rabix/composer

A graphical editor for CWL documents

Fran Sánchez

@fj-sanchez

Do you mean the generated code?

Michael R. Crusoe

@mr-c

Yes

Fran Sánchez

@fj-sanchez

class: CommandLineTool
cwlVersion: v1.0
$namespaces:
  sbg: 'https://www.sevenbridges.com/'
id: astrolabe
baseCommand: []
inputs:
  - id: output_dir
    type: Directory
    inputBinding:
      position: 2
      prefix: '-o'
    label: Output dir.
    doc: Output directory where artifacts will be extracted.
  - id: rosbag
    type: File
    inputBinding:
      position: 4
      prefix: '-b'
    label: Rosbag
    doc: Rosbag to analyse.
    'sbg:fileTypes': bag
  - id: json_file
    type:
      - 'null'
      - File
      - type: array
        items: File
    inputBinding:
      position: 5
      prefix: '-j'
    label: CC JSON file
    doc: JSON file generated by Control Centre for this bag session.
    'sbg:fileTypes': json
outputs: []
label: astrolabe extract rosbag
arguments:
  - position: 1
    prefix: ''
    valueFrom: extract
  - position: 3
    prefix: ''
    valueFrom: rosbag
requirements:
  - class: ResourceRequirement
    ramMin: 8000
    coresMin: 1
  - class: DockerRequirement
    dockerPull: >-
      registry.corp.XXXXXXX
successCodes:
  - 0
permanentFailCodes:
  - 1
  - 2
  - 4
  - 8
  - -1

I've removed the URL to our internal registry

Michael R. Crusoe

@mr-c

which element had an extra space associated?

Fran Sánchez

@fj-sanchez

And this is what I get when running it:

[1;30mINFO[0m [job astrolabe] /tmp/0w9w95jx$ docker \
    run \
    -i \
    --volume=/tmp/0w9w95jx:/wNBQGE:rw \
    --volume=/tmp/9s3zsfpo:/tmp:rw \
    --volume=/tmp/cwl_test:/var/lib/cwl/stg6b98f776-ed04-4573-9277-468824750333/cwl_test:ro \
    --volume=/home/francisco/data/tutorial/sample_bag.bag:/var/lib/cwl/stg6c041cb4-4701-4946-a682-64db82348ba0/sample_bag.bag:ro \
    --workdir=/wNBQGE \
    --read-only=true \
    --user=1000:106 \
    --rm \
    --env=TMPDIR=/tmp \
    --env=HOME=/wNBQGE \
    --cidfile=/tmp/ioxqfby4/20190812124926-745445.cid \
    registry.corp.XXXXXX \
    '' \
    extract \
    -o \
    /var/lib/cwl/stg6b98f776-ed04-4573-9277-468824750333/cwl_test \
    '' \
    rosbag \
    -b \
    /var/lib/cwl/stg6c041cb4-4701-4946-a682-64db82348ba0/sample_bag.bag

Michael R. Crusoe

@mr-c

Yes, the prefix entries are adding extra empty elements; you may want to remove them

Fran Sánchez

@fj-sanchez

But I'm not using any prefix for extract

Michael R. Crusoe

@mr-c

arguments:
  - position: 1
    prefix: ''
    valueFrom: extract

Maybe a GUI issue, but it is in the generated code

Fran Sánchez

@fj-sanchez

Oh I see...

Interesting... If I disable "Separate value and prefix" like this:

Then it completely removes the extract argument from the code...

Fran Sánchez

@fj-sanchez

Well, actually not from the code but from the execution line:

[1;30mINFO[0m [job astrolabe] /tmp/h8h5w59n$ docker \
    run \
    -i \
    --volume=/tmp/h8h5w59n:/TgQtgK:rw \
    --volume=/tmp/kyjn3x1b:/tmp:rw \
    --volume=/tmp/cwl_test:/var/lib/cwl/stgf9a1133b-6195-4328-bf98-186101e628d2/cwl_test:ro \
    --volume=/home/francisco/data/tutorial/sample_bag.bag:/var/lib/cwl/stg2393129f-2ad3-4c91-8f4b-70750efdf5e4/sample_bag.bag:ro \
    --workdir=/TgQtgK \
    --read-only=true \
    --user=1000:106 \
    --rm \
    --env=TMPDIR=/tmp \
    --env=HOME=/TgQtgK \
    --cidfile=/tmp/4rm9ytgr/20190812134540-480254.cid \
    registry.corp.XXXXXXX \
    '' \
    -o \
    /var/lib/cwl/stgf9a1133b-6195-4328-bf98-186101e628d2/cwl_test \
    '' \
    rosbag \
    -b \
    /var/lib/cwl/stg2393129f-2ad3-4c91-8f4b-70750efdf5e4/sample_bag.bag

