From 2ef5a46b00977a9f0831562a7b0577bd7a39299d Mon Sep 17 00:00:00 2001 From: Kenny Zhang Date: Mon, 17 Mar 2025 12:15:43 -0400 Subject: [PATCH 01/19] added markitdown conversion step to data api --- backend/graphrag_app/api/data.py | 8 ++++++-- notebooks/1-Quickstart.ipynb | 4 ++-- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/backend/graphrag_app/api/data.py b/backend/graphrag_app/api/data.py index 4d2ce553..71f6516a 100644 --- a/backend/graphrag_app/api/data.py +++ b/backend/graphrag_app/api/data.py @@ -14,6 +14,7 @@ HTTPException, UploadFile, ) +from markitdown import MarkItDown from graphrag_app.logger.load_logger import load_pipeline_logger from graphrag_app.typing.models import ( @@ -67,13 +68,16 @@ async def upload_file_async( upload_file: UploadFile, container_client: ContainerClient, overwrite: bool = True ) -> None: """ - Asynchronously upload a file to the specified blob container. + Asynchronously convert and upload a file to the specified blob container. Silently ignore errors that occur when overwrite=False. """ blob_client = container_client.get_blob_client(upload_file.filename) with upload_file.file as file_stream: try: - await blob_client.upload_blob(file_stream, overwrite=overwrite) + # Extract text from file and upload to Azure Blob Storage + md = MarkItDown() + result = md.convert(file_stream) + await blob_client.upload_blob(result.text_content, overwrite=overwrite) except Exception: pass diff --git a/notebooks/1-Quickstart.ipynb b/notebooks/1-Quickstart.ipynb index dec86222..683dcea8 100644 --- a/notebooks/1-Quickstart.ipynb +++ b/notebooks/1-Quickstart.ipynb @@ -402,7 +402,7 @@ ], "metadata": { "kernelspec": { - "display_name": "graphrag-venv", + "display_name": "Python 3", "language": "python", "name": "python3" }, @@ -416,7 +416,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.16" + "version": "3.10.12" } }, "nbformat": 4, From b684bb76482b143644c9827d85846441396a8e20 Mon Sep 17 00:00:00 2001 From: Kenny Zhang Date: Mon, 17 Mar 2025 12:34:55 -0400 Subject: [PATCH 02/19] use converted filename for blob client --- backend/graphrag_app/api/data.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/backend/graphrag_app/api/data.py b/backend/graphrag_app/api/data.py index 71f6516a..71e851df 100644 --- a/backend/graphrag_app/api/data.py +++ b/backend/graphrag_app/api/data.py @@ -71,7 +71,10 @@ async def upload_file_async( Asynchronously convert and upload a file to the specified blob container. Silently ignore errors that occur when overwrite=False. """ - blob_client = container_client.get_blob_client(upload_file.filename) + filename = upload_file.filename + converted_filename = filename.split(".")[0] + ".txt" + blob_client = container_client.get_blob_client(converted_filename) + with upload_file.file as file_stream: try: # Extract text from file and upload to Azure Blob Storage From c6e63a901d6693da8b9e8dbeba5e19164d717fd0 Mon Sep 17 00:00:00 2001 From: Kenny Zhang Date: Mon, 17 Mar 2025 16:28:26 -0400 Subject: [PATCH 03/19] added cache initialization and check function --- backend/graphrag_app/api/data.py | 46 +++++++++++++++++++++++++++----- 1 file changed, 40 insertions(+), 6 deletions(-) diff --git a/backend/graphrag_app/api/data.py b/backend/graphrag_app/api/data.py index 71e851df..bcbfffbb 100644 --- a/backend/graphrag_app/api/data.py +++ b/backend/graphrag_app/api/data.py @@ -2,10 +2,13 @@ # Licensed under the MIT License. import asyncio +import csv import re import traceback +from hashlib import sha256 +from io import StringIO from math import ceil -from typing import List +from typing import BinaryIO, List from azure.storage.blob.aio import ContainerClient from fastapi import ( @@ -73,18 +76,37 @@ async def upload_file_async( """ filename = upload_file.filename converted_filename = filename.split(".")[0] + ".txt" - blob_client = container_client.get_blob_client(converted_filename) - + converted_blob_client = container_client.get_blob_client(converted_filename) + with upload_file.file as file_stream: try: - # Extract text from file and upload to Azure Blob Storage + # extract text from file and upload to Azure Blob Storage md = MarkItDown() result = md.convert(file_stream) - await blob_client.upload_blob(result.text_content, overwrite=overwrite) + await converted_blob_client.upload_blob(result.text_content, overwrite=overwrite) except Exception: pass +async def check_cache(file_stream: BinaryIO, container_client: ContainerClient) -> bool: + """ + Check if the file has already been uploaded. + """ + # load the file cache + cache_blob_client = container_client.get_blob_client("uploaded_files_cache.csv") + cache_download_stream = await cache_blob_client.download_blob() + cache_bytes = await cache_download_stream.readall() + cache_content = StringIO(cache_bytes.decode("utf-8")) + cache_reader = csv.reader(cache_content) + + # comupte the sha256 hash of the file and check if it exists in the cache + file_hash = sha256(file_stream.read()).hexdigest() + for row in cache_reader: + if file_hash in row: + return True + return False + + class Cleaner: def __init__(self, file): self.file = file @@ -145,10 +167,22 @@ async def upload_files( # clean files - remove illegal XML characters files = [UploadFile(Cleaner(f.file), filename=f.filename) for f in files] - # upload files in batches of 1000 to avoid exceeding Azure Storage API limits blob_container_client = await get_blob_container_client( sanitized_container_name ) + + # create and upload the file cache if it doesn't exist + cache_blob_client = blob_container_client.get_blob_client("uploaded_files_cache.csv") + if not cache_blob_client.exists(): + headers = [ + ['Filename', 'Hash'] + ] + with open("uploaded_files_cache.csv", "w", newline="") as f: + writer = csv.writer(f) + writer.writerows(headers) + cache_blob_client.upload_blob(f, overwrite=True) + + # upload files in batches of 1000 to avoid exceeding Azure Storage API limits batch_size = 1000 num_batches = ceil(len(files) / batch_size) for i in range(num_batches): From 95f082be626f6619d33ca3b9e377696cf5f03fbd Mon Sep 17 00:00:00 2001 From: Kenny Zhang Date: Mon, 17 Mar 2025 16:32:27 -0400 Subject: [PATCH 04/19] upload file method calls checker function --- backend/graphrag_app/api/data.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/backend/graphrag_app/api/data.py b/backend/graphrag_app/api/data.py index bcbfffbb..e398b367 100644 --- a/backend/graphrag_app/api/data.py +++ b/backend/graphrag_app/api/data.py @@ -80,10 +80,11 @@ async def upload_file_async( with upload_file.file as file_stream: try: - # extract text from file and upload to Azure Blob Storage - md = MarkItDown() - result = md.convert(file_stream) - await converted_blob_client.upload_blob(result.text_content, overwrite=overwrite) + if not await check_cache(file_stream, container_client): + # extract text from file and upload to Azure Blob Storage + md = MarkItDown() + result = md.convert(file_stream) + await converted_blob_client.upload_blob(result.text_content, overwrite=overwrite) except Exception: pass From bcebb291c042cfe8bf31edbea6e751f6c0751ce6 Mon Sep 17 00:00:00 2001 From: Kenny Zhang Date: Tue, 18 Mar 2025 10:42:13 -0400 Subject: [PATCH 05/19] update file cache after conversion --- backend/graphrag_app/api/data.py | 30 +++++++++++++++++++++++++++--- 1 file changed, 27 insertions(+), 3 deletions(-) diff --git a/backend/graphrag_app/api/data.py b/backend/graphrag_app/api/data.py index e398b367..68b77059 100644 --- a/backend/graphrag_app/api/data.py +++ b/backend/graphrag_app/api/data.py @@ -85,6 +85,9 @@ async def upload_file_async( md = MarkItDown() result = md.convert(file_stream) await converted_blob_client.upload_blob(result.text_content, overwrite=overwrite) + + # update the file cache + await update_cache(filename, file_stream, container_client) except Exception: pass @@ -98,9 +101,9 @@ async def check_cache(file_stream: BinaryIO, container_client: ContainerClient) cache_download_stream = await cache_blob_client.download_blob() cache_bytes = await cache_download_stream.readall() cache_content = StringIO(cache_bytes.decode("utf-8")) - cache_reader = csv.reader(cache_content) # comupte the sha256 hash of the file and check if it exists in the cache + cache_reader = csv.reader(cache_content, delimiter=",") file_hash = sha256(file_stream.read()).hexdigest() for row in cache_reader: if file_hash in row: @@ -108,6 +111,26 @@ async def check_cache(file_stream: BinaryIO, container_client: ContainerClient) return False +async def update_cache(filename: str, file_stream: BinaryIO, container_client: ContainerClient) -> None: + """ + Update the file cache with the new file. + """ + # load the file cache + cache_blob_client = container_client.get_blob_client("uploaded_files_cache.csv") + cache_download_stream = await cache_blob_client.download_blob() + cache_bytes = await cache_download_stream.readall() + cache_content = StringIO(cache_bytes.decode("utf-8")) + + # compute the sha256 hash of the file and add it to the cache + cache_writer = csv.writer(cache_content, delimiter=",") + file_hash = sha256(file_stream.read()).hexdigest() + cache_writer.writerow([filename, file_hash]) + + # upload the updated cache to Azure Blob Storage + cache_content.seek(0) + await cache_blob_client.upload_blob(cache_content, overwrite=True) + + class Cleaner: def __init__(self, file): self.file = file @@ -179,9 +202,10 @@ async def upload_files( ['Filename', 'Hash'] ] with open("uploaded_files_cache.csv", "w", newline="") as f: - writer = csv.writer(f) + writer = csv.writer(f, delimiter=",") writer.writerows(headers) - cache_blob_client.upload_blob(f, overwrite=True) + f.seek(0) + await cache_blob_client.upload_blob(f, overwrite=True) # upload files in batches of 1000 to avoid exceeding Azure Storage API limits batch_size = 1000 From 1c35972770f00ba53138867055761c9264b67efe Mon Sep 17 00:00:00 2001 From: Kenny Zhang Date: Tue, 18 Mar 2025 11:13:25 -0400 Subject: [PATCH 06/19] move cache helpers to utils --- backend/graphrag_app/api/data.py | 45 ++-------------------------- backend/graphrag_app/utils/common.py | 43 ++++++++++++++++++++++++++ 2 files changed, 46 insertions(+), 42 deletions(-) diff --git a/backend/graphrag_app/api/data.py b/backend/graphrag_app/api/data.py index 68b77059..73b31d25 100644 --- a/backend/graphrag_app/api/data.py +++ b/backend/graphrag_app/api/data.py @@ -5,10 +5,8 @@ import csv import re import traceback -from hashlib import sha256 -from io import StringIO from math import ceil -from typing import BinaryIO, List +from typing import List from azure.storage.blob.aio import ContainerClient from fastapi import ( @@ -25,11 +23,13 @@ StorageNameList, ) from graphrag_app.utils.common import ( + check_cache, delete_cosmos_container_item_if_exist, delete_storage_container_if_exist, get_blob_container_client, get_cosmos_container_store_client, sanitize_name, + update_cache, ) data_route = APIRouter( @@ -92,45 +92,6 @@ async def upload_file_async( pass -async def check_cache(file_stream: BinaryIO, container_client: ContainerClient) -> bool: - """ - Check if the file has already been uploaded. - """ - # load the file cache - cache_blob_client = container_client.get_blob_client("uploaded_files_cache.csv") - cache_download_stream = await cache_blob_client.download_blob() - cache_bytes = await cache_download_stream.readall() - cache_content = StringIO(cache_bytes.decode("utf-8")) - - # comupte the sha256 hash of the file and check if it exists in the cache - cache_reader = csv.reader(cache_content, delimiter=",") - file_hash = sha256(file_stream.read()).hexdigest() - for row in cache_reader: - if file_hash in row: - return True - return False - - -async def update_cache(filename: str, file_stream: BinaryIO, container_client: ContainerClient) -> None: - """ - Update the file cache with the new file. - """ - # load the file cache - cache_blob_client = container_client.get_blob_client("uploaded_files_cache.csv") - cache_download_stream = await cache_blob_client.download_blob() - cache_bytes = await cache_download_stream.readall() - cache_content = StringIO(cache_bytes.decode("utf-8")) - - # compute the sha256 hash of the file and add it to the cache - cache_writer = csv.writer(cache_content, delimiter=",") - file_hash = sha256(file_stream.read()).hexdigest() - cache_writer.writerow([filename, file_hash]) - - # upload the updated cache to Azure Blob Storage - cache_content.seek(0) - await cache_blob_client.upload_blob(cache_content, overwrite=True) - - class Cleaner: def __init__(self, file): self.file = file diff --git a/backend/graphrag_app/utils/common.py b/backend/graphrag_app/utils/common.py index ad0dc29f..24f9728e 100644 --- a/backend/graphrag_app/utils/common.py +++ b/backend/graphrag_app/utils/common.py @@ -1,9 +1,13 @@ # Copyright (c) Microsoft Corporation. # Licensed under the MIT License. +import csv import hashlib import os import traceback +from hashlib import sha256 +from io import StringIO +from typing import BinaryIO import pandas as pd from azure.core.exceptions import ResourceNotFoundError @@ -189,3 +193,42 @@ def desanitize_name(sanitized_container_name: str) -> str | None: raise HTTPException( status_code=500, detail="Error retrieving original container name." ) + + +async def check_cache(file_stream: BinaryIO, container_client: ContainerClient) -> bool: + """ + Check if the file has already been uploaded. + """ + # load the file cache + cache_blob_client = container_client.get_blob_client("uploaded_files_cache.csv") + cache_download_stream = await cache_blob_client.download_blob() + cache_bytes = await cache_download_stream.readall() + cache_content = StringIO(cache_bytes.decode("utf-8")) + + # comupte the sha256 hash of the file and check if it exists in the cache + cache_reader = csv.reader(cache_content, delimiter=",") + file_hash = sha256(file_stream.read()).hexdigest() + for row in cache_reader: + if file_hash in row: + return True + return False + + +async def update_cache(filename: str, file_stream: BinaryIO, container_client: ContainerClient) -> None: + """ + Update the file cache with the new file. + """ + # load the file cache + cache_blob_client = container_client.get_blob_client("uploaded_files_cache.csv") + cache_download_stream = await cache_blob_client.download_blob() + cache_bytes = await cache_download_stream.readall() + cache_content = StringIO(cache_bytes.decode("utf-8")) + + # compute the sha256 hash of the file and add it to the cache + cache_writer = csv.writer(cache_content, delimiter=",") + file_hash = sha256(file_stream.read()).hexdigest() + cache_writer.writerow([filename, file_hash]) + + # upload the updated cache to Azure Blob Storage + cache_content.seek(0) + await cache_blob_client.upload_blob(cache_content, overwrite=True) From 2154882a50b1fe99159afbdbad2623b55de47ab1 Mon Sep 17 00:00:00 2001 From: Kenny Zhang Date: Tue, 18 Mar 2025 12:12:05 -0400 Subject: [PATCH 07/19] added helper function for cache creation --- backend/graphrag_app/api/data.py | 14 ++------------ backend/graphrag_app/utils/common.py | 22 ++++++++++++++++++++++ 2 files changed, 24 insertions(+), 12 deletions(-) diff --git a/backend/graphrag_app/api/data.py b/backend/graphrag_app/api/data.py index 73b31d25..3d860301 100644 --- a/backend/graphrag_app/api/data.py +++ b/backend/graphrag_app/api/data.py @@ -2,7 +2,6 @@ # Licensed under the MIT License. import asyncio -import csv import re import traceback from math import ceil @@ -24,6 +23,7 @@ ) from graphrag_app.utils.common import ( check_cache, + create_cache, delete_cosmos_container_item_if_exist, delete_storage_container_if_exist, get_blob_container_client, @@ -156,17 +156,7 @@ async def upload_files( sanitized_container_name ) - # create and upload the file cache if it doesn't exist - cache_blob_client = blob_container_client.get_blob_client("uploaded_files_cache.csv") - if not cache_blob_client.exists(): - headers = [ - ['Filename', 'Hash'] - ] - with open("uploaded_files_cache.csv", "w", newline="") as f: - writer = csv.writer(f, delimiter=",") - writer.writerows(headers) - f.seek(0) - await cache_blob_client.upload_blob(f, overwrite=True) + await create_cache(blob_container_client) # upload files in batches of 1000 to avoid exceeding Azure Storage API limits batch_size = 1000 diff --git a/backend/graphrag_app/utils/common.py b/backend/graphrag_app/utils/common.py index 24f9728e..4afde865 100644 --- a/backend/graphrag_app/utils/common.py +++ b/backend/graphrag_app/utils/common.py @@ -193,6 +193,28 @@ def desanitize_name(sanitized_container_name: str) -> str | None: raise HTTPException( status_code=500, detail="Error retrieving original container name." ) + + +async def create_cache(container_client: ContainerClient) -> None: + """ + Create a file cache to track the uploaded files if it doesn't exist. + """ + try: + cache_blob_client = container_client.get_blob_client("uploaded_files_cache.csv") + if not cache_blob_client.exists(): + headers = [ + ['Filename', 'Hash'] + ] + with open("uploaded_files_cache.csv", "w", newline="") as f: + writer = csv.writer(f, delimiter=",") + writer.writerows(headers) + f.seek(0) + await cache_blob_client.upload_blob(f, overwrite=True) + except Exception: + raise HTTPException( + status_code=500, + detail="Error creating file cache in Azure Blob Storage.", + ) async def check_cache(file_stream: BinaryIO, container_client: ContainerClient) -> bool: From c49ff489a1ebb96266c717f766863ca88259c472 Mon Sep 17 00:00:00 2001 From: Kenny Zhang Date: Wed, 19 Mar 2025 17:10:42 -0400 Subject: [PATCH 08/19] passed basic unit tests --- backend/graphrag_app/api/data.py | 23 ++++++-- backend/graphrag_app/utils/common.py | 86 ++++++++++++++++++---------- 2 files changed, 74 insertions(+), 35 deletions(-) diff --git a/backend/graphrag_app/api/data.py b/backend/graphrag_app/api/data.py index 3d860301..4501d0d5 100644 --- a/backend/graphrag_app/api/data.py +++ b/backend/graphrag_app/api/data.py @@ -2,6 +2,7 @@ # Licensed under the MIT License. import asyncio +import os import re import traceback from math import ceil @@ -14,7 +15,7 @@ HTTPException, UploadFile, ) -from markitdown import MarkItDown +from markitdown import MarkItDown, StreamInfo from graphrag_app.logger.load_logger import load_pipeline_logger from graphrag_app.typing.models import ( @@ -75,7 +76,8 @@ async def upload_file_async( Silently ignore errors that occur when overwrite=False. """ filename = upload_file.filename - converted_filename = filename.split(".")[0] + ".txt" + extension = os.path.splitext(filename)[1] + converted_filename = filename.replace(extension, ".txt") converted_blob_client = container_client.get_blob_client(converted_filename) with upload_file.file as file_stream: @@ -83,13 +85,24 @@ async def upload_file_async( if not await check_cache(file_stream, container_client): # extract text from file and upload to Azure Blob Storage md = MarkItDown() - result = md.convert(file_stream) + stream_info = StreamInfo( + extension=extension, + ) + file_stream.file._file.seek(0) + file_stream = file_stream.file._file + result = md.convert_stream( + stream=file_stream, + stream_info=stream_info, + ) await converted_blob_client.upload_blob(result.text_content, overwrite=overwrite) # update the file cache await update_cache(filename, file_stream, container_client) except Exception: - pass + raise HTTPException( + status_code=500, + detail=f"Error uploading file '{filename}' to container '{container_client.container_name}'.", + ) class Cleaner: @@ -107,7 +120,7 @@ def clean(self, val, replacement=""): self.changes += len(_illegal_xml_chars_RE.findall(val)) return _illegal_xml_chars_RE.sub(replacement, val) - def read(self, n): + def read(self, n: int = -1): return self.clean(self.file.read(n).decode()).encode( encoding="utf-8", errors="strict" ) diff --git a/backend/graphrag_app/utils/common.py b/backend/graphrag_app/utils/common.py index 4afde865..be788e72 100644 --- a/backend/graphrag_app/utils/common.py +++ b/backend/graphrag_app/utils/common.py @@ -201,15 +201,20 @@ async def create_cache(container_client: ContainerClient) -> None: """ try: cache_blob_client = container_client.get_blob_client("uploaded_files_cache.csv") - if not cache_blob_client.exists(): + if not await cache_blob_client.exists(): + # create the empty file cache csv headers = [ ['Filename', 'Hash'] ] with open("uploaded_files_cache.csv", "w", newline="") as f: writer = csv.writer(f, delimiter=",") writer.writerows(headers) - f.seek(0) + + # upload to Azure Blob Storage and remove the temporary file + with open("uploaded_files_cache.csv", "rb") as f: await