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					Install Hive Cells

The following order is recommended:
1. Review „i2b2 Database Strategy‟ in preparation for Data installation.
2. Data Installation (required) (includes table creation)
3. Project Management (PM) Cell (required)
4. Ontology (ONT) Cell Installation (required)
5. Data Repository (CRC) Cell Installation (required)
6. Workplace (WORK) Cell Installation (required)
7. File Repository (FR) Cell Installation (required)
8. PFT Processing (PFT) Cell Installation (optional)
9. Any remaining optional cells
Please refer to each cell‟s installation guide. If you have followed the Prerequisites
section in this guide, you may skip the Prerequisite sections for the individual cells.



Installing the i2b2 Data Package

1. Unzip the data package into a folder: (/opt/data)
You should see the project edu.harvard.i2b2.data.
„cd edu.harvard.i2b2.data /Release_1-4/NewInstall‟
This is considered your data installation working directory. Under this directory
are folders for Demodata, Metadata, and Workdata. These map to schemas
i2b2demodata, i2b2metadata and i2b2workdata for project Demo and
i2b2demodata2, i2b2metadata2 and i2b2workdata2 for project Demo2. Folder
Hivedata maps to the i2b2hive schema.

2 . Create user accounts in Oracle:
Log in as system user
Enter i2b2metadata user name and password. Check off Direct grant system
privileges as shown below. Repeat for users i2b2demodata, i2b2workdata for
project Demo, users i2b2metadata2, i2b2demodata2, i2b2workdata2 for project
Demo2 and user i2b2hive and i2b2pm.




3. Create Metadata tables and load data:
a) 'cd Metadata‟ of your working directory.
(edu.harvard.i2b2.data /Release_1-4/NewInstall)
b) Edit db.properties
Set database properties; be sure to set user/pswd to i2b2metadata and project to
demo;
Oracle:
db.type=oracle
db.username=i2b2metadata
db.password=demouser
db.server=127.0.0.1:1521:orcl
db.driver=oracle.jdbc.driver.OracleDriver
db.url=jdbc:oracle:thin:@127.0.0.1:1521:orcl
db.project=demo

In the above script we made the change from localhost to 127.0.0.1 as linux box doesn‟t map it to
localhost
c) To create metadata tables, indexes and sequences :
Run 'ant -f data_build.xml create_metadata_tables_release_1-4‟

d) To load data:
If you wish to load your own metadata, do that now.
Otherwise:
Run 'ant -f data_build.xml db_metadata_load_data'
This may take few minutes

e) Edit db.properties for user/pswd i2b2metadata2 and project demo2.
Repeat steps c and d.

4. Create Demodata tables and load data:
a) 'cd Demodata‟ of your working directory.
(edu.harvard.i2b2.data /Release_1-4/NewInstall)

b) Edit db.properties
Set database properties; be sure to set user/pswd to i2b2demodata and project
to demo.

Oracle:
db.type=oracle
db.username=i2b2demodata
db.password=demouser
db.server=127.0.0.1:1521:orcl
db.driver=oracle.jdbc.driver.OracleDriver
db.url=jdbc:oracle:thin:@127.0.0.1:1521:orcl
db.project=demo

c) To create demodata tables, indexes and sequences :
Run 'ant -f data_build.xml create_demodata_tables_release_1-4‟

d) To create new stored procedures:
Run 'ant -f data_build.xml create_procedures_release_1-4‟

e) To load data:
If you wish to load your own demo data, do that now.
Otherwise:
Run 'ant -f data_build.xml db_demodata_load_data'
This may take few minutes
f) Edit db.properties for user/pswd i2b2demodata2 and project demo2.
Repeat steps c, d and e.

5. Create Workdata tables and load data:

a) 'cd Workdata‟ of your working directory.
(edu.harvard.i2b2.data /Release_1-4/NewInstall)

b) Edit db.properties
Set database properties; be sure to set user/pswd to i2b2workdata, and project
to demo.

Oracle:
db.type=oracle
db.username=i2b2workdata
db.password=demouser
db.server=127.0.0.1:1521:orcl
db.driver=oracle.jdbc.driver.OracleDriver
db.url=jdbc:oracle:thin:@127.0.0.1:1521:orcl
db.project=demo

c) To create workdata tables, indexes and sequences :
Run 'ant -f data_build.xml create_workdata_tables_release_1-4‟

d) To load data:
If you wish to load your own work data, do that now.
Otherwise:
Run 'ant -f data_build.xml db_workdata_load_data'

e) Edit db.properties for user/pswd i2b2workdata2 and project demo2.
Repeat steps c and d.

6. Create Hive tables and load data:
a) 'cd Hivedata‟ of your working directory.
(edu.harvard.i2b2.data /Release_1-4/NewInstall)

b) Edit db.properties
Set database properties; be sure to set user/pswd to i2b2hive.
Oracle:
db.type=oracle
db.username=i2b2hive
db.password=demouser
db.server=127.0.0.1:1521:orcl
db.driver=oracle.jdbc.driver.OracleDriver
db.url=jdbc:oracle:thin:@127.0.0.1:1521:orcl

c) To create hive tables, indexes and sequences :
Run 'ant -f data_build.xml create_hivedata_tables_release_1-4‟
d) To load data:
If you wish to load your own hive data, do that now.
Otherwise:
Run 'ant -f data_build.xml db_hivedata_load_data'

The data loaded into the three i2b2hive db_lookup tables presumes that the
default target location pointing to the hive we are now setting up is 'i2b2demo'.

