Merge pull request 'move_images_to_minio' (#44) from move_images_to_minio into main

Reviewed-on: #44

other/transfer_images_mongo_minio.py

@@ -0,0 +1,122 @@
+"""Script to move all images from MongoDB to MinIO."""
+from __future__ import annotations
+
+import logging
+from io import BytesIO
+from pathlib import Path
+
+from bson import ObjectId
+from dotenv import load_dotenv
+from pymongo.collection import Collection
+
+from shared.data_store import connect as connect_minio
+from shared.data_store import put
+from shared.database import connect
+from shared.database import VisualCommunication
+from shared.utils import check_env
+from shared.utils import setup_logging
+
+
+def list_mongo_document_ids(
+    collection: Collection,
+) -> list[ObjectId]:
+    """Get list of all VisualCommunication documents in MongoDB."""
+    # prepare query
+    query = collection.find(
+        filter={},
+        projection={'_id': True},
+    )
+    # execute query
+    res_list = list(query)
+    logging.debug('got %s document(s)', len(res_list))
+    # convert result
+    id_list = [elem['_id'] for elem in res_list]
+    return id_list
+
+
+def get_visual_communication(
+    collection: Collection,
+    doc_id: ObjectId,
+) -> VisualCommunication:
+    """Get image from MongoDB."""
+    # prepare query
+    query = collection.find(
+        filter={'_id': doc_id},
+        projection={'_id': False},
+    )
+    # execute query
+    res_list = list(query)
+    logging.debug('got %s document(s)', len(res_list))
+    # convert result
+    vis_com = VisualCommunication.model_validate(res_list[0])
+    return vis_com
+
+
+def update_visual_communication(
+    collection: Collection,
+    vis_com: VisualCommunication,
+) -> None:
+    """Update VisualCommunication document in MongoDB."""
+    try:
+        collection.update_one(
+            filter={
+                'name': vis_com.name,
+            },
+            update={
+                '$set': vis_com.model_dump(),
+            },
+        )
+    except Exception as exc:
+        logging.error('failed saving %s', vis_com.name)
+        logging.debug(exc)
+        raise exc
+
+
+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()
+    # setup logging
+    setup_logging()
+    # connect to minIO
+    minio_client = connect_minio()
+    # connect to MongoDB
+    collection, db, client = connect()
+    # list documents in mongoDB
+    id_list = list_mongo_document_ids(collection)
+    for doc_id in id_list:
+        try:
+            # get image from MongoDB
+            vis_com = get_visual_communication(collection, doc_id)
+        except Exception as exc:
+            logging.debug(exc)
+            logging.error('failed getting image from document: %s', doc_id)
+            continue
+        try:
+            # save image to buffer
+            buffer = BytesIO()
+            vis_com.image.save(buffer, 'png')   # type: ignore
+            # put buffer in minio
+            object_name = put(
+                client=minio_client,
+                buffer=buffer,
+            )
+        except Exception as exc:
+            logging.debug(exc)
+            logging.error('failed saving image to minio')
+            continue
+        # update visual communication in mongodb
+        try:
+            vis_com.image = None    # type: ignore
+            vis_com.object_name = object_name
+            update_visual_communication(collection, vis_com)
+        except Exception as exc:
+            logging.debug(exc)
+            logging.error(
+                'failed updating visual communication %s', vis_com.name,
+            )
+            continue
+        logging.debug('updated visual communication %s', vis_com.name)

shared/data_store/__init__.py

@@ -0,0 +1,6 @@
+from __future__ import annotations
+
+from .connect import connect
+from .delete import delete
+from .get import get
+from .put import put

shared/data_store/connect.py

@@ -0,0 +1,45 @@
+"""Definition of connect function."""
+from __future__ import annotations
+
+import os
+
+from minio import Minio
+
+
+def connect(
+) -> Minio:
+    """Connect to MinIO server"""
+    # ensure necessary env vars available
+    necesasary_var_list = [
+        'MINIO_ENDPOINT',
+        'MINIO_ACCESS_KEY',
+        'MINIO_SECRET_KEY',
+        'MINIO_BUCKET_NAME',
+    ]
+    for env_var in necesasary_var_list:
+        # ensure env var set
+        assert (
+            env_var in os.environ
+        ), (
+            f"environment variable not set: {env_var}"
+        )
+    # prepare arguments
+    minio_endpoint = os.getenv('MINIO_ENDPOINT', default=None)
+    assert isinstance(minio_endpoint, str)
+    minio_access_key = os.getenv('MINIO_ACCESS_KEY', default=None)
+    assert isinstance(minio_access_key, str)
+    minio_secret_key = os.getenv('MINIO_SECRET_KEY', default=None)
+    assert isinstance(minio_secret_key, str)
+    minio_bucket_name = os.getenv('MINIO_BUCKET_NAME', default=None)
+    assert isinstance(minio_bucket_name, str)
+    # 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):
+        client.make_bucket(bucket_name=minio_bucket_name)
+    return client