cache_blob_client.upload_blob(f, overwrite=True) + if os.path.exists("uploaded_files_cache.csv"): + os.remove("uploaded_files_cache.csv") except Exception: raise HTTPException( status_code=500, @@ -221,36 +226,57 @@ async def check_cache(file_stream: BinaryIO, container_client: ContainerClient) """ Check if the file has already been uploaded. """ - # load the file cache - cache_blob_client = container_client.get_blob_client("uploaded_files_cache.csv") - cache_download_stream = await cache_blob_client.download_blob() - cache_bytes = await cache_download_stream.readall() - cache_content = StringIO(cache_bytes.decode("utf-8")) - - # comupte the sha256 hash of the file and check if it exists in the cache - cache_reader = csv.reader(cache_content, delimiter=",") - file_hash = sha256(file_stream.read()).hexdigest() - for row in cache_reader: - if file_hash in row: - return True - return False + try: + # load the file cache + cache_blob_client = container_client.get_blob_client("uploaded_files_cache.csv") + cache_download_stream = await cache_blob_client.download_blob() + cache_bytes = await cache_download_stream.readall() + cache_content = StringIO(cache_bytes.decode("utf-8")) + + # comupte the sha256 hash of the file and check if it exists in the cache + cache_reader = csv.reader(cache_content, delimiter=",") + file_hash = sha256(file_stream.read()).hexdigest() + for row in cache_reader: + if file_hash in row: + return True + return False + except Exception: + raise HTTPException( + status_code=500, + detail="Error checking file cache in Azure Blob Storage.", + ) async def update_cache(filename: str, file_stream: BinaryIO, container_client: ContainerClient) -> None: """ - Update the file cache with the new file. + Update the file cache with the new file by appending a new row to the cache. """ - # load the file cache - cache_blob_client = container_client.get_blob_client("uploaded_files_cache.csv") - cache_download_stream = await cache_blob_client.download_blob() - cache_bytes = await cache_download_stream.readall() - cache_content = StringIO(cache_bytes.decode("utf-8")) - - # compute the sha256 hash of the file and add it to the cache - cache_writer = csv.writer(cache_content, delimiter=",") - file_hash = sha256(file_stream.read()).hexdigest() - cache_writer.writerow([filename, file_hash]) - - # upload the updated cache to Azure Blob Storage - cache_content.seek(0) - await cache_blob_client.upload_blob(cache_content, overwrite=True) + try: + # Load the file cache + cache_blob_client = container_client.get_blob_client("uploaded_files_cache.csv") + cache_download_stream = await cache_blob_client.download_blob() + cache_bytes = await cache_download_stream.readall() + cache_content = StringIO(cache_bytes.decode("utf-8")) + + # Read existing rows and prepare to append + cache_reader = csv.reader(cache_content, delimiter=",") + existing_rows = list(cache_reader) + + # Compute the sha256 hash of the file and append it to the cache + file_hash = sha256(file_stream.read()).hexdigest() + new_row = [filename, file_hash] + existing_rows.append(new_row) + + # Write the updated content back to the StringIO object + updated_cache_content = StringIO() + cache_writer = csv.writer(updated_cache_content, delimiter=",") + cache_writer.writerows(existing_rows) + + # Upload the updated cache to Azure Blob Storage + updated_cache_content.seek(0) + await cache_blob_client.upload_blob(updated_cache_content.getvalue().encode("utf-8"), overwrite=True) + except Exception: + raise HTTPException( + status_code=500, + detail="Error updating file cache in Azure Blob Storage.", + ) \ No newline at end of file From 4c37ad6e07414f6da17c389b351f9da025d07802 Mon Sep 17 00:00:00 2001 From: Kenny Zhang Date: Thu, 20 Mar 2025 11:33:59 -0400 Subject: [PATCH 09/19] refactor cleaner class to single function --- backend/graphrag_app/api/data.py | 50 ++++++++++---------------------- 1 file changed, 15 insertions(+), 35 deletions(-) diff --git a/backend/graphrag_app/api/data.py b/backend/graphrag_app/api/data.py index 4501d0d5..6bdacbff 100644 --- a/backend/graphrag_app/api/data.py +++ b/backend/graphrag_app/api/data.py @@ -83,18 +83,21 @@ async def upload_file_async( with upload_file.file as file_stream: try: if not await check_cache(file_stream, container_client): - # extract text from file and upload to Azure Blob Storage + # extract text from file using MarkItDown md = MarkItDown() stream_info = StreamInfo( extension=extension, ) - file_stream.file._file.seek(0) - file_stream = file_stream.file._file + file_stream._file.seek(0) + file_stream = file_stream._file result = md.convert_stream( stream=file_stream, stream_info=stream_info, ) - await converted_blob_client.upload_blob(result.text_content, overwrite=overwrite) + + # clean the output and upload to blob storage + cleaned_result = clean_output(result.text_content) + await converted_blob_client.upload_blob(cleaned_result, overwrite=overwrite) # update the file cache await update_cache(filename, file_stream, container_client) @@ -103,36 +106,16 @@ async def upload_file_async( status_code=500, detail=f"Error uploading file '{filename}' to container '{container_client.container_name}'.", ) + - -class Cleaner: - def __init__(self, file): - self.file = file - self.name = file.name - self.changes = 0 - - def clean(self, val, replacement=""): - # fmt: off - _illegal_xml_chars_RE = re.compile( +def clean_output(val: str, replacement: str = ""): + """Remove illegal XML characters from a string.""" + # fmt: off + _illegal_xml_chars_RE = re.compile( "[\x00-\x08\x0b\x0c\x0e-\x1F\uD800-\uDFFF\uFFFE\uFFFF]" ) - # fmt: on - self.changes += len(_illegal_xml_chars_RE.findall(val)) - return _illegal_xml_chars_RE.sub(replacement, val) - - def read(self, n: int = -1): - return self.clean(self.file.read(n).decode()).encode( - encoding="utf-8", errors="strict" - ) - - def name(self): - return self.file.name - - def __enter__(self): - return self - - def __exit__(self, *args): - self.file.close() + # fmt: on + return _illegal_xml_chars_RE.sub(replacement, val) @data_route.post( @@ -162,13 +145,10 @@ async def upload_files( HTTPException: If the container name is invalid or if any error occurs during the upload process. """ try: - # clean files - remove illegal XML characters - files = [UploadFile(Cleaner(f.file), filename=f.filename) for f in files] - + # create the initial cache if it doesn't exist blob_container_client = await get_blob_container_client( sanitized_container_name ) - await create_cache(blob_container_client) # upload files in batches of 1000 to avoid exceeding Azure Storage API limits From c0f6f6c84ceba84cd6578d85efdc8446e2cf7ef1 Mon Sep 17 00:00:00 2001 From: Kenny Zhang Date: Thu, 20 Mar 2025 12:03:44 -0400 Subject: [PATCH 10/19] update toml and other small changes --- backend/graphrag_app/api/data.py | 7 ++----- backend/pyproject.toml | 1 + 2 files changed, 3 insertions(+), 5 deletions(-) diff --git a/backend/graphrag_app/api/data.py b/backend/graphrag_app/api/data.py index 6bdacbff..57b1d75c 100644 --- a/backend/graphrag_app/api/data.py +++ b/backend/graphrag_app/api/data.py @@ -102,11 +102,8 @@ async def upload_file_async( # update the file cache await update_cache(filename, file_stream, container_client) except Exception: - raise HTTPException( - status_code=500, - detail=f"Error uploading file '{filename}' to container '{container_client.container_name}'.", - ) - + pass + def clean_output(val: str, replacement: str = ""): """Remove illegal XML characters from a string.""" diff --git a/backend/pyproject.toml b/backend/pyproject.toml index e69c1c13..c1c37648 100644 --- a/backend/pyproject.toml +++ b/backend/pyproject.toml @@ -54,6 +54,7 @@ fsspec = ">=2024.2.0" graphrag = "==1.2.0" httpx = ">=0.25.2" kubernetes = ">=29.0.0" +markitdown = "0.1.0a3" networkx = ">=3.2.1" nltk = "*" pandas = ">=2.2.1" From 639ef9d952816f7799cdb189b408c6f749c62aa4 Mon Sep 17 00:00:00 2001 From: Kenny Zhang Date: Thu, 20 Mar 2025 12:05:20 -0400 Subject: [PATCH 11/19] ruff --- backend/graphrag_app/api/data.py | 4 +++- backend/graphrag_app/utils/common.py | 16 +++++++++------- notebooks/2-Advanced_Getting_Started.ipynb | 9 +++++++-- 3 files changed, 19 insertions(+), 10 deletions(-) diff --git a/backend/graphrag_app/api/data.py b/backend/graphrag_app/api/data.py index 57b1d75c..19b55245 100644 --- a/backend/graphrag_app/api/data.py +++ b/backend/graphrag_app/api/data.py @@ -97,7 +97,9 @@ async def upload_file_async( # clean the output and upload to blob storage cleaned_result = clean_output(result.text_content) - await converted_blob_client.upload_blob(cleaned_result, overwrite=overwrite) + await converted_blob_client.upload_blob( + cleaned_result, overwrite=overwrite + ) # update the file cache await update_cache(filename, file_stream, container_client) diff --git a/backend/graphrag_app/utils/common.py b/backend/graphrag_app/utils/common.py index be788e72..d5615116 100644 --- a/backend/graphrag_app/utils/common.py +++ b/backend/graphrag_app/utils/common.py @@ -193,7 +193,7 @@ def desanitize_name(sanitized_container_name: str) -> str | None: raise HTTPException( status_code=500, detail="Error retrieving original container name." ) - + async def create_cache(container_client: ContainerClient) -> None: """ @@ -203,9 +203,7 @@ async def create_cache(container_client: ContainerClient) -> None: cache_blob_client = container_client.get_blob_client("uploaded_files_cache.csv") if not await cache_blob_client.exists(): # create the empty file cache csv - headers = [ - ['Filename', 'Hash'] - ] + headers = [["Filename", "Hash"]] with open("uploaded_files_cache.csv", "w", newline="") as f: writer = csv.writer(f, delimiter=",") writer.writerows(headers) @@ -247,7 +245,9 @@ async def check_cache(file_stream: BinaryIO, container_client: ContainerClient) ) -async def update_cache(filename: str, file_stream: BinaryIO, container_client: ContainerClient) -> None: +async def update_cache( + filename: str, file_stream: BinaryIO, container_client: ContainerClient +) -> None: """ Update the file cache with the new file by appending a new row to the cache. """ @@ -274,9 +274,11 @@ async def update_cache(filename: str, file_stream: BinaryIO, container_client: C # Upload the updated cache to Azure Blob Storage updated_cache_content.seek(0) - await