How can one import data into a mongodb service in docker-compose

Question

I have been having problems using mongodb as a service in docker-compose. I managed to insert data into its container (csv, txt and json files, for instance) at data/db/ through a volume folder, but I still cant use it as a collection. I believe I should use the function mongoimport`, but it fails to connect to the host. All seems to be fine but the host. I have tried a lot of other addresses as hosts, but none have worked.

Below is my docker-compose.yml

version: '3'

services:

    mongodb:
        image: mongo:3.6
        container_name: mongodb
        restart: on-failure
        environment:
            - MONGO_INITDB_ROOT_USERNAME=root
            - MONGO_INITDB_ROOT_PASSWORD=example
        volumes:
            - ./mongodbvol:/data/db
        ports:
            - "27107:27107"
        command:
            mongoimport --host http://0.0.0.0:27017 -c col1 --type csv --file /data/db/tt.csv --headerline
        
    mongo-express:
        image: mongo-express
        container_name: mongo-express
        restart: on-failure
        environment:
            - ME_CONFIG_MONGODB_SERVER=mongodb
            - ME_CONFIG_MONGODB_ADMINUSERNAME=root
            - ME_CONFIG_MONGODB_ADMINPASSWORD=example
            - ME_CONFIG_BASICAUTH_USERNAME=necode
            - ME_CONFIG_BASICAUTH_PASSWORD=passwd
        ports:
            - "8081:8081"
        depends_on:
            - mongodb

    rshiny:
        image: guigo13/app
        container_name: rshiny
        restart: on-failure
        command: R -e "shiny::runApp('R/app.R', host = '0.0.0.0', port = 3838)"
        environment:
            - DB_URI=mongodb
            - DB_USERNAME=root
            - DB_PASSWORD=example
            - DB_NAME=appdb
            - DB_HOST=mongodb
            - DB_PORT=27017
        ports:
            - "3838:3838"
            - "3839:3838"
        depends_on:
            - mongodb

and here is the error from the logs

mongodb          | 2021-10-29T02:51:09.170+0000 [########################] test.col1    11B/11B (100.0%)
mongodb          | 2021-10-29T02:51:09.685+0000 [########################] test.col1    11B/11B (100.0%)
mongodb          | 2021-10-29T02:51:09.685+0000 Failed: error connecting to db server: no reachable servers
mongodb          | 2021-10-29T02:51:09.685+0000 imported 0 documents

Could someone, please, get me an alternative? Thanks in advance.

Answer 1

The problem is you are overriding the default CMD for the mongo image (which is running the db service - CMD ["mongod"]). This makes it impossible for the container to connect to itself). Also I think the default port for mongo is 27017, and not 27107.

I've seen people using a separate container to seed the data to the database, where all it does - it runs the mongoimport to populate the data and then dies. You could try thi approach. Check this answer, this may give you an idea.

Answer 2

If you want to import it just once, I would advice to create an own image:

Dockerfile:

FROM mongo:versiontag

ENV MONGO_INITDB_ROOT_USERNAME root
ENV MONGO_INITDB_ROOT_PASSWORD example
ENV MONGO_INITDB_DATABASE mydb

COPY mongodb.js /docker-entrypoint-initdb.d/
RUN mongod --fork --logpath=/tmp/mongodb.log && sleep 20 && \
  mongoimport -c=users -d=acrc --mode=upsert --file=/opt/acrc/config/users.json && \
  mongoimport -c=tasks -d=acrc --mode=upsert --file=/opt/acrc/config/tasks.json && \
  mongoimport -c=configs -d=acrc --mode=upsert --file=/opt/acrc/config/configs.json && \
  mongoimport -c=agentGroupConfigs -d=acrc --mode=upsert --file=/opt/acrc/config/agentGroupConfigs.json && \
  mongoimport -c=col1 --type=csv --file=/data/db/tt.csv --headerline

It is firing up the mongo while creating the container and fills it then.

in the mongodb.js you can script additional mongosh commands, like adding users, dbs or insert data and so on.

Edit: Small brainbug. Should do the RUN stuff in docker-entrypoint-initdb.d to be sure it just did once. Entrypoint-scripts are not executed if db-folder exists. Therefore:

COPY mongodb.js prefill.sh /docker-entrypoint-initdb.d/

prefill.sh

#!/bin/bash
mongod --fork --logpath=/tmp/mongodb.log 
sleep 20
mongoimport -c=users -d=acrc --mode=upsert --file=/opt/acrc/config/users.json
mongoimport -c=tasks -d=acrc --mode=upsert --file=/opt/acrc/config/tasks.json
mongoimport -c=configs -d=acrc --mode=upsert --file=/opt/acrc/config/configs.json
mongoimport -c=agentGroupConfigs -d=acrc --mode=upsert --file=/opt/acrc/config/agentGroupConfigs.json
mongoimport -c=col1 --type=csv --file=/data/db/tt.csv --headerline