shared/data_store/delete.py

@@ -0,0 +1,29 @@
+"""Definition of delete function."""
+from __future__ import annotations
+
+import logging
+import os
+
+from minio import Minio
+
+
+def delete(
+    client: Minio,
+    object_name: str,
+) -> None:
+    """Delete object from MinIO."""
+    assert isinstance(client, Minio)
+    assert isinstance(object_name, str)
+    bucket_name = os.getenv('MINIO_BUCKET_NAME', default=None)
+    assert isinstance(bucket_name, str)
+    # remove object
+    try:
+        client.remove_object(
+            bucket_name=bucket_name,
+            object_name=object_name,
+        )
+    except Exception as exc:
+        logging.debug(exc)
+        logging.error('failed deleting %s', object_name)
+    else:
+        logging.debug('deleted %s', object_name)

shared/data_store/get.py

@@ -0,0 +1,27 @@
+"""Definition of get function."""
+from __future__ import annotations
+
+import os
+from io import BytesIO
+
+from minio import Minio
+
+
+def get(
+    client: Minio,
+    object_name: str,
+) -> BytesIO:
+    """Get buffer from bucket in MinIO."""
+    assert isinstance(client, Minio)
+    assert isinstance(object_name, str)
+    bucket_name = os.getenv('MINIO_BUCKET_NAME', default=None)
+    assert isinstance(bucket_name, str)
+    # get buffer
+    try:
+        response = client.get_object(bucket_name, object_name)
+        buffer = BytesIO(response.data)
+    finally:
+        response.close()
+        response.release_conn()
+    buffer.seek(0)
+    return buffer

shared/data_store/put.py

@@ -0,0 +1,38 @@
+"""Definition of put function."""
+from __future__ import annotations
+
+import logging
+import os
+from hashlib import md5
+from io import BytesIO
+
+from minio import Minio
+
+
+def put(
+    client: Minio,
+    buffer: BytesIO,
+) -> str:
+    """Put buffer in bucket in MinIO and return MD5 checksum as object name."""
+    assert isinstance(client, Minio)
+    assert isinstance(buffer, BytesIO)
+    bucket_name = os.getenv('MINIO_BUCKET_NAME', default=None)
+    assert isinstance(bucket_name, str)
+    # get md5 of image
+    checksum = md5(buffer.getbuffer()).hexdigest()
+    # prepare for saving
+    num_bytes = buffer.tell()
+    buffer.seek(0)
+    # send data to bucket
+    try:
+        client.put_object(
+            bucket_name=bucket_name,
+            object_name=checksum,
+            length=num_bytes,
+            data=buffer,
+        )
+    except Exception as exc:
+        logging.error('failed saving data to MinIO')
+        raise exc
+    logging.debug('saved data to %s', checksum)
+    return checksum

shared/database/classes/visual_communication.py

@@ -7,11 +7,13 @@ from base64 import b64encode
 from io import BytesIO
 from pathlib import Path
 
+from minio import Minio
 from PIL import Image
 from pydantic import BaseModel
-from pydantic import field_serializer
-from pydantic import field_validator
+from pymongo.collection import Collection
 
+from shared.data_store import get
+from shared.data_store import put
 from shared.dto import ModelData
 
 
@@ -19,7 +21,7 @@ class VisualCommunication(BaseModel):
     """Visual communication model."""
 
     name: str
-    image: Image.Image
+    object_name: str
     annotation: ModelData | None = None
     prediction: ModelData | None = None
 
@@ -33,12 +35,59 @@ class VisualCommunication(BaseModel):
         return cls.__name__
 
     @classmethod
-    def from_file(cls, path: Path) -> VisualCommunication:
+    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)
+        buffer = BytesIO()
+        image.save(buffer, 'png')
+        object_name = put(
+            client=minio_client,
+            buffer=buffer,
+        )
+        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()
-        return VisualCommunication(name=name, image=image)
+        # 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:
@@ -46,35 +95,33 @@ class VisualCommunication(BaseModel):
         _, content_data = content.split(',')
         return Image.open(BytesIO(b64decode(content_data)))
 
