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bp2014n2 / i2b2

Bachelor project in order to use i2b2 with big data
http://bp2014n2.github.io/
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Queries in der History umbenennen oder löschen #37

Open SvenLehmann opened 9 years ago

SvenLehmann commented 9 years ago
philipp94831 commented 9 years ago

A request is send to the App-Server. It should be handled in the QueryToolService (CRC-Cell). edu.harvard.i2b2.crc.delegate.setfinder.QueryRequestDelegate and edu.harvard.i2b2.crc.delegate.setfinder.DeleteQueryMasterHandler are the relevant classes for execution. The RequestType ist dispatched in edu.harvard.i2b2.crc.datavo.setfinder.query.PsmRequestTypeType. The request is an XML request and handled by jaxb. In the jboss log it says:

11:57:00,318 WARN  [org.jboss.as.server.deployment] (MSC service thread 1-1) JBAS015960: Class Path entry jaxb-api.jar in /C:/Users/philipp.schirmer.HPI/Applications/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/WEB-INF/lib/jaxb-impl-2.1.7.jar  does not point to a valid jar for a Class-Path reference.
11:57:00,319 WARN  [org.jboss.as.server.deployment] (MSC service thread 1-1) JBAS015960: Class Path entry activation.jar in /C:/Users/philipp.schirmer.HPI/Applications/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/WEB-INF/lib/jaxb-impl-2.1.7.jar  does not point to a valid jar for a Class-Path reference.
11:57:00,319 WARN  [org.jboss.as.server.deployment] (MSC service thread 1-1) JBAS015960: Class Path entry jsr173_1.0_api.jar in /C:/Users/philipp.schirmer.HPI/Applications/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/WEB-INF/lib/jaxb-impl-2.1.7.jar  does not point to a valid jar for a Class-Path reference.
11:57:00,319 WARN  [org.jboss.as.server.deployment] (MSC service thread 1-1) JBAS015960: Class Path entry jaxb1-impl.jar in /C:/Users/philipp.schirmer.HPI/Applications/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/WEB-INF/lib/jaxb-impl-2.1.7.jar  does not point to a valid jar for a Class-Path reference.
11:57:00,319 WARN  [org.jboss.as.server.deployment] (MSC service thread 1-1) JBAS015960: Class Path entry jaxb-api.jar in /C:/Users/philipp.schirmer.HPI/Applications/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/WEB-INF/lib/jaxb-xjc-2.1.7.jar  does not point to a valid jar for a Class-Path reference.
11:57:00,320 WARN  [org.jboss.as.server.deployment] (MSC service thread 1-1) JBAS015960: Class Path entry jaxb-impl.jar in /C:/Users/philipp.schirmer.HPI/Applications/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/WEB-INF/lib/jaxb-xjc-2.1.7.jar  does not point to a valid jar for a Class-Path reference.
11:57:00,320 WARN  [org.jboss.as.server.deployment] (MSC service thread 1-1) JBAS015960: Class Path entry jsr173_1.0_api.jar in /C:/Users/philipp.schirmer.HPI/Applications/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/WEB-INF/lib/jaxb-xjc-2.1.7.jar  does not point to a valid jar for a Class-Path reference.
11:57:00,320 WARN  [org.jboss.as.server.deployment] (MSC service thread 1-1) JBAS015960: Class Path entry activation.jar in /C:/Users/philipp.schirmer.HPI/Applications/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/WEB-INF/lib/jaxb-xjc-2.1.7.jar  does not point to a valid jar for a Class-Path reference.
11:57:00,320 WARN  [org.jboss.as.server.deployment] (MSC service thread 1-1) JBAS015960: Class Path entry jaxws-rt.jar in /C:/Users/philipp.schirmer.HPI/Applications/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/WEB-INF/lib/jaxws-tools-2.1.3.jar  does not point to a valid jar for a Class-Path reference.
11:57:00,321 WARN  [org.jboss.as.server.deployment] (MSC service thread 1-1) JBAS015960: Class Path entry jaxb-xjc.jar in /C:/Users/philipp.schirmer.HPI/Applications/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/WEB-INF/lib/jaxws-tools-2.1.3.jar  does not point to a valid jar for a Class-Path reference.
11:57:00,321 WARN  [org.jboss.as.server.deployment] (MSC service thread 1-1) JBAS015960: Class Path entry relaxngDatatype.jar in /C:/Users/philipp.schirmer.HPI/Applications/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/WEB-INF/lib/jaxws-tools-2.1.3.jar  does not point to a valid jar for a Class-Path reference.
