Search on this blog

Search on this blog

View Categories

1. Configure cell properties

7 min read

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_cd param_name_cd value
T edu.harvard.i2b2.crc.pm.serviceaccount.password demouser
T edu.harvard.i2b2.crc.pm.serviceaccount.user AGG_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 #

Multiple servers

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.

https

If your Wildfly is set up to use https, you will also need to specify the full URL as shown below.

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_cd param_name_cd value
U edu.harvard.i2b2.crc.delegate.ontology.url /i2b2/services/OntologyService

could become

datatype_cd param_name_cd value
T edu.harvard.i2b2.crc.delegate.ontology.url http://localhost:9090/i2b2/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 first portion – i.e. Protocol (e.g., https://) hostname (e.g., localhost) and the port (e.g., 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_cd param_name_cd value
T ontology.terminal.delimiter true

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 Type Parameter Value
T queryprocessor.jndi.queryinfolocal ejb.querytool.QueryInfoLocal
T queryprocessor.jndi.querymanagerlocal ejb.querytool.QueryManagerLocal
T queryprocessor.jndi.querymanagerremote ejb.querytool.QueryManager
T applicationName Ontology Cell
T applicationName CRC Cell
T applicationVersion 1.7
T applicationVersion 1.7
T edu.harvard.i2b2.crc.analysis.queue.large.jobcheck.timemills 60000
T edu.harvard.i2b2.crc.analysis.queue.large.maxjobcount 1
T edu.harvard.i2b2.crc.analysis.queue.large.timeoutmills 43200000
T edu.harvard.i2b2.crc.analysis.queue.medium.jobcheck.timemills 60000
T edu.harvard.i2b2.crc.analysis.queue.medium.maxjobcount 4
T edu.harvard.i2b2.crc.analysis.queue.medium.timeoutmills 3000
T edu.harvard.i2b2.crc.delegate.ontology.operation.getchildren /getChildren
T edu.harvard.i2b2.crc.delegate.ontology.operation.getmodifierinfo /getModifierInfo
T edu.harvard.i2b2.crc.delegate.ontology.operation.getterminfo /getTermInfo
U edu.harvard.i2b2.crc.delegate.ontology.url /services/OntologyService
T edu.harvard.i2b2.crc.i2b2SocketServer 7070
T edu.harvard.i2b2.crc.jms.large.timeoutsec 43200
T edu.harvard.i2b2.crc.jms.medium.timeoutsec 14400
T edu.harvard.i2b2.crc.jms.small.timeoutsec 180
T edu.harvard.i2b2.crc.lockout.setfinderquery.count 7
T edu.harvard.i2b2.crc.lockout.setfinderquery.day 30
T edu.harvard.i2b2.crc.lockout.setfinderquery.zero.count -1
T edu.harvard.i2b2.crc.pdo.paging.inputlist.minpercent 20
T edu.harvard.i2b2.crc.pdo.paging.inputlist.minsize 1
T edu.harvard.i2b2.crc.pdo.paging.iteration 100
T edu.harvard.i2b2.crc.pdo.paging.method SUBDIVIDE_INPUT_METHOD 
T edu.harvard.i2b2.crc.pdo.paging.observation.size 7500
T edu.harvard.i2b2.crc.pdo.request.timeoutmills 600000
T edu.harvard.i2b2.crc.pm.serviceaccount.password demouser
T edu.harvard.i2b2.crc.pm.serviceaccount.user AGG_SERVICE_ACCOUNT
T edu.harvard.i2b2.crc.setfinder.querygenerator.version 1.7
T edu.harvard.i2b2.crc.setfinderquery.obfuscation.breakdowncount.sigma 1.6
T edu.harvard.i2b2.crc.setfinderquery.obfuscation.count.sigma 1.323
T edu.harvard.i2b2.crc.setfinderquery.obfuscation.minimum.value 3
T edu.harvard.i2b2.crc.setfinderquery.skiptemptable.maxconcept 40
U edu.harvard.i2b2.ontology.ws.crc.url /services/QueryToolService
T edu.harvard.i2b2.ontology.ws.fr.attachmentname cid
T edu.harvard.i2b2.ontology.ws.fr.filethreshold 4000
T edu.harvard.i2b2.ontology.ws.fr.operation urn:recvfileRequest
T edu.harvard.i2b2.ontology.ws.fr.tempspace /tmp
T edu.harvard.i2b2.ontology.ws.fr.timeout 10000
U edu.harvard.i2b2.ontology.ws.fr.url /services/FRService/
T I2B2_MESSAGE_ERROR_AUTHENTICATION_FAILURE Authentication failure.
T I2B2_MESSAGE_ERROR_INVALID_MESSAGE Invalid message body
T I2B2_MESSAGE_STATUS_COMPLETED COMPLETED
T I2B2_MESSAGE_STATUS_ERROR ERROR
T I2B2_MESSAGE_STATUS_FINISHED FINISHED
T I2B2_MESSAGE_STATUS_INCOMPLE INCOMPLETE
T I2B2_MESSAGE_STATUS_PROCESSING PROCESSING
T I2B2_MESSAGE_STATUS_QUEUED QUEUED
T ontology.terminal.delimiter true
U ontology.ws.pm.url /services/PMService/getServices
T queryprocessor.jndi.pdoquerylocal ejb.querytool.PdoQueryLocal
T queryprocessor.jndi.queryexecutormdblocal ejb.querytool.QueryExecutorMDBLocal
T queryprocessor.jndi.queryexecutormdbremote ejb.querytool.QueryExecutorMDB
T queryprocessor.jndi.querymasterlocal ejb.querytool.QueryMasterLocal
T queryprocessor.jndi.queryresultlocal ejb.querytool.QueryResultLocal
T queryprocessor.jndi.queryrunlocal ejb.querytool.QueryRunLocal
T queryprocessor.jndi.queue.connectionfactory ConnectionFactory
T queryprocessor.jndi.queue.executor_queue queue/jms.querytool.QueryExecutor
T queryprocessor.jndi.queue.response_queue queue/jms.querytool.QueryResponse
T queryprocessor.multifacttable false
U queryprocessor.ws.ontology.url /services/OntologyService/getTermInfo
U queryprocessor.ws.pm.url /services/PMService/getServices
U workplace.ws.pm.url /services/PMService/getServices
U im.ws.pm.url /services/PMService/getServices
T im.checkPatientInProject true
T im.empi.service none

