From 8368b12532c221fc1eac859944a3317acd51a610 Mon Sep 17 00:00:00 2001 From: KennyZhang1 <90438893+KennyZhang1@users.noreply.github.com> Date: Thu, 19 Dec 2024 14:43:21 -0500 Subject: [PATCH] Add Cosmos DB storage/cache option (#1431) * added cosmosdb constructor and database methods * added rest of abstract method headers * added cosmos db container methods * implemented has and delete methods * finished implementing abstract class methods * integrated class into storage factory * integrated cosmosdb class into cache factory * added support for new config file fields * replaced primary key cosmosdb initialization with connection strings * modified cosmosdb setter to require json * Fix non-default emitters * Format * Ruff * ruff * first successful run of cosmosdb indexing * removed extraneous container_name setting * require base_dir to be typed as str * reverted merged changed from closed branch * removed nested try statement * readded initial non-parquet emitter fix * added basic support for parquet emitter using internal conversions * merged with main and resolved conflicts * fixed more merge conflicts * added cosmosdb functionality to query pipeline * tested query for cosmosdb * collapsed cosmosdb schema to use minimal containers and databases * simplified create_database and create_container functions * ruff fixes and semversioner * spellcheck and ci fixes * updated pyproject toml and lock file * apply fixes after merge from main * add temporary comments * refactor cache factory * refactored storage factory * minor formatting * update dictionary * fix spellcheck typo * fix default value * fix pydantic model defaults * update pydantic models * fix init_content * cleanup how factory passes parameters to file storage * remove unnecessary output file type * update pydantic model * cleanup code * implemented clear method * fix merge from main * add test stub for cosmosdb * regenerate lock file * modified set method to collapse parquet rows * modified get method to collapse parquet rows * updated has and delete methods and docstrings to adhere to new schema * added prefix helper function * replaced delimiter for prefixed id * verified empty tests are passing * fix merges from main * add find test * update cicd step name * tested querying for new schema * resolved errors from merge conflicts * refactored set method to handle cache in new schema * refactored get method to handle cache in new schema * force unique ids to be written to cosmos for nodes * found bug with has and delete methods * modified has and delete to work with cache in new schema * fix the merge from main * minor typo fixes * update lock file * spellcheck fix * fix init function signature * minor formatting updates * remove https protocol * change localhost to 127.0.0.1 address * update pytest to use bacj engine * verified cache tests * improved speed of has function * resolved pytest error with find function * added test for child method * make container_name variable private as _container_name * minor variable name fix * cleanup cosmos pytest and make the cosmosdb storage class operations more efficient * update cicd to use different cosmosdb emulator * test with http protocol * added pytest for clear() * add longer timeout for cosmosdb emulator startup * revert http connection back to https * add comments to cicd code for future dev usage * set to container and database clients to none upon deletion * ruff changes * add comments to cicd code * removed unneeded None statements and ruff fixes * more ruff fixes * Update test_run.py * remove unnecessary call to delete container * ruff format updates * Reverted test_run.py * fix ruff formatter errors * cleanup variable names to be more consistent * remove extra semversioner file * revert pydantic model changes * revert pydantic model change * revert pydantic model change * re-enable inline formatting rule * update documentation in dev guide --------- Co-authored-by: Alonso Guevara Co-authored-by: Josh Bradley --- .../workflows/python-integration-tests.yml | 15 +- .../patch-20241121202210026640.json | 4 + DEVELOPING.md | 1 - dictionary.txt | 1 + graphrag/cache/factory.py | 3 + graphrag/config/create_graphrag_config.py | 3 + graphrag/config/enums.py | 4 + graphrag/config/init_content.py | 4 +- .../config/input_models/cache_config_input.py | 1 + .../input_models/storage_config_input.py | 1 + graphrag/config/models/cache_config.py | 3 + graphrag/config/models/storage_config.py | 3 + graphrag/index/config/cache.py | 28 +- graphrag/index/config/storage.py | 36 +- graphrag/index/create_pipeline_config.py | 42 ++ graphrag/index/run/workflow.py | 6 +- graphrag/query/input/loaders/utils.py | 3 +- graphrag/storage/blob_pipeline_storage.py | 20 +- graphrag/storage/cosmosdb_pipeline_storage.py | 348 +++++++++++ graphrag/storage/factory.py | 3 + graphrag/storage/file_pipeline_storage.py | 1 - graphrag/vector_stores/factory.py | 5 +- poetry.lock | 561 +++++++++--------- pyproject.toml | 4 +- tests/conftest.py | 2 + .../storage/test_blob_pipeline_storage.py | 6 +- .../storage/test_cosmosdb_storage.py | 109 ++++ tests/smoke/test_fixtures.py | 6 +- .../cache/test_file_pipeline_cache.py | 2 +- tests/verbs/test_extract_graph.py | 2 +- 30 files changed, 925 insertions(+), 302 deletions(-) create mode 100644 .semversioner/next-release/patch-20241121202210026640.json create mode 100644 graphrag/storage/cosmosdb_pipeline_storage.py create mode 100644 tests/integration/storage/test_cosmosdb_storage.py diff --git a/.github/workflows/python-integration-tests.yml b/.github/workflows/python-integration-tests.yml index