Error in building cbioportal from source

[Thankam Sreedharan Vipin]

Hello cbioportal list, 

I m trying to setup a local instance of cbioportal and following the documentation here: http://cbioportal.readthedocs.io/en/latest/Build-from-Source.html. At this step, I am encountering an error message with compiling the model building part. 

Details on my local environment:

OS Redhat Enterprise Linux Server release 7.4 (Maipo)

tomcat version 7.0.76

OpenJDK Runtime Environment version 1.7.0.151

Cbioportal latest code from master branch git clone https://github.com/cBioPortal/cbioportal.git

-bash-4.2$ mvn --version 

Apache Maven 3.0.5 (Red Hat 3.0.5-17)

Maven home: /usr/share/maven

Java version: 1.7.0_151, vendor: Oracle Corporation

Java home: /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.151-2.6.11.1.el7_4.x86_64/jre

Default locale: en_US, platform encoding: UTF-8

OS name: "linux", version: "3.10.0-693.2.2.el7.x86_64", arch: "amd64", family: “unix"

-bash-4.2$ java -version 

java version "1.7.0_151"

OpenJDK Runtime Environment (rhel-2.6.11.1.el7_4-x86_64 u151-b00)

OpenJDK 64-Bit Server VM (build 24.151-b00, mixed mode)

Here is the error from maven command: 

-bash-4.2$ mvn -DskipTests -e clean install

[INFO] Error stacktraces are turned on.

[INFO] Scanning for projects...

[INFO] ------------------------------------------------------------------------

[INFO] Reactor Build Order:

[INFO] 

[INFO] Portal Master

[INFO] model

[INFO] Portal Business Layer

[INFO] persistence

[INFO] persistence-api

[INFO] db-scripts

[INFO] persistence-mybatis

[INFO] security

[INFO] security-spring

[INFO] service

[INFO] Portal Core

[INFO] Portal Web Layer

[INFO] cBioPortal

[INFO] Portal Scripts

[INFO]                                                                         

[INFO] ------------------------------------------------------------------------

[INFO] Building Portal Master v1.8.3

[INFO] ------------------------------------------------------------------------

[INFO] 

[INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ master ---

[INFO] 

[INFO] --- maven-antrun-plugin:1.8:run (default) @ master ---

[INFO] Executing tasks

main:

[INFO] Executed tasks

[INFO] 

[INFO] --- jacoco-maven-plugin:0.7.6.201602180812:prepare-agent (pre-unit-test) @ master ---

[INFO] argLine set to -javaagent:/home/sky/.m2/repository/org/jacoco/org.jacoco.agent/0.7.6.201602180812/org.jacoco.agent-0.7.6.201602180812-runtime.jar=destfile=/home/sky/cbioportal/target/coverage-reports/jacoco-ut.exec

[INFO] 

[INFO] --- jacoco-maven-plugin:0.7.6.201602180812:report (post-unit-test) @ master ---

[INFO] Skipping JaCoCo execution due to missing execution data file:/home/sky/cbioportal/target/coverage-reports/jacoco-ut.exec

[INFO] 

[INFO] --- maven-install-plugin:2.3.1:install (default-install) @ master ---

[INFO] Installing /home/sky/cbioportal/pom.xml to /home/sky/.m2/repository/org/mskcc/cbio/master/v1.8.3/master-v1.8.3.pom

[INFO]                                                                         

[INFO] ------------------------------------------------------------------------

[INFO] Building model v1.8.3

[INFO] ------------------------------------------------------------------------

[INFO] 

[INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ model ---

[INFO] 

[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ model ---

[INFO] Using 'UTF-8' encoding to copy filtered resources.

[INFO] skip non existing resourceDirectory /home/sky/cbioportal/model/src/main/resources

[INFO] skip non existing resourceDirectory /home/sky/cbioportal/model/src/main/resources

[INFO] 

[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ model ---

[INFO] Changes detected - recompiling the module!

[INFO] Compiling 49 source files to /home/sky/cbioportal/model/target/classes

[INFO] ------------------------------------------------------------------------

[INFO] Reactor Summary:

[INFO] 

[INFO] Portal Master ..................................... SUCCESS [1.920s]

[INFO] model ............................................. FAILURE [0.571s]

[INFO] Portal Business Layer ............................. SKIPPED

[INFO] persistence ....................................... SKIPPED

[INFO] persistence-api ................................... SKIPPED

[INFO] db-scripts ........................................ SKIPPED

[INFO] persistence-mybatis ............................... SKIPPED

[INFO] security .......................................... SKIPPED

[INFO] security-spring ................................... SKIPPED

[INFO] service ........................................... SKIPPED

[INFO] Portal Core ....................................... SKIPPED

[INFO] Portal Web Layer .................................. SKIPPED

[INFO] cBioPortal ........................................ SKIPPED

[INFO] Portal Scripts .................................... SKIPPED

[INFO] ------------------------------------------------------------------------

[INFO] BUILD FAILURE

[INFO] ------------------------------------------------------------------------

[INFO] Total time: 2.970s

[INFO] Finished at: Thu Oct 12 14:40:12 CEST 2017

[INFO] Final Memory: 18M/427M

[INFO] ------------------------------------------------------------------------

[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.5.1:compile (default-compile) on project model: Fatal error compiling: invalid target release: 1.8 -> [Help 1]

org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.5.1:compile (default-compile) on project model: Fatal error compiling

