Problem of deploying cBioportal with docker

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Xiaoli Zhang

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Aug 31, 2021, 5:08:10 PM8/31/21
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Hi,

I am following the steps to install cBioportal with docker.  But with the command "docker-compose up", I got the messages as following:

'@'172.19.0.5' (using password: YES)1-08-31T09:58:28.255484Z 60 [Note] Access denied for user 'cbio_user
cbioportal-container           | Database connection success
cbioportal-container           | Migrating database if necessary...
cbioportal-container           | Checking database contents for reference genome information
cbioportal-container           | (1146, "Table 'cbioportal.mutation_event' doesn't exist")
cbioportal-container exited with code 1

Do you know what is wrong and any suggestions for this?
Thanks in advance.

Best regards,
Xiaoli

Pim van Nierop

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Sep 1, 2021, 2:13:01 AM9/1/21
to Xiaoli Zhang, cbiop...@googlegroups.com
Hi Xiaoli,

The problem is that the database was not initialized correctly. You would have to reset the system and make sure you proceed with starting the portal when the database has been provisioned.

Please perform the following steps:

  1. Stop and remove all containers with: 'docker stop $(docker ps -aq) && docker rm $(docker ps -aq) && docker system prune && docker volume prune'.
  2. Start only the mysql service with 'docker-compose up cbioportal_database_container'.
  3. Check the logs so that you are sure that the database is initialized. This may take up to 5 mins. When done, press ctrl-c to stop the database service.
  4. Start cbioportal and observe the logs for the database connection.

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Xiaoli Zhang

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Sep 2, 2021, 8:37:10 AM9/2/21
to Pim van Nierop, cbiop...@googlegroups.com
Hi Pim,

Thank you for your replying with detail steps.
I will follow up and do furter testings. Thanks again. :)

Best regards,
Xiaoli

From: Pim van Nierop [p...@thehyve.nl]
Sent: Wednesday, September 01, 2021 8:12 AM
To: Xiaoli Zhang
Cc: cbiop...@googlegroups.com
Subject: Re: [cbioportal] Problem of deploying cBioportal with docker

Xiaoli Zhang

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Sep 13, 2021, 8:50:14 AM9/13/21
to Pim van Nierop, cbiop...@googlegroups.com
Hello again,

Sorry for the late replying. Just get chance to test your steps today. But it is the same error as before. I did not see "ERROR" when I start mysql service with 'docker-compose up cbioportal_databse', just some "WARNING". But the table 'cbioportal.mutation_event' doesn't exist when I tried to start service cbioportal.

Here are the output messages, could you help to take a check? Thanks in advance.

