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Make constant value from valueFrom field override array inputs #639

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Merged
merged 3 commits into from
Feb 24, 2018
Merged

Make constant value from valueFrom field override array inputs #639

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3904447
Fix valueFrom field overriding default binding for arrays
Feb 1, 2018
2262ae1
Merge branch 'master' into fix/valuefrom
mr-c Feb 10, 2018
b114cc4
Merge branch 'master' into fix/valuefrom
mr-c Feb 24, 2018
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43 changes: 24 additions & 19 deletions cwltool/builder.py
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Original file line number Diff line number Diff line change
Expand Up @@ -78,6 +78,7 @@ def bind_input(self, schema, datum, lead_pos=None, tail_pos=None):
lead_pos = []
bindings = [] # type: List[Dict[Text,Text]]
binding = None # type: Dict[Text,Any]
value_from_expression = False
if "inputBinding" in schema and isinstance(schema["inputBinding"], dict):
binding = copy.copy(schema["inputBinding"])

Expand All @@ -87,29 +88,33 @@ def bind_input(self, schema, datum, lead_pos=None, tail_pos=None):
binding["position"] = aslist(lead_pos) + [0] + aslist(tail_pos)

binding["datum"] = datum
if "valueFrom" in binding:
value_from_expression = True

# Handle union types
if isinstance(schema["type"], list):
for t in schema["type"]:
if isinstance(t, (str, Text)) and self.names.has_name(t, ""):
avsc = self.names.get_name(t, "")
elif isinstance(t, dict) and "name" in t and self.names.has_name(t["name"], ""):
avsc = self.names.get_name(t["name"], "")
else:
avsc = AvroSchemaFromJSONData(t, self.names)
if validate.validate(avsc, datum):
schema = copy.deepcopy(schema)
schema["type"] = t
return self.bind_input(schema, datum, lead_pos=lead_pos, tail_pos=tail_pos)
raise validate.ValidationException(u"'%s' is not a valid union %s" % (datum, schema["type"]))
if not value_from_expression:
for t in schema["type"]:
if isinstance(t, (str, Text)) and self.names.has_name(t, ""):
avsc = self.names.get_name(t, "")
elif isinstance(t, dict) and "name" in t and self.names.has_name(t["name"], ""):
avsc = self.names.get_name(t["name"], "")
else:
avsc = AvroSchemaFromJSONData(t, self.names)
if validate.validate(avsc, datum):
schema = copy.deepcopy(schema)
schema["type"] = t
return self.bind_input(schema, datum, lead_pos=lead_pos, tail_pos=tail_pos)
raise validate.ValidationException(u"'%s' is not a valid union %s" % (datum, schema["type"]))
elif isinstance(schema["type"], dict):
st = copy.deepcopy(schema["type"])
if binding and "inputBinding" not in st and st["type"] == "array" and "itemSeparator" not in binding:
st["inputBinding"] = {}
for k in ("secondaryFiles", "format", "streamable"):
if k in schema:
st[k] = schema[k]
bindings.extend(self.bind_input(st, datum, lead_pos=lead_pos, tail_pos=tail_pos))
if not value_from_expression:
st = copy.deepcopy(schema["type"])
if binding and "inputBinding" not in st and st["type"] == "array" and "itemSeparator" not in binding:
st["inputBinding"] = {}
for k in ("secondaryFiles", "format", "streamable"):
if k in schema:
st[k] = schema[k]
bindings.extend(self.bind_input(st, datum, lead_pos=lead_pos, tail_pos=tail_pos))
else:
if schema["type"] in self.schemaDefs:
schema = self.schemaDefs[schema["type"]]
Expand Down