ffdbbef760..238d32c690 100644 --- a/.github/workflows/python-integration-tests.yml +++ b/.github/workflows/python-integration-tests.yml @@ -23,7 +23,7 @@ permissions: concurrency: group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} - # Only run the for the latest commit + # only run the for the latest commit cancel-in-progress: true env: @@ -37,7 +37,7 @@ jobs: matrix: python-version: ["3.10"] os: [ubuntu-latest, windows-latest] - fail-fast: false # Continue running all jobs even if one fails + fail-fast: false # continue running all jobs even if one fails env: DEBUG: 1 @@ -84,6 +84,17 @@ jobs: id: azuright uses: potatoqualitee/azuright@v1.1 + # For more information on installation/setup of Azure Cosmos DB Emulator + # https://learn.microsoft.com/en-us/azure/cosmos-db/how-to-develop-emulator?tabs=docker-linux%2Cpython&pivots=api-nosql + # Note: the emulator is only available on Windows runners. It can take longer than the default to initially startup so we increase the default timeout. + # If a job fails due to timeout, restarting the cicd job usually resolves the problem. + - name: Install Azure Cosmos DB Emulator + if: runner.os == 'Windows' + run: | + Write-Host "Launching Cosmos DB Emulator" + Import-Module "$env:ProgramFiles\Azure Cosmos DB Emulator\PSModules\Microsoft.Azure.CosmosDB.Emulator" + Start-CosmosDbEmulator -Timeout 500 + - name: Integration Test run: | poetry run poe test_integration diff --git a/.semversioner/next-release/patch-20241121202210026640.json b/.semversioner/next-release/patch-20241121202210026640.json new file mode 100644 index 0000000000..ac65aaf814 --- /dev/null +++ b/.semversioner/next-release/patch-20241121202210026640.json @@ -0,0 +1,4 @@ +{ + "type": "patch", + "description": "Implement cosmosdb storage option for cache and output" +} diff --git a/DEVELOPING.md b/DEVELOPING.md index be018e0583..d344bc7cd3 100644 --- a/DEVELOPING.md +++ b/DEVELOPING.md @@ -45,7 +45,6 @@ graphrag ├── config # configuration management ├── index # indexing engine | └─ run/run.py # main entrypoint to build an index -├── llm # generic llm interfaces ├── logger # logger module supporting several options │   └─ factory.py # └─ main entrypoint to create a logger ├── model # data model definitions associated with the knowledge graph diff --git a/dictionary.txt b/dictionary.txt index 0a18cd9272..575fe55548 100644 --- a/dictionary.txt +++ b/dictionary.txt @@ -28,6 +28,7 @@ ints # Azure abfs +cosmosdb Hnsw odata diff --git a/graphrag/cache/factory.py b/graphrag/cache/factory.py index 90f91a73b6..7490233cb7 100644 --- a/graphrag/cache/factory.py +++ b/graphrag/cache/factory.py @@ -9,6 +9,7 @@ from graphrag.config.enums import CacheType from graphrag.storage.blob_pipeline_storage import BlobPipelineStorage +from graphrag.storage.cosmosdb_pipeline_storage import create_cosmosdb_storage from graphrag.storage.file_pipeline_storage import FilePipelineStorage if TYPE_CHECKING: @@ -50,6 +51,8 @@ def create_cache( ) case CacheType.blob: return JsonPipelineCache(BlobPipelineStorage(**kwargs)) + case CacheType.cosmosdb: + return JsonPipelineCache(create_cosmosdb_storage(**kwargs)) case _: if cache_type in cls.cache_types: return cls.cache_types[cache_type](**kwargs) diff --git a/graphrag/config/create_graphrag_config.py b/graphrag/config/create_graphrag_config.py index c1da51126d..1155cee46f 100644 --- a/graphrag/config/create_graphrag_config.py +++ b/graphrag/config/create_graphrag_config.py @@ -362,6 +362,7 @@ def hydrate_parallelization_params( storage_account_blob_url=reader.str(Fragment.storage_account_blob_url), container_name=reader.str(Fragment.container_name), base_dir=reader.str(Fragment.base_dir) or defs.CACHE_BASE_DIR, + cosmosdb_account_url=reader.str(Fragment.cosmosdb_account_url), ) with ( reader.envvar_prefix(Section.reporting), @@ -383,6 +384,7 @@ def hydrate_parallelization_params( storage_account_blob_url=reader.str(Fragment.storage_account_blob_url), container_name=reader.str(Fragment.container_name), base_dir=reader.str(Fragment.base_dir) or defs.STORAGE_BASE_DIR, + cosmosdb_account_url=reader.str(Fragment.cosmosdb_account_url), ) with ( @@ -667,6 +669,7 @@ class Fragment(str, Enum): concurrent_requests = "CONCURRENT_REQUESTS" conn_string = "CONNECTION_STRING" container_name = "CONTAINER_NAME" + cosmosdb_account_url = "COSMOSDB_ACCOUNT_URL" deployment_name = "DEPLOYMENT_NAME" description = "DESCRIPTION" enabled = "ENABLED" diff --git a/graphrag/config/enums.py b/graphrag/config/enums.py index 4e27833395..4ff1e35571 100644 --- a/graphrag/config/enums.py +++ b/graphrag/config/enums.py @@ -19,6 +19,8 @@ class CacheType(str, Enum): """The none cache configuration type.""" blob = "blob" """The blob cache configuration type.""" + cosmosdb = "cosmosdb" + """The cosmosdb cache configuration type""" def __repr__(self): """Get a string representation.""" @@ -60,6 +62,8 @@ class StorageType(str, Enum): """The memory storage type.""" blob = "blob" """The blob storage type.""" + cosmosdb = "cosmosdb" + """The cosmosdb storage type""" def __repr__(self): """Get a string representation.""" diff --git a/graphrag/config/init_content.py b/graphrag/config/init_content.py index d34e6ea88b..8e3000ab3b 100644 --- a/graphrag/config/init_content.py +++ b/graphrag/config/init_content.py @@ -63,7 +63,7 @@ ## connection_string and container_name must be provided cache: - type: {defs.CACHE_TYPE.value} # or blob + type: {defs.CACHE_TYPE.value} # one of [blob, cosmosdb, file] base_dir: "{defs.CACHE_BASE_DIR}" reporting: @@ -71,7 +71,7 @@ base_dir: "{defs.REPORTING_BASE_DIR}" storage: - type: {defs.STORAGE_TYPE.value} # or