whoosis :
I have found many similar questions on internet and tried many solutions but still can't get around this error even after 10 hours. So please give ANY suggestion before marking it as a duplicate. I am also not familiar with hsqldb so please let me know if i am missing something very obvious.
I have a jar build with cTAKES pipeline code with spring-boot. The jar executes fine in windows but when i do this in ubuntu i get the error: user lacks privilege or object not found . I have tried following so far
- adding table name in qoutes and capitalizing table name ("cui_terms") in descriptor file (works fine in windows , doesnt work in ubuntu)
Giving absolute path to script file in descriptor (same) adding following properties in application.properties file
hibernate.dialect=org.hibernate.dialect.HSQLDialect hibernate.format_sql=true hibernate.show_sql=true hibernate.hbm2ddl.auto=create sql.ignore_case=true
Any suggestion would be extremely helpful Thanks in advance
This is the script file
SET DATABASE UNIQUE NAME HSQLDB5B3BA0CBCC
SET DATABASE GC 0
SET DATABASE DEFAULT RESULT MEMORY ROWS 0
SET DATABASE EVENT LOG LEVEL 0
SET DATABASE TRANSACTION CONTROL LOCKS
SET DATABASE DEFAULT ISOLATION LEVEL READ COMMITTED
SET DATABASE TRANSACTION ROLLBACK ON CONFLICT TRUE
SET DATABASE TEXT TABLE DEFAULTS ''
SET DATABASE SQL NAMES FALSE
SET DATABASE SQL REFERENCES FALSE
SET DATABASE SQL SIZE TRUE
SET DATABASE SQL TYPES FALSE
SET DATABASE SQL TDC DELETE TRUE
SET DATABASE SQL TDC UPDATE TRUE
SET DATABASE SQL TRANSLATE TTI TYPES TRUE
SET DATABASE SQL TRANSLATE TTI TYPES TRUE
SET DATABASE SQL CONCAT NULLS TRUE
SET DATABASE SQL UNIQUE NULLS TRUE
SET DATABASE SQL CONVERT TRUNCATE TRUE
SET DATABASE SQL AVG SCALE 0
SET DATABASE SQL DOUBLE NAN TRUE
SET DATABASE SQL SYNTAX ORA TRUE
SET FILES WRITE DELAY 10
SET FILES BACKUP INCREMENT TRUE
SET FILES CACHE SIZE 10000
SET FILES CACHE ROWS 50000
SET FILES SCALE 32
SET FILES LOB SCALE 32
SET FILES DEFRAG 0
SET FILES NIO TRUE
SET FILES NIO SIZE 256
SET FILES LOG TRUE
SET FILES LOG SIZE 50
CREATE USER SA PASSWORD DIGEST 'd41d8cd98f00b204e9800998ecf8427e'
ALTER USER SA SET LOCAL TRUE
CREATE SCHEMA PUBLIC AUTHORIZATION DBA
SET SCHEMA PUBLIC
CREATE MEMORY TABLE PUBLIC.CUI_TERMS(CUI BIGINT,RINDEX INTEGER,TCOUNT INTEGER,TEXT VARCHAR(255),RWORD VARCHAR(48))
CREATE INDEX IDX_CUI_TERMS ON PUBLIC.CUI_TERMS(RWORD)
CREATE MEMORY TABLE PUBLIC.TUI(CUI BIGINT,TUI INTEGER)
CREATE INDEX IDX_TUI ON PUBLIC.TUI(CUI)
CREATE MEMORY TABLE PUBLIC.PREFTERM(CUI BIGINT,PREFTERM VARCHAR(511))
CREATE INDEX IDX_PREFTERM ON PUBLIC.PREFTERM(CUI)
CREATE MEMORY TABLE PUBLIC.RXNORM(CUI BIGINT,RXNORM BIGINT)
CREATE INDEX IDX_RXNORM ON PUBLIC.RXNORM(CUI)
CREATE MEMORY TABLE PUBLIC.SNOMEDCT_US(CUI BIGINT,SNOMEDCT_US BIGINT)
CREATE INDEX IDX_SNOMEDCT_US ON PUBLIC.SNOMEDCT_US(CUI)
ALTER SEQUENCE SYSTEM_LOBS.LOB_ID RESTART WITH 1
SET DATABASE DEFAULT INITIAL SCHEMA PUBLIC
GRANT USAGE ON DOMAIN INFORMATION_SCHEMA.SQL_IDENTIFIER TO PUBLIC
GRANT USAGE ON DOMAIN INFORMATION_SCHEMA.YES_OR_NO TO PUBLIC
GRANT USAGE ON DOMAIN INFORMATION_SCHEMA.TIME_STAMP TO PUBLIC
GRANT USAGE ON DOMAIN INFORMATION_SCHEMA.CARDINAL_NUMBER TO PUBLIC
GRANT USAGE ON DOMAIN INFORMATION_SCHEMA.CHARACTER_DATA TO PUBLIC
GRANT DBA TO SA
SET SCHEMA SYSTEM_LOBS
INSERT INTO BLOCKS VALUES(0,2147483647,0)
SET SCHEMA PUBLIC
INSERT INTO CUI_TERMS VALUES(97,0,1,'mptp','mptp')
INSERT INTO CUI_TERMS VALUES(97,0,1,'methylphenyltetrahydropyridine','methylphenyltetrahydropyridine')
INSERT INTO CUI_TERMS VALUES(102,0,1,'naphthalidine','naphthalidine')
This is the annotator descriptor file where configurations are define
<?xml version="1.0" encoding="UTF-8"?>
<lookupSpecification>
<dictionaries>
<dictionary>
<name>sno_rx_16abTerms</name>
<implementationName>org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary</implementationName>
<properties>
<!-- urls for hsqldb memory connections must be file types in hsql 1.8.