   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:57)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:606)

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:414)

at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:357)

Caused by: org.apache.maven.plugin.MojoExecutionException: Fatal error compiling

at org.apache.maven.plugin.compiler.AbstractCompilerMojo.execute(AbstractCompilerMojo.java:897)

at org.apache.maven.plugin.compiler.CompilerMojo.execute(CompilerMojo.java:129)

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.codehaus.plexus.compiler.CompilerException: invalid target release: 1.8

at org.codehaus.plexus.compiler.javac.JavaxToolsCompiler.compileInProcess(JavaxToolsCompiler.java:172)

at org.codehaus.plexus.compiler.javac.JavacCompiler.performCompile(JavacCompiler.java:171)

at org.apache.maven.plugin.compiler.AbstractCompilerMojo.execute(AbstractCompilerMojo.java:886)

... 22 more

Caused by: java.lang.IllegalArgumentException: invalid target release: 1.8

at com.sun.tools.javac.main.RecognizedOptions$GrumpyHelper.error(RecognizedOptions.java:88)

at com.sun.tools.javac.main.RecognizedOptions$10.process(RecognizedOptions.java:359)

at com.sun.tools.javac.api.JavacTool.processOptions(JavacTool.java:242)

at com.sun.tools.javac.api.JavacTool.getTask(JavacTool.java:199)

at com.sun.tools.javac.api.JavacTool.getTask(JavacTool.java:68)

at org.codehaus.plexus.compiler.javac.JavaxToolsCompiler.compileInProcess(JavaxToolsCompiler.java:124)

... 24 more

[ERROR] 

[ERROR] Re-run Maven using the -X switch to enable full debug logging.

[ERROR] 

[ERROR] For more information about the errors and possible solutions, please read the following articles:

[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException

[ERROR] 

[ERROR] After correcting the problems, you can resume the build with the command

[ERROR]   mvn <goals> -rf :model

I am finding difficulty in understanding this error message and anybody have a same experience as above. 

Thanks! 

Vipin

[Thankam Sreedharan Vipin]

I have moved further in the build step, figured out a way to escape the below error message by pointing the right version number in the `pom.xml` file in the cbioportal root directory. 

```pom.xml 445-460 lines

<pluginManagement>

      <plugins>

        <plugin>

          <groupId>org.apache.maven.plugins</groupId>

          <artifactId>maven-compiler-plugin</artifactId>

          <version>3.5.1</version>

          <configuration>

          -  <source>1.8</source>

          -  <target>1.8</target>

          +  <source>1.7</source>

          +  <target>1.7</target>

            <compilerArgs>

              - <arg>-parameters</arg> 

        + <!—- <arg>-parameters</arg> —->

            </compilerArgs>

          </configuration>

        </plugin>

      </plugins>

</pluginManagement>

```

After the change I have re-run the install command as 

```

mvn -DskipTests clean install

```

This fix the few other module build process. Now the error is at `service` module: 

```

[INFO] Reactor Summary:

[INFO] 

[INFO] Portal Master ..................................... SUCCESS [2.033s]

[INFO] model ............................................. SUCCESS [4.698s]

[INFO] Portal Business Layer ............................. SUCCESS [2.278s]

[INFO] persistence ....................................... SUCCESS [0.039s]

[INFO] persistence-api ................................... SUCCESS [0.186s]

[INFO] db-scripts ........................................ SUCCESS [0.172s]

[INFO] persistence-mybatis ............................... SUCCESS [4.130s]

[INFO] security .......................................... SUCCESS [0.037s]

[INFO] security-spring ................................... SUCCESS [20.976s]

[INFO] service ........................................... FAILURE [0.273s]

[INFO] Portal Core ....................................... SKIPPED

[INFO] Portal Web Layer .................................. SKIPPED

[INFO] cBioPortal ........................................ SKIPPED

[INFO] Portal Scripts .................................... SKIPPED

[INFO] ------------------------------------------------------------------------

[INFO] BUILD FAILURE

[INFO] ------------------------------------------------------------------------

[INFO] Total time: 35.300s

[INFO] Finished at: Mon Oct 16 14:36:33 CEST 2017

[INFO] Final Memory: 33M/413M

[INFO] ------------------------------------------------------------------------

[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.5.1:compile (default-compile) on project service: Compilation failure: Compilation failure:

```

Any suggestions to fix this error message? 

Thank you, 

Vipin

[hds...@gmail.com]

Try java 1.8.

Are you make sure there is a folder ~/.m2?  and export M2 and  M2_HOME as export M2_HOME=/home/your_username/apache-maven-3.5.0, export M2=$M2_HOME/bin

Under your cbioportal folder, run

mvn -DskipTests clean install 

[kelse...@gmail.com]

Hi Vipin, 

since you are using java 7, you did right to change the following two lines, which ask maven compiler to build against java 7.

          +  <source>1.7</source>

          +  <target>1.7</target>

I believe your local maven repository has already been set, it is normally located at ${user.name}/.m2/repository, and you can verify the location  by looking at the maven configuration setting xml file.

Can you please rerun maven with -X option to send details error to the standout, so I could take a look.

mvn -X -DskipTests clean install

Thank you!

Kelsey

[JJ Gao]

Vipin,

Please see comments below.

-jj

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[vipi...@gmail.com]

Hi Kelsey, 

Sorry for the delay, Yes I have the the maven repository (.m2) under my username. 

