shahmanash
commented
5 years ago The biocachebackend is the image for running the biocache-cli tool. It is not a service and so when you start the services with docker-compose up it exits without error. It gets instantiated but exits as it does not have any running process.
To run the biocache CLI , say to ingest the data, you would run an instance of the service like
docker-compose run --rm biocachebackend ash
Note that in the above command , the service name is biocachebackend , which is as defined in the docker-compose.yml file, the option --rm removes the container once you exit from it and ash is the command line shell (equivalent to bash), as the docker image is based on Alpine Linux.
The above command would provide you access to the shell where you can execute the biocache command.
The image doesn't contain the necessary biocache-config.properties files , so a configured property file needs to mounted into the container https://github.com/bioatlas/ala-docker/blob/beta/docker-compose.yml#L117
Also, the biocache CLI requires the lucene nameindex while ingesting the occurrence data, so the necessary volume containing the lucene index needs to be mounted into this path /data/lucene/namematching as done here https://github.com/bioatlas/ala-docker/blob/beta/docker-compose.yml#L114
The configuration of biocache CLI for different components like cassandra database, SOLR and other services can be done from the config property file.
mskyttner
IuriGarcia
In the first place, thank you all for this work. It's really a big thing. I'm having some problem trying to execute in my dev station the biocache components. Biocachebackend exits code 0 and no logs is displayed. I have a docker-compose.yml to build and run Cassandra, Solr, and biocaches images, already downloaded the .war and .zips but don't know what is happening in biocachebackend.