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README.md
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| @@ -6,7 +6,9 @@ Tested on i2b2 VM 1.7.08b | |||
| ---- | |||
| All the steps up to and including **Create and admin user** are to be carried as root, inside the VM. | |||
| The package is best used locally on the VM. | |||
| All the steps involving file modifications **are to be run locally**, as root. | |||
| This includes the creation/deletion of projects. | |||
| ---- | |||
| @@ -14,18 +16,15 @@ All the steps up to and including **Create and admin user** are to be carried as | |||
| 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. | |||
| # Installation | |||
| Restart the machine. | |||
| Run `curl https://raw.githubusercontent.com/MaximeWack/R2b2/master/prepare.sh` to download the installation script, and run it as root. | |||
| # Installation | |||
| You might need to configure your internet connection if you are behind a proxy. | |||
| Install dependencies in R: | |||
| `install.packages(c("tidyverse", "RPostgreSQL", "devtools"))` | |||
| This script will add the EPEL repo, update the installed packages and package list on the system, and install system dependancies to run R2b2. It will also install R packages dependancies and install R2b2 from github. | |||
| Install with `devtools::install_github("maximewack/R2b2")` | |||
| Restart the machine. | |||
| # Usage | |||
| @@ -42,32 +41,3 @@ 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). | |||
| ---- | |||
| The subsequent steps up to and including **set domain** can be executed using the created admin system user, inside the VM. | |||
| ---- | |||
| ## 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. | |||
| ---- | |||
| 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) | |||
| ---- | |||
| ## 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. | |||