def get(self, args, render_format):
"""
Display dataset record.
"""
# pylint: disable=no-self-use
dataset = Dataset.objects.get(
id=args.dataset_id, include_metadata=args.metadata)
print(render(dataset, render_format))
if render_format == 'table':
from mtclient.models.datafile import DataFile
datafiles = DataFile.list("dataset__id=%s" % args.dataset_id)
if datafiles:
print(render(datafiles, render_format))
def get(self, args, render_format):
"""
Display experiment record.
"""
# pylint: disable=no-self-use
experiment = Experiment.objects.get(id=args.experiment_id,
include_metadata=args.metadata)
print(render(experiment, render_format))
if render_format == 'table':
datasets = Dataset.list(filters="experiments__id=%s" %
args.experiment_id)
if datasets:
print(render(datasets, render_format, display_heading=False))
def get(self, args, render_format):
"""
Display instrument record.
"""
# pylint: disable=no-self-use
instrument = Instrument.objects.get(id=args.instrument_id)
print(render(instrument, render_format))
def list(self, _args, render_format):
"""
Display list of API endpoints.
"""
# pylint: disable=no-self-use
api_endpoints = ApiEndpoint.list()
print(render(api_endpoints, render_format))
def get(self, args, render_format):
"""
Display schema for a model's API endpoint.
"""
# pylint: disable=no-self-use
api_schema = ApiSchema.get(args.api_model)
print(render(api_schema, render_format))
def get(self, args, render_format):
"""
Display datafile record.
"""
# pylint: disable=no-self-use
datafile = DataFile.objects.get(id=args.datafile_id,
include_metadata=args.metadata)
print(render(datafile, render_format))
def list(self, args, render_format):
"""
Display list of experiment records.
"""
# pylint: disable=no-self-use
experiments = Experiment.list(args.filter, args.limit, args.offset,
args.order_by)
print(render(experiments, render_format))
def update(self, args, render_format):
"""
Update dataset record.
"""
# pylint: disable=no-self-use
dataset = Dataset.update(args.dataset_id, args.description)
print(render(dataset, render_format))
print("Dataset updated successfully.")
def update(self, args, render_format):
"""
Update datafile record.
"""
# pylint: disable=no-self-use
datafile = DataFile.update(args.datafile_id, args.md5sum)
print(render(datafile, render_format))
print("DataFile updated successfully.")
def update(self, args, render_format):
"""
Update instrument record.
"""
# pylint: disable=no-self-use
instrument = Instrument.update(args.instrument_id, args.name)
print(render(instrument, render_format))
print("Instrument updated successfully.")
def create(self, args, render_format):
"""
Create dataset record.
"""
# pylint: disable=no-self-use
dataset = Dataset.create(
args.experiment_id, args.description, args.instrument, args.params)
print(render(dataset, render_format))
print("Dataset created successfully.")
def update(self, args, render_format):
"""
Update experiment record.
"""
# pylint: disable=no-self-use
experiment = Experiment.update(args.experiment_id, args.title,
args.description)
print(render(experiment, render_format))
print("Experiment updated successfully.")
def create(self, args, render_format):
"""
Create experiment record.
"""
# pylint: disable=no-self-use
experiment = Experiment.create(args.title, args.description,
args.institution, args.params)
print(render(experiment, render_format))
print("Experiment created successfully.")
def get(self, args, render_format):
"""
Display facility record
"""
super(FacilityController, self).get(args, render_format)
if render_format == 'table':
instruments = Instrument.list(filters="facility__id=%s" %
args.facility_id)
print(render(instruments, render_format))
def create(self, args, render_format):
"""
Create instrument record.
"""
# pylint: disable=no-self-use
facility_id = getattr(args, "facility_id",
getattr(args, "facility", None))
instrument = Instrument.create(facility_id, args.name)
print(render(instrument, render_format))
print("Instrument created successfully.")
def test_render_instrument():
"""
Test rendering a view of an instrument record
"""
mock_facility = {
"id": 1,
"manager_group": {
"id": 1,
"name": "test-facility-managers",
"resource_uri": "/api/v1/group/1/"
},
"name": "Test Facility",
"resource_uri": "/api/v1/facility/1/"
}
mock_facility_get_response = json.dumps(mock_facility)
mock_instrument = {
"created_time": None,
"facility": {
"created_time": None,
"id": 1,
"manager_group": {
"id": 1,
"name": "test-facility-managers",
"resource_uri": "/api/v1/group/1/"
},
"modified_time": None,
"name": "Test Facility",
"resource_uri": "/api/v1/facility/1/"
},
"id": 1,
"modified_time": None,
"name": "Test Instrument",
"resource_uri": "/api/v1/instrument/1/"
}
mock_instrument_get_response = json.dumps(mock_instrument)
expected = textwrap.dedent("""
+------------------+---------------------------+
| Instrument field | Value |
+==================+===========================+
| ID | 1 |
+------------------+---------------------------+
| Name | Test Instrument |
+------------------+---------------------------+
| Facility | <Facility: Test Facility> |
+------------------+---------------------------+
""")
with requests_mock.Mocker() as mocker:
get_facility_url = "%s/api/v1/facility/1/?format=json" % config.url
mocker.get(get_facility_url, text=mock_facility_get_response)
get_instrument_url = "%s/api/v1/instrument/1/?format=json" % config.url
mocker.get(get_instrument_url, text=mock_instrument_get_response)
instrument = Instrument.objects.get(id=1)
assert render(instrument).strip() == expected.strip()
def list(self, args, render_format):
"""
Display list of instrument records.
"""
# pylint: disable=no-self-use
facility_id = getattr(args, "facility_id",
getattr(args, "facility", None))
filters = ""
if facility_id:
filters = "facility__id=%s" % facility_id
instruments = Instrument.list(filters, args.limit, args.offset,
args.order_by)
print(render(instruments, render_format))
def list(self, args, render_format):
"""
Display list of dataset records.
"""
# pylint: disable=no-self-use
if args.exp:
filters = "experiments__id=%s" % args.exp
else:
filters = ""
if args.filter:
filters += "&%s" % args.filter
datasets = Dataset.list(
filters, args.limit, args.offset, args.order_by)
print(render(datasets, render_format))
def create(self, args, render_format):
"""
Create datafile record(s) for an existing file or for all files
within a directory.
"""
# pylint: disable=no-self-use
if os.path.isdir(args.path):
num_created = DataFile.create_datafiles(args.dataset_id,
args.storagebox,
args.dataset_path,
args.path)
print("%s datafiles created." % num_created)
else:
datafile = DataFile.create_datafile(args.dataset_id,
args.storagebox,
args.dataset_path, args.path)
print(render(datafile, render_format))
print("DataFile created successfully.")
def list(self, args, render_format):
"""
Display list of datafile records.
"""
# pylint: disable=no-self-use
if args.dataset:
filters = "dataset__id=%s" % args.dataset
else:
filters = ""
if args.directory:
filters += "&directory=%s" % args.directory
if args.filename:
filters += "&filename=%s" % args.filename
if args.filter:
filters += "&%s" % args.filter
datafiles = DataFile.list(filters, args.limit, args.offset,
args.order_by)
print(render(datafiles, render_format))