Merge pull request 'tests_for_datastore' (#63) from tests_for_datastore into main

Reviewed-on: #63

.gitea/workflows/pull.yaml

@@ -17,8 +17,8 @@ jobs:
           architecture: "x64"
       - name: Install Packages
         env:
-          PIP_INDEX_URL: http://192.168.1.2:5001/index/
+          PIP_INDEX_URL: ${{ vars.PIP_INDEX_URL }}
-          PIP_TRUSTED_HOST: 192.168.1.2
+          PIP_TRUSTED_HOST: ${{ vars.PIP_TRUSTED_HOST }}
         run: |
           pip install poetry
           poetry install
@@ -28,6 +28,13 @@ jobs:
       - name: Type Check
         run: |
           poetry run mypy .
-      - name: Pytest
+      - name: Pytest & Calculate Coverage
+        env:
+          MINIO_ENDPOINT: ${{ vars.MINIO_ENDPOINT }}
+          MINIO_ACCESS_KEY: ${{ secrets.MINIO_ACCESS_KEY }}
+          MINIO_SECRET_KEY: ${{ secrets.MINIO_SECRET_KEY }}
         run: |
-          poetry run pytest .
+          poetry run coverage run -m pytest .
+      - name: Coverage Report
+        run: |
+          poetry run coverage report -m

.pre-commit-config.yaml

@@ -58,4 +58,4 @@ repos:
       rev: 'v2.6'
       hooks:
       - id: vulture
-        entry: vulture . --min-confidence 90 --exclude */.venv/*.py
+        entry: vulture . --min-confidence 90 --exclude */.venv/*.py,*/tests/*.py

other/transfer_images_minio_subfolder.py

@@ -27,6 +27,7 @@ if __name__ == '__main__':
         # get image from minio
         buffer = get(
             client=minio_client,
+            bucket_name=BUCKET_NAME,
             object_name=obj.object_name,
         )
         # convert data to image

other/transfer_images_mongo_minio.py

@@ -3,16 +3,15 @@
 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.datastore import connect_minio, put
+from shared.datastore import connect_minio, put_image
 from shared.mongodb import connect_mongodb
-from shared.mongodb.classes import VisualCommunication
+from shared.mongodb.src.classes import VisualCommunication
 from shared.utils import check_env, setup_logging
 from web_ui.src.main import NECESSARY_ENV_VAR_LIST
 
@@ -96,13 +95,14 @@ if __name__ == '__main__':
             logging.error('failed getting image from document: %s', doc_id)
             continue
         try:
-            # save image to buffer
+            # get image
-            buffer = BytesIO()
+            image = vis_com.get_image(
-            vis_com.image.save(buffer, 'png')  # type: ignore
+                minio_client=minio_client,
+            )
             # put buffer in minio
-            object_name = put(
+            object_name = put_image(
                 client=minio_client,
-                buffer=buffer,
+                image=image,
             )
         except Exception as exc:
             logging.debug(exc)

poetry.lock

@@ -363,6 +363,85 @@ type = "legacy"
 url = "http://192.168.1.2:5001/index"
 reference = "threadripper"
 
+[[package]]
+name = "coverage"
+version = "7.6.4"
+description = "Code coverage measurement for Python"
+optional = false
+python-versions = ">=3.9"
+files = [
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+    {file = "coverage-7.6.4-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:8165b796df0bd42e10527a3f493c592ba494f16ef3c8b531288e3d0d72c1f6f0"},
+    {file = "coverage-7.6.4-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:c7c8b95bf47db6d19096a5e052ffca0a05f335bc63cef281a6e8fe864d450a72"},
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+    {file = "coverage-7.6.4-cp39-cp39-win_amd64.whl", hash = "sha256:c481b47f6b5845064c65a7bc78bc0860e635a9b055af0df46fdf1c58cebf8e8f"},
+    {file = "coverage-7.6.4-pp39.pp310-none-any.whl", hash = "sha256:3c65d37f3a9ebb703e710befdc489a38683a5b152242664b973a7b7b22348a4e"},
+    {file = "coverage-7.6.4.tar.gz", hash = "sha256:29fc0f17b1d3fea332f8001d4558f8214af7f1d87a345f3a133c901d60347c73"},
+]
+
+[package.extras]
+toml = ["tomli"]
+
+[package.source]
+type = "legacy"
+url = "http://192.168.1.2:5001/index"
+reference = "threadripper"
+
 [[package]]
 name = "dash"
 version = "2.17.0"
@@ -552,6 +631,33 @@ type = "legacy"
 url = "http://192.168.1.2:5001/index"
 reference = "threadripper"
 
+[[package]]
+name = "docker"
+version = "7.1.0"
+description = "A Python library for the Docker Engine API."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "docker-7.1.0-py3-none-any.whl", hash = "sha256:c96b93b7f0a746f9e77d325bcfb87422a3d8bd4f03136ae8a85b37f1898d5fc0"},
+    {file = "docker-7.1.0.tar.gz", hash = "sha256:ad8c70e6e3f8926cb8a92619b832b4ea5299e2831c14284663184e200546fa6c"},
+]
+
+[package.dependencies]
+pywin32 = {version = ">=304", markers = "sys_platform == \"win32\""}
+requests = ">=2.26.0"
+urllib3 = ">=1.26.0"
+
+[package.extras]
+dev = ["coverage (==7.2.7)", "pytest (==7.4.2)", "pytest-cov (==4.1.0)", "pytest-timeout (==2.1.0)", "ruff (==0.1.8)"]
+docs = ["myst-parser (==0.18.0)", "sphinx (==5.1.1)"]
+ssh = ["paramiko (>=2.4.3)"]
+websockets = ["websocket-client (>=1.3.0)"]
+
+[package.source]
+type = "legacy"
+url = "http://192.168.1.2:5001/index"
+reference = "threadripper"
+
 [[package]]
 name = "filelock"
 version = "3.14.0"
@@ -2040,6 +2146,29 @@ type = "legacy"
 url = "http://192.168.1.2:5001/index"
 reference = "threadripper"
 
