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-neo4j-arrow = {git = "https://github.com/neo4j-field/neo4j_arrow.git", rev = "0.6.1"} +graphdatascience = {git = "https://github.com/neo4j/graph-data-science-client", tag = "1.13"} [tool.poetry.group.dev.dependencies] pytest = "^7.4.3" @@ -35,6 +35,7 @@ flake8-bandit = "^4.1.1" types-protobuf = "^4.24.0.4" testcontainers = "^3.7.1" pandas = "^2.1.4" +pytest-flakefinder = "^1.1.0" [build-system] requires = ["poetry-core"] diff --git a/src/templates/bigquery.py b/src/templates/bigquery.py index 60ad652..1036a18 100644 --- a/src/templates/bigquery.py +++ b/src/templates/bigquery.py @@ -3,27 +3,7 @@ import argparse import logging import sys -import typing - -import neo4j -import neo4j.exceptions - import time - -from dataproc_templates import BaseTemplate - -import pyarrow as pa -from google.protobuf import descriptor_pb2 -from pyspark.sql import SparkSession - -import neo4j_arrow as na - -import pattern_parser -from .bq_client import BigQuerySource, BigQuerySink, BQStream -from . import constants as c, util - -from model import Node, Edge, arrow_to_nodes, arrow_to_edges - from typing import ( Any, Callable, @@ -38,15 +18,43 @@ cast, ) +import neo4j +import neo4j.exceptions +import pyarrow as pa +from dataproc_templates import BaseTemplate +from google.protobuf import descriptor_pb2 +from graphdatascience.query_runner import gds_arrow_client +from graphdatascience.query_runner.gds_arrow_client import GdsArrowClient +from pandas import DataFrame +from pyarrow import Table, RecordBatch +from pyspark.sql import SparkSession + +import pattern_parser +from model import Edge, Node, arrow_to_nodes, arrow_to_edges +from . import constants as c, util +from .bq_client import BigQuerySource, BigQuerySink, BQStream +from .mapper import node_mapper, edge_mapper, MappingFn +from .model import Graph + __all__ = [ "BigQueryToNeo4jGDSTemplate", "Neo4jGDSToBigQueryTemplate", ] Arrow = Union[pa.Table, pa.RecordBatch] +ArrowData = Union[pa.Table, Iterable[pa.RecordBatch]] +DataStream = Generator[Arrow, None, None] + +class ProgressTracker: + def __init__(self): + self.progress = 0 -def load_model_from_gcs(uri: str) -> Optional[na.model.Graph]: + def callback(self, progress: int) -> None: + self.progress = progress + + +def load_model_from_gcs(uri: str) -> Optional[Graph]: """ Attempt to load a Graph model from a GCS uri. Returns None on failure. """ @@ -54,58 +62,81 @@ def load_model_from_gcs(uri: str) -> Optional[na.model.Graph]: import fsspec with fsspec.open(uri, "rt") as f: - return na.model.Graph.from_json(f.read()) + return Graph.from_json(f.read()) except Exception: return None def flatten( - lists: List[List[Any]], fn: Optional[Callable[[Any], Any]] = None + lists: List[List[Any]], fn: Optional[Callable[[Any], Any]] = None ) -> List[Any]: """ Flatten a list of lists, applying an optional function (fn) to the initial list of lists. """ if not fn: - def fn(x: Any) -> Any: return x return [x for y in map(fn, lists) for x in y] +def map_tables(model: Graph, entity_type: str) -> Callable[[DataStream], List[ArrowData]]: + def _map_entity(table: Arrow, mapper: MappingFn): + if not table: + raise Exception("empty iterable of record batches provided") + mapped_table = mapper(table) + if isinstance(table, RecordBatch): + mapped_table = [mapped_table] + return mapped_table + + def _map_arrow_tables(table: DataStream) -> List[ArrowData]: + source_field = "_table" + if entity_type == "NODE": + mapper = node_mapper(model, source_field) + else: + mapper = edge_mapper(model, source_field) + + mapped_tables = [_map_entity(t, mapper) for t in table] + return mapped_tables + + return _map_arrow_tables + + def send_nodes( - client: na.Neo4jArrowClient, - model: Optional[na.model.Graph] = None, - source_field: str = "_table", -) -> Callable[[Any], Tuple[int, int]]: + client: GdsArrowClient, + model: Optional[Graph] = None, +) -> Callable[[ArrowData], int]: """ Wrap the given client, model, and (optional) source_field