def cli(ctx, path, job_path, **kwds):
"""Planemo command for running tools and jobs.
::
% planemo run cat1-tool.cwl cat-job.json
"""
kwds["cwl"] = path.endswith(".cwl")
conformance_test = kwds.get("conformance_test", False)
with conditionally_captured_io(conformance_test):
with engine_context(ctx, **kwds) as engine:
run_result = engine.run(path, job_path)
if not run_result.was_successful:
warn("Run failed [%s]" % str(run_result))
ctx.exit(1)
if conformance_test:
if hasattr(run_result, "cwl_command_state"):
command_state = run_result.cwl_command_state
dumped_json = json.dumps(command_state)
if hasattr(run_result, "galaxy_paths"):
for (local_path, galaxy_path) in run_result.galaxy_paths:
dumped_json = dumped_json.replace(galaxy_path, local_path)
print(dumped_json)
else:
outputs_dict = run_result.outputs_dict
print(outputs_dict)
output_json = kwds.get("output_json", None)
if output_json:
with open(output_json, "w") as f:
json.dump(outputs_dict, f)
return 0
def cli(ctx, uri, job_path, **kwds):
"""Planemo command for running tools and jobs.
\b
% planemo run cat1-tool.cwl cat-job.json
"""
path = uri_to_path(ctx, uri)
# TODO: convert UI to runnable and do a better test of cwl.
is_cwl = path.endswith(".cwl")
kwds["cwl"] = is_cwl
if kwds.get("engine", None) is None:
kwds["engine"] = "galaxy" if not is_cwl else "cwltool"
with engine_context(ctx, **kwds) as engine:
run_result = engine.run(path, job_path)
if not run_result.was_successful:
warn("Run failed [%s]" % unicodify(run_result))
ctx.exit(1)
outputs_dict = run_result.outputs_dict
print(outputs_dict)
output_json = kwds.get("output_json", None)
if output_json:
with open(output_json, "w") as f:
json.dump(outputs_dict, f)
return 0
def test_tutorial_create_hands_on_tutorial():
"""Test :func:`planemo.training.tutorial.tutorial.create_hands_on_tutorial`."""
tuto = Tutorial(
training=training,
topic=topic)
os.makedirs(tuto.wf_dir)
# with init_wf_id and no Galaxy URL
tuto.init_wf_id = 'ID'
tuto.training.galaxy_url = None
exp_exception = "No Galaxy URL given"
with assert_raises_regexp(Exception, exp_exception):
tuto.create_hands_on_tutorial(CTX)
# with init_wf_id and no Galaxy API key
tuto.init_wf_id = 'ID'
tuto.training.galaxy_url = 'http://%s:%s' % (KWDS['host'], KWDS['port'])
tuto.training.galaxy_api_key = None
exp_exception = "No API key to access the given Galaxy instance"
with assert_raises_regexp(Exception, exp_exception):
tuto.create_hands_on_tutorial(CTX)
# with init_wf_id
assert is_galaxy_engine(**KWDS)
with engine_context(CTX, **KWDS) as galaxy_engine:
with galaxy_engine.ensure_runnables_served([RUNNABLE]) as config:
tuto.init_wf_id = config.workflow_id(WF_FP)
tuto.training.galaxy_api_key = config.user_api_key
tuto.create_hands_on_tutorial(CTX)
assert os.path.exists(tuto.tuto_fp)
os.remove(tuto.tuto_fp)
# with init_wf_fp
tuto.init_wf_id = None
tuto.init_wf_fp = WF_FP
tuto.create_hands_on_tutorial(CTX)
assert os.path.exists(tuto.tuto_fp)
shutil.rmtree("topics")
def cli(ctx, runnable_identifier, job_path, **kwds):
"""Planemo command for running tools and jobs.
\b
% planemo run cat1-tool.cwl cat-job.json
"""
runnable = for_runnable_identifier(ctx, runnable_identifier, kwds)
is_cwl = runnable.type.is_cwl_artifact
kwds["cwl"] = is_cwl
if kwds.get("engine", None) is None:
if is_cwl:
kwds["engine"] = "cwltool"
elif kwds.get('galaxy_url', None):
kwds["engine"] = "external_galaxy"
else:
kwds["engine"] = "galaxy"
with engine_context(ctx, **kwds) as engine:
run_result = engine.run(runnable, job_path)
if not run_result.was_successful:
warn("Run failed [%s]" % unicodify(run_result))
ctx.exit(1)
outputs_dict = run_result.outputs_dict
output_json = kwds.get("output_json", None)
if output_json:
with open(output_json, "w") as f:
json.dump(outputs_dict, f)
return 0
def cli(ctx, workflow_path, output=None, force=False, **kwds):
"""Convert Format 2 workflow to a native Galaxy workflow.
