Increase worflow linting

planemo/commands/cmd_workflow_lint.py

@@ -4,8 +4,10 @@
 
 from planemo import options
 from planemo.cli import command_function
-from planemo.lint import build_lint_args
-from planemo.workflow_lint import lint_workflow_artifacts_on_paths
+from planemo.workflow_lint import (
+    build_wf_lint_args,
+    lint_workflow_artifacts_on_paths,
+)
 
 
 @click.command("workflow_lint")
@@ -14,11 +16,17 @@
 @options.report_xunit()
 @options.fail_level_option()
 @options.skip_option()
+@click.option(
+    "--iwc",
+    is_flag=True,
+    default=False,
+    help="Check workflows directory with the standards of iwc",
+)
 @command_function
 def cli(ctx, paths, **kwds):
     """Check workflows for syntax errors and best practices."""
     # Unlike tools, lets just make this recursive by default.
-    lint_args = build_lint_args(ctx, **kwds)
+    lint_args = build_wf_lint_args(ctx, **kwds)
     exit_code = lint_workflow_artifacts_on_paths(
         ctx,
         paths,

planemo/workflow_lint.py

@@ -39,6 +39,7 @@
     output_labels,
     required_input_labels,
 )
+from planemo.lint import build_lint_args
 from planemo.runnable import (
     cases,
     for_path,
@@ -59,6 +60,12 @@ class WorkflowLintContext(LintContext):
     training_topic = None
 
 
+def build_wf_lint_args(ctx, **kwds):
+    lint_args = build_lint_args(ctx, **kwds)
+    lint_args["iwc_grade"] = str(kwds.get("iwc", False))
+    return lint_args
+
+
 def generate_dockstore_yaml(directory: str, publish: bool = True) -> str:
     workflows = []
     all_workflow_paths = list(find_workflow_descriptions(directory))
@@ -138,9 +145,22 @@ def lint_workflow_artifacts_on_paths(
 def _lint_workflow_artifacts_on_path(
     lint_context: WorkflowLintContext, path: str, lint_args: Dict[str, Union[str, List[str]]]
 ) -> None:
+    iwc_grade = lint_args["iwc_grade"] == "True"
+    if iwc_grade:
+        if not os.path.isdir(path):
+            path = os.path.dirname(path)
+        lint_context.lint("lint_required_files", _lint_required_files_workflow_dir, path)
+        lint_context.lint("lint_changelog", _lint_changelog_version, path)
+
     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)
+            if iwc_grade:
+                lint_context.lint(
+                    "lint_dockstore_best_practices",
+                    _lint_dockstore_config_best_practices,
+                    potential_workflow_artifact_path,
+                )
 
         elif looks_like_a_workflow(potential_workflow_artifact_path):
 
@@ -152,6 +172,8 @@ def structure(path, lint_context):
                 lint_func(lint_context, workflow_dict, path=path)
 
             lint_context.lint("lint_structure", structure, potential_workflow_artifact_path)
+            if iwc_grade:
+                lint_context.lint("lint_release", _lint_release, 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)
@@ -394,6 +416,11 @@ def _lint_dockstore_config(path: str, lint_context: WorkflowLintContext) -> None
         lint_context.error("Invalid YAML contents found in %s" % DOCKSTORE_REGISTRY_CONF)
         return
 
+    if "version" not in dockstore_yaml:
+        lint_context.error("Invalid YAML contents found in %s, no version defined" % DOCKSTORE_REGISTRY_CONF)
+    if str(dockstore_yaml.get("version")) != DOCKSTORE_REGISTRY_CONF_VERSION:
+        lint_context.error("Invalid YAML version 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)
         return
@@ -403,8 +430,16 @@ def _lint_dockstore_config(path: str, lint_context: WorkflowLintContext) -> None
         lint_context.error("Invalid YAML contents found in %s, workflows not a list" % DOCKSTORE_REGISTRY_CONF)
         return
 