in a function that streams PyArrow data (Table or RecordBatch) to Neo4j as nodes. """ - def _send_nodes(table: Any) -> Tuple[int, int]: - result: Tuple[int, int] = client.write_nodes(table, model, source_field) - return result + def _send_nodes_gds(table: ArrowData) -> int: + nodes_progress = ProgressTracker() - return _send_nodes + client.upload_nodes(model.name, table, progress_callback=nodes_progress.callback) + return nodes_progress.progress + + return _send_nodes_gds def send_edges( - client: na.Neo4jArrowClient, - model: Optional[na.model.Graph] = None, - source_field: str = "_table", -) -> Callable[[Any], Tuple[int, int]]: + client: GdsArrowClient, + model: Optional[Graph] = None, +) -> Callable[[ArrowData], int]: """ Wrap the given client, model, and (optional) source_field in a function that streams PyArrow data (Table or RecordBatch) to Neo4j as relationships. """ - def _send_nodes(table: Any) -> Tuple[int, int]: - result: Tuple[int, int] = client.write_edges(table, model, source_field) - return result + def _send_edges_gds(table: ArrowData) -> int: + edge_progress = ProgressTracker() + + client.upload_relationships(model.name, table, progress_callback=edge_progress.callback) + return edge_progress.progress - return _send_nodes + return _send_edges_gds def tuple_sum(a: Tuple[int, int], b: Tuple[int, int]) -> Tuple[int, int]: @@ -116,7 +147,7 @@ def tuple_sum(a: Tuple[int, int], b: Tuple[int, int]) -> Tuple[int, int]: def node_to_stream_fn( - bq: BigQuerySource, graph: na.model.Graph + bq: BigQuerySource, graph: Graph ) -> Callable[[str], List[BQStream]]: """ Create a function that generates BigQuery streams with optional field @@ -139,7 +170,7 @@ def _node_to_stream(table_name: str) -> List[BQStream]: def edge_to_stream_fn( - bq: BigQuerySource, graph: na.model.Graph + bq: BigQuerySource, graph: Graph ) -> Callable[[str], List[BQStream]]: """ Create a function that generates BigQuery streams with optional field @@ -164,7 +195,7 @@ def _edge_to_stream(table_name: str) -> List[BQStream]: def convert_batch_fun( - converter: Callable[[Arrow], Generator[Any, None, None]] + converter: Callable[[Arrow], Generator[Any, None, None]] ) -> Callable[[Arrow], List[bytes]]: def _convert_batch(arrow: Arrow) -> List[bytes]: batch: List[bytes] = [] @@ -176,50 +207,60 @@ def _convert_batch(arrow: Arrow) -> List[bytes]: def read_nodes( - client: na.Neo4jArrowClient, pattern: pattern_parser.NodePattern -) -> Iterable[pa.RecordBatch]: - def _add_labels_column(batch: pa.RecordBatch, label: str) -> pa.RecordBatch: - if not batch.field("labels"): - labels_col = pa.array( - [[label]] * batch.num_rows, pa.large_list(pa.string()) - ) - new_schema = batch.schema.append(pa.field("labels", labels_col.type)) - return pa.RecordBatch.from_arrays( - batch.columns + [labels_col], schema=new_schema - ) - - return batch - - batches: Iterable[pa.RecordBatch] = client.read_nodes( - pattern.properties, labels=[pattern.label] + client: GdsArrowClient, pattern: pattern_parser.NodePattern, graph_name: str, database: str +) -> pa.RecordBatch: + labels = pattern.label + properties = pattern.properties + + dataframe: DataFrame = client.get_node_properties( + graph_name, + database, + properties if properties is not None else [], + labels if labels is not None else ["*"], + True, ) - return [_add_labels_column(batch, pattern.label) for batch in batches] + if 'labels' not in dataframe.columns: + dataframe['labels'] = pattern.label + + return pa.RecordBatch.from_pandas(df=dataframe) def read_edges( - client: na.Neo4jArrowClient, pattern: pattern_parser.EdgePattern -) -> Iterable[pa.RecordBatch]: - def _add_type_column( - batch: pa.RecordBatch, relationship_type: str - ) -> pa.RecordBatch: - type_col = pa.array([relationship_type] * batch.num_rows, pa.string()) - new_schema = batch.schema.append(pa.field("type", type_col.type)) - return pa.RecordBatch.from_arrays(batch.columns + [type_col], schema=new_schema) - - batches = client.read_edges( - properties=pattern.properties, relationship_types=[pattern.type] - ) - return [_add_type_column(batch, pattern.type) for batch in batches] + client: GdsArrowClient, pattern: pattern_parser.EdgePattern, graph_name: str, database: str +) -> pa.RecordBatch: + properties = pattern.properties + + relationship_types = pattern.type if pattern.type is not None else ["*"] + if properties: + dataframe: DataFrame = client.get_relationship_properties( + graph_name, + database, + properties, + relationship_types, + ) + else: + dataframe: DataFrame = client.get_relationships( + graph_name, + database, + relationship_types, + ) + + if 'type' not in dataframe.columns: + dataframe['type'] = pattern.type + + return pa.RecordBatch.from_pandas(df=dataframe) def read_by_pattern_fun( - client: na.Neo4jArrowClient, -) -> Callable[[pattern_parser.Pattern], Iterable[pa.RecordBatch]]: - def _read_by_pattern(pattern: pattern_parser.Pattern) -> Iterable[pa.RecordBatch]: + client: GdsArrowClient, + graph_name: str, + database: str, +) -> Callable[[pattern_parser.Pattern], pa.RecordBatch]: + def _read_by_pattern(pattern: pattern_parser.Pattern) -> pa.RecordBatch: if isinstance(pattern, pattern_parser.NodePattern): - return read_nodes(client, pattern) + return read_nodes(client, pattern, graph_name, database) elif isinstance(pattern, pattern_parser.EdgePattern): - return read_edges(client, pattern) + return read_edges(client, pattern, graph_name, database) else: raise ValueError( f"expected an instance of Pattern, but got {pattern.__class__.__name__}" @@ -229,7 +270,7 @@ def _read_by_pattern(pattern: pattern_parser.Pattern) -> Iterable[pa.RecordBatch def append_batch_fun( - sink_factory: Callable[[], BigQuerySink], + sink_factory: Callable[[], BigQuerySink], ) -> Callable[[Iterable[List[bytes]]], Iterable[Tuple[str, int]]]: def append_batch(batches: Iterable[List[bytes]]) -> Iterable[Tuple[str, int]]: sink = sink_factory() @@ -246,12 +287,12 @@ def append_batch(batches: Iterable[List[bytes]]) -> Iterable[Tuple[str, int]]: return append_batch -def load_graph(args: Dict[str, Any]) -> na.model.Graph: +def load_graph(args: Dict[str, Any]) -> Graph: # 1. Load the Graph Model. if args[c.NEO4J_GRAPH_JSON]: # Try loading a literal JSON-based model json_str = args[c.NEO4J_GRAPH_JSON] - graph = na.model.Graph.from_json(json_str) + graph = Graph.from_json(json_str) elif args[c.NEO4J_GRAPH_JSON_URI]: # Fall back to URI uri = args[c.NEO4J_GRAPH_JSON_URI] @@ -291,21 +332,19 @@ def apply_secrets(args: Dict[str, Any], debug: bool, logger: logging.Logger) -> args.update(secret) -def build_arrow_client( - graph: na.model.Graph, - neo4j_uri: str, - neo4j_username: str, - neo4j_password: str, - neo4j_concurrency: int, - *, - logger: Any = None, -) -> na.Neo4jArrowClient: +def build_gds_arrow_client( + neo4j_uri: str, + neo4j_username: str, + neo4j_password: str, + *, + logger: Any = None, +) -> GdsArrowClient: neo4j_logger = logging.getLogger("neo4j") neo4j_logger.handlers.clear() neo4j_logger.addHandler(util.SparkLogHandler(logger)) with neo4j.GraphDatabase.driver( - neo4j_uri, auth=neo4j.basic_auth(neo4j_username, neo4j_password) + neo4j_uri, auth=neo4j.basic_auth(neo4j_username, neo4j_password) ) as driver: try: record: Optional[neo4j.Record] = driver.execute_query( @@ -322,31 +361,17 @@ def build_arrow_client( raise Exception( "Please ensure that Arrow Flights Service is running." ) - advertised_listen_address = str(record["advertisedListenAddress"]) listen_address = str(record["listenAddress"]) - batch_size = int(record["batchSize"]) - uri = advertised_listen_address - if not uri: - uri = listen_address + host, port = listen_address.split(":") - arrow_logger = logging.getLogger("neo4j-arrow-client") - arrow_logger.handlers.clear() - arrow_logger.addHandler(util.SparkLogHandler(logger)) - - host, port = uri.split(":") - return na.Neo4jArrowClient( - host, - graph.name, + gds_client = gds_arrow_client.GdsArrowClient( + host=host, port=int(port), - tls=driver.encrypted, - database=graph.db, - user=neo4j_username, - password=neo4j_password, - concurrency=neo4j_concurrency, - max_chunk_size=batch_size, - logger=arrow_logger, + auth=(neo4j_username, neo4j_password), + encrypted=driver.encrypted, ) + return gds_client except neo4j.exceptions.ClientError as e: if e.code != "Neo.ClientError.Procedure.ProcedureNotFound": raise e @@ -358,10 +383,10 @@ def build_arrow_client( def sink_fun( - project_id: str, - dataset: str, - table: str, - descriptor: descriptor_pb2.DescriptorProto, + project_id: str, + dataset: str, + table: str, + descriptor: descriptor_pb2.DescriptorProto, ) -> Callable[[], BigQuerySink]: def sink() -> BigQuerySink: return BigQuerySink(project_id, dataset, table, descriptor) @@ -490,14 +515,14 @@ def run(self, spark: SparkSession, args: Dict[str, Any]) -> None: apply_secrets(args, args[c.DEBUG], logger) # 3. Initialize our clients for source and sink. - client = build_arrow_client( - na.model.Graph(name=graph_name, db=db_name), + + client = build_gds_arrow_client( str(args[c.NEO4J_URI]), str(args[c.NEO4J_USER]), str(args[c.NEO4J_PASSWORD]), - int(args[c.NEO4J_CONCURRENCY]), - logger=logger, + logger=logger ) + logger.info(f"using neo4j client {client}") patterns: list[pattern_parser.Pattern] = args[c.NEO4J_PATTERNS] @@ -510,14 +535,13 @@ def run(self, spark: SparkSession, args: Dict[str, Any]) -> None: start_time = time.time() def process_patterns( - filter_fun: Callable[[typing.Any], bool], - converter: Callable[[Arrow], Generator[Any, None, None]], - sink_factory: Callable[[], BigQuerySink], + filter_fun: Callable[[Any], bool], + converter: Callable[[Arrow], Generator[Any, None, None]], + sink_factory: Callable[[], BigQuerySink], ) -> Tuple[int, int]: results: List[Tuple[str, int]] = ( sc.parallelize([p for p in filter(filter_fun, patterns)]) - .flatMap(read_by_pattern_fun(client)) - .repartition(num_partitions) + .map(read_by_pattern_fun(client, graph_name, db_name)) .map(convert_batch_fun(converter)) .mapPartitions(append_batch_fun(sink_factory)) .collect() @@ -646,7 +670,7 @@ def parse_args(args: Optional[Sequence[str]] = None) -> Dict[str, Any]: default=False, type=bool, help="Whether to force the creation of the graph, by aborting an existing import or the database, " - "by overwriting the existing data files.", + "by overwriting the existing data files.", ) # BigQuery Parameters @@ -714,12 +738,14 @@ def run(self, spark: SparkSession, args: Dict[str, Any]) -> None: apply_secrets(args, debug, logger) # 2b. Initialize our clients for source and sink. - client = build_arrow_client( - graph, + + graph_name = args[c.NEO4J_GRAPH_NAME] + db_name = args[c.NEO4J_DB_NAME] + + client = build_gds_arrow_client( str(args[c.NEO4J_URI]), str(args[c.NEO4J_USER]), str(args[c.NEO4J_PASSWORD]), - int(args[c.NEO4J_CONCURRENCY]), logger=logger, ) bq = BigQuerySource(args[c.BQ_PROJECT], args[c.BQ_DATASET]) @@ -746,66 +772,71 @@ def run(self, spark: SparkSession, args: Dict[str, Any]) -> None: # 4. Begin our Graph import. force = bool(args[c.NEO4J_FORCE]) if str(args[c.NEO4J_ACTION]).lower() == "create_database": - result = client.start_create_database(force=force) + client.create_database(database=db_name, force=force) else: - result = client.start_create_graph(force=force) + client.create_graph(graph_name=graph_name, database=db_name) - logger.info(f"starting import for {result.get('name', graph.name)}") + logger.info(f"starting import for {graph_name}") # 5. Load our Nodes via PySpark workers. num_partitions = max(sc.defaultParallelism, args[c.NEO4J_CONCURRENCY]) logger.info(f"using {num_partitions:,} partitions") nodes_start = time.time() - cnt, size = ( - sc.parallelize(node_streams, num_partitions) - .map(bq.consume_stream, True) # don't shuffle - .map(send_nodes(client, graph)) - .reduce(tuple_sum) - ) + + nodes_count = (sc.parallelize(node_streams, num_partitions) + .map(bq.consume_stream, True) + .flatMap(map_tables(graph, "NODE")) + .map(send_nodes(client, graph)) + .sum() + ) + logger.info( - f"streamed {cnt:,} nodes, ~{size / (1 << 