From 99b5820ae6eff842fb0980a37083427236010319 Mon Sep 17 00:00:00 2001 From: brian Date: Mon, 6 Jan 2025 17:15:48 +0000 Subject: [PATCH 01/64] renamed module --- misc/generate_random_prediction.py | 4 ++-- misc/get_visual_communication.py | 2 +- misc/image_download.py | 4 ++-- misc/image_upload.py | 4 ++-- misc/image_upload_to_server.py | 4 ++-- misc/model_outputs_from_annotation.py | 2 +- misc/prediction_upload.py | 4 ++-- misc/total_annotated.py | 2 +- misc/total_documents.py | 2 +- model/src/main.py | 2 +- model/src/models/visual_communication.py | 2 +- other/transfer_images_mongo_minio.py | 4 ++-- pyproject.toml | 2 +- shared/{mongodb => docstore}/__init__.py | 0 shared/{mongodb => docstore}/src/__init__.py | 0 shared/{mongodb => docstore}/src/classes/__init__.py | 0 shared/{mongodb => docstore}/src/classes/angle.py | 0 shared/{mongodb => docstore}/src/classes/contact.py | 0 shared/{mongodb => docstore}/src/classes/data_model.py | 0 shared/{mongodb => docstore}/src/classes/distance.py | 0 shared/{mongodb => docstore}/src/classes/framing.py | 0 .../{mongodb => docstore}/src/classes/information_value.py | 0 shared/{mongodb => docstore}/src/classes/modality_color.py | 0 shared/{mongodb => docstore}/src/classes/modality_depth.py | 0 .../{mongodb => docstore}/src/classes/modality_lighting.py | 0 shared/{mongodb => docstore}/src/classes/model_data.py | 0 shared/{mongodb => docstore}/src/classes/point_of_view.py | 0 shared/{mongodb => docstore}/src/classes/salience.py | 0 .../src/classes/visual_communication.py | 2 +- shared/{mongodb => docstore}/src/classes/visual_syntax.py | 0 shared/{mongodb => docstore}/src/connect_mongodb.py | 0 shared/{mongodb => docstore}/src/count_documents.py | 0 shared/docstore/src/docstore_interface.py | 0 shared/{mongodb => docstore}/src/exceptions/__init__.py | 0 .../src/exceptions/no_document_found.py | 0 shared/{mongodb => docstore}/src/get_dataset.py | 0 .../{mongodb => docstore}/src/get_visual_communication.py | 4 ++-- shared/{mongodb => docstore}/src/list_names.py | 0 shared/{mongodb => docstore}/src/upsert_annotation.py | 2 +- shared/{mongodb => docstore}/src/upsert_prediction.py | 2 +- .../src/upsert_visual_communication.py | 2 +- web_ui/src/app/init_app.py | 6 +++--- web_ui/src/app/layout/labels.py | 2 +- web_ui/src/main.py | 2 +- 44 files changed, 30 insertions(+), 30 deletions(-) rename shared/{mongodb => docstore}/__init__.py (100%) rename shared/{mongodb => docstore}/src/__init__.py (100%) rename shared/{mongodb => docstore}/src/classes/__init__.py (100%) rename shared/{mongodb => docstore}/src/classes/angle.py (100%) rename shared/{mongodb => docstore}/src/classes/contact.py (100%) rename shared/{mongodb => docstore}/src/classes/data_model.py (100%) rename shared/{mongodb => docstore}/src/classes/distance.py (100%) rename shared/{mongodb => docstore}/src/classes/framing.py (100%) rename shared/{mongodb => docstore}/src/classes/information_value.py (100%) rename shared/{mongodb => docstore}/src/classes/modality_color.py (100%) rename shared/{mongodb => docstore}/src/classes/modality_depth.py (100%) rename shared/{mongodb => docstore}/src/classes/modality_lighting.py (100%) rename shared/{mongodb => docstore}/src/classes/model_data.py (100%) rename shared/{mongodb => docstore}/src/classes/point_of_view.py (100%) rename shared/{mongodb => docstore}/src/classes/salience.py (100%) rename shared/{mongodb => docstore}/src/classes/visual_communication.py (98%) rename shared/{mongodb => docstore}/src/classes/visual_syntax.py (100%) rename shared/{mongodb => docstore}/src/connect_mongodb.py (100%) rename shared/{mongodb => docstore}/src/count_documents.py (100%) create mode 100644 shared/docstore/src/docstore_interface.py rename shared/{mongodb => docstore}/src/exceptions/__init__.py (100%) rename shared/{mongodb => docstore}/src/exceptions/no_document_found.py (100%) rename shared/{mongodb => docstore}/src/get_dataset.py (100%) rename shared/{mongodb => docstore}/src/get_visual_communication.py (88%) rename shared/{mongodb => docstore}/src/list_names.py (100%) rename shared/{mongodb => docstore}/src/upsert_annotation.py (92%) rename shared/{mongodb => docstore}/src/upsert_prediction.py (92%) rename shared/{mongodb => docstore}/src/upsert_visual_communication.py (88%) diff --git a/misc/generate_random_prediction.py b/misc/generate_random_prediction.py index 3670fe9..080b9a8 100644 --- a/misc/generate_random_prediction.py +++ b/misc/generate_random_prediction.py @@ -5,8 +5,8 @@ from pathlib import Path from dotenv import load_dotenv from shared.datastore import Datastore -from shared.mongodb import connect_mongodb -from shared.mongodb.src.classes import VisualCommunication +from shared.docstore import connect_mongodb +from shared.docstore.src.classes import VisualCommunication from shared.utils import check_env, setup_logging from web_ui.src.main import NECESSARY_ENV_VAR_LIST diff --git a/misc/get_visual_communication.py b/misc/get_visual_communication.py index 9643a6c..2341957 100644 --- a/misc/get_visual_communication.py +++ b/misc/get_visual_communication.py @@ -5,7 +5,7 @@ from pathlib import Path from dotenv import load_dotenv from shared.datastore import Datastore -from shared.mongodb import connect_mongodb, get_visual_communication +from shared.docstore import connect_mongodb, get_visual_communication from shared.utils import check_env, setup_logging from web_ui.src.main import NECESSARY_ENV_VAR_LIST diff --git a/misc/image_download.py b/misc/image_download.py index cc8f28f..760560e 100644 --- a/misc/image_download.py +++ b/misc/image_download.py @@ -5,8 +5,8 @@ from pathlib import Path from dotenv import load_dotenv -from shared.mongodb import connect_mongodb -from shared.mongodb.classes import VisualCommunication +from shared.docstore import connect_mongodb +from shared.docstore.classes import VisualCommunication if __name__ == '__main__': # prepare env vars diff --git a/misc/image_upload.py b/misc/image_upload.py index 9db6652..9798c83 100644 --- a/misc/image_upload.py +++ b/misc/image_upload.py @@ -6,8 +6,8 @@ from dotenv import load_dotenv from pymongo.errors import DuplicateKeyError from shared.datastore import Datastore -from shared.mongodb import connect_mongodb -from shared.mongodb.src.classes import VisualCommunication +from shared.docstore import connect_mongodb +from shared.docstore.src.classes import VisualCommunication from shared.utils import check_env, setup_logging from web_ui.src.main import NECESSARY_ENV_VAR_LIST diff --git a/misc/image_upload_to_server.py b/misc/image_upload_to_server.py index 2333c27..8f401cb 100644 --- a/misc/image_upload_to_server.py +++ b/misc/image_upload_to_server.py @@ -6,8 +6,8 @@ from dotenv import load_dotenv from pymongo.errors import DuplicateKeyError from shared.datastore import Datastore -from shared.mongodb import connect_mongodb -from shared.mongodb.src.classes import VisualCommunication +from shared.docstore import connect_mongodb +from shared.docstore.src.classes import VisualCommunication from shared.utils import check_env, setup_logging from web_ui.src.main import NECESSARY_ENV_VAR_LIST diff --git a/misc/model_outputs_from_annotation.py b/misc/model_outputs_from_annotation.py index 1406b48..34d90e5 100644 --- a/misc/model_outputs_from_annotation.py +++ b/misc/model_outputs_from_annotation.py @@ -1,4 +1,4 @@ -from shared.mongodb.classes import ModelData +from shared.docstore.classes import ModelData if __name__ == '__main__': # instantiate data object diff --git a/misc/prediction_upload.py b/misc/prediction_upload.py index 2506fe7..e29cc74 100644 --- a/misc/prediction_upload.py +++ b/misc/prediction_upload.py @@ -5,8 +5,8 @@ from pathlib import Path from dotenv import load_dotenv from shared.datastore import Datastore -from shared.mongodb import connect_mongodb, upsert_prediction -from shared.mongodb.src.classes import VisualCommunication +from shared.docstore import connect_mongodb, upsert_prediction +from shared.docstore.src.classes import VisualCommunication from shared.utils import check_env, setup_logging from web_ui.src.main import NECESSARY_ENV_VAR_LIST diff --git a/misc/total_annotated.py b/misc/total_annotated.py index 66f6b04..a60bbd1 100644 --- a/misc/total_annotated.py +++ b/misc/total_annotated.py @@ -5,7 +5,7 @@ from pathlib import Path from dotenv import load_dotenv -from shared.mongodb import connect_mongodb, count_documents +from shared.docstore import connect_mongodb, count_documents if __name__ == '__main__': # prepare env vars diff --git a/misc/total_documents.py b/misc/total_documents.py index fa8b1c8..29c3750 100644 --- a/misc/total_documents.py +++ b/misc/total_documents.py @@ -5,7 +5,7 @@ from pathlib import Path from dotenv import load_dotenv -from shared.mongodb import connect_mongodb, count_documents +from shared.docstore import connect_mongodb, count_documents if __name__ == '__main__': # prepare env vars diff --git a/model/src/main.py b/model/src/main.py index 91d22c2..9b4cb3d 100644 --- a/model/src/main.py +++ b/model/src/main.py @@ -10,7 +10,7 @@ from tqdm import tqdm from utils import DEVICE, VCDADataset, load_model from shared.datastore import Datastore -from shared.mongodb.classes import ModelData +from shared.docstore.classes import ModelData from shared.utils import setup_logging if __name__ == '__main__': diff --git a/model/src/models/visual_communication.py b/model/src/models/visual_communication.py index 256203b..071d69f 100644 --- a/model/src/models/visual_communication.py +++ b/model/src/models/visual_communication.py @@ -4,7 +4,7 @@ from __future__ import annotations from torch import nn -from shared.mongodb.src.classes import ModelData +from shared.docstore.src.classes import ModelData from .angle import AngleTail from .contact import ContactTail diff --git a/other/transfer_images_mongo_minio.py b/other/transfer_images_mongo_minio.py index 8b8033c..482f5aa 100644 --- a/other/transfer_images_mongo_minio.py +++ b/other/transfer_images_mongo_minio.py @@ -10,8 +10,8 @@ from dotenv import load_dotenv from pymongo.collection import Collection from shared.datastore import Datastore -from shared.mongodb import connect_mongodb -from shared.mongodb.src.classes import VisualCommunication +from shared.docstore import connect_mongodb +from shared.docstore.src.classes import VisualCommunication from shared.utils import check_env, setup_logging from web_ui.src.main import NECESSARY_ENV_VAR_LIST diff --git a/pyproject.toml b/pyproject.toml index 314593d..ae87d37 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -119,7 +119,7 @@ module = "models.*" ignore_missing_imports = true [[tool.mypy.overrides]] -module = "shared.mongodb.*" +module = "shared.docstore.*" ignore_missing_imports = true [[tool.mypy.overrides]] diff --git a/shared/mongodb/__init__.py b/shared/docstore/__init__.py similarity index 100% rename from shared/mongodb/__init__.py rename to shared/docstore/__init__.py diff --git a/shared/mongodb/src/__init__.py b/shared/docstore/src/__init__.py similarity index 100% rename from shared/mongodb/src/__init__.py rename to shared/docstore/src/__init__.py diff --git a/shared/mongodb/src/classes/__init__.py b/shared/docstore/src/classes/__init__.py similarity index 100% rename from shared/mongodb/src/classes/__init__.py rename to shared/docstore/src/classes/__init__.py diff --git a/shared/mongodb/src/classes/angle.py b/shared/docstore/src/classes/angle.py similarity index 100% rename from shared/mongodb/src/classes/angle.py rename to shared/docstore/src/classes/angle.py diff --git a/shared/mongodb/src/classes/contact.py b/shared/docstore/src/classes/contact.py similarity index 100% rename from shared/mongodb/src/classes/contact.py rename to shared/docstore/src/classes/contact.py diff --git a/shared/mongodb/src/classes/data_model.py b/shared/docstore/src/classes/data_model.py similarity index 100% rename from shared/mongodb/src/classes/data_model.py rename to shared/docstore/src/classes/data_model.py diff --git a/shared/mongodb/src/classes/distance.py b/shared/docstore/src/classes/distance.py similarity index 100% rename from shared/mongodb/src/classes/distance.py rename to shared/docstore/src/classes/distance.py diff --git a/shared/mongodb/src/classes/framing.py b/shared/docstore/src/classes/framing.py similarity index 100% rename from shared/mongodb/src/classes/framing.py rename to shared/docstore/src/classes/framing.py diff --git a/shared/mongodb/src/classes/information_value.py b/shared/docstore/src/classes/information_value.py similarity index 100% rename from shared/mongodb/src/classes/information_value.py rename to shared/docstore/src/classes/information_value.py diff --git a/shared/mongodb/src/classes/modality_color.py b/shared/docstore/src/classes/modality_color.py similarity index 100% rename from shared/mongodb/src/classes/modality_color.py rename to shared/docstore/src/classes/modality_color.py diff --git a/shared/mongodb/src/classes/modality_depth.py b/shared/docstore/src/classes/modality_depth.py similarity index 100% rename from shared/mongodb/src/classes/modality_depth.py rename to shared/docstore/src/classes/modality_depth.py diff --git a/shared/mongodb/src/classes/modality_lighting.py b/shared/docstore/src/classes/modality_lighting.py similarity index 100% rename from shared/mongodb/src/classes/modality_lighting.py rename to shared/docstore/src/classes/modality_lighting.py diff --git a/shared/mongodb/src/classes/model_data.py b/shared/docstore/src/classes/model_data.py similarity index 100% rename from shared/mongodb/src/classes/model_data.py rename to shared/docstore/src/classes/model_data.py diff --git a/shared/mongodb/src/classes/point_of_view.py b/shared/docstore/src/classes/point_of_view.py similarity index 100% rename from shared/mongodb/src/classes/point_of_view.py rename to shared/docstore/src/classes/point_of_view.py diff --git a/shared/mongodb/src/classes/salience.py b/shared/docstore/src/classes/salience.py similarity index 100% rename from shared/mongodb/src/classes/salience.py rename to shared/docstore/src/classes/salience.py diff --git a/shared/mongodb/src/classes/visual_communication.py b/shared/docstore/src/classes/visual_communication.py similarity index 98% rename from shared/mongodb/src/classes/visual_communication.py rename to shared/docstore/src/classes/visual_communication.py index 2291e6b..e39afc2 100755 --- a/shared/mongodb/src/classes/visual_communication.py +++ b/shared/docstore/src/classes/visual_communication.py @@ -13,7 +13,7 @@ from pydantic import BaseModel, ConfigDict from pymongo.collection import Collection from shared.datastore import Datastore -from shared.mongodb.src.classes import ModelData +from shared.docstore.src.classes import ModelData class VisualCommunication(BaseModel): diff --git a/shared/mongodb/src/classes/visual_syntax.py b/shared/docstore/src/classes/visual_syntax.py similarity index 100% rename from shared/mongodb/src/classes/visual_syntax.py rename to shared/docstore/src/classes/visual_syntax.py diff --git a/shared/mongodb/src/connect_mongodb.py b/shared/docstore/src/connect_mongodb.py similarity index 100% rename from shared/mongodb/src/connect_mongodb.py rename to shared/docstore/src/connect_mongodb.py diff --git a/shared/mongodb/src/count_documents.py b/shared/docstore/src/count_documents.py similarity index 100% rename from shared/mongodb/src/count_documents.py rename to shared/docstore/src/count_documents.py diff --git a/shared/docstore/src/docstore_interface.py b/shared/docstore/src/docstore_interface.py new file mode 100644 index 0000000..e69de29 diff --git a/shared/mongodb/src/exceptions/__init__.py b/shared/docstore/src/exceptions/__init__.py similarity index 100% rename from shared/mongodb/src/exceptions/__init__.py rename to shared/docstore/src/exceptions/__init__.py diff --git a/shared/mongodb/src/exceptions/no_document_found.py b/shared/docstore/src/exceptions/no_document_found.py similarity index 100% rename from shared/mongodb/src/exceptions/no_document_found.py rename to shared/docstore/src/exceptions/no_document_found.py diff --git a/shared/mongodb/src/get_dataset.py b/shared/docstore/src/get_dataset.py similarity index 100% rename from shared/mongodb/src/get_dataset.py rename to shared/docstore/src/get_dataset.py diff --git a/shared/mongodb/src/get_visual_communication.py b/shared/docstore/src/get_visual_communication.py similarity index 88% rename from shared/mongodb/src/get_visual_communication.py rename to shared/docstore/src/get_visual_communication.py index 57a4071..5c85a88 100755 --- a/shared/mongodb/src/get_visual_communication.py +++ b/shared/docstore/src/get_visual_communication.py @@ -6,8 +6,8 @@ import logging from pymongo.collection import Collection -from shared.mongodb.src.classes import VisualCommunication -from shared.mongodb.src.exceptions import NoDocumentFoundException +from shared.docstore.src.classes import VisualCommunication +from shared.docstore.src.exceptions import NoDocumentFoundException def get_visual_communication( diff --git a/shared/mongodb/src/list_names.py b/shared/docstore/src/list_names.py similarity index 100% rename from shared/mongodb/src/list_names.py rename to shared/docstore/src/list_names.py diff --git a/shared/mongodb/src/upsert_annotation.py b/shared/docstore/src/upsert_annotation.py similarity index 92% rename from shared/mongodb/src/upsert_annotation.py rename to shared/docstore/src/upsert_annotation.py index d7c8c4d..4eec4c0 100755 --- a/shared/mongodb/src/upsert_annotation.py +++ b/shared/docstore/src/upsert_annotation.py @@ -4,7 +4,7 @@ import logging from pymongo.collection import Collection -from shared.mongodb.src.classes import ModelData +from shared.docstore.src.classes import ModelData def upsert_annotation( diff --git a/shared/mongodb/src/upsert_prediction.py b/shared/docstore/src/upsert_prediction.py similarity index 92% rename from shared/mongodb/src/upsert_prediction.py rename to shared/docstore/src/upsert_prediction.py index 7f1ca8f..81378a8 100755 --- a/shared/mongodb/src/upsert_prediction.py +++ b/shared/docstore/src/upsert_prediction.py @@ -4,7 +4,7 @@ import logging from pymongo.collection import Collection -from shared.mongodb.src.classes import ModelData +from shared.docstore.src.classes import ModelData def upsert_prediction( diff --git a/shared/mongodb/src/upsert_visual_communication.py b/shared/docstore/src/upsert_visual_communication.py similarity index 88% rename from shared/mongodb/src/upsert_visual_communication.py rename to shared/docstore/src/upsert_visual_communication.py index 8ea39af..b5a863c 100755 --- a/shared/mongodb/src/upsert_visual_communication.py +++ b/shared/docstore/src/upsert_visual_communication.py @@ -2,7 +2,7 @@ from __future__ import annotations from pymongo.collection import Collection -from shared.mongodb.src.classes import VisualCommunication +from shared.docstore.src.classes import VisualCommunication def upsert_visual_communication( diff --git a/web_ui/src/app/init_app.py b/web_ui/src/app/init_app.py index e479e74..ce2ade3 100644 --- a/web_ui/src/app/init_app.py +++ b/web_ui/src/app/init_app.py @@ -12,9 +12,9 @@ from pydantic import ValidationError from pymongo.collection import Collection from shared.datastore import Datastore -from shared.mongodb import count_documents, get_visual_communication, upsert_annotation -from shared.mongodb.src.classes import ModelData, VisualCommunication -from shared.mongodb.src.exceptions import NoDocumentFoundException +from shared.docstore import count_documents, get_visual_communication, upsert_annotation +from shared.docstore.src.classes import ModelData, VisualCommunication +from shared.docstore.src.exceptions import NoDocumentFoundException from .layout import app_layout diff --git a/web_ui/src/app/layout/labels.py b/web_ui/src/app/layout/labels.py index a4ec822..7021829 100644 --- a/web_ui/src/app/layout/labels.py +++ b/web_ui/src/app/layout/labels.py @@ -3,7 +3,7 @@ from __future__ import annotations import dash_mantine_components as dmc from dash import dcc, html -from shared.mongodb.classes import ( +from shared.docstore.classes import ( AngleData, ContactData, DistanceData, diff --git a/web_ui/src/main.py b/web_ui/src/main.py index 5546b47..88a1d09 100644 --- a/web_ui/src/main.py +++ b/web_ui/src/main.py @@ -5,7 +5,7 @@ from __future__ import annotations import os from shared.datastore import Datastore -from shared.mongodb import connect_mongodb +from shared.docstore import connect_mongodb from shared.utils import check_env, setup_logging from .app import init_app -- 2.54.0 From 0c762b55b22c37d20eaaf3003a7eec0c79c26a48 Mon Sep 17 00:00:00 2001 From: brian Date: Mon, 6 Jan 2025 17:32:33 +0000 Subject: [PATCH 02/64] corrected comment spelling --- shared/datastore/src/datastore_minio.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/shared/datastore/src/datastore_minio.py b/shared/datastore/src/datastore_minio.py index 8771740..d12edcb 100644 --- a/shared/datastore/src/datastore_minio.py +++ b/shared/datastore/src/datastore_minio.py @@ -30,7 +30,7 @@ class DatastoreMinio(DatastoreInterface): 'MINIO_BUCKET_NAME', } check_env(var_list) - # prepare interval variables + # prepare internal variables self._client: Minio | None = None self._bucket_name: str | None = None -- 2.54.0 From cbedc395bc6cd3cac2e00e42219636d2c4f24445 Mon Sep 17 00:00:00 2001 From: brian Date: Tue, 7 Jan 2025 17:48:10 +0000 Subject: [PATCH 03/64] corrected spelling --- shared/datastore/tests/unit/datastore_minio_test.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/shared/datastore/tests/unit/datastore_minio_test.py b/shared/datastore/tests/unit/datastore_minio_test.py index 2ce55c3..77f93d9 100644 --- a/shared/datastore/tests/unit/datastore_minio_test.py +++ b/shared/datastore/tests/unit/datastore_minio_test.py @@ -1,4 +1,4 @@ -"""Definition of unittests for Datastore instantiation.""" +"""Definition of unittests for Datastore Minio implementation.""" import os from hashlib import md5 -- 2.54.0 From ac6a305da8876dac8a649385263528453d7ef350 Mon Sep 17 00:00:00 2001 From: brian Date: Tue, 7 Jan 2025 17:50:17 +0000 Subject: [PATCH 04/64] fixed spelling --- shared/datastore/tests/unit/datastore_minio_test.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/shared/datastore/tests/unit/datastore_minio_test.py b/shared/datastore/tests/unit/datastore_minio_test.py index 77f93d9..e23ee67 100644 --- a/shared/datastore/tests/unit/datastore_minio_test.py +++ b/shared/datastore/tests/unit/datastore_minio_test.py @@ -13,7 +13,7 @@ from urllib3 import BaseHTTPResponse from shared.datastore.src.datastore_minio import DatastoreMinio -class TestDatastoreMinioInstantiation(TestCase): +class TestDatastoreMinioImplementation(TestCase): def setUp(self): # define relevant env vars -- 2.54.0 From 090a1cd8bb4071bd255cb7f89b70ec685c437741 Mon Sep 17 00:00:00 2001 From: brian Date: Fri, 28 Feb 2025 22:24:52 +0000 Subject: [PATCH 05/64] added integration tests and repository pattern for image, model and visual communication DTOs --- shared/docstore/src/docstore_interface.py | 83 ++++ shared/docstore/src/docstore_mongo.py | 241 ++++++++++ .../tests/unit/docstore_mongo_test.py | 45 ++ shared/repositories/__init__.py | 8 + shared/repositories/src/__init__.py | 3 + shared/repositories/src/dto/__init__.py | 7 + .../src/dto/bytes_io_pydantic_annotation.py | 37 ++ .../src/dto/hexadecimal_string.py | 24 + .../hexadecimal_string_pydantic_annotation.py | 38 ++ shared/repositories/src/dto/image_data.py | 16 + .../src/dto/image_pydantic_annotation.py | 37 ++ shared/repositories/src/dto/model_data.py | 60 +++ .../src/dto/type_checking_base_model.py | 12 + .../dto/visual_communication_data/__init__.py | 2 + .../visual_communication_data/angle_values.py | 11 + .../contact_values.py | 10 + .../distance_values.py | 11 + .../framing_values.py | 12 + .../information_value_values.py | 11 + .../modality_color_values.py | 11 + .../modality_depth_values.py | 11 + .../modality_lighting_values.py | 11 + .../point_of_view_values.py | 10 + .../salience_values.py | 13 + .../visual_communication_data/values_model.py | 60 +++ .../visual_communication_data.py | 14 + .../visual_communication_values.py | 49 ++ .../visual_syntax_values.py | 26 + shared/repositories/src/image_repository.py | 74 +++ .../src/implementations/__init__.py | 2 + .../implementations/minio_implementation.py | 186 ++++++++ .../implementations/mongo_implementation.py | 145 ++++++ .../repositories/src/interfaces/__init__.py | 4 + .../src/interfaces/database_interface.py | 28 ++ .../src/interfaces/image_interface.py | 26 + .../src/interfaces/model_interface.py | 26 + .../visual_communication_interface.py | 26 + shared/repositories/src/model_repository.py | 77 +++ .../src/visual_communication_repository.py | 56 +++ .../tests/integration/conftest.py | 444 ++++++++++++++++++ .../integration/image_repository_test.py | 156 ++++++ .../integration/minio_implementation_test.py | 133 ++++++ .../integration/model_repository_test.py | 136 ++++++ .../integration/mongo_implementation_test.py | 113 +++++ .../visual_communication_repository_test.py | 125 +++++ 45 files changed, 2630 insertions(+) create mode 100644 shared/docstore/src/docstore_mongo.py create mode 100644 shared/docstore/tests/unit/docstore_mongo_test.py create mode 100644 shared/repositories/__init__.py create mode 100644 shared/repositories/src/__init__.py create mode 100644 shared/repositories/src/dto/__init__.py create mode 100644 shared/repositories/src/dto/bytes_io_pydantic_annotation.py create mode 100644 shared/repositories/src/dto/hexadecimal_string.py create mode 100644 shared/repositories/src/dto/hexadecimal_string_pydantic_annotation.py create mode 100644 shared/repositories/src/dto/image_data.py create mode 100644 shared/repositories/src/dto/image_pydantic_annotation.py create mode 100644 shared/repositories/src/dto/model_data.py create mode 100644 shared/repositories/src/dto/type_checking_base_model.py create mode 100644 shared/repositories/src/dto/visual_communication_data/__init__.py create mode 100644 shared/repositories/src/dto/visual_communication_data/angle_values.py create mode 100644 shared/repositories/src/dto/visual_communication_data/contact_values.py create mode 100644 shared/repositories/src/dto/visual_communication_data/distance_values.py create mode 100644 shared/repositories/src/dto/visual_communication_data/framing_values.py create mode 100644 shared/repositories/src/dto/visual_communication_data/information_value_values.py create mode 100644 shared/repositories/src/dto/visual_communication_data/modality_color_values.py create mode 100644 shared/repositories/src/dto/visual_communication_data/modality_depth_values.py create mode 100644 shared/repositories/src/dto/visual_communication_data/modality_lighting_values.py create mode 100644 shared/repositories/src/dto/visual_communication_data/point_of_view_values.py create mode 100644 shared/repositories/src/dto/visual_communication_data/salience_values.py create mode 100644 shared/repositories/src/dto/visual_communication_data/values_model.py create mode 100644 shared/repositories/src/dto/visual_communication_data/visual_communication_data.py create mode 100644 shared/repositories/src/dto/visual_communication_data/visual_communication_values.py create mode 100644 shared/repositories/src/dto/visual_communication_data/visual_syntax_values.py create mode 100644 shared/repositories/src/image_repository.py create mode 100644 shared/repositories/src/implementations/__init__.py create mode 100644 shared/repositories/src/implementations/minio_implementation.py create mode 100644 shared/repositories/src/implementations/mongo_implementation.py create mode 100644 shared/repositories/src/interfaces/__init__.py create mode 100644 shared/repositories/src/interfaces/database_interface.py create mode 100644 shared/repositories/src/interfaces/image_interface.py create mode 100644 shared/repositories/src/interfaces/model_interface.py create mode 100644 shared/repositories/src/interfaces/visual_communication_interface.py create mode 100644 shared/repositories/src/model_repository.py create mode 100644 shared/repositories/src/visual_communication_repository.py create mode 100644 shared/repositories/tests/integration/conftest.py create mode 100644 shared/repositories/tests/integration/image_repository_test.py create mode 100644 shared/repositories/tests/integration/minio_implementation_test.py create mode 100644 shared/repositories/tests/integration/model_repository_test.py create mode 100644 shared/repositories/tests/integration/mongo_implementation_test.py create mode 100644 shared/repositories/tests/integration/visual_communication_repository_test.py diff --git a/shared/docstore/src/docstore_interface.py b/shared/docstore/src/docstore_interface.py index e69de29..eba250c 100644 --- a/shared/docstore/src/docstore_interface.py +++ b/shared/docstore/src/docstore_interface.py @@ -0,0 +1,83 @@ +"""Definition of docstore interface.""" + +from __future__ import annotations + +from abc import ABC, abstractmethod + +from shared.docstore.src.classes import ModelData, VisualCommunication + + +class DocstoreInterface(ABC): + """Docstore interface class.""" + + @abstractmethod + def connect( + self, + ) -> None: + pass + + @abstractmethod + def close( + self, + ) -> None: + pass + + @abstractmethod + def __enter__( + self, + ) -> DocstoreInterface: + pass + + @abstractmethod + def __exit__( + self, + exc_type, + exc_val, + exc_tb, + ) -> None: + pass + + @abstractmethod + def count_documents( + self, + only_with_annotation: bool, + ) -> int: + pass + + @abstractmethod + def list_names( + self, + only_with_annotation: bool, + ) -> list[str]: + pass + + @abstractmethod + def upsert_visual_comminucations( + self, + visual_communication_list: list[VisualCommunication], + ) -> None: + pass + + @abstractmethod + def upsert_annotations( + self, + visual_communication_name: str, + annotations: ModelData, + ) -> None: + pass + + @abstractmethod + def upsert_prediction( + self, + visual_communication_name: str, + predictions: ModelData, + ) -> None: + pass + + @abstractmethod + def get_visual_communication( + self, + with_annotation: bool, + name: str | None = None, + ) -> VisualCommunication: + pass diff --git a/shared/docstore/src/docstore_mongo.py b/shared/docstore/src/docstore_mongo.py new file mode 100644 index 0000000..9b83a6e --- /dev/null +++ b/shared/docstore/src/docstore_mongo.py @@ -0,0 +1,241 @@ +"""Definition of docstore mongodb implementation.""" + +from __future__ import annotations + +import logging +import os +from typing import Any + +from pymongo import MongoClient +from pymongo.collection import Collection +from pymongo.database import Database + +from shared.utils import check_env + +from .classes import ModelData, VisualCommunication +from .docstore_interface import DocstoreInterface +from .exceptions import NoDocumentFoundException + + +class DocstoreMongo(DocstoreInterface): + """Docstore interface.""" + + def __init__(self): + # ensure necessary env vars available + var_list = { + 'MONGO_ENDPOINT', + 'MONGO_DB', + 'MONGO_COLLECTION', + } + check_env(var_list) + # prepare