compiling JAVA for expression heatmap

classic Classic list List threaded Threaded
7 messages Options
Reply | Threaded
Open this post in threaded view
|

compiling JAVA for expression heatmap

Pengcheng Yang
Dear InterMiners,

This is maybe just a JAVA compiling issue with gradlew command. However,
with my little knowledge of JAVA, I cann't tackle this problem.

I have previously constructed the expression heatmap widget. After the
compiling process moved from ant to gradlew, the deploying work does not
compile these JAVA class any more. I have put the source code related to
expression heatmap to
https://github.com/pengchy/locustmine/tree/master/webapp/src/org/testmine/web.
It seems that these JAVA code files should be compiled to jar file
before deploying. However, I don't know how to use gradlew to compile
these files. Could anyone give a hint or some documentations.

Thank you and best,

Pengcheng Yang

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: compiling JAVA for expression heatmap

Daniela Butano-2

Dear Pengcheng,

I think you saved your classes in the wrong directory.

The correct structure is documented here . As you can see from here , gradle expects the source in src/main/java.

Daniela

On 26/02/2020 07:34, Pengcheng Yang wrote:
Dear InterMiners,

This is maybe just a JAVA compiling issue with gradlew command. However, with my little knowledge of JAVA, I cann't tackle this problem.

I have previously constructed the expression heatmap widget. After the compiling process moved from ant to gradlew, the deploying work does not compile these JAVA class any more. I have put the source code related to expression heatmap to https://github.com/pengchy/locustmine/tree/master/webapp/src/org/testmine/web. It seems that these JAVA code files should be compiled to jar file before deploying. However, I don't know how to use gradlew to compile these files. Could anyone give a hint or some documentations.

Thank you and best,

Pengcheng Yang

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: compiling JAVA for expression heatmap

Pengcheng Yang

Dear  Daniela,

Thank you for your helpful suggestions. I have moved the source code org under the directory webapp/src/main/java/. However, deploying the webapp has interrupted and returned the error said that "package javax.servlet.http does not exist". This package is required by the module webapp/src/main/java/org/testmine/web/HeatMapController.java. Please tell me how to tackle this problem?

Thank you and best,

Pengcheng


On 2020-2-26 18:01, Daniela Butano wrote:

Dear Pengcheng,

I think you saved your classes in the wrong directory.

The correct structure is documented here . As you can see from here , gradle expects the source in src/main/java.

Daniela

On 26/02/2020 07:34, Pengcheng Yang wrote:
Dear InterMiners,

This is maybe just a JAVA compiling issue with gradlew command. However, with my little knowledge of JAVA, I cann't tackle this problem.

I have previously constructed the expression heatmap widget. After the compiling process moved from ant to gradlew, the deploying work does not compile these JAVA class any more. I have put the source code related to expression heatmap to https://github.com/pengchy/locustmine/tree/master/webapp/src/org/testmine/web. It seems that these JAVA code files should be compiled to jar file before deploying. However, I don't know how to use gradlew to compile these files. Could anyone give a hint or some documentations.

Thank you and best,

Pengcheng Yang

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: compiling JAVA for expression heatmap

Daniela Butano-2

It's weird.

Could you please send me the whole log message? When you deploy fawmine, do you use .gradlew cargoredeployremote?

Tomcat comes with the servlet-api.jar library under {your-tomcat-installation}/lib, which contains the package javas.servlet.http.

If you commit your changes, on github, I can have a look.

Daniela

On 26/02/2020 15:06, Pengcheng Yang wrote:

Dear  Daniela,

Thank you for your helpful suggestions. I have moved the source code org under the directory webapp/src/main/java/. However, deploying the webapp has interrupted and returned the error said that "package javax.servlet.http does not exist". This package is required by the module webapp/src/main/java/org/testmine/web/HeatMapController.java. Please tell me how to tackle this problem?

Thank you and best,

Pengcheng


On 2020-2-26 18:01, Daniela Butano wrote:

Dear Pengcheng,

I think you saved your classes in the wrong directory.

The correct structure is documented here . As you can see from here , gradle expects the source in src/main/java.

Daniela

On 26/02/2020 07:34, Pengcheng Yang wrote:
Dear InterMiners,

This is maybe just a JAVA compiling issue with gradlew command. However, with my little knowledge of JAVA, I cann't tackle this problem.

I have previously constructed the expression heatmap widget. After the compiling process moved from ant to gradlew, the deploying work does not compile these JAVA class any more. I have put the source code related to expression heatmap to https://github.com/pengchy/locustmine/tree/master/webapp/src/org/testmine/web. It seems that these JAVA code files should be compiled to jar file before deploying. However, I don't know how to use gradlew to compile these files. Could anyone give a hint or some documentations.

Thank you and best,

Pengcheng Yang

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: compiling JAVA for expression heatmap

Pengcheng Yang

Hi Daniela,

I have committed the code on github at: https://github.com/pengchy/locustmine/tree/master/webapp/src/org/testmine/web (BTW: I am testing this feature using LocustMine).

