def cli(ctx, paths, **kwds):
"""Install conda packages for tool requirements."""
conda_context = build_conda_context(ctx, **kwds)
if not conda_context.is_conda_installed():
auto_init = kwds.get("conda_auto_init", False)
failed = True
if auto_init:
if conda_context.can_install_conda():
if conda_util.install_conda(conda_context):
error("Attempted to install conda and failed.")
else:
failed = False
else:
error("Cannot install conda, failing conda_install.")
else:
error(
"Conda not configured - run planemo conda_init' or pass --conda_auto_init to continue."
)
if failed:
raise ExitCodeException(EXIT_CODE_FAILED_DEPENDENCIES)
return_codes = []
for conda_target in collect_conda_targets(ctx, paths):
ctx.log("Install conda target %s" % conda_target)
return_code = conda_util.install_conda_target(
conda_target, conda_context=conda_context)
return_codes.append(return_code)
return coalesce_return_codes(return_codes, assert_at_least_one=True)
def cli(ctx, paths, **kwds):
"""Install conda packages for tool requirements."""
conda_context = build_conda_context(ctx, **kwds)
if not conda_context.is_conda_installed():
auto_init = kwds.get("conda_auto_init", False)
failed = True
if auto_init:
if conda_context.can_install_conda():
if conda_util.install_conda(conda_context):
error("Attempted to install conda and failed.")
else:
failed = False
else:
error("Cannot install conda, failing conda_install.")
else:
error("Conda not configured - run planemo conda_init' or pass --conda_auto_init to continue.")
if failed:
raise ExitCodeException(EXIT_CODE_FAILED_DEPENDENCIES)
return_codes = []
for conda_target in collect_conda_targets(ctx, paths):
ctx.log("Install conda target %s" % conda_target)
return_code = conda_util.install_conda_target(
conda_target, conda_context=conda_context
)
return_codes.append(return_code)
return coalesce_return_codes(return_codes, assert_at_least_one=True)
def cli(ctx, path, **kwds):
"""Install conda packages for tool requirements."""
conda_context = build_conda_context(**kwds)
return_codes = []
for conda_target in collect_conda_targets(path):
ctx.log("Install conda target %s" % conda_target)
return_code = conda_util.install_conda_target(
conda_target, conda_context=conda_context)
return_codes.append(return_code)
return coalesce_return_codes(return_codes, assert_at_least_one=True)
def cli(ctx, paths, **kwds):
"""Install conda packages for tool requirements."""
conda_context = build_conda_context(ctx, handle_auto_init=True, **kwds)
return_codes = []
for conda_target in collect_conda_targets(ctx, paths, recursive=kwds["recursive"]):
ctx.log("Install conda target %s" % conda_target)
return_code = conda_util.install_conda_target(
conda_target, conda_context=conda_context, skip_environment=kwds.get("global", False)
)
return_codes.append(return_code)
return coalesce_return_codes(return_codes, assert_at_least_one=True)
def lint_recipes_on_paths(ctx, paths, **kwds):
"""Apply conda linting procedure to recipes on supplied paths."""
assert_tools = kwds.get("assert_recipes", True)
recursive = kwds.get("recursive", False)
exit_codes = []
for recipe_dir in yield_recipes_on_paths(ctx, paths, recursive):
if lint_conda_recipe(ctx, recipe_dir, **kwds) != 0:
exit_codes.append(EXIT_CODE_GENERIC_FAILURE)
else:
exit_codes.append(EXIT_CODE_OK)
return coalesce_return_codes(exit_codes, assert_at_least_one=assert_tools)
def lint_recipes_on_paths(ctx, paths, **kwds):
"""Apply conda linting procedure to recipes on supplied paths."""
