def get_instruments_by_exercise_id_csv(exercise_id, session=None):
"""
Finds all collection instruments associated with an exercise and returns them in csv format
:param exercise_id
:param session: database session
:return: collection instruments in csv
"""
log.info('Getting csv for instruments', exercise_id=exercise_id)
validate_uuid(exercise_id)
csv_format = '"{count}","{file_name}","{length}","{date_stamp}"\n'
count = 1
csv = csv_format.format(count='Count',
file_name='File Name',
length='Length',
date_stamp='Time Stamp')
exercise = query_exercise_by_id(exercise_id, session)
if not exercise:
return None
for instrument in exercise.instruments:
csv += csv_format.format(count=count,
file_name=instrument.name,
length=instrument.seft_file.len if instrument.seft_file else None,
date_stamp=instrument.stamp)
count += 1
return csv
def upload_instrument_with_no_collection_exercise(self, survey_id, classifiers=None, session=None):
"""
Upload a collection instrument to the db without a collection exercise
:param classifiers: Classifiers associated with the instrument
:param session: database session
:param survey_id: database session
:return: a collection instrument instance
"""
log.info('Upload instrument', survey_id=survey_id)
validate_uuid(survey_id)
instrument = InstrumentModel(ci_type='EQ')
survey = self._find_or_create_survey_from_survey_id(survey_id, session)
instrument.survey = survey
if classifiers:
deserialized_classifiers = loads(classifiers)
instruments = self._get_instruments_by_classifier(deserialized_classifiers, None, session)
for instrument in instruments:
if instrument.classifiers == deserialized_classifiers:
raise RasError("Cannot upload an instrument with an identical set of classifiers", 400)
instrument.classifiers = deserialized_classifiers
session.add(instrument)
return instrument
def test_validate_uuid_error(self):
# Given a invalid uuid
uuid = "invalid_uuid"
# When a call is made to validate_uuid
# Then an RasError is raised
with self.assertRaises(RasError):
validate_uuid(uuid)
def get_instrument_by_id(instrument_id, session):
"""
Get the collection instrument from the db using the id
:param instrument_id: The id of the instrument we want
:param session: database session
:return: instrument
"""
log.info('Searching for instrument', instrument_id=instrument_id)
validate_uuid(instrument_id)
instrument = query_instrument_by_id(instrument_id, session)
return instrument
def get_exercise_by_id(exercise_id, session):
"""
Retrieves exercise
:param exercise_id: An exercise id (UUID)
:param session: database session
:return: exercise
"""
log.info('Searching for exercise', exercise_id=exercise_id)
validate_uuid(exercise_id)
exercise = query_exercise_by_id(exercise_id, session)
return exercise
def upload_to_bucket(self, exercise_id, file, ru_ref=None, classifiers=None, session=None):
"""
Encrypt and upload a collection instrument to the bucket and db
:param exercise_id: An exercise id (UUID)
:param ru_ref: The name of the file we're receiving
:param classifiers: Classifiers associated with the instrument
:param file: A file object from which we can read the file contents
:param session: database session
:return: a collection instrument instance
"""
log.info("Upload exercise", exercise_id=exercise_id)
validate_uuid(exercise_id)
self.validate_non_duplicate_instrument(file, exercise_id, session)
instrument = InstrumentModel(ci_type="SEFT")
seft_file = self._create_seft_file(instrument.instrument_id, file, encrypt_and_save_to_db=False)
instrument.seft_file = seft_file
exercise = self._find_or_create_exercise(exercise_id, session)
instrument.exercises.append(exercise)
survey = self._find_or_create_survey_from_exercise_id(exercise_id, session)
instrument.survey = survey
if ru_ref:
business = self._find_or_create_business(ru_ref, session)
self.validate_one_instrument_for_ru_specific_upload(exercise, business, session)
instrument.businesses.append(business)
if classifiers:
instrument.classifiers = loads(classifiers)
try:
survey_ref = get_survey_ref(instrument.survey.survey_id)
file.filename = survey_ref + "/" + exercise_id + "/" + file.filename
seft_ci_bucket = GoogleCloudSEFTCIBucket(current_app.config)
seft_ci_bucket.upload_file_to_bucket(file=file)
instrument.seft_file.gcs = True
except Exception as e:
log.exception("An error occurred when trying to put SEFT CI in bucket")
raise e
session.add(instrument)
return instrument
def get_instruments_by_exercise_id_csv(exercise_id, session=None):
"""
Finds all collection instruments associated with an exercise and returns them in csv format
:param exercise_id
:param session: database session
:return: collection instruments in csv
"""
log.info("Getting csv for instruments", exercise_id=exercise_id)
validate_uuid(exercise_id)
csv_format = '"{count}","{file_name}","{length}","{date_stamp}"\n'
count = 1