The full log information are pasted as below. Thank you!

pengcheng

=============== error messages=====================

-bash-4.2$ pwd
/home/pengchy/soft/intermine.4.0/git/locustmine
-bash-4.2$ ./gradlew cargoReDeployRemote -Dorg.gradle.project.release=beta --stacktrace

> Configure project :
Using properties file: '/home/pengchy/.intermine/locustmine.properties.beta'
cleaning
deleting idresolver cache
deleting datasources.xml
deleting organisms.xml
deleting publications.xml
deleted log files

> Task :webapp:unwarBioWebApp
    [unzip] Expanding: /home/pengchy/.gradle/caches/modules-2/files-2.1/org.intermine/bio-webapp/4.0.1/c9ec92f03d0bc99475272962dd63b2aa32c0abae/bio-webapp-4.0.1.war into /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/build/explodedWebApp

> Task :webapp:compileJava
/home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/java/org/testmine/web/HeatMapController.java:21: error: package javax.servlet.http does not exist
import javax.servlet.http.HttpServletRequest;
                         ^
/home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/java/org/testmine/web/HeatMapController.java:22: error: package javax.servlet.http does not exist
import javax.servlet.http.HttpServletResponse;
                         ^
/home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/java/org/testmine/web/HeatMapController.java:23: error: package javax.servlet.http does not exist
import javax.servlet.http.HttpSession;
                         ^
/home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/java/org/testmine/web/HeatMapController.java:91: error: cannot find symbol
            HttpServletRequest request,
            ^
  symbol:   class HttpServletRequest
  location: class HeatMapController
/home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/java/org/testmine/web/HeatMapController.java:92: error: cannot find symbol
            HttpServletResponse response) {
            ^
  symbol:   class HttpServletResponse
  location: class HeatMapController
/home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/java/org/testmine/web/HeatMapController.java:128: error: cannot find symbol
    private void findExpression(HttpServletRequest request, Model model,
                                ^
  symbol:   class HttpServletRequest
  location: class HeatMapController
6 errors


FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':webapp:compileJava'.
> Compilation failed; see the compiler error output for details.

* Try:
Run with --info or --debug option to get more log output.

* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':webapp:compileJava'.
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:100)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:70)
        at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:63)
        at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
        at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:58)
        at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:88)
        at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
        at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
        at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
        at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
        at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
        at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
        at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
        at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:124)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:80)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:105)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:99)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:625)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:580)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:99)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor.process(DefaultTaskPlanExecutor.java:60)
        at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter.execute(DefaultTaskGraphExecuter.java:128)
        at org.gradle.execution.SelectedTaskExecutionAction.execute(SelectedTaskExecutionAction.java:37)
        at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37)
        at org.gradle.execution.DefaultBuildExecuter.access$000(DefaultBuildExecuter.java:23)
        at org.gradle.execution.DefaultBuildExecuter$1.proceed(DefaultBuildExecuter.java:43)
        at org.gradle.execution.DryRunBuildExecutionAction.execute(DryRunBuildExecutionAction.java:46)
        at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37)
        at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:30)
        at org.gradle.initialization.DefaultGradleLauncher$ExecuteTasks.run(DefaultGradleLauncher.java:311)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
        at org.gradle.initialization.DefaultGradleLauncher.runTasks(DefaultGradleLauncher.java:202)
        at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:132)
        at org.gradle.initialization.DefaultGradleLauncher.executeTasks(DefaultGradleLauncher.java:107)
        at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:78)
        at org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:75)
        at org.gradle.internal.work.DefaultWorkerLeaseService.withLocks(DefaultWorkerLeaseService.java:152)
        at org.gradle.internal.invocation.GradleBuildController.doBuild(GradleBuildController.java:100)
        at org.gradle.internal.invocation.GradleBuildController.run(GradleBuildController.java:75)
        at org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28)
        at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35)
        at org.gradle.tooling.internal.provider.ValidatingBuildActionRunner.run(ValidatingBuildActionRunner.java:32)
        at org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner$1.run(RunAsBuildOperationBuildActionRunner.java:43)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
        at org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner.run(RunAsBuildOperationBuildActionRunner.java:40)
        at org.gradle.tooling.internal.provider.SubscribableBuildActionRunner.run(SubscribableBuildActionRunner.java:51)
        at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:45)
        at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:29)
        at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:39)
        at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:25)
        at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:71)
        at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:45)
        at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:51)
        at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:32)
        at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:36)
        at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:25)
        at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:43)
        at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:29)
        at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:64)
        at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:29)
        at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:55)
        at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:42)
        at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:58)
        at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:33)
        at org.gradle.launcher.cli.RunBuildAction.run(RunBuildAction.java:51)
        at org.gradle.internal.Actions$RunnableActionAdapter.execute(Actions.java:173)
        at org.gradle.launcher.cli.CommandLineActionFactory$ParseAndBuildAction.execute(CommandLineActionFactory.java:287)
        at org.gradle.launcher.cli.CommandLineActionFactory$ParseAndBuildAction.execute(CommandLineActionFactory.java:260)
        at org.gradle.launcher.cli.JavaRuntimeValidationAction.execute(JavaRuntimeValidationAction.java:33)
        at org.gradle.launcher.cli.JavaRuntimeValidationAction.execute(JavaRuntimeValidationAction.java:24)
        at org.gradle.launcher.cli.ExceptionReportingAction.execute(ExceptionReportingAction.java:33)
        at org.gradle.launcher.cli.ExceptionReportingAction.execute(ExceptionReportingAction.java:22)
        at org.gradle.launcher.cli.CommandLineActionFactory$WithLogging.execute(CommandLineActionFactory.java:253)
        at org.gradle.launcher.cli.CommandLineActionFactory$WithLogging.execute(CommandLineActionFactory.java:182)
        at org.gradle.launcher.Main.doAction(Main.java:33)
        at org.gradle.launcher.bootstrap.EntryPoint.run(EntryPoint.java:45)
        at org.gradle.launcher.bootstrap.ProcessBootstrap.runNoExit(ProcessBootstrap.java:60)
        at org.gradle.launcher.bootstrap.ProcessBootstrap.run(ProcessBootstrap.java:37)
        at org.gradle.launcher.GradleMain.main(GradleMain.java:23)
        at org.gradle.wrapper.BootstrapMainStarter.start(BootstrapMainStarter.java:31)
        at org.gradle.wrapper.WrapperExecutor.execute(WrapperExecutor.java:108)
        at org.gradle.wrapper.GradleWrapperMain.main(GradleWrapperMain.java:61)
Caused by: org.gradle.api.internal.tasks.compile.CompilationFailedException: Compilation failed; see the compiler error output for details.
        at org.gradle.api.internal.tasks.compile.JdkJavaCompiler.execute(JdkJavaCompiler.java:51)
        at org.gradle.api.internal.tasks.compile.JdkJavaCompiler.execute(JdkJavaCompiler.java:36)
        at org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.delegateAndHandleErrors(NormalizingJavaCompiler.java:99)
        at org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.execute(NormalizingJavaCompiler.java:52)
        at org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.execute(NormalizingJavaCompiler.java:37)
        at org.gradle.api.internal.tasks.compile.CleaningJavaCompilerSupport.execute(CleaningJavaCompilerSupport.java:35)
        at org.gradle.api.internal.tasks.compile.CleaningJavaCompilerSupport.execute(CleaningJavaCompilerSupport.java:25)
        at org.gradle.api.tasks.compile.JavaCompile.performCompilation(JavaCompile.java:198)
        at org.gradle.api.tasks.compile.JavaCompile.compile(JavaCompile.java:183)
        at org.gradle.api.tasks.compile.JavaCompile.compile(JavaCompile.java:120)
        at org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:73)
        at org.gradle.api.internal.project.taskfactory.DefaultTaskClassInfoStore$IncrementalTaskAction.doExecute(DefaultTaskClassInfoStore.java:173)
        at org.gradle.api.internal.project.taskfactory.DefaultTaskClassInfoStore$StandardTaskAction.execute(DefaultTaskClassInfoStore.java:134)
        at org.gradle.api.internal.project.taskfactory.DefaultTaskClassInfoStore$StandardTaskAction.execute(DefaultTaskClassInfoStore.java:121)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:122)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:111)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:92)
        ... 92 more


