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MassBank / MassBank-web

The web server application and directly connected components for a MassBank web server
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QuickSearchByPeak.search fails #155

Closed meier-rene closed 5 years ago

meier-rene commented 5 years ago

07-Jan-2019 10:46:23.264 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 8829 ms Error: Missing argument 'id' Error: Argument 'dsn' is missing or empty Error: Argument 'dsn' is missing or empty java.sql.SQLSyntaxErrorException: (conn=21891) You have an error in your SQL syntax; check the manual that corresponds to your MariaDB server version for the right syntax to use near ') ORDER BY ID' at line 1 at org.mariadb.jdbc.internal.util.exceptions.ExceptionMapper.get(ExceptionMapper.java:236) at org.mariadb.jdbc.internal.util.exceptions.ExceptionMapper.getException(ExceptionMapper.java:165) at org.mariadb.jdbc.MariaDbStatement.executeExceptionEpilogue(MariaDbStatement.java:238) at org.mariadb.jdbc.MariaDbPreparedStatementClient.executeInternal(MariaDbPreparedStatementClient.java:232) at org.mariadb.jdbc.MariaDbPreparedStatementClient.execute(MariaDbPreparedStatementClient.java:159) at org.mariadb.jdbc.MariaDbPreparedStatementClient.executeQuery(MariaDbPreparedStatementClient.java:174) at massbank.web.quicksearch.Search.searchPeak(Search.java:425) at massbank.web.quicksearch.Search.execute(Search.java:99) at massbank.web.quicksearch.Search.(Search.java:66) at massbank.web.quicksearch.QuickSearchByPeak.search(QuickSearchByPeak.java:18) at massbank.web.quicksearch.QuickSearchByPeak.search(QuickSearchByPeak.java:9) at massbank.web.SearchExecution.exec(SearchExecution.java:24) at org.apache.jsp.QpeakResult_jsp._jspService(QpeakResult_jsp.java:585) at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70) at javax.servlet.http.HttpServlet.service(HttpServlet.java:742) at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:443) at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:386) at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:330) 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.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:199) 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.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:650) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342) at org.apache.coyote.ajp.AjpProcessor.service(AjpProcessor.java:487) at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66) at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:800) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1463) 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: java.sql.SQLException: You have an error in your SQL syntax; check the manual that corresponds to your MariaDB server version for the right syntax to use near ') ORDER BY ID' at line 1 Query is: SELECT T.ID FROM (SELECT * FROM (SELECT AC_INSTRUMENT AS AC_INSTRUMENT, ACCESSION AS ID, AC_MASS_SPECTROMETRY_MS_TYPE AS MS_TYPE, RECORD_TITLE AS NAME, AC_MASS_SPECTROMETRY_ION_MODE AS ION FROM RECORD) AS R, (SELECT RECORD, VALUE FROM MS_FOCUSED_ION WHERE SUBTAG = 'PRECURSOR_M/Z') AS S WHERE R.ID= S.RECORD) AS T WHERE T.ION = ? AND T.MS_TYPE IN) ORDER BY ID, parameters ['POSITIVE'] java thread: ajp-nio-127.0.0.1-8009-exec-5 at org.mariadb.jdbc.internal.util.LogQueryTool.exceptionWithQuery(LogQueryTool.java:163) at org.mariadb.jdbc.internal.protocol.AbstractQueryProtocol.executeQuery(AbstractQueryProtocol.java:280) at org.mariadb.jdbc.MariaDbPreparedStatementClient.executeInternal(MariaDbPreparedStatementClient.java:223) ... 37 more

Treutler commented 5 years ago

@meier-rene does this error still happen?