From 2d27b9b0b35b56b724c61d834d20203ed8ca54db Mon Sep 17 00:00:00 2001
From: cristinamullin <46969696+cristinamullin@users.noreply.github.com>
Date: Thu, 30 May 2024 10:26:41 -0400
Subject: [PATCH 1/2] Censored and harmonize tab updates

- updates original columns referenced for censored tab table
- removes reference to columns that are no longer in the harmonization reference table in the TADA package (unit elements were removed)
---
 R/mod_censored_data.R |  6 +++---
 R/mod_harmonize_np.R  | 20 ++++++++++----------
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/R/mod_censored_data.R b/R/mod_censored_data.R
index 805105fff..5081b6cc3 100644
--- a/R/mod_censored_data.R
+++ b/R/mod_censored_data.R
@@ -264,16 +264,16 @@ mod_censored_data_server <- function(id, tadat) {
         dat[, c(
           "ResultIdentifier",
           "TADA.CharacteristicName",
-          "TADA.DetectionQuantitationLimitMeasure.MeasureValue",
+          "DetectionQuantitationLimitMeasure.MeasureValue",
           "DetectionQuantitationLimitMeasure.MeasureUnitCode",
           "TADA.ResultMeasureValue",
           "TADA.ResultMeasure.MeasureUnitCode"
         )]
       dat <-
         dat %>% dplyr::rename(
-          "Estimated Detection Limit Value" = TADA.ResultMeasureValue,
-          "Original Detection Limit Value" = TADA.DetectionQuantitationLimitMeasure.MeasureValue,
+          "Original Detection Limit Value" = DetectionQuantitationLimitMeasure.MeasureValue,
           "Original Unit" = DetectionQuantitationLimitMeasure.MeasureUnitCode,
+          "Estimated Detection Limit Value" = TADA.ResultMeasureValue,
           "Estimated Unit" = TADA.ResultMeasure.MeasureUnitCode
         )
       censdat$exdat <-
diff --git a/R/mod_harmonize_np.R b/R/mod_harmonize_np.R
index 91fdbfdf7..86290788c 100644
--- a/R/mod_harmonize_np.R
+++ b/R/mod_harmonize_np.R
@@ -52,9 +52,9 @@ mod_harmonize_np_server <- function(id, tadat) {
       "Target.TADA.MethodSpeciationName",
       "TADA.SpeciationAssumptions",
       "Target.TADA.SpeciationConversionFactor",
-      "TADA.ResultMeasure.MeasureUnitCode",
-      "Target.TADA.ResultMeasure.MeasureUnitCode",
-      "Target.TADA.UnitConversionFactor",
+      #"TADA.ResultMeasure.MeasureUnitCode", #no longer in harmonization template
+      #"Target.TADA.ResultMeasure.MeasureUnitCode", #no longer in harmonization template
+      #"Target.TADA.UnitConversionFactor", #no longer in harmonization template
       "HarmonizationGroup"
     )
 
@@ -77,9 +77,9 @@ mod_harmonize_np_server <- function(id, tadat) {
         Target.TADA.MethodSpeciationName = "Target Speciation",
         TADA.SpeciationAssumptions = "Speciation Assumptions",
         Target.TADA.SpeciationConversionFactor = "Speciation Conversion Factor (to AS N or AS P)",
-        TADA.ResultMeasure.MeasureUnitCode = "Unit",
-        Target.TADA.ResultMeasure.MeasureUnitCode = "Target Unit",
-        Target.TADA.UnitConversionFactor = "Unit Conversion Factor",
+        # TADA.ResultMeasure.MeasureUnitCode = "Unit",
+        # Target.TADA.ResultMeasure.MeasureUnitCode = "Target Unit",
+        # Target.TADA.UnitConversionFactor = "Unit Conversion Factor",
         HarmonizationGroup = "Harmonization Group"
       )
       harm$ref <- ref
@@ -123,9 +123,9 @@ mod_harmonize_np_server <- function(id, tadat) {
           Target.TADA.MethodSpeciationName = "Target Speciation",
           TADA.SpeciationAssumptions = "Speciation Assumptions",
           Target.TADA.SpeciationConversionFactor = "Speciation Conversion Factor (to AS N or AS P)",
-          TADA.ResultMeasure.MeasureUnitCode = "Unit",
-          Target.TADA.ResultMeasure.MeasureUnitCode = "Target Unit",
-          Target.TADA.UnitConversionFactor = "Unit Conversion Factor",
+          # TADA.ResultMeasure.MeasureUnitCode = "Unit",
+          # Target.TADA.ResultMeasure.MeasureUnitCode = "Target Unit",
+          # Target.TADA.UnitConversionFactor = "Unit Conversion Factor",
           HarmonizationGroup = "Harmonization Group"
         )
         harm$ref <- ref
@@ -157,7 +157,7 @@ mod_harmonize_np_server <- function(id, tadat) {
         selection = "none", rownames = FALSE
       ) %>%
         DT::formatStyle(columns = names(harm$ref), `font-size` = "12px") %>%
-        DT::formatStyle(columns = c("TADA.CharacteristicName", "TADA.ResultSampleFractionText", "TADA.MethodSpeciationName", "TADA.ResultMeasure.MeasureUnitCode"), backgroundColor = "#2e6da4", color = "white")
+        DT::formatStyle(columns = c("TADA.CharacteristicName", "TADA.ResultSampleFractionText", "TADA.MethodSpeciationName"), backgroundColor = "#2e6da4", color = "white")
     })
 
     # apply synonym ref to data when button is pushed

From e09c26e36bc25550013a2806a2f724d454e9e4a0 Mon Sep 17 00:00:00 2001
From: cristinamullin <46969696+cristinamullin@users.noreply.github.com>
Date: Thu, 30 May 2024 10:47:59 -0400
Subject: [PATCH 2/2] define global variables

---
 R/utils.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/utils.R b/R/utils.R
index f18fcf8e1..f04d2a9f1 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -22,5 +22,6 @@ utils::globalVariables(c(
   "nd_method", "nd_mult", "od_method", "org_table",
   "organization", "original_source", "project", "sampleMedia",
   "selected_filters", "selected_flags", "siteType",
-  "siteid", "startDate", "statecode", "od_mult", "field_sel"
+  "siteid", "startDate", "statecode", "od_mult", "field_sel", 
+  "DetectionQuantitationLimitMeasure.MeasureValue"
 ))