From e2bb91ab3e9c8dbf9e1312619fcc42ac35949cc8 Mon Sep 17 00:00:00 2001
From: Gordon Krieger <gordon.krieger@gmail.com>
Date: Wed, 7 Feb 2024 14:11:33 -0500
Subject: [PATCH 1/2] "negated" -> "excluded" for phenotypic features

---
 src/components/explorer/IndividualPhenotypicFeatures.js | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/components/explorer/IndividualPhenotypicFeatures.js b/src/components/explorer/IndividualPhenotypicFeatures.js
index 8af7edfb4..789cb6626 100644
--- a/src/components/explorer/IndividualPhenotypicFeatures.js
+++ b/src/components/explorer/IndividualPhenotypicFeatures.js
@@ -10,7 +10,7 @@ const PHENOTYPIC_FEATURES_COLUMNS = [
     {
         title: "Feature",
         key: "feature",
-        render: ({ header, type, negated }) => ({
+        render: ({ header, type, excluded }) => ({
             children: header ? (
                 <h4 style={{ marginBottom: 0 }} className="phenotypic-features--phenopacket-header">
                     Phenopacket:{" "}
@@ -20,7 +20,7 @@ const PHENOTYPIC_FEATURES_COLUMNS = [
                 </h4>
             ) : <>
                 <OntologyTerm term={type} />{" "}
-                {negated ? (
+                {excluded ? (
                     <span style={{ color: "#CC3333" }}>
                         (<span style={{ fontWeight: "bold" }}>Excluded:</span>{" "}
                         Found to be absent{" "}
@@ -73,7 +73,7 @@ const IndividualPhenotypicFeatures = ({ individual }) => {
             }] : []),  // If there is just 1 phenopacket, don't include a header row
             ...(p.phenotypic_features ?? []).map((pf) => ({
                 ...pf,
-                key: `${p.id}:${pf.type.id}:${pf.negated}`,
+                key: `${p.id}:${pf.type.id}:${pf.excluded}`,
             })),
         ]);
     }, [individual]);

From 1c78cbd1a900d24145ff4ab3c415567cb0c8bc48 Mon Sep 17 00:00:00 2001
From: Gordon Krieger <gordon.krieger@gmail.com>
Date: Thu, 8 Feb 2024 10:35:27 -0500
Subject: [PATCH 2/2] add excluded prop type to phenotypic features

---
 src/propTypes.js | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/propTypes.js b/src/propTypes.js
index 031a95541..144b13157 100644
--- a/src/propTypes.js
+++ b/src/propTypes.js
@@ -220,6 +220,7 @@ export const diseasePropTypesShape = PropTypes.shape({
 // Prop types object shape for a single phenopacket phenotypic feature object.
 export const phenotypicFeaturePropTypesShape = PropTypes.shape({
     type: ontologyShape.isRequired,
+    excluded: PropTypes.bool,
     created: PropTypes.string,  // ISO datetime string
     updated: PropTypes.string,  // ISO datetime string
 });