I reran the the build step as  

```

mvn -X -DskipTests clean install

```

produce the same error as before: 

```

[INFO] -------------------------------------------------------------

[INFO] ------------------------------------------------------------------------

[INFO] Reactor Summary:

[INFO] 

[INFO] Portal Master ..................................... SUCCESS [2.049s]

[INFO] model ............................................. SUCCESS [1.895s]

[INFO] Portal Business Layer ............................. SUCCESS [0.818s]

[INFO] persistence ....................................... SUCCESS [0.045s]

[INFO] persistence-api ................................... SUCCESS [0.269s]

[INFO] db-scripts ........................................ SUCCESS [0.178s]

[INFO] persistence-mybatis ............................... SUCCESS [1.001s]

[INFO] security .......................................... SUCCESS [0.036s]

[INFO] security-spring ................................... SUCCESS [0.503s]

[INFO] service ........................................... FAILURE [0.248s]

[INFO] Portal Core ....................................... SKIPPED

[INFO] Portal Web Layer .................................. SKIPPED

[INFO] cBioPortal ........................................ SKIPPED

[INFO] Portal Scripts .................................... SKIPPED

[INFO] ------------------------------------------------------------------------

[INFO] BUILD FAILURE

[INFO] ------------------------------------------------------------------------

[INFO] Total time: 7.541s

[INFO] Finished at: Thu Oct 19 09:43:06 CEST 2017

[INFO] Final Memory: 38M/427M

[INFO] ------------------------------------------------------------------------

…

org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.5.1:compile (default-compile) on project service: Compilation failure

at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:213)

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:57)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:606)

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:414)

at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:357)

Caused by: org.apache.maven.plugin.compiler.CompilationFailureException: Compilation failure

at org.apache.maven.plugin.compiler.AbstractCompilerMojo.execute(AbstractCompilerMojo.java:972)

at org.apache.maven.plugin.compiler.CompilerMojo.execute(CompilerMojo.java:129)

at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:101)

at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:209)

... 19 more

[ERROR] 

[ERROR] 

[ERROR] For more information about the errors and possible solutions, please read the following articles:

[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException

[ERROR] 

[ERROR] After correcting the problems, you can resume the build with the command

[ERROR]   mvn <goals> -rf :service

```

[Pieter Lukasse]

Hi Vipin,

we only support java 8 and later. I asked a colleague to update the documentation. Sorry for the confusion. 

Best regards,

Pieter.

[Pieter Lukasse]

Hi Vipin,

we only support java 8 and later. I asked a colleague to update the documentation. Sorry for the confusion. 

Best regards,

Pieter.

www.thehyve.nl
E pie...@thehyve.nl
T +31(0)30 700 9713
M +31(0)6 28 18 9540
Skype pieter.lukasse


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[Thankam Sreedharan Vipin]

Hi JJ, 

Please see comments below.

Thanks! 

-jj

On Mon, Oct 16, 2017 at 12:30 PM, <hds...@gmail.com> wrote:

Try java 1.8.

@Howard: Thank you for the suggestion. 

Are you make sure there is a folder ~/.m2?  and export M2 and  M2_HOME as export M2_HOME=/home/your_username/apache-maven-3.5.0, export M2=$M2_HOME/bin

Under your cbioportal folder, run

mvn -DskipTests clean install 

Regarding the above, Yes there is maven folder (.m2) under my username. /home/{username}/.m2/repository

I have installed the maven package using the RHEL 7 package distribution

yum install maven 

And set the environment variables as: 

export M2_HOME=/usr/share/maven/

export M2=$M2_HOME/bin

export PATH=$M2:$PATH

Now I have reloaded the shell and rerun the command as: 

```

mvn -DskipTests clean install

```

Returns me the error message as before: 

```

[INFO] ------------------------------------------------------------------------

[INFO] Reactor Summary:

[INFO] 

[INFO] Portal Master ..................................... SUCCESS [1.986s]

[INFO] model ............................................. SUCCESS [1.923s]

[INFO] Portal Business Layer ............................. SUCCESS [0.773s]

[INFO] persistence ....................................... SUCCESS [0.039s]

[INFO] persistence-api ................................... SUCCESS [0.235s]

[INFO] db-scripts ........................................ SUCCESS [0.163s]

[INFO] persistence-mybatis ............................... SUCCESS [0.981s]

[INFO] security .......................................... SUCCESS [0.034s]

[INFO] security-spring ................................... SUCCESS [0.493s]

[INFO] service ........................................... FAILURE [0.209s]

[INFO] Portal Core ....................................... SKIPPED

[INFO] Portal Web Layer .................................. SKIPPED

[INFO] cBioPortal ........................................ SKIPPED

[INFO] Portal Scripts .................................... SKIPPED

[INFO] ------------------------------------------------------------------------

[INFO] BUILD FAILURE

[INFO] ------------------------------------------------------------------------

[INFO] Total time: 7.336s

[INFO] Finished at: Thu Oct 19 10:24:05 CEST 2017

[INFO] Final Memory: 33M/441M

[INFO] ------------------------------------------------------------------------

[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.5.1:compile (default-compile) on project service: Compilation failure: Compilation failure:

```

Thanks! 

