Noctua Testing Deployment

This repository enables the deployment of the noctua editor (which includes minerva, barista, golr and noctua) locally, using self-generated GO-CAM models (in the form of .ttl files).

Note: For production deployment see this readme file

Deploy a version of the Noctua editor (including minerva, barista, golr and noctua locally via docker):

• important files:
  • build_images.yaml
    • builds all the docker images necessary to spin up a local instance.
  • push_images.yaml
    • pushes images to dockerhub if planning on staging to a remote machine.
  • stage.yaml
    • Tasks are executed on staging machine which can be local or remote.
    • The stages directory is created on build.

Deployment artifacts generated:

• blazegraph journal
• Solr Index
• Cloned repositories including:
  • noctua-form, noctua-landing-page, noctua-models, go-site.
• docker-compose and configuration files are generated from templates.

Notes:

• The docker images created by this repository have been successfully tested using:

  • MacOs (10.15.3)
  • Docker (19.03.5)
  • Docker Compose (1.25.2)
  • Ansible (2.10.3), Python (3.8.5), docker (4.3.1)

• Resources:

  • Docker should be given at least 3 CPUs and 8G RAM. (on mac see Docker Preferences | Resources)
  • python 2.7 should work as well.

Prerequisites:

There are two ways to install the requirements necessary for building this application stack:

A. Fast Install using miniconda

To install miniconda go to url

This will install ansible, docker ansible module, docker-compose, and terraform. See dependencies/bare-metal.yml

conda env create --file dependencies/bare-metal.yml
conda activate noctua_app_stack

# when done
conda deactivate

# delete a conda environment:
conda env remove  -n noctua_app_stack

B. Installing ansible and ansible docker plugin using Pip.

The ansible docker plugin is used to buid docker images.

pip install ansible
pip install docker 

After the prerequisits are installed:

1. Building Docker Images:

The playbook build_images.yaml clones minerva, noctua and amigo git repositories and builds corresponding docker images. The default branch used is master.

Note: To change the branch being cloned, see repo_map in docker-vars.yaml

ansible-playbook -e docker_hub_user=xxxx build_images.yaml
docker image list | egrep 'minerva|noctua|golr'

2. Modify vars.yaml to customize the connection information between barista and minerva:

• These can also be set on command line using the -e flag.
  • Barista:
    • uri
    • username
    • password

# on Mac:
export HOST=`ipconfig getifaddr en0`
ansible-playbook -e "host=$HOST" -i "localhost," --connection=local stage.yaml

3. Bring up stack using docker-compose.

Two docker-compose files are staged:

• docker-compose-golr.yaml
  • Uses a lightweight solr image for golr
• docker-compose-amigo.yaml
  • Uses the official geneontology/amigo-standalone for golr

# assuming stage_dir is in current directory and docker-compose-golr.yaml is used:
docker-compose -f stage_dir/docker-compose-golr.yaml up -d

# minerva takes a long time to start up the first time
# Tail minerva logs to see its progress
docker-compose -f stage_dir/docker-compose-golr.yaml logs -f minerva
# Or tail all logs
docker-compose -f stage_dir/docker-compose-golr.yaml logs -f

# When minerva is ready all other services should be up
docker-compose -f stage_dir/docker-compose-golr.yaml ps

4. Access noctua from a browser using http://localhost:{{ noctua_proxy_port }}

• Use http://localhost:8080 if default noctua_proxy_port was used

5. Bring down stack using docker-compose.

docker-compose -f stage_dir/docker-compose-golr.yaml down
# kill works faster ...
docker-compose -f stage_dir/docker-compose-golr.yaml kill
#delete containers:
docker-compose -f stage_dir/docker-compose-golr.yaml rm -f

Staging Remotely

If staging the stack to a remote machine:

1. Create an account on dockerhub if you do not have one.
2. Add a public dockerhub repository named minerva, noctua and golr.
3. set docker_hub_user in docker-vars.yaml or simply
4. use the -e option when using ansible-playbook command.
5. Refer to this document on provisionning an AWS.

Provision machine and stage app stack on the cloud:

• Skip this step if planning on staging locally.
• Refer to this document on provisionning an instance on AWS.

Push images:

• Skip this step if planning on staging locally.

ansible-playbook -e docker_hub_user=xxxx push_images.yaml