def write_tool_description(ctx, tool_description, **kwds):
"""Write a tool description to the file system guided by supplied CLI kwds."""
tool_id = kwds.get("id")
output = kwds.get("tool")
if not output:
extension = "cwl" if kwds.get("cwl") else "xml"
output = "%s.%s" % (tool_id, extension)
if not io.can_write_to_path(output, **kwds):
ctx.exit(1)
io.write_file(output, tool_description.contents)
io.info("Tool written to %s" % output)
test_contents = tool_description.test_contents
if test_contents:
sep = "-" if "-" in tool_id else "_"
tests_path = "%s%stests.yml" % (kwds.get("id"), sep)
if not io.can_write_to_path(tests_path, **kwds):
ctx.exit(1)
io.write_file(tests_path, test_contents)
io.info("Tool tests written to %s" % tests_path)
macros = kwds["macros"]
macros_file = "macros.xml"
if macros and not os.path.exists(macros_file):
io.write_file(macros_file, tool_description.macro_contents)
elif macros:
io.info(REUSING_MACROS_MESSAGE)
if tool_description.test_files:
if not os.path.exists("test-data"):
io.info("No test-data directory, creating one.")
io.shell("mkdir -p 'test-data'")
for test_file in tool_description.test_files:
io.info("Copying test-file %s" % test_file)
io.shell("cp '%s' 'test-data'" % test_file)
def shed_init(ctx, path, **kwds):
"""Initialize a new shed repository."""
if not os.path.exists(path):
os.makedirs(path)
shed_config_path = os.path.join(path, SHED_CONFIG_NAME)
if not can_write_to_path(shed_config_path, **kwds):
# .shed.yml exists and no --force sent.
return 1
create_failed = _create_shed_config(ctx, shed_config_path, **kwds)
if create_failed:
return 1
repo_dependencies_path = os.path.join(path, REPO_DEPENDENCIES_CONFIG_NAME)
from_workflow = kwds.get("from_workflow")
if from_workflow:
workflow_name = os.path.basename(from_workflow)
workflow_target = os.path.join(path, workflow_name)
if not os.path.exists(workflow_target):
shutil.copyfile(from_workflow, workflow_target)
if not can_write_to_path(repo_dependencies_path, **kwds):
return 1
repo_pairs = _parse_repos_from_workflow(from_workflow)
repository_dependencies = RepositoryDependencies(repo_pairs)
repository_dependencies.write_to_path(repo_dependencies_path)
return 0
def shed_init(ctx, path, **kwds):
if not os.path.exists(path):
os.makedirs(path)
shed_config_path = os.path.join(path, SHED_CONFIG_NAME)
if not can_write_to_path(shed_config_path, **kwds):
# .shed.yml exists and no --force sent.
return 1
create_failed = _create_shed_config(ctx, shed_config_path, **kwds)
if create_failed:
return 1
repo_dependencies_path = os.path.join(path, REPO_DEPENDENCIES_CONFIG_NAME)
from_workflow = kwds.get("from_workflow", None)
if from_workflow:
workflow_name = os.path.basename(from_workflow)
workflow_target = os.path.join(path, workflow_name)
if not os.path.exists(workflow_target):
shutil.copyfile(from_workflow, workflow_target)
if not can_write_to_path(repo_dependencies_path, **kwds):
return 1
repo_pairs = _parse_repos_from_workflow(from_workflow)
repository_dependencies = RepositoryDependencies()
repository_dependencies.repo_pairs = repo_pairs
repository_dependencies.write_to_path(repo_dependencies_path)
return 0
def shed_init(ctx, path, **kwds):
if not os.path.exists(path):
os.makedirs(path)
shed_config_path = os.path.join(path, SHED_CONFIG_NAME)
if not can_write_to_path(shed_config_path, **kwds):
# .shed.yml exists and no --force sent.
return 1
_create_shed_config(ctx, shed_config_path, **kwds)
repo_dependencies_path = os.path.join(path, "repository_dependencies.xml")
from_workflow = kwds.get("from_workflow", None)
if from_workflow:
workflow_name = os.path.basename(from_workflow)
workflow_target = os.path.join(path, workflow_name)
if not os.path.exists(workflow_target):
shutil.copyfile(from_workflow, workflow_target)
if not can_write_to_path(repo_dependencies_path, **kwds):
return 1
repo_pairs = _parse_repos_from_workflow(from_workflow)
contents = '<repositories description="">'
line_template = ' <repository owner="%s" name="%s" />'
for (owner, name) in repo_pairs:
contents += line_template % (owner, name)
contents += "</repositories>"
with open(repo_dependencies_path, "w") as f:
f.write(contents)
return 0
def write_tool_description(ctx, tool_description, **kwds):
"""Write a tool description to the file system guided by supplied CLI kwds."""
tool_id = kwds.get("id")
output = kwds.get("tool")
if not output:
extension = "cwl" if kwds.get("cwl") else "xml"
output = "%s.%s" % (tool_id, extension)
if not io.can_write_to_path(output, **kwds):
ctx.exit(1)
io.write_file(output, tool_description.contents)
io.info("Tool written to %s" % output)
test_contents = tool_description.test_contents
if test_contents:
sep = "-" if "-" in tool_id else "_"
tests_path = "%s%stests.yml" % (kwds.get("id"), sep)
if not io.can_write_to_path(tests_path, **kwds):
ctx.exit(1)
io.write_file(tests_path, test_contents)
io.info("Tool tests written to %s" % tests_path)
macros = kwds["macros"]
macros_file = "macros.xml"
if macros and not os.path.exists(macros_file):
io.write_file(macros_file, tool_description.macro_contents)
elif macros:
io.info(REUSING_MACROS_MESSAGE)
if tool_description.test_files:
if not os.path.exists("test-data"):
io.info("No test-data directory, creating one.")
io.shell("mkdir -p 'test-data'")
for test_file in tool_description.test_files:
io.info("Copying test-file %s" % test_file)
io.shell("cp '%s' 'test-data'" % test_file)
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, **kwds):
"""Generate a tool outline from supplied arguments.