[cbioportal-docker-compose]$ less docker-compose.yml 
[cbioportal-docker-compose]$ docker-compose up cbioportal-database
Creating cbioportal-database-container ... done
Attaching to cbioportal-database-container
cbioportal-database-container  | 2021-09-13 12:31:57+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.35-1debian10 started.
cbioportal-database-container  | 2021-09-13 12:31:57+00:00 [Note] [Entrypoint]: Switching to dedicated user 'mysql'
cbioportal-database-container  | 2021-09-13 12:31:57+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.35-1debian10 started.
cbioportal-database-container  | 2021-09-13 12:31:57+00:00 [Note] [Entrypoint]: Initializing database files
cbioportal-database-container  | 2021-09-13T12:31:57.435601Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
cbioportal-database-container  | 2021-09-13T12:31:58.162714Z 0 [Warning] InnoDB: New log files created, LSN=45790
cbioportal-database-container  | 2021-09-13T12:31:58.281874Z 0 [Warning] InnoDB: Creating foreign key constraint system tables.
cbioportal-database-container  | 2021-09-13T12:31:58.357088Z 0 [Warning] No existing UUID has been found, so we assume that this is the first time that this server has been started. Generating a new UUID: 96716f51-148e-11ec-828f-0242ac180002.
cbioportal-database-container  | 2021-09-13T12:31:58.360000Z 0 [Warning] Gtid table is not ready to be used. Table 'mysql.gtid_executed' cannot be opened.
cbioportal-database-container  | 2021-09-13T12:31:58.848979Z 0 [Warning] A deprecated TLS version TLSv1 is enabled. Please use TLSv1.2 or higher.
cbioportal-database-container  | 2021-09-13T12:31:58.849001Z 0 [Warning] A deprecated TLS version TLSv1.1 is enabled. Please use TLSv1.2 or higher.
cbioportal-database-container  | 2021-09-13T12:31:58.849627Z 0 [Warning] CA certificate ca.pem is self signed.
cbioportal-database-container  | 2021-09-13T12:31:59.022148Z 1 [Warning] root@localhost is created with an empty password ! Please consider switching off the --initialize-insecure option.
cbioportal-database-container  | 2021-09-13 12:32:02+00:00 [Note] [Entrypoint]: Database files initialized
cbioportal-database-container  | 2021-09-13 12:32:02+00:00 [Note] [Entrypoint]: Starting temporary server
cbioportal-database-container  | 2021-09-13 12:32:02+00:00 [Note] [Entrypoint]: Waiting for server startup
cbioportal-database-container  | 2021-09-13T12:32:02.803476Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
cbioportal-database-container  | 2021-09-13T12:32:02.805736Z 0 [Note] mysqld (mysqld 5.7.35) starting as process 76 ...
cbioportal-database-container  | 2021-09-13T12:32:02.809121Z 0 [Note] InnoDB: PUNCH HOLE support available
cbioportal-database-container  | 2021-09-13T12:32:02.809147Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
cbioportal-database-container  | 2021-09-13T12:32:02.809152Z 0 [Note] InnoDB: Uses event mutexes
cbioportal-database-container  | 2021-09-13T12:32:02.809155Z 0 [Note] InnoDB: GCC builtin __atomic_thread_fence() is used for memory barrier
cbioportal-database-container  | 2021-09-13T12:32:02.809159Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.11
cbioportal-database-container  | 2021-09-13T12:32:02.809164Z 0 [Note] InnoDB: Using Linux native AIO
cbioportal-database-container  | 2021-09-13T12:32:02.809453Z 0 [Note] InnoDB: Number of pools: 1
cbioportal-database-container  | 2021-09-13T12:32:02.809606Z 0 [Note] InnoDB: Using CPU crc32 instructions
cbioportal-database-container  | 2021-09-13T12:32:02.811673Z 0 [Note] InnoDB: Initializing buffer pool, total size = 128M, instances = 1, chunk size = 128M
cbioportal-database-container  | 2021-09-13T12:32:02.821225Z 0 [Note] InnoDB: Completed initialization of buffer pool
cbioportal-database-container  | 2021-09-13T12:32:02.824165Z 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
cbioportal-database-container  | 2021-09-13T12:32:02.836561Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
cbioportal-database-container  | 2021-09-13T12:32:02.847012Z 0 [Note] InnoDB: Creating shared tablespace for temporary tables
cbioportal-database-container  | 2021-09-13T12:32:02.847101Z 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
cbioportal-database-container  | 2021-09-13T12:32:02.921256Z 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
cbioportal-database-container  | 2021-09-13T12:32:02.922085Z 0 [Note] InnoDB: 96 redo rollback segment(s) found. 96 redo rollback segment(s) are active.
cbioportal-database-container  | 2021-09-13T12:32:02.922107Z 0 [Note] InnoDB: 32 non-redo rollback segment(s) are active.
