#335: reduce DataBuilder dependencies to i2b2 platform: ant, JVM, JDBC, jboss
--------------------------+------------------------
Reporter: dconnolly | Owner:
Type: enhancement | Status: closed
Priority: major | Milestone: gpc2sites
Component: data-sharing | Resolution: fixed
Keywords: | Blocked By:
Blocking: |
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Comment (by gkowalski):
Hacking on code I see in the builder-job.xml reference to "sql-200n" ,
lets change that to "sql-ora" :
{{{
103 <target name="queue-from-timeline"
104 description="queue a request based on timeline input and
filters">
105 <tempfile property="job.post.script"
destdir="${java.io.tmpdir}" suffix=".sql"/>
106 <echo level="info">
107 Building ${job.post.script} from ${timeline-xml}...
108 </echo>
109 <exec executable="python">
110 <arg value="${basedir}/timeline_to_job.py" />
111 <arg value="${timeline-xml}" />
112 <!-- <arg value="sql-200n" /> TODO: convert driver
classname -->
113 <arg value="sql-ora" /> <!-- TODO: convert driver
classname -->
114 <arg value="${job.post.script}" />
115 </exec>
}}}
yea that got it further :
{{{
gkowalsk$ ./run_mcw.sh
Buildfile: /Users/gkowalsk/Projects/seine-
minibuilder-0.5-f08eb078cb97/build.xml
builder-job.queue-from-timeline:
[echo]
[echo] Building
/var/folders/9f/lmmxyx7d1838n46rhj762s6d5tfklq/T/null1802194470.sql from
input.xml...
[echo]
sql-script.run:
[echo]
[echo] running as FH_CDWDEMODATA_DEV in
jdbc:oracle:thin:@fhoradev.ctsi.mcw.edu:1521:cdwdev1 ...
[echo]
[sql] Executing resource:
/var/folders/9f/lmmxyx7d1838n46rhj762s6d5tfklq/T/null1802194470.sql
[sql] Failed to execute: insert into qt_query_result_instance
(result_instance_id, start_date, result_type_id, status_type_id,
query_instance_id, description, path) select QT_SQ_QRI_QRIID.nextval,
sysdate, 20, -- EXPORT_CONCEPT
[sql] 1, -- QUEUED
[sql] (select max(query_instance_id) from qt_query_instance),
'Arterial vascular disease (440-447)', '\\I2B2_DIAG\Diagnoses\Circulatory
system (390-459)\Arterial vascular disease (440-447)\' from dual
BUILD FAILED
/Users/gkowalsk/Projects/seine-minibuilder-0.5-f08eb078cb97/build-tasks
/builder-job.xml:116: The following error occurred while executing this
line:
/Users/gkowalsk/Projects/seine-minibuilder-0.5-f08eb078cb97/build-tasks
/sql-script.xml:46: java.sql.SQLIntegrityConstraintViolationException:
ORA-02291: integrity constraint (FH_CDWDEMODATA_DEV.QT_FK_QRI_RTID)
violated - parent key not found
at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:447)
at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:396)
at oracle.jdbc.driver.T4C8Oall.processError(T4C8Oall.java:951)
at oracle.jdbc.driver.T4CTTIfun.receive(T4CTTIfun.java:513)
at oracle.jdbc.driver.T4CTTIfun.doRPC(T4CTTIfun.java:227)
at oracle.jdbc.driver.T4C8Oall.doOALL(T4C8Oall.java:531)
at oracle.jdbc.driver.T4CStatement.doOall8(T4CStatement.java:195)
at
oracle.jdbc.driver.T4CStatement.executeForRows(T4CStatement.java:1036)
at
oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleStatement.java:1336)
at
oracle.jdbc.driver.OracleStatement.executeInternal(OracleStatement.java:1916)
at
oracle.jdbc.driver.OracleStatement.execute(OracleStatement.java:1878)
at
oracle.jdbc.driver.OracleStatementWrapper.execute(OracleStatementWrapper.java:318)
at org.apache.tools.ant.taskdefs.SQLExec.execSQL(SQLExec.java:773)
at
org.apache.tools.ant.taskdefs.SQLExec.runStatements(SQLExec.java:743)
at
org.apache.tools.ant.taskdefs.SQLExec$Transaction.runTransaction(SQLExec.java:1053)
at
org.apache.tools.ant.taskdefs.SQLExec$Transaction.access$000(SQLExec.java:983)
at org.apache.tools.ant.taskdefs.SQLExec.execute(SQLExec.java:651)
at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:435)
at org.apache.tools.ant.Target.performTasks(Target.java:456)
at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
at
org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:440)
at
org.apache.tools.ant.taskdefs.CallTarget.execute(CallTarget.java:105)
at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:435)
at org.apache.tools.ant.Target.performTasks(Target.java:456)
at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
at org.apache.tools.ant.Project.executeTarget(Project.java:1364)
at
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
at org.apache.tools.ant.Main.runBuild(Main.java:851)
at org.apache.tools.ant.Main.startAnt(Main.java:235)
at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
Total time: 1 second
CTSI-iMac-gkowalski:seine-minibuilder-0.5-f08eb078cb97 gkowalsk$
}}}
I see it did use the proper SQL
{{{
-- insertJob:
4 insert into qt_query_instance
5 (user_id, group_id,
6 query_instance_id, patient_set,
7 start_date,
8 status_type_id,
9 message)
10 values
11 ('mcwcorp\gkowalsk', 'CDW',
12 QT_SQ_QI_QIID.nextval, ....
}}}
--
Ticket URL:
<http://informatics.gpcnetwork.org/trac/Project/ticket/335#comment:31>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Network - Informatics
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