renamed module

misc/generate_random_prediction.py

@@ -5,8 +5,8 @@ from pathlib import Path
 from dotenv import load_dotenv
 
 from shared.data_store import connect_minio
-from shared.database import connect_mongodb
+from shared.mongodb import connect_mongodb
-from shared.database.classes import VisualCommunication
+from shared.mongodb.classes import VisualCommunication
 from shared.utils import check_env, setup_logging
 from web_ui.src.main import NECESSARY_ENV_VAR_LIST
 

misc/get_visual_communication.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_mongodb, get_visual_communication
+from shared.mongodb import connect_mongodb, get_visual_communication
 from shared.utils import check_env, setup_logging
 from web_ui.src.main import NECESSARY_ENV_VAR_LIST
 

misc/image_download.py

@@ -5,8 +5,8 @@ from pathlib import Path
 
 from dotenv import load_dotenv
 
-from shared.database import connect_mongodb
+from shared.mongodb import connect_mongodb
-from shared.database.classes import VisualCommunication
+from shared.mongodb.classes import VisualCommunication
 
 if __name__ == '__main__':
     # prepare env vars

misc/image_upload.py

@@ -6,8 +6,8 @@ from dotenv import load_dotenv
 from pymongo.errors import DuplicateKeyError
 
 from shared.data_store import connect_minio
-from shared.database import connect_mongodb
+from shared.mongodb import connect_mongodb
-from shared.database.classes import VisualCommunication
+from shared.mongodb.classes import VisualCommunication
 from shared.utils import check_env, setup_logging
 from web_ui.src.main import NECESSARY_ENV_VAR_LIST
 

misc/image_upload_to_server.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 VisualCommunication, connect_mongodb
+from shared.mongodb import VisualCommunication, connect_mongodb
 from shared.utils import check_env, setup_logging
 from web_ui.src.main import NECESSARY_ENV_VAR_LIST
 

misc/prediction_upload.py

@@ -5,8 +5,8 @@ from pathlib import Path
 from dotenv import load_dotenv
 
 from shared.data_store import connect_minio
-from shared.database import connect_mongodb, upsert_prediction
+from shared.mongodb import connect_mongodb, upsert_prediction
-from shared.database.classes import VisualCommunication
+from shared.mongodb.classes import VisualCommunication
 from shared.utils import check_env, setup_logging
 from web_ui.src.main import NECESSARY_ENV_VAR_LIST
 

misc/total_annotated.py

@@ -5,7 +5,7 @@ from pathlib import Path
 
 from dotenv import load_dotenv
 
-from shared.database import connect_mongodb, count_documents
+from shared.mongodb import connect_mongodb, count_documents
 
 if __name__ == '__main__':
     # prepare env vars

misc/total_documents.py

@@ -5,7 +5,7 @@ from pathlib import Path
 
 from dotenv import load_dotenv
 
-from shared.database import connect_mongodb, count_documents
+from shared.mongodb import connect_mongodb, count_documents
 
 if __name__ == '__main__':
     # prepare env vars

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_mongodb
+from shared.mongodb import VisualCommunication, connect_mongodb
 from shared.utils import check_env, setup_logging
 from web_ui.src.main import NECESSARY_ENV_VAR_LIST
 

shared/mongodb/classes/__init__.py

@@ -1,4 +1,5 @@
 """Database classes module content."""
+
 from __future__ import annotations
 
 from .dataset import Dataset

shared/mongodb/classes/dataset.py

@@ -1,18 +1,18 @@
 """Definition of database Dataset class."""
+
 from __future__ import annotations
 
 import logging
 import random
-from datetime import datetime
+from datetime import UTC, datetime
-from datetime import UTC
 