blob + type: {defs.STORAGE_TYPE.value} # one of [blob, cosmosdb, file] base_dir: "{defs.STORAGE_BASE_DIR}" ## only turn this on if running `graphrag index` with custom settings diff --git a/graphrag/config/input_models/cache_config_input.py b/graphrag/config/input_models/cache_config_input.py index fe88d35b44..4c1ba35c57 100644 --- a/graphrag/config/input_models/cache_config_input.py +++ b/graphrag/config/input_models/cache_config_input.py @@ -16,3 +16,4 @@ class CacheConfigInput(TypedDict): connection_string: NotRequired[str | None] container_name: NotRequired[str | None] storage_account_blob_url: NotRequired[str | None] + cosmosdb_account_url: NotRequired[str | None] diff --git a/graphrag/config/input_models/storage_config_input.py b/graphrag/config/input_models/storage_config_input.py index cc5caf7952..4b0e85a2e5 100644 --- a/graphrag/config/input_models/storage_config_input.py +++ b/graphrag/config/input_models/storage_config_input.py @@ -16,3 +16,4 @@ class StorageConfigInput(TypedDict): connection_string: NotRequired[str | None] container_name: NotRequired[str | None] storage_account_blob_url: NotRequired[str | None] + cosmosdb_account_url: NotRequired[str | None] diff --git a/graphrag/config/models/cache_config.py b/graphrag/config/models/cache_config.py index 4589edce0b..fb4d22b229 100644 --- a/graphrag/config/models/cache_config.py +++ b/graphrag/config/models/cache_config.py @@ -27,3 +27,6 @@ class CacheConfig(BaseModel): storage_account_blob_url: str | None = Field( description="The storage account blob url to use.", default=None ) + cosmosdb_account_url: str | None = Field( + description="The cosmosdb account url to use.", default=None + ) diff --git a/graphrag/config/models/storage_config.py b/graphrag/config/models/storage_config.py index dcf41b9222..445a22b9a1 100644 --- a/graphrag/config/models/storage_config.py +++ b/graphrag/config/models/storage_config.py @@ -28,3 +28,6 @@ class StorageConfig(BaseModel): storage_account_blob_url: str | None = Field( description="The storage account blob url to use.", default=None ) + cosmosdb_account_url: str | None = Field( + description="The cosmosdb account url to use.", default=None + ) diff --git a/graphrag/index/config/cache.py b/graphrag/index/config/cache.py index 62d485d107..2ad6d5b8af 100644 --- a/graphrag/index/config/cache.py +++ b/graphrag/index/config/cache.py @@ -1,7 +1,7 @@ # Copyright (c) 2024 Microsoft Corporation. # Licensed under the MIT License -"""A module containing 'PipelineCacheConfig', 'PipelineFileCacheConfig', 'PipelineMemoryCacheConfig', 'PipelineBlobCacheConfig' models.""" +"""A module containing 'PipelineCacheConfig', 'PipelineFileCacheConfig', 'PipelineMemoryCacheConfig', 'PipelineBlobCacheConfig', 'PipelineCosmosDBCacheConfig' models.""" from __future__ import annotations @@ -71,9 +71,35 @@ class PipelineBlobCacheConfig(PipelineCacheConfig[Literal[CacheType.blob]]): """The storage account blob url for cache""" +class PipelineCosmosDBCacheConfig(PipelineCacheConfig[Literal[CacheType.cosmosdb]]): + """Represents the cosmosdb cache configuration for the pipeline.""" + + type: Literal[CacheType.cosmosdb] = CacheType.cosmosdb + """The type of cache.""" + + base_dir: str | None = Field( + description="The cosmosdb database name for the cache.", default=None + ) + """The cosmosdb database name for the cache.""" + + container_name: str = Field(description="The container name for cache.", default="") + """The container name for cache.""" + + connection_string: str | None = Field( + description="The cosmosdb primary key for the cache.", default=None + ) + """The cosmosdb primary key for the cache.""" + + cosmosdb_account_url: str | None = Field( + description="The cosmosdb account url for cache", default=None + ) + """The cosmosdb account url for cache""" + + PipelineCacheConfigTypes = ( PipelineFileCacheConfig | PipelineMemoryCacheConfig | PipelineBlobCacheConfig | PipelineNoneCacheConfig + | PipelineCosmosDBCacheConfig ) diff --git a/graphrag/index/config/storage.py b/graphrag/index/config/storage.py index 1e939cdf00..482b4056e4 100644 --- a/graphrag/index/config/storage.py +++ b/graphrag/index/config/storage.py @@ -1,7 +1,7 @@ # Copyright (c) 2024 Microsoft Corporation. # Licensed under the MIT License -"""A module containing 'PipelineStorageConfig', 'PipelineFileStorageConfig' and 'PipelineMemoryStorageConfig' models.""" +"""A module containing 'PipelineStorageConfig', 'PipelineFileStorageConfig','PipelineMemoryStorageConfig', 'PipelineBlobStorageConfig', and 'PipelineCosmosDBStorageConfig' models.""" from __future__ import annotations @@ -66,6 +66,38 @@ class PipelineBlobStorageConfig(PipelineStorageConfig[Literal[StorageType.blob]] """The storage account blob url.""" +class PipelineCosmosDBStorageConfig( + PipelineStorageConfig[Literal[StorageType.cosmosdb]] +): + """Represents the cosmosdb storage configuration for the pipeline.""" + + type: Literal[StorageType.cosmosdb] = StorageType.cosmosdb + """The type of storage.""" + + connection_string: str | None = Field( + description="The cosmosdb storage primary key for the storage.", default=None + ) + """The cosmosdb storage primary key for the storage.""" + + container_name: str = Field( + description="The container name for storage", default="" + ) + """The container name for storage.""" + + base_dir: str | None = Field( + description="The base directory for the storage.", default=None + ) + """The base directory for the storage.""" + + cosmosdb_account_url: str | None = Field( + description="The cosmosdb account url.", default=None + ) + """The cosmosdb account