Developers Getting Started With i2b2
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In i2b2 1.7.12, the cell properties have been moved to the database, in a table called hive_cell_params installed as part of the Hivedata. These must be manually modified in the database by a SQL editor. Most installations require only a few changes. The most commonly modified parameters are documented below and a list of all configurable parameters is at the end of this page.

Agg Service Account Password (important!)

When setting up the i2b2 to work in your environment we highly recommend you change the default password for the AGG_SERVICE_ACCOUNT and restart WildFly.

The AGG_SERVICE_ACCOUNT is an i2b2 user account used to run aggregate-counting queries in i2b2. These parameters should reflect the account name and password. We recommend changing the password. 

datatype_cdparam_name_cdvalue
Tedu.harvard.i2b2.crc.pm.serviceaccount.passworddemouser
Tedu.harvard.i2b2.crc.pm.serviceaccount.userAGG_SERVICE_ACCOUNT

It is also possible to change this password manually:

  1. Login using the AGG_SERVICE_ACCOUNT account on the webclient and in the top right select change password
  2. Update the hive_cell_param on using the following, where {password} is the password from step 1
update hive_cell_params set value='{password}' where param_name_cd='edu.harvard.i2b2.crc.pm.serviceaccount.password';

3. Restart i2b2

Cell URLs

If your cells are installed on different servers (e.g., Project Management is on a different server than the Ontology cell), you will need to make this change because the hostnames cannot be autodetected.

Each cell must communicate with other cells. To facilitate this, the cell URL properties allow each cell to know the URL of the other cells. Generally these do not need to be configured, because the hostname and port are automatically determined by the server and the rest of the URL is required to remain as written. If you do want to manually specify the hostname and port, change the data type to a T and append this to the text value. (Data type U is automatically resolved into a URL.)

For example,

datatype_cdparam_name_cdvalue
Uedu.harvard.i2b2.crc.delegate.ontology.url/services/OntologyService

could become

datatype_cdparam_name_cdvalue
Tedu.harvard.i2b2.crc.delegate.ontology.urlhttp://localhost:9090/services/OntologyService


Important

When you edit a .url property with the location of a cell it is extremely important that you only add/edit the hostname (localhost) and the port (9090). The remainder of the URL is required as it is written and should not be changed.

File Repository Cell Properties

13.4.3.3 Patient in Project Property

When a get request is sent to the IM cell it has the capability to verify whether or not a patient is part of the project requesting the patient data. By default the property is set to true, if you do not wish to check the project then you can set it to false.

13.4.3.4 Other EMPI Service Properties

The Identity Management (IM) Cell can be configured to work with a third party EMPI service such as OpenEMPI. To do this you will need to create the service to the other system and then update the im.properties file with the appropriate information.

Ontology Cell Properties (uncommon)

This uncommon change allows backward compatibility with i2b2 release 1.3.

datatype_cdparam_name_cdvalue
Tontology.terminal.delimitertrue


Value

Description

true

A backslash will be added automatically to the metadata fullpath name if it does not already exist.

false

This setting will not add a backslash to the fullpath name and will provide true backward compatibility with release 1.3

Appendix: All parameters

Below is a table of all configurable cell parameters and their default values. Data Type is T for text values, and U for URL values. URL values will automatically have protocol://hostname:port/ appended to the value, which is detected by the server. (For example, http://localhost:9090/)

