#!/usr/bin/python3 """ Creates reduced versions of the tree in the database: - A 'picked nodes' tree: Created from a minimal set of node names read from a file, possibly with some extra randmly-picked children. - An 'images only' tree: Created by removing nodes without an image or presence in the 'picked' tree. - A 'weakly trimmed' tree: Created by removing nodes that lack an image or description, or presence in the 'picked' tree. And, for nodes with 'many' children, removing some more, despite any node descriptions. """ import argparse import sys import re import sqlite3 DB_FILE = 'data.db' PICKED_NODES_FILE = 'picked_nodes.txt' COMP_NAME_REGEX = re.compile(r'\[.+ \+ .+]') # Used to recognise composite nodes class Node: def __init__(self, id, children, parent, tips, pSupport): self.id = id self.children = children self.parent = parent self.tips = tips self.pSupport = pSupport # ========== For data generation ========== def genData(tree: str, dbFile: str, pickedNodesFile: str) -> None: print('Opening database') dbCon = sqlite3.connect(dbFile) dbCur = dbCon.cursor() print('Finding root node') query = 'SELECT name FROM nodes LEFT JOIN edges ON nodes.name = edges.child WHERE edges.parent IS NULL LIMIT 1' (rootName,) = dbCur.execute(query).fetchone() print(f'Found \'{rootName}\'') print('=== Getting picked-nodes ===') pickedNames: set[str] = set() pickedTreeExists = False if dbCur.execute('SELECT name FROM sqlite_master WHERE type="table" AND name="nodes_p"').fetchone() is None: print(f'Reading from {pickedNodesFile}') with open(pickedNodesFile) as file: for line in file: name = line.rstrip() row = dbCur.execute('SELECT name from nodes WHERE name = ?', (name,)).fetchone() if row is None: row = dbCur.execute('SELECT name from names WHERE alt_name = ?', (name,)).fetchone() if row is not None: pickedNames.add(row[0]) if not pickedNames: raise Exception('ERROR: No picked names found') else: pickedTreeExists = True print('Picked-node tree already exists') if tree == 'picked': sys.exit() for (name,) in dbCur.execute('SELECT name FROM nodes_p'): pickedNames.add(name) print(f'Found {len(pickedNames)} names') if (tree == 'picked' or tree is None) and not pickedTreeExists: print('=== Generating picked-nodes tree ===') genPickedNodeTree(dbCur, pickedNames, rootName) if tree != 'picked': print('=== Finding \'non-low significance\' nodes ===') nodesWithImgOrPicked: set[str] = set() nodesWithImgDescOrPicked: set[str] = set() print('Finding nodes with descs') for (name,) in dbCur.execute('SELECT name FROM wiki_ids INNER JOIN descs ON wiki_ids.id = descs.wiki_id'): nodesWithImgDescOrPicked.add(name) print('Finding nodes with images') for (name,) in dbCur.execute('SELECT name FROM node_imgs'): nodesWithImgDescOrPicked.add(name) nodesWithImgOrPicked.add(name) print('Adding picked nodes') for name in pickedNames: nodesWithImgDescOrPicked.add(name) nodesWithImgOrPicked.add(name) if tree == 'images' or tree is None: print('=== Generating images-only tree ===') genImagesOnlyTree(dbCur, nodesWithImgOrPicked, pickedNames, rootName) if tree == 'trimmed' or tree is None: print('=== Generating weakly-trimmed tree ===') genWeaklyTrimmedTree(dbCur, nodesWithImgDescOrPicked, nodesWithImgOrPicked, rootName) print('Closing database') dbCon.commit() dbCon.close() def genPickedNodeTree(dbCur: sqlite3.Cursor, pickedNames: set[str], rootName: str) -> None: PREF_NUM_CHILDREN = 3 # Include extra children up to this limit print('Getting ancestors') nodeMap = genNodeMap(dbCur, pickedNames, 100) print(f'Result has {len(nodeMap)} nodes') print('Removing composite nodes') removedNames = removeCompositeNodes(nodeMap) print(f'Result has {len(nodeMap)} nodes') print('Removing \'collapsible\' nodes') temp = removeCollapsibleNodes(nodeMap, pickedNames) removedNames.update(temp) print(f'Result has {len(nodeMap)} nodes') print('Adding some additional nearby children') namesToAdd: list[str] = [] iterNum = 0 for name, node in nodeMap.items(): iterNum += 1 if iterNum % 100 == 0: print(f'At iteration {iterNum}') numChildren = len(node.children) if numChildren < PREF_NUM_CHILDREN: children = [row[0] for row in dbCur.execute('SELECT child FROM edges where parent = ?', (name,))] newChildren: