def cli(ctx, workflow_path, output=None, split_test=False, **kwds):
"""Initialize a Galaxy workflow test description for supplied workflow.
Be sure to your lint your workflow with ``workflow_lint`` before calling this
to ensure inputs and outputs comply with best practices that make workflow
testing easier.
"""
path_basename = os.path.basename(workflow_path)
job = job_template(workflow_path)
if output is None:
output = new_workflow_associated_path(workflow_path)
job_output = new_workflow_associated_path(workflow_path, suffix="job1")
if not can_write_to_path(output, **kwds):
ctx.exit(1)
test_description = [{
'doc': 'Test outline for %s' % path_basename,
'job': job,
'outputs': output_stubs_for_workflow(workflow_path),
}]
if split_test:
job_output = new_workflow_associated_path(workflow_path, suffix="job1")
if not can_write_to_path(job_output, **kwds):
ctx.exit(1)
test_description[0]['job'] = os.path.basename(job_output)
with open(job_output, "w") as f_job:
yaml.dump(job, f_job)
with open(output, "w") as f:
yaml.dump(test_description, f)
def cli(ctx, workflow_identifier, output=None, **kwds):
"""Initialize a Galaxy workflow job description for supplied workflow.
Be sure to your lint your workflow with ``workflow_lint`` before calling this
to ensure inputs and outputs comply with best practices that make workflow
testing easier.
Jobs can be run with the planemo run command (``planemo run workflow.ga job.yml``).
Planemo run works with Galaxy tools and CWL artifacts (both tools and workflows)
as well so this command may be renamed to to job_init at something along those
lines at some point.
"""
if kwds["from_invocation"]:
if not os.path.isdir('test-data'):
ctx.log("Creating test-data directory.")
os.makedirs("test-data")
path_basename = get_workflow_from_invocation_id(
workflow_identifier, kwds["galaxy_url"], kwds["galaxy_user_key"])
job = job_template(workflow_identifier, **kwds)
if output is None:
output = new_workflow_associated_path(
path_basename if kwds["from_invocation"] else workflow_identifier,
suffix="job")
if not can_write_to_path(output, **kwds):
ctx.exit(1)
with open(output, "w") as f_job:
yaml.dump(job, f_job)
def cli(ctx, workflow_identifier, output=None, **kwds):
"""Initialize a Galaxy workflow job description for supplied workflow.
Be sure to your lint your workflow with ``workflow_lint`` before calling this
to ensure inputs and outputs comply with best practices that make workflow
testing easier.
Jobs can be run with the planemo run command (``planemo run workflow.ga job.yml``).
Planemo run works with Galaxy tools and CWL artifacts (both tools and workflows)
as well so this command may be renamed to to job_init at something along those
lines at some point.
"""
job = job_template(workflow_identifier)
if output is None:
output = new_workflow_associated_path(workflow_identifier, suffix="job")
if not can_write_to_path(output, **kwds):
ctx.exit(1)
with open(output, "w") as f_job:
yaml.dump(job, f_job)
def cli(ctx, workflow_identifier, output=None, split_test=False, **kwds):
"""Initialize a Galaxy workflow test description for supplied workflow.
Be sure to your lint your workflow with ``workflow_lint`` before calling this
to ensure inputs and outputs comply with best practices that make workflow
testing easier.
"""
if kwds["from_invocation"]:
if not os.path.isdir('test-data'):
ctx.log("Creating test-data directory.")
os.makedirs("test-data")
path_basename = get_workflow_from_invocation_id(workflow_identifier, kwds["galaxy_url"], kwds["galaxy_user_key"])
else:
path_basename = os.path.basename(workflow_identifier)
job = job_template(workflow_identifier, **kwds)
if output is None:
output = new_workflow_associated_path(path_basename if kwds["from_invocation"] else workflow_identifier)
job_output = new_workflow_associated_path(path_basename if kwds["from_invocation"] else workflow_identifier, suffix="job1")
if not can_write_to_path(output, **kwds):
ctx.exit(1)
test_description = [{
'doc': 'Test outline for %s' % path_basename,
'job': job,
'outputs': output_stubs_for_workflow(workflow_identifier, **kwds),
}]
if split_test:
job_output = new_workflow_associated_path(path_basename if kwds["from_invocation"] else workflow_identifier, suffix="job1")
if not can_write_to_path(job_output, **kwds):
ctx.exit(1)
test_description[0]['job'] = os.path.basename(job_output)
with open(job_output, "w") as f_job:
yaml.dump(job, f_job)
with open(output, "w") as f:
yaml.dump(test_description, f)