move all configurable data to a well defined config module, so that we have all configs in one place for easier management

Description

Create environment for development.

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DoD (Definition of Done)

Testing

A command line script that loads example data to mongo that can then be queried for using the API

Write some documentation on:

• how to start web app locally for development
• how to start a database container for development
• how to build image
• how to deploy image
• how to configure (env vars)

documentation and deployment files are outdated

Currently searches return all samples that fit the sample criteria and they cannot be filtered by their biological beings.

Users should be able to search samples by biological beings.

Let's start following common style conventions (PEP8) that we are also using in other repositories.

• auto-format code with black . -l 160
• refactor camelCase functions and variables to snake_case
• check code style, format and linting with tox -p auto before committing

Switch from pymongo to motor for MongoDB driver, as it provides async connection

• https://github.com/mongodb/motor
• https://github.com/CSCfi/metadata-submitter can be used as reference

so that we can keep style consistent across projects and developers, add style checking conventions using:

• flake8
• black
• mypy

examples:

• https://github.com/CSCfi/beacon-python/blob/master/tox.ini
• https://github.com/CSCfi/metadata-submitter/blob/master/tox.ini
• checks can be run with tox -p auto
• black formatting can be applied by removing the --check param, e.g. black . -l 160

Biological being and anatomical search have multiple search terms and they should be queried from the beacon.

• add typing to code (avoid use of Any as much as possible) https://docs.python.org/3/library/typing.html
• add typing check with mypy to tox https://github.com/CSCfi/metadata-submitter/blob/master/tox.ini#L28-L39

add logging module

• api endpoints should have INFO logs
• add DEBUG logs to wherever they are useful to verifying internal workings
• add ERROR logs to all exceptions

examples for reference:

• https://github.com/CSCfi/metadata-submitter/blob/master/metadata_backend/helpers/logger.py
• https://github.com/CSCfi/beacon-network/blob/master/registry/utils/logging.py

Since the .json parsing has been updated the db structure changes as well. We need to update queries to work with these changes.

One of the possible search terms is all and this needs to work in the backend as well.

getSearchTerms should return only search options and datatypes. This should be a schema without any actual values.

Add login handling for queries.

Bug comes from .database import.