This target location is also referred to as the domain of the hive and should match
the domain set up in the PM setup.
In the client's i2b2.properties file:
I2b2.1=demo,REST,http://webservices:9090/i2b2/rest/PMService/
I2b2.2=HarvardDemo,REST,http://services.i2b2.org/PM/rest/PMService/
#I2b2.3=YourSite,REST,http://jbossHost:jbossPort/i2b2/rest/PMServ
ice/
The I2b2.1 target location ('demo') points to the hive residing on the vmware
image. The i2b2.2 target location, HarvardDemo points to the hive residing at
Harvard. The data installed at Harvard is identical to the data provided in this
package. The hive we are now setting up is I2b2.3. Please be sure to rename
'YourSite' to 'i2b2demo'.

7. Create PM tables and load data:
a) 'cd Pmdata‟ of your working directory.
(edu.harvard.i2b2.data /Release_1-4/NewInstall)

b) Edit db.properties
Set database properties; be sure to set user/pswd to i2b2pm

Oracle:
db.type=oracle
db.username=i2b2pm
db.password=i2b2pm_pswd
db.server=127.0.0.1:1521:orcl
db.driver=oracle.jdbc.driver.OracleDriver
db.url=jdbc:oracle:thin:@127.0.0.1:1521:orcl

c) To create pm tables, indexes and sequences :
Run 'ant -f data_build.xml create_pmdata_tables_release_1-4‟

d) To create pm triggers :
Run 'ant -f data_build.xml create_triggers_release_1-4‟

e) To load data:
If you wish to load your own pm data, do that now.
Otherwise:
Run 'ant -f data_build.xml db_pmdata_load_data'
   1. You are now ready to proceed with hive installation.

Installing or Upgrading the Project Management application

The 1.4 i2b2 Project Management cell now runs on the same JBoss platform as the Ontology and Data
Repository cells. As a result, all users need to perform the following installation procedures.

1. Download and extract the core server source code to a target area.
If this has been downloaded in a previous installation (e.g. ONT or CRC), there is no need to repeat this
step.

a) Set up a target source_directory. (/opt/i2b2/src)
b) Extract the core server source code to the target source_directory

2. Ensure that JBOSS is not running
a) 'cd $JBOSS_HOME/bin/'
b) './shutdown.sh -S' (rcjboss Stop/start/Status)

3. Deploy edu.harvard.i2b2.common

a) 'cd source_directory/edu.harvard.i2b2.common'

b) Edit the build.properties file and set jboss.home and axis2.war.name properties
jboss.home=/usr/jboss-4.2.2.GA
axis2.war.name=i2b2.war

c) „ant clean deploy jboss_pre_deployment_setup‟

4. Deploy edu.harvard.i2b2.pm
a) 'cd source_directory/edu.harvard.i2b2.pm'

b) Edit the build.properties file and set jboss.home and axis2.war.name properties
jboss.home=/usr/jboss-4.2.2.GA
axis2.war.name=i2b2.war

c) Edit etc/jboss/pm-ds.xml and configure your data sources:
PMBootStrapDS points to the location of your PM table.
Data source samples for both sqlserver and oracle are provided in pmds.
xml. Copy and modify the samples in pm-ds.xml as needed to create
the data sources shown below. If using Oracle rename
PMBootStrapDS_ORACLE to PMBootStrapDS, else if using SqlServer
name PMBootStrapDS_SQLSERVER to PMBootStrapDS.
<datasources>
<local-tx-datasource>
<jndi-name>PMBootStrapDS </jndi-name>
<driver-class>oracle.jdbc.driver.OracleDriver
</driver-class>
<connection-url>jdbc:oracle:thin:@127.0.0.1:1521:orcl
</connection-url>
<user-name>i2b2pm</user-name>
<password>demouser</password>
</local-tx-datasource>

f) „ant -f master_build.xml clean build-all deploy‟

5. Install the WebClient
a) Copy the Webclient directory, which is in the root directory of the core
server source code to your httpd directory; (/usr/local/apache2/htdocs)

The webclient is pre-configured for a localhost domain of „i2b2demo‟. If
you are upgrading from a system with a different domain or want to specify
a different domain, edit the file webclient/i2b2_config_data.js accordingly.
           { name: "oraMac1",
            domain: "i2b2demo",
            debug: true,
            urlCellPM: "http://oraMac1/i2b2/rest/PMService/"
           },

b) If your httpd server is not running, start it now.

