Details
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Bug
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Status: To Do
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Major
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Resolution: Unresolved
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None
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None
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None
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i2b2 Server VM 1.7.04
i2b2 Workbench
Version: 1.7.04.0004
Build id: 20141020
Description
Trying to synchronize ontologies in the "Edit Terms" view of the workbench leads to "Synchronize process is reporting an error.
Details are attached in the file i2b2-err.pdf
Server log shows following errors:
11:02:52,235 ERROR [stderr] (Thread-114) org.springframework.dao.InvalidDataAccessApiUsageException: 0 parameters were supplied, but 8 in parameters were declared in class [edu.harvard.i2b2.ontology.dao.OntProcessStatusDao$SaveOntProcessStatus]
11:02:52,243 ERROR [stderr] (Thread-114) at org.springframework.jdbc.object.RdbmsOperation.validateParameterCount(RdbmsOperation.java:436)
11:02:52,247 ERROR [stderr] (Thread-114) at org.springframework.jdbc.object.RdbmsOperation.validateParameters(RdbmsOperation.java:394)
11:02:52,248 ERROR [stderr] (Thread-114) at org.springframework.jdbc.object.SqlUpdate.update(SqlUpdate.java:167)
11:02:52,252 ERROR [stderr] (Thread-114) at edu.harvard.i2b2.ontology.dao.OntProcessStatusDao$SaveOntProcessStatus.save(Unknown Source)
11:02:52,253 ERROR [stderr] (Thread-114) at edu.harvard.i2b2.ontology.dao.OntProcessStatusDao.createOntologyProcessStatus(Unknown Source)
11:02:52,262 ERROR [stderr] (Thread-114) at edu.harvard.i2b2.ontology.delegate.CRCConceptUpdateHandler.execute(Unknown Source)
11:02:52,263 ERROR [stderr] (Thread-114) at edu.harvard.i2b2.ontology.ws.ExecutorRunnable.run(Unknown Source)
11:02:52,266 ERROR [stderr] (Thread-114) at java.lang.Thread.run(Thread.java:745)
11:02:52,267 ERROR [edu.harvard.i2b2.ontology.dao.OntProcessStatusDao] (Thread-114) Dao ontProcessStatus failed
11:02:52,268 ERROR [edu.harvard.i2b2.ontology.dao.OntProcessStatusDao] (Thread-114) 0 parameters were supplied, but 8 in parameters were declared in class [edu.harvard.i2b2.ontology.dao.OntProcessStatusDao$SaveOntProcessStatus]
11:02:52,277 ERROR [stderr] (Thread-114) edu.harvard.i2b2.common.exception.I2B2DAOException: Data access error
11:02:52,278 ERROR [stderr] (Thread-114) at edu.harvard.i2b2.ontology.dao.OntProcessStatusDao.createOntologyProcessStatus(Unknown Source)
11:02:52,292 ERROR [stderr] (Thread-114) at edu.harvard.i2b2.ontology.delegate.CRCConceptUpdateHandler.execute(Unknown Source)
11:02:52,297 ERROR [stderr] (Thread-114) at edu.harvard.i2b2.ontology.ws.ExecutorRunnable.run(Unknown Source)
11:02:52,298 ERROR [stderr] (Thread-114) at java.lang.Thread.run(Thread.java:745)
11:02:52,298 ERROR [stderr] (Thread-114) Caused by: org.springframework.dao.InvalidDataAccessApiUsageException: 0 parameters were supplied, but 8 in parameters were declared in class [edu.harvard.i2b2.ontology.dao.OntProcessStatusDao$SaveOntProcessStatus]
11:02:52,301 ERROR [stderr] (Thread-114) at org.springframework.jdbc.object.RdbmsOperation.validateParameterCount(RdbmsOperation.java:436)
11:02:52,306 ERROR [stderr] (Thread-114) at org.springframework.jdbc.object.RdbmsOperation.validateParameters(RdbmsOperation.java:394)
11:02:52,309 ERROR [stderr] (Thread-114) at org.springframework.jdbc.object.SqlUpdate.update(SqlUpdate.java:167)
11:02:52,310 ERROR [stderr] (Thread-114) at edu.harvard.i2b2.ontology.dao.OntProcessStatusDao$SaveOntProcessStatus.save(Unknown Source)
11:02:52,315 ERROR [stderr] (Thread-114) ... 4 more
11:03:47,025 ERROR [edu.harvard.i2b2.ontology.ws.OntologyService] (http--0.0.0.0-9090-2) er.jobException is Data access error
11:03:47,026 INFO [edu.harvard.i2b2.ontology.ws.OntologyService] (http--0.0.0.0-9090-2) waitTime is 120000
Details are attached in the file i2b2-err.pdf
Server log shows following errors:
11:02:52,235 ERROR [stderr] (Thread-114) org.springframework.dao.InvalidDataAccessApiUsageException: 0 parameters were supplied, but 8 in parameters were declared in class [edu.harvard.i2b2.ontology.dao.OntProcessStatusDao$SaveOntProcessStatus]
11:02:52,243 ERROR [stderr] (Thread-114) at org.springframework.jdbc.object.RdbmsOperation.validateParameterCount(RdbmsOperation.java:436)
11:02:52,247 ERROR [stderr] (Thread-114) at org.springframework.jdbc.object.RdbmsOperation.validateParameters(RdbmsOperation.java:394)
