Increase worflow linting

planemo/commands/cmd_workflow_lint.py

@@ -14,6 +14,12 @@
 @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."""
@@ -23,5 +29,6 @@ def cli(ctx, paths, **kwds):
         ctx,
         paths,
         lint_args,
+        iwc_grade=kwds.get("iwc", False)
     )
     ctx.exit(exit_code)

planemo/workflow_lint.py

@@ -57,6 +57,8 @@ class WorkflowLintContext(LintContext):
     # Setup training topic for linting - probably should pass this through
     # from click arguments.
     training_topic = None
+    release = None
+    iwc_grade = False
 
 
 def generate_dockstore_yaml(directory: str, publish: bool = True) -> str:
@@ -122,10 +124,11 @@ def generate_dockstore_yaml(directory: str, publish: bool = True) -> str:
 
 
 def lint_workflow_artifacts_on_paths(
-    ctx: "PlanemoCliContext", paths: Iterable[str], lint_args: Dict[str, Union[str, List[str]]]
+    ctx: "PlanemoCliContext", paths: Iterable[str], lint_args: Dict[str, Union[str, List[str]]], iwc_grade: bool
 ) -> int:
     report_level = lint_args["level"]
     lint_context = WorkflowLintContext(report_level, skip_types=lint_args["skip_types"])
+    lint_context.iwc_grade = iwc_grade
     for path in paths:
         _lint_workflow_artifacts_on_path(lint_context, path, lint_args)
 
@@ -138,6 +141,12 @@ 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:
+    if lint_context.iwc_grade:
+        if not os.path.isdir(path):
+            raise ValueError("iwc standards can only be checked on directories.")
+        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)
@@ -152,6 +161,8 @@ def structure(path, lint_context):
                 lint_func(lint_context, workflow_dict, path=path)
 
             lint_context.lint("lint_structure", structure, potential_workflow_artifact_path)
+            if lint_context.iwc_grade and lint_context.version is not None:
+                lint_context.lint("lint_version", check_version, 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 +405,11 @@ 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 +419,16 @@ 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 +444,21 @@ 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 lint_context.iwc_grade:
+        lint_fun = lint_context.error
+    else:
+        lint_fun = lint_context.warn
+    for recommended_key in ["testParameterFiles", "name"]:
         if recommended_key not in workflow_entry:
-            lint_context.warn(f"{DOCKSTORE_REGISTRY_CONF} workflow entry missing recommended key {recommended_key}")
+            lint_fun(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 +467,23 @@ 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 at least one author
+    if len(workflow_entry.get('authors', [])) == 0:
+        lint_fun(f"Workflow {workflow_name} have no "
+                 "'authors' in the .dockstore.yml.")
+    # 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 +584,41 @@ 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 _lint_changelog_version(path: str, lint_context: WorkflowLintContext) -> None:
+    lint_context.version = None
+    # Check the version can be get from the CHANGELOG.md
+    if not os.path.exists(os.path.join(path, 'CHANGELOG.md')):
+        return
+    with open(os.path.join(path, 'CHANGELOG.md'), 'r') as f:
+        for line in f:
+            if line.startswith('## ['):
+                lint_context.version = line.split(']')[0].replace('## [', '')
+                break
+
+    if lint_context.version is None:
+        lint_context.error("No version found in CHANGELOG. "
+                           "The version should be in a line that starts like "
+                           "'## [version number]'")
+
+
+def check_version(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:
+        if lint_context.version is not None and workflow_dict.get("release") != lint_context.version:
+            lint_context.error(f"The release of workflow {path} does not match "
+                               "the version in the CHANGELOG.")