This project is financed by France BioImaging.
A webapp to follow microscope performance over time.
Install OMERO_metrics in development mode as follows:
# within your python venv:
$ cd OMERO-metrics
$ pip install -e .
Run in your terminal to start the server:
$ docker compose up -d
Execute the following commands to create the database:
$ docker exec -it omero-web /bin/bash /opt/omero/web/venv3/bin/python /opt/omero/web/venv3/lib/python3.10/site-packages/omeroweb/manage.py migrate
Execute this code to generate some test data:
$ cd OMERO-metrics/
$ pip install -r requirements.txt
$ cd test/omero-server
$ python3 structure_generator.py
Now restart your omero-web server and go to
http://localhost:5080/omero_metrics/ in your browser.
This project is related to configuring Django settings for OMERO web application with Plotly Dash components.
$ cd OMERO-metrics
$ pip install -e .
-
Add the following lines to the
omeroweb/settings.pyfile: -
Make sure you have REACT_VERSION=18.2.0 installed and set ENV to REACT_VERSION=18.2.0 (export REACT_VERSION=18.2.0) .
STATICFILES_FINDERS = ['django.contrib.staticfiles.finders.FileSystemFinder','django.contrib.staticfiles.finders.AppDirectoriesFinder','django_plotly_dash.finders.DashAssetFinder', 'django_plotly_dash.finders.DashComponentFinder','django_plotly_dash.finders.DashAppDirectoryFinder'] PLOTLY_COMPONENTS = ['dpd_components', 'dash_bootstrap_components', 'dash_iconify', 'dash_mantine_components', 'dpd_static_support'] X_FRAME_OPTIONS = 'SAMEORIGIN' PLOTLY_DASH = {'ws_route' : 'dpd/ws/channel', 'http_route' : 'dpd/views', 'http_poke_enabled' : True, 'insert_demo_migrations' : False,'cache_timeout_initial_arguments': 60,'view_decorator': None,'cache_arguments': False, 'serve_locally': False}
you need to manually add the following apps to the INSTALLED_APPS list in the omeroweb/settings.py file:
"dpd_static_support", "bootstrap4", "corsheaders"
Add these additional configurations using the terminal:
export OMERODIR=$(pwd)
omero config set omero.web.application_server development
omero config set omero.web.debug True
omero config append omero.web.server_list '["localhost", 6063, "host"]'
omero config append omero.web.apps '"OMERO_metrics"'
omero config append omero.web.apps '"django_plotly_dash"'
omero config append omero.web.ui.top_links '["Metrics", "OMERO_metrics_index", {"title": "Open app in new tab", "target": "_blank"}]'
omero config append omero.web.middleware '{"index": 0.5, "class": "corsheaders.middleware.CorsMiddleware"}'
omero config append omero.web.middleware '{"index": 10, "class": "corsheaders.middleware.CorsPostCsrfMiddleware"}'
omero config set omero.web.cors_origin_allow_all True
omero config set omero.web.databases '{"default": {"ENGINE": "django.db.backends.sqlite3", "NAME": "mydatabase"}}'
omero config append omero.web.middleware '{"index": 7, "class": "django_plotly_dash.middleware.ExternalRedirectionMiddleware"}'
omero config append omero.web.middleware '{"index": 0.5, "class": "whitenoise.middleware.WhiteNoiseMiddleware"}'
omero config append omero.web.middleware '{"index": 8, "class": "django_plotly_dash.middleware.BaseMiddleware"}'
omero config append omero.web.middleware '{"index":0.1, "class": "OMERO_metrics.middleware.OmeroAuth"}'
omero config append omero.web.ui.center_plugins '["Metrics View", "OMERO_metrics/webclient_plugins/center_plugin.metricsview.js.html", "metrics_view_panel"]'
omero config append omero.web.ui.right_plugins '["ROIs", "OMERO_metrics/webclient_plugins/right_plugin.rois.js.html", "image_roi_tab"]'
python manage.py migrate
- This app was derived from cookiecutter-omero-webapp.
- For further info on depolyment, see Deployment
This project, similar to many Open Microscopy Environment (OME) projects, is licensed under the terms of the AGPL v3.
2024 CNRS