list[str] = [] for n in children: if n in nodeMap or n in removedNames: continue if COMP_NAME_REGEX.fullmatch(n) is not None: continue if dbCur.execute('SELECT name from node_imgs WHERE name = ?', (n,)).fetchone() is None and \ dbCur.execute('SELECT name from linked_imgs WHERE name = ?', (n,)).fetchone() is None: continue newChildren.append(n) newChildNames = newChildren[:(PREF_NUM_CHILDREN - numChildren)] node.children.extend(newChildNames) namesToAdd.extend(newChildNames) for name in namesToAdd: parent, pSupport = dbCur.execute('SELECT parent, 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] = Node(id, [], parent, 0, pSupport == 1) print(f'Result has {len(nodeMap)} nodes') print('Updating \'tips\' values') updateTips(rootName, nodeMap) print('Creating table') addTreeTables(nodeMap, dbCur, 'p') def genImagesOnlyTree( dbCur: sqlite3.Cursor, nodesWithImgOrPicked: set[str], pickedNames: set[str], rootName: str) -> None: print('Getting ancestors') nodeMap = genNodeMap(dbCur, nodesWithImgOrPicked, 1e4) print(f'Result has {len(nodeMap)} nodes') print('Removing composite nodes') removeCompositeNodes(nodeMap) print(f'Result has {len(nodeMap)} nodes') print('Removing \'collapsible\' nodes') removeCollapsibleNodes(nodeMap, pickedNames) print(f'Result has {len(nodeMap)} nodes') print('Updating \'tips\' values') # Needed for next trimming step updateTips(rootName, nodeMap) print('Trimming from nodes with \'many\' children') trimIfManyChildren(nodeMap, rootName, 300, pickedNames) print(f'Result has {len(nodeMap)} nodes') print('Updating \'tips\' values') updateTips(rootName, nodeMap) print('Creating table') addTreeTables(nodeMap, dbCur, 'i') def genWeaklyTrimmedTree( dbCur: sqlite3.Cursor, nodesWithImgDescOrPicked: set[str], nodesWithImgOrPicked: set[str], rootName: str) -> None: print('Getting ancestors') nodeMap = genNodeMap(dbCur, nodesWithImgDescOrPicked, 1e5) print(f'Result has {len(nodeMap)} nodes') print('Getting nodes to \'strongly keep\'') iterNum = 0 nodesFromImgOrPicked: set[str] = set() for name in nodesWithImgOrPicked: iterNum += 1 if iterNum % 1e4 == 0: print(f'At iteration {iterNum}') # while name is not None: if name not in nodesFromImgOrPicked: nodesFromImgOrPicked.add(name) name = nodeMap[name].parent else: break print(f'Node set has {len(nodesFromImgOrPicked)} nodes') print('Removing \'collapsible\' nodes') removeCollapsibleNodes(nodeMap, nodesWithImgDescOrPicked) print(f'Result has {len(nodeMap)} nodes') print('Updating \'tips\' values') # Needed for next trimming step updateTips(rootName, nodeMap) print('Trimming from nodes with \'many\' children') trimIfManyChildren(nodeMap, rootName, 600, nodesFromImgOrPicked) print(f'Result has {len(nodeMap)} nodes') print('Updating \'tips\' values') updateTips(rootName, nodeMap) print('Creating table') addTreeTables(nodeMap, dbCur, 't') # ========== Helper functions ========== def genNodeMap(dbCur: sqlite3.Cursor, nameSet: set[str], itersBeforePrint = 1) -> dict[str, Node]: """ Returns a subtree that includes nodes in 'nameSet', as a name-to-Node map """ nodeMap: dict[str, Node] = {} iterNum = 0 name: str | None for name in nameSet: iterNum += 1 if iterNum % itersBeforePrint == 0: print(f'At iteration {iterNum}') prevName: str | None = None while name is not None: if name not in nodeMap: # Add node id, tips = dbCur.execute('SELECT id, tips from nodes where name = ?', (name,)).fetchone() row: None | tuple[str, int] = dbCur.execute( 'SELECT parent, p_support from edges where child = ?', (name,)).fetchone() parent = None if row is None or row[0] == '' else row[0] pSupport = row is None or row[1] == 1 children = [] if prevName is None else [prevName] nodeMap[name] = Node(id, children, parent, 0, pSupport) # Iterate to parent prevName = name name = parent else: # Just add as child if prevName is not None: nodeMap[name].children.append(prevName) break return nodeMap def removeCompositeNodes(nodeMap: dict[str, Node]) -> set[str]: """ Given a tree, removes composite-name nodes, and returns the removed nodes' names """ namesToRemove: set[str] = set() for name, node in nodeMap.items(): parent = node.parent if parent is not None and COMP_NAME_REGEX.fullmatch(name) is not None: # Connect children to