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8a1dc5ceeb00e396702b8dacc06fcdc8dbdacc57 | bbt-t/simple-bot_discord | handlers/all_handlers.py | [
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] | Python | on_member_join | null | async def on_member_join(member):
"""
Registration of a new user in the DB.
:param member: user-object
:return: greeting to PM
"""
db.add_user(user_id=member.id, name=member.name, reg_time=time_now.date())
await member.send(embed=Embed(description=f'Привееет {member.name}! Рад тебя видеть!\n... |
Registration of a new user in the DB.
:param member: user-object
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db.add_user(user_id=member.id, name=member.name, reg_time=time_now.date())
await member.send(embed=Embed(description=f'Привееет {member.name}! Рад тебя видеть!\n'
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e44005a655d6d40187fd36f3b5830d29ca70cc70 | Newbas/beiwe-backend | libs/file_processing/data_qty_stats.py | [
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participant: Participant,
earliest_time_bin_number: Optional[int] = None,
latest_time_bin_number: Optional[int] = None,
):
""" Update the SummaryStatisticDaily stats for a participant, using ChunkRegistry data
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earliest_time_bin_number -- expressed in hours since 1/1/1970
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6d9ae30dbe6ceb0c1972306297da6fc70a8f58f2 | Newbas/beiwe-backend | api/survey_api.py | [
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] | Python | update_survey | <not_specific> | def update_survey(survey_id=None):
"""
Updates the survey when the 'Save & Deploy button on the edit_survey page is hit. Expects
content, weekly_timings, absolute_timings, relative_timings, and settings in the request body
"""
try:
survey = Survey.objects.get(pk=survey_id)
except ... |
Updates the survey when the 'Save & Deploy button on the edit_survey page is hit. Expects
content, weekly_timings, absolute_timings, relative_timings, and settings in the request body
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6d9ae30dbe6ceb0c1972306297da6fc70a8f58f2 | Newbas/beiwe-backend | api/survey_api.py | [
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count = 100
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6d9ae30dbe6ceb0c1972306297da6fc70a8f58f2 | Newbas/beiwe-backend | api/survey_api.py | [
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] | Python | make_slider_min_max_values_strings | <not_specific> | def make_slider_min_max_values_strings(json_content):
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backwards compatibility; when all the iOS apps involved in studies can handle ints,
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6b05db02c96cc08d1fc5438e18d689711bd8c807 | Newbas/beiwe-backend | api/tableau_api/web_data_connector.py | [
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] | Python | register_urls | null | def register_urls(cls, app):
"""
Register this class' URLs with Flask
"""
app.add_url_rule(cls.path, view_func=cls.as_view("web_data_connector_view")) |
Register this class' URLs with Flask
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4ccdeeadaba62f2ae5bf19d998bbc5bd3cb74b90 | Newbas/beiwe-backend | database/data_access_models.py | [
"BSD-3-Clause"
] | Python | update_registered_unchunked_data | null | def update_registered_unchunked_data(cls, data_type, chunk_path, file_contents):
""" Updates the data in case a user uploads an unchunkable file more than once,
and updates the file size just in case it changed. """
if data_type in CHUNKABLE_FILES:
raise ChunkableDataTypeError
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4ccdeeadaba62f2ae5bf19d998bbc5bd3cb74b90 | Newbas/beiwe-backend | database/data_access_models.py | [
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4ccdeeadaba62f2ae5bf19d998bbc5bd3cb74b90 | Newbas/beiwe-backend | database/data_access_models.py | [
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88f28cfa31d06f67bc38785a86abc33d3cea01fd | Newbas/beiwe-backend | pages/system_admin_pages.py | [
"BSD-3-Clause"
] | Python | validate_android_credentials | <not_specific> | def validate_android_credentials(credentials):
"""Ensure basic formatting and field validation for android firebase credential json file uploads
the credentials argument should contain a decoded string of such a file"""
try:
json_obj = json.dumps(credentials)
# keys are inconsistent in prese... | Ensure basic formatting and field validation for android firebase credential json file uploads
the credentials argument should contain a decoded string of such a file | Ensure basic formatting and field validation for android firebase credential json file uploads
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json_obj = json.dumps(credentials)
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except Exception:
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} |
88f28cfa31d06f67bc38785a86abc33d3cea01fd | Newbas/beiwe-backend | pages/system_admin_pages.py | [
"BSD-3-Clause"
] | Python | validate_ios_credentials | <not_specific> | def validate_ios_credentials(credentials):
"""Ensure basic formatting and field validation for ios firebase credential plist file uploads
the credentials argument should contain a decoded string of such a file"""
try:
plist_obj = plistlib.loads(str.encode(credentials))
# ios has different ke... | Ensure basic formatting and field validation for ios firebase credential plist file uploads
the credentials argument should contain a decoded string of such a file | Ensure basic formatting and field validation for ios firebase credential plist file uploads
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try:
plist_obj = plistlib.loads(str.encode(credentials))
if "API_KEY" not in plist_obj:
return False
except Exception:
return False
return True | [
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} |
c0e8d210ab173879e65c2faeb9225d62e3ab3312 | Newbas/beiwe-backend | database/schedule_models.py | [
"BSD-3-Clause"
] | Python | create_absolute_schedules | bool | def create_absolute_schedules(timings: List[List[int]], survey: Survey) -> bool:
""" Creates new AbsoluteSchedule objects from a frontend-style list of dates and times"""
survey.absolute_schedules.all().delete()
if survey.deleted or not timings:
return False
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survey.absolute_schedules.all().delete()
if survey.deleted or not timings:
return False
duplicated = False
for year, month, day, num_seconds in timings:
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... |
c0e8d210ab173879e65c2faeb9225d62e3ab3312 | Newbas/beiwe-backend | database/schedule_models.py | [
"BSD-3-Clause"
] | Python | create_relative_schedules | bool | def create_relative_schedules(timings: List[List[int]], survey: Survey) -> bool:
"""
Creates new RelativeSchedule objects from a frontend-style list of interventions and times
If you modify this please update create_relative_schedules_by_name in libs.copy_study too.
"""
surv... |
Creates new RelativeSchedule objects from a frontend-style list of interventions and times
If you modify this please update create_relative_schedules_by_name in libs.copy_study too.
| Creates new RelativeSchedule objects from a frontend-style list of interventions and times
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survey.relative_schedules.all().delete()
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duplicated = False
for intervention_id, days_after, num_seconds in timings:
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... |
c0e8d210ab173879e65c2faeb9225d62e3ab3312 | Newbas/beiwe-backend | database/schedule_models.py | [
"BSD-3-Clause"
] | Python | create_weekly_schedules | bool | def create_weekly_schedules(timings: List[List[int]], survey: Survey) -> bool:
""" Creates new WeeklySchedule objects from a frontend-style list of seconds into the day. """
if survey.deleted or not timings:
survey.weekly_schedules.all().delete()
return False
# a... | Creates new WeeklySchedule objects from a frontend-style list of seconds into the day. | Creates new WeeklySchedule objects from a frontend-style list of seconds into the day. | [
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if survey.deleted or not timings:
survey.weekly_schedules.all().delete()
return False
if len(timings) != 7:
raise Exception(
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... |
c0e8d210ab173879e65c2faeb9225d62e3ab3312 | Newbas/beiwe-backend | database/schedule_models.py | [
"BSD-3-Clause"
] | Python | export_survey_timings | List[List[int]] | def export_survey_timings(cls, survey: Survey) -> List[List[int]]:
"""Returns a json formatted list of weekly timings for use on the frontend"""
# this weird sort order results in correctly ordered output.
fields_ordered = ("hour", "minute", "day_of_week")
timings = [[], [], [], [], ... | Returns a json formatted list of weekly timings for use on the frontend | Returns a json formatted list of weekly timings for use on the frontend | [
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] | def export_survey_timings(cls, survey: Survey) -> List[List[int]]:
fields_ordered = ("hour", "minute", "day_of_week")
timings = [[], [], [], [], [], [], []]
schedule_components = WeeklySchedule.objects. \
filter(survey=survey).order_by(*fields_ordered).values_list(*fields_ordered)
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c0e8d210ab173879e65c2faeb9225d62e3ab3312 | Newbas/beiwe-backend | database/schedule_models.py | [
"BSD-3-Clause"
] | Python | find_pending_events | null | def find_pending_events(
participant: Participant = None, survey: Survey or str = None,
tz: tzinfo = gettz('America/New_York'),
):
""" THIS FUNCTION IS FOR DEBUGGING PURPOSES ONLY
Throw in a participant and or survey object, OR THEIR IDENTIFYING STRING and we make it w... | THIS FUNCTION IS FOR DEBUGGING PURPOSES ONLY
Throw in a participant and or survey object, OR THEIR IDENTIFYING STRING and we make it work
'tz' will normalize timestamps to that timezone, default is us east.
| THIS FUNCTION IS FOR DEBUGGING PURPOSES ONLY
Throw in a participant and or survey object, OR THEIR IDENTIFYING STRING and we make it work
'tz' will normalize timestamps to that timezone, default is us east. | [
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participant: Participant = None, survey: Survey or str = None,
tz: tzinfo = gettz('America/New_York'),
):
filters = {}
if participant:
filters['participant'] = participant
if survey:
filters["survey"] = survey
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18bcf5bb9065fe29676520dd7385ee9f6057769c | Newbas/beiwe-backend | api/push_notifications_api.py | [
"BSD-3-Clause"
] | Python | send_notification | <not_specific> | def send_notification():
"""
Sends a push notification to the participant, used for testing
Expects a patient_id in the request body.