-    @field_serializer('image')
-    @classmethod
-    def serialize_image(cls, image: Image.Image) -> bytes:   # type: ignore
-        """Convert image to bytes for storage in database."""
-        buffer = BytesIO()
-        image.save(buffer, format='JPEG')
-        return buffer.getvalue()
+    def get_image(self, minio_client: Minio) -> Image.Image:
+        """Load image data from minio."""
+        assert isinstance(minio_client, Minio)
+        # get buffer from minio
+        buffer = get(
+            client=minio_client,
+            object_name=self.object_name,
+        )
+        # convert data to image
+        im = Image.open(buffer)
+        return im
 
-    @field_validator('image', mode='before')
-    @classmethod
-    def convert_to_image(
-        cls,
-        image: Image.Image | BytesIO | bytes,
-    ) -> Image.Image:
-        """Convert bytes input from database into image."""
-        if isinstance(image, bytes):
-            image = BytesIO(image)
-        if isinstance(image, BytesIO):
-            image = Image.open(image)
-        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 __repr__(self) -> str:
-        return f"{self.classname()}(name='{self.name}')"
-
-    def webencoded_image(self) -> str:
+    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()
-        self.image.save(buffer, format='png')
+        image.save(buffer, format='png')
         img_enc = b64encode(buffer.getvalue()).decode('utf-8')
         return f"data:image/png;base64, {img_enc}"
 

shared/utils/check_env.py

@@ -14,6 +14,10 @@ def check_env() -> None:
         'MONGO_PASSWORD',
         'DASH_AUTH_USERNAME',
         'DASH_AUTH_PASSWORD',
+        'MINIO_ENDPOINT',
+        'MINIO_ACCESS_KEY',
+        'MINIO_SECRET_KEY',
+        'MINIO_BUCKET_NAME',
     }
     for env_var in necesasary_var_list:
         # ensure env var set

shared/utils/setup_logging.py

@@ -12,10 +12,14 @@ def setup_logging() -> None:
     fmt = (
         '%(asctime)s | '
         '%(levelname)s | '
-        '%(filename)s | '
+        '%(name)s | '
         '%(funcName)s | '
         '%(message)s'
     )
     datefmt = '%Y-%m-%d %H:%M:%S'
     logging.basicConfig(format=fmt, datefmt=datefmt, level=level)
+    # change levels for modules that spam the log
+    logging.getLogger('pymongo').setLevel(logging.WARNING)
+    logging.getLogger('urllib3').setLevel(logging.INFO)
+    logging.getLogger('PIL').setLevel(logging.INFO)
     logging.debug('finished')

tests/generate_random_prediction_test.py

@@ -2,10 +2,27 @@ from __future__ import annotations
 
 from pathlib import Path
 
-from shared.database.classes import VisualCommunication
+from dotenv import load_dotenv
 
+from shared.data_store import connect as connect_minio
+from shared.database import connect as connect_mongo
+from shared.database.classes import VisualCommunication
+from shared.utils import check_env
+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)
+    # ensure env vars set
+    check_env()
+    # setup logging
+    setup_logging()
+    # connect to minIO
+    minio_client = connect_minio()
+    # connect to MongoDB
+    collection, db, client = connect_mongo()
     # get list of image paths
     test_dir = Path(__file__).parent
     img_dir = test_dir / 'imgs'
@@ -13,7 +30,7 @@ if __name__ == '__main__':
     print(img_path_list)
     # instantiate data object
     vis_com_list = [
-        VisualCommunication.from_file(path)
+        VisualCommunication.from_file(path, minio_client=minio_client)
         for path
         in img_path_list
     ]

tests/get_visual_communication_test.py

@@ -1,22 +1,32 @@
 from __future__ import annotations
 
-import os
 from pathlib import Path
 
 from dotenv import load_dotenv
 
+from shared.data_store import (
+    connect as connect_minio,
+)
 from shared.database import connect
 from shared.database import get_visual_communication
+from shared.utils import check_env
+from shared.utils import setup_logging
 
 if __name__ == '__main__':
-    # prepare env vars
-    env_path = Path(__file__).parent.parent / 'local.env'
+    # load in env file
+    env_path = Path(__file__).parent.parent / 'server.env'
     assert env_path.exists()
     load_dotenv(env_path)
-    os.environ['MONGO_HOST'] = 'localhost'
-    # connect to database
+    # ensure env vars set
+    check_env()
+    # setup logging
+    setup_logging()
+    # connect to minIO
+    minio_client = connect_minio()
+    # connect to MongoDB
     collection, db, client = connect()
-    print(client.server_info())
     # get visual communication
     vis_com = get_visual_communication(collection)
-    print(vis_com)
+    print(repr(vis_com))
+    image = vis_com.get_image(minio_client=minio_client)
+    image.show()