internal variables + self.client: MongoClient | None = None + self.db: Database | None = None + self.collection: Collection | None = None + + def connect(self) -> None: + """Connect to Mongo server.""" + # prepare arguments + mongo_endpoint = str(os.getenv('MONGO_ENDPOINT')) + mongo_database = str(os.getenv('MONGO_DB')) + mongo_collection = str(os.getenv('MONGO_COLLECTION')) + # connect client + client = MongoClient(mongo_endpoint) + database = client[mongo_database] + collection = database[mongo_collection] + # set unique index on 'name' + collection.create_index(keys='name', unique=True) + # persist state + self._client = client + self._database = database + self._collection = collection + + def close(self) -> None: + """Close connection to Mongo server.""" + self._client.close() + self._client = None + self._database = None + self._collection = None + + def __enter__(self) -> DocstoreMongo: + self.connect() + return self + + def __exit__(self, exc_type, exc_val, exc_tb) -> None: + if any( + ( + exc_type is not None, + exc_val is not None, + exc_tb is not None, + ), + ): + logging.error('error while exiting context') + self.close() + + def count_documents( + self, + only_with_annotation: bool = False, + ): + """Get the total number of Visual Communication documents matching the + filter.""" + assert isinstance(only_with_annotation, bool) + # build query + query = {} + if only_with_annotation: + query['annotation'] = {'$ne': None} + # execute query + num_docs = self._collection.count_documents(filter=query) + return num_docs + + def list_names( + self, + only_with_annotation: bool, + ) -> list[str]: + """List names of Visual Communication documents that match the + filters.""" + assert isinstance(only_with_annotation, bool) + assert isinstance(self._collection, Collection) + # build query + query = {} + if only_with_annotation: + query['annotation'] = {'$ne': None} + # execute query + res_list = self._collection.find( + filter=query, + projection={ + '_id': False, # don't get id + 'name': True, # include document name + }, + ) + # extract info + name_list = [elem['name'] for elem in res_list] + return name_list + + def upsert_visual_comminucations( + self, + visual_communication_list: list[VisualCommunication], + ) -> None: + """Upsert Visual Communication document in the database.""" + assert isinstance(visual_communication_list, list) + assert all( + isinstance(vis_com, VisualCommunication) + for vis_com in visual_communication_list + ) + assert isinstance(self._collection, Collection) + # convert to dict + doc_list = [vis_com.model_dump() for vis_com in visual_communication_list] + # insert documents + response = self._collection.insert_many(documents=doc_list) + # check response + if not response.acknowledged: + raise OSError('failed inserting documents') + + def upsert_annotations( + self, + visual_communication_name: str, + annotations: ModelData, + ) -> None: + """Upsert annotation for the document with matching name.""" + assert isinstance(visual_communication_name, str) + assert len(visual_communication_name) > 0 + assert isinstance(annotations, ModelData) + assert isinstance(self._collection, Collection) + # convert to dict + doc = annotations.model_dump() + # build query + query = { + 'name': visual_communication_name, + } + update = { + '$set': { + 'annotation': doc, + }, + } + # execute query + res = self._collection.update_one( + filter=query, + update=update, + upsert=True, + ) + # check response + if not res.acknowledged: + raise OSError( + f'failed upserting annotations for {visual_communication_name}', + ) + + def upsert_prediction( + self, + visual_communication_name: str, + predictions: ModelData, + ) -> None: + """Upsert prediction for the document with matching name.""" + assert isinstance(visual_communication_name, str) + assert len(visual_communication_name) > 0 + assert isinstance(annotations, ModelData) + assert isinstance(self._collection, Collection) + # convert to dict + doc = predictions.model_dump() + # build query + query = { + 'name': visual_communication_name, + } + update = { + '$set': { + 'prediction': doc, + }, + } + # execute query + res = self._collection.update_one( + filter=query, + update=update, + upsert=True, + ) + # check response + if not res.acknowledged: + raise OSError( + f'failed upserting predictions for {visual_communication_name}', + ) + + def get_visual_communication( + self, + with_annotation: bool = False, + name: str | None = None, + ) -> VisualCommunication: + """Get a random Visual Communication document that matches annotation + filter. + + If name is not specified, a random document matching filter is + returned. + """ + assert isinstance(with_annotation, bool) + if name is not None: + assert isinstance(name, str) + assert len(name) > 0 + # build query + query: dict[str, Any] = {} + if with_annotation: + query['annotation'] = {'$ne': None} + else: + query['annotation'] = {'$eq': None} + if name is not None: + query['name'] = {'$eq': name} + # execute query + res_list = self._collection.aggregate( + pipeline=[ + { + '$match': query, # find using filters + }, + { + '$sample': { + 'size': 1, # get one random + }, + }, + ], + ) + doc_list = list(res_list) + # check result + if len(doc_list) == 0: + raise NoDocumentFoundException() + # convert + vis_com = VisualCommunication.model_validate(doc_list[0]) + return vis_com diff --git a/shared/docstore/tests/unit/docstore_mongo_test.py b/shared/docstore/tests/unit/docstore_mongo_test.py new file mode 100644 index 0000000..6e79b39 --- /dev/null +++ b/shared/docstore/tests/unit/docstore_mongo_test.py @@ -0,0 +1,45 @@ +"""Definition of unittests for Docstore MongoDB implementation.""" + +import os +from unittest import TestCase +from unittest.mock import MagicMock + +from pymongo import MongoClient +from pymongo.collection import Collection +from pymongo.database import Database + +from shared.docstore.src.docstore_mongo import DocstoreMongo + + +class TestDocstoreMongoImplementation(TestCase): + + def setUp(self): + # define relevant env vars + self.env_var_map = { + 'MONGO_ENDPOINT': '192.168.1.2:27017', + 'MONGO_DB': 'visual_critical_discourse_analysis', + 'MONGO_COLLECTION': 'test-collection', + } + # set env vars + for key, val in self.env_var_map.items(): + os.environ[key] = val + # set other variables + self.mongo_client_mock = MagicMock(MongoClient) + self.mongo_database_mock = MagicMock(Database) + self.mongo_collection_mock = MagicMock(Collection) + + def tearDown(self): + # clear env vars + for key in self.env_var_map: + _ = os.environ.pop(key, default=None) + # reset reuseable mocks + self.mongo_client_mock.reset_mock() + self.mongo_database_mock.reset_mock() + self.mongo_collection_mock.reset_mock() + + def test_instantiation_should_fail_when_env_not_set(self): + # ensure env not set + self.tearDown() + # run test + with self.assertRaises(OSError): + _ = DocstoreMongo() diff --git a/shared/repositories/__init__.py b/shared/repositories/__init__.py new file mode 100644 index 0000000..00b0de1 --- /dev/null +++ b/shared/repositories/__init__.py @@ -0,0 +1,8 @@ +from .src import ImageRepository, ModelRepository, VisualCommunicationRepository +from .src.dto import ( + HexadecimalString, + ImageData, + ModelData, + VisualCommunicationData, + VisualCommunicationValues, +) diff --git a/shared/repositories/src/__init__.py b/shared/repositories/src/__init__.py new file mode 100644 index 0000000..b2babd9 --- /dev/null +++ b/shared/repositories/src/__init__.py @@ -0,0 +1,3 @@ +from .image_repository import ImageRepository +from .model_repository import ModelRepository +from .visual_communication_repository import VisualCommunicationRepository diff --git a/shared/repositories/src/dto/__init__.py b/shared/repositories/src/dto/__init__.py new file mode 100644 index 0000000..0b34df9 --- /dev/null +++ b/shared/repositories/src/dto/__init__.py @@ -0,0 +1,7 @@ +from .hexadecimal_string import HexadecimalString +from .image_data import ImageData +from .model_data import ModelData +from .visual_communication_data import ( + VisualCommunicationData, + VisualCommunicationValues, +) diff --git a/shared/repositories/src/dto/bytes_io_pydantic_annotation.py b/shared/repositories/src/dto/bytes_io_pydantic_annotation.py new file mode 100644 index 0000000..b6c57dc --- /dev/null +++ b/shared/repositories/src/dto/bytes_io_pydantic_annotation.py @@ -0,0 +1,37 @@ +"""Definition of BytesIO Pydantic Annotation.""" + +from io import BytesIO +from typing import Any + +from pydantic.json_schema import JsonSchemaValue +from pydantic_core import core_schema + + +class BytesIOPydanticAnnotation: + """Pydantic annotation that defines input validation, as well as general + and json serialization.""" + + @classmethod + def validate_input(cls, v: Any, handler) -> BytesIO: + """Pydantic-related function to validate input on instantiation.""" + if isinstance(v, BytesIO): + return v + s = handler(v) + return BytesIO(s) + + @classmethod + def __get_pydantic_core_schema__( + cls, + source_type, + _handler, + ) -> core_schema.CoreSchema: + assert source_type is BytesIO + return core_schema.no_info_wrap_validator_function( + function=cls.validate_input, + schema=core_schema.str_schema(), + serialization=core_schema.to_string_ser_schema(), + ) + + @classmethod + def __get_pydantic_json_schema__(cls, _core_schema, handler) -> JsonSchemaValue: + return handler(core_schema.str_schema()) diff --git a/shared/repositories/src/dto/hexadecimal_string.py b/shared/repositories/src/dto/hexadecimal_string.py new file mode 100644 index 0000000..01a958f --- /dev/null +++ b/shared/repositories/src/dto/hexadecimal_string.py @@ -0,0 +1,24 @@ +"""Definition of Checksum DTO.""" + +from __future__ import annotations + +import re + + +class HexadecimalString(str): + """Hexadecimal-string class.""" + + def __new__(cls, string): + # ensure proper input format + pattern = r'[0-9-a-fA-F]{32}' + match = re.match(pattern, string) + if match is None: + raise ValueError(f'format does not match a hexadecimal-string: {string}') + return super().__new__(cls, string) + + def __repr__(self) -> str: + class_name = self.__class__.__name__ + return f"{class_name}('{self}')" + + def __reduce__(self): + return self.__class__, (self,) diff --git a/shared/repositories/src/dto/hexadecimal_string_pydantic_annotation.py b/shared/repositories/src/dto/hexadecimal_string_pydantic_annotation.py new file mode 100644 index 0000000..b1d5a7f --- /dev/null +++ b/shared/repositories/src/dto/hexadecimal_string_pydantic_annotation.py @@ -0,0 +1,38 @@ +"""Definition of HexadecimalString Pydantic Annotation.""" + +from typing import Any + +from pydantic.json_schema import JsonSchemaValue +from pydantic_core import core_schema + +from .hexadecimal_string import HexadecimalString + + +class HexadecimalStringPydanticAnnotation: + """Pydantic annotation that defines input validation, as well as general + and json serialization.""" + + @classmethod + def validate_input(cls, v: Any, handler) -> HexadecimalString: + """Pydantic-related function to validate input on instantiation.""" + if isinstance(v, HexadecimalString): + return v + s = handler(v) + return HexadecimalString(s) + + @classmethod + def __get_pydantic_core_schema__( + cls, + source_type, + _handler, + ) -> core_schema.CoreSchema: + assert source_type is HexadecimalString + return core_schema.no_info_wrap_validator_function( + function=cls.validate_input, + schema=core_schema.str_schema(), + serialization=core_schema.to_string_ser_schema(), + ) + + @classmethod + def __get_pydantic_json_schema__(cls, _core_schema, handler) -> JsonSchemaValue: + return handler(core_schema.str_schema()) diff --git a/shared/repositories/src/dto/image_data.py b/shared/repositories/src/dto/image_data.py new file mode 100644 index 0000000..e04dc66 --- /dev/null +++ b/shared/repositories/src/dto/image_data.py @@ -0,0 +1,16 @@ +"""Definition of VisualData DTO.""" + +from typing import Annotated + +from PIL import Image +from pydantic import Field + +from .image_pydantic_annotation import ImagePydanticAnnotation +from .type_checking_base_model import TypeCheckingBaseModel + + +class ImageData(TypeCheckingBaseModel): + """Visual data class.""" + + image: Annotated[Image.Image, ImagePydanticAnnotation] + name: str = Field(min_length=1) diff --git a/shared/repositories/src/dto/image_pydantic_annotation.py b/shared/repositories/src/dto/image_pydantic_annotation.py new file mode 100644 index 0000000..d92c625 --- /dev/null +++ b/shared/repositories/src/dto/image_pydantic_annotation.py @@ -0,0 +1,37 @@ +"""Definition of BytesIO Pydantic Annotation.""" + +from typing import Any + +from PIL import Image +from pydantic.json_schema import JsonSchemaValue +from pydantic_core import core_schema + + +class ImagePydanticAnnotation: + """Pydantic annotation that defines input validation, as well as general + and json serialization.""" + + @classmethod + def validate_input(cls, v: Any, handler) -> Image.Image: + """Pydantic-related function to validate input on instantiation.""" + if isinstance(v, Image.Image): + return v + s = handler(v) + return Image.open(s) + + @classmethod + def __get_pydantic_core_schema__( + cls, + source_type, + _handler, + ) -> core_schema.CoreSchema: + assert source_type is Image.Image + return core_schema.no_info_wrap_validator_function( + function=cls.validate_input, + schema=core_schema.str_schema(), + serialization=core_schema.to_string_ser_schema(), + ) + + @classmethod + def __get_pydantic_json_schema__(cls, _core_schema, handler) -> JsonSchemaValue: + return handler(core_schema.str_schema()) diff --git a/shared/repositories/src/dto/model_data.py b/shared/repositories/src/dto/model_data.py new file mode 100644 index 0000000..a8384d6 --- /dev/null +++ b/shared/repositories/src/dto/model_data.py @@ -0,0 +1,60 @@ +"""Definition of ModelData DTO.""" + +from __future__ import annotations + +from hashlib import md5 +from io import BytesIO +from typing import Annotated + +import torch +from pydantic import Field + +from .bytes_io_pydantic_annotation import BytesIOPydanticAnnotation +from .hexadecimal_string import HexadecimalString +from .hexadecimal_string_pydantic_annotation import HexadecimalStringPydanticAnnotation +from .type_checking_base_model import TypeCheckingBaseModel + + +class ModelData(TypeCheckingBaseModel): + """Model Data DTO.""" + + buffer: Annotated[BytesIO, BytesIOPydanticAnnotation] + buffer_checksum: Annotated[HexadecimalString, HexadecimalStringPydanticAnnotation] + class_name: str = Field( + min_length=1, + description='name of model class to generate data.', + ) + + @staticmethod + def calculate_checksum(buffer: BytesIO) -> HexadecimalString: + """Calculate buffer checksum.""" + checksum = md5(buffer.getbuffer()).hexdigest() + return HexadecimalString(checksum) + + @staticmethod + def model_to_buffer(model: torch.nn.Module) -> BytesIO: + """Save model to buffer.""" + assert isinstance(model, torch.nn.Module) + buffer = BytesIO() + torch.save(model.state_dict(), buffer) + return buffer + + @classmethod + def from_model(cls, model: torch.nn.Module) -> ModelData: + """Instantiate from torch module.""" + assert isinstance(model, torch.nn.Module) + # get model name + class_name = type(model).__name__ + # save data to buffer + buffer = cls.model_to_buffer(model) + buffer = BytesIO() + torch.save(model.state_dict(), buffer) + # calculate checksum + buffer_checksum = cls.calculate_checksum(buffer) + # instantiate from buffer + data = cls( + buffer=buffer, + buffer_checksum=buffer_checksum, + class_name=class_name, + ) + return data diff --git a/shared/repositories/src/dto/type_checking_base_model.py b/shared/repositories/src/dto/type_checking_base_model.py new file mode 100644 index 0000000..f4fbee1 --- /dev/null +++ b/shared/repositories/src/dto/type_checking_base_model.py @@ -0,0 +1,12 @@ +"""Definition of TypeCheckingBaseModel class.""" + +from pydantic import BaseModel, ConfigDict + + +class TypeCheckingBaseModel(BaseModel): + """BaseModel with added type checking on input types.""" + + model_config = ConfigDict( + validate_assignment=True, # argument type checking + frozen=True, # ensure data immutability + ) diff --git a/shared/repositories/src/dto/visual_communication_data/__init__.py b/shared/repositories/src/dto/visual_communication_data/__init__.py new file mode 100644 index 0000000..10d782b --- /dev/null +++ b/shared/repositories/src/dto/visual_communication_data/__init__.py @@ -0,0 +1,2 @@ +from .visual_communication_data import VisualCommunicationData +from .visual_communication_values import VisualCommunicationValues diff --git a/shared/repositories/src/dto/visual_communication_data/angle_values.py b/shared/repositories/src/dto/visual_communication_data/angle_values.py new file mode 100644 index 0000000..7fc735e --- /dev/null +++ b/shared/repositories/src/dto/visual_communication_data/angle_values.py @@ -0,0 +1,11 @@ +"""Definition of AngleValues DTO.""" + +from .values_model import ValuesModel + + +class AngleValues(ValuesModel): + """Angle values DTO.""" + + high: float + eye_level: float + low: float diff --git a/shared/repositories/src/dto/visual_communication_data/contact_values.py b/shared/repositories/src/dto/visual_communication_data/contact_values.py new file mode 100644 index 0000000..fa0a6bd --- /dev/null +++ b/shared/repositories/src/dto/visual_communication_data/contact_values.py @@ -0,0 +1,10 @@ +"""Definition of ContactValues DTO.""" + +from .values_model import ValuesModel + + +class ContactValues(ValuesModel): + """Contact values DTO.""" + + offer: float + demand: float diff --git a/shared/repositories/src/dto/visual_communication_data/distance_values.py b/shared/repositories/src/dto/visual_communication_data/distance_values.py new file mode 100644 index 0000000..e907cc3 --- /dev/null +++ b/shared/repositories/src/dto/visual_communication_data/distance_values.py @@ -0,0 +1,11 @@ +"""Definition of DistanceValues DTO.""" + +from .values_model import ValuesModel + + +class DistanceValues(ValuesModel): + """Distance values DTO.""" + + long: float + medium: float + close: float diff --git a/shared/repositories/src/dto/visual_communication_data/framing_values.py b/shared/repositories/src/dto/visual_communication_data/framing_values.py new file mode 100644 index 0000000..99139cb --- /dev/null +++ b/shared/repositories/src/dto/visual_communication_data/framing_values.py @@ -0,0 +1,12 @@ +"""Definition of FramingValues DTO.""" + +from .values_model import ValuesModel + + +class FramingValues(ValuesModel): + """Framing values DTO.""" + + frame_lines: float + empty_space: float + colour_contrast: float + form_contrast: float diff --git a/shared/repositories/src/dto/visual_communication_data/information_value_values.py b/shared/repositories/src/dto/visual_communication_data/information_value_values.py new file mode 100644 index 0000000..53025d9 --- /dev/null +++ b/shared/repositories/src/dto/visual_communication_data/information_value_values.py @@ -0,0 +1,11 @@ +"""Definition of InformationValueValues DTO.""" + +from .values_model import ValuesModel + + +class InformationValueValues(ValuesModel): + """Information value values DTO.""" + + given_new: float + ideal_real: float + central_marginal: float diff --git a/shared/repositories/src/dto/visual_communication_data/modality_color_values.py b/shared/repositories/src/dto/visual_communication_data/modality_color_values.py new file mode 100644 index 0000000..62dc497 --- /dev/null +++ b/shared/repositories/src/dto/visual_communication_data/modality_color_values.py @@ -0,0 +1,11 @@ +"""Definition of ModalityColorValues DTO.""" + +from .values_model import ValuesModel + + +class ModalityColorValues(ValuesModel): + """Modality color values DTO.""" + + high: float + medium: float + low: float diff --git a/shared/repositories/src/dto/visual_communication_data/modality_depth_values.py b/shared/repositories/src/dto/visual_communication_data/modality_depth_values.py new file mode 100644 index 0000000..ba73fb3 --- /dev/null +++ b/shared/repositories/src/dto/visual_communication_data/modality_depth_values.py @@ -0,0 +1,11 @@ +"""Definition of ModalityDepthValues DTO.""" + +from .values_model import ValuesModel + + +class ModalityDepthValues(ValuesModel): + """Modality depth values DTO.""" + + high: float + medium: float + low: float diff --git a/shared/repositories/src/dto/visual_communication_data/modality_lighting_values.py b/shared/repositories/src/dto/visual_communication_data/modality_lighting_values.py new file mode 100644 index 0000000..b01dba7 --- /dev/null +++ b/shared/repositories/src/dto/visual_communication_data/modality_lighting_values.py @@ -0,0 +1,11 @@ +"""Definition of ModalityLightingValues DTO.""" + +from .values_model import ValuesModel + + +class ModalityLightingValues(ValuesModel): + """Modality lighting values DTO.""" + + high: float + medium: float + low: float diff --git a/shared/repositories/src/dto/visual_communication_data/point_of_view_values.py b/shared/repositories/src/dto/visual_communication_data/point_of_view_values.py new file mode 100644 index 0000000..a6b02a9 --- /dev/null +++ b/shared/repositories/src/dto/visual_communication_data/point_of_view_values.py @@ -0,0 +1,10 @@ +"""Definition of PointOfViewValues DTO.""" + +from .values_model import ValuesModel + + +class PointOfViewValues(ValuesModel): + """Point-of-view values DTO.""" + + frontal: float + oblique: float diff --git a/shared/repositories/src/dto/visual_communication_data/salience_values.py b/shared/repositories/src/dto/visual_communication_data/salience_values.py new file mode 100644 index 0000000..7344377 --- /dev/null +++ b/shared/repositories/src/dto/visual_communication_data/salience_values.py @@ -0,0 +1,13 @@ +"""Definition of SalienceValues DTO.""" + +from .values_model import ValuesModel + + +class SalienceValues(ValuesModel): + """Salience values DTO.""" + + size: float + colour: float + tone: float + form: float + positioning: float diff --git a/shared/repositories/src/dto/visual_communication_data/values_model.py b/shared/repositories/src/dto/visual_communication_data/values_model.py new file mode 100644 index 0000000..28bdc58 --- /dev/null +++ b/shared/repositories/src/dto/visual_communication_data/values_model.py @@ -0,0 +1,60 @@ +"""Definition of ValuesModel base class.""" + +from __future__ import annotations + +import random + +from pydantic import BaseModel, ConfigDict +from torch import Tensor + + +class ValuesModel(BaseModel): + """ValuesModel base class.""" + + model_config = ConfigDict( + validate_assignment=True, # argument type checking + frozen=True, # ensure data immutability + ) + + @classmethod + def list_fields(cls) -> list[str]: + """List options that are stored as attributes.""" + return list(cls.model_fields.keys()) + + @classmethod + def from_random(cls): + """Instantiate with random numbers.""" + kwargs = {field: random.random() for field in cls.list_fields()} + return cls(**kwargs) + + @classmethod + def from_choice(cls, option: str) -> ValuesModel: + """Instantiate from choice.""" + assert isinstance(option, str) + assert len(option) > 0 + allowed_options_list = cls.list_fields() + if option not in allowed_options_list: + raise ValueError(f'option {option} must be in {allowed_options_list}') + # generate field values + kwargs = {field: 0 for field in allowed_options_list} + # set chosen value to max probability + kwargs[option] = 1 + return cls(**kwargs) + + @classmethod + def from_tensor(cls, tensor: Tensor): + """Instantiate from list of values.""" + assert tensor.size(dim=0) == 1, f'tensor batch larger than 1: {tensor}' + data_list = [float(t.item()) for t in tensor[0]] + kwargs = dict(zip(cls.list_fields(), data_list)) + return cls(**kwargs) + + def highest_score_field(self) -> str: + """Return name of field with highest score.""" + model_dict = self.model_dump() + return max(model_dict, key=lambda k: model_dict[k]) + + def highest_score_value(self) -> float: + """Return value of field with highest score.""" + model_dict = self.model_dump() + return max(model_dict.values()) diff --git a/shared/repositories/src/dto/visual_communication_data/visual_communication_data.py b/shared/repositories/src/dto/visual_communication_data/visual_communication_data.py new file mode 100644 index 0000000..3c28c42 --- /dev/null +++ b/shared/repositories/src/dto/visual_communication_data/visual_communication_data.py @@ -0,0 +1,14 @@ +"""Definition of VisualCommunicationData DTO.""" + +from pydantic import Field + +from ..type_checking_base_model import TypeCheckingBaseModel +from .visual_communication_values import VisualCommunicationValues + + +class VisualCommunicationData(TypeCheckingBaseModel): + """Visual communication data class.""" + + name: str = Field(min_length=1) + annotation: VisualCommunicationValues | None = None + prediction: VisualCommunicationValues | None = None diff --git a/shared/repositories/src/dto/visual_communication_data/visual_communication_values.py b/shared/repositories/src/dto/visual_communication_data/visual_communication_values.py new file mode 100644 index 0000000..e13bd71 --- /dev/null +++ b/shared/repositories/src/dto/visual_communication_data/visual_communication_values.py @@ -0,0 +1,49 @@ +"""Definition of VisualCommunicationValues DTO.""" + +from __future__ import annotations + +from ..type_checking_base_model import TypeCheckingBaseModel +from .angle_values import AngleValues +from .contact_values import ContactValues +from .distance_values import DistanceValues +from .framing_values import FramingValues +from .information_value_values import InformationValueValues +from .modality_color_values import ModalityColorValues +from .modality_depth_values import ModalityDepthValues +from .modality_lighting_values import ModalityLightingValues +from .point_of_view_values import PointOfViewValues +from .salience_values import SalienceValues +from .visual_syntax_values import VisualSyntaxValues + + +class VisualCommunicationValues(TypeCheckingBaseModel): + """Visual communication values class.""" + + visual_syntax: VisualSyntaxValues + contact: ContactValues + angle: AngleValues + point_of_view: PointOfViewValues + distance: DistanceValues + modality_lighting: ModalityLightingValues + modality_color: ModalityColorValues + modality_depth: ModalityDepthValues + information_value: InformationValueValues + framing: FramingValues + salience: SalienceValues + + @classmethod + def from_random(cls) -> VisualCommunicationValues: + """Create a random instance.""" + return cls( + visual_syntax=VisualSyntaxValues.from_random(), + contact=ContactValues.from_random(), + angle=AngleValues.from_random(), + point_of_view=PointOfViewValues.from_random(), + distance=DistanceValues.from_random(), + modality_lighting=ModalityLightingValues.from_random(), + modality_color=ModalityColorValues.from_random(), + modality_depth=ModalityDepthValues.from_random(), + information_value=InformationValueValues.from_random(), + framing=FramingValues.from_random(), + salience=SalienceValues.from_random(), + ) diff --git a/shared/repositories/src/dto/visual_communication_data/visual_syntax_values.py b/shared/repositories/src/dto/visual_communication_data/visual_syntax_values.py new file mode 100644 index 0000000..39ad9d3 --- /dev/null +++ b/shared/repositories/src/dto/visual_communication_data/visual_syntax_values.py @@ -0,0 +1,26 @@ +"""Definition of VisualSyntaxValues DTO.""" + +from .values_model import ValuesModel + + +class VisualSyntaxValues(ValuesModel): + """Visual syntax values DTO.""" + + non_transactional_action: float + non_transactional_reaction: float + unidirectional_transactional_action: float + unidirectional_transactional_reaction: float + bidirectional_transactional_action: float + bidirectional_transactional_reaction: float + conversion: float + speech_process: float + classification_overt_taxonomy: float + analytical_exhaustive: float + analytical_disarranged: float + analytical_temporal: float + analytical_distributed: float + analytical_topological: float + analytical_exploded: float + analytical_inclusive: float + symbolic_suggestive: float + symbolic_attributive: float diff --git a/shared/repositories/src/image_repository.py b/shared/repositories/src/image_repository.py new file mode 100644 index 0000000..306275d --- /dev/null +++ b/shared/repositories/src/image_repository.py @@ -0,0 +1,74 @@ +"""Definition of ImageRepository class.""" + +from __future__ import annotations + +from io import BytesIO +from pathlib import Path + +from PIL import Image + +from .dto import ImageData +from .implementations import MinioImplementation +from .interfaces import ImageInterface + + +class ImageRepository(ImageInterface, MinioImplementation): + """Image repository class that handles CRUD functionality for + VisualData.""" + + def __enter__(self) -> ImageRepository: + self.connect() + return self + + @staticmethod + def _build_path(image_name: str) -> Path: + """Build object path.""" + assert isinstance(image_name, str) + path = Path('images') / image_name + return path + + def get_data(self, image_name: str) -> ImageData | None: + """Get Visual data.""" + assert isinstance(image_name, str) + assert len(image_name) > 0 + # build path + path = self._build_path(image_name) + # get object from bucket + buffer = self._get(path) + # handle if no data found + if not buffer: + return None + # convert data + image = Image.open(buffer) + data = ImageData(image=image, name=image_name) + return data + + def put_data(self, data: ImageData) -> None: + """Put visual data.""" + assert isinstance(data, ImageData) + # build path + path = self._build_path(data.name) + # save image to buffer + buffer = BytesIO() + data.image.save(buffer, 'png') + # put object in bucket + self._put(path, buffer) + + def remove_data(self, image_name: str) -> None: + """Remove visual data.""" + assert isinstance(image_name, str) + assert len(image_name) > 0 + # build path + path = self._build_path(image_name) + # remove object + self._delete(path) + + def list_names(self) -> list[str]: + """List names of all images.""" + # build path + path = self._build_path('') + # list object paths + obj_path_list = self._list_objects(path) + # strip prefix + name_list = [obj_path.split('/')[-1] for obj_path in obj_path_list] + return name_list diff --git a/shared/repositories/src/implementations/__init__.py b/shared/repositories/src/implementations/__init__.py new file mode 100644 index 0000000..0e0fb0a --- /dev/null +++ b/shared/repositories/src/implementations/__init__.py @@ -0,0 +1,2 @@ +from .minio_implementation import MinioImplementation +from .mongo_implementation import MongoImplementation diff --git a/shared/repositories/src/implementations/minio_implementation.py b/shared/repositories/src/implementations/minio_implementation.py new file mode 100644 index 0000000..ddedb0c --- /dev/null +++ b/shared/repositories/src/implementations/minio_implementation.py @@ -0,0 +1,186 @@ +"""MinIO implementation.""" + +from __future__ import annotations + +import logging +import os +from io import BytesIO +from pathlib import