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Parsing error when the value includes == #110

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cgpu opened this issue Nov 10, 2022 · 0 comments
Open

Parsing error when the value includes == #110

cgpu opened this issue Nov 10, 2022 · 0 comments

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@cgpu
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cgpu commented Nov 10, 2022

In an example workflow, the parameter includes 2 equals, and this is breaking the parsing of parameters
Below there are the examples that work or fail respectively.

✅ Works, 1 = sign

--parameter meta_filter = 'TraitConceptCode = I21,I22; TotalSamples > 1000'

❌ Fails, 2 = signs from --parameter

--parameter meta_filter = 'TraitConceptCode == I21,I22; TotalSamples > 1000'

❌ Fails, 2 = signs from --job-config

--job-config params.config
// contents of params.config
params {
 meta_filter = 'TraitConceptCode == I21,I22; TotalSamples > 1000'
}

❌ Fails, 2 = signs from --job-config

--job-config params.config
// contents of params.config
params {
 meta_filter = 'TraitConceptCode = I21,I22; TotalSamples > 1000'
}
cloudos job run--cloudos-url $CLOUDOS --apikey $MY_API_KEY --workspace-id $WORKSPACE_ID --project-name $PROJECT_NAME --job-name $JOB_NAME --workflow-name $WORKFLOW_NAME $CLOUDOS_CLI_ARGS --job-config local2.config
CloudOS python package: a package for interacting with CloudOS.

Version: 1.2.0
CloudOS job functionality: run and check jobs in CloudOS.
Executing run...
Traceback (most recent call last):
File "/cloudos-cli/1.2.0-foss-2021a/bin/cloudos", line 8, in <module>
sys.exit(run_cloudos_cli())
File "/cloudos-cli/1.2.0-foss-2021a/lib/python3.9/site-packages/click/core.py", line 1137, in __call__
return self.main(*args, **kwargs)
File "/cloudos-cli/1.2.0-foss-2021a/lib/python3.9/site-packages/click/core.py", line 1062, in main
rv = self.invoke(ctx)
File "/cloudos-cli/1.2.0-foss-2021a/lib/python3.9/site-packages/click/core.py", line 1668, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/cloudos-cli/1.2.0-foss-2021a/lib/python3.9/site-packages/click/core.py", line 1668, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/cloudos-cli/1.2.0-foss-2021a/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/cloudos-cli/1.2.0-foss-2021a/lib/python3.9/site-packages/click/core.py", line 763, in invoke
return __callback(*args, **kwargs)
File "/apps/prod/easybuild/sl7.x86_64.foss-2021a/software/cloudos-cli/1.2.0-foss-2021a/lib/python3.9/site-packages/cloudos/__main__.py", line 265, in run
j_id = j.send_job(job_config,
File "/apps/prod/easybuild/sl7.x86_64.foss-2021a/software/cloudos-cli/1.2.0-foss-2021a/lib/python3.9/site-packages/cloudos/jobs/job.py", line 464, in send_job
params = self.convert_nextflow_to_json(job_config,
File "/apps/prod/easybuild/sl7.x86_64.foss-2021a/software/cloudos-cli/1.2.0-foss-2021a/lib/python3.9/site-packages/cloudos/jobs/job.py", line 277, in convert_nextflow_to_json
raise ValueError('Please, specify your ' +
ValueError: Please, specify your parameters in local2.config using the '=' as spacer. E.g: name = my_name
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