Merge branch 'dataset-permissions-auth-refactor' of github.com:topoteretes/cognee into dataset-permissions-auth-refactor

.github/workflows/test_memgraph.yml

@@ -1,9 +1,9 @@
 name: test | memgraph
 
-# on:
-#  workflow_dispatch:
-#  pull_request:
-#    types: [labeled, synchronize]
+on:
+  workflow_dispatch:
+  pull_request:
+    types: [labeled, synchronize]
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
@@ -17,13 +17,15 @@ jobs:
     name: test
     runs-on: ubuntu-22.04
 
-    defaults:
-      run:
-        shell: bash
+    services:
+      memgraph:
+        image: memgraph/memgraph-mage:latest
+        ports:
+          - 7687:7687
 
     steps:
       - name: Check out
-        uses: actions/checkout@master
+        uses: actions/checkout@v3
 
       - name: Setup Python
         uses: actions/setup-python@v5
@@ -38,7 +40,7 @@ jobs:
           installer-parallel: true
 
       - name: Install dependencies
-        run: poetry install -E memgraph --no-interaction
+        run: poetry install -E neo4j
 
       - name: Run default Memgraph
         env:
@@ -51,7 +53,7 @@ jobs:
           EMBEDDING_ENDPOINT: ${{ secrets.EMBEDDING_ENDPOINT }}
           EMBEDDING_API_KEY: ${{ secrets.EMBEDDING_API_KEY }}
           EMBEDDING_API_VERSION: ${{ secrets.EMBEDDING_API_VERSION }}
-          GRAPH_DATABASE_URL: ${{ secrets.MEMGRAPH_API_URL }}
-          GRAPH_DATABASE_PASSWORD: ${{ secrets.MEMGRAPH_API_KEY }}
-          GRAPH_DATABASE_USERNAME: " "
+          GRAPH_DATABASE_URL: "bolt://localhost:7687"
+          GRAPH_DATABASE_PASSWORD: "memgraph"
+          GRAPH_DATABASE_USERNAME: "memgraph"
         run: poetry run python ./cognee/tests/test_memgraph.py

cognee/infrastructure/databases/graph/memgraph/memgraph_adapter.py

@@ -614,7 +614,7 @@ class MemgraphAdapter(GraphDBInterface):
 
             return [result["successor"] for result in results]
 
-    async def get_neighbours(self, node_id: str) -> List[Dict[str, Any]]:
+    async def get_neighbors(self, node_id: str) -> List[Dict[str, Any]]:
         """
         Get both predecessors and successors of a node.
 
@@ -634,6 +634,25 @@ class MemgraphAdapter(GraphDBInterface):
 
         return predecessors + successors
 
+    async def get_node(self, node_id: str) -> Optional[Dict[str, Any]]:
+        """Get a single node by ID."""
+        query = """
+        MATCH (node {id: $node_id})
+        RETURN node
+        """
+        results = await self.query(query, {"node_id": node_id})
+        return results[0]["node"] if results else None
+
+    async def get_nodes(self, node_ids: List[str]) -> List[Dict[str, Any]]:
+        """Get multiple nodes by their IDs."""
+        query = """
+        UNWIND $node_ids AS id
+        MATCH (node {id: id})
+        RETURN node
+        """
+        results = await self.query(query, {"node_ids": node_ids})
+        return [result["node"] for result in results]
+
     async def get_connections(self, node_id: UUID) -> list:
         """
         Retrieve connections for a given node, including both predecessors and successors.

