Read all mappings from files

synoptic/L0-instrument.qmd

@@ -61,11 +61,15 @@ Working directory is `r getwd()`.
 
 ```{r AquaTROLL600}
 message("Reading aquaTROLL600 column mappings...")
-map_raw <- read_csv(file.path(INS_MAPS, "aquaTROLL600.csv"), col_types = "cc")
-map <- map_raw$datalogger_name
-names(map) <- map_raw$aquaTROLL600_name
+map_raw <- read_csv(file.path(INS_MAPS, "aquaTROLL600_fields.csv"), col_types = "cc")
+map <- map_raw$datalogger_field
+names(map) <- map_raw$aquaTROLL600_field
 
-logger_map <- c("26" = "Compass_CRC_TR_302") # TODO - put into a metadata table
+troll_map <- read_csv(file.path(INS_MAPS, "aquaTROLL600_devices.csv"), col_types = "ccc")
+logger_names <- troll_map$Logger
+names(logger_names) <- troll_map$Serial_number
+troll_letters <- troll_map$Letter
+names(troll_letters) <- troll_map$Serial_number
 
 files <- list.files(file.path(RAW, "aquaTROLL600"), 
                     pattern = "*.csv$", 
@@ -81,13 +85,13 @@ for(f in files) {
     if(!grepl("Format Version = 1", x_raw[2])) {
         stop("This file is not in the expected format")
     }
-    device_id <- gsub("Device Id = ", "", x_raw[3])
-    device_id <- gsub(",", "", device_id)
-    message("\tDevice ID = ", device_id)
-    if(!device_id %in% names(logger_map)) {
-        stop("Unknown device! No entry in the logger_map")
+    device_sn <- gsub("Device S/N = ", "", x_raw[6])
+    device_sn <- gsub(",", "", device_sn)
+    message("\tDevice S/N = ", device_sn)
+    if(!device_sn %in% troll_map$Serial_number) {
+        stop("Unknown device! No entry in the troll_map")
     }
-        
+    
     x <- read_csv(I(x_raw[-1:-9]), show_col_types = FALSE)
     message("\tData rows = ", nrow(x))
     
@@ -103,21 +107,21 @@ for(f in files) {
     }
     colnames(x) <- map[colnames(x)]
     # Add the "A" or "B", etc., as specified by the logger map
-    colnames(x)[-1] <- paste0(colnames(x)[-1], "B")
+    colnames(x)[-1] <- paste0(colnames(x)[-1], troll_letters[device_sn])
     
     # Change timestamp to datalogger format; restructure to
     # "Logger","Table","TIMESTAMP","loggernet_variable","value","ID"
     x$TIMESTAMP <- as.character(mdy_hm(x$TIMESTAMP))
     x_out <- pivot_longer(x, -TIMESTAMP, names_to = "loggernet_variable")
-    x_out$Table <- "WaterLevel600B"
-    x_out$Logger <- logger_map[device_id]
+    x_out$Table <- paste0("WaterLevel600", troll_letters[device_sn])
+    x_out$Logger <- logger_names[device_sn]
     
     x_out$ID <- sapply(apply(x_out, 1, paste, collapse = ""),
                        FUN = function(x) {
                            substr(digest::digest(x, algo = "md5"), 1, 16)
                            })
     
-    out_fn <- paste(logger_map[device_id], x_out$Table[1], basename(f), sep = "_")
+    out_fn <- paste(logger_names[device_sn], x_out$Table[1], basename(f), sep = "_")
     message("\tWriting ", out_fn)
     write.csv(x_out, file.path(L0, out_fn), row.names = FALSE)
 }

synoptic/metadata/raw-instrument-mappings/aquaTROLL600_devices.csv

@@ -0,0 +1,2 @@
+Serial_number,Logger,Letter
+848067,Compass_CRC_TR_302,B

synoptic/metadata/raw-instrument-mappings/aquaTROLL600.csv → synoptic/metadata/raw-instrument-mappings/aquaTROLL600_fields.csv

@@ -1,4 +1,4 @@
-datalogger_name,aquaTROLL600_name
+datalogger_field,aquaTROLL600_field
 TIMESTAMP,Date Time
 Aquatroll_ID(1),Device Id (in file header)
 Barometric_Pressure600,16: Barometer (16) mmHg (22)