Vipin

[vipi...@gmail.com]

Hi Peter & Kelsey, 

I have installed java-1.8.0-openjdk.x86_64 and the build the process completed successfully. 

```

[INFO] Installing /home/nexcbu/cbioportal/scripts/dependency-reduced-pom.xml to /home/nexcbu/.m2/repository/org/mskcc/cbio/scripts/v1.8.3/scripts-v1.8.3.pom

[INFO] ------------------------------------------------------------------------

[INFO] Reactor Summary:

[INFO] 

[INFO] Portal Master ..................................... SUCCESS [1.331s]

[INFO] model ............................................. SUCCESS [1.496s]

[INFO] Portal Business Layer ............................. SUCCESS [0.687s]

[INFO] persistence ....................................... SUCCESS [0.020s]

[INFO] persistence-api ................................... SUCCESS [0.130s]

[INFO] db-scripts ........................................ SUCCESS [0.137s]

[INFO] persistence-mybatis ............................... SUCCESS [0.927s]

[INFO] security .......................................... SUCCESS [0.017s]

[INFO] security-spring ................................... SUCCESS [0.467s]

[INFO] service ........................................... SUCCESS [1.499s]

[INFO] Portal Core ....................................... SUCCESS [29.825s]

[INFO] Portal Web Layer .................................. SUCCESS [12.992s]

[INFO] cBioPortal ........................................ SUCCESS [17.520s]

[INFO] Portal Scripts .................................... SUCCESS [10.407s]

[INFO] ------------------------------------------------------------------------

[INFO] BUILD SUCCESS

[INFO] ------------------------------------------------------------------------

[INFO] Total time: 1:17.713s

[INFO] Finished at: Fri Oct 20 15:53:02 CEST 2017

[INFO] Final Memory: 183M/883M

[INFO] ------------------------------------------------------------------------

```

Now I am continuing the next section for configuring the database. 

Thanks for the suggestion! 

Vipin 

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[vipi...@gmail.com]

Hi Peter & Kelsey, 

With the Java version 1.8 I am following the instance setup as described here:

http://cbioportal.readthedocs.io/en/latest/Load-Sample-Cancer-Study.html

At this point, 

```shell

cd ~/cbioportal/core/src/main/scripts

./importGenePanel.pl --data ../../test/scripts/test_data/study_es_0/gene_panel_example.txt

```

I am getting error message as: 

Here I am not seeing any issue with the JDBC part. I have provided the correct password in the ~/cbioportal/pom.xml file. 

```stdout

Reading data from:  ~/cbioportal/core/src/main/scripts/../../test/scripts/test_data/study_es_0/gene_panel_example.txt

ABORTED!

org.mybatis.spring.MyBatisSystemException: nested exception is org.apache.ibatis.exceptions.PersistenceException: 

### Error querying database.  Cause: org.springframework.jdbc.CannotGetJdbcConnectionException: Could not get JDBC Connection; nested exception is java.sql.SQLException: Cannot create PoolableConnectionFactory (Access denied for user 'cbio_user'@'localhost' (using password: YES))

### The error may exist in org/mskcc/cbio/portal/persistence/GenePanelMapperLegacy.xml

### The error may involve org.mskcc.cbio.portal.persistence.GenePanelMapperLegacy.getGeneByHugoSymbol

### The error occurred while executing a query

### Cause: org.springframework.jdbc.CannotGetJdbcConnectionException: Could not get JDBC Connection; nested exception is java.sql.SQLException: Cannot create PoolableConnectionFactory (Access denied for user 'cbio_user'@'localhost' (using password: YES))

```

Is there anything I am missing in this step?

Thanks! 

Vipin

[vipi...@gmail.com]

Hello support team, 

I have been following the documentation about the web component deployment of cbioportal here: 

http://cbioportal.readthedocs.io/en/latest/Deploying.html

I am working on redhat linux 7 version and installed the tomcat via system package. I have finished the first step of setting up the env variable CATALINA_HOME according to my system installation path. 

In the second step, I got confuse here. $CATALINA_HOME/bin/catalina.sh the tomcat startup file - is something different I think when you use the `systemctl` command. So in my case I have to add the env PORTAL_HOME in /usr/share/tomcat/conf/tomcat.conf

export PORTAL_HOME= $CATALINA_HOME + "/webapps/cbioportal/WEB-INF/classes/"

After the build step I can see the file here ~/cbioportal/portal/target/cbioportal-v1.8.3.war but I didn't understand how this has to be pointed to tomcat path. 

I have used this command to manage the tomcat: 

systemctl restart tomcat 

thanks! 

Vipin

On Friday, October 20, 2017 at 5:58:17 PM UTC+2, vi...@nexus.ethz.ch wrote:

[vipi...@gmail.com]

Hi Howard, 

Yeah I do have username and password for my cbioportal database. 

As of now, according to the documentation step [http://cbioportal.readthedocs.io/en/latest/Load-Sample-Cancer-Study.html], I have configured the database username and password to the Maven settings file: ~/.m2/settings.xml as 

```xml

-bash-4.2$ cat ~/.m2/settings.xml 

<settings>

  <servers>

    <server>

      <id>settingsKey</id>

      <username>cbio_user</username>

      <password>somepassword</password>

    </server>

  </servers>

</settings>

```

I have successfully imported the seed database by following these steps described here: http://cbioportal.readthedocs.io/en/latest/Import-the-Seed-Database.html

I think in the next step [http://cbioportal.readthedocs.io/en/latest/Deploying.html] while deploying the web application, as the third step mention about adding Mysql jdbc to tomcat. I didn't reach that step yet. I am working on the second step in the same above page, where I got stuck with re-defining PORTAL_HOME env variable. 

