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clulab / reach

Reach Biomedical Information Extraction
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Error installing REACH with sbt. #774

Closed Crispae closed 1 year ago

Crispae commented 1 year ago

I followed the steps mentioned in documentation:

git clone https://github.com/clulab/reach.git cd reach sbt 'runMain org.clulab.reach.export.server.ApiServer'

Gettiing this error

Screenshot 2022-10-27 122822
kwalcock commented 1 year ago

Can you try that command with double quotes instead of single ones? I don't see that step in the documentation. Can you point me to it? Thanks.

MihaiSurdeanu commented 1 year ago

@kwalcock : thanks for looking into this!

Crispae commented 1 year ago

Can you try that command with double quotes instead of single ones? I don't see that step in the documentation. Can you point me to it? Thanks.

I follow the steps mentioned in this documentation https://indra.readthedocs.io/en/latest/modules/sources/reach/index.html. In this there are 4 steps.

I tried INDRA communicating with a locally running REACH Server, on normal command line. It is giving error while in power shell it is working fine.

While i was trying the INDRA using a REACH JAR through a Python-Java bridge, using the command sbt assembly it is throwing new error

Screenshot 2022-10-28 153813

Although, i can successfully run the reach server with first method on power shell, but it would be better to look into why sbt assembly throwing error.

Thanks

kwalcock commented 1 year ago

Indeed, on Windows the two shells treat single quotes differently. I'm sending in a request to change the documentation to use double quotes so that it works on both.

I'm checking out the assembly error. One possible work-around is to use a version of reach that was available at the time the directions were written. They have you cloning the current version of reach, which may have changed in many ways in the meantime.

kwalcock commented 1 year ago

That's strange. I get a clean assembly. There is code in build.sbt to take care of the conflicts. Can you do a git status to check what you are working on? That code has been in place since 4/9/2022. Thanks.

Crispae commented 1 year ago
Screenshot 2022-10-31 100938

This is up to date with current changes. May be environment variables are causing this issue?

Crispae commented 1 year ago

I added all my environment variables in path

Screenshot 2022-10-31 101239
kwalcock commented 1 year ago

What has changed in build.sbt? To unchange it to match the current master branch, you would need to do git restore build.sbt. It would be nice to know what the change is first: git diff build.sbt.

kwalcock commented 1 year ago

I don't see anything suspicious in the environment variables. We generally use Java 8, but I don't think that's the problem.

Crispae commented 1 year ago

Assembly is working fine now, but still offline reading is not available. I already installed pyjnus.

Screenshot 2022-11-02 111750
kwalcock commented 1 year ago

If you have advice for others on how to get assembly to work, I'm sure they'd appreciate it.

Given those error messages, I wouldn't trust that jnius is installed or configured correctly. Is REACHPATH set, for example? For questions that are more about INDRA than REACH, you might have better luck at https://github.com/sorgerlab/indra/issues.

Crispae commented 1 year ago

Sorry for late response. offline system work fine, in the process_pmc function no need to add offline parameter, In url just use api.local_nxml_url.