skip non-draft3 CWL documents

Author: mr-c

Makefile

@@ -26,7 +26,7 @@ MODULE=cwl-upgrader
 # `SHELL=bash` Will break Titus's laptop, so don't use BASH-isms like
 # `[[` conditional expressions.
 PYSOURCES=$(wildcard ${MODULE}/**.py tests/*.py) setup.py
-DEVPKGS=pep8 diff_cover autopep8 pylint coverage pep257
+DEVPKGS=pep8 diff_cover autopep8 pylint coverage pep257 flake8
 MYPYPATH=typeshed/2or3
 MYPYFLAGS=--disallow-untyped-calls --disallow-untyped-defs \
 	  --warn-incomplete-stub --warn-redundant-casts
@@ -45,7 +45,7 @@ install-dep: install-dependencies
 
 install-dependencies:
 	pip install --upgrade $(DEVPKGS)
-	pip install -r requirements.txt
+	#pip install -r requirements.txt
 
 ## install     : install the ${MODULE} module and schema-salad-tool
 install: FORCE

README.rst

@@ -5,6 +5,9 @@ Common workflow language standalone document upgrader
 This is a standalone upgrader for Common Workflow Language documents from
 version "draft-3" to "v1.0".
 
+It does not check for correctness of the input document, for that one can use
+the CWL reference implementation.
+
 This is written and tested for Python 2.7, 3.4, and 3.5.
 
 Install

cwlupgrader/main.py

@@ -11,7 +11,11 @@ def main():  # type: () -> int
     for path in sys.argv[1:]:
         with open(path) as entry:
             document = ruamel.yaml.round_trip_load(entry)
-            draft3_to_v1_0(document)
+            if ('cwlVersion' in document
+                    and document['cwlVersion'] == 'cwl:draft-3'):
+                    draft3_to_v1_0(document)
+            else:
+                print("Skipping non draft-3 CWL document", file=sys.stderr)
             print(ruamel.yaml.round_trip_dump(document))
     return 0
 
@@ -45,7 +49,7 @@ def _draft3_to_v1_0(document):
         for i, sf in enumerate(document["secondaryFiles"]):
             if "$(" in sf or "${" in sf:
                 document["secondaryFiles"][i] = sf.replace(
-		    '"path"', '"location"').replace(".path", ".location")
+                    '"path"', '"location"').replace(".path", ".location")
 
     if "description" in document:
         document["doc"] = document["description"]
@@ -92,4 +96,3 @@ def shortenType(typeObj):
 
 if __name__ == "__main__":
     sys.exit(main())
-