This bug request documents the various problems/issues I ran into when deploying the LIMS (the nimbus-branch version) on our latest VM. They are in no particular order, I'll organize them later.
* when a user selects "Upload Sequence" under "My Studies" and they don't have any samples defined the upload page should just say something like "you need to have 1 or more samples defined in the database before you can associate sequence with them.
* if you click on bulk download with an empty database an "Internal Server Error" is displayed. An empty database should simply have a message saying "there are no files to download". This error does not appear under bulk download for the "my analysis" section
* launch workflows, if there are no workflows defined in the database then a message saying, there are no workflows defined in the database should be displayed instead of the normal page
* basically everywhere we display a tree or something, if there are no hits then a message say "No x found" should be displayed.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
* remove "Account Activity", "Useage Reports" from "My Account"
* We should simplify the name
* need to make sure the upload takes just plain fastq, either base or color space, and the whole process is configurable so that the data ends up in the right location on the filesystem
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
* need to make the navigation bar at the top and logo pluggable so we can swap out with the SeqWare version
* I get an error on the Show Sequencer Run page after adding a sequencer run:
SequencerRun length: 1
Get Analysis Files
Launch Files:
ROOT: source
[SeqWareLIMS] WARN [2011/05/13 10:49:16] | SQL Error: 0, SQLState: 42601
[SeqWareLIMS] ERROR [2011/05/13 10:49:16] | ERROR: syntax error at or near "WITH"
May 13, 2011 10:50:58 AM org.apache.catalina.core.StandardWrapperValve invoke
SEVERE: Servlet.service() for servlet dispatcher threw exception
org.postgresql.util.PSQLException: ERROR: syntax error at or near "WITH"
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1525)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1309)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:188)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:452)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:354)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:258)
at org.apache.commons.dbcp.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:96)
at org.apache.commons.dbcp.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:96)
at org.hibernate.jdbc.AbstractBatcher.getResultSet(AbstractBatcher.java:186)
at org.hibernate.loader.Loader.getResultSet(Loader.java:1787)
at org.hibernate.loader.Loader.doQuery(Loader.java:674)
at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:236)
at org.hibernate.loader.Loader.doList(Loader.java:2220)
at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2104)
at org.hibernate.loader.Loader.list(Loader.java:2099)
at org.hibernate.loader.custom.CustomLoader.list(CustomLoader.java:289)
at org.hibernate.impl.SessionImpl.listCustomQuery(SessionImpl.java:1695)
at org.hibernate.impl.AbstractSessionImpl.list(AbstractSessionImpl.java:142)
at org.hibernate.impl.SQLQueryImpl.list(SQLQueryImpl.java:152)
at net.sourceforge.solexatools.dao.hibernate.SequencerRunDAOHibernate.getProcStatuses(SequencerRunDAOHibernate.java:94)
at net.sourceforge.solexatools.business.impl.SequencerRunServiceImpl.setProcCountInfo(SequencerRunServiceImpl.java:214)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:139)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:107)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:161)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
at $Proxy3.setProcCountInfo(Unknown Source)
at net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController.handleRequestInternal(SequencerRunListDetailsController.java:72)
at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153)
at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48)
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:857)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:461)
at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:416)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:617)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298)
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:857)
at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:588)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)
at java.lang.Thread.run(Thread.java:619)
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Items from 20110513
* when a user selects "Upload Sequence" under "My Studies" and they don't have any samples defined the upload page should just say something like "you need to have 1 or more samples defined in the database before you can associate sequence with them.
* if you click on bulk download with an empty database an "Internal Server Error" is displayed. An empty database should simply have a message saying "there are no files to download". This error does not appear under bulk download for the "my analysis" section
* launch workflows, if there are no workflows defined in the database then a message saying, there are no workflows defined in the database should be displayed instead of the normal page
* basically everywhere we display a tree or something, if there are no hits then a message say "No x found" should be displayed.
20110513
* remove "Account Activity", "Useage Reports" from "My Account"
* We should simplify the name
* need to make sure the upload takes just plain fastq, either base or color space, and the whole process is configurable so that the data ends up in the right location on the filesystem
20110513
* need to make the navigation bar at the top and logo pluggable so we can swap out with the SeqWare version
* I get an error on the Show Sequencer Run page after adding a sequencer run:
SequencerRun length: 1
Get Analysis Files
Launch Files:
ROOT: source
[SeqWareLIMS] WARN [2011/05/13 10:49:16] | SQL Error: 0, SQLState: 42601
[SeqWareLIMS] ERROR [2011/05/13 10:49:16] | ERROR: syntax error at or near "WITH"
May 13, 2011 10:50:58 AM org.apache.catalina.core.StandardWrapperValve invoke
SEVERE: Servlet.service() for servlet dispatcher threw exception
org.postgresql.util.PSQLException: ERROR: syntax error at or near "WITH"
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1525)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1309)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:188)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:452)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:354)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:258)
at org.apache.commons.dbcp.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:96)
at org.apache.commons.dbcp.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:96)
at org.hibernate.jdbc.AbstractBatcher.getResultSet(AbstractBatcher.java:186)
at org.hibernate.loader.Loader.getResultSet(Loader.java:1787)
at org.hibernate.loader.Loader.doQuery(Loader.java:674)
at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:236)
at org.hibernate.loader.Loader.doList(Loader.java:2220)
at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2104)
at org.hibernate.loader.Loader.list(Loader.java:2099)
at org.hibernate.loader.custom.CustomLoader.list(CustomLoader.java:289)
at org.hibernate.impl.SessionImpl.listCustomQuery(SessionImpl.java:1695)
at org.hibernate.impl.AbstractSessionImpl.list(AbstractSessionImpl.java:142)
at org.hibernate.impl.SQLQueryImpl.list(SQLQueryImpl.java:152)
at net.sourceforge.solexatools.dao.hibernate.SequencerRunDAOHibernate.getProcStatuses(SequencerRunDAOHibernate.java:94)
at net.sourceforge.solexatools.business.impl.SequencerRunServiceImpl.setProcCountInfo(SequencerRunServiceImpl.java:214)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:139)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:107)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:161)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
at $Proxy3.setProcCountInfo(Unknown Source)
at net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController.handleRequestInternal(SequencerRunListDetailsController.java:72)
at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153)
at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48)
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:857)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:461)
at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:416)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:617)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298)
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:857)
at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:588)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)
at java.lang.Thread.run(Thread.java:619)