"""
assert is_galaxy_engine(**kwds)
kwds["no_dependency_resolution"] = True
if workflow_path.endswith(".ga"):
if output is None:
output = os.path.splitext(workflow_path)[0] + ".gxwf.yml"
with open(workflow_path, "r") as f:
workflow_dict = json.load(f)
format2_wrapper = from_galaxy_native(workflow_dict, json_wrapper=True)
with open(output, "w") as f:
f.write(format2_wrapper["yaml_content"])
else:
if output is None:
output = os.path.splitext(workflow_path)[0] + ".ga"
runnable = for_path(workflow_path)
with engine_context(ctx, **kwds) as galaxy_engine:
with galaxy_engine.ensure_runnables_served([runnable]) as config:
workflow_id = config.workflow_id(workflow_path)
output_dict = config.gi.workflows.export_workflow_dict(workflow_id)
output_contents = json.dumps(output_dict)
write_file(output, output_contents, force=force)
def cli(ctx, path, job_path, **kwds):
"""Planemo command for running tools and jobs.
::
% planemo run cat1-tool.cwl cat-job.json
"""
kwds["cwl"] = path.endswith(".cwl")
conformance_test = kwds.get("conformance_test", False)
with conditionally_captured_io(conformance_test):
with engine_context(ctx, **kwds) as engine:
run_result = engine.run(path, job_path)
if not run_result.was_successful:
warn("Run failed [%s]" % str(run_result))
ctx.exit(1)
if conformance_test:
if hasattr(run_result, "cwl_command_state"):
command_state = run_result.cwl_command_state
dumped_json = json.dumps(command_state)
if hasattr(run_result, "galaxy_paths"):
for (local_path, galaxy_path) in run_result.galaxy_paths:
dumped_json = dumped_json.replace(galaxy_path, local_path)
print(dumped_json)
else:
outputs_dict = run_result.outputs_dict
print(outputs_dict)
output_json = kwds.get("output_json", None)
if output_json:
with open(output_json, "w") as f:
json.dump(outputs_dict, f)
return 0
def cli(ctx, rerunnable_ids, **kwds):
"""Planemo command for rerunning and remapping failed jobs on an external Galaxy server.
Supply a list of history, invocation or job IDs, identifying the ID type using the
--invocation, --history or --job flag, and all associated failed jobs will be rerun.
Please note: attempting to rerun non-remappable jobs will result in an exit code of 1. As
jobs cannot be remapped more than once, running this command two or more times with the same
history or job IDs will therefore return an exit code of 1. If avoiding this is important,
you should specify the invocation ID instead if possible.
\b
% planemo rerun --invocation / --history / --job RERUNNABLE_IDS
"""
# Possible TODO: allow collection IDs to be specified as well
if not kwds.get('rerunnable_type'):
error(
"Please specify the type (invocation, history or job) of the IDs which should be rerun."
)
ctx.exit(1)
kwds["engine"] = "external_galaxy"
rerun_successful = True
with engine_context(ctx, **kwds) as engine:
for rerunnable_id in rerunnable_ids:
rerunnable = Rerunnable(rerunnable_id, kwds['rerunnable_type'],
kwds["galaxy_url"])
rerun_result = engine.rerun(ctx, rerunnable, **kwds)
if not rerun_result.was_successful:
rerun_successful = False
if rerun_successful:
info('All requested jobs were rerun successfully.')
ctx.exit(0)
else:
error('Some of the requested jobs could not be rerun.')
ctx.exit(1)
def cli(ctx, uri, job_path, **kwds):
"""Planemo command for running tools and jobs.
\b
% planemo run cat1-tool.cwl cat-job.json
"""
path = uri_to_path(ctx, uri)
# TODO: convert UI to runnable and do a better test of cwl.
is_cwl = path.endswith(".cwl")
kwds["cwl"] = is_cwl
if kwds.get("engine", None) is None:
kwds["engine"] = "galaxy" if not is_cwl else "cwltool"
with engine_context(ctx, **kwds) as engine:
run_result = engine.run(path, job_path)
if not run_result.was_successful:
warn("Run failed [%s]" % str(run_result))
ctx.exit(1)
outputs_dict = run_result.outputs_dict
print(outputs_dict)
output_json = kwds.get("output_json", None)
if output_json:
with open(output_json, "w") as f:
json.dump(outputs_dict, f)
return 0
def _cli(ctx, paths, glx, user_key, **kwds) -> Dict:
"""
Run specified tool's tests within Galaxy.
Returns a dict of the status and history_name of the finished workflow.
See https://github.com/galaxyproject/planemo/blob/master/planemo/commands/cmd_test.py
"""
kwds["engine"] = "external_galaxy"
kwds["shed_install"] = False
kwds["galaxy_url"] = glx.url
kwds["galaxy_admin_key"] = glx.user_key
kwds["history_name"] = "galaxy_benchmarker-" + str(time.time_ns()) + str(
random.randrange(0, 99999))
if user_key is not None:
kwds["galaxy_user_key"] = user_key
runnables = for_paths(paths)
try:
with engine_context(ctx, **kwds) as engine:
test_data = engine.test(runnables)
exit_code = handle_reports_and_summary(ctx,
test_data.structured_data,
kwds=kwds)
status = "success" if exit_code == 0 else "error"
except Exception as e:
log.error("There was an error: {e}".format(e=e))
status = "error"
return {"status": status, "history_name": kwds["history_name"]}
def cli(ctx, workflow_identifier, output=None, force=False, **kwds):
"""Convert Format 2 workflows to native Galaxy workflows, and vice-versa.
