From the error you've posted looks like there was something running on port 8080 already and you would need to kill that process before running the docker. For dataload part you would need to see the logs of docker to see exactly whats happening? Usually dataload fails if your ontology is not in the correct format and logs specify what exactly is failing.

I would suggest just to run your local ontologies you can follow the steps starting from here:

https://github.com/EBISPOT/ols4?tab=readme-ov-file#development-running-ols4-using-docker and use the following command to run everything up:

docker compose up --force-recreate --build --always-recreate-deps --attach-dependencies ols4-solr ols4-neo4j ols4-backend ols4-frontend

you don't need to copy your ontologies to testcases folder until unless you want to run our testcases on them

Ok. I will try your explanation and give you an feedback. Thanks @haideriqbal

@erfelipe Please can you post your config myontology.json? Using the testcases folder to put your ontology is what I do because it's mounted inside Docker, but you need to set the ontology_purl appropriately to reflect this.

So if you put myontology.owl in testcases the ontology_purl would be ./testcases/myontology.owl

@erfelipe Please can you post your config myontology.json? Using the testcases folder to put your ontology is what I do because it's mounted inside Docker, but you need to set the ontology_purl appropriately to reflect this.

Hi @jamesamcl thanks for your attention. In fact, I'm just copy the .json from efo.json and, change the purl link:

{
"ontologies": [
{
"id": "myontology",
"preferredPrefix": "myontology",
"title": "Teste local",
"uri": "http://www.ebi.ac.uk/efo",
"description": "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for external projects such as the NHGRI GWAS catalogue. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by many groups at the EBI and as the core ontology for OpenTargets.org",
"homepage": "http://www.ebi.ac.uk/efo",
"mailing_list": "[email protected]",
"definition_property": [
"http://purl.obolibrary.org/obo/IAO_0000115",
"http://www.ebi.ac.uk/efo/definition"
],
"synonym_property": [
"http://www.ebi.ac.uk/efo/alternative_term",
"http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"
],
"hierarchical_property": [
"http://purl.obolibrary.org/obo/BFO_0000050",
"http://purl.obolibrary.org/obo/RO_0002202"
],
"hidden_property": [
"http://www.ebi.ac.uk/efo/has_flag"
],
"base_uri": [
"http://www.ebi.ac.uk/efo/EFO_"
],
"reasoner": "OWL2",
"oboSlims": false,
"ontology_purl": "file:///opt/dataload/testcases/myontology.rdf"
}
]
}

So if you put myontology.owl in testcases the ontology_purl would be ./testcases/myontology.owl

Yep. I put the file in:

and try rdf version to.

And my last advances, I change the backend port from 8080 (http default port(?)) to 8082, and the services are working now:

But! The frontend not working yet:

But I'm will use the docker command sugest by @haideriqbal above.

I have the same problem. After exporting the docker logs I found:
"The "JAVA_OPTS" variable is not set. Defaulting to a blank string.
error while interpolating services.ols4-dataload.volumes.[]: required variable OLS4_CONFIG is missing a value: OLS4 dataload requires a config file"
The first problem (JAVA_OPTS) I've already solved. The second problem is strange because the docker-compose.yml seems to be correct.

@NCOR-BR i see its complaining about OLS4_CONFIG in your error. You would need to set OLS4_CONFIG to the json file containing your ontology config which you are trying to index. Please let us know if you still face the error after setting this variable.

unless

@haideriqbal this method works now! #development-running-ols4-using-docker
I'll try to load the local ontology with copy efo.json method.

closing this for now! feel free to reopen if you still have issues running OLS locally :)

@NCOR-BR whats the issue you are facing? from your previous comment it appears you were not specifying the OLS4_CONFIG variable correctly... did you try after initialising the variable correctly?

Hi @NCOR-BR i can't see the screen shot you attached. Looks like you replied by email and github can't seem to process the attached screenshot correctly

Thank you @haideriqbal .

@NCOR-BR can you share your docker logs? or let me know how you are running docker command? did you set OLS4_CONFIG variable before running the docker command?

Hi @haideriqbal I had a momentary breakthrough in getting the stack to work with efo.json
But the environment is not stable, there are rare moments when it works and most of the time it doesn't.
So I can't get it to work with a local ontology either.
Would it be possible, at some point, for us to meet via google meet to try to make the environment work locally? I'm in the GMT -3 time zone

Hi @erfelipe today might be short notice for you but would 2 pm UK time work for you tomorrow or Wednesday? I believe it would be 11 AM for you. Let me know if that works and we can have a chat :)

Hi @erfelipe today might be short notice for you but would 2 pm UK time work for you tomorrow or Wednesday? I believe it would be 11 AM for you. Let me know if that works and we can have a chat :)

Hi @haideriqbal, tomorrow will be great. Thanks for help! If you agree, can we meet in this room? I'm just want to share my screen to help in a possible solution. https://meet.google.com/sez-ropu-kzf
Best,

Sounds good! talk to you tomorrow :)

it might be a long shot but are you guys free now? We can start the call now? @erfelipe @NCOR-BR

it might be a long shot but are you guys free now? We can start the call now? @erfelipe @NCOR-BR

Yep @haideriqbal , we can. Please. https://meet.google.com/sez-ropu-kzf

cool joining now

Thank you very much for your support @haideriqbal !
We couldn't have done it without your knowledge.
Best wishes,