fixed mypy types

model/src/utils/get_class.py

@@ -1,8 +1,9 @@
 from importlib import import_module
-from types import ModuleType
+
+from torch.nn import Module
 
 
-def get_class(path: str) -> ModuleType:
+def get_class(path: str) -> Module:
     parts = path.split('.')
     module_path = '.'.join(parts[:-1])
     class_name = parts[-1]

model/src/utils/load_model.py

@@ -5,8 +5,8 @@ from pathlib import Path
 
 import torch
 from minio import Minio
-from src.models import VisualCommunicationModel
 
+from model.src.models import VisualCommunicationModel
 from shared.data_store import get_model
 
 from .get_model_name import get_model_name

model/train.py

@@ -13,11 +13,11 @@ from ignite.handlers.param_scheduler import create_lr_scheduler_with_warmup
 from ignite.handlers.tensorboard_logger import TensorboardLogger
 from ignite.handlers.tqdm_logger import ProgressBar
 from ignite.metrics import Average, Loss, RunningAverage
-from src.utils import VCDADataset, get_class
 from torch import nn
 from torch.optim.lr_scheduler import ExponentialLR
 from torch.utils.data import DataLoader
 
+from model.src.utils import VCDADataset, get_class
 from shared.data_store import connect_minio
 
 
@@ -90,7 +90,7 @@ val_metrics = {
 }
 evaluator = create_supervised_evaluator(
     model=model,
-    metrics=val_metrics,
+    metrics=val_metrics,  # type: ignore
     device=device,
 )
 ProgressBar(desc='Val', ncols=80).attach(evaluator)

other/transfer_images_mongo_minio.py

@@ -11,7 +11,7 @@ from dotenv import load_dotenv
 from pymongo.collection import Collection
 
 from shared.data_store import connect_minio, put
-from shared.database import VisualCommunication, connect
+from shared.database import VisualCommunication, connect_mongodb
 from shared.utils import check_env, setup_logging
 
 
@@ -82,7 +82,7 @@ if __name__ == '__main__':
     # connect to minIO
     minio_client = connect_minio()
     # connect to MongoDB
-    collection, db, client = connect()
+    collection, db, client = connect_mongodb()
     # list documents in mongoDB
     id_list = list_mongo_document_ids(collection)
     for doc_id in id_list:

shared/database/__init__.py

@@ -1,10 +1,11 @@
 """Database module content."""
+
 from __future__ import annotations
 
 from .classes.dataset import Dataset
 from .classes.exceptions import NoDocumentFoundException
 from .classes.visual_communication import VisualCommunication
-from .utils.connect import connect
+from .utils.connect_mongodb import connect_mongodb
 from .utils.count_documents import count_documents
 from .utils.get_visual_communication import get_visual_communication
 from .utils.list_names import list_names

shared/database/utils/save_dataset.py

@@ -20,10 +20,12 @@ def save_dataset(
 
 if __name__ == '__main__':
     from dotenv import load_dotenv
+
     load_dotenv('local.env')
-    from shared.database import list_names, connect
+    from shared.database import connect_mongodb, list_names
+
     # connect to database
-    collection, db, client = connect()
+    collection, db, client = connect_mongodb()
     print(client.server_info())
 
     name_list = list_names(collection=collection, only_with_annotation=True)

tests/generate_random_prediction_test.py

@@ -5,7 +5,7 @@ from pathlib import Path
 from dotenv import load_dotenv
 
 from shared.data_store import connect_minio
-from shared.database import connect as connect_mongo
+from shared.database import connect_mongodb
 from shared.database.classes import VisualCommunication
 from shared.utils import check_env, setup_logging
 
@@ -21,7 +21,7 @@ if __name__ == '__main__':
     # connect to minIO
     minio_client = connect_minio()
     # connect to MongoDB
-    collection, db, client = connect_mongo()
+    collection, db, client = connect_mongodb()
     # get list of image paths
     test_dir = Path(__file__).parent
     img_dir = test_dir / 'imgs'

tests/get_visual_communication_test.py

@@ -5,7 +5,7 @@ from pathlib import Path
 from dotenv import load_dotenv
 
 from shared.data_store import connect_minio
-from shared.database import connect, get_visual_communication
+from shared.database import connect_mongodb, get_visual_communication
 from shared.utils import check_env, setup_logging
 
