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Project to administer test ISPyB databases

Setup

Create a virtual environment and use pip to install dependencies $ pip install -r requirements.txt

This should install:

  • flask
  • SQLAlchemy
  • MySQL-Python (for python < 3) If on python < 3.4 than also
  • enum34

Running

Create/edit config.py module to reflect credentials (see ispyb/init.py for format)

python app.py

View in browser, http://localhost:9000/admin

Security

This is not a secure app and is only intended to run on development systems. There is a basic auth included - credentials are generated on startup (check console)

Setup/Update models

To recreate the database models you can use sqlacodegen

Install sqlacodegen

pip install 'sqlacodegen <= 2.0.0'

(Version 2.0.0 upwards has issues with VARCHAR length)

Generate models

sqlacodegen mysql://<user>:<password>@<host>/<db_name> --outfile gen_models.py

Then compare the generated models with ispyb/models.py

Some changes are required to fit the models file into flask SQLAlchemy conventions.

From newly generated file:

Changes to models.py:

  • - from sqlalchemy.ext.declarative import declarative_base
  • - Base = declarative_base()
  • - metadata = Base.metadata
  • + from . import Base
  • replace metadata with Base.metadata

Check model list is consistent

grep '(Base)' gen_models.py | sed s'/class //' | sed s'/(Base)://'

Add these to a model_list.py file within ispyb directory (replace existing one)