6. Start JBoss

7. Verify webservice is running


a) Check url „http://yourHost:9090/i2b2/services/listServices‟ in a browser.
Verify that PMService is listed as active.
Changing Server log level

By default JBOSS log will be in DEBUG mode, changing it to INFO mode will increase server
performance.

a) Edit $JBOSS_HOME /server/default/conf/jboss-log4j.xml file and add the
„Threshold‟ param.
<appender name="FILE"
class="org.jboss.logging.appender.DailyRollingFileAppender">
<errorHandlerclass="org.jboss.logging.util.OnlyOnceErrorHandler"/>
<param name="File" value="${jboss.server.home.dir}/log/server.log"/>
<param name="Append" value="false"/>
<param name="Threshold" value="INFO"/>
<!-- Rollover at midnight each day -->
<param name="DatePattern" value="'.'yyyy-MM-dd"/>
<layout class="org.apache.log4j.PatternLayout">
<!-- The default pattern: Date Priority [Category] Message\n -
->
<param name="ConversionPattern" value="%d %-5p [%c] %m%n"/>
.....
</layout>
</appender>

To switch back to DEBUG mode, comment out the „Threshold‟ param and wait a minute. THERE IS
NO NEED TO RESTART JBOSS.


Administration of the i2b2 Project Management application

Go to the site http://oraMac1/webclient

1. You will see a login screen. Log in with a user you know has ADMIN role.
For those installing for the first time, use the default ADMIN user of „i2b2‟ and password of
„demouser‟.




2. Once logged on you will be presented with a default setup, select „Admin‟ from the primary
navigation. You should see the following:
3. Click the „Hive‟ in the PM Navigation. This is where you can modify the Domains, Cells and Global
Params. Click on the Domain to see the Domain Information.
User creation in the i2b2 Project (Group) Management application

1. Continuing with the web client, select „Manage User‟ from the primary navigation. You should see
the following:
2. Click on the „Add New‟ link, and fill in the required fields for the user you wish to add, such as the
username, password, email address. Click the „Save Update‟ button once you are complete. Repeat the
process for as many users you wish to




3. To remove a user from the system, click on the row associated with that user, and click on the
„Delete‟ button.
4. To add a parameter to the user, select the row that contains the user you wish to add the parameter to
and a new table will appear below. Follow the same procedure by select „Add New‟ to add a parameter
to that user.

Registered Cell
1. Continuing with the web client, select „Hive‟ from the primary navigation, than „Cells‟ from the
secondary navigation. You should see the following:
2. Click on the URL column on the row that has the CRC on it. Change the 192.168.242.130 to the IP
or domain name that the CRC is installed on. Click the „Save Update‟ button once you are complete.
Repeat the process for the rest of the cells.
3. To add a new cell, click on the „Add New‟ button and fill out the new information for that cell. Click
the „Save Update‟ button when complete.
4. To add a parameter to the cell, select the row that contains the cell you wish to add the parameter to
and a new table will appear below. Follow the same procedure by select „Add New‟ to add a parameter
to that cell.


Existing Projects

1. Continuing with the web client, select „Projects from the primary navigation, than „i2b2demodata‟
from the secondary navigation. This is where you can update the information associated with the
project. You should see the following:
2. You can have cells that are associated with only this specific project, by selecting the cells in the
third level in the tree. And likewise, there will be parameters associated with that cell.

3. Parameters for this project can be added or deleted by selecting the Params from the tree.

4. The last item in the tree is Users, This item allows you to associate Users to a project. In the table,
enter the username that you want to grant permission to and than select the roles. You need to select an
Administration Role which is the first three roles and a Data Track which is the remaining roles. In the
example below, User and Data_Agg was selected. The user mem61 will inherit Data_Obfsc
automatically.
PM Cell Sanity Test via the i2b2Workbench

1. Configure the i2b2Workbench to communicate with your PM cell.
The i2b2Workbench may be configured via the i2b2Workbench.properties file. This file is found in the
top level directory of the binary package (see file /i2b2Workbench/i2b2Workbench.properties). Sample
contents of this file are shown below:

writeTimelineFile=yes
applicationName=i2b2
messageversion=1.1
I2b2.2=i2b2demo,REST,http://oraMac1/i2b2/rest/PMService/

The last lines in this file provide the location of the target PM cells. Its structure is as follows:
Identifier Label Protocol URL I2b2.1 HarvardDemo REST
http://webservices.i2b2.org/i2b2/rest/PMService/
#I2b2.2 YourSite REST http://host:port/i2b2/rest/PMService/ To set up the system to point to your
target PM cell, remove the comment tag („#‟) in the I2b2.2 identifier, provide a meaningful label and
configure the URL for the location of your PM cell.

