view env/lib/python3.9/site-packages/planemo/ @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
line wrap: on
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import os
import re

import yaml
from galaxy.tool_util.lint import LintContext
from galaxy.tool_util.loader_directory import EXCLUDE_WALK_DIRS
from gxformat2._yaml import ordered_load
from gxformat2.lint import lint_format2, lint_ga

from planemo.exit_codes import (
from planemo.galaxy.workflows import input_labels, output_labels, required_input_labels
from planemo.runnable import cases, for_path
from planemo.shed import DOCKSTORE_REGISTRY_CONF

POTENTIAL_WORKFLOW_FILES = re.compile(r'^.*(\.yml|\.yaml|\.ga)$')

class WorkflowLintContext(LintContext):
    # Setup training topic for linting - probably should pass this through
    # from click arguments.
    training_topic = None

def generate_dockstore_yaml(directory):
    workflows = []
    for workflow_path in find_workflow_descriptions(directory):
            # TODO: support CWL
            "subclass": "Galaxy",
            "primaryDescriptorPath": os.path.relpath(workflow_path, directory)
    # Force version to the top of file but serializing rest of config seprately
    contents = "version: %s\n" % DOCKSTORE_REGISTRY_CONF_VERSION
    contents += yaml.dump({"workflows": workflows})
    return contents

def lint_workflow_artifacts_on_paths(ctx, paths, lint_args):
    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_OK

def _lint_workflow_artifacts_on_path(lint_context, path, lint_args):
    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, "r") 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_tests", _lint_tsts, potential_workflow_artifact_path)
            # Allow linting ro crates and such also

# misspell for pytest
def _lint_tsts(path, lint_context):
    runnables = for_path(path, return_all=True)
    if not isinstance(runnables, list):
        runnables = [runnables]
    for runnable in runnables:
        test_cases = cases(runnable)
        all_tests_valid = False
        if len(test_cases) == 0:
            lint_context.warn("Workflow missing test cases.")
            all_tests_valid = True
        for test_case in test_cases:
            if not _lint_case(path, test_case, lint_context):
                all_tests_valid = False

        if all_tests_valid:
            lint_context.valid(f"Tests appear structurally correct for {runnable.path}")

def _lint_case(path, test_case, lint_context):
    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("Unknown workflow input in test job definition [%s], workflow inputs are [%s]" % (key, 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
            found_valid_expectation = True
        # TODO: validate structure of test expectations

    if not found_valid_expectation:
        lint_context.warn("Found no valid test expectations for workflow test")
        test_valid = False

    return test_valid

def _tst_input_valid(test_case, input_id, input_def, lint_context):
    if type(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
                    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, lint_context):
    dockstore_yaml = None
        with open(path, "r") as f:
            dockstore_yaml = yaml.safe_load(f)
    except Exception:
        lint_context.error("Invalid YAML found in %s" % DOCKSTORE_REGISTRY_CONF)

    if not isinstance(dockstore_yaml, dict):
        lint_context.error("Invalid YAML contents found in %s" % DOCKSTORE_REGISTRY_CONF)

    if "workflows" not in dockstore_yaml:
        lint_context.error("Invalid YAML contents found in %s, no workflows defined" % DOCKSTORE_REGISTRY_CONF)

    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)

    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, directory, workflow_entry):
    if not isinstance(workflow_entry, dict):
        lint_context.error("Invalid YAML contents found in %s, workflow entry not a dict" % DOCKSTORE_REGISTRY_CONF)

    found_errors = False
    for required_key in ["primaryDescriptorPath", "subclass"]:
        if required_key not in workflow_entry:
            lint_context.error("%s workflow entry missing required key %s" % (DOCKSTORE_REGISTRY_CONF, required_key))
            found_errors = True

    for recommended_key in ["testParameterFiles"]:
        if recommended_key not in workflow_entry:
            lint_context.warn("%s workflow entry missing recommended key %s" % (DOCKSTORE_REGISTRY_CONF, recommended_key))

    if found_errors:
        # Don't do the rest of the validation for a broken file.

    # 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("%s workflow entry references absent file %s" % (DOCKSTORE_REGISTRY_CONF, referenced_file))

def looks_like_a_workflow(path):
    """Return boolean indicating if this path looks like a workflow."""
    if POTENTIAL_WORKFLOW_FILES.match(os.path.basename(path)):
        with open(path, "r") 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 workflow_dict.get("class") == "GalaxyWorkflow" or workflow_dict.get("a_galaxy_workflow")
    return False

def find_workflow_descriptions(directory):
    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

def find_potential_workflow_files(directory):
    """Return a list of potential workflow files in a directory."""
    if not os.path.exists(directory):
        raise ValueError("Directory not found {}".format(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))
    return matches