* Get more help at https://help.gradle.org

BUILD FAILED in 17s
10 actionable tasks: 6 executed, 4 up-to-date


On 2020-2-26 23:46, Daniela Butano wrote:

It's weird.

Could you please send me the whole log message? When you deploy fawmine, do you use .gradlew cargoredeployremote?

Tomcat comes with the servlet-api.jar library under {your-tomcat-installation}/lib, which contains the package javas.servlet.http.

If you commit your changes, on github, I can have a look.

Daniela

On 26/02/2020 15:06, Pengcheng Yang wrote:

Dear  Daniela,

Thank you for your helpful suggestions. I have moved the source code org under the directory webapp/src/main/java/. However, deploying the webapp has interrupted and returned the error said that "package javax.servlet.http does not exist". This package is required by the module webapp/src/main/java/org/testmine/web/HeatMapController.java. Please tell me how to tackle this problem?

Thank you and best,

Pengcheng


On 2020-2-26 18:01, Daniela Butano wrote:

Dear Pengcheng,

I think you saved your classes in the wrong directory.

The correct structure is documented here . As you can see from here , gradle expects the source in src/main/java.

Daniela

On 26/02/2020 07:34, Pengcheng Yang wrote:
Dear InterMiners,

This is maybe just a JAVA compiling issue with gradlew command. However, with my little knowledge of JAVA, I cann't tackle this problem.

I have previously constructed the expression heatmap widget. After the compiling process moved from ant to gradlew, the deploying work does not compile these JAVA class any more. I have put the source code related to expression heatmap to https://github.com/pengchy/locustmine/tree/master/webapp/src/org/testmine/web. It seems that these JAVA code files should be compiled to jar file before deploying. However, I don't know how to use gradlew to compile these files. Could anyone give a hint or some documentations.

Thank you and best,

Pengcheng Yang

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: compiling JAVA for expression heatmap

Daniela Butano-2
Dear Pengcheng,
I haven't tried your code, but I have done a test on biotestmine adding
new CharRender class here
https://github.com/danielabutano/biotestmine/tree/pengchy/webapp/src/main/java/org/biotestmine/web
I run cargoredeplyremote; the war is generated properly. No compilation
error.
Sorry I didn't do too much, but I was very busy with the release.
I will have a look on it next week (tomorrow I am on holidays)

