But note taken
So I guess that due to this recommendation there is not other way to make Rabix composer avoid the
ShellCommandRequirement
Actually I figured out why it is adding it... If I change the default of "shellQuote" attribute it will add it, otherwise it won't
class: CommandLineTool
cwlVersion: v1.0
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: astrolabe
baseCommand: []
inputs:
- id: output_dir
type: Directory
inputBinding:
position: 2
prefix: '-o'
label: Output dir.
doc: Output directory where artifacts will be extracted.
- id: rosbag
type: File
inputBinding:
position: 4
prefix: '-b'
label: Rosbag
doc: Rosbag to analyse.
'sbg:fileTypes': bag
- id: json_file
type:
- 'null'
- File
- type: array
items: File
inputBinding:
position: 5
prefix: '-j'
label: CC JSON file
doc: JSON file generated by Control Centre for this bag session.
'sbg:fileTypes': json
outputs: []
label: astrolabe extract rosbag
arguments:
- position: 1
prefix: ''
valueFrom: extract
- position: 3
prefix: ''
valueFrom: rosbag
requirements:
- class: ResourceRequirement
ramMin: 8000
coresMin: 1
- class: DockerRequirement
dockerPull: >-
registry.corp.XXXXXXX
successCodes:
- 0
permanentFailCodes:
- 1
- 2
- 4
- 8
- -1
I've removed the URL to our internal registry
And this is what I get when running it:
[1;30mINFO[0m [job astrolabe] /tmp/0w9w95jx$ 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
Maybe a GUI issue, but it is in the generated code
Interesting... If I disable "Separate value and prefix" like this:
Then it completely removes the
extract argument from the code...
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
I have the same version listed int he GitHub issue
@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 ;)
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
I just manually changed it from the CSS
I changed the font-size for
.ace_editor class
and also generally for
body
I simply cannot stand the small font, 4 hours using it and already feeling the effects...
@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!