CGHub Python API

CGHub Python API.

Installation

To get the latest commit from GitHub

$ pip install -e git+git://github.com/42cc/cghub-python-api.git#egg=cghub_python_api

Usage

>>> from cghub_python_api import WSAPIRequest as Request
>>> results = []
>>> request = Request(query={'analysis_id': ['016cc2ca-db11-44af-b846-18e9275a4c4b', '01a589db-02d8-4d75-a2da-bb0bd8140a32']})
>>> for result in request.call():
...     print result.state.text
...     results.append(result)
...
live
live
>>> print results[0].disease_abbr.text
BRCA
>>> print results[0]['disease_abbr'].text
BRCA
>>> print results[1]['filename'].text
UNCID_1176640.2bdc311e-59cc-449f-b8dc-6662052678fd.sorted_genome_alignments.bam
>>> print results[1]['filename.0'].text
UNCID_1176640.2bdc311e-59cc-449f-b8dc-6662052678fd.sorted_genome_alignments.bam
>>> print results[1]['filename.1'].text
UNCID_1176640.2bdc311e-59cc-449f-b8dc-6662052678fd.sorted_genome_alignments.bam.bai
>>> print results[1]['checksum.0'].attrib
{'type': 'MD5'}
>>> results[0].analysis_id.exist
True
>>> results[0].somebadattr
<cghub_python_api.api.NonExistent object at 0x1ef1950>
>>> results[0].somebadattr.exist
False
>>> print results[0].somebadattr.text
None

Read more in docs/source/*.rst.

Running tests

python -m unittest -v tests

Contribute

If you want to contribute to this project, please perform the following steps

# Fork this repository
# Clone your fork
$ cd cghub-python-api
$ virtualenv .env --no-site-packages
$ source .env/bin/activate
$ python setup.py install
$ pip install -r test_requirements.txt

$ git co -b feature_branch master
# Implement your feature and tests
$ git add . && git commit
$ git push -u origin feature_branch
# Send us a pull request for your feature branch