OntoPortal docker development environment

This repo contains docker compose and DIP configuration for running and developing OntoPortal stack in 3 different ways:

1. docker-compose.backend_only.yml contains just the backend services required for developing and running API on your local system. To take advantage of that you would need to run docker compose -f docker-compose.backend_only.yml up -d
2. Run API/ncbo_cron and depenencies in docker using DIP
3. Run API/ncbo_cron in docker with mounted source code volumes from your local system. This will allow editing files on your local machine while running code inside docker container.

# clone this repo
git clone https://github.com/bioportal/ontoportal_docker.git

# clone ontologies_linked_data repo which is needed for creating solr configsets
git clone https://github.com/bioportal/ontologies_linked_data.git

# generate configsets:
cd ontologies_linked_data
./test/solr/generate_ncbo_configsets.sh

cd ../ontoportal_docker

# install DIP
bundle install

# export bioportal APIKEY which is needed for importing ontologies from bioportal when provisioning
cp .env.sample .env

# run provisioning via dip 
dip provision

dip provision will:

• clear existing volumes, i.e removing all data
• create 4store kb
• run ncbo_cron rake tasks for creating admin user acccount
• run bin/ncbo_ontology_import script on ncbo_cron container to import STY ontology from bioportal
• run ontology pull script
• process STY ontology

DIP commands:

list available dip commands

dip ls

starts api which you would be able to access on http://localhost:9393

dip api rackup

run ncbo_cron scripts:

dip cron bundle exe bin/<script>

For example, to import new ontology from BioPortal, pull and process it you would run:

dip cron bundle exec bin/ncbo_ontology_import --from-apikey ${BP_APIKEY} -o PO --from https://data.bioontology.org --admin-user admin
dip cron bundle exec bin/ncbo_ontology_pull -o PO
dip cron bundle exec bin/ncbo_ontology_process -o PO

API Development

When developing API it is possible to mount the source code from your local directory inside the container so that it runs your latest changes. To do that you need to make changes to dip.yml file and uncomment the line containing # - docker-compose.dev.yml. docker-compose.dev.yml contains overwrights to the docker-compose.yml which mounts your local directory.

to install gems inside the API container you would need to run dip api bundle install or dip api bundle update to get newer gems

to test your changes you would need to run dip api test

AllegroGraph

Ontoportal has support for running AllegroGraph as triple store backend. To change default 4store triple store to AllgegroGraph you would need to rename dip.override.yml.sample to dip.override.yml