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Bulk export all annotated samples from SQLite to EcoTaxa-ready ZIP

Source: R/database.R
export_all_db_to_zip.Rd

Exports annotated samples to class-organized PNG folders, writes one inventory .txt file per class folder, and then zips the result using iRfcb::ifcb_zip_pngs(include_txt = TRUE).

Usage

export_all_db_to_zip(
  db_path,
  zip_path,
  roi_path_map,
  skip_class = NULL,
  readme_file = system.file("exdata/README-template.md", package = "iRfcb")
)

Arguments

db_path

Path to the SQLite database file

zip_path

Full output path for the resulting ZIP archive

roi_path_map

Named list mapping sample names to .roi file paths. Samples without an entry are skipped.

skip_class

Character vector of class names to exclude from export (e.g. "unclassified"). Default NULL exports all classes.

readme_file

Optional README markdown file included in ZIP. Defaults to system.file("exdata/README-template.md", package = "iRfcb").

Value

Named list with counts: success, failed, skipped, inventory_files, and zip_path.