"""
assert is_galaxy_engine(**kwds)
kwds["no_dependency_resolution"] = True
if workflow_identifier.endswith(".ga"):
if output is None:
output = os.path.splitext(workflow_identifier)[0] + ".gxwf.yml"
with open(workflow_identifier, "r") as f:
workflow_dict = json.load(f)
format2_wrapper = from_galaxy_native(workflow_dict, json_wrapper=True)
with open(output, "w") as f:
f.write(format2_wrapper["yaml_content"])
else:
if output is None:
output = os.path.splitext(workflow_identifier)[0] + ".ga"
runnable = for_path(workflow_identifier)
with engine_context(ctx, **kwds) as galaxy_engine:
with galaxy_engine.ensure_runnables_served([runnable]) as config:
workflow_id = config.workflow_id(workflow_identifier)
output_dict = config.gi.workflows.export_workflow_dict(workflow_id)
output_contents = json.dumps(output_dict, indent=4, sort_keys=True)
write_file(output, output_contents, force=force)
def cli(ctx, paths, **kwds):
"""Run specified tool's tests within Galaxy.
All referenced tools (by default all the tools in the current working
directory) will be tested and the results quickly summarized.
To run these tests planemo needs a Galaxy instance to utilize, planemo
will search parent directories to see if any is a Galaxy instance
- but one can pick the Galaxy instance to use with the --galaxy_root
option or force planemo to download a disposable instance with the
``--install_galaxy`` flag.
In additon to to quick summary printed to the console - various detailed
output summaries can be configured. ``tool_test_output.html`` (settable
via ``--test_output``) will contain a human consumable HTML report
describing the test run. A JSON file (settable via ``--test_output_json``
and defaulting to ``tool_test_output.json``) will also be created. These
files can can be disabled by passing in empty arguments or globally by
setting the values ``default_test_output`` and/or
``default_test_output_json`` in ``~/.planemo.yml`` to ``null``. For
continuous integration testing a xUnit-style report can be confiured using
the ``--test_output_xunit``.
planemo uses temporarily generated config files and environment variables
to attempt to shield this execution of Galaxy from manually launched runs
against that same Galaxy root - but this may not be bullet proof yet so
please careful and do not try this against production Galaxy instances.
"""
runnables = for_paths(paths)
is_cwl = all([
r.type in [RunnableType.cwl_tool, RunnableType.cwl_workflow]
for r in runnables
])
if kwds.get("engine", None) is None:
kwds["engine"] = "galaxy" if not is_cwl else "cwltool"
engine_type = kwds["engine"]
enable_test_engines = any([
r.type not in [
RunnableType.galaxy_tool, RunnableType.galaxy_datamanager,
RunnableType.directory
] for r in runnables
])
enable_test_engines = enable_test_engines or engine_type != "galaxy"
if enable_test_engines:
ctx.vlog("Using test engine type %s" % engine_type)
with engine_context(ctx, **kwds) as engine:
test_data = engine.test(runnables)
return_value = handle_reports_and_summary(
ctx, test_data.structured_data, kwds=kwds)
else:
ctx.vlog(
"Running traditional Galaxy tool tests using run_tests.sh in Galaxy root %s"
% engine_type)
kwds["for_tests"] = True
with galaxy_config(ctx, runnables, **kwds) as config:
return_value = run_in_config(ctx, config, **kwds)
ctx.exit(return_value)
def get_hands_on_boxes_from_local_galaxy(kwds, wf_filepath, ctx):
"""Server local Galaxy and get the workflow dictionary."""
assert is_galaxy_engine(**kwds)
runnable = for_path(wf_filepath)
tuto_body = ''
with engine_context(ctx, **kwds) as galaxy_engine:
with galaxy_engine.ensure_runnables_served([runnable]) as config:
workflow_id = config.workflow_id(wf_filepath)
wf = config.gi.workflows.export_workflow_dict(workflow_id)
tuto_body = format_wf_steps(wf, config.gi)
return tuto_body
def test_format_wf_steps():
"""Test :func:`planemo.training.tutorial.format_wf_steps`."""
assert is_galaxy_engine(**KWDS)
with engine_context(CTX, **KWDS) as galaxy_engine:
with galaxy_engine.ensure_runnables_served([RUNNABLE]) as config:
workflow_id = config.workflow_id(WF_FP)
wf = config.gi.workflows.export_workflow_dict(workflow_id)
body = format_wf_steps(wf, config.gi)
assert '## Sub-step with **FastQC**' in body
assert '## Sub-step with **Query Tabular**' in body
assert '## Sub-step with **Select first**' in body
def get_hands_on_boxes_from_local_galaxy(kwds, wf_filepath, ctx):
"""Server local Galaxy and get the workflow dictionary."""
