dependency issue

[Masber]

Hi,

I am trying to build/install clinical-text-analysis but it complains about the dependencies.

[INFO] --- maven-dependency-plugin:3.1.1:analyze-only (check-dependencies) @ clinical-text-analysis-extension-biolark ---
[WARNING] Used undeclared dependencies found:
[WARNING]    commons-io:commons-io:jar:2.6:compile
[WARNING]    org.xwiki.commons:xwiki-commons-environment-api:jar:7.4.6:compile
[WARNING]    org.xwiki.commons:xwiki-commons-observation-api:jar:7.4.6:compile
[WARNING] Unused declared dependencies found:
[WARNING]    org.xwiki.platform:xwiki-platform-extension-distribution:jar:7.4.6:compile
[WARNING]    jdom:jdom:jar:1.0:compile
[WARNING]    org.apache.commons:commons-collections4:jar:4.0:compile
[WARNING]    log4j:log4j:jar:1.2.17:compile
[WARNING]    net.sf.jwordnet:jwnl:jar:1.3.3:compile
[WARNING]    uk.ac.shef.wit:simmetrics:jar:1.6.2:compile
[WARNING]    com.ibm.icu:icu4j:jar:51.1:compile
[WARNING]    net.sf.json-lib:json-lib:jar:jdk15:2.3:compile
[WARNING]    commons-collections:commons-collections:jar:3.2.1:compile
[WARNING]    org.biolark:biolark-ta:jar:1.0:compile
[WARNING]    org.biolark:biolark-commons:jar:1.0:compile
[WARNING]    org.biolark:biolemmatizer-core:jar:with-dependencies:1.1:compile
[WARNING]    org.apache.commons:commons-compress:jar:1.4.1:compile
[WARNING]    cc.mallet:mallet:jar:2.0.7:compile
[WARNING]    org.xwiki.platform:xwiki-platform-oldcore:jar:7.4.6:compile
[WARNING]    edu.mit:jwi:jar:2.2.4:compile
[WARNING]    nu.xom:xom:jar:1.2.8:compile
[WARNING]    org.phenotips:phenotips-constants:jar:1.4.1:compile
[WARNING]    com.googlecode.json-simple:json-simple:jar:1.1.1:compile
[WARNING]    xerces:xercesImpl:jar:2.9.1:compile
[WARNING]    com.googlecode.matrix-toolkits-java:mtj:jar:0.9.14:compile
[WARNING]    br.pro.lab:OpenJGraph:jar:0.9.1:compile
[WARNING]    com.google.code.gson:gson:jar:2.2.2:compile
[WARNING]    org.jsoup:jsoup:jar:1.7.2:compile
[WARNING]    org.biolark:biolark-input:jar:1.0:compile
[WARNING]    org.xwiki.commons:xwiki-commons-context:jar:7.4.6:compile
[WARNING]    org.beanshell:bsh:jar:2.0b5:compile
[WARNING]    org.mockito:mockito-all:jar:1.10.8:compile
[WARNING]    org.xwiki.platform:xwiki-platform-model:jar:7.4.6:compile
[WARNING]    org.biolark:biolark-search:jar:1.0:compile
[WARNING]    net.sf.trove4j:trove4j:jar:2.0.2:compile
[WARNING]    org.slf4j:slf4j-api:jar:1.7.25:compile
[WARNING]    org.biolark:biolark-variants:jar:1.0:compile
[WARNING]    org.xwiki.platform:xwiki-platform-bridge:jar:7.4.6:compile
[WARNING]    net.sourceforge.nekohtml:nekohtml:jar:1.9.17:compile
[WARNING]    org.biolark:biolark-input-pheno:jar:1.0:compile
[WARNING]    jgrapht:jgrapht:jar:0.6.0:compile
[WARNING]    org.biolark:lvg2013dist:jar:1.0:compile
[WARNING]    org.xwiki.platform:xwiki-platform-query-manager:jar:7.4.6:compile
[WARNING]    edu.stanford.nlp:stanford-corenlp:jar:3.5.1:compile
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] PhenoTips - Clinical Text Analysis ................. SUCCESS [  3.662 s]
[INFO] PhenoTips - Clinical Text Analysis - Java API ...... SUCCESS [ 30.231 s]
[INFO] PhenoTips - Clinical Text Analysis - Biolark implementation for the Java APIs FAILURE [ 18.808 s]
[INFO] PhenoTips - Clinical Text Analysis - Generic REST implementation for the Java APIs SKIPPED
[INFO] PhenoTips - Clinical Text Analysis - User Interface Components SKIPPED
[INFO] PhenoTips - Clinical Text Analysis - Page Objects .. SKIPPED
[INFO] PhenoTips - Clinical Text Analysis - Ctakes server . SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 53.812 s
[INFO] Finished at: 2018-11-28T13:15:48+11:00
[INFO] Final Memory: 56M/1782M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-dependency-plugin:3.1.1:analyze-only (check-dependencies) on project clinical-text-analysis-extension-biolark: Dependency problems found -> [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/MojoExecutionException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :clinical-text-analysis-extension-biolark

Process finished with exit code 1

Any thoughts?

thank you very much

[sdumitriu]

You can get it to build with mvn -Pquick (the quick profile disables all checks).

It's strange though, this works fine for me on master. Did you perhaps change the upstream version to 1.4?

[Masber]

I am using phenotips v.1.4.1 tar.gz file and clinical-text-analysis-extension v.1.0

not sure whether that asnwers your question. I am also putting here the changes I did to the pom files in order to make maven aware of clinical-text-analysis-extension

parent pom

...
  <groupId>org.phenotips</groupId>
  <artifactId>phenotips-parent</artifactId>
  <version>1.4.1</version>
  <packaging>pom</packaging>
...

components pom

<modules>
...
    <module>clinical-text-analysis</module>
</modules>

clinical-text-analysis-extension pom

<parent>
    <groupId>org.phenotips</groupId>
    <artifactId>phenotips-components</artifactId>
    <version>1.4.1</version>
</parent>

Please do not hesitate to let me know if need anything else

[Masber]

ok,

mvn -Pquick is successful on parent is successful and I can build the standalone distribution. However the clinical-text-analysis-extension is not present when I run phenotips standalone.

I created the build form master as suggested.

any idea?