import inspect
import json
import os
import re
from collections import OrderedDict
from typing import (
Any,
Dict,
Iterable,
Iterator,
List,
Optional,
Tuple,
TYPE_CHECKING,
Union,
)
import requests
import yaml
from bioblend import toolshed
from bioblend.toolshed import ToolShedInstance
from galaxy.tool_util.lint import LintContext
from galaxy.tool_util.loader_directory import EXCLUDE_WALK_DIRS
from galaxy.tool_util.parser.yaml import __to_test_assert_list
from galaxy.tool_util.verify import asserts
from gxformat2.lint import (
lint_format2,
lint_ga,
)
from gxformat2.yaml import ordered_load
from planemo.exit_codes import (
EXIT_CODE_GENERIC_FAILURE,
EXIT_CODE_OK,
)
from planemo.galaxy.workflows import (
input_labels,
output_labels,
required_input_labels,
)
from planemo.runnable import (
cases,
for_path,
TestCase,
)
from planemo.shed import DOCKSTORE_REGISTRY_CONF
if TYPE_CHECKING:
from planemo.cli import PlanemoCliContext
POTENTIAL_WORKFLOW_FILES = re.compile(r"^.*(\.yml|\.yaml|\.ga)$")
DOCKSTORE_REGISTRY_CONF_VERSION = "1.2"
MAIN_TOOLSHED_URL = "https://toolshed.g2.bx.psu.edu"
[docs]
class WorkflowLintContext(LintContext):
# Setup training topic for linting - probably should pass this through
# from click arguments.
training_topic = None
[docs]
def generate_dockstore_yaml(directory: str, publish: bool = True) -> str:
workflows = []
all_workflow_paths = list(find_workflow_descriptions(directory))
for workflow_path in all_workflow_paths:
test_parameter_path = f"{workflow_path.rsplit('.', 1)[0]}-tests.yml"
workflow_entry: Dict[str, Any] = {
# TODO: support CWL
"name": "main" if len(all_workflow_paths) == 1 else os.path.basename(workflow_path).split(".ga")[0],
"subclass": "Galaxy",
"publish": publish,
"primaryDescriptorPath": f"/{os.path.relpath(workflow_path, directory)}",
}
if os.path.exists(test_parameter_path):
workflow_entry["testParameterFiles"] = [f"/{os.path.relpath(test_parameter_path, directory)}"]
with open(workflow_path) as f:
workflow_dict = ordered_load(f)
# add author
if len(workflow_dict.get("creator", [])) > 0:
creators = workflow_dict["creator"]
authors = []
for creator in creators:
author = {}
# Put name first
if "name" in creator:
author["name"] = creator["name"]
for field, value in creator.items():
if field in ["class", "name"]:
continue
if field == "identifier":
# Check if it is an orcid:
# Read https://support.orcid.org/hc/en-us/articles/360006897674-Structure-of-the-ORCID-Identifier
orcid = re.findall(r"(?:\d{4}-){3}\d{3}[0-9X]", value)
if len(orcid) > 0:
# Check the orcid is valid
if (
requests.get(
f"https://orcid.org/{orcid[0]}",
headers={"Accept": "application/xml"},
allow_redirects=True,
).status_code
== 200
):
author["orcid"] = orcid[0]
else:
# If it is not put as identifier
author["identifier"] = value
else:
author["identifier"] = value
else:
author[field] = value
authors.append(author)
workflow_entry["authors"] = authors
workflows.append(workflow_entry)
# Force version to the top of file but serializing rest of config separately
contents = "version: %s\n" % DOCKSTORE_REGISTRY_CONF_VERSION
contents += yaml.dump({"workflows": workflows}, sort_keys=False)
return contents
[docs]
def lint_workflow_artifacts_on_paths(
ctx: "PlanemoCliContext", paths: Iterable[str], lint_args: Dict[str, Union[str, List[str]]]
) -> int:
report_level = lint_args["level"]
lint_context = WorkflowLintContext(report_level, skip_types=lint_args["skip_types"])
for path in paths:
_lint_workflow_artifacts_on_path(lint_context, path, lint_args)
if lint_context.failed(lint_args["fail_level"]):
return EXIT_CODE_GENERIC_FAILURE
else:
return EXIT_CODE_OK
def _lint_workflow_artifacts_on_path(
lint_context: WorkflowLintContext, path: str, lint_args: Dict[str, Union[str, List[str]]]
) -> None:
for potential_workflow_artifact_path in find_potential_workflow_files(path):
if os.path.basename(potential_workflow_artifact_path) == DOCKSTORE_REGISTRY_CONF:
lint_context.lint("lint_dockstore", _lint_dockstore_config, potential_workflow_artifact_path)
elif looks_like_a_workflow(potential_workflow_artifact_path):
def structure(path, lint_context):
with open(path) as f:
workflow_dict = ordered_load(f)
workflow_class = workflow_dict.get("class")
lint_func = lint_format2 if workflow_class == "GalaxyWorkflow" else lint_ga
lint_func(lint_context, workflow_dict, path=path)
lint_context.lint("lint_structure", structure, potential_workflow_artifact_path)
lint_context.lint("lint_best_practices", _lint_best_practices, potential_workflow_artifact_path)
lint_context.lint("lint_tests", _lint_tsts, potential_workflow_artifact_path)
lint_context.lint("lint_tool_ids", _lint_tool_ids, potential_workflow_artifact_path)
else:
# Allow linting ro crates and such also
pass
# misspell for pytest
def _lint_tsts(path: str, lint_context: WorkflowLintContext) -> None:
runnables = for_path(path)
if not isinstance(runnables, list):
runnables = [runnables]
for runnable in runnables:
test_cases = cases(runnable)
if len(test_cases) == 0:
lint_context.warn("Workflow missing test cases.")