But you are right @mr-c if I remove from the generated code the prefix it passes the arguments correctly

Michael R. Crusoe

@mr-c

Perhaps this common-workflow-language/cwltool#1165 is related

Fran Sánchez

@fj-sanchez

Indeed, at least if I manually remove it from the code it doesn't seem to add it anymore

I have the same version listed int he GitHub issue

Andrey Kartashov

@portah

@fj-sanchez about docker, I had the same confusion at the beginning https://stackoverflow.com/questions/33984937/docker-single-process-by-container-but-how-to-use-them-together

But stackoverflow gave a good hint ;)

Fran Sánchez

@fj-sanchez

Thanks @portah I'm going to read it

For me the issue might be that my entrypoint is actually preparing the execution environment sourcing some files, etc.

So I guess I'd have to set these variables ahead of run-time

Fran Sánchez

@fj-sanchez

Is there any way to see the stdout of a container while I run it in the Rabix composer UI?

Andrey Kartashov

@portah

docker logs 01cbb30ebf10

Fran Sánchez

@fj-sanchez

But I don't see the container Id while it is executing, only at the end if I check the output in stderr.log

Andrey Kartashov

@portah

docker ps ?

Fran Sánchez

@fj-sanchez

Ok, but no way to see it from the Rabix UI, right?

Fran Sánchez

@fj-sanchez

Any way to increase the font size in Rabix Composer?

Michael R. Crusoe

@mr-c

@fj-sanchez Not at this time, alas rabix/composer#225

Fran Sánchez

@fj-sanchez

Mmmm, it seems to have been there for a while now...

Michael R. Crusoe

@mr-c

Sadly, yes

Fran Sánchez

@fj-sanchez

Mmmm, I think it's very easy to change...

I just manually changed it from the CSS

I changed the font-size for .ace_editor class

and also generally for body

Michael R. Crusoe

@mr-c

@fj-sanchez Can you add that to the issue?

Fran Sánchez

@fj-sanchez

Will do

Michael R. Crusoe

@mr-c

Thanks!

Fran Sánchez

@fj-sanchez

Done, I'm running from source code but I guess that it should be applicable also to a deployed electron instance if you change the proper file or alternatively you can just re-compile it with the changes.

I simply cannot stand the small font, 4 hours using it and already feeling the effects...

Michael R. Crusoe

@mr-c

:+1:

Ian

@ionox0

@kaushik-work I actually see a few comments here rabix/composer#348 rabix/composer#329 and it looks like it's actually already addressed! I may have been wrong about how we have our development environment set up actually, thank you!

ccflorece

@ccflorece

Hi! I installed rabix composer in my windows laptop and i also have a docker and java installed by there's something wrong during execution

Kaushik Ghose

@kaushik-work

Hi @ccflorece there is a path problem with Rabix executor on windows. The best would be to invoke the CWL runner manually after exporting the job file from composer

ccflorece

@ccflorece

Hi, Kaushik! Thanks for responding. It has something to do with Java. This is what appears in my error log: "java.net.URISyntaxException: Illegal character in opaque part at index 2"

Kaushik Ghose

@kaushik-work

Hi @ccflorece , yes. That is a problem with Rabix Executor on windows.

This happens when you click "Run", is that right?

ccflorece

@ccflorece

Yes, @kaushik-work . Well, that's disappointing. Does that mean it only works in Ubuntu?

Kaushik Ghose

@kaushik-work

Rabix Executor works on macOS and Linux. For windows I believe Cwltool is the only one that works. Neither Cromwell nor Toil work on windows, I believe.

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