From b59d3ef1472b88cf19d131fc40ee6e18703711b1 Mon Sep 17 00:00:00 2001
From: Lanny W <lanzhenwang9@gmail.com>
Date: Sat, 23 Nov 2024 21:24:23 -0600
Subject: [PATCH 1/2] intialize from no sample selected state to optimize
 performance

---
 .../SchemaIO/components/TreeSelectionView.tsx | 22 +++----------------
 1 file changed, 3 insertions(+), 19 deletions(-)

diff --git a/app/packages/core/src/plugins/SchemaIO/components/TreeSelectionView.tsx b/app/packages/core/src/plugins/SchemaIO/components/TreeSelectionView.tsx
index 74a187d764..68d8730566 100644
--- a/app/packages/core/src/plugins/SchemaIO/components/TreeSelectionView.tsx
+++ b/app/packages/core/src/plugins/SchemaIO/components/TreeSelectionView.tsx
@@ -39,12 +39,7 @@ export default function TreeSelectionView(props: ViewPropsType) {
   const { view = {} } = schema;
 
   if (data == undefined) {
-    const sampleIds = view?.data.flatMap(([parentId, children]) => {
-      return children.map((childId) =>
-        typeof childId === "string" ? childId : childId[0]
-      );
-    });
-    onChange(path, sampleIds);
+    onChange(path, []);
   }
 
   const structure = view?.data || [];
@@ -78,7 +73,7 @@ export default function TreeSelectionView(props: ViewPropsType) {
   const initialCollapsedState: CollapsedState = React.useMemo(() => {
     const state: CollapsedState = {};
     structure.forEach(([parentId]) => {
-      state[parentId] = false; // start as expanded
+      state[parentId] = true; // start as expanded
     });
     return state;
   }, [structure]);
@@ -87,7 +82,7 @@ export default function TreeSelectionView(props: ViewPropsType) {
     initialCollapsedState
   );
 
-  const [allCollapsed, setAllCollapsed] = React.useState(false);
+  const [allCollapsed, setAllCollapsed] = React.useState(true);
 
   const handleExpandCollapseAll = () => {
     setCollapsedState((prevState) => {
@@ -209,17 +204,6 @@ export default function TreeSelectionView(props: ViewPropsType) {
     return idx === -1 ? 0 : idx + 1;
   };
 
-  // On init, all samples are selected by default
-  useEffect(() => {
-    const sampleIds = view?.data.flatMap(([parentId, children]) => {
-      return children.map((childId) =>
-        typeof childId === "string" ? childId : childId[0]
-      );
-    });
-    onChange(path, sampleIds);
-    // eslint-disable-next-line react-hooks/exhaustive-deps
-  }, []);
-
   // this only runs when data and checkboxstate are different
   // meaning the user selected samples from the grid
   // we will handle the state change of checkedState here

From 14bcfcda77ba8abb606379e7ca5c44c07f5dcf67 Mon Sep 17 00:00:00 2001
From: Lanny W <lanzhenwang9@gmail.com>
Date: Sun, 24 Nov 2024 13:57:33 -0600
Subject: [PATCH 2/2] cleanup

---
 .../src/plugins/SchemaIO/components/TreeSelectionView.tsx  | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/app/packages/core/src/plugins/SchemaIO/components/TreeSelectionView.tsx b/app/packages/core/src/plugins/SchemaIO/components/TreeSelectionView.tsx
index 68d8730566..e8c20164a1 100644
--- a/app/packages/core/src/plugins/SchemaIO/components/TreeSelectionView.tsx
+++ b/app/packages/core/src/plugins/SchemaIO/components/TreeSelectionView.tsx
@@ -73,7 +73,7 @@ export default function TreeSelectionView(props: ViewPropsType) {
   const initialCollapsedState: CollapsedState = React.useMemo(() => {
     const state: CollapsedState = {};
     structure.forEach(([parentId]) => {
-      state[parentId] = true; // start as expanded
+      state[parentId] = true; // start as folded
     });
     return state;
   }, [structure]);
@@ -92,7 +92,7 @@ export default function TreeSelectionView(props: ViewPropsType) {
       });
       return newState;
     });
-    setAllCollapsed(!allCollapsed); // Toggle the expand/collapse state
+    setAllCollapsed(!allCollapsed);
   };
 
   const handleCheckboxChange = (id: string, isChecked: boolean) => {
@@ -178,7 +178,7 @@ export default function TreeSelectionView(props: ViewPropsType) {
         const isSample =
           !structure.some(([parentId]) => parentId === key) &&
           key !== "selectAll";
-        return isSample && updatedState[key].checked; // Only checked samples
+        return isSample && updatedState[key].checked;
       });
 
       // We update the actual output value (ctx.params.value \ data) here.
@@ -188,7 +188,6 @@ export default function TreeSelectionView(props: ViewPropsType) {
     });
   };
 
-  // Function to handle expand/collapse toggle
   const handleToggleCollapse = (id: string) => {
     setCollapsedState((prevState) => ({
       ...prevState,