Repo Doctor

The Repo Doctor is a diagnostic tool that analyzes your Arraylake repositories to ensure they are compatible with Flux services. It checks for CF convention compliance and helps you fix any issues that would prevent your data from being served through Flux protocols.

Overview

Before enabling Flux services on a repository, the Repo Doctor validates that your data meets the requirements for each protocol. It checks for proper coordinate system metadata, dimension attributes, and data structure compliance with CF conventions.

Running Repo Doctor

The Repo Doctor can be run via the Arraylake CLI to diagnose and optionally fix CF compliance issues in your datasets.

Diagnose Only

arraylake repo doctor {org}/{repo}

This will analyze your repository and report any CF compliance issues without making changes.

Diagnose and Fix

arraylake repo doctor {org}/{repo} --treat

This will diagnose issues and prompt you to fix them automatically.

Specific Group

arraylake repo doctor {org}/{repo} --group /path/to/group

Target a specific group within your Zarr hierarchy.

Checking Service Compatibility

While the Repo Doctor doesn't have a flag to check for a single service, it always reports which services your data is compatible with. Look for the compatibility section in the output:

  ✅ edr
  ✅ tiles
  ✅ wms
  ❌ dap2

To check if your data is ready for a specific service like WMS:

1. Run arraylake repo doctor {org}/{repo} --group /your/group
2. Look for "wms" in the "Compatible services" list
3. If WMS is incompatible, check the missing attributes - WMS requires latitude and longitude standard names

Compatibility Checks

Service Requirements

The Repo Doctor checks compatibility with each Flux service:

Service	Required CF Attributes	Description
EDR	X, Y axes	Environmental Data Retrieval requires spatial coordinates
WMS	latitude, longitude	Web Map Service needs geographic coordinates
Tiles	X, Y or lat/lon	Tile service works with either coordinate system
DAP2	None (always compatible)	OPeNDAP has no specific CF requirements

CF Convention Attributes

The doctor checks for two types of CF attributes:

1. Axis Attributes (axis): Identifies dimension roles (X, Y, Z, T)
2. Standard Name Attributes (standard_name): Identifies physical quantities (latitude, longitude, time, vertical)

Example of properly attributed coordinates:

# X axis / Longitude
ds.lon.attrs = {
    'axis': 'X',
    'standard_name': 'longitude',
    'units': 'degrees_east'
}

# Y axis / Latitude
ds.lat.attrs = {
    'axis': 'Y',
    'standard_name': 'latitude',
    'units': 'degrees_north'
}

# Time dimension
ds.time.attrs = {
    'axis': 'T',
    'standard_name': 'time'
}