Rescan folders and rebuild the file index cache — rescan_file

Scans the configured (or specified) ROI, classification, and output folders for IFCB sample files and saves the results to the file index cache. This can be called outside the Shiny app, e.g. from a cron job, to keep the cache up to date without manually clicking the rescan button.

Usage

rescan_file_index(
  roi_folder = NULL,
  csv_folder = NULL,
  output_folder = NULL,
  verbose = TRUE,
  db_folder = NULL,
  data_source = "local",
  dashboard_url = NULL,
  dashboard_autoclass = FALSE,
  progress = NULL
)

Arguments

roi_folder: Path to ROI/PNG data folder. If NULL, read from saved settings.
csv_folder: Path to classification folder (CSV/H5/MAT). If NULL, read from saved settings.
output_folder: Path to output folder for MAT annotations. If NULL, read from saved settings.
verbose: If TRUE, print progress messages. Default TRUE.
db_folder: Path to the database folder for SQLite annotations. If NULL, read from saved settings; if not found in settings, defaults to get_default_db_dir().
data_source: Either "local" (default) for local folder scanning, or "dashboard" to fetch the sample list from a remote IFCB Dashboard.
dashboard_url: When data_source = "dashboard", the full Dashboard URL (e.g. "https://habon-ifcb.whoi.edu/timeline?dataset=tangosund").
dashboard_autoclass: Logical. When TRUE and data_source = "dashboard", skip scanning the local csv_folder for classifier output files (the dashboard's own auto-classifications are used instead). Defaults to FALSE.
progress: Optional callback function used to report scan progress. The callback receives named arguments value (numeric in [0, 1]) and detail (character message). Mainly intended for Shiny progress bars.

Value

Invisibly returns the file index list, or NULL if roi_folder is invalid.

Details

If folder paths are not provided, they are read from saved settings.

Examples

if (FALSE) { # \dontrun{
# Rescan using saved settings
rescan_file_index()

# Rescan with explicit paths
rescan_file_index(
  roi_folder = "/data/ifcb/raw",
  csv_folder = "/data/ifcb/classified",
  output_folder = "/data/ifcb/manual"
)

# Scan from a remote Dashboard
rescan_file_index(data_source = "dashboard",
                  dashboard_url = "https://habon-ifcb.whoi.edu/timeline?dataset=tangosund")

# Use in a cron job:
# Rscript -e 'ClassiPyR::rescan_file_index()'
} # }