parent nodeMap[parent].children.remove(name) nodeMap[parent].children.extend(node.children) for n in node.children: nodeMap[n].parent = parent nodeMap[n].pSupport &= node.pSupport # Remember for removal namesToRemove.add(name) for name in namesToRemove: del nodeMap[name] return namesToRemove def removeCollapsibleNodes(nodeMap: dict[str, Node], nodesToKeep: set[str] = set()) -> set[str]: """ Given a tree, removes single-child parents, then only-childs, with given exceptions, and returns the set of removed nodes' names """ namesToRemove: set[str] = set() # Remove single-child parents for name, node in nodeMap.items(): if len(node.children) == 1 and node.parent is not None and name not in nodesToKeep: # Connect parent and children parent = node.parent child = node.children[0] nodeMap[parent].children.remove(name) nodeMap[parent].children.append(child) nodeMap[child].parent = parent nodeMap[child].pSupport &= node.pSupport # Remember for removal namesToRemove.add(name) for name in namesToRemove: del nodeMap[name] # Remove only-childs (not redundant because 'nodesToKeep' can cause single-child parents to be kept) namesToRemove.clear() for name, node in nodeMap.items(): isOnlyChild = node.parent is not None and len(nodeMap[node.parent].children) == 1 if isOnlyChild and name not in nodesToKeep: # Connect parent and children parent = node.parent nodeMap[parent].children = node.children for n in node.children: nodeMap[n].parent = parent nodeMap[n].pSupport &= node.pSupport # Remember for removal namesToRemove.add(name) for name in namesToRemove: del nodeMap[name] return namesToRemove def trimIfManyChildren( nodeMap: dict[str, Node], rootName: str, childThreshold: int, nodesToKeep: set[str] = set()) -> None: namesToRemove: set[str] = set() def findTrimmables(nodeName: str) -> None: nonlocal nodeMap, nodesToKeep node = nodeMap[nodeName] if len(node.children) > childThreshold: numToTrim = len(node.children) - childThreshold # Try removing nodes, preferring those with less tips candidatesToTrim = [n for n in node.children if n not in nodesToKeep] childToTips = {n: nodeMap[n].tips for n in candidatesToTrim} candidatesToTrim.sort(key=lambda n: childToTips[n], reverse=True) childrenToRemove = set(candidatesToTrim[-numToTrim:]) node.children = [n for n in node.children if n not in childrenToRemove] # Mark nodes for deletion for n in childrenToRemove: markForRemoval(n) # Recurse on children for n in node.children: findTrimmables(n) def markForRemoval(nodeName: str) -> None: nonlocal nodeMap, namesToRemove namesToRemove.add(nodeName) for child in nodeMap[nodeName].children: markForRemoval(child) findTrimmables(rootName) for nodeName in namesToRemove: del nodeMap[nodeName] def updateTips(nodeName: str, nodeMap: dict[str, Node]) -> int: """ Updates the 'tips' values for a node and it's descendants, returning the node's new 'tips' value """ node = nodeMap[nodeName] tips = sum([updateTips(childName, nodeMap) for childName in node.children]) tips = max(1, tips) node.tips = tips return tips def addTreeTables(nodeMap: dict[str, Node], dbCur: sqlite3.Cursor, suffix: str): """ Adds a tree to the database, as tables nodes_X and edges_X, where X is the given suffix """ nodesTbl = f'nodes_{suffix}' edgesTbl = f'edges_{suffix}' dbCur.execute(f'CREATE TABLE {nodesTbl} (name TEXT PRIMARY KEY, id TEXT UNIQUE, tips INT)') dbCur.execute(f'CREATE INDEX {nodesTbl}_idx_nc ON {nodesTbl}(name COLLATE NOCASE)') dbCur.execute(f'CREATE TABLE {edgesTbl} (parent TEXT, child TEXT, p_support INT, PRIMARY KEY (parent, child))') dbCur.execute(f'CREATE INDEX {edgesTbl}_child_idx ON {edgesTbl}(child)') for name, node in nodeMap.items(): dbCur.execute(f'INSERT INTO {nodesTbl} VALUES (?, ?, ?)', (name, node.id, node.tips)) for childName in node.children: pSupport = 1 if nodeMap[childName].pSupport else 0 dbCur.execute(f'INSERT INTO {edgesTbl} VALUES (?, ?, ?)', (name, childName, pSupport)) # ========== Main block ========== if __name__ == '__main__': parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter) parser.add_argument('--tree', choices=['picked', 'images', 'trimmed'], help='Only generate the specified tree') args = parser.parse_args() genData(args.tree, DB_FILE, PICKED_NODES_FILE)