Data TypeParameterValue
Tqueryprocessor.jndi.queryinfolocalejb.querytool.QueryInfoLocal
Tqueryprocessor.jndi.querymanagerlocalejb.querytool.QueryManagerLocal
Tqueryprocessor.jndi.querymanagerremoteejb.querytool.QueryManager
TapplicationNameOntology Cell
TapplicationNameCRC Cell
TapplicationVersion1.7
TapplicationVersion1.7
Tedu.harvard.i2b2.crc.analysis.queue.large.jobcheck.timemills60000
Tedu.harvard.i2b2.crc.analysis.queue.large.maxjobcount1
Tedu.harvard.i2b2.crc.analysis.queue.large.timeoutmills43200000
Tedu.harvard.i2b2.crc.analysis.queue.medium.jobcheck.timemills60000
Tedu.harvard.i2b2.crc.analysis.queue.medium.maxjobcount4
Tedu.harvard.i2b2.crc.analysis.queue.medium.timeoutmills3000
Tedu.harvard.i2b2.crc.delegate.ontology.operation.getchildren/getChildren
Tedu.harvard.i2b2.crc.delegate.ontology.operation.getmodifierinfo/getModifierInfo
Tedu.harvard.i2b2.crc.delegate.ontology.operation.getterminfo/getTermInfo
Uedu.harvard.i2b2.crc.delegate.ontology.url/services/OntologyService
Tedu.harvard.i2b2.crc.i2b2SocketServer7070
Tedu.harvard.i2b2.crc.jms.large.timeoutsec43200
Tedu.harvard.i2b2.crc.jms.medium.timeoutsec14400
Tedu.harvard.i2b2.crc.jms.small.timeoutsec180
Tedu.harvard.i2b2.crc.lockout.setfinderquery.count7
Tedu.harvard.i2b2.crc.lockout.setfinderquery.day30
Tedu.harvard.i2b2.crc.lockout.setfinderquery.zero.count-1
Tedu.harvard.i2b2.crc.pdo.paging.inputlist.minpercent20
Tedu.harvard.i2b2.crc.pdo.paging.inputlist.minsize1
Tedu.harvard.i2b2.crc.pdo.paging.iteration100
Tedu.harvard.i2b2.crc.pdo.paging.methodSUBDIVIDE_INPUT_METHOD 
Tedu.harvard.i2b2.crc.pdo.paging.observation.size7500
Tedu.harvard.i2b2.crc.pdo.request.timeoutmills600000
Tedu.harvard.i2b2.crc.pm.serviceaccount.passworddemouser
Tedu.harvard.i2b2.crc.pm.serviceaccount.userAGG_SERVICE_ACCOUNT
Tedu.harvard.i2b2.crc.setfinder.querygenerator.version1.7
Tedu.harvard.i2b2.crc.setfinderquery.obfuscation.breakdowncount.sigma1.6
Tedu.harvard.i2b2.crc.setfinderquery.obfuscation.count.sigma1.323
Tedu.harvard.i2b2.crc.setfinderquery.obfuscation.minimum.value3
Tedu.harvard.i2b2.crc.setfinderquery.skiptemptable.maxconcept40
Uedu.harvard.i2b2.ontology.ws.crc.url/services/QueryToolService
Tedu.harvard.i2b2.ontology.ws.fr.attachmentnamecid
Tedu.harvard.i2b2.ontology.ws.fr.filethreshold4000
Tedu.harvard.i2b2.ontology.ws.fr.operationurn:recvfileRequest
Tedu.harvard.i2b2.ontology.ws.fr.tempspace/tmp
Tedu.harvard.i2b2.ontology.ws.fr.timeout10000
Uedu.harvard.i2b2.ontology.ws.fr.url/services/FRService/
TI2B2_MESSAGE_ERROR_AUTHENTICATION_FAILUREAuthentication failure.
TI2B2_MESSAGE_ERROR_INVALID_MESSAGEInvalid message body
TI2B2_MESSAGE_STATUS_COMPLETEDCOMPLETED
TI2B2_MESSAGE_STATUS_ERRORERROR
TI2B2_MESSAGE_STATUS_FINISHEDFINISHED
TI2B2_MESSAGE_STATUS_INCOMPLEINCOMPLETE
TI2B2_MESSAGE_STATUS_PROCESSINGPROCESSING
TI2B2_MESSAGE_STATUS_QUEUEDQUEUED
Tontology.terminal.delimitertrue
Uontology.ws.pm.url/services/PMService/getServices
Tqueryprocessor.jndi.pdoquerylocalejb.querytool.PdoQueryLocal
Tqueryprocessor.jndi.queryexecutormdblocalejb.querytool.QueryExecutorMDBLocal
Tqueryprocessor.jndi.queryexecutormdbremoteejb.querytool.QueryExecutorMDB
Tqueryprocessor.jndi.querymasterlocalejb.querytool.QueryMasterLocal
Tqueryprocessor.jndi.queryresultlocalejb.querytool.QueryResultLocal
Tqueryprocessor.jndi.queryrunlocalejb.querytool.QueryRunLocal
Tqueryprocessor.jndi.queue.connectionfactoryConnectionFactory
Tqueryprocessor.jndi.queue.executor_queuequeue/jms.querytool.QueryExecutor
Tqueryprocessor.jndi.queue.response_queuequeue/jms.querytool.QueryResponse
Tqueryprocessor.multifacttablefalse
Uqueryprocessor.ws.ontology.url/services/OntologyService/getTermInfo
Uqueryprocessor.ws.pm.url/services/PMService/getServices
Uworkplace.ws.pm.url/services/PMService/getServices
Uim.ws.pm.url/services/PMService/getServices
Tim.checkPatientInProjecttrue
Tim.empi.servicenone

Deprecated parameters in 1.7.12

Note for those upgrading that many parameters were deprecated in 1.7.12 and are not part of the new table: CRC loader properties (now sharing CRC properties), datasource lookups (now using hive db lookup table, configured by admin tool), application directory (no longer needed), ws.pm.bypass, ontology.ws.pm.webServiceMethod, ontology.pm.serviceaccount.user (was never used)
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