Python interface to the GenoLogics LIMS server via its REST API.

A basic module for interacting with the Illumina Basespace Clarity LIMS server via its REST API. The goal is to provide simple access to the most common entities and their attributes in a reasonably Pythonic fashion.

Compatibility

From version 1.0.0 the scripts have been ported to support Python 3, and it is backwards compatible with Python 2 as well. The previous versions (<0.4.6) are only compatible with Python 2.

Design

All instances of Project, Sample, Artifact, etc should be obtained using the get_* methods of the Lims class, which keeps an internal cache of current instances. The idea is to create one and only one instance in a running script for representing an item in the database. If one has more than one instance representing the same item, there is a danger that one of them gets updated and not the others.

An instance of Project, Sample, Artifact, etc, retrieves lazily (i.e. only when required) its XML representation from the database. This is parsed and kept as an ElementTree within the instance. All access to predefined attributes goes via descriptors which read from or modify the ElementTree. This simplifies writing back an updated instance to the database.

Installation

pip install genologics

or for the cutting edge version:

pip install https://github.com/SciLifeLab/genologics/tarball/master

For installing an older version:

pip install "genologics==0.4.*"

Usage

The URL and credentials should be written in a new file in any of those config files (ordered by preference):

$HOME/.genologicsrc, .genologicsrc, genologics.conf, genologics.cfg

or if installed system_wide:

/etc/genologics.conf

[genologics]
BASEURI=https://yourlims.example.com:8443
USERNAME=your_username
PASSWORD=your_password
[logging]
MAIN_LOG=/home/glsai/your_main_log_file

Example scripts

Usage example scripts are provided in the subdirectory 'examples'.

NOTE: The example files rely on specific entities and configurations on the server, and use base URI, user name and password, so to work for your server, all these must be reviewed and modified.

EPPs

The EPPs in use at Scilifelab can be found in the subdirectory 'scripts' of the repository scilifelab_epps.

Tests

The limsmock serves as a LIMS REST API mock for testing purposes. It can be used for building tests for the genologicas package or other packages querying the clarity lims rest api.

Some examples of how it can be used can be fount in tests directory.

Pull requests policy

Pull requests are welcome, and will be tested internally before merging. Be aware that this process might take a fair amount of time.

Known bugs

• Artifact state is part of its URL (as a query parameter). It is not entirely clear how to deal with this in the Lims.cache: Currently, an artifact that has the current state may be represented by a URL that includes the state, and another that does not contain it.