pydata / pydata/xarray

Zarr file over HTTP fetches several times the same time axis variable

Open
#10,560 8 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

topic-backends topic-performance
Dominant language
Python
Stars
4.2k
Forks
1.4k
Avg merge
2d 15h
Merged PRs (30d)
14

Description

What happened?

When loading a Dataset from Zarr over HTTP the time chunk is fetched 3 times from the remote location.

Example Zarr dataset (on google bucket) :
https://storage.googleapis.com/test_zarr_oie/IEA_PVPS.zarr/ADR/zarr.json

What did you expect to happen?

I expect the following URL to be fetched once only :
https://storage.googleapis.com/test_zarr_oie/IEA_PVPS.zarr/ADR/time/c/0

Instead it is fetched 3 times (logs from mitmproxy) :

16:28:07 HTTPS GET    storage.googleapis.com /test_zarr_oie/IEA_PVPS.zarr/ADR/.zattrs                                                       404 application/xml  201b 358ms 
16:28:07 HTTPS GET    storage.googleapis.com /test_zarr_oie/IEA_PVPS.zarr/ADR/.zgroup                                                       404 application/xml  201b 384ms 
16:28:07 HTTPS GET    storage.googleapis.com /test_zarr_oie/IEA_PVPS.zarr/ADR/.zmetadata                                                    404 application/xml  204b 346ms 
16:28:07 HTTPS GET    storage.googleapis.com /test_zarr_oie/IEA_PVPS.zarr/ADR/zarr.json                                                     200 …plication/json 40.5k 204ms 
16:28:07 HTTPS GET    storage.googleapis.com /test_zarr_oie/IEA_PVPS.zarr/ADR/time/c/0                                                      200 …n/octet-stream ….04k  26ms 
16:28:07 HTTPS GET    storage.googleapis.com /test_zarr_oie/IEA_PVPS.zarr/ADR/time/c/0                                                      200 …n/octet-stream ….04k  24ms 
16:28:07 HTTPS GET    storage.googleapis.com /test_zarr_oie/IEA_PVPS.zarr/ADR/station_name/c                                                200 …n/octet-stream   27b  31ms 
16:28:07 HTTPS GET    storage.googleapis.com /test_zarr_oie/IEA_PVPS.zarr/ADR/time/c/0                                                200 …n/octet-stream ….04k  25ms 
Minimal Complete Verifiable Example
# To spy the request, you may setup a local proxy first : 
# `mitmproxy --mode reverse:https://storage.googleapis.com/ --listen-port 1111`

# Initial URL
# URL="https://storage.googleapis.com/test_zarr_oie/IEA_PVPS.zarr/ADR"

# Proxy URL 
URL="http://localhost:1111/test_zarr_oie/IEA_PVPS.zarr/ADR"

ds = xr.open_dataset(URL, engine="zarr")
print(ds)
MVCE confirmation
  • Minimal example — the example is as focused as reasonably possible to demonstrate the underlying issue in xarray.
  • Complete example — the example is self-contained, including all data and the text of any traceback.
  • Verifiable example — the example copy & pastes into an IPython prompt or Binder notebook, returning the result.
  • New issue — a search of GitHub Issues suggests this is not a duplicate.
  • Recent environment — the issue occurs with the latest version of xarray and its dependencies.
Relevant log output
16:28:07 HTTPS GET    storage.googleapis.com /test_zarr_oie/IEA_PVPS.zarr/ADR/.zattrs                                                       404 application/xml  201b 358ms 
16:28:07 HTTPS GET    storage.googleapis.com /test_zarr_oie/IEA_PVPS.zarr/ADR/.zgroup                                                       404 application/xml  201b 384ms 
16:28:07 HTTPS GET    storage.googleapis.com /test_zarr_oie/IEA_PVPS.zarr/ADR/.zmetadata                                                    404 application/xml  204b 346ms 
16:28:07 HTTPS GET    storage.googleapis.com /test_zarr_oie/IEA_PVPS.zarr/ADR/zarr.json                                                     200 …plication/json 40.5k 204ms 
16:28:07 HTTPS GET    storage.googleapis.com /test_zarr_oie/IEA_PVPS.zarr/ADR/time/c/0                                                      200 …n/octet-stream ….04k  26ms 
16:28:07 HTTPS GET    storage.googleapis.com /test_zarr_oie/IEA_PVPS.zarr/ADR/time/c/0                                                      200 …n/octet-stream ….04k  24ms 
16:28:07 HTTPS GET    storage.googleapis.com /test_zarr_oie/IEA_PVPS.zarr/ADR/station_name/c                                                200 …n/octet-stream   27b  31ms 
16:28:07 HTTPS GET    storage.googleapis.com /test_zarr_oie/IEA_PVPS.zarr/ADR/time/c/0
Anything else we need to know?

No response

Environment

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the provided xr.open_dataset(URL, engine="zarr") MVCE and inspect the repeated remote request for time/c/0 while loading the example dataset. Confirm that the time chunk is fetched once rather than three times, while preserving successful dataset loading.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data, performance
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
45/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.