2. Launch the i2b2Workbench (double-click on i2b2Workbench.exe)

Login to i2b2:
a. Select your target location (YourSite)
b. Enter a valid username and password that you set up in gridsphere (demo/demouser)
Installing the Ontology Management Application

1. Download and extract the core server source code to a target area.
If this has been downloaded in a previous installation (e.g. PM or CRC), there is no need to repeat this
step.
a) Set up a target source_directory. (/opt/i2b2/src)
b) Extract the core server source code to the target source_directory

2. Ensure that JBOSS is not running
a) 'cd $JBOSS_HOME/bin/'
b) './shutdown.sh -S'

3. Deploy edu.harvard.i2b2.common
If this has been deployed in a previous installation (e.g. CRC), there is no need to repeat this step.
a) 'cd source_directory/edu.harvard.i2b2.common'
b) Edit the build.properties file and set jboss.home and axis2.war.name properties
jboss.home=/usr/jboss-4.2.2.GA
axis2.war.name=i2b2.war
c) „ant clean deploy jboss_pre_deployment_setup‟

4. Deploy edu.harvard.i2b2.ontology
a) 'cd source_directory/edu.harvard.i2b2.ontology'
b) Edit the build.properties file and set jboss.home and axis2.war.name properties
jboss.home=/usr/jboss-4.2.2.GA
axis2.war.name=i2b2.war
c) Edit the etc/spring/ontology_application_directory.properties file and specify a location for the
application properties directory. This location can be anything you desire but must be a directory path
that your linux
user has access permission for.
edu.harvard.i2b2.ontology.applicationdir= /usr/jboss-4.2.2.GA
/server/default/conf/ontologyapp

d) Edit the etc/spring/ontology.properties file and set database and project management properties Set
metadata bootstrap database schema name to the location of the ONT_DB_LOOKUP table
#######################################
# METADATA schema name
#######################################
ontology.bootstrapdb.metadataschema=i2b2hive
Set the Project Management property settings
Note the new address for the jboss-based PMService.
ontology.ws.pm.url=http://oraMac1/i2b2/rest/PMService/getServices
# Flag to bypass project management cell
ontology.ws.pm.bypass=false
ontology.ws.pm.bypass.role=ADMIN
ontology.ws.pm.bypass.project=Demo

Set the METADATA delimiter (backslash) setting
ontology.terminal.delimiter=true

If set to „true‟, this parameter adds a backslash automatically to the metadata fullpath name if it does
not already exist. This was added to fix a bug related to leaf-level metadata concepts with similar
names: such as //i2b2/i2b2/metadata/pul and //i2b2/i2b2/metadata/pulm Set this to „false‟ if you want
true Release 1.3 backward compatibility.
e) Edit etc/jboss/ont-ds..xml and configure your data sources:
OntologyBootStrapDS points to the location of your ONT_DB_LOOKUP table. Any additional data
source specified in the lookup table must be specified here as well (shown below as
"OntologyDemoDS" for project
Demo and "OntologyDemo2DS" for project Demo2). Data source samples for both sqlserver and
oracle are provided in ontds.xml. Copy and modify the samples in ont-ds.xml as needed to create the
three data sources shown below. Comment out or remove any unused samples.
<datasources>
<local-tx-datasource>
<jndi-name>OntologyBootStrapDS</jndi-name>
<driver-class>oracle.jdbc.driver.OracleDriver
</driver-class>
<connection-url>jdbc:oracle:thin:@127.0.0.1:1521:orcl
</connection-url>
<user-name>i2b2hive</user-name>
<password>demouser</password>
</local-tx-datasource>
<local-tx-datasource>
<jndi-name>OntologyDemoDS</jndi-name>
<driver-class>oracle.jdbc.driver.OracleDriver
</driver-class>
<connection-url>jdbc:oracle:thin:@127.0.0.1:1521:orcl
</connection-url>
<user-name>i2b2metadata</user-name>
<password>demouser</password>
</local-tx-datasource>
<local-tx-datasource>
<jndi-name>OntologyDemo2DS</jndi-name>
<driver-class>oracle.jdbc.driver.OracleDriver
</driver-class>
<connection-url>jdbc:oracle:thin:@127.0.0.1:1521:orcl
</connection-url>
<user-name>i2b2metadata2</user-name>
<password>demouser</password>
</local-tx-datasource>
</datasources>

f) „ant -f master_build.xml clean build-all deploy‟

5. Start JBOSS
6. Verify webservice is running
a) Check url „http://oraMac1/i2b2/services/listServices‟ in a browser.
Verify that OntologyService is listed as active.




Verify Installation

Ontology (ONT) Cell Sanity Test via the i2b2Workbench

1. Configure the i2b2Workbench to communicate with your ONT cell.

Cell configuration is addressed in the Project Management (PM) Cell installation and set up. Please
refer to this document if the Ontology Cell has not yet been configured. To verify this data, go to the
web client site http://oraMac1/webclient.
Once logged on, select „Cells‟ under the „Hive primary navigation tab. If the Ontology Cell has been
configured it will be listed as an existing, registered cell:




2. Launch the i2b2Workbench (double-click on i2b2Workbench.exe)

Login to i2b2:
a. Select your target location (YourSite)
b. Enter a valid username and password (demo/demouser)

c. The URL at the bottom of the login screen should be the address of your PM cell.
If not, edit the i2b2workbench.properties file to point to the location of your PM cell.
I2b2.1=oraMac1,REST,http://oraMac1/i2b2/rest/PMService/




3. Open the Navigate Terms view in the workbench.
If all is configured properly, you will be greeted with a top level folder called
“Ontology”. Double click on this folder to expand.




