Feature #15028
closed[CWL] Support CWL draft v1.1
Description
- Update cwltool dependency
- Support v1.1 process requirements on Arvados
- Warn about Arvados extensions that are superseded by v1.1 process requirements
- Pass v1.1 conformance test suite
Updated by Peter Amstutz over 5 years ago
- Subject changed from [CWL] Support CWL draft v1.1 to [CWL] Support CWL draft v1.1
- Assigned To set to Peter Amstutz
- Story points set to 2.0
Updated by Peter Amstutz over 5 years ago
- Target version changed from 2019-04-10 Sprint to 2019-04-24 Sprint
Updated by Peter Amstutz over 5 years ago
- Status changed from New to In Progress
- Target version changed from 2019-04-24 Sprint to 2019-05-08 Sprint
Updated by Tom Morris over 5 years ago
- Target version changed from 2019-05-08 Sprint to 2019-05-22 Sprint
Updated by Tom Morris over 5 years ago
- Target version changed from 2019-05-22 Sprint to Arvados Future Sprints
Updated by Tom Morris over 5 years ago
- Target version changed from Arvados Future Sprints to 2019-06-05 Sprint
Updated by Peter Amstutz over 5 years ago
Updated by Eric Biagiotti over 5 years ago
No comments on the code, but running:
./test_with_arvbox.sh --no-reset-container --config dev --leave-running --suite conformance-v1.1
All the tests return the following:
The CWL reference runner no longer supports pre CWL v1.0 documents. Supported versions are: v1.0 v1.1.0-dev1 (with --enable-dev flag only)
Also, would be nice to be able to pass the -j flag through test_with_arvbox.sh. Should work with both integration and conformance tests.
Updated by Peter Amstutz over 5 years ago
Eric Biagiotti wrote:
No comments on the code, but running:
[...]
All the tests return the following:
The CWL reference runner no longer supports pre CWL v1.0 documents. Supported versions are:
You need to run test_with_arvbox.sh with "--build" so that it builds a jobs image with the local checkout instead of fetching arvados/jobs:latest.
Also, would be nice to be able to pass the -j flag through test_with_arvbox.sh. Should work with both integration and conformance tests.
That ought to work. Did you try it?
Updated by Eric Biagiotti over 5 years ago
Gave up on running the tests with test_with_arvbox. Maybe we need some better documentation for running that script.
./run_test.sh -j8 RUNNER=arvados-cwl-runner EXTRA="--api=containers --compute-checksum --disable-reuse --local"
resulted in the following:
Test 253 failed: /home/eric/projects/cwl_env/venv/bin/arvados-cwl-runner --api=containers --compute-checksum --disable-reuse --local --outdir=/tmp/tmpZhRx2l --quiet tests/optional-numerical-output-0.cwl tests/empty.json Test that optional number output is returned as 0, not null Compare failure expected: { "out": 0 } got: { "out": null } caused by: failed comparison for key 'out': expected: 0 got: null 250 tests passed, 1 failures, 2 unsupported features
Updated by Peter Amstutz over 5 years ago
- Target version changed from 2019-06-05 Sprint to 2019-06-19 Sprint
Updated by Peter Amstutz over 5 years ago
- Target version changed from 2019-06-19 Sprint to 2019-07-03 Sprint
- Story points changed from 2.0 to 0.5
Updated by Peter Amstutz over 5 years ago
- Target version changed from 2019-07-03 Sprint to 2019-07-17 Sprint
Updated by Peter Amstutz about 5 years ago
Documentation branch: 15028-cwl11-doc-update @ b23721a01f61c6d9862ea6cb4d15bd620e06eeef
Updated by Eric Biagiotti about 5 years ago
Peter Amstutz wrote:
Documentation branch: 15028-cwl11-doc-update @ b23721a01f61c6d9862ea6cb4d15bd620e06eeef
- Remove "this" in:
The one exception to the @hints@ section this is @arv:APIRequirement@
- Would be nice to link back to the API Requirement extension from the reference to it in the cwl workflow tutorial
- The Portability section in cwl-style.html:
- The first sentence seems like it should go above the portability section
- The subsequent sentences kind of come out of no where. Maybe a lead in sentence about why portability is important would help, or "Consider the following recommendations to improve portability of your workflows...".
- The tip to
Avoid declaring InlineJavascriptRequirement
is a performance problem and should probably be in the performance section.
- I think a separate page for Upgrading CWL might be helpful going forward. At the very least it shouldn't be a subsection under Portability.
Updated by Peter Amstutz about 5 years ago
- Target version changed from 2019-07-17 Sprint to 2019-07-31 Sprint
Updated by Peter Amstutz about 5 years ago
- Target version deleted (
2019-07-31 Sprint)
Eric Biagiotti wrote:
Peter Amstutz wrote:
Documentation branch: 15028-cwl11-doc-update @ b23721a01f61c6d9862ea6cb4d15bd620e06eeef
- Remove "this" in: [...]
Fixed. Actually I rewrote this whole thing to add more detail.
- Would be nice to link back to the API Requirement extension from the reference to it in the cwl workflow tutorial
Added link.
- The Portability section in cwl-style.html:
- The first sentence seems like it should go above the portability section
- The subsequent sentences kind of come out of no where. Maybe a lead in sentence about why portability is important would help, or "Consider the following recommendations to improve portability of your workflows...".
- The tip to
Avoid declaring InlineJavascriptRequirement
is a performance problem and should probably be in the performance section.
I rearranged this a bit and added lead-in sentences to set up each section.
- I think a separate page for Upgrading CWL might be helpful going forward. At the very least it shouldn't be a subsection under Portability.
I made a separate "Version and API support" page.
15028-cwl11-doc-update @ ad76d059c306a73af45b6b7525aabb5f54c73f8b
Updated by Peter Amstutz about 5 years ago
- Status changed from In Progress to Resolved