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Jul 19, 2024
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1 change: 1 addition & 0 deletions .github/workflows/build-and-deploy.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@ jobs:
github.ref == 'refs/heads/main' ||
github.ref == 'refs/heads/staging' ||
github.ref == 'refs/heads/development'

strategy:
matrix:
# Specify the docker-compose services to build images from
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54 changes: 28 additions & 26 deletions Pipfile
Original file line number Diff line number Diff line change
Expand Up @@ -4,42 +4,44 @@ verify_ssl = true
name = "pypi"

[packages]
django = "*"
django-filter = "*"
django-extensions = "*"
pillow = "*"
pre-commit = "*"
'sentry-sdk[django]' = "*"
python-dotenv = "*"
django-health-check = "*"
django-cors-headers = "*"
django-debug-toolbar = "*"
factory-boy = "*"
linkpreview = "*"
django-redis = "*"
mysqlclient = "*"
django-import-export = "*"
celery = {version = "*", extras = ["redis"]}
coverage = "*"
crispy-bootstrap5 = "*"
django = "*"
django-celery-beat = "*"
django-cors-headers = "*"
django-coverage-plugin = "*"
django-crispy-forms = "*"
django-debug-toolbar = "*"
django-docs = "*"
django-extensions = "*"
django-extensions-models = "*"
mypy = "*"
django-filter = "*"
django-health-check = "*"
django-import-export = "*"
django-redis = "*"
django-stubs = "*"
tzdata = "*"
djangorestframework = "*"
pyparsing = "*"
pydot = "*"
markdown = "*"
drf-spectacular = "*"
django-docs = "*"
sphinxcontrib-django = "*"
sphinx-rtd-theme = "*"
django-crispy-forms = "*"
crispy-bootstrap5 = "*"
django-celery-beat = "*"
celery = {version = "*", extras = ["redis"]}
factory-boy = "*"
flower = "*"
gunicorn = "*"
linkpreview = "*"
markdown = "*"
mypy = "*"
mysqlclient = "*"
mysql-connector-python = "*"
pillow = "*"
pre-commit = "*"
pydot = "*"
pyparsing = "*"
python-dotenv = "*"
sphinx-rtd-theme = "*"
sphinxcontrib-django = "*"
sqlalchemy = "*"
types-requests = "*"
tzdata = "*"

[dev-packages]
flake8 = "*"
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167 changes: 167 additions & 0 deletions src/sync-signals-with-metadata.py
Original file line number Diff line number Diff line change
@@ -0,0 +1,167 @@
import logging
import os
from datetime import datetime

import requests
import sqlalchemy
from sqlalchemy import create_engine, update
from sqlalchemy.engine import Engine
from sqlalchemy.orm import DeclarativeBase, sessionmaker

logger = logging.getLogger(__name__)

SQLALCHEMY_DATABASE_URI = os.environ.get(
"SQLALCHEMY_DATABASE_URI",
"mysql+mysqlconnector://root:ROOT_PASSWORD@localhost:3306/mysql_database",
)
engine: Engine = create_engine(
SQLALCHEMY_DATABASE_URI, execution_options={"engine_id": "default"}
)
Session = sessionmaker(bind=engine)


COVID_CAST_META_URL = os.environ.get(
"COVID_CAST_META_URL", "https://api.delphi.cmu.edu/epidata/covidcast/meta"
)


class Base(DeclarativeBase):
pass


class Signal(Base):

