Award Numbers function

R/award_script.R

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+###Produce a list of award numbers in our metadata and their information
+
+#####First use download_data_objects from datamgmt
+download_data_objects <- function(mn, data_pids, out_paths, n_max = 3) {
+  stopifnot(methods::is(mn, "MNode"))
+  stopifnot(is.character(data_pids))
+
+  for (i in seq_along(out_paths)) {
+
+    if (file.exists(out_paths[i])) {
+      warning(call. = FALSE,
+              paste0("The file ", out_paths[i], " already exists. Skipping download."))
+    } else {
+      n_tries <- 0
+      dataObj <- "error"
+
+      while (dataObj[1] == "error" & n_tries < n_max) {
+        dataObj <- tryCatch({
+          dataone::getObject(mn, data_pids[i])
+        }, error = function(e) {return("error")})
+
+        n_tries <- n_tries + 1
+      }
+      writeBin(dataObj, out_paths[i])
+    }
+  }
+
+  return(invisible())
+}
+######
+
+#Function with arguments: mn, metapid
+getAwardNumbers <- function(mn, metapid){
+  #outputs list of pid, raw_award_string, award_number, title of xml file
+
+  stopifnot(methods::is(mn, "MNode"))
+  stopifnot(is.character(metapid))
+
+  #get outpath name from metapid
+  systema <- getSystemMetadata(mn, metapid)
+  systema_name <- systema@fileName
+  outpath <- paste("/home/mnguyen/", systema_name, sep = "")
+
+  #download data from metapid
+  download_data_objects(mn, c(metapid), c(outpath))
+  eml_file <- outpath
+
+  #get xml from metapid
+  eml <- read_eml(eml_file) #read in eml_file
+  list <- list() #will be output list
+
+  #filename 
+  filename <- eml_file
+  list[["filename"]] <- filename
+
+  #pid
+  list[["metapid"]] <- metapid
+
+  #the raw award string numbers
+  raw_award_string <- c()
+  funding <- eml@dataset@project@funding@para
+  for(i in 1:length(funding)){
+    award <- funding@.Data[[i]]@.Data[[1]]
+    raw_award_string[i] <- as_list(award)[[1]]
+  }
+  list[["raw_award_string"]] <- raw_award_string
+
+  #award_number
+  award_number <- str_extract_all(string = raw_award_string, pattern ="[0-9]+")
+  list[["award_number"]] <- unlist(award_number)
+
+  #title
+  title <- eml@dataset@title@.Data[[1]]@.Data
+  list[["title"]] <- title
+
+  return(list)
+}

R/function.R

@@ -0,0 +1,77 @@
+###Produce a list of award numbers in our metadata and their information
+
+#####First use download_data_objects from datamgmt
+download_data_objects <- function(mn, data_pids, out_paths, n_max = 3) {
+  stopifnot(methods::is(mn, "MNode"))
+  stopifnot(is.character(data_pids))
+
+  for (i in seq_along(out_paths)) {
+
+    if (file.exists(out_paths[i])) {
+      warning(call. = FALSE,
+              paste0("The file ", out_paths[i], " already exists. Skipping download."))
+    } else {
+      n_tries <- 0
+      dataObj <- "error"
+
+      while (dataObj[1] == "error" & n_tries < n_max) {
+        dataObj <- tryCatch({
+          dataone::getObject(mn, data_pids[i])
+        }, error = function(e) {return("error")})
+
+        n_tries <- n_tries + 1
+      }
+      writeBin(dataObj, out_paths[i])
+    }
+  }
+
+  return(invisible())
+}
+######
+
+#Function with arguments: mn, metapid
+getAwardNumbers <- function(mn, metapid){
+  #outputs list of pid, raw_award_string, award_number, title of xml file
+
+  stopifnot(methods::is(mn, "MNode"))
+  stopifnot(is.character(metapid))
+
+  #get outpath name from metapid
+  systema <- getSystemMetadata(mn, metapid)
+  systema_name <- systema@fileName
+  outpath <- paste("/home/mnguyen/", systema_name, sep = "")
+
+  #download data from metapid
+  download_data_objects(mn, c(metapid), c(outpath))
+  eml_file <- outpath
+
+  #get xml from metapid
+  eml <- read_eml(eml_file) #read in eml_file
+  list <- list() #will be output list
+
+  #filename 
+  filename <- eml_file
+  list[["filename"]] <- filename
+
+  #pid
+  list[["metapid"]] <- metapid
+
+  #the raw award string numbers
+  raw_award_string <- c()
+  funding <- eml@dataset@project@funding@para
+  for(i in 1:length(funding)){
+    award <- funding@.Data[[i]]@.Data[[1]]
+    raw_award_string[i] <- as_list(award)[[1]]
+  }
+  list[["raw_award_string"]] <- raw_award_string
+
+  #award_number
+  award_number <- str_extract_all(string = raw_award_string, pattern ="[0-9]+")
+  list[["award_number"]] <- unlist(award_number)
+
+  #title
+  title <- eml@dataset@title@.Data[[1]]@.Data
+  list[["title"]] <- title
+
+  return(list)
+}