examples/relational_db_with_dlt/fix_foreign_keys.sql

@@ -0,0 +1,290 @@
+BEGIN TRANSACTION;
+
+PRAGMA foreign_keys=OFF;
+
+/*------------------------------------------------------------------------
+1) pokemon_list
+------------------------------------------------------------------------*/
+CREATE TABLE IF NOT EXISTS new_pokemon_list (
+    name TEXT,
+    url TEXT,
+    _dlt_load_id TEXT NOT NULL,
+    _dlt_id VARCHAR(128) NOT NULL PRIMARY KEY
+);
+INSERT INTO new_pokemon_list
+    SELECT name, url, _dlt_load_id, _dlt_id
+    FROM pokemon_list;
+DROP TABLE pokemon_list;
+ALTER TABLE new_pokemon_list RENAME TO pokemon_list;
+
+/*------------------------------------------------------------------------
+2) pokemon_details (Parent for most child tables)
+   _dlt_id is a PRIMARY KEY so children can FK to it.
+------------------------------------------------------------------------*/
+CREATE TABLE IF NOT EXISTS new_pokemon_details (
+    base_experience BIGINT,
+    height BIGINT,
+    id BIGINT,
+    is_default BOOLEAN,
+    name TEXT,
+    "order" BIGINT,
+    species__name,
+    weight BIGINT,
+    _dlt_load_id TEXT NOT NULL,
+    _dlt_id VARCHAR(128) NOT NULL PRIMARY KEY
+);
+INSERT INTO new_pokemon_details
+    SELECT base_experience,
+           height,
+           id,
+           is_default,
+           name,
+           "order",
+           species__name,
+           weight,
+           _dlt_load_id,
+           _dlt_id
+    FROM pokemon_details;
+DROP TABLE pokemon_details;
+ALTER TABLE new_pokemon_details RENAME TO pokemon_details;
+
+/*------------------------------------------------------------------------
+3) pokemon_details_abilities (Child)
+   Foreign key from _dlt_parent_id → pokemon_details(_dlt_id)
+------------------------------------------------------------------------*/
+CREATE TABLE IF NOT EXISTS new_pokemon_details__abilities (
+    ability__name TEXT,
+    ability__url TEXT,
+    is_hidden BOOLEAN,
+    slot BIGINT,
+    _dlt_parent_id VARCHAR(128) NOT NULL,
+    _dlt_list_idx BIGINT NOT NULL,
+    _dlt_id VARCHAR(128) NOT NULL PRIMARY KEY,
+    CONSTRAINT fk_abilities
+      FOREIGN KEY (_dlt_parent_id)
+      REFERENCES pokemon_details(_dlt_id)
+      ON DELETE CASCADE
+);
+INSERT INTO new_pokemon_details__abilities
+    SELECT ability__name,
+           ability__url,
+           is_hidden,
+           slot,
+           _dlt_parent_id,
+           _dlt_list_idx,
+           _dlt_id
+    FROM pokemon_details__abilities;
+DROP TABLE pokemon_details__abilities;
+ALTER TABLE new_pokemon_details__abilities RENAME TO pokemon_details__abilities;
+
+/*------------------------------------------------------------------------
+4) pokemon_details_forms (Child)
+------------------------------------------------------------------------*/
+CREATE TABLE IF NOT EXISTS new_pokemon_details_forms (
+    name TEXT,
+    url TEXT,
+    _dlt_parent_id VARCHAR(128) NOT NULL,
+    _dlt_list_idx BIGINT NOT NULL,
+    _dlt_id VARCHAR(128) NOT NULL PRIMARY KEY,
+    FOREIGN KEY (_dlt_parent_id)
+      REFERENCES pokemon_details(_dlt_id)
+      ON DELETE CASCADE
+);
+INSERT INTO new_pokemon_details_forms
+    SELECT name,
+           url,
+           _dlt_parent_id,
+           _dlt_list_idx,
+           _dlt_id
+    FROM pokemon_details__forms;
+DROP TABLE pokemon_details__forms;
+ALTER TABLE new_pokemon_details_forms RENAME TO pokemon_details__forms;
+
