ficolo/impc-reference-harvester

IMPC Reference harvester

IMPC Reference harvester

IMPC harvester for comsortium's resources citing papers

Requirements

• Python 3+
• NLTK
• MongoDB
• Solr with the Allele2 core loaded

How to run

1. Clone this repo:

git clone https://github.com/mpi2/impc-reference-harvester.git
cd impc-reference-harvester

2. Edit the config_example.ini file.
3. Create a new pyvenv and activate it:

python3 -m venv .venv
source .venv/bin/activate

4. Install python dependecies:

pip install -r requirements.txt

5. Run the script:

python reference_harvester.py 

Development environment setup

1. Fork this repo and then clone your forked version:

   git clone https://github.com/USERNAME/impc-reference-harvester.git
   cd impc-reference-harvester

2. Use your favorite IDE to make your awesome changes and make sure the project is pointing to the venv generated. To do that using Pycharm fo to the instructions here.

3. And finally commit and push your changes to your fork and the make a pull request to the original repo when you are ready to go. Another member of the team will review your changes and after having two +1 you will be ready to merge them to the base repo.

   In order to sync your forked local version with the base repo you need to add an upstream remote:

   git remote add upstream https://github.com/mpi2/impc-reference-harvester.git

   Please procure to have your version in sync with the base repo to avoid merging hell.

   git fetch upstream
   git checkout master
   git merge upstream/master
   git push origin master