SEMC Sinedon

Overview

SEMC Sinedon is a reimplementation of the Leginon Cryo-EM suite's Sinedon library (classic Sinedon). Classic Sinedon is a full-fledged object-relational mapping (ORM) package written in Python. SEMC Sinedon differs from classic Sinedon in that it only implements the data model used by Appion and Leginon, and delegates ORM functionality to Django. The reason for creating this version of Sinedon is to reduce the scope of what is maintained by the research computing staff at the Simons Electron Microscopy Center (SEMC). Phrased differently, we strove to reduce the maintenance burden of our primary data pipeline.

Installation

SEMC Sinedon requires poetry. After installing poetry, SEMC Sinedon may be installed by running the following command in a cloned copy of this repository:

poetry install

Configuration File

SEMC Sinedon retrieves database connection parameters from the same configuration file used by classic Sinedon (sinedon.cfg). The SINEDON_CFG_PATH shell environment variable should be defined so that SEMC Sinedon knows where to find this configuration file. If this is variable is not defined, SEMC Sinedon will try to find sinedon.cfg in the current user's home directory.

Developers Guide

Adding a new database model/table to sinedon.

1. Create the model in a new file under the appropriate location (e.g., models/appion for Appion DB tables, models/leginon for Leginon DB tables)
2. Ensure that the Django Meta class is defined and that db_table is set.
3. Add the model to the __init__.py file under models/{appion,leginon,projects}.
4. Add the table name to the list of database table names in the appropriate router class under routers/{appion,leginon,projects}.py.
5. Create a serializer for the model under serializers.