These file urls must be either absolute path or relative to current working directory.
They cannot be based upon the classpath.
Though JdbcConnectionFactory will attempt to "find" a db based upon the parent dir of the url
for the sake of ide ease-of-use, the user should be aware of these hsql limitations.
-->
<property key="jdbcDriver" value="org.hsqldb.jdbcDriver"/>
<property key="jdbcUrl" value="jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab"/>
<property key="jdbcUser" value="sa"/>
<property key="jdbcPass" value=""/>
<property key="rareWordTable" value="cui_terms"/>
<property key="umlsUrl" value="https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser"/>
<property key="umlsVendor" value="NLM-6515182895"/>
<property key="umlsUser" value="CHANGE_ME"/>
<property key="umlsPass" value="CHANGE_ME"/>
</properties>
</dictionary>
</dictionaries>
<conceptFactories>
<conceptFactory>
<name>sno_rx_16abConcepts</name>
<implementationName>org.apache.ctakes.dictionary.lookup2.concept.UmlsJdbcConceptFactory</implementationName>
<properties>
<property key="jdbcDriver" value="org.hsqldb.jdbcDriver"/>
<property key="jdbcUrl" value="jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab"/>
<property key="jdbcUser" value="sa"/>
<property key="jdbcPass" value=""/>
<property key="umlsUrl" value="https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser"/>
<property key="umlsVendor" value="NLM-6515182895"/>
<property key="umlsUser" value="CHANGE_ME"/>
<property key="umlsPass" value="CHANGE_ME"/>
<property key="tuiTable" value="tui"/>
<property key="prefTermTable" value="prefTerm"/>
<!-- Optional tables for optional term info.
Uncommenting these lines alone may not persist term information;
persistence depends upon the TermConsumer. -->
<property key="rxnormTable" value="long"/>
<property key="snomedct_usTable" value="long"/>
</properties>
</conceptFactory>
</conceptFactories>
<!-- Defines what terms and concepts will be used -->
<dictionaryConceptPairs>
<dictionaryConceptPair>
<name>sno_rx_16abPair</name>
<dictionaryName>sno_rx_16abTerms</dictionaryName>
<conceptFactoryName>sno_rx_16abConcepts</conceptFactoryName>
</dictionaryConceptPair>
</dictionaryConceptPairs>
<rareWordConsumer>
<name>Term Consumer</name>
<implementationName>org.apache.ctakes.dictionary.lookup2.consumer.DefaultTermConsumer</implementationName>
</rareWordConsumer>
</lookupSpecification>
And this is the java class where connection is made
package org.apache.ctakes.dictionary.lookup2.dictionary;
import org.apache.ctakes.dictionary.lookup2.term.RareWordTerm;
import org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory;
import org.apache.log4j.Logger;
import org.apache.uima.UimaContext;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.Properties;
import static org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.*;
final public class JdbcRareWordDictionary extends AbstractRareWordDictionary {
/**
* Column (field) indices in the database. Notice that these are constant and not configurable.
* If a configurable implementation is desired then create an extension.
