Python API client for WikiPathways webservices.

How to Use

Clone and cd into this repo:

git clone https://github.com/wikipathways/wikipathways-api-client-py.git
cd wikipathways-api-client-py

Install virtualenvwrapper and create a new virtualenv (if pip is available on your system, the virtualenvwrapper steps are optional):

mkvirtualenv your_preferred_name

Install wikipathways-api-client-py:

pip install -e .

Try one of the examples:

python ./examples/example_get_pathway_as.py

Now that your virtualenv is created, you can leave it at anytime with:

deactivate

And come back to it later with:

workon your_preferred_name

To list all your virtualenvs:

ls $WORKON_HOME

Troubleshooting

This set of commands was required for one user to install on Linux:

sudo apt-get update
sudo apt-get install aptitude
sudo aptitude install libxslt1-dev libxml2-dev
git clone https://github.com/wikipathways/wikipathways-api-client-py.git
cd wikipathways-api-client-py
pip install -e .
python wikipathways-api-client-py/examples/example_get_pathway_as.py

Supported API calls

If it's checked in the following list, the WikiPathways API call is implemented in this client. If it's not checked, we'd be happy to accept your pull request with code implementing it! You can find more details about the calls in the WikiPathways API documentation.

• [x] listOrganisms
• [x] listPathways
• [x] getPathwayInfo
• [ ] getPathwayHistory
• [ ] getRecentChanges
• [ ] login
• [x] getPathwayAs
• [ ] updatePathway
• [x] createPathway
• [x] findPathwaysByText
• [x] findPathwaysByXref
• [ ] findInteractions
• [ ] saveCurationTag
• [ ] removeCurationTag
• [ ] getCurationTags
• [ ] getCurationTagsByName
• [x] getColoredPathway
• [ ] getXrefList
• [ ] findPathwaysByLiterature
• [ ] getOntologyTermsByPathway
• [ ] getOntologyTermsByOntology
• [ ] getPathwaysByOntologyTerm
• [ ] getPathwaysByParentOntologyTerm

Future Enhancements

• [ ] Add tests
• [ ] Add documentation and build docs with PyDoc
• [ ] Publish on PyPI so it can be installed with pip