birm / DynamicServices

DynamicServices

Overview

DynamicServices is a suit of web-services to run containerized algorithms on large bio-medical image data. It can used to run the algorithm on a region of interest (ROI) tile or on the whole image.

Architecture assumptions

DynamicServices pulls an image ROI from an image server based on JSON orders. The following describes the workflow and underground architecture assumptions.

Dependencies:

• yum install curl-devel
• yum install jsoncpp-devel or use http://ask.xmodulo.com/fix-fatal-error-jsoncpp.html
• Install redox: https://github.com/hmartiro/redox

Build:

• mkdir obj
• make

Config file

Refer to sample_config.json

Deployment

Dependencies

DynamicServices requires following tools installed and setup

Camicroscope (Dependency)

• Install all components of camicroscope from (https://github.com/camicroscope/Distro)
  • In config.json update annotations.server and annotations.redis to IP address of Loader container.
  • Set the API key in api_key_file as the API key of Bindaas(from Data container)
• Install Kue(https://github.com/Automattic/kue) and redis on the host machine.
  • In config.json updated orders.kue and orders.redis with host and port of kue and redis.
  • Configure camicroscope viewer in /Configuration/api/config.php set ordering service as this Kue.

To run use: LD_LIBRARY_PATH=/usr/local/lib64/ ./dynamicservices config.json To deploy using nohup: LD_LIBRARY_PATH=/usr/local/lib64/ nohup ./dynamicservices config.json > dynamicservices.log &

Deployment inside an algorithm docker container

To deploy inside an algorithm docker container. Take alogorithm image as base and use the given Dockerfile to build a new image with DynamicServices installed inside it. The given Dockerfile uses sbubmi/test_segmentation:latest as the base image.

• Build the docker image docker build -t dynamic_services_segmentation .
• Create a new directory (let's call it configs)
• Update and place config.json & api_key.json inside configs
• Run the container using docker run --net="host" -itd -v <path_to_configs>:/tmp/DynamicServices/configs dynamic_services_segmentation
• Make sure that all the entries in config.json are updated. "api_key_file" should have the complete path inside the docker container.
• To check the log of DynamicServices use tail -f configs/dynamicservices.log

Algorithm execution pipeline

As soon as DynamicServices gets a notification about a new job on orders' Redis, it fetces the order from Kue for that job id. The order json is used to extract the case_id, subject_id and ROI information along with other algorithm parameters. DynamicServices then fetches the ROI using an image service and runs the algorithm on the tile with all the paramaters. The resultant zip file is then posted to the annotations server.