Tidy flatten

R/buildRecord.R

@@ -284,10 +284,10 @@ setMethod("buildRecord", "RmbSpectrum2", function(o, ..., cpd = NULL, mbdata = l
  # Here is the right place to fix the name of the INTERNAL ID field.
  if(!is.null(getOption("RMassBank")$annotations$internal_id_fieldname))
  {
- id.col <- which(names(mbdata[["COMMENT"]]) == "ID")
- if(length(id.col) > 0)
+ id_col <- which(names(mbdata[["COMMENT"]]) == "ID")
+ if(length(id_col) > 0)
  {
- names(mbdata[["COMMENT"]])[[id.col]] <-
+ names(mbdata[["COMMENT"]])[[id_col]] <-
  getOption("RMassBank")$annotations$internal_id_fieldname
  }
  }

R/createMassBank.R

@@ -90,14 +90,14 @@ loadInfolist <- function(mb, fileName)
  # dbname_e will be dropped because of the select= in the subset below.
  }
 
- if("COMMENT.EAWAG_UCHEM_ID" %in% colnames(mbdata_new)) {
- colnames(mbdata_new)[[which(colnames(mbdata_new)== "COMMENT.EAWAG_UCHEM_ID")]] <-
- "COMMENT.ID"
+ if("COMMENT_EAWAG_UCHEM_ID" %in% colnames(mbdata_new)) {
+ colnames(mbdata_new)[[which(colnames(mbdata_new) == "COMMENT_EAWAG_UCHEM_ID")]] <-
+ "COMMENT_ID"
  }
 
  # use only the columns present in mbdata_archive, no other columns added in excel
  col_names <- colnames(mb@mbdata_archive)
- comment_colnames <- colnames(mbdata_new)[grepl(x = colnames(mbdata_new), pattern = "^COMMENT\\.(?!CONFIDENCE)(?!ID)", perl = TRUE)]
+ comment_colnames <- colnames(mbdata_new)[grepl(x = colnames(mbdata_new), pattern = "^COMMENT\\_(?!CONFIDENCE)(?!ID)", perl = TRUE)]
  col_names <- c(col_names, comment_colnames)
 
  ## The read infolists might not have all required / expected columns
@@ -138,8 +138,8 @@ resetInfolists <- function(mb)
 { 
  mb@mbdata_archive <-
  structure(list(id = integer(0), dbcas = character(0), 
- dbname = character(0), dataused = character(0), COMMENT.CONFIDENCE = character(0), 
- COMMENT.ID = integer(0), `CH$NAME1` = character(0), 
+ dbname = character(0), dataused = character(0), COMMENT_CONFIDENCE = character(0), 
+ COMMENT_ID = integer(0), `CH$NAME1` = character(0), 
  `CH$NAME2` = character(0), `CH$NAME3` = character(0), `CH$NAME4` = character(0),
  `CH$NAME5` = character(0), `CH$COMPOUND_CLASS` = character(0), 
  `CH$FORMULA` = character(0), `CH$EXACT_MASS` = numeric(0),` CH$SMILES` = character(0), 
@@ -149,7 +149,7 @@ resetInfolists <- function(mb)
  `CH$LINK_CHEMSPIDER` = integer(0), `CH$LINK_COMPTOX` = character(0), 
  AUTHORS = character(0), COPYRIGHT = character(0)
  ), .Names = c("id", "dbcas", 
- "dbname", "dataused", "COMMENT.CONFIDENCE", "COMMENT.ID", 
+ "dbname", "dataused", "COMMENT_CONFIDENCE", "COMMENT_ID", 
  "CH$NAME1", "CH$NAME2", "CH$NAME3", "CH$NAME4", "CH$NAME5", "CH$COMPOUND_CLASS", "CH$FORMULA", 
  "CH$EXACT_MASS", "CH$SMILES", "CH$IUPAC", "CH$LINK_CAS", "CH$LINK_CHEBI", 
  "CH$LINK_HMDB", "CH$LINK_KEGG", "CH$LINK_LIPIDMAPS", "CH$LINK_PUBCHEM",
@@ -254,7 +254,7 @@ mbWorkflow <- function(mb, steps=c(1,2,3,4,5,6,7,8), infolist_path="./infolist.c
  rmb_log_info("mbWorkflow: Step 2. Export infolist (if required)")
  if(length(mb@mbdata)>0)
  {
- mbdata <- tibble::as_tibble(flatten(mb@mbdata))
+ mbdata <- flatten(mb@mbdata)
  readr::write_csv(x = mbdata, file = infolist_path, col_names = TRUE, na = "", quote = "needed")
  rmb_log_info(paste("The file", infolist_path, "was generated with new compound information. Please check and edit the table, and add it to your infolist folder."))
  return(mb)
@@ -585,14 +585,19 @@ gatherData <- function(id)
 