csv = csv_format.format(count="Count", file_name="File Name", length="Length", date_stamp="Time Stamp")
exercise = query_exercise_by_id(exercise_id, session)
if not exercise:
return None
for instrument in exercise.instruments:
if instrument.seft_file.gcs:
try:
survey_ref = get_survey_ref(instrument.survey.survey_id)
exercise_id = str(instrument.exids[0])
file_path = survey_ref + "/" + exercise_id + "/" + instrument.seft_file.file_name
seft_ci_bucket = GoogleCloudSEFTCIBucket(current_app.config)
file = seft_ci_bucket.download_file_from_bucket(file_path)
csv += csv_format.format(
count=count,
file_name=instrument.seft_file.file_name,
length=len(file),
date_stamp=instrument.stamp,
)
except Exception:
log.exception("Couldn't find SEFT CI in bucket")
else:
csv += csv_format.format(
count=count,
file_name=instrument.name,
length=instrument.seft_file.len if instrument.seft_file else None,
date_stamp=instrument.stamp,
)
count += 1
return csv
def link_instrument_to_exercise(self, instrument_id, exercise_id, session=None):
"""
Link a collection instrument to a collection exercise
:param instrument_id: A collection instrument id (UUID)
:param exercise_id: A collection exercise id (UUID)
:param session: database session
:return: True if instrument has been successfully linked to exercise
"""
log.info('Linking instrument to exercise', instrument_id=instrument_id, exercise_id=exercise_id)
validate_uuid(instrument_id)
validate_uuid(exercise_id)
instrument = self.get_instrument_by_id(instrument_id, session)
exercise = self._find_or_create_exercise(exercise_id, session)
instrument.exercises.append(exercise)
log.info('Successfully linked instrument to exercise', instrument_id=instrument_id, exercise_id=exercise_id)
return True
def test_validate_uuid(self):
# Given a valid uuid
uuid = "6710e50e-224b-4918-9706-c6b28f7481cd"
# When a call is made to validate_uuid
is_valid_uuid = validate_uuid(uuid)
# Then True is returned
self.assertTrue(is_valid_uuid)
def patch_seft_instrument(self, instrument_id: str, file, session):
"""
Replaces the the seft_file for an instrument with the one provided.
:param instrument_id: The top level instrument id that needs changing
:param file: A FileStorage object with the new file
:param session: A database session
:raises RasError: Raised when instrument id is invalid, instrument not found, or instrument isn't of type SEFT
"""
validate_uuid(instrument_id)
instrument = self.get_instrument_by_id(instrument_id, session)
if instrument is None:
log.error('Instrument not found')
raise RasError('Instrument not found', 400)
if instrument.type != 'SEFT':
log.error('Not a SEFT instrument')
raise RasError('Not a SEFT instrument', 400)
seft_model = self._update_seft_file(instrument.seft_file, file)
session.add(seft_model)
def patch_seft_instrument(self, instrument_id: str, file, session):
"""
Replaces the the seft_file for an instrument with the one provided.
:param instrument_id: The top level instrument id that needs changing
:param file: A FileStorage object with the new file
:param session: A database session
:raises RasError: Raised when instrument id is invalid, instrument not found, or instrument isn't of type SEFT
"""
validate_uuid(instrument_id)
instrument = self.get_instrument_by_id(instrument_id, session)
if instrument is None:
log.error("Instrument not found")
raise RasError("Instrument not found", 400)
if instrument.type != "SEFT":
log.error("Not a SEFT instrument")
raise RasError("Not a SEFT instrument", 400)
survey_ref = get_survey_ref(instrument.survey.survey_id)
exercise_id = str(instrument.exids[0])
seft_model = self._update_seft_file(instrument.seft_file, file, survey_ref, exercise_id)
session.add(seft_model)
def upload_instrument(self, exercise_id, file, ru_ref=None, classifiers=None, session=None):
"""
Encrypt and upload a collection instrument to the db
:param exercise_id: An exercise id (UUID)
:param ru_ref: The name of the file we're receiving
:param classifiers: Classifiers associated with the instrument
:param file: A file object from which we can read the file contents
:param session: database session
:return: a collection instrument instance
"""
log.info('Upload exercise', exercise_id=exercise_id)
validate_uuid(exercise_id)
instrument = InstrumentModel(ci_type='SEFT')
seft_file = self._create_seft_file(instrument.instrument_id, file)
instrument.seft_file = seft_file
exercise = self._find_or_create_exercise(exercise_id, session)
instrument.exercises.append(exercise)
survey = self._find_or_create_survey_from_exercise_id(exercise_id, session)
instrument.survey = survey
if ru_ref:
business = self._find_or_create_business(ru_ref, session)
self.validate_one_instrument_for_ru_specific_upload(exercise, business, session)
instrument.businesses.append(business)
if classifiers:
instrument.classifiers = loads(classifiers)
session.add(instrument)
return instrument