"""Graph analytics operations. To be split into separate files when we have more.""" import os from lynxkite.core import ops from collections import deque import dataclasses import functools import matplotlib import networkx as nx import pandas as pd import polars as pl import traceback import typing op = ops.op_registration("LynxKite Graph Analytics") @dataclasses.dataclass class RelationDefinition: """Defines a set of edges.""" df: str # The DataFrame that contains the edges. source_column: ( str # The column in the edge DataFrame that contains the source node ID. ) target_column: ( str # The column in the edge DataFrame that contains the target node ID. ) source_table: str # The DataFrame that contains the source nodes. target_table: str # The DataFrame that contains the target nodes. source_key: str # The column in the source table that contains the node ID. target_key: str # The column in the target table that contains the node ID. @dataclasses.dataclass class Bundle: """A collection of DataFrames and other data. Can efficiently represent a knowledge graph (homogeneous or heterogeneous) or tabular data. It can also carry other data, such as a trained model. """ dfs: dict[str, pd.DataFrame] = dataclasses.field(default_factory=dict) relations: list[RelationDefinition] = dataclasses.field(default_factory=list) other: dict[str, typing.Any] = None @classmethod def from_nx(cls, graph: nx.Graph): edges = nx.to_pandas_edgelist(graph) d = dict(graph.nodes(data=True)) nodes = pd.DataFrame(d.values(), index=d.keys()) nodes["id"] = nodes.index return cls( dfs={"edges": edges, "nodes": nodes}, relations=[ RelationDefinition( df="edges", source_column="source", target_column="target", source_table="nodes", target_table="nodes", source_key="id", target_key="id", ) ], ) @classmethod def from_df(cls, df: pd.DataFrame): return cls(dfs={"df": df}) def to_nx(self): # TODO: Use relations. graph = nx.from_pandas_edgelist(self.dfs["edges"]) if "nodes" in self.dfs: nx.set_node_attributes( graph, self.dfs["nodes"].set_index("id").to_dict("index") ) return graph def copy(self): """Returns a medium depth copy of the bundle. The Bundle is completely new, but the DataFrames and RelationDefinitions are shared.""" return Bundle( dfs=dict(self.dfs), relations=list(self.relations), other=dict(self.other) if self.other else None, ) def nx_node_attribute_func(name): """Decorator for wrapping a function that adds a NetworkX node attribute.""" def decorator(func): @functools.wraps(func) def wrapper(graph: nx.Graph, **kwargs): graph = graph.copy() attr = func(graph, **kwargs) nx.set_node_attributes(graph, attr, name) return graph return wrapper return decorator def disambiguate_edges(ws): """If an input plug is connected to multiple edges, keep only the last edge.""" seen = set() for edge in reversed(ws.edges): if (edge.target, edge.targetHandle) in seen: ws.edges.remove(edge) seen.add((edge.target, edge.targetHandle)) @ops.register_executor("LynxKite") async def execute(ws): catalog = ops.CATALOGS["LynxKite"] disambiguate_edges(ws) outputs = {} failed = 0 while len(outputs) + failed < len(ws.nodes): for node in ws.nodes: if node.id in outputs: continue # TODO: Take the input/output handles into account. inputs = [edge.source for edge in ws.edges if edge.target == node.id] if all(input in outputs for input in inputs): inputs = [outputs[input] for input in inputs] data = node.data op = catalog[data.title] params = {**data.params} # Convert inputs. try: for i, (x, p) in enumerate(zip(inputs, op.inputs.values())): if p.type == nx.Graph and isinstance(x, Bundle): inputs[i] = x.to_nx() elif p.type == Bundle and isinstance(x, nx.Graph): inputs[i] = Bundle.from_nx(x) elif p.type == Bundle and isinstance(x, pd.DataFrame): inputs[i] = Bundle.from_df(x) output = op(*inputs, **params) except Exception as e: traceback.print_exc() data.error = str(e) failed += 1 continue if len(op.inputs) == 1 and op.inputs.get("multi") == "*": # It's a flexible input. Create n+1 handles. data.inputs = {f"input{i}": None for i in range(len(inputs) + 1)} data.error = None outputs[node.id] = output if ( op.type == "visualization" or op.type == "table_view" or op.type == "image" ): data.display = output @op("Import Parquet") def import_parquet(*, filename: str): """Imports a Parquet file.""" return pd.read_parquet(filename) @op("Import CSV") def import_csv( *, filename: str, columns: str = "", separator: str = "" ): """Imports a CSV file.""" return pd.read_csv( filename, names=pd.api.extensions.no_default if columns == "" else columns.split(","), sep=pd.api.extensions.no_default if separator == "" else separator, ) @op("Create scale-free graph") def create_scale_free_graph(*, nodes: int = 10): """Creates a scale-free graph with the given number of nodes.""" return nx.scale_free_graph(nodes) @op("Compute PageRank") @nx_node_attribute_func("pagerank") def compute_pagerank(graph: nx.Graph, *, damping=0.85, iterations=100): return nx.pagerank(graph, alpha=damping, max_iter=iterations) @op("Compute betweenness centrality") @nx_node_attribute_func("betweenness_centrality") def compute_betweenness_centrality(graph: nx.Graph, *, k=10): return nx.betweenness_centrality(graph, k=k, backend="cugraph") @op("Discard loop edges") def discard_loop_edges(graph: nx.Graph): graph = graph.copy() graph.remove_edges_from(nx.selfloop_edges(graph)) return graph @op("SQL") def sql(bundle: Bundle, *, query: ops.LongStr, save_as: str = "result"): """Run a SQL query on the DataFrames in the bundle. Save the results as a new DataFrame.""" bundle = bundle.copy() if os.environ.get("NX_CUGRAPH_AUTOCONFIG", "").strip().lower() == "true": with pl.Config() as cfg: cfg.set_verbose(True) res = ( pl.SQLContext(bundle.dfs) .execute(query) .collect(engine="gpu") .to_pandas() ) # TODO: Currently `collect()` moves the data from cuDF to Polars. Then we convert it to Pandas, # which (hopefully) puts it back into cuDF. Hopefully we will be able to keep it in cuDF. else: res = pl.SQLContext(bundle.dfs).execute(query).collect().to_pandas() bundle.dfs[save_as] = res return bundle @op("Organize bundle") def organize_bundle(bundle: Bundle, *, code: ops.LongStr): """Lets you rename/copy/delete DataFrames, and modify relations. TODO: Use a declarative solution instead of Python code. Add UI.""" bundle = bundle.copy() exec(code, globals(), {"bundle": bundle}) return bundle @op("Sample graph") def sample_graph(graph: nx.Graph, *, nodes: int = 100): """Takes a (preferably connected) subgraph.""" sample = set() to_expand = deque([0]) while to_expand and len(sample) < nodes: node = to_expand.pop() for n in graph.neighbors(node): if n not in sample: sample.add(n) to_expand.append(n) if len(sample) == nodes: break return nx.Graph(graph.subgraph(sample)) def _map_color(value): cmap = matplotlib.cm.get_cmap("viridis") value = (value - value.min()) / (value.max() - value.min()) rgba = cmap(value) return [ "#{:02x}{:02x}{:02x}".format(int(r * 255), int(g * 255), int(b * 255)) for r, g, b in rgba[:, :3] ] @op("Visualize graph", view="visualization") def visualize_graph(graph: Bundle, *, color_nodes_by: ops.NodeAttribute = None): nodes = graph.dfs["nodes"].copy() if color_nodes_by: nodes["color"] = _map_color(nodes[color_nodes_by]) nodes = nodes.to_records() edges = graph.dfs["edges"].drop_duplicates(["source", "target"]) edges = edges.to_records() pos = nx.spring_layout(graph.to_nx(), iterations=max(1, int(10000 / len(nodes)))) v = { "animationDuration": 500, "animationEasingUpdate": "quinticInOut", "series": [ { "type": "graph", "roam": True, "lineStyle": { "color": "gray", "curveness": 0.3, }, "emphasis": { "focus": "adjacency", "lineStyle": { "width": 10, }, }, "data": [ { "id": str(n.id), "x": float(pos[n.id][0]), "y": float(pos[n.id][1]), # Adjust node size to cover the same area no matter how many nodes there are. "symbolSize": 50 / len(nodes) ** 0.5, "itemStyle": {"color": n.color} if color_nodes_by else {}, } for n in nodes ], "links": [ {"source": str(r.source), "target": str(r.target)} for r in edges ], }, ], } return v def collect(df: pd.DataFrame): if isinstance(df, pl.LazyFrame): df = df.collect() if isinstance(df, pl.DataFrame): return [[d[c] for c in df.columns] for d in df.to_dicts()] return df.values.tolist() @op("View tables", view="table_view") def view_tables(bundle: Bundle): v = { "dataframes": { name: { "columns": [str(c) for c in df.columns], "data": collect(df), } for name, df in bundle.dfs.items() }, "relations": bundle.relations, "other": bundle.other, } return v