  if(usebabel){
  cmdinchikey <- paste0(babeldir, 'obabel -:"',smiles,'" ', '-oinchikey')
- inchikey_split <- system(cmdinchikey, intern=TRUE, input=smiles, ignore.stderr=TRUE)
- } else{
- inchikey <- getCactus(smiles, 'stdinchikey')
+ inchikey_split <- system(cmdinchikey, intern = TRUE, input = smiles, ignore.stderr = TRUE)
+ } else {
+ inchi_key <- getCactus(identifier = smiles, representation = "stdinchikey")
+
+ if(is.na(inchi_key)) {
+ inchi_key <- getPcInchiKey(query = smiles, from = "smiles")
+ }
+
  if(!is.na(inchikey)){
  ##Split the "InChiKey=" part off the key
- inchikey_split <- strsplit(inchikey, "=", fixed=TRUE)[[1]][[2]]
- } else{
- inchikey_split <- getPcInchiKey(smiles)
+ inchikey_split <- strsplit(inchi_key, "=", fixed = TRUE)[[1]][[2]]
+ } else {
+ inchikey_split <- getPcInchiKey(query = smiles, from = "smiles")
  }
  }
 
@@ -1120,7 +1125,7 @@ gatherDataUnknown <- function(id, mode, retrieval){
 #' \code{\link{gatherData}}.
 #' @param row One row of MassBank compound information retrieved from an
 #' infolist.
-#' @return \code{flatten} returns a matrix (not a data frame) to be written to
+#' @return \code{flatten} returns a tibble (not a data frame or matrix) to be written to
 #' CSV.
 #' 
 #' \code{readMbdata} returns a list of type \code{list(id= \var{compoundID},
@@ -1146,19 +1151,19 @@ flatten <- function(mbdata)
  .checkMbSettings()
 
  colNames <- names(unlist(mbdata[[1]]))
- commentNames <- colNames[grepl(x = colNames, pattern = "^COMMENT\\.")]
+ commentNames <- colNames[grepl(x = colNames, pattern = "^COMMENT\\_")]
 
