troubleshooting.md

Troubleshooting

Starting and stopping the ireceptor system service

sudo systemctl start ireceptor
sudo systemctl stop ireceptor

Checking if the Docker containers are running

sudo docker ps

will return:

CONTAINER ID        IMAGE                          COMMAND                  CREATED             STATUS              PORTS                      NAMES
7bd5da46b2a6        ireceptor/repository-mongo     "docker-entrypoint.s…"   59 seconds ago      Up 59 seconds       0.0.0.0:27017->27017/tcp   irdn-mongo
469743631ac3        ireceptor/service-js-mongodb   "node --harmony /ser…"   59 seconds ago      Up 58 seconds       0.0.0.0:8080->8080/tcp     irdn-api

irdn-mongo is the Docker container for the database, irdn-api is the one for the web application.

Logging into the Docker containers

# log as root into the database container
sudo docker exec -t -i irdn-mongo /bin/bash

# log as root into the web application container
sudo docker exec -t -i irdn-api /bin/bash

More generally, docker exec -t -i <container name> <command> executes a given command in the given container.

Logging into the MongoDB database as an admin user

# load the admin user credentials
source scripts/export.sh

# launch a mongo client using these credentials
sudo docker exec -it irdn-mongo mongo --authenticationDatabase admin $MONGODB_DB -u $MONGODB_SERVICE_USER -p $MONGODB_SERVICE_SECRET

You can then execute standard MongoDB commands:

// switch to the "ireceptor" database
use ireceptor

// show sampless
db.sample.find()

// show sequence annotations
db.sequence.find()

For more, see the MongoDB documentation

View the database log

MongoDB logs to the standard output of the Docker container, which can be accessed with:

sudo docker logs irdn-mongo

View the web application log

node.js logs to the standard output of the Docker container, which can be accessed with:

sudo docker logs irdn-api

Other useful information

• the database data folder and the import tools were installed in /opt/ireceptor