patrickkwang/robokop-rabbitmq repository overview

⁠ROBOKOP

ROBOKOP is a tool for reasoning over structured biomedical knowledge databases as part of the NCATS translator and reasoner programs. The ROBOKOP system consists of a web based user interface, an API server, and several worker servers. The code is separated into three separate repositories.

• robokop - https://github.com/ncats-Gamma/robokop⁠ - UI and entry point
• robokop-interfaces - https://github.com/ncats-Gamma/robokop-interfaces⁠ - Knowledge source interfaces and knowledge graph building
• robokop-rank - https://github.com/ncats-Gamma/robokop-rank⁠ - Find and ranks subgraphs based on a supplied question

This repository is the main repository for the user interface and common storage modules. It is also used f or issues associated with the entire stack.

⁠Example Installation

See an instance at http://robokop.renci.org⁠

• http://robokop.renci.org⁠ - The Robokop user interface
• http://robokop.renci.org/api⁠ - The Robokop user interface API
• http://robokop.renci.org:6010/apidocs⁠ - The robokop-interfaces API
• http://robokop.renci.org:6011/apidocs⁠ - The robokop-rank API
• http://robokop.renci.org:7474⁠ - NEO4j http interface
• bolt://robokop.renci.org:7687 - NEO4j bolt interface
• http://robokop.renci.org:5555⁠ - UI to see the worker queues for the UI - Requires authentication
• http://robokop.renci.org:5556⁠ - UI to see the worker queues for the builder - Requires authentication
• http://robokop.renci.org:5557⁠ - UI to see the worker queues for the ranker - Requires authentication

⁠Setup Instructions

⁠Installation

ROBOKOP uses several docker containers managed through docker-compose. Both should be installed and configured properly.

⁠Source Code Structure

We create a robokop directory and clone three repos into it: robokop, robokop-interfaces, and robokop-rank.

In the root directory, we create shared and logs diretories.

Into the shared directory we copy a "robokop.env" file with environment variables. A template is included below.

This is our directory structure:

robokop
├── logs
├── robokop
├── robokop-interfaces
├── robokop-rank
└── shared
    └── robokop.env

⁠Environment settings

robokop.env looks like this:

#################### Locations of things ####################
NEO4J_HTTP_PORT=7474
NEO4J_BOLT_PORT=7687

REDIS_PORT=6379

POSTGRES_PORT=5432
POSTGRES_USER=murphy
POSTGRES_DB=robokop

ROBOKOP_HOST=127.0.0.1
RANKER_HOST=127.0.0.1
BUILDER_HOST=127.0.0.1
MANAGER_PORT=80
BUILDER_PORT=6010
RANKER_PORT=6011

# Services can be REACHED at these addresses. They should generally publish to 0.0.0.0.
NEO4J_HOST=127.0.0.1
REDIS_HOST=127.0.0.1
POSTGRES_HOST=127.0.0.1
FLOWER_HOST=127.0.0.1
SUPERVISOR_HOST=127.0.0.1

GREENT_REDIS_DB=0
MANAGER_REDIS_DB=1
BUILDER_REDIS_DB=2
RANKER_REDIS_DB=3

FLOWER_ADDRESS=0.0.0.0
MANAGER_FLOWER_PORT=5555
BUILDER_FLOWER_PORT=5556
RANKER_FLOWER_PORT=5557
FLOWER_USER=admin

MANAGER_SUPERVISOR_PORT=9001
BUILDER_SUPERVISOR_PORT=9002
RANKER_SUPERVISOR_PORT=9003
SUPERVISOR_USER=admin

COMPOSE_PROJECT_NAME=robokop
#############################################################

####################### Secret stuff ########################
ADMIN_EMAIL=<[email protected]>
ADMIN_PASSWORD=----------------------------------

NEO4J_PASSWORD=----------------------------------

FLOWER_PASSWORD=----------------------------------

SUPERVISOR_PASSWORD=----------------------------------

ROBOKOP_SECRET_KEY=----------------------------------
ROBOKOP_SECURITY_PASSWORD_SALT=----------------------------------

ROBOKOP_MAIL_SERVER=----------------------------------
ROBOKOP_MAIL_USERNAME=----------------------------------
ROBOKOP_MAIL_PASSWORD=----------------------------------
ROBOKOP_DEFAULT_MAIL_SENDER=----------------------------------
ROBOKOP_SECURITY_EMAIL_SENDER=----------------------------------
#############################################################

You'll need to supply values for the secret things at the end.

⁠Build

Environemnts are configured in several docker containers managed by docker-compose.

• robokop/robokop/helpers - Common storage databases - Redis, Neo4j, Postgres
• robokop/robokop/deploy - UI API and web server
• robokop/robokop-interfaces/deploy - robokop-interfaces API server
• robokop/robokop-rank/deploy - robokop-interfaces API server

First we must build the containers. For each of robokop, robokop-interfaces, and robokop-rank,

• cd into /deploy
• docker-compose build

When those are all complete, we must start the helpers (storage containers).

• cd robokop/robokop/helpers
• docker-compose up

Then for each of robokop, robokop-interfaces, and robokop-rank,

• cd into /deploy
• docker-compose up

With all containers started you can now monitor each component using the urls below.

⁠Interfaces

• http://127.0.0.1⁠ - The Robokop user interface
• http://127.0.0.1/api/⁠ - The Robokop user interface API
• http://127.0.0.1:6010/apidocs⁠ - The robokop-interfaces API
• http://127.0.0.1:6011/apidocs⁠ - The robokop-rank API
• http://127.0.0.1:7474⁠ - NEO4j http interface
• bolt://127.0.0.1:7687 - NEO4j bolt interface
• http://127.0.0.1:5555⁠ - UI to see the queues for the UI - Requires authentication
• http://127.0.0.1:5556⁠ - UI to see the queues for the builder - Requires authentication
• http://127.0.0.1:5557⁠ - UI to see the queues for the ranker - Requires authentication