> Hi Daniela,
>
> I have committed the code on github at:
> https://github.com/pengchy/locustmine/tree/master/webapp/src/org/testmine/web
> (BTW: I am testing this feature using LocustMine).
>
> The full log information are pasted as below. Thank you!
>
> pengcheng
>
> =============== error messages=====================
>
> -bash-4.2$ pwd
> /home/pengchy/soft/intermine.4.0/git/locustmine
> -bash-4.2$ ./gradlew cargoReDeployRemote
> -Dorg.gradle.project.release=beta --stacktrace
>
>> Configure project :
> Using properties file:
> '/home/pengchy/.intermine/locustmine.properties.beta'
> cleaning
> deleting idresolver cache
> deleting datasources.xml
> deleting organisms.xml
> deleting publications.xml
> deleted log files
>
>> Task :webapp:unwarBioWebApp
>     [unzip] Expanding:
> /home/pengchy/.gradle/caches/modules-2/files-2.1/org.intermine/bio-webapp/4.0.1/c9ec92f03d0bc99475272962dd63b2aa32c0abae/bio-webapp-4.0.1.war
> into
> /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/build/explodedWebApp
>
>> Task :webapp:compileJava
> /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/java/org/testmine/web/HeatMapController.java:21:
> error: package javax.servlet.http does not exist
> import javax.servlet.http.HttpServletRequest;
>                          ^
> /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/java/org/testmine/web/HeatMapController.java:22:
> error: package javax.servlet.http does not exist
> import javax.servlet.http.HttpServletResponse;
>                          ^
> /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/java/org/testmine/web/HeatMapController.java:23:
> error: package javax.servlet.http does not exist
> import javax.servlet.http.HttpSession;
>                          ^
> /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/java/org/testmine/web/HeatMapController.java:91:
> error: cannot find symbol
>             HttpServletRequest request,
>             ^
>   symbol:   class HttpServletRequest
>   location: class HeatMapController
> /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/java/org/testmine/web/HeatMapController.java:92:
> error: cannot find symbol
>             HttpServletResponse response) {
>             ^
>   symbol:   class HttpServletResponse
>   location: class HeatMapController
> /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/java/org/testmine/web/HeatMapController.java:128:
> error: cannot find symbol
>     private void findExpression(HttpServletRequest request, Model
> model,
>                                 ^
>   symbol:   class HttpServletRequest
>   location: class HeatMapController
> 6 errors
>
> FAILURE: Build failed with an exception.
>
> * What went wrong:
> Execution failed for task ':webapp:compileJava'.
>> Compilation failed; see the compiler error output for details.
>
> * Try:
> Run with --info or --debug option to get more log output.
>
> * Exception is:
> org.gradle.api.tasks.TaskExecutionException: Execution failed for task
> ':webapp:compileJava'.
>         at
> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:100)
>         at
> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:70)
>         at
> org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:63)
>         at
> org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
>         at
> org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:58)
>         at
> org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:88)
>         at
> org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
>         at
> org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
>         at
> org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
>         at
> org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
>         at
> org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
>         at
> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
>         at
> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
>         at
> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
>         at
> org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
>         at
> org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
>         at
> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
>         at
> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
>         at
> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:124)
>         at
> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:80)
>         at
> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:105)
>         at
> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:99)
>         at
> org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:625)
>         at
> org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:580)
>         at
> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:99)
>         at
> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor.process(DefaultTaskPlanExecutor.java:60)
>         at
> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter.execute(DefaultTaskGraphExecuter.java:128)
>         at
> org.gradle.execution.SelectedTaskExecutionAction.execute(SelectedTaskExecutionAction.java:37)
>         at
> org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37)
>         at
> org.gradle.execution.DefaultBuildExecuter.access$000(DefaultBuildExecuter.java:23)
>         at
> org.gradle.execution.DefaultBuildExecuter$1.proceed(DefaultBuildExecuter.java:43)
>         at
> org.gradle.execution.DryRunBuildExecutionAction.execute(DryRunBuildExecutionAction.java:46)
>         at
> org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37)
>         at
> org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:30)
>         at
> org.gradle.initialization.DefaultGradleLauncher$ExecuteTasks.run(DefaultGradleLauncher.java:311)
>         at
> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
>         at
> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
>         at
> org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
>         at
> org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
>         at
> org.gradle.initialization.DefaultGradleLauncher.runTasks(DefaultGradleLauncher.java:202)
>         at
> org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:132)
>         at
> org.gradle.initialization.DefaultGradleLauncher.executeTasks(DefaultGradleLauncher.java:107)
>         at
> org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:78)
>         at
> org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:75)
>         at
> org.gradle.internal.work.DefaultWorkerLeaseService.withLocks(DefaultWorkerLeaseService.java:152)
>         at
> org.gradle.internal.invocation.GradleBuildController.doBuild(GradleBuildController.java:100)
>         at
> org.gradle.internal.invocation.GradleBuildController.run(GradleBuildController.java:75)
>         at
> org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28)
>         at
> org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35)
>         at
> org.gradle.tooling.internal.provider.ValidatingBuildActionRunner.run(ValidatingBuildActionRunner.java:32)
>         at
> org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner$1.run(RunAsBuildOperationBuildActionRunner.java:43)
>         at
> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
>         at
> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
>         at
> org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
>         at
> org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
>         at
> org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner.run(RunAsBuildOperationBuildActionRunner.java:40)
>         at
> org.gradle.tooling.internal.provider.SubscribableBuildActionRunner.run(SubscribableBuildActionRunner.java:51)
>         at
> org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:45)
