[ARVADOS-WORKBENCH2] updated: 2.1.0-357-gfc11c583
Git user
git at public.arvados.org
Wed May 12 21:49:28 UTC 2021
Summary of changes:
cypress/fixtures/workflow_with_array_fields.yaml | 116 ++---------------------
cypress/integration/favorites.spec.js | 6 +-
2 files changed, 13 insertions(+), 109 deletions(-)
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from 43c92c8e2518642fa1033d66a0f72fcb026c0308 (commit)
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commit fc11c583c589346256f63a53491f262363c611f7
Author: Daniel Kutyła <daniel.kutyla at contractors.roche.com>
Date: Wed May 12 23:48:42 2021 +0200
17595: Added new workflow
Arvados-DCO-1.1-Signed-off-by: Daniel Kutyła <daniel.kutyla at contractors.roche.com>
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]')
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