Fix bug in finding character attribute for quality. Update SBT.

.gitignore

@@ -5,3 +5,4 @@
 /dist
 .DS_Store
 target
+/.idea

build.sbt

@@ -4,7 +4,7 @@ organization  := "org.phenoscape"
 
 name          := "Phenex"
 
-version       := "1.21.0"
+version       := "1.21.1"
 
 mainClass in Compile := Some("org.phenoscape.main.Phenex")
 

project/build.properties

@@ -1 +1 @@
-sbt.version=0.13.15
+sbt.version=1.3.4

project/plugins.sbt

@@ -1 +1 @@
-addSbtPlugin("com.typesafe.sbt" % "sbt-native-packager" % "1.1.5")
+addSbtPlugin("com.typesafe.sbt" % "sbt-native-packager" % "1.5.1")

src/main/java/org/obo/annotation/base/OBOUtil.java

@@ -262,6 +262,17 @@ public static OBOClass getIsaParentForTerm(OBOClass term) {
 		return null;
 	}
 
+	public static Set<OBOClass> getIsaParentsForTerm(OBOClass term) {
+		final Collection<Link> parents = term.getParents();
+		final Set<OBOClass> isaParents = new HashSet<>();
+		for (Link link : parents) {
+			if (link.getType().getName().equals("is_a")) {
+				isaParents.add((OBOClass) (link.getParent()));
+			}
+		}
+		return isaParents;
+	}
+
 	// if (ObjectUtils.equals(this.validName, validName)) return;
 	// final OBOClass oldValue = this.validName;
 	// this.validName = validName;

src/main/java/org/phenoscape/io/TabDelimitedWriter.java

@@ -195,6 +195,15 @@ private String getCharacterHeader() {
 	}
 
 	private OBOClass getCharacterAttributeForValue(OBOClass valueTerm) {
+		OBOClass attribute = getCharacterAttributeForValueRecurse(valueTerm);
+		if (attribute != null) {
+			return attribute;
+		} else {
+			return valueTerm;
+		}
+	}
+
+	private OBOClass getCharacterAttributeForValueRecurse(OBOClass valueTerm) {
 		@SuppressWarnings("unchecked")
 		final Set<TermSubset> categories = valueTerm.getSubsets() != null ? valueTerm.getSubsets() : Collections.EMPTY_SET;
 		final Set<String> categoryNames = new HashSet<String>();
@@ -204,12 +213,14 @@ private OBOClass getCharacterAttributeForValue(OBOClass valueTerm) {
 		if (categoryNames.contains("character_slim")) {
 			return valueTerm;
 		} else {
-			final OBOClass parent = OBOUtil.getIsaParentForTerm(valueTerm);
-			if (parent != null) {
-				return getCharacterAttributeForValue(parent);
-			} else {
-				return valueTerm;
+			final Set<OBOClass> parents = OBOUtil.getIsaParentsForTerm(valueTerm);
+			final Set<OBOClass> attributes = new HashSet<>();
+			for (OBOClass parent : parents) {
+				final OBOClass attribute = getCharacterAttributeForValueRecurse(parent);
+				if (attribute != null) attributes.add(attribute);
 			}
+			if (parents.isEmpty()) return null;
+			else return parents.iterator().next();
 		}
 	}