cbioportal-database-container  | 2021-09-13T12:32:02.922801Z 0 [Note] InnoDB: 5.7.35 started; log sequence number 2748441
cbioportal-database-container  | 2021-09-13T12:32:02.923003Z 0 [Note] InnoDB: Loading buffer pool(s) from /var/lib/mysql/ib_buffer_pool
cbioportal-database-container  | 2021-09-13T12:32:02.923232Z 0 [Note] Plugin 'FEDERATED' is disabled.
cbioportal-database-container  | 2021-09-13T12:32:02.925062Z 0 [Note] InnoDB: Buffer pool(s) load completed at 210913 12:32:02
cbioportal-database-container  | 2021-09-13T12:32:02.931091Z 0 [Note] Found ca.pem, server-cert.pem and server-key.pem in data directory. Trying to enable SSL support using them.
cbioportal-database-container  | 2021-09-13T12:32:02.931114Z 0 [Note] Skipping generation of SSL certificates as certificate files are present in data directory.
cbioportal-database-container  | 2021-09-13T12:32:02.931123Z 0 [Warning] A deprecated TLS version TLSv1 is enabled. Please use TLSv1.2 or higher.
cbioportal-database-container  | 2021-09-13T12:32:02.931126Z 0 [Warning] A deprecated TLS version TLSv1.1 is enabled. Please use TLSv1.2 or higher.
cbioportal-database-container  | 2021-09-13T12:32:02.931933Z 0 [Warning] CA certificate ca.pem is self signed.
cbioportal-database-container  | 2021-09-13T12:32:02.931991Z 0 [Note] Skipping generation of RSA key pair as key files are present in data directory.
cbioportal-database-container  | 2021-09-13T12:32:02.935133Z 0 [Warning] Insecure configuration for --pid-file: Location '/var/run/mysqld' in the path is accessible to all OS users. Consider choosing a different directory.
cbioportal-database-container  | 2021-09-13T12:32:02.945752Z 0 [Note] Event Scheduler: Loaded 0 events
cbioportal-database-container  | 2021-09-13T12:32:02.945979Z 0 [Note] mysqld: ready for connections.
cbioportal-database-container  | Version: '5.7.35'  socket: '/var/run/mysqld/mysqld.sock'  port: 0  MySQL Community Server (GPL)
cbioportal-database-container  | 2021-09-13 12:32:03+00:00 [Note] [Entrypoint]: Temporary server started.
cbioportal-database-container  | Warning: Unable to load '/usr/share/zoneinfo/iso3166.tab' as time zone. Skipping it.
cbioportal-database-container  | Warning: Unable to load '/usr/share/zoneinfo/leap-seconds.list' as time zone. Skipping it.
cbioportal-database-container  | Warning: Unable to load '/usr/share/zoneinfo/zone.tab' as time zone. Skipping it.
cbioportal-database-container  | Warning: Unable to load '/usr/share/zoneinfo/zone1970.tab' as time zone. Skipping it.
cbioportal-database-container  | 2021-09-13 12:32:05+00:00 [Note] [Entrypoint]: Creating database cbioportal
cbioportal-database-container  | 2021-09-13 12:32:05+00:00 [Note] [Entrypoint]: Creating user cbio_user
cbioportal-database-container  | 2021-09-13 12:32:05+00:00 [Note] [Entrypoint]: Giving user cbio_user access to schema cbioportal
cbioportal-database-container  | 
cbioportal-database-container  | 2021-09-13 12:32:05+00:00 [Note] [Entrypoint]: /usr/local/bin/docker-entrypoint.sh: running /docker-entrypoint-initdb.d/cgds.sql
cbioportal-database-container  | 
cbioportal-database-container  | 
cbioportal-database-container  | 2021-09-13 12:32:05+00:00 [Note] [Entrypoint]: /usr/local/bin/docker-entrypoint.sh: running /docker-entrypoint-initdb.d/seed.sql.gz
cbioportal-database-container  | gzip: /docker-entrypoint-initdb.d/seed.sql.gz is a directory -- ignored


[cbioportal-docker-compose]$ docker-compose up cbioportal
cbioportal-database-container is up-to-date
Creating cbioportal-session-database-container ... done
Creating cbioportal-session-container          ... done
Creating cbioportal-container                  ... done
Attaching to cbioportal-container
cbioportal-container           | Using database config:
cbioportal-container           | db.host=cbioportal-database:3306
cbioportal-container           | db.user=cbio_user
cbioportal-container           | db.portal_db_name=cbioportal
cbioportal-container           | db.password=somepassword
cbioportal-container           | Database connection success
cbioportal-container           | Migrating database if necessary...
cbioportal-container           | Checking database contents for reference genome information
cbioportal-container           | (1146, "Table 'cbioportal.mutation_event' doesn't exist")


Best regards,
Xiaoli

From: Pim van Nierop [p...@thehyve.nl]
Sent: Wednesday, September 01, 2021 8:12 AM
To: Xiaoli Zhang
Cc: cbiop...@googlegroups.com
Subject: Re: [cbioportal] Problem of deploying cBioportal with docker

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