cache_blob_client.upload_blob(updated_cache_content.getvalue().encode("utf-8"), overwrite=True) + await cache_blob_client.upload_blob( + updated_cache_content.getvalue().encode("utf-8"), overwrite=True + ) except Exception: raise HTTPException( status_code=500, detail="Error updating file cache in Azure Blob Storage.", - ) \ No newline at end of file + ) diff --git a/notebooks/2-Advanced_Getting_Started.ipynb b/notebooks/2-Advanced_Getting_Started.ipynb index 37af6111..d57d58b2 100644 --- a/notebooks/2-Advanced_Getting_Started.ipynb +++ b/notebooks/2-Advanced_Getting_Started.ipynb @@ -290,7 +290,10 @@ " return requests.post(\n", " url,\n", " files=prompts if len(prompts) > 0 else None,\n", - " params={\"index_container_name\": index_name, \"storage_container_name\": storage_name},\n", + " params={\n", + " \"index_container_name\": index_name,\n", + " \"storage_container_name\": storage_name,\n", + " },\n", " headers=headers,\n", " )\n", "\n", @@ -619,7 +622,9 @@ " community_summarization_prompt = prompts[\"community_summarization_prompt\"]\n", " summarize_description_prompt = prompts[\"entity_summarization_prompt\"]\n", "else:\n", - " entity_extraction_prompt = community_summarization_prompt = summarize_description_prompt = None\n", + " entity_extraction_prompt = community_summarization_prompt = (\n", + " summarize_description_prompt\n", + " ) = None\n", "\n", "response = build_index(\n", " storage_name=storage_name,\n", From a2bb00c6bae67fb32a5dfcf4079c4a007f980de2 Mon Sep 17 00:00:00 2001 From: Kenny Zhang Date: Thu, 20 Mar 2025 12:06:07 -0400 Subject: [PATCH 12/19] update lockfile --- backend/poetry.lock | 2349 +++++++++++++++++++++++-------------------- 1 file changed, 1278 insertions(+), 1071 deletions(-) diff --git a/backend/poetry.lock b/backend/poetry.lock index f3506626..f8da1d0f 100644 --- a/backend/poetry.lock +++ b/backend/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.5 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. 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"19e01bb5835a96beebc3bab6ecbdee4519fad7f218db09cd08b960beea7e5978" From 591950a6c7b02880bc4d74d055b1731c1c57be91 Mon Sep 17 00:00:00 2001 From: Josh Bradley Date: Wed, 2 Apr 2025 23:22:52 -0400 Subject: [PATCH 14/19] ruff fixes --- backend/graphrag_app/api/data.py | 2 +- backend/graphrag_app/utils/common.py | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/backend/graphrag_app/api/data.py b/backend/graphrag_app/api/data.py index a4a278dc..166acd5b 100644 --- a/backend/graphrag_app/api/data.py +++ b/backend/graphrag_app/api/data.py @@ -30,8 +30,8 @@ get_blob_container_client, get_cosmos_container_store_client, sanitize_name, - update_cache, subscription_key_check, + update_cache, ) data_route = APIRouter( diff --git a/backend/graphrag_app/utils/common.py b/backend/graphrag_app/utils/common.py index cdd80480..01577167 100644 --- a/backend/graphrag_app/utils/common.py +++ b/backend/graphrag_app/utils/common.py @@ -7,8 +7,7 @@ import traceback from hashlib import sha256 from io import StringIO -from typing import BinaryIO -from typing import Annotated +from typing import Annotated, BinaryIO import pandas as pd from azure.core.exceptions import ResourceNotFoundError From a77806fb8003528ef9cfeff268065822cc8c5cbf Mon Sep 17 00:00:00 2001 From: Josh Bradley Date: Sun, 6 Apr 2025 02:19:05 -0400 Subject: [PATCH 15/19] update successful response status code --- backend/graphrag_app/api/data.py | 39 +- backend/graphrag_app/api/graph.py | 2 + backend/graphrag_app/api/index.py | 8 +- backend/graphrag_app/api/prompt_tuning.py | 2 + backend/graphrag_app/api/query.py | 5 +- backend/graphrag_app/api/query_streaming.py | 3 + backend/graphrag_app/api/source.py | 17 +- backend/graphrag_app/utils/common.py | 8 +- backend/poetry.lock | 1150 ++++++++++++------- backend/pyproject.toml | 2 +- notebooks/1-Quickstart.ipynb | 6 +- notebooks/2-Advanced_Getting_Started.ipynb | 14 +- 12 files changed, 812 insertions(+), 444 deletions(-) diff --git a/backend/graphrag_app/api/data.py b/backend/graphrag_app/api/data.py index 166acd5b..95a71069 100644 --- a/backend/graphrag_app/api/data.py +++ b/backend/graphrag_app/api/data.py @@ -14,6 +14,7 @@ Depends, HTTPException, UploadFile, + status, ) from markitdown import MarkItDown, StreamInfo @@ -98,7 +99,7 @@ async def upload_file_async( stream_info=stream_info, ) - # clean the output and upload to blob storage + # remove illegal unicode characters and upload to blob storage cleaned_result = clean_output(result.text_content) await converted_blob_client.upload_blob( cleaned_result, overwrite=overwrite @@ -107,11 +108,12 @@ async def upload_file_async( # update the file cache await update_cache(filename, file_stream, container_client) except Exception: - pass + # if any exception occurs, return the filename to indicate conversion/upload failures + return upload_file.filename def clean_output(val: str, replacement: str = ""): - """Remove illegal XML characters from a string.""" + """Removes unicode characters that are invalid XML characters (not valid for graphml files at least).""" # fmt: off _illegal_xml_chars_RE = re.compile( "[\x00-\x08\x0b\x0c\x0e-\x1F\uD800-\uDFFF\uFFFE\uFFFF]" @@ -124,7 +126,7 @@ def clean_output(val: str, replacement: str = ""): "", summary="Upload data to a data storage container", response_model=BaseResponse, - responses={200: {"model": BaseResponse}}, + responses={status.HTTP_201_CREATED: {"model": BaseResponse}}, ) async def upload_files( files: List[UploadFile], @@ -133,18 +135,8 @@ async def upload_files( overwrite: bool = True, ): """ - Create a Azure Storage container and upload files to it. - - Args: - files (List[UploadFile]): A list of files to be uploaded. - storage_name (str): The name of the Azure Blob Storage container to which files will be uploaded. - overwrite (bool): Whether to overwrite existing files with the same name. Defaults to True. If False, files that already exist will be skipped. - - Returns: - BaseResponse: An instance of the BaseResponse model with a status message indicating the result of the upload. - - Raises: - HTTPException: If the container name is invalid or if any error occurs during the upload process. + Create a Azure Storage container (if needed) and upload files. Multiple file types are supported, including pdf, powerpoint, word, excel, html, csv, json, xml, etc. + The complete set of supported file types can be found in the MarkItDown (https://github.com/microsoft/markitdown) library. """ try: # create the initial cache if it doesn't exist @@ -153,8 +145,9 @@ async def upload_files( ) await create_cache(blob_container_client) - # upload files in batches of 1000 to avoid exceeding Azure Storage API limits - batch_size = 1000 + # upload files in batches of 100 to avoid exceeding Azure Storage API limits + processing_errors = [] + batch_size = 100 num_batches = ceil(len(files) / batch_size) for i in range(num_batches): batch_files = files[i * batch_size : (i + 1) * batch_size] @@ -162,7 +155,9 @@ async def upload_files( upload_file_async(file, blob_container_client, overwrite) for file in batch_files ] - await asyncio.gather(*tasks) + results = await asyncio.gather(*tasks) + results = [r for r in results if r is not None] + processing_errors.extend(results) # update container-store entry in cosmosDB once upload process is successful cosmos_container_store_client = get_cosmos_container_store_client() @@ -171,6 +166,12 @@ async def upload_files( "human_readable_name": container_name, "type": "data", }) + + if len(processing_errors) > 0: + raise HTTPException( + status_code=400, + detail=f"Error uploading files: {processing_errors}.", + ) return BaseResponse(status="File upload successful.") except Exception as e: logger = load_pipeline_logger() diff --git a/backend/graphrag_app/api/graph.py b/backend/graphrag_app/api/graph.py index 47910f79..bd2bc592 100644 --- a/backend/graphrag_app/api/graph.py +++ b/backend/graphrag_app/api/graph.py @@ -8,6 +8,7 @@ APIRouter, Depends, HTTPException, + status, ) from fastapi.responses import StreamingResponse @@ -31,6 +32,7 @@ "/graphml/{container_name}", summary="Retrieve a GraphML file of the knowledge graph", response_description="GraphML file successfully downloaded", + status_code=status.HTTP_200_OK, ) async def get_graphml_file( container_name, sanitized_container_name: str = Depends(sanitize_name) diff --git a/backend/graphrag_app/api/index.py b/backend/graphrag_app/api/index.py index 6ec3d550..5166601a 100644 --- a/backend/graphrag_app/api/index.py +++ b/backend/graphrag_app/api/index.py @@ -12,6 +12,7 @@ Depends, HTTPException, UploadFile, + status, ) from kubernetes import ( client as kubernetes_client, @@ -49,7 +50,7 @@ "", summary="Build an index", response_model=BaseResponse, - responses={200: {"model": BaseResponse}}, + responses={status.HTTP_202_ACCEPTED: {"model": BaseResponse}}, ) async def schedule_index_job( storage_container_name: str, @@ -142,7 +143,7 @@ async def schedule_index_job( "", summary="Get all index names", response_model=IndexNameList, - responses={200: {"model": IndexNameList}}, + responses={status.HTTP_200_OK: {"model": IndexNameList}}, ) async def get_all_index_names( container_store_client=Depends(get_cosmos_container_store_client), @@ -218,7 +219,7 @@ def _delete_k8s_job(job_name: str, namespace: str) -> None: "/{container_name}", summary="Delete a specified index", response_model=BaseResponse, - responses={200: {"model": BaseResponse}}, + responses={status.HTTP_200_OK: {"model": BaseResponse}}, ) async def delete_index( container_name: str, @@ -267,6 +268,7 @@ async def delete_index( "/status/{container_name}", summary="Track the status of an indexing job", response_model=IndexStatusResponse, + status_code=status.HTTP_200_OK, ) async def get_index_status( container_name: str, sanitized_container_name: str = Depends(sanitize_name) diff --git a/backend/graphrag_app/api/prompt_tuning.py b/backend/graphrag_app/api/prompt_tuning.py index 1a6f078c..9fb4c5c5 100644 --- a/backend/graphrag_app/api/prompt_tuning.py +++ b/backend/graphrag_app/api/prompt_tuning.py @@ -11,6 +11,7 @@ APIRouter, Depends, HTTPException, + status, ) from graphrag.config.create_graphrag_config import create_graphrag_config @@ -27,6 +28,7 @@ "/prompts", summary="Generate