Help with i2b2 installation

Niveditha Thota

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Feb 1, 2011, 1:37:19 PM2/1/11

to mem...@i2b2aug.org, i2b2-ins...@googlegroups.com

Hi,

I am working with i2b2 version 1.3 VM here at UAB. The VM is installed in UNIX environment. We are trying to point the cells in i2b2 to our production database which is located on a remote machine. To achieve this, I have modified the relevant database files and recompiled the source files for the cells following the directions from the installation guide. But, we are facing trouble getting the workbench to work with the i2b2 instance configured for the production database.

Three of the cells in the workbench are giving the following errors:

Ontology cell is unavailable

Workplace cell is unavailable

Data Repository cell is unavailable

The logs from the JBOSS have the error below:

13:12:19,830 ERROR [AxisRESTServlet] org.apache.axis2.AxisFault: Could not locate hive= demo; nested exception is:

edu.harvard.i2b2.common.exception.I2B2Exception: Could not locate hive= demo; nested exception is:

org.apache.axis2.AxisFault: Could not locate hive= demo; nested exception is:

edu.harvard.i2b2.common.exception.I2B2Exception: Could not locate hive= demo

13:12:21,494 INFO [PropertiesFactoryBean] Loading properties file from class path resource [crc_application_directory.properties]

13:12:21,754 INFO [XmlBeanDefinitionReader] Loading XML bean definitions from URL [file:/opt/jboss/server/default/conf/crcapp/CRCApplicationContext.xml]

13:12:22,164 INFO [CollectionFactory] JDK 1.4+ collections available

13:12:22,192 INFO [CollectionFactory] Commons Collections 3.x available

13:12:22,195 INFO [FileSystemXmlApplicationContext] Bean factory for application context [org.springframework.context.support.FileSystemXmlApplicationContext;hashCode=15850979]: org.springframework.beans.factory.support.DefaultListableBeanFactory defining beans [jaxbPackage,appType,message_header,TestDataSourceLookup,TestDataSource,CRCDataSourceLookup,defaultSetfinderResultType,setFinderResultGeneratorMap]; root of BeanFactory hierarchy

13:12:22,208 INFO [FileSystemXmlApplicationContext] 8 beans defined in application context [org.springframework.context.support.FileSystemXmlApplicationContext;hashCode=15850979]

13:12:22,214 INFO [FileSystemXmlApplicationContext] Unable to locate MessageSource with name 'messageSource': using default [org.springframework.context.support.DelegatingMessageSource@b05409]

13:12:22,218 INFO [FileSystemXmlApplicationContext] Unable to locate ApplicationEventMulticaster with name 'applicationEventMulticaster': using default [org.springframework.context.event.SimpleApplicationEventMulticaster@13dff89]

13:12:22,219 INFO [DefaultListableBeanFactory] Pre-instantiating singletons in factory [org.springframework.beans.factory.support.DefaultListableBeanFactory defining beans [jaxbPackage,appType,message_header,TestDataSourceLookup,TestDataSource,CRCDataSourceLookup,defaultSetfinderResultType,setFinderResultGeneratorMap]; root of BeanFactory hierarchy]

13:12:23,429 INFO [PropertiesFactoryBean] Loading properties file from class path resource [crc_application_directory.properties]

13:12:23,429 INFO [PropertiesFactoryBean] Loading properties file from file [/opt/jboss/server/default/conf/crcapp/crc.properties]

13:12:23,592 INFO [QueryRequestDelegate] project name from PM Demo Group

13:12:23,593 INFO [QueryRequestDelegate] project id from PM Demo

13:12:23,593 ERROR [QueryRequestDelegate] Project role not set for the user

13:12:23,762 INFO [DataSourceLookupHelper] Could not match Project id=[/Demo/] Trying with hive =demo

13:12:24,239 INFO [PropertiesFactoryBean] Loading properties file from class path resource [workplace_application_directory.properties]

13:12:24,241 INFO [PropertiesFactoryBean] Loading properties file from file [/opt/jboss/server/default/conf/workplaceapp/workplace.properties]