Do I need to move ~/cbioportal/portal/target/cbioportal-v1.8.3.war to $CATLINA_HOME/webapps/cbioportal/WEB-INF/classes/ (my CATALINA_HOME is /usr/share/tomcat) 

I also have added the portal.properties file with correct username and password for the cbioportal mysql database.

Regards, 

Vipin

[cBioPortal for Cancer Genomics Discussion Group]

Hi Vipin, 

yes, here are list of things you need to do:

1. download mysql connect from http://dev.mysql.com/downloads/connector/j/ and put the jar file under /usr/share/tomcat/lib
   
2. deploy ~/cbioportal/portal/target/cbioportal-v1.8.3.war to /usr/share/tomcat/webapps directory and adjust the logging path in the log4j.properties file 
3. double check from a sql terminal if user "cbio_user" can login into the database. If not then in sql terminal type "grant all privileges on cbioportal.* to 'cbio_user'@'localhost' identified by 'somepassword'", assume your db name is 'cbioportal'.
   

I would not suggest use systemctl to start tomcat, rather use /usr/share/tomcat/bin/catalina.sh start in this way CATALINA_HOME will automatically be set, but you do need to export POTAL_HOME variable manually. Or alternatively, you can create a shell script have following lines:

================================

CATALINA_HOME=/usr/share/tomcat

PORTAL_HOME="$CATLINA_HOME/webapps/cbioportal/WEB-INF/classes/"

export CATALINA_HOME PORTAL_HOME

$CATALINE_HOME/bin/catalina.sh start

=================================

then use the script to start tomcat.

All the best!

Kelsey

[vipi...@gmail.com]

Hi Kelsey, 

Thank you for the information which is helpful to debug the issue with my setup environment. 

I have followed the steps which you mentioned below: 

yes, here are list of things you need to do:

1. download mysql connect from http://dev.mysql.com/downloads/connector/j/ and put the jar file under /usr/share/tomcat/lib

Downloaded the file and placed the JAR file under the folder specified in the above line.

 

1. deploy ~/cbioportal/portal/target/cbioportal-v1.8.3.war to /usr/share/tomcat/webapps directory and adjust the logging path in the log4j.properties file 

 

I have moved the cbioportal-v1.8.3.war to tomcat webapps folder. I have adjusted the log files variables in the log4j.properties file. 

1. double check from a sql terminal if user "cbio_user" can login into the database. If not then in sql terminal type "grant all privileges on cbioportal.* to 'cbio_user'@'localhost' identified by 'somepassword'", assume your db name is 'cbioportal'.
   

Everything granted properly to the database. double checked. 

 

I would not suggest use systemctl to start tomcat, rather use /usr/share/tomcat/bin/catalina.sh start in this way CATALINA_HOME will automatically be set, but you do need to export POTAL_HOME variable manually. Or alternatively, you can create a shell script have following lines:

================================

CATALINA_HOME=/usr/share/tomcat

PORTAL_HOME="$CATLINA_HOME/webapps/cbioportal/WEB-INF/classes/"

export CATALINA_HOME PORTAL_HOME

$CATALINE_HOME/bin/catalina.sh start

=================================

then use the script to start tomcat.

Thanks for the bash script. But I am not sure what will be the content of catalina.sh file. I think in RHEL 7 distribution, I have /usr/share/tomcat/conf/tomcat.conf which defines the JAVA_OPTS env variables etc.

Thanks! 

Vipin

[Pieter Lukasse]

Hi Vipin, 

sorry for the late answer. Before building with maven, did you update the portal.properties file in src/main/resources/ to contain the correct DB credentials?

Thanks,

Pieter

[Pieter Lukasse]

Hi Vipin, 

sorry for the late answer. Before building with maven, did you update the portal.properties file in src/main/resources/ to contain the correct DB credentials?

Thanks,

Pieter

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E pie...@thehyve.nl
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[vipi...@gmail.com]

Hi Peter, 

Yeah I added the database user credentials to the file: 

~/cbioportal/src/main/resources/portal.properties

Thanks! 

Vipin

[vipi...@gmail.com]

As far as I understood, under RHEL the tomcat daemon is not calling catalina.sh file but simply call the tomcat bootstrap class directly. The file /usr/share/tomcat/bin/catalina.sh doesn’t exists when you install tomcat on an RHEL distribution and I can see the tomcat bootstrap file as /usr/share/tomcat/bin/bootstrap.jar 

[Pieter Lukasse]

The tomcat is not used in this case. All importGenePanel.pl does is do a java call:

exec("$JAVA_HOME/bin/java -Xmx1524M -Dspring.profiles.active=dbcp -cp $cp -DPORTAL_HOME='$portalHome' org.mskcc.cbio.portal.scripts.ImportGenePanel @ARGV");

The -Dspring.profiles.active=dbcp most likely links to what is configured in /cbioportal/business/src/main/resources/applicationContext-business.xml . Can you try:

1. to replace the values there by the hard-coded credentials for your DB
   
2. build with maven again
3. run the importGenePanel once more

Step 1 above should not be needed...just suggesting this here for troubleshooting purposes.

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[vipi...@gmail.com]

Hi Peter and Kelsey, 

I have recompiled the codebase and still got stuck at the web component deployment part. 

