R/BiodbSdfEntry.R

In pkrog/biodb: biodb, a library and a development framework for connecting to chemical and biological databases

#' 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
    }
}
))