4. Open the Find Terms view in the workbench
Enter a diagnostic term to search on such as “asthma”. Click on the Find button. If all is configured
properly, you will see a list of entries each containing the work „asthma‟.
Installing the Clinical Research Chart Application

1. Download and extract the core server source code to a target area.
If this has been downloaded in a previous installation (e.g. PM or ONT), there
is no need to repeat this step.
a) Set up a target source_directory. (/opt/i2b2/src)
b) Extract core server source code to the target source_directory.

2. Ensure that JBOSS is not running
a) ./$JBOSS_HOME/bin/shutdown.sh –S

3. Deploy edu.harvard.i2b2.common
If this has been deployed in a previous installation (eg. ONT), there is no need to repeat this step.
a) 'cd source_directory/edu.harvard.i2b2.common'
b) Edit the build.properties file and set jboss.home and axis2.war.name properties

jboss.home=/usr/jboss-4.2.2.GA
axis2.war.name=i2b2.war

c) „ant clean dist deploy jboss_pre_deployment_setup‟

4. Deploy edu.harvard.i2b2.crc and edu.harvard.i2b2.crc.loader
4.1. Build edu.harvard.i2b2.crc.loader
The Uploader service is added to the CRC as part of the Release 1.3. The source for the Uploader
resides in edu.harvard.i2b2.crc.loader project and it uses the CRC‟s datasource setup.

a) 'cd source_directory/edu.harvard.i2b2.crc.loader'
b) Edit the build.properties file and set jboss.home and axis2.war.name properties

jboss.home=/usr/jboss-4.2.2.GA
axis2.war.name=i2b2.war

c) Edit the etc/spring/crc_loader_application_directory.properties file and specify a location for the
application properties directory. This location can be anything you desire but must be a directory path
that your linux
user has access permission for.

edu.harvard.i2b2.crc.applicationdir= /usr/jboss-4.2.2.GA/server/default/conf/crcloaderapp

d)Edit the etc/spring/edu.harvard.i2b2.crc.loader.properties file and set project management properties
Set Project Management property settings:

Note the new location of the PM URL.

edu.harvard.i2b2.crc.loader.ws.pm.url=http://oraMac1/i2b2/rest/PMService/getServices
# Flag to bypass project management cell
edu.harvard.i2b2.crc.loader.ws.pm.bypass=false
edu.harvard.i2b2.crc.loader.ws.pm.bypass.role=ADMIN
edu.harvard.i2b2.crc.loader.ws.pm.bypass.project=Demo


If you are using file repository cell and want to connect the CRC loader to it,
then set the FileRepository cell property setting
#######################################
# File Management Cell
#######################################
edu.harvard.i2b2.crc.loader.ws.fr.url=http://oraMac1/i2b2/services/FRService/

e) Edit the etc/spring/CRCLoaderApplicationContext.xml Specify the jdbc properties to locate the
„CRC_DB_LOOKUP‟ table.
<bean id="LoaderLookupDS" class="org.apache.commons.dbcp.BasicDataSource" destroymethod="
close">
<property name="driverClassName" value=" oracle.jdbc.driver.OracleDriver"/>
<property name="url" value="jdbc:oracle:thin:@127.0.0.1:1521:orcl"/>
<property name="username" value="i2b2hive"/>
<property name="password" value="demouser"/>
</bean>
Update entry in edu.harvard.i2b2.crc.loader.properties to reflect the above change.

#######################################
# Datasource Lookup properties
#######################################
edu.harvard.i2b2.crc.loader.ds.lookup.datasource=LoaderLookupDS
edu.harvard.i2b2.crc.loader.ds.lookup.servertype=ORACLE
edu.harvard.i2b2.crc.loader.ds.lookup.schemaname=i2b2hive
f) „ant -f build.xml clean dist‟

Note : No „deploy‟ target is used. The loader will be deployed as part of edu.harvard.i2b2.crc project.

4.2 Setup edu.harvard.i2b2.crc
a) 'cd source_directory/edu.harvard.i2b2.crc'
b) Edit the build.properties file and set jboss.home and axis2.war.name properties
jboss.home=/usr/jboss-4.2.2.GA
axis2.war.name=i2b2.war
#jms persistance could be either oracle or mssql
jboss.jms.persistance=oracle

c) Edit the etc/spring/crc_application_directory.properties file and specify a location for the application
properties directory. This location can be anything you desire but must be a directory path that your
linux user has access permission for.
edu.harvard.i2b2.crc.applicationdir= /usr/jboss-4.2.2.GA/server/default/conf/crcapp

d)Edit the etc/spring/crc.properties file and set project management properties
Set Project Management property settings
Note the new location of the PM Service.
#######################################
# Project Management Cell
#######################################
queryprocessor.ws.pm.url=http://localhost:9090/i2b2/rest/PMService/getServices
# Flag to bypass project management cell
queryprocessor.ws.pm.bypass=false
queryprocessor.ws.pm.bypass.role=ADMIN
queryprocessor.ws.pm.bypass.project=Demo
e)Set Ontology property settings, change the hostname and port
#######################################
# Ontology Cell
#######################################
queryprocessor.ws.ontology.url=http://localhost:9090/i2b2/rest/OntologyService/getTermInfo
f)Create the CRC service user account in the Project Management cell and assign the „User‟ and
„Data_Obfsc‟ role to the user. CRC uses this PM user in the Ontology and PM cell calls.
#####################################################
# CRC service account properties
#####################################################
edu.harvard.i2b2.crc.pm.serviceaccount.user=OBFSC_SERVICE_ACCOUNT
edu.harvard.i2b2.crc.pm.serviceaccount.password=demouser

