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wikipathways / cytoscape-wikipathways-app

WikiPathways app for Cytoscape to open and access pathways from WikiPathways
Apache License 2.0
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jdom issues for 3.3.10 #125

Closed DeniseSl22 closed 2 years ago

DeniseSl22 commented 2 years ago

Hi @yihangx , I reported these issues first in Slack but @AlexanderPico mentioned to me you're not in that channel. I recently checked out the code in this repo to work on #123 myself, however I could not compile the app from the command line (mvn install resulted in errors). After some digging, I found that several maven artifacts required a higher version in the pom.xml, then which were added in the localSettings.sh file (leading to this PR #124 ). But, the jdom artifact is still causing me issues.

  1. The pom.xml requires version 2.0.1 for com.springsource.org.jdom-2.0.1.jar
  2. Several other users have reported issues with the jdom artifact version 2.0.1 not being downloadable: https://groups.google.com/a/opencast.org/g/dev/c/J7SU8zsM5SA ; I recently cleaned out my .m2 folder, so don't have an old version of this artifact lying about unfortunately
  3. It seem that this specific jdom maven library is not maintained anymore, so that might need to be replaced (in the long run) for the WikiPathways-Cytoscape app.
  4. According to the jdom website, there is a 2.0.6.1 version: http://www.jdom.org/ , And the jdom github repo seems to be maintained: https://github.com/hunterhacker/jdom/ . The artifact is now called jdom2, but should still be an XML parser.
  5. I'm trying to get this maven artifact (https://mvnrepository.com/artifact/org.jdom/jdom2/2.0.6.1) in my localSettings, however I have been unsuccessful for the time being: 
    mvn install:install-file -Dfile=localRepo/org.jdom-2.0.6.1.jar -DgroupId=org.jdom -DartifactId=jdom2 -Dversion=2.0.6.1 -Dpackaging=jar

    The error might be cause by the 'path-to-file' not being correct, or another issue which I cannot see right now, so any help would be much appreciated @yihangx (and also @mkutmon :smile: )

DeniseSl22 commented 2 years ago

I can now compile the code and create an App, however I believe the XML parser library is not working correctly. Top network view: app 3.3.10 from the GitHub repo, bottom network view: build I created from code locally (with jdom 2.6.0.1): image

DeniseSl22 commented 2 years ago

@yihangx ; I'm sending a new PR in stead of #126 ; this includes a jdom2 library (which is not compatible with PathVisio 3.x at the moment). I will discuss with @mkutmon and other PV developers, if jdom2 will be used for PV4 (or not).

DeniseSl22 commented 2 years ago

127

DeniseSl22 commented 2 years ago

jdom issues have been resolved for current release.