moved webui and updated poetry packages

model/src/dataloader.py

@@ -14,7 +14,7 @@ from torchvision.transforms.functional import pad
 from torchvision.transforms.functional import resize
 from torchvision.transforms.functional import rotate
 
-from core.database import connect
+from shared.database import connect
 
 # resnet18 original normalization values
 RESNET_NORMALIZE_MEAN = [0.485, 0.456, 0.406]

model/src/models/visual_communication.py

@@ -14,17 +14,17 @@ from .point_of_view import PointOfViewTail
 from .resnet18_head import ResNet18Head
 from .salience import SalienceTail
 from .visual_syntax import VisualSyntaxTail
-from core.dto import AngleData
+from shared.dto import AngleData
-from core.dto import ContactData
+from shared.dto import ContactData
-from core.dto import DistanceData
+from shared.dto import DistanceData
-from core.dto import FramingData
+from shared.dto import FramingData
-from core.dto import InformationValueData
+from shared.dto import InformationValueData
-from core.dto import ModalityColorData
+from shared.dto import ModalityColorData
-from core.dto import ModalityDepthData
+from shared.dto import ModalityDepthData
-from core.dto import ModalityLightingData
+from shared.dto import ModalityLightingData
-from core.dto import PointOfViewData
+from shared.dto import PointOfViewData
-from core.dto import SalienceData
+from shared.dto import SalienceData
-from core.dto import VisualSyntaxData
+from shared.dto import VisualSyntaxData
 
 
 class VisualCommunicationModel(nn.Module):

poetry.lock

@@ -32,13 +32,13 @@ tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "p
 
 [[package]]
 name = "blinker"
-version = "1.8.1"
+version = "1.8.2"
 description = "Fast, simple object-to-object and broadcast signaling"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "blinker-1.8.1-py3-none-any.whl", hash = "sha256:5f1cdeff423b77c31b89de0565cd03e5275a03028f44b2b15f912632a58cced6"},
+    {file = "blinker-1.8.2-py3-none-any.whl", hash = "sha256:1779309f71bf239144b9399d06ae925637cf6634cf6bd131104184531bf67c01"},
-    {file = "blinker-1.8.1.tar.gz", hash = "sha256:da44ec748222dcd0105ef975eed946da197d5bdf8bafb6aa92f5bc89da63fa25"},
+    {file = "blinker-1.8.2.tar.gz", hash = "sha256:8f77b09d3bf7c795e969e9486f39c2c5e9c39d4ee07424be2bc594ece9642d83"},
 ]
 
 [[package]]
@@ -242,13 +242,13 @@ files = [
 
 [[package]]
 name = "dash"
-version = "2.16.1"
+version = "2.17.0"
 description = "A Python framework for building reactive web-apps. Developed by Plotly."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "dash-2.16.1-py3-none-any.whl", hash = "sha256:8a9d2a618e415113c0b2a4d25d5dc4df5cb921f733b33dde75559db2316b1df1"},
+    {file = "dash-2.17.0-py3-none-any.whl", hash = "sha256:2421569023b2cd46ea2d4b2c14fe72c71b7436527a3102219b2265fa361e7c67"},
-    {file = "dash-2.16.1.tar.gz", hash = "sha256:b2871d6b8d4c9dfd0a64f89f22d001c93292910b41d92d9ff2bb424a28283976"},
+    {file = "dash-2.17.0.tar.gz", hash = "sha256:d065cd88771e45d0485993be0d27565e08918cb7edd18e31ee1c5b41252fc2fa"},
 ]
 
 [package.dependencies]
@@ -267,7 +267,7 @@ Werkzeug = "<3.1"
 
 [package.extras]
 celery = ["celery[redis] (>=5.1.2)", "redis (>=3.5.3)"]
-ci = ["black (==22.3.0)", "dash-dangerously-set-inner-html", "dash-flow-example (==0.0.5)", "flake8 (==7.0.0)", "flaky (==3.7.0)", "flask-talisman (==1.0.0)", "jupyterlab (<4.0.0)", "mimesis (<=11.1.0)", "mock (==4.0.3)", "numpy (<=1.26.3)", "openpyxl", "orjson (==3.9.12)", "pandas (>=1.4.0)", "pyarrow", "pylint (==3.0.3)", "pytest-mock", "pytest-rerunfailures", "pytest-sugar (==0.9.6)", "pyzmq (==25.1.2)", "xlrd (>=2.0.1)"]
+ci = ["black (==22.3.0)", "dash-dangerously-set-inner-html", "dash-flow-example (==0.0.5)", "flake8 (==7.0.0)", "flaky (==3.8.1)", "flask-talisman (==1.0.0)", "jupyterlab (<4.0.0)", "mimesis (<=11.1.0)", "mock (==4.0.3)", "numpy (<=1.26.3)", "openpyxl", "orjson (==3.9.12)", "pandas (>=1.4.0)", "pyarrow", "pylint (==3.0.3)", "pytest-mock", "pytest-rerunfailures", "pytest-sugar (==0.9.6)", "pyzmq (==25.1.2)", "xlrd (>=2.0.1)"]
 compress = ["flask-compress"]
 dev = ["PyYAML (>=5.4.1)", "coloredlogs (>=15.0.1)", "fire (>=0.4.0)"]
 diskcache = ["diskcache (>=5.2.1)", "multiprocess (>=0.70.12)", "psutil (>=5.8.0)"]
@@ -440,13 +440,13 @@ dotenv = ["python-dotenv"]
 
