Merge branch 'main' of https://github.com/open-sciencelab/GraphGen into fix/fix-kuzudb-error

Author: ChenZiHong-Gavin

.github/workflows/translator.yml

@@ -0,0 +1,29 @@
+name: Translator
+on:
+  issues:
+    types: [opened, edited]
+  issue_comment:
+    types: [created, edited]
+  discussion:
+    types: [created, edited]
+  discussion_comment:
+    types: [created, edited]
+  pull_request_target:
+    types: [opened, edited]
+  pull_request_review_comment:
+    types: [created, edited]
+
+jobs:
+  translate:
+    permissions:
+      issues: write
+      discussions: write
+      pull-requests: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: lizheming/[email protected]
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          IS_MODIFY_TITLE: true
+          APPEND_TRANSLATION: true

graphgen/common/init_llm.py

@@ -4,7 +4,6 @@
 import ray
 
 from graphgen.bases import BaseLLMWrapper
-from graphgen.common.init_storage import get_actor_handle
 from graphgen.models import Tokenizer
 
 
@@ -74,9 +73,9 @@ class LLMServiceProxy(BaseLLMWrapper):
     A proxy class to interact with the LLMServiceActor for distributed LLM operations.
     """
 
-    def __init__(self, actor_name: str):
+    def __init__(self, actor_handle: ray.actor.ActorHandle):
         super().__init__()
-        self.actor_handle = get_actor_handle(actor_name)
+        self.actor_handle = actor_handle
         self._create_local_tokenizer()
 
     async def generate_answer(
@@ -128,25 +127,25 @@ def create_llm(
 
         actor_name = f"Actor_LLM_{model_type}"
         try:
-            ray.get_actor(actor_name)
+            actor_handle = ray.get_actor(actor_name)
+            print(f"Using existing Ray actor: {actor_name}")
         except ValueError:
             print(f"Creating Ray actor for LLM {model_type} with backend {backend}.")
             num_gpus = float(config.pop("num_gpus", 0))
-            actor = (
+            actor_handle = (
                 ray.remote(LLMServiceActor)
                 .options(
                     name=actor_name,
                     num_gpus=num_gpus,
-                    lifetime="detached",
                     get_if_exists=True,
                 )
                 .remote(backend, config)
             )
 
             # wait for actor to be ready
-            ray.get(actor.ready.remote())
+            ray.get(actor_handle.ready.remote())
 
-        return LLMServiceProxy(actor_name)
+        return LLMServiceProxy(actor_handle)
 
 
 def _load_env_group(prefix: str) -> Dict[str, Any]:

graphgen/common/init_storage.py

@@ -48,6 +48,9 @@ def drop(self):
     def reload(self):
         return self.kv.reload()
 
+    def ready(self) -> bool:
+        return True
+
 
 class GraphStorageActor:
     def __init__(self, backend: str, working_dir: str, namespace: str):
@@ -114,22 +117,14 @@ def delete_node(self, node_id: str):
     def reload(self):
         return self.graph.reload()
 
-
-def get_actor_handle(name: str):
-    try:
-        return ray.get_actor(name)
-    except ValueError as exc:
-        raise RuntimeError(
-            f"Actor {name} not found. Make sure it is created before accessing."
-        ) from exc
+    def ready(self) -> bool:
+        return True
 
 
 class RemoteKVStorageProxy(BaseKVStorage):
-    def __init__(self, namespace: str):
+    def __init__(self, actor_handle: ray.actor.ActorHandle):
         super().__init__()
-        self.namespace = namespace
-        self.actor_name = f"Actor_KV_{namespace}"
-        self.actor = get_actor_handle(self.actor_name)
+        self.actor = actor_handle
 
     def data(self) -> Dict[str, Any]:
         return ray.get(self.actor.data.remote())
@@ -163,11 +158,9 @@ def reload(self):
 
 
 class RemoteGraphStorageProxy(BaseGraphStorage):
-    def __init__(self, namespace: str):
+    def __init__(self, actor_handle: ray.actor.ActorHandle):
         super().__init__()
-        self.namespace = namespace
-        self.actor_name = f"Actor_Graph_{namespace}"
-        self.actor = get_actor_handle(self.actor_name)
+        self.actor = actor_handle
 
     def index_done_callback(self):
         return ray.get(self.actor.index_done_callback.remote())
@@ -235,27 +228,23 @@ class StorageFactory:
     def create_storage(backend: str, working_dir: str, namespace: str):
         if backend in ["json_kv", "rocksdb"]:
             actor_name = f"Actor_KV_{namespace}"
-            try:
-                ray.get_actor(actor_name)
-            except ValueError:
-                ray.remote(KVStorageActor).options(
-                    name=actor_name,
-                    lifetime="detached",
-                    get_if_exists=True,
-                ).remote(backend, working_dir, namespace)
-            return RemoteKVStorageProxy(namespace)
-        if backend in ["networkx", "kuzu"]:
+            actor_class = KVStorageActor
+            proxy_class = RemoteKVStorageProxy
+        elif backend in ["networkx", "kuzu"]:
             actor_name = f"Actor_Graph_{namespace}"
-            try:
-                ray.get_actor(actor_name)
-            except ValueError:
-                ray.remote(GraphStorageActor).options(
-                    name=actor_name,
-                    lifetime="detached",
-                    get_if_exists=True,
-                ).remote(backend, working_dir, namespace)
-            return RemoteGraphStorageProxy(namespace)
-        raise ValueError(f"Unknown storage backend: {backend}")
+            actor_class = GraphStorageActor
+            proxy_class = RemoteGraphStorageProxy
+        else:
+            raise ValueError(f"Unknown storage backend: {backend}")
+        try:
+            actor_handle = ray.get_actor(actor_name)
+        except ValueError:
+            actor_handle = ray.remote(actor_class).options(
+                name=actor_name,
+                get_if_exists=True,
+            ).remote(backend, working_dir, namespace)
+            ray.get(actor_handle.ready.remote())
+        return proxy_class(actor_handle)
 
