galithil / genologics Goto Github PK

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.

Supported python versions :

2.6
2.7 (recommended)
3.4
3.5

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.

pip install genologics

or for the cutting edge version:

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

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

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.

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

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

• 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.