assert is_galaxy_engine(**kwds)
runnable = for_path(wf_filepath)
tuto_body = ''
with engine_context(ctx, **kwds) as galaxy_engine:
with galaxy_engine.ensure_runnables_served([runnable]) as config:
workflow_id = config.workflow_id(wf_filepath)
wf = config.gi.workflows.export_workflow_dict(workflow_id)
tuto_body = format_wf_steps(wf, config.gi)
return tuto_body
def test_get_hands_on_boxes_from_running_galaxy():
"""Test :func:`planemo.training.tutorial.get_hands_on_boxes_from_running_galaxy`."""
assert is_galaxy_engine(**KWDS)
galaxy_url = 'http://%s:%s' % (KWDS['host'], KWDS['port'])
with engine_context(CTX, **KWDS) as galaxy_engine:
with galaxy_engine.ensure_runnables_served([RUNNABLE]) as config:
wf_id = config.workflow_id(WF_FP)
tuto_body = get_hands_on_boxes_from_running_galaxy(wf_id, galaxy_url, config.user_api_key)
assert '## Sub-step with **FastQC**' in tuto_body
assert '## Sub-step with **Query Tabular**' in tuto_body
assert '## Sub-step with **Select first**' in tuto_body
def cli(ctx, workflow_path, output=None, force=False, **kwds):
"""Open a synchronized Galaxy workflow editor.
"""
assert is_galaxy_engine(**kwds)
kwds["workflows_from_path"] = True
runnable = for_path(workflow_path)
with engine_context(ctx, **kwds) as galaxy_engine:
with galaxy_engine.ensure_runnables_served([runnable]) as config:
workflow_id = config.workflow_id(workflow_path)
url = "%s/workflow/editor?id=%s" % (config.galaxy_url, workflow_id)
click.launch(url)
sleep_for_serve()
def cli(ctx, workflow_identifier, output=None, force=False, **kwds):
"""Open a synchronized Galaxy workflow editor.
"""
assert is_galaxy_engine(**kwds)
runnable = for_runnable_identifier(ctx, workflow_identifier, kwds.get("profile"))
kwds["workflows_from_path"] = True
with engine_context(ctx, **kwds) as galaxy_engine:
with galaxy_engine.ensure_runnables_served([runnable]) as config:
workflow_id = config.workflow_id_for_runnable(runnable)
url = "%s/workflow/editor?id=%s" % (config.galaxy_url, workflow_id)
click.launch(url)
if kwds["engine"] != "external_galaxy":
sleep_for_serve()
def cli(ctx, paths, **kwds):
"""Run specified tool's tests within Galaxy.
All referenced tools (by default all the tools in the current working
directory) will be tested and the results quickly summarized.
To run these tests planemo needs a Galaxy instance to utilize, planemo
will search parent directories to see if any is a Galaxy instance
- but one can pick the Galaxy instance to use with the --galaxy_root
option or force planemo to download a disposable instance with the
``--install_galaxy`` flag.
In additon to to quick summary printed to the console - various detailed
output summaries can be configured. ``tool_test_output.html`` (settable
via ``--test_output``) will contain a human consumable HTML report
describing the test run. A JSON file (settable via ``--test_output_json``
and defaulting to ``tool_test_output.json``) will also be created. These
files can can be disabled by passing in empty arguments or globally by
setting the values ``default_test_output`` and/or
``default_test_output_json`` in ``~/.planemo.yml`` to ``null``. For
continuous integration testing a xUnit-style report can be confiured using
the ``--test_output_xunit``.
planemo uses temporarily generated config files and environment variables
to attempt to shield this execution of Galaxy from manually launched runs
against that same Galaxy root - but this may not be bullet proof yet so
please careful and do not try this against production Galaxy instances.
"""
runnables = for_paths(paths)
is_cwl = all([r.type in [RunnableType.cwl_tool, RunnableType.cwl_workflow] for r in runnables])
if kwds.get("engine", None) is None:
kwds["engine"] = "galaxy" if not is_cwl else "cwltool"
engine_type = kwds["engine"]
enable_test_engines = any([r.type not in [RunnableType.galaxy_tool, RunnableType.directory] for r in runnables])
enable_test_engines = enable_test_engines or engine_type != "galaxy"
if enable_test_engines:
ctx.vlog("Using test engine type %s" % engine_type)
with engine_context(ctx, **kwds) as engine:
test_data = engine.test(runnables)
return_value = handle_reports_and_summary(ctx, test_data.structured_data, kwds=kwds)
else:
ctx.vlog("Running traditional Galaxy tool tests using run_tests.sh in Galaxy root %s" % engine_type)
kwds["for_tests"] = True
with galaxy_config(ctx, runnables, **kwds) as config:
return_value = run_in_config(ctx, config, **kwds)
ctx.exit(return_value)
def cli(ctx, workflow_path, output=None, force=False, **kwds):
"""Convert Format 2 workflow to a native Galaxy workflow.
