search

logicahealth / InfoButtons

Infobuttons are context-sensitive links embedded in the electronic health record (EHR). They use clinical context information from the EHR, such as patient demographics, medications, diagnoses, user role, and clinical setting to help find answers to clinicians' and patients' questions using online health information resources.
28 stars 29 forks source link

Error during final "mvn clean install" routine. #25

Open jxfish2 opened 5 years ago

jxfish2 commented 5 years ago

I finally got everything setup, and to the "Run" section of your BuildGuide.

But, when I get to this point, the "mvn clean install" routine throws a lot of errors.

I am sending a copy of the errors inline:

[INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for oib-request 2.3-SNAPSHOT: [INFO] [INFO] oib-request ........................................ SUCCESS [ 0.445 s] [INFO] oib-profile-schema ................................. FAILURE [ 0.724 s] [INFO] oib-service-test ................................... SKIPPED [INFO] oib-request-schema ................................. SKIPPED [INFO] OIB Core Utility Module ............................ SKIPPED [INFO] oib-valueset-matcher ............................... SKIPPED [INFO] oib-request-db ..................................... SKIPPED [INFO] oib-request-inference-rxnorm ....................... SKIPPED [INFO] oib-ext-resources .................................. SKIPPED [INFO] oib-request-service ................................ SKIPPED [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 1.399 s [INFO] Finished at: 2019-01-29T14:00:13-05:00 [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:0.13.1:generate (xsd-generate) on project oib-profile-schema: Execution xsd-generate of goal org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:0.13.1:generate failed: A required class was missing while executing org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:0.13.1:generate: com/sun/xml/bind/api/ErrorListener [ERROR] ----------------------------------------------------- [ERROR] realm = plugin>org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:0.13.1 [ERROR] strategy = org.codehaus.plexus.classworlds.strategy.SelfFirstStrategy [ERROR] urls[0] = file:/root/.m2/repository/org/jvnet/jaxb2/maven2/maven-jaxb2-plugin/0.13.1/maven-jaxb2-plugin-0.13.1.jar [ERROR] urls[1] = file:/root/.m2/repository/org/jvnet/jaxb2/maven2/maven-jaxb2-plugin-core/0.13.1/maven-jaxb2-plugin-core-0.13.1.jar [ERROR] urls[2] = file:/root/.m2/repository/org/apache/commons/commons-lang3/3.2.1/commons-lang3-3.2.1.jar [ERROR] urls[3] = file:/root/.m2/repository/com/sun/org/apache/xml/internal/resolver/20050927/resolver-20050927.jar [ERROR] urls[4] = file:/root/.m2/repository/org/sonatype/plexus/plexus-build-api/0.0.7/plexus-build-api-0.0.7.jar [ERROR] urls[5] = file:/root/.m2/repository/junit/junit/4.8.1/junit-4.8.1.jar [ERROR] urls[6] = file:/root/.m2/repository/org/codehaus/plexus/plexus-utils/1.5.15/plexus-utils-1.5.15.jar [ERROR] urls[7] = file:/root/.m2/repository/org/jvnet/jaxb2/maven2/maven-jaxb22-plugin/0.13.1/maven-jaxb22-plugin-0.13.1.jar [ERROR] urls[8] = file:/root/.m2/repository/org/glassfish/jaxb/jaxb-runtime/2.2.11/jaxb-runtime-2.2.11.jar [ERROR] urls[9] = file:/root/.m2/repository/org/glassfish/jaxb/jaxb-xjc/2.2.11/jaxb-xjc-2.2.11.jar [ERROR] urls[10] = file:/root/.m2/repository/org/apache/maven/plugin-tools/maven-plugin-annotations/3.4/maven-plugin-annotations-3.4.jar [ERROR] Number of foreign imports: 1 [ERROR] import: Entry[import from realm ClassRealm[maven.api, parent: null]] [ERROR] [ERROR] ----------------------------------------------------- [ERROR] : com.sun.xml.bind.api.ErrorListener [ERROR] -> [Help 1] org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:0.13.1:generate (xsd-generate) on project oib-profile-schema: Execution xsd-generate of goal org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:0.13.1:generate failed: A required class was missing while executing org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:0.13.1:generate: com/sun/xml/bind/api/ErrorListener

