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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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Using docker-compose in Windows 10 #467

Closed b-fran closed 3 years ago

b-fran commented 3 years ago

I am trying to setup OLS via docker using Windows 10 (version 20H2) and receiving the following error when entering the command.

Command: docker run --net=host -v $(pwd)/config:/config ebispot/ols-config-importer:stable

Error Message: 2021-03-08 10:52:59,804 INFO main YamlLoader.logStarting - Starting YamlLoader v3.2.1-SNAPSHOT on docker-desktop with PID 1 (/opt/ols-config-importer.jar started by root in /) 2021-03-08 10:52:59,823 DEBUG main YamlLoader.logStarting - Running with Spring Boot v1.3.8.RELEASE, Spring v4.2.8.RELEASE 2021-03-08 10:52:59,823 INFO main YamlLoader.logStartupProfileInfo - No active profile set, falling back to default profiles: default 2021-03-08 10:53:04,797 INFO main YamlLoader$$EnhancerBySpringCGLIB$$2efc129c.run - OBO Ontologies will be imported using config at 'file:///config/obo-config.yaml' 2021-03-08 10:53:04,798 WARN main YamlLoader$$EnhancerBySpringCGLIB$$2efc129c.run - Resource 'URL [file:/config/obo-config.yaml]' could not be found and will therefore not be loaded 2021-03-08 10:53:04,798 INFO main YamlLoader$$EnhancerBySpringCGLIB$$2efc129c.run - Ontologies will be imported using config at 'file:///config/ols-config.yaml' 2021-03-08 10:53:04,799 WARN main YamlLoader$$EnhancerBySpringCGLIB$$2efc129c.run - Resource 'URL [file:/config/ols-config.yaml]' could not be found and will not be loaded 2021-03-08 10:53:04,801 INFO main YamlLoader.logStarted - Started YamlLoader in 6.407 seconds (JVM running for 8.33)

I am using: GNU bash, version 4.4.23(1) I have not changed anything inside the repository. I copied the config files from a colleague. These config files work under the same configuration with ubuntu. Has the setup of OLS been confirmed using docker with a windows 10 system?

Also, the OLS webpage will load, however the indexing fails.

Any information on this topic would be greatly appreciated. Thank you.

matentzn commented 3 years ago

Hello @b-fran

Indeed, these commands are rarely tested on windows; but in my experience you can make them work.

I will assume that in the same directory as you run the command, there is a subdirectory config containing ols-config.yaml.

My guess is that -v $(pwd)/config:/config fails;

Some potential things to check:

  1. docker has access to your directory (docker settings)
  2. $(pwd) somehow does not work on windows? this is supposed to give you an absolute path to the current directory.. Play with that a bit, and perhaps provide the full absolute path here instead.
  3. Never used GNU bash on windows, but maybe this ($(pwd)/config) is not the right syntax for the path (\)?
rpandey19 commented 3 years ago

It worked for me when provided the full path for the config folder. However I have not been able to load a owl file from my local machine (custom ontology). Have you tried that? If it worked for you please let me know

b-fran commented 3 years ago

Thanks for the insight. I gave up using bash and just replaced $(pwd) with %cd%. Unfortunately, I have not dealt with local owl files.