 [[package]]
 name = "fsspec"
-version = "2024.3.1"
+version = "2024.5.0"
 description = "File-system specification"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "fsspec-2024.3.1-py3-none-any.whl", hash = "sha256:918d18d41bf73f0e2b261824baeb1b124bcf771767e3a26425cd7dec3332f512"},
+    {file = "fsspec-2024.5.0-py3-none-any.whl", hash = "sha256:e0fdbc446d67e182f49a70b82cf7889028a63588fde6b222521f10937b2b670c"},
-    {file = "fsspec-2024.3.1.tar.gz", hash = "sha256:f39780e282d7d117ffb42bb96992f8a90795e4d0fb0f661a70ca39fe9c43ded9"},
+    {file = "fsspec-2024.5.0.tar.gz", hash = "sha256:1d021b0b0f933e3b3029ed808eb400c08ba101ca2de4b3483fbc9ca23fcee94a"},
 ]
 
 [package.extras]
@@ -454,7 +454,7 @@ abfs = ["adlfs"]
 adl = ["adlfs"]
 arrow = ["pyarrow (>=1)"]
 dask = ["dask", "distributed"]
-devel = ["pytest", "pytest-cov"]
+dev = ["pre-commit", "ruff"]
 dropbox = ["dropbox", "dropboxdrivefs", "requests"]
 full = ["adlfs", "aiohttp (!=4.0.0a0,!=4.0.0a1)", "dask", "distributed", "dropbox", "dropboxdrivefs", "fusepy", "gcsfs", "libarchive-c", "ocifs", "panel", "paramiko", "pyarrow (>=1)", "pygit2", "requests", "s3fs", "smbprotocol", "tqdm"]
 fuse = ["fusepy"]
@@ -471,6 +471,9 @@ s3 = ["s3fs"]
 sftp = ["paramiko"]
 smb = ["smbprotocol"]
 ssh = ["paramiko"]
+test = ["aiohttp (!=4.0.0a0,!=4.0.0a1)", "numpy", "pytest", "pytest-asyncio (!=0.22.0)", "pytest-benchmark", "pytest-cov", "pytest-mock", "pytest-recording", "pytest-rerunfailures", "requests"]
+test-downstream = ["aiobotocore (>=2.5.4,<3.0.0)", "dask-expr", "dask[dataframe,test]", "moto[server] (>4,<5)", "pytest-timeout", "xarray"]
+test-full = ["adlfs", "aiohttp (!=4.0.0a0,!=4.0.0a1)", "cloudpickle", "dask", "distributed", "dropbox", "dropboxdrivefs", "fastparquet", "fusepy", "gcsfs", "jinja2", "kerchunk", "libarchive-c", "lz4", "notebook", "numpy", "ocifs", "pandas", "panel", "paramiko", "pyarrow", "pyarrow (>=1)", "pyftpdlib", "pygit2", "pytest", "pytest-asyncio (!=0.22.0)", "pytest-benchmark", "pytest-cov", "pytest-mock", "pytest-recording", "pytest-rerunfailures", "python-snappy", "requests", "smbprotocol", "tqdm", "urllib3", "zarr", "zstandard"]
 tqdm = ["tqdm"]
 
 [[package]]
@@ -547,13 +550,13 @@ files = [
 
 [[package]]
 name = "jinja2"
-version = "3.1.3"
+version = "3.1.4"
 description = "A very fast and expressive template engine."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "Jinja2-3.1.3-py3-none-any.whl", hash = "sha256:7d6d50dd97d52cbc355597bd845fabfbac3f551e1f99619e39a35ce8c370b5fa"},
+    {file = "jinja2-3.1.4-py3-none-any.whl", hash = "sha256:bc5dd2abb727a5319567b7a813e6a2e7318c39f4f487cfe6c89c6f9c7d25197d"},
-    {file = "Jinja2-3.1.3.tar.gz", hash = "sha256:ac8bd6544d4bb2c9792bf3a159e80bba8fda7f07e81bc3aed565432d5925ba90"},
+    {file = "jinja2-3.1.4.tar.gz", hash = "sha256:4a3aee7acbbe7303aede8e9648d13b8bf88a429282aa6122a993f0ac800cb369"},
 ]
 
 [package.dependencies]
@@ -1113,13 +1116,13 @@ xmp = ["defusedxml"]
 
 [[package]]
 name = "plotly"
-version = "5.21.0"
+version = "5.22.0"
 description = "An open-source, interactive data visualization library for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "plotly-5.21.0-py3-none-any.whl", hash = "sha256:a33f41fd5922e45b2b253f795b200d14452eb625790bb72d0a72cf1328a6abbf"},
+    {file = "plotly-5.22.0-py3-none-any.whl", hash = "sha256:68fc1901f098daeb233cc3dd44ec9dc31fb3ca4f4e53189344199c43496ed006"},
-    {file = "plotly-5.21.0.tar.gz", hash = "sha256:69243f8c165d4be26c0df1c6f0b7b258e2dfeefe032763404ad7e7fb7d7c2073"},
+    {file = "plotly-5.22.0.tar.gz", hash = "sha256:859fdadbd86b5770ae2466e542b761b247d1c6b49daed765b95bb8c7063e7469"},
 ]
 
