xcube patch

Synopsis

Patch and consolidate the metadata of a xcube dataset.

$ xcube patch --help

Usage: xcube patch [OPTIONS] DATASET

  Patch and consolidate the metadata of a dataset.

  DATASET can be either a local filesystem path or a URL. It must point to
  either a Zarr dataset (*.zarr) or a xcube multi-level dataset (*.levels).
  Additional storage options for a given protocol may be passed by the OPTIONS
  option.

  In METADATA, the special attribute value "__delete__" can be used to remove
  that attribute from dataset or array metadata.

Options:
  --metadata METADATA  The metadata to be patched. Must be a JSON or YAML file
                       using Zarr consolidated metadata format.
  --options OPTIONS    Protocol-specific storage options (see fsspec). Must be
                       a JSON or YAML file.
  -q, --quiet          Disable output of log messages to the console entirely.
                       Note, this will also suppress error and warning
                       messages.
  -v, --verbose        Enable output of log messages to the console. Has no
                       effect if --quiet/-q is used. May be given multiple
                       times to control the level of log messages, i.e., -v
                       refers to level INFO, -vv to DETAIL, -vvv to DEBUG,
                       -vvvv to TRACE. If omitted, the log level of the
                       console is WARNING.
  -d, --dry-run        Do not change any data, just report what would have
                       been changed.
  --help               Show this message and exit.

Patch file example

Patch files use the Zarr Consolidated Metadata Format, v1. For example, the following patch file (YAML) will delete the global attribute TileSize and change the value of the attribute long_name of variable conc_chl:

zarr_consolidated_format: 1
metadata:

  .zattrs:
    TileSize: __delete__

  conc_chl/.zattrs:
    long_name: Chlorophyll concentration

Storage options file example

Here is a storage options file for the “s3” protocol that provides credentials for AWS S3 access:

key: AJDKJCLSKKA
secret: kjkl456lkj45632k45j63l

Usage example

$ xcube patch s3://my-cubes-bucket/test.zarr --metadata patch.yml -v