13:12:24,262 ERROR [RESTSender] Error in processing POST request

org.apache.axis2.AxisFault: Transport error 404 . Error Message is <html><head><title>JBossWeb/2.0.1.GA - Error report</title><style></style> </head><body><h1>HTTP Status 404 - /axis2/rest/PMService/getServices</h1><HR size="1" noshade="noshade"><p><b>type</b> Status report</p><p><b>message</b> <u>/axis2/rest/PMService/getServices</u></p><p><b>description</b> <u>The requested resource (/axis2/rest/PMService/getServices) is not available.</u></p><HR size="1" noshade="noshade"><h3>JBossWeb/2.0.1.GA</h3></body></html>

at org.apache.axis2.transport.http.RESTSender.sendViaPost(RESTSender.java:295)

at org.apache.axis2.transport.http.RESTSender.send(RESTSender.java:141)

at org.apache.axis2.transport.http.CommonsHTTPTransportSender.writeMessageWithCommons(CommonsHTTPTransportSender.java:334)

at org.apache.axis2.transport.http.CommonsHTTPTransportSender.invoke(CommonsHTTPTransportSender.java:205)

at org.apache.axis2.engine.AxisEngine.send(AxisEngine.java:670)

at org.apache.axis2.description.OutInAxisOperationClient.send(OutInAxisOperation.java:365)

at org.apache.axis2.description.OutInAxisOperationClient.execute(OutInAxisOperation.java:295)

at org.apache.axis2.client.ServiceClient.sendReceive(ServiceClient.java:579)

at org.apache.axis2.client.ServiceClient.sendReceive(ServiceClient.java:508)

at edu.harvard.i2b2.pm.ws.PMServiceDriver.sendREST(Unknown Source)

at edu.harvard.i2b2.pm.ws.PMServiceDriver.getRoles(Unknown Source)

at edu.harvard.i2b2.workplace.delegate.RequestHandler.getRoleInfo(Unknown Source)

at edu.harvard.i2b2.workplace.delegate.GetFoldersByProjectHandler.<init>(Unknown Source)

at edu.harvard.i2b2.workplace.ws.WorkplaceService.getFoldersByProject(Unknown Source)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

at java.lang.reflect.Method.invoke(Method.java:585)

at org.apache.axis2.receivers.RawXMLINOutMessageReceiver.invokeBusinessLogic(RawXMLINOutMessageReceiver.java:88)

at org.apache.axis2.receivers.AbstractInOutSyncMessageReceiver.receive(AbstractInOutSyncMessageReceiver.java:39)

at org.apache.axis2.engine.AxisEngine.receive(AxisEngine.java:493)

at org.apache.axis2.transport.http.util.RESTUtil.invokeAxisEngine(RESTUtil.java:153)

at org.apache.axis2.transport.http.util.RESTUtil.processPostRequest(RESTUtil.java:102)

at org.apache.axis2.transport.http.AxisRESTServlet.doPost(AxisRESTServlet.java:66)

at javax.servlet.http.HttpServlet.service(HttpServlet.java:710)

at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

at org.jboss.web.tomcat.filters.ReplyHeaderFilter.doFilter(ReplyHeaderFilter.java:96)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:230)

at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:175)

at org.jboss.web.tomcat.security.SecurityAssociationValve.invoke(SecurityAssociationValve.java:179)

at org.jboss.web.tomcat.security.JaccContextValve.invoke(JaccContextValve.java:84)

at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)

at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)

at org.jboss.web.tomcat.service.jca.CachedConnectionValve.invoke(CachedConnectionValve.java:157)

at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)

at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:262)

at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:844)

at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:583)

at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:446)

at java.lang.Thread.run(Thread.java:595)

13:12:24,263 ERROR [PMServiceDriver] Incoming message input stream is null

13:12:24,263 ERROR [GetFoldersByProjectHandler] Cant connect to PM service

13:12:24,322 ERROR [AxisRESTServlet] org.apache.axis2.AxisFault: Could not locate hive= demo; nested exception is:

edu.harvard.i2b2.common.exception.I2B2Exception: Could not locate hive= demo; nested exception is:

org.apache.axis2.AxisFault: Could not locate hive= demo; nested exception is:

edu.harvard.i2b2.common.exception.I2B2Exception: Could not locate hive= demo

Any thoughts on what might be wrong?