Path +from traceback import format_exc + +from minio import Minio + +from shared.utils import check_env + +from ..interfaces import DatabaseInterface + + +class MinioImplementation(DatabaseInterface): + """MinIO basic CRUD implementation.""" + + def __init__(self): + # ensure necessary env vars available + var_list = { + 'MINIO_ENDPOINT', + 'MINIO_ACCESS_KEY', + 'MINIO_SECRET_KEY', + 'MINIO_BUCKET_NAME', + } + check_env(var_list) + # prepare internal variables + self._client: Minio | None = None + self._bucket_name: str | None = None + + def connect(self): + """Connect to MinIO server.""" + # prepare arguments + minio_endpoint = str(os.getenv('MINIO_ENDPOINT')) + minio_access_key = str(os.getenv('MINIO_ACCESS_KEY')) + minio_secret_key = str(os.getenv('MINIO_SECRET_KEY')) + minio_bucket_name = str(os.getenv('MINIO_BUCKET_NAME')) + # connect client + client = Minio( + endpoint=minio_endpoint, + access_key=minio_access_key, + secret_key=minio_secret_key, + secure=False, + ) + # ensure bucket exists + if not client.bucket_exists(bucket_name=minio_bucket_name): + logging.debug('creating bucket: %s', minio_bucket_name) + client.make_bucket(bucket_name=minio_bucket_name) + # persist state + self._client = client + self._bucket_name = minio_bucket_name + + def close(self) -> None: + """Close connection to MinIO server. + + N.B. MinIO connection cannot be closed manually. + """ + self._client = None + self._bucket_name = None + + def connected(self): + """Check connection to Minio.""" + res = isinstance(self._client, Minio) + logging.debug(res) + return res + + def __enter__(self) -> MinioImplementation: + self.connect() + return self + + def __exit__(self, exc_type, exc_val, exc_tb) -> None: + if any( + ( + exc_type is not None, + exc_val is not None, + exc_tb is not None, + ), + ): + logging.error('error while exiting context') + self.close() + + def _put( + self, + path: Path, + buffer: BytesIO, + ) -> None: + """Save in-memory buffer as object in MinIO.""" + assert isinstance(path, Path) + assert isinstance(buffer, BytesIO) + assert isinstance(self._client, Minio) + assert isinstance(self._bucket_name, str) + # prepare for saving + num_bytes = len(buffer.getvalue()) + buffer.seek(0) + # send data to bucket + try: + self._client.put_object( + bucket_name=self._bucket_name, + object_name=path.as_posix(), + length=num_bytes, + data=buffer, + ) + logging.debug('saved data to %s', path) + except Exception as exc: + logging.error('failed saving data to MinIO') + raise exc + + def _get( + self, + path: Path, + ) -> BytesIO | None: + """Get object from MinIO as in-memory buffer.""" + assert isinstance(path, Path) + assert isinstance(self._client, Minio) + assert isinstance(self._bucket_name, str) + try: + # make request + response = self._client.get_object( + bucket_name=self._bucket_name, + object_name=path.as_posix(), + ) + assert response.status == 200 + # get buffer + buffer = BytesIO() + chunk_size = 2**14 + while chunk := response.read(chunk_size): + buffer.write(chunk) + buffer.seek(0) + logging.debug('got %s', path) + return buffer + except Exception: + logging.error('failed getting data from MinIO') + logging.debug(format_exc()) + return None + finally: + # close connection if established + if 'response' in locals(): + response.close() + response.release_conn() + + def _delete( + self, + path: Path, + ) -> None: + """Delete object from MinIO.""" + assert isinstance(path, Path) + assert isinstance(self._client, Minio) + assert isinstance(self._bucket_name, str) + # remove object + try: + self._client.remove_object( + bucket_name=self._bucket_name, + object_name=path.as_posix(), + ) + logging.debug('deleted %s', path) + except Exception as exc: + logging.error('failed deleting %s', path) + logging.debug(format_exc()) + raise exc + + def _list_objects( + self, + path: Path, + ) -> list[str]: + """List objects in bucket under path.""" + assert isinstance(path, Path) + assert isinstance(self._client, Minio) + assert isinstance(self._bucket_name, str) + try: + # list objects + obj_list = self._client.list_objects( + bucket_name=self._bucket_name, + prefix=path.as_posix(), + recursive=True, + ) + # extract info + name_list = [obj.object_name for obj in obj_list] + logging.debug('got %s objects matching %s', len(name_list), path) + return name_list + except Exception as exc: + logging.error('failed listing objects under %s', path) + logging.debug(format_exc()) + raise exc diff --git a/shared/repositories/src/implementations/mongo_implementation.py b/shared/repositories/src/implementations/mongo_implementation.py new file mode 100644 index 0000000..1d43439 --- /dev/null +++ b/shared/repositories/src/implementations/mongo_implementation.py @@ -0,0 +1,145 @@ +"""Mongo implementation.""" + +from __future__ import annotations + +import logging +import os +import traceback + +from pymongo import MongoClient +from pymongo.collection import Collection +from pymongo.database import Database +from pymongo.errors import ServerSelectionTimeoutError + +from shared.utils import check_env + +from ..interfaces import DatabaseInterface + + +class MongoImplementation(DatabaseInterface): + """MongoDB basic CRUD implementation.""" + + def __init__(self): + # ensure necessary env vars available + var_list = { + 'MONGO_ENDPOINT', + 'MONGO_DB', + 'MONGO_COLLECTION', + } + check_env(var_list) + # prepare internal variables + self.client: MongoClient | None = None + self.db: Database | None = None + self.collection: Collection | None = None + + def connect(self) -> None: + """Connect to Mongo server.""" + # prepare arguments + mongo_endpoint = str(os.getenv('MONGO_ENDPOINT')) + mongo_database = str(os.getenv('MONGO_DB')) + mongo_collection = str(os.getenv('MONGO_COLLECTION')) + # connect client + client = MongoClient(mongo_endpoint) + database = client[mongo_database] + collection = database[mongo_collection] + # set unique index on 'name' + collection.create_index(keys='name', unique=True) + # persist state + self._client = client + self._database = database + self._collection = collection + + def close(self) -> None: + """Close connection to Mongo server.""" + self._client.close() + self._client = None + self._database = None + self._collection = None + + def connected(self) -> bool: + """Check connection to Mongo.""" + if self._client is None: + return False + try: + # trigger fetch data + _ = self._client.server_info() + res = True + except ServerSelectionTimeoutError: + res = False + logging.debug(res) + return res + + def __enter__(self) -> MongoImplementation: + self.connect() + return self + + def __exit__(self, exc_type, exc_val, exc_tb) -> None: + if any( + ( + exc_type is not None, + exc_val is not None, + exc_tb is not None, + ), + ): + logging.error('error while exiting context') + traceback.print_exception(exc_type, exc_val, exc_tb) + self.close() + + def _save( + self, + data: dict, + query: dict, + ) -> None: + """Save document in Mongo.""" + assert isinstance(data, dict) + assert isinstance(query, dict) + assert 'name' in data + assert self.connected() + self._collection.update_one( + filter=query, + update={ + '$set': data.copy(), + }, + upsert=True, + ) + logging.debug('Save %s', data) + + def _get( + self, + query: dict, + ) -> dict | None: + """Get document from Mongo.""" + assert isinstance(query, dict) + assert self.connected() + doc = self._collection.find_one(query, projection={'_id': False}) + logging.debug('Found %s', doc) + return doc + + def _delete( + self, + query: dict, + ) -> None: + """Remove document from Mongo.""" + assert isinstance(query, dict) + assert self.connected() + doc = self._collection.delete_one(query) + logging.debug('Deleted %s', doc) + + def _list_documents(self, key='name') -> list[str]: + """List documents in Mongo.""" + assert isinstance(key, str) + assert len(key) > 0 + # build query + doc_list = list( + self._collection.find( + filter={}, + projection={ + '_id': False, + key: True, + }, + ), + ) + # extract values + value_list = [doc[key] for doc in doc_list] + logging.debug('Got %s document(s)', len(doc_list)) + return value_list diff --git a/shared/repositories/src/interfaces/__init__.py b/shared/repositories/src/interfaces/__init__.py new file mode 100644 index 0000000..0250cfd --- /dev/null +++ b/shared/repositories/src/interfaces/__init__.py @@ -0,0 +1,4 @@ +from .database_interface import DatabaseInterface +from .image_interface import ImageInterface +from .model_interface import ModelInterface +from .visual_communication_interface import VisualCommunicationInterface diff --git a/shared/repositories/src/interfaces/database_interface.py b/shared/repositories/src/interfaces/database_interface.py new file mode 100644 index 0000000..2a7f6e3 --- /dev/null +++ b/shared/repositories/src/interfaces/database_interface.py @@ -0,0 +1,28 @@ +"""Definition of DatabaseInterface class.""" + +from abc import ABC, abstractmethod + + +class DatabaseInterface(ABC): + """Interface base class adding 'connect', 'close' and context + functionalities.""" + + @abstractmethod + def connect(self): + raise NotImplementedError() + + @abstractmethod + def close(self): + raise NotImplementedError() + + @abstractmethod + def connected(self) -> bool: + raise NotImplementedError() + + @abstractmethod + def __enter__(self): + raise NotImplementedError() + + @abstractmethod + def __exit__(self, exc_type, exc_val, exc_tb): + raise NotImplementedError() diff --git a/shared/repositories/src/interfaces/image_interface.py b/shared/repositories/src/interfaces/image_interface.py new file mode 100644 index 0000000..ab003ec --- /dev/null +++ b/shared/repositories/src/interfaces/image_interface.py @@ -0,0 +1,26 @@ +"""Definition of ImageInterface.""" + +from abc import abstractmethod + +from ..dto import ImageData +from .database_interface import DatabaseInterface + + +class ImageInterface(DatabaseInterface): + """Image interface class.""" + + @abstractmethod + def get_data(self, image_name: str) -> ImageData | None: + raise NotImplementedError() + + @abstractmethod + def put_data(self, data: ImageData) -> None: + raise NotImplementedError() + + @abstractmethod + def remove_data(self, image_name: str) -> None: + raise NotImplementedError() + + @abstractmethod + def list_names(self) -> list[str]: + raise NotImplementedError() diff --git a/shared/repositories/src/interfaces/model_interface.py b/shared/repositories/src/interfaces/model_interface.py new file mode 100644 index 0000000..974148e --- /dev/null +++ b/shared/repositories/src/interfaces/model_interface.py @@ -0,0 +1,26 @@ +"""Definition of ModelInterface.""" + +from abc import abstractmethod + +from ..dto import ModelData +from .database_interface import DatabaseInterface + + +class ModelInterface(DatabaseInterface): + """Model interface class.""" + + @abstractmethod + def get_data(self, object_name: str) -> ModelData | None: + raise NotImplementedError() + + @abstractmethod + def put_data(self, data: ModelData) -> None: + raise NotImplementedError() + + @abstractmethod + def remove_data(self, object_name: str) -> None: + raise NotImplementedError() + + @abstractmethod + def list_names(self) -> list[str]: + raise NotImplementedError() diff --git a/shared/repositories/src/interfaces/visual_communication_interface.py b/shared/repositories/src/interfaces/visual_communication_interface.py new file mode 100644 index 0000000..6030e5f --- /dev/null +++ b/shared/repositories/src/interfaces/visual_communication_interface.py @@ -0,0 +1,26 @@ +"""Definition of VisualCommunicationInterface.""" + +from abc import abstractmethod + +from ..dto import VisualCommunicationData +from .database_interface import DatabaseInterface + + +class VisualCommunicationInterface(DatabaseInterface): + """Visual communication interface class.""" + + @abstractmethod + def get_data(self, name: str) -> VisualCommunicationData | None: + raise NotImplementedError() + + @abstractmethod + def put_data(self, data: VisualCommunicationData) -> None: + raise NotImplementedError() + + @abstractmethod + def remove_data(self, name: str) -> None: + raise NotImplementedError() + + @abstractmethod + def list_names(self) -> list[str]: + raise NotImplementedError() diff --git a/shared/repositories/src/model_repository.py b/shared/repositories/src/model_repository.py new file mode 100644 index 0000000..cb42777 --- /dev/null +++ b/shared/repositories/src/model_repository.py @@ -0,0 +1,77 @@ +"""Definition of ModelRepository class.""" + +from __future__ import annotations + +from pathlib import Path + +from .dto import HexadecimalString, ModelData +from .implementations import MinioImplementation +from .interfaces import ModelInterface + + +class ModelRepository(ModelInterface, MinioImplementation): + """Model repository class that handles CRUD functionality for ModelData.""" + + def __enter__(self) -> ModelRepository: + self.connect() + return self + + @staticmethod + def _prefix() -> Path: + """Object name prefix.""" + return Path('models') + + @classmethod + def _build_object_name(cls, data: ModelData) -> str: + """Build object name from data.""" + return f'{data.class_name}-{data.buffer_checksum}' + + def get_data(self, object_name: str) -> ModelData | None: + """Get model data.""" + assert isinstance(object_name, str) + # build path + path = self._prefix() / object_name + # get object from bucket + buffer = self._get(path) + # handle if no data found + if not buffer: + return None + # extract info + class_name, buffer_checksum_str = object_name.split('-') + # convert data + buffer_checksum = HexadecimalString(buffer_checksum_str) + # instantiate data + data = ModelData( + buffer=buffer, + buffer_checksum=buffer_checksum, + class_name=class_name, + ) + return data + + def put_data(self, data: ModelData) -> None: + """Put model data.""" + assert isinstance(data, ModelData) + # build object name + object_name = self._build_object_name(data) + # build path + path = self._prefix() / object_name + # put object in bucket + self._put(path, data.buffer) + + def remove_data(self, object_name: str) -> None: + """Remove model data.""" + assert isinstance(object_name, str) + # build path + path = self._prefix() / object_name + # remove object + self._delete(path) + + def list_names(self) -> list[str]: + """List names of all models.""" + # build path + path = self._prefix() + # list object paths + obj_path_list = self._list_objects(path) + # strip prefix + name_list = [obj_path.split('/')[-1] for obj_path in obj_path_list] + return name_list diff --git a/shared/repositories/src/visual_communication_repository.py b/shared/repositories/src/visual_communication_repository.py new file mode 100644 index 0000000..5322906 --- /dev/null +++ b/shared/repositories/src/visual_communication_repository.py @@ -0,0 +1,56 @@ +"""Definition of VisualCommunicationRepository class.""" + +from __future__ import annotations + +from .dto import VisualCommunicationData +from .implementations import MongoImplementation +from .interfaces import VisualCommunicationInterface + + +class VisualCommunicationRepository(VisualCommunicationInterface, MongoImplementation): + """Visual communication repository class that handles CRUD functionality + for VisualCommunicationData.""" + + def __enter__(self) -> VisualCommunicationRepository: + self.connect() + return self + + def get_data(self, name: str) -> VisualCommunicationData | None: + """Get visual communication data.""" + assert isinstance(name, str) + assert len(name) > 0 + # build query + query = {'name': name} + # get document from mongo + doc = self._get(query) + # handle if no data found + if doc is None: + return None + # instantiate object + data = VisualCommunicationData(**doc) + return data + + def put_data(self, data: VisualCommunicationData) -> None: + """Put visual communication data.""" + assert isinstance(data, VisualCommunicationData) + # convert to dict + data = data.model_dump(mode='json') + # build query + query = {'name': data['name']} + # save to mongo + self._save(data, query) + + def remove_data(self, name: str) -> None: + """Remove visual communication data.""" + assert isinstance(name, str) + assert len(name) > 0 + # build query + query = {'name': name} + # remove document from mongo + self._delete(query) + + def list_names(self) -> list[str]: + """List names of all documents.""" + # list documents + name_list = self._list_documents(key='name') + return name_list diff --git a/shared/repositories/tests/integration/conftest.py b/shared/repositories/tests/integration/conftest.py new file mode 100644 index 0000000..a17e012 --- /dev/null +++ b/shared/repositories/tests/integration/conftest.py @@ -0,0 +1,444 @@ +"""Integration tests configuration.""" + +import os +import random +from collections.abc import Iterator +from io import BytesIO +from pathlib import Path + +import minio +import pytest +from PIL import Image +from pymongo import MongoClient +from testcontainers.minio import MinioContainer +from testcontainers.mongodb import MongoDbContainer + +from model.src.models import VisualCommunicationModel +from shared.repositories import ( + HexadecimalString, + ImageData, + ImageRepository, + ModelData, + ModelRepository, + VisualCommunicationData, + VisualCommunicationRepository, + VisualCommunicationValues, +) +from shared.repositories.src.implementations import ( + MinioImplementation, + MongoImplementation, +) + +# set random seed for reproducibility +random.seed(13) + +# define test static variables +MINIO_PORT = 9000 +MINIO_ACCESS_KEY = 'minioadmin' +MINIO_SECRET_KEY = 'minioadmin' +MONGO_PORT = 27017 +MONGO_USERNAME = 'admin' +MONGO_PASSWORD = 'password' + +env_var_map = { + 'MINIO_ENDPOINT': f'localhost:{MINIO_PORT}', # updated when container is running + 'MINIO_ACCESS_KEY': MINIO_ACCESS_KEY, + 'MINIO_SECRET_KEY': MINIO_SECRET_KEY, + 'MINIO_BUCKET_NAME': 'test-bucket', + 'MINIO_OBJECT_NAME': 'test-object', + 'MINIO_IMAGE_NAME': 'test-image', + 'MONGO_ENDPOINT': ( + f'mongodb://{MONGO_USERNAME}:{MONGO_PASSWORD}' f'@localhost:{MONGO_PORT}/' + ), # updated when container is running + 'MONGO_DB': 'test-db', + 'MONGO_COLLECTION': 'test-collection', +} +container_map = { + 'minio': MinioContainer( + port=MINIO_PORT, + access_key=MINIO_ACCESS_KEY, + secret_key=MINIO_SECRET_KEY, + ), + 'mongo': MongoDbContainer( + port=MONGO_PORT, + username=MONGO_USERNAME, + password=MONGO_PASSWORD, + dbname=env_var_map['MONGO_DB'], + ), +} + + +@pytest.fixture(scope='session', autouse=True) +def setup_infrastructure(request: pytest.FixtureRequest) -> None: + """Prepare infrastructure for integration test.""" + # prepare infrastructure + for container in container_map.values(): + container.start() + # update env var map + minio_host = container_map['minio'].get_container_host_ip() + minio_port = container_map['minio'].get_exposed_port(MINIO_PORT) + env_var_map['MINIO_ENDPOINT'] = f'{minio_host}:{minio_port}' + mongo_host = container_map['mongo'].get_container_host_ip() + mongo_port = container_map['mongo'].get_exposed_port(MONGO_PORT) + env_var_map['MONGO_ENDPOINT'] = ( + f'mongodb://{MONGO_USERNAME}:{MONGO_PASSWORD}@{mongo_host}:{mongo_port}/' + ) + + # ensure cleanup + def cleanup_infrastructure(): + for container in container_map.values(): + container.stop() + + request.addfinalizer(cleanup_infrastructure) + + +@pytest.fixture(scope='session', autouse=True) +def populate_env( + request: pytest.FixtureRequest, + setup_infrastructure, +) -> None: + """Populate environment with variables used for testing.""" + # update env + for key, val in env_var_map.items(): + os.environ[key] = val + + # ensure cleanup + def cleanup_env(): + for key in env_var_map: + _ = os.environ.pop(key, default=None) + + request.addfinalizer(cleanup_env) + + +@pytest.fixture(scope='session') +def raw_minio_client( + setup_infrastructure, + populate_env, +) -> Iterator[minio.Minio]: + """Raw Minio client fixture.""" + # prepare arguments + minio_endpoint = str(os.getenv('MINIO_ENDPOINT')) + minio_access_key = str(os.getenv('MINIO_ACCESS_KEY')) + minio_secret_key = str(os.getenv('MINIO_SECRET_KEY')) + minio_bucket_name = str(os.getenv('MINIO_BUCKET_NAME')) + # connect client + client = minio.Minio( + endpoint=minio_endpoint, + access_key=minio_access_key, + secret_key=minio_secret_key, + secure=False, + ) + # ensure bucket exists + if not client.bucket_exists(bucket_name=minio_bucket_name): + client.make_bucket(bucket_name=minio_bucket_name) + # expose client + yield client + # cleanup + object_list = client.list_objects(minio_bucket_name, recursive=True) + for obj in object_list: + client.remove_object( + bucket_name=obj.bucket_name, + object_name=obj.object_name, + ) + client.remove_bucket(minio_bucket_name) + + +@pytest.fixture +def minio_client( + setup_infrastructure, + populate_env, +) -> Iterator[MinioImplementation]: + """MinioImplementation fixture.""" + # instantiate and connect client + minio_client = MinioImplementation() + minio_client.connect() + # expose client + yield minio_client + # cleanup + object_name_list = minio_client._list_objects(Path('*')) + for name in object_name_list: + minio_client._delete(Path(name)) + minio_client.close() + + +@pytest.fixture +def buffer() -> Iterator[BytesIO]: + """Bytes buffer fixture.""" + # generate reproducible random data + data = random.randbytes(n=2**21) # 2 MB + # convert data + buffer = BytesIO(data) + # expose buffer + yield buffer + + +@pytest.fixture +def buffer_in_minio( + raw_minio_client: minio.Minio, + buffer: BytesIO, +) -> Iterator[tuple[Path, BytesIO]]: + """Buffer in Minio fixture.""" + # prepare arguments + minio_bucket_name = str(os.getenv('MINIO_BUCKET_NAME')) + minio_object_name = str(os.getenv('MINIO_OBJECT_NAME')) + # prepare for saving + num_bytes = len(buffer.getvalue()) + buffer.seek(0) + # put data in bucket + raw_minio_client.put_object( + bucket_name=minio_bucket_name, + object_name=minio_object_name, + length=num_bytes, + data=buffer, + ) + # expose data + yield Path(minio_object_name), buffer + # cleanup + raw_minio_client.remove_object( + bucket_name=minio_bucket_name, + object_name=minio_object_name, + ) + + +@pytest.fixture +def image_data() -> Iterator[ImageData]: + """Image data fixture.""" + # prepare arguments + name = str(os.getenv('MINIO_IMAGE_NAME')) + image = Image.new(mode='RGB', size=(480, 480)) + # instantiate data + image_data = ImageData(image=image, name=name) + # expose data + yield image_data + + +@pytest.fixture +def image_data_in_minio( + raw_minio_client: minio.Minio, + image_data: ImageData, +) -> Iterator[ImageData]: + """Image data in Minio fixture.""" + # prepare arguments + minio_bucket_name = str(os.getenv('MINIO_BUCKET_NAME')) + image_name = image_data.name + # build object path + object_path = ImageRepository._build_path(image_name) + # save image to buffer + buffer = BytesIO() + image_data.image.save(buffer, 'png') + # prepare for saving + num_bytes = len(buffer.getvalue()) + buffer.seek(0) + # put data in bucket + raw_minio_client.put_object( + bucket_name=minio_bucket_name, + object_name=object_path.as_posix(), + length=num_bytes, + data=buffer, + ) + # expose data + yield image_data + # cleanup + raw_minio_client.remove_object( + bucket_name=minio_bucket_name, + object_name=object_path.as_posix(), + ) + + +@pytest.fixture(scope='session') +def image_repo( + setup_infrastructure, + populate_env, +) -> Iterator[ImageRepository]: + """Image repository fixture.""" + repo = ImageRepository() + repo.connect() + yield repo + repo.close() + + +@pytest.fixture +def model_data() -> Iterator[ModelData]: + """Model data fixture.""" + # prepare arguments + vis_com_model = VisualCommunicationModel().to('cpu') + class_name = type(vis_com_model).__name__ + buffer = ModelData.model_to_buffer(vis_com_model) + buffer_checksum = HexadecimalString('77dcab1769563654a6e24f92d40f29bd') + # instantiate data + model_data = ModelData( + buffer=buffer, + buffer_checksum=buffer_checksum, + class_name=class_name, + ) + # expose model + yield model_data + + +@pytest.fixture +def model_data_in_minio( + raw_minio_client: minio.Minio, + model_data: ModelData, +) -> Iterator[ModelData]: + """Model data in Minio fixture.""" + # prepare arguments + minio_bucket_name = str(os.getenv('MINIO_BUCKET_NAME')) + object_name = ModelRepository._build_object_name(model_data) + buffer = model_data.buffer + # build object path + object_path = ModelRepository._prefix() / object_name + # prepare for saving + num_bytes = len(buffer.getvalue()) + buffer.seek(0) + # put data in bucket + raw_minio_client.put_object( + bucket_name=minio_bucket_name, + object_name=object_path.as_posix(), + length=num_bytes, + data=buffer, + ) + # expose data + yield model_data + # cleanup + raw_minio_client.remove_object( + bucket_name=minio_bucket_name, + object_name=object_path.as_posix(), + ) + + +@pytest.fixture(scope='session') +def model_repo( + setup_infrastructure, + populate_env, +) -> Iterator[ModelRepository]: + """Model repository fixture.""" + repo = ModelRepository() + repo.connect() + yield repo + repo.close() + + +@pytest.fixture +def raw_mongo_client( + setup_infrastructure, + populate_env, +) -> Iterator[MongoClient]: + """Raw mongo client fixture.""" + # prepare arguments + mongo_endpoint = str(os.getenv('MONGO_ENDPOINT')) + mongo_database = str(os.getenv('MONGO_DB')) + # connect client + client = MongoClient(mongo_endpoint) + _ = client[mongo_database] + # expose client + yield client + # cleanup + client.drop_database(mongo_database) + + +@pytest.fixture +def mongo_client( + setup_infrastructure, + populate_env, +) -> Iterator[MongoImplementation]: + """MongoImplementation fixture.""" + # instantiate and connect client + mongo_client = MongoImplementation() + mongo_client.connect() + # expose client + yield mongo_client + # cleanup + mongo_client._collection.drop() + mongo_client.close() + + +@pytest.fixture +def dictionary() -> Iterator[dict]: + """Dictionary fixture.""" + # prepare data + data = { + 'name': 'test-dictionary', + 'str_key': 'value', + 'int_key': 100, + 'float_key': 3.14, + 'list_key': [1, 2, 3], + 'dict_key': { + 'nested_key': 'nested_value', + }, + } + # expose data + yield data + + +@pytest.fixture +def dictionary_in_mongo( + raw_mongo_client: MongoClient, + dictionary: dict, +) -> Iterator[dict]: + """Dictionary in Mongo fixture.""" + # prepare arguments + database = str(os.getenv('MONGO_DB')) + collection = str(os.getenv('MONGO_COLLECTION')) + # save data + _ = raw_mongo_client[database][collection].insert_one(dictionary.copy()) + # expose data + yield dictionary + # cleanup + raw_mongo_client[database][collection].delete_one(dictionary) + + +@pytest.fixture +def visual_communication_values() -> Iterator[VisualCommunicationValues]: + """Visual communication values fixture.""" + # instantiate with random values + visual_communication_values = VisualCommunicationValues.from_random() + # expose values + yield visual_communication_values + + +@pytest.fixture +def visual_communication_data( + visual_communication_values: VisualCommunicationValues, +) -> Iterator[VisualCommunicationData]: + """Visual communication data fixture.""" + # prepare arguments + name = 'test-visual-communication' + annotation = visual_communication_values + # instantiate data + visual_communication_data = VisualCommunicationData( + name=name, + annotation=annotation, + ) + # expose data + yield visual_communication_data + + +@pytest.fixture +def visual_communication_data_in_mongo( + raw_mongo_client: MongoClient, + visual_communication_data: VisualCommunicationData, +) -> Iterator[VisualCommunicationData]: + """Visual communication data in Mongo fixture.""" + # prepare arguments + database = str(os.getenv('MONGO_DB')) + collection = str(os.getenv('MONGO_COLLECTION')) + # convert data + dictionary = visual_communication_data.model_dump(mode='dict') + # save data + _ = raw_mongo_client[database][collection].insert_one(dictionary.copy()) + # expose data + yield visual_communication_data + # cleanup + raw_mongo_client[database][collection].delete_one(dictionary) + + +@pytest.fixture(scope='session') +def visual_communication_repo( + setup_infrastructure, + populate_env, +) -> Iterator[VisualCommunicationRepository]: + """Visual communication repository fixture.""" + repo = VisualCommunicationRepository() + repo.connect() + yield repo + repo.close() diff --git a/shared/repositories/tests/integration/image_repository_test.py b/shared/repositories/tests/integration/image_repository_test.py new file mode 100644 index 0000000..89011e6 --- /dev/null +++ b/shared/repositories/tests/integration/image_repository_test.py @@ -0,0 +1,156 @@ +"""Integration tests for ImageRepository class.""" + +import numpy as np +import pytest +from PIL import Image + +from shared.repositories import ImageData, ImageRepository + + +def same_image( + img_a: Image.Image, + img_b: Image.Image, +) -> bool: + """Check if two images contain the same data.""" + assert isinstance(img_a, Image.Image) + assert isinstance(img_b, Image.Image) + # check if images have a comparable number of channels + if img_a.getbands() != img_b.getbands(): + return False + # calculate pixel difference between images + img_a_arr = np.asarray(img_a) + img_b_arr = np.asarray(img_b) + diff = np.subtract(img_a_arr, img_b_arr) + if np.sum(diff) != 0: + return False + return True + + +def same_image_data( + data_a: ImageData, + data_b: ImageData, +) -> bool: + """Check if two ImageData-objects contain the same data.""" + assert isinstance(data_a, ImageData) + assert isinstance(data_b, ImageData) + # compare names + if data_a.name != data_b.name: + return False + # compare images + if not same_image(data_a.image, data_b.image): + return False + return True + + +def test_should_have_context_handler(): + """Test that class has a working context handler implemented.""" + # ACT + with ImageRepository() as repo: + # ASSERT + assert repo.connected() + + +def test_should_get_image_data( + image_repo: ImageRepository, + image_data_in_minio: ImageData, +): + """Test getting image data.""" + # ARRANGE + image_name = image_data_in_minio.name + # ACT + received_image_data = image_repo.get_data(image_name) + # ASSERT + assert received_image_data is not None + assert isinstance(received_image_data, ImageData) + assert same_image_data(image_data_in_minio, received_image_data) + + +def test_should_get_none_when_no_image_data( + image_repo: ImageRepository, + image_data: ImageData, +): + """Test getting None when no data is available.""" + # ARRANGE + image_name = image_data.name + # ACT + received_image_data = image_repo.get_data(image_name) + # ASSERT + assert received_image_data is None + + +def test_should_delete_image_data( + image_repo: ImageRepository, + image_data_in_minio: ImageData, +): + """Test deleting image data.""" + # ARRANGE + image_name = image_data_in_minio.name + # ACT + image_repo.remove_data(image_name) + received_image_data = image_repo.get_data(image_name) + # ASSERT + assert received_image_data is None + + +def test_should_put_image_data( + image_repo: ImageRepository, + image_data: ImageData, +): + """Test putting image data.""" + # ARRANGE + image_name = image_data.name + # ACT + image_repo.put_data(image_data) + received_image_data = image_repo.get_data(image_name) + # ASSERT + assert received_image_data is not None + assert same_image_data(image_data, received_image_data) + + +def test_should_update_image_data( + image_repo: ImageRepository, + image_data_in_minio: ImageData, +): + """Test updating image data.""" + # ARRANGE + updated_image_data = image_data_in_minio.model_copy( + update={ + 'image': Image.new(mode='RGB', size=(480, 480), color='white'), + }, + ) + image_name = updated_image_data.name + # ACT + image_repo.put_data(updated_image_data) + received_image_data = image_repo.get_data(image_name) + # ASSERT + assert not same_image_data(image_data_in_minio, updated_image_data) + assert received_image_data is not None + assert same_image_data(updated_image_data, received_image_data) + + +def test_should_list_names( + image_repo: ImageRepository, + image_data_in_minio: ImageData, +): + """Test get all image names.""" + # ARRANGE + updated_image_data = image_data_in_minio.model_copy( + update={ + 'name': 'updated-test-image', + }, + ) + image_repo.put_data(updated_image_data) + expected_name_list = [ + image_data_in_minio.name, + updated_image_data.name, + ] + # ACT + name_list = image_repo.list_names() + # ASSERT + assert len(name_list) == 2 + for name in name_list: + assert name in expected_name_list + + +if __name__ == '__main__': + pytest.main(['-s', '-v', __file__]) diff --git a/shared/repositories/tests/integration/minio_implementation_test.py b/shared/repositories/tests/integration/minio_implementation_test.py new file mode 100644 index 0000000..4c43da6 --- /dev/null +++ b/shared/repositories/tests/integration/minio_implementation_test.py @@ -0,0 +1,133 @@ +"""Integration tests related to Minio implementation.""" + +import logging +import os +from io import BytesIO +from pathlib import Path + +import pytest + +from shared.repositories.src.implementations import MinioImplementation + + +def same_data( + data_a: BytesIO, + data_b: BytesIO, +) -> bool: + """Check if two BytesIO-objects contain the same data.""" + assert isinstance(data_a, BytesIO) + assert isinstance(data_b, BytesIO) + # prepare for being read + data_a.seek(0) + data_b.seek(0) + # convert to bytes + data_a_bytes = data_a.read() + data_b_bytes = data_b.read() + # compare size + if len(data_a_bytes) != len(data_b_bytes): + logging.error( + 'data has different length: %s and %s', + len(data_a_bytes), + len(data_b_bytes), + ) + return False + # compare content + if data_a_bytes != data_b_bytes: + logging.error('data has different bytes') + return False + return True + + +def test_should_connect_to_minio(): + """Test connection to Minio.""" + # ARRANGE + client = MinioImplementation() + # ACT + client.connect() + # ASSERT + assert client.connected() + client.close() + + +def test_should_have_context_handler(): + """Test that class has a working context handler implemented.""" + # ACT + with MinioImplementation() as client: + # ASSERT + assert client.connected() + + +def test_should_get_data( + minio_client: MinioImplementation, + buffer_in_minio: tuple[Path, BytesIO], +): + """Test getting data from Minio.""" + # ARRANGE + path, buffer = buffer_in_minio + # ACT + received_buffer = minio_client._get(path) + # ASSERT + assert received_buffer is not None + assert same_data(received_buffer, buffer) + + +def test_should_get_none_when_no_data( + minio_client: MinioImplementation, +): + """Test getting None when no data is available in Minio.""" + # ARRANGE + nonexistent_path = Path('nonexistent-object-name') + # ACT + received_buffer = minio_client._get(nonexistent_path) + # ASSERT + assert received_buffer is None + + +def test_should_delete_data( + minio_client: MinioImplementation, + buffer_in_minio: tuple[Path, BytesIO], +): + """Test deleting data from Minio.""" + # ARRANGE + path, _ = buffer_in_minio + # ACT + minio_client._delete(path) + # ASSERT + received_buffer = minio_client._get(path) + assert received_buffer is None + + +def test_should_put_data( + minio_client: MinioImplementation, + buffer: BytesIO, +): + """Test putting data in Minio.""" + # ARRANGE + path = Path(os.getenv('MINIO_OBJECT_NAME', default='')) + # ACT + minio_client._put(path, buffer) + received_buffer = minio_client._get(path) + # ASSERT + assert received_buffer is not None + assert same_data(received_buffer, buffer) + + +def test_should_update_data( + minio_client: MinioImplementation, + buffer_in_minio: tuple[Path, BytesIO], +): + """Test updating data in Minio.""" + # ARRANGE + path, buffer = buffer_in_minio + updated_buffer = BytesIO(buffer.getvalue() + b'extra data') + # ACT + minio_client._put(path, updated_buffer) + received_buffer = minio_client._get(path) + # ASSERT + assert not same_data(updated_buffer, buffer) + assert received_buffer is not None + assert same_data(received_buffer, updated_buffer) + + +if __name__ == '__main__': + pytest.main(['-s', '-v', __file__]) diff --git a/shared/repositories/tests/integration/model_repository_test.py b/shared/repositories/tests/integration/model_repository_test.py new file mode 100644 index 0000000..1226e1f --- /dev/null +++ b/shared/repositories/tests/integration/model_repository_test.py @@ -0,0 +1,136 @@ +"""Integration tests for ModelRepository class.""" + +from io import BytesIO + +import pytest + +from shared.repositories import ModelData, ModelRepository + + +def same_buffer( + buffer_a: BytesIO, + buffer_b: BytesIO, +) -> bool: + """Check if 2 buffers contain the same data.""" + assert isinstance(buffer_a, BytesIO) + assert isinstance(buffer_b, BytesIO) + # read buffers + a_values = buffer_a.getvalue() + b_values = buffer_b.getvalue() + # compare length of buffers + if len(a_values) != len(b_values): + return False + # compare content of buffers + if a_values != b_values: + return False + return True + + +def same_model_data( + data_a: ModelData, + data_b: ModelData, +) -> bool: + """Check if to ModelData-objects contain the same data.""" + assert isinstance(data_a, ModelData) + assert isinstance(data_b, ModelData) + # compare names + if data_a.buffer_checksum != data_b.buffer_checksum: + return False + # compare buffer + if not same_buffer(data_a.buffer, data_b.buffer): + return False + return True + + +def test_should_have_context_handler(): + """Test that class has a working context handler implemented.""" + # ACT + with ModelRepository() as repo: + # ASSERT + assert repo.connected() + + +def test_should_get_model_data( + model_repo: ModelRepository, + model_data_in_minio: ModelData, +): + """Test getting model data.""" + # ARRANGE + object_name = ModelRepository._build_object_name(model_data_in_minio) + # ACT + received_model_data = model_repo.get_data(object_name) + # ASSERT + assert received_model_data is not None + assert isinstance(received_model_data, ModelData) + assert same_model_data(model_data_in_minio, received_model_data) + + +def test_should_get_none_when_no_model_data( + model_repo: ModelRepository, + model_data: ModelData, +): + """Test getting None whne no data is available.""" + # ARRANGE + object_name = ModelRepository._build_object_name(model_data) + # ACT + received_model_data = model_repo.get_data(object_name) + # ASSERT + assert received_model_data is None + + +def test_should_delete_model_data( + model_repo: ModelRepository, + model_data_in_minio: ModelData, +): + """Test deleting model data.""" + # ARRANGE + object_name = ModelRepository._build_object_name(model_data_in_minio) + # ACT + model_repo.remove_data(object_name) + received_model_data = model_repo.get_data(object_name) + # ASSERT + assert received_model_data is None + + +def test_should_put_model_data( + model_repo: ModelRepository, + model_data: ModelData, +): + """Test putting model data.""" + # ARRANGE + object_name = ModelRepository._build_object_name(model_data) + # ACT + model_repo.put_data(model_data) + received_model_data = model_repo.get_data(object_name) + # ASSERT + assert received_model_data is not None + assert same_model_data(model_data, received_model_data) + + +def test_should_list_names( + model_repo: ModelRepository, + model_data_in_minio: ModelData, +): + """Test get all model names.""" + # ARRANGE + new_buffer_checksum = ModelData.calculate_checksum(model_data_in_minio.buffer) + updated_model_data = model_data_in_minio.model_copy( + update={ + 'buffer_checksum': new_buffer_checksum, + }, + ) + model_repo.put_data(updated_model_data) + expected_name_list = [ + ModelRepository._build_object_name(model_data_in_minio), + ModelRepository._build_object_name(updated_model_data), + ] + # ACT + name_list = model_repo.list_names() + # ASSERT + assert len(name_list) == 2 + for name in name_list: + assert name in expected_name_list + + +if __name__ == '__main__': + pytest.main(['-s', '-v', __file__]) diff --git a/shared/repositories/tests/integration/mongo_implementation_test.py b/shared/repositories/tests/integration/mongo_implementation_test.py new file mode 100644 index 0000000..c0101bd --- /dev/null +++ b/shared/repositories/tests/integration/mongo_implementation_test.py @@ -0,0 +1,113 @@ +"""Integration tests related to Mongo implementation.""" + +import pytest + +from shared.repositories.src.implementations import MongoImplementation + + +def test_should_connect_mongo(): + """Test connecting to Mongo.""" + # ARRANGE + client = MongoImplementation() + # ACT + client.connect() + # ASSERT + assert client.connected() + client.close() + + +def test_should_have_context_handler(): + """Test that class has a working context handler implemented.""" + # ACT + with MongoImplementation() as client: + # ASSERT + assert client.connected() + + +def test_should_get_data( + mongo_client: MongoImplementation, + dictionary_in_mongo: dict, +): + """Test getting data from mongo.""" + # ARRANGE + name = dictionary_in_mongo['name'] + query = {'name': name} + # ACT + received_dictionary = mongo_client._get(query) + # ASSERT + assert received_dictionary is not None + assert isinstance(received_dictionary, dict) + assert received_dictionary == dictionary_in_mongo + + +def test_should_get_none_when_no_data( + mongo_client: MongoImplementation, + dictionary: dict, +): + """Test getting None when no data is available in mongo.""" + # ARRANGE + name = dictionary['name'] + query = {'name': name} + # ACT + received_dictionary = mongo_client._get(query) + # ASSERT + assert received_dictionary is None + + +def test_should_delete_data( + mongo_client: MongoImplementation, + dictionary_in_mongo: dict, +): + """Test deleting data from mongo.""" + # ARRANGE + name = dictionary_in_mongo['name'] + query = {'name': name} + # ACT + mongo_client._delete(query) + received_dictionary = mongo_client._get(query) + # ASSERT + assert received_dictionary is None + + +def test_should_save_data( + mongo_client: MongoImplementation, + dictionary: dict, +): + """Test saving data to mongo.""" + # ARRANGE + name = dictionary['name'] + query = {'name': name} + # ACT + mongo_client._save( + data=dictionary, + query=query, + ) + # ASSERT + received_dictionary = mongo_client._get(query) + assert received_dictionary is not None + assert isinstance(received_dictionary, dict) + assert received_dictionary == dictionary + + +def test_should_update_data( + mongo_client: MongoImplementation, + dictionary_in_mongo: dict, +): + """Test updating data in mongo.""" + # ARRANGE + name = dictionary_in_mongo['name'] + query = {'name': name} + # ACT + dictionary_in_mongo['str-key'] = 'updated-value' + mongo_client._save( + data=dictionary_in_mongo, + query=query, + ) + # ASSERT + received_dictionary = mongo_client._get(query) + assert received_dictionary is not None + assert received_dictionary == dictionary_in_mongo + + +if __name__ == '__main__': + pytest.main(['-s', '-v', __file__]) diff --git a/shared/repositories/tests/integration/visual_communication_repository_test.py b/shared/repositories/tests/integration/visual_communication_repository_test.py new file mode 100644 index 0000000..31dd119 --- /dev/null +++ b/shared/repositories/tests/integration/visual_communication_repository_test.py @@ -0,0 +1,125 @@ +"""Integration tests for VisualCommunicationRepository class.""" + +import pytest + +from shared.repositories import ( + VisualCommunicationData, + VisualCommunicationRepository, + VisualCommunicationValues, +) + + +def test_should_have_context_handler(): + """Test that class has a working context handler implemented.""" + # ACT + with VisualCommunicationRepository() as repo: + # ASSERT + assert repo.connected() + + +def test_should_get_visual_communication_data( + visual_communication_repo: VisualCommunicationRepository, + visual_communication_data_in_mongo: VisualCommunicationData, +): + """Test getting visual communication data.""" + # ARRANGE + name = visual_communication_data_in_mongo.name + # ACT + received_visual_communication_data = visual_communication_repo.get_data(name) + # ASSERT + assert received_visual_communication_data is not None + assert isinstance(received_visual_communication_data, VisualCommunicationData) + assert received_visual_communication_data == visual_communication_data_in_mongo + + +def test_should_get_none_when_no_visual_communication_data( + visual_communication_repo: VisualCommunicationRepository, + visual_communication_data: VisualCommunicationData, +): + """Test getting None when no data is available.""" + # ARRANGE + name = visual_communication_data.name + # ACT + received_visual_communication_data = visual_communication_repo.get_data(name) + # ASSERT + assert received_visual_communication_data is None + + +def test_should_delete_image_data( + visual_communication_repo: VisualCommunicationRepository, + visual_communication_data_in_mongo: VisualCommunicationData, +): + """Test deleting visual communication data.""" + # ARRANGE + name = visual_communication_data_in_mongo.name + # ACT + visual_communication_repo.remove_data(name) + received_visual_communication_data = visual_communication_repo.get_data(name) + # ASSERT + assert received_visual_communication_data is None + + +def test_should_put_visual_communication_data( + visual_communication_repo: VisualCommunicationRepository, + visual_communication_data: VisualCommunicationData, +): + """Test putting visual communication data.""" + # ARRANGE + name = visual_communication_data.name + # ACT + visual_communication_repo.put_data(visual_communication_data) + received_visual_communication_data = visual_communication_repo.get_data(name) + # ASSERT + assert received_visual_communication_data is not None + assert isinstance(received_visual_communication_data, VisualCommunicationData) + assert received_visual_communication_data == visual_communication_data + + +def test_should_update_visual_communication_data( + visual_communication_repo: VisualCommunicationRepository, + visual_communication_data_in_mongo: VisualCommunicationData, +): + """Test updating visual communication data.""" + # ARRANGE + name = visual_communication_data_in_mongo.name + updated_annotation = VisualCommunicationValues.from_random() + updated_visual_communication = VisualCommunicationData( + name=name, + annotation=updated_annotation, + ) + # ACT + visual_communication_repo.put_data(updated_visual_communication) + received_visual_communication_data = visual_communication_repo.get_data(name) + # ASSERT + assert received_visual_communication_data is not None + assert isinstance(received_visual_communication_data, VisualCommunicationData) + assert received_visual_communication_data == updated_visual_communication + + +def test_should_list_names( + visual_communication_repo: VisualCommunicationRepository, + visual_communication_data_in_mongo: VisualCommunicationData, +): + """Test listing names of all documents.""" + # ARRANGE + name = 'test-visual-communication-2' + annotation = VisualCommunicationValues.from_random() + second_visual_communication = VisualCommunicationData( + name=name, + annotation=annotation, + ) + visual_communication_repo.put_data(second_visual_communication) + expected_name_list = [ + visual_communication_data_in_mongo.name, + second_visual_communication.name, + ] + # ACT + name_list = visual_communication_repo.list_names() + # ASSERT + assert len(name_list) == 2 + for name in name_list: + assert name in expected_name_list + + +if __name__ == '__main__': + pytest.main(['-s', '-v', __file__]) -- 2.54.0 From 88a20c4b0b862e0d48379d5da96bed8c7be8ae07 Mon Sep 17 00:00:00 2001 From: brian Date: Fri, 28 Feb 2025 22:54:53 +0000 Subject: [PATCH 06/64] corrected type hints --- shared/docstore/src/docstore_mongo.py | 8 ++++---- .../src/implementations/mongo_implementation.py | 8 ++++---- .../repositories/src/visual_communication_repository.py | 6 +++--- shared/repositories/tests/integration/conftest.py | 2 +- 4 files changed, 12 insertions(+), 12 deletions(-) diff --git a/shared/docstore/src/docstore_mongo.py b/shared/docstore/src/docstore_mongo.py index 9b83a6e..cd665b8 100644 --- a/shared/docstore/src/docstore_mongo.py +++ b/shared/docstore/src/docstore_mongo.py @@ -40,7 +40,7 @@ class DocstoreMongo(DocstoreInterface): mongo_database = str(os.getenv('MONGO_DB')) mongo_collection = str(os.getenv('MONGO_COLLECTION')) # connect client - client = MongoClient(mongo_endpoint) + client: MongoClient = MongoClient(mongo_endpoint) database = client[mongo_database] collection = database[mongo_collection] # set unique index on 'name' @@ -53,9 +53,9 @@ class DocstoreMongo(DocstoreInterface): def close(self) -> None: """Close connection to Mongo server.""" self._client.close() - self._client = None - self._database = None - self._collection = None + self._client = None # type: ignore + self._database = None # type: ignore + self._collection = None # type: ignore def __enter__(self) -> DocstoreMongo: self.connect() diff --git a/shared/repositories/src/implementations/mongo_implementation.py b/shared/repositories/src/implementations/mongo_implementation.py index 1d43439..853cf9b 100644 --- a/shared/repositories/src/implementations/mongo_implementation.py +++ b/shared/repositories/src/implementations/mongo_implementation.py @@ -39,7 +39,7 @@ class MongoImplementation(DatabaseInterface): mongo_database = str(os.getenv('MONGO_DB')) mongo_collection = str(os.getenv('MONGO_COLLECTION')) # connect client - client = MongoClient(mongo_endpoint) + client: MongoClient = MongoClient(mongo_endpoint) database = client[mongo_database] collection = database[mongo_collection] # set unique index on 'name' @@ -52,9 +52,9 @@ class MongoImplementation(DatabaseInterface): def close(self) -> None: """Close connection to Mongo server.""" self._client.close() - self._client = None - self._database = None - self._collection = None + self._client = None # type: ignore + self._database = None # type: ignore + self._collection = None # type: ignore def connected(self) -> bool: """Check connection to Mongo.""" diff --git a/shared/repositories/src/visual_communication_repository.py b/shared/repositories/src/visual_communication_repository.py index 5322906..376ed8f 100644 --- a/shared/repositories/src/visual_communication_repository.py +++ b/shared/repositories/src/visual_communication_repository.py @@ -34,11 +34,11 @@ class VisualCommunicationRepository(VisualCommunicationInterface, MongoImplement """Put visual communication data.""" assert isinstance(data, VisualCommunicationData) # convert to dict - data = data.model_dump(mode='json') + data_dict: dict = data.model_dump(mode='json') # build query - query = {'name': data['name']} + query = {'name': data.name} # save to mongo - self._save(data, query) + self._save(data_dict, query) def remove_data(self, name: str) -> None: """Remove visual communication data.""" diff --git a/shared/repositories/tests/integration/conftest.py b/shared/repositories/tests/integration/conftest.py index a17e012..9f2775a 100644 --- a/shared/repositories/tests/integration/conftest.py +++ b/shared/repositories/tests/integration/conftest.py @@ -328,7 +328,7 @@ def raw_mongo_client( mongo_endpoint = str(os.getenv('MONGO_ENDPOINT')) mongo_database = str(os.getenv('MONGO_DB')) # connect client - client = MongoClient(mongo_endpoint) + client: MongoClient = MongoClient(mongo_endpoint) _ = client[mongo_database] # expose client yield client -- 2.54.0 From 10ce0d9124c914be8ff75006cff5e74bd90de6c6 Mon Sep 17 00:00:00 2001 From: brian Date: Thu, 6 Mar 2025 20:19:52 +0000 Subject: [PATCH 07/64] updated to recommended CI install method --- .gitea/workflows/pull.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitea/workflows/pull.yaml b/.gitea/workflows/pull.yaml index 452ad07..9aa175a 100644 --- a/.gitea/workflows/pull.yaml +++ b/.gitea/workflows/pull.yaml @@ -20,7 +20,7 @@ jobs: PIP_INDEX_URL: ${{ vars.PIP_INDEX_URL }} PIP_TRUSTED_HOST: ${{ vars.PIP_TRUSTED_HOST }} run: | - pip install poetry + pipx install poetry==1.8.3 poetry install - name: PEP8 Check run: | -- 2.54.0 From d92051f5c442980fcb9b6c3d85fda71980f96e16 Mon Sep 17 00:00:00 2001 From: brian Date: Thu, 6 Mar 2025 20:23:16 +0000 Subject: [PATCH 08/64] new attempt at installing poetry --- .gitea/workflows/pull.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitea/workflows/pull.yaml b/.gitea/workflows/pull.yaml index 9aa175a..453e8ba 100644 --- a/.gitea/workflows/pull.yaml +++ b/.gitea/workflows/pull.yaml @@ -20,7 +20,7 @@ jobs: PIP_INDEX_URL: ${{ vars.PIP_INDEX_URL }} PIP_TRUSTED_HOST: ${{ vars.PIP_TRUSTED_HOST }} run: | - pipx install poetry==1.8.3 + curl -sSL https://install.python-poetry.org | POETRY_VERSION=1.8.3 python3 - poetry install - name: PEP8 Check run: | -- 2.54.0 From 4827a3f7ddf543de6bc0f43a2c85e07d9b6f4177 Mon Sep 17 00:00:00 2001 From: brian Date: Thu, 6 Mar 2025 20:26:56 +0000 Subject: [PATCH 09/64] next attempt at installing poetry --- .gitea/workflows/pull.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.gitea/workflows/pull.yaml b/.gitea/workflows/pull.yaml index 453e8ba..e884f1b 100644 --- a/.gitea/workflows/pull.yaml +++ b/.gitea/workflows/pull.yaml @@ -19,8 +19,10 @@ jobs: env: PIP_INDEX_URL: ${{ vars.PIP_INDEX_URL }} PIP_TRUSTED_HOST: ${{ vars.PIP_TRUSTED_HOST }} + POETRY_VERSION: 1.8.3 + POETRY_HOME: /etc/poetry run: | - curl -sSL https://install.python-poetry.org | POETRY_VERSION=1.8.3 python3 - + curl -sSL https://install.python-poetry.org | python3 - poetry install - name: PEP8 Check run: | -- 2.54.0 From ee304f1a75497a9391f4ce972a080424f6fbd6d8 Mon Sep 17 00:00:00 2001 From: brian Date: Thu, 6 Mar 2025 20:36:42 +0000 Subject: [PATCH 10/64] yet another attempt at installing poetry --- .gitea/workflows/pull.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitea/workflows/pull.yaml b/.gitea/workflows/pull.yaml index e884f1b..4384048 100644 --- a/.gitea/workflows/pull.yaml +++ b/.gitea/workflows/pull.yaml @@ -23,6 +23,7 @@ jobs: POETRY_HOME: /etc/poetry run: | curl -sSL https://install.python-poetry.org | python3 - + export PATH=$POETRY_HOME/bin:$PATH poetry install - name: PEP8 Check run: | -- 2.54.0 From 6840ac72f1c8982e8b71949bb4b1518eb36a18a9 Mon Sep 17 00:00:00 2001 From: brian Date: Thu, 6 Mar 2025 20:56:59 +0000 Subject: [PATCH 11/64] try again with poetry --- .gitea/workflows/pull.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.gitea/workflows/pull.yaml b/.gitea/workflows/pull.yaml index 4384048..1cdd82e 100644 --- a/.gitea/workflows/pull.yaml +++ b/.gitea/workflows/pull.yaml @@ -22,7 +22,8 @@ jobs: POETRY_VERSION: 1.8.3 POETRY_HOME: /etc/poetry run: | - curl -sSL https://install.python-poetry.org | python3 - + python3 -m venv $POETRY_HOME + $POETRY_HOME/bin/pip install poetry export PATH=$POETRY_HOME/bin:$PATH poetry install - name: PEP8 Check -- 2.54.0 From 9e66981d3e2a6e5422c6bcf0f634e36a3a9fe3f7 Mon Sep 17 00:00:00 2001 From: brian Date: Thu, 6 Mar 2025 21:02:17 +0000 Subject: [PATCH 12/64] next attempt --- .gitea/workflows/pull.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitea/workflows/pull.yaml b/.gitea/workflows/pull.yaml index 1cdd82e..79dbc43 100644 --- a/.gitea/workflows/pull.yaml +++ b/.gitea/workflows/pull.yaml @@ -23,7 +23,7 @@ jobs: POETRY_HOME: /etc/poetry run: | python3 -m venv $POETRY_HOME - $POETRY_HOME/bin/pip install poetry + $POETRY_HOME/bin/pip install poetry==$POETRY_VERSION export PATH=$POETRY_HOME/bin:$PATH poetry install - name: PEP8 Check -- 2.54.0 From c2a2c3496764947600f0803e7788e496ecd84eaf Mon Sep 17 00:00:00 2001 From: brian Date: Thu, 6 Mar 2025 21:04:24 +0000 Subject: [PATCH 13/64] again --- .gitea/workflows/pull.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.gitea/workflows/pull.yaml b/.gitea/workflows/pull.yaml index 79dbc43..4384048 100644 --- a/.gitea/workflows/pull.yaml +++ b/.gitea/workflows/pull.yaml @@ -22,8 +22,7 @@ jobs: POETRY_VERSION: 1.8.3 POETRY_HOME: /etc/poetry run: | - python3 -m venv $POETRY_HOME - $POETRY_HOME/bin/pip install poetry==$POETRY_VERSION + curl -sSL https://install.python-poetry.org | python3 - export PATH=$POETRY_HOME/bin:$PATH poetry install - name: PEP8 Check -- 2.54.0 From d9bd5be46d6076e6e275555f5547a30fc51a6117 Mon Sep 17 00:00:00 2001 From: brian Date: Thu, 6 Mar 2025 21:06:50 +0000 Subject: [PATCH 14/64] again again --- .gitea/workflows/pull.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitea/workflows/pull.yaml b/.gitea/workflows/pull.yaml index 4384048..9af9aa1 100644 --- a/.gitea/workflows/pull.yaml +++ b/.gitea/workflows/pull.yaml @@ -21,6 +21,7 @@ jobs: PIP_TRUSTED_HOST: ${{ vars.PIP_TRUSTED_HOST }} POETRY_VERSION: 1.8.3 POETRY_HOME: /etc/poetry + POETRY_NO_INTERACTION: 1 run: | curl -sSL https://install.python-poetry.org | python3 - export PATH=$POETRY_HOME/bin:$PATH -- 2.54.0 From 29bf41c7da029336b11fc14f734b318ae9fe5f67 Mon Sep 17 00:00:00 2001 From: brian Date: Thu, 6 Mar 2025 21:16:06 +0000 Subject: [PATCH 15/64] next try --- .gitea/workflows/pull.yaml | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/.gitea/workflows/pull.yaml b/.gitea/workflows/pull.yaml index 9af9aa1..45dfeac 100644 --- a/.gitea/workflows/pull.yaml +++ b/.gitea/workflows/pull.yaml @@ -20,11 +20,8 @@ jobs: PIP_INDEX_URL: ${{ vars.PIP_INDEX_URL }} PIP_TRUSTED_HOST: ${{ vars.PIP_TRUSTED_HOST }} POETRY_VERSION: 1.8.3 - POETRY_HOME: /etc/poetry - POETRY_NO_INTERACTION: 1 run: | - curl -sSL https://install.python-poetry.org | python3 - - export PATH=$POETRY_HOME/bin:$PATH + pipx install poetry==$POETRY_VERSION poetry install - name: PEP8 Check run: | -- 2.54.0 From 813daa0c90f72f92b94fdd9e2b26fae3d5ce70e5 Mon Sep 17 00:00:00 2001 From: brian Date: Thu, 6 Mar 2025 21:22:52 +0000 Subject: [PATCH 16/64] next attempt --- .gitea/workflows/pull.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.gitea/workflows/pull.yaml b/.gitea/workflows/pull.yaml index 45dfeac..4294f16 100644 --- a/.gitea/workflows/pull.yaml +++ b/.gitea/workflows/pull.yaml @@ -20,8 +20,11 @@ jobs: PIP_INDEX_URL: ${{ vars.PIP_INDEX_URL }} PIP_TRUSTED_HOST: ${{ vars.PIP_TRUSTED_HOST }} POETRY_VERSION: 1.8.3 + POETRY_HOME: /opt/poetry + POETRY_NO_INTERACTION: 1 run: | - pipx install poetry==$POETRY_VERSION + curl -sSL https://install.python-poetry.org | python3 - + export PATH=$POETRY_HOME/bin:$PATH poetry install - name: PEP8 Check run: | -- 2.54.0 From d4c9738db439ef63835835564acaf37851fe72e7 Mon Sep 17 00:00:00 2001 From: brian Date: Thu, 6 Mar 2025 21:29:52 +0000 Subject: [PATCH 17/64] next try --- .gitea/workflows/pull.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/.gitea/workflows/pull.yaml b/.gitea/workflows/pull.yaml index 4294f16..e48e7a5 100644 --- a/.gitea/workflows/pull.yaml +++ b/.gitea/workflows/pull.yaml @@ -15,16 +15,19 @@ jobs: with: python-verison: "3.12" architecture: "x64" - - name: Install Packages + - name: Setup poetry env: - PIP_INDEX_URL: ${{ vars.PIP_INDEX_URL }} - PIP_TRUSTED_HOST: ${{ vars.PIP_TRUSTED_HOST }} POETRY_VERSION: 1.8.3 POETRY_HOME: /opt/poetry POETRY_NO_INTERACTION: 1 run: | curl -sSL https://install.python-poetry.org | python3 - export PATH=$POETRY_HOME/bin:$PATH + - name: Install Dependencies + env: + PIP_INDEX_URL: ${{ vars.PIP_INDEX_URL }} + PIP_TRUSTED_HOST: ${{ vars.PIP_TRUSTED_HOST }} + run: | poetry install - name: PEP8 Check run: | -- 2.54.0 From 31be0d7aac0315c14f6ef54a2916fcaa007e2d00 Mon Sep 17 00:00:00 2001 From: brian Date: Thu, 6 Mar 2025 21:34:14 +0000 Subject: [PATCH 18/64] added check for poetry installation --- .gitea/workflows/pull.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitea/workflows/pull.yaml b/.gitea/workflows/pull.yaml index e48e7a5..7a4b55f 100644 --- a/.gitea/workflows/pull.yaml +++ b/.gitea/workflows/pull.yaml @@ -23,6 +23,7 @@ jobs: run: | curl -sSL https://install.python-poetry.org | python3 - export PATH=$POETRY_HOME/bin:$PATH + poetry --version - name: Install Dependencies env: PIP_INDEX_URL: ${{ vars.PIP_INDEX_URL }} -- 2.54.0 From 4bcfbbed0a98f138e14e07077176d1f4afa63922 Mon Sep 17 00:00:00 2001 From: brian Date: Thu, 6 Mar 2025 22:02:06 +0000 Subject: [PATCH 19/64] removed usage of testcontainers --- .../tests/integration/conftest.py | 53 ++----------------- 1 file changed, 5 insertions(+), 48 deletions(-) diff --git a/shared/repositories/tests/integration/conftest.py b/shared/repositories/tests/integration/conftest.py index 9f2775a..16f25e7 100644 --- a/shared/repositories/tests/integration/conftest.py +++ b/shared/repositories/tests/integration/conftest.py @@ -10,8 +10,6 @@ import minio import pytest from PIL import Image from pymongo import MongoClient -from testcontainers.minio import MinioContainer -from testcontainers.mongodb import MongoDbContainer from model.src.models import VisualCommunicationModel from shared.repositories import ( @@ -48,58 +46,24 @@ env_var_map = { 'MINIO_OBJECT_NAME': 'test-object', 'MINIO_IMAGE_NAME': 'test-image', 'MONGO_ENDPOINT': ( - f'mongodb://{MONGO_USERNAME}:{MONGO_PASSWORD}' f'@localhost:{MONGO_PORT}/' + f'mongodb://{MONGO_USERNAME}:{MONGO_PASSWORD}@localhost:{MONGO_PORT}/' ), # updated when container is running 'MONGO_DB': 'test-db', 'MONGO_COLLECTION': 'test-collection', } -container_map = { - 'minio': MinioContainer( - port=MINIO_PORT, - access_key=MINIO_ACCESS_KEY, - secret_key=MINIO_SECRET_KEY, - ), - 'mongo': MongoDbContainer( - port=MONGO_PORT, - username=MONGO_USERNAME, - password=MONGO_PASSWORD, - dbname=env_var_map['MONGO_DB'], - ), -} - - -@pytest.fixture(scope='session', autouse=True) -def setup_infrastructure(request: pytest.FixtureRequest) -> None: - """Prepare infrastructure for integration test.""" - # prepare infrastructure - for container in container_map.values(): - container.start() - # update env var map - minio_host = container_map['minio'].get_container_host_ip() - minio_port = container_map['minio'].get_exposed_port(MINIO_PORT) - env_var_map['MINIO_ENDPOINT'] = f'{minio_host}:{minio_port}' - mongo_host = container_map['mongo'].get_container_host_ip() - mongo_port = container_map['mongo'].get_exposed_port(MONGO_PORT) - env_var_map['MONGO_ENDPOINT'] = ( - f'mongodb://{MONGO_USERNAME}:{MONGO_PASSWORD}@{mongo_host}:{mongo_port}/' - ) - - # ensure cleanup - def cleanup_infrastructure(): - for container in container_map.values(): - container.stop() - - request.addfinalizer(cleanup_infrastructure) @pytest.fixture(scope='session', autouse=True) def populate_env( request: pytest.FixtureRequest, - setup_infrastructure, ) -> None: """Populate environment with variables used for testing.""" # update env for key, val in env_var_map.items(): + # skip if already set by CI pipeline + if key in os.environ: + continue + # set env var os.environ[key] = val # ensure cleanup @@ -112,7 +76,6 @@ def populate_env( @pytest.fixture(scope='session') def raw_minio_client( - setup_infrastructure, populate_env, ) -> Iterator[minio.Minio]: """Raw Minio client fixture.""" @@ -145,7 +108,6 @@ def raw_minio_client( @pytest.fixture def minio_client( - setup_infrastructure, populate_env, ) -> Iterator[MinioImplementation]: """MinioImplementation fixture.""" @@ -247,7 +209,6 @@ def image_data_in_minio( @pytest.fixture(scope='session') def image_repo( - setup_infrastructure, populate_env, ) -> Iterator[ImageRepository]: """Image repository fixture.""" @@ -308,7 +269,6 @@ def model_data_in_minio( @pytest.fixture(scope='session') def model_repo( - setup_infrastructure, populate_env, ) -> Iterator[ModelRepository]: """Model repository fixture.""" @@ -320,7 +280,6 @@ def model_repo( @pytest.fixture def raw_mongo_client( - setup_infrastructure, populate_env, ) -> Iterator[MongoClient]: """Raw mongo client fixture.""" @@ -338,7 +297,6 @@ def raw_mongo_client( @pytest.fixture def mongo_client( - setup_infrastructure, populate_env, ) -> Iterator[MongoImplementation]: """MongoImplementation fixture.""" @@ -434,7 +392,6 @@ def visual_communication_data_in_mongo( @pytest.fixture(scope='session') def visual_communication_repo( - setup_infrastructure, populate_env, ) -> Iterator[VisualCommunicationRepository]: """Visual communication repository fixture.""" -- 2.54.0 From a2f892e35c713a4e27cfc2aec4fd7d1d4c8cc021 Mon Sep 17 00:00:00 2001 From: brian Date: Thu, 6 Mar 2025 22:02:21 +0000 Subject: [PATCH 20/64] added env var for CI testing --- .gitea/workflows/pull.