  colList <- c(
  "id",
  "dbcas",
  "dbname",
  "dataused",
  commentNames,
- #"COMMENT.CONFIDENCE",
+ #"COMMENT_CONFIDENCE",
  # Note: The field name of the internal id field is replaced with the real name
  # at "compilation" time. Therefore, functions DOWNSTREAM from compileRecord() 
  # must use the full name including the info from options("RMassBank").
- #"COMMENT.ID",
+ #"COMMENT_ID",
  "CH$NAME1",
  "CH$NAME2",
  "CH$NAME3",
@@ -1177,27 +1182,35 @@ flatten <- function(mbdata)
  "CH$LINK_PUBCHEM",
  "CH$LINK_INCHIKEY",
  "CH$LINK_CHEMSPIDER",
- "CH$LINK_COMPTOX"
+  "CH$LINK_COMPTOX"
  )
  # make an empty data frame with the right length
  rows <- length(mbdata)
  cols <- length(colList)
- mbframe <- matrix(data=NA, nrow=rows, ncol=cols)
- colnames(mbframe) <- colList
+
+ mbtbl <- tibble::tibble(!!!colList, .rows = 0, .name_repair = ~ colList)
+
+
+ #mbframe <- matrix(data = NA, nrow = rows, ncol = cols)
+ #colnames(mbframe) <- colList
  #browser()
- for(row in 1:rows)
- {
+ for(i in 1:rows) {
  # fill in all the data into the dataframe: all columns which 
  # a) exist in the target dataframe and b) exist in the (unlisted) MB record
  # are written into the dataframe.
- data <- unlist(mbdata[[row]])
+ data <- unlist(mbdata[[i]], use.names = TRUE)
+ names(data) <- gsub("\\.", "_", names(data))
  # bugfix for the case of only one name
- if(!("CH$NAME1" %in% names(data)))
- data[["CH$NAME1"]] <- data[["CH$NAME"]]
- datacols <- intersect(colList, names(data))
- mbframe[row,datacols] <- data[datacols]
+ if(!("CH$NAME1" %in% names(data))) {
+ data[["CH$NAME1"]] <- data[["CH$NAME"]]
+ }
+ datacols <- intersect(colList, names(data))
+
+ mbtbl <- mbtbl |> dplyr::bind_rows(data[datacols])
+
  }
- return(mbframe)
+
+ return(mbtbl)
 
 }
 
@@ -1231,8 +1244,8 @@ readMbdata <- function(row)
  # This is not very flexible, as you can see...
  colList <- c(
  commentNames,
- #"COMMENT.CONFIDENCE",
- #"COMMENT.ID",
+ #"COMMENT_CONFIDENCE",
+ #"COMMENT_ID",
  "CH$NAME1",
  "CH$NAME2",
  "CH$NAME3",
@@ -1253,10 +1266,10 @@ readMbdata <- function(row)
  "CH$LINK_CHEMSPIDER",
  "CH$LINK_COMPTOX")
  mbdata[["COMMENT"]] = list()
- #mbdata[["COMMENT"]][["CONFIDENCE"]] <- row[["COMMENT.CONFIDENCE"]]
+ #mbdata[["COMMENT"]][["CONFIDENCE"]] <- row[["COMMENT_CONFIDENCE"]]
  # Again, our ID field. 
- #mbdata[["COMMENT"]][["ID"]] <- row[["COMMENT.ID"]]
- mbdata[["COMMENT"]][gsub(x = commentNames, pattern = "^COMMENT\\.", replacement = "")] <- row[commentNames]
+ #mbdata[["COMMENT"]][["ID"]] <- row[["COMMENT_D"]]
+ mbdata[["COMMENT"]][gsub(x = commentNames, pattern = "^COMMENT\\_", replacement = "")] <- row[commentNames]
 
  names = c(row[["CH$NAME1"]], row[["CH$NAME2"]], row[["CH$NAME3"]], row[["CH$NAME4"]], row[["CH$NAME5"]])
  names = names[which(!is.na(names))]
@@ -1283,8 +1296,8 @@ readMbdata <- function(row)
  mbdata[["CH$LINK"]] <- link
 
  ## SP$SAMPLE
- if(all(nchar(row[["SP.SAMPLE"]]) > 0, row[["SP.SAMPLE"]] != "NA", !is.na(row[["SP.SAMPLE"]]), na.rm = TRUE))
- mbdata[['SP$SAMPLE']] <- row[["SP.SAMPLE"]]
+ if(all(nchar(row[["SP_SAMPLE"]]) > 0, row[["SP_SAMPLE"]] != "NA", !is.na(row[["SP_SAMPLE"]]), na.rm = TRUE))
+ mbdata[['SP$SAMPLE']] <- row[["SP_SAMPLE"]]
 
  if(!is.na(row[["AUTHORS"]]))
  mbdata[["AUTHORS"]] = row[["AUTHORS"]]