*/
static private enum FIELD_INDEX {
CUI( 1 ), RINDEX( 2 ), TCOUNT( 3 ), TEXT( 4 ), RWORD( 5 );
final private int __index;
private FIELD_INDEX( final int index ) {
__index = index;
}
}
static final private Logger LOGGER = Logger.getLogger( "JdbcRareWordDictionary" );
static public final String RARE_WORD_TABLE = "rareWordTable";
private PreparedStatement _selectTermCall;
public JdbcRareWordDictionary( final String name, final UimaContext uimaContext, final Properties properties )
throws SQLException {
this( name,
properties.getProperty( JDBC_DRIVER ), properties.getProperty( JDBC_URL ),
properties.getProperty( JDBC_USER ), properties.getProperty( JDBC_PASS ),
properties.getProperty( RARE_WORD_TABLE ) );
}
public JdbcRareWordDictionary( final String name,
final String jdbcDriver,
final String jdbcUrl,
final String jdbcUser,
final String jdbcPass,
final String tableName )
throws SQLException {
super( name );
boolean connected = false;
try {
// DO NOT use try with resources here. Try with resources uses a closable and closes it when exiting the try
final Connection connection = JdbcConnectionFactory.getInstance()
.getConnection( jdbcDriver, jdbcUrl, jdbcUser, jdbcPass );
connected = connection != null;
_selectTermCall = createSelectCall( connection, tableName );
} catch ( SQLException sqlE ) {
if ( !connected ) {
LOGGER.error( "Could not Connect to Dictionary " + name );
} else {
LOGGER.error( "Could not create Term Data Selection Call", sqlE );
}
throw sqlE;
}
LOGGER.info( "Connected to cui and term table " + tableName.toUpperCase() );
}
@Override
public Collection<RareWordTerm> getRareWordHits( final String rareWordText ) {
final List<RareWordTerm> rareWordTerms = new ArrayList<>();
try {
fillSelectCall( rareWordText );
final ResultSet resultSet = _selectTermCall.executeQuery();
while ( resultSet.next() ) {
final RareWordTerm rareWordTerm = new RareWordTerm( resultSet.getString( FIELD_INDEX.TEXT.__index ),
resultSet.getLong( FIELD_INDEX.CUI.__index ),
resultSet.getString( FIELD_INDEX.RWORD.__index ),
resultSet.getInt( FIELD_INDEX.RINDEX.__index ),
resultSet.getInt( FIELD_INDEX.TCOUNT.__index ) );
rareWordTerms.add( rareWordTerm );
}
resultSet.close();
} catch ( SQLException e ) {
LOGGER.error( e.getMessage() );
}
return rareWordTerms;
}
static private PreparedStatement createSelectCall( final Connection connection, final String tableName )
throws SQLException {
final String lookupSql = "SELECT * FROM " + tableName + " WHERE RWORD = ?";
return connection.prepareStatement( lookupSql );
}
/**
* @param rareWordText text of the rare word to use for term lookup
* @return an sql call to use for term lookup
* @throws SQLException if the {@code PreparedStatement} could not be created or changed
*/
private PreparedStatement fillSelectCall( final String rareWordText ) throws SQLException {
_selectTermCall.clearParameters();
_selectTermCall.setString( 1, rareWordText );
return _selectTermCall;
}
}
Following is the exception occurred
11 Apr 2019 12:14:47 INFO AbstractJCasTermAnnotator - Exclusion tagset loaded: CC CD DT EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB VBD VBG VBN VBP VBZ WDT WP WPS WRB
11 Apr 2019 12:14:47 INFO AbstractJCasTermAnnotator - Using minimum term text span: 3
11 Apr 2019 12:14:47 INFO AbstractJCasTermAnnotator - Using Dictionary Descriptor: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml
11 Apr 2019 12:14:48 INFO DictionaryDescriptorParser - Parsing dictionary specifications:
11 Apr 2019 12:14:49 INFO JdbcConnectionFactory - Connecting to jdbc:hsqldb:file:org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab:
2019-04-11 12:14:49.223 INFO 5458 --- [nio-8080-exec-1] hsqldb.db.HSQLDB6A0B3FC2C1.ENGINE : Checkpoint start
2019-04-11 12:14:49.224 INFO 5458 --- [nio-8080-exec-1] hsqldb.db.HSQLDB6A0B3FC2C1.ENGINE : checkpointClose start
2019-04-11 12:14:49.300 INFO 5458 --- [nio-8080-exec-1] hsqldb.db.HSQLDB6A0B3FC2C1.ENGINE : checkpointClose synched
2019-04-11 12:14:49.317 INFO 5458 --- [nio-8080-exec-1] hsqldb.db.HSQLDB6A0B3FC2C1.ENGINE : checkpointClose script done
2019-04-11 12:14:49.323 INFO 5458 --- [nio-8080-exec-1] hsqldb.db.HSQLDB6A0B3FC2C1.ENGINE : checkpointClose end
2019-04-11 12:14:49.327 INFO 5458 --- [nio-8080-exec-1] hsqldb.db.HSQLDB6A0B3FC2C1.ENGINE : Checkpoint end - txts: 1
11 Apr 2019 12:14:49 INFO JdbcConnectionFactory - Database connected
11 Apr 2019 12:14:49 ERROR JdbcRareWordDictionary - Could not create Term Data Selection Call
java.sql.SQLSyntaxErrorException: user lacks privilege or object not found: CUI_TERMS in statement [SELECT * FROM CUI_TERMS WHERE RWORD = ?]
