remove unecessary codepaths (#1152)

Author: mr-c

cwltool/load_tool.py

@@ -305,16 +305,9 @@ def resolve_and_validate_document(loadingContext,
     if loadingContext.do_update in (True, None):
         if "cwlVersion" not in metadata:
             metadata["cwlVersion"] = cwlVersion
-        processobj = cast(CommentedMap, cmap(update.update(
-            processobj, document_loader, fileuri, loadingContext.enable_dev, metadata)))
-        if isinstance(processobj, MutableMapping):
-            document_loader.idx[processobj["id"]] = processobj
-        elif isinstance(processobj, MutableSequence):
-            document_loader.idx[metadata["id"]] = metadata
-            for po in processobj:
-                document_loader.idx[po["id"]] = po
-        else:
-            raise Exception("'processobj' was not MutableMapping or MutableSequence %s" % type(processobj))
+        processobj = update.update(
+            processobj, document_loader, fileuri, loadingContext.enable_dev, metadata)
+        document_loader.idx[processobj["id"]] = processobj
 
     if jobobj is not None:
         loadingContext.jobdefaults = jobobj

cwltool/update.py

@@ -46,12 +46,17 @@ def rewrite_requirements(t):
                 rewrite_requirements(s)
 
     def update_secondaryFiles(t):
-        if isinstance(t, MutableSequence):
-            return [update_secondaryFiles(p) for p in t]
+        if isinstance(t, CommentedSeq):
+            new_seq = copy.deepcopy(t)
+            for index, entry in enumerate(t):
+                new_seq[index] = update_secondaryFiles(entry)
+            return new_seq
+        elif isinstance(t, MutableSequence):
+            return CommentedSeq([update_secondaryFiles(p) for p in t])
         elif isinstance(t, MutableMapping):
             return t
         else:
-            return {"pattern": t}
+            return CommentedMap([("pattern", t)])
 
     def fix_inputBinding(t):
         for i in t["inputs"]:
@@ -71,9 +76,9 @@ def fix_inputBinding(t):
     if isinstance(upd, MutableMapping) and "$graph" in upd:
         upd = upd["$graph"]
     for proc in aslist(upd):
-        proc.setdefault("hints", [])
-        proc["hints"].insert(0, {"class": "NetworkAccess", "networkAccess": True})
-        proc["hints"].insert(0, {"class": "LoadListingRequirement", "loadListing": "deep_listing"})
+        proc.setdefault("hints", CommentedSeq())
+        proc["hints"].insert(0, CommentedMap([("class", "NetworkAccess"),( "networkAccess", True)]))
+        proc["hints"].insert(0, CommentedMap([("class", "LoadListingRequirement"),("loadListing", "deep_listing")]))
         if "cwlVersion" in proc:
             del proc["cwlVersion"]
 
@@ -108,7 +113,7 @@ def checkversion(doc,        # type: Union[CommentedSeq, CommentedMap]
                  metadata,   # type: CommentedMap
                  enable_dev  # type: bool
 ):
-    # type: (...) -> Tuple[Union[CommentedSeq, CommentedMap], Text]
+    # type: (...) -> Tuple[CommentedMap, Text]
     """Check the validity of the version of the give CWL document.
 
     Returns the document and the validated version string.
@@ -151,16 +156,15 @@ def checkversion(doc,        # type: Union[CommentedSeq, CommentedMap]
 
 
 def update(doc, loader, baseuri, enable_dev, metadata):
-    # type: (Union[CommentedSeq, CommentedMap], Loader, Text, bool, Any) -> Union[CommentedSeq, CommentedMap]
+    # type: (Union[CommentedSeq, CommentedMap], Loader, Text, bool, Any) -> CommentedMap
 
-    if (metadata.get("http://commonwl.org/cwltool#original_cwlVersion") or
-        (isinstance(doc, CommentedMap) and doc.get("http://commonwl.org/cwltool#original_cwlVersion"))):
-        return doc
-
-    (cdoc, originalversion) = checkversion(doc, metadata, enable_dev)
-    version = originalversion
+    if isinstance(doc, CommentedMap):
+            if metadata.get("http://commonwl.org/cwltool#original_cwlVersion") \
+                    or doc.get("http://commonwl.org/cwltool#original_cwlVersion"):
+                return doc
 
     (cdoc, version) = checkversion(doc, metadata, enable_dev)
+    originalversion = copy.copy(version)
 
     nextupdate = identity  # type: Optional[Callable[[Any, Loader, Text], Tuple[Any, Text]]]
 

tests/test_toolargparse.py

@@ -79,6 +79,7 @@
 @needs_docker
 @pytest.mark.parametrize('name,script_contents,params', scripts_argparse_params)
 def test_argparse(name, script_contents, params, tmpdir):
+    script = None
     try:
         script = NamedTemporaryFile(mode='w', delete=False)
         script.write(script_contents)
@@ -91,5 +92,5 @@ def test_argparse(name, script_contents, params, tmpdir):
     except SystemExit as err:
         assert err.code == 0, name
     finally:
-        if os.path.exists(script.name):
+        if script and script.name and os.path.exists(script.name):
             os.unlink(script.name)