wiki:i2b2/installation_notes

Version 15 (modified by overbyc, 10 years ago) (diff)

--

Recommended order of installation (from Hive Installation Guide)

  1. Project Management Cell (required)
  2. Data Installation (required)
  3. Ontology Cell (required)
  4. Data Repository (CRC) Cell (required)
  5. Any remaining optional cells

i2b2 lingo

  • Hive - a set of Cells that interact through a SOA (Service Oriented Architecture)
  • Cell - an independent and changeable service that can send and receive messages using REST protocol

Prerequisite installation & notes

Steps:

  • Follow steps from Hive Installation Guide
  • Add environment variables from step h to a startup file e.g. ~/.bash_profile
  • Add Oracle XE environment variables to startup file
    export ORACLE_HOME=/usr/lib/oracle/xe/app/oracle/product/10.2.0/server
    export ORACLE_SID=XE
    export PATH=$ORACLE_HOME/bin:$PATH
    

Project Management Cell installation documents & notes

Note: built within the gridsphere portal framework (provides an open-source portlet-based Web portal)

Functions:

  • Manages user accounts
  • Contains mechanisms for collaboration
  • Manage cells

Steps:

  • Follow PM Cell Installation Guide (skip prerequisite installation steps)

Note: edu.harvard.i2b2.pm located in core-src-10.zip

  • Configure i2b2Workbench to communicate with PM cell (pg. 25 of PM Cell Installation Guide)
  • See i2b2Workbench installation documents & notes section below for how to connect to UW server

Problems encountered & solutions:

  • Tomcat log error message: “...NoClassDefFoundError?: org/apache/xml/serialize/XMLSerializer.”
    • Possible cause (found on gridsphere thread): The new version of tomcat doesn’t come with the org/apache/xml/serialize/XMLSerializer class
    • Solution: Download Xerces from http://xml.apache.org/xalan-j/downloads.html and put the xercesImpl.jar and xml-apis.jar files in $CATALINA_HOME/common/endorsed
    • Unix command:
      curl -O http://mirrors.24-7-solutions.net/pub/apache/xml/xalan-j/xalan-j_2_7_1-bin-2jars.zip
      

Documents:

Data installation documents & notes

Steps:

  • DBA account should be created in Oracle Express
  • While logged in as DBA, create the following DBs: I2B2METADATA & I2B2DEMODATA (password: DEMO)
  • Run scripts located in demodata-10.zip

SQL commands:

SQL> GRANT CONNECT, RESOURCE, DBA O I2B2METADATA IDENTIFIED BY DEMO;
SQL> CONNECT I2B2METADATA/DEMO@XE
SQL> @i2b2metadata_create.sql 
SQL> @i2b2metadata_data.sql 

SQL> GRANT CONNECT, RESOURCE, DBA O I2B2DEMODATA IDENTIFIED BY DEMO;
SQL> CONNECT I2B2DEMODATA/DEMO@XE
SQL> @i2b2demodata_create.sql 
SQL> @i2b2demodata_data.sql 
SQL> @i2b2demodata_seq.sql 
  • Metadata - schema and data used by the ontology cell
  • Demodata - schema and data used by the CRC cell

Note: Integration of data from other data sources involves determining what data fits into the schema used for the demodata

Ontology Cell installation documents & notes

Functions:

  • Data representation for the CRC
  • Includes International Disease Classification Version 9 -CM (ICD9-CM), National Drug Classification (NDC), and Logical Observation Identifiers Names and Codes (LOINC) vocabulary definitions

Steps:

  • Follow ONT Cell Installation Guide (skip prerequisite installation steps)

Note: edu.harvard.i2b2.ontology located in core-src-10.zip

  • Register ONT Cell by adding information as described on pages 17-18 of PM Cell Installation Guide in the Project Manager

Problems encountered & solutions:

  • i2b2Workbench error message: ‘Ontology cell is unavailable’
    • Cause: Ontology cell address in gridsphere (PM Cell) is incorrect
    • Solution: Review pages 17-18 of PM Cell installation guide.
      • Make sure the Base URL is in the correct format (replace host & port with the correct values)
        http://host:port/i2b2/rest/OntologyServerce/
        
  • i2b2Workbench error message: ‘Database error’
    • Cause: Problems connecting to the database
    • Solution: Review pages 5-7 of ONT Cell installation guide.
      • Make sure the following line in the PM property settings of the ontology.properties file is exactly as follows:
        ontology.ws.pm.url= http://localhost:7070/axis2/rest/PMService/getServices
        
      • Edit the following line in the etc/spring/OntologyApplicationContext.xml file (replace host with the correct value):
        <property name=”url”
        	value=”jdbc:oracle:thin:@host:1521:xe”/>
        

Note: apply changes by running ‘ant -f master_build.xml build-all deploy’

Documents:

Data Repository (CRC) Cell installation documents & notes

Functions:

  • Query web services (PDO Webservice & Setfinder Webservice)
  • PDO Webservice is for querying the database based on patient data object (PDO) requests
  • Setfinder Webservice supports operations like create query, delete query, save query definition & results

Steps:

  • Follow CRC Cell Installation Guide (skip prerequisite installation steps)

Note: edu.harvard.i2b2.common & edu.harvard.i2b2.crc located in core-src-10.zip

  • Register CRC Cell by adding information as described on pages 17-18 of PM Cell Installation Guide in the Project Manager.

Problems encountered & solutions:

  • i2b2Workbench error message: ‘Database error’
    • Cause: Problems connecting to the database
    • Solution: Review pages 5-6 of CRC Cell installation guide.
      • Edit database properties in the etc/spring/crc.properties file (replace host with the correct value):
        queryprocessor.database.connection_string=jdbc:oracle:thin:@host:1521:xe
        
      • Edit database properties in in the etc/jboss/crc-oracle-ds.xml file (replace host with the correct value):
        <xa-datasource-property name="URL">jdbc:oracle:thin:@host:1521:xe</xa-datasource-property>
        
      • Edit database properties in in the etc/jboss/crc-oracle-jms-ds.xml file (replace host with the correct value):
        <connection-url>jdbc:oracle:thin:@host:1521:xe</connection-url>
        

Note: apply changes by running ‘ant -f master_build.xml build-all deploy’

Documents:

I2b2 Workbench documents & notes

Functions:

  • Communicate with i2b2 Cells
  • Helps aggregate Cell functionality in the Hive
  • Can browse concepts from ontology and use them to define criteria in a patient set (PDO) query
  • A PDO query interaction allows the user to select the type of data to be returned on a set of patients

Configure to work with UW server:

  • Add the following line to i2b2Workbench.properties file to connect with the UW server
    I2b2.2=UW Demo Site, REST, http://oculus.biostr.washington.edu:7070/axis2/rest/PMService 
    

Note: i2b2Workbench.properties file may be access by Ctrl clicking the i2b2workbench icon and selecting “Show Package Contents” (for Mac OS X)

  • Log into i2b2Workbench with User privileges using uwdemo/uwpassword for username/password

Documents:

Future work

  • Expanding vocabulary used by ONT cell
  • Building your own cell
  • Building applications on top of the Hive (e.g. i2b2Workbench)
  • Adding functionality to the i2b2Workbench using Eclipse
  • Automating mapping between the Ontology and the CRC schema

Note: All figures borrowed from i2b2 documentation

Attachments