+[[package]]
+name = "pytest-cov"
+version = "6.0.0"
+description = "Pytest plugin for measuring coverage."
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "pytest-cov-6.0.0.tar.gz", hash = "sha256:fde0b595ca248bb8e2d76f020b465f3b107c9632e6a1d1705f17834c89dcadc0"},
+    {file = "pytest_cov-6.0.0-py3-none-any.whl", hash = "sha256:eee6f1b9e61008bd34975a4d5bab25801eb31898b032dd55addc93e96fcaaa35"},
+]
+
+[package.dependencies]
+coverage = {version = ">=7.5", extras = ["toml"]}
+pytest = ">=4.6"
+
+[package.extras]
+testing = ["fields", "hunter", "process-tests", "pytest-xdist", "virtualenv"]
+
+[package.source]
+type = "legacy"
+url = "http://192.168.1.2:5001/index"
+reference = "threadripper"
+
 [[package]]
 name = "python-dateutil"
 version = "2.9.0.post0"
@@ -2114,6 +2243,38 @@ type = "legacy"
 url = "http://192.168.1.2:5001/index"
 reference = "threadripper"
 
+[[package]]
+name = "pywin32"
+version = "308"
+description = "Python for Window Extensions"
+optional = false
+python-versions = "*"
+files = [
+    {file = "pywin32-308-cp310-cp310-win32.whl", hash = "sha256:796ff4426437896550d2981b9c2ac0ffd75238ad9ea2d3bfa67a1abd546d262e"},
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+    {file = "pywin32-308-cp310-cp310-win_arm64.whl", hash = "sha256:a5ab5381813b40f264fa3495b98af850098f814a25a63589a8e9eb12560f450c"},
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+url = "http://192.168.1.2:5001/index"
+reference = "threadripper"
+
 [[package]]
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 version = "2.32.3"
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 url = "http://192.168.1.2:5001/index"
 reference = "threadripper"
 
+[[package]]
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+optional = false
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+wrapt = "*"
+
+[package.extras]
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+clickhouse = ["clickhouse-driver"]
+cosmosdb = ["azure-cosmos"]
+db2 = ["ibm_db_sa", "sqlalchemy"]
+generic = ["httpx", "redis"]
+google = ["google-cloud-datastore (>=2)", "google-cloud-pubsub (>=2)"]
+influxdb = ["influxdb", "influxdb-client"]
+k3s = ["kubernetes", "pyyaml"]
+keycloak = ["python-keycloak"]
+localstack = ["boto3"]
+mailpit = ["cryptography"]
+minio = ["minio"]
+mongodb = ["pymongo"]
+mssql = ["pymssql", "sqlalchemy"]
+mysql = ["pymysql[rsa]", "sqlalchemy"]
+nats = ["nats-py"]
+neo4j = ["neo4j"]
+opensearch = ["opensearch-py"]
+oracle = ["oracledb", "sqlalchemy"]
+oracle-free = ["oracledb", "sqlalchemy"]
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+rabbitmq = ["pika"]
+redis = ["redis"]
+registry = ["bcrypt"]
+scylla = ["cassandra-driver (==3.29.1)"]
+selenium = ["selenium"]
+sftp = ["cryptography"]
+test-module-import = ["httpx"]
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+url = "http://192.168.1.2:5001/index"
+reference = "threadripper"
+
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 version = "2.2.2"
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 url = "http://192.168.1.2:5001/index"
 reference = "threadripper"
 
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+    {file = "wrapt-1.16.0-cp39-cp39-win32.whl", hash = "sha256:ed867c42c268f876097248e05b6117a65bcd1e63b779e916fe2e33cd6fd0d3c3"},
+    {file = "wrapt-1.16.0-cp39-cp39-win_amd64.whl", hash = "sha256:eb1b046be06b0fce7249f1d025cd359b4b80fc1c3e24ad9eca33e0dcdb2e4a35"},
+    {file = "wrapt-1.16.0-py3-none-any.whl", hash = "sha256:6906c4100a8fcbf2fa735f6059214bb13b97f75b1a61777fcf6432121ef12ef1"},
+    {file = "wrapt-1.16.0.tar.gz", hash = "sha256:5f370f952971e7d17c7d1ead40e49f32345a7f7a5373571ef44d800d06b1899d"},
+]
+
+[package.source]
+type = "legacy"
+url = "http://192.168.1.2:5001/index"
+reference = "threadripper"
+
 [[package]]
 name = "wsproto"
 version = "1.2.0"
@@ -2772,4 +3074,4 @@ reference = "threadripper"
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.12"
-content-hash = "33dbc73047d591ae63dd2d934519882654074a1f3c9ca757d0571d869b8541c2"
+content-hash = "539b697eb7c6ea07594c923ca2aaf26ea841be843c18e696882ccd5dc83339f7"

pyproject.toml

@@ -22,6 +22,9 @@ flake8-pyproject = "^1.2.3"
 pandas-stubs = "^2.2.2.240603"
 types-tqdm = "^4.66.0.20240417"
 pytest = "^8.3.3"
+testcontainers = "^4.8.2"
+coverage = "^7.6.4"
+pytest-cov = "^6.0.0"
 
