From 9f0dcdea1049a59cd1fb4f0872edee1b7a87a4e6 Mon Sep 17 00:00:00 2001
From: Terry Truong <terry06890@gmail.com>
Date: Sat, 28 May 2022 11:30:32 +1000
Subject: Fix tree-trimming to not discard certain nodes

Was trimming off nodes without an image/desc/reduced_tree_presence,
including those with a descdendant that has them. Was using a
linked-image association to prevent this, but this wasn't reliable.
---
 backend/data/README.md      |  6 +++---
 backend/data/genOtolData.py | 19 +++++++++++++++++--
 src/App.vue                 | 10 +++++-----
 3 files changed, 25 insertions(+), 10 deletions(-)

diff --git a/backend/data/README.md b/backend/data/README.md
index d444e4f..4655c2d 100644
--- a/backend/data/README.md
+++ b/backend/data/README.md
@@ -65,6 +65,6 @@ Other Files
     of possibly-significant nodes are removed, using a short-sighted
     heuristic. <br>
     One way to generate this list is to generate the files as usual,
-    then get node names that have an associated image, linked-image,
-    description, or presence in r_nodes. Then run the genOtolData.py
-    and genEolNameData.py scripts again.
+    then get node names that have an associated image, description, or
+    presence in r_nodes. Then run the genOtolData.py and genEolNameData.py
+    scripts again (after deleting their created tables).
diff --git a/backend/data/genOtolData.py b/backend/data/genOtolData.py
index 252e9f2..87db2c4 100755
--- a/backend/data/genOtolData.py
+++ b/backend/data/genOtolData.py
@@ -141,14 +141,29 @@ def parseNewickName():
 		return [match.group(1).replace("_", " "), match.group(2)]
 rootId = parseNewick()
 # For nodes with *many* children, remove some of those children
-print("Trimming nodes from tree")
+print("Getting nodes for which to avoid trimming")
 namesToKeep = set()
 if os.path.exists(keptNamesFile):
-	with open(keptNamesFile) as file: # Contains names with an image (incl linked), desc, or reduced-tree-presence
+	with open(keptNamesFile) as file: # Contains names with an image, desc, or reduced-tree-presence
 		for line in file:
 			namesToKeep.add(line.rstrip())
 else:
 	print("WARNING: No '{}' file found".format(keptNamesFile))
+print("Read in {} nodes".format(len(namesToKeep)))
+keptAncestors = set()
+for name in namesToKeep:
+	if name in nameToFirstId:
+		ids = [nameToFirstId[name]] if name not in dupNameToIds else dupNameToIds[name]
+		for id in ids:
+			parentId = nodeMap[id]["parent"]
+			while parentId != None:
+				parentObj = nodeMap[parentId]
+				keptAncestors.add(parentObj["name"])
+				parentId = parentObj["parent"]
+oldNamesToKeepSz = len(namesToKeep)
+namesToKeep.update(keptAncestors)
+print("Added {} ancestor nodes".format(len(namesToKeep) - oldNamesToKeepSz))
+print("Trimming nodes from tree")
 def trimChildren(nodeId):
 	""" Traverse node tree, looking for nodes with too many children """
 	nodeObj = nodeMap[nodeId]
diff --git a/src/App.vue b/src/App.vue
index 9fda4de..6f8f7a8 100644
--- a/src/App.vue
+++ b/src/App.vue
@@ -65,7 +65,7 @@ const defaultUiOpts = {
 	shadowFocused: '0 0 1px 2px orange',
 	infoIconSz: 18, //px
 	infoIconMargin: 2, //px
-	tipThresholds: [[1, 'greenyellow'], [30, 'orange'], [100, 'red']],
+	tipThresholds: [[1, 'greenyellow'], [100, 'orange'], [1000, 'red']],
 	headerColor: '#fafaf9',
 	// For leaf tiles
 	leafTilePadding: 4, //px
@@ -770,15 +770,15 @@ export default defineComponent({
 		</div>
 	</div>
 	<!-- Modals -->
+	<transition name="fade">
+		<search-modal v-if="searchOpen" :tolMap="tolMap" :uiOpts="uiOpts" ref="searchModal"
+			@search-close="searchOpen = false" @search-node="onSearchNode" @info-icon-click="onInfoIconClick"/>
+	</transition>
 	<transition name="fade">
 		<tile-info-modal v-if="infoModalNodeName != null"
 			:nodeName="infoModalNodeName" :tolMap="tolMap" :lytOpts="lytOpts" :uiOpts="uiOpts"
 			@info-modal-close="infoModalNodeName = null"/>
 	</transition>
-	<transition name="fade">
-		<search-modal v-if="searchOpen" :tolMap="tolMap" :uiOpts="uiOpts" ref="searchModal"
-			@search-close="searchOpen = false" @search-node="onSearchNode" @info-icon-click="onInfoIconClick"/>
-	</transition>
 	<transition name="fade">
 		<help-modal v-if="helpOpen" :uiOpts="uiOpts"
 			@help-modal-close="helpOpen = false" @start-tutorial="onStartTutorial"/>
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