metahq-build metadata¶

Command group for OmicIDX queries.

Usage:

metahq-build metadata [OPTIONS] COMMAND [ARGS]...

Options:

  --help  Show this message and exit.

list-fields¶

Show queriable metadata fields from OmicIDX.

Usage:

metahq-build metadata list-fields [OPTIONS]

Options:

  -l, --level [sample|series]  Which metadata level for which to show
                               available fields.
  --metadata-db PATH           Path to OmicIDX DuckDB file (default:
                               data/omicidx.duckdb)
  --help                       Show this message and exit.

sample¶

Retrieve sample-level metadata from OmicIDX for samples in a MetaHQ BSON database.

Usage:

metahq-build metadata sample [OPTIONS]

Options:

  -f, --fields TEXT   A comma-delimited string of fields to query
  -o, --outfile PATH  Path to parquet outfile.
  --sample-bson PATH  Path to sample-level BSON database storing MetaHQ sample
                      anntotations.
  --metadata-db PATH  Path to OmicIDX DuckDB file (default:
                      data/omicidx.duckdb)
  --null-values TEXT  Values for which to fill null values.
  --help              Show this message and exit.

series¶

Retrieve series-level metadata from OmicIDX for series in a MetaHQ BSON database.

Usage:

metahq-build metadata series [OPTIONS]

Options:

  -f, --fields TEXT   A comma-delimited string of fields to query
  -o, --outfile PATH  Path to parquet outfile.
  --series-bson PATH  Path to series-level BSON database storing MetaHQ series
                      anntotations.
  --metadata-db PATH  Path to OmicIDX DuckDB file (default:
                      data/omicidx.duckdb)
  --null-values TEXT  Values for which to fill null values.
  --help              Show this message and exit.