g) Update QT_BREAKDOWN_PATH table: Based on your Ontology mapping,
update the parent item key values used in the analysis break down calculation.
Name Value
PATIENT_GENDER_COUNT_XML \\i2b2\i2b2\Demographics\Gender\
PATIENT_RACE_COUNT_XML \\i2b2\i2b2\Demographics\Race\
PATIENT_VITALSTATUS_COUNT_XML \\i2b2\i2b2\Demographics\Vital Status\
PATIENT_AGE_COUNT_XML \\i2b2\i2b2\Demographics\Age\
h) The following steps tells CRC, where the “CRC_DB_LOOKUP” table is located.

       code_lookup
PK c_domain_id varchar(255)
PK c_project_path varchar(255)
PK c_owner_id varchar(255)
   c_db_fullschema varchar(255)
   c_db_datasource varchar(255)
   c_db_servertype varchar(255)
   c_db_nicename varchar(255)
   c_db_tooltip varchar(255)
   c_comment text
   c_entry_date datetime
   c_change_date datetime
   c_status_cd char(1)

Edit etc/spring/CRCApplicationContext.xml:
<bean id="CRCDataSourceLookup"
class="org.apache.commons.dbcp.BasicDataSource" destroymethod="close">
<property name="driverClassName" value="oracle.jdbc.driver.OracleDriver"/>
<property name="url" value="jdbc:oracle:thin:@127.0.0.1:1521:orcl"/>
<property name="username" value="i2b2hive"/>
<property name="password" value="demouser"/>
</bean>
Update entry in etc/spring/crc.properties to reflect the above change.
#######################################
# Datasource Lookup properties
#######################################
queryprocessor.ds.lookup.datasource=CRCDataSourceLookup
queryprocessor.ds.lookup.servertype=ORACLE
queryprocessor.ds.lookup.schemaname=i2b2hive
Continuing in file etc/spring/crc.properties:
i)The PDO paging size can be adjusted based on the runtime jvm setting.
#######################################
# PDO Paging properties
#######################################
edu.harvard.i2b2.crc.pdo.paging.observation.size=75000
j)You can tune the default max job count for the Analysis job queue
#######################################
# Analysis Queue properties
#######################################
edu.harvard.i2b2.crc.analysis.queue.medium.timeoutmills=1800000
edu.harvard.i2b2.crc.analysis.queue.medium.maxjobcount=4
edu.harvard.i2b2.crc.analysis.queue.large.timeoutmills=3600000
9
edu.harvard.i2b2.crc.analysis.queue.large.maxjobcount=4
edu.harvard.i2b2.crc.analysis.queue.medium.jobcheck.timemills=120000
edu.harvard.i2b2.crc.analysis.queue.large.jobcheck.timemills=120000
k)If required adjust the default query queues timeout in second.
#####################################################
# Setfinder JMS Queue transaction timeout properties
#####################################################
edu.harvard.i2b2.crc.jms.small.timeoutsec=180
edu.harvard.i2b2.crc.jms.medium.timeoutsec=14400
edu.harvard.i2b2.crc.jms.large.timeoutsec=43200
l)If required change the default user‟s setfinder lockout parameter
#####################################################
# CRC setfinder query lockout parameter
#####################################################
edu.harvard.i2b2.crc.lockout.setfinderquery.count=7
edu.harvard.i2b2.crc.lockout.setfinderquery.day=30

m)Configure JBoss Datasource:
CRC supports both Oracle and SqlServer. Edit etc/jboss/crc-ds.xml and set the database connection
properties. For SqlServer data source, please use the sample provided in the crc-ds.xml. The following
steps show the configuring Oracle data source for two projects. If your setup has multiple projects
pointing to different data sources, then copy <local-tx-datasource> in ds-xml for each project data
source.
<jndi-name>QueryToolDemoDS</jndi-name>
<connectionurl>
   jdbc:oracle:thin:@127.0.0.1:1521:orcl</connection-url>
   <driver-class>oracle.jdbc.driver.OracleDriver</driver-class>
<user-name>i2b2demodata</user-name>
<password>demouser</password>
For example, project Demo2 would have this entry:
<jndi-name>QueryToolDemo2DS</jndi-name> with connection-url:
<connectionurl>
jdbc:oracle:thin:@127.0.0.1:1521:orcl</connection-url>
<driver-class>oracle.jdbc.driver.OracleDriver</driver-class>
<user-name>i2b2demodata2</user-name>
<password>demouser</password>

n)Edit etc/jboss/crc-jms-ds.xml and set „DefaultDS‟ JMS database connection properties If the data
source is Sqlserver, then comment the oracle section and uncomment sqlserver datasource section.
<local-tx-datasource>
<jndi-name>DefaultDS</jndi-name>
<connectionurl>
jdbc:oracle:thin:@127.0.0.1:1521:orcl</connection-url>
<driver-class>oracle.jdbc.driver.OracleDriver</driverclass>
<user-name>i2b2hive_uname</user-name>
<password>demouser</password>
...
</local-tx-datasource>

4.3 Build and deploy edu.harvard.i2b2.crc and edu.harvard.i2b2.crc.loader
„ant -f master_build.xml clean build-all deploy‟

Note: If you are deploying on an existing JBoss instance with CRC 1.3, then please remove the
QueryProcessor-EJB.jar from the $JBOSS_HOME/server/default/deploy directory.

