R/str_match_with_rearrangement.R

In patelm9/cartographR:

#' Inverts concepts with a single dash to see if a string match in MRCONSO can occur with a rearrangement, typically with drug combinations with {asdfasd}-{asdfadsf} naming convention
#' @import stringr
#' @import dplyr
#' @import typewriteR
#' @export

str_match_with_rearrangement <-
        function(progress_list) {
                for (i in 1:nrow(progress_list$QUEUE)) {
                        if (i == 1) {
                                total_obs <- nrow(progress_list$QUEUE)
                        }
                        KEY_CONCEPT_NAME <- progress_list$QUEUE$KEY_CONCEPT_NAME[1]
                        if (grepl("^.*[-]{1}.*$", KEY_CONCEPT_NAME) == TRUE) {
                                cat("\n\n")
                                typewriteR::tell_me(Sys.time(), "Starting row", i, "of", total_obs)
                                cat("\n")
                                typewriteR::tell_me(Sys.time(), "Concept:", KEY_CONCEPT_NAME)
                                cat("\n\n")
                                
                                KEY_CONCEPT_NAME <- stringr::str_replace(KEY_CONCEPT_NAME, "(^.*)([-]{1})(.*$)", "\\3-\\1")
                                first_match <- get_first_possible_cui(KEY_CONCEPT_NAME)
                                if (nrow(first_match) == 1) {
                                        progress_list$QUEUE$KEY_CUI[1] <- first_match$CUI
                                        progress_list$QUEUE$KEY_CUI_MRCONSO_STR[1] <- first_match$STR
                                        progress_list$QUEUE$KEY_TIMESTAMP[1] <- mirroR::get_timestamp()
                                        
                                        progress_list$STAGED <-
                                                dplyr::bind_rows(progress_list$STAGED,
                                                                 progress_list$QUEUE %>%
                                                                         filter(row_number() == 1)
                                                )
                                        
                                        progress_list$QUEUE <- progress_list$QUEUE[-1,]
                                        assign("PROGRESS_LIST", progress_list, envir = globalenv())
                                } else {
                                        progress_list$STAGED <-
                                                dplyr::bind_rows(progress_list$STAGED,
                                                                 progress_list$QUEUE %>%
                                                                         filter(row_number() == 1)
                                                )
                                        
                                        progress_list$QUEUE <- progress_list$QUEUE[-1,]
                                        assign("PROGRESS_LIST", progress_list, envir = globalenv())
                                }
                        } else {
                                progress_list$STAGED <-
                                        dplyr::bind_rows(progress_list$STAGED,
                                                         progress_list$QUEUE %>%
                                                                 filter(row_number() == 1)
                                        )
                                
                                progress_list$QUEUE <- progress_list$QUEUE[-1,]
                                assign("PROGRESS_LIST", progress_list, envir = globalenv())
                        }
                }
                
        }