url.""" + + PipelineStorageConfigTypes = ( - PipelineFileStorageConfig | PipelineMemoryStorageConfig | PipelineBlobStorageConfig + PipelineFileStorageConfig + | PipelineMemoryStorageConfig + | PipelineBlobStorageConfig + | PipelineCosmosDBStorageConfig ) diff --git a/graphrag/index/create_pipeline_config.py b/graphrag/index/create_pipeline_config.py index 2c8fe4fc05..4d88c5ad57 100644 --- a/graphrag/index/create_pipeline_config.py +++ b/graphrag/index/create_pipeline_config.py @@ -20,6 +20,7 @@ from graphrag.index.config.cache import ( PipelineBlobCacheConfig, PipelineCacheConfigTypes, + PipelineCosmosDBCacheConfig, PipelineFileCacheConfig, PipelineMemoryCacheConfig, PipelineNoneCacheConfig, @@ -44,6 +45,7 @@ ) from graphrag.index.config.storage import ( PipelineBlobStorageConfig, + PipelineCosmosDBStorageConfig, PipelineFileStorageConfig, PipelineMemoryStorageConfig, PipelineStorageConfigTypes, @@ -420,6 +422,26 @@ def _get_storage_config( base_dir=storage_settings.base_dir, storage_account_blob_url=storage_account_blob_url, ) + case StorageType.cosmosdb: + cosmosdb_account_url = storage_settings.cosmosdb_account_url + connection_string = storage_settings.connection_string + base_dir = storage_settings.base_dir + container_name = storage_settings.container_name + if cosmosdb_account_url is None: + msg = "CosmosDB account url must be provided for cosmosdb storage." + raise ValueError(msg) + if base_dir is None: + msg = "Base directory must be provided for cosmosdb storage." + raise ValueError(msg) + if container_name is None: + msg = "Container name must be provided for cosmosdb storage." + raise ValueError(msg) + return PipelineCosmosDBStorageConfig( + cosmosdb_account_url=cosmosdb_account_url, + connection_string=connection_string, + base_dir=storage_settings.base_dir, + container_name=container_name, + ) case _: # relative to the root_dir base_dir = storage_settings.base_dir @@ -457,6 +479,26 @@ def _get_cache_config( base_dir=settings.cache.base_dir, storage_account_blob_url=storage_account_blob_url, ) + case CacheType.cosmosdb: + cosmosdb_account_url = settings.cache.cosmosdb_account_url + connection_string = settings.cache.connection_string + base_dir = settings.cache.base_dir + container_name = settings.cache.container_name + if base_dir is None: + msg = "Base directory must be provided for cosmosdb cache." + raise ValueError(msg) + if container_name is None: + msg = "Container name must be provided for cosmosdb cache." + raise ValueError(msg) + if connection_string is None and cosmosdb_account_url is None: + msg = "Connection string or cosmosDB account url must be provided for cosmosdb cache." + raise ValueError(msg) + return PipelineCosmosDBCacheConfig( + cosmosdb_account_url=cosmosdb_account_url, + connection_string=connection_string, + base_dir=base_dir, + container_name=container_name, + ) case _: # relative to root dir return PipelineFileCacheConfig(base_dir="./cache") diff --git a/graphrag/index/run/workflow.py b/graphrag/index/run/workflow.py index 4379f36b7f..e4758fd951 100644 --- a/graphrag/index/run/workflow.py +++ b/graphrag/index/run/workflow.py @@ -95,8 +95,12 @@ async def _process_workflow( return None context.stats.workflows[workflow_name] = {"overall": 0.0} + await _inject_workflow_data_dependencies( - workflow, workflow_dependencies, dataset, context.storage + workflow, + workflow_dependencies, + dataset, + context.storage, ) workflow_start_time = time.time() diff --git a/graphrag/query/input/loaders/utils.py b/graphrag/query/input/loaders/utils.py index 3c680f0faa..3878232985 100644 --- a/graphrag/query/input/loaders/utils.py +++ b/graphrag/query/input/loaders/utils.py @@ -165,8 +165,7 @@ def to_optional_float(data: pd.Series, column_name: str | None) -> float | None: if value is None: return None if not isinstance(value, float): - msg = f"value is not a float: {value} ({type(value)})" - raise ValueError(msg) + return float(value) else: msg = f"Column {column_name} not found in data" raise ValueError(msg) diff --git a/graphrag/storage/blob_pipeline_storage.py b/graphrag/storage/blob_pipeline_storage.py index c7081644e8..701e59e25c 100644 --- a/graphrag/storage/blob_pipeline_storage.py +++ b/graphrag/storage/blob_pipeline_storage.py @@ -65,11 +65,11 @@ def __init__( self._container_name, self._path_prefix, ) - self.create_container() + self._create_container() - def create_container(self) -> None: + def _create_container(self) -> None: """Create the container if it does not exist.""" - if not self.container_exists(): + if not self._container_exists(): container_name = self._container_name container_names = [ container.name @@ -78,12 +78,12 @@ def create_container(self) -> None: if container_name not in container_names: self._blob_service_client.create_container(container_name) - def delete_container(self) -> None: + def _delete_container(self) -> None: """Delete the container.""" - if self.container_exists(): + if self._container_exists(): self._blob_service_client.delete_container(self._container_name) - def container_exists(self) -> bool: + def _container_exists(self) -> bool: """Check if the container exists.""" container_name = self._container_name container_names = [ @@ -119,7 +119,7 @@ def find( file_pattern.pattern, ) - def blobname(blob_name: str) -> str: + def _blobname(blob_name: str) -> str: if blob_name.startswith(self._path_prefix): blob_name = blob_name.replace(self._path_prefix, "", 1) if blob_name.startswith("/"): @@ -146,7 +146,7 @@ def item_filter(item: dict[str, Any]) -> bool: if match and blob.name.startswith(base_dir): group = match.groupdict() if item_filter(group): - yield (blobname(blob.name), group) + yield (_blobname(blob.name), group) num_loaded += 1 if max_count > 0 and num_loaded >= max_count: break @@ -203,7 +203,7 @@ async def set(self, key: str, value: Any, encoding: str | None = None) -> None: except Exception: log.exception("Error setting key %s: %s", key) - def set_df_json(self, key: str, dataframe: Any) -> None: + def _set_df_json(self, key: str, dataframe: Any) -> None: """Set a json dataframe.""" if self._connection_string is None and self._storage_account_name: dataframe.to_json( @@ -225,7 +225,7 @@ def set_df_json(self, key: str, dataframe: Any) -> None: force_ascii=False, ) - def set_df_parquet(self, key: str, dataframe: Any) -> None: + def _set_df_parquet(self, key: str, dataframe: Any) -> None: """Set a parquet dataframe.""" if self._connection_string is None and self._storage_account_name: dataframe.to_parquet( diff --git a/graphrag/storage/cosmosdb_pipeline_storage.py b/graphrag/storage/cosmosdb_pipeline_storage.py new file mode 100644 index 0000000000..9de9cf6dc0 --- /dev/null +++ b/graphrag/storage/cosmosdb_pipeline_storage.py @@ -0,0 +1,348 @@ +# Copyright (c) 2024 Microsoft Corporation. +# Licensed under the MIT License + +"""Azure CosmosDB Storage implementation of PipelineStorage.""" + +import json +import logging +import re +from collections.abc import Iterator +from io import BytesIO, StringIO +from typing import Any + +import pandas as pd +from azure.cosmos import ContainerProxy, CosmosClient, DatabaseProxy +from azure.cosmos.exceptions import CosmosResourceNotFoundError +from azure.cosmos.partition_key import PartitionKey +from azure.identity import DefaultAzureCredential +from datashaper import Progress + +from graphrag.logger.base import ProgressLogger +from graphrag.storage.pipeline_storage import PipelineStorage + +log = logging.getLogger(__name__) + + +class CosmosDBPipelineStorage(PipelineStorage): + """The CosmosDB-Storage Implementation.""" + + _cosmos_client: CosmosClient + _database_client: DatabaseProxy | None + _container_client: ContainerProxy | None + _cosmosdb_account_url: str | None + _connection_string: str | None + _database_name: str + _container_name: str + _encoding: str + + def __init__( + self, + database_name: str, + container_name: str, + cosmosdb_account_url: str | None = None, + connection_string: str | None = None, + encoding: str = "utf-8", + ): + """Initialize the CosmosDB Storage.""" + if connection_string: + self._cosmos_client = CosmosClient.from_connection_string(connection_string) + else: + if cosmosdb_account_url is None: + msg = ( + "Either connection_string or cosmosdb_account_url must be provided." + ) + raise ValueError(msg) + self._cosmos_client = CosmosClient( + url=cosmosdb_account_url, + credential=DefaultAzureCredential(), + ) + self._encoding = encoding + self._database_name = database_name + self._connection_string = connection_string + self._cosmosdb_account_url = cosmosdb_account_url + self._container_name = container_name + self._cosmosdb_account_name = ( + cosmosdb_account_url.split("//")[1].split(".")[0] + if cosmosdb_account_url + else None + ) + log.info( + "creating cosmosdb storage with account: %s and database: %s and container: %s", + self._cosmosdb_account_name, + self._database_name, + self._container_name, + ) + self._create_database() + self._create_container() + + def _create_database(self) -> None: + """Create the database if it doesn't exist.""" + self._database_client = self._cosmos_client.create_database_if_not_exists( + id=self._database_name + ) + + def _delete_database(self) -> None: + """Delete the database if it exists.""" + if self._database_client: + self._database_client = self._cosmos_client.delete_database( + self._database_client + ) + self._container_client = None + + def _create_container(self) -> None: + """Create a container for the current container name if it doesn't exist.""" + partition_key = PartitionKey(path="/id", kind="Hash") + if self._database_client: + self._container_client = ( + self._database_client.create_container_if_not_exists( + id=self._container_name, + partition_key=partition_key, + ) + ) + + def _delete_container(self) -> None: + """Delete the container with the current container name if it exists.""" + if self._database_client and self._container_client: + self._container_client = self._database_client.delete_container( + self._container_client + ) + + def find( + self, + file_pattern: re.Pattern[str], + base_dir: str | None = None, + progress: ProgressLogger | None = None, + file_filter: dict[str, Any] | None = None, + max_count=-1, + ) -> Iterator[tuple[str, dict[str, Any]]]: + """Find documents in a Cosmos DB container using a file pattern regex and custom file filter (optional). + + Params: + base_dir: The name of the base directory (not used in Cosmos DB context). + file_pattern: The file pattern to use. + file_filter: A dictionary of key-value pairs to filter the documents. + max_count: The maximum number of documents to return. If -1, all documents are returned. + + Returns + ------- + An iterator of document IDs and their corresponding regex matches. + """ + base_dir = base_dir or "" + log.info( + "search container %s for documents matching %s", + self._container_name, + file_pattern.pattern, + ) + if not self._database_client or not self._container_client: + return + + def item_filter(item: dict[str, Any]) -> bool: + if file_filter is None: + return True + return all( + re.match(value, item.get(key, "")) for key, value in file_filter.items() + ) + + try: + query = "SELECT * FROM c WHERE RegexMatch(c.id, @pattern)" + parameters: list[dict[str, Any]] = [ + {"name": "@pattern", "value": file_pattern.pattern} + ] + if file_filter: + for key, value in file_filter.items(): + query += f" AND c.