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.
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 |
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. |
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. |
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 |
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 |
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) |