 [package.dependencies]
@@ -1282,71 +1285,71 @@ files = [
 
 [[package]]
 name = "pymongo"
-version = "4.7.1"
+version = "4.7.2"
 description = "Python driver for MongoDB <http://www.mongodb.org>"
 optional = false
 python-versions = ">=3.7"
 files = [
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 [package.dependencies]
@@ -1414,13 +1417,13 @@ files = [
 
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+version = "2.32.0"
 description = "Python HTTP for Humans."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
@@ -1464,13 +1467,13 @@ six = ">=1.7.0"
 
 [[package]]
 name = "selenium"
-version = "4.20.0"
+version = "4.21.0"
 description = ""
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -1545,17 +1548,18 @@ mpmath = ">=0.19"
 
 [[package]]
 name = "tenacity"
-version = "8.2.3"
+version = "8.3.0"
 description = "Retry code until it succeeds"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
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 ]
 
 [package.extras]
-doc = ["reno", "sphinx", "tornado (>=4.5)"]
+doc = ["reno", "sphinx"]
+test = ["pytest", "tornado (>=4.5)", "typeguard"]
 
 [[package]]
 name = "torch"
@@ -1658,13 +1662,13 @@ scipy = ["scipy"]
 
 [[package]]
 name = "trio"
-version = "0.25.0"
+version = "0.25.1"
 description = "A friendly Python library for async concurrency and I/O"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "trio-0.25.0-py3-none-any.whl", hash = "sha256:e6458efe29cc543e557a91e614e2b51710eba2961669329ce9c862d50c6e8e81"},
+    {file = "trio-0.25.1-py3-none-any.whl", hash = "sha256:e42617ba091e7b2e50c899052e83a3c403101841de925187f61e7b7eaebdf3fb"},
-    {file = "trio-0.25.0.tar.gz", hash = "sha256:9b41f5993ad2c0e5f62d0acca320ec657fdb6b2a2c22b8c7aed6caf154475c4e"},
+    {file = "trio-0.25.1.tar.gz", hash = "sha256:9f5314f014ea3af489e77b001861c535005c3858d38ec46b6b071ebfa339d7fb"},
 ]
 
 [package.dependencies]
@@ -1692,13 +1696,13 @@ wsproto = ">=0.14"
 
 [[package]]
 name = "types-pillow"
-version = "10.2.0.20240423"
+version = "10.2.0.20240520"
 description = "Typing stubs for Pillow"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "types-Pillow-10.2.0.20240423.tar.gz", hash = "sha256:696e68b9b6a58548fc307a8669830469237c5b11809ddf978ac77fafa79251cd"},
+    {file = "types-Pillow-10.2.0.20240520.tar.gz", hash = "sha256:130b979195465fa1e1676d8e81c9c7c30319e8e95b12fae945e8f0d525213107"},
-    {file = "types_Pillow-10.2.0.20240423-py3-none-any.whl", hash = "sha256:bd12923093b96c91d523efcdb66967a307f1a843bcfaf2d5a529146c10a9ced3"},
+    {file = "types_Pillow-10.2.0.20240520-py3-none-any.whl", hash = "sha256:33c36494b380e2a269bb742181bea5d9b00820367822dbd3760f07210a1da23d"},
 ]
 
 [[package]]
@@ -1761,13 +1765,13 @@ requests = "*"
 
 [[package]]
 name = "werkzeug"
-version = "3.0.2"
+version = "3.0.3"
 description = "The comprehensive WSGI web application library."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "werkzeug-3.0.2-py3-none-any.whl", hash = "sha256:3aac3f5da756f93030740bc235d3e09449efcf65f2f55e3602e1d851b8f48795"},
+    {file = "werkzeug-3.0.3-py3-none-any.whl", hash = "sha256:fc9645dc43e03e4d630d23143a04a7f947a9a3b5727cd535fdfe155a17cc48c8"},
-    {file = "werkzeug-3.0.2.tar.gz", hash = "sha256:e39b645a6ac92822588e7b39a692e7828724ceae0b0d702ef96701f90e70128d"},
+    {file = "werkzeug-3.0.3.tar.gz", hash = "sha256:097e5bfda9f0aba8da6b8545146def481d06aa7d3266e7448e2cccf67dd8bd18"},
 ]
 
 [package.dependencies]
@@ -1792,20 +1796,20 @@ h11 = ">=0.9.0,<1"
 