return
all_tests_valid = True
for test_case in test_cases:
if isinstance(test_case, TestCase):
if not _lint_case(path, test_case, lint_context):
all_tests_valid = False
else:
lint_context.warn(f"Test case of type {type(test_case)} not currently supported.")
all_tests_valid = False
if all_tests_valid:
lint_context.valid(f"Tests appear structurally correct for {runnable.path}")
def _lint_best_practices(path: str, lint_context: WorkflowLintContext) -> None: # noqa: C901
"""
This function duplicates the checks made by Galaxy's best practices panel:
https://github.com/galaxyproject/galaxy/blob/5396bb15fe8cfcf2e89d46c1d061c49b60e2f0b1/client/src/components/Workflow/Editor/Lint.vue
"""
def check_json_for_untyped_params(j):
values = j.values() if isinstance(j, dict) else j
for value in values:
if type(value) in [list, dict, OrderedDict]:
if check_json_for_untyped_params(value):
return True
elif isinstance(value, str):
if re.match(r"\$\{.+?\}", value):
return True
return False
with open(path) as f:
workflow_dict = ordered_load(f)
steps = workflow_dict.get("steps", {})
# annotation
if not workflow_dict.get("annotation"):
lint_context.warn("Workflow is not annotated.")
# creator
if not len(workflow_dict.get("creator", [])) > 0:
lint_context.warn("Workflow does not specify a creator.")
# license
if not workflow_dict.get("license"):
lint_context.warn("Workflow does not specify a license.")
# checks on individual steps
for step in steps.values():
# disconnected inputs
if step.get("type") not in ["data_collection_input", "parameter_input"]:
for input in step.get("inputs", []):
if input.get("name") not in step.get("input_connections"): # TODO: check optional
lint_context.warn(
f"Input {input.get('name')} of workflow step {step.get('annotation') or step.get('id')} is disconnected."
)
# missing metadata
if not step.get("annotation"):
lint_context.warn(f"Workflow step with ID {step.get('id')} has no annotation.")
if not step.get("label"):
lint_context.warn(f"Workflow step with ID {step.get('id')} has no label.")
# untyped parameters
if workflow_dict.get("class") == "GalaxyWorkflow":
tool_state = step.get("tool_state", {})
pjas = step.get("out", {})
else:
tool_state = json.loads(step.get("tool_state", "{}"))
pjas = step.get("post_job_actions", {})
if check_json_for_untyped_params(tool_state):
lint_context.warn(f"Workflow step with ID {step.get('id')} specifies an untyped parameter as an input.")
if check_json_for_untyped_params(pjas):
lint_context.warn(
f"Workflow step with ID {step.get('id')} specifies an untyped parameter in the post-job actions."