I have performed all the actions described in the page here: 

http://cbioportal.readthedocs.io/en/latest/Deploying.html

As I said in my RHEL distribution I don't have a catalina.sh script but all the available env variables are available environment. So if I start the tomcat technically I should able to render the landing page right? 

Regards, 

Vipin

[vipi...@gmail.com]

Hi Pieter, 

Thanks! I understand the tomcat server is not used in this purpose. 

I have performed the steps which you mentioned below, starting from 2 step on. After building maven again, I was able to upload the sample study described here:

http://cbioportal.readthedocs.io/en/latest/Load-Sample-Cancer-Study.html

Now I have deployed the cbioportal WAR files to the tomcat folder and started my tomcat server using 

systemctl start tomcat 

But not able to render the application page via a browser. I have checked whether the application is listening to the port which assigned and it is yes. 

[root@cbp logs]# netstat -pant | grep LISTEN

…

tcp6       0      0 :::8080                 :::*                    LISTEN      33105/java 

tcp        0      0 0.0.0.0:3306            0.0.0.0:*               LISTEN      17737/mysqld 

…

If you want any information on the log files, I am happy to provide. 

Thanks! 

Vipin

[Vipin TS]

Hi Howard, 

Thanks for the comments. 

As I mentioned before I am working on a RHEL 7 version of enterprise edition linux distribution. When I installed `tomcat` from the RHEL distribution repo (tomcat version 7.0.76), the CATALINA_HOME is set to `/usr/share/tomcat/`. This is my tomcat setup and I have a `bin` folder under the path as `CATALINA_HOME/bin`. In `/usr/share/tomcat/bin` I am not able to find the `catalina.sh` file. This is the reason why I started the tomcat service as `systemctl start tomcat`. I personally don't know how this `catalina.sh` file will looks like. 

Regarding the errors from tomcat logs, I am attaching the errors which I got from todays test run which is completely followed the instructions available from http://cbioportal.readthedocs.io/en/latest/Deploying.html

I have also looked at my `cbioportal.log` file to see whether this has some issues, but I found something strange there: 

...

2017-11-17 15:10:09 [main] INFO  org.mskcc.cbio.portal.util.GlobalProperties - Attempting to read properties file: /home/vipin/cbioportal/portal.properties

2017-11-17 15:10:09 [main] INFO  org.mskcc.cbio.portal.util.GlobalProperties - Failed to read properties file: /home/vipin/cbioportal/portal.properties

...

I don't know how this is happening, in my understanding this file is in the folder /home/nexcbu/cbioportal/src/main/resources/

I am pretty much following the instructions from the deployment doc to set up the web component of the instance. I do have some experience in setting up java application with tomcat. 

If you would like to have more information from my side please let me know. 

Regards,

Vipin 

Vipin 

On Fri, Nov 17, 2017 at 7:15 PM, Howard Sun <hds...@gmail.com> wrote:

Vipin,

You must have catalina.sh from tomcat. It is in your tomcat folder as /home/vipin/apache-tomcat-9.0.0M26/bin/catalina.sh.

If you run into errors, please look at /home/vipin/apache-tomcat-9.0.0M26/logs and cbioportal.log

If you follow cbioportal doc, you should set it to work easily,otherwise think about tomcat and java mechanism.

Howard 

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[Pieter Lukasse]

Hi Vipin,

From the log messages you shared in the email I would say that your PORTAL_HOME is configured as /home/vipin/cbioportal/ . However in your next comment you also refer to /home/nexcbu/cbioportal/ . Please make sure you have only one location for all of your cBioPortal code. 

The log file line below looks strange. Perhaps you can also try on tomcat8 instead of 9?

INFO: validateJarFile(/usr/share/tomcat/webapps/cbioportal-1.9.0/WEB-INF/lib/javax.el-api-2.2.4.jar) - jar not loaded. See Servlet Spec 3.0, section 10.7.2. Offending class: javax/el/Expression.class

You can also check the cbioportal .log file itself. Check cbioportal/src/main/resources/log4j.properties for what would be the location of this file on your server. Regarding the ports: please check with your sysadmin if there is no firewall blocking your access to this server port (8080) from the outside. 

Finally, you might want to consider the Docker solution we have for cBioPortal installation: https://github.com/thehyve/cbioportal-docker  (check with your sysadmin first if he can get docker on your server - docker installation itself is not always that easy unfortunately on older versions of CentOS or RHEL). 

I hope this helps.

Best regards,

Pieter

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E pie...@thehyve.nl

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[vipi...@gmail.com]

Hi Pieter, 

On Wednesday, November 22, 2017 at 2:51:41 PM UTC+1, Pieter Lukasse wrote:

Hi Vipin,

From the log messages you shared in the email I would say that your PORTAL_HOME is configured as /home/vipin/cbioportal/ . However in your next comment you also refer to /home/nexcbu/cbioportal/ . Please make sure you have only one location for all of your cBioPortal code. 

This was a typo in my previous mail thread. Sorry about that. There is only one codebase for cbioportal and the value for the env variable PORTAL_HOME is /home/vipin/cbioportal/. 

 

The log file line below looks strange. Perhaps you can also try on tomcat8 instead of 9?

INFO: validateJarFile(/usr/share/tomcat/webapps/cbioportal-1.9.0/WEB-INF/lib/javax.el-api-2.2.4.jar) - jar not loaded. See Servlet Spec 3.0, section 10.7.2. Offending class: javax/el/Expression.class

Ok, let me see. 