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitea/workflows/pull.yaml b/.gitea/workflows/pull.yaml index 7a4b55f..b635f51 100644 --- a/.gitea/workflows/pull.yaml +++ b/.gitea/workflows/pull.yaml @@ -41,6 +41,7 @@ jobs: MINIO_ENDPOINT: ${{ vars.MINIO_ENDPOINT }} MINIO_ACCESS_KEY: ${{ secrets.MINIO_ACCESS_KEY }} MINIO_SECRET_KEY: ${{ secrets.MINIO_SECRET_KEY }} + MONGO_ENDPOINT: ${{ vars.MONGO_ENDPOINT }} run: | 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"pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] [package.source] type = "legacy" -- 2.54.0 From 9af3d9bc54d682eec5d886cfef156fc298ef7675 Mon Sep 17 00:00:00 2001 From: brian Date: Sat, 8 Mar 2025 21:19:18 +0000 Subject: [PATCH 31/64] update pre-commit --- .pre-commit-config.yaml | 14 +- poetry.lock | 2444 +++++++++++++++++++++++---------------- pyproject.toml | 1 + 3 files changed, 1485 insertions(+), 974 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 12c3384..9c3e5d3 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.5.0 + rev: v5.0.0 hooks: - id: trailing-whitespace - id: end-of-file-fixer @@ -9,7 +9,7 @@ repos: - id: double-quote-string-fixer - id: name-tests-test - repo: https://github.com/asottile/setup-cfg-fmt - rev: v2.5.0 + rev: v2.7.0 hooks: - id: setup-cfg-fmt - repo: https://github.com/pre-commit/mirrors-isort @@ -23,24 +23,24 @@ repos: hooks: - id: add-trailing-comma - repo: https://github.com/asottile/pyupgrade - rev: v3.15.1 + rev: v3.19.1 hooks: - id: pyupgrade args: [--py39-plus] - repo: https://github.com/PyCQA/flake8 - rev: 7.0.0 + rev: 7.1.2 hooks: - id: flake8 entry: pflake8 additional_dependencies: - "pyproject-flake8" - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.8.0 + rev: v1.15.0 hooks: - id: mypy exclude: ^testing/resources/ - repo: https://github.com/psf/black - rev: 24.4.2 + rev: 25.1.0 hooks: - id: black language_version: python3.12 @@ -55,7 +55,7 @@ repos: language: python types: [ python ] - repo: https://github.com/jendrikseipp/vulture - rev: 'v2.6' + rev: 'v2.14' hooks: - id: vulture entry: vulture . --min-confidence 90 --exclude */.venv/*.py,*/tests/*.py diff --git a/poetry.lock b/poetry.lock index 18dd9a7..8d72f9b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.1.1 and should not be changed by hand. 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4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.gitea/workflows/pull.yaml b/.gitea/workflows/pull.yaml index a41da31..4778cfd 100644 --- a/.gitea/workflows/pull.yaml +++ b/.gitea/workflows/pull.yaml @@ -9,9 +9,9 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout Code - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Setup Environment - uses: https://github.com/actions/setup-python@v3 + uses: https://github.com/actions/setup-python@v5 with: python-verison: "3.12" architecture: "x64" -- 2.54.0 From df2c2b7e5f3ce3a3d6333220af7c6128019003a0 Mon Sep 17 00:00:00 2001 From: brian Date: Mon, 10 Mar 2025 19:17:42 +0000 Subject: [PATCH 38/64] corrected spelling mistake --- .gitea/workflows/pull.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitea/workflows/pull.yaml b/.gitea/workflows/pull.yaml index 4778cfd..1ebed4d 100644 --- a/.gitea/workflows/pull.yaml +++ b/.gitea/workflows/pull.yaml @@ -13,7 +13,7 @@ jobs: - name: Setup Environment uses: https://github.com/actions/setup-python@v5 with: - python-verison: "3.12" + python-version: "3.12" architecture: "x64" - name: Setup poetry env: -- 2.54.0 From cb8d17cbc3cc9647beac2c7acaedc71f260d98cf Mon Sep 17 00:00:00 2001 From: brian Date: Mon, 10 Mar 2025 19:25:12 +0000 Subject: [PATCH 39/64] fixed poetry path --- .gitea/workflows/pull.yaml | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/.gitea/workflows/pull.yaml b/.gitea/workflows/pull.yaml index 1ebed4d..6149f35 100644 --- a/.gitea/workflows/pull.yaml +++ b/.gitea/workflows/pull.yaml @@ -26,18 +26,16 @@ jobs: poetry --version - name: Install Dependencies env: - POETRY_HOME: /opt/poetry PIP_INDEX_URL: ${{ vars.PIP_INDEX_URL }} PIP_TRUSTED_HOST: ${{ vars.PIP_TRUSTED_HOST }} run: | - export PATH=$POETRY_HOME/bin:$PATH - poetry install + /opt/poetry/bin/poetry install - name: PEP8 Check run: | - poetry run flake8 . --benchmark + /opt/poetry/bin/poetry run flake8 . --benchmark - name: Type Check run: | - poetry run mypy . + /opt/poetry/bin/poetry run mypy . - name: Pytest & Calculate Coverage env: MINIO_ENDPOINT: ${{ vars.MINIO_ENDPOINT }} @@ -45,7 +43,7 @@ jobs: MINIO_SECRET_KEY: ${{ secrets.MINIO_SECRET_KEY }} MONGO_ENDPOINT: ${{ vars.MONGO_ENDPOINT }} run: | - poetry run coverage run -m pytest . + /opt/poetry/bin/poetry run coverage run -m pytest . - name: Coverage Report run: | - poetry run coverage report -m + /opt/poetry/bin/poetry run coverage report -m -- 2.54.0 From 33d30941a6c1bbadb7956a1190e48fb63cd27ffc Mon Sep 17 00:00:00 2001 From: brian Date: Mon, 17 Mar 2025 18:06:46 +0000 Subject: [PATCH 40/64] updated to run locally --- .../repositories/tests/integration/conftest.py | 18 +++++------------- 1 file changed, 5 insertions(+), 13 deletions(-) diff --git a/shared/repositories/tests/integration/conftest.py b/shared/repositories/tests/integration/conftest.py index 16f25e7..209c951 100644 --- a/shared/repositories/tests/integration/conftest.py +++ b/shared/repositories/tests/integration/conftest.py @@ -8,6 +8,7 @@ from pathlib import Path import minio import pytest +from dotenv import load_dotenv from PIL import Image from pymongo import MongoClient @@ -30,24 +31,15 @@ from shared.repositories.src.implementations import ( # set random seed for reproducibility random.seed(13) -# define test static variables -MINIO_PORT = 9000 -MINIO_ACCESS_KEY = 'minioadmin' -MINIO_SECRET_KEY = 'minioadmin' -MONGO_PORT = 27017 -MONGO_USERNAME = 'admin' -MONGO_PASSWORD = 'password' +# load loca test environment variables +test_env_path = Path(__file__).parent.parent.parent.parent.parent / 'test.env' +load_dotenv('test.env') +# define test environment variables env_var_map = { - 'MINIO_ENDPOINT': f'localhost:{MINIO_PORT}', # updated when container is running - 'MINIO_ACCESS_KEY': MINIO_ACCESS_KEY, - 'MINIO_SECRET_KEY': MINIO_SECRET_KEY, 'MINIO_BUCKET_NAME': 'test-bucket', 'MINIO_OBJECT_NAME': 'test-object', 'MINIO_IMAGE_NAME': 'test-image', - 'MONGO_ENDPOINT': ( - f'mongodb://{MONGO_USERNAME}:{MONGO_PASSWORD}@localhost:{MONGO_PORT}/' - ), # updated when container is running 'MONGO_DB': 'test-db', 'MONGO_COLLECTION': 'test-collection', } -- 2.54.0 From 282fee08062ab5411bec046e615415210bf9b2ee Mon Sep 17 00:00:00 2001 From: brian Date: Mon, 17 Mar 2025 20:57:30 +0000 Subject: [PATCH 41/64] fixed spelling mistake --- shared/repositories/tests/integration/conftest.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/shared/repositories/tests/integration/conftest.py b/shared/repositories/tests/integration/conftest.py index 209c951..30802c7 100644 --- a/shared/repositories/tests/integration/conftest.py +++ b/shared/repositories/tests/integration/conftest.py @@ -31,7 +31,7 @@ from shared.repositories.src.implementations import ( # set random seed for reproducibility random.seed(13) -# load loca test environment variables +# load local test environment variables test_env_path = Path(__file__).parent.parent.parent.parent.parent / 'test.env' load_dotenv('test.env') -- 2.54.0 From e9340f17c4c1b8ac4f0292ae885475329fb6d9bd Mon Sep 17 00:00:00 2001 From: brian Date: Mon, 17 Mar 2025 20:57:43 +0000 Subject: [PATCH 42/64] print out env vars for debugging --- .gitea/workflows/pull.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.gitea/workflows/pull.yaml b/.gitea/workflows/pull.yaml index 6149f35..3cfda55 100644 --- a/.gitea/workflows/pull.yaml +++ b/.gitea/workflows/pull.yaml @@ -43,6 +43,10 @@ jobs: MINIO_SECRET_KEY: ${{ secrets.MINIO_SECRET_KEY }} MONGO_ENDPOINT: ${{ vars.MONGO_ENDPOINT }} run: | + echo "MINIO_ENDPOINT=${MINIO_ENDPOINT}" + echo "MINIO_ACCESS_KEY=${MINIO_ACCESS_KEY}" + echo "MINIO_SECRET_KEY=${MINIO_SECRET_KEY}" + echo "MONGO_ENDPOINT=${MONGO_ENDPOINT}" /opt/poetry/bin/poetry run coverage run -m pytest . - name: Coverage Report run: | -- 2.54.0 From 5870c3b0a3a0d5769ee0e655db329711e5739e9c Mon Sep 17 00:00:00 2001 From: brian Date: Mon, 17 Mar 2025 21:11:52 +0000 Subject: [PATCH 43/64] added no chache-option to poetry --- .gitea/workflows/pull.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitea/workflows/pull.yaml b/.gitea/workflows/pull.yaml index 3cfda55..3851ca4 100644 --- a/.gitea/workflows/pull.yaml +++ b/.gitea/workflows/pull.yaml @@ -20,6 +20,7 @@ jobs: POETRY_VERSION: 2.1.1 POETRY_HOME: /opt/poetry POETRY_NO_INTERACTION: 1 + POETRY_NO_CACHE: 1 run: | curl -sSL https://install.python-poetry.org | python3 - export PATH=$POETRY_HOME/bin:$PATH -- 2.54.0 From 66370a33c270779728451c661f22aa55df1ce6cc Mon Sep 17 00:00:00 2001 From: brian Date: Mon, 17 Mar 2025 21:12:19 +0000 Subject: [PATCH 44/64] tried to add if-statement to load_dotenv to see if this disturbs CI tests --- shared/repositories/tests/integration/conftest.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/shared/repositories/tests/integration/conftest.py b/shared/repositories/tests/integration/conftest.py index 30802c7..1c97d4e 100644 --- a/shared/repositories/tests/integration/conftest.py +++ b/shared/repositories/tests/integration/conftest.py @@ -33,7 +33,8 @@ random.seed(13) # load local test environment variables test_env_path = Path(__file__).parent.parent.parent.parent.parent / 'test.env' -load_dotenv('test.env') +if test_env_path.exists(): + load_dotenv('test.env') # define test environment variables env_var_map = { -- 2.54.0 From 77a3219f396bf308180383bf6b5a0d060de606a0 Mon Sep 17 00:00:00 2001 From: brian Date: Mon, 17 Mar 2025 21:13:21 +0000 Subject: [PATCH 45/64] fixed path variable --- shared/repositories/tests/integration/conftest.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/shared/repositories/tests/integration/conftest.py b/shared/repositories/tests/integration/conftest.py index 1c97d4e..9e47163 100644 --- a/shared/repositories/tests/integration/conftest.py +++ b/shared/repositories/tests/integration/conftest.py @@ -34,7 +34,7 @@ random.seed(13) # load local test environment variables test_env_path = Path(__file__).parent.parent.parent.parent.parent / 'test.env' if test_env_path.exists(): - load_dotenv('test.env') + load_dotenv(test_env_path.as_posix()) # define test environment variables env_var_map = { -- 2.54.0 From 9c8089d091c86f4a5440cc193d238a1bd4e76410 Mon Sep 17 00:00:00 2001 From: brian Date: Mon, 17 Mar 2025 21:34:17 +0000 Subject: [PATCH 46/64] tried explicit export statements --- .gitea/workflows/pull.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.gitea/workflows/pull.yaml b/.gitea/workflows/pull.yaml index 3851ca4..3a9557f 100644 --- a/.gitea/workflows/pull.yaml +++ b/.gitea/workflows/pull.yaml @@ -44,10 +44,10 @@ jobs: MINIO_SECRET_KEY: ${{ secrets.MINIO_SECRET_KEY }} MONGO_ENDPOINT: ${{ vars.MONGO_ENDPOINT }} run: | - echo "MINIO_ENDPOINT=${MINIO_ENDPOINT}" - echo "MINIO_ACCESS_KEY=${MINIO_ACCESS_KEY}" - echo "MINIO_SECRET_KEY=${MINIO_SECRET_KEY}" - echo "MONGO_ENDPOINT=${MONGO_ENDPOINT}" + export "MINIO_ENDPOINT=${MINIO_ENDPOINT}" + export "MINIO_ACCESS_KEY=${MINIO_ACCESS_KEY}" + export "MINIO_SECRET_KEY=${MINIO_SECRET_KEY}" + export "MONGO_ENDPOINT=${MONGO_ENDPOINT}" /opt/poetry/bin/poetry run coverage run -m pytest . - name: Coverage Report run: | -- 2.54.0 From 62519c371eb6d134eb3969bc33e12c6b274a7218 Mon Sep 17 00:00:00 2001 From: brian Date: Mon, 17 Mar 2025 21:41:42 +0000 Subject: [PATCH 47/64] removed explicitly setting env vars --- .gitea/workflows/pull.yaml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/.gitea/workflows/pull.yaml b/.gitea/workflows/pull.yaml index 3a9557f..03597f2 100644 --- a/.gitea/workflows/pull.yaml +++ b/.gitea/workflows/pull.yaml @@ -44,10 +44,6 @@ jobs: MINIO_SECRET_KEY: ${{ secrets.MINIO_SECRET_KEY }} MONGO_ENDPOINT: ${{ vars.MONGO_ENDPOINT }} run: | - export "MINIO_ENDPOINT=${MINIO_ENDPOINT}" - export "MINIO_ACCESS_KEY=${MINIO_ACCESS_KEY}" - export "MINIO_SECRET_KEY=${MINIO_SECRET_KEY}" - export "MONGO_ENDPOINT=${MONGO_ENDPOINT}" /opt/poetry/bin/poetry run coverage run -m pytest . - name: Coverage Report run: | -- 2.54.0 From 14a41256884579a4d21ab8de82b47f0631d3aef1 Mon Sep 17 00:00:00 2001 From: brian Date: Mon, 17 Mar 2025 21:44:13 +0000 Subject: [PATCH 48/64] updated to give full list of missing env vars --- shared/utils/check_env.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/shared/utils/check_env.py b/shared/utils/check_env.py index d35d23c..61af197 100644 --- a/shared/utils/check_env.py +++ b/shared/utils/check_env.py @@ -10,6 +10,9 @@ def check_env( assert isinstance(var_list, set) assert all(isinstance(elem, str) for elem in var_list) # check that env vars are set + missing_vars = [] for env_var in var_list: if env_var not in os.environ: - raise OSError(f"environment variable not set: {env_var}") + missing_vars.append(env_var) + if len(missing_vars) > 0: + raise OSError(f"environment variable(s) not set: {missing_vars}") -- 2.54.0 From 790204af6aa91ad0c001d11e79c005b4007161b2 Mon Sep 17 00:00:00 2001 From: brian Date: Mon, 17 Mar 2025 21:48:43 +0000 Subject: [PATCH 49/64] updated logical check --- shared/utils/check_env.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/shared/utils/check_env.py b/shared/utils/check_env.py index 61af197..95a0a03 100644 --- a/shared/utils/check_env.py +++ b/shared/utils/check_env.py @@ -14,5 +14,5 @@ def check_env( for env_var in var_list: if env_var not in os.environ: missing_vars.append(env_var) - if len(missing_vars) > 0: + if missing_vars: raise OSError(f"environment variable(s) not set: {missing_vars}") -- 2.54.0 From 096ffd56e9b8f496d9c431e88388674870eee2f2 Mon Sep 17 00:00:00 2001 From: brian Date: Mon, 17 Mar 2025 21:54:52 +0000 Subject: [PATCH 50/64] added explicit env var checking --- shared/repositories/tests/integration/conftest.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/shared/repositories/tests/integration/conftest.py b/shared/repositories/tests/integration/conftest.py index 9e47163..a34243d 100644 --- a/shared/repositories/tests/integration/conftest.py +++ b/shared/repositories/tests/integration/conftest.py @@ -37,6 +37,10 @@ if test_env_path.exists(): load_dotenv(test_env_path.as_posix()) # define test environment variables +assert 'MINIO_ENDPOINT' in os.environ, 'MINIO_ENDPOINT not set' +assert 'MINIO_ACCESS_KEY' in os.environ, 'MINIO_ACCESS_KEY not set' +assert 'MINIO_SECRET_KEY' in os.environ, 'MINIO_SECRET_KEY not set' +assert 'MONGO_ENDPOINT' in os.environ, 'MONGO_ENDPOINT not set' env_var_map = { 'MINIO_BUCKET_NAME': 'test-bucket', 'MINIO_OBJECT_NAME': 'test-object', -- 2.54.0 From 400706e7304e77649cab6a5e1ca3f6dd6c957093 Mon Sep 17 00:00:00 2001 From: brian Date: Mon, 17 Mar 2025 22:09:48 +0000 Subject: [PATCH 51/64] moved env var checks --- shared/repositories/tests/integration/conftest.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/shared/repositories/tests/integration/conftest.py b/shared/repositories/tests/integration/conftest.py index a34243d..10d88a6 100644 --- a/shared/repositories/tests/integration/conftest.py +++ b/shared/repositories/tests/integration/conftest.py @@ -209,6 +209,11 @@ def image_repo( populate_env, ) -> Iterator[ImageRepository]: """Image repository fixture.""" + # define test environment variables + assert 'MINIO_ENDPOINT' in os.environ, 'MINIO_ENDPOINT not set' + assert 'MINIO_ACCESS_KEY' in os.environ, 'MINIO_ACCESS_KEY not set' + assert 'MINIO_SECRET_KEY' in os.environ, 'MINIO_SECRET_KEY not set' + assert 'MONGO_ENDPOINT' in os.environ, 'MONGO_ENDPOINT not set' repo = ImageRepository() repo.connect() yield repo -- 2.54.0 From ad82ad4591cc8bae59b634a8b8101554642fbd8d Mon Sep 17 00:00:00 2001 From: brian Date: Mon, 17 Mar 2025 22:19:14 +0000 Subject: [PATCH 52/64] added explicit check for necessary env vars --- .../tests/integration/conftest.py | 34 ++++++++++--------- 1 file changed, 18 insertions(+), 16 deletions(-) diff --git a/shared/repositories/tests/integration/conftest.py b/shared/repositories/tests/integration/conftest.py index 10d88a6..870dd8c 100644 --- a/shared/repositories/tests/integration/conftest.py +++ b/shared/repositories/tests/integration/conftest.py @@ -37,10 +37,12 @@ if test_env_path.exists(): load_dotenv(test_env_path.as_posix()) # define test environment variables -assert 'MINIO_ENDPOINT' in os.environ, 'MINIO_ENDPOINT not set' -assert 'MINIO_ACCESS_KEY' in os.environ, 'MINIO_ACCESS_KEY not set' -assert 'MINIO_SECRET_KEY' in os.environ, 'MINIO_SECRET_KEY not set' -assert 'MONGO_ENDPOINT' in os.environ, 'MONGO_ENDPOINT not set' +necessary_env_vars = { + 'MINIO_ENDPOINT', + 'MINIO_ACCESS_KEY', + 'MINIO_SECRET_KEY', + 'MONGO_ENDPOINT', +} env_var_map = { 'MINIO_BUCKET_NAME': 'test-bucket', 'MINIO_OBJECT_NAME': 'test-object', @@ -51,15 +53,15 @@ env_var_map = { @pytest.fixture(scope='session', autouse=True) -def populate_env( +def setup_env( request: pytest.FixtureRequest, ) -> None: """Populate environment with variables used for testing.""" - # update env + # check if necessary env vars are set + for key in necessary_env_vars: + assert key in os.environ, f'{key} not set' + # set testing env vars for key, val in env_var_map.items(): - # skip if already set by CI pipeline - if key in os.environ: - continue # set env var os.environ[key] = val @@ -73,7 +75,7 @@ def populate_env( @pytest.fixture(scope='session') def raw_minio_client( - populate_env, + setup_env, ) -> Iterator[minio.Minio]: """Raw Minio client fixture.""" # prepare arguments @@ -105,7 +107,7 @@ def raw_minio_client( @pytest.fixture def minio_client( - populate_env, + setup_env, ) -> Iterator[MinioImplementation]: """MinioImplementation fixture.""" # instantiate and connect client @@ -206,7 +208,7 @@ def image_data_in_minio( @pytest.fixture(scope='session') def image_repo( - populate_env, + setup_env, ) -> Iterator[ImageRepository]: """Image repository fixture.""" # define test environment variables @@ -271,7 +273,7 @@ def model_data_in_minio( @pytest.fixture(scope='session') def model_repo( - populate_env, + setup_env, ) -> Iterator[ModelRepository]: """Model repository fixture.""" repo = ModelRepository() @@ -282,7 +284,7 @@ def model_repo( @pytest.fixture def raw_mongo_client( - populate_env, + setup_env, ) -> Iterator[MongoClient]: """Raw mongo client fixture.""" # prepare arguments @@ -299,7 +301,7 @@ def raw_mongo_client( @pytest.fixture def mongo_client( - populate_env, + setup_env, ) -> Iterator[MongoImplementation]: """MongoImplementation fixture.""" # instantiate and connect client @@ -394,7 +396,7 @@ def visual_communication_data_in_mongo( @pytest.fixture(scope='session') def visual_communication_repo( - populate_env, + setup_env, ) -> Iterator[VisualCommunicationRepository]: """Visual communication repository fixture.""" repo = VisualCommunicationRepository() -- 2.54.0 From ab7e346939f0078440408052b87ce7b455f79ce6 Mon Sep 17 00:00:00 2001 From: brian Date: Mon, 17 Mar 2025 22:32:06 +0000 Subject: [PATCH 53/64] tried loading github env file --- shared/repositories/tests/integration/conftest.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/shared/repositories/tests/integration/conftest.py b/shared/repositories/tests/integration/conftest.py index 870dd8c..15bde11 100644 --- a/shared/repositories/tests/integration/conftest.py +++ b/shared/repositories/tests/integration/conftest.py @@ -33,8 +33,8 @@ random.seed(13) # load local test environment variables test_env_path = Path(__file__).parent.parent.parent.parent.parent / 'test.env' -if test_env_path.exists(): - load_dotenv(test_env_path.as_posix()) +load_dotenv(test_env_path.as_posix()) +load_dotenv(os.getenv('GITHUB_ENV', default='.')) # define test environment variables necessary_env_vars = { -- 2.54.0 From 280dbb579e0dd122ea743c2e38b4e4c4bd5cb4f6 Mon Sep 17 00:00:00 2001 From: brian Date: Mon, 17 Mar 2025 22:46:52 +0000 Subject: [PATCH 54/64] added more explicit env var loading --- shared/repositories/tests/integration/conftest.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/shared/repositories/tests/integration/conftest.py b/shared/repositories/tests/integration/conftest.py index 15bde11..c759876 100644 --- a/shared/repositories/tests/integration/conftest.py +++ b/shared/repositories/tests/integration/conftest.py @@ -31,11 +31,6 @@ from shared.repositories.src.implementations import ( # set random seed for reproducibility random.seed(13) -# load local test environment variables -test_env_path = Path(__file__).parent.parent.parent.parent.parent / 'test.env' -load_dotenv(test_env_path.as_posix()) -load_dotenv(os.getenv('GITHUB_ENV', default='.')) - # define test environment variables necessary_env_vars = { 'MINIO_ENDPOINT', @@ -57,6 +52,11 @@ def setup_env( request: pytest.FixtureRequest, ) -> None: """Populate environment with variables used for testing.""" + # load in optional local test environment variables + test_env_path = Path(__file__).parent.parent.parent.parent.parent / 'test.env' + load_dotenv(test_env_path) + # load in optional CI environment variables + load_dotenv(os.getenv('GITHUB_ENV')) # check if necessary env vars are set for key in necessary_env_vars: assert key in os.environ, f'{key} not set' -- 2.54.0 From 49d2c48d31d5db2645f680de0a40bb8c38a75e9c Mon Sep 17 00:00:00 2001 From: brian Date: Tue, 18 Mar 2025 15:34:39 +0000 Subject: [PATCH 55/64] explicitly adding local env vars to file --- .gitea/workflows/pull.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.gitea/workflows/pull.yaml b/.gitea/workflows/pull.yaml index 03597f2..0c4f15c 100644 --- a/.gitea/workflows/pull.yaml +++ b/.gitea/workflows/pull.yaml @@ -44,6 +44,10 @@ jobs: MINIO_SECRET_KEY: ${{ secrets.MINIO_SECRET_KEY }} MONGO_ENDPOINT: ${{ vars.MONGO_ENDPOINT }} run: | + echo "MINIO_ENDPOINT=${MINIO_ENDPOINT}" >> .env + echo "MINIO_ACCESS_KEY=${MINIO_ACCESS_KEY}" >> .env + echo "MINIO_SECRET_KEY=${MINIO_SECRET_KEY}" >> .env + echo "MONGO_ENDPOINT=${MONGO_ENDPOINT}" >> .env /opt/poetry/bin/poetry run coverage run -m pytest . - name: Coverage Report run: | -- 2.54.0 From ac8ca830e1bca881ccaff65ec58b3221135dcd3a Mon Sep 17 00:00:00 2001 From: brian Date: Tue, 18 Mar 2025 19:12:06 +0000 Subject: [PATCH 56/64] manually set needed environment variables in conftest --- .gitea/workflows/pull.yaml | 9 --------- shared/repositories/tests/integration/conftest.py | 10 ++++------ 2 files changed, 4 insertions(+), 15 deletions(-) diff --git a/.gitea/workflows/pull.yaml b/.gitea/workflows/pull.yaml index 0c4f15c..960a1e7 100644 --- a/.gitea/workflows/pull.yaml +++ b/.gitea/workflows/pull.yaml @@ -38,16 +38,7 @@ jobs: run: | /opt/poetry/bin/poetry run mypy . - name: Pytest & Calculate Coverage - env: - MINIO_ENDPOINT: ${{ vars.MINIO_ENDPOINT }} - MINIO_ACCESS_KEY: ${{ secrets.MINIO_ACCESS_KEY }} - MINIO_SECRET_KEY: ${{ secrets.MINIO_SECRET_KEY }} - MONGO_ENDPOINT: ${{ vars.MONGO_ENDPOINT }} run: | - echo "MINIO_ENDPOINT=${MINIO_ENDPOINT}" >> .env - echo "MINIO_ACCESS_KEY=${MINIO_ACCESS_KEY}" >> .env - echo "MINIO_SECRET_KEY=${MINIO_SECRET_KEY}" >> .env - echo "MONGO_ENDPOINT=${MONGO_ENDPOINT}" >> .env /opt/poetry/bin/poetry run coverage run -m pytest . - name: Coverage Report run: | diff --git a/shared/repositories/tests/integration/conftest.py b/shared/repositories/tests/integration/conftest.py index c759876..adba948 100644 --- a/shared/repositories/tests/integration/conftest.py +++ b/shared/repositories/tests/integration/conftest.py @@ -33,15 +33,18 @@ random.seed(13) # define test environment variables necessary_env_vars = { - 'MINIO_ENDPOINT', 'MINIO_ACCESS_KEY', 'MINIO_SECRET_KEY', 'MONGO_ENDPOINT', } env_var_map = { + 'MINIO_ENDPOINT': '192.168.1.2:9000', + 'MINIO_ACCESS_KEY': '1rMQTezbALeJyOgAbYYE', + 'MINIO_SECRET_KEY': 'O76GM756ybKYLFokZFJneaCoYwpaIbAlOdB7mcc0', 'MINIO_BUCKET_NAME': 'test-bucket', 'MINIO_OBJECT_NAME': 'test-object', 'MINIO_IMAGE_NAME': 'test-image', + 'MONGO_ENDPOINT': 'mongodb://192.168.1.2:27017/', 'MONGO_DB': 'test-db', 'MONGO_COLLECTION': 'test-collection', } @@ -55,11 +58,6 @@ def setup_env( # load in optional local test environment variables test_env_path = Path(__file__).parent.parent.parent.parent.parent / 'test.env' load_dotenv(test_env_path) - # load in optional CI environment variables - load_dotenv(os.getenv('GITHUB_ENV')) - # check if necessary env vars are set - for key in necessary_env_vars: - assert key in os.environ, f'{key} not set' # set testing env vars for key, val in env_var_map.items(): # set env var -- 2.54.0 From 0b54ccaadb02465c06d43c8ae4744b6295e9ef22 Mon Sep 17 00:00:00 2001 From: brian Date: Tue, 18 Mar 2025 19:12:51 +0000 Subject: [PATCH 57/64] removed unused variable --- shared/repositories/tests/integration/conftest.