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troubleshooting.md

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Troubleshooting

Logging into the MongoDB database of the database Docker container

scripts/mongo.sh

You can then execute standard MongoDB commands:

// show sampless
db.sample.find()

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

For more, see the MongoDB documentation.

Starting and stopping the Turnkey

This will start and stop the Docker containers:

scripts/start_turnkey.sh

scripts/stop_turnkey.sh

List the Docker containers

You can use docker-compose:

sudo docker-compose --file scripts/docker-compose.yml --project-name turnkey-service ps

which will return the state of the services defined in docker-compose.yml:

                 Name                                Command               State          Ports       
------------------------------------------------------------------------------------------------------
turnkey-service_ireceptor-api_1           docker-php-entrypoint apac ...   Up       0.0.0.0:80->80/tcp
turnkey-service_ireceptor-database_1      docker-entrypoint.sh mongod      Up       27017/tcp         
turnkey-service_ireceptor-dataloading_1   python3                          Exit 0

or directly Docker:

sudo docker ps

which will return the list of Docker containers currently running:

CONTAINER ID        IMAGE                                   COMMAND                  CREATED             STATUS              PORTS                NAMES
9641ed06f008        ireceptorj/service-php-mongodb:latest   "docker-php-entrypoi…"   3 hours ago         Up 3 hours          0.0.0.0:80->80/tcp   turnkey-service_ireceptor-api_1
0265683d92cd        ireceptorj/repository-mongodb:dev       "docker-entrypoint.s…"   3 hours ago         Up 3 hours          27017/tcp            turnkey-service_ireceptor-database_1

Logging into the Docker containers

Log into the database container as root

sudo docker-compose --file scripts/docker-compose.yml --project-name turnkey-service exec ireceptor-database bash

Log into the web application container as root

sudo docker-compose --file scripts/docker-compose.yml --project-name turnkey-service exec ireceptor-api bash

Launch the dataloading container and log into it as root

sudo docker-compose --file scripts/docker-compose.yml --project-name turnkey-service run ireceptor-dataloading bash

Logs

View the database log (MongoDB log)

sudo docker-compose --file scripts/docker-compose.yml --project-name turnkey-service logs ireceptor-database

View the web application log (Apache log)

sudo docker-compose --file scripts/docker-compose.yml --project-name turnkey-service logs ireceptor-api

View the dataloading logs (generated by the data import script)

Look into the log folder:

ls -l log

which contains a log file for each file imported into the database.

total 28
-rw-rw-r-- 1 ubuntu ubuntu 486 Jan 12 02:00 2019-01-12_02-00-53_metadata_mixcr.csv.log
-rw-rw-r-- 1 ubuntu ubuntu 563 Jan 12 02:01 2019-01-12_02-01-01_rearrangements_mixcr.txt.log
-rw-rw-r-- 1 ubuntu ubuntu 563 Jan 12 02:01 2019-01-12_02-01-07_rearrangements_mixcr.txt.log
-rw-rw-r-- 1 ubuntu ubuntu 762 Jan 14 21:46 2019-01-14_21-46-52_metadata_mixcr.csv.log
-rw-rw-r-- 1 ubuntu ubuntu 541 Jan 14 21:48 2019-01-14_21-48-08_metadata_mixcr.csv.log
-rw-rw-r-- 1 ubuntu ubuntu 550 Jan 14 21:48 2019-01-14_21-48-44_rearrangements_mixcr.txt.log
-rw-rw-r-- 1 ubuntu ubuntu 549 Jan 14 21:51 2019-01-14_21-51-04_rearrangements_mixcr.txt.log