gpkg-io.R

#' Read data from a GeoPackage
#'
#' This function creates a _geopackage_ object with references to all tables from the GeoPackage source specified in `x`. For a simple list of tables see `gpkg_tables()`.
#'
#' @param x Path to GeoPackage
#' @param connect Connect to database and store connection in result? Default: `FALSE`
#' @param quiet Hide printing of gdalinfo description to stdout. Default: `TRUE`
#' @return A _geopackage_ object (list containing tables, grids and vector data)
#' @export
#' @seealso [gpkg_tables()]
#' @keywords io
gpkg_read <- function(x, connect = FALSE, quiet = TRUE) {
  if (inherits(x, 'geopackage')) {
    x <- x$dsn
  }
  res <- lapply(x, function(xx) {
    res <- list()
    contents <- gpkg_contents(x, create = TRUE)
    # read grids
    if (!any(contents$data_type %in%  c("attributes", "features"))) {
        r <- try(terra::rast(xx), silent = TRUE)
        if (inherits(r, 'try-error')) {
          grids <- list()
        } else {
          # convert to list of single-layer SpatRaster
          grids <- as.list(r)
          # assign raster table names
          names(grids) <- names(r)
        }
    } else grids <- list()

    # read vector layers (error if there aren't any)
    if (any(contents$data_type == "features")) {
        vects <- lapply(contents$table_name, function(xxx){
            # create SpatVectorProxy
            try(terra::vect(path.expand(xx), xxx, proxy = TRUE), silent = quiet)
          })
        names(vects) <- contents$table_name
        vects <- vects[!vapply(vects, FUN.VALUE = logical(1), inherits, 'try-error')]
    } else vects <- list()

    # TODO: get table references
    tables <- list()

    # spatial results (grid+vect+tabular) in `tables`
    res$tables <- c(grids, vects, tables)

    # descriptions in `gdalinfo`
    res$gdalinfo <- terra::describe(xx)

    # verbose gdalinfo output
    if (!quiet) cat(res$gdalinfo, sep = "\n")
    res
  })

  res2 <- do.call('c', lapply(res, function(x) x$tables))
  names(res2) <- do.call('c', lapply(res, function(x) names(x$tables)))
  
  obj <- .geopackage(dsn = x, connect = connect)
  obj$tables <- x
  obj  
}

#' Write data to a GeoPackage
#' @param x Vector of source file path(s), or a list containing one or more SpatRaster, SpatRasterCollection, or SpatVectorProxy objects.
#' @param destfile Character. Path to output GeoPackage
#' @param table_name Character. Default `NULL` name is derived from source file. Required if `x` is a _data.frame_.
#' @param datatype Data type. Defaults to `"FLT4S"` for GeoTIFF files, `"INT2U"` otherwise. See documentation for `terra::writeRaster()`.
#' @param append Append to existing data source? Default: `FALSE`. Setting `append=TRUE` overrides `overwrite=TRUE`
#' @param overwrite Overwrite existing data source? Default `FALSE`.
#' @param NoData Value to use as GDAL `NoData` Value
#' @param gdal_options Additional `gdal_options`, passed to `terra::writeRaster()`
#' @param ... Additional arguments are passed as GeoPackage "creation options." See Details.
#' @details Additional, non-default GeoPackage creation options can be specified as arguments to this function. The full list of creation options can be viewed [here](https://gdal.org/drivers/raster/gpkg.html#creation-options) or in the `gpkg_creation_options` dataset. The name of the argument is `creation_option` and the value is selected from one of the elements of `values` for that option.
#' 
#' If `x` contains source file paths, any comma-separated value (CSV) files are treated as attribute data--even if they contain a geometry column. GeoPackage source file paths are always treated as vector data sources, and only one layer will be read from the source and written to the target. If you need to read raster data from a GeoPackage first create a `SpatRaster`  from the layer of interest (see `gpkg_rast()`) before passing to `gpkg_write()`. If you need to read multiple layers from any multi-layer source read them individually into suitable objects. For a source GeoPackage containing multiple layers you can use `gpkg_read()` (returns a _geopackage_ object) or `gpkg_tables()` (returns a _list_ object).
#' 
#' @return Logical. `TRUE` on successful write of at least one grid.
#' @seealso [gpkg_creation_options]
#' @export
#' @keywords io
gpkg_write <- function(x,
                       destfile,
                       table_name = NULL,
                       datatype = "FLT4S",
                       append = FALSE,
                       overwrite = FALSE,
                       NoData = NULL,
                       gdal_options = NULL,
                       ...) {
  res <- .gpkg_process_sources(x, 
                               destfile,
                               table_name = table_name,
                               datatype = datatype,
                               append = append,
                               overwrite = overwrite,
                               NoData = NoData,
                               gdal_options = gdal_options,
                               ...)
  invisible(.gpkg_postprocess_sources(res))
}

