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civic-api-client

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:

  1. variants-list

  2. evidence-items-list

  3. action-items-web-view

  4. tsv-create

  5. 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
  1. 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
  1. 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
  1. 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

Git repositories related to the CIViC project

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.