diff options
Diffstat (limited to 'backend')
| -rwxr-xr-x | backend/data/genOtolData.py | 23 | ||||
| -rwxr-xr-x | backend/server.py | 10 |
2 files changed, 18 insertions, 15 deletions
diff --git a/backend/data/genOtolData.py b/backend/data/genOtolData.py index a7d9c03..696d59b 100755 --- a/backend/data/genOtolData.py +++ b/backend/data/genOtolData.py @@ -6,9 +6,8 @@ import os.path usageInfo = f"usage: {sys.argv[0]}\n" usageInfo += "Reads labelled_supertree_ottnames.tre & annotations.json (from an Open Tree of Life release), \n" usageInfo += "and creates a sqlite database, which holds entries of the form (name text, data text).\n" -usageInfo += "Each row holds a tree-of-life node name, and a JSON string with the form \n" -usageInfo += "{\"children\": [name1, ...], \"parent\": name1, \"tips\": int1, \"pSupport\": bool1}, holding \n" -usageInfo += "child names, a parent name or null, descendant 'tips', and a phylogeny-support indicator\n" +usageInfo += "Each row holds a tree-of-life node's name, JSON-encoded child name array, a parent name or '', \n" +usageInfo += "number of descendant 'tips', and a 1 or 0 indicating phylogenetic-support.\n" usageInfo += "\n" usageInfo += "Expected labelled_supertree_ottnames.tre format:\n" usageInfo += " Represents a tree-of-life in Newick format, roughly like (n1,n2,(n3,n4)n5)n6,\n" @@ -82,7 +81,7 @@ def parseNewick(): name2 = name + " [" + str(count) + "]" name = name2 nodeMap[name] = { - "n": name, "id": id, "children": childNames, "parent": None, "tips": tips, "pSupport": False + "name": name, "id": id, "children": childNames, "parent": None, "tips": tips, "pSupport": False } # Update childrens' parent reference for childName in childNames: @@ -91,7 +90,7 @@ def parseNewick(): else: # Parse node name [name, id] = parseNewickName() idToName[id] = name - nodeMap[name] = {"n": name, "id": id, "children": [], "parent": None, "tips": 1, "pSupport": False} + nodeMap[name] = {"name": name, "id": id, "children": [], "parent": None, "tips": 1, "pSupport": False} return name def parseNewickName(): """Helper that parses an input node name, and returns a [name,id] pair""" @@ -182,7 +181,7 @@ def applyMrcaNameConvert(name, namesToSwap): return childName1 namesToSwap = {} # Maps mrca* names to replacement names for node in nodeMap.values(): - name = node["n"] + name = node["name"] if (name.startswith("mrca") and name not in namesToSwap): applyMrcaNameConvert(name, namesToSwap) for [oldName, newName] in namesToSwap.items(): @@ -198,7 +197,7 @@ for node in nodeMap.values(): if (childName in namesToSwap): childNames[i] = namesToSwap[childName] -# Add annotations data, and delete certain fields +# Add annotations data for node in nodeMap.values(): # Set has-support value using annotations id = node["id"] @@ -210,15 +209,15 @@ for node in nodeMap.values(): # Root node gets support if node["parent"] == None: node["pSupport"] = True - # Delete some no-longer-needed fields - del node["n"] - del node["id"] # Create db dbCon = sqlite3.connect(dbFile) dbCur = dbCon.cursor() -dbCur.execute("CREATE TABLE nodes (name TEXT PRIMARY KEY, data TEXT)") +dbCur.execute("CREATE TABLE nodes (name TEXT PRIMARY KEY, children TEXT, parent TEXT, tips INT, p_support INT)") for name in nodeMap.keys(): - dbCur.execute("INSERT INTO nodes VALUES (?, ?)", (name, json.dumps(nodeMap[name]))) + node = nodeMap[name] + dbCur.execute("INSERT INTO nodes VALUES (?, ?, ?, ?, ?)", + (name, json.dumps(node["children"]), "" if node["parent"] == None else node["parent"], + node["tips"], 1 if node["pSupport"] else 0)) dbCon.commit() dbCon.close() diff --git a/backend/server.py b/backend/server.py index 0786ee8..ef6d9cf 100755 --- a/backend/server.py +++ b/backend/server.py @@ -31,11 +31,15 @@ dbCon = sqlite3.connect(dbFile) def lookupNode(name): # Get from db cur = dbCon.cursor() - cur.execute("SELECT name, data FROM nodes WHERE name = ?", (name,)) - row = cur.fetchone() + row = cur.execute("SELECT name, children, parent, tips, p_support FROM nodes WHERE name = ?", (name,)).fetchone() if row == None: return None - nodeObj = json.loads(row[1]) + nodeObj = { + "children": json.loads(row[1]), + "parent": None if row[2] == "" else row[2], + "tips": row[3], + "pSupport": True if row[4] == 1 else False, + } # Check for image file match = re.fullmatch(r"\[(.+) \+ (.+)]", name) if match == None: |