custom graphrag prompts based on user-provided data.", description="Generating custom prompts from user-provided data may take several minutes to run based on the amount of data used.", + status_code=status.HTTP_200_OK, ) async def generate_prompts( container_name: str, diff --git a/backend/graphrag_app/api/query.py b/backend/graphrag_app/api/query.py index a406b602..c994db9d 100644 --- a/backend/graphrag_app/api/query.py +++ b/backend/graphrag_app/api/query.py @@ -10,6 +10,7 @@ APIRouter, Depends, HTTPException, + status, ) from graphrag.api.query import global_search, local_search from graphrag.config.create_graphrag_config import create_graphrag_config @@ -42,7 +43,7 @@ summary="Perform a global search across the knowledge graph index", description="The global query method generates answers by searching over all AI-generated community reports in a map-reduce fashion. This is a resource-intensive method, but often gives good responses for questions that require an understanding of the dataset as a whole.", response_model=GraphResponse, - responses={200: {"model": GraphResponse}}, + responses={status.HTTP_200_OK: {"model": GraphResponse}}, ) async def global_query(request: GraphRequest): # this is a slightly modified version of the graphrag.query.cli.run_global_search method @@ -122,7 +123,7 @@ async def global_query(request: GraphRequest): summary="Perform a local search across the knowledge graph index.", description="The local query method generates answers by combining relevant data from the AI-extracted knowledge-graph with text chunks of the raw documents. This method is suitable for questions that require an understanding of specific entities mentioned in the documents (e.g. What are the healing properties of chamomile?).", response_model=GraphResponse, - responses={200: {"model": GraphResponse}}, + responses={status.HTTP_200_OK: {"model": GraphResponse}}, ) async def local_query(request: GraphRequest): index_name = request.index_name diff --git a/backend/graphrag_app/api/query_streaming.py b/backend/graphrag_app/api/query_streaming.py index 86d0252d..bef5511b 100644 --- a/backend/graphrag_app/api/query_streaming.py +++ b/backend/graphrag_app/api/query_streaming.py @@ -12,6 +12,7 @@ APIRouter, Depends, HTTPException, + status, ) from fastapi.responses import StreamingResponse from graphrag.api.query import ( @@ -47,6 +48,7 @@ "/global", summary="Stream a response back after performing a global search", description="The global query method generates answers by searching over all AI-generated community reports in a map-reduce fashion. This is a resource-intensive method, but often gives good responses for questions that require an understanding of the dataset as a whole.", + status_code=status.HTTP_200_OK, ) async def global_search_streaming(request: GraphRequest): # this is a slightly modified version of graphrag_app.api.query.global_query() method @@ -204,6 +206,7 @@ async def global_search_streaming(request: GraphRequest): "/local", summary="Stream a response back after performing a local search", description="The local query method generates answers by combining relevant data from the AI-extracted knowledge-graph with text chunks of the raw documents. This method is suitable for questions that require an understanding of specific entities mentioned in the documents (e.g. What are the healing properties of chamomile?).", + status_code=status.HTTP_200_OK, ) async def local_search_streaming(request: GraphRequest): # this is a slightly modified version of graphrag_app.api.query.local_query() method diff --git a/backend/graphrag_app/api/source.py b/backend/graphrag_app/api/source.py index 5b91fdd2..9692e239 100644 --- a/backend/graphrag_app/api/source.py +++ b/backend/graphrag_app/api/source.py @@ -5,7 +5,12 @@ import traceback import pandas as pd -from fastapi import APIRouter, Depends, HTTPException +from fastapi import ( + APIRouter, + Depends, + HTTPException, + status, +) from graphrag_app.logger.load_logger import load_pipeline_logger from graphrag_app.typing.models import ( @@ -43,7 +48,7 @@ "/report/{container_name}/{report_id}", summary="Return a single community report.", response_model=ReportResponse, - responses={200: {"model": ReportResponse}}, + responses={status.HTTP_200_OK: {"model": ReportResponse}}, ) async def get_report_info( report_id: int, @@ -88,7 +93,7 @@ async def get_report_info( "/text/{container_name}/{text_unit_id}", summary="Return a single base text unit.", response_model=TextUnitResponse, - responses={200: {"model": TextUnitResponse}}, + responses={status.HTTP_200_OK: {"model": TextUnitResponse}}, ) async def get_chunk_info( text_unit_id: str, @@ -148,7 +153,7 @@ async def get_chunk_info( "/entity/{container_name}/{entity_id}", summary="Return a single entity.", response_model=EntityResponse, - responses={200: {"model": EntityResponse}}, + responses={status.HTTP_200_OK: {"model": EntityResponse}}, ) async def get_entity_info( entity_id: int, @@ -190,7 +195,7 @@ async def get_entity_info( "/claim/{container_name}/{claim_id}", summary="Return a single claim.", response_model=ClaimResponse, - responses={200: {"model": ClaimResponse}}, + responses={status.HTTP_200_OK: {"model": ClaimResponse}}, ) async def get_claim_info( claim_id: int, @@ -240,7 +245,7 @@ async def get_claim_info( "/relationship/{container_name}/{relationship_id}", summary="Return a single relationship.", response_model=RelationshipResponse, - responses={200: {"model": RelationshipResponse}}, + responses={status.HTTP_200_OK: {"model": RelationshipResponse}}, ) async def get_relationship_info( relationship_id: int, diff --git a/backend/graphrag_app/utils/common.py b/backend/graphrag_app/utils/common.py index 01577167..85e41f9f 100644 --- a/backend/graphrag_app/utils/common.py +++ b/backend/graphrag_app/utils/common.py @@ -213,7 +213,7 @@ async def subscription_key_check( async def create_cache(container_client: ContainerClient) -> None: """ - Create a file cache to track the uploaded files if it doesn't exist. + Create a file cache (csv) to track uploaded files. """ try: cache_blob_client = container_client.get_blob_client("uploaded_files_cache.csv") @@ -238,7 +238,9 @@ async def create_cache(container_client: ContainerClient) -> None: async def check_cache(file_stream: BinaryIO, container_client: ContainerClient) -> bool: """ - Check if the file has already been uploaded. + Check a cache file to determine if a file has previously been uploaded. + + Note: This function creates/checks a CSV file in azure storage to act as a cache of previously uploaded files. """ try: # load the file cache @@ -265,7 +267,7 @@ async def update_cache( filename: str, file_stream: BinaryIO, container_client: ContainerClient ) -> None: """ - Update the file cache with the new file by appending a new row to the cache. + Update the file cache (csv) with a new file by adding a new row. """ try: # Load the file cache diff --git a/backend/poetry.lock b/backend/poetry.lock index 0d3262f3..9972f3bc 100644 --- a/backend/poetry.lock +++ b/backend/poetry.lock @@ -403,6 +403,22 @@ numpy = "*" [package.extras] scipy = ["scipy"] +[[package]] +name = "azure-ai-documentintelligence" +version = "1.0.2" +description = "Microsoft Azure AI Document Intelligence Client Library for Python" +optional = false +python-versions = ">=3.8" +files = [ + {file = "azure_ai_documentintelligence-1.0.2-py3-none-any.whl", hash = "sha256:e1fb446abbdeccc9759d897898a0fe13141ed29f9ad11fc705f951925822ed59"}, + {file = "azure_ai_documentintelligence-1.0.2.tar.gz", hash = "sha256:4d75a2513f2839365ebabc0e0e1772f5601b3a8c9a71e75da12440da13b63484"}, +] + +[package.dependencies] +azure-core = ">=1.30.0" +isodate = ">=0.6.1" +typing-extensions = ">=4.6.0" + [[package]] name = "azure-common" version = "1.1.28" @@ -416,13 +432,13 @@ files = [ [[package]] name = "azure-core" -version = "1.32.0" +version = 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recognition, with support for several engines and APIs, online and offline." +optional = false +python-versions = ">=3.9" +files = [ + {file = "speechrecognition-3.14.2-py3-none-any.whl", hash = "sha256:42940b95295b358fdd7415daa01260c8b20025d6b4000fbbaa3458f005d912b7"}, + {file = "speechrecognition-3.14.2.tar.gz", hash = "sha256:2daa467f0b5686017ff3f9a64dcfa1a789ee10d1b0ada3be74bfad10eaef5f49"}, +] + +[package.dependencies] +typing-extensions = "*" + +[package.extras] +assemblyai = ["requests"] +audio = ["PyAudio (>=0.2.11)"] +dev = ["numpy", "pytest", "pytest-randomly", "respx"] +faster-whisper = ["faster-whisper"] +google-cloud = ["google-cloud-speech"] +groq = ["groq", "httpx (<0.28)"] +openai = ["httpx (<0.28)", "openai"] +pocketsphinx = ["pocketsphinx"] +whisper-local = ["openai-whisper", "soundfile"] + [[package]] name = "stack-data" version = "0.6.3" @@ -6261,13 +6581,13 @@ files = [ [[package]] name = "typing-extensions" -version = "4.13.0" +version = "4.13.1" description = 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">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" +files = [ + {file = "xlrd-2.0.1-py2.py3-none-any.whl", hash = "sha256:6a33ee89877bd9abc1158129f6e94be74e2679636b8a205b43b85206c3f0bbdd"}, + {file = "xlrd-2.0.1.tar.gz", hash = "sha256:f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88"}, +] + +[package.extras] +build = ["twine", "wheel"] +docs = ["sphinx"] +test = ["pytest", "pytest-cov"] + +[[package]] +name = "xlsxwriter" +version = "3.2.2" +description = "A Python module for creating Excel XLSX files." +optional = false +python-versions = ">=3.6" +files = [ + {file = "XlsxWriter-3.2.2-py3-none-any.whl", hash = "sha256:272ce861e7fa5e82a4a6ebc24511f2cb952fde3461f6c6e1a1e81d3272db1471"}, + {file = "xlsxwriter-3.2.2.tar.gz", hash = "sha256:befc7f92578a85fed261639fb6cde1fd51b79c5e854040847dde59d4317077dc"}, +] + [[package]] name = "yarl" version = "1.18.3" @@ -6647,6 +6994,21 @@ idna = ">=2.0" multidict = ">=4.0" propcache = ">=0.2.0" +[[package]] +name = "youtube-transcript-api" +version = "1.0.3" +description = "This is an python API which allows you to get the transcripts/subtitles for a given YouTube video. It also works for automatically generated subtitles, supports translating subtitles and it does not require a headless browser, like other selenium based solutions