Taxonify_backend: v0.8.2

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)