Thanks,

Nive

Niveditha Thota

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Feb 1, 2011, 3:56:19 PM2/1/11

to Jerem...@cchmc.org, mem...@i2b2aug.org, i2b2-ins...@googlegroups.com

Hi,

Thanks for looking into the issue. I followed your instruction and checked the C_DOMAIN_ID value for the CRC_DB_LOOKUP and ONT_DB_LOOKUP tables. Both the tables have value ‘i2b2demo’ instead of ‘demo’. Instead of changing the database value, I modified the entry in the i2b2workbench.properties file to use the domain – i2b2demo. I also changed the domain name under environment variables under GLOBAL HIVE DATA in the gridsphere to i2b2demo. Doing this got rid of the the error - "Could not locate hive= demo".

The Workplace cell still has some problem. It gives error message – ‘User was not validated’

JBOSS log shows:

15:03:33,107 ERROR [RESTSender] Error in processing POST request

15:03:33,108 ERROR [PMServiceDriver] Incoming message input stream is null

15:03:33,108 ERROR [GetFoldersByProjectHandler] Cant connect to PM service

Nivi

From: Jeremy Nix [mailto:Jerem...@cchmc.org]
Sent: Tuesday, February 01, 2011 1:36 PM
To: Niveditha Thota
Cc: mem...@i2b2aug.org; i2b2-ins...@googlegroups.com
Subject: Re: Help with i2b2 installation

The message of importance here is "Could not locate hive= demo". This error is thrown in both the Ontology Cell and the CRC cell if the cell is unable to read out the proper datasource information from the crc_db_lookup or ont_db_lookup table in the i2b2hive schema. Verify the entries in these tables to make sure that there are entries with a C_DOMAIN_ID of "demo". If none exist, then that's at least a starting point. If the records do exist, then you will want to verify the contents of the following files:

jboss/server/default/conf/crcapp/CRCApplicationContext.xml
- make sure that the datasource entry for CRCDataSourceLookup is using the same i2b2hive schema/user/database that you used above to verify the contents of the crc_db_lookup table.

jboss/server/deploy/ont-ds.xml
- make sure that the datasource entry for OntologyBootStrapDS is using the same i2b2hive schema/user/database that you used above to verify the contents of the ont_db_lookup table.

Hope this helps

Jeremy Nix
Senior Application Developer
Cincinnati Children's Hospital Medical Center

Phillips, Lori C.

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Feb 1, 2011, 4:34:28 PM2/1/11

to Niveditha Thota, Jerem...@cchmc.org, mem...@i2b2aug.org, i2b2-ins...@googlegroups.com

Not sure if this is your problem, but WORK_DB_LOOKUP would also have to be modified up in the same manner.

Is the address of the PM service configured correctly in the workplace properties file ?

workplace.ws.pm.url= ????

/axis2/rest/PMService/getServices --- maybe should be /i2b2/rest/.....?

From: Niveditha Thota [mailto:tho...@uab.edu]
Sent: Tuesday, February 01, 2011 3:56 PM
To: Jerem...@cchmc.org
Cc: mem...@i2b2aug.org; i2b2-ins...@googlegroups.com
Subject: RE: Help with i2b2 installation

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Niveditha Thota

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Feb 1, 2011, 5:13:43 PM2/1/11

to Phillips, Lori C., Jerem...@cchmc.org, mem...@i2b2aug.org, i2b2-ins...@googlegroups.com

The port number for the PM cell was wrong in the workplace.properties file.

Changed it to 7070 and that took care of the error.

Thanks for your help.

Nivi

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