Add generic funtion for parsing ncbi data

R/ncbi_meta.R

@@ -0,0 +1,54 @@
+#' Parse NCBI sequence metadata
+#' 
+#' This function can be used to parse various non-sequence data sets from NCBI
+#' into a tibble. The function currently supports parsing NCBI BioSample data
+#' from XML format.
+#' @param meta character; either a character vector containing a data set that
+#' was retrieved through \code{rentrez::entrez_fetch()} or a path to an file
+#' that was downloaded from NCBI.
+#' @param db character; the NCBI database from which the data was retrieved.
+#' Currently only \code{"biosample"} is supported.
+#' @param format character; the format of the data set. Currently only
+#' \code{"xml"} is supported.
+#' @param verbose logical; Should verbose messages be printed to console?
+#' @examples
+#' \dontrun{
+#' data(examples)
+#' 
+#' # NCBI BioSample, fully programmatic access
+#' 
+#' # Get internal BioSample UID for BioSample ID
+#' biosample_uid <- get_uid(examples$biosample, db = "biosample")
+#' # Get metadata in XML format
+#' meta_xml <- rentrez::entrez_fetch(
+#'   db = "biosample",
+#'   id = biosample_uid$uid,
+#'   rettype = "full",
+#'   retmode = "xml"
+#' )
+#' # Parse XML
+#' ncbi_meta(meta = meta_xml, db = "biosample", format = "xml")
+#' 
+#' # NCBI BioSample, download XML file from NCBI and parse
+#' 
+#' # Manually download the XML file
+#' # https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN02714232
+#' # upper right corner -> send to -> file -> format = full (xml) -> create file
+#' # Parse XML
+#' ncbi_meta(meta = "biosample_result.xml", db = "biosample", format = "xml")
+#' }
+#' @export
+ncbi_meta <- function(
+  meta,
+  db,
+  format = "xml",
+  verbose = getOption("verbose")
+) {
+  f <- get(paste("ncbi_meta", db, format, sep = "_"))
+  if (db == "biosample" & format == "xml") {
+    out <- f(meta, verbose)
+  } else {
+    out <- tibble::tibble()
+  }
+  return(out)
+}

R/ncbi_meta_biosample.R

@@ -6,32 +6,6 @@
 #' that was retrieved through \code{rentrez::entrez_fetch()} or a path to an xml
 #' file that was downloaded from NCBI BioSample.
 #' @param verbose logical; Should verbose messages be printed to console?
-#' @examples
-#' \dontrun{
-#' data(examples)
-#' 
-#' # Option 1 - fully programmatic access
-#' 
-#' # Get internal BioSample UID for BioSample ID
-#' biosample_uid <- get_uid(examples$biosample, db = "biosample")
-#' # Get metadata in XML format
-#' meta_xml <- rentrez::entrez_fetch(
-#'   db = "biosample",
-#'   id = biosample_uid$uid,
-#'   rettype = "full",
-#'   retmode = "xml"
-#' )
-#' # Parse XML
-#' ncbi_meta_biosample_xml(meta_xml)
-#' 
-#' # Option 2 - download XML file from NCBI and parse
-#' 
-#' # Manually download the XML file
-#' # https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN02714232
-#' # upper right corner -> send to -> file -> format = full (xml) -> create file
-#' # Parse XML
-#' ncbi_meta_biomsample_xml("biosample_result.xml")
-#' }
 ncbi_meta_biosample_xml <- function(
     biosample_xml,
     verbose = getOption("verbose")