 if __name__ == '__main__':
@@ -20,7 +20,7 @@ if __name__ == '__main__':
     # connect to minIO
     minio_client = connect_minio()
     # connect to MongoDB
-    collection, db, client = connect()
+    collection, db, client = connect_mongodb()
     # get visual communication
     vis_com = get_visual_communication(collection)
     print(repr(vis_com))

tests/image_upload_test.py

@@ -6,7 +6,7 @@ from dotenv import load_dotenv
 from pymongo.errors import DuplicateKeyError
 
 from shared.data_store import connect_minio
-from shared.database import connect as connect_mongo
+from shared.database import connect_mongodb
 from shared.database.classes import VisualCommunication
 from shared.utils import check_env, setup_logging
 
@@ -22,7 +22,7 @@ if __name__ == '__main__':
     # connect to minIO
     minio_client = connect_minio()
     # connect to MongoDB
-    collection, db, client = connect_mongo()
+    collection, db, client = connect_mongodb()
     # get list of image paths
     test_dir = Path(__file__).parent
     img_dir = test_dir / 'imgs'

tests/image_upload_to_server_test.py

@@ -6,8 +6,7 @@ from dotenv import load_dotenv
 from pymongo.errors import DuplicateKeyError
 
 from shared.data_store import connect_minio
-from shared.database import VisualCommunication
-from shared.database import connect as connect_mongo
+from shared.database import VisualCommunication, connect_mongodb
 from shared.utils import check_env, setup_logging
 
 if __name__ == '__main__':
@@ -22,7 +21,7 @@ if __name__ == '__main__':
     # connect to minIO
     minio_client = connect_minio()
     # connect to MongoDB
-    collection, db, client = connect_mongo()
+    collection, db, client = connect_mongodb()
     # get list of image paths
     ext_img_dir = Path('/Volumes/BW-PSSD/Mixed Methods/')
     assert ext_img_dir.exists()

tests/prediction_upload_test.py

@@ -5,8 +5,7 @@ from pathlib import Path
 from dotenv import load_dotenv
 
 from shared.data_store import connect_minio
-from shared.database import connect as connect_mongo
-from shared.database import upsert_prediction
+from shared.database import connect_mongodb, upsert_prediction
 from shared.database.classes import VisualCommunication
 from shared.utils import check_env, setup_logging
 
@@ -22,7 +21,7 @@ if __name__ == '__main__':
     # connect to minIO
     minio_client = connect_minio()
     # connect to MongoDB
-    collection, db, client = connect_mongo()
+    collection, db, client = connect_mongodb()
     # get list of image paths
     test_dir = Path(__file__).parent
     img_dir = test_dir / 'imgs'

tests/total_annotated_test.py

@@ -5,8 +5,7 @@ from pathlib import Path
 
 from dotenv import load_dotenv
 
-from shared.database import connect
-from shared.database import count_documents
+from shared.database import connect_mongodb, count_documents
 
 if __name__ == '__main__':
     # prepare env vars
@@ -15,7 +14,7 @@ if __name__ == '__main__':
     load_dotenv(env_path)
     os.environ['MONGO_HOST'] = 'localhost'
     # connect to database
-    collection, db, client = connect()
+    collection, db, client = connect_mongodb()
     # get visual communication
     num_docs = count_documents(
         collection=collection,

tests/total_documents_test.py

@@ -5,8 +5,7 @@ from pathlib import Path
 
 from dotenv import load_dotenv
 
-from shared.database import connect
-from shared.database import count_documents
+from shared.database import connect_mongodb, count_documents
 
 if __name__ == '__main__':
     # prepare env vars
@@ -15,7 +14,7 @@ if __name__ == '__main__':
     load_dotenv(env_path)
     os.environ['MONGO_HOST'] = 'localhost'
     # connect to database
-    collection, db, client = connect()
+    collection, db, client = connect_mongodb()
     # get visual communication
     num_docs = count_documents(
         collection=collection,

web_ui/src/main.py

@@ -5,7 +5,7 @@ from __future__ import annotations
 import os
 
 from shared.data_store import connect_minio
-from shared.database import connect
+from shared.database import connect_mongodb
 from shared.utils import check_env, setup_logging
 
 from .app import init_app
@@ -17,7 +17,7 @@ check_env()
 setup_logging()
 
 # connect to database
-collection, db, client = connect()
+collection, db, client = connect_mongodb()
 
 # connect to minio
 minio_client = connect_minio()