do!" +optional = false +python-versions = "<3.14,>=3.8" +files = [ + {file = "youtube_transcript_api-1.0.3-py3-none-any.whl", hash = "sha256:d1874e57de65cf14c9d7d09b2b37c814d6287fa0e770d4922c4cd32a5b3f6c47"}, + {file = "youtube_transcript_api-1.0.3.tar.gz", hash = "sha256:902baf90e7840a42e1e148335e09fe5575dbff64c81414957aea7038e8a4db46"}, +] + +[package.dependencies] +defusedxml = ">=0.7.1,<0.8.0" +requests = "*" + [[package]] name = "zipp" version = "3.21.0" @@ -6669,4 +7031,4 @@ type = ["pytest-mypy"] [metadata] lock-version = "2.0" python-versions = "~3.10" -content-hash = "19e01bb5835a96beebc3bab6ecbdee4519fad7f218db09cd08b960beea7e5978" +content-hash = "b3eab1568863563f4279757a54ea24ed126136606711c60b042468a79a3a2183" diff --git a/backend/pyproject.toml b/backend/pyproject.toml index 93ee530e..6877b7c6 100644 --- a/backend/pyproject.toml +++ b/backend/pyproject.toml @@ -53,7 +53,7 @@ fsspec = ">=2024.2.0" graphrag = "==1.2.0" httpx = ">=0.25.2" kubernetes = ">=29.0.0" -markitdown = "0.1.0a3" +markitdown = {extras = ["all"], version = "^0.1.1"} networkx = ">=3.2.1" nltk = "*" pandas = ">=2.2.1" diff --git a/notebooks/1-Quickstart.ipynb b/notebooks/1-Quickstart.ipynb index 683dcea8..1a08d921 100644 --- a/notebooks/1-Quickstart.ipynb +++ b/notebooks/1-Quickstart.ipynb @@ -181,11 +181,7 @@ " filepaths = list(Path(file_directory).iterdir())\n", " for file in tqdm(filepaths):\n", " # validate that file is a file, has acceptable file type, has a .txt extension, and has utf-8 encoding\n", - " if (\n", - " not file.is_file()\n", - " or file.suffix != \".txt\"\n", - " or magic.from_file(str(file), mime=True) not in accepted_file_types\n", - " ):\n", + " if (not file.is_file()):\n", " print(f\"Skipping invalid file: {file}\")\n", " continue\n", " # open and decode file as utf-8, ignore bad characters\n", diff --git a/notebooks/2-Advanced_Getting_Started.ipynb b/notebooks/2-Advanced_Getting_Started.ipynb index d57d58b2..ce7cd443 100644 --- a/notebooks/2-Advanced_Getting_Started.ipynb +++ b/notebooks/2-Advanced_Getting_Started.ipynb @@ -27,17 +27,14 @@ "| DELETE | /index/{index_name}\n", "| GET | /index/status/{index_name}\n", "| POST | /query/global\n", - "| POST | /query/streaming/global\n", "| POST | /query/local\n", - "| POST | /query/streaming/local\n", "| GET | /index/config/prompts\n", "| GET | /source/report/{index_name}/{report_id}\n", "| GET | /source/text/{index_name}/{text_unit_id}\n", "| GET | /source/entity/{index_name}/{entity_id}\n", "| GET | /source/claim/{index_name}/{claim_id}\n", "| GET | /source/relationship/{index_name}/{relationship_id}\n", - "| GET | /graph/graphml/{index_name}\n", - "| GET | /graph/stats/{index_name}" + "| GET | /graph/graphml/{index_name}" ] }, { @@ -229,15 +226,10 @@ " return response\n", "\n", " batch_files = []\n", - " accepted_file_types = [\"text/plain\"]\n", " filepaths = list(Path(file_directory).iterdir())\n", " for file in tqdm(filepaths):\n", " # validate that file is a file, has acceptable file type, has a .txt extension, and has utf-8 encoding\n", - " if (\n", - " not file.is_file()\n", - " or file.suffix != \".txt\"\n", - " or magic.from_file(str(file), mime=True) not in accepted_file_types\n", - " ):\n", + " if (not file.is_file()):\n", " print(f\"Skipping invalid file: {file}\")\n", " continue\n", " # open and decode file as utf-8, ignore bad characters\n", @@ -961,7 +953,7 @@ ], "metadata": { "kernelspec": { - "display_name": "graphrag-venv", + "display_name": "3.10", "language": "python", "name": "python3" }, From 088ebdf4b568a6c4f631814dd68b5741a0184b0f Mon Sep 17 00:00:00 2001 From: Josh Bradley Date: Sun, 6 Apr 2025 11:44:14 -0400 Subject: [PATCH 16/19] clean up http status code usage --- backend/graphrag_app/api/data.py | 12 ++++---- backend/graphrag_app/api/index.py | 12 ++++---- backend/graphrag_app/api/query.py | 4 +-- backend/graphrag_app/main.py | 7 +++-- backend/graphrag_app/utils/common.py | 42 +++++++++++++++++----------- 5 files changed, 46 insertions(+), 31 deletions(-) diff --git a/backend/graphrag_app/api/data.py b/backend/graphrag_app/api/data.py index 95a71069..2a3a6fdc 100644 --- a/backend/graphrag_app/api/data.py +++ b/backend/graphrag_app/api/data.py @@ -47,7 +47,7 @@ "", summary="Get list of data containers.", response_model=StorageNameList, - responses={200: {"model": StorageNameList}}, + responses={status.HTTP_200_OK: {"model": StorageNameList}}, ) async def get_all_data_containers(): """ @@ -169,20 +169,20 @@ async def upload_files( if len(processing_errors) > 0: raise HTTPException( - status_code=400, + status_code=status.HTTP_422_UNPROCESSABLE_ENTITY, detail=f"Error uploading files: {processing_errors}.", ) - return BaseResponse(status="File upload successful.") + return BaseResponse(status="Success.") except Exception as e: logger = load_pipeline_logger() logger.error( message="Error uploading files.", cause=e, stack=traceback.format_exc(), - details={"files": [f.filename for f in files]}, + details={"files": processing_errors}, ) raise HTTPException( - status_code=500, + status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=f"Error uploading files to container '{container_name}'.", ) @@ -191,7 +191,7 @@ async def upload_files( "/{container_name}", summary="Delete a data storage container", response_model=BaseResponse, - responses={200: {"model": BaseResponse}}, + responses={status.HTTP_200_OK: {"model": BaseResponse}}, ) async def delete_files( container_name: str, sanitized_container_name: str = Depends(sanitize_name) diff --git a/backend/graphrag_app/api/index.py b/backend/graphrag_app/api/index.py index 5166601a..40941321 100644 --- a/backend/graphrag_app/api/index.py +++ b/backend/graphrag_app/api/index.py @@ -72,7 +72,7 @@ async def schedule_index_job( sanitized_storage_container_name ).exists(): raise HTTPException( - status_code=500, + status_code=status.HTTP_412_PRECONDITION_FAILED, detail=f"Storage container '{storage_container_name}' does not exist", ) @@ -102,7 +102,7 @@ async def schedule_index_job( PipelineJobState(existing_job.status) == PipelineJobState.RUNNING ): raise HTTPException( - status_code=202, # request has been accepted for processing but is not complete. + status_code=status.HTTP_425_TOO_EARLY, # request has been accepted for processing but is not complete. detail=f"Index '{index_container_name}' already exists and has not finished building.", ) # if indexing job is in a failed state, delete the associated K8s job and pod to allow for a new job to be scheduled @@ -258,7 +258,8 @@ async def delete_index( details={"container": container_name}, ) raise HTTPException( - status_code=500, detail=f"Error deleting '{container_name}'." + status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, + detail=f"Error deleting '{container_name}'.", ) return BaseResponse(status="Success") @@ -277,7 +278,7 @@ async def get_index_status( if pipelinejob.item_exist(sanitized_container_name): pipeline_job = pipelinejob.load_item(sanitized_container_name) return IndexStatusResponse( - status_code=200, + status_code=status.HTTP_200_OK, index_name=pipeline_job.human_readable_index_name, storage_name=pipeline_job.human_readable_storage_name, status=pipeline_job.status.value, @@ -286,5 +287,6 @@ async def get_index_status( ) else: raise HTTPException( - status_code=404, detail=f"'{container_name}' does not exist." + status_code=status.HTTP_404_NOT_FOUND, + detail=f"'{container_name}' does not exist.", ) diff --git a/backend/graphrag_app/api/query.py b/backend/graphrag_app/api/query.py index c994db9d..11d11b22 100644 --- a/backend/graphrag_app/api/query.py +++ b/backend/graphrag_app/api/query.py @@ -52,7 +52,7 @@ async def global_query(request: GraphRequest): if not _is_index_complete(sanitized_index_name): raise HTTPException( - status_code=500, + status_code=status.HTTP_425_TOO_EARLY, detail=f"{index_name} not ready for querying.", ) @@ -131,7 +131,7 @@ async def local_query(request: GraphRequest): if not _is_index_complete(sanitized_index_name): raise HTTPException( - status_code=500, + status_code=status.HTTP_425_TOO_EARLY, detail=f"{index_name} not ready for querying.", ) diff --git a/backend/graphrag_app/main.py b/backend/graphrag_app/main.py index a21770a4..53984842 100644 --- a/backend/graphrag_app/main.py +++ b/backend/graphrag_app/main.py @@ -33,7 +33,7 @@ async def catch_all_exceptions_middleware(request: Request, call_next): - """a function to globally catch all exceptions and return a 500 response with the exception message""" + """A global function to catch all exceptions and produce a standard error message""" try: return await call_next(request) except Exception as e: @@ -44,7 +44,10 @@ async def catch_all_exceptions_middleware(request: Request, call_next): cause=e, stack=stack, ) - return Response("Unexpected internal server error.", status_code=500) + return Response( + "Unexpected internal server error.", + status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, + ) # NOTE: this function is not currently used, but it is a placeholder for future use once RBAC issues have been resolved diff --git a/backend/graphrag_app/utils/common.py b/backend/graphrag_app/utils/common.py index 85e41f9f..73ce0b19 100644 --- a/backend/graphrag_app/utils/common.py +++ b/backend/graphrag_app/utils/common.py @@ -14,15 +14,18 @@ from azure.cosmos import ContainerProxy, exceptions from azure.identity import DefaultAzureCredential from azure.storage.blob.aio import ContainerClient -from fastapi import Header, HTTPException +from fastapi import Header, HTTPException, status from graphrag_app.logger.load_logger import load_pipeline_logger from graphrag_app.utils.azure_clients import AzureClientManager +FILE_UPLOAD_CACHE = "cache/uploaded_files.csv" + def get_df( table_path: str, ) -> pd.DataFrame: + """Read a parquet file from Azure Storage and return it as a pandas DataFrame.""" df = pd.read_parquet( table_path, storage_options=pandas_storage_options(), @@ -126,7 +129,10 @@ def get_cosmos_container_store_client() -> ContainerProxy: cause=e, stack=traceback.format_exc(), ) - raise HTTPException(status_code=500, detail="Error fetching cosmosdb client.") + raise HTTPException( + status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, + detail="Error fetching cosmosdb client.", + ) async def