MongoDB and Pymongo Cheats

Set up a MondoDB

Create a new Directory in your repository with a db folder in it. Directory/db

Create a YAML file named docker-compose.yaml and copy this script to it.

version: '3.6'
services:

  mongo-client:
    image: mongo:3.6
    restart: unless-stopped
    volumes:
      - ./beacon/db:/data/db
    ports:
      - "27017:27017"

  mongo-express:
    image: mongo-express
    restart: unless-stopped
    environment:
      - ME_CONFIG_MONGODB_SERVER=mongo-client
      - ME_CONFIG_MONGODB_PORT=27017
      - ME_CONFIG_BASICAUTH_USERNAME=admin
      - ME_CONFIG_BASICAUTH_PASSWORD=adminpass
    ports:
      - "8081:8081"

Run the commands below to create a docker container.

docker-compose up -d
docker exec -it mongo-client bash

To get more information about the created container for example NAMES and PORTS run the docker ps command

Database Manipulation in Python

The following code creates a databas with a variants collection.

from pymongo import MongoClient
from datetime import datetime

db_client = MongoClient() # if you work on a vertual machine you might need to change this into db_client = MongoClient("<docker ps IP>",27017)
database = db_client["cnv_reference_db"]
var_coll = database["variants"]

variants = [
    {
      "info": { "cn_count": 1 },
      "biosample_id": "testsample-0001",
      "variant_internal_id": '11:52900000-134452384:EFO_0030067',
      "variant_state": { "id": 'EFO:0030067', "label": 'copy number loss' },
      "location": {
        "sequence_id": 'refseq:NC_000011.10',
        "chromosome": '11',
        "start": 52900000,
        "end": 134452384
      },
      "relative_copy_class": 'partial loss',
      "updated": datetime.now().isoformat()
    }
]

for v in variants:
    vid = var_coll.insert_one(v).inserted_id
    vstr = f'refvar-{vid}'
    var_coll.update_one({'_id':vid},{'$set':{ 'id':vstr }})
    print(f'==> inserted {vstr}')