From 6a190a35bb51eac6f16cf097b72cbd2faf4f7292 Mon Sep 17 00:00:00 2001 From: kdu14933 Date: Fri, 29 Nov 2024 14:57:10 +0000 Subject: [PATCH 01/24] Added function decorator to handle db issues --- operationsgateway_api/src/mongo/interface.py | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/operationsgateway_api/src/mongo/interface.py b/operationsgateway_api/src/mongo/interface.py index a21d54b1..f3a81f3f 100644 --- a/operationsgateway_api/src/mongo/interface.py +++ b/operationsgateway_api/src/mongo/interface.py @@ -14,6 +14,7 @@ from operationsgateway_api.src.config import Config from operationsgateway_api.src.exceptions import DatabaseError from operationsgateway_api.src.mongo.connection import ConnectionInstance +from operationsgateway_api.src.mongo.mongo_error_handling import mongodb_error_handling log = logging.getLogger() ProjectionAlias = Optional[Union[Mapping[str, Any], Iterable[str]]] @@ -22,16 +23,17 @@ class MongoDBInterface: """ An implementation of various PyMongo and Motor functions that suit our specific - database and colllection names + database and collection names Motor doesn't support type annotations (see https://jira.mongodb.org/browse/MOTOR-331 for any updates) so type annotations are - used from PyMongo which from a user perspective, acts almost identically (exlcuding + used from PyMongo which from a user perspective, acts almost identically (excluding async support of course). This means the type hinting can actually be useful for developers of this repo """ @staticmethod + @mongodb_error_handling("get_collection_object") def get_collection_object(collection_name: str) -> Collection: """ Simple getter function which gets a particular collection so it can be @@ -44,6 +46,7 @@ def get_collection_object(collection_name: str) -> Collection: raise DatabaseError("Invalid collection name given") from exc @staticmethod + @mongodb_error_handling("find") def find( collection_name: str = "images", filter_: dict = None, @@ -99,6 +102,7 @@ async def query_to_list(query: Cursor) -> List[Dict[str, Any]]: return await query.to_list(length=Config.config.mongodb.max_documents) @staticmethod + @mongodb_error_handling("find_one") async def find_one( collection_name: str, filter_: Dict[str, Any] = None, @@ -120,6 +124,7 @@ async def find_one( return await collection.find_one(filter_, sort=sort, projection=projection) @staticmethod + @mongodb_error_handling("update_one") async def update_one( collection_name: str, filter_: Dict[str, Any] = None, @@ -153,6 +158,7 @@ async def update_one( ) from exc @staticmethod + @mongodb_error_handling("update_many") async def update_many( collection_name: str, filter_: Dict[str, Any] = {}, # noqa: B006 @@ -177,6 +183,7 @@ async def update_many( ) from exc @staticmethod + @mongodb_error_handling("insert_one") async def insert_one(collection_name: str, data: Dict[str, Any]) -> InsertOneResult: """ Using the input data, insert a single document into a given collection @@ -194,6 +201,7 @@ async def insert_one(collection_name: str, data: Dict[str, Any]) -> InsertOneRes ) from exc @staticmethod + @mongodb_error_handling("insert_many") async def insert_many( collection_name: str, data: List[Dict[str, Any]], @@ -215,6 +223,7 @@ async def insert_many( ) from exc @staticmethod + @mongodb_error_handling("delete_one") async def delete_one( collection_name: str, filter_: Dict[str, Any] = None, @@ -245,6 +254,7 @@ async def delete_one( ) from exc @staticmethod + @mongodb_error_handling("count_documents") async def count_documents( collection_name: str, filter_: Dict[str, Any] = None, @@ -273,6 +283,7 @@ async def count_documents( ) from exc @staticmethod + @mongodb_error_handling("aggregate") async def aggregate( collection_name: str, pipeline, From 50273e9ff2af6ca9614044b3ac22828f970c850a Mon Sep 17 00:00:00 2001 From: kdu14933 Date: Fri, 29 Nov 2024 14:57:24 +0000 Subject: [PATCH 02/24] Created function decorator to handle db issues --- .../src/mongo/mongo_error_handling.py | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 operationsgateway_api/src/mongo/mongo_error_handling.py diff --git a/operationsgateway_api/src/mongo/mongo_error_handling.py b/operationsgateway_api/src/mongo/mongo_error_handling.py new file mode 100644 index 00000000..ce98ffc0 --- /dev/null +++ b/operationsgateway_api/src/mongo/mongo_error_handling.py @@ -0,0 +1,39 @@ +from functools import wraps +from inspect import iscoroutinefunction + +from operationsgateway_api.src.exceptions import DatabaseError + + +def mongodb_error_handling(operation: str): + """ + Decorator for consistent error handling in MongoDB operations, supporting