 
 [tool.poetry.group.dev.dependencies]
@@ -118,3 +121,7 @@ ignore_missing_imports = true
 [[tool.mypy.overrides]]
 module = "shared.mongodb.*"
 ignore_missing_imports = true
+
+[[tool.mypy.overrides]]
+module = "testcontainers.*"
+ignore_missing_imports = true

shared/datastore/__init__.py

@@ -1,8 +1,10 @@
-from .connect_minio import connect_minio
+from .src import (
-from .delete import delete
+    connect_minio,
-from .get import get
+    delete,
-from .get_image import get_image
+    get,
-from .get_model import get_model
+    get_image,
-from .put import put
+    get_model,
-from .put_image import put_image
+    put,
-from .put_model import put_model
+    put_image,
+    put_model,
+)

shared/datastore/get_image.py

@@ -1,41 +0,0 @@
-"""Definition of get_image function."""
-
-import logging
-import os
-from io import BytesIO
-
-from minio import Minio
-from PIL import Image
-
-
-def get_image(
-    client: Minio,
-    object_name: str,
-) -> Image.Image:
-    """Get image from image subfolder in bucket in Minio."""
-    assert isinstance(client, Minio)
-    assert isinstance(object_name, str)
-    assert len(object_name) > 0
-    # prepare arguments
-    assert 'MINIO_BUCKET_NAME' in os.environ
-    bucket_name = os.getenv('MINIO_BUCKET_NAME', default='')
-    subfolder = 'images'
-    # get object from bucket
-    object_name = f'{subfolder}/{object_name}'
-    try:
-        response = client.get_object(
-            bucket_name=bucket_name,
-            object_name=object_name,
-        )
-        buffer = BytesIO(response.data)
-    except Exception as exc:
-        logging.error('failed getting data from MinIO')
-        raise exc
-    finally:
-        response.close()
-        response.release_conn()
-    buffer.seek(0)
-    # convert data to image
-    image = Image.open(buffer)
-    logging.debug('got data from %s', object_name)
-    return image

shared/datastore/src/__init__.py

@@ -0,0 +1,8 @@
+from .connect_minio import connect_minio
+from .delete import delete
+from .get import get
+from .get_image import get_image
+from .get_model import get_model
+from .put import put
+from .put_image import put_image
+from .put_model import put_model

shared/datastore/src/connect_minio.py

@@ -5,28 +5,24 @@ import os
 
 from minio import Minio
 
+from shared.utils import check_env
+
 
 def connect_minio() -> Minio:
     """Connect to MinIO server."""
     # ensure necessary env vars available
-    env_var_list = [
+    var_list = {
         'MINIO_ENDPOINT',
         'MINIO_ACCESS_KEY',
         'MINIO_SECRET_KEY',
         'MINIO_BUCKET_NAME',
-    ]
+    }
-    for env_var in env_var_list:
+    check_env(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='')
+    minio_endpoint = str(os.getenv('MINIO_ENDPOINT'))
-    minio_access_key = os.getenv('MINIO_ACCESS_KEY', default='')
+    minio_access_key = str(os.getenv('MINIO_ACCESS_KEY'))
-    minio_secret_key = os.getenv('MINIO_SECRET_KEY', default='')
+    minio_secret_key = str(os.getenv('MINIO_SECRET_KEY'))
-    minio_bucket_name = os.getenv('MINIO_BUCKET_NAME', default='')
+    minio_bucket_name = str(os.getenv('MINIO_BUCKET_NAME'))
     # connect client
     client = Minio(
         endpoint=minio_endpoint,

shared/datastore/src/delete.py

@@ -1,22 +1,22 @@
 """Definition of delete function."""
 
-from __future__ import annotations
-
 import logging
-import os
+from traceback import print_exc
 
 from minio import Minio
 
 
 def delete(
     client: Minio,
+    bucket_name: str,
     object_name: str,
 ) -> None:
     """Delete object from MinIO."""
     assert isinstance(client, Minio)
-    assert isinstance(object_name, str)
+    assert isinstance(bucket_name, str)
-    bucket_name = os.getenv('MINIO_BUCKET_NAME', default='')
     assert len(bucket_name) > 0
+    assert isinstance(object_name, str)
+    assert len(object_name) > 0
     # remove object
     try:
         client.remove_object(
@@ -24,7 +24,8 @@ def delete(
             object_name=object_name,
         )
     except Exception as exc:
-        logging.debug(exc)
         logging.error('failed deleting %s', object_name)
+        print_exc()
+        raise exc
     else:
         logging.debug('deleted %s', object_name)

shared/datastore/src/get.py

@@ -1,7 +1,6 @@
 """Definition of get function."""
 
 import logging
-import os
 from io import BytesIO
 from traceback import print_exc
 
@@ -10,19 +9,23 @@ from minio import Minio
 
 def get(
     client: Minio,
+    bucket_name: str,
     object_name: str,
 ) -> BytesIO:
     """Get buffer from bucket in MinIO."""
     assert isinstance(client, Minio)
+    assert isinstance(bucket_name, str)
+    assert len(bucket_name) > 0
     assert isinstance(object_name, str)
-    bucket_name = os.getenv('MINIO_BUCKET_NAME', default='')
+    assert len(object_name) > 0
-    # get buffer
     try:
+        # make request
         response = client.get_object(
             bucket_name=bucket_name,
             object_name=object_name,
         )
         assert response.status == 200
+        # get buffer
         buffer = BytesIO()
         chunk_size = 2**14
         while chunk := response.read(chunk_size):
@@ -35,5 +38,7 @@ def get(
         print_exc()
         raise exc
     finally:
+        # close connection if established
+        if 'response' in locals():
             response.close()
             response.release_conn()

