def from_json(cls, value):
"""init this request from json back again
:param value: the json (not string) representation
"""
process = Process.from_json(value['process'])
wps_request = WPSRequest()
wps_request.json = json.loads(value['wps_request'])
wps_response = ExecuteResponse(wps_request=wps_request,
uuid=process.uuid,
process=process)
wps_response.store_status_file = True
new_job = Job(process=Process.from_json(value['process']),
wps_request=wps_request,
wps_response=wps_response)
return new_job
def test_insert_request(self):
requests = self.session.query(RequestInstance)
assert requests.count() == 0
obj = {
'operation': 'execute',
'version': '1.0.0',
'language': 'eng',
'identifier': 'multiple-outputs',
'store_execute': True,
'status': True,
'lineage': True,
'inputs': {
'count': [{
'identifier': 'count',
'type': 'literal',
'data': 3
}]
},
'outputs': {},
'raw': False
}
request = WPSRequest()
request.json = obj
from .processes.metalinkprocess import MultipleOutputs
process = MultipleOutputs()
process.uuid = uuid.uuid4()
store_request(process.uuid, request, process)
requests = self.session.query(RequestInstance)
assert requests.count() == 1
stored_request = pop_first_stored()
job = Job.from_json({
"process": json.loads(stored_request.process),
"wps_request": json.loads(stored_request.request)
})
assert job.process.identifier == "multiple-outputs"
assert str(job.process.uuid) == str(process.uuid)
requests = self.session.query(RequestInstance)
assert requests.count() == 0
def test_parse_wps_input():
obj = {
"operation": "execute",
"version": "1.0.0",
"language": "eng",
"identifier": "subset",
"identifiers": "subset", # TODO: why identifierS?
"store_execute": True,
"status": True,
"lineage": True,
"inputs": {
"time": [{
"identifier": "time",
"type": "literal",
"data_type": "string",
"allowed_values": [{
"type": "anyvalue"
}],
"data": "1970/1980",
}],
"time_components": [{
"identifier": "time",
"type": "literal",
"data_type": "string",
"allowed_values": [{
"type": "anyvalue"
}],
"data": "year:1970,1980|month=01,02,03",
}],
},
"outputs": {},
"raw": False,
}
request = WPSRequest()
request.json = obj
assert parse_wps_input(request.inputs, "time", default=None) == "1970/1980"
assert (parse_wps_input(request.inputs, "time_components",
default=None) == "year:1970,1980|month=01,02,03")
def test_stdout_stderr_logging_for_commandline_tool_failure():
"""
Execute a process and assert that stderr is correctly logged to log file.
"""
process = Process({
"title": "test-stdout-stderr",
"id": "test-stdout-stderr",
"package": {
"cwlVersion": "v1.0",
"class": "CommandLineTool",
"baseCommand": "not_existing_command",
"inputs": {
"message": {
"type": "string",
"inputBinding": {
"position": 1
}
}
},
"outputs": {}
}
})
payload = process
package = process["package"]
title = process["title"]
identifier = process["id"]
# WPSPackage._handle()
log_file = tempfile.NamedTemporaryFile()
status_location = log_file.name
workdir = tempfile.TemporaryDirectory()
class TestWpsPackage(WpsPackage):
@property
def status_location(self):
return status_location
wps_package_instance = TestWpsPackage(identifier=identifier,
title=title,
payload=payload,
package=package)
wps_package_instance.set_workdir(workdir.name)
# WPSRequest mock
wps_request = WPSRequest()
wps_request.json = {
"identifier": "test-stdout-stderr",
"operation": "execute",
"version": "1.0.0",
"language": "null",
"identifiers": "null",
"store_execute": "true",
"status": "true",
"lineage": "true",
"raw": "false",
"inputs": {
"message": [{
"identifier": "message",
"title": "A dummy message",
"type": "literal",
"data_type": "string",
"data": "Dummy message",
"allowed_values": [],
}]
},
"outputs": {}
}
# ExecuteResponse mock
wps_response = type("", (object, ), {
"_update_status": lambda *_, **__: 1
})()
from weaver.exceptions import PackageExecutionError
try:
wps_package_instance._handler(wps_request, wps_response)
except PackageExecutionError as exception:
assert "Completed permanentFail" in exception.args[0]
else:
fail(
"\"wps_package._handler()\" was expected to throw \"PackageExecutionError\" exception"
)
def test_stdout_stderr_logging_for_commandline_tool_success():
"""
Execute a process and assert that stdout is correctly logged to log file.
"""
process = Process({
"title": "test-stdout-stderr",
"id": "test-stdout-stderr",
"package": {
"cwlVersion": "v1.0",
"class": "CommandLineTool",
"baseCommand": "echo",
"inputs": {
"message": {
"type": "string",
"inputBinding": {
"position": 1
}
}
},
"outputs": {}
}
})
payload = process
package = process["package"]
title = process["title"]
identifier = process["id"]
# WPSPackage._handle()
log_file = tempfile.NamedTemporaryFile()
status_location = log_file.name
workdir = tempfile.TemporaryDirectory()
class TestWpsPackage(WpsPackage):
@property
def status_location(self):
return status_location
wps_package_instance = TestWpsPackage(identifier=identifier,
title=title,
payload=payload,
package=package)
wps_package_instance.set_workdir(workdir.name)
# WPSRequest mock
wps_request = WPSRequest()
wps_request.json = {
"identifier": "test-stdout-stderr",
"operation": "execute",
"version": "1.0.0",
"language": "null",
"identifiers": "null",
"store_execute": "true",
"status": "true",
"lineage": "true",
"raw": "false",
"inputs": {
"message": [{
"identifier": "message",
"title": "A dummy message",
"type": "literal",
"data_type": "string",
"data": "Dummy message",
"allowed_values": [],
}]
},
"outputs": {}
}
# ExecuteResponse mock
wps_response = type("", (object, ), {
"_update_status": lambda *_, **__: 1
})()
wps_package_instance._handler(wps_request, wps_response)
# log assertions
with open(status_location + ".log", "r") as file:
log_data = file.read()
assert "Dummy message" in log_data