.is.file <- function(y, pattern) {
  is.character(y) && grepl(sprintf("\\.(%s)$", pattern), y, ignore.case = TRUE)
}

.gpkg_process_sources <- function(x, ...) {
  
  if (!is.list(x) || is.data.frame(x)) {
    x <- list(x)
  }
  
  # objects with a file source
  src_raster <- vapply(x, inherits, logical(1), c('SpatRaster', 'SpatRasterCollection'))
  src_vector <- vapply(x, inherits, logical(1), 'SpatVectorProxy')
  obj_vector <- vapply(x, inherits, logical(1), c('sf', 'SpatVector'))
  obj_attrib <- vapply(x, inherits, logical(1), 'data.frame')
  
  # pth_raster <- vapply(x, .is.file, logical(1),  "tif+|vrt|grd|png")
  # pth_vector <- vapply(x, .is.file, logical(1),  "shp|gpkg")
  # pth_attrib <- vapply(x, .is.file, logical(1),  "csv")
  pth_file <- vapply(x, .is.file, logical(1), ".*")
  
  # TODO: gdal is not used to read attributes,
  #       provide support for some other tabular data formats?
  #       arrow? openxlsx? 
  pth_attrib <- pth_file & vapply(x, .is.file, logical(1),  "csv")
  pth_raster <- rep(FALSE, length(x))  
  pth_vector <- rep(FALSE, length(x))
  
  if (any(pth_file)) {
    if (!requireNamespace("vapour")) {
      stop("package 'vapour' is required to auto-detect GDAL drivers needed to read from arbitrary file paths", call. = FALSE)
    }
    
    gdal_drv <- vapply(x, function(y) {
      if (!is.character(y)) {
        ""
      } else
        vapour::vapour_driver(y)
    }, character(1))
    
    drv <- vapour::vapour_all_drivers()
    drm <- match(gdal_drv, drv$driver)
    
    
    pth_raster <- pth_file & drv$raster[drm]
    
    # TODO: how to handle GPKG as a raster and vector source?
    pth_raster[gdal_drv == "GPKG"] <- FALSE
    
    pth_vector <- pth_file & drv$vector[drm]
    
    # TODO: handling of CSV files as attributes/without GDAL
    #       filter vapour drivers to subset that terra can readwrite
    pth_vector[gdal_drv == "CSV"] <- FALSE
  }
  
  
  # classify list of object input  grid, features, attributes
  #  - each processing function handles local objects and/or file paths
  list(
    grids = .gpkg_process_grids(c(x[src_raster], x[pth_raster]), ...),
    features = .gpkg_process_features(c(x[obj_vector], x[src_vector], x[pth_vector]), ...),
    attributes = .gpkg_process_attributes(c(x[obj_attrib], x[pth_attrib]), ...)
  )
}

#' @importFrom utils read.csv
.gpkg_process_attributes <- function(ldsn, destfile, table_name, overwrite=FALSE, append=TRUE, ...) {
  sapply(names(ldsn), function(x) {
    # attribute tables
    if (!inherits(ldsn[[x]], 'data.frame')) {
      ldsn[[x]] <- utils::read.csv(ldsn[[x]])
    }
    g <- geopackage(destfile, connect = TRUE)
    on.exit(gpkg_disconnect(g))
    x <- gpkg_write_attributes(
      g,
      ldsn[[x]],
      table_name = x,
      overwrite = overwrite,
      append = append
    )
    return(inherits(x, 'try-error'))
  })
}
    
.gpkg_process_grids <- function(ldsn, destfile, datatype, append = TRUE, overwrite = FALSE, NoData, gdal_options, ...) {
  res <- list()
  if (length(ldsn) > 0) {
    gdal_options_sub <- .gpkg_gdaloptions_add(gdal_options, 
                                              key = "RASTER_TABLE", 
                                              value = names(ldsn)[[1]])
    res <- list(.gpkg_write_grid_subdataset_terra(
      x = ldsn[[1]],
      destfile = destfile,
      datatype = datatype,
      append = append,
      overwrite = overwrite,
      NoData = NoData,
      gdal_options = gdal_options_sub,
      ...
    ))
    names(res) <- names(ldsn)[[1]]
  }
  sds <- list()
  if (length(ldsn) > 1) {
    # subsequent grids append=TRUE
    sds <- sapply(names(ldsn[2:length(ldsn)]), function(n) {
      gdal_options_sub <- .gpkg_gdaloptions_add(gdal_options, 
                                                key = "RASTER_TABLE", 
                                                value = n)
      .gpkg_write_grid_subdataset_terra(
        ldsn[[n]],
        destfile = destfile,
        datatype = datatype,
        append = TRUE,
        overwrite = overwrite,
        NoData = NoData,
        gdal_options = gdal_options_sub,
        ...
      )
    })
  }
  c(res, sds)
}

