R/h5ls.R

In rhdf5: R Interface to HDF5

h5lsConvertToDataframe <- function(L, all=FALSE, native) {
  if (is.data.frame(L)) {
    L$ltype <- h5const2String("H5L_TYPE", L$ltype)
    L$otype <- h5const2String("H5I_TYPE", L$otype)
    if (!all) {
      L <- L[,c("group", "name", "otype", "dclass","dim")]
    }
  } else {
    for (i in seq_len(length(L))) {
      L[i] <- list(h5lsConvertToDataframe(L[[i]],all=all, native = native))
    }
  }
  L
}

h5ls <- function( file, recursive = TRUE, all=FALSE, datasetinfo=TRUE, 
                  index_type = h5default("H5_INDEX"), order = h5default("H5_ITER"), 
                  s3 = FALSE, s3credentials = NULL, native = FALSE) {
  
    if(isTRUE(s3)) {
      fapl <- H5Pcreate("H5P_FILE_ACCESS")
      on.exit(H5Pclose(fapl))
      H5Pset_fapl_ros3(fapl, s3credentials)
      loc <- h5checktypeOrOpenLocS3(file, readonly = TRUE, fapl = fapl, native = native)
    } else {
      loc <- h5checktypeOrOpenLoc(file, readonly = TRUE, fapl = NULL, native = native)
    }
    on.exit(h5closeitLoc(loc), add = TRUE)
    
    if (length(datasetinfo)!=1 || !is.logical(datasetinfo)) stop("'datasetinfo' must be a logical of length 1")
    index_type <- h5checkConstants( "H5_INDEX", index_type )
    order <- h5checkConstants( "H5_ITER", order )
    if (is.logical(recursive)) {
        if (recursive) {
            depth = -1L
        } else {
            depth = 1L
        }
    } else if ( is.numeric(recursive) | is.integer(recursive) ) {
        depth = as.integer(recursive)
        if( length(recursive) > 1 ) {
            warning("'recursive' must be of length 1.  Only using first value.")
        } else if (recursive == 0) {
            stop("value 0 for 'recursive' is undefined, either a positive integer or negative (maximum recursion)")
        } 
    } else {
        stop("'recursive' must be number or a logical")
    }
    di <- ifelse(datasetinfo, 1L, 0L)
    L <- .Call("_h5ls", loc$H5Identifier@ID, depth, di, index_type, order, loc$H5Identifier@native, PACKAGE='rhdf5')
    h5lsConvertToDataframe(L, all=all, native = loc$H5Identifier@native)
}