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  • Nov 29 15:30

    marijanlekic on 1.0.2

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  • Nov 29 15:18

    marijanlekic on 1.0.2

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  • Nov 29 15:13
    dependabot[bot] labeled #440
  • Nov 29 15:13
    dependabot[bot] opened #440
  • Nov 29 15:13

    dependabot[bot] on npm_and_yarn

    chore(deps): bump mixin-deep fr… (compare)

  • Nov 29 15:11

    marijanlekic on master

    Unable to sync platform data … chore: add build/ and ng-dist/ … Merge pull request #439 from mi… (compare)

  • Nov 29 15:11
    marijanlekic closed #439
  • Nov 29 15:01
    milosdanilov opened #439
  • Nov 18 20:56
    truatpasteurdotfr closed #438
  • Nov 18 20:56
    truatpasteurdotfr commented #438
  • Nov 15 11:51
    kaushik-work commented #438
  • Nov 15 08:02
    gungorbudak commented #438
  • Nov 14 09:06
    truatpasteurdotfr opened #438
  • Oct 22 19:34
    gungorbudak commented #433
  • Sep 09 16:52
    kaushik-work commented #225
  • Sep 06 08:34
    pvanheus commented #432
  • Aug 23 07:16
    Silberbear commented #437
  • Aug 22 14:28
    kaushik-work commented #424
  • Aug 22 14:22
    kaushik-work commented #437
  • Aug 19 11:59
    Silberbear opened #437
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
$namespaces:
  sbg: 'https://www.sevenbridges.com/'
id: astrolabe
baseCommand: []
inputs:
  - id: output_dir
    type: Directory
    inputBinding:
      position: 2
      prefix: '-o'
    label: Output dir.
    doc: Output directory where artifacts will be extracted.
  - id: rosbag
    type: File
    inputBinding:
      position: 4
      prefix: '-b'
    label: Rosbag
    doc: Rosbag to analyse.
    'sbg:fileTypes': bag
  - id: json_file
    type:
      - 'null'
      - File
      - type: array
        items: File
    inputBinding:
      position: 5
      prefix: '-j'
    label: CC JSON file
    doc: JSON file generated by Control Centre for this bag session.
    'sbg:fileTypes': json
outputs: []
label: astrolabe extract rosbag
arguments:
  - position: 1
    prefix: ''
    valueFrom: extract
  - position: 3
    prefix: ''
    valueFrom: rosbag
requirements:
  - class: ResourceRequirement
    ramMin: 8000
    coresMin: 1
  - class: DockerRequirement
    dockerPull: >-
      registry.corp.XXXXXXX
successCodes:
  - 0
permanentFailCodes:
  - 1
  - 2
  - 4
  - 8
  - -1
I've removed the URL to our internal registry
Michael R. Crusoe
@mr-c
which element had an extra space associated?
Fran Sánchez
@fj-sanchez
And this is what I get when running it:
INFO [job astrolabe] /tmp/0w9w95jx$ 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:
image.png
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:
INFO [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
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.