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/shared/repositories/tests/integration/conftest.py b/shared/repositories/tests/integration/conftest.py index adba948..ecc1cf0 100644 --- a/shared/repositories/tests/integration/conftest.py +++ b/shared/repositories/tests/integration/conftest.py @@ -32,11 +32,6 @@ from shared.repositories.src.implementations import ( random.seed(13) # define test environment variables -necessary_env_vars = { - 'MINIO_ACCESS_KEY', - 'MINIO_SECRET_KEY', - 'MONGO_ENDPOINT', -} env_var_map = { 'MINIO_ENDPOINT': '192.168.1.2:9000', 'MINIO_ACCESS_KEY': '1rMQTezbALeJyOgAbYYE', -- 2.54.0 From a379270add7aa7c71d032525c83781a40e409cd8 Mon Sep 17 00:00:00 2001 From: brian Date: Tue, 18 Mar 2025 19:21:17 +0000 Subject: [PATCH 58/64] removed deprecated modules --- shared/datastore/__init__.py | 1 - shared/datastore/src/__init__.py | 1 - shared/datastore/src/datastore_interface.py | 69 ----- shared/datastore/src/datastore_minio.py | 241 ------------------ .../tests/integration/base_crud_test.py | 112 -------- .../datastore/tests/integration/conftest.py | 196 -------------- .../tests/integration/connect_test.py | 10 - .../tests/integration/image_crud_test.py | 82 ------ .../tests/integration/model_crud_test.py | 90 ------- .../tests/unit/datastore_minio_test.py | 230 ----------------- shared/docstore/__init__.py | 8 - shared/docstore/src/__init__.py | 3 - shared/docstore/src/classes/__init__.py | 13 - shared/docstore/src/classes/angle.py | 13 - shared/docstore/src/classes/contact.py | 12 - shared/docstore/src/classes/data_model.py | 67 ----- shared/docstore/src/classes/distance.py | 13 - shared/docstore/src/classes/framing.py | 14 - .../docstore/src/classes/information_value.py | 13 - shared/docstore/src/classes/modality_color.py | 13 - shared/docstore/src/classes/modality_depth.py | 13 - .../docstore/src/classes/modality_lighting.py | 13 - shared/docstore/src/classes/model_data.py | 115 --------- shared/docstore/src/classes/point_of_view.py | 12 - shared/docstore/src/classes/salience.py | 15 -- .../src/classes/visual_communication.py | 122 --------- shared/docstore/src/classes/visual_syntax.py | 28 -- shared/docstore/src/connect_mongodb.py | 30 --- shared/docstore/src/count_documents.py | 20 -- shared/docstore/src/docstore_interface.py | 83 ------ shared/docstore/src/docstore_mongo.py | 241 ------------------ shared/docstore/src/exceptions/__init__.py | 1 - .../src/exceptions/no_document_found.py | 5 - shared/docstore/src/get_dataset.py | 16 -- .../docstore/src/get_visual_communication.py | 40 --- shared/docstore/src/list_names.py | 30 --- shared/docstore/src/upsert_annotation.py | 30 --- shared/docstore/src/upsert_prediction.py | 30 --- .../src/upsert_visual_communication.py | 19 -- .../tests/unit/docstore_mongo_test.py | 45 ---- .../tests/integration/conftest.py | 14 +- 41 files changed, 10 insertions(+), 2113 deletions(-) delete mode 100644 shared/datastore/__init__.py delete mode 100644 shared/datastore/src/__init__.py delete mode 100644 shared/datastore/src/datastore_interface.py delete mode 100644 shared/datastore/src/datastore_minio.py delete mode 100644 shared/datastore/tests/integration/base_crud_test.py delete mode 100644 shared/datastore/tests/integration/conftest.py delete mode 100644 shared/datastore/tests/integration/connect_test.py delete mode 100644 shared/datastore/tests/integration/image_crud_test.py delete mode 100644 shared/datastore/tests/integration/model_crud_test.py delete mode 100644 shared/datastore/tests/unit/datastore_minio_test.py delete mode 100644 shared/docstore/__init__.py delete mode 100755 shared/docstore/src/__init__.py delete mode 100755 shared/docstore/src/classes/__init__.py delete mode 100644 shared/docstore/src/classes/angle.py delete mode 100644 shared/docstore/src/classes/contact.py delete mode 100644 shared/docstore/src/classes/data_model.py delete mode 100644 shared/docstore/src/classes/distance.py delete mode 100644 shared/docstore/src/classes/framing.py delete mode 100644 shared/docstore/src/classes/information_value.py delete mode 100644 shared/docstore/src/classes/modality_color.py delete mode 100644 shared/docstore/src/classes/modality_depth.py delete mode 100644 shared/docstore/src/classes/modality_lighting.py delete mode 100644 shared/docstore/src/classes/model_data.py delete mode 100644 shared/docstore/src/classes/point_of_view.py delete mode 100644 shared/docstore/src/classes/salience.py delete mode 100755 shared/docstore/src/classes/visual_communication.py delete mode 100644 shared/docstore/src/classes/visual_syntax.py delete mode 100644 shared/docstore/src/connect_mongodb.py delete mode 100755 shared/docstore/src/count_documents.py delete mode 100644 shared/docstore/src/docstore_interface.py delete mode 100644 shared/docstore/src/docstore_mongo.py delete mode 100644 shared/docstore/src/exceptions/__init__.py delete mode 100755 shared/docstore/src/exceptions/no_document_found.py delete mode 100755 shared/docstore/src/get_dataset.py delete mode 100755 shared/docstore/src/get_visual_communication.py delete mode 100755 shared/docstore/src/list_names.py delete mode 100755 shared/docstore/src/upsert_annotation.py delete mode 100755 shared/docstore/src/upsert_prediction.py delete mode 100755 shared/docstore/src/upsert_visual_communication.py delete mode 100644 shared/docstore/tests/unit/docstore_mongo_test.py diff --git a/shared/datastore/__init__.py b/shared/datastore/__init__.py deleted file mode 100644 index aec85ae..0000000 --- a/shared/datastore/__init__.py +++ /dev/null @@ -1 +0,0 @@ -from .src import Datastore diff --git a/shared/datastore/src/__init__.py b/shared/datastore/src/__init__.py deleted file mode 100644 index 2d860b3..0000000 --- a/shared/datastore/src/__init__.py +++ /dev/null @@ -1 +0,0 @@ -from .datastore_minio import DatastoreMinio as Datastore diff --git a/shared/datastore/src/datastore_interface.py b/shared/datastore/src/datastore_interface.py deleted file mode 100644 index 7cd5445..0000000 --- a/shared/datastore/src/datastore_interface.py +++ /dev/null @@ -1,69 +0,0 @@ -"""Definition of datastore interface.""" - -from __future__ import annotations - -from abc import ABC, abstractmethod -from collections import OrderedDict - -from PIL import Image -from torch.nn import Module - - -class DatastoreInterface(ABC): - """Datastore interface class.""" - - @abstractmethod - def connect( - self, - ) -> None: - pass - - @abstractmethod - def close( - self, - ) -> None: - pass - - @abstractmethod - def __enter__( - self, - ) -> DatastoreInterface: - self.connect() - return self - - @abstractmethod - def __exit__( - self, - exc_type, - exc_val, - exc_tb, - ) -> None: - self.close() - - @abstractmethod - def put_image( - self, - image: Image.Image, - ) -> str: - pass - - @abstractmethod - def get_image( - self, - object_name: str, - ) -> Image.Image: - pass - - @abstractmethod - def put_model( - self, - model: Module, - ) -> str: - pass - - @abstractmethod - def get_model( - self, - object_name: str, - ) -> OrderedDict: - pass diff --git a/shared/datastore/src/datastore_minio.py b/shared/datastore/src/datastore_minio.py deleted file mode 100644 index d12edcb..0000000 --- a/shared/datastore/src/datastore_minio.py +++ /dev/null @@ -1,241 +0,0 @@ -"""Definition of datastore minio implementation.""" - -from __future__ import annotations - -import logging -import os -from collections import OrderedDict -from hashlib import md5 -from io import BytesIO -from traceback import format_exc - -import torch -from minio import Minio -from PIL import Image - -from shared.utils import check_env - -from .datastore_interface import DatastoreInterface - - -class DatastoreMinio(DatastoreInterface): - """Datastore interface.""" - - def __init__(self): - # ensure necessary env vars available - var_list = { - 'MINIO_ENDPOINT', - 'MINIO_ACCESS_KEY', - 'MINIO_SECRET_KEY', - 'MINIO_BUCKET_NAME', - } - check_env(var_list) - # prepare internal variables - self._client: Minio | None = None - self._bucket_name: str | None = None - - def connect(self) -> None: - """Connect to Minio server.""" - # prepare arguments - minio_endpoint = str(os.getenv('MINIO_ENDPOINT')) - minio_access_key = str(os.getenv('MINIO_ACCESS_KEY')) - minio_secret_key = str(os.getenv('MINIO_SECRET_KEY')) - minio_bucket_name = str(os.getenv('MINIO_BUCKET_NAME')) - # connect client - client = Minio( - endpoint=minio_endpoint, - access_key=minio_access_key, - secret_key=minio_secret_key, - secure=False, - ) - # ensure bucket exists - if not client.bucket_exists(bucket_name=minio_bucket_name): - logging.debug('creating bucket: %s', minio_bucket_name) - client.make_bucket(bucket_name=minio_bucket_name) - logging.debug('finished') - # persist state - self._client = client - self._bucket_name = minio_bucket_name - - def close(self) -> None: - """Close connection to Minio server. - - N.B. Minio connection cannot be closed manually. - """ - self._client = None - self._bucket_name = None - - def __enter__(self) -> DatastoreMinio: - self.connect() - return self - - def __exit__(self, exc_type, exc_val, exc_tb) -> None: - if any( - ( - exc_type is not None, - exc_val is not None, - exc_tb is not None, - ), - ): - logging.error('error while exiting context') - self.close() - - def _put( - self, - object_name: str, - buffer: BytesIO, - ) -> None: - """Save in-memory buffer as object in Minio.""" - assert isinstance(object_name, str) - assert len(object_name) > 0 - assert isinstance(buffer, BytesIO) - assert isinstance(self._client, Minio) - assert isinstance(self._bucket_name, str) - # prepare for saving - num_bytes = len(buffer.getvalue()) - buffer.seek(0) - # send data to bucket - try: - self._client.put_object( - bucket_name=self._bucket_name, - object_name=object_name, - length=num_bytes, - data=buffer, - ) - logging.debug('saved data to %s', object_name) - except Exception as exc: - logging.error('failed saving data to MinIO') - raise exc - - def _get( - self, - object_name: str, - ) -> BytesIO: - """Get object from Minio as in-memory buffer.""" - assert isinstance(object_name, str) - assert len(object_name) > 0 - assert isinstance(self._client, Minio) - assert isinstance(self._bucket_name, str) - try: - # make request - response = self._client.get_object( - bucket_name=self._bucket_name, - object_name=object_name, - ) - assert response.status == 200 - # get buffer - buffer = BytesIO() - chunk_size = 2**14 - while chunk := response.read(chunk_size): - buffer.write(chunk) - buffer.seek(0) - logging.debug('got %s', object_name) - return buffer - except Exception as exc: - logging.error('failed getting data from MinIO') - logging.debug(format_exc()) - raise exc - finally: - # close connection if established - if 'response' in locals(): - response.close() - response.release_conn() - - def _delete( - self, - object_name: str, - ) -> None: - """Delete object from Minio.""" - assert isinstance(object_name, str) - assert len(object_name) > 0 - assert isinstance(self._client, Minio) - assert isinstance(self._bucket_name, str) - # remove object - try: - self._client.remove_object( - bucket_name=self._bucket_name, - object_name=object_name, - ) - logging.debug('deleted %s', object_name) - except Exception as exc: - logging.error('failed deleting %s', object_name) - logging.debug(format_exc()) - raise exc - - def put_image( - self, - image: Image.Image, - ) -> str: - """Put image in Minio.""" - assert isinstance(image, Image.Image) - # save data to buffer - buffer = BytesIO() - image.save(buffer, 'png') - # get md5 of buffer - checksum = md5(buffer.getbuffer()).hexdigest() - # build object path - object_path = f'images/{checksum}' - # send data to bucket - self._put( - object_name=object_path, - buffer=buffer, - ) - logging.debug('saved data to %s', object_path) - return checksum - - def get_image( - self, - object_name: str, - ) -> Image.Image: - """Get image from Minio.""" - assert isinstance(object_name, str) - assert len(object_name) > 0 - # build object path - object_path = f'images/{object_name}' - # get object from bucket - buffer = self._get( - object_name=object_path, - ) - # convert data to image - image = Image.open(buffer) - logging.debug('got data from %s', object_path) - return image - - def put_model( - self, - model: torch.nn.Module, - ) -> str: - """Put model in Minio.""" - assert isinstance(model, torch.nn.Module) - # save data to buffer - buffer = BytesIO() - torch.save(model.state_dict(), buffer) - # get md5 of image - checksum = md5(buffer.getbuffer()).hexdigest() - # build object path - object_path = f'models/{checksum}' - # send data to bucket - self._put( - object_name=object_path, - buffer=buffer, - ) - logging.debug('saved data to %s', object_path) - return checksum - - def get_model( - self, - object_name: str, - ) -> OrderedDict: - """Get model data from Minio.""" - assert isinstance(object_name, str) - assert len(object_name) > 0 - # build object path - object_path = f'models/{object_name}' - # get object from bucket - buffer = self._get( - object_name=object_path, - ) - # convert data to model checkpoint - model_content = torch.load(buffer) - logging.debug('got data from %s', object_path) - return model_content diff --git a/shared/datastore/tests/integration/base_crud_test.py b/shared/datastore/tests/integration/base_crud_test.py deleted file mode 100644 index 723ffc7..0000000 --- a/shared/datastore/tests/integration/base_crud_test.py +++ /dev/null @@ -1,112 +0,0 @@ -"""Integration tests related to base CRUD functions.""" - -import logging -import os -from io import BytesIO - -import minio -import pytest - -from shared.datastore import Datastore - - -def same_data( - data_a: BytesIO, - data_b: BytesIO, -) -> bool: - """Check if two BytesIO-objects contain the same data.""" - assert isinstance(data_a, BytesIO) - assert isinstance(data_b, BytesIO) - # prepare for being read - data_a.seek(0) - data_b.seek(0) - # convert to bytes - data_a_bytes = data_a.read() - data_b_bytes = data_b.read() - # compare size - if len(data_a_bytes) != len(data_b_bytes): - logging.error( - 'data has different length: %s and %s', - len(data_a_bytes), - len(data_b_bytes), - ) - return False - # compare content - if data_a_bytes != data_b_bytes: - logging.error('data has different bytes') - return False - return True - - -def test_should_get_data( - datastore: Datastore, - data_in_minio, -): - # ARRANGE - data, _, object_name = data_in_minio - # ACT - received_data = datastore._get( - object_name=object_name, - ) - # ASSERT - assert isinstance(data, BytesIO) - assert same_data(data, received_data) - - -def test_should_delete_data( - datastore: Datastore, - data_in_minio, -): - # ARRANGE - _, _, object_name = data_in_minio - # ACT - datastore._delete( - object_name=object_name, - ) - # ASSERT - with pytest.raises(minio.error.S3Error): - _ = datastore._get( - object_name=object_name, - ) - - -def test_should_put_data( - datastore: Datastore, - data, -): - # ARRANGE - minio_object_name = str(os.getenv('MINIO_OBJECT_NAME')) - buffer = BytesIO(data) - # ACT - datastore._put( - object_name=minio_object_name, - buffer=buffer, - ) - received_data = datastore._get( - object_name=minio_object_name, - ) - # ASSERT - assert isinstance(received_data, BytesIO) - assert same_data(received_data, buffer) - - -def test_should_update_data( - datastore: Datastore, - data_in_minio, -): - # ARRANGE - buffer, _, object_name = data_in_minio - # ACT - datastore._put( - object_name=object_name, - buffer=buffer, - ) - received_data = datastore._get( - object_name=object_name, - ) - # ASSERT - assert same_data(received_data, buffer) - - -if __name__ == '__main__': - pytest.main() diff --git a/shared/datastore/tests/integration/conftest.py b/shared/datastore/tests/integration/conftest.py deleted file mode 100644 index 741fb25..0000000 --- a/shared/datastore/tests/integration/conftest.py +++ /dev/null @@ -1,196 +0,0 @@ -"""Integration test configurations.""" - -import os -import random -from collections.abc import Iterator -from hashlib import md5 -from io import BytesIO -from pathlib import Path - -import pytest -import torch -from dotenv import load_dotenv -from PIL import Image - -from model.src.models import VisualCommunicationModel -from shared.datastore import Datastore - -env_var_map = { - 'MINIO_BUCKET_NAME': 'test-bucket', - 'MINIO_OBJECT_NAME': '46KXJMFIAPVLM0TKRFZR5YPPTVJ6PJNX', -} - - -@pytest.fixture(scope='session', autouse=True) -def populate_env( - request: pytest.FixtureRequest, -) -> None: - """Populate environment with variables used for testing.""" - # read env-file for local testing - load_dotenv( - dotenv_path=Path(__file__).parent.parent.parent.parent.parent / 'server.env', - ) - # update env - for key, val in env_var_map.items(): - os.environ[key] = val - - # ensure cleanup - def cleanup_env(): - for key in env_var_map: - _ = os.environ.pop(key, default=None) - - request.addfinalizer(cleanup_env) - - -@pytest.fixture(scope='session') -def datastore( - populate_env, -) -> Iterator[Datastore]: - # prepare arguments - minio_bucket_name = str(os.getenv('MINIO_BUCKET_NAME')) - # connect to minio - datastore_client = Datastore() - datastore_client.connect() - assert datastore_client._client is not None - # ensure bucket exists - if not datastore_client._client.bucket_exists(bucket_name=minio_bucket_name): - datastore_client._client.make_bucket(bucket_name=minio_bucket_name) - # expose client - yield datastore_client - # remove objects left behind by tests - for obj in datastore_client._client.list_objects( - bucket_name=minio_bucket_name, - recursive=True, - ): - datastore_client._client.remove_object( - bucket_name=obj.bucket_name, - object_name=obj.object_name, - ) - # remove bucket - datastore_client._client.remove_bucket(bucket_name=minio_bucket_name) - assert not datastore_client._client.bucket_exists(bucket_name=minio_bucket_name) - # disconnect from minio - datastore_client.close() - - -@pytest.fixture -def data() -> Iterator[bytes]: - # generate random data - num_bytes = 2**21 # 2 MB - data = random.randbytes(n=num_bytes) - # expose data - yield data - - -@pytest.fixture -def data_in_minio( - datastore: Datastore, - data: bytes, -) -> Iterator[tuple[BytesIO, str, str]]: - assert datastore._client is not None - # prepare arguments - minio_bucket_name = str(os.getenv('MINIO_BUCKET_NAME')) - minio_object_name = str(os.getenv('MINIO_OBJECT_NAME')) - # convert data - buffer = BytesIO(data) - # prepare for saving - num_bytes = len(buffer.getvalue()) - buffer.seek(0) - # send data to bucket - datastore._client.put_object( - bucket_name=minio_bucket_name, - object_name=minio_object_name, - length=num_bytes, - data=buffer, - ) - # expose data - yield buffer, minio_bucket_name, minio_object_name - # clean up - datastore._client.remove_object( - bucket_name=minio_bucket_name, - object_name=minio_object_name, - ) - - -@pytest.fixture -def image() -> Iterator[Image.Image]: - # generate image - image = Image.new(mode='RGB', size=(480, 480)) - # expose image - yield image - - -@pytest.fixture -def image_in_minio( - datastore: Datastore, - image: Image.Image, -) -> Iterator[tuple[Image.Image, str]]: - assert datastore._client is not None - # prepare arguments - minio_bucket_name = str(os.getenv('MINIO_BUCKET_NAME')) - # save data to buffer - buffer = BytesIO() - image.save(buffer, 'png') - # get md5 of buffer - checksum = md5(buffer.getbuffer()).hexdigest() - # build object path - object_path = f'images/{checksum}' - # prepare for saving - num_bytes = len(buffer.getvalue()) - buffer.seek(0) - # send data to bucket - datastore._client.put_object( - bucket_name=minio_bucket_name, - object_name=object_path, - length=num_bytes, - data=buffer, - ) - # expose image and object name - yield image, checksum - # cleanup - datastore._client.remove_object( - bucket_name=minio_bucket_name, - object_name=object_path, - ) - - -@pytest.fixture -def model() -> Iterator[torch.nn.Module]: - # generate model - model = VisualCommunicationModel().to('cpu') - # expose model - yield model - - -@pytest.fixture -def model_in_minio( - datastore: Datastore, - model: torch.nn.Module, -) -> Iterator[tuple[torch.nn.Module, str]]: - assert datastore._client is not None - # prepare arguments - minio_bucket_name = str(os.getenv('MINIO_BUCKET_NAME')) - # save data to buffer - buffer = BytesIO() - torch.save(model.state_dict(), buffer) - # get md5 of image - checksum = md5(buffer.getbuffer()).hexdigest() - # build object path - object_path = f'models/{checksum}' - # prepare for saving - num_bytes = len(buffer.getvalue()) - buffer.seek(0) - # send data to bucket - datastore._client.put_object( - bucket_name=minio_bucket_name, - object_name=object_path, - length=num_bytes, - data=buffer, - ) - # expose model and object name - yield model, checksum - # cleanup - datastore._client.remove_object( - bucket_name=minio_bucket_name, - object_name=object_path, - ) diff --git a/shared/datastore/tests/integration/connect_test.py b/shared/datastore/tests/integration/connect_test.py deleted file mode 100644 index ea5868e..0000000 --- a/shared/datastore/tests/integration/connect_test.py +++ /dev/null @@ -1,10 +0,0 @@ -"""Integration test for connect_minio function.""" - -from minio import Minio - -from shared.datastore import Datastore - - -def test_should_return_correct_type(): - with Datastore() as ds: - assert isinstance(ds._client, Minio) diff --git a/shared/datastore/tests/integration/image_crud_test.py b/shared/datastore/tests/integration/image_crud_test.py deleted file mode 100644 index c3b0dbb..0000000 --- a/shared/datastore/tests/integration/image_crud_test.py +++ /dev/null @@ -1,82 +0,0 @@ -"""Integration tests related to image CRUD.""" - -import numpy as np -import pytest -from PIL import Image - -from shared.datastore import Datastore - - -def same_image( - img_a: Image.Image, - img_b: Image.Image, -) -> bool: - """Check if two images contain the same data.""" - assert isinstance(img_a, Image.Image) - assert isinstance(img_b, Image.Image) - # check if images have a comparable number of channels - if img_a.getbands() != img_b.getbands(): - return False - # calculate pixel difference between images - img_a_arr = np.asarray(img_a) - img_b_arr = np.asarray(img_b) - diff = np.subtract(img_a_arr, img_b_arr) - if np.sum(diff) != 0: - return False - return True - - -def test_should_get_image( - datastore: Datastore, - image_in_minio: tuple[Image.Image, str], -): - # ARRANGE - image, object_name = image_in_minio - # ACT - received_image = datastore.get_image( - object_name=object_name, - ) - # ASSERT - assert isinstance(image, Image.Image) - assert same_image(image, received_image) - - -def test_should_put_image( - datastore: Datastore, - image: Image.Image, -): - # ARRANGE - object_name = datastore.put_image( - image=image, - ) - assert isinstance(object_name, str) - assert len(object_name) > 0 - # ACT - received_image = datastore.get_image( - object_name=object_name, - ) - # ASSERT - assert same_image(image, received_image) - - -def test_should_update_image( - datastore: Datastore, - image_in_minio: tuple[Image.Image, str], -): - # ARRANGE - image, object_name = image_in_minio - object_name = datastore.put_image( - image=image, - ) - assert isinstance(object_name, str) - assert len(object_name) > 0 - # ACT - received_image = datastore.get_image( - object_name=object_name, - ) - # ASSERT - assert same_image(image, received_image) - - -if __name__ == '__main__': - pytest.main() diff --git a/shared/datastore/tests/integration/model_crud_test.py b/shared/datastore/tests/integration/model_crud_test.py deleted file mode 100644 index 2f41472..0000000 --- a/shared/datastore/tests/integration/model_crud_test.py +++ /dev/null @@ -1,90 +0,0 @@ -"""Integration tests related to model CRUD.""" - -from collections import OrderedDict - -from torch.nn import Module - -from model.src.models import VisualCommunicationModel -from shared.datastore import Datastore - - -def same_model( - model_a: Module, - model_b: Module, -) -> bool: - """Check if two models are the same class, have the same number of - parameters and contain the same weights.""" - assert isinstance(model_a, Module) - assert isinstance(model_b, Module) - # compare model classes - assert type(model_a) is type(model_b) - # compare number of parameters - params_a = list(model_a.parameters()) - params_b = list(model_b.parameters()) - if len(params_a) != len(params_b): - return False - # compare model weights - for p_a, p_b in zip(params_a, params_b): - if p_a.data.ne(p_b.data).sum() > 0: - return False - return True - - -def test_should_get_model( - datastore: Datastore, - model_in_minio: tuple[Module, str], -): - # ARRANGE - model, object_name = model_in_minio - # ACT - model_data = datastore.get_model( - object_name=object_name, - ) - assert isinstance(model_data, OrderedDict) - received_model = VisualCommunicationModel().to('cpu') - received_model.load_state_dict(model_data) - # ASSERT - assert same_model(model, received_model) - - -def test_should_put_model( - datastore: Datastore, - model: Module, -): - # ARRANGE - object_name = datastore.put_model( - model=model, - ) - assert isinstance(object_name, str) - assert len(object_name) > 0 - # ACT - model_data = datastore.get_model( - object_name=object_name, - ) - assert isinstance(model_data, OrderedDict) - received_model = VisualCommunicationModel().to('cpu') - received_model.load_state_dict(model_data) - # ASSERT - assert same_model(model, received_model) - - -def test_should_update_model( - datastore: Datastore, - model_in_minio: tuple[Module, str], -): - # ARRANGE - model, object_name = model_in_minio - object_name = datastore.put_model( - model=model, - ) - assert isinstance(object_name, str) - assert len(object_name) > 0 - # ACT - model_data = datastore.get_model( - object_name=object_name, - ) - assert isinstance(model_data, OrderedDict) - received_model = VisualCommunicationModel().to('cpu') - received_model.load_state_dict(model_data) - # ASSERT - assert same_model(model, received_model) diff --git a/shared/datastore/tests/unit/datastore_minio_test.py b/shared/datastore/tests/unit/datastore_minio_test.py deleted file mode 100644 index e23ee67..0000000 --- a/shared/datastore/tests/unit/datastore_minio_test.py +++ /dev/null @@ -1,230 +0,0 @@ -"""Definition of unittests for Datastore Minio implementation.""" - -import os -from hashlib import md5 -from io import BytesIO -from unittest import TestCase -from unittest.mock import ANY, MagicMock, patch - -from minio import Minio -from PIL import Image -from urllib3 import BaseHTTPResponse - -from shared.datastore.src.datastore_minio import DatastoreMinio - - -class TestDatastoreMinioImplementation(TestCase): - - def setUp(self): - # define relevant env vars - self.env_var_map = { - 'MINIO_ENDPOINT': '192.168.1.2', - 'MINIO_ACCESS_KEY': 'randomAccess_key', - 'MINIO_SECRET_KEY': 'randomSecret_key', - 'MINIO_BUCKET_NAME': 'test-bucket-name', - } - # set env vars - for key, val in self.env_var_map.items(): - os.environ[key] = val - # set other variables - self.object_name = '46KXJMFIAPVLM0TKRFZR5YPPTVJ6PJNX' - self.image = Image.new(mode='RGB', size=(480, 480)) - self.buffer = BytesIO() - self.image.save(self.buffer, 'png') - self.num_bytes = len(self.buffer.getvalue()) - self.checksum = md5(self.buffer.getbuffer()).hexdigest() - - def tearDown(self): - # clear env vars - for key in self.env_var_map: - _ = os.environ.pop(key, default=None) - - def test_instantiation_should_fail_when_env_not_set(self): - # ensure env not set - self.tearDown() - # run test - with self.assertRaises(OSError): - _ = DatastoreMinio() - - @patch('shared.datastore.src.datastore_minio.Minio') - def test_connect_should_call_Minio_with_env_vars(self, minio_mock): - # ARRANGE - datastore = DatastoreMinio() - minio_mock().bucket_exists.return_value = False - # ACT - datastore.connect() - # ASSERT - minio_mock.assert_called_with( - endpoint=self.env_var_map['MINIO_ENDPOINT'], - access_key=self.env_var_map['MINIO_ACCESS_KEY'], - secret_key=self.env_var_map['MINIO_SECRET_KEY'], - secure=False, - ) - minio_mock().bucket_exists.assert_called_with( - bucket_name=self.env_var_map['MINIO_BUCKET_NAME'], - ) - minio_mock().make_bucket.assert_called_with( - bucket_name=self.env_var_map['MINIO_BUCKET_NAME'], - ) - - def test_close_should_overwrite_private_variables(self): - # ARRANGE - datastore = DatastoreMinio() - datastore._client = MagicMock() - datastore._bucket_name = MagicMock() - assert isinstance(datastore._client, MagicMock) - assert isinstance(datastore._bucket_name, MagicMock) - # ACT - datastore.close() - # ASSERT - assert datastore._client is None - assert datastore._bucket_name is None - - @patch('shared.datastore.src.datastore_minio.DatastoreMinio.connect') - @patch('shared.datastore.src.datastore_minio.DatastoreMinio.close') - def test_context_management_implemented( - self, - mocked_close_method, - mocked_connect_method, - ): - # ARRANGE, ACT and ASSERT - with DatastoreMinio() as ds: - mocked_connect_method.assert_called_once() - assert isinstance(ds, DatastoreMinio) - mocked_close_method.assert_called_once() - - def test_should_call_put_object_with_arguments(self): - # ARRANGE - datastore = DatastoreMinio() - datastore._client = MagicMock(Minio) - datastore._bucket_name = self.env_var_map['MINIO_BUCKET_NAME'] - self.buffer.seek(0) - # ACT - datastore._put( - object_name=self.object_name, - buffer=self.buffer, - ) - # ASSERT - datastore._client.put_object.assert_called_with( - bucket_name=self.env_var_map['MINIO_BUCKET_NAME'], - object_name=self.object_name, - length=self.num_bytes, - data=self.buffer, - ) - - def test_should_call_get_object_with_arguments(self): - # ARRANGE - datastore = DatastoreMinio() - datastore._client = MagicMock(Minio) - datastore._client.get_object.return_value = MagicMock( - BaseHTTPResponse, - status=200, - ) - # datastore._client.get_object.read.side_effect = [b'random ', b'test', b'text'] - datastore._bucket_name = self.env_var_map['MINIO_BUCKET_NAME'] - # ACT - with self.assertRaises(TypeError): # dont care to mock even more... - datastore._get( - object_name=self.object_name, - ) - # ASSERT - datastore._client.get_object.assert_called_with( - bucket_name=self.env_var_map['MINIO_BUCKET_NAME'], - object_name=self.object_name, - ) - - def test_should_call_remove_object_with_arguments(self): - # ARRANGE - datastore = DatastoreMinio() - datastore._client = MagicMock(Minio) - datastore._bucket_name = self.env_var_map['MINIO_BUCKET_NAME'] - # ACT - datastore._delete( - object_name=self.object_name, - ) - # ASSERT - datastore._client.remove_object.assert_called_with( - bucket_name=self.env_var_map['MINIO_BUCKET_NAME'], - object_name=self.object_name, - ) - - def test_put_image_should_call_put_object_with_arguments(self): - # ARRANGE - datastore = DatastoreMinio() - datastore._client = MagicMock(Minio) - datastore._bucket_name = self.env_var_map['MINIO_BUCKET_NAME'] - object_path = f'images/{self.checksum}' - # ACT - datastore.put_image( - image=self.image, - ) - # ASSERT - datastore._client.put_object.assert_called_with( - bucket_name=self.env_var_map['MINIO_BUCKET_NAME'], - object_name=object_path, - length=self.num_bytes, - data=ANY, # saved to different buffer when converting image - ) - - def test_get_image_should_call_get_object_with_arguments(self): - # ARRANGE - datastore = DatastoreMinio() - datastore._client = MagicMock(Minio) - datastore._client.get_object.return_value = MagicMock( - BaseHTTPResponse, - status=200, - ) - datastore._bucket_name = self.env_var_map['MINIO_BUCKET_NAME'] - object_path = f'images/{self.checksum}' - # ACT - with self.assertRaises(TypeError): # dont care to mock even more... - datastore.get_image( - object_name=self.checksum, - ) - # ASSERT - datastore._client.get_object.assert_called_with( - bucket_name=self.env_var_map['MINIO_BUCKET_NAME'], - object_name=object_path, - ) - - # @patch('shared.datastore.src.datastore_minio.torch.serialization.save') - # def test_put_model_should_call_put_object_with_arguments(self, mocked_torch_fn): - # # ARRANGE - # datastore = DatastoreMinio() - # datastore._client = MagicMock(Minio) - # datastore._bucket_name = self.env_var_map['MINIO_BUCKET_NAME'] - # object_path = f'images/{self.checksum}' - # mocked_torch_fn.return_value = None - # model = MagicMock(torch.nn.Module) - # # ACT - # datastore.put_model( - # model=model, - # ) - # # ASSERT - # datastore._client.put_object.assert_called_with( - # bucket_name=self.env_var_map['MINIO_BUCKET_NAME'], - # object_name=object_path, - # length=self.num_bytes, - # data=ANY, # saved to different buffer when converting data - # ) - - def test_get_model_should_call_get_object_with_arguments(self): - # ARRANGE - datastore = DatastoreMinio() - datastore._client = MagicMock(Minio) - datastore._client.get_object.return_value = MagicMock( - BaseHTTPResponse, - status=200, - ) - datastore._bucket_name = self.env_var_map['MINIO_BUCKET_NAME'] - object_path = f'models/{self.checksum}' - # ACT - with self.assertRaises(TypeError): # dont care to mock even more... - datastore.get_model( - object_name=self.checksum, - ) - # ASSERT - datastore._client.get_object.assert_called_with( - bucket_name=self.env_var_map['MINIO_BUCKET_NAME'], - object_name=object_path, - ) diff --git a/shared/docstore/__init__.py b/shared/docstore/__init__.py deleted file mode 100644 index 6ca8e30..0000000 --- a/shared/docstore/__init__.py +++ /dev/null @@ -1,8 +0,0 @@ -from .src import classes, exceptions -from .src.connect_mongodb import connect_mongodb -from .src.count_documents import count_documents -from .src.get_visual_communication import get_visual_communication -from .src.list_names import list_names -from .src.upsert_annotation import upsert_annotation -from .src.upsert_prediction import upsert_prediction -from .src.upsert_visual_communication import upsert_visual_communication diff --git a/shared/docstore/src/__init__.py b/shared/docstore/src/__init__.py deleted file mode 100755 index c6267c3..0000000 --- a/shared/docstore/src/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -"""Database utils module content.""" - -from .connect_mongodb import connect_mongodb diff --git a/shared/docstore/src/classes/__init__.py b/shared/docstore/src/classes/__init__.py deleted file mode 100755 index 84090da..0000000 --- a/shared/docstore/src/classes/__init__.py +++ /dev/null @@ -1,13 +0,0 @@ -from .angle import AngleData -from .contact import ContactData -from .distance import DistanceData -from .framing import FramingData -from .information_value import InformationValueData -from .modality_color import ModalityColorData -from .modality_depth import ModalityDepthData -from .modality_lighting import ModalityLightingData -from .model_data import ModelData -from .point_of_view import PointOfViewData -from .salience import SalienceData -from .visual_communication import VisualCommunication -from .visual_syntax import VisualSyntaxData diff --git a/shared/docstore/src/classes/angle.py b/shared/docstore/src/classes/angle.py deleted file mode 100644 index 12491da..0000000 --- a/shared/docstore/src/classes/angle.py +++ /dev/null @@ -1,13 +0,0 @@ -"""Definition of Angle data model.""" - -from __future__ import annotations - -from .data_model import DataModel - - -class AngleData(DataModel): - """Angle data model.""" - - high: float - eye_level: float - low: float diff --git a/shared/docstore/src/classes/contact.py b/shared/docstore/src/classes/contact.py deleted file mode 100644 index fc08a0a..0000000 --- a/shared/docstore/src/classes/contact.py +++ /dev/null @@ -1,12 +0,0 @@ -"""Definition of ContactData data model.""" - -from __future__ import annotations - -from .data_model import DataModel - - -class ContactData(DataModel): - """ContactData data model.""" - - offer: float - demand: float diff --git a/shared/docstore/src/classes/data_model.py b/shared/docstore/src/classes/data_model.py deleted file mode 100644 index f19b0c8..0000000 --- a/shared/docstore/src/classes/data_model.py +++ /dev/null @@ -1,67 +0,0 @@ -"""Definition of DataModel base class.""" - -import random - -from pydantic import BaseModel, ValidationError -from torch import Tensor - - -class DataModel(BaseModel): - """DataModel base class.""" - - @classmethod - def classname(cls) -> str: - """Return classname.""" - return cls.