shared/datastore/src/get_image.py

@@ -0,0 +1,35 @@
+"""Definition of get_image function."""
+
+import logging
+import os
+
+from minio import Minio
+from PIL import Image
+
+from shared.utils import check_env
+
+from .get import get
+
+
+def get_image(
+    client: Minio,
+    object_name: str,
+) -> Image.Image:
+    """Get image from image subfolder in bucket in Minio."""
+    assert isinstance(client, Minio)
+    assert isinstance(object_name, str)
+    assert len(object_name) > 0
+    # prepare arguments
+    check_env({'MINIO_BUCKET_NAME'})
+    bucket_name = str(os.getenv('MINIO_BUCKET_NAME'))
+    object_name = f'images/{object_name}'
+    # get object from bucket
+    buffer = get(
+        client=client,
+        bucket_name=bucket_name,
+        object_name=object_name,
+    )
+    # convert data to image
+    image = Image.open(buffer)
+    logging.debug('got data from %s', object_name)
+    return image

shared/datastore/src/get_model.py

@@ -1,11 +1,14 @@
 """Definition of get_model function."""
 
 import logging
+import os
 from collections import OrderedDict
 
 import torch
 from minio import Minio
 
+from shared.utils import check_env
+
 from .get import get
 
 
@@ -16,15 +19,18 @@ def get_model(
     """Get model from model subfolder in bucket in Minio."""
     assert isinstance(client, Minio)
     assert isinstance(object_name, str)
-    subfolder = 'models'
+    assert len(object_name) > 0
-    object_name = f'{subfolder}/{object_name}'
+    # prepare arguments
-    # get buffer
+    check_env({'MINIO_BUCKET_NAME'})
+    bucket_name = str(os.getenv('MINIO_BUCKET_NAME'))
+    object_name = f'models/{object_name}'
+    # get object from bucket
     buffer = get(
         client=client,
+        bucket_name=bucket_name,
         object_name=object_name,
     )
     # convert data to model checkpoint
-    buffer.seek(0)
     model_content = torch.load(buffer)
     logging.debug('finished')
     return model_content

shared/datastore/src/put.py

@@ -1,10 +1,6 @@
 """Definition of put function."""
 
-from __future__ import annotations
-
 import logging
-import os
-from hashlib import md5
 from io import BytesIO
 
 from minio import Minio
@@ -13,27 +9,28 @@ from minio import Minio
 def put(
     client: Minio,
     buffer: BytesIO,
-) -> str:
+    bucket_name: str,
+    object_name: str,
+) -> None:
     """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='')
+    assert isinstance(bucket_name, str)
     assert len(bucket_name) > 0
-    # get md5 of image
+    assert isinstance(object_name, str)
-    checksum = md5(buffer.getbuffer()).hexdigest()
+    assert len(object_name) > 0
     # prepare for saving
-    num_bytes = buffer.tell()
+    num_bytes = len(buffer.getvalue())
     buffer.seek(0)
     # send data to bucket
     try:
         client.put_object(
             bucket_name=bucket_name,
-            object_name=checksum,
+            object_name=object_name,
             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)
+    logging.debug('saved data to %s', object_name)
-    return checksum

shared/datastore/src/put_image.py

@@ -8,6 +8,8 @@ from io import BytesIO
 from minio import Minio
 from PIL import Image
 
+from .put import put
+
 
 def put_image(
     client: Minio,
@@ -17,28 +19,22 @@ def put_image(
     used as object name."""
     assert isinstance(client, Minio)
     assert isinstance(image, Image.Image)
+    # get bucket name from env
     bucket_name = os.getenv('MINIO_BUCKET_NAME', default='')
     assert len(bucket_name) > 0
-    subfolder = 'images'
+    # save data to buffer
-    # save image to buffer
     buffer = BytesIO()
     image.save(buffer, 'png')
-    # get md5 of image
+    # get md5 of buffer
     checksum = md5(buffer.getbuffer()).hexdigest()
-    # prepare for saving
+    # set object name
-    num_bytes = buffer.tell()
+    object_name = f'images/{checksum}'
-    buffer.seek(0)
     # send data to bucket
-    object_name = f'{subfolder}/{checksum}'
+    put(
-    try:
+        client=client,
-        client.put_object(
+        buffer=buffer,
         bucket_name=bucket_name,
         object_name=object_name,
-            length=num_bytes,
-            data=buffer,
     )
-    except Exception as exc:
+    logging.debug('finished')
-        logging.error('failed saving data to MinIO')
-        raise exc
-    logging.debug('saved data to %s', object_name)
     return checksum

shared/datastore/src/put_model.py

@@ -9,6 +9,10 @@ import torch
 from minio import Minio
 from torch.nn import Module
 
+from shared.utils import check_env
+
+from .put import put
+
 
 def put_model(
     client: Minio,
@@ -18,28 +22,22 @@ def put_model(
     used as object name."""
     assert isinstance(client, Minio)
     assert isinstance(model, Module)
-    bucket_name = os.getenv('MINIO_BUCKET_NAME', default='')
+    # get bucket name from env
-    assert len(bucket_name) > 0
+    check_env({'MINIO_BUCKET_NAME'})
-    subfolder = 'models'
+    bucket_name = str(os.getenv('MINIO_BUCKET_NAME'))
-    # save image to buffer
+    # save data to buffer
     buffer = BytesIO()
     torch.save(model.state_dict(), buffer)
     # get md5 of image
     checksum = md5(buffer.getbuffer()).hexdigest()
-    # prepare for saving
+    # set object name
-    num_bytes = buffer.tell()
+    object_name = f'models/{checksum}'
-    buffer.seek(0)
     # send data to bucket
-    object_name = f'{subfolder}/{checksum}'
+    put(
-    try:
+        client=client,
-        client.put_object(
+        buffer=buffer,
         bucket_name=bucket_name,
         object_name=object_name,
-            length=num_bytes,
-            data=buffer,
     )
-    except Exception as exc:
+    logging.debug('finished')
-        logging.error('failed saving data to MinIO')
-        raise exc
-    logging.debug('saved data to %s', object_name)
     return checksum