 

You can also check the cbioportal .log file itself. Check cbioportal/src/main/resources/log4j.properties for what would be the location of this file on your server. Regarding the ports: please check with your sysadmin if there is no firewall blocking your access to this server port (8080) from the outside. 

 

There is no firewall block to the instance port number 8080. I have double checked this. I am accessing the instance's default pages. As I mentioned, the only error message I can see from the `cbioportal.log` is 

```shell

2017-11-17 15:09:31 [main] INFO  org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from URL [file:////home/vipin/cbioportal/portal.properties]

2017-11-17 15:09:31 [main] WARN  org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Could not load properties from URL [file:////home/vipin/cbioportal/portal.properties]: /home/vipin/cbioportal/portal.properties (No such file or directory)

2017-11-17 15:09:31 [main] INFO  org.springframework.beans.factory.config.PropertyPlaceholderConfigurer - Loading properties file from class path resource [portal.properties]

2017-11-17 15:09:31 [main] INFO  org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor - JSR-330 'javax.inject.Inject' annotation found and supported for autowiring

2017-11-17 15:09:36 [main] INFO  org.mskcc.cbio.portal.util.ServerDetector - Detected server null

2017-11-17 15:10:09 [main] INFO  org.mskcc.cbio.portal.util.GlobalProperties - Attempting to read properties file: /home/vipin/cbioportal/portal.properties

2017-11-17 15:10:09 [main] INFO  org.mskcc.cbio.portal.util.GlobalProperties - Failed to read properties file: /home/vipin/cbioportal/portal.properties

2017-11-17 15:10:09 [main] INFO  org.mskcc.cbio.portal.util.GlobalProperties - Attempting to read properties file from classpath

2017-11-17 15:10:09 [main] INFO  org.mskcc.cbio.portal.util.GlobalProperties - Successfully read properties file

```

To get the portal.properties file, it has to look at the complete path as /home/vipin/cbioportal/src/main/resources/portal.properties

Finally, you might want to consider the Docker solution we have for cBioPortal installation: https://github.com/thehyve/cbioportal-docker  (check with your sysadmin first if he can get docker on your server - docker installation itself is not always that easy unfortunately on older versions of CentOS or RHEL). 

We are running the recent version of RHEL server. I have to check this with server management group here and I think it is difficult to get docker on this king of managed instances. 

Thank your for the comments, let me go through the steps one again to resolve the issue. 

Regards, 

Vipin

[Pieter Lukasse]

Hi Vipin,

The message

2017-11-17 15:10:09 [main] INFO  org.mskcc.cbio.portal.util.GlobalProperties - Attempting to read properties file: /home/vipin/cbioportal/portal.properties

2017-11-17 15:10:09 [main] INFO  org.mskcc.cbio.portal.util.GlobalProperties - Failed to read properties file: /home/vipin/cbioportal/portal.properties

2017-11-17 15:10:09 [main] INFO  org.mskcc.cbio.portal.util.GlobalProperties - Attempting to read properties file from classpath

2017-11-17 15:10:09 [main] INFO  org.mskcc.cbio.portal.util.GlobalProperties - Successfully read properties file

is not a problem. It is just telling you that it is looking for the file at PORTAL_HOME first (/home/vipin/cbioportal/) before attempting to read from classpath (i.e. within the .war). The last message above states that it successfully parsed the one from the .war. 

A closer look at your log file reveals more problems:

WARNING: Failed to register in JMX: javax.naming.NamingException: Could not create resource factory instance [Root exception is java.lang.ClassNotFoundException: org.apache.tomcat.dbcp.dbcp.BasicDataSourceFactory]

Nov 17, 2017 10:17:30 AM org.apache.catalina.core.StandardContext startInternal

SEVERE: One or more listeners failed to start. Full details will be found in the appropriate container log file

Nov 17, 2017 10:17:30 AM org.apache.catalina.core.StandardContext startInternal

SEVERE: Context [/cbioportal-1.9.0] startup failed due to previous errors

This "ClassNotFoundException" also makes me suspect tomcat9. I think most of us are using tomcat7 or tomcat8. 

Best regards,

Pieter

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[vipi...@gmail.com]

Hi Pieter, 

Ok good to know about the details on portal.properties file reading. 

Regarding the `catalina.log` file "ClassNotFoundException" error, I have double checked here about my tomcat installation. 

```shell

# yum list installed | grep tomcat 

tomcat.noarch                      7.0.76-2.el7            @rhel-x86_64-server-7

```

Thanks! 

Vipin

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[philipp....@fau.de]

Hi Pieter,

although this thread is quite old, I'm having the same issues and simply installing Java 8 did not solve my issue.

I'm on macOS and PORTAL_HOME, CATALINA_HOME, M2, and M2_HOME are all correctly set.

Maybe you can take a look at my error messages and point me in the right direction?