both + sync and async functions. + """ + + def decorator(func): + if iscoroutinefunction(func): # Check if the function is async + + @wraps(func) + async def async_wrapper(*args, **kwargs): + try: + return await func(*args, **kwargs) + except Exception as exc: + raise DatabaseError( + f"Database operation failed during {operation}", + ) from exc + + return async_wrapper + else: # Handle synchronous functions + + @wraps(func) + def sync_wrapper(*args, **kwargs): + try: + return func(*args, **kwargs) + except Exception as exc: + raise DatabaseError( + f"Database operation failed during {operation}", + ) from exc + + return sync_wrapper + + return decorator From f9f491a8d47980cdd7376b761f73f3aed1bafc92 Mon Sep 17 00:00:00 2001 From: kdu14933 Date: Fri, 29 Nov 2024 14:58:32 +0000 Subject: [PATCH 03/24] Added test to check that a db error is caught and returned --- test/mongo/test_mongo_error_handling.py | 48 +++++++++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 test/mongo/test_mongo_error_handling.py diff --git a/test/mongo/test_mongo_error_handling.py b/test/mongo/test_mongo_error_handling.py new file mode 100644 index 00000000..aa458190 --- /dev/null +++ b/test/mongo/test_mongo_error_handling.py @@ -0,0 +1,48 @@ +from unittest.mock import AsyncMock, patch + +from fastapi.testclient import TestClient +import pytest + + +class TestMongoDBErrorHandling: + @pytest.mark.asyncio + @pytest.mark.parametrize( + "record_id, expected_status_code, expected_response", + [ + pytest.param( + "20230605100000", + 500, + {"detail": "Database operation failed during find_one"}, + id="Simulated error during find_one", + ), + ], + ) + # This test simulates an exception being raised in the collection.find_one call + # (within interface.py), which the decorator should handle and produce a + # DatabaseError, ultimately flowing this back up to the user in the endpoint, + # producing a 500 + async def test_find_one_exception_in_interface( + self, + test_app: TestClient, + login_and_get_token, + record_id, + expected_status_code, + expected_response, + ): + with patch( + "operationsgateway_api.src.mongo.interface.MongoDBInterface.get_collection_object", + ) as mock_get_collection_object: + # Mock the `collection.find_one` to raise an exception + mock_collection = AsyncMock() + mock_collection.find_one.side_effect = Exception("Simulated exception") + mock_get_collection_object.return_value = mock_collection + + # Make the GET request to the endpoint + response = test_app.get( + f"/records/{record_id}", + headers={"Authorization": f"Bearer {login_and_get_token}"}, + ) + + # Assert the status code and responseAsyncMock + assert response.status_code == expected_status_code + assert response.json() == expected_response From c9745698d2e801f7364ad9770b046a1ff71ad054 Mon Sep 17 00:00:00 2001 From: kdu14933 Date: Mon, 20 Jan 2025 13:37:51 +0000 Subject: [PATCH 04/24] Wrapped the upload in a try/catch and return the failed channel if nessesary --- operationsgateway_api/src/records/image.py | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/operationsgateway_api/src/records/image.py b/operationsgateway_api/src/records/image.py index f4a25c4d..35e6bb61 100644 --- a/operationsgateway_api/src/records/image.py +++ b/operationsgateway_api/src/records/image.py @@ -2,7 +2,7 @@ from io import BytesIO import logging -from typing import Tuple +from typing import Tuple, Optional from botocore.exceptions import ClientError import numpy as np @@ -79,7 +79,7 @@ def extract_metadata_from_path(self) -> Tuple[str, str]: return record_id, channel_name @staticmethod - def upload_image(input_image: Image) -> None: + def upload_image(input_image: Image) -> Optional[str]: """ Save the image on Echo S3 object storage """ @@ -96,7 +96,15 @@ def upload_image(input_image: Image) -> None: echo = EchoInterface() storage_path = Image.get_full_path(input_image.image.path) log.info("Storing image on S3: %s", storage_path) - echo.upload_file_object(image_bytes, storage_path) + + try: + echo.upload_file_object(image_bytes, storage_path) + return None # No failure + except EchoS3Error: + # Extract the channel name and propagate it + record_id, channel_name = input_image.extract_metadata_from_path() + log.error("Failed to upload image for channel: %s", channel_name) + return channel_name @staticmethod async def get_image( From cbd62c5dfb802bc63f6a35566bb25d23dc615c4c Mon Sep 17 00:00:00 2001 From: kdu14933 Date: Mon, 20 Jan 2025 13:39:00 +0000 Subject: [PATCH 05/24] Added a function to remove a channel from the record. Used when the channel fails to upload to echo --- operationsgateway_api/src/records/record.