 
 def init_storage(backend: str, working_dir: str, namespace: str):

graphgen/engine.py

@@ -1,15 +1,20 @@
+import os
 import inspect
 import logging
 from collections import defaultdict, deque
 from functools import wraps
 from typing import Any, Callable, Dict, List, Set
+from dotenv import load_dotenv
 
 import ray
 import ray.data
+from ray.data import DataContext
 
 from graphgen.bases import Config, Node
 from graphgen.utils import logger
+from graphgen.common import init_llm, init_storage
 
+load_dotenv()
 
 class Engine:
     def __init__(
@@ -19,6 +24,26 @@ def __init__(
         self.global_params = self.config.global_params
         self.functions = functions
         self.datasets: Dict[str, ray.data.Dataset] = {}
+        self.llm_actors = {}
+        self.storage_actors = {}
+
+        ctx = DataContext.get_current()
+        ctx.enable_rich_progress_bars = False
+        ctx.use_ray_tqdm = False
+        # Disable tensor extension casting to avoid conversion errors with complex types
+        # (e.g., gene_synonyms, gene_names which are lists/arrays)
+        ctx.enable_tensor_extension_casting = False
+        ctx._metrics_export_port = 0  # Disable metrics exporter to avoid RpcError
+
+        all_env_vars = os.environ.copy()
+        if "runtime_env" not in ray_init_kwargs:
+            ray_init_kwargs["runtime_env"] = {}
+
+        existing_env_vars = ray_init_kwargs["runtime_env"].get("env_vars", {})
+        ray_init_kwargs["runtime_env"]["env_vars"] = {
+            **all_env_vars,
+            **existing_env_vars
+        }
 
         if not ray.is_initialized():
             context = ray.init(
@@ -29,6 +54,59 @@ def __init__(
             )
             logger.info("Ray Dashboard URL: %s", context.dashboard_url)
 
+        self._init_llms()
+        self._init_storage()
+
+    def _init_llms(self):
+        self.llm_actors["synthesizer"] = init_llm("synthesizer")
+        self.llm_actors["trainee"] = init_llm("trainee")
+
+    def _init_storage(self):
+        kv_namespaces, graph_namespaces = self._scan_storage_requirements()
+        working_dir = self.global_params["working_dir"]
+
+        for node_id in kv_namespaces:
+            proxy = init_storage(self.global_params["kv_backend"], working_dir, node_id)
+            self.storage_actors[f"kv_{node_id}"] = proxy
+            logger.info("Create KV Storage Actor: namespace=%s", node_id)
+
+        for ns in graph_namespaces:
+            proxy = init_storage(self.global_params["graph_backend"], working_dir, ns)
+            self.storage_actors[f"graph_{ns}"] = proxy
+            logger.info("Create Graph Storage Actor: namespace=%s", ns)
+
+    def _scan_storage_requirements(self) -> tuple[set[str], set[str]]:
+        kv_namespaces = set()
+        graph_namespaces = set()
+
+        # TODO: Temporarily hard-coded; node storage will be centrally managed later.
+        for node in self.config.nodes:
+            op_name = node.op_name
+            if self._function_needs_param(op_name, "kv_backend"):
+                kv_namespaces.add(op_name)
+            if self._function_needs_param(op_name, "graph_backend"):
+                graph_namespaces.add("graph")
+        return kv_namespaces, graph_namespaces
+
+    def _function_needs_param(self, op_name: str, param_name: str) -> bool:
+        if op_name not in self.functions:
+            return False
+
+        func = self.functions[op_name]
+
+        if inspect.isclass(func):
+            try:
+                sig = inspect.signature(func.__init__)
+                return param_name in sig.parameters
+            except (ValueError, TypeError):
+                return False
+
+        try:
+            sig = inspect.signature(func)
+            return param_name in sig.parameters
+        except (ValueError, TypeError):
+            return False
+
     @staticmethod
     def _topo_sort(nodes: List[Node]) -> List[Node]:
         id_to_node: Dict[str, Node] = {}

graphgen/run.py

@@ -6,7 +6,6 @@
 
 import ray
 import yaml
-from dotenv import load_dotenv
 from ray.data.block import Block
 from ray.data.datasource.filename_provider import FilenameProvider
 
@@ -16,8 +15,6 @@
 
 sys_path = os.path.abspath(os.path.dirname(__file__))
 
-load_dotenv()
-
 
 def set_working_dir(folder):
     os.makedirs(folder, exist_ok=True)

requirements.txt

@@ -23,6 +23,8 @@ aiohttp
 socksio
 pydantic
 ray==2.52.1
+kuzu
+pyarrow
 
 leidenalg
 igraph