tests/image_upload_test.py

@@ -1,15 +1,29 @@
 from __future__ import annotations
 
-import os
 from pathlib import Path
 
 from dotenv import load_dotenv
 from pymongo.errors import DuplicateKeyError
 
-from shared.database import connect
+from shared.data_store import connect as connect_minio
+from shared.database import connect as connect_mongo
 from shared.database.classes import VisualCommunication
+from shared.utils import check_env
+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)
+    # ensure env vars set
+    check_env()
+    # setup logging
+    setup_logging()
+    # connect to minIO
+    minio_client = connect_minio()
+    # connect to MongoDB
+    collection, db, client = connect_mongo()
     # get list of image paths
     test_dir = Path(__file__).parent
     img_dir = test_dir / 'imgs'
@@ -17,20 +31,12 @@ if __name__ == '__main__':
     print(img_path_list)
     # instantiate data object
     vis_com_list = [
-        VisualCommunication.from_file(path)
+        VisualCommunication.from_file(path, minio_client=minio_client)
         for path
         in img_path_list
     ]
     for vis_com in vis_com_list:
         print(repr(vis_com))
-    # prepare env vars
-    env_path = test_dir.parent / 'local.env'
-    assert env_path.exists()
-    load_dotenv(env_path)
-    os.environ['MONGO_HOST'] = 'localhost'
-    # connect to database
-    collection, db, client = connect()
-    print(client.server_info())
     # upload images
     for vis_com in vis_com_list:
         try:

tests/image_upload_to_server_test.py

@@ -5,10 +5,25 @@ from pathlib import Path
 from dotenv import load_dotenv
 from pymongo.errors import DuplicateKeyError
 
-from shared.database import connect
+from shared.data_store import connect as connect_minio
+from shared.database import connect as connect_mongo
 from shared.database import VisualCommunication
+from shared.utils import check_env
+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)
+    # ensure env vars set
+    check_env()
+    # setup logging
+    setup_logging()
+    # connect to minIO
+    minio_client = connect_minio()
+    # connect to MongoDB
+    collection, db, client = connect_mongo()
     # get list of image paths
     ext_img_dir = Path('/Volumes/BW-PSSD/Mixed Methods/')
     assert ext_img_dir.exists()
@@ -20,19 +35,11 @@ if __name__ == '__main__':
     print(f"found {len(img_path_list)} images")
     # create visual communication objects
     vis_com_list = [
-        VisualCommunication.from_file(path)
+        VisualCommunication.from_file(path, minio_client=minio_client)
         for path
         in img_path_list
     ]
     print(f"created {len(vis_com_list)} visual communication objects")
-    # prepare env vars
-    env_path = Path(__file__).parent.parent / 'server.env'
-    assert env_path.exists()
-    load_dotenv(env_path)
-    # connect to database
-    collection, db, client = connect()
-    assert client.server_info() is not None
-    print('connected to database')
     # upload images
     for vis_com in vis_com_list:
         try:

tests/prediction_upload_test.py

@@ -1,46 +1,42 @@
 from __future__ import annotations
 
-import logging
-import os
 from pathlib import Path
 
 from dotenv import load_dotenv
 
-from shared.database import connect
+from shared.data_store import connect as connect_minio
+from shared.database import connect as connect_mongo
 from shared.database import upsert_prediction
 from shared.database.classes import VisualCommunication
+from shared.utils import check_env
+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)
+    # ensure env vars set
+    check_env()
     # setup logging
-    fmt = (
-        '%(asctime)s | '
-        '%(levelname)s | '
-        '%(filename)s | '
-        '%(funcName)s | '
-        '%(message)s'
-    )
-    datefmt = '%Y-%m-%d %H:%M:%S'
-    logging.basicConfig(format=fmt, datefmt=datefmt, level=logging.INFO)
+    setup_logging()
+    # connect to minIO
+    minio_client = connect_minio()
+    # connect to MongoDB
+    collection, db, client = connect_mongo()
     # 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)
+        VisualCommunication.from_file(path, minio_client=minio_client)
         for path
         in img_path_list
     ]
     # generate random predictions
     for vis_com in vis_com_list:
         vis_com.generate_random_prediction()
-    # prepare env vars
-    env_path = test_dir.parent / 'local.env'
-    assert env_path.exists()
-    load_dotenv(env_path)
-    os.environ['MONGO_HOST'] = 'localhost'
-    # connect to database
-    collection, db, client = connect()
     # upload visual communication
     for vis_com in vis_com_list:
         if vis_com.prediction is None:

web_ui/src/app/init_app.py

@@ -11,21 +11,23 @@ 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 upsert_visual_communication
 from shared.database import VisualCommunication
 from shared.dto import ModelData
 
 
 def init_app(
-    collection: Collection,
+    mongo_collection: Collection,
+    minio_client: Minio,
 ) -> Dash:
     """Initialise web UI application."""
     # setup app
@@ -92,11 +94,11 @@ def init_app(
             assert isinstance(filename_list, list)
         # get values from database
         num_total = count_documents(
-            collection=collection,
+            collection=mongo_collection,
             only_with_annotation=False,
         )
         num_handled = count_documents(
-            collection=collection,
+            collection=mongo_collection,
             only_with_annotation=True,
         )
         limit = int(num_total/20)
@@ -118,34 +120,52 @@ def init_app(
         filename_list: list[str] | None,
     ) -> tuple[str | None, str | None]:
         """Upload image to database through web ui."""
-        # stop early if possible
-        if content_list is None or filename_list is None:
-            logging.info('nothing to upload.')
-            return None, 'nothing to upload'.title()
-        # build list of visual communication
-        vis_com_list = []
-        for content, filename in zip(content_list, filename_list):
-            try:
-                image = VisualCommunication.decode_image(content=content)
-                vis_com = VisualCommunication(
-                    name=filename,
-                    image=image,
-                )
-            except Exception as exc:
-                logging.error('failed handling data from file: %s', filename)
-                logging.debug(exc)
-                continue
-            vis_com_list.append(vis_com)
-        # upsert documents
-        success = upsert_visual_communication(
-            collection=collection,
-            visual_communication_list=vis_com_list,
-        )
-        if success:
-            logging.info('uploaded %s files to database', len(vis_com_list))
-            return 'successfully uploaded images'.title(), None
-        logging.error('failed uploading images to database')
-        return None, 'failed uploading images'.title()
+        try:
+            # stop if no input
+            assert (
+                content_list is not None
+            ) and (
+                filename_list is not None
+            ), 'nothing to upload'
+            # handle input
+            failed_filename_list = []
+            for content, filename in zip(content_list, filename_list):
+                try:
+                    # decode image content
+                    image = VisualCommunication.decode_image(content=content)
+                except Exception:
+                    logging.debug('failed decoding %s', filename)
+                    failed_filename_list.append(filename)
+                    continue
+                try:
+                    # instantiate to upload image to minio
+                    vis_com = VisualCommunication.from_name_and_image(
+                        name=filename,
+                        image=image,
+                        minio_client=minio_client,
+                    )
+                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
+                    delete_from_minio(
+                        client=minio_client,
+                        object_name=vis_com.object_name,
+                    )
+            assert len(failed_filename_list) == 0, f"failed uploading:{
+                '\n'.join(failed_filename_list)
+            }"
+        except Exception as exc:
+            logging.debug(exc)
+            return None, str(exc).title()
+        return 'successfully uploaded images'.title(), None
 
     # define callback: cycle visual communication data
     @app.callback(
@@ -217,7 +237,7 @@ def init_app(
                 annotations = ModelData.from_annotations(**annotation_map)
                 # save data to database
                 upsert_annotation(
-                    collection=collection,
+                    collection=mongo_collection,
                     vis_com_name=vis_com_name,
                     annotations=annotations,
                 )
@@ -231,12 +251,12 @@ def init_app(
         try:
             # get data
             vis_com = get_visual_communication(
-                collection=collection,
+                collection=mongo_collection,
                 with_annotation=False,
             )
             # set variables
             vis_com_name = vis_com.name
-            image_src = vis_com.webencoded_image()
+            image_src = vis_com.webencoded_image(minio_client=minio_client)
             if vis_com.prediction is not None:
                 # TODO: update to use optional predictions
                 pass

web_ui/src/main.py

@@ -4,6 +4,7 @@ from __future__ import annotations
 import os
 
 from .app import init_app
+from shared.data_store import connect as connect_minio
 from shared.database import connect
 from shared.utils import check_env
 from shared.utils import setup_logging
@@ -17,7 +18,13 @@ setup_logging()
 # connect to database
 collection, db, client = connect()
 
+# connect to minio
+minio_client = connect_minio()
+
 # initialise application
-app = init_app(collection=collection)
+app = init_app(
+    mongo_collection=collection,
+    minio_client=minio_client,
+)
 server = app.server
 server.config.update(SECRET_KEY=os.urandom(24))