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/operationsgateway_api/src/records/record.py b/operationsgateway_api/src/records/record.py index 41630b27..2a8cad10 100644 --- a/operationsgateway_api/src/records/record.py +++ b/operationsgateway_api/src/records/record.py @@ -109,6 +109,14 @@ async def update(self) -> None: }, ) + def remove_channel(self, channel_name: str) -> None: + if channel_name in self.record.channels: + log.info("Removing channel '%s' from record.", channel_name) + del self.record.channels[channel_name] + else: + log.warning("Channel '%s' not found in record.", channel_name) + raise KeyError(f"Channel '{channel_name}' does not exist in the record.") + async def find_existing_record(self) -> Union[RecordModel, None]: """ Using the ID, check if the object's record is currently stored in the database From 63d2366bc6f1a68cb7aee7b948235d56909b4257 Mon Sep 17 00:00:00 2001 From: kdu14933 Date: Mon, 20 Jan 2025 13:39:36 +0000 Subject: [PATCH 06/24] Wrapped the upload in a try/catch and return the failed channel if nessesary --- operationsgateway_api/src/records/waveform.py | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/operationsgateway_api/src/records/waveform.py b/operationsgateway_api/src/records/waveform.py index 16c65b10..b9d423a4 100644 --- a/operationsgateway_api/src/records/waveform.py +++ b/operationsgateway_api/src/records/waveform.py @@ -2,6 +2,7 @@ from io import BytesIO import json import logging +from typing import Optional from botocore.exceptions import ClientError import matplotlib @@ -35,17 +36,24 @@ def to_json(self): b.seek(0) return b - def insert_waveform(self) -> None: + def insert_waveform(self) -> Optional[str]: """ Store the waveform from this object in Echo """ log.info("Storing waveform: %s", self.waveform.path) bytes_json = self.to_json() echo = EchoInterface() - echo.upload_file_object( - bytes_json, - Waveform.get_full_path(self.waveform.path), - ) + try: + echo.upload_file_object( + bytes_json, + Waveform.get_full_path(self.waveform.path), + ) + return None # Successful upload + except EchoS3Error as e: + # Extract the channel name and propagate it + channel_name = self.get_channel_name_from_id() + log.error("Failed to upload waveform for channel '%s': %s", channel_name, str(e)) + return channel_name def create_thumbnail(self) -> None: """ From b89d078c18a221a25b845e487efd0d4be43bbcc5 Mon Sep 17 00:00:00 2001 From: kdu14933 Date: Mon, 20 Jan 2025 13:41:07 +0000 Subject: [PATCH 07/24] Updated versions --- poetry.lock | 1098 ++++++++++++++++++++++++--------------------------- 1 file changed, 524 insertions(+), 574 deletions(-) diff --git a/poetry.lock b/poetry.lock index 590ee427..e5c93bcf 100644 --- a/poetry.lock +++ b/poetry.lock @@ -13,39 +13,40 @@ files = [ [[package]] name = "anyio" -version = "4.6.2.post1" +version = "4.8.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false python-versions = ">=3.9" files = [ - 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(==1.14.*)", "pytest-mypy"] [[package]] name = "six" From 2270606dc790737eb5ee72da488b6c9533acd103 Mon Sep 17 00:00:00 2001 From: kdu14933 Date: Mon, 20 Jan 2025 13:43:06 +0000 Subject: [PATCH 08/24] Black formatting --- operationsgateway_api/src/records/waveform.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/operationsgateway_api/src/records/waveform.py b/operationsgateway_api/src/records/waveform.py index b9d423a4..32d7c998 100644 --- a/operationsgateway_api/src/records/waveform.py +++ b/operationsgateway_api/src/records/waveform.py @@ -36,7 +36,7 @@ def to_json(self): b.seek(0) return b - def insert_waveform(self) -> Optional[str]: + def insert_waveform(self) -> Optional[str]: """ Store the waveform from this object in Echo """ @@ -52,7 +52,9 @@ def insert_waveform(self) -> Optional[str]: except EchoS3Error as e: # Extract the channel name and propagate it channel_name = self.get_channel_name_from_id() - log.error("Failed to upload waveform for channel '%s': %s", channel_name, str(e)) + log.error( + "Failed to upload waveform for channel '%s': %s", channel_name, str(e) + ) return channel_name def create_thumbnail(self) -> None: From ce92c48e4efeea168e89d2fca236e01b20516f24 Mon Sep 17 00:00:00 2001 From: kdu14933 Date: Mon, 20 Jan 2025 16:51:48 +0000 Subject: [PATCH 09/24] Added to list of aliases --- operationsgateway_api/src/records/colourmap_mapping.json | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/operationsgateway_api/src/records/colourmap_mapping.json b/operationsgateway_api/src/records/colourmap_mapping.json index 6c7ccc73..4a389fa6 100644 --- a/operationsgateway_api/src/records/colourmap_mapping.json +++ b/operationsgateway_api/src/records/colourmap_mapping.json @@ -107,7 +107,13 @@ "bwr", "bwr_r", "seismic", - "seismic_r" + "seismic_r", + "berlin", + "berlin_r", + "managua", + "managua_r", + "vanimo", + "vanimo_r" ], "Cyclic": [ "twilight", From eb73d4dea1e93526120baba073734f02c322ad67 Mon Sep 17 00:00:00 2001 From: kdu14933 Date: Mon, 20 Jan 2025 16:52:44 +0000 Subject: [PATCH 10/24] Linting --- operationsgateway_api/src/records/image.py | 2 +- operationsgateway_api/src/records/waveform.py | 7 ++++--- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/operationsgateway_api/src/records/image.py b/operationsgateway_api/src/records/image.py index 35e6bb61..d84a07c3 100644 --- a/operationsgateway_api/src/records/image.py +++ b/operationsgateway_api/src/records/image.py @@ -2,7 +2,7 @@ from io import BytesIO import logging -from typing import Tuple, Optional +from typing import Optional, Tuple from botocore.exceptions import ClientError import numpy as np diff --git a/operationsgateway_api/src/records/waveform.py b/operationsgateway_api/src/records/waveform.py index 32d7c998..eedb5623 100644 --- a/operationsgateway_api/src/records/waveform.py +++ b/operationsgateway_api/src/records/waveform.py @@ -49,11 +49,12 @@ def insert_waveform(self) -> Optional[str]: Waveform.get_full_path(self.waveform.path), ) return None # Successful upload - except EchoS3Error as e: + except EchoS3Error: # Extract the channel name and propagate it channel_name = self.get_channel_name_from_id() - log.error( - "Failed to upload waveform for channel '%s': %s", channel_name, str(e) + log.exception( + "Failed to upload waveform for channel '%s'", + channel_name, ) return channel_name From 18ad3b6069f62cdedaf6c0e1da1826bcddf25039 Mon Sep 17 00:00:00 2001 From: kdu14933 Date: Mon, 20 Jan 2025 16:53:17 +0000 Subject: [PATCH 11/24] Added to list of aliases --- test/images/test_colourmap_mapping.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/images/test_colourmap_mapping.py b/test/images/test_colourmap_mapping.py index d15a888a..9a9bfbf4 100644 --- a/test/images/test_colourmap_mapping.py +++ b/test/images/test_colourmap_mapping.py @@ -72,7 +72,7 @@ def test_mapping_file_contains_all_colourmaps(self): # Checking the mapping file contains all colourmaps available in Matplotlib # From Matplotlib v3.9, they have introduced alias for common typos so # excluding these. - alias = {"grey", "gist_grey", "gist_yerg", "Grays"} + alias = {"grey", "grey_r","gist_grey", "gist_grey_r", "gist_yerg", "gist_yerg_r", "Grays", "Grays_r"} for colourmap in plt.colormaps(): if colourmap in alias: continue From 2f6bd61b73296147fc3bce170deb11ec4a3fd9f8 Mon Sep 17 00:00:00 2001 From: kdu14933 Date: Tue, 21 Jan 2025 11:08:40 +0000 Subject: [PATCH 12/24] Created a way to monitor the result of the echo uploads and remove the channels from the record if any of them fail. --- .../src/routes/ingest_data.py | 42 +++++++++++++++---- 1 file changed, 35 insertions(+), 7 deletions(-) diff --git a/operationsgateway_api/src/routes/ingest_data.py b/operationsgateway_api/src/routes/ingest_data.py index 00bec144..91426136 100644 --- a/operationsgateway_api/src/routes/ingest_data.py +++ b/operationsgateway_api/src/routes/ingest_data.py @@ -111,24 +111,52 @@ async def submit_hdf( record = Record(record_data) log.debug("Processing waveforms") + failed_waveform_uploads = [] for w in waveforms: waveform = Waveform(w) - waveform.insert_waveform() - waveform.create_thumbnail() - record.store_thumbnail(waveform) - + # Call insert_waveform and track failures + failed_upload = waveform.insert_waveform() # Returns channel name if failed + # if the upload to echo fails, don't process the waveform any further + if failed_upload: + failed_waveform_uploads.append(failed_upload) + else: + waveform.create_thumbnail() + record.store_thumbnail(waveform) # in the record not echo + + # This section distributes the Image.upload_image calls across + # the threads in the pool.It takes the image_instances list, + # applies the Image.upload_image function to each item, and collects + # the return values in upload_results. The map function blocks the main + # thread until all the tasks in the pool are complete. log.debug("Processing images") + failed_image_uploads = [] image_instances = [Image(i) for i in images] for image in image_instances: image.create_thumbnail() - record.store_thumbnail(image) - + record.store_thumbnail(image) # in the record not echo if len(image_instances) > 0: pool = ThreadPool(processes=Config.config.images.upload_image_threads) - pool.map(Image.upload_image, image_instances) + upload_results = pool.map(Image.upload_image, image_instances) + # Filter out successful uploads, collect only failed ones + failed_image_uploads = [channel for channel in upload_results if channel] pool.close() image_instances = None + # Combine failed channels from waveforms and images and remove them from the record + # Update the channel checker to reflect failed uploads + all_failed_upload_channels = failed_waveform_uploads + failed_image_uploads + for channel in all_failed_upload_channels: + record.remove_channel(channel) + if channel in checker_response["accepted_channels"]: + # Remove from accepted_channels and add to rejected_channels + checker_response["accepted_channels"].remove(channel) + checker_response["rejected_channels"][channel] = ["Upload to Echo failed"] + elif channel in checker_response["rejected_channels"]: + # Append the failure reason to the existing reasons + checker_response["rejected_channels"][channel].append( + "Upload to Echo failed", + ) + if stored_record and accept_type == "accept_merge": log.debug( "Record matching ID %s already exists in the database, updating existing" From 1a4dd989586101053f11cab211d56945b6a0b619 Mon Sep 17 00:00:00 2001 From: kdu14933 Date: Tue, 21 Jan 2025 11:09:16 +0000 Subject: [PATCH 13/24] added tests to check various db and echo related failures --- test/endpoints/test_submit_hdf.py | 193 ++++++++++++++++++++++++++++++ 1 file changed, 193 insertions(+) diff --git a/test/endpoints/test_submit_hdf.py b/test/endpoints/test_submit_hdf.py index e5d990a5..8dd397cd 100644 --- a/test/endpoints/test_submit_hdf.py +++ b/test/endpoints/test_submit_hdf.py @@ -1,8 +1,11 @@ +from unittest.mock import patch + from fastapi.testclient import TestClient import h5py import numpy as np import pytest +from operationsgateway_api.src.exceptions import DatabaseError, EchoS3Error from test.records.ingestion.create_test_hdf import create_test_hdf_file @@ -331,3 +334,193 @@ async def test_channel_multiple_reject_types( assert test_response.json() == expected_response assert test_response.status_code == 200 + + # The DB is but ECHO is not accessible before ingestion starts. + @pytest.mark.asyncio + async def test_echo_failure_on_start( + self, + reset_record_storage, + test_app: TestClient, + login_and_get_token, + ): + with patch( + "operationsgateway_api.src.records.echo_interface.EchoInterface.upload_file_object", + side_effect=EchoS3Error(), + ): + create_integration_test_hdf() + + test_file = "test.h5" + files = {"file": (test_file, open(test_file, "rb"))} + + test_response = test_app.post( + "/submit/hdf", + headers={"Authorization": f"Bearer {login_and_get_token}"}, + files=files, + ) + + assert test_response.status_code == 201 + + expected_response = { + "message": "Added as 20200407142816", + "response": { + "accepted_channels": ["PM-201-TJ-CAM-2-FWHMY"], + "rejected_channels": { + "PM-201-FE-CAM-2": [ + "Upload to Echo failed", + ], + "PM-201-HJ-PD": [ + "Upload to Echo failed", + ], + }, + "warnings": [], + }, + } + print("-----------------------") + print(test_response.json()) + print("-----------------------") + assert test_response.json() == expected_response + + # DB and ECHO become inaccessible mid-way through ingesting a NEW .h5 file + @pytest.mark.asyncio + async def test_partial_s3_and_db_upload_failure( + self, + reset_record_storage, + test_app: TestClient, + login_and_get_token, + ): + + # Define a side_effect function for the mock upload + def mock_upload_file_object(file_object, object_path): + # Extract channel name from the path + channel_name = object_path.split("/")[-1] + if channel_name == "PM-201-FE-CAM-2.json": + raise EchoS3Error() + + # Define a side_effect function for the database insert + def mock_insert_one(collection_name, data): + if "PM-201-HJ-PD" in data["channels"]: + raise DatabaseError() + + # Patch both the S3 upload method and the MongoDB insert_one method + with patch( + "operationsgateway_api.src.records.echo_interface.EchoInterface.upload_file_object", + side_effect=mock_upload_file_object, + ), patch( + "operationsgateway_api.src.mongo.interface.MongoDBInterface.insert_one", + side_effect=mock_insert_one, + ): + + # Create a test HDF file with the defined channels + create_integration_test_hdf() + + # Simulate the file upload + test_file = "test.h5" + files = {"file": (test_file, open(test_file, "rb"))} + + # Call the endpoint + test_response = test_app.post( + "/submit/hdf", + headers={"Authorization": f"Bearer {login_and_get_token}"}, + files=files, + ) + + # Check the status code + assert