diff env/lib/python3.9/site-packages/galaxy/tool_util/linters/cwl.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/galaxy/tool_util/linters/cwl.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,48 @@
+"""Linter for CWL tools."""
+
+lint_tool_types = ["cwl"]
+
+from galaxy.tool_util.cwl.schema import schema_loader
+
+
+def lint_cwl_validation(tool_source, lint_ctx):
+    """Determine in CWL tool validates against spec."""
+    raw_reference = schema_loader.raw_process_reference(tool_source._source_path)
+    validation_exception = None
+    try:
+        schema_loader.process_definition(raw_reference)
+    except Exception as e:
+        validation_exception = e
+    if validation_exception:
+        lint_ctx.error("Failed to valdiate CWL artifact [%s]", validation_exception)
+    else:
+        lint_ctx.info("CWL appears to be valid.")
+
+
+def lint_new_draft(tool_source, lint_ctx):
+    """Determine in CWL tool is valid, modern draft."""
+    raw_reference = schema_loader.raw_process_reference(tool_source._source_path)
+    cwl_version = raw_reference.process_object.get("cwlVersion", None)
+    if cwl_version is None:
+        lint_ctx.error("CWL file does not contain a 'cwlVersion'")
+    if cwl_version not in ["v1.0"]:
+        lint_ctx.warn("CWL version [%s] is unknown, we recommend the v1.0 the stable release." % cwl_version)
+    else:
+        lint_ctx.info("Modern CWL version [%s]", cwl_version)
+
+
+def lint_docker_image(tool_source, lint_ctx):
+    _, containers = tool_source.parse_requirements_and_containers()
+    if len(containers) == 0:
+        lint_ctx.warn("Tool does not specify a DockerPull source.")
+    else:
+        identifier = containers[0].identifier
+        lint_ctx.info("Tool will run in Docker image [%s]." % identifier)
+
+
+def lint_description(tool_source, lint_ctx):
+    help = tool_source.parse_help()
+    if not help:
+        lint_ctx.warn("Description of tool is empty or absent.")
+    elif "TODO" in help:
+        lint_ctx.warn("Help contains TODO text.")