assert_tools = kwds.get("assert_recipes", True)
recursive = kwds.get("recursive", False)
exit_codes = []
for recipe_dir in yield_recipes_on_paths(ctx, paths, recursive):
if lint_conda_recipe(ctx, recipe_dir, **kwds) != 0:
exit_codes.append(EXIT_CODE_GENERIC_FAILURE)
else:
exit_codes.append(EXIT_CODE_OK)
return coalesce_return_codes(exit_codes, assert_at_least_one=assert_tools)
def cli(ctx, path, **kwds):
"""Install conda packages for tool requirements."""
conda_context = build_conda_context(**kwds)
return_codes = []
for conda_target in collect_conda_targets(path):
ctx.log("Install conda target %s" % conda_target)
return_code = conda_util.install_conda_target(
conda_target, conda_context=conda_context
)
return_codes.append(return_code)
return coalesce_return_codes(return_codes, assert_at_least_one=True)
def cli(ctx, paths, **kwds):
"""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 []
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(
"{} could not be updated - the following error was raised: {}".
format(tool_path, 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)
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, 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 for_each_repository(ctx, function, paths, **kwds):
ret_codes = []
for path in paths:
with _path_on_disk(ctx, path) as raw_path:
try:
for realized_repository in _realize_effective_repositories(
ctx, raw_path, **kwds):
ret_codes.append(function(realized_repository))
except RealizationException:
error(REALIZAION_PROBLEMS_MESSAGE)
return 254
return coalesce_return_codes(ret_codes)
def cli(ctx, paths, **kwds):
"""Install conda packages for tool requirements."""
conda_context = build_conda_context(ctx, handle_auto_init=True, **kwds)
return_codes = []
for conda_target in collect_conda_targets(ctx,
paths,
recursive=kwds["recursive"]):
ctx.log("Install conda target %s" % conda_target)
return_code = conda_util.install_conda_target(
conda_target,
conda_context=conda_context,
skip_environment=kwds.get("global", False))
return_codes.append(return_code)
return coalesce_return_codes(return_codes, assert_at_least_one=True)
def lint_tools_on_path(ctx, paths, lint_args, **kwds):
assert_tools = kwds.get("assert_tools", True)
recursive = kwds.get("recursive", False)
exit_codes = []
for (tool_path, tool_xml) in yield_tool_sources_on_paths(ctx, paths, recursive):
if handle_tool_load_error(tool_path, tool_xml):
exit_codes.append(EXIT_CODE_GENERIC_FAILURE)
continue
info("Linting tool %s" % tool_path)
if not lint_tool_source(tool_xml, **lint_args):
error("Failed linting")
exit_codes.append(EXIT_CODE_GENERIC_FAILURE)
else:
exit_codes.append(EXIT_CODE_OK)
return coalesce_return_codes(exit_codes, assert_at_least_one=assert_tools)
def for_each_repository(ctx, function, paths, **kwds):
ret_codes = []
for path in paths:
with _path_on_disk(path) as raw_path:
try:
for realized_repository in _realize_effective_repositories(
ctx, raw_path, **kwds
):
ret_codes.append(
function(realized_repository)
)
except RealizationException:
error(REALIZAION_PROBLEMS_MESSAGE)
return 254
return coalesce_return_codes(ret_codes)
def lint_tools_on_path(ctx, paths, lint_args, **kwds):
assert_tools = kwds.get("assert_tools", True)
recursive = kwds.get("recursive", False)
exit_codes = []
for (tool_path,
tool_xml) in yield_tool_sources_on_paths(ctx, paths, recursive):
if handle_tool_load_error(tool_path, tool_xml):
exit_codes.append(EXIT_CODE_GENERIC_FAILURE)
continue
info("Linting tool %s" % tool_path)
if not lint_tool_source(tool_xml, **lint_args):
error("Failed linting")
exit_codes.append(EXIT_CODE_GENERIC_FAILURE)
else:
exit_codes.append(EXIT_CODE_OK)
return coalesce_return_codes(exit_codes, assert_at_least_one=assert_tools)
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)
