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开源软件名称:pekrau/genologics开源软件地址:https://github.com/SciLifeLab/genologics开源编程语言:Python 100.0%开源软件介绍: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. CompatibilityFrom 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. DesignAll 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
or for the cutting edge version:
For installing an older version:
UsageThe URL and credentials should be written in a new file in any of those config files (ordered by preference):
or if installed system_wide:
Example scriptsUsage 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. EPPsThe EPPs in use at Scilifelab can be found in the subdirectory 'scripts' of the repository scilifelab_epps. TestsThe 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 policyPull requests are welcome, and will be tested internally before merging. Be aware that this process might take a fair amount of time. Known bugs
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2023-10-27
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