LNCD scheduler (DB management)

Schedule and record visits to the Laboratory of NeuroCognitive Development.

This is unlikely to be too useful to the world at large. Integrations are specific to the lab's tools (gcal, qualtrics) and firewall. The database schema is tied to internal organization of multimodal experiments with human participates.

Instead see components:

• google calendar: https://github.com/LabNeuroCogDevel/LNCDcal.py
• qualtrics - Qualtrics.py

Run without install within UPMC firewall

schedule.py is in the path on the main LNCD server.

• connect to rhea (via Mobaxterm/ssh)
• run scheduler: schedule.py

Development

• make install will use pipenv to manage the python virtual environment. requirements.txt also exists, but is currently (2021-11-30) only for travis CI.
• make test runs tests. see Testing section and Travis CI

DB

for an example postgres database, see make lncddb_test (scripts/fake_db.bash creates lncddb_test DB with example data)

GUI

• qtcreator for visual ui files (designer.exe with anaconda on windows)
• consider __name == "__main__" tests for individual modules so they can be run indpenednetly with sys.argv (example CheckinVisit.py)

Automatic hooks

hook	runs	script
commit	black	scripts/pre-commit
push	pytest w/optional Xvfb	scripts/pre-push

Hooks are installed by by make install (ln -s $(pwd)/scripts/pre-* .git/hooks/). They can be ingored using git push --no-verify

Install on windows

Use anaconda to manage python and the dependencies.

• python: https://www.anaconda.com/download/#windows (install as user, not system)
• python libaries/dependencies:anaconda navigator -> environments -> root play -> terminal
  • upmc cert issue: conda config --set ssl_verify False
  • version control: conda install git
  • LNCDcal: pip install --trusted-host github.com git+https://github.com/LabNeuroCogDevel/LNCDcal.py
  • sql: conda install psycopg2 pip install pyesql
  • gui: conda install pyQt5
• app:
  • anaconda navigator -> projects -> import -> from folder

20190712 - pyqt5 update issue, current fix pip install pyqt5==5.12.2 pyinstaller/pyinstaller#4293

Secrets

There are two files needed but not in the repo. These carry google (gcal), qualtircs (api), and database authentication.

• config.ini configuration settings (db info, qualtrics, cal info). See config.ini.example.
• *.p12 gcal cred file for service account

Notes

Testing

use make test, same as pipenv run python -m pytest

• Depends on pytest, pytest-qt and pytest-pgsql. see make install (pipenv install --dev)
• within tests directory, but expects to be run at root directory (./sql/ and ./*py files)
• makes use of pytest autoloaded conftest.py to provided schema loading through shared test fixture create_db

UI

• qtbot w/lncdapp fixture (defined in tests/conftest.py)

DB

create_db fixture in tests/conftest.py uses transacted_postgresql_db from pytest-pgsql. This creates a mocked database using the same sql/*csv files with which scripts/fake_db.bash creates an actual testing postgres dblncddb_test.

Database

• See scripts/fake_db.bash to build a testing database.
• DBeaver is an excellent tool to visually explore.

Summary tables

Visit has some confusing views (with triggers):

• visits_view : json columns full info for visit, no drop info
• visits_summary: most recent note (+ drop values) and action

Providence

Schema and triggers are in sql/ they mirror database building code (not public, ~/src/db/mdb_psql_clj/resources/sql/)