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clulab / reach

Reach Biomedical Information Extraction
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Uncompressed bioresources kb files #744

Closed enoriega closed 3 years ago

enoriega commented 3 years ago

Expanded the gz files and modified the code to work this way. After this change, editing the KBs should be easier

MihaiSurdeanu commented 3 years ago

LGTM!

enoriega commented 3 years ago

Thanks for those missing updates @bgyori

kwalcock commented 3 years ago

Thanks, @enoriega. I hadn't intended to create a task for someone else, but if it's already finished, I'll just sit back and be grateful.

enoriega commented 3 years ago

Serendipity :)

kwalcock commented 3 years ago

I'm not sure the testing completed. It looks like the network tests might be interfering with each other. Ports are reported already in use and that kind of thing. I will try to get the green badge out of it.

enoriega commented 3 years ago

Unfortunately I already merged. I'll give priority on fixing it to do a new pull request

kwalcock commented 3 years ago

I was just going to resubmit the test to Jenkins when it isn't as busy. It's doing processors and eidos tests at the same time. Some of them want ports as well. I wonder if there is a way to notify Jenkins that certain system resources are required for a test so that it doesn't run two at a time that contend for them.

enoriega commented 3 years ago

I ran them on my computer, these are the test suits that need some work:

TestAdHocIMKBs
TestProteinResolutions
TestOverrides

I started to fixing them now