def get_input_from_form(request):
"""Gets the sidecar processing input arguments from a request object.
Parameters
----------
request: Request object
A Request object containing user data from the sidecar processing form.
Returns
-------
dict
A dictionary containing input arguments for calling the underlying sidecar processing functions.
"""
arguments = {
base_constants.SCHEMA:
get_hed_schema_from_pull_down(request),
base_constants.JSON_SIDECAR:
None,
base_constants.COMMAND:
request.form.get(base_constants.COMMAND_OPTION, None),
base_constants.CHECK_FOR_WARNINGS:
form_has_option(request, base_constants.CHECK_FOR_WARNINGS, 'on'),
base_constants.EXPAND_DEFS:
form_has_option(request, base_constants.EXPAND_DEFS, 'on')
}
if base_constants.JSON_FILE in request.files:
f = request.files[base_constants.JSON_FILE]
fb = io.StringIO(f.read(file_constants.BYTE_LIMIT).decode('ascii'))
arguments[base_constants.JSON_SIDECAR] = models.Sidecar(
file=fb, name=secure_filename(f.filename))
return arguments
def test_process_services_sidecar(self):
from hedweb.services import process
json_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data/bids_events.json')
with open(json_path) as f:
data = json.load(f)
json_text = json.dumps(data)
fb = io.StringIO(json_text)
schema_url = 'https://raw.githubusercontent.com/hed-standard/hed-specification/master/' \
+ 'hedxml/HED8.0.0.xml'
hed_schema = hedschema.load_schema(schema_url)
json_sidecar = models.Sidecar(file=fb, name='JSON_Sidecar')
arguments = {base_constants.SERVICE: 'sidecar_validate', base_constants.SCHEMA: hed_schema,
base_constants.COMMAND: 'validate', base_constants.COMMAND_TARGET: 'sidecar',
base_constants.JSON_SIDECAR: json_sidecar}
with self.app.app_context():
response = process(arguments)
self.assertFalse(response['error_type'],
'sidecar_validation services should not have a fatal error when file is invalid')
results = response['results']
self.assertEqual('success', results['msg_category'],
"sidecar_validation services has success on bids_events.json")
self.assertEqual('8.0.0', results[base_constants.SCHEMA_VERSION], 'Version 8.0.0 was used')
schema_url = 'https://raw.githubusercontent.com/hed-standard/hed-specification/master/' \
+ 'hedxml/HED7.2.0.xml'
arguments[base_constants.SCHEMA] = hedschema.load_schema(schema_url)
with self.app.app_context():
response = process(arguments)
self.assertFalse(response['error_type'],
'sidecar_validation services should not have a error when file is valid')
results = response['results']
self.assertTrue(results['data'], 'sidecar_validation produces errors when file not valid')
self.assertEqual('warning', results['msg_category'], "sidecar_validation did not valid with 7.2.0")
self.assertEqual('7.2.0', results['schema_version'], 'Version 7.2.0 was used')
def test_sidecar_convert_to_short_invalid(self):
from hed import models
from hedweb.sidecar import sidecar_convert
json_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data/bids_events_bad.json')
json_sidecar = models.Sidecar(file=json_path, name='bids_events_bad')
schema_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data/HED8.0.0.xml')
hed_schema = hedschema.load_schema(schema_path)
with self.app.app_context():
results = sidecar_convert(hed_schema, json_sidecar)
self.assertTrue(results['data'], 'sidecar_convert results should have data key')
self.assertEqual('warning', results['msg_category'],
'sidecar_convert msg_category should be warning for errors')
def test_sidecar_validate_valid(self):
from hed import models
from hedweb.sidecar import sidecar_validate
json_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data/bids_events.json')
json_sidecar = models.Sidecar(file=json_path, name='bids_events')
schema_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data/HED8.0.0.xml')
hed_schema = hedschema.load_schema(schema_path)
with self.app.app_context():
results = sidecar_validate(hed_schema, json_sidecar)
self.assertFalse(results['data'],
'sidecar_validate results should not have a data key when no validation errors')
self.assertEqual('success', results["msg_category"],
'sidecar_validate msg_category should be success when no errors')
def test_sidecar_convert_to_long_valid(self):
from hed import models
from hedweb.sidecar import sidecar_convert
from hedweb.constants import base_constants
json_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data/bids_events.json')
json_sidecar = models.Sidecar(file=json_path, name='bids_events')
schema_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data/HED8.0.0.xml')
hed_schema = hedschema.load_schema(schema_path)
with self.app.app_context():
results = sidecar_convert(hed_schema, json_sidecar, command=base_constants.COMMAND_TO_LONG)
self.assertTrue(results['data'],
'sidecar_convert to long results should have data key')
self.assertEqual('success', results["msg_category"],
'sidecar_convert to long msg_category should be success when no errors')
def test_events_validate_invalid(self):
from hedweb.events import validate
events_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data/bids_events.tsv')
json_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data/bids_events_bad.json')
schema_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data/HED8.0.0.xml')
hed_schema = hedschema.load_schema(schema_path)
json_sidecar = models.Sidecar(file=json_path, name='bids_events_bad')
events = models.EventsInput(file=events_path, sidecars=json_sidecar, name='bids_events')
with self.app.app_context():
results = validate(hed_schema, events)
self.assertTrue(results['data'],
'validate results should have a data key when validation errors')
self.assertEqual('warning', results["msg_category"],
'validate msg_category should be warning when errors')
def test_events_assemble_valid(self):
from hedweb.events import assemble
events_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data/bids_events.tsv')
json_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data/bids_events.json')