"""
invalid = _validate_kwds(kwds)
if invalid:
return invalid
output = kwds.get("tool")
if not output:
output = "%s.xml" % kwds.get("id")
if not io.can_write_to_path(output, **kwds):
sys.exit(1)
tool_description = tool_builder.build(**kwds)
open(output, "w").write(tool_description.contents)
io.info("Tool written to %s" % output)
macros = kwds["macros"]
macros_file = "macros.xml"
if macros and not os.path.exists(macros_file):
open(macros_file, "w").write(tool_description.macro_contents)
elif macros:
io.info(REUSING_MACROS_MESSAGE)
if tool_description.test_files:
if not os.path.exists("test-data"):
io.info("No test-data directory, creating one.")
io.shell("mkdir -p 'test-data'")
for test_file in tool_description.test_files:
io.info("Copying test-file %s" % test_file)
io.shell("cp '%s' 'test-data'" % test_file)
def cli(ctx, **kwds):
"""Generate a tool outline from supplied arguments.
"""
invalid = _validate_kwds(kwds)
if invalid:
return invalid
output = kwds.get("tool")
if not output:
output = "%s.xml" % kwds.get("id")
if not io.can_write_to_path(output, **kwds):
sys.exit(1)
tool_description = tool_builder.build(**kwds)
open(output, "w").write(tool_description.contents)
io.info("Tool written to %s" % output)
macros = kwds["macros"]
macros_file = "macros.xml"
if macros and not os.path.exists(macros_file):
open(macros_file, "w").write(tool_description.macro_contents)
else:
io.info(REUSING_MACROS_MESSAGE)
if tool_description.test_files:
if not os.path.exists("test-data"):
io.info("No test-data directory, creating one.")
io.shell("mkdir -p 'test-data'")
for test_file in tool_description.test_files:
io.info("Copying test-file %s" % test_file)
io.shell("cp '%s' 'test-data'" % test_file)
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 write_tool_description(ctx, tool_description, **kwds):
"""Write a tool description to the file system guided by supplied CLI kwds."""
tool_id = kwds.get("id")
output = kwds.get("tool")
if not output:
extension = "cwl" if kwds.get("cwl") else "xml"
output = "%s.%s" % (tool_id, extension)
if not io.can_write_to_path(output, **kwds):
ctx.exit(1)
io.write_file(output, tool_description.contents)
io.info("Tool written to %s" % output)
for tool_file in tool_description.tool_files:
if tool_file.contents is None:
continue
path = tool_file.filename
if not io.can_write_to_path(path, **kwds):
ctx.exit(1)
io.write_file(path, tool_file.contents)
io.info("Tool %s written to %s" % (tool_file.description, path))
macros = kwds["macros"]
macros_file = "macros.xml"
if macros and not os.path.exists(macros_file):
io.write_file(macros_file, tool_description.macro_contents)
elif macros:
io.info(REUSING_MACROS_MESSAGE)
if tool_description.test_files:
if not os.path.exists("test-data"):
io.info("No test-data directory, creating one.")
os.makedirs('test-data')
for test_file in tool_description.test_files:
io.info("Copying test-file %s" % test_file)
try:
shutil.copy(test_file, 'test-data')
except Exception as e:
io.info("Copy of %s failed: %s" % (test_file, e))
def write_tool_description(ctx, tool_description, **kwds):
"""Write a tool description to the file system guided by supplied CLI kwds."""
tool_id = kwds.get("id")
output = kwds.get("tool")
if not output:
extension = "cwl" if kwds.get("cwl") else "xml"
output = "%s.%s" % (tool_id, extension)
if not io.can_write_to_path(output, **kwds):
ctx.exit(1)
io.write_file(output, tool_description.contents)
io.info("Tool written to %s" % output)
for tool_file in tool_description.tool_files:
if tool_file.contents is None:
continue
path = tool_file.filename
if not io.can_write_to_path(path, **kwds):
ctx.exit(1)
io.write_file(path, tool_file.contents)
io.info("Tool %s written to %s" % (tool_file.description, path))
macros = kwds["macros"]
macros_file = "macros.xml"
if macros and not os.path.exists(macros_file):
io.write_file(macros_file, tool_description.macro_contents)
elif macros:
io.info(REUSING_MACROS_MESSAGE)
if tool_description.test_files:
if not os.path.exists("test-data"):
io.info("No test-data directory, creating one.")
os.makedirs('test-data')
for test_file in tool_description.test_files:
io.info("Copying test-file %s" % test_file)
try:
shutil.copy(test_file, 'test-data')
except Exception as e:
io.info("Copy of %s failed: %s" % (test_file, e))
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)
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)
