Cannot login to Libreclinica 1.3

[GSTTDMS]

I am unable to login to Libreclinica 1.3 even though I can get to the login screen. system is ubuntu 20.04, tomcat 9, postgres 14. Every time I try and login I get the error page (Oops ...). Below is the error I see in the logs.

21-Oct-2024 14:39:00.316 SEVERE [http-nio-8080-exec-1] org.apache.catalina.core.StandardWrapperValve.invoke Servlet.service() for servlet [default] in context with path [/LibreClinica] threw exception [java.lang.NullPointerException] with root cause
java.lang.NullPointerException
at org.akaza.openclinica.dao.login.UserAccountDAO.findByUserName(UserAccountDAO.java:541)
at org.akaza.openclinica.web.filter.OpenClinicaUsernamePasswordAuthenticationFilter.attemptAuthentication(OpenClinicaUsernamePasswordAuthenticationFilter.java:137)
at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:212)
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:74)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:56)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.session.ConcurrentSessionFilter.doFilter(ConcurrentSessionFilter.java:155)
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.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:168)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:144)
at net.sf.ehcache.constructs.web.filter.GzipFilter.doFilter(GzipFilter.java:95)
at net.sf.ehcache.constructs.web.filter.Filter.doFilter(Filter.java:86)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:168)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:144)
at org.akaza.openclinica.web.filter.LocaleFilter.doFilter(LocaleFilter.java:48)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:168)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:144)
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:168)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:144)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:168)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:90)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:482)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:130)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:93)
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:660)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:74)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:346)
at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:383)
at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:63)
at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:937)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1791)
at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:52)
at org.apache.tomcat.util.threads.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1190)
at org.apache.tomcat.util.threads.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:659)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:63)
at java.base/java.lang.Thread.run(Thread.java:829)

Any ideas? Thanks.

[toskrip]

This is error from data access layer which looks like the initialisation of the data access objects was not successful. Can you check if the initial table structure was created in the database and that there is the user_account table with initial root user present? To me a looks like some miss-configuration... are there maybe some errors present also within log files?

[GSTTDMS]

Thanks. I decided to do a clean install and still get the same error. Just as before the database has been created, the user_account table with the initial root user is present. Attached are my log files.

localhost.2024-10-22.log
libreclinica-db.log
libreclinica.2024-10-22.log

[toskrip]

the log shows that database connection string was not initialized properly (failing with null pointer). Looks like it is failing while setting the database connection url but that is supposed to be created automatically when postgres is detected as dbType in datainfo properties file. I would suspect other the properties file not copied out of WEB-INF/classes into libreclinica.config location or tomcat cannot read the properties file (permissions not set correctly).

[GSTTDMS]

Thanks again for your quick reply. All permissions seem to be in place. As a check if I remove the dataInfo.properties from
the tomcat/libreclinica.conf folder LibreClinica 1.3 does not start. I decided to try version 1.2.1 with exactly the same setup and I did not get any errors. Thanks.

[toskrip]

now I noticed on your screenshot from 1.3 opps! page that the changeset corresponds to the current state of lc-develop branch which is unreleased development state (supposed to be released as 1.4 eventually). This means that you was compiling it on your own from the sources. Could you try to use the actually released 1.3 war from the release page and let me know if you are still getting the same error in the log?

[GSTTDMS]

Hi, I installed the actual release 1.3 war from the release page and got the same error. Attached are the log files. Many thanks.
libreclinica-db.2024-10-23.log
localhost.2024-10-23.log

[toskrip]

This is really strange, not sure if I will manage to reproduce it. There is lots of errors in logs that would indicate not just database layer is not initialized but also other things from spring application context failed to start. Almost like if it would have in classpath some incompatible or conflicting libraries but this is hard to imagine because also between 1.2.1 and 1.3 there have not been that many changes. You can try to describe in more detail your deployment environment, maybe somebody else will have an idea (I exhausted my initial list of typical troublemakers).

[GSTTDMS]

Thanks toskrip for looking into this. These are my deployment details:

ubuntu version
lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 20.04.6 LTS
Release: 20.04
Codename: focal

tomcat version
java -cp catalina.jar org.apache.catalina.util.ServerInfo
Server version: Apache Tomcat/9.0.96
Server built: Oct 3 2024 19:44:30 UTC
Server number: 9.0.96.0
OS Name: Linux
OS Version: 5.4.0-198-generic
Architecture: amd64
JVM Version: 1.8.0_432-b06
JVM Vendor: Amazon.com Inc.

java version
java -version
openjdk version "1.8.0_432"
OpenJDK Runtime Environment Corretto-8.432.06.1 (build 1.8.0_432-b06)
OpenJDK 64-Bit Server VM Corretto-8.432.06.1 (build 25.432-b06, mixed mode)

Note that jdk-11 was initially used but got the same error from LibreClinica, also it won't compile with jdk 11.

postgres version
select version();
PostgreSQL 14.13 (Ubuntu 14.13-1.pgdg20.04+1) on x86_64-pc-linux-gnu, compiled by gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0, 64-bit

[GSTTDMS]

Hello, just to let you know that I recently reinstalled lc 1.3.0 on my system and it worked. Both the released one and the latest lc_develop one worked. The only change from earlier was to update the OS when I had to install a new package (swaks) on the system so seems more like an environment issue. Thanks.

[toskrip]

thanks for letting us know... I was trying to reproduce it with different fresh setups (also in docker) but could not really reproduce it. So it is now confirmed that it was something specific in your environment.