| Jon (LabKey DevOps) responded: |
2018-02-02 13:13 |
Hi Joakim,
This is actually expected since 17.2, the ownership of specific files were moved out of the labkeywebapp directory and are now being handled by the API module.
What actually happens when you try to install LabKey? Are you getting any error messages? If so, can you either attach them to your response or copy/paste them in?
Regards,
Jon |
| |
| Joakim Bygdell responded: |
2018-02-04 23:28 |
Hi,
So this happens when upgrading from 16.3 to 17.3 using your upgrade script.
While the actual upgrade works the app will not start, one of the issues are related to changes in the labkey.xml file:
diff new vs old.
< <Loader loaderClass="org.labkey.bootstrap.LabKeyBootstrapClassLoader" />
---
> <Loader loaderClass="org.labkey.bootstrap.LabkeyServerBootstrapClassLoader" />
Fixing that allows the app to be started from tomacts dashboard but the app throws an 500 error.
500: Unexpected server error. If contacting support regarding this error, please refer to error code: ZKMHZM
java.lang.NoClassDefFoundError: Could not initialize class org.labkey.api.jsp.JspLoader
at org.labkey.api.view.JspView.<init>(JspView.java:89)
at org.labkey.api.view.template.PrintTemplate.<init>(PrintTemplate.java:32)
at org.labkey.api.view.template.HomeTemplate.<init>(HomeTemplate.java:65)
at org.labkey.core.view.template.bootstrap.BootstrapTemplate.<init>(BootstrapTemplate.java:66)
at org.labkey.core.view.template.bootstrap.factory.TemplateFactoryBootstrap.createTemplate(TemplateFactoryBootstrap.java:75)
at org.labkey.api.view.ViewServiceImpl.getTemplate(ViewServiceImpl.java:52)
at org.labkey.core.portal.ProjectController$BeginAction.getView(ProjectController.java:333)
at org.labkey.core.portal.ProjectController$BeginAction.getView(ProjectController.java:293)
at org.labkey.api.action.SimpleViewAction.handleRequest(SimpleViewAction.java:82)
at org.labkey.api.action.BaseViewAction.handleRequest(BaseViewAction.java:177)
at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:414)
at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1228)
at org.labkey.api.view.ViewServlet._service(ViewServlet.java:205)
at org.labkey.api.view.ViewServlet.service(ViewServlet.java:132)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:725)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:291)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:38)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:1148)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:217)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:506)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:142)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:610)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:537)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1081)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:658)
at org.apache.coyote.http11.Http11NioProtocol$Http11ConnectionHandler.process(Http11NioProtocol.java:222)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1580)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1537)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:745)
request attributes
LABKEY.OriginalURL = http://10.0.0.90:8080/labkey/home/project-begin.view?
LABKEY.StartTime = 1517814934585
LABKEY.action = begin
org.springframework.web.servlet.DispatcherServlet.CONTEXT = Root WebApplicationContext: startup date 14:54 UTC 2018; parent: Root WebApplicationContext
LABKEY.controller = project
LABKEY.Counter = 0
X-LABKEY-CSRF = 5a12294c8c3aa33db8edcc4ffa36f90d
LABKEY.container = /home
LABKEY.RequestURL = /labkey/home/project-begin.view?
LABKEY.OriginalURLHelper = /labkey/home/project-begin.view?