schema_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data/HED8.0.0.xml')
hed_schema = hedschema.load_schema(schema_path)
json_sidecar = models.Sidecar(file=json_path, name='bids_json')
events = models.EventsInput(file=events_path, sidecars=json_sidecar, name='bids_events')
with self.app.app_context():
results = assemble(hed_schema, events, expand_defs=True)
self.assertTrue(results['data'],
'assemble results should have a data key when no errors')
self.assertEqual('success', results['msg_category'],
'assemble msg_category should be success when no errors')
def test_sidecar_process_valid_to_short_defs_expanded(self):
from hedweb.sidecar import process
json_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data/bids_events.json')
json_sidecar = models.Sidecar(file=json_path, name='bids_events')
schema_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data/HED8.0.0.xml')
hed_schema = hedschema.load_schema(schema_path)
arguments = {base_constants.SCHEMA: hed_schema, base_constants.JSON_SIDECAR: json_sidecar,
base_constants.JSON_DISPLAY_NAME: 'bids_events',
base_constants.EXPAND_DEFS: True,
base_constants.COMMAND: base_constants.COMMAND_TO_SHORT}
with self.app.app_context():
results = process(arguments)
self.assertTrue(isinstance(results, dict),
'process to short should return a dict when no errors and defs expanded')
self.assertEqual('success', results['msg_category'],
'process to short should return success if no errors and defs_expanded')
def test_events_process_invalid(self):
from hedweb.events import process
events_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data/bids_events.tsv')
json_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data/bids_events_bad.json')
schema_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data/HED8.0.0.xml')
hed_schema = hedschema.load_schema(schema_path)
json_sidecar = models.Sidecar(file=json_path, name='bids_events_bad')
events = models.EventsInput(file=events_path, sidecars=json_sidecar, name='bids_events')
arguments = {base_constants.EVENTS: events, base_constants.COMMAND: base_constants.COMMAND_VALIDATE,
base_constants.EXPAND_DEFS: True,
base_constants.CHECK_FOR_WARNINGS: True, base_constants.SCHEMA: hed_schema}
with self.app.app_context():
results = process(arguments)
self.assertTrue(isinstance(results, dict),
'process validation should return a result dictionary when validation errors')
self.assertEqual('warning', results['msg_category'],
'process validate should return warning when errors')
def test_sidecar_process_invalid(self):
from hedweb.sidecar import process
json_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data/bids_events_bad.json')
json_sidecar = models.Sidecar(file=json_path, name='bids_events_bad')
schema_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data/HED8.0.0.xml')
hed_schema = hedschema.load_schema(schema_path)
arguments = {base_constants.SCHEMA: hed_schema, base_constants.JSON_SIDECAR: json_sidecar,
base_constants.JSON_DISPLAY_NAME: 'bids_events_bad',
base_constants.COMMAND: base_constants.COMMAND_TO_SHORT}
with self.app.app_context():
results = process(arguments)
self.assertTrue(isinstance(results, dict),
'process to short should return a dictionary when errors')
self.assertEqual('warning', results['msg_category'],
'process to short should give warning when JSON with errors')
self.assertTrue(results['data'],
'process to short should not convert using HED 8.0.0.xml')
def get_input_from_events_form(request):
"""Gets the validation function input arguments from a request object associated with the validation form.
Parameters
----------
request: Request object
A Request object containing user data from the validation form.
Returns
-------
dictionary
A dictionary containing input arguments for calling the underlying validation function.
"""
arguments = {
base_constants.SCHEMA:
get_hed_schema_from_pull_down(request),
base_constants.EVENTS:
None,
base_constants.COMMAND:
request.form.get(base_constants.COMMAND_OPTION, ''),
base_constants.CHECK_FOR_WARNINGS:
form_has_option(request, base_constants.CHECK_FOR_WARNINGS, 'on'),
base_constants.EXPAND_DEFS:
form_has_option(request, base_constants.EXPAND_DEFS, 'on'),
base_constants.COLUMNS_SELECTED:
create_column_selections(request.form)
}
json_sidecar = None
if base_constants.JSON_FILE in request.files:
f = request.files[base_constants.JSON_FILE]
json_sidecar = models.Sidecar(file=f, name=secure_filename(f.filename))
arguments[base_constants.JSON_SIDECAR] = json_sidecar
if base_constants.EVENTS_FILE in request.files:
f = request.files[base_constants.EVENTS_FILE]
arguments[base_constants.EVENTS] = \
models.EventsInput(file=f, sidecars=json_sidecar, name=secure_filename(f.filename))
return arguments
def get_input_objects(arguments, params):
if base_constants.JSON_STRING in params and params[
base_constants.JSON_STRING]:
arguments[base_constants.JSON_SIDECAR] = \
models.Sidecar(file=io.StringIO(params[base_constants.JSON_STRING]), name='JSON_Sidecar')
if base_constants.EVENTS_STRING in params and params[
base_constants.EVENTS_STRING]:
arguments[base_constants.EVENTS] = \
models.EventsInput(file=io.StringIO(params[base_constants.EVENTS_STRING]),
sidecars=arguments[base_constants.JSON_SIDECAR], name='Events')
if base_constants.SPREADSHEET_STRING in params and params[
base_constants.SPREADSHEET_STRING]:
tag_columns, prefix_dict = spreadsheet.get_prefix_dict(params)
arguments[base_constants.SPREADSHEET] = \
models.HedInput(file=io.StringIO(params[base_constants.SPREADSHEET_STRING]), file_type=".tsv",
tag_columns=tag_columns,
has_column_names=arguments.get(base_constants.HAS_COLUMN_NAMES, None),
column_prefix_dictionary=prefix_dict, name='spreadsheet.tsv')
if base_constants.STRING_LIST in params and params[
base_constants.STRING_LIST]:
s_list = []
for s in params[base_constants.STRING_LIST]:
s_list.append(models.HedString(s))
arguments[base_constants.STRING_LIST] = s_list