shared/datastore/tests/integration/base_crud_test.py

@@ -0,0 +1,117 @@
+"""Integration tests related to base CRUD functions."""
+
+import logging
+import os
+from io import BytesIO
+
+import minio
+import pytest
+
+from shared.datastore import delete, get, put
+
+
+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(
+    minio_client,
+    data_in_minio,
+):
+    data, bucket_name, object_name = data_in_minio
+    received_data = get(
+        client=minio_client,
+        bucket_name=bucket_name,
+        object_name=object_name,
+    )
+
+    assert isinstance(data, BytesIO)
+    assert same_data(data, received_data)
+
+
+def test_should_delete_data(
+    minio_client,
+    data_in_minio,
+):
+    _, bucket_name, object_name = data_in_minio
+    delete(
+        client=minio_client,
+        bucket_name=bucket_name,
+        object_name=object_name,
+    )
+    with pytest.raises(minio.error.S3Error):
+        _ = get(
+            client=minio_client,
+            bucket_name=bucket_name,
+            object_name=object_name,
+        )
+
+
+def test_should_put_data(
+    minio_client,
+    data,
+):
+    # prepare variables
+    minio_bucket_name = str(os.getenv('MINIO_BUCKET_NAME'))
+    minio_object_name = str(os.getenv('MINIO_OBJECT_NAME'))
+    buffer = BytesIO(data)
+    put(
+        client=minio_client,
+        buffer=buffer,
+        bucket_name=minio_bucket_name,
+        object_name=minio_object_name,
+    )
+    received_data = get(
+        client=minio_client,
+        bucket_name=minio_bucket_name,
+        object_name=minio_object_name,
+    )
+    assert isinstance(received_data, BytesIO)
+    assert same_data(received_data, buffer)
+
+
+def test_should_update_data(
+    minio_client,
+    data_in_minio,
+):
+    buffer, bucket_name, object_name = data_in_minio
+    put(
+        client=minio_client,
+        buffer=buffer,
+        bucket_name=bucket_name,
+        object_name=object_name,
+    )
+    received_data = get(
+        client=minio_client,
+        bucket_name=bucket_name,
+        object_name=object_name,
+    )
+    assert same_data(received_data, buffer)
+
+
+if __name__ == '__main__':
+    pytest.main()

shared/datastore/tests/integration/conftest.py

@@ -0,0 +1,128 @@
+"""Integration test configurations."""
+
+import os
+import random
+from collections.abc import Iterator
+from io import BytesIO
+from pathlib import Path
+
+import pytest
+from dotenv import load_dotenv
+from minio import Minio
+from PIL import Image
+
+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 minio_client(
+    populate_env,
+) -> Iterator[Minio]:
+    # 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 to minio
+    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)
+    # expose client
+    yield client
+    # remove objects left behind by tests
+    for obj in client.list_objects(bucket_name=minio_bucket_name, recursive=True):
+        client.remove_object(
+            bucket_name=obj.bucket_name,
+            object_name=obj.object_name,
+        )
+    # remove bucket
+    client.remove_bucket(bucket_name=minio_bucket_name)
+    assert not client.bucket_exists(bucket_name=minio_bucket_name)
+
+
+@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(
+    minio_client,
+    data,
+) -> Iterator[tuple[BytesIO, str, str]]:
+    # 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
+    minio_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
+    minio_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(
+#     image: Image.Image,
+# ) -> tuple(Image.Image, str):
+#     #
+
+
+#     # expose image and object name
+#     yield image, object_name
+#     # cleanup

shared/datastore/tests/integration/connect_test.py

@@ -0,0 +1,10 @@
+"""Integration test for connect_minio function."""
+
+from minio import Minio
+
+from shared.datastore import connect_minio
+
+
+def test_should_return_correct_type():
+    client = connect_minio()
+    assert isinstance(client, Minio)

shared/datastore/tests/integration/image_crud_test.py

@@ -0,0 +1,73 @@
+"""Integration tests related to image CRUD."""
+
+import numpy as np
+from PIL import Image
+
+# from shared.datastore import connect_minio, get_image, put_image
+
+
+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(
+#     image_in_minio,
+# ):
+#     image, object_name = image_in_minio
+#     client = connect_minio()
+#     received_image = get_image(
+#         client=client,
+#         object_name=object_name,
+#     )
+#     assert isinstance(image, Image.Image)
+#     assert received_image == image
+
+
+# def test_should_put_image(
+#     image,
+# ):
+#     client = connect_minio()
+#     object_name = put_image(
+#         client=client,
+#         image=image,
+#     )
+#     assert isinstance(object_name, str)
+#     assert len(object_name) > 0
+#     received_image = get_image(
+#         client=client,
+#         object_name=object_name,
+#     )
+#     assert same_image(received_image, image)
+
+
+# def test_should_update_image(
+#     image_in_minio,
+# ):
+#     image, object_name = image_in_minio
+#     client = connect_minio()
+#     object_name = put_image(
+#         client=client,
+#         image=image,
+#     )
+#     assert isinstance(object_name, str)
+#     assert len(object_name) > 0
+#     received_image = get_image(
+#         client=client,
+#         object_name=object_name,
+#     )
+#     assert received_image == image

