Starts the Cloud SQL proxy and runs mysql so that you can issue SQL commands directly against a Cloud SQL instance.
Generates an Alembic schema migration in alembic/versions after altering the SQLAlchemy schema in model/.
To regenerate an initial schema:
# Remove the existing schema definition.
rm alembic/versions/*.py
# Clear the database. (The setup script clears the db, creates an empty one,
# and then fails everything else leaving it empty.)
tools/setup_local_database.sh
# Optionally add any new imports to the Alembic bootstrap.
$EDITOR alembic/script.py.mako
# Regenerate the schema.
tools/generate_schema.sh 'Initial schema with manual edits for HPO IDs.'
# Re-add the HPO IDs.
$EDITOR alembic/versions/*.py
# Start a dev appserver and set up the db according to the new schema (and
# import the codebook).
dev_appserver.py test.yaml --require_indexes &
tools/setup_local_database.sh
Imports a set of fake participants into the database.
Imports questionnaires into the database
Imports the codebook, questionnaires, and fake participants into the database.
Populates configuration JSON in Datastore, for use by the AppEngine app.
Example updating the local config:
tools/install_config.sh --config config/config_dev.json --update
Launches a local Jupyter notebook environment that's connected to an RDR instance.
If your system pip -V is earlier than 9.0.1, you can upgrade it, or use the newer version from a virtualenv by running:
virtualenv newpip
. newpip/bin/activate
and then continuing as below.
You can install Jupyter locally via:
pip install --upgrade setuptools pip
pip install --upgrade jupyter
tools/jupyter.sh --project all-of-us-rdr-staging --account [email protected]
Within the notebook web UI, navigate to "tools/jupyter-debugging-environment.ipynb" and run all cells.
And updating a deployed environment:
tools/install_config.sh --project pmi-drc-api-test --account [email protected] \
--update --config config/config_test.json
Sets up a Cloud SQL database instance, sets the root password, creates an rdr database in it, and populates database configuration in Datastore.
Sets up your workspace after checking out the code, or when something changes in requirements.txt.
Sets up an rdr database on your local MySQL instance, for use when running a local server.
Upgrades a database (either local or in Cloud SQL) to the latest or a specified Alembic revision, applying schema migrations. (If the schema is already up to date, this is a no-op.)
Trim trailing whitespace form all files and optionally commit changes.
Returns nonzero if there are uncommitted changes, for use as a pre-push hook.
Creates credentials in a temp file, exports run_cloud_sql_proxy function used to run Cloud SQL.
Sets PYTHONPATH to include everything in libs and the AppEngine SDK. For use when running python scripts that rely on these libraries.
Retrieves metadata about all physical measurements in use in the database; or when run with --run_backfill, backfills all physical measurement rows and their children to match parsed resources.