"""
assert is_galaxy_engine(**kwds)
kwds["no_dependency_resolution"] = True
if output is None:
output = os.path.splitext(workflow_path)[0] + ".ga"
runnable = for_path(workflow_path)
with engine_context(ctx, **kwds) as galaxy_engine:
with galaxy_engine.serve_runnables([runnable]) as config:
workflow_id = config.workflow_id(workflow_path)
output_dict = config.gi.workflows.export_workflow_dict(workflow_id)
output_contents = json.dumps(output_dict)
write_file(output, output_contents, force=force)
def test_tutorial_export_workflow_file():
"""Test :func:`planemo.training.tutorial.tutorial.export_workflow_file`."""
tuto = Tutorial(training=training, topic=topic)
os.makedirs(tuto.wf_dir)
# with worflow fp
tuto.init_wf_fp = WF_FP
tuto.export_workflow_file()
assert os.path.exists(tuto.wf_fp)
# with workflow id
tuto.init_wf_fp = None
os.remove(tuto.wf_fp)
assert is_galaxy_engine(**KWDS)
galaxy_url = 'http://%s:%s' % (KWDS['host'], KWDS['port'])
with engine_context(CTX, **KWDS) as galaxy_engine:
with galaxy_engine.ensure_runnables_served([RUNNABLE]) as config:
tuto.init_wf_id = config.workflow_id(WF_FP)
tuto.training.galaxy_url = galaxy_url
tuto.training.galaxy_api_key = config.user_api_key
tuto.export_workflow_file()
assert os.path.exists(tuto.wf_fp)
shutil.rmtree("topics")
def cli(ctx, workflow_identifier, output=None, force=False, **kwds):
"""Open a synchronized Galaxy workflow editor.
"""
assert is_galaxy_engine(**kwds)
workflow_identifier = translate_alias(ctx, workflow_identifier,
kwds.get('profile'))
if os.path.exists(workflow_identifier):
runnable = for_path(workflow_identifier)
else: # assume galaxy workflow id
runnable = for_id(workflow_identifier)
kwds["workflows_from_path"] = True
with engine_context(ctx, **kwds) as galaxy_engine:
with galaxy_engine.ensure_runnables_served([runnable]) as config:
workflow_id = config.workflow_id_for_runnable(runnable)
url = "%s/workflow/editor?id=%s" % (config.galaxy_url, workflow_id)
click.launch(url)
if kwds["engine"] != "external_galaxy":
sleep_for_serve()
def test_runnables(ctx, runnables, original_paths=None, **kwds):
"""Return exit code indicating test or failure."""
engine_type = kwds["engine"]
test_engine_testable = {RunnableType.galaxy_tool, RunnableType.galaxy_datamanager, RunnableType.directory}
enable_test_engines = any(r.type not in test_engine_testable for r in runnables)
enable_test_engines = enable_test_engines or engine_type != "galaxy"
if enable_test_engines:
ctx.vlog("Using test engine type %s" % engine_type)
with engine_context(ctx, **kwds) as engine:
test_data = engine.test(runnables)
ctx.vlog("engine.test returning [%s]" % test_data)
return_value = handle_reports_and_summary(ctx, test_data.structured_data, kwds=kwds)
else:
ctx.vlog("Running traditional Galaxy tool tests using run_tests.sh in Galaxy root %s" % engine_type)
kwds["for_tests"] = True
if kwds.get('update_test_data'):
non_copied_runnables = for_paths(original_paths)
kwds['test_data_target_dir'] = _find_test_data(non_copied_runnables, **kwds)
with galaxy_config(ctx, runnables, **kwds) as config:
return_value = run_in_config(ctx, config, **kwds)
return return_value
def test_tutorial_export_workflow_file():
"""Test :func:`planemo.training.tutorial.tutorial.export_workflow_file`."""
tuto = Tutorial(
training=training,
topic=topic)
os.makedirs(tuto.wf_dir)
# with worflow fp
tuto.init_wf_fp = WF_FP
tuto.export_workflow_file()
assert os.path.exists(tuto.wf_fp)
# with workflow id
tuto.init_wf_fp = None
os.remove(tuto.wf_fp)
assert is_galaxy_engine(**KWDS)
galaxy_url = 'http://%s:%s' % (KWDS['host'], KWDS['port'])
with engine_context(CTX, **KWDS) as galaxy_engine:
with galaxy_engine.ensure_runnables_served([RUNNABLE]) as config:
tuto.init_wf_id = config.workflow_id(WF_FP)
tuto.training.galaxy_url = galaxy_url
tuto.training.galaxy_api_key = config.user_api_key
tuto.export_workflow_file()
assert os.path.exists(tuto.wf_fp)
shutil.rmtree("topics")
def cli(ctx, uri, job_path, **kwds):
"""Planemo command for running tools and jobs.
