Arvados

The newly created container request should set up the following mounts:

            "mounts": {
                "/var/lib/cwl/workflow.json": {
                    "kind": "json",
                    "content": {"class": "Workflow", ...},
                },
                "/var/lib/cwl/cwl.input.json": {
                    "kind": "json",
                    "content": {}
                }

(note: edited "/var/lib/cwl/jobs/cwl.input.json" -> "/var/lib/cwl/cwl.input.json")

Sounds good to me.

{
  "command": ["arvados-cwl-runner", "--local", "--api=containers", "/var/lib/cwl/workflow.json", "/var/lib/cwl/cwl.input.json"],
  "output_path": "/var/spool/cwl",
  "cwd": "/var/spool/cwl",
  "priority": 1,
  "state": "Uncommitted",
  "container_image": "arvados/jobs",
  "mounts": {
    "/var/lib/cwl/workflow.json": {
      "kind": "json",
      "content": {"class": "Workflow", ...},
    },
    "/var/lib/cwl/cwl.input.json": {
      "kind": "json",
      "content": {}
    },
    "stdout": {
      "kind": "file",
      "path": "/var/spool/cwl/cwl.output.json" 
    },
    "/var/spool/cwl": {
      "kind": "collection",
      "writable": True
    }
  },
  "runtime_constraints": {
    "vcpus": 1,
    "ram": 256000000,
    "API": True
  }
}

The above container request is based on the one already in use by arvados-cwl-runner --submit so it should work.

Please clarify the workflow.json mount point's content attribute. What key name should I use to pass the workflow json? Thanks.

  "mounts": {
    "/var/lib/cwl/workflow.json": {
      "kind": "json",
      "content": {"class": "Workflow", ...},
    },

Radhika Chippada wrote:

Please clarify the workflow.json mount point's content attribute. What key name should I use to pass the workflow json? Thanks.

The content of the "workflow" field from the "workflow" record should be assigned to the "content" field under "/var/lib/cwl/workflow.json".

Branch 9767-workflows-in-chooser is ready for review at c837f9d95

I manually added workflow yaml to 4xphq-7fd4e-2fkoj19vfnbc6j1, and created the container_request 4xphq-xvhdp-emh6t3cmt038ssa via the dashboard. (And I am able to see the inputs I added in the yaml in #9043 branch updates)

In work_units_controller.rb:51

wf_json = JSON.dump(YAML::load(workflow.workflow))

The mounts field is a structured/serialized field, so this should be:

wf_json = YAML::load(workflow.workflow)

For the chooser title, instead of "Choose a pipeline or process to run" suggest this say "Choose a pipeline or workflow to run".

In the chooser, I'm not sure showing the raw text of the workflow is very useful. Perhaps remove the workflow text, and if there is no description, perhaps render "No description provided" so that the box isn't empty?

Don't forget to add safe_yaml, if Workbench is parsing user-supplied YAML.

The container requests page should have a link back to the workflow object, similar to the way the pipeline instance page has a link to the pipeline template.

Suggest setting a default container request name based on the name of the workflow. Something like "%s container" or "%s run" (where %s = the workflow name).

wf_json = JSON.dump(YAML::load(workflow.workflow)) ... wf_json = YAML::load(workflow.workflow)

Updated

For the chooser title, instead of "Choose a pipeline or process to run" suggest this say "Choose a pipeline or workflow to run".

Done

In the chooser, I'm not sure showing the raw text of the workflow is very useful. Perhaps remove the workflow text, and if there is no description, perhaps render "No description provided" so that the box isn't empty?

Removed the workflow display from preview pane

Tom said: Don't forget to add safe_yaml, if Workbench is parsing user-supplied YAML.

Added safe_yaml gem and updated the load_config similar to API load_config

The container requests page should have a link back to the workflow object, similar to the way the pipeline instance page has a link to the pipeline template.

Will do this in a separate branch. Created task #9847

Suggest setting a default container request name based on the name of the workflow. Something like "%s container" or "%s run" (where %s = the workflow name).

Added this

The "Run a pipeline..." on project pages should also be updated to display workflows in the chooser dialog.

Good catch. Commit a485bcb2 addresses this. Thanks.

a485bcb LGTM, thanks.

Branch 9767-workflow-link-in-container-request at ac36412 adds a link to workflow in the container_request#show page.

9767-workflow-link-in-container-request @ commit:a720aab7961883fe3541dc68ed7ad0d5f91edbee LGTM