20):,.2f} MiB original size" + f"streamed {nodes_count} nodes" ) - # 5b. Assert we actually got nodes - if cnt < 1: + # # 5b. Assert we actually got nodes + if nodes_count < 1: logger.error("failed to load nodes; aborting.") sys.exit(1) # 6. Signal we're done with Nodes before moving onto Edges. - result = client.nodes_done() + result = client.node_load_done(graph.name) duration = time.time() - nodes_start - total = result["node_count"] + total = result.node_count logger.info( f"signalled nodes complete, imported {total:,} nodes" f" in {duration:,.3f}s ({total / duration:,.2f} nodes/s)" ) - if cnt != total: - logger.warning(f"sent {cnt} nodes, but imported {total}!") + if nodes_count != total: + logger.warning(f"sent {nodes_count} nodes, but imported {total}!") # 7. Now stream Edges via the PySpark workers. edges_start = time.time() - cnt, size = ( + edges_count = ( sc.parallelize(edge_streams, num_partitions) .map(bq.consume_stream, True) # don't shuffle + .flatMap(map_tables(graph, "EDGE")) .map(send_edges(client, graph)) - .reduce(tuple_sum) + .sum() ) + logger.info( - f"streamed {cnt:,} edges, ~{size / (1 << 20):,.2f} MiB original size" + f"streamed {edges_count} edges" ) # 8. Signal we're done with Edges. - result = client.edges_done() + result = client.relationship_load_done(graph.name) duration = time.time() - edges_start - total = result["relationship_count"] + total = result.relationship_count logger.info( f"signalled edges complete, imported {total:,} edges" f" in {duration:,.3f}s ({total / duration:,.2f} edges/s)" ) - if cnt != total: - logger.warning(f"sent {cnt} edges, but imported {total}!") + if edges_count != total: + logger.warning(f"sent {edges_count} edges, but imported {total}!") # 9. TODO: await import completion and GDS projection available + duration = time.time() - start_time logger.info(f"completed in {duration:,.3f} seconds") diff --git a/src/templates/mapper.py b/src/templates/mapper.py new file mode 100644 index 0000000..1d4ef34 --- /dev/null +++ b/src/templates/mapper.py @@ -0,0 +1,88 @@ +from typing import Optional, Callable, Union, List, Tuple +import pyarrow as pa + +from templates.model import Graph + +Arrow = Union[pa.Table, pa.RecordBatch] +MappingFn = Callable[[Arrow], Arrow] + + +def node_mapper(model: Graph, source_field: Optional[str] = None) -> MappingFn: + """ + Generate a mapping function for a Node. + """ + + def _map(data: Arrow) -> Arrow: + schema = data.schema + if source_field: + src = schema.metadata.get(source_field.encode("utf8")) + node = model.node_for_src(src.decode("utf8")) + else: # guess at labels + my_label = data["labels"][0].as_py() + node = model.node_by_label(my_label) + if not node: + raise Exception("cannot find matching node in model given " f"{data.schema}") + + columns, fields = _rename_and_add_column([], [], data, node.key_field, "nodeId") + if node.label: + columns.append(pa.array([node.label] * len(data), pa.string())) + fields.append(pa.field("labels", pa.string())) + if node.label_field: + columns, fields = _rename_and_add_column(columns, fields, data, node.label_field, "labels") + for name in node.properties: + columns, fields = _rename_and_add_column(columns, fields, data, name, node.properties[name]) + + return data.from_arrays(columns, schema=pa.schema(fields)) + + return _map + + +def edge_mapper(model: Graph, source_field: Optional[str] = None) -> MappingFn: + """ + Generate a mapping function for an Edge. + """ + + def _map(data: Arrow) -> Arrow: + schema = data.schema + if source_field: + src = schema.metadata.get(source_field.encode("utf8")) + edge = model.edge_for_src(src.decode("utf8")) + else: # guess at type + my_type = data["type"][0].as_py() + edge = model.edge_by_type(my_type) + if not edge: + raise Exception("cannot find matching edge in model given " f"{data.schema}") + + columns, fields = _rename_and_add_column([], [], data, edge.source_field, "sourceNodeId") + columns, fields = _rename_and_add_column(columns, fields, data, edge.target_field, "targetNodeId") + if