__name__ - - @classmethod - def list_fields(cls) -> list[str]: - """List options that are stored as attributes.""" - return list(cls.model_fields.keys()) - - @classmethod - def from_random(cls): - """Instantiate with random numbers.""" - kwargs = {field: random.random() for field in cls.list_fields()} - return cls(**kwargs) - - @classmethod - def from_choice(cls, option: str): - """Instantiate from choice.""" - if option is None: - raise ValidationError() - assert isinstance(option, str), 'option is not a string' - allowed_options_list = cls.list_fields() - assert ( - option in allowed_options_list - ), f"{option} is not among allowed fields {allowed_options_list}" - kwargs = {field: 0 for field in cls.list_fields()} - kwargs[option] = 1 - return cls(**kwargs) - - @classmethod - def from_tensor(cls, tensor: Tensor): - """Instantiate from list of values.""" - assert tensor.size(dim=0) == 1, f'tensor batch larger than 1: {tensor}' - data_list = [float(t.item()) for t in tensor[0]] - kwargs = dict(zip(cls.list_fields(), data_list)) - return cls(**kwargs) - - def __repr__(self) -> str: - model_dict = self.model_dump() - model_repr_str = f'{self.classname()}(' - model_repr_str += ', '.join( - [f'{field}={value:.3f}' for field, value in model_dict.items()], - ) - model_repr_str += ')' - return model_repr_str - - def highest_score_field(self) -> str: - """Return name of field with highest score.""" - model_dict = self.model_dump() - return max(model_dict, key=lambda k: model_dict[k]) - - def highest_score_value(self) -> float: - """Return value of field with highest score.""" - model_dict = self.model_dump() - return max(model_dict.values()) diff --git a/shared/docstore/src/classes/distance.py b/shared/docstore/src/classes/distance.py deleted file mode 100644 index 0aebbe6..0000000 --- a/shared/docstore/src/classes/distance.py +++ /dev/null @@ -1,13 +0,0 @@ -"""Definition of DistanceData data model.""" - -from __future__ import annotations - -from .data_model import DataModel - - -class DistanceData(DataModel): - """DistanceData data model.""" - - long: float - medium: float - close: float diff --git a/shared/docstore/src/classes/framing.py b/shared/docstore/src/classes/framing.py deleted file mode 100644 index eca22e3..0000000 --- a/shared/docstore/src/classes/framing.py +++ /dev/null @@ -1,14 +0,0 @@ -"""Definition of FramingData data model.""" - -from __future__ import annotations - -from .data_model import DataModel - - -class FramingData(DataModel): - """FramingData data model.""" - - frame_lines: float - empty_space: float - colour_contrast: float - form_contrast: float diff --git a/shared/docstore/src/classes/information_value.py b/shared/docstore/src/classes/information_value.py deleted file mode 100644 index fd4bf48..0000000 --- a/shared/docstore/src/classes/information_value.py +++ /dev/null @@ -1,13 +0,0 @@ -"""Definition of InformationValueData data model.""" - -from __future__ import annotations - -from .data_model import DataModel - - -class InformationValueData(DataModel): - """InformationValueData data model.""" - - given_new: float - ideal_real: float - central_marginal: float diff --git a/shared/docstore/src/classes/modality_color.py b/shared/docstore/src/classes/modality_color.py deleted file mode 100644 index 458e568..0000000 --- a/shared/docstore/src/classes/modality_color.py +++ /dev/null @@ -1,13 +0,0 @@ -"""Definition of ModalityColorData data model.""" - -from __future__ import annotations - -from .data_model import DataModel - - -class ModalityColorData(DataModel): - """ModalityColorData data model.""" - - high: float - medium: float - low: float diff --git a/shared/docstore/src/classes/modality_depth.py b/shared/docstore/src/classes/modality_depth.py deleted file mode 100644 index e0446f4..0000000 --- a/shared/docstore/src/classes/modality_depth.py +++ /dev/null @@ -1,13 +0,0 @@ -"""Definition of ModalityDepthData data model.""" - -from __future__ import annotations - -from .data_model import DataModel - - -class ModalityDepthData(DataModel): - """ModalityDepthData data model.""" - - high: float - medium: float - low: float diff --git a/shared/docstore/src/classes/modality_lighting.py b/shared/docstore/src/classes/modality_lighting.py deleted file mode 100644 index 508ad57..0000000 --- a/shared/docstore/src/classes/modality_lighting.py +++ /dev/null @@ -1,13 +0,0 @@ -"""Definition of ModalityLightingData data model.""" - -from __future__ import annotations - -from .data_model import DataModel - - -class ModalityLightingData(DataModel): - """ModalityLightingData data model.""" - - high: float - medium: float - low: float diff --git a/shared/docstore/src/classes/model_data.py b/shared/docstore/src/classes/model_data.py deleted file mode 100644 index 5bbbf07..0000000 --- a/shared/docstore/src/classes/model_data.py +++ /dev/null @@ -1,115 +0,0 @@ -"""Definition of ModelData data model.""" - -from __future__ import annotations - -from .angle import AngleData -from .contact import ContactData -from .data_model import DataModel -from .distance import DistanceData -from .framing import FramingData -from .information_value import InformationValueData -from .modality_color import ModalityColorData -from .modality_depth import ModalityDepthData -from .modality_lighting import ModalityLightingData -from .point_of_view import PointOfViewData -from .salience import SalienceData -from .visual_syntax import VisualSyntaxData - - -class ModelData(DataModel): - """ModelData model for data IO with combined ML model.""" - - visual_syntax: VisualSyntaxData - contact: ContactData - angle: AngleData - point_of_view: PointOfViewData - distance: DistanceData - modality_lighting: ModalityLightingData - modality_color: ModalityColorData - modality_depth: ModalityDepthData - information_value: InformationValueData - framing: FramingData - salience: SalienceData - - @classmethod - def from_random(cls) -> ModelData: - """Instantiate with random numbers.""" - kwargs = { - field: field_info.annotation.from_random() # type: ignore - for field, field_info in cls.model_fields.items() - } - return cls(**kwargs) - - @classmethod - def from_prediction_dict( - cls, - prediction_dict: dict, - ) -> ModelData: - """Instantiate from prediction dictionary.""" - kwargs = { - 'visual_syntax': VisualSyntaxData.from_tensor( - prediction_dict['visual_syntax'], - ), - 'contact': ContactData.from_tensor( - prediction_dict['contact'], - ), - 'angle': AngleData.from_tensor( - prediction_dict['angle'], - ), - 'point_of_view': PointOfViewData.from_tensor( - prediction_dict['point_of_view'], - ), - 'distance': DistanceData.from_tensor( - prediction_dict['distance'], - ), - 'modality_lighting': ModalityLightingData.from_tensor( - prediction_dict['modality_lighting'], - ), - 'modality_color': ModalityColorData.from_tensor( - prediction_dict['modality_color'], - ), - 'modality_depth': ModalityDepthData.from_tensor( - prediction_dict['modality_depth'], - ), - 'information_value': InformationValueData.from_tensor( - prediction_dict['information_value'], - ), - 'framing': FramingData.from_tensor( - prediction_dict['framing'], - ), - 'salience': SalienceData.from_tensor( - prediction_dict['salience'], - ), - } - return cls(**kwargs) - - @classmethod - def from_annotations( - cls, - visual_syntax: str, - contact: str, - angle: str, - point_of_view: str, - distance: str, - modality_lighting: str, - modality_color: str, - modality_depth: str, - information_value: str, - framing: str, - salience: str, - ) -> ModelData: - """Instantiate from annotation.""" - kwargs = { - 'visual_syntax': VisualSyntaxData.from_choice(visual_syntax), - 'contact': ContactData.from_choice(contact), - 'angle': AngleData.from_choice(angle), - 'point_of_view': PointOfViewData.from_choice(point_of_view), - 'distance': DistanceData.from_choice(distance), - 'modality_lighting': ModalityLightingData.from_choice(modality_lighting), - 'modality_color': ModalityColorData.from_choice(modality_color), - 'modality_depth': ModalityDepthData.from_choice(modality_depth), - 'information_value': InformationValueData.from_choice(information_value), - 'framing': FramingData.from_choice(framing), - 'salience': SalienceData.from_choice(salience), - } - return cls(**kwargs) diff --git a/shared/docstore/src/classes/point_of_view.py b/shared/docstore/src/classes/point_of_view.py deleted file mode 100644 index b1e4543..0000000 --- a/shared/docstore/src/classes/point_of_view.py +++ /dev/null @@ -1,12 +0,0 @@ -"""Definition of PointOfViewData data model.""" - -from __future__ import annotations - -from .data_model import DataModel - - -class PointOfViewData(DataModel): - """PointOfViewData data model.""" - - frontal: float - oblique: float diff --git a/shared/docstore/src/classes/salience.py b/shared/docstore/src/classes/salience.py deleted file mode 100644 index 186132c..0000000 --- a/shared/docstore/src/classes/salience.py +++ /dev/null @@ -1,15 +0,0 @@ -"""Definition of SalienceData data model.""" - -from __future__ import annotations - -from .data_model import DataModel - - -class SalienceData(DataModel): - """SalienceData data model.""" - - size: float - colour: float - tone: float - form: float - positioning: float diff --git a/shared/docstore/src/classes/visual_communication.py b/shared/docstore/src/classes/visual_communication.py deleted file mode 100755 index e39afc2..0000000 --- a/shared/docstore/src/classes/visual_communication.py +++ /dev/null @@ -1,122 +0,0 @@ -"""Definition of VisualCommunication model.""" - -from __future__ import annotations - -import logging -from base64 import b64decode, b64encode -from io import BytesIO -from pathlib import Path - -from minio import Minio -from PIL import Image -from pydantic import BaseModel, ConfigDict -from pymongo.collection import Collection - -from shared.datastore import Datastore -from shared.docstore.src.classes import ModelData - - -class VisualCommunication(BaseModel): - """Visual communication model.""" - - name: str - object_name: str - annotation: ModelData | None = None - prediction: ModelData | None = None - model_config = ConfigDict(arbitrary_types_allowed=True) - - @classmethod - def classname(cls) -> str: - """Return classname.""" - return cls.__name__ - - @classmethod - def upload_image_to_minio( - cls, - image: Image.Image, - minio_client: Minio, - ) -> str: - """Upload image to MinIO and return MD5 checksum of hashed image.""" - assert isinstance(image, Image.Image) - assert isinstance(minio_client, Minio) - with Datastore() as ds: - object_name = ds.put_image( - image=image, - ) - return object_name - - @classmethod - def from_name_and_image( - cls, - name: str, - image: Image.Image, - minio_client: Minio, - ) -> VisualCommunication: - """Instantiate from filename and image that is automatically uploaded - to MinIO.""" - assert isinstance(name, str) - assert isinstance(image, Image.Image) - assert isinstance(minio_client, Minio) - # upload file to minio - object_name = VisualCommunication.upload_image_to_minio( - image=image, - minio_client=minio_client, - ) - return VisualCommunication(name=name, object_name=object_name) - - @classmethod - def from_file(cls, path: Path, minio_client: Minio) -> VisualCommunication: - """Instantiate from file.""" - assert isinstance(path, Path) - assert isinstance(minio_client, Minio) - # determine name - name = path.stem - # open image - image = Image.open(path) - image.load() - # instantiate object - return VisualCommunication.from_name_and_image( - name=name, - image=image, - minio_client=minio_client, - ) - - @classmethod - def decode_image(cls, content: str) -> Image.Image: - """Extract image from webencoded content.""" - _, content_data = content.split(',') - return Image.open(BytesIO(b64decode(content_data))) - - def get_image(self, minio_client: Minio) -> Image.Image: - """Load image data from minio.""" - assert isinstance(minio_client, Minio) - # get image from minio - with Datastore() as ds: - image = ds.get_image( - object_name=self.object_name, - ) - return image - - def save_to_mongo(self, collection: Collection) -> None: - """Save self as document in MongoDB.""" - res = collection.insert_one( - document=self.model_dump(), - ) - assert res.acknowledged - - def webencoded_image(self, minio_client: Minio) -> str: - """Convert image to be displayed on webpage.""" - assert isinstance(minio_client, Minio) - # get image from minio - image = self.get_image(minio_client) - # convert images to bytes string - buffer = BytesIO() - image.save(buffer, format='png') - img_enc = b64encode(buffer.getvalue()).decode('utf-8') - return f"data:image/png;base64, {img_enc}" - - def generate_random_prediction(self, force: bool = False) -> None: - """Generate random prediction values.""" - if not force and self.prediction is not None: - logging.warning('set force=True to overwrite existing values.') - self.prediction = ModelData.from_random() diff --git a/shared/docstore/src/classes/visual_syntax.py b/shared/docstore/src/classes/visual_syntax.py deleted file mode 100644 index 4483e7f..0000000 --- a/shared/docstore/src/classes/visual_syntax.py +++ /dev/null @@ -1,28 +0,0 @@ -"""Definition of VisualSyntaxData data model.""" - -from __future__ import annotations - -from .data_model import DataModel - - -class VisualSyntaxData(DataModel): - """VisualSyntaxData data model.""" - - non_transactional_action: float - non_transactional_reaction: float - unidirectional_transactional_action: float - unidirectional_transactional_reaction: float - bidirectional_transactional_action: float - bidirectional_transactional_reaction: float - conversion: float - speech_process: float - classification_overt_taxonomy: float - analytical_exhaustive: float - analytical_disarranged: float - analytical_temporal: float - analytical_distributed: float - analytical_topological: float - analytical_exploded: float - analytical_inclusive: float - symbolic_suggestive: float - symbolic_attributive: float diff --git a/shared/docstore/src/connect_mongodb.py b/shared/docstore/src/connect_mongodb.py deleted file mode 100644 index c9743bc..0000000 --- a/shared/docstore/src/connect_mongodb.py +++ /dev/null @@ -1,30 +0,0 @@ -"""Definition of function to connect to database using environment -variables.""" - -import logging -import os - -from dotenv import load_dotenv -from pymongo import MongoClient - - -def connect_mongodb(): - """Connect to MongoDB using env vars.""" - # load env vars - load_dotenv() - necessary_env_vars = [ - 'MONGO_HOST', - 'MONGO_DB', - 'MONGO_COLLECTION', - ] - for env_var in necessary_env_vars: - assert env_var in os.environ, f"{env_var} not found" - # connect to database - client = MongoClient(os.getenv('MONGO_HOST')) - db = client[os.getenv('MONGO_DB')] - # extract collection - collection = db[os.getenv('MONGO_COLLECTION')] - # set unique index on "name" - collection.create_index('name', unique=True) - logging.debug('finished') - return collection, db, client diff --git a/shared/docstore/src/count_documents.py b/shared/docstore/src/count_documents.py deleted file mode 100755 index eb9af6b..0000000 --- a/shared/docstore/src/count_documents.py +++ /dev/null @@ -1,20 +0,0 @@ -"""Definition of function to count documents in database.""" - -from __future__ import annotations - -from pymongo.collection import Collection - - -def count_documents( - collection: Collection, - only_with_annotation: bool = False, -) -> int: - """Get the total number of documents in database that matches the - filters.""" - assert isinstance(collection, Collection) - assert isinstance(only_with_annotation, bool) - # build query - query = {} - if only_with_annotation: - query['annotation'] = {'$ne': None} - return collection.count_documents(filter=query) diff --git a/shared/docstore/src/docstore_interface.py b/shared/docstore/src/docstore_interface.py deleted file mode 100644 index eba250c..0000000 --- a/shared/docstore/src/docstore_interface.py +++ /dev/null @@ -1,83 +0,0 @@ -"""Definition of docstore interface.""" - -from __future__ import annotations - -from abc import ABC, abstractmethod - -from shared.docstore.src.classes import ModelData, VisualCommunication - - -class DocstoreInterface(ABC): - """Docstore interface class.""" - - @abstractmethod - def connect( - self, - ) -> None: - pass - - @abstractmethod - def close( - self, - ) -> None: - pass - - @abstractmethod - def __enter__( - self, - ) -> DocstoreInterface: - pass - - @abstractmethod - def __exit__( - self, - exc_type, - exc_val, - exc_tb, - ) -> None: - pass - - @abstractmethod - def count_documents( - self, - only_with_annotation: bool, - ) -> int: - pass - - @abstractmethod - def list_names( - self, - only_with_annotation: bool, - ) -> list[str]: - pass - - @abstractmethod - def upsert_visual_comminucations( - self, - visual_communication_list: list[VisualCommunication], - ) -> None: - pass - - @abstractmethod - def upsert_annotations( - self, - visual_communication_name: str, - annotations: ModelData, - ) -> None: - pass - - @abstractmethod - def upsert_prediction( - self, - visual_communication_name: str, - predictions: ModelData, - ) -> None: - pass - - @abstractmethod - def get_visual_communication( - self, - with_annotation: bool, - name: str | None = None, - ) -> VisualCommunication: - pass diff --git a/shared/docstore/src/docstore_mongo.py b/shared/docstore/src/docstore_mongo.py deleted file mode 100644 index cd665b8..0000000 --- a/shared/docstore/src/docstore_mongo.py +++ /dev/null @@ -1,241 +0,0 @@ -"""Definition of docstore mongodb implementation.""" - -from __future__ import annotations - -import logging -import os -from typing import Any - -from pymongo import MongoClient -from pymongo.collection import Collection -from pymongo.database import Database - -from shared.utils import check_env - -from .classes import ModelData, VisualCommunication -from .docstore_interface import DocstoreInterface -from .exceptions import NoDocumentFoundException - - -class DocstoreMongo(DocstoreInterface): - """Docstore interface.""" - - def __init__(self): - # ensure necessary env vars available - var_list = { - 'MONGO_ENDPOINT', - 'MONGO_DB', - 'MONGO_COLLECTION', - } - check_env(var_list) - # prepare internal variables - self.client: MongoClient | None = None - self.db: Database | None = None - self.collection: Collection | None = None - - def connect(self) -> None: - """Connect to Mongo server.""" - # prepare arguments - mongo_endpoint = str(os.getenv('MONGO_ENDPOINT')) - mongo_database = str(os.getenv('MONGO_DB')) - mongo_collection = str(os.getenv('MONGO_COLLECTION')) - # connect client - client: MongoClient = MongoClient(mongo_endpoint) - database = client[mongo_database] - collection = database[mongo_collection] - # set unique index on 'name' - collection.create_index(keys='name', unique=True) - # persist state - self._client = client - self._database = database - self._collection = collection - - def close(self) -> None: - """Close connection to Mongo server.""" - self._client.close() - self._client = None # type: ignore - self._database = None # type: ignore - self._collection = None # type: ignore - - def __enter__(self) -> DocstoreMongo: - self.connect() - return self - - def __exit__(self, exc_type, exc_val, exc_tb) -> None: - if any( - ( - exc_type is not None, - exc_val is not None, - exc_tb is not None, - ), - ): - logging.error('error while exiting context') - self.close() - - def count_documents( - self, - only_with_annotation: bool = False, - ): - """Get the total number of Visual Communication documents matching the - filter.""" - assert isinstance(only_with_annotation, bool) - # build query - query = {} - if only_with_annotation: - query['annotation'] = {'$ne': None} - # execute query - num_docs = self._collection.count_documents(filter=query) - return num_docs - - def list_names( - self, - only_with_annotation: bool, - ) -> list[str]: - """List names of Visual Communication documents that match the - filters.""" - assert isinstance(only_with_annotation, bool) - assert isinstance(self._collection, Collection) - # build query - query = {} - if only_with_annotation: - query['annotation'] = {'$ne': None} - # execute query - res_list = self._collection.find( - filter=query, - projection={ - '_id': False, # don't get id - 'name': True, # include document name - }, - ) - # extract info - name_list = [elem['name'] for elem in res_list] - return name_list - - def upsert_visual_comminucations( - self, - visual_communication_list: list[VisualCommunication], - ) -> None: - """Upsert Visual Communication document in the database.""" - assert isinstance(visual_communication_list, list) - assert all( - isinstance(vis_com, VisualCommunication) - for vis_com in visual_communication_list - ) - assert isinstance(self._collection, Collection) - # convert to dict - doc_list = [vis_com.model_dump() for vis_com in visual_communication_list] - # insert documents - response = self._collection.insert_many(documents=doc_list) - # check response - if not response.acknowledged: - raise OSError('failed inserting documents') - - def upsert_annotations( - self, - visual_communication_name: str, - annotations: ModelData, - ) -> None: - """Upsert annotation for the document with matching name.""" - assert isinstance(visual_communication_name, str) - assert len(visual_communication_name) > 0 - assert isinstance(annotations, ModelData) - assert isinstance(self._collection, Collection) - # convert to dict - doc = annotations.model_dump() - # build query - query = { - 'name': visual_communication_name, - } - update = { - '$set': { - 'annotation': doc, - }, - } - # execute query - res = self._collection.update_one( - filter=query, - update=update, - upsert=True, - ) - # check response - if not res.acknowledged: - raise OSError( - f'failed upserting annotations for {visual_communication_name}', - ) - - def upsert_prediction( - self, - visual_communication_name: str, - predictions: ModelData, - ) -> None: - """Upsert prediction for the document with matching name.""" - assert isinstance(visual_communication_name, str) - assert len(visual_communication_name) > 0 - assert isinstance(annotations, ModelData) - assert isinstance(self._collection, Collection) - # convert to dict - doc = predictions.model_dump() - # build query - query = { - 'name': visual_communication_name, - } - update = { - '$set': { - 'prediction': doc, - }, - } - # execute query - res = self._collection.update_one( - filter=query, - update=update, - upsert=True, - ) - # check response - if not res.acknowledged: - raise OSError( - f'failed upserting predictions for {visual_communication_name}', - ) - - def get_visual_communication( - self, - with_annotation: bool = False, - name: str | None = None, - ) -> VisualCommunication: - """Get a random Visual Communication document that matches annotation - filter. - - If name is not specified, a random document matching filter is - returned. - """ - assert isinstance(with_annotation, bool) - if name is not None: - assert isinstance(name, str) - assert len(name) > 0 - # build query - query: dict[str, Any] = {} - if with_annotation: - query['annotation'] = {'$ne': None} - else: - query['annotation'] = {'$eq': None} - if name is not None: - query['name'] = {'$eq': name} - # execute query - res_list = self._collection.aggregate( - pipeline=[ - { - '$match': query, # find using filters - }, - { - '$sample': { - 'size': 1, # get one random - }, - }, - ], - ) - doc_list = list(res_list) - # check result - if len(doc_list) == 0: - raise NoDocumentFoundException() - # convert - vis_com = VisualCommunication.model_validate(doc_list[0]) - return vis_com diff --git a/shared/docstore/src/exceptions/__init__.py b/shared/docstore/src/exceptions/__init__.py deleted file mode 100644 index 6daba63..0000000 --- a/shared/docstore/src/exceptions/__init__.py +++ /dev/null @@ -1 +0,0 @@ -from .no_document_found import NoDocumentFoundException diff --git a/shared/docstore/src/exceptions/no_document_found.py b/shared/docstore/src/exceptions/no_document_found.py deleted file mode 100755 index dfe1c99..0000000 --- a/shared/docstore/src/exceptions/no_document_found.py +++ /dev/null @@ -1,5 +0,0 @@ -"""Definition of database exception.""" - - -class NoDocumentFoundException(Exception): - """Database exception for when no documents are found.""" diff --git a/shared/docstore/src/get_dataset.py b/shared/docstore/src/get_dataset.py deleted file mode 100755 index 0c823cc..0000000 --- a/shared/docstore/src/get_dataset.py +++ /dev/null @@ -1,16 +0,0 @@ -"""Definition of get_dataset function.""" - -from typing import Literal - -from pymongo.collection import Collection - - -def get_dataset( - collection: Collection, - type: Literal['train', 'test', 'validation'], -) -> list[str]: - """Get list of data names for the corresponding type.""" - assert isinstance(collection, Collection) - assert isinstance(type, str) - assert type in ['train', 'test', 'validation'] - return [] diff --git a/shared/docstore/src/get_visual_communication.py b/shared/docstore/src/get_visual_communication.py deleted file mode 100755 index 5c85a88..0000000 --- a/shared/docstore/src/get_visual_communication.py +++ /dev/null @@ -1,40 +0,0 @@ -"""Definition of function to get visual communication from database.""" - -from __future__ import annotations - -import logging - -from pymongo.collection import Collection - -from shared.docstore.src.classes import VisualCommunication -from shared.docstore.src.exceptions import NoDocumentFoundException - - -def get_visual_communication( - collection: Collection, - with_annotation: bool = False, -) -> VisualCommunication: - """Get a random visual communication from the database.""" - query = {} - if with_annotation: - query['annotation'] = {'$ne': None} - else: - query['annotation'] = {'$eq': None} - data = collection.aggregate( - pipeline=[ - { - '$match': query, # find using filters - }, - { - '$sample': { - 'size': 1, # get one random - }, - }, - ], - ) - data_list = list(data) # read data from cursor object - if len(data_list) == 0: - raise NoDocumentFoundException() - vis_com = VisualCommunication.model_validate(data_list[0]) - logging.debug('finished') - return vis_com diff --git a/shared/docstore/src/list_names.py b/shared/docstore/src/list_names.py deleted file mode 100755 index 86e09dc..0000000 --- a/shared/docstore/src/list_names.py +++ /dev/null @@ -1,30 +0,0 @@ -"""Definition of function to list names of all visual communication documents -in database.""" - -from __future__ import annotations - -from pymongo.collection import Collection - - -def list_names( - collection: Collection, - only_with_annotation: bool = True, -) -> list[str]: - """List the names of entries that match the filters.""" - assert isinstance(collection, Collection) - assert isinstance(only_with_annotation, bool) - # build query - query = {} - if only_with_annotation: - query['annotation'] = {'$ne': None} - # execute query - res_list = collection.find( - filter=query, - projection={ - '_id': False, - 'name': True, - }, - ) - # extract information - name_list = [elem['name'] for elem in res_list] - return name_list diff --git a/shared/docstore/src/upsert_annotation.py b/shared/docstore/src/upsert_annotation.py deleted file mode 100755 index 4eec4c0..0000000 --- a/shared/docstore/src/upsert_annotation.py +++ /dev/null @@ -1,30 +0,0 @@ -from __future__ import annotations - -import logging - -from pymongo.collection import Collection - -from shared.docstore.src.classes import ModelData - - -def upsert_annotation( - collection: Collection, - vis_com_name: str, - annotations: ModelData, -) -> None: - """Upserts annotation data in the database.""" - query = { - 'name': vis_com_name, - } - update = { - '$set': { - 'annotation': annotations.model_dump(), - }, - } - res = collection.update_one( - filter=query, - update=update, - upsert=True, - ) - logging.info('upserted document: %s', res) - logging.info('finished') diff --git a/shared/docstore/src/upsert_prediction.py b/shared/docstore/src/upsert_prediction.py deleted file mode 100755 index 81378a8..0000000 --- a/shared/docstore/src/upsert_prediction.py +++ /dev/null @@ -1,30 +0,0 @@ -from __future__ import annotations - -import logging - -from pymongo.collection import Collection - -from shared.docstore.src.classes import ModelData - - -def upsert_prediction( - collection: Collection, - vis_com_name: str, - predictions: ModelData, -) -> None: - """Upsert prediction data in the database.""" - query = { - 'name': vis_com_name, - } - update = { - '$set': { - 'prediction': predictions.model_dump(), - }, - } - res = collection.update_one( - filter=query, - update=update, - upsert=True, - ) - logging.debug('upserted document: %s', res) - logging.info('finished') diff --git a/shared/docstore/src/upsert_visual_communication.py b/shared/docstore/src/upsert_visual_communication.py deleted file mode 100755 index b5a863c..0000000 --- a/shared/docstore/src/upsert_visual_communication.py +++ /dev/null @@ -1,19 +0,0 @@ -from __future__ import annotations - -from pymongo.collection import Collection - -from shared.docstore.src.classes import VisualCommunication - - -def upsert_visual_communication( - collection: Collection, - visual_communication_list: list[VisualCommunication], -) -> bool: - """Upsert VisualCommunication object in the database. - - Returns bool stating success. - """ - response = collection.insert_many( - [vis_com.model_dump() for vis_com in visual_communication_list], - ) - return response.acknowledged diff --git a/shared/docstore/tests/unit/docstore_mongo_test.py b/shared/docstore/tests/unit/docstore_mongo_test.py deleted file mode 100644 index 6e79b39..0000000 --- a/shared/docstore/tests/unit/docstore_mongo_test.py +++ /dev/null @@ -1,45 +0,0 @@ -"""Definition of unittests for Docstore MongoDB implementation.""" - -import os -from unittest import TestCase -from unittest.mock import MagicMock - -from pymongo import MongoClient -from pymongo.collection import Collection -from pymongo.database import Database - -from shared.docstore.src.docstore_mongo import DocstoreMongo - - -class TestDocstoreMongoImplementation(TestCase): - - def setUp(self): - # define relevant env vars - self.env_var_map = { - 'MONGO_ENDPOINT': '192.168.1.2:27017', - 'MONGO_DB': 'visual_critical_discourse_analysis', - 'MONGO_COLLECTION': 'test-collection', - } - # set env vars - for key, val in self.env_var_map.items(): - os.environ[key] = val - # set other variables - self.mongo_client_mock = MagicMock(MongoClient) - self.mongo_database_mock = MagicMock(Database) - self.mongo_collection_mock = MagicMock(Collection) - - def tearDown(self): - # clear env vars - for key in self.env_var_map: - _ = os.environ.pop(key, default=None) - # reset reuseable mocks - self.mongo_client_mock.reset_mock() - self.mongo_database_mock.reset_mock() - self.mongo_collection_mock.reset_mock() - - def test_instantiation_should_fail_when_env_not_set(self): - # ensure env not set - self.tearDown() - # run test - with self.assertRaises(OSError): - _ = DocstoreMongo() diff --git a/shared/repositories/tests/integration/conftest.py b/shared/repositories/tests/integration/conftest.py index ecc1cf0..a44910b 100644 --- a/shared/repositories/tests/integration/conftest.py +++ b/shared/repositories/tests/integration/conftest.py @@ -32,14 +32,17 @@ from shared.repositories.src.implementations import ( random.seed(13) # define test environment variables +necessary_env_vars = { + 'MINIO_ENDPOINT', + 'MINIO_ACCESS_KEY', + 'MINIO_SECRET_KEY', + 'MONGO_ENDPOINT', +} env_var_map = { - 'MINIO_ENDPOINT': '192.168.1.2:9000', - 'MINIO_ACCESS_KEY': '1rMQTezbALeJyOgAbYYE', - 'MINIO_SECRET_KEY': 'O76GM756ybKYLFokZFJneaCoYwpaIbAlOdB7mcc0', + 'MINIO_ENDPOINT': 'localhost:9000', 'MINIO_BUCKET_NAME': 'test-bucket', 'MINIO_OBJECT_NAME': 'test-object', 'MINIO_IMAGE_NAME': 'test-image', - 'MONGO_ENDPOINT': 'mongodb://192.168.1.2:27017/', 'MONGO_DB': 'test-db', 'MONGO_COLLECTION': 'test-collection', } @@ -53,6 +56,9 @@ def setup_env( # load in optional local test environment variables test_env_path = Path(__file__).parent.parent.parent.parent.parent / 'test.env' load_dotenv(test_env_path) + # check if necessary env vars are set + for key in necessary_env_vars: + assert key in os.environ, f'{key} not set' # set testing env vars for key, val in env_var_map.items(): # set env var -- 2.54.0 From 7d8af1c5827cfb8413819075fdbe72ee56fc91ae Mon Sep 17 00:00:00 2001 From: brian Date: Tue, 18 Mar 2025 19:28:12 +0000 Subject: [PATCH 59/64] changed returned class type --- model/src/models/visual_communication.py | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/model/src/models/visual_communication.py b/model/src/models/visual_communication.py index 071d69f..c5734bf 100644 --- a/model/src/models/visual_communication.py +++ b/model/src/models/visual_communication.py @@ -4,8 +4,6 @@ from __future__ import annotations from torch import nn -from shared.docstore.src.classes import ModelData - from .angle import AngleTail from .contact import ContactTail from .distance import DistanceTail @@ -39,7 +37,7 @@ class VisualCommunicationModel(nn.Module): self.framing_tail = FramingTail() self.salience_tail = SalienceTail() - def forward(self, x) -> ModelData: + def forward(self, x) -> dict: """Calculate model output on data.""" # generate visual representation features = self.resnet_head(x) @@ -57,6 +55,4 @@ class VisualCommunicationModel(nn.Module): 'framing': self.framing_tail(features), 'salience': self.salience_tail(features), } - # convert to respective classes - data = ModelData.from_prediction_dict(prediction_dict) - return data + return prediction_dict -- 2.54.0 From c5bcd09bbab872946f59952af1333e1add5147d2 Mon Sep 17 00:00:00 2001 From: brian Date: Tue, 18 Mar 2025 19:30:12 +0000 Subject: [PATCH 60/64] removed already defined environment variable --- shared/repositories/tests/integration/conftest.py | 1 - 1 file changed, 1 deletion(-) diff --git a/shared/repositories/tests/integration/conftest.py b/shared/repositories/tests/integration/conftest.py index a44910b..6027ece 100644 --- a/shared/repositories/tests/integration/conftest.py +++ b/shared/repositories/tests/integration/conftest.py @@ -39,7 +39,6 @@ necessary_env_vars = { 'MONGO_ENDPOINT', } env_var_map = { - 'MINIO_ENDPOINT': 'localhost:9000', 'MINIO_BUCKET_NAME': 'test-bucket', 'MINIO_OBJECT_NAME': 'test-object', 'MINIO_IMAGE_NAME': 'test-image', -- 2.54.0 From 6399b88adea7b6d3c5022267a1575bbf0e6dbef2 Mon Sep 17 00:00:00 2001 From: brian Date: Tue, 18 Mar 2025 19:33:50 +0000 Subject: [PATCH 61/64] clarified comment --- shared/repositories/tests/integration/conftest.