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Single quote instead of backticks in output #661

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Merged
merged 1 commit into from
Feb 15, 2018
Merged

Single quote instead of backticks in output #661

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2 changes: 1 addition & 1 deletion cwltool/argparser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -193,7 +193,7 @@ def arg_parser(): # type: () -> argparse.ArgumentParser
parser.add_argument("--default-container",
help="Specify a default docker container that will be used if the workflow fails to specify one.")
parser.add_argument("--no-match-user", action="store_true",
help="Disable passing the current uid to 'docker run --user`")
help="Disable passing the current uid to `docker run --user`")
parser.add_argument("--disable-net", action="store_true",
help="Use docker's default networking for containers;"
" the default is to enable networking.")
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3 changes: 2 additions & 1 deletion cwltool/draft2tool.py
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Original file line number Diff line number Diff line change
Expand Up @@ -151,7 +151,8 @@ def revmap_file(builder, outdir, f):
return f


raise WorkflowException(u"Output File object is missing both `location` and `path` fields: %s" % f)
raise WorkflowException(u"Output File object is missing both 'location' "
"and 'path' fields: %s" % f)


class CallbackJob(object):
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11 changes: 7 additions & 4 deletions cwltool/process.py
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Expand Up @@ -401,7 +401,7 @@ def fillInDefaults(inputs, job):
elif job.get(fieldname) is None and u"null" in aslist(inp[u"type"]):
job[fieldname] = None
else:
raise WorkflowException("Missing required input parameter `%s`" % shortname(inp["id"]))
raise WorkflowException("Missing required input parameter '%s'" % shortname(inp["id"]))


def avroize_type(field_type, name_prefix=""):
Expand Down Expand Up @@ -506,7 +506,8 @@ def __init__(self, toolpath_object, **kwargs):
del c["id"]

if "type" not in c:
raise validate.ValidationException(u"Missing `type` in parameter `%s`" % c["name"])
raise validate.ValidationException(u"Missing 'type' in "
"parameter '%s'" % c["name"])

if "default" in c and "null" not in aslist(c["type"]):
c["type"] = ["null"] + aslist(c["type"])
Expand All @@ -522,15 +523,17 @@ def __init__(self, toolpath_object, **kwargs):
self.inputs_record_schema = cast(Dict[six.text_type, Any], schema_salad.schema.make_valid_avro(self.inputs_record_schema, {}, set()))
AvroSchemaFromJSONData(self.inputs_record_schema, self.names)
except avro.schema.SchemaParseException as e:
raise validate.ValidationException(u"Got error `%s` while processing inputs of %s:\n%s" %
raise validate.ValidationException(u"Got error '%s' while "
"processing inputs of %s:\n%s" %
(Text(e), self.tool["id"],
json.dumps(self.inputs_record_schema, indent=4)))

try:
self.outputs_record_schema = cast(Dict[six.text_type, Any], schema_salad.schema.make_valid_avro(self.outputs_record_schema, {}, set()))
AvroSchemaFromJSONData(self.outputs_record_schema, self.names)
except avro.schema.SchemaParseException as e:
raise validate.ValidationException(u"Got error `%s` while processing outputs of %s:\n%s" %
raise validate.ValidationException(u"Got error '%s' while "
"processing outputs of %s:\n%s" %
(Text(e), self.tool["id"],
json.dumps(self.outputs_record_schema, indent=4)))

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2 changes: 1 addition & 1 deletion cwltool/workflow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ def defaultMakeTool(toolpath_object, # type: Dict[Text, Any]
):
# type: (...) -> Process
if not isinstance(toolpath_object, dict):
raise WorkflowException(u"Not a dict: `%s`" % toolpath_object)
raise WorkflowException(u"Not a dict: '%s'" % toolpath_object)
if "class" in toolpath_object:
if toolpath_object["class"] == "CommandLineTool":
return draft2tool.CommandLineTool(toolpath_object, **kwargs)
Expand Down