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, 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 test_io_capture():
"""Test :func:`planemo.io.conditionally_captured_io`."""
with io.conditionally_captured_io(True, tee=False) as capture:
io.warn("Problem...")
assert_equal(capture[0]["data"], "Problem...")
with io.conditionally_captured_io(True, tee=False) as capture:
io.shell("echo 'Problem...'")
assert_equal(capture[0]["data"], "echo 'Problem...'")
assert_equal(capture[1]["data"], "Problem...")
with io.conditionally_captured_io(True, tee=False) as capture:
io.communicate("echo 'Problem...'")
assert_equal(capture[0]["data"], "echo 'Problem...'")
assert_equal(capture[1]["data"], "Problem...")
with io.conditionally_captured_io(False, tee=False) as capture:
io.communicate("echo 'Test...'")
assert capture is None
def test_io_capture():
"""Test :func:`planemo.io.conditionally_captured_io`."""
with io.conditionally_captured_io(True, tee=False) as capture:
io.warn("Problem...")
assert_equal(capture[0]["data"], "Problem...")
with io.conditionally_captured_io(True, tee=False) as capture:
io.shell("echo 'Problem...'")
assert_equal(capture[0]["data"], "echo 'Problem...'")
assert_equal(capture[1]["data"], "Problem...")
with io.conditionally_captured_io(True, tee=False) as capture:
io.communicate("echo 'Problem...'")
assert_equal(capture[0]["data"], "echo 'Problem...'")
assert_equal(capture[1]["data"], "Problem...")
with io.conditionally_captured_io(False, tee=False) as capture:
io.communicate("echo 'Test...'")
assert capture is None
def run_galaxy(ctx, path, job_path, **kwds):
kwds["cwl"] = True
conformance_test = kwds.get("conformance_test", False)
with conditionally_captured_io(conformance_test):
with serve_daemon(ctx, [path], **kwds) as config:
try:
cwl_run = run_cwl_tool(path, job_path, config, **kwds)
except Exception:
io.warn("Problem running cwl tool...")
print(config.log_contents)
raise
print(cwl_run.cwl_command_state)
return 0
