Merge pull request #45 from common-workflow-language/improve-makerdf

Bugfix makerdf (helper function for converting to RDF).

Author: mr-c

schema_salad/jsonld_context.py

@@ -188,11 +188,11 @@ def fix_jsonld_ids(obj, ids):
         for entry in obj:
             fix_jsonld_ids(entry, ids)
 
-def makerdf(workflow, wf, ctx):
-    # type: (Union[str, unicode], Union[List[Dict[unicode, Any]], Dict[unicode, Any]], Loader.ContextType) -> Graph
+def makerdf(workflow, wf, ctx, graph=None):
+    # type: (Union[str, unicode], Union[List[Dict[unicode, Any]], Dict[unicode, Any]], Loader.ContextType, Graph) -> Graph
     prefixes = {}
     idfields = []
-    for k,v in ctx.iteritems():
+    for k, v in ctx.iteritems():
         if isinstance(v, dict):
             url = v["@id"]
         else:
@@ -201,26 +201,29 @@ def makerdf(workflow, wf, ctx):
             idfields.append(k)
         doc_url, frg = urlparse.urldefrag(url)
         if "/" in frg:
-            p, _ = frg.split("/")
+            p = frg.split("/")[0]
             prefixes[p] = u"%s#%s/" % (doc_url, p)
 
+    fix_jsonld_ids(wf, idfields)
+
+    if graph is None:
+        g = Graph()
+    else:
+        g = graph
+
     if isinstance(wf, list):
-        wf = {
-            "@context": ctx,
-            "@graph": wf
-        }
+        for w in wf:
+            w["@context"] = ctx
+            g.parse(data=json.dumps(w), format='json-ld', location=workflow)
     else:
         wf["@context"] = ctx
-
-    fix_jsonld_ids(wf, idfields)
-
-    g = Graph().parse(data=json.dumps(wf), format='json-ld', location=workflow)
+        g.parse(data=json.dumps(wf), format='json-ld', location=workflow)
 
     # Bug in json-ld loader causes @id fields to be added to the graph
-    for s,p,o in g.triples((None, URIRef("@id"), None)):
-        g.remove((s, p, o))
+    for sub, pred, obj in g.triples((None, URIRef("@id"), None)):
+        g.remove((sub, pred, obj))
 
-    for k2,v2 in prefixes.iteritems():
+    for k2, v2 in prefixes.iteritems():
         g.namespace_manager.bind(k2, v2)
 
     return g

schema_salad/main.py

@@ -2,6 +2,7 @@
 import argparse
 import logging
 import sys
+import traceback
 import pkg_resources  # part of setuptools
 from . import schema
 from . import jsonld_context
@@ -103,7 +104,7 @@ def main(argsl=None):  # type: (List[str]) -> int
             schema_raw_doc, schema_uri)
     except (validate.ValidationException) as e:
         _logger.error("Schema `%s` failed link checking:\n%s",
-                      args.schema, e, exc_info=(e if args.debug else False))
+                args.schema, e, exc_info=(True if args.debug else False))
         _logger.debug("Index is %s", metaschema_loader.idx.keys())
         _logger.debug("Vocabulary is %s", metaschema_loader.vocab.keys())
         return 1
@@ -148,7 +149,8 @@ def main(argsl=None):  # type: (List[str]) -> int
 
     if isinstance(avsc_names, Exception):
         _logger.error("Schema `%s` error:\n%s", args.schema,
-                      avsc_names, exc_info=(avsc_names if args.debug else False))
+                avsc_names, exc_info=((type(avsc_names), avsc_names,
+                    None) if args.debug else None))
         if args.print_avro:
             print(json.dumps(avsc_obj, indent=4))
         return 1

schema_salad/ref_resolver.py

@@ -553,7 +553,7 @@ def resolve_all(self, document, base_url, file_base=None, checklinks=True):
                     document[key], _ = loader.resolve_all(
                         val, base_url, file_base=file_base, checklinks=False)
             except validate.ValidationException as v:
-                _logger.warn("loader is %s", id(loader), exc_info=v)
+                _logger.warn("loader is %s", id(loader), exc_info=True)
                 raise validate.ValidationException("(%s) (%s) Validation error in field %s:\n%s" % (
                     id(loader), file_base, key, validate.indent(str(v))))
 
@@ -577,7 +577,7 @@ def resolve_all(self, document, base_url, file_base=None, checklinks=True):
                             val, base_url, file_base=file_base, checklinks=False)
                         i += 1
             except validate.ValidationException as v:
-                _logger.warn("failed", exc_info=v)
+                _logger.warn("failed", exc_info=True)
                 raise validate.ValidationException("(%s) (%s) Validation error in position %i:\n%s" % (
                     id(loader), file_base, i, validate.indent(str(v))))
 

setup.py

@@ -41,7 +41,7 @@
 extras_require = {}               # TODO: to be removed when the above is added
 
 setup(name='schema-salad',
-      version='1.14',
+      version='1.15',
       description='Schema Annotations for Linked Avro Data (SALAD)',
       long_description=open(README).read(),
       author='Common workflow language working group',

typeshed/2.7/rdflib/graph.pyi

@@ -25,7 +25,7 @@ class Graph(Node):
     def close(self, commit_pending_transaction=False): ...
     def add(self, __tuple_arg_2: Tuple[Node, Node, Node]) -> None: ...
     def addN(self, quads): ...
-    def remove(self, __tuple_arg_2): ...
+    def remove(self, __tuple_arg_2: Tuple[Union[AnyStr, URIRef], AnyStr, Union[AnyStr, URIRef]]) -> None: ...
     def triples(self, __tuple_arg_2: Tuple[Union[AnyStr, URIRef], AnyStr, Union[AnyStr, URIRef]]) -> Iterator[Tuple[AnyStr, AnyStr, AnyStr]]: ...
     def __getitem__(self, item): ...
     def __len__(self): ...