+    if len(workflow_entries) == 0:
+        lint_context.error("No workflow specified in the .dockstore.yml.")
+
+    workflow_names_in_dockstore = []
     for workflow_entry in workflow_entries:
         _lint_dockstore_workflow_entry(lint_context, os.path.dirname(path), workflow_entry)
+        workflow_name = workflow_entry.get("name", "")
+        if workflow_name in workflow_names_in_dockstore:
+            lint_context.error(f"{DOCKSTORE_REGISTRY_CONF} has multiple workflow entries with the same name")
+        workflow_names_in_dockstore.append(workflow_name)
 
 
 def _lint_dockstore_workflow_entry(
@@ -420,15 +455,13 @@ def _lint_dockstore_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
+    if workflow_entry.get("subclass") != "Galaxy":
+        lint_context.error(f"{DOCKSTORE_REGISTRY_CONF} workflow entry subclass must be 'Galaxy'.")
+
     descriptor_path = workflow_entry["primaryDescriptorPath"]
     test_files = workflow_entry.get("testParameterFiles", [])
 
@@ -437,6 +470,20 @@ def _lint_dockstore_workflow_entry(
         if not os.path.exists(referenced_path):
             lint_context.error(f"{DOCKSTORE_REGISTRY_CONF} workflow entry references absent file {referenced_file}")
 
+    # Check there is no space in name:
+    workflow_name = workflow_entry.get("name", "")
+    # Check the name has no space
+    if " " in workflow_name:
+        lint_context.error(
+            "Dockstore does not accept workflow names with space.",
+            f"Change '{workflow_name}' in {DOCKSTORE_REGISTRY_CONF}.",
+        )
+
+    # Check there is not mailto
+    for author in workflow_entry.get("authors", []):
+        if author.get("email", "").startswith("mailto:"):
+            lint_context.error("email field of the .dockstore.yml must not " "contain 'mailto:'")
+
 
 def looks_like_a_workflow(path: str) -> bool:
     """Return boolean indicating if this path looks like a workflow."""
@@ -537,3 +584,80 @@ def _lint_tool_ids_steps(lint_context: WorkflowLintContext, wf_dict: Dict, ts: T
     if not failed:
         lint_context.valid("All tool ids appear to be valid.")
     return None
+
+
+def _lint_required_files_workflow_dir(path: str, lint_context: WorkflowLintContext) -> None:
+    # Check all required files are present
+    required_files = ["README.md", "CHANGELOG.md", ".dockstore.yml"]
+    for required_file in required_files:
+        if not os.path.exists(os.path.join(path, required_file)):
+            lint_context.error(f"The file {required_file} is" " missing but required.")
+
+
+def _get_changelog_version(path: str) -> str:
+    # Get the version from the CHANGELOG.md
+    version = ""
+    if not os.path.exists(os.path.join(path, "CHANGELOG.md")):
+        return version
+    with open(os.path.join(path, "CHANGELOG.md"), "r") as f:
+        for line in f:
+            if line.startswith("## ["):
+                version = line.split("]")[0].replace("## [", "")
+                break
+    return version
+
+
+def _lint_changelog_version(path: str, lint_context: WorkflowLintContext) -> None:
+    # Check the version can be get from the CHANGELOG.md
+    if not os.path.exists(os.path.join(path, "CHANGELOG.md")):
+        return
+    if _get_changelog_version(path) == "":
+        lint_context.error(
+            "No version found in CHANGELOG. "
+            "The version should be in a line that starts like "
+            "'## [version number]'"
+        )
+
+
+def _lint_release(path, lint_context):
+    with open(path) as f:
+        workflow_dict = ordered_load(f)
+    if "release" not in workflow_dict:
+        lint_context.error(f"The workflow {path} has no release")
+    else:
+        # Try to get the version from the CHANGELOG:
+        version = _get_changelog_version(os.path.dirname(path))
+        if version != "" and workflow_dict.get("release") != version:
+            lint_context.error(f"The release of workflow {path} does not match " "the version in the CHANGELOG.")
+
+
+def _lint_dockstore_config_best_practices(path: str, lint_context: WorkflowLintContext) -> None:
+    dockstore_yaml = None
+    try:
+        with open(path) as f:
+            dockstore_yaml = yaml.safe_load(f)
+    except Exception:
+        return
+
+    if not isinstance(dockstore_yaml, dict):
+        return
+
+    workflow_entries = dockstore_yaml.get("workflows")
+    if not isinstance(workflow_entries, list):
+        return
+
+    for workflow_entry in workflow_entries:
+        _lint_dockstore_workflow_entry_best_practices(lint_context, os.path.dirname(path), workflow_entry)
+
+
+def _lint_dockstore_workflow_entry_best_practices(
+    lint_context: WorkflowLintContext, directory: str, workflow_entry: Dict[str, Any]
+) -> None:
+    for recommended_key in ["testParameterFiles", "name"]:
+        if recommended_key not in workflow_entry:
+            lint_context.error(f"{DOCKSTORE_REGISTRY_CONF} workflow entry missing recommended key {recommended_key}")
+
+    workflow_name = workflow_entry.get("name", "")
+    # Check there is at least one author
+    if len(workflow_entry.get("authors", [])) == 0:
+        lint_context.error(f"Workflow {workflow_name} have no 'authors' in the {DOCKSTORE_REGISTRY_CONF}.")