get_blob_container_client(name: str) -> ContainerClient: @@ -144,7 +150,10 @@ async def get_blob_container_client(name: str) -> ContainerClient: cause=e, stack=traceback.format_exc(), ) - raise HTTPException(status_code=500, detail="Error fetching storage client.") + raise HTTPException( + status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, + detail="Error fetching storage client.", + ) def sanitize_name(container_name: str) -> str: @@ -191,7 +200,8 @@ def desanitize_name(sanitized_container_name: str) -> str | None: return None except Exception: raise HTTPException( - status_code=500, detail="Error retrieving original container name." + status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, + detail="Error retrieving original container name.", ) @@ -199,14 +209,14 @@ async def subscription_key_check( Ocp_Apim_Subscription_Key: Annotated[str, Header()], ): """ - Verifies if user has passed the Ocp_Apim_Subscription_Key (APIM subscription key) in the request header. - If it is not present, an HTTPException with a 400 status code is raised. - Note: this check is unnecessary (APIM validates subscription keys automatically), but this will add the key + Verify if user has passed the Ocp_Apim_Subscription_Key (APIM subscription key) in the request header. + Note: this check is unnecessary (APIM validates subscription keys automatically), but it effectively adds the key as a required parameter in the swagger docs page, enabling users to send requests using the swagger docs "Try it out" feature. """ if not Ocp_Apim_Subscription_Key: raise HTTPException( - status_code=400, detail="Ocp-Apim-Subscription-Key required" + status_code=status.HTTP_400_BAD_REQUEST, + detail="Ocp-Apim-Subscription-Key required", ) return Ocp_Apim_Subscription_Key @@ -216,7 +226,7 @@ async def create_cache(container_client: ContainerClient) -> None: Create a file cache (csv) to track uploaded files. """ try: - cache_blob_client = container_client.get_blob_client("uploaded_files_cache.csv") + cache_blob_client = container_client.get_blob_client(FILE_UPLOAD_CACHE) if not await cache_blob_client.exists(): # create the empty file cache csv headers = [["Filename", "Hash"]] @@ -231,20 +241,20 @@ async def create_cache(container_client: ContainerClient) -> None: os.remove("uploaded_files_cache.csv") except Exception: raise HTTPException( - status_code=500, + status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail="Error creating file cache in Azure Blob Storage.", ) async def check_cache(file_stream: BinaryIO, container_client: ContainerClient) -> bool: """ - Check a cache file to determine if a file has previously been uploaded. + Check a file cache (csv) to determine if a file has previously been uploaded. Note: This function creates/checks a CSV file in azure storage to act as a cache of previously uploaded files. """ try: # load the file cache - cache_blob_client = container_client.get_blob_client("uploaded_files_cache.csv") + cache_blob_client = container_client.get_blob_client(FILE_UPLOAD_CACHE) cache_download_stream = await cache_blob_client.download_blob() cache_bytes = await cache_download_stream.readall() cache_content = StringIO(cache_bytes.decode("utf-8")) @@ -258,7 +268,7 @@ async def check_cache(file_stream: BinaryIO, container_client: ContainerClient) return False except Exception: raise HTTPException( - status_code=500, + status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail="Error checking file cache in Azure Blob Storage.", ) @@ -267,11 +277,11 @@ async def update_cache( filename: str, file_stream: BinaryIO, container_client: ContainerClient ) -> None: """ - Update the file cache (csv) with a new file by adding a new row. + Update a file cache (csv) with a new file by adding a new row. """ try: # Load the file cache - cache_blob_client = container_client.get_blob_client("uploaded_files_cache.csv") + cache_blob_client = container_client.get_blob_client(FILE_UPLOAD_CACHE) cache_download_stream = await cache_blob_client.download_blob() cache_bytes = await cache_download_stream.readall() cache_content = StringIO(cache_bytes.decode("utf-8")) @@ -297,6 +307,6 @@ async def update_cache( ) except Exception: raise HTTPException( - status_code=500, + status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail="Error updating file cache in Azure Blob Storage.", ) From b4aed6ec1a8f253d584bc4127c472fd1d457e934 Mon Sep 17 00:00:00 2001 From: Josh Bradley Date: Mon, 7 Apr 2025 18:01:32 -0400 Subject: [PATCH 17/19] update notebooks to align with API and to support upload multi-filetype --- backend/graphrag_app/api/data.py | 44 +++++++++++++--------- backend/graphrag_app/utils/common.py | 44 +++++++++++----------- notebooks/1-Quickstart.ipynb | 17 ++------- notebooks/2-Advanced_Getting_Started.ipynb | 14 +++---- 4 files changed, 59 insertions(+), 60 deletions(-) diff --git a/backend/graphrag_app/api/data.py b/backend/graphrag_app/api/data.py index 2a3a6fdc..dae1c6c0 100644 --- a/backend/graphrag_app/api/data.py +++ b/backend/graphrag_app/api/data.py @@ -2,6 +2,7 @@ # Licensed under the MIT License. import asyncio +import hashlib import os import re import traceback @@ -72,21 +73,26 @@ async def get_all_data_containers(): return StorageNameList(storage_name=items) -async def upload_file_async( +async def upload_file( upload_file: UploadFile, container_client: ContainerClient, overwrite: bool = True -) -> None: +): """ - Asynchronously convert and upload a file to the specified blob container. - Silently ignore errors that occur when overwrite=False. + Convert and upload a file to a specified blob container. + + Returns a list of objects where each object will have one of the following types: + * Tuple[str, str] - a tuple of (filename, file_hash) for successful uploads + * Tuple[str, None] - a tuple of (filename, None) for failed uploads or + * None for skipped files """ filename = upload_file.filename extension = os.path.splitext(filename)[1] - converted_filename = filename.replace(extension, ".txt") + converted_filename = filename + ".txt" converted_blob_client = container_client.get_blob_client(converted_filename) with upload_file.file as file_stream: try: - if not await check_cache(file_stream, container_client): + file_hash = hashlib.sha256(file_stream.read()).hexdigest() + if not await check_cache(file_hash, container_client): # extract text from file using MarkItDown md = MarkItDown() stream_info = StreamInfo( @@ -100,19 +106,19 @@ async def upload_file_async( ) # remove illegal unicode characters and upload to blob storage - cleaned_result = clean_output(result.text_content) + cleaned_result = _clean_output(result.text_content) await converted_blob_client.upload_blob( cleaned_result, overwrite=overwrite ) - # update the file cache - await update_cache(filename, file_stream, container_client) + # return tuple of (filename, file_hash) to indicate success + return (filename, file_hash) except Exception: - # if any exception occurs, return the filename to indicate conversion/upload failures - return upload_file.filename + # if any exception occurs, return a tuple of (filename, None) to indicate conversion/upload failure + return (upload_file.filename, None) -def clean_output(val: str, replacement: str = ""): +def _clean_output(val: str, replacement: str = ""): """Removes unicode characters that are invalid XML characters (not valid for graphml files at least).""" # fmt: off _illegal_xml_chars_RE = re.compile( @@ -145,19 +151,23 @@ async def upload_files( ) await create_cache(blob_container_client) - # upload files in batches of 100 to avoid exceeding Azure Storage API limits + # process file uploads in batches to avoid exceeding Azure Storage API limits processing_errors = [] batch_size = 100 num_batches = ceil(len(files) / batch_size) for i in range(num_batches): batch_files = files[i * batch_size : (i + 1) * batch_size] tasks = [ - upload_file_async(file, blob_container_client, overwrite) + upload_file(file, blob_container_client, overwrite) for file in batch_files ] - results = await asyncio.gather(*tasks) - results = [r for r in results if r is not None] - processing_errors.extend(results) + upload_results = await asyncio.gather(*tasks) + successful_uploads = [r for r in upload_results if r and r[1] is not None] + # update the file cache with successful uploads + await update_cache(successful_uploads, blob_container_client) + # collect failed uploads + failed_uploads = [r[0] for r in upload_results if r and r[1] is None] + processing_errors.extend(failed_uploads) # update container-store entry in cosmosDB once upload process is successful cosmos_container_store_client = get_cosmos_container_store_client() diff --git a/backend/graphrag_app/utils/common.py b/backend/graphrag_app/utils/common.py index 73ce0b19..6d002b3b 100644 --- a/backend/graphrag_app/utils/common.py +++ b/backend/graphrag_app/utils/common.py @@ -1,13 +1,15 @@ # Copyright (c) Microsoft Corporation. # Licensed under the MIT License. +""" +Common utility functions used by the API endpoints. +""" import csv import hashlib import os import traceback -from hashlib import sha256 from io import StringIO -from typing import Annotated, BinaryIO +from typing import Annotated, Tuple import pandas as pd from azure.core.exceptions import ResourceNotFoundError @@ -23,11 +25,11 @@ def get_df( - table_path: str, + filepath: str, ) -> pd.DataFrame: """Read a parquet file from Azure Storage and return it as a pandas DataFrame.""" df = pd.read_parquet( - table_path, + filepath, storage_options=pandas_storage_options(), ) return df @@ -223,22 +225,23 @@ async def subscription_key_check( async def create_cache(container_client: ContainerClient) -> None: """ - Create a file cache (csv) to track uploaded files. + Create a file cache (csv). """ try: cache_blob_client = container_client.get_blob_client(FILE_UPLOAD_CACHE) if not await cache_blob_client.exists(): # create the empty file cache csv headers = [["Filename", "Hash"]] - with open("uploaded_files_cache.csv", "w", newline="") as f: + tmp_cache_file = "uploaded_files_cache.csv" + with open(tmp_cache_file, "w", newline="") as f: writer = csv.writer(f, delimiter=",") writer.writerows(headers) # upload to Azure Blob Storage and remove the temporary file - with open("uploaded_files_cache.csv", "rb") as f: + with open(tmp_cache_file, "rb") as f: await cache_blob_client.upload_blob(f, overwrite=True) - if os.path.exists("uploaded_files_cache.csv"): - os.remove("uploaded_files_cache.csv") + if os.path.exists(tmp_cache_file): + os.remove(tmp_cache_file) except Exception: raise HTTPException( status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, @@ -246,9 +249,9 @@ async def create_cache(container_client: ContainerClient) -> None: ) -async def check_cache(file_stream: BinaryIO, container_client: ContainerClient) -> bool: +async def check_cache(file_hash: str, container_client: ContainerClient) -> bool: """ - Check a file cache (csv) to determine if a file has previously been uploaded. + Check a file cache (csv) to determine if a file hash has previously been uploaded. Note: This function creates/checks a CSV file in azure storage to act as a cache of previously uploaded files. """ @@ -261,7 +264,6 @@ async def check_cache(file_stream: BinaryIO, container_client: ContainerClient) # comupte the sha256 hash of the file and check if it exists in the cache cache_reader = csv.reader(cache_content, delimiter=",") - file_hash = sha256(file_stream.read()).hexdigest() for row in cache_reader: if file_hash in row: return True @@ -274,26 +276,24 @@ async def check_cache(file_stream: BinaryIO, container_client: ContainerClient) async def update_cache( - filename: str, file_stream: BinaryIO, container_client: ContainerClient + new_files: Tuple[str, str], container_client: ContainerClient ) -> None: """ - Update a file cache (csv) with a new file by adding a new row. + Update an existing file cache (csv) with new files. """ try: - # Load the file cache + # Load the existing cache cache_blob_client = container_client.get_blob_client(FILE_UPLOAD_CACHE) cache_download_stream = await cache_blob_client.download_blob() cache_bytes = await cache_download_stream.readall() cache_content = StringIO(cache_bytes.decode("utf-8")) - - # Read existing rows and prepare to append cache_reader = csv.reader(cache_content, delimiter=",") - existing_rows = list(cache_reader) - # Compute the sha256 hash of the file and append it to the cache - file_hash = sha256(file_stream.read()).hexdigest() - new_row = [filename, file_hash] - existing_rows.append(new_row) + # append new data + existing_rows = list(cache_reader) + for filename, file_hash in new_files: + row = [filename, file_hash] + existing_rows.append(row) # Write the updated content back to the StringIO object updated_cache_content = StringIO() diff --git a/notebooks/1-Quickstart.ipynb b/notebooks/1-Quickstart.ipynb index 1a08d921..840334fb 100644 --- a/notebooks/1-Quickstart.ipynb +++ b/notebooks/1-Quickstart.ipynb @@ -21,7 +21,7 @@ "metadata": {}, "outputs": [], "source": [ - "! pip install devtools python-magic requests tqdm" + "! pip install devtools requests tqdm" ] }, { @@ -35,7 +35,6 @@ "import time\n", "from pathlib import Path\n", "\n", - "import magic\n", "import requests\n", "from devtools import pprint\n", "from tqdm import tqdm" @@ -177,16 +176,14 @@ " return response\n", "\n", " batch_files = []\n", - " accepted_file_types = [\"text/plain\"]\n", " filepaths = list(Path(file_directory).iterdir())\n", " for file in tqdm(filepaths):\n", " # validate that file is a file, has acceptable file type, has a .txt extension, and has utf-8 encoding\n", " if (not file.is_file()):\n", " print(f\"Skipping invalid file: {file}\")\n", " continue\n", - " # open and decode file as utf-8, ignore bad characters\n", " batch_files.append(\n", - " (\"files\", open(file=file, mode=\"r\", encoding=\"utf-8\", errors=\"ignore\"))\n", + " (\"files\", open(file=file, mode=\"rb\"))\n", " )\n", " # upload batch of files\n", " if len(batch_files) == batch_size:\n", @@ -195,7 +192,7 @@ " if not response.ok:\n", " return response\n", " batch_files.clear()\n", - " # upload remaining files\n", + " # upload last batch of remaining files\n", " if len(batch_files) > 0:\n", " response = upload_batch(batch_files, container_name, overwrite, max_retries)\n", " return response\n", @@ -326,9 +323,6 @@ "metadata": {}, "outputs": [], "source": [ - "%%time\n", - "\n", - "\n", "def global_search(\n", " index_name: str | list[str], query: str, community_level: int\n", ") -> requests.Response:\n", @@ -368,9 +362,6 @@ "metadata": {}, "outputs": [], "source": [ - "%%time\n", - "\n", - "\n", "def local_search(\n", " index_name: str | list[str], query: str, community_level: int\n", ") -> requests.Response:\n", @@ -412,7 +403,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.12" + "version": "3.10.16" } }, "nbformat": 4, diff --git a/notebooks/2-Advanced_Getting_Started.ipynb b/notebooks/2-Advanced_Getting_Started.ipynb index ce7cd443..1724f5af 100644 --- a/notebooks/2-Advanced_Getting_Started.ipynb +++ b/notebooks/2-Advanced_Getting_Started.ipynb @@ -53,7 +53,7 @@ "metadata": {}, "outputs": [], "source": [ - "! pip install devtools pandas python-magic requests tqdm" + "! pip install devtools pandas requests tqdm" ] }, { @@ -69,7 +69,6 @@ "import time\n", "from pathlib import Path\n", "\n", - "import magic\n", "import pandas as pd\n", "import requests\n", "from devtools import pprint\n", @@ -232,9 +231,8 @@ " if (not file.is_file()):\n", " print(f\"Skipping invalid file: {file}\")\n", " continue\n", - " # open and decode file as utf-8, ignore bad characters\n", " batch_files.append(\n", - " (\"files\", open(file=file, mode=\"r\", encoding=\"utf-8\", errors=\"ignore\"))\n", + " (\"files\", open(file=file, mode=\"rb\"))\n", " )\n", " # upload batch of files\n", " if len(batch_files) == batch_size:\n", @@ -243,7 +241,7 @@ " if not response.ok:\n", " return response\n", " batch_files.clear()\n", - " # upload remaining files\n", + " # upload last batch of remaining files\n", " if len(batch_files) > 0:\n", " response = upload_batch(batch_files, container_name, overwrite, max_retries)\n", " return response\n", @@ -742,8 +740,8 @@ "# pass in a single index name as a string or to query across multiple indexes, set index_name=[myindex1, myindex2]\n", "global_response = global_search(\n", " index_name=index_name,\n", - " query=\"Summarize the main topics found in this data\",\n", - " community_level=1,\n", + " query=\"Summarize the qualifications to being a delivery data scientist\",\n", + " community_level=2,\n", ")\n", "# print the result and save context data in a variable\n", "global_response_data = parse_query_response(global_response, return_context_data=True)\n", @@ -953,7 +951,7 @@ ], "metadata": { "kernelspec": { - "display_name": "3.10", + "display_name": "Python 3", "language": "python", "name": "python3" }, From 7534b85fbf7258eee2726280dcd75e7ac2bdcdac Mon Sep 17 00:00:00 2001 From: Josh Bradley Date: Mon, 7 Apr 2025 18:04:57 -0400 Subject: [PATCH 18/19] update notebook documentation --- notebooks/1-Quickstart.ipynb | 2 +- notebooks/2-Advanced_Getting_Started.ipynb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/notebooks/1-Quickstart.ipynb b/notebooks/1-Quickstart.ipynb index 840334fb..1c9f86b7 100644 --- a/notebooks/1-Quickstart.ipynb +++ b/notebooks/1-Quickstart.ipynb @@ -126,7 +126,7 @@ "source": [ "## Upload Files\n", "\n", - "For a demonstration of how to index data in graphrag, we first need to ingest a few files into graphrag." + "For a demonstration of how to index data in graphrag, we first need to ingest a few files into graphrag. **Multiple filetypes are now supported via the [MarkItDown](https://github.com/microsoft/markitdown) library.**" ] }, { diff --git a/notebooks/2-Advanced_Getting_Started.ipynb b/notebooks/2-Advanced_Getting_Started.ipynb index 1724f5af..f4f06cf0 100644 --- a/notebooks/2-Advanced_Getting_Started.ipynb +++ b/notebooks/2-Advanced_Getting_Started.ipynb @@ -479,7 +479,7 @@ "source": [ "## Upload files\n", "\n", - "Use the API to upload a collection of local files. The API will create a new storage blob container to host these files in. For a set of large files, consider reducing the batch upload size in order to not overwhelm the API endpoint and prevent out-of-memory problems." + "Use the API to upload a collection of files. **Multiple filetypes are now supported via the [MarkItDown](https://github.com/microsoft/markitdown) library.** The API will create a new storage blob container to host these files in. For a set of large files, consider reducing the batch upload size in order to not overwhelm the API endpoint and prevent out-of-memory problems." ] }, { From 4017f51cf35bebcf40428e4d83e5edc32c55f698 Mon Sep 17 00:00:00 2001 From: Josh Bradley Date: Mon, 7 Apr 2025 18:19:51 -0400 Subject: [PATCH 19/19] fix test --- backend/poetry.lock | 202 ++++++++++---------- backend/tests/integration/test_api_index.py | 2 +- 2 files changed, 105 insertions(+), 99 deletions(-) diff --git a/backend/poetry.lock b/backend/poetry.lock index 9972f3bc..7dad142d 100644 --- a/backend/poetry.lock +++ b/backend/poetry.lock @@ -516,13 +516,13 @@ typing-extensions = ">=4.0.0" [[package]] name = "azure-monitor-opentelemetry" -version = "1.6.5" +version = "1.6.6" description = "Microsoft Azure Monitor Opentelemetry Distro Client Library for Python" optional = false python-versions = ">=3.8" files = [ - {file = "azure_monitor_opentelemetry-1.6.5-py3-none-any.whl", hash = "sha256:9e04fe20db099765ad17a4542ee89dccc59ef152b9c279d45c4e2148d020bb44"}, - {file = "azure_monitor_opentelemetry-1.6.5.tar.gz", hash = "sha256:5a25b0748b0f5785d7ed8141019125574984d78b8ca0ae8fe11849bf514a1331"}, + {file = "azure_monitor_opentelemetry-1.6.6-py3-none-any.whl", hash = "sha256:934bfaef0829714641bd7d68d9dd348b5fe8b44aca99c385431df8b1c414d6ee"}, + {file = "azure_monitor_opentelemetry-1.6.6.tar.gz", hash = "sha256:e27031f9759e1dfcf63e2c39b079a83e61c664c51e28044456cb3767851f91e5"}, ] [package.dependencies] @@ -541,17 +541,18 @@ opentelemetry-sdk = ">=1.28,<2.0" [[package]] name = "azure-monitor-opentelemetry-exporter" -version = "1.0.0b35" +version = "1.0.0b36" description = "Microsoft Azure Monitor Opentelemetry Exporter Client Library for Python" optional = false python-versions = ">=3.8" files = [ - {file = "azure_monitor_opentelemetry_exporter-1.0.0b35-py2.py3-none-any.whl", hash = "sha256:93c8824f6c2589905159b4c27640f4be65ce96e1b51959b6b32ea63f518c3944"}, - {file = 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