>         at
> org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:29)
>         at
> org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:39)
>         at
> org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:25)
>         at
> org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:71)
>         at
> org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:45)
>         at
> org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:51)
>         at
> org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:32)
>         at
> org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:36)
>         at
> org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:25)
>         at
> org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:43)
>         at
> org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:29)
>         at
> org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:64)
>         at
> org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:29)
>         at
> org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:55)
>         at
> org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:42)
>         at
> org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:58)
>         at
> org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:33)
>         at
> org.gradle.launcher.cli.RunBuildAction.run(RunBuildAction.java:51)
>         at
> org.gradle.internal.Actions$RunnableActionAdapter.execute(Actions.java:173)
>         at
> org.gradle.launcher.cli.CommandLineActionFactory$ParseAndBuildAction.execute(CommandLineActionFactory.java:287)
>         at
> org.gradle.launcher.cli.CommandLineActionFactory$ParseAndBuildAction.execute(CommandLineActionFactory.java:260)
>         at
> org.gradle.launcher.cli.JavaRuntimeValidationAction.execute(JavaRuntimeValidationAction.java:33)
>         at
> org.gradle.launcher.cli.JavaRuntimeValidationAction.execute(JavaRuntimeValidationAction.java:24)
>         at
> org.gradle.launcher.cli.ExceptionReportingAction.execute(ExceptionReportingAction.java:33)
>         at
> org.gradle.launcher.cli.ExceptionReportingAction.execute(ExceptionReportingAction.java:22)
>         at
> org.gradle.launcher.cli.CommandLineActionFactory$WithLogging.execute(CommandLineActionFactory.java:253)
>         at
> org.gradle.launcher.cli.CommandLineActionFactory$WithLogging.execute(CommandLineActionFactory.java:182)
>         at org.gradle.launcher.Main.doAction(Main.java:33)
>         at
> org.gradle.launcher.bootstrap.EntryPoint.run(EntryPoint.java:45)
>         at
> org.gradle.launcher.bootstrap.ProcessBootstrap.runNoExit(ProcessBootstrap.java:60)
>         at
> org.gradle.launcher.bootstrap.ProcessBootstrap.run(ProcessBootstrap.java:37)
>         at org.gradle.launcher.GradleMain.main(GradleMain.java:23)
>         at
> org.gradle.wrapper.BootstrapMainStarter.start(BootstrapMainStarter.java:31)
>         at
> org.gradle.wrapper.WrapperExecutor.execute(WrapperExecutor.java:108)
>         at
> org.gradle.wrapper.GradleWrapperMain.main(GradleWrapperMain.java:61)
> Caused by:
> org.gradle.api.internal.tasks.compile.CompilationFailedException:
> Compilation failed; see the compiler error output for details.
>         at
> org.gradle.api.internal.tasks.compile.JdkJavaCompiler.execute(JdkJavaCompiler.java:51)
>         at
> org.gradle.api.internal.tasks.compile.JdkJavaCompiler.execute(JdkJavaCompiler.java:36)
>         at
> org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.delegateAndHandleErrors(NormalizingJavaCompiler.java:99)
>         at
> org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.execute(NormalizingJavaCompiler.java:52)
>         at
> org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.execute(NormalizingJavaCompiler.java:37)
>         at
> org.gradle.api.internal.tasks.compile.CleaningJavaCompilerSupport.execute(CleaningJavaCompilerSupport.java:35)
>         at
> org.gradle.api.internal.tasks.compile.CleaningJavaCompilerSupport.execute(CleaningJavaCompilerSupport.java:25)
>         at
> org.gradle.api.tasks.compile.JavaCompile.performCompilation(JavaCompile.java:198)
>         at
> org.gradle.api.tasks.compile.JavaCompile.compile(JavaCompile.java:183)
>         at
> org.gradle.api.tasks.compile.JavaCompile.compile(JavaCompile.java:120)
>         at
> org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:73)
>         at
> org.gradle.api.internal.project.taskfactory.DefaultTaskClassInfoStore$IncrementalTaskAction.doExecute(DefaultTaskClassInfoStore.java:173)
>         at
> org.gradle.api.internal.project.taskfactory.DefaultTaskClassInfoStore$StandardTaskAction.execute(DefaultTaskClassInfoStore.java:134)
>         at
> org.gradle.api.internal.project.taskfactory.DefaultTaskClassInfoStore$StandardTaskAction.execute(DefaultTaskClassInfoStore.java:121)
>         at
> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:122)
>         at
> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
>         at
> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
>         at
> org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
>         at
> org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
>         at
> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:111)
>         at
> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:92)
>         ... 92 more
>
> * Get more help at https://help.gradle.org
>
> BUILD FAILED in 17s
> 10 actionable tasks: 6 executed, 4 up-to-date
>
> On 2020-2-26 23:46, Daniela Butano wrote:
>
>> It's weird.
>>
>> Could you please send me the whole log message? When you deploy
>> fawmine, do you use .gradlew cargoredeployremote?
>>
>> Tomcat comes with the servlet-api.jar library under
>> {your-tomcat-installation}/lib, which contains the package
>> javas.servlet.http.
>>
>> If you commit your changes, on github, I can have a look.
>>
>> Daniela
>> On 26/02/2020 15:06, Pengcheng Yang wrote:
>>
>> Dear  Daniela,
>>
>> Thank you for your helpful suggestions. I have moved the source code
>> _org_ under the directory _webapp/src/main/java/_. However,
>> deploying the webapp has interrupted and returned the error said
>> that "package javax.servlet.http does not exist". This package is
>> required by the module
>> _webapp/src/main/java/org/testmine/web/HeatMapController.java_.
>> Please tell me how to tackle this problem?
>>
>> Thank you and best,
>>
>> Pengcheng
>>
>> On 2020-2-26 18:01, Daniela Butano wrote:
>>
>> Dear Pengcheng,
>>
>> I think you saved your classes in the wrong directory.
>>
>> The correct structure is documented here [1] . As you can see from
>> here [2], gradle expects the source in src/main/java.
>>
>> Daniela
>>
>> On 26/02/2020 07:34, Pengcheng Yang wrote:
>> Dear InterMiners,
>>
>> This is maybe just a JAVA compiling issue with gradlew command.
>> However, with my little knowledge of JAVA, I cann't tackle this
>> problem.
>>
>> I have previously constructed the expression heatmap widget. After
>> the compiling process moved from ant to gradlew, the deploying work
>> does not compile these JAVA class any more. I have put the source
>> code related to expression heatmap to
>>
> https://github.com/pengchy/locustmine/tree/master/webapp/src/org/testmine/web.
>> It seems that these JAVA code files should be compiled to jar file
>> before deploying. However, I don't know how to use gradlew to
>> compile these files. Could anyone give a hint or some
>> documentations.
>>
>> Thank you and best,
>>
>> Pengcheng Yang
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
>
>
>
> Links:
> ------
> [1]
> https://intermine.readthedocs.io/en/latest/intermine/upgrade/#new-directory-structure
> [2]
> https://github.com/pengchy/locustmine/blob/master/webapp/build.gradle#L8
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: compiling JAVA for expression heatmap

