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implement enum type in cwltool #104

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Merged
merged 5 commits into from
Jun 28, 2016
Merged

implement enum type in cwltool #104

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fbecf5f
parse enum type in generate_parser()
hmenager Jun 27, 2016
a7a54d6
create a 'name' field for enum types where missing (#101)
hmenager Jun 27, 2016
cef0de5
remove dummy print.
hmenager Jun 28, 2016
2212479
remove irrelevant comment
hmenager Jun 28, 2016
332196a
add other tests in generate_parser()
hmenager Jun 28, 2016
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3 changes: 2 additions & 1 deletion cwltool/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -277,7 +277,8 @@ def generate_parser(toolparser, tool, namemap):
action = cast(argparse.Action, FileAppendAction)
else:
action = "append"

elif isinstance(inptype, dict) and inptype["type"] == "enum":
atype = str
if inptype == "string":
atype = str
elif inptype == "int":
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20 changes: 18 additions & 2 deletions cwltool/process.py
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Original file line number Diff line number Diff line change
Expand Up @@ -223,6 +223,22 @@ def fillInDefaults(inputs, job):
else:
raise validate.ValidationException("Missing input parameter `%s`" % shortname(inp["id"]))


def avroize_type(field_type, name_prefix=""):
"""
adds missing information to a type so that CWL types are valid in schema_salad.
"""
if type(field_type) == list:
field_type_result = []
for idx, field_type_item in enumerate(field_type):
field_type_result.append(avroize_type(field_type_item, name_prefix+"_"+str(idx)))
return field_type_result
elif type(field_type) == dict and "type" in field_type and field_type["type"] == "enum":
if "name" not in field_type:
field_type["name"] = name_prefix+"_type_enum"
return field_type


class Process(object):
__metaclass__ = abc.ABCMeta

Expand Down Expand Up @@ -252,7 +268,7 @@ def __init__(self, toolpath_object, **kwargs):

if sd:
sdtypes = sd["types"]
av = schema_salad.schema.make_valid_avro(sdtypes, {t["name"]: t for t in sdtypes}, set())
av = schema_salad.schema.make_valid_avro(sdtypes, {t["name"]: t for t in avroize_type(sdtypes)}, set())
for i in av:
self.schemaDefs[i["name"]] = i
avro.schema.make_avsc_object(av, self.names)
Expand All @@ -278,7 +294,7 @@ def __init__(self, toolpath_object, **kwargs):
c["type"] = ["null"] + aslist(c["type"])
else:
c["type"] = c["type"]

c["type"] = avroize_type(c["type"],c["name"])
if key == "inputs":
self.inputs_record_schema["fields"].append(c) # type: ignore
elif key == "outputs":
Expand Down