add column that indicates when otoliths were the type of age structur…

…e collected, and an option to include an additional column for alternate types of structures collected
pbs-assess · Nov 15, 2024 · 894117e · 894117e
1 parent 5495a76
commit 894117e
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diff --git a/R/get-all-survey-samples.R b/R/get-all-survey-samples.R
@@ -43,6 +43,9 @@
 #' @param return_dna_info Should DNA container ids and sample type be returned?
 #'   This can create duplication of specimen ids for some species.  Defaults to
 #'   FALSE.
+#' @param return_specimen_type Should non-otolith structure types be returned?
+#'   This can create duplication of specimen ids for some species.  Defaults to
+#'   FALSE.
 #' @param quiet_option Default option, `"message"`, suppresses messages from
 #'   sections of code with lots of `join_by` messages. Any other string will allow
 #'   messages.
@@ -63,6 +66,7 @@ get_all_survey_samples <- function(species, ssid = NULL,
                                    remove_bad_data = TRUE,
                                    remove_duplicates = TRUE,
                                    return_dna_info = FALSE,
+                                   return_specimen_type = FALSE,
                                    drop_na_columns = TRUE,
                                    quiet_option = "message") {
   .q <- read_sql("get-all-survey-samples.sql")
@@ -115,6 +119,14 @@ get_all_survey_samples <- function(species, ssid = NULL,
 
   .d <- run_sql("GFBioSQL", .q)
 
+  ## ALTERNATE_SPECIMEN_TYPE can cause duplication for some species with multiple types collected per individual
+  ## Could do something about record duplication with multiple samples like combining or not returning them?
+  if (!return_specimen_type) {
+    .d <- .d |>
+      select(-ALTERNATE_SPECIMEN_TYPE) |>
+      distinct()
+  }
+
   names(.d) <- tolower(names(.d))
 
   if (nrow(.d) < 1) {

diff --git a/inst/sql/get-all-survey-samples.sql b/inst/sql/get-all-survey-samples.sql
@@ -38,6 +38,8 @@ SELECT
   SM.SPECIES_CATEGORY_CODE,
   SM.SAMPLE_SOURCE_CODE,
   CASE WHEN SC.SPECIMEN_COLLECTED_IND = 'Y' OR SC.SPECIMEN_COLLECTED_IND = 'y' THEN 1 ELSE 0 END AS AGE_SPECIMEN_COLLECTED,
+  CASE WHEN SC1.SPECIMEN_COLLECTED_IND = 'Y' OR SC1.SPECIMEN_COLLECTED_IND = 'y' THEN 1 ELSE 0 END AS OTOLITH_COLLECTED,
+  CA.COLLECTED_ATTRIBUTE_DESC AS ALTERNATE_SPECIMEN_TYPE,
   DNA.STORAGE_CONTAINER_TYPE_CODE AS DNA_SAMPLE_TYPE,
   DNA.STORAGE_CONTAINER_SUB_ID AS DNA_CONTAINER_ID,
   CASE WHEN SM.GEAR_CODE IN (1, 6, 8, 11, 14, 16) THEN ISNULL(TRSP.USABILITY_CODE, 0)
@@ -82,6 +84,19 @@ SELECT
 		FROM GFBioSQL.dbo.SPECIMEN_COLLECTED
 		WHERE COLLECTED_ATTRIBUTE_CODE BETWEEN 20 AND 25
 		GROUP BY SAMPLE_ID, SPECIMEN_ID, SPECIMEN_COLLECTED_IND) SC ON SP.SPECIMEN_ID = SC.SPECIMEN_ID AND SP.SAMPLE_ID = SC.SAMPLE_ID
+  LEFT JOIN (SELECT SAMPLE_ID,
+                    MIN(SPECIMEN_ID) AS SPECIMEN_ID,
+                    SPECIMEN_COLLECTED_IND AS SPECIMEN_COLLECTED_IND
+		FROM GFBioSQL.dbo.SPECIMEN_COLLECTED
+		WHERE COLLECTED_ATTRIBUTE_CODE = 20
+		GROUP BY SAMPLE_ID, SPECIMEN_ID, SPECIMEN_COLLECTED_IND) SC1 ON SP.SPECIMEN_ID = SC1.SPECIMEN_ID AND SP.SAMPLE_ID = SC1.SAMPLE_ID
+  LEFT JOIN (SELECT SAMPLE_ID,
+                    MIN(SPECIMEN_ID) AS SPECIMEN_ID,
+                    COLLECTED_ATTRIBUTE_CODE
+		FROM GFBioSQL.dbo.SPECIMEN_COLLECTED
+		WHERE COLLECTED_ATTRIBUTE_CODE BETWEEN 21 AND 29 AND (SPECIMEN_COLLECTED_IND = 'Y' OR SPECIMEN_COLLECTED_IND = 'y')
+		GROUP BY SAMPLE_ID, SPECIMEN_ID, COLLECTED_ATTRIBUTE_CODE) SC2 ON SP.SPECIMEN_ID = SC2.SPECIMEN_ID AND SP.SAMPLE_ID = SC2.SAMPLE_ID
+  LEFT JOIN COLLECTED_ATTRIBUTE CA ON CA.COLLECTED_ATTRIBUTE_CODE = SC2.COLLECTED_ATTRIBUTE_CODE
 WHERE TRIP_SUB_TYPE_CODE IN (2, 3) AND
    ISNULL(G.SURVEY_SERIES_ID, S.SURVEY_SERIES_ID) <> 0
 -- insert species here