Add tile-info otol links

5 files changed, 19 insertions, 10 deletions

diff --git a/backend/data/genOtolData.py b/backend/data/genOtolData.py
index 2ea548a..cc2d854 100755
--- a/backend/data/genOtolData.py
+++ b/backend/data/genOtolData.py
@@ -32,7 +32,7 @@ nodeMap = {} # Maps node IDs to node objects
 nameToFirstId = {} # Maps node names to first found ID (names might have multiple IDs)
 dupNameToIds = {} # Maps names of nodes with multiple IDs to those node IDs
 softChildLimit = 100
-keptNamesFile = "namesToKeep.txt" # Contains names to keep when doing node trimming
+keptNamesFile = "genOtolNamesToKeep.txt" # Contains names to keep when doing node trimming
 
 # Parse treeFile
 print("Parsing tree file")
@@ -289,12 +289,12 @@ for [id, node] in nodeMap.items():
 print("Creating nodes and edges tables")
 dbCon = sqlite3.connect(dbFile)
 dbCur = dbCon.cursor()
-dbCur.execute("CREATE TABLE nodes (name TEXT PRIMARY KEY, tips INT)")
+dbCur.execute("CREATE TABLE nodes (name TEXT PRIMARY KEY, id TEXT UNIQUE, tips INT)")
 dbCur.execute("CREATE INDEX nodes_idx_nc ON nodes(name COLLATE NOCASE)")
 dbCur.execute("CREATE TABLE edges (node TEXT, child TEXT, p_support INT, PRIMARY KEY (node, child))")
 dbCur.execute("CREATE INDEX edges_child_idx ON edges(child)")
-for node in nodeMap.values():
-	dbCur.execute("INSERT INTO nodes VALUES (?, ?)", (node["name"], node["tips"]))
+for (otolId, node) in nodeMap.items():
+	dbCur.execute("INSERT INTO nodes VALUES (?, ?, ?)", (node["name"], otolId, node["tips"]))
 	childIds = node["children"]
 	for childId in childIds:
 		childNode = nodeMap[childId]
diff --git a/backend/data/genReducedTreeData.py b/backend/data/genReducedTreeData.py
index a88573d..7dc3acc 100755
--- a/backend/data/genReducedTreeData.py
+++ b/backend/data/genReducedTreeData.py
@@ -49,11 +49,12 @@ for name in minimalNames:
 	prevName = None
 	while name != None:
 		if name not in nodeMap:
-			(tips,) = dbCur.execute("SELECT tips from nodes where name = ?", (name,)).fetchone()
+			(id, tips) = dbCur.execute("SELECT id, tips from nodes where name = ?", (name,)).fetchone()
 			row = dbCur.execute("SELECT node, p_support from edges where child = ?", (name,)).fetchone()
 			parent = None if row == None or row[0] == "" else row[0]
 			pSupport = 1 if row == None or row[1] == 1 else 0
 			nodeMap[name] = {
+				"id": id,
 				"children": [] if prevName == None else [prevName],
 				"parent": parent,
 				"tips": 0,
@@ -124,8 +125,10 @@ for (name, nodeObj) in nodeMap.items():
 		namesToAdd.extend(newChildNames)
 for name in namesToAdd:
 	(parent, pSupport) = dbCur.execute("SELECT node, p_support from edges WHERE child = ?", (name,)).fetchone()
+	(id,) = dbCur.execute("SELECT id FROM nodes WHERE name = ?", (name,)).fetchone()
 	parent = None if parent == "" else parent
 	nodeMap[name] = {
+		"id": id,
 		"children": [],
 		"parent": parent,
 		"tips": 0,
@@ -145,12 +148,13 @@ def setTips(nodeName):
 setTips(rootName)
 # Add new nodes to db
 print("Adding to db")
-dbCur.execute("CREATE TABLE r_nodes (name TEXT PRIMARY KEY, tips INT)")
+dbCur.execute("CREATE TABLE r_nodes (name TEXT PRIMARY KEY, id TEXT UNIQUE, tips INT)")
+dbCur.execute("CREATE INDEX r_nodes_idx_nc ON r_nodes(name COLLATE NOCASE)")
 dbCur.execute("CREATE TABLE r_edges (node TEXT, child TEXT, p_support INT, PRIMARY KEY (node, child))")
 dbCur.execute("CREATE INDEX r_edges_child_idx ON r_edges(child)")
 for (name, nodeObj) in nodeMap.items():
 	parentName = "" if nodeObj["parent"] == None else nodeObj["parent"]
-	dbCur.execute("INSERT INTO r_nodes VALUES (?, ?)", (name, nodeObj["tips"]))
+	dbCur.execute("INSERT INTO r_nodes VALUES (?, ?, ?)", (name, nodeObj["id"], nodeObj["tips"]))
 	for childName in nodeObj["children"]:
 		pSupport = 1 if nodeMap[childName]["pSupport"] else 0
 		dbCur.execute("INSERT INTO r_edges VALUES (?, ?, ?)", (name, childName, pSupport))
diff --git a/backend/server.py b/backend/server.py
index c564466..05cba2d 100755
--- a/backend/server.py
+++ b/backend/server.py
@@ -35,9 +35,10 @@ def lookupNodes(names, useReducedTree):
 	nodesTable = "nodes" if not useReducedTree else "r_nodes"
 	edgesTable = "edges" if not useReducedTree else "r_edges"
 	queryParamStr = ",".join(["?"] * len(names))
-	query = f"SELECT name, tips FROM {nodesTable} WHERE name IN ({queryParamStr})"
-	for (nodeName, tips) in cur.execute(query, names):
+	query = f"SELECT name, id, tips FROM {nodesTable} WHERE name IN ({queryParamStr})"
+	for (nodeName, otolId, tips) in cur.execute(query, names):
 		nodeObjs[nodeName] = {
+			"otolId": otolId,
 			"children": [],
 			"parent": None,
 			"tips": tips,
diff --git a/src/components/TileInfoModal.vue b/src/components/TileInfoModal.vue
index 1123387..6e1a8ab 100644
--- a/src/components/TileInfoModal.vue
+++ b/src/components/TileInfoModal.vue
@@ -123,7 +123,9 @@ export default defineComponent({
 		<h1 class="text-center text-xl font-bold mb-2">
 			{{displayName}}
 			<div v-if="tolNode != null">
-				({{tolNode.children.length}} children, {{tolNode.tips}} tips)
+				({{tolNode.children.length}} children, {{tolNode.tips}} tips,
+					<a :href="'https://tree.opentreeoflife.org/opentree/argus/opentree13.4@' + tolNode.otolId">
+						OTOL Link</a>)
 			</div>
 		</h1>
 		<hr class="mb-4 border-stone-400"/>
diff --git a/src/tol.ts b/src/tol.ts
index aa9a9b1..59ecadc 100644
--- a/src/tol.ts
+++ b/src/tol.ts
@@ -6,6 +6,7 @@
 export type TolMap = Map<string, TolNode>;
 // Represents a tree-of-life node
 export class TolNode {
+	otolId: string | null;
 	children: string[];
 	parent: string | null;
 	tips: number;
@@ -13,6 +14,7 @@ export class TolNode {
 	commonName: null | string;
 	imgName: null | string | [string, string] | [null, string] | [string, null];
 	constructor(children: string[] = [], parent = null, tips = 0, pSupport = false){
+		this.otolId = null;
 		this.children = children;
 		this.parent = parent;
 		this.tips = tips;