+/*------------------------------------------------------------------------
+5) pokemon_details_game_indices (Child)
+------------------------------------------------------------------------*/
+CREATE TABLE IF NOT EXISTS new_pokemon_details__game_indices (
+    game_index BIGINT,
+    version__name TEXT,
+    version__url TEXT,
+    _dlt_parent_id VARCHAR(128) NOT NULL,
+    _dlt_list_idx BIGINT NOT NULL,
+    _dlt_id VARCHAR(128) NOT NULL PRIMARY KEY,
+    FOREIGN KEY (_dlt_parent_id)
+      REFERENCES pokemon_details(_dlt_id)
+      ON DELETE CASCADE
+);
+INSERT INTO new_pokemon_details__game_indices
+    SELECT game_index,
+           version__name,
+           version__url,
+           _dlt_parent_id,
+           _dlt_list_idx,
+           _dlt_id
+    FROM pokemon_details__game_indices;
+DROP TABLE pokemon_details__game_indices;
+ALTER TABLE new_pokemon_details__game_indices RENAME TO pokemon_details__game_indices;
+
+
+/*------------------------------------------------------------------------
+6) pokemon_details_moves (Child of pokemon_details)
+------------------------------------------------------------------------*/
+CREATE TABLE IF NOT EXISTS new_pokemon_details__moves (
+    move__name TEXT,
+    move__url TEXT,
+    _dlt_parent_id VARCHAR(128) NOT NULL,
+    _dlt_list_idx BIGINT NOT NULL,
+    _dlt_id VARCHAR(128) NOT NULL PRIMARY KEY,
+    FOREIGN KEY (_dlt_parent_id)
+      REFERENCES pokemon_details(_dlt_id)
+      ON DELETE CASCADE
+);
+INSERT INTO new_pokemon_details__moves
+    SELECT move__name,
+           move__url,
+           _dlt_parent_id,
+           _dlt_list_idx,
+           _dlt_id
+    FROM pokemon_details__moves;
+DROP TABLE pokemon_details__moves;
+ALTER TABLE new_pokemon_details__moves RENAME TO pokemon_details__moves;
+
+/*------------------------------------------------------------------------
+7) pokemon_details_moves_version_group_details (Child of pokemon_details_moves)
+------------------------------------------------------------------------*/
+CREATE TABLE IF NOT EXISTS new_pokemon_details__moves__version_group_details (
+    level_learned_at BIGINT,
+    version_group__name TEXT,
+    version_group__url TEXT,
+    move_learn_method__name TEXT,
+    move_learn_method__url TEXT,
+    _dlt_parent_id VARCHAR(128) NOT NULL,
+    _dlt_list_idx BIGINT NOT NULL,
+    _dlt_id VARCHAR(128) NOT NULL PRIMARY KEY,
+    "order" BIGINT,
+    FOREIGN KEY (_dlt_parent_id)
+      REFERENCES pokemon_details__moves(_dlt_id)
+      ON DELETE CASCADE
+);
+INSERT INTO new_pokemon_details__moves__version_group_details
+    SELECT level_learned_at,
+           version_group__name,
+           version_group__url,
+           move_learn_method__name,
+           move_learn_method__url,
+           _dlt_parent_id,
+           _dlt_list_idx,
+           _dlt_id,
+           "order"
+    FROM pokemon_details__moves__version_group_details;
+DROP TABLE pokemon_details__moves__version_group_details;
+ALTER TABLE new_pokemon_details__moves__version_group_details
+    RENAME TO pokemon_details__moves__version_group_details;
+
+/*------------------------------------------------------------------------
+8) pokemon_details_past_abilities (Child of pokemon_details)
+------------------------------------------------------------------------*/
+CREATE TABLE IF NOT EXISTS new_pokemon_details__past_abilities (
+    generation__name TEXT,
+    generation__url TEXT,
+    _dlt_parent_id VARCHAR(128) NOT NULL,