shared/datastore/tests/integration/model_crud_test.py

@@ -0,0 +1,52 @@
+"""Integration tests related to model CRUD."""
+
+# from torch.nn import Module
+
+# from shared.datastore import connect_minio, get_model, put_model
+
+# def test_should_get_model(
+#     model_in_minio,
+# ):
+#     model, object_name = model_in_minio
+#     client = connect_minio()
+#     received_model = get_model(
+#         client=client,
+#         object_name=object_name,
+#     )
+#     assert isinstance(model, Module)
+#     assert received_model == model
+
+
+# def test_should_put_model(
+#     model,
+# ):
+#     client = connect_minio()
+#     object_name = put_model(
+#         client=client,
+#         model=model,
+#     )
+#     assert isinstance(object_name, str)
+#     assert len(object_name) > 0
+#     received_model = get_model(
+#         client=client,
+#         object_name=object_name,
+#     )
+#     assert received_model == model
+
+
+# def test_should_update_model(
+#     model_in_minio,
+# ):
+#     model, object_name = model_in_minio
+#     client = connect_minio()
+#     object_name = put_model(
+#         client=client,
+#         model=model,
+#     )
+#     assert isinstance(object_name, str)
+#     assert len(object_name) > 0
+#     received_model = get_model(
+#         client=client,
+#         object_name=object_name,
+#     )
+#     assert received_model == model

shared/datastore/tests/unit/connect_minio_test.py

@@ -0,0 +1,33 @@
+"""Definition of unittests for connect_minio function."""
+
+import os
+import unittest
+
+from shared.datastore import connect_minio
+
+
+class TestConnectMinio(unittest.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
+
+    def tearDown(self):
+        # clear env vars
+        for key in self.env_var_map:
+            _ = os.environ.pop(key, default=None)
+
+    def test_should_fail_when_env_not_set(self):
+        # ensure env not set
+        self.tearDown()
+        # run test
+        with self.assertRaises(AssertionError):
+            _ = connect_minio()

shared/datastore/tests/unit/delete_test.py

@@ -0,0 +1,61 @@
+"""Definition of unittests for delete function."""
+
+import unittest
+from unittest.mock import Mock
+
+from minio import Minio
+
+from shared.datastore import delete
+
+
+class TestDelete(unittest.TestCase):
+
+    def setUp(self):
+        # set relevant variables
+        self.client = Mock(spec=Minio)
+        self.bucket_name = 'test-bucket'
+        self.object_name = '46KXJMFIAPVLM0TKRFZR5YPPTVJ6PJNX'
+        # set bad arguments
+        self.bad_client = 'not-minio-type'
+        self.bad_string = float(0.0)
+        self.len_0_string = ''
+
+    def test_should_fail_on_wrong_input_type_client(self):
+        with self.assertRaises(AssertionError):
+            delete(
+                client=self.bad_client,
+                bucket_name=self.bucket_name,
+                object_name=self.object_name,
+            )
+
+    def test_should_fail_on_wrong_input_type_bucket_name(self):
+        with self.assertRaises(AssertionError):
+            delete(
+                client=self.client,
+                bucket_name=self.bad_string,
+                object_name=self.object_name,
+            )
+
+    def test_should_fail_on_wrong_input_length_bucket_name(self):
+        with self.assertRaises(AssertionError):
+            delete(
+                client=self.client,
+                bucket_name=self.len_0_string,
+                object_name=self.object_name,
+            )
+
+    def test_should_fail_on_wrong_input_type_object_name(self):
+        with self.assertRaises(AssertionError):
+            delete(
+                client=self.client,
+                bucket_name=self.bucket_name,
+                object_name=self.bad_string,
+            )
+
+    def test_should_fail_on_wrong_input_length_object_name(self):
+        with self.assertRaises(AssertionError):
+            delete(
+                client=self.client,
+                bucket_name=self.bucket_name,
+                object_name=self.len_0_string,
+            )

shared/datastore/tests/unit/get_image_test.py

@@ -0,0 +1,63 @@
+"""Definition of unittests for get_image function."""
+
+import os
+import unittest
+from unittest.mock import MagicMock
+
+from minio import Minio
+
+from shared.datastore import get_image
+
+
+class TestGetImage(unittest.TestCase):
+
+    def setUp(self):
+        # set relevant variables
+        self.client = MagicMock(spec=Minio)
+        self.object_name = '46KXJMFIAPVLM0TKRFZR5YPPTVJ6PJNX'
+        self.env_var_map = {
+            'MINIO_BUCKET_NAME': 'test-bucket',
+        }
+        # set bad arguments
+        self.bad_client = 'not-minio-type'
+        self.bad_string = float(0.0)
+        self.len_0_string = ''
+        # populate env
+        for key, val in self.env_var_map.items():
+            os.environ[key] = val
+
+    def tearDown(self):
+        # clean env
+        for key in self.env_var_map:
+            _ = os.environ.pop(key, default=None)
+
+    def test_should_fail_when_env_not_set(self):
+        # ensure env not set
+        self.tearDown()
+        # run test
+        with self.assertRaises(AssertionError):
+            get_image(
+                client=self.client,
+                object_name=self.object_name,
+            )
+
+    def test_should_fail_on_wrong_input_type_client(self):
+        with self.assertRaises(AssertionError):
+            get_image(
+                client=self.bad_client,
+                object_name=self.object_name,
+            )
+
+    def test_should_fail_on_wrong_input_type_object_name(self):
+        with self.assertRaises(AssertionError):
+            get_image(
+                client=self.client,
+                object_name=self.bad_string,
+            )
+
+    def test_should_fail_on_wrong_input_length_object_name(self):
+        with self.assertRaises(AssertionError):
+            get_image(
+                client=self.client,
+                object_name=self.len_0_string,
+            )