11:02:52,248 ERROR [stderr] (Thread-114) at org.springframework.jdbc.object.SqlUpdate.update(SqlUpdate.java:167)
11:02:52,252 ERROR [stderr] (Thread-114) at edu.harvard.i2b2.ontology.dao.OntProcessStatusDao$SaveOntProcessStatus.save(Unknown Source)
11:02:52,253 ERROR [stderr] (Thread-114) at edu.harvard.i2b2.ontology.dao.OntProcessStatusDao.createOntologyProcessStatus(Unknown Source)
11:02:52,262 ERROR [stderr] (Thread-114) at edu.harvard.i2b2.ontology.delegate.CRCConceptUpdateHandler.execute(Unknown Source)
11:02:52,263 ERROR [stderr] (Thread-114) at edu.harvard.i2b2.ontology.ws.ExecutorRunnable.run(Unknown Source)
11:02:52,266 ERROR [stderr] (Thread-114) at java.lang.Thread.run(Thread.java:745)
11:02:52,267 ERROR [edu.harvard.i2b2.ontology.dao.OntProcessStatusDao] (Thread-114) Dao ontProcessStatus failed
11:02:52,268 ERROR [edu.harvard.i2b2.ontology.dao.OntProcessStatusDao] (Thread-114) 0 parameters were supplied, but 8 in parameters were declared in class [edu.harvard.i2b2.ontology.dao.OntProcessStatusDao$SaveOntProcessStatus]
11:02:52,277 ERROR [stderr] (Thread-114) edu.harvard.i2b2.common.exception.I2B2DAOException: Data access error
11:02:52,278 ERROR [stderr] (Thread-114) at edu.harvard.i2b2.ontology.dao.OntProcessStatusDao.createOntologyProcessStatus(Unknown Source)
11:02:52,292 ERROR [stderr] (Thread-114) at edu.harvard.i2b2.ontology.delegate.CRCConceptUpdateHandler.execute(Unknown Source)
11:02:52,297 ERROR [stderr] (Thread-114) at edu.harvard.i2b2.ontology.ws.ExecutorRunnable.run(Unknown Source)
11:02:52,298 ERROR [stderr] (Thread-114) at java.lang.Thread.run(Thread.java:745)
11:02:52,298 ERROR [stderr] (Thread-114) Caused by: org.springframework.dao.InvalidDataAccessApiUsageException: 0 parameters were supplied, but 8 in parameters were declared in class [edu.harvard.i2b2.ontology.dao.OntProcessStatusDao$SaveOntProcessStatus]
11:02:52,301 ERROR [stderr] (Thread-114) at org.springframework.jdbc.object.RdbmsOperation.validateParameterCount(RdbmsOperation.java:436)
11:02:52,306 ERROR [stderr] (Thread-114) at org.springframework.jdbc.object.RdbmsOperation.validateParameters(RdbmsOperation.java:394)
11:02:52,309 ERROR [stderr] (Thread-114) at org.springframework.jdbc.object.SqlUpdate.update(SqlUpdate.java:167)
11:02:52,310 ERROR [stderr] (Thread-114) at edu.harvard.i2b2.ontology.dao.OntProcessStatusDao$SaveOntProcessStatus.save(Unknown Source)
11:02:52,315 ERROR [stderr] (Thread-114) ... 4 more
11:03:47,025 ERROR [edu.harvard.i2b2.ontology.ws.OntologyService] (http--0.0.0.0-9090-2) er.jobException is Data access error
11:03:47,026 INFO [edu.harvard.i2b2.ontology.ws.OntologyService] (http--0.0.0.0-9090-2) waitTime is 120000
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Affects Database/s | PostgreSQL [ 10188 ] | All databases [ 10219 ] |
| Fix Version/s | 1.7.06 [ 10200 ] | |
| Reproduction Notes |
This can be reproduced in both the demo and test environments.
STEPS TO REPRODUCE / TEST: Pre-requisite: i2b2 User has to have the Edit role in order to use the Edit Terms view in the i2b2 Workbench. 1. Log into the i2b2 Workbench. 2. Go to the Edit Terms view. 3. Enter a new term or edit an existing term. 4. Click on the Database Synchronization icon located at the top of the view. 5. Select Synchronize all and click on the Run button. 6. An error message will be displayed to the user saying an error has occurred with the synchronization process. IMPORTANT NOTE: This issue was reported for PostgreSQL databases but it is an issue for all supported databases (Oracle, PostgreSQL and SQL Server) |
|
| Affects Version/s | 1.7.05 [ 10164 ] | |
| Assignee | Mike Mendis [ mem61 ] | |
| i2b2 Feature/s | Synchronization Process [ 10066 ] | |
| i2b2 Sponsored Project/s | i2b2 Core [ 10196 ] | |
| Status | New [ 10000 ] | Open [ 1 ] |
| Fix Version/s | 1.7.07 [ 10201 ] | |
| Fix Version/s | 1.7.06 [ 10200 ] |
| Fix Version/s | 1.7.08 [ 10204 ] | |
| Fix Version/s | 1.7.07 [ 10201 ] |
| Fix Version/s | 1.7.09 [ 10306 ] | |
| Fix Version/s | 1.7.08 [ 10204 ] |
| Fix Version/s | 1.7.09 [ 10306 ] |
| Component/s | CRC Cell [ 10049 ] | |
| Component/s | Ontology Cell [ 10054 ] | |
| Component/s | Workbench [ 10057 ] | |
| Key | CORE-176 | WORKBENCH-3 |
| Affects Version/s | 1.7.04 [ 10160 ] | |
| Affects Version/s | 1.7.05 [ 10164 ] | |
| Workflow | i2b2 Issues Workflow [ 10824 ] | Software Simplified Workflow for Project WORKBENCH [ 11384 ] |
| Project | i2b2 Core Software [ 10034 ] | i2b2 Workbench [ 10333 ] |
| Status | Open [ 1 ] | To Do [ 10006 ] |