+    _dlt_list_idx BIGINT NOT NULL,
+    _dlt_id VARCHAR(128) NOT NULL PRIMARY KEY,
+    FOREIGN KEY (_dlt_parent_id)
+      REFERENCES pokemon_details(_dlt_id)
+      ON DELETE CASCADE
+);
+INSERT INTO new_pokemon_details__past_abilities
+    SELECT generation__name,
+           generation__url,
+           _dlt_parent_id,
+           _dlt_list_idx,
+           _dlt_id
+    FROM pokemon_details__past_abilities;
+DROP TABLE pokemon_details__past_abilities;
+ALTER TABLE new_pokemon_details__past_abilities
+    RENAME TO pokemon_details__past_abilities;
+
+/*------------------------------------------------------------------------
+9) pokemon_details_stats (Child of pokemon_details)
+------------------------------------------------------------------------*/
+CREATE TABLE IF NOT EXISTS new_pokemon_details_stats (
+    base_stat BIGINT,
+    effort BIGINT,
+    stat__name TEXT,
+    stat__url TEXT,
+    _dlt_parent_id VARCHAR(128) NOT NULL,
+    _dlt_list_idx BIGINT NOT NULL,
+    _dlt_id VARCHAR(128) NOT NULL PRIMARY KEY,
+    FOREIGN KEY (_dlt_parent_id)
+      REFERENCES pokemon_details(_dlt_id)
+      ON DELETE CASCADE
+);
+INSERT INTO new_pokemon_details_stats
+    SELECT base_stat,
+           effort,
+           stat__name,
+           stat__url,
+           _dlt_parent_id,
+           _dlt_list_idx,
+           _dlt_id
+    FROM pokemon_details__stats;
+DROP TABLE pokemon_details__stats;
+ALTER TABLE new_pokemon_details_stats
+    RENAME TO pokemon_details__stats;
+
+/*------------------------------------------------------------------------
+10) pokemon_details_types (Child of pokemon_details)
+------------------------------------------------------------------------*/
+CREATE TABLE IF NOT EXISTS new_pokemon_details__types (
+    slot BIGINT,
+    type__name TEXT,
+    type__url TEXT,
+    _dlt_parent_id VARCHAR(128) NOT NULL,
+    _dlt_list_idx BIGINT NOT NULL,
+    _dlt_id VARCHAR(128) NOT NULL PRIMARY KEY,
+    FOREIGN KEY (_dlt_parent_id)
+      REFERENCES pokemon_details(_dlt_id)
+      ON DELETE CASCADE
+);
+INSERT INTO new_pokemon_details__types
+    SELECT slot,
+           type__name,
+           type__url,
+           _dlt_parent_id,
+           _dlt_list_idx,
+           _dlt_id
+    FROM pokemon_details__types;
+DROP TABLE pokemon_details__types;
+ALTER TABLE new_pokemon_details__types
+    RENAME TO pokemon_details__types;
+
+/*------------------------------------------------------------------------
+11) pokemon_details_past_abilities_abilities (Child of pokemon_details_past_abilities)
+------------------------------------------------------------------------*/
+CREATE TABLE IF NOT EXISTS new_pokemon_details__past_abilities__abilities (
+    is_hidden BOOLEAN,
+    slot BIGINT,
+    _dlt_parent_id VARCHAR(128) NOT NULL,
+    _dlt_list_idx BIGINT NOT NULL,
+    _dlt_id VARCHAR(128) NOT NULL PRIMARY KEY,
+    FOREIGN KEY (_dlt_parent_id)
+      REFERENCES pokemon_details__past_abilities(_dlt_id)
+      ON DELETE CASCADE
+);
+INSERT INTO new_pokemon_details__past_abilities__abilities
+    SELECT is_hidden,
+           slot,
+           _dlt_parent_id,
+           _dlt_list_idx,
+           _dlt_id
+    FROM pokemon_details__past_abilities__abilities;
+DROP TABLE pokemon_details__past_abilities__abilities;
+ALTER TABLE new_pokemon_details__past_abilities__abilities
+    RENAME TO pokemon_details__past_abilities__abilities;
+
+
+/* Re-enable FK checks */
+PRAGMA foreign_keys=ON;
+
+COMMIT;