shared/datastore/tests/unit/get_model_test.py

@@ -0,0 +1,63 @@
+"""Definition of unittest for get_model function."""
+
+import os
+import unittest
+from unittest.mock import MagicMock
+
+from minio import Minio
+
+from shared.datastore import get_model
+
+
+class TestGetModel(unittest.TestCase):
+
+    def setUp(self):
+        # set relevant variables
+        self.client = MagicMock(spec=Minio)
+        self.object_name = '46KXJMFIAPVLM0TKRFZR5YPPTVJ6PJNX'
+        self.env_var_map = {
+            'MINIO_BUCKET_NAME': 'test-bucket',
+        }
+        # set bad arguments
+        self.bad_client = 'not-minio-type'
+        self.bad_string = float(0.0)
+        self.len_0_string = ''
+        # populate env
+        for key, val in self.env_var_map.items():
+            os.environ[key] = val
+
+    def tearDown(self):
+        # clean env
+        for key in self.env_var_map:
+            _ = os.environ.pop(key, default=None)
+
+    def test_should_fail_when_env_not_set(self):
+        # ensure env not set
+        self.tearDown()
+        # run test
+        with self.assertRaises(AssertionError):
+            get_model(
+                client=self.client,
+                object_name=self.object_name,
+            )
+
+    def test_should_fail_on_wrong_input_type_client(self):
+        with self.assertRaises(AssertionError):
+            get_model(
+                client=self.bad_client,
+                object_name=self.object_name,
+            )
+
+    def test_should_fail_on_wrong_input_type_object_name(self):
+        with self.assertRaises(AssertionError):
+            get_model(
+                client=self.client,
+                object_name=self.bad_string,
+            )
+
+    def test_should_fail_on_wrong_input_length_object_name(self):
+        with self.assertRaises(AssertionError):
+            get_model(
+                client=self.client,
+                object_name=self.len_0_string,
+            )

shared/datastore/tests/unit/get_test.py

@@ -0,0 +1,60 @@
+"""Definition of unittests for get function."""
+
+import unittest
+from unittest.mock import MagicMock
+
+from minio import Minio
+
+from shared.datastore import get
+
+
+class TestGet(unittest.TestCase):
+    def setUp(self):
+        # set relevant variables
+        self.client = MagicMock(spec=Minio)
+        self.bucket_name = 'test-bucket'
+        self.object_name = '46KXJMFIAPVLM0TKRFZR5YPPTVJ6PJNX'
+        # set bad arguments
+        self.bad_client = 'not-minio-type'
+        self.bad_string = float(0.0)
+        self.len_0_string = ''
+
+    def test_should_fail_on_wrong_input_type_client(self):
+        with self.assertRaises(AssertionError):
+            get(
+                client=self.bad_client,
+                bucket_name=self.bucket_name,
+                object_name=self.object_name,
+            )
+
+    def test_should_fail_on_wrong_input_type_bucket_name(self):
+        with self.assertRaises(AssertionError):
+            get(
+                client=self.client,
+                bucket_name=self.bad_string,
+                object_name=self.object_name,
+            )
+
+    def test_should_fail_on_wrong_input_length_bucket_name(self):
+        with self.assertRaises(AssertionError):
+            get(
+                client=self.client,
+                bucket_name=self.len_0_string,
+                object_name=self.object_name,
+            )
+
+    def test_should_fail_on_wrong_input_type_object_name(self):
+        with self.assertRaises(AssertionError):
+            get(
+                client=self.client,
+                bucket_name=self.bucket_name,
+                object_name=self.bad_string,
+            )
+
+    def test_should_fail_on_wrong_input_length_object_name(self):
+        with self.assertRaises(AssertionError):
+            get(
+                client=self.client,
+                bucket_name=self.bucket_name,
+                object_name=self.len_0_string,
+            )

shared/datastore/tests/unit/put_image_test.py

@@ -0,0 +1,41 @@
+"""Definition of unittests for put_image function."""
+
+import os
+import unittest
+from unittest.mock import MagicMock
+
+from minio import Minio
+from PIL import Image
+
+from shared.datastore import put_image
+
+
+class TestPutImage(unittest.TestCase):
+
+    def setUp(self):
+        # set relevant variables
+        self.client = MagicMock(spec=Minio)
+        self.image = Image.new(mode='RGB', size=(480, 480))
+        self.env_var_map = {
+            'MINIO_BUCKET_NAME': 'test-bucket',
+        }
+        # set bad arguments
+        self.bad_client = 'not-minio-type'
+        self.bad_image = 'not-image-type'
+        # populate env
+        for key, val in self.env_var_map.items():
+            os.environ[key] = val
+
+    def test_should_fail_on_wrong_input_type_client(self):
+        with self.assertRaises(AssertionError):
+            put_image(
+                client=self.bad_client,
+                image=self.image,
+            )
+
+    def test_should_fail_on_wrong_input_type_image(self):
+        with self.assertRaises(AssertionError):
+            put_image(
+                client=self.client,
+                image=self.bad_image,
+            )