-from pydantic import BaseModel
+from pydantic import BaseModel, Field
-from pydantic import Field
 from pymongo.collection import Collection
 
 
 class Dataset(BaseModel):
     """Database Dataset model."""
+
     create_time: datetime = Field(default_factory=lambda: datetime.now(UTC))
     train_names: list[str]
     test_names: list[str]
@@ -44,13 +44,9 @@ class Dataset(BaseModel):
         num_test = round(num_total * fraction_map['test'])
         # split data
         validation_name_list = random.choices(name_list, k=num_validation)
-        name_list = [
+        name_list = [name for name in name_list if name not in validation_name_list]
-            name for name in name_list if name not in validation_name_list
-        ]
         test_name_list = random.choices(name_list, k=num_test)
-        train_name_list = [
+        train_name_list = [name for name in name_list if name not in test_name_list]
-            name for name in name_list if name not in test_name_list
-        ]
         # instantiate object
         dataset = Dataset(
             train_names=train_name_list,

shared/mongodb/classes/exceptions.py

@@ -1,4 +1,5 @@
 """Definition of database exception."""
+
 from __future__ import annotations
 
 

shared/mongodb/utils/count_documents.py

@@ -1,4 +1,5 @@
 """Definition of function to count documents in database."""
+
 from __future__ import annotations
 
 from pymongo.collection import Collection
@@ -8,10 +9,8 @@ def count_documents(
     collection: Collection,
     only_with_annotation: bool = False,
 ) -> int:
-    """
+    """Get the total number of documents in database that matches the
-    Get the total number of documents
+    filters."""
-    in database that matches the filters.
-    """
     assert isinstance(collection, Collection)
     assert isinstance(only_with_annotation, bool)
     # build query

shared/mongodb/utils/get_visual_communication.py

@@ -1,12 +1,12 @@
 """Definition of function to get visual communication from database."""
+
 from __future__ import annotations
 
 import logging
 
 from pymongo.collection import Collection
 
-from shared.database import NoDocumentFoundException
+from shared.mongodb import NoDocumentFoundException, VisualCommunication
-from shared.database import VisualCommunication
 
 
 def get_visual_communication(
@@ -22,16 +22,16 @@ def get_visual_communication(
     data = collection.aggregate(
         pipeline=[
             {
-                '$match': query,     # find using filters
+                '$match': query,  # find using filters
             },
             {
                 '$sample': {
-                    'size': 1,   # get one random
+                    'size': 1,  # get one random
                 },
             },
         ],
     )
-    data_list = list(data)   # read data from cursor object
+    data_list = list(data)  # read data from cursor object
     if len(data_list) == 0:
         raise NoDocumentFoundException()
     vis_com = VisualCommunication.model_validate(data_list[0])

shared/mongodb/utils/list_names.py

@@ -1,7 +1,6 @@
-"""
+"""Definition of function to list names of all visual communication documents
-Definition of function to list names
+in database."""
-of all visual communication documents in database.
+
-"""
 from __future__ import annotations
 
 from pymongo.collection import Collection

shared/mongodb/utils/save_dataset.py

@@ -4,7 +4,7 @@ import logging
 
 from pymongo.collection import Collection
 
-from shared.database import Dataset
+from shared.mongodb import Dataset
 
 
 def save_dataset(
@@ -22,7 +22,7 @@ if __name__ == '__main__':
     from dotenv import load_dotenv
 
     load_dotenv('local.env')
-    from shared.database import connect_mongodb, list_names
+    from shared.mongodb import connect_mongodb, list_names
 
     # connect to database
     collection, db, client = connect_mongodb()

shared/mongodb/utils/upsert_visual_communication.py

@@ -2,22 +2,18 @@ from __future__ import annotations
 
 from pymongo.collection import Collection
 
-from shared.database import VisualCommunication
+from shared.mongodb import VisualCommunication
 
 
 def upsert_visual_communication(
     collection: Collection,
     visual_communication_list: list[VisualCommunication],
 ) -> bool:
-    """
+    """Upsert VisualCommunication object in the database.
-    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],
-            vis_com.model_dump()
-            for vis_com
-            in visual_communication_list
-        ],
     )
     return response.acknowledged

web_ui/src/app/init_app.py

@@ -1,28 +1,28 @@
 """Definition of init_app function."""
+
 from __future__ import annotations
 
 import logging
 import os
 
 import dash_bootstrap_components as dbc
-from dash import ALL
+from dash import ALL, Dash, Input, Output, State
-from dash import Dash
-from dash import Input
-from dash import Output
-from dash import State
 from dash_auth import BasicAuth
 from minio import Minio
 from pydantic import ValidationError
 from pymongo.collection import Collection
 