Thanks,

Philipp

 

mvn -version

Apache Maven 3.5.4 (1edded0938998edf8bf061f1ceb3cfdeccf443fe; 2018-06-17T20:33:14+02:00)

Maven home: /usr/local/Cellar/maven@3.5/3.5.4/libexec

Java version: 1.8.0_202, vendor: Oracle Corporation, runtime: /Library/Java/JavaVirtualMachines/jdk1.8.0_202.jdk/Contents/Home/jre

Default locale: de_DE, platform encoding: UTF-8

OS name: "mac os x", version: "10.14.3", arch: "x86_64", family: "mac"

[ERROR] COMPILATION ERROR : 

[INFO] -------------------------------------------------------------

[ERROR] /Users/philipp/dev/cbioportal/service/src/main/java/org/cbioportal/service/impl/CancerTypeServiceImpl.java:[15,24] package javax.annotation does not exist

[ERROR] /Users/philipp/dev/cbioportal/service/src/main/java/org/cbioportal/service/impl/GeneServiceImpl.java:[13,24] package javax.annotation does not exist

[ERROR] /Users/philipp/dev/cbioportal/service/src/main/java/org/cbioportal/service/impl/CancerTypeServiceImpl.java:[27,6] cannot find symbol

  symbol:   class PostConstruct

  location: class org.cbioportal.service.impl.CancerTypeServiceImpl

[ERROR] /Users/philipp/dev/cbioportal/service/src/main/java/org/cbioportal/service/impl/GeneServiceImpl.java:[33,6] cannot find symbol

  symbol:   class PostConstruct

  location: class org.cbioportal.service.impl.GeneServiceImpl

[INFO] 4 errors 

[INFO] -------------------------------------------------------------

[INFO] ------------------------------------------------------------------------

[INFO] Reactor Summary:

[INFO] 

[INFO] Portal Master 2.2.0-SNAPSHOT ....................... SUCCESS [  1.057 s]

[INFO] model .............................................. SUCCESS [  1.998 s]

[INFO] Portal Business Layer .............................. SUCCESS [  1.079 s]

[INFO] persistence ........................................ SUCCESS [  0.026 s]

[INFO] persistence-api .................................... SUCCESS [  0.567 s]

[INFO] db-scripts ......................................... SUCCESS [  0.540 s]

[INFO] persistence-mybatis ................................ SUCCESS [  1.095 s]

[INFO] service ............................................ FAILURE [  0.777 s]

[INFO] Portal Web Layer ................................... SKIPPED

[INFO] security ........................................... SKIPPED

[INFO] security-spring .................................... SKIPPED

[INFO] Portal Core ........................................ SKIPPED

[INFO] cBioPortal ......................................... SKIPPED

[INFO] Portal Scripts 2.2.0-SNAPSHOT ...................... SKIPPED

[INFO] ------------------------------------------------------------------------

[INFO] BUILD FAILURE

[INFO] ------------------------------------------------------------------------

[INFO] Total time: 17.061 s

[INFO] Finished at: 2019-04-17T11:26:23+02:00

[INFO] ------------------------------------------------------------------------

[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.5.1:compile (default-compile) on project service: Compilation failure: Compilation failure: 

[ERROR] /Users/philipp/dev/cbioportal/service/src/main/java/org/cbioportal/service/impl/CancerTypeServiceImpl.java:[15,24] package javax.annotation does not exist

[ERROR] /Users/philipp/dev/cbioportal/service/src/main/java/org/cbioportal/service/impl/GeneServiceImpl.java:[13,24] package javax.annotation does not exist

[ERROR] /Users/philipp/dev/cbioportal/service/src/main/java/org/cbioportal/service/impl/CancerTypeServiceImpl.java:[27,6] cannot find symbol

[ERROR]   symbol:   class PostConstruct

[ERROR]   location: class org.cbioportal.service.impl.CancerTypeServiceImpl

[ERROR] /Users/philipp/dev/cbioportal/service/src/main/java/org/cbioportal/service/impl/GeneServiceImpl.java:[33,6] cannot find symbol

[ERROR]   symbol:   class PostConstruct

[ERROR]   location: class org.cbioportal.service.impl.GeneServiceImpl

[ERROR] -> [Help 1]

org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.5.1:compile (default-compile) on project service: Compilation failure

    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:213)

    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:154)

    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:146)

    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)

    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81)

    at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:56)

    at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:128)

    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:305)

    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:192)

    at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:105)

    at org.apache.maven.cli.MavenCli.execute (MavenCli.java:954)

    at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:288)

    at org.apache.maven.cli.MavenCli.main (MavenCli.java:192)

    at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)

    at jdk.internal.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)

    at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)

    at java.lang.reflect.Method.invoke (Method.java:566)

    at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:289)

    at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:229)

    at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:415)

    at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:356)

Caused by: org.apache.maven.plugin.compiler.CompilationFailureException: Compilation failure

    at org.apache.maven.plugin.compiler.AbstractCompilerMojo.execute (AbstractCompilerMojo.java:972)

    at org.apache.maven.plugin.compiler.CompilerMojo.execute (CompilerMojo.java:129)

    at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo (DefaultBuildPluginManager.java:137)

    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:208)

    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:154)

    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:146)

    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)

    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81)

    at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:56)

    at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:128)

    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:305)

    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:192)

    at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:105)

    at org.apache.maven.cli.MavenCli.execute (MavenCli.java:954)

    at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:288)

    at org.apache.maven.cli.MavenCli.main (MavenCli.java:192)

    at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)

    at jdk.internal.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)

    at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)

    at java.lang.reflect.Method.invoke (Method.java:566)

    at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:289)

    at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:229)

    at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:415)

    at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:356)

[ERROR] 

[ERROR] Re-run Maven using the -X switch to enable full debug logging.

[ERROR] 

[ERROR] For more information about the errors and possible solutions, please read the following articles:

[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException

[ERROR] 

[ERROR] After correcting the problems, you can resume the build with the command

[ERROR]   mvn <goals> -rf :service