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 execute(*params):
parser = parser_execute()
helps = any([True for ht in ["--help", "-h"] if ht in params])
if len(params) <= 1 and helps:
parser.print_help()
raise SystemExit
args, params = parser.parse_known_args(params)
mode = args.mode
params += ["--help"] if args.help is True else []
if mode == "launch":
parser = parser_executeLaunch()
results = parser.parse_args(params)
descriptor = results.descriptor
inp = results.invocation
# Validate invocation and descriptor
arguments = [descriptor, '-i', inp]
if results.sandbox:
arguments.append('--sandbox')
valid = invocation(*arguments)
# Generate object that will perform the commands
from boutiques.localExec import LocalExecutor
executor = LocalExecutor(
descriptor, inp, {
"forcePathType": True,
"debug": results.debug,
"changeUser": results.user,
"stream": results.stream,
"imagePath": results.imagepath,
"skipDataCollect": results.skip_data_collection,
"forceDocker": results.force_docker,
"forceSingularity": results.force_singularity,
"provenance": results.provenance,
"noContainer": results.no_container,
"sandbox": results.sandbox
})
# Execute it
return executor.execute(results.volumes)
if mode == "simulate":
parser = parser_executeSimulate()
results = parser.parse_args(params)
descriptor = results.descriptor
# Do some basic input scrubbing
inp = results.input
arguments = [descriptor]
if inp:
arguments.append('-i')
arguments.append(inp)
if results.sandbox:
arguments.append('--sandbox')
valid = invocation(*arguments)
# Generate object that will perform the commands
from boutiques.localExec import LocalExecutor
executor = LocalExecutor(
descriptor, inp, {
"forcePathType": True,
"destroyTempScripts": True,
"changeUser": True,
"skipDataCollect": True,
"requireComplete": results.complete,
"sandbox": results.sandbox
})
if not inp:
# Add optional inputs with default-value to inputs_dict,
# which is then populated with random params
executor.in_dict = addDefaultValues(executor.desc_dict, {})
executor.generateRandomParams(generateCmdLineFromInDict=True)
if results.json:
sout = [
json.dumps(customSortInvocationByInput(executor.in_dict,
descriptor),
indent=4)
]
print(sout[0])
else:
executor.printCmdLine()
sout = executor.cmd_line
# for consistency with execute
# Adding hide to "container location" field since it's an invalid
# value, can parse that to hide the summary print
return ExecutorOutput(os.linesep.join(sout), "", 0, "", [], [],
os.linesep.join(sout), "", "hide")
if mode == "prepare":
parser = parser_executePrepare()
results = parser.parse_args(params)
descriptor = results.descriptor
# Validate descriptor
arguments = [descriptor]
if results.sandbox:
arguments.append('--sandbox')
valid = invocation(*arguments)
# Generate object that will perform the commands
from boutiques.localExec import LocalExecutor
executor = LocalExecutor(
descriptor, None, {
"forcePathType": True,
"debug": results.debug,
"stream": results.stream,
"imagePath": results.imagepath,
"skipDataCollect": True,
"sandbox": results.sandbox
})
container_location = executor.prepare()[1]
print("Container location: " + container_location)
# Adding hide to "container location" field since it's an invalid
# value, and we can parse that to hide the summary print
return ExecutorOutput(container_location, "", 0, "", [], [], "", "",
"hide")
