taxonify_backend GUI repository: https://github.com/MicroscopeIT/taxonify_gui Getting started After you clone the repo please make sure you have also pulled LFS data. If not then run the following command: git lfs pull Environment files Stack needs .env files to run. The files are filled in with some default values in the repo so you do not have to take any action here. The files are tracked by git however so if you make some local modifications to them that you do not want to push upstream please run git update-index --skip-worktree <filepath> on each changed .env file. Run the stack locally with Docker In order to run the stack locally you need to define all required environment files and execute the following commands: Starting the stack mkdir db_data touch webserver.log docker-compose build docker-compose up -d Removing the stack docker-compose stop ; docker-compose rm -v -f Running unit tests Assuming you have already prepared python environment, in order to run unit tests ensure that you have set two variables STORAGE_CONNECTION_STRING and MONGO_TEST_DB_CONNECTION_STRING, then type in your command line python -m unittest discover -s aquascope/tests -t . Ensure that you included the STORAGE_CONENCTION_STRING in quotation marks. Seeding database with exemplary data If you want to seed the DB with exemplary data please make sure you have your local stack up and running and please execute the following command: bash ./seed_db.bash Environment files description In order to run the stack you need to setup a few environment files and fill required values. celery.env RABBITMQ_DEFAULT_PASS - password used for celery/rabbitmq authentication. Should be the same as CELERY_PASS CELERY_PASS - password used for celery/rabbitmq authentication. Should be the same as RABBITMQ_DEFAULT_PASS mongodb_root_credentials.env MONGO_INITDB_ROOT_USERNAME - root db username MONGO_INITDB_ROOT_PASSWORD - root db password MONGO_INITDB_DATABASE - root db name mongodb_user_credentials.env MONGO_CONNECTION_STRING - It should be mongodb://<USERNAME>:<PASSWORD>@<DB_ADDRESS>/<DB_NAME>. <DB_ADDRESS> for local stack is just localhost. These values don't need to (and even shouldn't be) the same as values proviede in mongodb_root_credentials.env. Example: MONGO_CONNECTION_STRING=mongodb://aquascopeuser:dummypass@localhost/aquascopedb storage_credentials.env STORAGE_CONNECTION_STRING - value of Azure Storage Account connection string (DefaultEndpointsProtocol=http;AccountName=devstoreaccount1;AccountKey=Eby8vdM02xNOcqFlqUwJPLlmEtlCDXJ1OUzFT50uSRZ6IFsuFq2UVErCz4I6tq/K1SZFPTOtr/KBHBeksoGMGw==;BlobEndpoint=http://0.0.0.0:10000/devstoreaccount1; if using local Docker stack) user_authentication.env JWT_SECRET_KEY - key for signing JWT tokens AQUASCOPE_TEST_USER - username of the only user in the system AQUASCOPE_TEST_PASS - password of the only user in the system encoded with pbkdf2_sha256 algorithm from passlib library. AQUASCOPE_SECONDARY_PASS - secondary password to the system encoded with pbkdf2_sha256 algorithm from passlib library. Release v0.8.2 emergency fix of pyyaml vulnerability that was patched in 4.2b1 annotation bug fix (items projection error)