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OpenReadout

search

search queries an index made by index, reports its storage health, or exports what a query selects as a dataset.

openreadout search [OPTIONS] <INDEX_DIR> [QUERY]

Query syntax

Terms are combined with AND; OR separates alternatives.

  • field=value, field!=value: equal, not equal.
  • field~text: contains.
  • field<v, <=, >, >=: compare numbers, sizes and dates (size>1GB, acquired<2020).
  • field:TERM_ID: match an ontology term, such as technique:FBbi_00000246.
  • a|b: either value.
  • -term: negate a term.
  • Bare words search paths, samples, channels and descriptions.

An empty query selects everything. The fields are the index columns listed in the lab share guide.

Flags

Results

  • --sort FIELD: sort by a field; -size sorts descending. Default: path order.
  • --limit N: most results, 0 = all. Default 50. With --export, most data sets exported (default all).
  • --fields FIELDS: fields to return, comma-separated, or all.
  • --jsonl: one JSON object per result and line, without the wrapper.
  • --json: print the JSON wrapper instead of text.

Storage health (--health)

  • --health: report on the whole index instead of results: truncated or corrupt files, unreadable formats, duplicates, the same experiment stored twice, files at risk, totals and personal data.
  • --no-hash: do not confirm duplicate candidates by hashing their content.
  • --max-list N: most entries listed per section. Default 100. Counts are always complete.
  • -o, --output FILE: also write the report as Markdown.

Dataset export (--export)

  • --export OUT: export the selected data sets into this directory: images as OME-Zarr, tables, traces and spectra as Parquet (or CSV), metadata JSON and a datasheet. Resumable and verified.
  • --tables parquet|csv: file format for tables, traces and spectra. Default parquet.
  • --redact: replace values flagged as personal data with stable salted hashes.
  • --salt-file FILE: file holding the redaction salt (or set OPENREADOUT_REDACT_SALT).
  • --license SPDX: license of the whole export. Default: the nearest LICENSE file of each source.
  • --no-images: leave images out.

Examples

Terminal window
openreadout search /lab/index "format=czi objective=63x acquired<2020" --sort -size
openreadout search /lab/index "status=truncated|corrupt" --jsonl --fields path,format,check_codes
openreadout search /lab/index --health -o health.md
openreadout search /lab/index "sample~A12" --export dataset/ --redact --salt-file ~/.salt

Redaction and the personal-data rules: Personal data.

JSON

search, search --health, search --export.

Run openreadout search --help for the full help of your installed version.