Infrastructure for parsing CWL tools.

lib/galaxy/tools/cwl/__init__.py

@@ -0,0 +1,18 @@
+from .parser import tool_proxy
+from .runtime_actions import handle_outputs
+from .representation import to_cwl_job, to_galaxy_parameters
+
+from .cwltool_deps import (
+    needs_shell_quoting,
+    shellescape,
+)
+
+
+__all__ = [
+    'tool_proxy',
+    'handle_outputs',
+    'to_cwl_job',
+    'to_galaxy_parameters',
+    'needs_shell_quoting',
+    'shellescape',
+]

lib/galaxy/tools/cwl/cwltool_deps.py

@@ -0,0 +1,48 @@
+""" This module contains logic for dealing with cwltool as an optional
+dependency for Galaxy and/or applications which use Galaxy as a library.
+"""
+
+try:
+    import requests
+except ImportError:
+    requests = None
+
+try:
+    from cwltool import (
+        main,
+        workflow,
+        job,
+    )
+except ImportError:
+    main = None
+    workflow = None
+    job = None
+
+try:
+    import shellescape
+except ImportError:
+    shellescape = None
+
+if job is not None:
+    needs_shell_quoting = job.needs_shell_quoting
+else:
+    needs_shell_quoting = None
+
+
+def ensure_cwltool_available():
+    if main is None or workflow is None or shellescape is None:
+        message = "This feature requires cwltool and dependencies to be available, they are not."
+        if requests is None:
+            message += " Library 'requests' unavailable."
+        if shellescape is None:
+            message += " Library 'shellescape' unavailable."
+        raise ImportError(message)
+
+
+__all__ = [
+    'main',
+    'workflow',
+    'ensure_cwltool_available',
+    'shellescape',
+    'needs_shell_quoting',
+]