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Docs: OlsDatasetExtractor: CSV not generated #62
Comments
@joeflack4 Thank you for logging the issue in such detail. We will look into it as soon as we can. |
We should probably unify custom deployments in https://github.com/EBISPOT/ontotools-docker These kinds of issues are mostly problems with mount points etc.. @joeflack4 did you try using the docker compose setup? |
@matentzn https://github.com/EBISPOT/ontotools-docker addresses the complete Ontology Tools stack. However, not everyone wants to install the complete stack. |
I agree, I was more thinking of moving the docs there, and using docker compose even for the individual services; it would just be less support work in the future, bypassing typical mistakes in Following readme docs. |
Hey guys. Thanks for looking into this! @matentzn Yep, I was just following the documentation. It asks to do |
It seems the paths are wrong in the supplied config.ini.
should be
I will get this updated. As @matentzn says we should probably in the long term unify all of these separate Docker instructions into the ontotools-docker repository, which is more up to date but currently only deploys the whole stack. |
Makes sense that that is the issue! For now, Nico has instructed me to use the full ontotools stack for my purposes, as it should serve my purposes just fine. But thanks for looking into this. |
Description
I'm trying to learn about OXO and I have set up a local instance using docker. I'm following the docs, and I want to create
datasets.csv
and follow the rest of the documentation walkthrough. But either (a) the file is not being generated, or (b) I can't find it.This is the command that I'm running:
Expected behavior
After running command, a CSV file should be created within the docker container
oxo_oxo-web-1
at the path/mnt/neo4j/datasources.csv
.Actual behavior
After running the command, no such file is found at
/mnt/neo4j/datasources.csv
is not found in that container. The/mnt
directory exists, but/mnt/neo4j/
directory does not exist.Additional information
I simply followed the documentation (https://github.com/EBISPOT/OXO) prior to running this command. I had done the following:
Neo4j and the other containers are up and running and appear to be healthy.
My
config.ini
(I didn't create this; it was already there)Command output
Examining
oxo_oxo-web-1
to find CSVThe text was updated successfully, but these errors were encountered: