i2b2 r plugin

Introduction

They was a strong need to provide a new export plugin to i2b2. This one is :

• based on open-source softwares
• securised (auth, audit table, i2b2 roles)
• fast (direct SQL calls to the i2b2 database)
• compressed export
• flexible, and modifiable

Screenshot

1 Specify the export

2 Get the zip file

3 Open the zip file

prerequired

• i2b2 1.7 and higher
• postgresql database
• linux (debian/ubunu prefered)
• opencpu
• RPostgres R package
  • libpq (postgresql development library)
• data.table R package
• jsonlite R package
• the i2b2rplugin plugin installed & configured in the i2b2 webclient

installation

• i2b2pm
  • create the audit table running the config/i2b2_create_postgresql.sql
• i2b2rplugin R package
  • clone this repository
  • configure the config/*.csv in order to choose exported columns and roles
  • configure the config/*.R in order to transform the data for users
  • rename the config/*_observation_fact.R in order to map your concept_mapping_prefix
  • copy/edit the config file to a securized destination accessible to openCPU user
  • place some documentation files in it
  • edit the R/function.R#PATH_CONFIG accordingly
  • compile the package
  • install the package as root on the OpenCPU server (in order openCPU access to it)
• ExportOCPU i2B2 web plugin
  • moove the plugins/ExportOCPU to /i2b2/js-i2b2/cells/plugins/standard/
  • edit the i2b2/default.htm add the javascript dependencies

<script type="text/javascript" src="//code.jquery.com/jquery-3.1.0.min.js"></script>
<script type="text/javascript" src="//cdn.opencpu.org/opencpu-0.5.js"></script>

• /i2b2/js-i2b2/i2b2_loader.js add the plugin to the list

{ code: "ExportOCPU",
        forceLoading: true,
        forceConfigMsg: { params: [] },
        roles: [ "DATA_DEID", "DATA_PROT" ],
        forceDir: "cells/plugins/standard"
}

• /i2b2/js-i2b2/cells/plugins/standard/ExportOCPU/cell_config_data.js : replace with your host

ocpuUrl : "//<your-ip>/ocpu/library/i2b2rplugin/R",
ocpuHost :  "http://<your-ip>"

to be done

• oracle/msql connectors
• statistical functions