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QUICK_INSTALL.md

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Quick Installation Guide for the OntologyStore v0.5.0

A guide for installing the OntologyStore software.

The OntologyStore has two components:

  1. The i2b2 OntologyStore cell (back-end).
  2. The i2b2 OntologyStore plugin (front-end).

Installing the i2b2 OntologyStore Cell

The following instructions assume that the Wildfly is installed on the server and is located at /opt/wildfly.

Prerequisites

  • i2b2 Core Server 1.7.13 Release or 1.8.0 Release.
  • System administrator privileges for adding AAR file, JAR file, and datasource file (*-ds.xml) to Wildfly.

1. Stop Wildfly Server

  • Stop the current Wildfly server where the i2b2 cells are deployed.

2. Download the Cell

  • Click on ontologystore_cell.zip to download the file.

  • Extract ontologystore_cell.zip file. Once extracted, there should be a folder called ontologystore_cell containing the followin files:

    • OntologyStore.aar
    • OntologyStore.jar

3. Deploy the OntologyStore Cell in Wildfly

  • Copy the OntologyStore.aar file from the ontologystore_cell folder to the i2b2 WEB-INF/services directory /opt/wildfly/standalone/deployments/i2b2.war/WEB-INF/services.

  • Copy the OntologyStore.jar file from the ontologystore_cell folder to the i2b2 WEB-INF/lib directory /opt/wildfly/standalone/deployments/i2b2.war/WEB-INF/lib.

Note that the i2b2.war in the Wildfly directory /opt/wildfly/standalone/deployments may be an actual WAR file instead of a directory. In this case, you will need to open up the i2b2.war file and add the OntologyStore.aar file to the WEB-INF/services folder and the OntologyStore.jar file to the WEB-INF/lib folder.

4. Add the Datasource Configuration File

  • Download the datasource file ontstore-ds.xml based on your database vendor:

    Database Vendor Datasource File
    Oracle ontstore-ds.xml
    SQL Server ontstore-ds.xml
    PostgreSQL ontstore-ds.xml

  • Replace the value for the connection-url, user-name, and password in the file ontstore-ds.xml with your database connection url, username, and password, respectively.

  • Place the file ontstore-ds.xml in the directory /opt/wildfly/standalone/deployments.

See the i2b2 documentation on Data Source Configuration for more detail.

5. Restart Wildfly Server

Configuring the OntologyStore Cell

Prerequisites

  • i2b2 database administrator privileges for adding entries into the i2b2 database tables.

1. Add the Cell

All of the back-end communications go through the PM Cell first then get pass to the designated cell. For the PM cell to recognize the OntologyStore cell, the cell information must be added to the pm_cell_data table in the i2b2 database.

Assume that the i2b2 Core Servers is deployed in Wildfly with the hostname localhost on port 9090

2. Configure Cell Properties

The OntologyStore has two properties that need to be set:

  1. The location (URL) of the file (JSON) containing a list of ontologies to download.
  2. The location on the server to download the ontologies to.
Set the URL Location
Set the Download Location

The configuration below tells the OntologyStore cell where to download the ontologies. Assume that the directory where the ontologies are downloaded to is /home/wildfly/ontology

  • Insert the following data to the pm_cell_params table to set the additional cell properties:

    Column Value
    datatype_cd T
    cell_id ONTSTORE
    project_path /
    param_name_cd ontstore.dir.download
    value /home/wildfly/ontology
    status_cd A

    See the i2b2 documentation on Add Cell Parameters for more detail.

Installing the Plugin

The following instructions assume that the i2b2 webclient directory is /var/www/html/webclient.

Prerequisites

  • i2b2 Web Client 1.7.13 Release or 1.8.0 Release.
  • System administrator privileges for updating the Web Client.

1. Stop the Apache HTTP Server

  • Stop the web server running the i2b2 webclient.

2. Add the OntologyStore Plugin Communicator

The plugin communicator is the communication channel between the OntologyStore plugin and the OntologyStore cell.

  • Click on ONTSTORE.zip to download the file.

  • Extract the ONTSTORE.zip file to the following i2b2 webclient directory:

    Web Client Version Directory
    1.7.13 Release /var/www/html/webclient/js-i2b2/cells
    1.8.x Release /var/www/html/webclient/js-i2b2/cells/LEGACYPLUGIN/legacy_plugin/js-i2b2/cells

3. Add the Plugin to the i2b2 Webclient

  • Click on OntologyStore.zip to download the file.

  • Extract file OntologyStore.zip to the following i2b2 webclient plugin directory:

    Web Client Version Directory
    1.7.13 Release /var/www/html/webclient/js-i2b2/cells/plugins/community
    1.8.x Release /var/www/html/webclient/js-i2b2/cells/LEGACYPLUGIN/legacy_plugin/js-i2b2/cells/plugins/community

4. Configure the i2b2 Webclient

  • Add the following code to the Javascript array i2b2.hive.tempCellsList in the module loader configuration file i2b2_loader.js:

    {code: "ONTSTORE"},
{code: "OntologyStore",
    forceLoading: true,
    forceConfigMsg: {params: []},
    roles: [ "MANAGER" ],
    forceDir: "cells/plugins/community"
}

    The i2b2_loader.js file is located in the following directory:

    Web Client Version Directory
    1.7.13 Release /var/www/html/webclient/js-i2b2
    1.8.x Release /var/www/html/webclient/js-i2b2/cells/LEGACYPLUGIN/legacy_plugin/js-i2b2

    Remember to make a backup copy of the file before modifying it.

5. Restart the Apache HTTP Server

  • Restart the web server running the i2b2 webcleint.