JuliaDataCubes / JuliaDataCubes/YAXArrays.jl

overwrite in savedataset fails for S3

Open
#559 0 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

bug
Dominant language
Julia
Stars
132
Forks
25
PR merge metrics
No merged PRs in 30d

Description

When I try to overwrite an old dataset on S3 in savedataset this doesn't remove the already laying data and fails with the following error:

julia>     dsout = savedataset(outds_skeleton,path=outpath*".zarr",skeleton=true,overwrite=true)
ERROR: Store is not empty
Stacktrace:
 [1] error(s::String)
   @ Base ./error.jl:44
 [2] zgroup(s::S3Store, path::String; attrs::Dict{String, Any}, indent_json::Bool)
   @ Zarr ~/Documents/baresoilfraction_opengeohub/dev/Zarr/src/ZGroup.jl:133
 [3] zgroup(s::String; kwargs::@Kwargs{attrs::Dict{String, Any}})
   @ Zarr ~/Documents/baresoilfraction_opengeohub/dev/Zarr/src/ZGroup.jl:147
 [4] zgroup
   @ ~/Documents/baresoilfraction_opengeohub/dev/Zarr/src/ZGroup.jl:147 [inlined]
 [5] create_empty
   @ ~/.julia/packages/YAXArrayBase/lAdRh/ext/ZarrExt.jl:55 [inlined]
 [6] create_dataset(T::Type, path::String, gatts::Dict{…}, dimnames::Vector{…}, dimvals::Vector{…}, dimattrs::Vector{…}, vartypes::Vector{…}, varnames::Vector{…}, vardims::Vector{…}, varattrs::Vector{…}, varchunks::Vector{…}; kwargs::@Kwargs{})
   @ YAXArrayBase ~/.julia/packages/YAXArrayBase/lAdRh/src/datasets/datasetinterface.jl:59
 [7] create_dataset(T::Type, path::String, gatts::Dict{…}, dimnames::Vector{…}, dimvals::Vector{…}, dimattrs::Vector{…}, vartypes::Vector{…}, varnames::Vector{…}, vardims::Vector{…}, varattrs::Vector{…}, varchunks::Vector{…})
   @ YAXArrayBase ~/.julia/packages/YAXArrayBase/lAdRh/src/datasets/datasetinterface.jl:58
 [8] savedataset(ds::Dataset; path::String, persist::Nothing, overwrite::Bool, append::Bool, skeleton::Bool, backend::Symbol, driver::Symbol, max_cache::Float64, writefac::Float64, kwargs::@Kwargs{})
   @ YAXArrays.Datasets ~/.julia/packages/YAXArrays/x5iTf/src/DatasetAPI/Datasets.jl:714
 [9] top-level scope
   @ REPL[145]:1
Some type information was truncated. Use `show(err)` to see complete types.

Contributor guide

No contributing guide indexed for this repository

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 at the savedataset call in YAXArrays.Datasets and follow create_empty in YAXArrayBase's ZarrExt.jl to the zgroup implementation in Zarr/src/ZGroup.jl. Reproduce the S3 overwrite case, then verify that an existing dataset can be overwritten without the "Store is not empty" error.

Written by the indexing model from the issue text.

Assessment

Tech stack
aws, julia
Domain
cloud, data
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 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.