R2b2

Manage an i2b2 instance installed from the VM from i2b2.org.

Tested on i2b2 VM 1.7.08b

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All the steps up to and including Create and admin user are to be carried as root, inside the VM.

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Prerequisites

Download and install the VM image from i2b2.org and run it inside VMWare.

yum install epel-release && yum update to use the epel repo and update the system.

yum install R openssl-devel libxml2-devel postgresql-devel postgresql91-devel libcurl-devel to install R and necessary dependencies.

Restart the machine.

Installation

Install dependencies in R:
install.packages(c("tidyverse", "RPostgreSQL", "devtools"))

Install with devtools::install_github("maximewack/R2b2")

Usage

Set permissions

The set_permissions function sets group owning, setgid and group rights +rwx to the webclient and wildfly folders so that the admin(s) can manage them.

Create an admin user

By default, create_admin creates a i2b2admin system user, with a random generated password containing numbers and letters of all cases.
You can set a preferred username as the first argument (name), an arbitrary password (pass), or set the desired password length (pass_length).

The user is created for the system, with membership to the wildfly group.
An user with the same name, and their corresponding database are also created in PostgreSQL, with the generated or given password.

You are still responsible for managing the root account and its password (default = demouser), and optionally granting additional privileges to the admin user (such as sudo rights).

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The subsequent steps up to and including set domain can be executed using the created admin system user, inside the VM.

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Securing the database

This step is only necessary if you want to access the database remotely. Otherwise, the default settings are secure enough.

All the databases have the default demouser password.
secure_db takes a database admin credentials (name and pass) and a password length (pass_length) to generate random passwords for the i2b2{demodata, hive, imdata, metadata, pm, workdata} databases. Those passwords are updated in the {crc, im, ont, pm, work}-ds.xml files in $JBOSS_HOME/standalone/deployments/.

You are still responsible for managing the access rights to the PostgreSQL database (listening addresses in $PSQL_HOME/data/postgresql.conf and access methods in $PSQL_HOME/data/pg_hba.conf) if you want to be able to access it remotely.

Set the domain

set_domain takes a database admin credentials (name and pass) and a domain_id (the internal id) and domain_name (the name of the host on the webclient login page) and sets the corresponding columns in i2b2hive and i2b2pm, and configures the webclient to connect to this domain.

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The next steps can be carried with another user, as long as you provide the necessary credentials (database admin account), and even from a different machine (you'll have to configure the pg_hba.conf and postgresql.conf files accordingly)

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Set the project

set_project takes a host address, a database admin credentials (name and pass) and a project_id (the internal id, also the project path. It must not contain spaces) and project_name (the name of the project displayed in the webclient) and sets the corresponding columns in i2b2hive and i2b2pm.