Merge pull request #19 from ocean-tracking-network/shannon_fixes_rece…

…iver Shannon fixes receiver
ocean-tracking-network · Apr 1, 2024 · 9ad4bda · 9ad4bda
2 parents 3847fd0 + cdfb060
commit 9ad4bda
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Showing 2 changed files with 36 additions and 10 deletions.
diff --git a/R/imos_to_otn_receivers.R b/R/imos_to_otn_receivers.R
@@ -22,31 +22,57 @@ imos_to_otn_receivers <- function(rcvr_dataframe) {
       depth_below_surface,
       receiver_name,
       receiver_status,
-      receiver_recovery_datetime
+      receiver_recovery_datetime,
+      receiver_recovery_latitude,
+      receiver_recovery_longitude
     ) %>%
     mutate(
       BOTTOM_DEPTH = NA,
       RISER_LENGTH = NA,
       CODE_SET = NA,
-      AR_MODEL_NUMBER = NA,
-      AR_SERIAL_NUMBER = NA,
+      AR_MODEL_NO = NA,
+      AR_SERIAL_NO = NA,
       DATA_DOWNLOADED = NA,
       DOWNLOAD_DATE_TIME = NA,
-      COMMENTS = NA
+      COMMENTS = NA,
+      TRANSMITTER = NA,
+      TRANSMITTER_MODEL = NA,
+      DEPLOYED_BY = NA,
+      FILENAME = NA
     ) %>%
     rename(
       OTN_ARRAY = receiver_project_name,
       STATION_NO = station_name,
-      DEPLOY_DATE_TIME = receiver_deployment_datetime,
+      `DEPLOY_DATE_TIME (yyyy-mm-ddThh:mm:ss)` = receiver_deployment_datetime,
       DEPLOY_LAT = receiver_deployment_latitude,
       DEPLOY_LONG = receiver_deployment_longitude,
       INSTRUMENT_DEPTH = depth_below_surface,
       RECOVERED = receiver_status,
-      RECOVER_DATE_TIME = receiver_recovery_datetime
+      RECOVER_DATE_TIME = receiver_recovery_datetime,
+      RECOVER_LAT = receiver_recovery_latitude,
+      RECOVER_LONG = receiver_recovery_longitude
     ) %>%
-    separate(
-      col = receiver_name,
-      into = c("INS_MODEL_NUMBER", "INS_SERIAL_NUMBER", sep = "-")
+    separate_wider_delim(
+      cols = receiver_name,
+      delim = "-",
+      names = c("INS_MODEL_NO", "INS_SERIAL_NO")
+    )
+
+  # We have to do some cleaning up of date formats in the appropriate columns.
+  # First we'll hit them with Lubridate to make sure they're real dates, formatted correctly.
+  # Then, since they need a "T" in there, we'll cast them back to character strings and slot a 'T'
+  # in where once there was whitespace. Simple! I don't love calling multiple near-identical mutates, but I also
+  # don't like how unreadable and cursed it is to do the requisite jiggery-pokery to get multiple functions into a single
+  # mutate(across())
+  rcvr_return <- rcvr_return %>%
+    mutate(
+      across(ends_with("_DATE_TIME"), lubridate::ymd_hms)
+    ) %>%
+    mutate(
+      across(ends_with("_DATE_TIME"), as.character)
+    ) %>%
+    mutate(
+      across(ends_with("_DATE_TIME"), ~ stringr::str_replace(.x, " ", "T"))
     )
 
   # Have to do a little extra manipulation on the dataframe to give "RECOVERED"

diff --git a/R/otn_imos_column_map.R b/R/otn_imos_column_map.R
@@ -94,7 +94,7 @@ otn_imos_column_map <- function(det_dataframe, rcvr_dataframe = NULL, tag_datafr
       WORMS_species_aphia_id = sapply(det_dataframe$scientificname, USE.NAMES = FALSE, FUN = get_aphiaid_from_lookup, lookup = lookup),
       animal_sex = NA,
       receiver_name = receiver,
-      receiver_project_name = receiver_group,
+      receiver_project_name = detectedby,
       transmitter_serial_number = NA,
       transmitter_type = NA,
       transmitter_sensor_type = NA,