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EBISPOT / OLS

Ontology Lookup Service from SPOT at EBI
http://www.ebi.ac.uk/ols
Apache License 2.0
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Unable to setup with docker-compose per README: `missing required field: language` #561

Open bpow opened 2 years ago

bpow commented 2 years ago

When following the instructions from the README.md to run using docker-compose (against the docker-compose.yml in 30c29a16c), when running the docker run --net=host -v $(pwd)/config:/config ebispot/ols-config-importer:stable (after a lot of other output, some of which looks like general debug output and some of which includes exceptions), I get the error:

OLS loading complete with the following messages:

No ontologies were updated
---------------------------

The following ontologies failed
--------------------------------
foodon
[doc=shellfish-like product (fully preserved)foodon] missing required field: language; nested exception is org.apache.solr.client.solrj.impl.HttpSolrServer$RemoteSolrException: [doc=shellfish-like product (fully preserved)foodon] missing required field: language

duo
[doc=duo:class:http://purl.obolibrary.org/obo/IAO_0000631] missing required field: language; nested exception is org.apache.solr.client.solrj.impl.HttpSolrServer$RemoteSolrException: [doc=duo:class:http://purl.obolibrary.org/obo/IAO_0000631] missing required field: language

I'm not sure if this is strictly-speaking an issue with OLS (since maybe these ontologies should be providing language fields with each term), but it seems to happen with a lot of ontologies.

My best guess is that maybe this can be traced back to 0230a3c5 changes to various schemata where language is made to be a required field.

Is there some way to set a default language for terms that do not otherwise define them, or to allow language to be a non-required field? Or am I looking in the wrong place to try to address this?

henrietteharmse commented 2 years ago

@bpow Thanks for bringing this to our attention!

jamesamcl commented 2 years ago

Hi, please ignore my previous comment, I made an incorrect assumption!

Please can you try checking out the stable branch? This is an issue with the solr config in dev which I will fix shortly, but in the mean time it should be fine in stable.

bpow commented 2 years ago

Thanks for the ultra-rapid response!

This does indeed work for the stable branch, I hadn't even realized that I had checked out the dev branch. So from my standpoint, I can (and probably should) be working from stable anyway, which certainly reduces the priority of this issue.

KonradHoeffner commented 2 years ago

I just experienced the same problem and didn't realize it as well, it seems that the dev branch is checked out by default on git clone git@github.com:EBISPOT/OLS.git. Could this repository be configured so that stable is checked out by default?