5. Start JBOSS

6. Verify webservice is running
a) Check url „http://yourHost:9090/i2b2/services/listServices‟ in a browser.
Verify that QueryToolService is listed as active.




Verify Installation
CRC Cell Sanity Test via the i2b2Workbench

1. Configure the i2b2Workbench to communicate with your CRC cell.
Cell configuration is addressed in the Project Management (PM) Cell installation and set up. Please
refer to this document if the CRC Cell has not yet been configured.
To verify this data, go to the web client site http://oraMac1/webclient.
Once logged on, select „Cells‟ under the „Hive primary navigation tab. If the CRC Cell has been
configured it will be listed as an existing, registered cell: To verify cell data, select cell name(CRC) and
click on Edit Cell Info.




2. Launch the i2b2Workbench (double-click on i2b2Workbench.exe)
Login to i2b2:
a. Select your target location (YourSite)
b. Enter a valid username and password (demo/demouser)




3. Open the Query Tool, Previous Queries and Timeline views in the workbench
If all is configured properly, you will be greeted with the following
Installing the Workplace Application

1. Download and extract the core server source code to a target area.
If this has been downloaded in a previous installation (e.g. PM or CRC), there is no need to repeat this
step.
a) Set up a target source_directory. (/opt/i2b2/src)
b) Extract the core server source code to the target source_directory

2. Ensure that JBOSS is not running

3. Deploy edu.harvard.i2b2.common
If this has been deployed in a previous installation (e.g. CRC, ONT), there is no need to repeat this
step.
a) 'cd source_directory/edu.harvard.i2b2.common'
b) Edit the build.properties file and set jboss.home and axis2.war.name properties
jboss.home=/usr/jboss-4.2.2.GA
axis2.war.name=i2b2.war
c) „ant clean deploy jboss_pre_deployment_setup‟

4. Deploy edu.harvard.i2b2.workplace
a) 'cd source_directory/edu.harvard.i2b2.workplace'
b) Edit the build.properties file and set jboss.home and axis2.war.name properties
jboss.home=/usr/jboss-4.2.2.GA
axis2.war.name=i2b2.war
c) Edit the etc/jboss/work-ds.xml file and configure your data sources: WorkplaceBootStrapDS points
to the location of your WORK_DB_LOOKUP table. Any additional data source specified in the lookup
table must be
specified here as well (shown below as "WorkplaceDemoDS" and "WorkplaceDemo2DS"). Data
source samples for both sqlserver and oracle are provided in workds.xml. Copy and modify the samples
in work-ds.xml as needed to create the three data sources shown below. Comment out or remove any
unused samples.
<datasource>
<local-tx-datasource>
<jndi-name>WorkplaceBootStrapDS</jndi-name>
<driver-class>oracle.jdbc.driver.OracleDriver</driverclass>
<connectionurl>
jdbc:oracle:thin:@127.0.0.1:1521:orcl</connection-url>
<user-name>i2b2hive</user-name>
<password>demouser</password>
</local-tx-datasource>
<local-tx-datasource>
<jndi-name>WorkplaceDemoDS</jndi-name>
<driver-class>oracle.jdbc.driver.OracleDriver</driverclass>
<connection-url>jdbc:oracle:thin:@127.0.0.1:1521:orcl</connection-url>
<user-name>i2b2workdata</user-name>
<password>demouser</password>
</local-tx-datasource>
<local-tx-datasource>
<jndi-name>WorkplaceDemo2DS</jndi-name>
<driver-class>oracle.jdbc.driver.OracleDriver</driverclass>
<connection-url>jdbc:oracle:thin:@yourHost:1521:orcl
</connection-url>
<user-name>i2b2workdata2</user-name>
<password>demouser</password>
</local-tx-datasource>
</datasources>

d) Edit the etc/spring/workplace_application_directory.properties file and specify a location for the
application properties directory. This location can be anything you desire but must be a directory path
that your linux user has access permission for.
edu.harvard.i2b2.workplace.applicationdir=/usr/jboss-4.2.2.GA/server/default/conf/workplaceapp

e) Edit the etc/spring/workplace.properties file and set database and project management properties
Set WORK_DB_LOOKUP schema name
#######################################
# METADATA schema name
#######################################
workplace.bootstrapdb.metadataschema=i2b2hive
Set the Project Management property settings
workplace.ws.pm.url=http://oraMac1/i2b2/rest/PMService/getServices
workplace.ws.pm.webServiceMethod=REST
# Flag to bypass project management cell
workplace.ws.pm.bypass=false
workplace.ws.pm.bypass.role=ADMIN
workplace.ws.pm.bypass.project=Demo

f) ant -f master_build.xml clean build-all deploy‟

5. Start JBOSS
6. Verify webservice is running
a) Check url „http://oraMac1/i2b2/services/listServices‟ in a browser.
Verify that WorkplaceService is listed as active.
Verify Installation