.gpkg_process_features <- function(ldsn, destfile, insert = TRUE, overwrite = FALSE, ...) {
  if (is.null(names(ldsn)) && length(ldsn) > 0) {
    names(ldsn) <- paste0("layer", 1:length(ldsn))
  }
  sapply(names(ldsn), function(vv) {
    .gpkg_write_vector_terra(
      ldsn[[vv]],
      layername = vv,
      destfile = destfile,
      insert = insert,
      overwrite = overwrite
    )
  })
}

.gpkg_postprocess_sources <- function(result, ...) {
  result
 # TODO gpkg_validate? 
}

.lut_gpkg_creation <- function(...) {
  kv <- list(...)
  gpkg_creation_options <- get("gpkg_creation_options")
  kvn <- trimws(names(kv)[names(kv) %in% gpkg_creation_options$creation_option])
  kvn <- kvn[nchar(kvn) > 0]
  if (length(kvn) > 0) {
    return(paste0(kvn, "=", as.character(kv[kvn])))
  }
  character(0)
}

.gpkg_debug <- function(x, ...) if (getOption("gpkg.debug", default = FALSE)) message("DEBUG:\n\n", x, ...)

.gpkg_gdaloptions_add <- function(gdal_options, key, value, force = FALSE) {
  # add a gdaloption (if 'key' not already defined)
  if (force || !any(grepl(key, gdal_options, ignore.case = TRUE))) 
    return(c(gdal_options, ifelse(nchar(value) > 0, paste0(key, "=", value), "")))
  else ""
}

#' .gpkg_write_grid_subdataset_terra
#' @return A SpatRaster reference to grid written to GeoPackage, or `NULL` on error
#' @noRd
#' @keywords internal
.gpkg_write_grid_subdataset_terra <- function(x,
                                              destfile,
                                              datatype,
                                              append = FALSE,
                                              overwrite = FALSE,
                                              NoData = NULL,
                                              gdal_options = NULL,
                                              ...) {
  res <- NULL
  if (!requireNamespace('terra', quietly = TRUE)) stop('the `terra` package is required to write gridded data to GeoPackage', call. = FALSE)

  if (!inherits(x, 'SpatRaster')) {
    r <- terra::rast(x)
  } else {
    r <- x
  }

  gdal_options <- unique(c(gdal_options, .lut_gpkg_creation(...)))

  .gpkg_debug(paste0(gdal_options, collapse = "\n"))

  if (append) {
    if (!any(grepl("APPEND_SUBDATASET", gdal_options, ignore.case = TRUE))) {
      gdal_options <- c(gdal_options, "APPEND_SUBDATASET=YES")
    }
  }
  
  res <- terra::writeRaster(
    x = r,
    filename = destfile,
    datatype = datatype,
    overwrite = overwrite,
    gdal = gdal_options
  )

  if (!is.null(NoData)) {
    ctn <- gsub("RASTER_TABLE=(.*)|.*", "\\1", gdal_options)
    ctn <- ctn[nchar(ctn) > 0]
    if (length(ctn) > 0) {
      gpkg_tile_set_data_null(destfile, ctn, NoData)
    } else message("NOTE: NoData specified without setting RASTER_TABLE")
  }

  invisible(res)

}

#' .gpkg_write_vector_terra
#' @return A SpatVectorProxy reference to grid written to GeoPackage, or `NULL` on error
#' @noRd
#' @keywords internal
.gpkg_write_vector_terra <- function(x,
                                     destfile,
                                     layername,
                                     insert = FALSE,
                                     overwrite = FALSE,
                                     gdal_options = NULL,
                                     ...) {

  gdal_options <- unique(c(gdal_options, .lut_gpkg_creation(...)))
  
  if (inherits(x, 'SpatVectorProxy')) {
    x <- terra::query(x)
  }
  
  if (!inherits(x, 'SpatVector')) {
    x <- terra::vect(x)
  }
  
  res <- terra::writeVector(x,
            destfile,
            layer = layername,
            insert = insert,
            overwrite = overwrite,
            options = gdal_options
          )
  invisible(res)
}