From 3b105e543a0e2e7097e3156d3daa1bdc0bd3fc2b Mon Sep 17 00:00:00 2001 From: Terry Truong Date: Sat, 4 Jun 2022 14:09:05 +1000 Subject: Add tile-info otol links --- backend/data/genOtolData.py | 8 ++++---- backend/data/genReducedTreeData.py | 10 +++++++--- backend/server.py | 5 +++-- src/components/TileInfoModal.vue | 4 +++- src/tol.ts | 2 ++ 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({

{{displayName}}
- ({{tolNode.children.length}} children, {{tolNode.tips}} tips) + ({{tolNode.children.length}} children, {{tolNode.tips}} tips, + + OTOL Link)

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; // 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; -- cgit v1.2.3