From b0a8c314b021a11b334cd7533f938b46c05a9bfb Mon Sep 17 00:00:00 2001
From: labkey-jeckels <jeckels@labkey.com>
Date: Thu, 29 Apr 2021 15:05:24 -0700
Subject: [PATCH] Omit pedigree plot generations where both dam and sire are
 unknown

---
 .../reports/schemas/study/Pedigree/Pedigree.r   | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/ehr/resources/reports/schemas/study/Pedigree/Pedigree.r b/ehr/resources/reports/schemas/study/Pedigree/Pedigree.r
index 5b51f09ce..b9b6386b6 100644
--- a/ehr/resources/reports/schemas/study/Pedigree/Pedigree.r
+++ b/ehr/resources/reports/schemas/study/Pedigree/Pedigree.r
@@ -15,8 +15,7 @@ library(Rlabkey)
 
 labkey.setCurlOptions(ssl_verifypeer = FALSE, ssl_verifyhost = FALSE)
 
-
-if ((length(labkey.data$id) == 0) || all(is.na(labkey.data$dam) & is.na(labkey.data$sire))) {
+if ((length(labkey.data$id) == 0) | (is.na(labkey.data$dam) & is.na(labkey.data$sire))){
     png(filename="${imgout:myscatterplot}", width = 650, height = 150);
     plot(0, 0, type='n', xaxt='n', yaxt='n', bty='n', ann=FALSE  )
     title(main = "No pedigree data found for selected animal(s).", sub = NULL, xlab = NULL, ylab = NULL,
@@ -185,6 +184,8 @@ if ((length(labkey.data$id) == 0) || all(is.na(labkey.data$dam) & is.na(labkey.d
         return (substr(lineNL, 1, nchar(lineNL) - 1));
      };
 
+    unknownIdIndex = 1
+
     #[Quoc: remove ]
     #The pedigree program expects all individuals to have either 2 parents or 1.
     #Sometimes the father is not known. For missing parents we give them a unique id and
@@ -200,8 +201,9 @@ if ((length(labkey.data$id) == 0) || all(is.na(labkey.data$dam) & is.na(labkey.d
         if (length(damIndex) == 0) damIndex <- which(allPed$Id == ped$Dam[i]);
         if (length(sireIndex) == 0) sireIndex <- which(allPed$Id == ped$Sire[i]);
 
-        if(is.na(ped$Sire[i])){
-            xt <- sample (1:99,1)
+        if((is.na(ped$Sire[i]))& (!is.na(ped$Dam[i]))){
+            xt <- unknownIdIndex
+            unknownIdIndex <- unknownIdIndex + 1
             #typeof(ped$Sire);
             #typeof(xt);
             ped$Sire[i] <- paste('xxs',xt)
@@ -209,8 +211,9 @@ if ((length(labkey.data$id) == 0) || all(is.na(labkey.data$dam) & is.na(labkey.d
             #print(ped$Dam[i])
             #print(ped$Sire[i])
         }
-        if(is.na(ped$Dam[i])){
-                xt <- sample (1:99,1)
+        if((is.na(ped$Dam[i]))& (!is.na(ped$Sire[i]))){
+                xt <- unknownIdIndex
+                unknownIdIndex <- unknownIdIndex + 1
                 #typeof(ped$Sire);
                 #typeof(xt);
                 ped$Dam[i] <- paste ('xxd',xt);
@@ -302,4 +305,4 @@ if ((length(labkey.data$id) == 0) || all(is.na(labkey.data$dam) & is.na(labkey.d
         legend(x = "bottomright", legend=leg.txt, pch=c(0, 1, 47), col=c('blue', 'red', 'black'), inset = 0.1, cex=1, pt.cex = 1.8)
         #dev.off();
     }
-};
\ No newline at end of file
+};