\b
% planemo run cat1-tool.cwl cat-job.json
"""
path = uri_to_path(ctx, uri)
kwds["cwl"] = path.endswith(".cwl")
with engine_context(ctx, **kwds) as engine:
run_result = engine.run(path, job_path)
if not run_result.was_successful:
warn("Run failed [%s]" % str(run_result))
ctx.exit(1)
outputs_dict = run_result.outputs_dict
print(outputs_dict)
output_json = kwds.get("output_json", None)
if output_json:
with open(output_json, "w") as f:
json.dump(outputs_dict, f)
return 0
def cli(ctx, runnable_identifier, job_path, **kwds):
"""Planemo command for running tools and jobs.
\b
% planemo run cat1-tool.cwl cat-job.json
"""
runnable_identifier = translate_alias(ctx, runnable_identifier,
kwds.get('profile'))
path = uri_to_path(ctx, runnable_identifier)
if os.path.exists(path):
runnable = for_path(path)
else: # assume galaxy workflow id
runnable = for_id(runnable_identifier)
# TODO: do a better test of cwl.
is_cwl = path.endswith(".cwl")
kwds["cwl"] = is_cwl
if kwds.get("engine", None) is None:
if is_cwl:
kwds["engine"] = "cwltool"
elif kwds.get('galaxy_url', None):
kwds["engine"] = "external_galaxy"
else:
kwds["engine"] = "galaxy"
with engine_context(ctx, **kwds) as engine:
run_result = engine.run(runnable, job_path)
if not run_result.was_successful:
warn("Run failed [%s]" % unicodify(run_result))
ctx.exit(1)
outputs_dict = run_result.outputs_dict
output_json = kwds.get("output_json", None)
if output_json:
with open(output_json, "w") as f:
json.dump(outputs_dict, f)
return 0
def cli(ctx, uri, job_path, **kwds):
"""Planemo command for running tools and jobs.
\b
% planemo run cat1-tool.cwl cat-job.json
"""
path = uri_to_path(ctx, uri)
kwds["cwl"] = path.endswith(".cwl")
with engine_context(ctx, **kwds) as engine:
run_result = engine.run(path, job_path)
if not run_result.was_successful:
warn("Run failed [%s]" % str(run_result))
ctx.exit(1)
outputs_dict = run_result.outputs_dict
print(outputs_dict)
output_json = kwds.get("output_json", None)
if output_json:
with open(output_json, "w") as f:
json.dump(outputs_dict, f)
return 0
def cli(ctx, runnable_identifier, job_path, **kwds):
"""Planemo command for running tools and jobs.
\b
% planemo run cat1-tool.cwl cat-job.json
"""
runnable = for_runnable_identifier(ctx, runnable_identifier, kwds)
is_cwl = runnable.type.is_cwl_artifact
kwds["cwl"] = is_cwl
kwds["execution_type"] = "Run"
if kwds.get("engine", None) is None:
if is_cwl:
kwds["engine"] = "cwltool"
elif kwds.get('galaxy_url', None):
kwds["engine"] = "external_galaxy"
else:
kwds["engine"] = "galaxy"
with engine_context(ctx, **kwds) as engine:
run_result = engine.run(runnable, job_path)
if not run_result.was_successful:
warn("Run failed [%s]" % unicodify(run_result))
elif kwds.get('no_wait'):
info('Run successfully executed - exiting without waiting for results.')
else:
output_json = kwds.get("output_json", None)
outputs_dict = run_result.outputs_dict
if output_json:
with open(output_json, "w") as f:
json.dump(outputs_dict, f)
info('Run completed successfully.')