examples/relational_db_with_dlt/relational_db_and_dlt.py

@@ -0,0 +1,174 @@
+import dlt
+import requests
+import asyncio
+import threading
+import sqlalchemy as sa
+import pathlib
+import os
+from dlt.destinations.impl.sqlalchemy.configuration import SqlalchemyCredentials
+
+
+import cognee
+from cognee.infrastructure.databases.graph import get_graph_engine
+from cognee.api.v1.visualize.visualize import visualize_graph
+from cognee.infrastructure.databases.relational import (
+    get_migration_relational_engine,
+    create_db_and_tables as create_relational_db_and_tables,
+)
+from cognee.infrastructure.databases.vector.pgvector import (
+    create_db_and_tables as create_pgvector_db_and_tables,
+)
+from cognee.tasks.ingestion.migrate_relational_database import migrate_relational_database
+from cognee.modules.search.types import SearchType
+
+from cognee.root_dir import get_absolute_path
+
+
+class PatchedSqlalchemyCredentials(SqlalchemyCredentials):
+    def __init__(self, connection_string=None):
+        super().__init__(connection_string)
+        if not hasattr(self, "_conn_lock"):
+            self._conn_lock = threading.Lock()
+
+
+BASE_URL = "https://pokeapi.co/api/v2/"
+
+
+@dlt.resource(write_disposition="replace")
+def pokemon_list(limit: int = 5):
+    """Fetch Pokémon list (first 5 Pokémon)."""
+    response = requests.get(f"{BASE_URL}pokemon", params={"limit": limit})
+    response.raise_for_status()
+    yield response.json()["results"]
+
+
+@dlt.transformer(data_from=pokemon_list)
+def pokemon_details(pokemons):
+    """Fetch full detail for each Pokémon."""
+    for pokemon in pokemons:
+        response = requests.get(pokemon["url"])
+        response.raise_for_status()
+        yield response.json()
+
+
+async def setup_and_process_data():
+    """
+    Setup configuration and process Pokemon data into a SQLite database with dlt.
+    """
+    engine = sa.create_engine("sqlite:///pokemon_data.db")
+
+    pipeline = dlt.pipeline(
+        pipeline_name="pokemon_pipeline",
+        destination=dlt.destinations.sqlalchemy(
+            PatchedSqlalchemyCredentials("sqlite:///pokemon_data.db?timeout=15")
+        ),
+        dataset_name="main",
+        dev_mode=False,
+    )
+
+    info = pipeline.run([pokemon_list, pokemon_details])
+    print(f"[setup_and_process_data] Pipeline run complete. Pipeline info:\n{info}")
+
+    # (Optional) Inspect tables for debugging
+    print("[setup_and_process_data] Verifying data was written to the database.")
+    with engine.connect() as conn:
+        tables = conn.execute(
+            sa.text("SELECT name FROM sqlite_master WHERE type='table';")
+        ).fetchall()
+        print(f"[setup_and_process_data] Tables in database: {tables}")
+        # Example: if 'pokemon_details' is expected, we can see how many rows:
+        for table_tuple in tables:
+            table_name = table_tuple[0]
+            row_count = conn.execute(sa.text(f"SELECT COUNT(*) FROM {table_name}")).fetchone()[0]
+            print(f"    -> Table '{table_name}' has {row_count} row(s).")
+
+    print("[setup_and_process_data] Data loading step finished.\n")
+    return None
+
+
+async def apply_foreign_key_fixes():
+    """
+    Apply foreign key fixes to the SQLite database after data processing.
+    """
+    engine = sa.create_engine("sqlite:///pokemon_data.db")
+    with engine.connect() as conn:
+        raw_conn = conn.connection.connection
+        with open(
+            "examples/relational_db_with_dlt/fix_foreign_keys.sql", "r", encoding="utf-8"
+        ) as f:
+            sql_script = f.read()
+        raw_conn.executescript(sql_script)  # runs multiple statements
+        print("[apply_foreign_key_fixes] Applied foreign key fixes")
+
+    return None
+
+
+async def migrate_to_cognee():
+    """
+    Migrate the data from the SQLite database to cognee's knowledge graph.
+    """
+
+    # Use cognee's absolute path function instead of relative paths
+    data_directory_path = get_absolute_path(".data_storage")
+    cognee.config.data_root_directory(data_directory_path)
+
+    cognee_directory_path = get_absolute_path(".cognee_system")
+    cognee.config.system_root_directory(cognee_directory_path)
+
+    await cognee.prune.prune_data()
+    await cognee.prune.prune_system(metadata=True)
+    engine = get_migration_relational_engine()
+
+    await create_relational_db_and_tables()
+    await create_pgvector_db_and_tables()
+
+    schema = await engine.extract_schema()
+
+    graph_engine = await get_graph_engine()
+
+    await migrate_relational_database(graph_engine, schema=schema)
+
+
+async def visualize_knowledge_graph():
+    """
+    Generate and save an HTML visualization of the knowledge graph.
+    """
+    home_dir = os.path.expanduser("~")
+    html_path = os.path.join(home_dir, "graph_visualization.html")
+
+    await visualize_graph(html_path)
+
+
+async def search_knowledge_graph():
+    """
+    Perform a search query against the knowledge graph.
+    """
+    search_results = await cognee.search(
+        query_type=SearchType.GRAPH_COMPLETION, query_text="What kind of data do you contain?"
+    )
+    print(search_results)
+
+
+async def main():
+    print("[main] Starting main function, running setup_and_process_data...")
+    await setup_and_process_data()
+    print("[main] Data loaded into SQLite.")
+    await apply_foreign_key_fixes()
+    print("[main] Foreign key fixes applied.")
+    await migrate_to_cognee()
+    print("[main] Migration to cognee finished.")
+    await visualize_knowledge_graph()
+    print("[main] Knowledge graph visualization created.")
+    await search_knowledge_graph()
+    print("[main] Knowledge graph search completed.")
+
+
+if __name__ == "__main__":
+    print("[__main__] Creating and running event loop.")
+    loop = asyncio.new_event_loop()
+    asyncio.set_event_loop(loop)
+    try:
+        loop.run_until_complete(main())
+    finally:
+        loop.run_until_complete(loop.shutdown_asyncgens())
+    print("[__main__] Event loop closed. Exiting.")