together with - specified metainformation files. Mostly used to create a collection for genestack - upload. Can only be run on the WB2. + cwlVersion: v1.2 hints: - - class: ResourceRequirement - coresMin: 1 - ramMin: 85000 + - acrContainerImage: 7009415fdc959d0c2819ee2e9db96561+261 + class: http://arvados.org/cwl#WorkflowRunnerResources id: "#main" inputs: - - default: - - basename: metainfo.txt - class: File - location: keep:1cd1dbc27dc10fa8aaaf8fa19efd3bb8+237/metainfo.txt - nameext: ".txt" - nameroot: metainfo - size: 0 - - basename: test11.txt - class: File - location: keep:1cd1dbc27dc10fa8aaaf8fa19efd3bb8+237/test11.txt - nameext: ".txt" - nameroot: test11 - size: 0 - doc: This input allows you to add any number of additional files to be integrated - in the output collection. - id: "#main/additionalFileArray" - label: Files - type: - items: File - type: array - - default: - - basename: collection1 - class: Directory - location: keep:1cd1dbc27dc10fa8aaaf8fa19efd3bb8+237/collection1 - - basename: collection2 - class: Directory - location: keep:1cd1dbc27dc10fa8aaaf8fa19efd3bb8+237/collection2 - doc: This input allows you to specify collections to integrate. From these collections, - all files that end with .gct or .vcf will be extracted. - id: "#main/collectionArray" - label: Collections + - default: [] + id: "#main/bar" type: items: Directory type: array - outputs: - - id: "#main/genestackArray" - outputSource: "#main/collectFiles/collectedArray" + - default: [] + id: "#main/foo" type: items: File type: array - requirements: - - class: SubworkflowFeatureRequirement - - class: ScatterFeatureRequirement - - class: StepInputExpressionRequirement - - class: InlineJavascriptRequirement - steps: - - id: "#main/collectFiles" - in: - - id: "#main/collectFiles/additionalFileArray" - source: "#main/additionalFileArray" - - id: "#main/collectFiles/collectionArray" - source: "#main/collectionArray" - out: - - "#main/collectFiles/collectedArray" - run: "#collectFiles.cwl" -cwlVersion: v1.0 \ No newline at end of file + outputs: [] + steps: [] +cwlVersion: v1.2 diff --git a/cypress/integration/favorites.spec.js b/cypress/integration/favorites.spec.js index e48adebf..e49d8b30 100644 --- a/cypress/integration/favorites.spec.js +++ b/cypress/integration/favorites.spec.js @@ -205,7 +205,7 @@ describe('Favorites tests', function () { }); }); - it.only('can select multi files when creating workflow', () => { + it('can select multi files when creating workflow', () => { cy.createProject({ owningUser: activeUser, projectName: 'myProject1', @@ -250,7 +250,7 @@ describe('Favorites tests', function () { cy.get('main').contains(testWorkflow.name).click(); cy.get('[data-cy=run-process-next-button]').click(); - cy.get('label').contains('Files').parent('div').find('input').click(); + cy.get('label').contains('#main/foo').parent('div').find('input').click(); cy.get('div[role=dialog]') .within(() => { cy.get('p').contains('Projects').closest('div[role=button]') @@ -269,7 +269,7 @@ describe('Favorites tests', function () { cy.get('[data-cy=ok-button]').click(); }); - cy.get('label').contains('Collections').parent('div').find('input').click(); + cy.get('label').contains('#main/bar').parent('div').find('input').click(); cy.get('div[role=dialog]') .within(() => { cy.get('p').contains('Projects').closest('div[role=button]') -- 2.30.2