"""
print(check_firebase_instance())
message = messaging.Message(
data={
'type': 'fake',
'content': 'hello good sir',
... |
Sends a push notification to the participant, used for testing
Expects a patient_id in the request body.
| Sends a push notification to the participant, used for testing
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print(check_firebase_instance())
message = messaging.Message(
data={
'type': 'fake',
'content': 'hello good sir',
},
token=get_session_participant().get_fcm_token().token,
)
response = messaging.send(message)
print('Successfull... | [
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18bcf5bb9065fe29676520dd7385ee9f6057769c | Newbas/beiwe-backend | api/push_notifications_api.py | [
"BSD-3-Clause"
] | Python | send_survey_notification | <not_specific> | def send_survey_notification():
"""
Sends a push notification to the participant with survey data, used for testing
Expects a patient_id in the request body
"""
participant = get_session_participant()
survey_ids = list(
participant.study.surveys.filter(deleted=False).exclude(surve... |
Sends a push notification to the participant with survey data, used for testing
Expects a patient_id in the request body
| Sends a push notification to the participant with survey data, used for testing
Expects a patient_id in the request body | [
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participant = get_session_participant()
survey_ids = list(
participant.study.surveys.filter(deleted=False).exclude(survey_type="image_survey")
.values_list("object_id", flat=True)[:4]
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c7a1976da6893d5b2a4508b7653617472f44f759 | Newbas/beiwe-backend | api/participant_administration.py | [
"BSD-3-Clause"
] | Python | reset_participant_password | <not_specific> | def reset_participant_password():
""" Takes a patient ID and resets its password. Returns the new random password."""
patient_id = request.values['patient_id']
study_id = request.values['study_id']
try:
participant = Participant.objects.get(patient_id=patient_id)
except Participant.DoesNotE... | Takes a patient ID and resets its password. Returns the new random password. | Takes a patient ID and resets its password. Returns the new random password. | [
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patient_id = request.values['patient_id']
study_id = request.values['study_id']
try:
participant = Participant.objects.get(patient_id=patient_id)
except Participant.DoesNotExist:
flash(f'The participant {patient_id} does not exist', 'danger')
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c7a1976da6893d5b2a4508b7653617472f44f759 | Newbas/beiwe-backend | api/participant_administration.py | [
"BSD-3-Clause"
] | Python | reset_device | <not_specific> | def reset_device():
"""
Resets a participant's device. The participant will not be able to connect until they
register a new device.
"""
patient_id = request.values['patient_id']
study_id = request.values['study_id']
try:
participant = Participant.objects.get(patient_id=patient_id)... |
Resets a participant's device. The participant will not be able to connect until they
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patient_id = request.values['patient_id']
study_id = request.values['study_id']
try:
participant = Participant.objects.get(patient_id=patient_id)
except Participant.DoesNotExist:
flash(f'The participant {patient_id} does not exist', 'danger')
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c7a1976da6893d5b2a4508b7653617472f44f759 | Newbas/beiwe-backend | api/participant_administration.py | [
"BSD-3-Clause"
] | Python | unregister_participant | <not_specific> | def unregister_participant():
"""
Block participant from uploading further data
"""
patient_id = request.values['patient_id']
study_id = request.values['study_id']
try:
participant = Participant.objects.get(patient_id=patient_id)
except Participant.DoesNotExist:
flash(f'The... |
Block participant from uploading further data
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patient_id = request.values['patient_id']
study_id = request.values['study_id']
try:
participant = Participant.objects.get(patient_id=patient_id)
except Participant.DoesNotExist:
flash(f'The participant {patient_id} does not exist', 'danger')
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c7a1976da6893d5b2a4508b7653617472f44f759 | Newbas/beiwe-backend | api/participant_administration.py | [
"BSD-3-Clause"
] | Python | create_new_participant | <not_specific> | def create_new_participant():
"""
Creates a new user, generates a password and keys, pushes data to s3 and user database, adds
user to the study they are supposed to be attached to and returns a string containing
password and patient id.
"""
study_id = request.values['study_id']
patient_id,... |
Creates a new user, generates a password and keys, pushes data to s3 and user database, adds
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study_id = request.values['study_id']
patient_id, password = Participant.create_with_password(study_id=study_id)
participant = Participant.objects.get(patient_id=patient_id)
study = Study.objects.get(id=study_id)
add_fields_and_interventions(participant, study)
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c7a1976da6893d5b2a4508b7653617472f44f759 | Newbas/beiwe-backend | api/participant_administration.py | [
"BSD-3-Clause"
] | Python | create_many_patients | <not_specific> | def create_many_patients(study_id=None):
""" Creates a number of new users at once for a study. Generates a password and keys for
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number_of_new_patients = int(request.form.get('number_of_new_patients', 0))
desired_filename = request.form.get('desired_filename', '')
filename_spaces_to_underscores = sub(r'[\ =]', '_', desired_filename)
filename = sub(r'[^a-zA-Z0-9_\.=]', '', filename_spaces_t... | [
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c7a1976da6893d5b2a4508b7653617472f44f759 | Newbas/beiwe-backend | api/participant_administration.py | [
"BSD-3-Clause"
] | Python | add_fields_and_interventions | null | def add_fields_and_interventions(participant: Participant, study: Study):
""" Creates empty ParticipantFieldValue and InterventionDate objects for newly created
participants, doesn't affect existing instances. """
for field in study.fields.all():
ParticipantFieldValue.objects.get_or_create(particip... | Creates empty ParticipantFieldValue and InterventionDate objects for newly created
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for field in study.fields.all():
ParticipantFieldValue.objects.get_or_create(participant=participant, field=field)
for intervention in study.interventions.all():
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9f77fad167ad960a1df52146616494604bb8a1b8 | Newbas/beiwe-backend | database/tableau_api_models.py | [
"BSD-3-Clause"
] | Python | construct_summary_statistics | <not_specific> | def construct_summary_statistics(self):
"""
Construct summary statistics from forest output, returning whether or not any
SummaryStatisticDaily has potentially been created or updated.
"""
if not os.path.exists(self.forest_results_path):
return False
if self.... |
Construct summary statistics from forest output, returning whether or not any
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if not os.path.exists(self.forest_results_path):
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if self.forest_tree == ForestTree.jasmine:
task_attribute = "jasmine_task"
elif self.forest_tree == ForestTree.willow:
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9f77fad167ad960a1df52146616494604bb8a1b8 | Newbas/beiwe-backend | database/tableau_api_models.py | [
"BSD-3-Clause"
] | Python | clean_up_files | null | def clean_up_files(self):
"""
Delete temporary input and output files from this Forest run.
"""
shutil.rmtree(self.data_base_path) |
Delete temporary input and output files from this Forest run.
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9f77fad167ad960a1df52146616494604bb8a1b8 | Newbas/beiwe-backend | database/tableau_api_models.py | [
"BSD-3-Clause"
] | Python | data_base_path | <not_specific> | def data_base_path(self):
"""
Return the path to the base data folder, creating it if it doesn't already exist.
"""
return os.path.join("/tmp", str(self.external_id), self.forest_tree) |
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9f77fad167ad960a1df52146616494604bb8a1b8 | Newbas/beiwe-backend | database/tableau_api_models.py | [
"BSD-3-Clause"
] | Python | data_input_path | <not_specific> | def data_input_path(self):
"""
Return the path to the input data folder, creating it if it doesn't already exist.
"""
return os.path.join(self.data_base_path, "data") |
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9f77fad167ad960a1df52146616494604bb8a1b8 | Newbas/beiwe-backend | database/tableau_api_models.py | [
"BSD-3-Clause"
] | Python | data_output_path | <not_specific> | def data_output_path(self):
"""
Return the path to the output data folder, creating it if it doesn't already exist.
"""
return os.path.join(self.data_base_path, "output") |
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9f77fad167ad960a1df52146616494604bb8a1b8 | Newbas/beiwe-backend | database/tableau_api_models.py | [
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] | Python | forest_results_path | <not_specific> | def forest_results_path(self):
"""
Return the path to the file that contains the output of Forest.
