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https://issues.apache.org/jira/browse/CTAKES-469?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16416353#comment-16416353
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Sean Mullane commented on CTAKES-469:
-------------------------------------
It seems likely that this is being caused by
https://issues.apache.org/jira/browse/CTAKES-446.
Can you share the piper file you used with this? If you used something like
{code:java}
reader org.apache.ctakes.ytex.uima.DBCollectionReader
queryGetDocumentKeys="select txt.NOTE_ID instance_id, txt.Note_Entry_Dtm
doc_date from dbo.document txt where txt.doctype = 'Progress Notes'",
queryGetDocument="select Note_text from dbo.document txt where txt.NOTE_ID =
:instance_id" {code}
then the regex parser fails on the 2nd "=" on the line and causes the
"queryGetDocument" parameter to be null, resulting in the error you're seeing.
> could not able to run ytex with DBCollection reader
> ----------------------------------------------------
>
> Key: CTAKES-469
> URL: https://issues.apache.org/jira/browse/CTAKES-469
> Project: cTAKES
> Issue Type: Bug
> Components: ctakes-ytex, ctakes-ytex-uima
> Affects Versions: 4.0.0, 4.0.1
> Environment: windows 10, java 8, catkes-4 , MS SQL SERVER
> fix-SetupAuiFirstWord.CTAKES-334.svn-01.patch
> Reporter: athyanarayana
> Assignee: Alex Zbarcea
> Priority: Critical
> Labels: error
> Fix For: 4.0.0, 4.0.1
>
> Attachments: out1.txt, ytexerror.png
>
> Original Estimate: 168h
> Remaining Estimate: 168h
>
> i cant abel to run ctakes CPE with ytex db collection reder , below is the
> error i am getting
> {code:java}
> Loading model:
> ................................
> Loading model:
> .............................
> org.apache.uima.resource.ResourceInitializationException: Initialization of
> CAS Processor with name "DBCollectionReader.xml" failed.
> at
> org.apache.uima.collection.impl.CollectionProcessingEngine_impl.initialize(CollectionProcessingEngine_impl.java:81)
> at
> org.apache.uima.impl.UIMAFramework_impl._produceCollectionProcessingEngine(UIMAFramework_impl.java:420)
> at
> org.apache.uima.UIMAFramework.produceCollectionProcessingEngine(UIMAFramework.java:918)
> at org.apache.uima.tools.cpm.CpmPanel.startProcessing(CpmPanel.java:573)
> at org.apache.uima.tools.cpm.CpmPanel.access$000(CpmPanel.java:105)
> at org.apache.uima.tools.cpm.CpmPanel$1.run(CpmPanel.java:713)
> Caused by: org.apache.uima.resource.ResourceConfigurationException:
> Initialization of CAS Processor with name "DBCollectionReader.xml" failed.
> at
> org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1101)
> at
> org.apache.uima.collection.impl.cpm.container.CPEFactory.getCasProcessors(CPEFactory.java:547)
> at
> org.apache.uima.collection.impl.cpm.BaseCPMImpl.init(BaseCPMImpl.java:253)
> at
> org.apache.uima.collection.impl.cpm.BaseCPMImpl.<init>(BaseCPMImpl.java:127)
> at
> org.apache.uima.collection.impl.CollectionProcessingEngine_impl.initialize(CollectionProcessingEngine_impl.java:73)
> ... 5 more
> Caused by: org.apache.uima.resource.ResourceInitializationException:
> Initialization of annotator class
> "org.apache.ctakes.ytex.uima.DBCollectionReader" failed. (Descriptor:
> file:/c:/cn/desc/ctakes-ytex-uima/desc/collection_reader/DBCollectionReader.xml)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:271)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:170)
> at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:279)
> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:331)
> at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:448)
> at
> org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1085)
> ... 9 more
> Caused by: java.lang.IllegalArgumentException: SQL must not be null
> at org.springframework.util.Assert.notNull(Assert.java:112)
> at
> org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:432)
> at
> org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:464)
> at
> org.springframework.jdbc.core.JdbcTemplate.queryForList(JdbcTemplate.java:495)
> at
> org.springframework.jdbc.core.simple.SimpleJdbcTemplate.queryForList(SimpleJdbcTemplate.java:238)
> at
> org.apache.ctakes.ytex.uima.DBCollectionReader$1.doInTransaction(DBCollectionReader.java:179)
> at
> org.apache.ctakes.ytex.uima.DBCollectionReader$1.doInTransaction(DBCollectionReader.java:1)
> at
> org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:130)
> at
> org.apache.ctakes.ytex.uima.DBCollectionReader.loadDocumentIds(DBCollectionReader.java:173)
> at
> org.apache.ctakes.ytex.uima.DBCollectionReader.initialize(DBCollectionReader.java:116)
> at
> org.apache.uima.collection.CollectionReader_ImplBase.initialize(CollectionReader_ImplBase.java:70)
> at
> org.apache.uima.analysis_engine.impl.compatibility.CollectionReaderAdapter.initialize(CollectionReaderAdapter.java:87)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:266)
> ... 16 more
> {code}
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