Pengcheng Yang
Dear Daniela,

Thank you for your reply and the testing. I have performed "clean" and
"redeploy", the error remain.

I will scrutinize this problem after finishing the work at hand.

Thanks!

Pengcheng


On 2020-3-6 3:24, [hidden email] wrote:

> Dear Pengcheng,
> I haven't tried your code, but I have done a test on biotestmine
> adding new CharRender class here
> https://github.com/danielabutano/biotestmine/tree/pengchy/webapp/src/main/java/org/biotestmine/web
> I run cargoredeplyremote; the war is generated properly. No
> compilation error.
> Sorry I didn't do too much, but I was very busy with the release.
> I will have a look on it next week (tomorrow I am on holidays)
>
>> Hi Daniela,
>>
>> I have committed the code on github at:
>> https://github.com/pengchy/locustmine/tree/master/webapp/src/org/testmine/web 
>>
>> (BTW: I am testing this feature using LocustMine).
>>
>> The full log information are pasted as below. Thank you!
>>
>> pengcheng
>>
>> =============== error messages=====================
>>
>> -bash-4.2$ pwd
>> /home/pengchy/soft/intermine.4.0/git/locustmine
>> -bash-4.2$ ./gradlew cargoReDeployRemote
>> -Dorg.gradle.project.release=beta --stacktrace
>>
>>> Configure project :
>> Using properties file:
>> '/home/pengchy/.intermine/locustmine.properties.beta'
>> cleaning
>> deleting idresolver cache
>> deleting datasources.xml
>> deleting organisms.xml
>> deleting publications.xml
>> deleted log files
>>
>>> Task :webapp:unwarBioWebApp
>>     [unzip] Expanding:
>> /home/pengchy/.gradle/caches/modules-2/files-2.1/org.intermine/bio-webapp/4.0.1/c9ec92f03d0bc99475272962dd63b2aa32c0abae/bio-webapp-4.0.1.war
>>
>> into
>> /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/build/explodedWebApp
>>
>>
>>> Task :webapp:compileJava
>> /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/java/org/testmine/web/HeatMapController.java:21:
>>
>> error: package javax.servlet.http does not exist
>> import javax.servlet.http.HttpServletRequest;
>>                          ^
>> /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/java/org/testmine/web/HeatMapController.java:22:
>>
>> error: package javax.servlet.http does not exist
>> import javax.servlet.http.HttpServletResponse;
>>                          ^
>> /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/java/org/testmine/web/HeatMapController.java:23:
>>
>> error: package javax.servlet.http does not exist
>> import javax.servlet.http.HttpSession;
>>                          ^
>> /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/java/org/testmine/web/HeatMapController.java:91:
>>
>> error: cannot find symbol
>>             HttpServletRequest request,
>>             ^
>>   symbol:   class HttpServletRequest
>>   location: class HeatMapController
>> /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/java/org/testmine/web/HeatMapController.java:92:
>>
>> error: cannot find symbol
>>             HttpServletResponse response) {
>>             ^
>>   symbol:   class HttpServletResponse
>>   location: class HeatMapController
>> /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/java/org/testmine/web/HeatMapController.java:128:
>>
>> error: cannot find symbol
>>     private void findExpression(HttpServletRequest request, Model
>> model,
>>                                 ^
>>   symbol:   class HttpServletRequest
>>   location: class HeatMapController
>> 6 errors
>>
>> FAILURE: Build failed with an exception.
>>
>> * What went wrong:
>> Execution failed for task ':webapp:compileJava'.
>>> Compilation failed; see the compiler error output for details.
>>
>> * Try:
>> Run with --info or --debug option to get more log output.
>>
>> * Exception is:
>> org.gradle.api.tasks.TaskExecutionException: Execution failed for task
>> ':webapp:compileJava'.
>>         at
>> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:100)
>>
>>         at
>> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:70)
>>
>>         at
>> org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:63)
>>
>>         at
>> org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
>>
>>         at
>> org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:58)
>>
>>         at
>> org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:88)
>>
>>         at
>> org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
>>
>>         at
>> org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
>>
>>         at
>> org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
>>
>>         at
>> org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
>>
>>         at
>> org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
>>
>>         at
>> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
>>
>>         at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
>>
>>         at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
>>
>>         at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
>>
>>         at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
>>
>>         at
>> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
>>
>>         at
>> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
>>
>>         at
>> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:124)
>>
>>         at
>> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:80)
>>
>>         at
>> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:105)
>>
>>         at
>> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:99)
>>
>>         at
>> org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:625)
>>
>>         at
>> org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:580)
>>
>>         at
>> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:99)
>>
>>         at
>> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor.process(DefaultTaskPlanExecutor.java:60)
>>
>>         at
>> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter.execute(DefaultTaskGraphExecuter.java:128)
>>
>>         at
>> org.gradle.execution.SelectedTaskExecutionAction.execute(SelectedTaskExecutionAction.java:37)
>>
>>         at
>> org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37)
>>
>>         at
>> org.gradle.execution.DefaultBuildExecuter.access$000(DefaultBuildExecuter.java:23)
>>
>>         at
>> org.gradle.execution.DefaultBuildExecuter$1.proceed(DefaultBuildExecuter.java:43)
>>
>>         at
>> org.gradle.execution.DryRunBuildExecutionAction.execute(DryRunBuildExecutionAction.java:46)
>>
>>         at
>> org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37)
>>
>>         at
>> org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:30)
>>
>>         at
>> org.gradle.initialization.DefaultGradleLauncher$ExecuteTasks.run(DefaultGradleLauncher.java:311)
>>
>>         at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
>>
>>         at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
>>
>>         at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
>>
>>         at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
>>
>>         at
>> org.gradle.initialization.DefaultGradleLauncher.runTasks(DefaultGradleLauncher.java:202)
>>
>>         at
>> org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:132)
>>
>>         at
>> org.gradle.initialization.DefaultGradleLauncher.executeTasks(DefaultGradleLauncher.java:107)
>>
>>         at
>> org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:78)
>>
>>         at
>> org.gradle.internal.invocation.GradleBuildController$1.call(GradleBuildController.java:75)
>>
>>         at
>> org.gradle.internal.work.DefaultWorkerLeaseService.withLocks(DefaultWorkerLeaseService.java:152)
>>
>>         at
>> org.gradle.internal.invocation.GradleBuildController.doBuild(GradleBuildController.java:100)
>>
>>         at
>> org.gradle.internal.invocation.GradleBuildController.run(GradleBuildController.java:75)
>>
>>         at
>> org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28)
>>
>>         at
>> org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35)
>>
>>         at
>> org.gradle.tooling.internal.provider.ValidatingBuildActionRunner.run(ValidatingBuildActionRunner.java:32)
>>
>>         at
>> org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner$1.run(RunAsBuildOperationBuildActionRunner.java:43)
>>
>>         at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
>>
>>         at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
>>
>>         at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
>>
>>         at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
>>
>>         at
>> org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner.run(RunAsBuildOperationBuildActionRunner.java:40)
>>
>>         at
>> org.gradle.tooling.internal.provider.SubscribableBuildActionRunner.run(SubscribableBuildActionRunner.java:51)
>>
>>         at
>> org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:45)
>>
>>         at
>> org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:29)
>>
>>         at
>> org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:39)
>>
>>         at
>> org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:25)
>>
>>         at
>> org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:71)
>>
>>         at
>> org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:45)
>>
>>         at
>> org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:51)
>>
>>         at
>> org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:32)
>>
>>         at
>> org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:36)
>>
>>         at
>> org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:25)
>>
>>         at
>> org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:43)
>>
>>         at
>> org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:29)
>>
>>         at
>> org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:64)
>>
>>         at
>> org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:29)
>>
>>         at
>> org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:55)
>>
>>         at
>> org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:42)
>>
>>         at
>> org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:58)
>>
>>         at
>> org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:33)
>>
>>         at
>> org.gradle.launcher.cli.RunBuildAction.run(RunBuildAction.java:51)
>>         at
>> org.gradle.internal.Actions$RunnableActionAdapter.execute(Actions.java:173)
>>
>>         at
>> org.gradle.launcher.cli.CommandLineActionFactory$ParseAndBuildAction.execute(CommandLineActionFactory.java:287)
>>
>>         at
>> org.gradle.launcher.cli.CommandLineActionFactory$ParseAndBuildAction.execute(CommandLineActionFactory.java:260)
>>
>>         at
>> org.gradle.launcher.cli.JavaRuntimeValidationAction.execute(JavaRuntimeValidationAction.java:33)
>>
>>         at
>> org.gradle.launcher.cli.JavaRuntimeValidationAction.execute(JavaRuntimeValidationAction.java:24)
>>
>>         at
>> org.gradle.launcher.cli.ExceptionReportingAction.execute(ExceptionReportingAction.java:33)
>>
>>         at
>> org.gradle.launcher.cli.ExceptionReportingAction.execute(ExceptionReportingAction.java:22)
>>
>>         at
>> org.gradle.launcher.cli.CommandLineActionFactory$WithLogging.execute(CommandLineActionFactory.java:253)
>>
>>         at
>> org.gradle.launcher.cli.CommandLineActionFactory$WithLogging.execute(CommandLineActionFactory.java:182)
>>
>>         at org.gradle.launcher.Main.doAction(Main.java:33)