"""
return os.path.join(self.data_output_path, f"{self.participant.patient_id}.csv") |
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9f77fad167ad960a1df52146616494604bb8a1b8 | Newbas/beiwe-backend | database/tableau_api_models.py | [
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] | Python | params_dict | <not_specific> | def params_dict(self):
"""
Return a dict of params to pass into the Forest function.
"""
other_params = {
"output_folder": self.data_output_path,
"study_folder": self.data_input_path,
# Need to add a day since this model tracks time end inclusively, bu... |
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"time_end": datetime_to_list(self.data_date_end + datetime.timedelta(days=1)),
"time_start": datetime_to_list(self.data_date_start),
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9f77fad167ad960a1df52146616494604bb8a1b8 | Newbas/beiwe-backend | database/tableau_api_models.py | [
"BSD-3-Clause"
] | Python | generate_all_bv_set_s3_key | <not_specific> | def generate_all_bv_set_s3_key(self):
"""
Generate the S3 key that all_bv_set_s3_key should live in (whereas the direct
all_bv_set_s3_key field on the instance is where it currently lives, regardless
of how generation changes).
"""
return os.path.join(self.s3_base_folder,... |
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9f77fad167ad960a1df52146616494604bb8a1b8 | Newbas/beiwe-backend | database/tableau_api_models.py | [
"BSD-3-Clause"
] | Python | generate_all_memory_dict_s3_key | <not_specific> | def generate_all_memory_dict_s3_key(self):
"""
Generate the S3 key that all_memory_dict_s3_key should live in (whereas the direct
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"""
return os.path.join(self.... |
Generate the S3 key that all_memory_dict_s3_key should live in (whereas the direct
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0fbfac9bbdd2da12f57b522080dad6bfc6ea7df8 | Newbas/beiwe-backend | services/celery_push_notifications.py | [
"BSD-3-Clause"
] | Python | celery_send_push_notification | <not_specific> | def celery_send_push_notification(fcm_token: str, survey_obj_ids: List[str], schedule_pks: List[int]):
''' Celery task that sends push notifications. Note that this list of pks may contain duplicates.'''
# Oh. The reason we need the patient_id is so that we can debug anything ever. lol...
patient_id = Part... | Celery task that sends push notifications. Note that this list of pks may contain duplicates. | Celery task that sends push notifications. Note that this list of pks may contain duplicates. | [
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patient_id = ParticipantFCMHistory.objects.filter(token=fcm_token) \
.values_list("participant__patient_id", flat=True).get()
with make_error_sentry(sentry_type=SentryTypes.data_processing):
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3a2fc409837822733ad287784881a10d07dc7af9 | Newbas/beiwe-backend | cluster_management/launch_script.py | [
"BSD-3-Clause"
] | Python | load_git_repo | null | def load_git_repo():
""" Get a local copy of the git repository """
# Git clone the repository into the remote beiwe-backend folder
# git operations print to both stderr *and* stdout, so redirect them both to the log file
run(f'cd {REMOTE_HOME_DIR}; git clone https://github.com/onnela-lab/beiwe-backend.... | Get a local copy of the git repository | Get a local copy of the git repository | [
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run(f'cd {REMOTE_HOME_DIR}; git clone https://github.com/onnela-lab/beiwe-backend.git 2>> {LOG_FILE}')
if DEV_MODE:
branch = environ.get("DEV_BRANCH", "development")
else:
branch = "main"
run(f'cd {REMOTE_HOME_DIR}/beiwe-backend; git checkout {branch} 1>> {LOG_FILE} ... | [
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3a2fc409837822733ad287784881a10d07dc7af9 | Newbas/beiwe-backend | cluster_management/launch_script.py | [
"BSD-3-Clause"
] | Python | do_create_single_server_ami | null | def do_create_single_server_ami(ip_address, key_filename):
"""
Set up a beiwe-backend deployment on a single server suitable for turning into an AMI
:param ip_address: IP address of the server you're setting up as an AMI
:param key_filename: Full filepath of the key that lets you SSH into that server
... |
Set up a beiwe-backend deployment on a single server suitable for turning into an AMI
:param ip_address: IP address of the server you're setting up as an AMI
:param key_filename: Full filepath of the key that lets you SSH into that server
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configure_fabric(None, ip_address, key_filename=key_filename)
push_home_directory_files()
apt_installs(single_server_ami=True)
load_git_repo()
setup_python()
push_beiwe_configuration(None, single_server_ami=True)
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3add3bb29df4dabf8d424746b22a065a3a3a2cde | Newbas/beiwe-backend | libs/celery_control.py | [
"BSD-3-Clause"
] | Python | safe_apply_async | <not_specific> | def safe_apply_async(a_task_for_a_celery_queue, *args, **kwargs):
""" Enqueuing a new task, for which we use Celery's most flexible `apply_async` function,
can fail deep inside amqp/transport.py with an OperationalError. Use this common wrapper to
handle that case.
An "a_task_for_a_celery_queue" is eit... | Enqueuing a new task, for which we use Celery's most flexible `apply_async` function,
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handle that case.
An "a_task_for_a_celery_queue" is either a "@celery_app.task"-wrapped function' or it is a
FalseCeleryApp.... | Enqueuing a new task, for which we use Celery's most flexible `apply_async` function,
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for i in range(10):
try:
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except OperationalError:
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7d7fdf71fdca90d240ef0fe72471937a9d524e99 | Newbas/beiwe-backend | libs/sentry.py | [
"BSD-3-Clause"
] | Python | make_error_sentry | <not_specific> | def make_error_sentry(sentry_type:str, tags:dict=None):
""" Creates an ErrorSentry, defaults to error limit 10.
If the applicable sentry DSN is missing will return an ErrorSentry,
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return null_error_ha... | Creates an ErrorSentry, defaults to error limit 10.
If the applicable sentry DSN is missing will return an ErrorSentry,
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tags = tags or {}
tags["sentry_type"] = sentry_type
try:
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fd41ae0c3cf36af6460c35ba500f21e65d4aaa6a | Newbas/beiwe-backend | database/survey_models.py | [
"BSD-3-Clause"
] | Python | create_with_settings | <not_specific> | def create_with_settings(cls, survey_type: str, **kwargs):
"""
Create a new Survey with the provided survey type and attached to the given Study,
as well as any other given keyword arguments. If the Survey is audio/image and no other
settings are given, give it the default audio/image su... |
Create a new Survey with the provided survey type and attached to the given Study,
as well as any other given keyword arguments. If the Survey is audio/image and no other
settings are given, give it the default audio/image survey settings.
| Create a new Survey with the provided survey type and attached to the given Study,
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settings are given, give it the default audio/image survey settings. | [
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if survey_type == cls.AUDIO_SURVEY and 'settings' not in kwargs:
kwargs['settings'] = json.dumps(AUDIO_SURVEY_SETTINGS)
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fd41ae0c3cf36af6460c35ba500f21e65d4aaa6a | Newbas/beiwe-backend | database/survey_models.py | [
"BSD-3-Clause"
] | Python | weekly_timings | <not_specific> | def weekly_timings(self):
"""
Returns a json serializable object that represents the weekly schedules of this survey.
The return object is a list of 7 lists of ints
"""
from database.schedule_models import WeeklySchedule
return WeeklySchedule.export_survey_timings(self) |
Returns a json serializable object that represents the weekly schedules of this survey.
The return object is a list of 7 lists of ints
| Returns a json serializable object that represents the weekly schedules of this survey.
The return object is a list of 7 lists of ints | [
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from database.schedule_models import WeeklySchedule
return WeeklySchedule.export_survey_timings(self) | [
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} |
fd41ae0c3cf36af6460c35ba500f21e65d4aaa6a | Newbas/beiwe-backend | database/survey_models.py | [
"BSD-3-Clause"
] | Python | relative_timings | <not_specific> | def relative_timings(self):
"""
Returns a json serializable object that represents the relative schedules of the survey
The return object is a list of lists of intervention ids, days offset, and seconds offset.
"""
schedules = []
for schedule in self.relative_schedules.al... |
Returns a json serializable object that represents the relative schedules of the survey
The return object is a list of lists of intervention ids, days offset, and seconds offset.
| Returns a json serializable object that represents the relative schedules of the survey
The return object is a list of lists of intervention ids, days offset, and seconds offset. | [
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schedules = []
for schedule in self.relative_schedules.all():
num_seconds = schedule.minute * 60 + schedule.hour * 3600
schedules.append([schedule.intervention.id, schedule.days_after, num_seconds])
return schedules | [
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} |
fd41ae0c3cf36af6460c35ba500f21e65d4aaa6a | Newbas/beiwe-backend | database/survey_models.py | [
"BSD-3-Clause"
] | Python | relative_timings_by_name | <not_specific> | def relative_timings_by_name(self):
"""
Returns a json serializable object that represents the relative schedules of the survey
The return object is a list of lists of intervention names, days offset, and seconds offset.
