Fix --print-rdf to include dependent documents (tools etc) in graph (#180)

* Fix --print-rdf to include dependent documents (tools etc) in graph, and update
--print-dot for CWL v1.0

* Fix type annotations

* Bump schema salad dependency, make version pin less restrictive.

Author: tetron

cwltool/cwlrdf.py

@@ -1,14 +1,24 @@
 import json
 import urlparse
+from .process import Process
 from schema_salad.ref_resolver import Loader
 from schema_salad.jsonld_context import makerdf
 from rdflib import Graph, plugin, URIRef
 from rdflib.serializer import Serializer
 from typing import Any, Dict, IO, Text, Union
 
-def printrdf(workflow, wf, ctx, sr, stdout):
-    # type: (Union[Text, Text], Union[List[Dict[Text, Any]], Dict[Text, Any]], Loader.ContextType, Text, IO[Any]) -> None
-    stdout.write(makerdf(workflow, wf, ctx).serialize(format=sr))
+def gather(tool, ctx):  # type: (Process, Loader.ContextType) -> Graph
+    g = Graph()
+
+    def visitor(t):
+        makerdf(t["id"], t, ctx, graph=g)
+
+    tool.visit(visitor)
+    return g
+
+def printrdf(wf, ctx, sr, stdout):
+    # type: (Process, Loader.ContextType, Text, IO[Any]) -> None
+    stdout.write(gather(wf, ctx).serialize(format=sr))
 
 def lastpart(uri):  # type: (Any) -> Text
     uri = Text(uri)
@@ -129,9 +139,9 @@ def dot_without_parameters(g, stdout):  # type: (Graph, IO[Any]) -> None
            WHERE {
               ?wf1 Workflow:steps ?src .
               ?wf2 Workflow:steps ?sink .
-              ?src cwl:outputs ?out .
+              ?src cwl:out ?out .
               ?inp cwl:source ?out .
-              ?sink cwl:inputs ?inp .
+              ?sink cwl:in ?inp .
               ?src cwl:run ?srcrun .
               ?sink cwl:run ?sinkrun .
            }""")
@@ -147,9 +157,9 @@ def dot_without_parameters(g, stdout):  # type: (Graph, IO[Any]) -> None
         stdout.write(u'"%s" -> "%s" [%s]\n' % (dotname[src], dotname[sink], attr))
 
 
-def printdot(workflow, wf, ctx, stdout, include_parameters=False):
-    # type: (Union[Text, Text], Union[List[Dict[Text, Any]], Dict[Text, Any]], Loader.ContextType, Any, bool) -> None
-    g = makerdf(workflow, wf, ctx)
+def printdot(wf, ctx, stdout, include_parameters=False):
+    # type: (Process, Loader.ContextType, Any, bool) -> None
+    g = gather(wf, ctx)
 
     stdout.write("digraph {")
 

cwltool/main.py

@@ -598,16 +598,17 @@ def main(argsl=None,
                 stdout.write(json.dumps(processobj, indent=4))
                 return 0
 
+            tool = make_tool(document_loader, avsc_names, metadata, uri,
+                    makeTool, vars(args))
+
             if args.print_rdf:
-                printrdf(uri, processobj, document_loader.ctx, args.rdf_serializer, stdout)
+                printrdf(tool, document_loader.ctx, args.rdf_serializer, stdout)
                 return 0
 
             if args.print_dot:
-                printdot(uri, processobj, document_loader.ctx, stdout)
+                printdot(tool, document_loader.ctx, stdout)
                 return 0
 
-            tool = make_tool(document_loader, avsc_names, metadata, uri,
-                    makeTool, vars(args))
         except (validate.ValidationException) as exc:
             _logger.error(u"Tool definition failed validation:\n%s", exc,
                           exc_info=args.debug)

cwltool/process.py

@@ -561,7 +561,7 @@ def validate_hints(self, avsc_names, hints, strict):
     def get_requirement(self, feature):  # type: (Any) -> Tuple[Any, bool]
         return get_feature(self, feature)
 
-    def visit(self, op):
+    def visit(self, op):  # type: (Callable[[Dict[Text, Any]], None]) -> None
         op(self.tool)
 
     @abc.abstractmethod

setup.py

@@ -46,7 +46,7 @@
           'rdflib >= 4.1.0',
           'rdflib-jsonld >= 0.3.0',
           'shellescape',
-          'schema-salad==1.17.20160820171034',
+          'schema-salad >= 1.18',
           'typing >= 3.5.2',
           'cwltest >= 1.0.20160907111242'],
       test_suite='tests',