From 1b14464a6c7594997ae2bf595ba9c69b3dd6a74a Mon Sep 17 00:00:00 2001
From: Brian Schlining <bschlining@gmail.com>
Date: Mon, 21 Oct 2024 16:52:15 -0700
Subject: [PATCH] empty values are returned as null

---
 project/build.properties                         |  2 +-
 src/main/scala/org/fathomnet/worms/Data.scala    |  2 ++
 .../fathomnet/worms/io/MutableWormsNode.scala    |  2 +-
 .../org/fathomnet/worms/io/WormsConcept.scala    | 10 +++++-----
 .../scala/org/fathomnet/worms/io/model.scala     | 16 +++++++++-------
 5 files changed, 18 insertions(+), 14 deletions(-)

diff --git a/project/build.properties b/project/build.properties
index ee4c672..bc73906 100644
--- a/project/build.properties
+++ b/project/build.properties
@@ -1 +1 @@
-sbt.version=1.10.1
+sbt.version=1.10.3
diff --git a/src/main/scala/org/fathomnet/worms/Data.scala b/src/main/scala/org/fathomnet/worms/Data.scala
index 217aebc..8e19010 100644
--- a/src/main/scala/org/fathomnet/worms/Data.scala
+++ b/src/main/scala/org/fathomnet/worms/Data.scala
@@ -69,3 +69,5 @@ final case class Data(rootNode: WormsNode, wormsConcepts: Seq[WormsConcept]):
             case (parent, Some(child)) =>
                 val newParent = parent.copy(children = Seq(child))
                 Some(newParent)
+
+
diff --git a/src/main/scala/org/fathomnet/worms/io/MutableWormsNode.scala b/src/main/scala/org/fathomnet/worms/io/MutableWormsNode.scala
index 23e4351..621b861 100644
--- a/src/main/scala/org/fathomnet/worms/io/MutableWormsNode.scala
+++ b/src/main/scala/org/fathomnet/worms/io/MutableWormsNode.scala
@@ -71,7 +71,7 @@ object MutableWormsNodeBuilder:
         rows.filter(wc =>
             val lr = wc.rank.toLowerCase
             // (!lr.contains("species") && !lr.contains("variety")) || (!wc.isExtinct && wc.isMarine)
-            (!lr.contains("species") && !lr.contains("variety")) || (!wc.isExtinct)
+            (!lr.contains("species") && !lr.contains("variety")) || (!wc.isExtinct.getOrElse(false))
         )
 
     /**
diff --git a/src/main/scala/org/fathomnet/worms/io/WormsConcept.scala b/src/main/scala/org/fathomnet/worms/io/WormsConcept.scala
index 717bc05..5c8b696 100644
--- a/src/main/scala/org/fathomnet/worms/io/WormsConcept.scala
+++ b/src/main/scala/org/fathomnet/worms/io/WormsConcept.scala
@@ -21,11 +21,11 @@ final case class WormsConcept(
     parentId: Option[Long],
     names: Seq[WormsConceptName],
     rank: String,
-    isMarine: Boolean = false, 
-    isFreshwater: Boolean = false,
-    isTerrestrial: Boolean = false,
-    isExtinct: Boolean = false,
-    isBrackish: Boolean = false
+    isMarine: Option[Boolean] = None, 
+    isFreshwater: Option[Boolean] = None,
+    isTerrestrial: Option[Boolean] = None,
+    isExtinct: Option[Boolean] = None,
+    isBrackish: Option[Boolean] = None
 )
 
 object WormsConcept:
diff --git a/src/main/scala/org/fathomnet/worms/io/model.scala b/src/main/scala/org/fathomnet/worms/io/model.scala
index b3b6317..5811bbc 100644
--- a/src/main/scala/org/fathomnet/worms/io/model.scala
+++ b/src/main/scala/org/fathomnet/worms/io/model.scala
@@ -62,17 +62,19 @@ object VernacularName:
     def read(file: String): List[VernacularName] = readFile(file, VernacularName.from)
 
 final case class SpeciesProfile(taxonID: String, 
-        isMarine: Boolean, 
-        isFreshwater: Boolean,
-        isTerrestrial: Boolean,
-        isExtinct: Boolean,
-        isBrackish: Boolean):
+        isMarine: Option[Boolean], 
+        isFreshwater: Option[Boolean],
+        isTerrestrial: Option[Boolean],
+        isExtinct: Option[Boolean],
+        isBrackish: Option[Boolean]):
     val id = taxonIDToKey(taxonID)
 
 object SpeciesProfile:
 
-    private def toBool(value: String): Boolean =
-        value == "1"
+    private def toBool(value: String): Option[Boolean] =
+        if value.isBlank then None
+        else Some(value == "1")
+
 
     def from(row: String): Option[SpeciesProfile] =
         Try {