printrdf & printdot: add support for multi-document CWL files

Author: mr-c

cwltool/cwlrdf.py

@@ -6,7 +6,7 @@
 from typing import Any, Union, Dict, IO
 
 def makerdf(workflow, wf, ctx):
-    # type: (Union[str, unicode], Dict[unicode, Any], Loader.ContextType) -> Graph
+    # type: (Union[str, unicode], Union[List[Dict[unicode, Any]], Dict[unicode, Any]], Loader.ContextType) -> Graph
     prefixes = {}
     for k,v in ctx.iteritems():
         if isinstance(v, dict):
@@ -18,7 +18,11 @@ def makerdf(workflow, wf, ctx):
             p, _ = frg.split("/")
             prefixes[p] = u"%s#%s/" % (doc_url, p)
 
-    wf["@context"] = ctx
+    if isinstance(wf, list):
+        for entry in wf:
+            entry["@context"] = ctx
+    else:
+        wf["@context"] = ctx
     g = Graph().parse(data=json.dumps(wf), format='json-ld', location=workflow)
 
     # Bug in json-ld loader causes @id fields to be added to the graph
@@ -31,7 +35,7 @@ def makerdf(workflow, wf, ctx):
     return g
 
 def printrdf(workflow, wf, ctx, sr, stdout):
-    # type: (Union[str, unicode], Dict[unicode, Any], Loader.ContextType, str, IO[Any]) -> None
+    # type: (Union[str, unicode], Union[List[Dict[unicode, Any]], Dict[unicode, Any]], Loader.ContextType, str, IO[Any]) -> None
     stdout.write(makerdf(workflow, wf, ctx).serialize(format=sr))
 
 def lastpart(uri):  # type: (Any) -> str
@@ -172,7 +176,7 @@ def dot_without_parameters(g, stdout):  # type: (Graph, IO[Any]) -> None
 
 
 def printdot(workflow, wf, ctx, stdout, include_parameters=False):
-    # type: (Union[str, unicode], Dict[unicode, Any], Loader.ContextType, Any, bool) -> None
+    # type: (Union[str, unicode], Union[List[Dict[unicode, Any]], Dict[unicode, Any]], Loader.ContextType, Any, bool) -> None
     g = makerdf(workflow, wf, ctx)
 
     stdout.write("digraph {")

cwltool/load_tool.py

@@ -44,7 +44,7 @@ def fetch_document(argsworkflow):
 
 def validate_document(document_loader, workflowobj, uri,
                       enable_dev=False, strict=True, preprocess_only=False):
-    # type: (Loader, Dict[unicode, Any], unicode, bool, bool, bool) -> Tuple[Loader, Names, Dict[unicode, Any], Dict[unicode, Any], unicode]
+    # type: (Loader, Dict[unicode, Any], unicode, bool, bool, bool) -> Tuple[Loader, Names, Union[Dict[unicode, Any], List[Dict[unicode, Any]]], Dict[unicode, Any], unicode]
     """Validate a CWL document."""
     jobobj = None
     if "cwl:tool" in workflowobj:
@@ -83,10 +83,13 @@ def validate_document(document_loader, workflowobj, uri,
 
     workflowobj["id"] = fileuri
     processobj, metadata = document_loader.resolve_all(workflowobj, fileuri)
-    if not isinstance(processobj, dict):
-        raise validate.ValidationException("Workflow must be a dict.")
+    if not isinstance(processobj, (dict, list)):
+        raise validate.ValidationException("Workflow must be a dict or list.")
 
     if not metadata:
+        if not isinstance(processobj, dict):
+            raise validate.ValidationException(
+                    "Draft-2 workflows must be a dict.")
         metadata = {"$namespaces": processobj.get("$namespaces", {}),
                    "$schemas": processobj.get("$schemas", []),
                    "cwlVersion": processobj["cwlVersion"]}
@@ -106,9 +109,8 @@ def validate_document(document_loader, workflowobj, uri,
     return document_loader, avsc_names, processobj, metadata, uri
 
 
-def make_tool(document_loader, avsc_names, processobj, metadata, uri, makeTool,
-              kwargs):
-    # type: (Loader, Names, Dict[unicode, Any], Dict[unicode, Any], unicode, Callable[..., Process], Dict[str, Any]) -> Process
+def make_tool(document_loader, avsc_names, metadata, uri, makeTool, kwargs):
+    # type: (Loader, Names, Dict[unicode, Any], unicode, Callable[..., Process], Dict[str, Any]) -> Process
     """Make a Python CWL object."""
     resolveduri = document_loader.resolve_ref(uri)[0]
 
@@ -122,7 +124,7 @@ def make_tool(document_loader, avsc_names, processobj, metadata, uri, makeTool,
                     urlparse.urldefrag(i["id"])[1] for i in resolveduri
                     if "id" in i))
     else:
-        processobj = cast(Dict[unicode, Any], resolveduri)
+        processobj = resolveduri
 
     kwargs = kwargs.copy()
     kwargs.update({
@@ -150,5 +152,5 @@ def load_tool(argsworkflow, makeTool, kwargs=None,
     document_loader, avsc_names, processobj, metadata, uri = validate_document(
         document_loader, workflowobj, uri, enable_dev=enable_dev,
         strict=strict)
-    return make_tool(document_loader, avsc_names, processobj, metadata, uri,
+    return make_tool(document_loader, avsc_names, metadata, uri,
                      makeTool, kwargs if kwargs else {})

cwltool/main.py

@@ -593,8 +593,8 @@ def main(argsl=None,
                 printdot(uri, processobj, document_loader.ctx, stdout)
                 return 0
 
-            tool = make_tool(document_loader, avsc_names, processobj, metadata,
-                             uri, makeTool, {})
+            tool = make_tool(document_loader, avsc_names, metadata, uri,
+                    makeTool, {})
         except (validate.ValidationException) as exc:
             _logger.error(u"Tool definition failed validation:\n%s", exc,
                           exc_info=(exc if args.debug else False))

cwltool/update.py

@@ -386,7 +386,7 @@ def identity(doc, loader, baseuri):  # pylint: disable=unused-argument
     return (doc, doc["cwlVersion"])
 
 def checkversion(doc, metadata, enable_dev):
-    # type: (Union[List, Dict[unicode, Any]], Dict[unicode, Any], bool) -> Tuple[Dict[unicode, Any], unicode]  # pylint: disable=line-too-long
+    # type: (Union[List[Dict[unicode, Any]], Dict[unicode, Any]], Dict[unicode, Any], bool) -> Tuple[Dict[unicode, Any], unicode]  # pylint: disable=line-too-long
     """Checks the validity of the version of the give CWL document.
 
     Returns the document and the validated version string.
@@ -418,7 +418,7 @@ def checkversion(doc, metadata, enable_dev):
     return (cdoc, version)
 
 def update(doc, loader, baseuri, enable_dev, metadata):
-    # type: (Union[List, Dict[unicode, Any]], Loader, str, bool, Any) -> Dict[unicode, Any]
+    # type: (Union[List[Dict[unicode, Any]], Dict[unicode, Any]], Loader, str, bool, Any) -> Dict[unicode, Any]
 
     (cdoc, version) = checkversion(doc, metadata, enable_dev)