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MyGeneset.info

MyGeneset.info is a web API for accessing gene set data.

Setting Up and Running BioThings Hub

1. Pre-requisites:

  • Python>=3.6 (Python versions lower than 3.8 also require PyPI package singledispatchmethod)
  • Git
  • MongoDB
  • Elasticsearch>=6.0.0, <7.0.0

Elasticsearch and MongoDB can be installed locally, or run from Docker containers:

MongoDB:

docker run -d -p 27017-27019:27017-27019 --name mongodb mongo:latest

Elasticsearch:

docker run -d -p 9200:9200 -p 9300:9300 -e "discovery.type=single-node" --name elasticsearch docker.elastic.co/elasticsearch/elasticsearch:6.8.13

2. Clone this repo:

git clone https://github.com/biothings/mygeneset.info.git

3. Setup a Python virtual environment (optional, but highly recommended):

With virtualenv:

mkdir -p ~/venvs
virtualenv ~/venvs/mygeneset
source ~/venvs/mygeneset/bin/activate

Alternatively, using miniconda:

conda create -n mygeneset python=3.8
conda activate mygeneset

4. Install required Python modules:

cd mygeneset.info
pip install -r ./requirements_hub.txt

5. Make your own "config.py" file

cd src
vim config.py

from config_hub import * # Add additional customizations

6. Generate SSH keys

# from src folder:
ssh-keygen -f bin/ssh_host_key

7. Start BioThings Hub

# from src folder:
python -m bin.hub

8. Connect to the Hub from web interface (BioThings Studio)

Navigate to https://studio.biothings.io/ and create a connection to http://localhost:HUB_API_PORT, in which HUB_API_PORT is the port number specified in your configuration (default is 19480).

Running the Production API

1. Configure the Web Component

The API configuration file is located under /src/config_web.py.

The value of STATUS_CHECK.id should match an _id in the data.

STATUS_CHECK = {
    'id': 'WP4966',
    'index': 'mygeneset_current',
    'doc_type': 'geneset'
}

Optionally, edit the port number and host in ES_HOST.

2. Run API

python index.py