https://github.com/ispyb/ispyb-models

https://github.com/ispyb/ispyb-models

Last synced: 2 months ago
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• Host: GitHub
• URL: https://github.com/ispyb/ispyb-models
• Owner: ispyb
• Created: 2022-07-13T12:18:02.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2023-01-24T09:36:28.000Z (about 2 years ago)
• Last Synced: 2024-11-01T20:47:03.137Z (3 months ago)
• Language: Python
• Size: 130 KB
• Stars: 3
• Watchers: 6
• Forks: 1
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • Changelog: HISTORY.md

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README

        
This provides a set of [SQLAlchemy](https://www.sqlalchemy.org/) ORM models for the [ISPyB database](https://github.com/ispyb/ispyb-database/).

## Installation

Install from pypi [ispyb-models](https://pypi.org/project/ispyb-models):

```bash

pip install ispyb-models

```

## Basic Usage

```python

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:

```bash

$ 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:

```bash

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

```

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

```bash

$ sh build.sh

```

Generate the models with [sqlacodegen](https://pypi.org/project/sqlacodegen/)

in `src/ispyb/models/`:

```bash

. generate_models.sh

```