diff options
Diffstat (limited to 'backend/data/genReducedTreeData.py')
| -rwxr-xr-x | backend/data/genReducedTreeData.py | 29 |
1 files changed, 17 insertions, 12 deletions
diff --git a/backend/data/genReducedTreeData.py b/backend/data/genReducedTreeData.py index ed8fae9..508e751 100755 --- a/backend/data/genReducedTreeData.py +++ b/backend/data/genReducedTreeData.py @@ -47,14 +47,15 @@ for name in minimalNames: prevName = None while name != None: if name not in nodeMap: - (parent, tips, p_support) = dbCur.execute( - "SELECT parent, tips, p_support from nodes WHERE name = ?", (name,)).fetchone() - parent = None if parent == "" else parent + (tips,) = dbCur.execute("SELECT 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] = { "children": [] if prevName == None else [prevName], "parent": parent, "tips": 0, - "pSupport": p_support == 1, + "pSupport": pSupport, } prevName = name name = parent @@ -112,20 +113,21 @@ for (name, nodeObj) in nodeMap.items(): # numChildren = len(nodeObj["children"]) if numChildren < PREF_NUM_CHILDREN: - row = dbCur.execute("SELECT children from nodes WHERE name = ?", (name,)).fetchone() - newChildren = [n for n in json.loads(row[0]) if + children = [row[0] for row in dbCur.execute("SELECT child FROM edges where node = ?", (name,))] + newChildren = [n for n in children if not (n in nodeMap or n in namesToRemove) and compNameRegex.fullmatch(n) == None] newChildNames = newChildren[:max(0, PREF_NUM_CHILDREN - numChildren)] nodeObj["children"].extend(newChildNames) namesToAdd.extend(newChildNames) for name in namesToAdd: - (parent, pSupport) = dbCur.execute("SELECT parent, p_support from nodes WHERE name = ?", (name,)).fetchone() + (parent, pSupport) = dbCur.execute("SELECT node, p_support from edges WHERE child = ?", (name,)).fetchone() + parent = None if parent == "" else parent nodeMap[name] = { "children": [], "parent": parent, "tips": 0, - "pSupport": pSupport, + "pSupport": pSupport == 1, } print("New node set has {} nodes".format(len(nodeMap))) # set tips vals @@ -141,12 +143,15 @@ def setTips(nodeName): setTips(rootName) # Add new nodes to db print("Adding to db") -dbCur.execute( - "CREATE TABLE reduced_nodes (name TEXT PRIMARY KEY, children TEXT, parent TEXT, tips INT, p_support INT)") +dbCur.execute("CREATE TABLE r_nodes (name TEXT PRIMARY KEY, tips INT)") +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 reduced_nodes VALUES (?, ?, ?, ?, ?)", - (name, json.dumps(nodeObj["children"]), parentName, nodeObj["tips"], 1 if nodeObj["pSupport"] else 0)) + dbCur.execute("INSERT INTO r_nodes VALUES (?, ?)", (name, 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)) # Close db dbCon.commit() dbCon.close() |