Overview

This document outlines the high-level structure of the CaeNDR repository, with notes on external data sources.

The codebase primarily consists of two types of components, contained in the src directory. These form almost all of the source code for the project - 99% of the work happens in this directory.

Name	Path	Description	Code	Wiki
Modules	src/modules	Individual applications that may be run separately. Many different modules across the project.	link	link
Package	src/pkg/caendr	A library of shared code used by all modules. One single package shared across the project.	link	link

In addition, there are a few other top-level folders that might be of interest:

• env - Environment files for configuring variables, secrets, etc.
• tf - Terraform configuration, for deployment. (Might be deprecated?)

Service Modules

Directories containing source code, Dockerfiles, Makefiles, etc. for each service module ("module"). Modules are individual applications that may be run separately, either constantly in the background or on-demand.

Site Module(s)

These modules are used to build the user-facing CaeNDR website. NOTE that only site-v2 should be used!

Name	Path	Description	Code	Wiki
Site v1 (DEPRECATED)	src/modules/site	The original codebase for the old "CeNDR" site (not a typo).	link	link
Site v2 (Current)	src/modules/site-v2	The codebase for the current CaeNDR site, as of early 2025.	link	link

Tool Modules

These modules are used to build & run the site tools, i.e. the lab-produced tool codebases that perform specific data operations.

Name	Path	Description	Code	Wiki
Database Operations	src/modules/db_operations	The parent module that runs all tools.	link	link
Heritability Proxy	src/modules/heritability_proxy	Code to pull, build, & run the Heritability tool Docker image.	link	link
Indel Primer	src/modules/indel_primer	Source code for the Pairwise Indel Finder tool.	link	link
Nemascan Proxy	src/modules/nemascan-proxy	Code to pull, build, & run the NemaScan tool Docker image.	link	link

Note that the Heritability and Nemascan tools are built & run entirely from separate repositories, whereas the Indel Finder tool is defined in this repository.

Background Modules

These are miscellaneous modules that run in the background of the site. They are typically specialized for a single task or set of tasks, and are run as needed.

Name	Path	Description	Code	Wiki
API Pipeline Tasks	src/modules/api/pipeline-task	API that handles requests for jobs - scheduling marking as complete, etc.	link	link
Image Thumbnail Generator	src/modules/img_thumb_gen	Automatically generates thumbnail-size images on strain picture file uploads.	link	link
Maintenance	src/modules/maintenance	Fallback "maintenance" page if site is down (?)	link	link

Package

The CaeNDR python package which contains, among other things:

• libraries for accessing cloud services
• models defining CaeNDR internal data
• utility functions that are commonly reused
• service libraries for interacting with CaeNDR data

The service modules (described above) include the CaeNDR package in addition to their requirements.txt file.