Workplace (WORK) Cell Sanity Test via the i2b2Workbench

1. Configure the i2b2Workbench to communicate with your WORK cell.
Cell configuration is addressed the Project Management (PM) Cell installation and setup. Please refer
to this document if the Workplace Cell has not yet been configured. To verify this data, go to the web
client site http://oraMac1/webclient.
Once logged on, select „Cells‟ under the „Hive primary navigation tab. If the Workplace Cell has been
configured it will be listed as an existing, registered cell:
To verify cell data, select cell name and click on Edit Cell Info.

If the Workplace has not been configured yet, select Add New. Properties for the Workplace cell are as
follows:

ID    Name Base             URL                                            Method
WORK Workplace Cell http://host:port/i2b2/rest/WorkplaceService/           REST

2. Launch the i2b2Workbench (double-click on i2b2Workbench.exe)

Login to i2b2:
a. Select your target location (YourSite)
b. Enter a valid username and password (demo/demouser)

3. Open the Workplace view in the workbench

If all is configured properly, you will be greeted with two top level workplace containers: „SHARED‟
and „yourUserId‟. Double click on either container to expand.
Installing the File Repository cell

1. Download and extract the core server source code to a target area.
If this has been downloaded in a previous installation (e.g. PM or ONT), there is no need to repeat this
step.
a) Set up a target source_directory. (/opt/i2b2/src)
b) Extract core server source code to the target source_directory.

2. Ensure that JBOSS is not running

3. Deploy edu.harvard.i2b2.common
If this has been deployed in a previous installation (eg. ONT), there is no need to repeat this step.
a) 'cd source_directory/edu.harvard.i2b2.common'
b) Edit the build.properties file and set jboss.home and axis2.war.name properties
jboss.home=/usr/jboss-4.2.2.GA
axis2.war.name=i2b2.war
c) „ant clean deploy jboss_pre_deployment_setup‟

4. Deploy edu.harvard.i2b2.fr
a) 'cd source_directory/edu.harvard.i2b2.fr'
b) Edit the build.properties file and set jboss.home, axis2.war.name
jboss.home=/usr/jboss-4.2.2.GA
axis2.war.name=i2b2.war

c) Edit the etc/spring/fr_application_directory.properties file and specify a location for the application
properties directory. This location can be anything you desire but must be a directory path that your
linux user has access permission for.

edu.harvard.i2b2.fr.applicationdir= /usr/jboss-4.2.2.GA/server/default/conf/frapp

d) Edit the etc/spring/edu.harvard.i2b2.fr.properties file and set project management properties

Set Project Management property settings
Note the new location of the PM Service:

edu.harvard.i2b2.fr.ws.pm.url=http://oraMac1/i2b2/rest/PMService/getServices
# Flag to bypass project management cell
edu.harvard.i2b2.fr.ws.pm.bypass=false
edu.harvard.i2b2.fr.ws.pm.bypass.role=ADMIN
edu.harvard.i2b2.fr.ws.pm.bypass.project=Demo
e) „ant -f master_build.xml clean build-all deploy‟

5. Update Project Management
a) Logon to Project Manager Web Interface
Once logged on, select „Hive‟ from the primary navigation tab and „Cell‟ from the secondary
navigation menu. If the Data Importer Cell (FR Cell) has not been configured, select „Add New‟ and
fill in the required cell information in step 1.

Please note that the correct ID for this cell is „FRC‟.




b) Enter the parameters by selecting the row that has the „FRC‟ as the ID.

PathSeperator is the default path separator for the host machine running the cell, on Mac OS and Linux
is it /, while on Windows it is \ DestDir is the destination where the files will be hosted.

c) (optional) To allow admin users to transfer files directly via SFTP, create a Group Variable called
FRMethod with the value of SFTP and FRHost with the name of the machine. FRPort is an optional
field, usually set at 22. To allow the CRC loader to retrieve the files locally when it is on the same
JBoss as FR, set the FRMethod to 'local'. This will prevent the CRC Loader from accessing the FR via
a web service call, resulting in faster responses.

d) To create a directory on the server to host the files, logon as the same user that will be running jBoss.
1. „mkdir /opt/FRC‟

6. Start JBOSS
7. Verify webservice is running
a) Check url „http://oraMac1/i2b2/services/listServices‟ in a browser.
Verify that FRService is listed as active.




FR Cell Sanity Test via the i2b2Workbench
1. Launch the i2b2Workbench (double-click on i2b2Workbench.exe)

Login to i2b2:
a. Select your target location (YourSite)
b. Enter a valid username and password (demo/demouser)

2. Open the Import Data view in the workbench
If all is configured properly, you will be greeted with the following

				
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