MyGeneset.info

MyGeneset.info is a web API for storing, searching, and accessing geneset data.

Setting Up and Running BioThings Hub

1. BioThings Hub: Pre-requisites

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

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:7.17.1

2. Clone this repo

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

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

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

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).

Setting up the Web Server

1. Web Server: Pre-requisites

MongoDB is not required for running the web server

• Python>=3.6 (Python versions lower than 3.8 also require PyPI package singledispatchmethod)
• Git
• Elasticsearch>=6.0.0 (See installation steps above)

2. Install requirements

pip install -r ./requirements_web.txt

3. 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'
}

You can override any settings from config_web.py in config.py:

from config_web import * # Add additional customizations

Some required configurations:

```python
# A random string
COOKIE_SECRET =

# GitHub keys
GITHUB_CLIENT_ID =
GITHUB_CLIENT_SECRET =

# ORCID keys
ORCID_CLIENT_ID =
ORCID_CLIENT_SECRET =

WEB_HOST = "http://localhost:8000"

# Path to local webapp folder
FRONTEND_PATH =
```

FRONTEND_PATH is only required for running the API with the user interface. You need to first clone and build the web app project: "https://github.com/biothings/mygeneset.info-website"

4. Create Elasticsearch Indices

The ES indices defined in the ES_INDEX setting must exist.

For example:

```bash
# Creating an empty user_genesets index
curl -X PUT "localhost:9200/user_genesets"
```

5. Run API

python index.py

For launching alongside the web app:

python index.py --webapp

To see debugging messages:

python index.py --debug