__tablename__ = "signals_signal"

id = sqlalchemy.Column(sqlalchemy.Integer, primary_key=True)
name = sqlalchemy.Column(sqlalchemy.String)
display_name = sqlalchemy.Column(sqlalchemy.String)
active = sqlalchemy.Column(sqlalchemy.Boolean)
short_description = sqlalchemy.Column(sqlalchemy.String)
description = sqlalchemy.Column(sqlalchemy.String)
format_type = sqlalchemy.Column(sqlalchemy.String)
time_type = sqlalchemy.Column(sqlalchemy.String)
time_label = sqlalchemy.Column(sqlalchemy.String)
is_smoothed = sqlalchemy.Column(sqlalchemy.Boolean)
is_weighted = sqlalchemy.Column(sqlalchemy.Boolean)
is_cumulative = sqlalchemy.Column(sqlalchemy.Boolean)
has_stderr = sqlalchemy.Column(sqlalchemy.Boolean)
has_sample_size = sqlalchemy.Column(sqlalchemy.Boolean)
high_values_are = sqlalchemy.Column(sqlalchemy.String)
base_id = sqlalchemy.Column(sqlalchemy.Integer)
category_id = sqlalchemy.Column(sqlalchemy.Integer)
source_id = sqlalchemy.Column(sqlalchemy.Integer)
created = sqlalchemy.Column(sqlalchemy.DateTime)
modified = sqlalchemy.Column(sqlalchemy.DateTime)
last_updated = sqlalchemy.Column(sqlalchemy.Date)
age_breakdown = sqlalchemy.Column(sqlalchemy.String)
data_censoring = sqlalchemy.Column(sqlalchemy.Text)
gender_breakdown = sqlalchemy.Column(sqlalchemy.Integer)
missingness = sqlalchemy.Column(sqlalchemy.Text)
race_breakdown = sqlalchemy.Column(sqlalchemy.Integer)
reporting_cadence = sqlalchemy.Column(sqlalchemy.String)
restrictions = sqlalchemy.Column(sqlalchemy.Text)
severenity_pyramid_rungs = sqlalchemy.Column(sqlalchemy.String)
temporal_scope_end = sqlalchemy.Column(sqlalchemy.String)
temporal_scope_end_note = sqlalchemy.Column(sqlalchemy.Text)
temporal_scope_start = sqlalchemy.Column(sqlalchemy.String)
temporal_scope_start_note = sqlalchemy.Column(sqlalchemy.Text)
typical_reporting_lag = sqlalchemy.Column(sqlalchemy.String)
typical_revision_cadence = sqlalchemy.Column(sqlalchemy.String)
license_id = sqlalchemy.Column(sqlalchemy.Integer)
signal_type_id = sqlalchemy.Column(sqlalchemy.Integer)
from_date = sqlalchemy.Column(sqlalchemy.Date)
to_date = sqlalchemy.Column(sqlalchemy.Date)
geographic_scope_id = sqlalchemy.Column(sqlalchemy.Integer)
signal_availability_days = sqlalchemy.Column(sqlalchemy.Integer)


class Source(Base):
__tablename__ = "datasources_sourcesubdivision"

id = sqlalchemy.Column(sqlalchemy.Integer, primary_key=True)
name = sqlalchemy.Column(sqlalchemy.String)
display_name = sqlalchemy.Column(sqlalchemy.String)
description = sqlalchemy.Column(sqlalchemy.String)
db_source = sqlalchemy.Column(sqlalchemy.String)
data_source_id = sqlalchemy.Column(sqlalchemy.Integer)
created = sqlalchemy.Column(sqlalchemy.DateTime)
modified = sqlalchemy.Column(sqlalchemy.DateTime)
external_name = sqlalchemy.Column(sqlalchemy.String)


class SignalLastUpdatedParser:

def __init__(self, covidcast_meta_data: list) -> None:
self.covidcast_meta_data = covidcast_meta_data
self.year_week_date_format = "%Y-%W-%w"
self.year_month_day_date_format = "%Y%m%d"

def format_date(
self,
date: str,
) -> datetime:
"""
Format the date string to a specific format.

:param date: The date string to format.
:return: The formatted date string.
:rtype: str
"""
formated_date: datetime
if len(date) == 6:
year, week = date[:4], date[4:]
logger.info(f"Date: {date}, year: {year}, week: {int(week)-1}")
formated_date = datetime.strptime(
f"{int(year)}-{int(week)-1}-1", self.year_week_date_format
)
elif len(date) == 8:
formated_date = datetime.strptime(date, self.year_month_day_date_format)
return formated_date

def set_data(self) -> None:
"""
Set the last updated date for signals in the database.
"""
with Session() as session:
for db_source in self.covidcast_meta_data:
for signal_data in db_source["signals"]:
source = (
session.query(Source)
.filter(Source.name == signal_data["source"])
.first()
)
last_updated = self.format_date(str(signal_data["max_issue"]))
from_date = self.format_date(str(signal_data["min_time"]))
to_date = self.format_date(str(signal_data["max_time"]))
signal_availability_days = abs((to_date - from_date).days)
try:
session.execute(
update(Signal)
.where(Signal.name == signal_data["signal"])
.where(Signal.source_id == source.id)
.values(
last_updated=last_updated,
from_date=from_date,
to_date=to_date,
signal_availability_days=signal_availability_days,
)
)
session.commit()
logger.info(f"Signal {signal_data['signal']} successfully updated.")
except AttributeError:
logger.error(f"Failed to update signal {signal_data['signal']}. Probably the issue is with the source or source with name {signal_data['source']} does not exist.")


def main():
response = requests.get(COVID_CAST_META_URL)
if response.status_code == 200:
covidcast_meta_data = response.json()
parser = SignalLastUpdatedParser(covidcast_meta_data)
parser.set_data()
else:
logger.error(f"Failed to get data from {COVID_CAST_META_URL}")


if __name__ == "__main__":
main()
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