report_data = StructuredData(data={'tests': [run_result.structured_data()], 'version': '0.1'})
report_data.calculate_summary_data()
return_value = handle_reports_and_summary(ctx, report_data.structured_data, kwds=kwds)
ctx.exit(return_value)
def test_plain_init(self):
ctx = cli.PlanemoCliContext()
ctx.planemo_directory = "/tmp/planemo-test-workspace"
cat_tool = os.path.join(PROJECT_TEMPLATES_DIR, "demo", "cat.xml")
test_workflow_path = os.path.join(TEST_DATA_DIR, 'wf2.ga')
with engine_context(ctx, extra_tools=(cat_tool, )) as galaxy_engine:
with galaxy_engine.ensure_runnables_served(
[for_path(test_workflow_path)]) as config:
wfid = config.workflow_id(test_workflow_path)
# commands to test
profile_list_cmd = ["profile_list"]
profile_create_cmd = [
"profile_create", "test_ext_profile", "--galaxy_url",
config.galaxy_url, "--galaxy_user_key", config.user_api_key
]
alias_create_cmd = [
"create_alias", wfid, "--alias", "test_wf_alias",
"--profile", "test_ext_profile"
]
alias_list_cmd = [
"list_alias", "--profile", "test_ext_profile"
]
alias_delete_cmd = [
"delete_alias", "--alias", "test_wf_alias", "--profile",
"test_ext_profile"
]
profile_delete_cmd = ["profile_delete", "test_ext_profile"]
run_cmd = [
"run", "test_wf_alias",
os.path.join(TEST_DATA_DIR, "wf2-job.yml"), "--profile",
"test_ext_profile"
]
list_invocs_cmd = [
"list_invocations", "test_wf_alias", "--profile",
"test_ext_profile"
]
rerun_cmd = [
"rerun", "--invocation", "invocation_id", "--profile",
"test_ext_profile"
]
upload_data_cmd = [
"upload_data", "test_wf_alias",
os.path.join(TEST_DATA_DIR, "wf2-job.yml"), "new-job.yml",
"--profile", "test_ext_profile"
]
workflow_test_init_cmd = [
"workflow_test_init", "invocation_id", "--from_invocation",
"--profile", "test_ext_profile"
]
test_workflow_test_init_cmd = [
"test", "TestWorkflow1.ga", "--profile", "test_ext_profile"
]
# test alias and profile creation
result = self._check_exit_code(profile_list_cmd)
assert 'test_ext_profile' not in result.output
result = self._check_exit_code(profile_create_cmd)
assert 'Profile [test_ext_profile] created' in result.output
result = self._check_exit_code(profile_list_cmd)
assert 'test_ext_profile' in result.output
result = self._check_exit_code(alias_create_cmd)
assert 'Alias test_wf_alias created.' in result.output
result = self._check_exit_code(alias_list_cmd)
assert 'test_wf_alias' in result.output
assert wfid in result.output
assert '1 aliases were found for profile test_ext_profile.' in result.output
# test upload_data command
self._check_exit_code(upload_data_cmd)
with open("new-job.yml") as f:
new_job = yaml.safe_load(f)
assert list(new_job['WorkflowInput1']) == list(
new_job['WorkflowInput2']) == ["class", "galaxy_id"]
# test WF execution (from wfid) using created profile and alias
result = self._check_exit_code(run_cmd)
assert 'Run failed' not in result.output
result = self._check_exit_code(run_cmd + ["--no_wait"])
assert 'Run successfully executed' in result.output
result = self._check_exit_code(list_invocs_cmd)
assert '2 invocations found.' in result.output
assert '1 jobs ok' in result.output or '"ok": 1' in result.output # so it passes regardless if tabulate is installed or not
# test rerun
invocation_id = config.user_gi.workflows.get_invocations(
wfid)[0]['id']
rerun_cmd[2] = invocation_id
result = self._check_exit_code(rerun_cmd)
assert 'No jobs matching the specified invocation' in result.output
# test generating test case from invocation_id
workflow_test_init_cmd[1] = invocation_id
self._check_exit_code(workflow_test_init_cmd)
assert os.path.exists('TestWorkflow1.ga')
assert os.path.exists('TestWorkflow1-tests.yml')
self._check_exit_code(test_workflow_test_init_cmd)
# test alias and profile deletion
result = self._check_exit_code(alias_delete_cmd)
assert 'Alias test_wf_alias was successfully deleted from profile test_ext_profile' in result.output
result = self._check_exit_code(alias_list_cmd)
assert '0 aliases were found for profile test_ext_profile.' in result.output
result = self._check_exit_code(profile_delete_cmd)
assert 'Profile deleted.' in result.output
result = self._check_exit_code(profile_list_cmd)
assert 'test_ext_profile' not in result.output
def cli(ctx, paths, **kwds): # noqa C901
"""Auto-update tool requirements by checking against Conda and updating if newer versions are available."""
assert_tools = kwds.get("assert_tools", True)
recursive = kwds.get("recursive", False)
exit_codes = []
modified_files = set()
tools_to_skip = [line.rstrip() for line in open(kwds['skiplist'])
] if kwds['skiplist'] else []
runnables = for_paths(paths)
if any(r.type in {RunnableType.galaxy_tool, RunnableType.directory}
for r in runnables):
# update Galaxy tools
for (tool_path,
tool_xml) in yield_tool_sources_on_paths(ctx, paths, recursive):
if tool_path.split('/')[-1] in tools_to_skip:
info("Skipping tool %s" % tool_path)
continue
info("Auto-updating tool %s" % tool_path)
try:
updated = autoupdate.autoupdate_tool(
ctx, tool_path, modified_files=modified_files, **kwds)
if updated:
modified_files.update(updated)
except Exception as e:
error(
f"{tool_path} could not be updated - the following error was raised: {e.__str__()}"
)
if handle_tool_load_error(tool_path, tool_xml):
exit_codes.append(EXIT_CODE_GENERIC_FAILURE)
continue
else:
exit_codes.append(EXIT_CODE_OK)
workflows = [
r for r in runnables if r.type == RunnableType.galaxy_workflow
]
modified_workflows = []
if workflows:
assert is_galaxy_engine(**kwds)
if kwds.get("engine") != "external_galaxy":
kwds["install_most_recent_revision"] = True
kwds["install_resolver_dependencies"] = False
kwds["install_repository_dependencies"] = False
kwds['shed_install'] = True
with engine_context(ctx, **kwds) as galaxy_engine:
with galaxy_engine.ensure_runnables_served(workflows) as config:
for workflow in workflows:
if config.updated_repos.get(workflow.path) or kwds.get(
"engine") == "external_galaxy":
info("Auto-updating workflow %s" % workflow.path)
updated_workflow = autoupdate.autoupdate_wf(
ctx, config, workflow)
if workflow.path.endswith(".ga"):
with open(workflow.path, 'w') as f:
json.dump(updated_workflow,
f,
indent=4,
sort_keys=True)
else:
format2_wrapper = from_galaxy_native(
updated_workflow, json_wrapper=True)
with open(workflow.path, "w") as f:
f.write(format2_wrapper["yaml_content"])
modified_workflows.append(workflow.path)
else:
info(
"No newer tool versions were found, so the workflow was not updated."