{key} = @{key}" + parameters.append({"name": f"@{key}", "value": value}) + items = list( + self._container_client.query_items( + query=query, + parameters=parameters, + enable_cross_partition_query=True, + ) + ) + num_loaded = 0 + num_total = len(items) + if num_total == 0: + return + num_filtered = 0 + for item in items: + match = file_pattern.match(item["id"]) + if match: + group = match.groupdict() + if item_filter(group): + yield (item["id"], group) + num_loaded += 1 + if max_count > 0 and num_loaded >= max_count: + break + else: + num_filtered += 1 + else: + num_filtered += 1 + if progress is not None: + progress( + _create_progress_status(num_loaded, num_filtered, num_total) + ) + except Exception: + log.exception( + "An error occurred while searching for documents in Cosmos DB." + ) + + async def get( + self, key: str, as_bytes: bool | None = None, encoding: str | None = None + ) -> Any: + """Fetch all items in a container that match the given key.""" + try: + if not self._database_client or not self._container_client: + return None + if as_bytes: + prefix = self._get_prefix(key) + query = f"SELECT * FROM c WHERE STARTSWITH(c.id, '{prefix}')" # noqa: S608 + queried_items = self._container_client.query_items( + query=query, enable_cross_partition_query=True + ) + items_list = list(queried_items) + for item in items_list: + item["id"] = item["id"].split(":")[1] + + items_json_str = json.dumps(items_list) + + items_df = pd.read_json( + StringIO(items_json_str), orient="records", lines=False + ) + return items_df.to_parquet() + item = self._container_client.read_item(item=key, partition_key=key) + item_body = item.get("body") + return json.dumps(item_body) + except Exception: + log.exception("Error reading item %s", key) + return None + + async def set(self, key: str, value: Any, encoding: str | None = None) -> None: + """Insert the contents of a file into a cosmosdb container for the given filename key. + + For better optimization, the file is destructured such that each row is a unique cosmosdb item. + """ + try: + if not self._database_client or not self._container_client: + msg = "Database or container not initialized" + raise ValueError(msg) # noqa: TRY301 + # value represents a parquet file + if isinstance(value, bytes): + prefix = self._get_prefix(key) + value_df = pd.read_parquet(BytesIO(value)) + value_json = value_df.to_json( + orient="records", lines=False, force_ascii=False + ) + if value_json is None: + log.exception("Error converting output %s to json", key) + else: + cosmosdb_item_list = json.loads(value_json) + for cosmosdb_item in cosmosdb_item_list: + # Append an additional prefix to the id to force a unique identifier for the create_final_nodes rows + if prefix == "create_final_nodes": + prefixed_id = f"{prefix}-community_{cosmosdb_item['community']}:{cosmosdb_item['id']}" + else: + prefixed_id = f"{prefix}:{cosmosdb_item['id']}" + cosmosdb_item["id"] = prefixed_id + self._container_client.upsert_item(body=cosmosdb_item) + # value represents a cache output or stats.json + else: + cosmosdb_item = { + "id": key, + "body": json.loads(value), + } + self._container_client.upsert_item(body=cosmosdb_item) + except Exception: + log.exception("Error writing item %s", key) + + async def has(self, key: str) -> bool: + """Check if the contents of the given filename key exist in the cosmosdb storage.""" + if not self._database_client or not self._container_client: + return False + if ".parquet" in key: + prefix = self._get_prefix(key) + query = f"SELECT * FROM c WHERE STARTSWITH(c.id, '{prefix}')" # noqa: S608 + queried_items = self._container_client.query_items( + query=query, enable_cross_partition_query=True + ) + return len(list(queried_items)) > 0 + query = f"SELECT * FROM c WHERE c.id = '{key}'" # noqa: S608 + queried_items = self._container_client.query_items( + query=query, enable_cross_partition_query=True + ) + return len(list(queried_items)) == 1 + + async def delete(self, key: str) -> None: + """Delete all cosmosdb items belonging to the given filename key.""" + if not self._database_client or not self._container_client: + return + try: + if ".parquet" in key: + prefix = self._get_prefix(key) + query = f"SELECT * FROM c WHERE STARTSWITH(c.id, '{prefix}')" # noqa: S608 + queried_items = self._container_client.query_items( + query=query, enable_cross_partition_query=True + ) + for item in queried_items: + self._container_client.delete_item( + item=item["id"], partition_key=item["id"] + ) + else: + self._container_client.delete_item(item=key, partition_key=key) + except CosmosResourceNotFoundError: + return + except Exception: + log.exception("Error deleting item %s", key) + + async def clear(self) -> None: + """Clear all contents from storage. + + # This currently deletes the database, including all containers and data within it. + # TODO: We should decide what granularity of deletion is the ideal behavior (e.g. delete all items within a container, delete the current container, delete the current database) + """ + self._delete_database() + + def keys(self) -> list[str]: + """Return the keys in the storage.""" + msg = "CosmosDB storage does yet not support listing keys." + raise NotImplementedError(msg) + + def child(self, name: str | None) -> PipelineStorage: + """Create a child storage instance.""" + return self + + def _get_prefix(self, key: str) -> str: + """Get the prefix of the filename key.""" + return key.split(".")