Release 1.8.2 DataExpert parameters #

Cell ID Parameter Name Example Value Notes
CRC edu.harvard.i2b2.crc.smtp.host smtp.partners.org SMTP host
CRC edu.harvard.i2b2.crc.smtp.port 25 SMTP port
CRC edu.harvard.i2b2.crc.smtp.ssl.enabled FALSE TRUE will enable SSL
CRC edu.harvard.i2b2.crc.smtp.auth FALSE TRUE will enable SMTP authentication
CRC edu.harvard.i2b2.crc.smtp.username none SMTP username (required for SMTP authentication)
CRC edu.harvard.i2b2.crc.smtp.password none SMTP password (required for SMTP authentication)
CRC edu.harvard.i2b2.crc.smtp.enabled FALSE TRUE will enable e-mails
CRC edu.harvard.i2b2.crc.exportcsv.defaultescapecharacter Escape character for export files
CRC edu.harvard.i2b2.crc.exportcsv.maxfetchrows -1 Maximum number of rows to export, or -1 for no limit
CRC edu.harvard.i2b2.crc.exportcsv.defaultlineend n Line ending for export files
CRC edu.harvard.i2b2.crc.exportcsv.defaultseperator t Field separator for export files
CRC edu.harvard.i2b2.crc.exportcsv.resultfetchsize 50000 Number of records retrieved during each database fetch.
CRC edu.harvard.i2b2.crc.exportcsv.filename {{{PROJECT_ID}}}/{{{DATE_yyyyMMdd}}}_{{{FULL_NAME}}}.tsv Parameterized template for export file names. If the extension is .zip, the file is zipped.
CRC edu.harvard.i2b2.crc.exportcsv.defaultquotechar Quote character for export files
CRC edu.harvard.i2b2.crc.exportcsv.workfolder /tmp/i2b2 Folder on the i2b2 server for data exports
CRC edu.harvard.i2b2.crc.exportcsv.zipencryptmethod none Encryption method for the exported ZIP file. One of STANDARD, NONE, or AES.

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)