edge.type: + columns.append(pa.array([edge.type] * len(data), pa.string())) + fields.append(pa.field("relationshipType", pa.string())) + if edge.type_field: + columns, fields = _rename_and_add_column(columns, fields, data, edge.type_field, "relationshipType") + for name in edge.properties: + columns, fields = _rename_and_add_column(columns, fields, data, name, edge.properties[name]) + + return data.from_arrays(columns, schema=pa.schema(fields)) + + return _map + + +def nop_mapper(data: Arrow) -> Arrow: + """ + Used as a no-op mapping function. + """ + return data + + +def _rename_and_add_column( + columns: List[Union[pa.Array, pa.ChunkedArray]], + fields: List[pa.Field], + data: Arrow, + current_name: str, + new_name: str, +) -> Tuple[List[Union[pa.Array, pa.ChunkedArray]], List[pa.Field]]: + idx = data.schema.get_field_index(current_name) + columns.append(data.columns[idx]) + fields.append(data.schema.field(idx).with_name(new_name)) + return columns, fields diff --git a/src/templates/model.py b/src/templates/model.py new file mode 100644 index 0000000..4cad79f --- /dev/null +++ b/src/templates/model.py @@ -0,0 +1,301 @@ +""" +-------------------------------------------------------------- +bigquery_connector.model: A graph model for mapping over source data. +-------------------------------------------------------------- +""" +from json import dumps, loads, JSONEncoder +import re + +from typing import Any, Dict, Generic, List, Optional, Union, TypeVar + + +class ValidationError(Exception): + def __init__(self, message: str): + self.message = message + + +class _NodeEncoder(JSONEncoder): + def default(self, n: "Node") -> object: + return n.to_dict() + + +class _EdgeEncoder(JSONEncoder): + def default(self, e: "Edge") -> object: + return e.to_dict() + + +class _GraphEncoder(JSONEncoder): + def default(self, g: "Graph") -> object: + return g.to_dict() + + +class Node: + def __init__( + self, + *, + source: str, + label: str = "", + label_field: str = "", + key_field: str, + properties: Optional[Dict[str, Any]] = None, + **kwargs: Any, + ): + self._source = source + self._label = label + self._label_field = label_field + self._key_field = key_field + self._properties = dict(properties or {}, **kwargs) + self._pattern: Optional[re.Pattern[str]] = None + try: + self._pattern = re.compile(self._source) + except Exception: + pass + + @property + def source(self) -> str: + return self._source + + @property + def label(self) -> str: + return self._label + + @property + def key_field(self) -> str: + return self._key_field + + @property + def label_field(self) -> str: + return self._label_field + + @property + def properties(self) -> Dict[str, Any]: + return self._properties + + def matches(self, s: str) -> bool: + if self._pattern: + return self._pattern.match(s) is not None + else: + return self._source == s + + def to_dict(self) -> Dict[str, Any]: + return { + "source": self._source, + "label": self._label, + "label_field": self._label_field, + "key_field": self._key_field, + "properties": self._properties, + } + + def validate(self) -> None: + if not self._source: + raise ValidationError(f"source must be provided in {self}") + if not self._key_field: + raise ValidationError(f"key_field must be provided in {self}") + if not self._label and not self._label_field: + raise ValidationError(f"either label or label_field must be provided in {self}") + if self._label and self._label_field: + raise ValidationError(f"use of label and label_field at the same time is not allowed " f"in {self}") + + def __str__(self) -> str: + return str(self.to_dict()) + + +class Edge: + def __init__( + self, + *, + source: str, + edge_type: str = "", + type_field: str = "", + type: str = "", + source_field: str, + target_field: str, + properties: Optional[Dict[str, Any]] = None, + **kwargs: Any, + ): + self._source = source + self._type = edge_type + if not self._type and type: + self._type = type + self._type_field = type_field + self._source_field = source_field + self._target_field = target_field + self._properties = dict(properties or {}, **kwargs) + self._pattern: Optional[re.Pattern[str]] = None + try: + self._pattern = re.compile(source) + except ValueError: + pass + except TypeError: + pass + + @property + def source(self) -> str: + return self._source + + @property + def type(self) -> str: + return self._type + + @property + def type_field(self) -> str: + return self._type_field + + @property + def source_field(self) -> str: + return self._source_field + + @property + def target_field(self) -> str: + return self._target_field + + @property + def properties(self) -> Dict[str, Any]: + return self._properties + + def matches(self, s: str) -> bool: + if self._pattern: + return self._pattern.match(s) is not None + else: + return self._source == s + + def to_dict(self) -> Dict[str, Any]: + return { + "source": self.source, + "type": self._type, + "type_field": self._type_field, + "source_field": self._source_field, + "target_field": self._target_field, + "properties": self._properties, + } + + def validate(self) -> None: + if not self._source: + raise ValidationError(f"source must be provided in {self}") + if not self._source_field: + raise ValidationError(f"source_field must be provided in {self}") + if not self._target_field: + raise ValidationError(f"target_field must be provided in {self}") + if not self._type_field and not self._type: + raise ValidationError(f"either type or type_field must be provided in {self}") + if self._type_field and self._type: + raise ValidationError(f"use of type and type_field at the same time is not allowed in {self}") + + def __str__(self) -> str: + return str(self.to_dict()) + + +class Graph: + """ + ------------------------------- + A Graph model over source data. + ------------------------------- + + A Graph consists of: + * A name + * A db name (optional, default = "neo4j") + * A List of Nodes (optional, but should have at least 1) + * A List of Edges (optional, though boring if none!) + """ + + def __init__(self, *, name: str, db: str = "", nodes: List[Node] = [], edges: List[Edge] = []): + self.name = name + self.db = db + self.nodes = nodes + self.edges = edges + + def named(self, name: str) -> "Graph": + return Graph(name=name, db=self.db, nodes=self.nodes, edges=self.edges) + + def in_db(self, db: str) -> "Graph": + return Graph(name=self.name, db=db, nodes=self.nodes, edges=self.edges) + + def with_nodes(self, nodes: List[Node]) -> "Graph": + return Graph(name=self.name, db=self.db, nodes=nodes, edges=self.edges) + + def with_edges(self, edges: List[Edge]) -> "Graph": + return Graph(name=self.name, db=self.db, nodes=self.nodes, edges=edges) + + def with_node(self, node: Node) -> "Graph": + return Graph(name=self.name, db=self.db, nodes=self.nodes + [node], edges=self.edges) + + def with_edge(self, edge: Edge) -> "Graph": + return Graph(name=self.name, db=self.db, nodes=self.nodes, edges=self.edges + [edge]) + + def node_for_src(self, source: str) -> Union[None, Node]: + """Find a Node in a Graph based on matching source pattern.""" + for node in self.nodes: + if node.matches(source): + return node + return None + + def edge_for_src(self, source: str) -> Union[None, Edge]: + for edge in self.edges: + if edge.matches(source): + return edge + return None + + def edge_by_type(self, _type: str) -> Union[None, Edge]: + for edge in self.edges: + if edge.type == _type: + return edge + return None + + def node_by_label(self, label: str) -> Union[None, Node]: + for node in self.nodes: + if node.label == label: + return node + return None + + def validate(self) -> None: + for node in self.nodes: + node.validate() + for edge in self.edges: + edge.validate() + + @classmethod + def from_json(cls, json: str) -> "Graph": + obj = loads(json) + nodes = [ + Node( + source=n["source"], + label=n.get("label", ""), + label_field=n.get("label_field", ""), + key_field=n["key_field"], + **n.get("properties", {}), + ) + for n in obj.get("nodes", []) + ] + edges = [ + Edge( + source=e["source"], + edge_type=e.get("type", ""), + type_field=e.get("type_field", ""), + source_field=e["source_field"], + target_field=e["target_field"], + **e.get("properties", {}), + ) + for e in obj.get("edges", []) + ] + return Graph(name=obj["name"], db=obj.get("db", "neo4j"), nodes=nodes, edges=edges) + + def to_dict(self) -> Dict[str, Any]: + return { + "name": self.name, + "db": self.db, + "nodes": [n.to_dict() for n in self.nodes], + "edges": [e.to_dict() for e in self.edges], + } + + def to_json(self) -> str: + return dumps(self, cls=_GraphEncoder) + + def __str__(self) -> str: + return str(self.to_dict()) + + def __eq__(self, other: Any) -> bool: + if not other: + return False + if not isinstance(other, Graph): + return False + return self.to_dict() == other.to_dict() diff --git a/tests/integration/conftest.py b/tests/integration/conftest.py index 026273b..4d0c721 100644 --- a/tests/integration/conftest.py +++ b/tests/integration/conftest.py @@ -9,9 +9,7 @@ import pytest import testcontainers.neo4j -import neo4j_arrow._client from google.cloud import bigquery -from neo4j_arrow import Neo4jArrowClient user_count = 10 user_id_base = 1000 @@ -193,24 +191,8 @@ def driver(neo4j): driver.close() -@pytest.fixture(scope="module") -def arrow_client_factory(neo4j, driver) -> Callable[[str], Neo4jArrowClient]: - def _arrow_client_factory(graph_name: str) -> Neo4jArrowClient: - return Neo4jArrowClient( - neo4j.get_container_host_ip(), - graph=graph_name, - user=neo4j.NEO4J_USER, - password=neo4j.NEO4J_ADMIN_PASSWORD, - port=int(neo4j.get_exposed_port(8491)), - tls=False, - proc_names=neo4j_arrow._client.procedure_names(gds_version(driver)), - ) - - return _arrow_client_factory - - @pytest.fixture(autouse=True) -def setup(driver, arrow_client_factory): +def setup(driver): with driver.session() as session: session.run("CREATE OR REPLACE DATABASE neo4j WAIT").consume() diff --git a/tests/unit/templates/mapper_test.py b/tests/unit/templates/mapper_test.py new file mode 100644 index 0000000..8dd2436 --- /dev/null +++ b/tests/unit/templates/mapper_test.py @@ -0,0 +1,71 @@ +from templates.mapper import node_mapper, nop_mapper, edge_mapper + +import pyarrow as pa + +from templates.model import Graph, Node, Edge + + +def test_nop_mapper(): + mapper = nop_mapper + t = pa.table({"labels": ["Junk"], "nodeId": ["junk_id"]}) + result = mapper(t) + assert result is not None + assert "nodeId" in result.schema.names + assert "labels" in result.schema.names + + +def test_node_mapper(): + SRC_KEY = "gcs_source" + g = Graph( + name="junk", + nodes=[ + Node( + source="gs://.*/junk.*parquet", + label_field="my_labels", + key_field="my_key", + ) + ], + ) + mapper = node_mapper(g, SRC_KEY) + + src = "gs://bucket/folder/junk_0001.parquet" + t = pa.table({"my_labels": ["Junk"], "my_key": ["junk_id"]}) + schema = t.schema.with_metadata({SRC_KEY: src}) + table = pa.Table.from_arrays(t.columns, schema=schema) + + result = mapper(table) + assert result is not None + assert "nodeId" in result.schema.names + assert "labels" in result.schema.names + assert "my_labels" not in result.schema.names + assert "my_key" not in result.schema.names + + +def test_edge_mapper(): + SRC_KEY = "gcs_source" + g = Graph( + name="junk", + edges=[ + Edge( + source="gs://.*/junk.*parquet", + type_field="my_type", + source_field="my_src", + target_field="my_tgt", + ) + ], + ) + mapper = edge_mapper(g, SRC_KEY) + + src = "gs://bucket/folder/junk_0001.parquet" + t = pa.table({"my_type": ["JUNK"], "my_src": ["junk_id"], "my_tgt": ["junk_id"]}) + schema = t.schema.with_metadata({SRC_KEY: src}) + table = pa.Table.from_arrays(t.columns, schema=schema) + + result = mapper(table) + assert result is not None + assert "relationshipType" in result.schema.names + assert "sourceNodeId" in result.schema.names + assert "targetNodeId" in result.schema.names + assert "my_type" not in result.schema.names + assert "my_src" not in result.schema.names + assert "my_tgt" not in result.schema.names