at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source)
at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source)
at org.hsqldb.jdbc.JDBCPreparedStatement.<init>(Unknown Source)
at org.hsqldb.jdbc.JDBCConnection.prepareStatement(Unknown Source)
at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.createSelectCall(JdbcRareWordDictionary.java:139)
at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:93)
at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:75)
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:488)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:196)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionaries(DictionaryDescriptorParser.java:156)
at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:128)
at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:129)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:261)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:175)
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.produceAnalysisEngine(UIMAFramework.java:407)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:256)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:435)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:379)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:192)
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.produceAnalysisEngine(UIMAFramework.java:407)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:256)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:435)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:379)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:192)
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.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:140)
at com.canehealth.spring.ctakes.service.CtakesService.runCollectionProccesingEngine(CtakesService.java:284)
at com.canehealth.spring.ctakes.service.CtakesService.Jcas2json(CtakesService.java:146)
at com.canehealth.spring.ctakes.controller.RestApiController.post_text(RestApiController.java:61)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:564)
at org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:209)
at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:136)
at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:102)
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:877)
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:783)
at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:87)
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:991)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:925)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:974)
at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:877)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:661)
at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:851)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:320)
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:127)
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:91)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:119)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:137)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:111)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:170)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:63)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:200)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:116)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:66)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:105)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:56)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at com.canehealth.spring.ctakes.configuration.CORSFilter.doFilter(CORSFilter.java:30)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:215)
at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:178)
at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:357)
at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:270)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.springframework.web.filter.RequestContextFilter.doFilterInternal(RequestContextFilter.java:99)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.springframework.web.filter.HttpPutFormContentFilter.doFilterInternal(HttpPutFormContentFilter.java:109)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.springframework.web.filter.HiddenHttpMethodFilter.doFilterInternal(HiddenHttpMethodFilter.java:81)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:200)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:496)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342)
at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:803)
at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:790)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1468)
at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1135)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.base/java.lang.Thread.run(Thread.java:844)
Caused by: org.hsqldb.HsqlException: user lacks privilege or object not found: CUI_TERMS
at org.hsqldb.error.Error.error(Unknown Source)
at org.hsqldb.error.Error.error(Unknown Source)
at org.hsqldb.ParserDQL.readTableName(Unknown Source)
at org.hsqldb.ParserDQL.readTableOrSubquery(Unknown Source)
at org.hsqldb.ParserDQL.XreadTableReference(Unknown Source)
at org.hsqldb.ParserDQL.XreadFromClause(Unknown Source)
at org.hsqldb.ParserDQL.XreadTableExpression(Unknown Source)
at org.hsqldb.ParserDQL.XreadQuerySpecification(Unknown Source)
at org.hsqldb.ParserDQL.XreadSimpleTable(Unknown Source)
at org.hsqldb.ParserDQL.XreadQueryPrimary(Unknown Source)
at org.hsqldb.ParserDQL.XreadQueryTerm(Unknown Source)
at org.hsqldb.ParserDQL.XreadQueryExpressionBody(Unknown Source)
at org.hsqldb.ParserDQL.XreadQueryExpression(Unknown Source)
at org.hsqldb.ParserDQL.compileCursorSpecification(Unknown Source)
at org.hsqldb.ParserCommand.compilePart(Unknown Source)
at org.hsqldb.ParserCommand.compileStatement(Unknown Source)
at org.hsqldb.Session.compileStatement(Unknown Source)
at org.hsqldb.StatementManager.compile(Unknown Source)
at org.hsqldb.Session.execute(Unknown Source)
... 128 more
fredt :
The issue here is: Where are the database files? By default, HSQLDB creates an empty database when none exists at the given URL. In order to ensure your database URL points to the correct location, append ;ifexists=true at the end of both jdbcUrl properties. See http://hsqldb.org/doc/2.0/guide/dbproperties-chapt.html#dpc_connection_props
Second, the paths in the jdbcUrl's that you specify are file:, which means a directory structure, but the paths look like pointing to a jar (res:) resource. If the database is in a jar, use the correct type of URL.
If the database files are not in a jar, but are stored in a read-only location in the given directory structure, you may still be able to connect with res:.