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phyloref / jphyloref

MIT License
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Quick fix for the context download issue #107

Open gaurav opened 6 months ago

gaurav commented 6 months ago

This PR provides a quick fix for the context download issue, but storing the two most recent contexts in the JAR file so that they can used even without an internet connection. We will need the internet to download the Phyloref, CDAO and TCAN ontologies, but those can be stored in an ontologies/ directory, so in theory this gets us to the point where JPhyloRef can be run without an internet connection. However, this has not yet been tested on HiPerGaTor as we are in the process of moving from one server to another there.

WIP: Hopefully this will not be needed at all if I can get the more comprehensive solution in PR #106 to work. But I wanted to hold onto this code if it is needed as an intermediate solution.

hlapp commented 6 months ago

@gaurav did you mean to assign this to me for review when you changed it to ready for review?

gaurav commented 6 months ago

@hlapp Sorry, I should have been clearer: nope, this PR doesn't need to be reviewed yet. I'm hoping that once we're properly set up on HiPerGator again I can install a more recent version of Java and then get the more comprehensive solution in PR https://github.com/phyloref/jphyloref/pull/106 working. In that case, I'll close this issue. But if that doesn't work and I need to a temporary fix just to get Klados working again sooner, I'll use the code from this PR and submit it to you for review then.