CLI reference#

The sddb-cli console script wraps the same catalog queries as the Python API.

sddb-cli#

Query and download spatialdata-db datasets.

Usage:

$ sddb-cli [OPTIONS] COMMAND [ARGS]...

Options:

  • --help: Show this message and exit.

Commands:

  • query: List datasets matching the given facets.

  • facets: List facet columns, or the distinct values...

  • download: Download datasets (by uid, or every member...

  • viewer-url: Print the browser viewer link for a...

  • genes: List datasets expressing all GENES (one...

  • cite: Write BibTeX for the studies of the...

sddb-cli query#

List datasets matching the given facets.

A facet value that is not in the catalog resolves through aliases (case, spaces and hyphens are ignored; --technology also takes the assay label, e.g. "10x Xenium"), or fails with a "did you mean" hint.

Usage:

$ sddb-cli query [OPTIONS]

Options:

  • --organism <str>

  • --assay <str>

  • --tissue <str>

  • --disease <str>

  • --technology <str>

  • --tier <str>

  • --source <str>: Data source: the study_id prefix (geo, hest, 10x, ...).

  • --preservation-method <str>: Preservation method, for example FFPE or fresh frozen.

  • --hne-image / --no-hne-image: Keep datasets with (or without) an H&E image.

  • --redistributable / --no-redistributable: Keep datasets whose known license allows redistribution (or the rest, which includes unknown licenses).

  • --validation <str>: 'pass' (default) or 'all'. [default: pass]

  • --gene, --expressing <str>: Gene symbol or Ensembl id; repeat to require all (downloads the gene index once).

  • --min-fraction <float>: With --gene: min fraction_obs_detected.

  • --search <str>: Free-text search over facet values.

  • --min-obs <int>: Keep datasets with n_obs >= this.

  • --min-features <int>: Keep datasets with n_features >= this.

  • --catalog <str>: Catalog URL (default: $SDDB_CATALOG_URL).

  • --json: Emit JSON records.

  • --help: Show this message and exit.

sddb-cli facets#

List facet columns, or the distinct values of FIELD.

Usage:

$ sddb-cli facets [OPTIONS] [field]

Arguments:

  • field: Facet column; omit to list columns.

Options:

  • --catalog <str>: Catalog URL (default: $SDDB_CATALOG_URL).

  • --help: Show this message and exit.

sddb-cli download#

Download datasets (by uid, or every member of --collection) to DEST and print the manifest path.

Usage:

$ sddb-cli download [OPTIONS] [uids]...

Arguments:

  • uids...: Dataset uid(s).

Options:

  • --collection <str>: A collection slug instead of uids.

  • --dest <path>: Destination directory. [default: .]

  • --catalog <str>: Catalog URL (default: $SDDB_CATALOG_URL).

  • --workers <int>: Parallel downloads. [default: 4]

  • --help: Show this message and exit.

sddb-cli viewer-url#

Print the browser viewer link for a dataset; fails when the link loads another dataset's store.

Usage:

$ sddb-cli viewer-url [OPTIONS] {uid}

Arguments:

  • uid: [required]

Options:

  • --catalog <str>: Catalog URL (default: $SDDB_CATALOG_URL).

  • --help: Show this message and exit.

sddb-cli genes#

List datasets expressing all GENES (one gene: ranked by fraction of observations detected).

The first call downloads the cross-dataset gene index (~900 MB, one-time; cached and read in batches).

Usage:

$ sddb-cli genes [OPTIONS] {genes}...

Arguments:

  • genes...: Gene symbol(s) or Ensembl id(s), case-insensitive. [required]

Options:

  • --limit <int>: Max datasets to list. [default: 20]

  • --validation <str>: 'all' (default, includes bronze) or 'pass'. [default: all]

  • --catalog <str>: Catalog URL (default: $SDDB_CATALOG_URL).

  • --help: Show this message and exit.

sddb-cli cite#

Write BibTeX for the studies of the datasets matching the given facets/search.

Usage:

$ sddb-cli cite [OPTIONS]

Options:

  • -o, --output <path>: BibTeX file to write. [required]

  • --organism <str>

  • --assay <str>

  • --tissue <str>

  • --disease <str>

  • --technology <str>

  • --tier <str>

  • --source <str>: Data source: the study_id prefix (geo, hest, 10x, ...).

  • --hne-image / --no-hne-image: Keep datasets with (or without) an H&E image.

  • --redistributable / --no-redistributable: Keep datasets whose known license allows redistribution (or the rest, which includes unknown licenses).

  • --search <str>: Free-text search over facet values.

  • --validation <str>: 'pass' (default) or 'all'. [default: pass]

  • --bib-url <str>: citations.bib URL/path (default: next to the catalog).

  • --catalog <str>: Catalog URL (default: $SDDB_CATALOG_URL).

  • --help: Show this message and exit.