#' Entry class for content in SDF format.
#'
#' This is an abstract class for handling database entries whose content is in
#' SDF format.
#'
#' @seealso Super class \code{\link{BiodbTxtEntry}}.
#'
#' @examples
#' # Create a concrete entry class inheriting from CSV class:
#' MyEntry <- R6::R6Class("MyEntry", inherit=biodb::BiodbSdfEntry)
#'
#' @include BiodbTxtEntry.R
#' @export
BiodbSdfEntry <- R6::R6Class("BiodbSdfEntry",
inherit=BiodbTxtEntry,
public=list(
#' @description
#' New instance initializer. Entry objects must not be created directly.
#' Instead, they are retrieved through the connector instances.
#' @param ... All parameters are passed to the super class initializer.
#' @return Nothing.
initialize=function(...) {
super$initialize(...)
abstractClass('BiodbSdfEntry', self)
return(invisible(NULL))
}
),
private=list(
doParseFieldsStep1=function(parsed.content) {
# Get parsing expressions
parsing.expr <- self$getParent()$getPropertyValue('parsing.expr')
chk::chk_character(parsed.content)
if ( ! chk::vld_character(parsing.expr) && ! chk::vld_list(parsing.expr))
error("parsing.expr must be either a character vector or a list.")
if (is.list(parsing.expr))
chk::chk_all(parsing.expr, chk::chk_character)
chk::chk_named(parsing.expr)
# Tags to field
tag2field <- character()
for (field in names(parsing.expr)) {
tag <- parsing.expr[[field]][[1]]
tag2field[[tag]] <- field
}
# Loop on lines
tag <- NULL
for (line in parsed.content) {
# Remove spaces at start and end
line <- sub('^ *', '', line)
line <- sub(' *$', '', line)
# Read tag
g <- stringr::str_match(line, '^> *<(.+)>$')
if ( ! is.na(g[1, 1]))
tag <- g[1, 2]
# Read and set value
else if (nchar(line) > 0 && ! is.null(tag)
&& tag %in% names(tag2field)) {
# Get biodb field
field <- tag2field[[tag]]
# Use regex to modify value
if (length(parsing.expr[[field]]) > 1) {
regex <- parsing.expr[[field]][[2]]
line <- sub(regex, '\\1', line, perl = TRUE)
}
# Set/append value to field
self$appendFieldValue(field, line)
}
# Reset tag
else
tag <- NULL
}
}
))
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