diff options
Diffstat (limited to 'backend/data')
| -rwxr-xr-x | backend/data/genOtolData.py | 8 | ||||
| -rwxr-xr-x | backend/data/genReducedTreeData.py | 10 |
2 files changed, 11 insertions, 7 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)) |