From 4b7e59dc75373eb3200631d19f58771e44227546 Mon Sep 17 00:00:00 2001
From: Andrew Gene Brown <andrew.g.brown@usda.gov>
Date: Tue, 24 Sep 2024 18:23:41 -0700
Subject: [PATCH] fetchNASIS: update QC messages by adding to soilDB.env as
 needed for fragments/artifacts >100%

---
 R/fetchNASIS_pedons.R           | 15 ++++++++++++++-
 R/get_site_data_from_NASIS_db.R |  2 +-
 R/simplifyArtifactData.R        |  5 ++++-
 R/simplifyFragmentData.R        |  7 +++++--
 4 files changed, 24 insertions(+), 5 deletions(-)

diff --git a/R/fetchNASIS_pedons.R b/R/fetchNASIS_pedons.R
index 70fa3081..9d1c428f 100644
--- a/R/fetchNASIS_pedons.R
+++ b/R/fetchNASIS_pedons.R
@@ -256,10 +256,23 @@
       )
     }
   }
+  
   if (exists('dup.pedon.ids', envir = get_soilDB_env()))
     if (length(get('dup.pedon.ids', envir = get_soilDB_env())) > 0)
       message("-> QC: duplicate pedons: \n\tUse `get('dup.pedon.ids', envir=get_soilDB_env())` for pedon record IDs (peiid)")
-
+  
+  if (exists('rock.fragment.volume.gt100.phiid', envir = get_soilDB_env()))
+    if (length(get('rock.fragment.volume.gt100.phiid', envir = get_soilDB_env())) > 0)
+      message("-> QC: pedon horizons with rock fragment volume >=100%: \n\tUse `get('rock.fragment.volume.gt100.phiid', envir=get_soilDB_env())` for pedon horizon record IDs (phiid)")
+  
+  if (exists('artifact.volume.gt100.phiid', envir = get_soilDB_env()))
+    if (length(get('artifact.volume.gt100.phiid', envir = get_soilDB_env())) > 0)
+      message("-> QC: pedon horizons with artifact volume >=100%: \n\tUse `get('artifact.volume.gt100.phiid', envir=get_soilDB_env())` for pedon horizon record IDs (phiid)")
+  
+  if (exists('surface.fragment.cover.gt100.siteobsiid', envir = get_soilDB_env()))
+    if (length(get('surface.fragment.cover.gt100.siteobsiid', envir = get_soilDB_env())) > 0)
+      message("-> QC: pedons with surface fragment cover >=100%: \n\tUse `get('surface.fragment.cover.gt100.siteobsiid', envir=get_soilDB_env())` for site observation record IDs (siteobsiid)")
+  
   # set NASIS component specific horizon identifier
   if (!fill & length(filled.ids) == 0) {
     res <- try(hzidname(hz_data) <- 'phiid')
diff --git a/R/get_site_data_from_NASIS_db.R b/R/get_site_data_from_NASIS_db.R
index bbc3f4d2..d7594ebb 100644
--- a/R/get_site_data_from_NASIS_db.R
+++ b/R/get_site_data_from_NASIS_db.R
@@ -136,7 +136,7 @@ ORDER BY pedon_View_1.peiid ;"
 	
 	phs <- simplifyFragmentData(
 	  uncode(sfr, dsn = dsn),
-	  id.var = "peiid",
+	  id.var = "siteobsiid",
 	  vol.var = "sfragcov",
 	  prefix = "sfrag",
 	  msg = "surface fragment cover"
diff --git a/R/simplifyArtifactData.R b/R/simplifyArtifactData.R
index 1ccfa49c..fa23f5cf 100644
--- a/R/simplifyArtifactData.R
+++ b/R/simplifyArtifactData.R
@@ -102,7 +102,10 @@ simplifyArtifactData <- function(art, id.var, vol.var = "huartvol", nullFragsAre
     idx <- unique(unlist(lapply(gt.100[class.idx], which)))
     flagged.ids <- art.wide[[id.var]][idx]
     
-    message(sprintf("NOTE: artifact volume >= 100%% in %s: %s", id.var, paste(flagged.ids, collapse = ",")))
+    gt100nm <- paste0("artifact.volume.gt100.", id.var)
+    assign(gt100nm, value = flagged.ids, envir = get_soilDB_env())
+    
+    message(sprintf("NOTE: some %s have artifact volume >= 100%%", id.var))
   }
 
   # compute total artifacts
diff --git a/R/simplifyFragmentData.R b/R/simplifyFragmentData.R
index fbe67dba..78ab570b 100644
--- a/R/simplifyFragmentData.R
+++ b/R/simplifyFragmentData.R
@@ -229,8 +229,11 @@ simplifyFragmentData <- function(rf, id.var, vol.var = "fragvol", prefix = "frag
     class.idx <- which(gt.100.matches)
     idx <- unique(unlist(lapply(gt.100[class.idx], which)))
     flagged.ids <- rf.wide[[id.var]][idx]
-
-    message(sprintf("NOTE: %s >= 100%% in %s: %s", msg, id.var, paste(flagged.ids, collapse = ",")))
+    
+    gt100nm <- paste0(gsub(" ", ".", msg), ".gt100.", id.var)
+    assign(gt100nm, value = flagged.ids, envir = get_soilDB_env())
+    
+    message(sprintf("NOTE: some %s have %s >= 100%%", id.var, msg))
   }
 
   # compute total fragments