"""
schedules = []
for schedule in self.relative_sc... |
Returns a json serializable object that represents the relative schedules of the survey
The return object is a list of lists of intervention names, days offset, and seconds offset.
| Returns a json serializable object that represents the relative schedules of the survey
The return object is a list of lists of intervention names, days offset, and seconds offset. | [
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schedules = []
for schedule in self.relative_schedules.all():
num_seconds = schedule.minute * 60 + schedule.hour * 3600
schedules.append([schedule.intervention.name, schedule.days_after, num_seconds])
return schedules | [
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} |
fd41ae0c3cf36af6460c35ba500f21e65d4aaa6a | Newbas/beiwe-backend | database/survey_models.py | [
"BSD-3-Clause"
] | Python | absolute_timings | <not_specific> | def absolute_timings(self):
"""
Returns a json serializable object that represents the absolute schedules of the survey
The return object is a list of lists of the year, month, day and seconds within the day.
"""
schedules = []
for schedule in self.absolute_schedules.all(... |
Returns a json serializable object that represents the absolute schedules of the survey
The return object is a list of lists of the year, month, day and seconds within the day.
| Returns a json serializable object that represents the absolute schedules of the survey
The return object is a list of lists of the year, month, day and seconds within the day. | [
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schedules = []
for schedule in self.absolute_schedules.all():
event_time = schedule.event_time
num_seconds = event_time.minute * 60 + event_time.hour * 3600
schedules.append([event_time.year, event_time.month, event_time.day, num_seconds])
... | [
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} |
fd41ae0c3cf36af6460c35ba500f21e65d4aaa6a | Newbas/beiwe-backend | database/survey_models.py | [
"BSD-3-Clause"
] | Python | format_survey_for_study | <not_specific> | def format_survey_for_study(self):
"""
Returns a dict with the values of the survey fields for download to the app
"""
survey_dict = self.as_unpacked_native_python()
# Make the dict look like the old Mongolia-style dict that the frontend is expecting
survey_dict.pop('id')... |
Returns a dict with the values of the survey fields for download to the app
| Returns a dict with the values of the survey fields for download to the app | [
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survey_dict = self.as_unpacked_native_python()
survey_dict.pop('id')
survey_dict.pop('deleted')
survey_dict['_id'] = survey_dict.pop('object_id')
from database.schedule_models import WeeklySchedule
survey_dict['timings'] = WeeklySchedule... | [
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} |
fd41ae0c3cf36af6460c35ba500f21e65d4aaa6a | Newbas/beiwe-backend | database/survey_models.py | [
"BSD-3-Clause"
] | Python | archive | <not_specific> | def archive(self):
""" Create an archive if there were any changes to the data since the last archive was
created, or if no archive exists. """
# get self as dictionary representation, remove fields that don't exist, extract last
# updated and the survey id.
new_data = self.as_d... | Create an archive if there were any changes to the data since the last archive was
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] | def archive(self):
new_data = self.as_dict()
archive_start = new_data.pop("last_updated")
survey_id = new_data.pop("id")
new_data.pop("object_id")
new_data.pop("created_on")
new_data.pop("study")
try:
prior_archive = self.most_recent_archive().as_dict(... | [
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} |
69846b2aac527ec8fe3c4a6814eeb217bab94d37 | Newbas/beiwe-backend | authentication/admin_authentication.py | [
"BSD-3-Clause"
] | Python | is_logged_in | <not_specific> | def is_logged_in():
""" automatically logs out the researcher if their session is timed out. """
if EXPIRY_NAME in session:
expiry_datetime = session[EXPIRY_NAME]
if is_naive(expiry_datetime):
if expiry_datetime > datetime.now():
return SESSION_UUID in session
... | automatically logs out the researcher if their session is timed out. | automatically logs out the researcher if their session is timed out. | [
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if EXPIRY_NAME in session:
expiry_datetime = session[EXPIRY_NAME]
if is_naive(expiry_datetime):
if expiry_datetime > datetime.now():
return SESSION_UUID in session
else:
if expiry_datetime > timezone.now():
return SE... | [
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69846b2aac527ec8fe3c4a6814eeb217bab94d37 | Newbas/beiwe-backend | authentication/admin_authentication.py | [
"BSD-3-Clause"
] | Python | assert_admin | <not_specific> | def assert_admin(study_id):
""" This function will throw a 403 forbidden error and stop execution. Note that the abort
directly raises the 403 error, if we don't hit that return True. """
session_researcher = get_session_researcher()
if not session_researcher.site_admin and not session_researcher.c... | This function will throw a 403 forbidden error and stop execution. Note that the abort
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session_researcher = get_session_researcher()
if not session_researcher.site_admin and not session_researcher.check_study_admin(study_id):
flash("This user does not have admin privilages on this study.", "danger")
return abort(403)
return True | [
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69846b2aac527ec8fe3c4a6814eeb217bab94d37 | Newbas/beiwe-backend | authentication/admin_authentication.py | [
"BSD-3-Clause"
] | Python | assert_researcher_under_admin | <not_specific> | def assert_researcher_under_admin(researcher, study=None):
""" Asserts that the researcher provided is allowed to be edited by the session user.
If study is provided then the admin test is strictly for that study, otherwise it checks
for admin status anywhere. """
session_researcher = get_sessio... | Asserts that the researcher provided is allowed to be edited by the session user.
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69846b2aac527ec8fe3c4a6814eeb217bab94d37 | Newbas/beiwe-backend | authentication/admin_authentication.py | [
"BSD-3-Clause"
] | Python | forest_enabled | <not_specific> | def forest_enabled(func):
"""
Decorator for validating that Forest is enabled for this study.
"""
@functools.wraps(func)
def wrapped(*args, **kwargs):
try:
study = Study.objects.get(id=kwargs.get("study_id", None))
except Study.DoesNotExist:
return abort(404)
... |
Decorator for validating that Forest is enabled for this study.
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@functools.wraps(func)
def wrapped(*args, **kwargs):
try:
study = Study.objects.get(id=kwargs.get("study_id", None))
except Study.DoesNotExist:
return abort(404)
if not study.forest_enabled:
return abort(404)
return fu... | [
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} |
e028eb49bb2978411f0d0b3b6ee85fef8e48c7e0 | Newbas/beiwe-backend | api/study_api.py | [
"BSD-3-Clause"
] | Python | delete_intervention | <not_specific> | def delete_intervention(study_id=None):
"""Deletes the specified Intervention. Expects intervention in the request body."""
study = Study.objects.get(pk=study_id)
intervention_id = request.values.get('intervention')
if intervention_id:
try:
intervention = Intervention.objects.g... | Deletes the specified Intervention. Expects intervention in the request body. | Deletes the specified Intervention. Expects intervention in the request body. | [
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study = Study.objects.get(pk=study_id)
intervention_id = request.values.get('intervention')
if intervention_id:
try:
intervention = Intervention.objects.get(id=intervention_id)
except Intervention.DoesNotExist:
intervention = No... | [
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e028eb49bb2978411f0d0b3b6ee85fef8e48c7e0 | Newbas/beiwe-backend | api/study_api.py | [
"BSD-3-Clause"
] | Python | edit_intervention | <not_specific> | def edit_intervention(study_id=None):
"""
Edits the name of the intervention. Expects intervention_id and edit_intervention in the
request body
"""
study = Study.objects.get(pk=study_id)
intervention_id = request.values.get('intervention_id', None)
new_name = request.values.get('edit_... |
Edits the name of the intervention. Expects intervention_id and edit_intervention in the
request body
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study = Study.objects.get(pk=study_id)
intervention_id = request.values.get('intervention_id', None)
new_name = request.values.get('edit_intervention', None)
if intervention_id:
try:
intervention = Intervention.objects.get(id=intervention_id)
... | [
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} |
e028eb49bb2978411f0d0b3b6ee85fef8e48c7e0 | Newbas/beiwe-backend | api/study_api.py | [
"BSD-3-Clause"
] | Python | delete_field | <not_specific> | def delete_field(study_id=None):
"""Deletes the specified Custom Field. Expects field in the request body."""