 [[package]]
 name = "zipp"
-version = "3.18.1"
+version = "3.18.2"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.18.1-py3-none-any.whl", hash = "sha256:206f5a15f2af3dbaee80769fb7dc6f249695e940acca08dfb2a4769fe61e538b"},
+    {file = "zipp-3.18.2-py3-none-any.whl", hash = "sha256:dce197b859eb796242b0622af1b8beb0a722d52aa2f57133ead08edd5bf5374e"},
-    {file = "zipp-3.18.1.tar.gz", hash = "sha256:2884ed22e7d8961de1c9a05142eb69a247f120291bc0206a00a7642f09b5b715"},
+    {file = "zipp-3.18.2.tar.gz", hash = "sha256:6278d9ddbcfb1f1089a88fde84481528b07b0e10474e09dcfe53dad4069fa059"},
 ]
 
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.12"
-content-hash = "6c4bb66c774e93a08e4180f3148942edf91e2b5620ea1f6c3e4c30045bb643e5"
+content-hash = "2db221a28d46b210a8fa0b78ad2fa3ac606a52052ad5e02b50d5b07db1e1c5b7"

pyproject.toml

@@ -5,20 +5,11 @@ description = ""
 authors = ["Brian Bjarke Jensen <[email protected]>"]
 readme = "README.md"
 packages = [
-    { include = "core" },
+    { include = "shared" },
 ]
 
 [tool.poetry.dependencies]
 python = "^3.12"
-gunicorn = "^21.2.0"
-python-dotenv = "^1.0.1"
-dash = "^2.15.0"
-dash-bootstrap-components = "^1.5.0"
-dash-mantine-components = "^0.12.1"
-pydantic = "^2.6.1"
-pillow = "^10.2.0"
-pymongo = "^4.6.1"
-dash-auth = "^2.2.0"
 
 
 [tool.poetry.group.test.dependencies]
@@ -38,6 +29,20 @@ retry = "^0.9.2"
 torch = "^2.2.1"
 torchvision = "^0.17.1"
 
+
+[tool.poetry.group.shared.dependencies]
+pymongo = "^4.7.2"
+pydantic = "^2.6.1"
+pillow = "^10.2.0"
+
+
+[tool.poetry.group.web_ui.dependencies]
+dash = "^2.17.0"
+gunicorn = "^21.2.0"
+dash-bootstrap-components = "^1.5.0"
+dash-mantine-components = "^0.12.1"
+dash-auth = "^2.2.0"
+
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"

shared/database/classes/visual_communication.py

@@ -12,7 +12,7 @@ from pydantic import BaseModel
 from pydantic import field_serializer
 from pydantic import field_validator
 
-from core.dto import ModelData
+from shared.dto import ModelData
 
 
 class VisualCommunication(BaseModel):

shared/database/utils/get_visual_communication.py

@@ -5,8 +5,8 @@ import logging
 
 from pymongo.collection import Collection
 
-from core.database import NoDocumentFoundException
+from shared.database import NoDocumentFoundException
-from core.database import VisualCommunication
+from shared.database import VisualCommunication
 
 
 def get_visual_communication(

shared/database/utils/save_dataset.py

@@ -4,7 +4,7 @@ import logging
 
 from pymongo.collection import Collection
 
-from core.database import Dataset
+from shared.database import Dataset
 
 
 def save_dataset(
@@ -21,7 +21,7 @@ def save_dataset(
 if __name__ == '__main__':
     from dotenv import load_dotenv
     load_dotenv('local.env')
-    from core.database import list_names, connect
+    from shared.database import list_names, connect
     # connect to database
     collection, db, client = connect()
     print(client.server_info())

shared/database/utils/upsert_annotation.py

@@ -4,7 +4,7 @@ import logging
 
 from pymongo.collection import Collection
 
-from core.dto import ModelData
+from shared.dto import ModelData
 
 
 def upsert_annotation(

shared/database/utils/upsert_prediction.py

@@ -4,7 +4,7 @@ import logging
 
 from pymongo.collection import Collection
 
-from core.dto import ModelData
+from shared.dto import ModelData
 
 
 def upsert_prediction(

shared/database/utils/upsert_visual_communication.py

@@ -2,7 +2,7 @@ from __future__ import annotations
 
 from pymongo.collection import Collection
 
-from core.database import VisualCommunication
+from shared.database import VisualCommunication
 
 
 def upsert_visual_communication(

shared/utils/__init__.py

@@ -0,0 +1,4 @@
+from __future__ import annotations
+
+from .check_env import check_env
+from .setup_logging import setup_logging

shared/utils/check_env.py

@@ -0,0 +1,24 @@
+"""Definition of check_env function."""
+from __future__ import annotations
+
+import os
+
+
+def check_env() -> None:
+    """Check necessary environment variables are set."""
+    necesasary_var_list = {
+        'MONGO_HOST',
+        'MONGO_DB',
+        'MONGO_COLLECTION',
+        'MONGO_USER',
+        'MONGO_PASSWORD',
+        'DASH_AUTH_USERNAME',
+        'DASH_AUTH_PASSWORD',
+    }
+    for env_var in necesasary_var_list:
+        # ensure env var set
+        assert (
+            env_var in os.environ
+        ), (
+            f"environment variable not set: {env_var}"
+        )

