/i2b2rplugin

This collection of i2b2 plugins are based on a R package loaded in OpenCPU

Primary LanguageR

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

Screenshot1

2 Get the zip file

Screenshot2

3 Open the zip file

Screenshot3

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