study = Study.objects.get(pk=study_id)
field = request.values.get('field', None)
if field:
try:
study_field = StudyField.objects.get(study=study, id=field)
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study = Study.objects.get(pk=study_id)
field = request.values.get('field', None)
if field:
try:
study_field = StudyField.objects.get(study=study, id=field)
except StudyField.DoesNotExist:
study_field = None
try:
if ... | [
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e028eb49bb2978411f0d0b3b6ee85fef8e48c7e0 | Newbas/beiwe-backend | api/study_api.py | [
"BSD-3-Clause"
] | Python | edit_custom_field | <not_specific> | def edit_custom_field(study_id=None):
"""Edits the name of a Custom field. Expects field_id anf edit_custom_field in request body"""
field_id = request.values.get("field_id")
new_field_name = request.values.get("edit_custom_field")
if field_id:
try:
field = StudyField.objects.g... | Edits the name of a Custom field. Expects field_id anf edit_custom_field in request body | Edits the name of a Custom field. Expects field_id anf edit_custom_field in request body | [
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field_id = request.values.get("field_id")
new_field_name = request.values.get("edit_custom_field")
if field_id:
try:
field = StudyField.objects.get(id=field_id)
except StudyField.DoesNotExist:
field = None
if field and new... | [
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4326d61916e26b22505bfdd27b897898d9a5a26c | Newbas/beiwe-backend | api/copy_study_api.py | [
"BSD-3-Clause"
] | Python | export_study_settings_file | <not_specific> | def export_study_settings_file(study_id):
""" Endpoint that returns a json representation of a study. """
study = Study.objects.get(pk=study_id)
filename = study.name.replace(' ', '_') + "_surveys_and_settings.json"
return Response(
format_study(study),
mimetype="application/json",
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] | def export_study_settings_file(study_id):
study = Study.objects.get(pk=study_id)
filename = study.name.replace(' ', '_') + "_surveys_and_settings.json"
return Response(
format_study(study),
mimetype="application/json",
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4326d61916e26b22505bfdd27b897898d9a5a26c | Newbas/beiwe-backend | api/copy_study_api.py | [
"BSD-3-Clause"
] | Python | import_study_settings_file | <not_specific> | def import_study_settings_file(study_id):
""" Endpoint that takes the output of export_study_settings_file and creates a new study. """
study = Study.objects.get(pk=study_id)
file = request.files.get('upload', None)
if not file:
abort(400)
if not allowed_file_extension(file.filename):
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study = Study.objects.get(pk=study_id)
file = request.files.get('upload', None)
if not file:
abort(400)
if not allowed_file_extension(file.filename):
flash("You can only upload .json files!", 'danger')
return redirect(request.referrer)
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cc1e511f912d2b318b82b9a20284af5f231ec619 | Newbas/beiwe-backend | libs/firebase_config.py | [
"BSD-3-Clause"
] | Python | update_firebase_instance | None | def update_firebase_instance(rucur_depth=3) -> None:
""" Creates or destroys the firebase app, handling basic credential errors. """
junk_creds = False
encoded_credentials = None # IDE complains
try:
encoded_credentials = json.loads(safely_get_db_credential(BACKEND_FIREBASE_CREDENTIALS))
e... | Creates or destroys the firebase app, handling basic credential errors. | Creates or destroys the firebase app, handling basic credential errors. | [
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] | def update_firebase_instance(rucur_depth=3) -> None:
junk_creds = False
encoded_credentials = None
try:
encoded_credentials = json.loads(safely_get_db_credential(BACKEND_FIREBASE_CREDENTIALS))
except (JSONDecodeError, TypeError):
junk_creds = True
try:
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8e38e010bd96aef3252b428bf4bf53db51cadbd0 | Newbas/beiwe-backend | api/mobile_api.py | [
"BSD-3-Clause"
] | Python | upload | <not_specific> | def upload(OS_API=""):
""" Entry point to upload GPS, Accelerometer, Audio, PowerState, Calls Log, Texts Log,
Survey Response, and debugging files to s3.
Behavior:
The Beiwe app is supposed to delete the uploaded file if it receives an html 200 response.
The API returns a 200 response when the file... | Entry point to upload GPS, Accelerometer, Audio, PowerState, Calls Log, Texts Log,
Survey Response, and debugging files to s3.
Behavior:
The Beiwe app is supposed to delete the uploaded file if it receives an html 200 response.
The API returns a 200 response when the file has A) been successfully hand... | Entry point to upload GPS, Accelerometer, Audio, PowerState, Calls Log, Texts Log,
Survey Response, and debugging files to s3.
The Beiwe app is supposed to delete the uploaded file if it receives an html 200 response.
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file_name = request.values.get("file_name", None)
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8e38e010bd96aef3252b428bf4bf53db51cadbd0 | Newbas/beiwe-backend | api/mobile_api.py | [
"BSD-3-Clause"
] | Python | register_user | <not_specific> | def register_user(OS_API=""):
""" Checks that the patient id has been granted, and that there is no device registered with
that id. If the patient id has no device registered it registers this device and logs the
bluetooth mac address.
Check the documentation in user_authentication to ensure you have p... | Checks that the patient id has been granted, and that there is no device registered with
that id. If the patient id has no device registered it registers this device and logs the
bluetooth mac address.
Check the documentation in user_authentication to ensure you have provided the proper credentials.
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patient_id = request.values['patient_id']
phone_number = request.values['phone_number']
device_id = request.values['device_id']
device_os = request.values.get('device_os', "none")
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4d68cdc3eb4dee714fe22a454d12624cb0b2dee6 | Newbas/beiwe-backend | services/celery_data_processing.py | [
"BSD-3-Clause"
] | Python | create_file_processing_tasks | null | def create_file_processing_tasks():
""" Generates tasks to enqueue. This is called every 6 minutes, and tasks have a lifetime
of 6 minutes. Note that tasks are not removed from the queue by RabbitMQ, but by Celery.
inspecting the queue will continue to display the tasks that have not been sent to Celery
... | Generates tasks to enqueue. This is called every 6 minutes, and tasks have a lifetime
of 6 minutes. Note that tasks are not removed from the queue by RabbitMQ, but by Celery.
inspecting the queue will continue to display the tasks that have not been sent to Celery
until the most recent job is finished.
... | Generates tasks to enqueue. This is called every 6 minutes, and tasks have a lifetime
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expiry = (datetime.utcnow() + timedelta(minutes=5)).replace(second=30, microsecond=0)
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participant_set = set(
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4d68cdc3eb4dee714fe22a454d12624cb0b2dee6 | Newbas/beiwe-backend | services/celery_data_processing.py | [
"BSD-3-Clause"
] | Python | celery_process_file_chunks | null | def celery_process_file_chunks(participant_id):
""" This is the function is queued up, it runs through all new uploads from a specific user and
'chunks' them. Handles logic for skipping bad files, raising errors. """
# celery doesn't clean up after itself very well, either memory or open network connection... | This is the function is queued up, it runs through all new uploads from a specific user and
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number_bad_files = 0
tags = {'user_id': participant.patient_id}
error_sentry = make_error_sentry(sentry_type=SentryTypes.data_processing)
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380d8a14e965244c01afb9e20fb07b52ee2de4fc | Newbas/beiwe-backend | database/migrations/0061_historical_data_qty_stats.py | [
"BSD-3-Clause"
] | Python | calculate_data_quantity_stats | null | def calculate_data_quantity_stats(participant: Participant):
""" Update the SummaryStatisticDaily stats for a participant, using ChunkRegistry data """
study_timezone = gettz(participant.study.timezone_name)
query = ChunkRegistry.objects.filter(participant=participant)
daily_data_quant... | Update the SummaryStatisticDaily stats for a participant, using ChunkRegistry data | Update the SummaryStatisticDaily stats for a participant, using ChunkRegistry data | [
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study_timezone = gettz(participant.study.timezone_name)
query = ChunkRegistry.objects.filter(participant=participant)
daily_data_quantities = defaultdict(lambda: defaultdict(int))
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c1e813284ebece2db43a334aba04ee9dc832cd53 | Newbas/beiwe-backend | database/study_models.py | [
"BSD-3-Clause"
] | Python | save | null | def save(self, *args, **kwargs):
""" Ensure there is a study device settings attached to this study. """
# First we just save. This code has vacillated between throwing a validation error and not
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c1e813284ebece2db43a334aba04ee9dc832cd53 | Newbas/beiwe-backend | database/study_models.py | [
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] | Python | _get_data_time_bin | Optional[datetime] | def _get_data_time_bin(self, earliest=True, only_after_epoch: bool = True,
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"""
Return the earliest ChunkRegistry time bin datetime for this study.
Note: As of 2021-07-01, running the query as a QuerySet filt... |
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e3d76597b34c9806c579afe966d279acb6b7601b | Newbas/beiwe-backend | libs/file_processing/file_processing_core.py | [
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] | Python | do_process_user_file_chunks | <not_specific> | def do_process_user_file_chunks(
page_size: int, error_handler: ErrorHandler, position: int, participant: Participant
):
"""
Run through the files to process, pull their data, put it into s3 bins. Run the file through
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All files except for the audio r... | Run through the files to process, pull their data, put it into s3 bins. Run the file through
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ftps_to_remove = set()
pool = ThreadPool(CONCURRENT_NETWORK_OPS)
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e3d76597b34c9806c579afe966d279acb6b7601b | Newbas/beiwe-backend | libs/file_processing/file_processing_core.py | [
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] | Python | process_one_file | <not_specific> | def process_one_file(
file_for_processing: FileForProcessing, survey_id_dict: dict, all_binified_data: DefaultDict,
ftps_to_remove: set
):
""" This function is the inner loop of the chunking process. """
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e3d76597b34c9806c579afe966d279acb6b7601b | Newbas/beiwe-backend | libs/file_processing/file_processing_core.py | [
"BSD-3-Clause"
] | Python | upload_binified_data | <not_specific> | def upload_binified_data(binified_data, error_handler, survey_id_dict):
""" Takes in binified csv data and handles uploading/downloading+updating
older data to/from S3 for each chunk.
