ispyb-models 1.0.5

SQLAlchemy ORM models for the ISPyB database

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()
)

Manually generate 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/:

sqlacodegen mysql+mysqlconnector://user:password@host:port/ispyb_build --noinflect --outfile _auto_db_schema.py

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.