tests/data/wf_repos/basic_wf_iwc_invalid_version/.dockstore.yml

@@ -0,0 +1,11 @@
+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /Super-simple-workflow.ga
+  testParameterFiles:
+  - /Super-simple-workflow-tests.yml
+  authors:
+  - name: Lucille Delisle
+    orcid: 0000-0002-1964-4960

tests/data/wf_repos/basic_wf_iwc_invalid_version/CHANGELOG.md

@@ -0,0 +1,5 @@
+# Changelog
+
+## [0.1] 2024-06-17
+
+First release.

tests/data/wf_repos/basic_wf_iwc_invalid_version/README.md

@@ -0,0 +1,3 @@
+# Super simple workflow
+
+This is a super simple workflow which generates a file with x lines with 'hello'

tests/data/wf_repos/basic_wf_iwc_invalid_version/Super-simple-workflow-tests.yml

@@ -0,0 +1,10 @@
+- doc: Test outline for Super-simple-workflow
+  job:
+    n_rows: 5
+  outputs:
+    outfile:
+      asserts:
+        has_n_lines:
+          n: 5
+        has_line:
+          line: "hello"

tests/data/wf_repos/basic_wf_iwc_invalid_version/Super-simple-workflow.ga

@@ -0,0 +1,95 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "This workflow generates a file with x lines with 'hello'",
+    "comments": [],
+    "creator": [
+        {
+            "class": "Person",
+            "identifier": "https://orcid.org/0000-0002-1964-4960",
+            "name": "Lucille Delisle"
+        }
+    ],
+    "format-version": "0.1",
+    "license": "MIT",
+    "release": "0.2",
+    "name": "Super simple workflow",
+    "report": {
+        "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+    },
+    "steps": {
+        "0": {
+            "annotation": "Number of rows to generate",
+            "content_id": null,
+            "errors": null,
+            "id": 0,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Number of rows to generate",
+                    "name": "n_rows"
+                }
+            ],
+            "label": "n_rows",
+            "name": "Input parameter",
+            "outputs": [],
+            "position": {
+                "left": 0,
+                "top": 0
+            },
+            "tool_id": null,
+            "tool_state": "{\"parameter_type\": \"integer\", \"optional\": false}",
+            "tool_version": null,
+            "type": "parameter_input",
+            "uuid": "2ee42c13-83f5-4ac4-b35d-74294edf7dea",
+            "when": null
+        },
+        "1": {
+            "annotation": "this creates a file with a given number of lines",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1",
+            "errors": null,
+            "id": 1,
+            "input_connections": {
+                "token_set_0|repeat_select|times": {
+                    "id": 0,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [],
+            "label": "create file",
+            "name": "Create text file",
+            "outputs": [
+                {
+                    "name": "outfile",
+                    "type": "txt"
+                }
+            ],
+            "position": {
+                "left": 236,
+                "top": 11
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1",
+            "tool_shed_repository": {
+                "changeset_revision": "fbf99087e067",
+                "name": "text_processing",
+                "owner": "bgruening",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"token_set\": [{\"__index__\": 0, \"line\": \"hello\", \"repeat_select\": {\"repeat_select_opts\": \"user\", \"__current_case__\": 0, \"times\": {\"__class__\": \"ConnectedValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "9.3+galaxy1",
+            "type": "tool",
+            "uuid": "a86ff433-8dce-417c-baf0-bc106a93ee48",
+            "when": null,
+            "workflow_outputs": [
+                {
+                    "label": "outfile",
+                    "output_name": "outfile",
+                    "uuid": "34572088-8ad8-4661-81a2-6dfe2d83a0fe"
+                }
+            ]
+        }
+    },
+    "tags": [],
+    "uuid": "72c87042-27a8-4bcc-92af-ca74704e6161",
+    "version": 3
+}