)
# unlabeled outputs are checked by gxformat2, no need to check here
def _lint_case(path: str, test_case: TestCase, lint_context: WorkflowLintContext) -> bool:
test_valid = True
i_labels = input_labels(workflow_path=path)
job_keys = test_case.input_ids
for key in job_keys:
if key not in i_labels:
# consider an error instead?
lint_context.warn(
f"Unknown workflow input in test job definition [{key}], workflow inputs are [{i_labels}]"
)
test_valid = False
# check non-optional parameters are set
for required_label in required_input_labels(path):
if required_label not in job_keys:
template = "Non-optional input has no value specified in workflow test job [%s], job specifies inputs [%s]"
lint_context.error(template % (required_label, job_keys))
test_valid = False
for input_id, input_def in test_case._job.items():
if not _tst_input_valid(test_case, input_id, input_def, lint_context):
test_valid = False
test_output_ids = test_case.tested_output_ids
o_labels = output_labels(path)
found_valid_expectation = False
for test_output_id in test_output_ids:
if test_output_id not in o_labels:
template = "Test found for unknown workflow output [%s], workflow outputs [%s]"
lint_context.error(template % (test_output_id, o_labels))
test_valid = False
else:
found_valid_expectation = True
# TODO: validate structure of test expectations
output_expectations = test_case.output_expectations[test_output_id]
test_valid = is_valid_output_expectations(lint_context=lint_context, output_expectations=output_expectations)
if not found_valid_expectation:
lint_context.warn("Found no valid test expectations for workflow test")
test_valid = False
return test_valid
[docs]
def is_valid_output_expectations(lint_context, output_expectations):
all_assertion_definitions = []
if isinstance(output_expectations, (int, str, float, bool)):
# CWL style parameter output
return True
elif "element_tests" in output_expectations:
# This is a collection
for element_id in output_expectations["element_tests"]:
all_assertion_definitions.append(output_expectations["element_tests"][element_id].get("asserts"))
else:
all_assertion_definitions.append(output_expectations.get("asserts"))
for assertion_definitions in all_assertion_definitions:
if not _check_test_assertions(lint_context, assertion_definitions):
return False
return True
def _check_test_assertions(
lint_context: WorkflowLintContext, assertion_definitions: Optional[Dict[str, Dict[str, Any]]]
) -> bool:
# we are already in Python, not XML, so it is simpler to lint assertions by checking against the
# Python functions directly, rather than checking against galaxy.xsd as for tool linting
assertions_valid = True
if assertion_definitions:
# Can be either a dictionary with different assert
# Or a list with max of asserts and potentially identical
# We transform to list:
assertion_definitions_list = __to_test_assert_list(assertion_definitions)
for assertion_description in assertion_definitions_list:
function = asserts.assertion_functions.get(f"assert_{assertion_description['tag']}")
if function is None:
lint_context.error(f"Invalid assertion: assert_{assertion_description['tag']} does not exists")
assertions_valid = False
continue
signature = inspect.signature(function)
function_args = inspect.getfullargspec(function).args
assertion_params = assertion_description["attributes"].copy()
if "verify_assertions_function" in function_args:
assertion_params["verify_assertions_function"] = asserts.verify_assertion
if "children" in function_args:
if "asserts" in assertion_params:
assertion_params["children"] = assertion_params["asserts"]
del assertion_params["asserts"]
if "children" not in assertion_params:
assertion_params["children"] = []
_check_test_assertions(lint_context, assertion_params["children"])
del assertion_params["that"]
try:
# try mapping the function with the attributes supplied and check for TypeError
signature.bind("", **assertion_params)
except AssertionError:
pass
except TypeError as e:
lint_context.error(f"Invalid assertion in tests: assert_{assertion_description['tag']} {str(e)}")
assertions_valid = False
return assertions_valid
def _tst_input_valid(
test_case: TestCase,
input_id: str,
input_def: Dict[str, Any],
lint_context: WorkflowLintContext,
) -> bool:
if isinstance(input_def, dict): # else assume it is a parameter
clazz = input_def.get("class")
if clazz == "File":
input_path = input_def.get("path")
if input_path:
if not os.path.isabs(input_path):
input_path = os.path.join(test_case.tests_directory, input_path)
if not os.path.exists(input_path):
message = "Test referenced File path [%s] not found" % input_path
lint_context.warn(message)
return False
elif clazz == "Collection":
for elem in input_def.get("elements", []):
elem_valid = _tst_input_valid(test_case, input_id, elem, lint_context)
if not elem_valid:
return False
return True
def _lint_dockstore_config(path: str, lint_context: WorkflowLintContext) -> None:
dockstore_yaml = None
try:
with open(path) as f:
dockstore_yaml = yaml.safe_load(f)
except Exception:
lint_context.error("Invalid YAML found in %s" % DOCKSTORE_REGISTRY_CONF)
return
if not isinstance(dockstore_yaml, dict):
lint_context.error("Invalid YAML contents found in %s" % DOCKSTORE_REGISTRY_CONF)
return
if "workflows" not in dockstore_yaml:
lint_context.error("Invalid YAML contents found in %s, no workflows defined" % DOCKSTORE_REGISTRY_CONF)
return
workflow_entries = dockstore_yaml.get("workflows")
if not isinstance(workflow_entries, list):
lint_context.error("Invalid YAML contents found in %s, workflows not a list" % DOCKSTORE_REGISTRY_CONF)
return
for workflow_entry in workflow_entries:
_lint_dockstore_workflow_entry(lint_context, os.path.dirname(path), workflow_entry)
def _lint_dockstore_workflow_entry(
lint_context: WorkflowLintContext, directory: str, workflow_entry: Dict[str, Any]
) -> None:
if not isinstance(workflow_entry, dict):
lint_context.error("Invalid YAML contents found in %s, workflow entry not a dict" % DOCKSTORE_REGISTRY_CONF)
return
found_errors = False
for required_key in ["primaryDescriptorPath", "subclass"]:
if required_key not in workflow_entry:
lint_context.error(f"{DOCKSTORE_REGISTRY_CONF} workflow entry missing required key {required_key}")
found_errors = True
for recommended_key in ["testParameterFiles"]:
if recommended_key not in workflow_entry:
lint_context.warn(f"{DOCKSTORE_REGISTRY_CONF} workflow entry missing recommended key {recommended_key}")
if found_errors:
# Don't do the rest of the validation for a broken file.
return
# TODO: validate subclass
descriptor_path = workflow_entry["primaryDescriptorPath"]
test_files = workflow_entry.get("testParameterFiles", [])
for referenced_file in [descriptor_path] + test_files:
referenced_path = os.path.join(directory, referenced_file[1:])
if not os.path.exists(referenced_path):
lint_context.error(f"{DOCKSTORE_REGISTRY_CONF} workflow entry references absent file {referenced_file}")
[docs]
def looks_like_a_workflow(path: str) -> bool:
"""Return boolean indicating if this path looks like a workflow."""
if POTENTIAL_WORKFLOW_FILES.match(os.path.basename(path)):
with open(path) as f:
workflow_dict = ordered_load(f)
if not isinstance(workflow_dict, dict):
# Not exactly right - could have a #main def - do better and sync with Galaxy.
return False
return bool(workflow_dict.get("class") == "GalaxyWorkflow" or workflow_dict.get("a_galaxy_workflow"))
return False
[docs]
def find_workflow_descriptions(directory: str) -> Iterator[str]:
for potential_workflow_artifact_path in find_potential_workflow_files(directory):
if looks_like_a_workflow(potential_workflow_artifact_path):
yield potential_workflow_artifact_path
[docs]
def find_potential_workflow_files(directory: str) -> List[str]:
"""Return a list of potential workflow files in a directory."""
if not os.path.exists(directory):
raise ValueError(f"Directory not found {directory}")
matches = []
if os.path.isdir(directory):
for root, dirnames, filenames in os.walk(directory):
# exclude some directories (like .hg) from traversing
dirnames[:] = [dir for dir in dirnames if dir not in EXCLUDE_WALK_DIRS]
for filename in filenames:
if POTENTIAL_WORKFLOW_FILES.match(filename):
matches.append(os.path.join(root, filename))
else:
matches.append(directory)
return matches
def _lint_tool_ids(path: str, lint_context: WorkflowLintContext) -> None:
def _lint_tool_ids_steps(lint_context: WorkflowLintContext, wf_dict: Dict, ts: ToolShedInstance) -> bool:
"""Returns whether a single tool_id was invalid"""
failed = False
steps = wf_dict.get("steps", {})
for step in steps.values():
if step.get("type", "tool") == "tool" and not step.get("run", {}).get("class") == "GalaxyWorkflow":
warning_msg, _ = find_repos_from_tool_id(step["tool_id"], ts)
if warning_msg != "":
lint_context.error(warning_msg)
failed = True
elif step.get("type") == "subworkflow": # GA SWF
sub_failed = _lint_tool_ids_steps(lint_context, step["subworkflow"], ts)
if sub_failed:
failed = True
elif step.get("run", {}).get("class") == "GalaxyWorkflow": # gxformat2 SWF
sub_failed = _lint_tool_ids_steps(lint_context, step["run"], ts)
if sub_failed:
failed = True
else:
continue
return failed
with open(path) as f:
workflow_dict = ordered_load(f)
ts = toolshed.ToolShedInstance(url=MAIN_TOOLSHED_URL)
failed = _lint_tool_ids_steps(lint_context, workflow_dict, ts)
if not failed:
lint_context.valid("All tools_id appear to be valid.")
return None