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.
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 | /services/OntologyService |
could become
datatype_cd | param_name_cd | value |
T | edu.harvard.i2b2.crc.delegate.ontology.url | http://localhost:9090/services/OntologyService |
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. |
When setting up the i2b2 to work in your environment we highly recommend you change the default password for the AGG_SERVICE_ACCOUNT. Once you have changed the password you will need to redeploy JBoss. Please see Chapter 10.5 Deployment for additional information on how to deploy the CRC cell. Reminder: The Ontology Cell also uses the AGG_SERVICE_ACCOUNT, therefore you need to also make the change in the ontology.properties. |
|
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 |
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_METHODÂ |
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 |