shared/datastore/tests/unit/put_model_test.py

@@ -0,0 +1,40 @@
+"""Definition of unittests for put_model function."""
+
+import os
+import unittest
+from unittest.mock import MagicMock
+
+from minio import Minio
+from torch.nn import Module
+
+from shared.datastore import put_model
+
+
+class TestPutModel(unittest.TestCase):
+    def setUp(self):
+        # set relevant variables
+        self.client = MagicMock(spec=Minio)
+        self.model = MagicMock(spec=Module)
+        self.env_var_map = {
+            'MINIO_BUCKET_NAME': 'test-bucket',
+        }
+        # set bad arguments
+        self.bad_client = 'not-minio-type'
+        self.bad_model = 'not-image-type'
+        # populate env
+        for key, val in self.env_var_map.items():
+            os.environ[key] = val
+
+    def test_should_fail_on_wrong_input_type_client(self):
+        with self.assertRaises(AssertionError):
+            put_model(
+                client=self.bad_client,
+                model=self.model,
+            )
+
+    def test_should_fail_on_wrong_input_type_model(self):
+        with self.assertRaises(AssertionError):
+            put_model(
+                client=self.client,
+                model=self.bad_model,
+            )

shared/datastore/tests/unit/put_test.py

@@ -0,0 +1,80 @@
+"""Definition of unittests for put function."""
+
+import unittest
+from io import BytesIO
+from unittest.mock import MagicMock
+
+from minio import Minio
+from PIL import Image
+
+from shared.datastore import put
+
+
+class TestPut(unittest.TestCase):
+    def setUp(self):
+        # set relevant variables
+        self.client = MagicMock(spec=Minio)
+        self.bucket_name = 'test-bucket'
+        self.object_name = '46KXJMFIAPVLM0TKRFZR5YPPTVJ6PJNX'
+        self.image = Image.new(mode='RGB', size=(480, 480))
+        self.buffer = BytesIO()
+        self.image.save(self.buffer, 'png')
+        # set bad arguments
+        self.bad_client = 'not-minio-type'
+        self.bad_string = float(0.0)
+        self.bad_buffer = 'not-buffer-type'
+        self.len_0_string = ''
+
+    def test_should_fail_on_wrong_input_type_client(self):
+        with self.assertRaises(AssertionError):
+            put(
+                client=self.bad_client,
+                buffer=self.buffer,
+                bucket_name=self.bucket_name,
+                object_name=self.object_name,
+            )
+
+    def test_should_fail_on_wrong_input_type_buffer(self):
+        with self.assertRaises(AssertionError):
+            put(
+                client=self.client,
+                buffer=self.bad_buffer,
+                bucket_name=self.bucket_name,
+                object_name=self.object_name,
+            )
+
+    def test_should_fail_on_wrong_input_type_bucket_name(self):
+        with self.assertRaises(AssertionError):
+            put(
+                client=self.client,
+                buffer=self.buffer,
+                bucket_name=self.bad_string,
+                object_name=self.object_name,
+            )
+
+    def test_should_fail_on_wrong_input_length_bucket_name(self):
+        with self.assertRaises(AssertionError):
+            put(
+                client=self.client,
+                buffer=self.buffer,
+                bucket_name=self.len_0_string,
+                object_name=self.object_name,
+            )
+
+    def test_should_fail_on_wrong_input_type_object_name(self):
+        with self.assertRaises(AssertionError):
+            put(
+                client=self.client,
+                buffer=self.buffer,
+                bucket_name=self.bucket_name,
+                object_name=self.bad_string,
+            )
+
+    def test_should_fail_on_wrong_input_length_object_name(self):
+        with self.assertRaises(AssertionError):
+            put(
+                client=self.client,
+                buffer=self.buffer,
+                bucket_name=self.bucket_name,
+                object_name=self.len_0_string,
+            )

shared/mongodb/src/classes/visual_communication.py

@@ -12,8 +12,8 @@ from PIL import Image
 from pydantic import BaseModel, ConfigDict
 from pymongo.collection import Collection
 
-from shared.datastore import get, put
+from shared.datastore import get_image, put_image
-from shared.mongodb.classes import ModelData
+from shared.mongodb.src.classes import ModelData
 
 
 class VisualCommunication(BaseModel):
@@ -39,11 +39,9 @@ class VisualCommunication(BaseModel):
         """Upload image to MinIO and return MD5 checksum of hashed image."""
         assert isinstance(image, Image.Image)
         assert isinstance(minio_client, Minio)
-        buffer = BytesIO()
+        object_name = put_image(
-        image.save(buffer, 'png')
-        object_name = put(
             client=minio_client,
-            buffer=buffer,
+            image=image,
         )
         return object_name
 
@@ -92,14 +90,12 @@ class VisualCommunication(BaseModel):
     def get_image(self, minio_client: Minio) -> Image.Image:
         """Load image data from minio."""
         assert isinstance(minio_client, Minio)
-        # get buffer from minio
+        # get image from minio
-        buffer = get(
+        image = get_image(
             client=minio_client,
             object_name=self.object_name,
         )
-        # convert data to image
+        return image
-        im = Image.open(buffer)
-        return im
 
     def save_to_mongo(self, collection: Collection) -> None:
         """Save self as document in MongoDB."""

web_ui/src/app/init_app.py

@@ -14,8 +14,8 @@ from pymongo.collection import Collection
 
 from shared.datastore import delete as delete_from_minio
 from shared.mongodb import count_documents, get_visual_communication, upsert_annotation
-from shared.mongodb.classes import ModelData, VisualCommunication
+from shared.mongodb.src.classes import ModelData, VisualCommunication
-from shared.mongodb.exceptions import NoDocumentFoundException
+from shared.mongodb.src.exceptions import NoDocumentFoundException
 
 from .layout import app_layout
 
@@ -146,8 +146,10 @@ def init_app(
                     logging.debug(exc)
                     failed_filename_list.append(filename)
                     # remove document from minio
+                    bucket_name = os.getenv('MINIO_BUCKET_NAME', default='')
                     delete_from_minio(
                         client=minio_client,
+                        bucket_name=bucket_name,
                         object_name=vis_com.object_name,
                     )
             assert (