VEuPathDB / VEuPathDB/install

Investigate build issues when adding dependencies to TypeHandler in EbrcModelCommon

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Description

Overview

Issue 1: FgpUtil is not resolved when running rebuilder-jenkins https://ci.apidb.org/job/integrate.plasmodb.org/1722/console
Issue 2: Jackson is not resolved when running wb model

mavenCleanInstall:
     [exec] [ERROR] COMPILATION ERROR : 
     [exec] [ERROR] /var/www/TriTrypDB/tritrypdb.crouchk/project_home/EbrcModelCommon/Model/src/main/java/org/apidb/apicommon/model/userdataset/ISASimpleTypeHandler.java:[3,37] error: package com.fasterxml.jackson.databind does not exist
     [exec] [ERROR] /var/www/TriTrypDB/tritrypdb.crouchk/project_home/EbrcModelCommon/Model/src/main/java/org/apidb/apicommon/model/userdataset/ISASimpleTypeHandler.java:[19,23] error: cannot find symbol
     [exec]   symbol:   class ObjectMapper
     [exec]   location: class ISASimpleTypeHandler
     [exec] [ERROR] /var/www/TriTrypDB/tritrypdb.crouchk/project_home/EbrcModelCommon/Model/src/main/java/org/apidb/apicommon/model/userdataset/ISASimpleTypeHandler.java:[19,56] error: cannot find symbol
     [exec]   symbol:   class ObjectMapper
     [exec]   location: class ISASimpleTypeHandler
     [exec] [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.0:compile (default-compile) on project ebrc-model-common-model: Compilation failure: Compilation failure:
     [exec] [ERROR] /var/www/TriTrypDB/tritrypdb.crouchk/project_home/EbrcModelCommon/Model/src/main/java/org/apidb/apicommon/model/userdataset/ISASimpleTypeHandler.java:[3,37] error: package com.fasterxml.jackson.databind does not exist
     [exec] [ERROR] /var/www/TriTrypDB/tritrypdb.crouchk/project_home/EbrcModelCommon/Model/src/main/java/org/apidb/apicommon/model/userdataset/ISASimpleTypeHandler.java:[19,23] error: cannot find symbol
     [exec] [ERROR] symbol:   class ObjectMapper
     [exec] [ERROR] location: class ISASimpleTypeHandler
     [exec] [ERROR] /var/www/TriTrypDB/tritrypdb.crouchk/project_home/EbrcModelCommon/Model/src/main/java/org/apidb/apicommon/model/userdataset/ISASimpleTypeHandler.java:[19,56] error: cannot find symbol
     [exec] [ERROR] symbol:   class ObjectMapper
     [exec] [ERROR] location: class ISASimpleTypeHandler
     [exec] [ERROR] -> [Help 1]
     [exec] [ERROR] 
     [exec] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
     [exec] [ERROR] Re-run Maven using the -X switch to enable full debug logging.
     [exec] [ERROR] 
     [exec] [ERROR] For more information about the errors and possible solutions, please read the following articles:
     [exec] [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException

  • rebuilder seems to succeed locally in both cases.

Contributor guide

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing the rebuilder-jenkins and wb model builds, then inspect the Maven configuration and EbrcModelCommon/Model/src/main/java/org/apidb/apicommon/model/userdataset/ISASimpleTypeHandler.java. Compare dependency resolution in the local and Jenkins environments, including the missing FgpUtil and Jackson classes. Done means both builds resolve their dependencies and compile successfully.

Written by the indexing model from the issue text.

Assessment

Tech stack
java
Domain
build-system, ci-cd
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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