core schema database configuration
Server URL jdbc:postgresql://localhost/labkey
Product Name PostgreSQL
Product Version 9.4.13
Driver Name PostgreSQL Native Driver
Driver Version PostgreSQL 9.4.1210
and
java.lang.ExceptionInInitializerError
at org.labkey.api.view.JspView.<init>(JspView.java:89)
at org.labkey.api.view.template.PrintTemplate.<init>(PrintTemplate.java:32)
at org.labkey.api.view.template.HomeTemplate.<init>(HomeTemplate.java:65)
at org.labkey.core.view.template.bootstrap.BootstrapTemplate.<init>(BootstrapTemplate.java:66)
at org.labkey.core.view.template.bootstrap.factory.TemplateFactoryBootstrap.createTemplate(TemplateFactoryBootstrap.java:75)
at org.labkey.api.view.ViewServiceImpl.getTemplate(ViewServiceImpl.java:52)
at org.labkey.core.portal.ProjectController$BeginAction.getView(ProjectController.java:333)
at org.labkey.core.portal.ProjectController$BeginAction.getView(ProjectController.java:293)
at org.labkey.api.action.SimpleViewAction.handleRequest(SimpleViewAction.java:82)
at org.labkey.api.action.BaseViewAction.handleRequest(BaseViewAction.java:177)
at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:414)
at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1228)
at org.labkey.api.view.ViewServlet._service(ViewServlet.java:205)
at org.labkey.api.view.ViewServlet.service(ViewServlet.java:132)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:725)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:291)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:38)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:1148)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:217)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:506)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:142)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:610)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:537)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1081)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:658)
at org.apache.coyote.http11.Http11NioProtocol$Http11ConnectionHandler.process(Http11NioProtocol.java:222)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1580)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1537)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.NullPointerException
at org.labkey.api.jsp.JspClassLoader.<init>(JspClassLoader.java:49)
at org.labkey.api.jsp.JspLoader.<clinit>(JspLoader.java:42)
… 49 more
request attributes
LABKEY.OriginalURL = http://10.0.0.90:8080/labkey/home/project-begin.view?
LABKEY.StartTime = 1517815276460
LABKEY.action = begin
org.springframework.web.servlet.DispatcherServlet.CONTEXT = Root WebApplicationContext: startup date 20:52 UTC 2018; parent: Root WebApplicationContext
LABKEY.controller = project
LABKEY.Counter = 0
X-LABKEY-CSRF = 5a12294c8c3aa33db8edcc4ffa36f90d
LABKEY.container = /home
LABKEY.RequestURL = /labkey/home/project-begin.view?
LABKEY.OriginalURLHelper = /labkey/home/project-begin.view?
core schema database configuration
Server URL jdbc:postgresql://localhost/labkey
Product Name PostgreSQL
Product Version 9.4.13
Driver Name PostgreSQL Native Driver
Driver Version PostgreSQL 9.4.1210 |
| |
| Jon (LabKey DevOps) responded: |
2018-02-05 14:37 |
Hi Joakim,
Thank you for the errors. It looks like one of the JSP resources wasn't extracted properly upon the initial installation.
Do you think it would be possible for you to attach the full labkey.log file from your TOMCAT_HOME/logs directory? We can examine the log and see what occurred at the time when the server tried run after the files were extracted from the archive.
Regards,
Jon |
| |
| Joakim Bygdell responded: |
2018-02-15 23:23 |
Error log from startup sequence after 16.3 -> 17.3 upgrade. |
|
| |
| Jon (LabKey DevOps) responded: |
2018-02-15 23:34 |
Hi Joakim,
Just curious, when you did your upgrade, did you remember to copy the JAR files in the tomcat-lib directory to the TOMCAT_HOME/lib directory?
I had just ran into that same error and that was caused by having JAR files for LabKey that were too old in the Tomcat lib directory.
Once I copied over the newest ones with my build, it installed without issue.
Regards,
Jon |
| |
| Joakim Bygdell responded: |
2018-02-15 23:36 |
The upgrade was performed using the upgrade script. |
| |
| Jon (LabKey DevOps) responded: |
2018-02-16 00:11 |
Hi Joakim,
Can you manually copy the files over? Although the script should do the work, I'd like to rule this possibility out.
Regards,
Jon |
| |
| Joakim Bygdell responded: |
2018-02-16 00:13 |
I have performed the upgrade both manually and using the script, same result both times. |
| |
| Jon (LabKey DevOps) responded: |
2018-02-16 22:54 |
Hi Joakim,
I've tested the build in question via an upgrade from 16.3 to 17.3 and haven't had an issue. This particular stack error that I've seen usually is due to having old JAR files that need to be replaced, so I'm not certain as to why your build is doing this when you're upgrading. However, I think you can use a build that is in-between 16.3 and 17.3 to possibly allow the upgrade to work.
Is it possible for you to reload your old 16.3 database and try to upgrade to 17.2, then try to upgrade to 17.3?
You can obtain the binaries for 17.2 here: https://www.labkey.org/Documentation/wiki-page.view?name=prevReleasesDetails&release=17.2
Regards,
Jon |
| |
labkey.log