test_response.status_code == 500 + + assert test_response.json() == {"detail": "Database error"} + + # The DB is but ECHO is not accessible mid-way through ingesting a NEW .h5 file. + @pytest.mark.asyncio + async def test_partial_s3_upload_failure( + self, + reset_record_storage, + test_app: TestClient, + login_and_get_token, + ): + + # Track uploaded channels + uploaded_channels = [] + + # Define a side_effect function for the mock + def mock_upload_file_object(file_object, object_path): + # Extract channel name from the path + channel_name = object_path.split("/")[-1] + if channel_name == "PM-201-HJ-PD.json": # Simulate success for the first + uploaded_channels.append(channel_name) + else: + raise EchoS3Error() + + # Patch the S3 upload method + with patch( + "operationsgateway_api.src.records.echo_interface.EchoInterface.upload_file_object", + side_effect=mock_upload_file_object, + ): + # Create a test HDF file with the defined channels + create_integration_test_hdf() + + # Simulate the file upload + test_file = "test.h5" + files = {"file": (test_file, open(test_file, "rb"))} + + # Call the endpoint + test_response = test_app.post( + "/submit/hdf", + headers={"Authorization": f"Bearer {login_and_get_token}"}, + files=files, + ) + + # Check the status code + assert test_response.status_code == 201 + + expected_response = { + "message": "Added as 20200407142816", + "response": { + "accepted_channels": ["PM-201-HJ-PD", "PM-201-TJ-CAM-2-FWHMY"], + "rejected_channels": { + "PM-201-FE-CAM-2": [ + "Upload to Echo failed", + ], + }, + "warnings": [], + }, + } + assert test_response.json() == expected_response + + # ECHO is but the db is not accessible mid-way through ingesting a NEW .h5 file. + @pytest.mark.asyncio + async def test_partial_db_failure( + self, + reset_record_storage, + test_app: TestClient, + login_and_get_token, + ): + + # Define a side_effect function for the database insert + def mock_insert_one(collection_name, data): + if "PM-201-HJ-PD" in data["channels"]: + raise DatabaseError() + + # Patch both the MongoDB insert_one method + with patch( + "operationsgateway_api.src.mongo.interface.MongoDBInterface.insert_one", + side_effect=mock_insert_one, + ): + + # Create a test HDF file with the defined channels + create_integration_test_hdf() + + # Simulate the file upload + test_file = "test.h5" + files = {"file": (test_file, open(test_file, "rb"))} + + # Call the endpoint + test_response = test_app.post( + "/submit/hdf", + headers={"Authorization": f"Bearer {login_and_get_token}"}, + files=files, + ) + + # Check the status code + assert test_response.status_code == 500 + + assert test_response.json() == {"detail": "Database error"} From b89d73a2cea9e3eb4c36e2d729a989a9c37da99e Mon Sep 17 00:00:00 2001 From: kdu14933 Date: Tue, 21 Jan 2025 11:31:38 +0000 Subject: [PATCH 14/24] Linting --- test/images/test_colourmap_mapping.py | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/test/images/test_colourmap_mapping.py b/test/images/test_colourmap_mapping.py index 9a9bfbf4..92027462 100644 --- a/test/images/test_colourmap_mapping.py +++ b/test/images/test_colourmap_mapping.py @@ -72,7 +72,16 @@ def test_mapping_file_contains_all_colourmaps(self): # Checking the mapping file contains all colourmaps available in Matplotlib # From Matplotlib v3.9, they have introduced alias for common typos so # excluding these. - alias = {"grey", "grey_r","gist_grey", "gist_grey_r", "gist_yerg", "gist_yerg_r", "Grays", "Grays_r"} + alias = { + "grey", + "grey_r", + "gist_grey", + "gist_grey_r", + "gist_yerg", + "gist_yerg_r", + "Grays", + "Grays_r", + } for colourmap in plt.colormaps(): if colourmap in alias: continue From f7c53a46bfca55b2537e14f7b3668349183d250e Mon Sep 17 00:00:00 2001 From: kdu14933 Date: Tue, 21 Jan 2025 11:59:06 +0000 Subject: [PATCH 15/24] Update vulnerable dependencies --- poetry.lock | 367 +++++++++++++++++++++++++------------------------ pyproject.toml | 4 +- 2 files changed, 193 insertions(+), 178 deletions(-) diff --git a/poetry.lock b/poetry.lock index e5c93bcf..92888d70 100644 --- a/poetry.lock +++ b/poetry.lock @@ -135,32 +135,32 @@ uvloop = ["uvloop (>=0.15.2)"] [[package]] name = "boto3" -version = "1.35.95" +version = "1.36.2" description = "The AWS SDK for Python" optional = false python-versions = ">=3.8" files = [ - {file = "boto3-1.35.95-py3-none-any.whl", hash = "sha256:c81223488607457dacb7829ee0c99803c664593b34a2b0f86c71d421e7c3469a"}, - {file = "boto3-1.35.95.tar.gz", hash = "sha256:d5671226819f6a78e31b1f37bd60f194afb8203254a543d06bdfb76de7d79236"}, + {file = "boto3-1.36.2-py3-none-any.whl", hash = "sha256:76cfc9a705be46e8d22607efacc8d688c064f923d785a01c00b28e9a96425d1a"}, + {file = "boto3-1.36.2.tar.gz", hash = "sha256:fde1c29996b77274a60b7bc9f741525afa6267bb1716eb644a764fb7c124a0d2"}, ] 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a/operationsgateway_api/src/mongo/interface.py +++ b/operationsgateway_api/src/mongo/interface.py @@ -86,6 +86,7 @@ def find( ) @staticmethod + @mongodb_error_handling("query_to_list") async def query_to_list(query: Cursor) -> List[Dict[str, Any]]: """ Sends the query to MongoDB and converts the query results into a list From 5da3e018ea0d86d4b60f361182b38c51f2799583 Mon Sep 17 00:00:00 2001 From: kdu14933 Date: Thu, 30 Jan 2025 16:32:15 +0000 Subject: [PATCH 17/24] Removing redundant KeyError --- operationsgateway_api/src/records/record.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/operationsgateway_api/src/records/record.py b/operationsgateway_api/src/records/record.py index 2a8cad10..a343456a 100644 --- a/operationsgateway_api/src/records/record.py +++ b/operationsgateway_api/src/records/record.py @@ -114,8 +114,7 @@ def remove_channel(self, channel_name: str) -> None: log.info("Removing channel '%s' from record.", channel_name) del self.record.channels[channel_name] else: - log.warning("Channel '%s' not found in record.", channel_name) - raise KeyError(f"Channel '{channel_name}' does not exist in the record.") + log.error("Channel '%s' not found in record.", channel_name) async def find_existing_record(self) -> Union[RecordModel, None]: """ From b65af8e3bec1885c621b81731ca0bd806f9f47bb Mon Sep 17 00:00:00 2001 From: kdu14933 Date: Fri, 31 Jan 2025 16:06:50 +0000 Subject: [PATCH 18/24] Added passthrough for DatabaseErrors --- operationsgateway_api/src/mongo/mongo_error_handling.py | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/operationsgateway_api/src/mongo/mongo_error_handling.py b/operationsgateway_api/src/mongo/mongo_error_handling.py index ce98ffc0..32ac1356 100644 --- a/operationsgateway_api/src/mongo/mongo_error_handling.py +++ b/operationsgateway_api/src/mongo/mongo_error_handling.py @@ -1,8 +1,11 @@ from functools import wraps from inspect import iscoroutinefunction +import logging from operationsgateway_api.src.exceptions import DatabaseError +log = logging.getLogger() + def mongodb_error_handling(operation: str): """ @@ -17,7 +20,10 @@ def decorator(func): async def async_wrapper(*args, **kwargs): try: return await func(*args, **kwargs) + except DatabaseError: + raise # If it's already a DatabaseError, propagate it as-is except Exception as exc: + log.error("Database operation: %s failed", operation) raise DatabaseError( f"Database operation failed during {operation}", ) from exc @@ -29,7 +35,10 @@ async def async_wrapper(*args, **kwargs): def sync_wrapper(*args, **kwargs): try: return func(*args, **kwargs) + except DatabaseError: + raise # If it's already a DatabaseError, propagate it as-is except Exception as exc: + log.error("Database operation: %s failed", operation) raise DatabaseError( f"Database operation failed during {operation}", ) from exc From f048abc1639b02d42f3094326a3f5bd4f40db94c Mon Sep 17 00:00:00 2001 From: kdu14933 Date: Fri, 31 Jan 2025 16:07:19 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PyJWT = "2.10.1" cryptography = "^43.0.1" python-ldap = "3.4.2" -boto3 = "^1.26.97" +boto3 = ">=1.26.97,<1.36.0" cron-converter = "^1.0.1" zeep = "^4.2.1" # Indirect dependency lxml 5.1.0 causes symbol not found in flat namespace '_exsltDateXpathCtxtRegister' error From 6d07ad42effbe716f69ffcb042820c524318cf85 Mon Sep 17 00:00:00 2001 From: kdu14933 Date: Mon, 3 Feb 2025 10:58:26 +0000 Subject: [PATCH 20/24] Updated tests for coverage --- test/mongo/test_mongo_error_handling.py | 59 ++++++++++++++++++++++--- 1 file changed, 53 insertions(+), 6 deletions(-) diff --git a/test/mongo/test_mongo_error_handling.py b/test/mongo/test_mongo_error_handling.py index aa458190..8f3ee6ee 100644 --- a/test/mongo/test_mongo_error_handling.py +++ b/test/mongo/test_mongo_error_handling.py @@ -3,9 +3,12 @@ from fastapi.testclient import TestClient import pytest +from operationsgateway_api.src.exceptions import DatabaseError +from operationsgateway_api.src.mongo.mongo_error_handling import mongodb_error_handling + class TestMongoDBErrorHandling: - @pytest.mark.asyncio + @pytest.mark.parametrize( "record_id, expected_status_code, expected_response", [ @@ -17,11 +20,8 @@ class TestMongoDBErrorHandling: ), ], ) - # This test simulates an exception being raised in the collection.find_one call - # (within interface.py), which the decorator should handle and produce a - # DatabaseError, ultimately flowing this back up to the user in the endpoint, - # producing a 500 - async def test_find_one_exception_in_interface( + @pytest.mark.asyncio + async def test_async_integration_failure( self, test_app: TestClient, login_and_get_token, @@ -29,6 +29,11 @@ async def test_find_one_exception_in_interface( expected_status_code, expected_response, ): + """This test simulates an exception being raised in the collection.find_one call + (within interface.py), which the decorator should handle and produce a + DatabaseError, ultimately flowing this back up to the user in the endpoint, + producing a 500""" + with patch( "operationsgateway_api.src.mongo.interface.MongoDBInterface.get_collection_object", ) as mock_get_collection_object: @@ -46,3 +51,45 @@ async def test_find_one_exception_in_interface( # Assert the status code and responseAsyncMock assert response.status_code == expected_status_code assert response.json() == expected_response + + @pytest.mark.asyncio + async def test_async_unit_success(self): + """Ensure the async decorator allows normal execution + if no exception occurs.""" + + @mongodb_error_handling("find_one") + async def mock_find_one(): + return {"key": "value"} + + result = await mock_find_one() + assert result == {"key": "value"} + + def test_sync_unit_failure(self): + """Test the sync version of the MongoDB error + handling decorator in isolation.""" + + @mongodb_error_handling("insert_one") + def mock_insert_one(): + raise Exception("Simulated database error") + + with patch( + "operationsgateway_api.src.mongo.mongo_error_handling.log", + ) as mock_log: + with pytest.raises(DatabaseError) as exc_info: + mock_insert_one() + + assert "Database operation failed during insert_one" in str(exc_info.value) + mock_log.error.assert_called_once_with( + "Database operation: %s failed", + "insert_one", + ) + + def test_sync_unit_success(self): + """Ensure the sync decorator allows normal execution if no exception occurs.""" + + @mongodb_error_handling("insert_one") + def mock_insert_one(): + return {"key": "value"} + + result = mock_insert_one() + assert result == {"key": "value"} From abfe6fdd26adf6141c1337e787a0661b33a92063 Mon Sep 17 00:00:00 2001 From: kdu14933 Date: Mon, 3 Feb 2025 11:46:37 +0000 Subject: [PATCH 21/24] Updated test to cover for propagated db errors. --- test/mongo/test_mongo_error_handling.py | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/test/mongo/test_mongo_error_handling.py b/test/mongo/test_mongo_error_handling.py index 8f3ee6ee..2c286e29 100644 --- a/test/mongo/test_mongo_error_handling.py +++ b/test/mongo/test_mongo_error_handling.py @@ -64,6 +64,19 @@ async def mock_find_one(): result = await mock_find_one() assert result == {"key": "value"} + @pytest.mark.asyncio + async def test_async_propagate_database_error(self): + """Ensure the async decorator does not wrap an existing DatabaseError.""" + + @mongodb_error_handling("find_one") + async def mock_find_one(): + raise DatabaseError("Simulated DatabaseError") + + with pytest.raises(DatabaseError) as exc_info: + await mock_find_one() + + assert "Simulated DatabaseError" in str(exc_info.value) + def test_sync_unit_failure(self): """Test the sync version of the MongoDB error handling decorator in isolation.""" @@ -93,3 +106,15 @@ def mock_insert_one(): result = mock_insert_one() assert result == {"key": "value"} + + def test_sync_propagate_database_error(self): + """Ensure the sync decorator does not wrap an existing DatabaseError.""" + + @mongodb_error_handling("insert_one") + def mock_insert_one(): + raise DatabaseError("Simulated DatabaseError") + + with pytest.raises(DatabaseError) as exc_info: + mock_insert_one() + + assert "Simulated DatabaseError" in str(exc_info.value) From fdc730965d33413e35a95f2bbcc6b55903226b4c Mon Sep 17 00:00:00 2001 From: kdu14933 Date: Mon, 3 Feb 2025 17:00:02 +0000 Subject: [PATCH 22/24] updated to working versions --- poetry.lock | 236 ++++++++++++++++++++++++++++------------------------ 1 file changed, 125 insertions(+), 111 deletions(-) diff --git a/poetry.lock b/poetry.lock index 37f05564..9fcbe87a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -173,13 +173,13 @@ crt = ["awscrt (==0.22.0)"] [[package]] name = "certifi" -version = "2025.1.31" +version = "2024.12.14" description = "Python package for providing Mozilla's CA Bundle." optional = false python-versions = ">=3.6" files = [ - {file = "certifi-2025.1.31-py3-none-any.whl", hash = "sha256:ca78db4565a652026a4db2bcdf68f2fb589ea80d0be70e03929ed730746b84fe"}, - {file = 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