realm = plugin>org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:0.13.1 strategy = org.codehaus.plexus.classworlds.strategy.SelfFirstStrategy urls[0] = file:/root/.m2/repository/org/jvnet/jaxb2/maven2/maven-jaxb2-plugin/0.13.1/maven-jaxb2-plugin-0.13.1.jar urls[1] = file:/root/.m2/repository/org/jvnet/jaxb2/maven2/maven-jaxb2-plugin-core/0.13.1/maven-jaxb2-plugin-core-0.13.1.jar urls[2] = file:/root/.m2/repository/org/apache/commons/commons-lang3/3.2.1/commons-lang3-3.2.1.jar urls[3] = file:/root/.m2/repository/com/sun/org/apache/xml/internal/resolver/20050927/resolver-20050927.jar urls[4] = file:/root/.m2/repository/org/sonatype/plexus/plexus-build-api/0.0.7/plexus-build-api-0.0.7.jar urls[5] = file:/root/.m2/repository/junit/junit/4.8.1/junit-4.8.1.jar urls[6] = file:/root/.m2/repository/org/codehaus/plexus/plexus-utils/1.5.15/plexus-utils-1.5.15.jar urls[7] = file:/root/.m2/repository/org/jvnet/jaxb2/maven2/maven-jaxb22-plugin/0.13.1/maven-jaxb22-plugin-0.13.1.jar urls[8] = file:/root/.m2/repository/org/glassfish/jaxb/jaxb-runtime/2.2.11/jaxb-runtime-2.2.11.jar urls[9] = file:/root/.m2/repository/org/glassfish/jaxb/jaxb-xjc/2.2.11/jaxb-xjc-2.2.11.jar urls[10] = file:/root/.m2/repository/org/apache/maven/plugin-tools/maven-plugin-annotations/3.4/maven-plugin-annotations-3.4.jar Number of foreign imports: 1 import: Entry[import from realm ClassRealm[maven.api, parent: null]]

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

Caused by: org.apache.maven.plugin.PluginExecutionException: Execution xsd-generate of goal org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:0.13.1:generate failed: A required class was missing while executing org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:0.13.1:generate: com/sun/xml/bind/api/ErrorListener

realm = plugin>org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:0.13.1 strategy = org.codehaus.plexus.classworlds.strategy.SelfFirstStrategy urls[0] = file:/root/.m2/repository/org/jvnet/jaxb2/maven2/maven-jaxb2-plugin/0.13.1/maven-jaxb2-plugin-0.13.1.jar urls[1] = file:/root/.m2/repository/org/jvnet/jaxb2/maven2/maven-jaxb2-plugin-core/0.13.1/maven-jaxb2-plugin-core-0.13.1.jar urls[2] = file:/root/.m2/repository/org/apache/commons/commons-lang3/3.2.1/commons-lang3-3.2.1.jar urls[3] = file:/root/.m2/repository/com/sun/org/apache/xml/internal/resolver/20050927/resolver-20050927.jar urls[4] = file:/root/.m2/repository/org/sonatype/plexus/plexus-build-api/0.0.7/plexus-build-api-0.0.7.jar urls[5] = file:/root/.m2/repository/junit/junit/4.8.1/junit-4.8.1.jar urls[6] = file:/root/.m2/repository/org/codehaus/plexus/plexus-utils/1.5.15/plexus-utils-1.5.15.jar urls[7] = file:/root/.m2/repository/org/jvnet/jaxb2/maven2/maven-jaxb22-plugin/0.13.1/maven-jaxb22-plugin-0.13.1.jar urls[8] = file:/root/.m2/repository/org/glassfish/jaxb/jaxb-runtime/2.2.11/jaxb-runtime-2.2.11.jar urls[9] = file:/root/.m2/repository/org/glassfish/jaxb/jaxb-xjc/2.2.11/jaxb-xjc-2.2.11.jar urls[10] = file:/root/.m2/repository/org/apache/maven/plugin-tools/maven-plugin-annotations/3.4/maven-plugin-annotations-3.4.jar Number of foreign imports: 1 import: Entry[import from realm ClassRealm[maven.api, parent: null]]