shared/utils/setup_logging.py

@@ -0,0 +1,21 @@
+"""Definition of setup_logging function."""
+from __future__ import annotations
+
+import logging
+import os
+
+
+def setup_logging() -> None:
+    """Setup logging."""
+    requested_log_level = os.getenv('LOG_LEVEL', default='info')
+    level = getattr(logging, requested_log_level.upper())
+    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=level)
+    logging.debug('finished')

tests/generate_random_prediction_test.py

@@ -2,7 +2,7 @@ from __future__ import annotations
 
 from pathlib import Path
 
-from core.database.classes import VisualCommunication
+from shared.database.classes import VisualCommunication
 
 
 if __name__ == '__main__':

tests/get_visual_communication_test.py

@@ -5,8 +5,8 @@ from pathlib import Path
 
 from dotenv import load_dotenv
 
-from core.database import connect
+from shared.database import connect
-from core.database import get_visual_communication
+from shared.database import get_visual_communication
 
 if __name__ == '__main__':
     # prepare env vars

tests/image_download_test.py

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

tests/image_upload_test.py

@@ -6,8 +6,8 @@ from pathlib import Path
 from dotenv import load_dotenv
 from pymongo.errors import DuplicateKeyError
 
-from core.database import connect
+from shared.database import connect
-from core.database.classes import VisualCommunication
+from shared.database.classes import VisualCommunication
 
 if __name__ == '__main__':
     # get list of image paths

tests/image_upload_to_server_test.py

@@ -5,8 +5,8 @@ from pathlib import Path
 from dotenv import load_dotenv
 from pymongo.errors import DuplicateKeyError
 
-from core.database import connect
+from shared.database import connect
-from core.database import VisualCommunication
+from shared.database import VisualCommunication
 
 if __name__ == '__main__':
     # get list of image paths

tests/model_outputs_from_annotation_test.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from core.dto import ModelData
+from shared.dto import ModelData
 
 
 if __name__ == '__main__':

tests/prediction_upload_test.py

@@ -6,9 +6,9 @@ from pathlib import Path
 
 from dotenv import load_dotenv
 
-from core.database import connect
+from shared.database import connect
-from core.database import upsert_prediction
+from shared.database import upsert_prediction
-from core.database.classes import VisualCommunication
+from shared.database.classes import VisualCommunication
 
 if __name__ == '__main__':
     # setup logging

tests/total_annotated_test.py

@@ -5,8 +5,8 @@ from pathlib import Path
 
 from dotenv import load_dotenv
 
-from core.database import connect
+from shared.database import connect
-from core.database import count_documents
+from shared.database import count_documents
 
 if __name__ == '__main__':
     # prepare env vars

tests/total_documents_test.py

@@ -5,8 +5,8 @@ from pathlib import Path
 
 from dotenv import load_dotenv
 
-from core.database import connect
+from shared.database import connect
-from core.database import count_documents
+from shared.database import count_documents
 
 if __name__ == '__main__':
     # prepare env vars

web_ui/Dockerfile

@@ -30,7 +30,8 @@ ENV PATH="${POETRY_HOME}/bin:$PATH"
 # install runtime dependencies
 WORKDIR ${APP_HOME}
 COPY poetry.lock pyproject.toml ./
-RUN --mount=type=cache,target=${POETRY_CACHE_DIR} poetry install --without model
+RUN --mount=type=cache,target=${POETRY_CACHE_DIR} poetry install \
+    --with shared,web_ui
 
 # final stage
 FROM python:3.12-slim-bookworm
@@ -48,7 +49,7 @@ RUN mkdir -p /home/app && \
 
 # add code while changing ownership
 WORKDIR $APP_HOME
-COPY --chown=app:app ./core ./core
+COPY --chown=app:app ./shared ./shared
 COPY --chown=app:app ./web_ui/src ./src
 
 # change to the app user

web_ui/docker-compose.server.yml

@@ -0,0 +1,13 @@
+services:
+  web:
+    image: visual_critical_discourse_analysis:test
+    container_name: visual_critical_discourse_analysis_alone
+    build:
+      context: ../
+      dockerfile: ./web_ui/Dockerfile
+    ports:
+      - 8050:8050
+    env_file:
+      - ../server.env
+    environment:
+      - ENV=TEST