[0] + + +# TODO remove this helper function and have the factory instantiate the class directly +# once the new config system is in place and will enforce the correct types/existence of certain fields +def create_cosmosdb_storage(**kwargs: Any) -> PipelineStorage: + """Create a CosmosDB storage instance.""" + log.info("Creating cosmosdb storage") + cosmosdb_account_url = kwargs.get("cosmosdb_account_url") + connection_string = kwargs.get("connection_string") + base_dir = kwargs["base_dir"] + container_name = kwargs["container_name"] + if not base_dir: + msg = "No base_dir provided for database name" + raise ValueError(msg) + if connection_string is None and cosmosdb_account_url is None: + msg = "connection_string or cosmosdb_account_url is required." + raise ValueError(msg) + return CosmosDBPipelineStorage( + cosmosdb_account_url=cosmosdb_account_url, + connection_string=connection_string, + database_name=base_dir, + container_name=container_name, + ) + + +def _create_progress_status( + num_loaded: int, num_filtered: int, num_total: int +) -> Progress: + return Progress( + total_items=num_total, + completed_items=num_loaded + num_filtered, + description=f"{num_loaded} files loaded ({num_filtered} filtered)", + ) diff --git a/graphrag/storage/factory.py b/graphrag/storage/factory.py index d245442a75..e3346af401 100644 --- a/graphrag/storage/factory.py +++ b/graphrag/storage/factory.py @@ -9,6 +9,7 @@ from graphrag.config.enums import StorageType from graphrag.storage.blob_pipeline_storage import create_blob_storage +from graphrag.storage.cosmosdb_pipeline_storage import create_cosmosdb_storage from graphrag.storage.file_pipeline_storage import create_file_storage from graphrag.storage.memory_pipeline_storage import MemoryPipelineStorage @@ -37,6 +38,8 @@ def create_storage( match storage_type: case StorageType.blob: return create_blob_storage(**kwargs) + case StorageType.cosmosdb: + return create_cosmosdb_storage(**kwargs) case StorageType.file: return create_file_storage(**kwargs) case StorageType.memory: diff --git a/graphrag/storage/file_pipeline_storage.py b/graphrag/storage/file_pipeline_storage.py index 895616d62a..f64df723b4 100644 --- a/graphrag/storage/file_pipeline_storage.py +++ b/graphrag/storage/file_pipeline_storage.py @@ -47,7 +47,6 @@ def find( def item_filter(item: dict[str, Any]) -> bool: if file_filter is None: return True - return all(re.match(value, item[key]) for key, value in file_filter.items()) search_path = Path(self._root_dir) / (base_dir or "") diff --git a/graphrag/vector_stores/factory.py b/graphrag/vector_stores/factory.py index eedbefab13..c1fc89abe1 100644 --- a/graphrag/vector_stores/factory.py +++ b/graphrag/vector_stores/factory.py @@ -19,7 +19,10 @@ class VectorStoreType(str, Enum): class VectorStoreFactory: - """A factory class for vector stores.""" + """A factory for vector stores. + + Includes a method for users to register a custom vector store implementation. + """ vector_store_types: ClassVar[dict[str, type]] = {} diff --git a/poetry.lock b/poetry.lock index 841b2c8c39..dc21b3802e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -190,19 +190,19 @@ typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""} [[package]] name = "attrs" -version = "24.2.0" +version = "24.3.0" description = "Classes Without Boilerplate" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2"}, - {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"}, + {file = 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python-versions = ">=3.10,<3.13" -content-hash = "35b7e6ca1c91915781f6e010d7c070a3a66f3071b8e241854b9b034f63c261e1" +content-hash = "54d5f5d253d47c5c28c874c9aa56eaeba543fa3c27fed6143ae266b0a07ed391" diff --git a/pyproject.toml b/pyproject.toml index 1efc3ea8fd..7d27132548 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -81,8 +81,9 @@ devtools = "^0.12.2" typing-extensions = "^4.12.2" #Azure -azure-storage-blob = "^12.24.0" +azure-cosmos = "^4.9.0" azure-identity = "^1.19.0" +azure-storage-blob = "^12.24.0" future = "^1.0.0" # Needed until graspologic fixes their dependency typer = "^0.15.1" @@ -267,6 +268,7 @@ include = ["graphrag", "tests", "examples", "examples_notebooks"] exclude = ["**/node_modules", "**/__pycache__"] [tool.pytest.ini_options] +asyncio_default_fixture_loop_scope = "function" asyncio_mode = "auto" timeout = 1000 env_files = [".env"] diff --git a/tests/conftest.py b/tests/conftest.py index c6536014b8..17a8835feb 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,5 +1,7 @@ # Copyright (c) 2024 Microsoft Corporation. # Licensed under the MIT License + + def pytest_addoption(parser): parser.addoption( "--run_slow", action="store_true", default=False, help="run slow tests" diff --git a/tests/integration/storage/test_blob_pipeline_storage.py b/tests/integration/storage/test_blob_pipeline_storage.py index af5b26e071..6883920136 100644 --- a/tests/integration/storage/test_blob_pipeline_storage.py +++ b/tests/integration/storage/test_blob_pipeline_storage.py @@ -44,7 +44,7 @@ async def test_find(): output = await storage.get("test.txt") assert output is None finally: - storage.delete_container() + storage._delete_container() # noqa: SLF001 async def test_dotprefix(): @@ -59,7 +59,7 @@ async def test_dotprefix(): items = [item[0] for item in items] assert items == ["input/christmas.txt"] finally: - storage.delete_container() + storage._delete_container() # noqa: SLF001 async def test_child(): @@ -93,4 +93,4 @@ async def test_child(): has_test = await parent.has("input/test.txt") assert not has_test finally: - parent.delete_container() + parent._delete_container() # noqa: SLF001 diff --git a/tests/integration/storage/test_cosmosdb_storage.py b/tests/integration/storage/test_cosmosdb_storage.py new file mode 100644 index 0000000000..5b82e0d83e --- /dev/null +++ b/tests/integration/storage/test_cosmosdb_storage.py @@ -0,0 +1,109 @@ +# Copyright (c) 2024 Microsoft Corporation. +# Licensed under the MIT License +"""CosmosDB Storage Tests.""" + +import json +import re +import sys + +import pytest + +from graphrag.storage.cosmosdb_pipeline_storage import CosmosDBPipelineStorage + +# cspell:disable-next-line well-known-key +WELL_KNOWN_COSMOS_CONNECTION_STRING = "AccountEndpoint=https://127.0.0.1:8081/;AccountKey=C2y6yDjf5/R+ob0N8A7Cgv30VRDJIWEHLM+4QDU5DE2nQ9nDuVTqobD4b8mGGyPMbIZnqyMsEcaGQy67XIw/Jw==" + +# the cosmosdb emulator is only available on windows runners at this time +if not sys.platform.startswith("win"): + pytest.skip( + "encountered windows-only tests -- will skip for now", allow_module_level=True + ) + + +async def test_find(): + storage = CosmosDBPipelineStorage( + connection_string=WELL_KNOWN_COSMOS_CONNECTION_STRING, + database_name="testfind", + container_name="testfindcontainer", + ) + try: + try: + items = list(storage.find(file_pattern=re.compile(r".*\.json$"))) + items = [item[0] for item in items] + assert items == [] + + json_content = { + "content": "Merry Christmas!", + } + await storage.set( + "christmas.json", json.dumps(json_content), encoding="utf-8" + ) + items = list(storage.find(file_pattern=re.compile(r".*\.json$"))) + items = [item[0] for item in items] + assert items == ["christmas.json"] + + json_content = { + "content": "Hello, World!", + } + await storage.set("test.json", json.dumps(json_content), encoding="utf-8") + items = list(storage.find(file_pattern=re.compile(r".*\.json$"))) + items = [item[0] for item in items] + assert items == ["christmas.json", "test.json"] + + output = await storage.get("test.json") + output_json = json.loads(output) + assert output_json["content"] == "Hello, World!" + + json_exists = await storage.has("christmas.json") + assert json_exists is True + json_exists = await storage.has("easter.json") + assert json_exists is False + finally: + await storage.delete("test.json") + output = await storage.get("test.json") + assert output is None + finally: + await storage.clear() + + +async def test_child(): + storage = CosmosDBPipelineStorage( + connection_string=WELL_KNOWN_COSMOS_CONNECTION_STRING, + database_name="testchild", + container_name="testchildcontainer", + ) + try: + child_storage = storage.child("child") + assert type(child_storage) is CosmosDBPipelineStorage + finally: + await storage.clear() + + +async def test_clear(): + storage = CosmosDBPipelineStorage( + connection_string=WELL_KNOWN_COSMOS_CONNECTION_STRING, + database_name="testclear", + container_name="testclearcontainer", + ) + try: + json_exists = { + "content": "Merry Christmas!", + } + await storage.set("christmas.json", json.dumps(json_exists), encoding="utf-8") + json_exists = { + "content": "Happy Easter!", + } + await storage.set("easter.json", json.dumps(json_exists), encoding="utf-8") + await storage.clear() + + items = list(storage.find(file_pattern=re.compile(r".*\.json$"))) + items = [item[0] for item in items] + assert items == [] + + output = await storage.get("easter.json") + assert output is None + + assert storage._container_client is None # noqa: SLF001 + assert storage._database_client is None # noqa: SLF001 + finally: + await storage.clear() diff --git a/tests/smoke/test_fixtures.py b/tests/smoke/test_fixtures.py index 1f0c449753..af6a5cd96d 100644 --- a/tests/smoke/test_fixtures.py +++ b/tests/smoke/test_fixtures.py @@ -100,8 +100,8 @@ async def prepare_azurite_data(input_path: str, azure: dict) -> Callable[[], Non container_name=input_container, ) # Bounce the container if it exists to clear out old run data - input_storage.delete_container() - input_storage.create_container() + input_storage._delete_container() # noqa: SLF001 + input_storage._create_container() # noqa: SLF001 # Upload data files txt_files = list((root / "input").glob("*.txt")) @@ -116,7 +116,7 @@ async def prepare_azurite_data(input_path: str, azure: dict) -> Callable[[], Non ) await input_storage.set(file_path, text, encoding="utf-8") - return lambda: input_storage.delete_container() + return lambda: input_storage._delete_container() # noqa: SLF001 class TestIndexer: diff --git a/tests/unit/indexing/cache/test_file_pipeline_cache.py b/tests/unit/indexing/cache/test_file_pipeline_cache.py index 045581ad49..d08bd6ebfc 100644 --- a/tests/unit/indexing/cache/test_file_pipeline_cache.py +++ b/tests/unit/indexing/cache/test_file_pipeline_cache.py @@ -13,7 +13,7 @@ def create_cache(): - storage = FilePipelineStorage(os.path.join(os.getcwd(), ".tmp")) + storage = FilePipelineStorage(root_dir=os.path.join(os.getcwd(), ".tmp")) return JsonPipelineCache(storage) diff --git a/tests/verbs/test_extract_graph.py b/tests/verbs/test_extract_graph.py index 9e4d0a4280..3ccc1d22b6 100644 --- a/tests/verbs/test_extract_graph.py +++ b/tests/verbs/test_extract_graph.py @@ -92,7 +92,7 @@ async def test_extract_graph(): # we need to update the mocking to provide somewhat unique graphs so a true merge happens # the assertion should grab a node and ensure the description matches the mock description, not the original as we are doing below - assert nodes_actual["description"].values[0] == "Company_A is a test company" + assert nodes_actual["description"].to_numpy()[0] == "Company_A is a test company" assert len(context.storage.keys()) == 0, "Storage should be empty"