Closed bgyori closed 2 years ago
As a minor side-issue, note how in the logging message in the case I was running this from the reach repo folder, it says
22:41:45.838 [main] INFO o.c.p.bionlp.BioNLPProcessor -
Done. Read org.clulab.processors.bionlp.ner.ReachSingleStandardKbSource$$anon$1@7e27b77a.lineCount
lines from bio_process.tsv
so the line count is not shown as intended.
At runtime (except maybe during testing, so testtime), nothing should refer to the directory structure of the source code. So, I think you've found a problem. I'm looking into what to do about it.
Thank you Keith!
On Tue, Aug 24, 2021 at 8:14 AM Keith Alcock @.***> wrote:
At runtime (except maybe during testing, so testtime), nothing should refer to the directory structure of the source code. So, I think you've found a problem. I'm looking into what to do about it.
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The logging statement does have a bug as well, but it is readily fixed.
This is being addressed with #760.
Thank you! I have now been using this and everything seems to work.
I am trying to create a fat JAR of the latest Reach using
sbt assembly
and then using it to process text with the ApiRuler's annotate_text method (this has been our standard integration approach, no change here). If I do this exactly from the Reach repo's main folder, it works, i.e. it is able to load all the resource files and return a resultHowever, if I move to any other folder, loading the resource files fails when attempting to load the first resource file:
-> process exits here.
So I suspect the issue is with the path by which the bioresources are referred to in the context of a JAR file. In particular, I am wondering if this line: https://github.com/clulab/reach/blob/master/bioresources/src/main/resources/application.conf#L1 could be responsible for the issue.
Any help would be appreciated!