i2b2 Docker Images

[Andrew Hoffmann]

Hello,

I am looking for the source code for the Docker images published on DockerHub at https://hub.docker.com/u/i2b2

Are these available?

Andrew Hoffmann
University of Wisconsin-Madison

[Jeff Klann]

Yes, they are! Kavi put them here:  https://github.com/i2b2/i2b2-docker-generator 

Thanks,

Jeff Klann

[Andrew Hoffmann]

Hi Jeff,

 

Thanks for the link.  This appears to be a private repository; I am getting a 404.

 

Andrew Hoffmann

 

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[Kavishwar Wagholikar]

Hi Andrew,
Please send us your github id, so that you can be added to the repo.
Thanks,
kavi

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[cmc]

Is there any documentation or examples on how to use the Docker images? I see the i2b2-docker sub-project which has a Docker compose file to bring up an example server complete with a psql database. 

But what I'd like to have is an image I can start up and just set environment variables configure the data sources, etc. The Docker compose version exposes some env variables - but not the jdbc connection strings, for example. 

Thanks. 

[Mauro Bucalo]

Hi Kavi,

is it possible to add also me (mbucalo) and my colleagues Gabriele (gguazzardi) and Rita (rdemolfetta).

Thanks for your work

Mauro

[Kavishwar Wagholikar]

Added you all for access to the docker generator repo.
Thanks,
kavi

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[Kavishwar Wagholikar]

Thats correct! The documentation at https://github.com/i2b2/i2b2-docker/,
shows how to setup a i2b2 with a demo database in pgsql.

You can modify the variables in the .env file to auto-configure the
jdbc connection strings, if you already have an existing pg database.
Let us know if you have any other questions.

Thanks,
kavi

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[cmc]

Thanks Kavi, my goal is to create (or use) a Docker image to run i2b2 against my own data source (not an example server). 

Ideally, I could pull the i2b2 image, set environment variables for the DB connection strings and other properties and run it (vs having to compile i2b2 myself, install an instance of wildfly, etc. etc.)  

I can see in the example, it is setting environment variables for the various parts, but it doesn't set JDBC connection URLs. 

And it's not clear to me what the defaults for the I2B2_xxx variables are, etc. 

If the private github project you're referencing shows those things, my github user id is :  XcrigX

Thanks!

```

    environment:

      - DS_TYPE=${I2B2_DS_TYPE}
     
      - DS_CRC_IP=${I2B2_DS_CRC_IP}
      - DS_CRC_PORT=${I2B2_DS_CRC_PORT}
      - DS_CRC_USER=${I2B2_DS_CRC_USER}
      - DS_CRC_PASS=${I2B2_DS_CRC_PASS}
      - DS_CRC_DB=${I2B2_DS_CRC_DB}
      - DS_CRC_SCHEMA=${I2B2_DS_CRC_SCHEMA}
     ...

```

[cmc]

Are "you" constructing the JDBC URL from the  different  env variable parts? In my case I need to set additional parameters for the connection (authentication mode for SQL Server, etc) so I need to set the raw/full JDBC url. 

[cmc]

Kavi, if you could please add me to the repo also - XcrigX - I might be able to work out what I need. Thanks! 

[Jeff Klann]

I agree that this would be a great feature, and it's necessary for anyone using a physical database that is not running Postgres or the i2b2.public schema.

I know Kavi & team are working on support for physical databases with the Wildfly docker image, so maybe we will get this capability soon?

Thanks,

Jeff Klann