web_ui/src/app/__init__.py

@@ -1,3 +1,3 @@
 from __future__ import annotations
 
-from .app import app
+from .init_app import init_app

web_ui/src/app/app.py

@@ -1,251 +0,0 @@
-from __future__ import annotations
-
-import logging
-import os
-
-import dash_bootstrap_components as dbc
-from dash import ALL
-from dash import Dash
-from dash import Input
-from dash import Output
-from dash import State
-from dash_auth import BasicAuth
-from pydantic import ValidationError
-
-from .layout import app_layout
-from core.database import connect
-from core.database import count_documents
-from core.database import get_visual_communication
-from core.database import NoDocumentFoundException
-from core.database import upsert_annotation
-from core.database import upsert_visual_communication
-from core.database import VisualCommunication
-from core.dto import ModelData
-
-# setup app
-app = Dash(__name__, external_stylesheets=[dbc.themes.BOOTSTRAP])
-app.title = 'visual critical discourse analysis'.title()
-app.layout = app_layout
-server = app.server
-
-# setup authentication
-AUTH_DICT = {
-    os.getenv('DASH_AUTH_USERNAME'): os.getenv('DASH_AUTH_PASSWORD'),
-}
-BasicAuth(app, AUTH_DICT)
-
-# connect to database
-collection, db, client = connect()
-
-
-# define callbacks
-@app.callback(
-    Output('alert-element', 'is_open'),
-    Output('alert-element', 'children'),
-    Input('alert-message', 'data'),
-)
-def show_alert(
-    msg: str | None,
-):
-    if msg is None or msg == '':
-        return False, ''
-    logging.info(f'updated alert message: {msg}')
-    return True, msg
-
-
-@app.callback(
-    Output('success-element', 'is_open'),
-    Output('success-element', 'children'),
-    Input('success-message', 'data'),
-)
-def show_success(
-    msg: str | None,
-):
-    if msg is None or msg == '':
-        return False, ''
-    logging.info(f"updated success message: {msg}")
-    return True, msg
-
-
-@app.callback(
-    Output('progress-bar', 'value'),
-    Output('progress-bar', 'max'),
-    Output('progress-bar', 'label'),
-    Input('next-button', 'n_clicks'),
-    Input('upload-data', 'filename'),
-)
-def update_progress_bar(
-    n_clicks: int,
-    filename_list: list[str] | None,
-):
-    logging.info('began updating progress bar')
-    global collection
-    # get values from database
-    num_total = count_documents(
-        collection=collection,
-        only_with_annotation=False,
-    )
-    num_handled = count_documents(
-        collection=collection,
-        only_with_annotation=True,
-    )
-    limit = int(num_total/20)
-    label_str = f"{num_handled}/{num_total}" if num_handled >= limit else ''
-    return num_handled, num_total, label_str
-
-
-@app.callback(
-    Output('success-message', 'data', allow_duplicate=True),
-    Output('alert-message', 'data', allow_duplicate=True),
-    Input('upload-data', 'contents'),
-    State('upload-data', 'filename'),
-    prevent_initial_call=True,
-)
-def upload_images(
-    content_list: list[str] | None,
-    filename_list: list[str] | None,
-):
-    logging.info('began uploading images')
-    global collection
-    # stop early if possible
-    if content_list is None or filename_list is None:
-        logging.warning('content_list is None -> nothing to upload')
-        return None, 'nothing selected to upload'.title()
-    # build list of visual communication
-    visual_communication_list = []
-    for content, filename in zip(content_list, filename_list):
-        try:
-            image = VisualCommunication.decode_image(content)
-            vis_com = VisualCommunication(
-                name=filename,
-                image=image,
-            )
-        except Exception as exc:
-            logging.warning(
-                (
-                    'failed creating VisualCommunication object '
-                    f"from file {filename}"
-                ),
-                exc,
-            )
-        else:
-            visual_communication_list.append(vis_com)
-    # upsert documents
-    success = upsert_visual_communication(
-        collection=collection,
-        visual_communication_list=visual_communication_list,
-    )
-    if success:
-        logging.info(f"succesfully uploaded {len(filename_list)} images")
-        return 'successfully uploaded images'.title(), None
-    logging.warning('failed inserting images into database')
-    return None, 'failed uploading images'.title()
-
-
-@app.callback(
-    Output('alert-message', 'data', allow_duplicate=True),
-    Output('vis-com-name', 'data'),
-    Output('image-container', 'src'),
-    Output({'type': 'annotation', 'index': ALL}, 'value'),
-    Input('next-button', 'n_clicks'),
-    State('vis-com-name', 'data'),
-    State('image-container', 'src'),
-    State({'type': 'annotation', 'index': ALL}, 'id'),
-    State({'type': 'annotation', 'index': ALL}, 'value'),
-    prevent_initial_call=True,
-)
-def cycle_visual_communication_data(
-    n_clicks: int,
-    vis_com_name: str,
-    image_src: str,
-    annotation_keys: list,
-    annotation_values: list,
-):
-    logging.info('began cycling visual communication data')
-    global collection
-    # prepare default response
-    response = [
-        '',
-        vis_com_name,
-        image_src,
-        annotation_values,
-    ]
-    # check if next-button clicked
-    if n_clicks == 0:
-        logging.info('stopping early: next-button has not yet been clicked')
-        return response
-    # check if visual communication name is set
-    if len(vis_com_name) > 0:
-        logging.info('saving annotations to database: %s', vis_com_name)
-        try:
-            # extract option keys
-            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 = [
-                elem.replace(' ', '_')
-                for elem
-                in annotation_keys
-            ]
-            annotation_values = [
-                elem.replace(' ', '_').lower()
-                for elem
-                in annotation_values
-            ]
-            annotation_map = {
-                key: value
-                for key, value
-                in zip(annotation_keys, annotation_values)
-            }
-            # instantiate ModelOutputs object
-            annotations = ModelData.from_annotations(**annotation_map)
-            # save data to database
-            upsert_annotation(
-                collection=collection,
-                vis_com_name=vis_com_name,
-                annotations=annotations,
-            )
-        except (ValueError, ValidationError) as exc:
-            msg = f"failed saving annotation: {exc}"
-            logging.warning(msg)
-            response[0] = msg
-            return tuple(response)
-    # get new visual communication
-    logging.info('trying to get new visual communication')
-    try:
-        # get data
-        vis_com = get_visual_communication(
-            collection=collection,
-            with_annotation=False,
-        )
-        # set variables
-        vis_com_name = vis_com.name
-        image_src = vis_com.webencoded_image()
-        if vis_com.prediction is not None:
-            # TODO: update to use optional predictions
-            pass
-        else:
-            # reset annotations
-            annotation_values = [None for elem in annotation_values]
-    except NoDocumentFoundException:
-        msg = 'no unannotated data in database'
-        logging.warning(msg)
-        response[0] = msg
-        return tuple(response)
-    else:
-        response[1] = vis_com_name
-        response[2] = image_src
-        response[3] = annotation_values
-        logging.info('finished getting visual communication: %s', vis_com_name)
-    return tuple(response)
-
-
-if __name__ == '__main__':
-    app.run(debug=True)