-from .layout import app_layout
 from shared.data_store import delete as delete_from_minio
-from shared.database import count_documents
-from shared.database import get_visual_communication
-from shared.database import NoDocumentFoundException
-from shared.database import upsert_annotation
-from shared.database import VisualCommunication
 from shared.dto import ModelData
+from shared.mongodb import (
+    NoDocumentFoundException,
+    VisualCommunication,
+    count_documents,
+    get_visual_communication,
+    upsert_annotation,
+)
+
+from .layout import app_layout
 
 
 def init_app(
@@ -101,10 +101,8 @@ def init_app(
             collection=mongo_collection,
             only_with_annotation=True,
         )
-        limit = int(num_total/20)
+        limit = int(num_total / 20)
-        label_str = f"{
+        label_str = f'{num_handled}/{num_total}' if num_handled >= limit else ''
-            num_handled
-        }/{num_total}" if num_handled >= limit else ''
         return num_handled, num_total, label_str
 
     # define callback: upload image
@@ -122,9 +120,7 @@ def init_app(
         """Upload image to database through web ui."""
         try:
             # stop if no input
-            assert (
+            assert (content_list is not None) and (
-                content_list is not None
-            ) and (
                 filename_list is not None
             ), 'nothing to upload'
             # handle input
@@ -159,7 +155,9 @@ def init_app(
                         client=minio_client,
                         object_name=vis_com.object_name,
                     )
-            assert len(failed_filename_list) == 0, f"failed uploading:{
+            assert (
+                len(failed_filename_list) == 0
+            ), f"failed uploading:{
                 '\n'.join(failed_filename_list)
             }"
         except Exception as exc:
@@ -208,30 +206,19 @@ def init_app(
             logging.info('saving annotations to database: %s', vis_com_name)
             try:
                 # extract option keys
-                annotation_keys = [
+                annotation_keys = [elem['index'] for elem in annotation_keys]
-                    elem['index']
-                    for elem in annotation_keys
-                ]
                 # ensure all options are set
                 logging.info(annotation_keys)
                 for option, value in zip(annotation_keys, annotation_values):
                     if value is None:
                         raise ValueError(f"{option} is not set")
                 # prepare data to save
-                annotation_keys = [
+                annotation_keys = [elem.replace(' ', '_') for elem in annotation_keys]
-                    elem.replace(' ', '_')
-                    for elem
-                    in annotation_keys
-                ]
                 annotation_values = [
-                    elem.replace(' ', '_').lower()
+                    elem.replace(' ', '_').lower() for elem in annotation_values
-                    for elem
-                    in annotation_values
                 ]
                 annotation_map = {
-                    key: value
+                    key: value for key, value in zip(annotation_keys, annotation_values)
-                    for key, value
-                    in zip(annotation_keys, annotation_values)
                 }
                 # instantiate ModelOutputs object
                 annotations = ModelData.from_annotations(**annotation_map)
@@ -273,8 +260,10 @@ def init_app(
             response[2] = image_src
             response[3] = annotation_values
             logging.info(
-                'finished getting visual communication: %s', vis_com_name,
+                'finished getting visual communication: %s',
+                vis_com_name,
             )
         return tuple(response)
+
     logging.info('initialised app')
     return app

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_mongodb
+from shared.mongodb import connect_mongodb
 from shared.utils import check_env, setup_logging
 
 from .app import init_app