tschoonj / ispyb-api

Package for writing acquisition and processing results into an ISPyB database

ISPyB API

This package provides a way to write acquisition and processing results into an ISPyB database. Currently, the only supported method is through stored procedures, but the package is designed to allow for other methods as well, such as webservices.

Documentation

Please see https://ispyb.readthedocs.io.

Requirements

• Python 2.7, 3.4, 3.5, 3.6, 3.7
• The mysql.connector Python package.
• MariaDB 10.0+ or MySQL 5.6+, but we recommend MariaDB 10.2 or later.
• An ISPyB database installed on the above. See the ispyb-database repo for details.

Installation

From PyPI:

pip install --user ispyb

The --user option installs the package for your own user only. You can leave it out if you want to install the package system-wide.

To install the source code in editable mode for development:

git clone [email protected]:DiamondLightSource/ispyb-api.git
pip install -e --user ispyb-api

Examples

import ispyb
from datetime import datetime

# Get a connection and data area objects
with ispyb.open('config.cfg') as conn:
  core = conn.core
  mx_acquisition = conn.mx_acquisition

  # Find the id for a given visit
  sessionid = core.retrieve_visit_id('cm14451-2')

  # Create a new data collection group entry:
  params = mx_acquisition.get_data_collection_group_params()
  params['parentid'] = sessionid
  params['experimenttype'] = 'OSC'
  params['starttime'] = datetime.strptime('2017-09-21 13:00:00', '%Y-%m-%d %H:%M:%S')
  params['endtime'] = datetime.strptime('2017-09-21 13:00:10', '%Y-%m-%d %H:%M:%S')
  params['comments'] = 'This is a test of data collection group.'
  dcg_id = mx_acquisition.insert_data_collection_group(list(params.values()))
  print("dcg_id: %i" % dcg_id)

See docs/pipeline2ispyb.py for a more detailed example of how to use the package.

Tests

Unit tests (pytests) are run automatically by Travis against a real MariaDB ISPyB database schema. You can also run the tests in your Development environment if you have an ISPyB database.