Example tools using the CIVIC API. Very basic docs on using the API is here. The schemas can be viewed here
##Dependencies
brew install wget
wget https://bootstrap.pypa.io/get-pip.py
sudo python get-pip.py
sudo pip install virtualenv
##Setup Install like any other Python package, I like using the Virtualenv setup.
git clone https://github.com/griffithlab/civic-api-client
cd civic-api-client
virtualenv myenv
#virtualenv myenv --python=python2.7 #if you have problems with your python version
source myenv/bin/activate
pip install .
To deactivate the virtual environment,
deactivate
##Usage Command options:
-
variants-list
-
evidence-items-list
-
action-items-web-view
-
tsv-create
-
List variants errors Basic usage (check for all variants and print out all errors):
civic-api-client variants-list
Error type can be specified, for example:
civic-api-client variants-list --wrong-base
Command above will print variants where ref/var base is not in [A,C,G,T,N,None] For more error types, see help manu with following command:
civic-api-client variants-list -h
- List evidence errors Basic usage (check for all evidence and print out all errors):
civic-api-client evidence-items-list
Error type can be specified, for example, search for missing drug items: Print out on screen(All types):
civic-api-client evidence-items-list --drug
Specify evidence types and print on web page(Predictive,for example):
civic-api-client evidence-items-list --drug --evi-type Predictive --web
For more error types, see help manu with following command:
civic-api-client evidence-items-list -h
- Check for variants or evidences errors on web Basic functionality for now, this will run a web-server on http://127.0.0.1:5000/ , this page will list the items that need work.
civic-api-client action-items-web-view
Can also be done by following command:
civic-api-client variants-list --web
civic-api-client evidence-items-list --web
- Export all evidence items as tsv file
civic-api-client tsv-create
##Development To contribute to the code for this project, please fork the repo and submit a pull request.
To test your own changes (after editing code) you can rebuild the package as follows:
pip install . --upgrade
To install the latest changes
git pull
pip install . --upgrade
The CIViC source code and application are organized in a client-server model. The backend code is available in the civic-server repository and frontend code is available in the civic-client repository. Issues relating to curation are tracked in the civic-curation repository. An example of a Python client is available in the civic-api-client repository. Issues relating to public CIViC meetings are tracked in the civic-meeting repository.