>>         at
>> org.gradle.launcher.bootstrap.EntryPoint.run(EntryPoint.java:45)
>>         at
>> org.gradle.launcher.bootstrap.ProcessBootstrap.runNoExit(ProcessBootstrap.java:60)
>>
>>         at
>> org.gradle.launcher.bootstrap.ProcessBootstrap.run(ProcessBootstrap.java:37)
>>
>>         at org.gradle.launcher.GradleMain.main(GradleMain.java:23)
>>         at
>> org.gradle.wrapper.BootstrapMainStarter.start(BootstrapMainStarter.java:31)
>>
>>         at
>> org.gradle.wrapper.WrapperExecutor.execute(WrapperExecutor.java:108)
>>         at
>> org.gradle.wrapper.GradleWrapperMain.main(GradleWrapperMain.java:61)
>> Caused by:
>> org.gradle.api.internal.tasks.compile.CompilationFailedException:
>> Compilation failed; see the compiler error output for details.
>>         at
>> org.gradle.api.internal.tasks.compile.JdkJavaCompiler.execute(JdkJavaCompiler.java:51)
>>
>>         at
>> org.gradle.api.internal.tasks.compile.JdkJavaCompiler.execute(JdkJavaCompiler.java:36)
>>
>>         at
>> org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.delegateAndHandleErrors(NormalizingJavaCompiler.java:99)
>>
>>         at
>> org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.execute(NormalizingJavaCompiler.java:52)
>>
>>         at
>> org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.execute(NormalizingJavaCompiler.java:37)
>>
>>         at
>> org.gradle.api.internal.tasks.compile.CleaningJavaCompilerSupport.execute(CleaningJavaCompilerSupport.java:35)
>>
>>         at
>> org.gradle.api.internal.tasks.compile.CleaningJavaCompilerSupport.execute(CleaningJavaCompilerSupport.java:25)
>>
>>         at
>> org.gradle.api.tasks.compile.JavaCompile.performCompilation(JavaCompile.java:198)
>>
>>         at
>> org.gradle.api.tasks.compile.JavaCompile.compile(JavaCompile.java:183)
>>         at
>> org.gradle.api.tasks.compile.JavaCompile.compile(JavaCompile.java:120)
>>         at
>> org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:73)
>>         at
>> org.gradle.api.internal.project.taskfactory.DefaultTaskClassInfoStore$IncrementalTaskAction.doExecute(DefaultTaskClassInfoStore.java:173)
>>
>>         at
>> org.gradle.api.internal.project.taskfactory.DefaultTaskClassInfoStore$StandardTaskAction.execute(DefaultTaskClassInfoStore.java:134)
>>
>>         at
>> org.gradle.api.internal.project.taskfactory.DefaultTaskClassInfoStore$StandardTaskAction.execute(DefaultTaskClassInfoStore.java:121)
>>
>>         at
>> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:122)
>>
>>         at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
>>
>>         at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
>>
>>         at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
>>
>>         at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
>>
>>         at
>> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:111)
>>
>>         at
>> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:92)
>>
>>         ... 92 more
>>
>> * Get more help at https://help.gradle.org
>>
>> BUILD FAILED in 17s
>> 10 actionable tasks: 6 executed, 4 up-to-date
>>
>> On 2020-2-26 23:46, Daniela Butano wrote:
>>
>>> It's weird.
>>>
>>> Could you please send me the whole log message? When you deploy
>>> fawmine, do you use .gradlew cargoredeployremote?
>>>
>>> Tomcat comes with the servlet-api.jar library under
>>> {your-tomcat-installation}/lib, which contains the package
>>> javas.servlet.http.
>>>
>>> If you commit your changes, on github, I can have a look.
>>>
>>> Daniela
>>> On 26/02/2020 15:06, Pengcheng Yang wrote:
>>>
>>> Dear  Daniela,
>>>
>>> Thank you for your helpful suggestions. I have moved the source code
>>> _org_ under the directory _webapp/src/main/java/_. However,
>>> deploying the webapp has interrupted and returned the error said
>>> that "package javax.servlet.http does not exist". This package is
>>> required by the module
>>> _webapp/src/main/java/org/testmine/web/HeatMapController.java_.
>>> Please tell me how to tackle this problem?
>>>
>>> Thank you and best,
>>>
>>> Pengcheng
>>>
>>> On 2020-2-26 18:01, Daniela Butano wrote:
>>>
>>> Dear Pengcheng,
>>>
>>> I think you saved your classes in the wrong directory.
>>>
>>> The correct structure is documented here [1] . As you can see from
>>> here [2], gradle expects the source in src/main/java.
>>>
>>> Daniela
>>>
>>> On 26/02/2020 07:34, Pengcheng Yang wrote:
>>> Dear InterMiners,
>>>
>>> This is maybe just a JAVA compiling issue with gradlew command.
>>> However, with my little knowledge of JAVA, I cann't tackle this
>>> problem.
>>>
>>> I have previously constructed the expression heatmap widget. After
>>> the compiling process moved from ant to gradlew, the deploying work
>>> does not compile these JAVA class any more. I have put the source
>>> code related to expression heatmap to
>>>
>> https://github.com/pengchy/locustmine/tree/master/webapp/src/org/testmine/web.
>>
>>> It seems that these JAVA code files should be compiled to jar file
>>> before deploying. However, I don't know how to use gradlew to
>>> compile these files. Could anyone give a hint or some
>>> documentations.
>>>
>>> Thank you and best,
>>>
>>> Pengcheng Yang
>>>
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> https://lists.intermine.org/mailman/listinfo/dev
>>>
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> https://lists.intermine.org/mailman/listinfo/dev
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev
>>
>>
>>
>> Links:
>> ------
>> [1]
>> https://intermine.readthedocs.io/en/latest/intermine/upgrade/#new-directory-structure 
>>
>> [2]
>> https://github.com/pengchy/locustmine/blob/master/webapp/build.gradle#L8
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev