Merge pull request #2959 from mashehu/handle-request-errors

Linting: handle request errors more gracefully for actions validation

CHANGELOG.md

@@ -26,6 +26,7 @@
 - Include test for presence of versions in snapshot ([#2888](https://github.com/nf-core/tools/pull/2888))
 - Components: set correct sha before running component lint tests ([#2952](https://github.com/nf-core/tools/pull/2952))
 - Less strict logo comparison ([#2956](https://github.com/nf-core/tools/pull/2956))
+- Handle request errors more gracefully for actions validation ([#2959](https://github.com/nf-core/tools/pull/2959))
 
 ### Download
 

nf_core/lint/actions_schema_validation.py

@@ -1,13 +1,14 @@
 import glob
 import logging
 import os
+from typing import Any, Dict, List
 
 import jsonschema
 import requests
 import yaml
 
 
-def actions_schema_validation(self):
+def actions_schema_validation(self) -> Dict[str, List[str]]:
     """Checks that the GitHub Action workflow yml/yaml files adhere to the correct schema
 
     nf-core pipelines use GitHub actions workflows to run CI tests, check formatting and also linting, among others.
@@ -17,8 +18,9 @@ def actions_schema_validation(self):
     To pass this test, make sure that all your workflows contain the required properties ``on`` and ``jobs`` and that
     all other properties are of the correct type, as specified in the schema (link above).
     """
-    passed = []
-    failed = []
+    passed: List[str] = []
+    failed: List[str] = []
+    warned: List[str] = []
 
     # Only show error messages from schema
     logging.getLogger("nf_core.schema").setLevel(logging.ERROR)
@@ -28,7 +30,13 @@ def actions_schema_validation(self):
 
     # Load the GitHub workflow schema
     r = requests.get("https://json.schemastore.org/github-workflow", allow_redirects=True)
-    schema = r.json()
+    # handle "Service Unavailable" error
+    if r.status_code not in [200, 301]:
+        warned.append(
+            f"Failed to fetch schema: Response code for `https://json.schemastore.org/github-workflow` was {r.status_code}"
+        )
+        return {"passed": passed, "failed": failed, "warned": warned}
+    schema: Dict[str, Any] = r.json()
 
     # Validate all workflows against the schema
     for wf_path in action_workflows:
@@ -46,7 +54,7 @@ def actions_schema_validation(self):
         try:
             wf_json["on"] = wf_json.pop(True)
         except Exception:
-            failed.append("Missing 'on' keyword in {}.format(wf)")
+            failed.append(f"Missing 'on' keyword in {wf}")
 
         # Validate the workflow
         try:
@@ -55,4 +63,4 @@ def actions_schema_validation(self):
         except Exception as e:
             failed.append(f"Workflow validation failed for {wf}: {e}")
 
-    return {"passed": passed, "failed": failed}
+    return {"passed": passed, "failed": failed, "warned": warned}

tests/lint/actions_schema_validation.py

@@ -1,4 +1,4 @@
-import os
+from pathlib import Path
 
 import yaml
 
@@ -9,10 +9,11 @@ def test_actions_schema_validation_missing_jobs(self):
     """Missing 'jobs' field should result in failure"""
     new_pipeline = self._make_pipeline_copy()
 
-    with open(os.path.join(new_pipeline, ".github", "workflows", "awstest.yml")) as fh:
+    awstest_yml_path = Path(new_pipeline) / ".github" / "workflows" / "awstest.yml"
+    with open(awstest_yml_path) as fh:
         awstest_yml = yaml.safe_load(fh)
     awstest_yml.pop("jobs")
-    with open(os.path.join(new_pipeline, ".github", "workflows", "awstest.yml"), "w") as fh:
+    with open(awstest_yml_path, "w") as fh:
         yaml.dump(awstest_yml, fh)
 
     lint_obj = nf_core.lint.PipelineLint(new_pipeline)
@@ -27,29 +28,31 @@ def test_actions_schema_validation_missing_on(self):
     """Missing 'on' field should result in failure"""
     new_pipeline = self._make_pipeline_copy()
 
-    with open(os.path.join(new_pipeline, ".github", "workflows", "awstest.yml")) as fh:
+    awstest_yml_path = Path(new_pipeline) / ".github" / "workflows" / "awstest.yml"
+    with open(awstest_yml_path) as fh:
         awstest_yml = yaml.safe_load(fh)
     awstest_yml.pop(True)
-    with open(os.path.join(new_pipeline, ".github", "workflows", "awstest.yml"), "w") as fh:
+    with open(awstest_yml_path, "w") as fh:
         yaml.dump(awstest_yml, fh)
 
     lint_obj = nf_core.lint.PipelineLint(new_pipeline)
     lint_obj._load()
 
     results = lint_obj.actions_schema_validation()
 
-    assert results["failed"][0] == "Missing 'on' keyword in {}.format(wf)"
+    assert results["failed"][0] == "Missing 'on' keyword in awstest.yml"
     assert "Workflow validation failed for awstest.yml: 'on' is a required property" in results["failed"][1]
 
 
 def test_actions_schema_validation_fails_for_additional_property(self):
     """Missing 'jobs' field should result in failure"""
     new_pipeline = self._make_pipeline_copy()
 
-    with open(os.path.join(new_pipeline, ".github", "workflows", "awstest.yml")) as fh:
+    awstest_yml_path = Path(new_pipeline) / ".github" / "workflows" / "awstest.yml"
+    with open(awstest_yml_path) as fh:
         awstest_yml = yaml.safe_load(fh)
     awstest_yml["not_jobs"] = awstest_yml["jobs"]
-    with open(os.path.join(new_pipeline, ".github", "workflows", "awstest.yml"), "w") as fh:
+    with open(awstest_yml_path, "w") as fh:
         yaml.dump(awstest_yml, fh)
 
     lint_obj = nf_core.lint.PipelineLint(new_pipeline)