Phaedra 2 – Technical Documentation

Documentation: Architecture

Mon, 01 Jan 0001 00:00:00 +0000

Overview

The Phaedra II platform is based on a microservices architecture pattern.

The following list of services are currently implemented in Phaedra II:

These services communicate with each other using an event-based mechanism, Apache Kafka, to perform various tasks:

In addition, each service exposes a public API that is accessible by way of an API Gateway.

Plate Service

Plate service is responsible for managing projects, experiments and plates created in Phaedra II. It is implemented with Spring Boot framework.

Protocol Service

Protocol service is responsible for managing protocols, features and calculations formulas. It is implemented with Spring Boot framework.

Data Capture Service

Data capture service is responsible for importing data measurements and managing/executing capture jobs. It it implemented with JavaScript that runs on a Node.js runtime environment.

Measurement Service

Measurement service is responsible for managing the imported data measurements. It is implemented with Spring Boot framework.

Calculation Service

Calculation service is responsible for executing formula calculations created and defined with Protocol service. It consists of 1 or more calculation engines (this can be scaled) that can execute R code. It is implemented with Spring Boot framework.

Resultdata Service

Resultdata service is responsible for managing the calculated result data coming from the Calculation service. It is implemented with Spring Boot framework.

Metadata Service

Metadata service is responsible for managing metadata like tags and properties for different Phaedra II entity objects like projects, experiments, plates, protocols, plate templates and wells. It is implemented with Spring Boot framework.

Charting Service

Charting service is responsible for building different types of charts for specific input data. The charting service collects the data from other Phaedra II services and combines the collected data in charts that can be displayed. The chart types that are available at the moment of the writing are Scatter, Box-plot and Bar charts for selected plate. It is implemented with Spring Boot framework.

Pipeline Service

Pipeline service manages pipelines and their executions, which perform common tasks in an automated fashion. Typically, these tasks are triggered from the arrival of new measurements in Phaedra, and include plate measurement linking, plate definition linking, protocol calculation, etc.

Phaedra UI

Phaedra UI is an implementation of the Phaedra Web client application. It is implemented with Vue.js web framework. Phaedra UI relies on the REST and GraphQL apis of the Phaedra II back-end services to visualise and update the data.

Documentation: Infrastructure

Mon, 01 Jan 0001 00:00:00 +0000

Overview

Phaedra 2 is deployed as a set of services on a Kubernetes cluster. For a full list of these services, see Architecture.

In addition to these services, a Phaedra 2 cluster also contains:

Script Engine workers, to perform script executions, mainly for the CalculationService and the DataCaptureService
A public Keycloak server, used for authentication and authorization
A public API gateway, to expose the service APIs outside the cluster
A set of Kafka brokers, to manage the Kafka topics that the services use for inter-service communication

From within the cluster, the Phaedra services will need access to:

An object store that persists binary data such as images
A relational database that persists numerical and other data for most of the services

Deployment

Phaedra 2 components are deployed using a set of Kustomize yaml files, which are split up into 2 parts:

A set of generic files which can be reused across deployments,
A set of specific configuration files which are edited to match the environment they will be deployed on.

Helm Chart

A Helm chart is currently under development to assist with the deployment of a Phaedra 2 cluster.

Please check back soon for updates on this topic.

Documentation: Kafka Events

Mon, 01 Jan 0001 00:00:00 +0000

Introduction

Phaedra 2 uses Kafka for inter-service communication as well as some external communication. This document provides a full list of all events Phaedra 2 services provide, and consume.

Notes

All message formats are JSON, unless specified otherwise
Each services has its own group ID, noted in snake-case. E.g. PlateService has group id plate-service
Additional/external consumers MUST NOT use these predefined group IDs.

Calculation Events

Topic: calculations

Event Key	Description	Producer	Consumers
requestPlateCalculation	Request a plate calculation	UI	CalculationService
requestCurveFit	Request a curve fit	CalculationService	CalculationService
notifyCalculationEvent	Progress notification about a running calculation job	CalculationService	*

Plate Events

Topic: plates

Event Key	Description	Producer	Consumers
requestPlateCalculationStatusUpdate	Request a plate status change	CalculationService	PlateService
requestPlateMeasurementLink	Request a plate-measurement link	PipelineService	PlateService
requestPlateDefinitionLink	Request a plate-definition link	PipelineService	PlateService
notifyPlateModified	Notification about a plate modification	PlateService	*
notifyPlateMeasLinked	Notification that a plate has been linked with a measurement	PlateService	*
notifyPlateDefinitionLinked	Notification that a plate has b een linked with a plate definition	PlateService	*

ResultData Events

Topic: resultdata

Event Key	Description	Producer	Consumers
saveResultData	Save calculation result data	CalculationService	ResultDataService
saveResultStats	Save calculation result stats	CalculationService	ResultDataService
resultSetUpdated	Notification that a resultset has been updated	ResultDataService	*
resultDataUpdated	Notification that a resultset’s data has been updated	ResultDataService	*
resultFeatureStatUpdated	Notification that a resultset’s feature stat has been updated	ResultDataService	*

CurveData Events

Topic: curvedata

Event Key	Description	Producer	Consumers
saveCurve	Save a DRC	CalculationService	CurveDataService

DataCapture Events

Topic: datacapture

Event Key	Description	Producer	Consumers
requestCaptureJob	Request a new datacapture job	PipelineService	DataCaptureService
notifyCaptureJobUpdated	Notification about progress of a datacapture job	DataCaptureService	*

Measurement Events

Topic: measurements

Event Key	Description	Producer	Consumers
requestMeasurementSaveWellData	Save measurement’s well data	DataCaptureService	MeasurementService
requestMeasurementSaveSubwellData	Save measurement’s subwell data	DataCaptureService	MeasurementService
notifyNewMeasurement	Notification that a new measurement is available	MeasurementService	*