Test DB

Requirements

• uv: https://docs.astral.sh/uv/getting-started/installation/
• docker and docker compose: https://docs.docker.com/compose/install/

Setup the virtualenv

$ uv sync

Run the server in Docker

This will bring up a persistent database and run tests in Docker. The server is automatically reloaded whenever the source code changes.

make run-docker

Alternatively, run the server locally from the source code

This will bring up a persistent database and run tests locally: The server is automatically reloaded whenever the source code changes.

make run-local

Run tests in Docker

This will bring up a non-persistent database and run tests in Docker:

$ make test-docker

Alternatively, run tests locally from the source code

This will bring up a non-persistent database and run tests locally:

$ make test-local

Available make targets

$ make
help                    Show this help
format                  Run formatters
lint                    Run linters
build                   Build the Docker image
test-local              Run tests locally
test-docker             Run tests in Docker
run-local               Run the application locally
run-docker              Run the application in Docker
kill                    Take down the application and remove the volumes
migration               Create or update the alembic migration

Optional, populate the database with sample data

• Download the hierarchy:

aws s3 cp --no-sign-request s3://openbluebrain/Model_Data/Brain_atlas/Mouse/resolution_25_um/version_1.1.0/Parcellation_ontology/mba_hierarchy.json . 

• Download the Nexus data (only metadata) from:

https://openbraininstitute-my.sharepoint.com/:u:/g/personal/jean-denis_courcol_openbraininstitute_org/EVY7UqF-iHtFs1SmpWoykC4B5vdckmGWlM9OQTe8aTTqIA?e=dHJ9Os

• Untar in a directory called out

tar xzf out.tar.gz

• Import data into the specified database:

make import

Legacy notes, to be cleaned up

# setup postgres to use full text search (VectorTS)

# test_legacy / test_dump can be used to test legacy calls
# test_dump is going through all the nexus rest calls in nexus_use_case_dump and executes these calls

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