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ISA-tools / ISAcreator

ISAcreator is a Java desktop application which allows for the creation and editing of ISA-Tab files. Originally developed by Eamonn Maguire, with further contributions by Alejandra Gonzalez-Beltran, David Johnson and Philippe Rocca-Serra (Uni. of Oxford).
http://www.isa-tools.org
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Missing dependency management section, other dependency issues #271

Closed heuermh closed 7 years ago

heuermh commented 10 years ago

I found some minor issues with dependencies:

$ mvn dependency:analyze
[INFO] Scanning for projects...
...
[INFO] >>> maven-dependency-plugin:2.8:analyze (default-cli) @ ISAcreator >>>
[WARNING] The POM for xalan:xalan:jar:2.4 is missing, no dependency information available
[WARNING] The POM for org.codehaus.jackson:jackson-core-asl:jar:1.7.0-SNAPSHOT-20101126.221009-1 is missing, no dependency information available
[INFO] 
[INFO] --- maven-dependency-plugin:2.8:analyze (default-cli) @ ISAcreator ---
[WARNING] Used undeclared dependencies found:
[WARNING]    net.java.dev.fuse:fuse-core:jar:0.4:compile
[WARNING]    javax.xml.bind:jaxb-api:jar:2.2.3:compile
[WARNING]    javax.jws:jsr181-api:jar:1.0-MR1:compile
[WARNING]    javax.activation:activation:jar:1.1:compile
[WARNING]    xml-apis:xml-apis:jar:1.3.02:compile
[WARNING]    javax.xml.stream:stax-api:jar:1.0-2:compile
[WARNING] Unused declared dependencies found:
[WARNING]    net.java.dev.fuse:fuse-swing:jar:0.4:compile
[WARNING]    javax.xml:jaxrpc-api:jar:1.1:compile
[WARNING]    org.jets3t:com.springsource.org.jets3t:jar:0.8.0:compile
[WARNING]    genomespace:identityServer-messages:jar:1.0:compile
[WARNING]    com.google.zxing:javase:jar:2.1:compile
[WARNING]    genomespace:org.genomespace.jersey-apache-client:jar:1.11:runtime
[WARNING]    com.sun.jersey:jersey-bundle:jar:1.11:compile
[WARNING]    com.sun.jersey:jersey-json:jar:1.11:runtime
[WARNING]    com.amazonaws:aws-java-sdk:jar:1.3.0:compile
[WARNING]    org.glassfish:javax.json:jar:1.0:compile

Some of these are easy to fix with a <dependencyManagement> section but I'm not sure about many of them. What are all the unused declared dependencies for? Why are you using the strange springsource httpclient?

I can't see where the 1.7.0-SNAPSHOT version for jackson-core-asl is coming from either.

heuermh commented 10 years ago

Started to fix these here

https://github.com/heuermh/ISAcreator/tree/dep-mgt

Let me know if you'd like me to submit a pull request.

eamonnmag commented 10 years ago

Thanks Michael,

Yes, submit a pull request. I’ll check that everything still works with the changes and then we can integrate it with the development branch. The dependencies, and in particular the unused dependencies can be a little misleading. The dependency plugin seems to get it wrong on occasions wrt what can be removed. I have gone through multiple rounds of removing dependencies marked by this plugin in the past only to see the software stops working.

Some of the weird dependencies in the tree, like the Spring one are indirect dependencies of the direct dependencies we actually use.

On 13 Mar 2014, at 21:49, Michael L Heuer notifications@github.com wrote:

Started to fix these here

https://github.com/heuermh/ISAcreator/tree/dep-mgt

Let me know if you'd like me to submit a pull request.

— Reply to this email directly or view it on GitHub.

eamonnmag commented 10 years ago

Hi, I had a look at your changes. Can you submit a pull request? I can then try it out.

heuermh commented 7 years ago

Thanks for following up on this, @djcomlab! Sorry I dropped the ball.

djcomlab commented 7 years ago

No worries! :)