This provides a set of SQLAlchemy ORM models for the ISPyB database.

Installation

Install from pypi ispyb-models:

pip install ispyb-models

Basic Usage

from ispyb import models

dataCollection = models.DataCollection(
    ...
)

ses.add(dataCollection)
ses.commit()

...

datacollections = (
    ses.query(
        models.DataCollection
    ).filter(models.DataCollection.dataCollectionId == 1)
    ).first()
)

Generate a new version

To update the models you need to run the workflow Update Models through GitHub Actions panel. This will create a new branch with models matching the latest DB release and create a pull request for merge this branch into main. Before merging there are some things you need to do:

• Make sure py-ispyb tests still pass with these new models
• Update HISTORY.md to reflect the changes
• Bump version number with bump2version

⚠️ Do not edit the output file yourself

The resulting _auto_db_schema.py should not be edited (other than automatic formatting with black or sorting of imports with isort). All models are imported into and accessed via the __init__.py. Any modifications, e.g. injecting additional relationships between models should be done here.

⚠️ [for local test] Manually update the DB schema

Checkout the specific tag for a given ispyb-database version:

$ git clone -b v1.18.1 https://github.com/ispyb/ispyb-database.git
$ # or, if you have an existing copy of the repository:
$ git checkout v1.18.1

Apply the schema patch in patches/circular_references.patch to avoid circular foreign key references:

$ patch -p1 < ispyb-models/patches/circular_references.patch

Then run the ispyb-database build.sh script to generate the database:

$ sh build.sh

Generate the models with sqlacodegen in src/ispyb/models/:

. generate_models.sh