web_ui/src/app/init_app.py

@@ -0,0 +1,260 @@
+"""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 Dash
+from dash import Input
+from dash import Output
+from dash import State
+from dash_auth import BasicAuth
+from pydantic import ValidationError
+from pymongo.collection import Collection
+
+from .layout import app_layout
+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,
+) -> Dash:
+    """Initialise web UI application."""
+    # setup app
+    app = Dash(
+        name='visual_critical_discourse_analysis_web_ui',
+        external_stylesheets=[
+            dbc.themes.BOOTSTRAP,
+        ],
+    )
+    app.title = 'visual critical discourse analysis'.title()
+    app.layout = app_layout
+
+    # setup authentication
+    auth_dict = {
+        os.getenv('DASH_AUTH_USERNAME'): os.getenv('DASH_AUTH_PASSWORD'),
+    }
+    BasicAuth(app, auth_dict)
+
+    # define callback: show warning
+    @app.callback(
+        Output('warning-element', 'is_open'),
+        Output('warning-element', 'children'),
+        Input('warning-message', 'data'),
+    )
+    def show_warning(
+        msg: str | None,
+    ) -> tuple[bool, str]:
+        """Show warning message in web ui."""
+        if msg is None or msg == '':
+            return False, ''
+        logging.debug('updated warning message: %s', msg)
+        return True, msg
+
+    # define callback: show info
+    @app.callback(
+        Output('info-element', 'is_open'),
+        Output('info-element', 'children'),
+        Input('info-message', 'data'),
+    )
+    def show_info(
+        msg: str | None,
+    ) -> tuple[bool, str]:
+        """Show info message in web ui."""
+        if msg is None or msg == '':
+            return False, ''
+        logging.debug('updated info message: %s', msg)
+        return True, msg
+
+    # define callback: update progress bar
+    @app.callback(
+        Output('progress-bar', 'value'),
+        Output('progress-bar', 'max'),
+        Output('progress-bar', 'label'),
+        Input('next-button', 'n_clicks'),
+        Input('upload-data', 'filename'),
+    )
+    def update_progress_bar(
+        n_clicks: int,
+        filename_list: list[str] | None,
+    ) -> tuple[int, int, str]:
+        """Update progress bar in web ui."""
+        assert isinstance(n_clicks, int)
+        if filename_list is not None:
+            assert isinstance(filename_list, list)
+        # get values from database
+        num_total = count_documents(
+            collection=collection,
+            only_with_annotation=False,
+        )
+        num_handled = count_documents(
+            collection=collection,
+            only_with_annotation=True,
+        )
+        limit = int(num_total/20)
+        label_str = f"{
+            num_handled
+        }/{num_total}" if num_handled >= limit else ''
+        return num_handled, num_total, label_str
+
+    # define callback: upload image
+    @app.callback(
+        Output('info-message', 'data', allow_duplicate=True),
+        Output('warning-message', 'data', allow_duplicate=True),
+        Input('upload-data', 'contents'),
+        State('upload-data', 'filename'),
+        prevent_initial_call=True,
+    )
+    def upload_images(
+        content_list: list[str] | None,
+        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()
+
+    # define callback: cycle visual communication data
+    @app.callback(
+        Output('warning-message', 'data', allow_duplicate=True),
+        Output('vis-com-name', 'data'),
+        Output('image-container', 'src'),
+        Output({'type': 'annotation', 'index': ALL}, 'value'),
+        Input('next-button', 'n_clicks'),
+        State('vis-com-name', 'data'),
+        State('image-container', 'src'),
+        State({'type': 'annotation', 'index': ALL}, 'id'),
+        State({'type': 'annotation', 'index': ALL}, 'value'),
+        prevent_initial_call=True,
+    )
+    def cycle_vis_com_data(
+        n_clicks: int,
+        vis_com_name: str,
+        image_src: str,
+        annotation_keys: list,
+        annotation_values: list,
+    ) -> tuple:
+        """Cycle visual communcation data."""
+        assert isinstance(n_clicks, int)
+        assert isinstance(vis_com_name, str)
+        assert isinstance(image_src, str)
+        assert isinstance(annotation_keys, list)
+        assert isinstance(annotation_values, list)
+        # prepare default response
+        response = [
+            '',
+            vis_com_name,
+            image_src,
+            annotation_values,
+        ]
+        # stop early if possible
+        if n_clicks == 0:
+            return tuple(response)
+        # check if visual communication name is set
+        if len(vis_com_name) > 0:
+            logging.info('saving annotations to database: %s', vis_com_name)
+            try:
+                # extract option keys
+                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 = [
+                    elem.replace(' ', '_')
+                    for elem
+                    in annotation_keys
+                ]
+                annotation_values = [
+                    elem.replace(' ', '_').lower()
+                    for elem
+                    in annotation_values
+                ]
+                annotation_map = {
+                    key: value
+                    for key, value
+                    in zip(annotation_keys, annotation_values)
+                }
+                # instantiate ModelOutputs object
+                annotations = ModelData.from_annotations(**annotation_map)
+                # save data to database
+                upsert_annotation(
+                    collection=collection,
+                    vis_com_name=vis_com_name,
+                    annotations=annotations,
+                )
+            except (ValueError, ValidationError) as exc:
+                msg = f"failed saving annotation: {exc}"
+                logging.warning(msg)
+                response[0] = msg
+                return tuple(response)
+        # get new visual communication
+        logging.info('trying to get new visual communication')
+        try:
+            # get data
+            vis_com = get_visual_communication(
+                collection=collection,
+                with_annotation=False,
+            )
+            # set variables
+            vis_com_name = vis_com.name
+            image_src = vis_com.webencoded_image()
+            if vis_com.prediction is not None:
+                # TODO: update to use optional predictions
+                pass
+            else:
+                # reset annotations
+                annotation_values = [None for elem in annotation_values]
+        except NoDocumentFoundException:
+            msg = 'no unannotated data in database'
+            logging.warning(msg)
+            response[0] = msg
+            return tuple(response)
+        else:
+            response[1] = vis_com_name
+            response[2] = image_src
+            response[3] = annotation_values
+            logging.info(
+                'finished getting visual communication: %s', vis_com_name,
+            )
+        return tuple(response)
+    logging.info('initialised app')
+    return app