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

Caused by: org.apache.maven.plugin.PluginContainerException: A required class was missing while executing org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:0.13.1:generate: com/sun/xml/bind/api/ErrorListener

realm = plugin>org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:0.13.1 strategy = org.codehaus.plexus.classworlds.strategy.SelfFirstStrategy urls[0] = file:/root/.m2/repository/org/jvnet/jaxb2/maven2/maven-jaxb2-plugin/0.13.1/maven-jaxb2-plugin-0.13.1.jar urls[1] = file:/root/.m2/repository/org/jvnet/jaxb2/maven2/maven-jaxb2-plugin-core/0.13.1/maven-jaxb2-plugin-core-0.13.1.jar urls[2] = file:/root/.m2/repository/org/apache/commons/commons-lang3/3.2.1/commons-lang3-3.2.1.jar urls[3] = file:/root/.m2/repository/com/sun/org/apache/xml/internal/resolver/20050927/resolver-20050927.jar urls[4] = file:/root/.m2/repository/org/sonatype/plexus/plexus-build-api/0.0.7/plexus-build-api-0.0.7.jar urls[5] = file:/root/.m2/repository/junit/junit/4.8.1/junit-4.8.1.jar urls[6] = file:/root/.m2/repository/org/codehaus/plexus/plexus-utils/1.5.15/plexus-utils-1.5.15.jar urls[7] = file:/root/.m2/repository/org/jvnet/jaxb2/maven2/maven-jaxb22-plugin/0.13.1/maven-jaxb22-plugin-0.13.1.jar urls[8] = file:/root/.m2/repository/org/glassfish/jaxb/jaxb-runtime/2.2.11/jaxb-runtime-2.2.11.jar urls[9] = file:/root/.m2/repository/org/glassfish/jaxb/jaxb-xjc/2.2.11/jaxb-xjc-2.2.11.jar urls[10] = file:/root/.m2/repository/org/apache/maven/plugin-tools/maven-plugin-annotations/3.4/maven-plugin-annotations-3.4.jar Number of foreign imports: 1 import: Entry[import from realm ClassRealm[maven.api, parent: null]]

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

[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/PluginContainerException [ERROR] [ERROR] After correcting the problems, you can resume the build with the command [ERROR] mvn -rf :oib-profile-schema

Am I missing something?

Any idea why this failed?

Any specific log files I could look at?

aniskand commented 5 years ago

I would double check that your JAVA_HOME is pointing to a JDK and not a JRE. That missing class is part of the core java APIs, not an included dependency.

jxfish2 commented 5 years ago

Ok, still got some errors, but MUCH better this time.

Here are the latest errors:

[INFO] Reactor Summary for oib-request 2.3-SNAPSHOT: [INFO] [INFO] oib-request ........................................ SUCCESS [ 0.267 s] [INFO] oib-profile-schema ................................. SUCCESS [ 6.395 s] [INFO] oib-service-test ................................... SUCCESS [ 0.765 s] [INFO] oib-request-schema ................................. SUCCESS [ 2.338 s] [INFO] OIB Core Utility Module ............................ SUCCESS [ 1.417 s] [INFO] oib-valueset-matcher ............................... SUCCESS [ 0.237 s] [INFO] oib-request-db ..................................... SUCCESS [ 1.444 s] [INFO] oib-request-inference-rxnorm ....................... SUCCESS [ 0.144 s] [INFO] oib-ext-resources .................................. FAILURE [ 0.024 s] [INFO] oib-request-service ................................ SKIPPED [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 13.249 s [INFO] Finished at: 2019-01-29T15:44:15-05:00 [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal on project oib-ext-resources: Could not resolve dependencies for project org.openinfobutton:oib-ext-resources:jar:2.3-SNAPSHOT: Could not find artifact org.openinfobutton:rest-impl:jar:1.1-SNAPSHOT -> [Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. [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/DependencyResolutionException [ERROR] [ERROR] After correcting the problems, you can resume the build with the command [ERROR] mvn -rf :oib-ext-resources

aniskand commented 5 years ago

Sorry, you need to build the "rest-terminology-services" project first. It's on the same folder level as "oib-request". You can use the same mvn command.

jxfish2 commented 5 years ago

Output with the "-e -X" options:

[INFO] Reactor Summary for oib-request 2.3-SNAPSHOT: [INFO] [INFO] oib-request ........................................ SUCCESS [ 0.312 s] [INFO] oib-profile-schema ................................. SUCCESS [ 4.368 s] [INFO] oib-service-test ................................... SUCCESS [ 0.288 s] [INFO] oib-request-schema ................................. SUCCESS [ 0.815 s] [INFO] OIB Core Utility Module ............................ SUCCESS [ 0.542 s] [INFO] oib-valueset-matcher ............................... SUCCESS [ 0.413 s] [INFO] oib-request-db ..................................... SUCCESS [ 0.586 s] [INFO] oib-request-inference-rxnorm ....................... SUCCESS [ 0.307 s] [INFO] oib-ext-resources .................................. FAILURE [ 0.109 s] [INFO] oib-request-service ................................ SKIPPED [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 7.924 s [INFO] Finished at: 2019-01-29T15:47:25-05:00 [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal on project oib-ext-resources: Could not resolve dependencies for project org.openinfobutton:oib-ext-resources:jar:2.3-SNAPSHOT: Could not find artifact org.openinfobutton:rest-impl:jar:1.1-SNAPSHOT -> [Help 1] org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal on project oib-ext-resources: Could not resolve dependencies for project org.openinfobutton:oib-ext-resources:jar:2.3-SNAPSHOT: Could not find artifact org.openinfobutton:rest-impl:jar:1.1-SNAPSHOT

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

Caused by: org.apache.maven.project.DependencyResolutionException: Could not resolve dependencies for project org.openinfobutton:oib-ext-resources:jar:2.3-SNAPSHOT: Could not find artifact org.openinfobutton:rest-impl:jar:1.1-SNAPSHOT

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

Caused by: org.eclipse.aether.resolution.DependencyResolutionException: Could not find artifact org.openinfobutton:rest-impl:jar:1.1-SNAPSHOT

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

Caused by: org.eclipse.aether.resolution.ArtifactResolutionException: Could not find artifact org.openinfobutton:rest-impl:jar:1.1-SNAPSHOT

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

Caused by: org.eclipse.aether.transfer.ArtifactNotFoundException: Could not find artifact org.openinfobutton:rest-impl:jar:1.1-SNAPSHOT

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

[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/DependencyResolutionException [ERROR] [ERROR] After correcting the problems, you can resume the build with the command [ERROR] mvn -rf :oib-ext-resources

Any ideas? :P

aniskand commented 5 years ago

Sorry, you need to build the "rest-terminology-services" project first. It's on the same folder level as "oib-request". You can use the same mvn command.

jxfish2 commented 5 years ago

Actually, I was pretty certain that I already did.

But, to be safe, I rebuilt it again.

There are no errors that I can see, when building the rest-terminoloty-services project.

But, I still get the same errors, when building the oib-request project.

After re-running both again,

Here is what I am getting from the oib-request build:

[WARNING] The POM for org.openinfobutton:rest-impl:jar:1.1-SNAPSHOT is missing, no dependency information available [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for oib-request 2.3-SNAPSHOT: [INFO] [INFO] oib-request ........................................ SUCCESS [ 0.230 s] [INFO] oib-profile-schema ................................. SUCCESS [ 3.728 s] [INFO] oib-service-test ................................... SUCCESS [ 0.097 s] [INFO] oib-request-schema ................................. SUCCESS [ 0.495 s] [INFO] OIB Core Utility Module ............................ SUCCESS [ 0.258 s] [INFO] oib-valueset-matcher ............................... SUCCESS [ 0.250 s] [INFO] oib-request-db ..................................... SUCCESS [ 0.325 s] [INFO] oib-request-inference-rxnorm ....................... SUCCESS [ 0.105 s] [INFO] oib-ext-resources .................................. FAILURE [ 0.033 s] [INFO] oib-request-service ................................ SKIPPED [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 5.712 s [INFO] Finished at: 2019-01-29T16:20:23-05:00 [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal on project oib-ext-resources: Could not resolve dependencies for project org.openinfobutton:oib-ext-resources:jar:2.3-SNAPSHOT: Could not find artifact org.openinfobutton:rest-impl:jar:1.1-SNAPSHOT -> [Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. [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/DependencyResolutionException [ERROR] [ERROR] After correcting the problems, you can resume the build with the command [ERROR] mvn -rf :oib-ext-resources

aniskand commented 5 years ago

Ok I see the problem, the version number in one of the poms wasn't correct. Do a git pull on the repository and try again.