EMhub is a web application for data management at scientific core facilities, specially designed for operations of middle-size CryoEM centers. It allows the creation of users and resources (e.g. microscopes or other instruments). It also coordinates access to resources through applications and bookings, providing full traceability and reporting of usage.
Additionally, a REST API is exposed that permits the writing of external scripts to communicate with the application. This feature allows to write "workers" that can monitor new data collection sessions and handle different tasks such as data transfer or on-the-fly processing.
For more detailed information check the documentation at:
https://3dem.github.io/emdocs/emhub/
conda create --name=emhub python=3.8 conda activate emhub git clone https://github.com/3dem/emhub.git # OR git clone git@github.com:3dem/emhub.git cd emhub # If you want to use the development branch, then do: # git checkout devel pip install -e . # Generate some test data emh-data --create_instance export FLASK_APP=emhub export EMHUB_INSTANCE=~/.emhub/instances/test # Now launch the built-in Flask development server: flask run --debug # or with gunicorn: gunicorn -k gevent --workers=2 'emhub:create_app()' --bind 0.0.0.0:5000 # Then launch a web browser at http://127.0.0.1:5000/ # user: admin, password: adminIn order to make the emhub available to install with pip install emhub, we need to:
python install twine restructuredtext-lint cd emhub # It might be a good idea to check the README.rst before uploading: rst-lint README.rst python setup.py sdist twine upload dist/emhub-0.0.1a3.tar.gzA Dockerfile has been include to create Docker images.
cd emhub docker build . -t emhub docker run --rm -p 8080:8080 --name=emhub -v $PWD/instance:/instanceIf we modify the database models, then an update/migration is required.
# Do changes in the model (data_models.py) alembic revision --autogenerate # Review the generated script alembic upgrade head # or use first the --sql option to see the commandsA Python environment with Sphinx and other dependencies is required to build the documentation.
# Install environment conda create -y --name=emhub-docs python=3.8 conda activate emhub-docs conda install nodejs=20 -c conda-forge -y npm install -g jsdoc pip install -e . # install emhub pip install -r docs/requirements.txt # install doc requirements # Build the docs python build_docs.py # or just sphinx-build -b html docs/ html/ # Rsync the generated html files to the emdocs repo rsync -av html/ ~/work/documentation/emdocs/emhub/ cd ../emhub-docs/ git ci -am "Updated html files"