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/shared/repositories/tests/integration/conftest.py b/shared/repositories/tests/integration/conftest.py index 6027ece..a052e36 100644 --- a/shared/repositories/tests/integration/conftest.py +++ b/shared/repositories/tests/integration/conftest.py @@ -58,7 +58,7 @@ def setup_env( # check if necessary env vars are set for key in necessary_env_vars: assert key in os.environ, f'{key} not set' - # set testing env vars + # set env vars unique to this test for key, val in env_var_map.items(): # set env var os.environ[key] = val -- 2.54.0 From 7176dfdf90c35e0b6685ea880e86d51464e6c07e Mon Sep 17 00:00:00 2001 From: brian Date: Tue, 18 Mar 2025 19:34:03 +0000 Subject: [PATCH 62/64] added env vars back in --- .gitea/workflows/pull.yaml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.gitea/workflows/pull.yaml b/.gitea/workflows/pull.yaml index 960a1e7..844db93 100644 --- a/.gitea/workflows/pull.yaml +++ b/.gitea/workflows/pull.yaml @@ -38,6 +38,11 @@ jobs: run: | /opt/poetry/bin/poetry run mypy . - name: Pytest & Calculate Coverage + env: + MINIO_ENDPOINT: ${{ vars.MINIO_ENDPOINT }} + MINIO_ACCESS_KEY: ${{ vars.MINIO_ACCESS_KEY }} + MINIO_SECRET_KEY: ${{ secrets.MINIO_SECRET_KEY }} + MONGO_ENDPOINT: ${{ vars.MONGO_ENDPOINT }} run: | /opt/poetry/bin/poetry run coverage run -m pytest . - name: Coverage Report -- 2.54.0 From 08062ad87daf2b344aa355b96b0688aa103900c8 Mon Sep 17 00:00:00 2001 From: brian Date: Tue, 15 Apr 2025 21:56:33 +0000 Subject: [PATCH 63/64] removed unused packages --- misc/generate_random_prediction.py | 42 -------- misc/get_visual_communication.py | 31 ------ misc/image_upload.py | 48 --------- misc/image_upload_to_server.py | 53 --------- misc/model_io.py | 34 ------ misc/new_model_to_minio.py | 32 ------ misc/prediction_upload.py | 48 --------- model/src/main.py | 12 +-- model/src/utils/load_model.py | 17 ++- model/src/utils/vcda_dataset.py | 14 ++- model/train.py | 10 +- other/transfer_images_minio_subfolder.py | 42 -------- web_ui/src/app/init_app.py | 130 ++++++++++++----------- web_ui/src/main.py | 17 +-- 14 files changed, 91 insertions(+), 439 deletions(-) delete mode 100644 misc/generate_random_prediction.py delete mode 100644 misc/get_visual_communication.py delete mode 100644 misc/image_upload.py delete mode 100644 misc/image_upload_to_server.py delete mode 100644 misc/model_io.py delete mode 100644 misc/new_model_to_minio.py delete mode 100644 misc/prediction_upload.py delete mode 100644 other/transfer_images_minio_subfolder.py diff --git a/misc/generate_random_prediction.py b/misc/generate_random_prediction.py deleted file mode 100644 index 080b9a8..0000000 --- a/misc/generate_random_prediction.py +++ /dev/null @@ -1,42 +0,0 @@ -from __future__ import annotations - -from pathlib import Path - -from dotenv import load_dotenv - -from shared.datastore import Datastore -from shared.docstore import connect_mongodb -from shared.docstore.src.classes import VisualCommunication -from shared.utils import check_env, setup_logging -from web_ui.src.main import NECESSARY_ENV_VAR_LIST - -if __name__ == '__main__': - # load in env file - env_path = Path(__file__).parent.parent / 'server.env' - assert env_path.exists() - load_dotenv(env_path) - # ensure env vars set - check_env(NECESSARY_ENV_VAR_LIST) - # setup logging - setup_logging() - # connect to minIO - datastore = Datastore() - datastore.connect() - assert datastore._client is not None - # connect to MongoDB - collection, db, client = connect_mongodb() - # get list of image paths - test_dir = Path(__file__).parent - img_dir = test_dir / 'imgs' - img_path_list = [path for path in img_dir.glob('*.jpeg') if path.is_file()] - print(img_path_list) - # instantiate data object - vis_com_list = [ - VisualCommunication.from_file(path, minio_client=datastore._client) - for path in img_path_list - ] - # generate random predictions - for vis_com in vis_com_list: - vis_com.generate_random_prediction() - for vis_com in vis_com_list: - print(vis_com) diff --git a/misc/get_visual_communication.py b/misc/get_visual_communication.py deleted file mode 100644 index 2341957..0000000 --- a/misc/get_visual_communication.py +++ /dev/null @@ -1,31 +0,0 @@ -from __future__ import annotations - -from pathlib import Path - -from dotenv import load_dotenv - -from shared.datastore import Datastore -from shared.docstore import connect_mongodb, get_visual_communication -from shared.utils import check_env, setup_logging -from web_ui.src.main import NECESSARY_ENV_VAR_LIST - -if __name__ == '__main__': - # load in env file - env_path = Path(__file__).parent.parent / 'server.env' - assert env_path.exists() - load_dotenv(env_path) - # ensure env vars set - check_env(NECESSARY_ENV_VAR_LIST) - # setup logging - setup_logging() - # connect to minIO - datastore = Datastore() - datastore.connect() - assert datastore._client is not None - # connect to MongoDB - collection, db, client = connect_mongodb() - # get visual communication - vis_com = get_visual_communication(collection) - print(repr(vis_com)) - image = vis_com.get_image(minio_client=datastore._client) - image.show() diff --git a/misc/image_upload.py b/misc/image_upload.py deleted file mode 100644 index 9798c83..0000000 --- a/misc/image_upload.py +++ /dev/null @@ -1,48 +0,0 @@ -from __future__ import annotations - -from pathlib import Path - -from dotenv import load_dotenv -from pymongo.errors import DuplicateKeyError - -from shared.datastore import Datastore -from shared.docstore import connect_mongodb -from shared.docstore.src.classes import VisualCommunication -from shared.utils import check_env, setup_logging -from web_ui.src.main import NECESSARY_ENV_VAR_LIST - -if __name__ == '__main__': - # load in env file - env_path = Path(__file__).parent.parent / 'server.env' - assert env_path.exists() - load_dotenv(env_path) - # ensure env vars set - check_env(NECESSARY_ENV_VAR_LIST) - # setup logging - setup_logging() - # connect to minIO - datastore = Datastore() - datastore.connect() - assert datastore._client is not None - # connect to MongoDB - collection, db, client = connect_mongodb() - # get list of image paths - test_dir = Path(__file__).parent - img_dir = test_dir / 'imgs' - img_path_list = [path for path in img_dir.glob('*.jpeg') if path.is_file()] - print(img_path_list) - # instantiate data object - vis_com_list = [ - VisualCommunication.from_file(path, minio_client=datastore._client) - for path in img_path_list - ] - for vis_com in vis_com_list: - print(repr(vis_com)) - # upload images - for vis_com in vis_com_list: - try: - result = collection.insert_one(vis_com.model_dump()) - except DuplicateKeyError as exc: - print('ignoring:\n', exc) - else: - print(f"inserted document: {result}") diff --git a/misc/image_upload_to_server.py b/misc/image_upload_to_server.py deleted file mode 100644 index 8f401cb..0000000 --- a/misc/image_upload_to_server.py +++ /dev/null @@ -1,53 +0,0 @@ -from __future__ import annotations - -from pathlib import Path - -from dotenv import load_dotenv -from pymongo.errors import DuplicateKeyError - -from shared.datastore import Datastore -from shared.docstore import connect_mongodb -from shared.docstore.src.classes import VisualCommunication -from shared.utils import check_env, setup_logging -from web_ui.src.main import NECESSARY_ENV_VAR_LIST - -if __name__ == '__main__': - # load in env file - env_path = Path(__file__).parent.parent / 'server.env' - assert env_path.exists() - load_dotenv(env_path) - # ensure env vars set - check_env(NECESSARY_ENV_VAR_LIST) - # setup logging - setup_logging() - # connect to minIO - datastore = Datastore() - datastore.connect() - assert datastore._client is not None - # connect to MongoDB - collection, db, client = connect_mongodb() - # get list of image paths - ext_img_dir = Path('/Volumes/BW-PSSD/Mixed Methods/') - assert ext_img_dir.exists() - img_path_list = [ - path - for path in ext_img_dir.glob( - '*.jpg', - ) - if path.is_file() - ] - print(f"found {len(img_path_list)} images") - # create visual communication objects - vis_com_list = [ - VisualCommunication.from_file(path, minio_client=datastore._client) - for path in img_path_list - ] - print(f"created {len(vis_com_list)} visual communication objects") - # upload images - for vis_com in vis_com_list: - try: - result = collection.insert_one(vis_com.model_dump()) - except DuplicateKeyError as exc: - print('ignoring:\n', exc) - else: - print(f"inserted document: {result}") diff --git a/misc/model_io.py b/misc/model_io.py deleted file mode 100644 index b5bec6d..0000000 --- a/misc/model_io.py +++ /dev/null @@ -1,34 +0,0 @@ -"""Test that a model can be saved and loaded again.""" - -from pathlib import Path - -import torch -from dotenv import load_dotenv -from torchinfo import summary - -from model.src.models import VisualCommunicationModel -from shared.datastore import Datastore -from shared.utils import setup_logging - -DEVICE = torch.device('cuda' if torch.cuda.is_available() else 'cpu') - -if __name__ == '__main__': - # load in env file - env_path = Path(__file__).parent.parent / 'server.env' - assert env_path.exists() - load_dotenv(env_path) - # setup logging - setup_logging() - # connect to minio - datastore = Datastore() - datastore.connect() - # instantiate model - model = VisualCommunicationModel().to(DEVICE) - # show model weights - summary(model) - # put buffer in minio bucket - hash_str = datastore.put_model( - model=model, - ) - print(f"hash string: {hash_str}") - print('saved to Minio') diff --git a/misc/new_model_to_minio.py b/misc/new_model_to_minio.py deleted file mode 100644 index 416dd25..0000000 --- a/misc/new_model_to_minio.py +++ /dev/null @@ -1,32 +0,0 @@ -"""Definition of function to generate a new randomly initialized model and save -it in Minio datastore.""" - -from pathlib import Path - -from dotenv import load_dotenv -from torchinfo import summary - -from model.src.models import VisualCommunicationModel -from shared.datastore import Datastore -from shared.utils import setup_logging - -if __name__ == '__main__': - # load in env file - env_path = Path(__file__).parent.parent / 'server.env' - assert env_path.exists() - load_dotenv(env_path) - # setup logging - setup_logging() - # connect to minio - datastore = Datastore() - datastore.connect() - # instantiate model - model = VisualCommunicationModel(download_resnet_weights=True) - # show model weights - summary(model) - # put buffer in minio bucket - hash_str = datastore.put_model( - model=model, - ) - print(f"hash string: {hash_str}") - print('saved to Minio') diff --git a/misc/prediction_upload.py b/misc/prediction_upload.py deleted file mode 100644 index e29cc74..0000000 --- a/misc/prediction_upload.py +++ /dev/null @@ -1,48 +0,0 @@ -from __future__ import annotations - -from pathlib import Path - -from dotenv import load_dotenv - -from shared.datastore import Datastore -from shared.docstore import connect_mongodb, upsert_prediction -from shared.docstore.src.classes import VisualCommunication -from shared.utils import check_env, setup_logging -from web_ui.src.main import NECESSARY_ENV_VAR_LIST - -if __name__ == '__main__': - # load in env file - env_path = Path(__file__).parent.parent / 'server.env' - assert env_path.exists() - load_dotenv(env_path) - # ensure env vars set - check_env(NECESSARY_ENV_VAR_LIST) - # setup logging - setup_logging() - # connect to minIO - datastore = Datastore() - datastore.connect() - assert datastore._client is not None - # connect to MongoDB - collection, db, client = connect_mongodb() - # get list of image paths - test_dir = Path(__file__).parent - img_dir = test_dir / 'imgs' - img_path_list = [path for path in img_dir.glob('*.jpeg') if path.is_file()] - # instantiate data object - vis_com_list = [ - VisualCommunication.from_file(path, minio_client=datastore._client) - for path in img_path_list - ] - # generate random predictions - for vis_com in vis_com_list: - vis_com.generate_random_prediction() - # upload visual communication - for vis_com in vis_com_list: - if vis_com.prediction is None: - continue - upsert_prediction( - collection=collection, - vis_com_name=vis_com.name, - predictions=vis_com.prediction, - ) diff --git a/model/src/main.py b/model/src/main.py index 9b4cb3d..82ac444 100644 --- a/model/src/main.py +++ b/model/src/main.py @@ -9,22 +9,16 @@ from models import VisualCommunicationModel from tqdm import tqdm from utils import DEVICE, VCDADataset, load_model -from shared.datastore import Datastore -from shared.docstore.classes import ModelData from shared.utils import setup_logging if __name__ == '__main__': # setup logging setup_logging() - # connect to minio - datastore = Datastore() - datastore.connect() # instantiate model - model: VisualCommunicationModel = load_model(client=datastore._client) + model: VisualCommunicationModel = load_model() model.eval() # setup dataset dataset = VCDADataset( - minio_client=datastore._client, data_name_list=[ '02dbaf48d713e4e6d3a6b98fd2dc866e', ], @@ -40,10 +34,10 @@ if __name__ == '__main__': image = torch.unsqueeze(image, 0) # add artificial batch dimension image = image.to(DEVICE) # make prediction - pred: ModelData = model(image) + pred: dict = model(image) except Exception: print_exc() continue else: - print(json.dumps(pred.model_dump(), indent=4)) + print(json.dumps(pred, indent=4)) logging.debug('finished') diff --git a/model/src/utils/load_model.py b/model/src/utils/load_model.py index 992f498..b5121cb 100644 --- a/model/src/utils/load_model.py +++ b/model/src/utils/load_model.py @@ -6,29 +6,28 @@ from pathlib import Path import torch from model.src.models import VisualCommunicationModel -from shared.datastore import Datastore +from shared.repositories import ModelRepository from .get_model_name import get_model_name DEVICE = torch.device('cuda' if torch.cuda.is_available() else 'cpu') -def load_model( - datastore: Datastore, -) -> VisualCommunicationModel: +def load_model() -> VisualCommunicationModel: """Instantiate model with weights loaded from latest model saved in MinIO.""" - assert isinstance(datastore, Datastore) # instantiate model model = VisualCommunicationModel() # get model object name model_name_path = Path('model_name.txt') model_object_name = get_model_name(path=model_name_path) logging.info('using model: %s', model_object_name) - # load model from minio - model_checkpoint = datastore.get_model( - object_name=model_object_name, - ) + # load model data + with ModelRepository() as repo: + model_data = repo.get_data(model_object_name) + if model_data is None: + raise FileNotFoundError(f'model {model_object_name} not found') + model_checkpoint = torch.load(model_data.buffer) model.load_state_dict(model_checkpoint) # clean memory model_checkpoint.clear() diff --git a/model/src/utils/vcda_dataset.py b/model/src/utils/vcda_dataset.py index 43f57e7..418681d 100644 --- a/model/src/utils/vcda_dataset.py +++ b/model/src/utils/vcda_dataset.py @@ -15,7 +15,7 @@ from torchvision.transforms.functional import ( to_tensor, ) -from shared.datastore import Datastore +from shared.repositories import ImageRepository # resnet18 original normalization values RESNET_NORMALIZE_MEAN = [0.485, 0.456, 0.406] @@ -27,13 +27,11 @@ class VCDADataset(Dataset): def __init__( self, - datastore: Datastore, data_name_list: list[str], do_augment: bool = False, random_annotations: bool = False, ): super().__init__() - self.datastore = datastore self.data_name_list = data_name_list self.do_augment = do_augment self.random_annotations = random_annotations @@ -55,11 +53,11 @@ class VCDADataset(Dataset): def __getitem__(self, idx): # get image from database - object_name = self.data_name_list[idx] - image = self.datastore.get_image( - object_name=object_name, - ) - tensor = self.image_to_tensor(image) + image_name = self.data_name_list[idx] + with ImageRepository() as repo: + image_data = repo.get_data(image_name) + assert image_data is not None + tensor = self.image_to_tensor(image_data.image) if self.do_augment: tensor = self.augment(tensor) return tensor diff --git a/model/train.py b/model/train.py index 0446285..1ad1ffa 100644 --- a/model/train.py +++ b/model/train.py @@ -18,7 +18,6 @@ from torch.optim.lr_scheduler import ExponentialLR from torch.utils.data import DataLoader from model.src.utils import VCDADataset, get_class -from shared.datastore import Datastore def parse_arguments(): @@ -57,19 +56,16 @@ optimizer = torch.optim.Adam(model.parameters(), lr=args.lr) loss_fn = nn.CrossEntropyLoss() # create datasets and loaders -datastore = Datastore() -datastore.connect() with open('model/src/dataset/train.csv', encoding='utf-8') as fh: train_data_name_list = fh.read().split('\n') train_dataset = VCDADataset( - datastore=datastore, data_name_list=train_data_name_list, ) train_loader = DataLoader(dataset=train_dataset, num_workers=args.loader_workers) with open('model/src/dataset/val.csv', encoding='utf-8') as fh: val_data_name_list = fh.read().split('\n') -val_dataset = VCDADataset(datastore=datastore, data_name_list=val_data_name_list) +val_dataset = VCDADataset(data_name_list=val_data_name_list) val_loader = DataLoader(dataset=val_dataset, num_workers=args.loader_workers) # create trainer and evaluator @@ -141,7 +137,7 @@ to_save = { } checkpoint_handler = Checkpoint( to_save, - f"runs/checkpoints/{run_name}", + f'runs/checkpoints/{run_name}', n_saved=3, filename_prefix='best', score_function=lambda engine: -engine.state.metrics['loss'], @@ -155,7 +151,7 @@ if args.checkpoint: # save model config os.makedirs('runs/configs/', exist_ok=True) -with open(f"runs/configs/{run_name}.json", 'w', encoding='utf-8') as fh: +with open(f'runs/configs/{run_name}.json', 'w', encoding='utf-8') as fh: json.dump(config, fh) # start training diff --git a/other/transfer_images_minio_subfolder.py b/other/transfer_images_minio_subfolder.py deleted file mode 100644 index 4c960a8..0000000 --- a/other/transfer_images_minio_subfolder.py +++ /dev/null @@ -1,42 +0,0 @@ -"""Script to move minio images to subfolder.""" - -import os -from pathlib import Path - -from dotenv import load_dotenv -from PIL import Image - -from shared.datastore import Datastore -from shared.utils import setup_logging - -if __name__ == '__main__': - # load in env file - env_path = Path(__file__).parent.parent / 'server.env' - assert env_path.exists() - load_dotenv(env_path) - # setup logging - setup_logging() - # connect to minio - datastore = Datastore() - datastore.connect() - assert datastore._client is not None - # list images in bucket - BUCKET_NAME = os.getenv( - 'MINIO_BUCKET_NAME', - default='visual-critical-discourse-analysis', - ) - obj_list = datastore._client.list_objects( - bucket_name=BUCKET_NAME, - ) - # begin moving images - for obj in obj_list: - # get image from minio - buffer = datastore._get( - object_name=obj.object_name, - ) - # convert data to image - image = Image.open(buffer) - # put image into minio subfolder - _ = datastore.put_image( - image=image, - ) diff --git a/web_ui/src/app/init_app.py b/web_ui/src/app/init_app.py index ce2ade3..e5af2f0 100644 --- a/web_ui/src/app/init_app.py +++ b/web_ui/src/app/init_app.py @@ -4,29 +4,28 @@ from __future__ import annotations import logging import os +import random +from base64 import b64decode, b64encode +from io import BytesIO import dash_bootstrap_components as dbc from dash import ALL, Dash, Input, Output, State from dash_auth import BasicAuth +from PIL import Image from pydantic import ValidationError -from pymongo.collection import Collection -from shared.datastore import Datastore -from shared.docstore import count_documents, get_visual_communication, upsert_annotation -from shared.docstore.src.classes import ModelData, VisualCommunication -from shared.docstore.src.exceptions import NoDocumentFoundException +from shared.repositories import ( + ImageData, + ImageRepository, + VisualCommunicationData, + VisualCommunicationRepository, +) from .layout import app_layout -def init_app( - mongo_collection: Collection, - datastore: Datastore, -) -> Dash: +def init_app() -> Dash: """Initialise web UI application.""" - assert isinstance(mongo_collection, Collection) - assert isinstance(datastore, Datastore) - assert datastore._client is not None # setup app app = Dash( name='visual_critical_discourse_analysis_web_ui', @@ -90,14 +89,10 @@ def init_app( if filename_list is not None: assert isinstance(filename_list, list) # get values from database - num_total = count_documents( - collection=mongo_collection, - only_with_annotation=False, - ) - num_handled = count_documents( - collection=mongo_collection, - only_with_annotation=True, - ) + with VisualCommunicationRepository() as repo: + name_list = repo.list_names() + num_total = len(name_list) + num_handled = 0 limit = int(num_total / 20) label_str = f'{num_handled}/{num_total}' if num_handled >= limit else '' return num_handled, num_total, label_str @@ -125,38 +120,37 @@ def init_app( for content, filename in zip(content_list, filename_list): try: # decode image content - image = VisualCommunication.decode_image(content=content) + content_data = content.split(',')[-1] + image = Image.open(BytesIO(b64decode(content_data))) + # instantiate ImageData object + image_data = ImageData( + name=filename, + image=image, + ) + # instantiate VisualCommunicationData object + vis_com_data = VisualCommunicationData(name=filename) except Exception: logging.debug('failed decoding %s', filename) failed_filename_list.append(filename) continue try: - assert datastore._client is not None - # instantiate to upload image to minio - vis_com = VisualCommunication.from_name_and_image( - name=filename, - image=image, - minio_client=datastore._client, - ) + # save ImageData + with ImageRepository() as repo: + repo.put_data(image_data) + # save VisualCommunicationData + with VisualCommunicationRepository() as repo: + repo.put_data(vis_com_data) except Exception as exc: logging.debug(exc) failed_filename_list.append(filename) - continue - try: - # save to mongodb - vis_com.save_to_mongo(collection=mongo_collection) - except Exception as exc: - logging.debug(exc) - failed_filename_list.append(filename) - # remove document from minio - datastore._delete( - object_name=vis_com.object_name, - ) - assert ( - len(failed_filename_list) == 0 - ), f"failed uploading:{ - '\n'.join(failed_filename_list) - }" + # cleanup failed uploads + with ImageRepository() as repo: + repo.remove_data(image_data.name) + with VisualCommunicationRepository() as repo: + repo.remove_data(vis_com_data.name) + if len(failed_filename_list) == 0: + err_msg = 'failed uploading:' + '\n'.join(failed_filename_list) + raise FileNotFoundError(err_msg) except Exception as exc: logging.debug(exc) return None, str(exc).title() @@ -208,7 +202,7 @@ def init_app( logging.info(annotation_keys) for option, value in zip(annotation_keys, annotation_values): if value is None: - raise ValueError(f"{option} is not set") + raise ValueError(f'{option} is not set') # prepare data to save annotation_keys = [elem.replace(' ', '_') for elem in annotation_keys] annotation_values = [ @@ -217,16 +211,21 @@ def init_app( annotation_map = { key: value for key, value in zip(annotation_keys, annotation_values) } - # instantiate ModelOutputs object - annotations = ModelData.from_annotations(**annotation_map) - # save data to database - upsert_annotation( - collection=mongo_collection, - vis_com_name=vis_com_name, - annotations=annotations, - ) + # get data + with VisualCommunicationRepository() as repo: + vis_com_data = repo.get_data(vis_com_name) + # data already present, as it was loaded earlier to get here + assert vis_com_data is not None + # update annotations + vis_com_data_updated = vis_com_data.model_copy( + update={ + 'annotations': annotation_map, + }, + ) + # save updated data + repo.put_data(vis_com_data_updated) except (ValueError, ValidationError) as exc: - msg = f"failed saving annotation: {exc}" + msg = f'failed saving annotation: {exc}' logging.warning(msg) response[0] = msg return tuple(response) @@ -234,21 +233,30 @@ def init_app( logging.info('trying to get new visual communication') try: # get data - vis_com = get_visual_communication( - collection=mongo_collection, - with_annotation=False, - ) + with VisualCommunicationRepository() as repo: + name_list = repo.list_names() + random_name = random.choice(name_list) + vis_com = repo.get_data(random_name) + # could not get here if data doesn't exist + assert vis_com is not None # set variables vis_com_name = vis_com.name - assert datastore._client is not None - image_src = vis_com.webencoded_image(minio_client=datastore._client) + with ImageRepository() as repo: + image_data = repo.get_data(vis_com_name) + # could not get here if data doesn't exist + assert image_data is not None + buffer = BytesIO() + image_data.image.save(buffer, format='PNG') + image_src = 'data:image/png;base64,' + b64encode(buffer.getvalue()).decode( + 'utf-8', + ) if vis_com.prediction is not None: # TODO: update to use optional predictions pass else: # reset annotations annotation_values = [None for elem in annotation_values] - except NoDocumentFoundException: + except Exception: msg = 'no unannotated data in database' logging.warning(msg) response[0] = msg diff --git a/web_ui/src/main.py b/web_ui/src/main.py index 88a1d09..6d0fdf2 100644 --- a/web_ui/src/main.py +++ b/web_ui/src/main.py @@ -4,15 +4,13 @@ from __future__ import annotations import os -from shared.datastore import Datastore -from shared.docstore import connect_mongodb from shared.utils import check_env, setup_logging from .app import init_app # ensure env vars set NECESSARY_ENV_VAR_LIST = { - 'MONGO_HOST', + 'MONGO_ENDPOINT', 'MONGO_DB', 'MONGO_COLLECTION', 'MONGO_USER', @@ -23,24 +21,13 @@ NECESSARY_ENV_VAR_LIST = { 'MINIO_ACCESS_KEY', 'MINIO_SECRET_KEY', 'MINIO_BUCKET_NAME', - 'MINIO_BUCKET_NAME_MODELS', } check_env(NECESSARY_ENV_VAR_LIST) # setup logging stream handler setup_logging() -# connect to database -collection, db, client = connect_mongodb() - -# connect to minio -datastore = Datastore() -datastore.connect() - # initialise application -app = init_app( - mongo_collection=collection, - datastore=datastore, -) +app = init_app() server = app.server server.config.update(SECRET_KEY=os.urandom(24)) -- 2.54.0 From a2b818bbccf116179ce51341d81f7cca5105bd94 Mon Sep 17 00:00:00 2001 From: brian Date: Tue, 15 Apr 2025 21:56:45 +0000 Subject: [PATCH 64/64] updated ignored packages --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index e4a48bb..75db744 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -112,7 +112,7 @@ module = "utils.*" ignore_missing_imports = true [[tool.mypy.overrides]] -module = "datastore.*" +module = "shared.datastore.*" ignore_missing_imports = true [[tool.mypy.overrides]] -- 2.54.0