)
if kwds['test']:
if not modified_files:
info("No tools were updated, so no tests were run.")
else:
with temp_directory(dir=ctx.planemo_directory) as temp_path:
# only test tools in updated directories
modified_paths = [
path for path, tool_xml in yield_tool_sources_on_paths(
ctx, paths, recursive) if path in modified_files
]
info(
f"Running tests for the following auto-updated tools: {', '.join(modified_paths)}"
)
runnables = for_paths(modified_paths + modified_workflows,
temp_path=temp_path)
kwds["engine"] = "galaxy"
return_value = test_runnables(ctx,
runnables,
original_paths=paths,
**kwds)
exit_codes.append(return_value)
return coalesce_return_codes(exit_codes, assert_at_least_one=assert_tools)
def test_can_handle():
ctx = test_context()
for engine_type in ["galaxy", "cwltool"]:
with engine_context(ctx, engine=engine_type) as e:
for key, value in CAN_HANDLE[engine_type].items():
assert bool(e.can_run(for_path(key))) is value
def test_plain_init(self):
ctx = cli.PlanemoCliContext()
ctx.planemo_directory = "/tmp/planemo-test-workspace"
cat_tool = os.path.join(PROJECT_TEMPLATES_DIR, "demo", "cat.xml")
test_workflow_path = os.path.join(TEST_DATA_DIR, 'wf2.ga')
with engine_context(ctx, extra_tools=(cat_tool, )) as galaxy_engine:
with galaxy_engine.ensure_runnables_served(
[for_path(test_workflow_path)]) as config:
wfid = config.workflow_id(test_workflow_path)
# commands to test
profile_list_cmd = ["profile_list"]
profile_create_cmd = [
"profile_create", "test_ext_profile", "--galaxy_url",
config.galaxy_url, "--galaxy_user_key", config.user_api_key
]
alias_create_cmd = [
"create_alias", wfid, "--alias", "test_wf_alias",
"--profile", "test_ext_profile"
]
alias_list_cmd = [
"list_alias", "--profile", "test_ext_profile"
]
alias_delete_cmd = [
"delete_alias", "--alias", "test_wf_alias", "--profile",
"test_ext_profile"
]
profile_delete_cmd = ["profile_delete", "test_ext_profile"]
run_cmd = [
"run", "test_wf_alias",
os.path.join(TEST_DATA_DIR, "wf2-job.yml"), "--profile",
"test_ext_profile"
]
list_invocs_cmd = [
"list_invocations", "test_wf_alias", "--profile",
"test_ext_profile"
]
# test alias and profile creation
result = self._check_exit_code(profile_list_cmd)
assert 'test_ext_profile' not in result.output
result = self._check_exit_code(profile_create_cmd)
assert 'Profile [test_ext_profile] created' in result.output
result = self._check_exit_code(profile_list_cmd)
assert 'test_ext_profile' in result.output
result = self._check_exit_code(alias_create_cmd)
assert 'Alias test_wf_alias created.' in result.output
result = self._check_exit_code(alias_list_cmd)
assert 'test_wf_alias' in result.output
assert wfid in result.output
assert '1 aliases were found for profile test_ext_profile.' in result.output
# test WF execution (from wfid) using created profile and alias
result = self._check_exit_code(run_cmd)
assert 'Run failed' not in result.output
result = self._check_exit_code(list_invocs_cmd)
assert '1 invocations found.' in result.output
assert '1 jobs ok' in result.output or '"ok": 1' in result.output # so it passes regardless if tabulate is installed or not
# test alias and profile deletion
result = self._check_exit_code(alias_delete_cmd)
assert 'Alias test_wf_alias was successfully deleted from profile test_ext_profile' in result.output
result = self._check_exit_code(alias_list_cmd)
assert '0 aliases were found for profile test_ext_profile.' in result.output
result = self._check_exit_code(profile_delete_cmd)
assert 'Profile deleted.' in result.output
result = self._check_exit_code(profile_list_cmd)
assert 'test_ext_profile' not in result.output