11:57:00,321 WARN  [org.jboss.as.server.deployment] (MSC service thread 1-1) JBAS015960: Class Path entry bcel.jar in /C:/Users/philipp.schirmer.HPI/Applications/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/WEB-INF/lib/jibx-bind-1.2.jar  does not point to a valid jar for a Class-Path reference.
11:57:00,321 WARN  [org.jboss.as.server.deployment] (MSC service thread 1-1) JBAS015960: Class Path entry jibx-run.jar in /C:/Users/philipp.schirmer.HPI/Applications/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/WEB-INF/lib/jibx-bind-1.2.jar  does not point to a valid jar for a Class-Path reference.
11:57:00,322 WARN  [org.jboss.as.server.deployment] (MSC service thread 1-1) JBAS015960: Class Path entry xpp3.jar in /C:/Users/philipp.schirmer.HPI/Applications/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/WEB-INF/lib/jibx-bind-1.2.jar  does not point to a valid jar for a Class-Path reference.
11:57:00,322 WARN  [org.jboss.as.server.deployment] (MSC service thread 1-1) JBAS015960: Class Path entry stax-api.jar in /C:/Users/philipp.schirmer.HPI/Applications/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/WEB-INF/lib/jibx-bind-1.2.jar  does not point to a valid jar for a Class-Path reference.
11:57:00,322 WARN  [org.jboss.as.server.deployment] (MSC service thread 1-1) JBAS015960: Class Path entry wstx-asl.jar in /C:/Users/philipp.schirmer.HPI/Applications/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/WEB-INF/lib/jibx-bind-1.2.jar  does not point to a valid jar for a Class-Path reference.
11:57:00,322 WARN  [org.jboss.as.server.deployment] (MSC service thread 1-1) JBAS015960: Class Path entry xpp3.jar in /C:/Users/philipp.schirmer.HPI/Applications/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/WEB-INF/lib/jibx-run-1.2.jar  does not point to a valid jar for a Class-Path reference.
11:57:00,322 WARN  [org.jboss.as.server.deployment] (MSC service thread 1-1) JBAS015960: Class Path entry stax-api.jar in /C:/Users/philipp.schirmer.HPI/Applications/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/WEB-INF/lib/jibx-run-1.2.jar  does not point to a valid jar for a Class-Path reference.
11:57:00,323 WARN  [org.jboss.as.server.deployment] (MSC service thread 1-1) JBAS015960: Class Path entry wstx-asl.jar in /C:/Users/philipp.schirmer.HPI/Applications/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/WEB-INF/lib/jibx-run-1.2.jar  does not point to a valid jar for a Class-Path reference.
11:57:00,323 WARN  [org.jboss.as.server.deployment] (MSC service thread 1-1) JBAS015960: Class Path entry activation.jar in /C:/Users/philipp.schirmer.HPI/Applications/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/WEB-INF/lib/mail-1.4.jar  does not point to a valid jar for a Class-Path reference.
11:57:00,325 WARN  [org.jboss.as.server.deployment] (MSC service thread 1-1) JBAS015960: Class Path entry xercesImpl.jar in /C:/Users/philipp.schirmer.HPI/Applications/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/WEB-INF/lib/xalan-2.7.0.jar  does not point to a valid jar for a Class-Path reference.
11:57:00,326 WARN  [org.jboss.as.server.deployment] (MSC service thread 1-1) JBAS015960: Class Path entry xml-apis.jar in /C:/Users/philipp.schirmer.HPI/Applications/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/WEB-INF/lib/xalan-2.7.0.jar  does not point to a valid jar for a Class-Path reference.
11:57:00,326 WARN  [org.jboss.as.server.deployment] (MSC service thread 1-1) JBAS015960: Class Path entry serializer.jar in /C:/Users/philipp.schirmer.HPI/Applications/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/WEB-INF/lib/xalan-2.7.0.jar  does not point to a valid jar for a Class-Path reference.
philipp94831 commented 9 years ago

Doesn't even work in the i2b2 1.7.04 VMWare Image

philipp94831 commented 9 years ago

Google Groups Thread

philipp94831 commented 9 years ago

Jira Thread

Seems to be on roadmap for 1.7.05

philipp94831 commented 9 years ago

Answer from i2b2 community in Google Group

Hi Philipp,

I have seen this before, but was unable to reproduce it on our environment. I think now I know why, this is a postgres bug. The live web client is on oracle which is why i think it works. Let me do some testing and should be resolved in the next version

thanks mike