web_ui/src/app/layout/labels.py

@@ -4,17 +4,17 @@ import dash_mantine_components as dmc
 from dash import dcc
 from dash import html
 
-from core.dto import AngleData
+from shared.dto import AngleData
-from core.dto import ContactData
+from shared.dto import ContactData
-from core.dto import DistanceData
+from shared.dto import DistanceData
-from core.dto import FramingData
+from shared.dto import FramingData
-from core.dto import InformationValueData
+from shared.dto import InformationValueData
-from core.dto import ModalityColorData
+from shared.dto import ModalityColorData
-from core.dto import ModalityDepthData
+from shared.dto import ModalityDepthData
-from core.dto import ModalityLightingData
+from shared.dto import ModalityLightingData
-from core.dto import PointOfViewData
+from shared.dto import PointOfViewData
-from core.dto import SalienceData
+from shared.dto import SalienceData
-from core.dto import VisualSyntaxData
+from shared.dto import VisualSyntaxData
 
 
 def generate_visual_syntax_options_map():

web_ui/src/app/layout/stores.py

@@ -6,8 +6,8 @@ from dash import html
 
 stores_element = html.Div(
     children=[
-        dcc.Store(id='alert-message', data=''),
+        dcc.Store(id='warning-message', data=''),
-        dcc.Store(id='success-message', data=''),
+        dcc.Store(id='info-message', data=''),
         dcc.Store(id='vis-com-name', data=''),
     ],
 )

web_ui/src/main.py

@@ -1,53 +1,23 @@
+"""Definition of web_ui main script."""
 from __future__ import annotations
 
-import logging
 import os
-from pathlib import Path
 
-from dotenv import load_dotenv
+from .app import init_app
-
+from shared.database import connect
-from .app import app
+from shared.utils import check_env
-
+from shared.utils import setup_logging
-# prepare optional local setup
-env_path = Path(__file__).parent.parent.parent / 'local.env'
-load_dotenv(env_path)
 
 # ensure env vars set
-necesasary_var_list = {
+check_env()
-    'MONGO_HOST',
-    'MONGO_DB',
-    'MONGO_COLLECTION',
-    'MONGO_USER',
-    'MONGO_PASSWORD',
-    'DASH_AUTH_USERNAME',
-    'DASH_AUTH_PASSWORD',
-}
-for env_var in necesasary_var_list:
-    # ensure env var set
-    assert (
-        env_var in os.environ
-    ), (
-        f"environment variable not set: {env_var}"
-    )
 
 # setup logging stream handler
-FMT = (
+setup_logging()
-    '%(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)
 
-logging.info('initialized app')
+# connect to database
+collection, db, client = connect()
+
+# initialise application
+app = init_app(collection=collection)
 server = app.server
 server.config.update(SECRET_KEY=os.urandom(24))
-
-if __name__ == '__main__':
-    # prepare local env vars
-    os.environ['MONGO_HOST'] = 'localhost'
-    # run app
-    app.run(debug=True)
-    logging.info('started app')