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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.
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Cell URLs
Each cell must communicate with other cells. To facilitate this, you must set cell URL properties for each cell to accurately reflect the URL of the other cells.
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When you edit the queryprocessor.ws.pm.url property with the location of your PM Cell it is extremely important that you only edit the hostname (localhost) and the port (9090). The remainder of the URL is required as it is written and should not be changed. |
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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.
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Agg Service Account Password (important!)
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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. |
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pm.serviceaccount.user | AGG_SERVICE_ACCOUNT |
It is also possible to change this password manually:
- Login using the AGG_SERVICE_ACCOUNT account on the webclient and in the top right select change password
- 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
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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 autodetectedontology.url properties with the location of your Ontology Cell it is extremely important that you only edit the hostname (localhost) and the port (9090). The remainder of the URL is required as it is written and should not be changed. |
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| When you edit the ontology.ws.pm.url property with the location of your PM Cell it is extremely important that you only edit the hostname (localhost) and the port (9090). The remainder
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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
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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,
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datatype_cd | param_name_cd | value |
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edu.harvard.i2b2. |
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crc. |
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delegate. |
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title | Important |
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ontology.url | /i2b2/services/OntologyService |
could become
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datatype_cd | param_name_cd | value |
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edu.harvard.i2b2. |
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crc. |
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delegate. |
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When you edit the im.ws.pm.a .url property with the location of your PM Cell 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. | ||
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When you edit the workplace.ws.pm.url property with the location of your PM Cell it is extremely important that you only edit the hostname (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. |
Agg Service Account Password
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File Repository Cell Properties
13.4.3.3 Patient in Project Property
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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.
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13.4.3.4 Other EMPI Service Properties
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borderColor | #ccc |
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bgColor | #ffffff |
titleBGColor | #E5DFEC |
borderStyle | solid |
title | METADATA delimiter (backslash) |
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Level | 2 |
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Ontology Cell Properties (uncommon)
This uncommon change allows backward compatibility with i2b2 release 1.3.
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datatype_cd | param_name_cd | value |
T | ontology.terminal.delimiter |
true |
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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 |
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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) |