Development Guide

• Introduction
  • Terminology
  • List of Technologies
• Developing a Processing-Container
  • The processing-container.json File
    • ProcessingContainer
    • TaskTemplate
    • TaskTemplateEnv
    • IOMount
    • ScaleRule
    • Resources
    • Example
  • The Task API Command Line Interface (CLI)
    • Installation
    • Validating a processing-container.json File
    • Running a Task Locally with Docker
  • Input and output channel data structure convention
    • Output channel
    • Item identifiers in input and output channels
    • Item identifiers when combining multiple inputs items into one output item
  • Best practice for developing a processing-container
    • Example processing-container
  • Using a processing-container in an Airflow DAG
    • Minimal DAG Example
    • Passing data between operators
    • Passing user input to a task-run
    • Container images from an external registry
  • Migrating from KaapanaBaseOperator
    • Legacy Data Mounting (KaapanaBaseOperator)
    • Migrated Data Mounting (KaapanaTaskOperator)
    • Features not yet supported by the KaapanaTaskOperator
• Developing Workflow Extensions
  • Introduction
  • Step 1: Helm Chart Configuration
  • Step 2: Airflow Configuration
  • Step 3: Code for Data Processing
  • Step 4: Building All Containers of the Extension
  • Step 5: Putting Containers in a Running Platform
  • Step 6: Packaging the Helm Chart
  • Step 7: Putting the Chart in a Running Platform
  • Step 8: Installing and Running the Workflow
  • Step 9: Debugging the Workflow
  • Step 10: Advanced Options for Workflow Extensions
• Developing Applications
  • Introduction
  • Deploy a Flask Application on the platform
    • Step 1: Create and run our Flask app locally
    • Step 2: Create a Docker container with the Flask application
    • Step 3: Write the Kubernetes deployments
    • Step 4: Write a helm chart
    • Step 5: Provide the application as an extension
    • Step 6: Advanced Options for Applications
• Developing a Workflow Extension with a Custom Registry
  • Prerequisites
  • Provide processing-container images
    • Build and Push the Processing-Container Image
    • Launch a New Registry extension with scope Project-Secret
  • Prepraing the extension-chart
    • Prepare the Airflow Code and Build the DAG Installer Image
    • Prepare, Package, and Upload the Workflow Helm Chart
    • Launch a New Registry Extension with scope Service-Secret
• Uploading a Workflow Extension via the Extensions View
  • Prerequisites
  • Build Processing Containers
  • Prepare the Airflow Code and Build the DAG Installer Image
  • Save and Upload Docker Images
  • Prepare, Package, and Upload the Helm Chart
• Upgrading an Extension in the Kaapana Extension Collection
  • Prerequisites
  • Update the Helm Chart
  • Package the Helm Chart and Add It to the Extension Collection
  • Build and Push the Updated Extension Collection Image
  • Update the Extension Collection in Kaapana
• Existing Operators
  • Base operators
    • KaapanaBaseOperator
    • KaapanaPythonBaseOperator
    • KaapanaApplicationOperator
  • DICOM operators
    • Bin2DcmOperator
    • Dcm2MetaJsonConverter
    • DcmConverterOperator
    • DcmModifyOperator
    • DcmQueryOperator
    • DcmSeg2ItkOperator
    • Json2DcmSROperator
    • LocalDcm2JsonOperator
    • LocalDcmAnonymizerOperator
    • Mask2nifitiOperator
    • Pdf2DcmOperator
    • DcmValidatorOperator
  • File-based operators
    • LocalConcatJsonOperator
    • ZipUnzipOperator
  • NIFTI and nrrd operators
    • MergeMasksOperator
    • Itk2DcmOperator
    • Itk2DcmSegOperator
    • PyRadiomicsOperator
    • ResampleOperator
    • ConnectedComponentAnalysisOperator
  • Opensearch operators
    • DeleteFromMetaOperator
    • Json2MetaOperator
  • Service operators
    • GenerateThumbnailOperator
    • LocalAddToDatasetOperator
    • LocalAutoTriggerOperator
    • LocalCleanUpExpiredWorkflowDataOperator
    • LocalCtpQuarantineCheckOperator
    • LocalEmailSendOperator
    • LocalServiceSyncDagsDbOperator
  • Store operators (MinIO and PACS)
    • DcmSendOperator
    • DeleteFromPacsOperator
    • LocalDicomSendOperator
    • GetRefSeriesOperator
    • MinioOperator
    • LocalTaggingOperator
  • Project operators
    • LocalAssignDataToProjectOperator
  • Uncategorized operators
    • LocalDagTriggerOperator
    • ClearValidationResultOperator
    • JupyterlabReportingOperator
    • TrainTestSplitOperator
  • Workflow management operators
    • GetInputOperator
    • LocalWorkflowCleanerOperator
• Kaapana Services
  • Notification Service
    • Notification Model
• Advanced: How Kaapana uses Helm
  • How Kaapana uses Helm charts
  • Useful Commands
  • Chart Dependency Tree
• Best Practices
  • Writing Dockerfile
    • Base images
    • Labels
    • Package managers: apt, apk
    • Installation of python packages: pip install
    • Utilizing Multi-Stage Dockerfiles
    • General Guidelines
    • Example of a Kaapana Dockerfile for a workflow
  • Code Formatting
    • Black Code Formatter
    • Installation
    • Usage
    • Pre-commit hook