From a696075ada2c5c3f84dc7c46634e7f26b55c989c Mon Sep 17 00:00:00 2001
From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com>
Date: Wed, 25 Oct 2023 13:05:44 -0400
Subject: [PATCH 1/4] parse NAs when reading in json

---
 lib/Utils.groovy | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/Utils.groovy b/lib/Utils.groovy
index fa61a6af..cebda435 100644
--- a/lib/Utils.groovy
+++ b/lib/Utils.groovy
@@ -15,6 +15,8 @@ class Utils {
      */
   static def readMeta(file) {
     def meta = new JsonSlurper().parse(file)
+    meta = meta.each{ key, value -> meta[key] = Utils.parseNA(value) }
+
     return(meta)
   }
 
@@ -38,8 +40,9 @@ class Utils {
    */
   static def getMetaVal(file, key){
     def obj = new JsonSlurper().parse(file)
+    value = Utils.parseNA(obj[key])
 
-    return(obj[key])
+    return(value)
   }
 
 

From cd8135c9116373cc57fa0b681f5e5d736b9cbbb9 Mon Sep 17 00:00:00 2001
From: Ally Hawkins <ally.hawkins@ccdatalab.org>
Date: Thu, 26 Oct 2023 09:25:56 -0500
Subject: [PATCH 2/4] update parseNA to deal with non strings

---
 lib/Utils.groovy | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/lib/Utils.groovy b/lib/Utils.groovy
index cebda435..49bb6b85 100644
--- a/lib/Utils.groovy
+++ b/lib/Utils.groovy
@@ -55,9 +55,12 @@ class Utils {
    */
   static def parseNA(str) {
     if (str){
-      str.toLowerCase() in ['na','n/a','nan']? '' : str
-    } else {
+      if (str instanceof String) { // has to be a string to have NA vals replaced
+        str.toLowerCase() in ['na','n/a','nan']? '' : str
+      } else { // not a string, so just return the unmodified value
+        str
+      }
+    } else { // all falsey values get turned into empty strings
       ''
     }
-   }
 }

From d1fa12b4ed9da32fe647d676fda20e037b58cbef Mon Sep 17 00:00:00 2001
From: Ally Hawkins <ally.hawkins@ccdatalab.org>
Date: Thu, 26 Oct 2023 11:15:59 -0500
Subject: [PATCH 3/4] Use this and missing bracket

---
 lib/Utils.groovy | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/lib/Utils.groovy b/lib/Utils.groovy
index 49bb6b85..de3df690 100644
--- a/lib/Utils.groovy
+++ b/lib/Utils.groovy
@@ -15,7 +15,7 @@ class Utils {
      */
   static def readMeta(file) {
     def meta = new JsonSlurper().parse(file)
-    meta = meta.each{ key, value -> meta[key] = Utils.parseNA(value) }
+    meta = meta.each{ key, value -> meta[key] = this.parseNA(value) }
 
     return(meta)
   }
@@ -40,7 +40,7 @@ class Utils {
    */
   static def getMetaVal(file, key){
     def obj = new JsonSlurper().parse(file)
-    value = Utils.parseNA(obj[key])
+    def value = this.parseNA(obj[key])
 
     return(value)
   }
@@ -63,4 +63,5 @@ class Utils {
     } else { // all falsey values get turned into empty strings
       ''
     }
-}
+  }
+}
\ No newline at end of file

From bddcbd1c8ade4548f9a9ed362d9594c9104af0ce Mon Sep 17 00:00:00 2001
From: Ally Hawkins <ally.hawkins@ccdatalab.org>
Date: Thu, 26 Oct 2023 11:23:02 -0500
Subject: [PATCH 4/4] new line

---
 lib/Utils.groovy | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/Utils.groovy b/lib/Utils.groovy
index de3df690..01242ac4 100644
--- a/lib/Utils.groovy
+++ b/lib/Utils.groovy
@@ -64,4 +64,4 @@ class Utils {
       ''
     }
   }
-}
\ No newline at end of file
+}