Returns a set of concatenations that have succeeded and can be removed.
Returns the number of failed FTPS so... | Takes in binified csv data and handles uploading/downloading+updating
older data to/from S3 for each chunk.
Returns a set of concatenations that have succeeded and can be removed.
Returns the number of failed FTPS so that we don't retry them.
Returns the earliest and latest time bins ha... | Takes in binified csv data and handles uploading/downloading+updating
older data to/from S3 for each chunk.
Returns a set of concatenations that have succeeded and can be removed.
Returns the number of failed FTPS so that we don't retry them.
Returns the earliest and latest time bins handled
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failed_ftps = set([])
ftps_to_retire = set([])
upload_these = []
earliest_time_bin = None
latest_time_bin = None
for data_bin, (data_rows_list, ftp_list) in binified_data.items():
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7508e4702a25641614b751eb73de5ba5211b7921 | ivan866/smoothPursuitClassification | parsers/DataExporter.py | [
"MIT"
] | Python | createDir | str | def createDir(self, prefix:str = 'OUTPUT', dryRun:bool = False) -> str:
"""Creates timestamped directory to save data into.
:param prefix: directory name prefix.
:param dryRun: whether to actually create the dir or just generate the path
:return: Directory path str.
"""
... | Creates timestamped directory to save data into.
:param prefix: directory name prefix.
:param dryRun: whether to actually create the dir or just generate the path
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if self.settingsReader.check(full=True):
now = datetime.now().strftime('%Y-%m-%d %H_%M_%S')
dateTag = ET.Element('date')
dateTag.text = now
self.settingsReader.settings.append(dateTag)
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7508e4702a25641614b751eb73de5ba5211b7921 | ivan866/smoothPursuitClassification | parsers/DataExporter.py | [
"MIT"
] | Python | copyMeta | None | def copyMeta(self, saveDir:str = '') -> None:
"""Writes settings and report to previously created save directory.
:param saveDir:
:return:
"""
if self.settingsReader.check():
if saveDir:
metaDir = saveDir
else:
metaDir = se... | Writes settings and report to previously created save directory.
:param saveDir:
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] | def copyMeta(self, saveDir:str = '') -> None:
if self.settingsReader.check():
if saveDir:
metaDir = saveDir
else:
metaDir = self.saveDir
self.settingsReader.save(metaDir)
self.main.printToOut('Current settings copied to output.')
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7508e4702a25641614b751eb73de5ba5211b7921 | ivan866/smoothPursuitClassification | parsers/DataExporter.py | [
"MIT"
] | Python | exportCSV | None | def exportCSV(self, multiData:object, format:str='csv') -> None:
"""Writes all data to CSV files.
:param multiData:
:param format:
:return:
"""
if self.settingsReader.check() and multiData.check():
self.main.printToOut('Exporting data channels to {0}.'.format... | Writes all data to CSV files.
:param multiData:
:param format:
:return:
| Writes all data to CSV files. | [
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] | def exportCSV(self, multiData:object, format:str='csv') -> None:
if self.settingsReader.check() and multiData.check():
self.main.printToOut('Exporting data channels to {0}.'.format(format.upper()))
saveDir = self.createDir()
for type in multiData.multiData.keys():
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0a376419afd1b5e4f4d34742f35e50b5b4b724ff | ivan866/smoothPursuitClassification | algo/IVTFilter.py | [
"MIT"
] | Python | printParams | str | def printParams(self) -> str:
"""Returns a str describing the parameters set.
:return: all parameters for this filter.
"""
res=[]
for k,v in self.params.items():
res.append('{0}: {1}'.format(k,v))
return '; '.join(res) | Returns a str describing the parameters set.
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res=[]
for k,v in self.params.items():
res.append('{0}: {1}'.format(k,v))
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0a376419afd1b5e4f4d34742f35e50b5b4b724ff | ivan866/smoothPursuitClassification | algo/IVTFilter.py | [
"MIT"
] | Python | runJob | None | def runJob(self, data:DataFrame, min_velocity:float, noise_level:float, min_static:float, min_motion:float) -> None:
"""Sets filter parameters, processes the data and returns the filtered result.
:param data: pandas dataframe with only 2 columns - time and speed
:param min_velocity: min saccad... | Sets filter parameters, processes the data and returns the filtered result.
:param data: pandas dataframe with only 2 columns - time and speed
:param min_velocity: min saccade velocity, otherwise consider as fixation
:param noise_level: max noise velocity, what counts as saccade border
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self.setParameter('min_velocity', min_velocity)
self.setParameter('noise_level', noise_level)
self.setParameter('min_static', min_static)
self.setParameter('min_motion', ... | [
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0a376419afd1b5e4f4d34742f35e50b5b4b724ff | ivan866/smoothPursuitClassification | algo/IVTFilter.py | [
"MIT"
] | Python | traverseOffsets | tuple | def traverseOffsets(self, data, sindex:int, eindex:int, thres:float) -> tuple:
"""Runs step by step through data in given direction and finds nearest threshold value.
:param data:
:param sindex: start index
:param eindex: end index
:param thres: value to search for
:retu... | Runs step by step through data in given direction and finds nearest threshold value.
:param data:
:param sindex: start index
:param eindex: end index
:param thres: value to search for
:return: found indices
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0a376419afd1b5e4f4d34742f35e50b5b4b724ff | ivan866/smoothPursuitClassification | algo/IVTFilter.py | [
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] | Python | filterValues | DataFrame | def filterValues(self, values:DataFrame) -> DataFrame:
"""Filter out results based on condition.
:param values: data to filter
:return: filtered data
"""
dur = []
minMotion = self.getParameter('min_motion')
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dur = []
minMotion = self.getParameter('min_motion')
values.apply(lambda x: dur.append(x['max'] - x['min']), axis=1)
values['dur'] = dur
res = values[values['dur'] >= minMotion]
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bc0bed69667f1b6b6c57108a65fd4d8af9f2ffeb | ivan866/smoothPursuitClassification | SmoothPursuitClassification.py | [
"MIT"
] | Python | printError | None | def printError(self) -> None:
"""Prints current Exception info to console.
:return: None.
"""
eInfo = sys.exc_info()
text = '{0}: {1}.'.format(eInfo[0].__name__, eInfo[1])
self.consoleContents += f'{text}\n'
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eInfo = sys.exc_info()
text = '{0}: {1}.'.format(eInfo[0].__name__, eInfo[1])
self.consoleContents += f'{text}\n'
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bc0bed69667f1b6b6c57108a65fd4d8af9f2ffeb | ivan866/smoothPursuitClassification | SmoothPursuitClassification.py | [
"MIT"
] | Python | saveConsole | None | def saveConsole(self, saveDir:str) -> None:
"""Write current console contents to file.
:param saveDir: Path to write into.
:return:
"""
reportFile = open(saveDir + '/console.txt', 'w')
reportFile.write(self.consoleContents)
reportFile.close()
self.printTo... | Write current console contents to file.
:param saveDir: Path to write into.
:return:
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reportFile = open(saveDir + '/console.txt', 'w')
reportFile.write(self.consoleContents)
reportFile.close()
self.printToOut('Console contents saved to file.') | [
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6d1af6423bdbc7cdc99894903b528dc66a147f41 | ivan866/smoothPursuitClassification | utils/SettingsReader.py | [
"MIT"
] | Python | select | None | def select(self, file:str=None) -> None:
"""Selects file with settings, specified literally by path string, opens dialog otherwise.
:param file: Path string.
:return: None
"""
if not file:
self.settingsFile = filedialog.askopenfilename(filetypes = (("eXtensib... | Selects file with settings, specified literally by path string, opens dialog otherwise.
:param file: Path string.
:return: None
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if not file:
self.settingsFile = filedialog.askopenfilename(filetypes = (("eXtensible Markup Language","*.xml"),("all files","*.*")))
else:
self.settingsFile = file
if self.settingsFile:
self.dataDir = os.path.dirname(s... | [
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6d1af6423bdbc7cdc99894903b528dc66a147f41 | ivan866/smoothPursuitClassification | utils/SettingsReader.py | [
"MIT"
] | Python | read | None | def read(self) -> None:
"""Actually reads and parses xml file contents.
:return:
"""
#self.main.logger.debug('reading settings...')
try:
self.settingsTree = ET.parse(self.settingsFile)
self.settings = self.settingsTree.getroot()
except xml.etree.... | Actually reads and parses xml file contents.
