def invocation(*params):
parser = ArgumentParser("Creates invocation schema and validates"
" invocations. Uses descriptor's invocation"
" schema if it exists, otherwise creates one.")
parser.add_argument("descriptor", action="store",
help="The Boutiques descriptor as a JSON file, JSON "
"string or Zenodo ID (prefixed by 'zenodo.').")
parser.add_argument("-i", "--invocation", action="store",
help="Input values in a JSON file or as a JSON "
"object to be validated against "
"the invocation schema.")
parser.add_argument("-w", "--write-schema", action="store_true",
help="If descriptor doesn't have an invocation "
"schema, creates one and writes it to the descriptor"
" file ")
result = parser.parse_args(params)
validate(result.descriptor)
descriptor = loadJson(result.descriptor)
if descriptor.get("invocation-schema"):
invSchema = descriptor.get("invocation-schema")
else:
from boutiques.invocationSchemaHandler import generateInvocationSchema
invSchema = generateInvocationSchema(descriptor)
if result.write_schema:
descriptor["invocation-schema"] = invSchema
with open(result.descriptor, "w") as f:
f.write(json.dumps(descriptor, indent=4, sort_keys=True))
if result.invocation:
from boutiques.invocationSchemaHandler import validateSchema
data = addDefaultValues(descriptor, loadJson(result.invocation))
validateSchema(invSchema, data)
def invocation(*params):
parser = parser_invocation()
result = parser.parse_args(params)
validate(result.descriptor)
descriptor = loadJson(result.descriptor)
if descriptor.get("invocation-schema"):
invSchema = descriptor.get("invocation-schema")
else:
from boutiques.invocationSchemaHandler import generateInvocationSchema
invSchema = generateInvocationSchema(descriptor)
if result.write_schema:
descriptor["invocation-schema"] = invSchema
with open(result.descriptor, "w") as f:
f.write(json.dumps(descriptor, indent=4, sort_keys=True))
if result.invocation:
from boutiques.invocationSchemaHandler import validateSchema
data = addDefaultValues(descriptor, loadJson(result.invocation))
validateSchema(invSchema, data)
def invocation(*params):
parser = parser_invocation()
results = parser.parse_args(params)
arguments = [results.descriptor]
if results.sandbox:
arguments.append('--sandbox')
validate(*arguments)
descriptor = loadJson(results.descriptor, sandbox=results.sandbox)
if descriptor.get("invocation-schema"):
invSchema = descriptor.get("invocation-schema")
else:
from boutiques.invocationSchemaHandler import generateInvocationSchema
invSchema = generateInvocationSchema(descriptor)
if results.write_schema:
descriptor["invocation-schema"] = invSchema
with open(results.descriptor, "w") as f:
f.write(json.dumps(descriptor, indent=4))
if results.invocation:
from boutiques.invocationSchemaHandler import validateSchema
data = addDefaultValues(descriptor, loadJson(results.invocation))
validateSchema(invSchema, data)
def invocation(*params):
parser = ArgumentParser(
"Creates invocation schema and validates invocations")
parser.add_argument("descriptor",
action="store",
help="The Boutiques descriptor.")
parser.add_argument(
"-i",
"--invocation",
action="store",
help="Input values in a JSON file to be validated against "
"the invocation schema.")
result = parser.parse_args(params)
try:
from jsonschema import ValidationError
validate(result.descriptor)
if result.invocation:
data = json.loads(open(result.invocation).read())
except ValidationError as e:
print("Error reading JSON:")
raise ValidationError(e.message)
descriptor = json.loads(open(result.descriptor).read())
if descriptor.get("invocation-schema"):
invSchema = descriptor.get("invocation-schema")
else:
from boutiques.invocationSchemaHandler import generateInvocationSchema
invSchema = generateInvocationSchema(descriptor)
descriptor["invocation-schema"] = invSchema
with open(result.descriptor, "w") as f:
f.write(json.dumps(descriptor, indent=4, sort_keys=True))
if result.invocation:
from boutiques.invocationSchemaHandler import validateSchema
try:
validateSchema(invSchema, data)
except ValidationError as e:
print("Invalid invocation:")
raise ValidationError(e.message)