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Issue tracker for the beta release of PeptideShaker 2.0
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Weird error with streams in CommandParameter.isInList #28

Closed CarlosHorro closed 5 years ago

CarlosHorro commented 5 years ago

Some days ago I had a problem when trying to set IdentificationParametersCLI with -specificy "0,1" (ie: with more than 1 value) I though it was something just happening to -specificity param, but I've checked that it also happened with params as -fi "a,b" or -ri "y,z"

When executing in the command line there was no message shown, the app just stopped without any result or message. I've fixed this problem (already pushed), but I still see that it occurs now when the value provided is not among the valid ones and the code manages the stream here:

if (!supportedInput.anyMatch(value -> value.equals(arg))) {

            valid = false;
            String errorMessage = System.getProperty("line.separator") + "Error parsing the " + argType + " option: Found " + arg + ". Supported input: ["
                    + supportedInput.collect(Collectors.joining(",")) + "]." + System.getProperty("line.separator");
            System.out.println(errorMessage);

        }

When debugging in Netbeans we can see this:

Command execution failed.
org.apache.commons.exec.ExecuteException: Process exited with an error: 1 (Exit value: 1)
    at org.apache.commons.exec.DefaultExecutor.executeInternal(DefaultExecutor.java:404)
    at org.apache.commons.exec.DefaultExecutor.execute(DefaultExecutor.java:166)
    at org.codehaus.mojo.exec.ExecMojo.executeCommandLine(ExecMojo.java:804)
    at org.codehaus.mojo.exec.ExecMojo.executeCommandLine(ExecMojo.java:751)
    at org.codehaus.mojo.exec.ExecMojo.execute(ExecMojo.java:313)
    at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:101)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:209)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:84)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:59)
    at org.apache.maven.lifecycle.internal.LifecycleStarter.singleThreadedBuild(LifecycleStarter.java:183)
    at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:161)
    at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:320)
    at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:156)
    at org.apache.maven.cli.MavenCli.execute(MavenCli.java:537)
    at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:196)
    at org.apache.maven.cli.MavenCli.main(MavenCli.java:141)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:290)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:230)
    at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:409)
    at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:352)
------------------------------------------------------------------------
BUILD FAILURE
------------------------------------------------------------------------
Total time: 2.846s
Finished at: Tue Jun 18 10:41:42 CEST 2019
Final Memory: 9M/309M
------------------------------------------------------------------------
Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.6.0:exec (default-cli) on project SearchGUI: Command execution failed. Process exited with an error: 1 (Exit value: 1) -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.6.0:exec (default-cli) on project SearchGUI: Command execution failed.
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:217)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:84)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:59)
    at org.apache.maven.lifecycle.internal.LifecycleStarter.singleThreadedBuild(LifecycleStarter.java:183)
    at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:161)
    at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:320)
    at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:156)
    at org.apache.maven.cli.MavenCli.execute(MavenCli.java:537)
    at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:196)
    at org.apache.maven.cli.MavenCli.main(MavenCli.java:141)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:290)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:230)
    at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:409)
    at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:352)
Caused by: org.apache.maven.plugin.MojoExecutionException: Command execution failed.
    at org.codehaus.mojo.exec.ExecMojo.execute(ExecMojo.java:326)
    at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:101)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:209)
    ... 19 more
Caused by: org.apache.commons.exec.ExecuteException: Process exited with an error: 1 (Exit value: 1)
    at org.apache.commons.exec.DefaultExecutor.executeInternal(DefaultExecutor.java:404)
    at org.apache.commons.exec.DefaultExecutor.execute(DefaultExecutor.java:166)
    at org.codehaus.mojo.exec.ExecMojo.executeCommandLine(ExecMojo.java:804)
    at org.codehaus.mojo.exec.ExecMojo.executeCommandLine(ExecMojo.java:751)
    at org.codehaus.mojo.exec.ExecMojo.execute(ExecMojo.java:313)
    ... 21 more

It makes sense that the stream can be used just once (there, seems to be used twice, with anyMatch and building the errorMessage) , but still the error happens when removing 

String errorMessage = System.getProperty("line.separator") + "Error parsing the " + argType + " option: Found " + arg + ". Supported input: ["
                   + supportedInput.collect(Collectors.joining(",")) + "]." + System.getProperty("line.separator");
            System.out.println(errorMessage);
hbarsnes commented 5 years ago

Is it an option to simply revert to not using the streams for this particular method?

As this is what we used to do (https://github.com/compomics/compomics-utilities/blob/master/src/main/java/com/compomics/software/cli/CommandParameter.java) and I think this worked fine?

CarlosHorro commented 5 years ago

Yes, it seems old implementation works fine, so I've reused it and it's already pushed.