:return:
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try:
self.settingsTree = ET.parse(self.settingsFile)
self.settings = self.settingsTree.getroot()
except xml.etree.ElementTree.ParseError:
self.main.printError()
self.main.printToOut('ERROR: Bad settings file. Check your XML is valid... | [
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6d1af6423bdbc7cdc99894903b528dc66a147f41 | ivan866/smoothPursuitClassification | utils/SettingsReader.py | [
"MIT"
] | Python | genTypeFile | object | def genTypeFile(self, type:str) -> object:
"""Generator of ids of particular type present in settings.
:param type:
:return: File XML element from settings, if such file exists on disk.
"""
found=False
if self.check(full=True):
for elem in self.getTypes(type)... | Generator of ids of particular type present in settings.
:param type:
:return: File XML element from settings, if such file exists on disk.
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found=False
if self.check(full=True):
for elem in self.getTypes(type):
file= '{0}/{1}'.format(self.dataDir, elem.get('path'))
if os.path.exists(file):
if not found:
self.mai... | [
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6d1af6423bdbc7cdc99894903b528dc66a147f41 | ivan866/smoothPursuitClassification | utils/SettingsReader.py | [
"MIT"
] | Python | substVersatileChannels | str | def substVersatileChannels(self, channel: str) -> str:
"""Substitutes related versatile channel names, which should be the name of the source file type channel in settings.
:param channel: versatile channel name, like samples or gaze.
:return: master channel name.
"""
#FIXME hot... | Substitutes related versatile channel names, which should be the name of the source file type channel in settings.
:param channel: versatile channel name, like samples or gaze.
:return: master channel name.
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if channel in self.main.SAMPLES_COMPONENTS_LIST and self.hasType('samples') and not self.hasType('saccade'):
return 'samples'
elif channel in self.main.GAZE_COMPONENTS_LIST and self.hasType('gaze') and not self.hasType('fixations'):
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6d1af6423bdbc7cdc99894903b528dc66a147f41 | ivan866/smoothPursuitClassification | utils/SettingsReader.py | [
"MIT"
] | Python | unique | list | def unique(self, element:str='file', field:str='') -> list:
"""Filters all specified elements by field and returns unique.
:param element: On what element of settings to filter on.
:param field: For what field to search for.
:return: List of unique fields in these elements.
... | Filters all specified elements by field and returns unique.
:param element: On what element of settings to filter on.
:param field: For what field to search for.
:return: List of unique fields in these elements.
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] | def unique(self, element:str='file', field:str='') -> list:
elements = self.settings.findall(element)
l=[]
for el in elements:
l.append(el.get(field))
return np.unique(l) | [
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6d1af6423bdbc7cdc99894903b528dc66a147f41 | ivan866/smoothPursuitClassification | utils/SettingsReader.py | [
"MIT"
] | Python | totalDuration | object | def totalDuration(self, block:str, parse:bool=True) -> object:
"""Returns total duration of all intervals.
:param block:
:param parse: bool whether to parse str to timedelta or not.
:return: Duration of interval in timedelta or str format.
"""
dur = pd.DataFrame(... | Returns total duration of all intervals.
:param block:
:param parse: bool whether to parse str to timedelta or not.
:return: Duration of interval in timedelta or str format.
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dur = pd.DataFrame(self.getDurations(block=block, parse=True)).sum()[0]
if parse:
return dur
else:
return dur.strftime('%M:%S.%f') | [
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6d1af6423bdbc7cdc99894903b528dc66a147f41 | ivan866/smoothPursuitClassification | utils/SettingsReader.py | [
"MIT"
] | Python | hasType | bool | def hasType(self, type:str) -> bool:
"""Checks if such file type present.
:param type:
:return:
"""
if type in self.unique(field='type'):
return True
else:
return False | Checks if such file type present.
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6d1af6423bdbc7cdc99894903b528dc66a147f41 | ivan866/smoothPursuitClassification | utils/SettingsReader.py | [
"MIT"
] | Python | check | bool | def check(self, full:bool=False) -> bool:
"""Returns True if settings are already selected, False otherwise.
:param full: if to check settings actually read and parsed already.
:return: A bool representing presence of settings file path.
"""
#self.main.logger.debug('check settin... | Returns True if settings are already selected, False otherwise.
:param full: if to check settings actually read and parsed already.
:return: A bool representing presence of settings file path.
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if not full:
if self.settingsFile:
return True
else:
self.main.printToOut('WARNING: Select settings first!')
return False
else:
if self.settings:
return True
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6d1af6423bdbc7cdc99894903b528dc66a147f41 | ivan866/smoothPursuitClassification | utils/SettingsReader.py | [
"MIT"
] | Python | save | None | def save(self, saveDir:str)->None:
"""Write current settings to file.
:param saveDir: Path to write into.
:return:
"""
self.main.logger.debug('writing settings...')
self.settingsTree.write(saveDir + '/' + os.path.basename(self.settingsFile))
#TODO
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self.main.logger.debug('writing settings...')
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6d1af6423bdbc7cdc99894903b528dc66a147f41 | ivan866/smoothPursuitClassification | utils/SettingsReader.py | [
"MIT"
] | Python | md5 | str | def md5(self, fname:str)->str:
"""Calculates and returns MD5 hash checksum of a file.
From https://stackoverflow.com/a/3431838/2795533
:param fname: file path.
:return: md5 hex value.
"""
hash_md5 = hashlib.md5()
with open(fname, "rb") as f:
for chun... | Calculates and returns MD5 hash checksum of a file.
From https://stackoverflow.com/a/3431838/2795533
:param fname: file path.
:return: md5 hex value.
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hash_md5 = hashlib.md5()
with open(fname, "rb") as f:
for chunk in iter(lambda: f.read(4096), b""):
hash_md5.update(chunk)
return hash_md5.hexdigest() | [
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e6442a01314cad1c19c867a6a896489979174e57 | ivan866/smoothPursuitClassification | algo/IBDT.py | [
"MIT"
] | Python | addPoint | None | def addPoint(self, entry:object) -> None:
"""Calculates velocity and classifies event type of the given sample, if already trained.
Not a method for aggregating data samples. Method is for using the classifier.
:param entry: IBDT_Data to classify event on.
:return:
"""
... | Calculates velocity and classifies event type of the given sample, if already trained.
Not a method for aggregating data samples. Method is for using the classifier.
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| Calculates velocity and classifies event type of the given sample, if already trained.
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e6442a01314cad1c19c867a6a896489979174e57 | ivan866/smoothPursuitClassification | algo/IBDT.py | [
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] | Python | train | None | def train(self, gaze:list) -> None:
"""Perform training on the data specified, split velocity means on 2 clusters and update model hyperparameters.
:param gaze: list of IBDT_Data to train on.
:return:
"""
samples = deque()
#Find first valid sample
for index in... | Perform training on the data specified, split velocity means on 2 clusters and update model hyperparameters.
:param gaze: list of IBDT_Data to train on.
:return:
| Perform training on the data specified, split velocity means on 2 clusters and update model hyperparameters. | [
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samples = deque()
for index in range(0, len(gaze)):
previous = gaze[index]
if (previous != gaze[len(gaze)-1]) and (previous.base.confidence < self.minSampleConfidence):
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e6442a01314cad1c19c867a6a896489979174e57 | ivan866/smoothPursuitClassification | algo/IBDT.py | [
"MIT"
] | Python | estimateVelocity | float | def estimateVelocity(self, cur:object, prev:object) -> float:
"""Simple velocity, no smoothing, no angular speed.
:param cur:
:param prev:
:return: velocity from trigonometric distance (incorrect)
"""
#TODO simple trigonometric distance, must be cosine law for spherical ... | Simple velocity, no smoothing, no angular speed.
:param cur:
:param prev:
:return: velocity from trigonometric distance (incorrect)
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dist = cv2.norm( np.array([cur.base.x, cur.base.y]), np.array([prev.base.x, prev.base.y]) )
dt = cur.base.ts - prev.base.ts
return dist / dt | [
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e6442a01314cad1c19c867a6a896489979174e57 | ivan866/smoothPursuitClassification | algo/IBDT.py | [
"MIT"
] | Python | runJob | list | def runJob(self, data:DataFrame, maxSaccadeDurationMs:float, minSampleConfidence:float, classification:int) -> list:
"""Sets classifier parameters, runs classification and returns list of specified event type.
:param data: pandas dataframe with 4 columns - time(ms), validity(higher is more valid), x(p... | Sets classifier parameters, runs classification and returns list of specified event type.
:param data: pandas dataframe with 4 columns - time(ms), validity(higher is more valid), x(px or mm), y(px or mm).
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self.maxSaccadeDurationMs = maxSaccadeDurationMs
self.minSampleConfidence = minSampleConfidence
self.classification = classification
ibdtData = []
for index, row ... | [
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e6442a01314cad1c19c867a6a896489979174e57 | ivan866/smoothPursuitClassification | algo/IBDT.py | [
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] | Python | updatePursuitPrior | None | def updatePursuitPrior(self) -> None:
"""Calculates mean of all ?but last window values.
:return:
"""
#TODO refactor whole method to list comprehension
previousLikelihoods = []
for index in range(0, len(self.window)-1):
d = self.window[index]
prev... | Calculates mean of all ?but last window values.
:return:
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previousLikelihoods = []
for index in range(0, len(self.window)-1):
d = self.window[index]
previousLikelihoods.append(d.pursuit.likelihood)
self.cur.pursuit.prior = np.mean(previousLikelihoods) | [
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... |
e6442a01314cad1c19c867a6a896489979174e57 | ivan866/smoothPursuitClassification | algo/IBDT.py | [
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] | Python | updateFixationAndSaccadeLikelihood | None | def updateFixationAndSaccadeLikelihood(self) -> None:
"""Queries the model for predicted likelihoods, writes them to cur sample.
:return:
"""
if self.cur.base.v < self.fMean:
self.cur.fixation.likelihood = 1
self.cur.saccade.likelihood = 0
return None... | Queries the model for predicted likelihoods, writes them to cur sample.
:return:
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if self.cur.base.v < self.fMean:
self.cur.fixation.likelihood = 1
self.cur.saccade.likelihood = 0
return None
if self.cur.base.v > self.sMean:
self.cur.fixation.likelihood = 0
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e6442a01314cad1c19c867a6a896489979174e57 | ivan866/smoothPursuitClassification | algo/IBDT.py | [
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] | Python | binaryClassification | None | def binaryClassification(self) -> None:
"""Simple 2-class likelihood comparison.
:return:
"""
if self.cur.fixation.likelihood > self.cur.saccade.likelihood:
self.cur.classification = MOVEMENT['FIXATION']
else:
self.cur.classification = MOVEMENT['SACCADE'] | Simple 2-class likelihood comparison.
:return:
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if self.cur.fixation.likelihood > self.cur.saccade.likelihood:
self.cur.classification = MOVEMENT['FIXATION']
else:
self.cur.classification = MOVEMENT['SACCADE'] | [
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... |
e6442a01314cad1c19c867a6a896489979174e57 | ivan866/smoothPursuitClassification | algo/IBDT.py | [
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] | Python | ternaryClassification | None | def ternaryClassification(self) -> None:
"""3-class Bayesian posterior comparison.
:return:
"""
#Class that maximizes posterior probability
maxPosterior = self.cur.fixation.posterior
self.cur.base.classification = MOVEMENT['FIXATION']
if self.cur.saccade.poster... | 3-class Bayesian posterior comparison.
:return:
| 3-class Bayesian posterior comparison. | [
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maxPosterior = self.cur.fixation.posterior
self.cur.base.classification = MOVEMENT['FIXATION']
if self.cur.saccade.posterior > maxPosterior:
self.cur.base.classification = MOVEMENT['SACCADE']
maxPosterior = self.cur.saccade.posteri... | [
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95a1dbcd7206b07712b8abcfd7db96c2bb07a806 | ivan866/smoothPursuitClassification | parsers/DataReader.py | [
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] | Python | read | None | def read(self, settingsReader:object, multiData:object) -> None:
"""Actual data parsing code.
Depends on pandas module.
:param settingsReader: SettingsReader object to get xml settings tree from.
:param multiData: MultiData object to write into.
:return:
"""
... | Actual data parsing code.
Depends on pandas module.
:param settingsReader: SettingsReader object to get xml settings tree from.
:param multiData: MultiData object to write into.
:return:
| Actual data parsing code.
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if settingsReader.check():
settingsReader.read()
else:
return
multiData.reset()
try:
self.readSMISamples(settingsReader, multiData)
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95a1dbcd7206b07712b8abcfd7db96c2bb07a806 | ivan866/smoothPursuitClassification | parsers/DataReader.py | [
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] | Python | readTobiiGaze | None | def readTobiiGaze(self, settingsReader:object, multiData:object) -> None:
"""Reads Tobii Glasses 2 gaze data from .tsv file.
:param settingsReader: same as everywhere
:param multiData: same
:return:
"""
for fileElem in settingsReader.genTypeFile('gaze'):
... | Reads Tobii Glasses 2 gaze data from .tsv file.
:param settingsReader: same as everywhere
:param multiData: same
:return:
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for fileElem in settingsReader.genTypeFile('gaze'):
filePath = settingsReader.getPathAttrById('gaze', fileElem.get('id'), absolute=True)
fileExt = os.path.splitext(filePath)[1]
self.main.printToOut('Rea... | [
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"# узнаем какие столбцы присутствуют",
"# переводим в секунды",
"#gazeData['Gaze event duration'] /= 1000",
"# убираем пусты... | [
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... |
6a88b9f26a8a20121162c5474c09f2e23fce6154 | ivan866/smoothPursuitClassification | parsers/MultiData.py | [
"MIT"
] | Python | genChannelIds | tuple | def genChannelIds(self, channel:str) -> tuple:
"""Generator of ids present in multiData in particular channel (i.e. 'type' tag).
:param channel:
:return: Tuple with current channel and id, if such id present in multiData.
"""
if self.settingsReader.check() and self.check():
... | Generator of ids present in multiData in particular channel (i.e. 'type' tag).
:param channel:
:return: Tuple with current channel and id, if such id present in multiData.
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channelZeroName = self.settingsReader.substVersatileChannels(channel)
typeList = self.settingsReader.getTypes(channelZeroName)
if not len(typeList):
typeList = self... | [
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6a88b9f26a8a20121162c5474c09f2e23fce6154 | ivan866/smoothPursuitClassification | parsers/MultiData.py | [
"MIT"
] | Python | tagIntervals | DataFrame | def tagIntervals(self, chData:object, startFrom:object, block:str, ignoreEmpty:bool=True) -> DataFrame:
"""Tags given data by intervals, then returns a single dataframe.
:param chData: data to stack intervals from, usually after getChannelById method.
:param startFrom: zeroTime to start... | Tags given data by intervals, then returns a single dataframe.
:param chData: data to stack intervals from, usually after getChannelById method.
:param startFrom: zeroTime to start from.
:param block: which type of block to tag by.
:param ignoreEmpty: Whether to cut off the empt... | Tags given data by intervals, then returns a single dataframe. | [
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] | def tagIntervals(self, chData:object, startFrom:object, block:str, ignoreEmpty:bool=True) -> DataFrame:
data = []
ints = self.settingsReader.getIntervals(block=block, ignoreEmpty=ignoreEmpty)
for interval in ints:
intData = self.getDataInterval(chData, startFrom, interval.get('id'), ... | [
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6a88b9f26a8a20121162c5474c09f2e23fce6154 | ivan866/smoothPursuitClassification | parsers/MultiData.py | [
"MIT"
] | Python | hasColumn | bool | def hasColumn(self, column:str, id:str) -> bool:
"""Checks if multiData contains such column in its gaze channel.
:param column: Column name from Tobii gaze data.
:param id: string of channel id from settings.
:return: True if column present, False otherwise.
"""
... | Checks if multiData contains such column in its gaze channel.
:param column: Column name from Tobii gaze data.
:param id: string of channel id from settings.
:return: True if column present, False otherwise.
| Checks if multiData contains such column in its gaze channel. | [
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] | def hasColumn(self, column:str, id:str) -> bool:
return column in self.multiData['availColumns'][id] | [
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6a88b9f26a8a20121162c5474c09f2e23fce6154 | ivan866/smoothPursuitClassification | parsers/MultiData.py | [
"MIT"
] | Python | hasAllColumns | bool | def hasAllColumns(self, columns:list, id:str) -> bool:
"""Checks if multiData contains ALL these columns passed in list.
:param columns: List of strings with column names.
:param id: string of channel id from settings.
:return: True if all columns present, False otherwise.
... | Checks if multiData contains ALL these columns passed in list.
:param columns: List of strings with column names.
:param id: string of channel id from settings.
:return: True if all columns present, False otherwise.
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] | def hasAllColumns(self, columns:list, id:str) -> bool:
for col in columns:
if col not in self.multiData['availColumns'][id]:
return False
return True | [
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6a88b9f26a8a20121162c5474c09f2e23fce6154 | ivan866/smoothPursuitClassification | parsers/MultiData.py | [
"MIT"
] | Python | hasChannelById | bool | def hasChannelById(self, channel:str, id:str) -> bool:
"""Checks if multiData contains this channel.id node in its hierarchy.
:param channel: string of type from settings.
:param id: string of channel id from settings.
:return: True if such id in such channel present, False othe... | Checks if multiData contains this channel.id node in its hierarchy.
:param channel: string of type from settings.
:param id: string of channel id from settings.
:return: True if such id in such channel present, False otherwise.
| Checks if multiData contains this channel.id node in its hierarchy. | [
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] | def hasChannelById(self, channel:str, id:str) -> bool:
try:
self.multiData[channel][id]
return True
except KeyError:
return False | [
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... |
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