Bug #17595: Selecting multiple collections as inputs to a workflow - Arvados

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Bug #17595

closed

Selecting multiple collections as inputs to a workflow

Added by Peter Amstutz over 3 years ago. Updated 8 months ago.

Status:

Resolved

Priority:

Normal

Assigned To:

Daniel Kutyła

Category:

Workbench2

Target version:

2021-05-26 sprint

Story points:

Release:

Arvados 2.2.0

Release relationship:

Auto

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duplicated-selections.png (158 KB) duplicated-selections.png		Peter Amstutz, 05/10/2021 07:37 PM
Untitled.jpg (81 KB) Untitled.jpg		Daniel Kutyła, 05/12/2021 04:35 PM

Subtasks 1 (0 open — 1 closed)

Related issues 1 (0 open — 1 closed)

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Updated by Peter Amstutz over 3 years ago

Assigned To set to Daniel Kutyła

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Updated by Daniel Kutyła over 3 years ago

Status changed from New to In Progress

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Updated by Peter Amstutz over 3 years ago

Blocks Idea #17512: Release Arvados 2.2 added

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Updated by Daniel Kutyła over 3 years ago

New version: https://dev.arvados.org/projects/arvados/repository/arvados-workbench2/revisions/43c92c8e2518642fa1033d66a0f72fcb026c0308
Test run: developer-tests-workbench2: #399
Branch: 17595-Selecting-multiple-collections-as-inputs-to-a-workflow

Added multiselect, added tests

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Updated by Peter Amstutz over 3 years ago

File duplicated-selections.png duplicated-selections.png added

You test cases are sort of complex. Here's the simplest possible test case:

cwlVersion: v1.2
class: Workflow
inputs:
  foo: File[]
  bar: Directory[]
outputs: []
steps: []

When I try this, I get a crash because the initial value for the "foo" and "bar" parameters is assigned "null" instead of an empty list. I tried to track down where the initial values are set, but didn't manage to find it.

I did notice that your test cases have "default" values for the arrays, which is probably why you didn't encounter this.

Here's the simplest test case, with defaults. This one doesn't crash.

cwlVersion: v1.2
class: Workflow
inputs:
  foo:
    type: File[]
    default: []
  bar:
    type: Directory[]
    default: []
outputs: []
steps: []

This is not exactly wrong, but the behavior is confusing:

There's only two collections in "Selected collections" but more than two collections are checked. I believe what is happening is that the duplicated selections have the same portable data hash as one of the selected collections. If you delete the collection from "Selected collections" it only clears the first checkbox, but not the duplicates.

For the checkboxes, it should do the comparison based on the uuid, not the portable data hash.

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Updated by Peter Amstutz over 3 years ago

Target version changed from 2021-05-12 sprint to 2021-05-26 sprint

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Updated by Daniel Kutyła over 3 years ago

File Untitled.jpg Untitled.jpg added

Can you please verify if provided workflow is ok? As I do not see any inputs that allow me to test files and collections popups

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Updated by Peter Amstutz over 3 years ago

Daniel Kutyła wrote:

Can you please verify if provided workflow is ok? As I do not see any inputs that allow me to test files and collections popups

Ah, you are right. What I posted in #note-5 is the workflow that you would use with "arvados-cwl-runner --create-workflow" and not what actually appears in the workflow record. Here's the processed/encoded version:

"{\n \"$graph\": [\n {\n \"class\": \"Workflow\",\n \"cwlVersion\": \"v1.2\",\n \"hints\": [\n {\n \"acrContainerImage\": \"7009415fdc959d0c2819ee2e9db96561+261\",\n \"class\": \"http://arvados.org/cwl#WorkflowRunnerResources\"\n }\n ],\n \"id\": \"#main\",\n \"inputs\": [\n {\n \"default\": [],\n \"id\": \"#main/bar\",\n \"type\": {\n \"items\": \"Directory\",\n \"type\": \"array\"\n }\n },\n {\n \"default\": [],\n \"id\": \"#main/foo\",\n \"type\": {\n \"items\": \"File\",\n \"type\": \"array\"\n }\n }\n ],\n \"outputs\": [],\n \"steps\": []\n }\n ],\n \"cwlVersion\": \"v1.2\"\n}"

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Updated by Peter Amstutz over 3 years ago

Release set to 38

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#10

Updated by Daniel Kutyła over 3 years ago

Release deleted (38)

New version: https://dev.arvados.org/projects/arvados/repository/arvados-workbench2/revisions/1739b7bc6b6602cdfbaca0f5fe899c9e6fd7fe1f
Test run: developer-tests-workbench2: #636
Branch: 17595-Selecting-multiple-collections-as-inputs-to-a-workflow

Added multiselect, added tests

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#11

Updated by Peter Amstutz over 3 years ago

You need a separate test with a version without default:

"$graph":
- class: Workflow
  cwlVersion: v1.2
  hints:
  - acrContainerImage: 7009415fdc959d0c2819ee2e9db96561+261
    class: http://arvados.org/cwl#WorkflowRunnerResources
  id: "#main" 
  inputs:
  - id: "#main/bar" 
    type:
      items: Directory
      type: array
  - id: "#main/foo" 
    type:
      items: File
      type: array
  outputs: []
  steps: []
cwlVersion: v1.2

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#12