feat: add base classes and docs

[JaeAeich]

Summary by Sourcery

This pull request introduces new base classes for the TESK API, including TeskApp for application initialization and running, BaseValidator for custom validation logic, and BaseTeskRequest for common TES API endpoint logic. Additionally, it refactors the existing application initialization logic to utilize the new TeskApp class.

• New Features:
  • Introduced TeskApp class to encapsulate the initialization and running of the TESK API server, extending the Foca framework.
  • Added BaseValidator class for custom validation logic, which must be implemented by all custom validators.
  • Created BaseTeskRequest class to define common properties and methods for TES API endpoint business logic.
• Enhancements:
  • Refactored the application initialization and running logic from app.py to the new TeskApp class.

[sourcery-ai[bot]]

Reviewer's Guide by Sourcery

This pull request introduces new base classes TESK, requests, and model validators. It also includes significant enhancements to the documentation, Helm chart configurations, and Kubernetes Ingress settings. Additionally, new unit tests have been added for various modules, and a GitHub Actions workflow has been set up to check for vulnerabilities.

File-Level Changes

Files	Changes
tesk/app.py tesk/tesk_app.py	Refactored the application initialization to use the new TeskApp class, simplifying the main entry point and configuration loading.
tesk/api/ga4gh/tes/models/base/base_validator.py tesk/api/ga4gh/tes/base/base_tesk_request.py tesk/api/ga4gh/tes/base/__init__.py tesk/api/ga4gh/tes/models/base/__init__.py	Introduced new base classes for TES API requests and custom Pydantic validators, providing a structured approach for request handling and validation.

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[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 98.21%. Comparing base (c5128a9) to head (bf33bc8).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #191 +/- ## ======================================= Coverage 98.21% 98.21% ======================================= Files 8 8 Lines 561 561 ======================================= Hits 551 551 Misses 10 10 ``` | [Flag](https://app.codecov.io/gh/elixir-cloud-aai/TESK/pull/191/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=elixir-cloud-aai) | Coverage Δ | | |---|---|---| | [test_unit](https://app.codecov.io/gh/elixir-cloud-aai/TESK/pull/191/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=elixir-cloud-aai) | `98.21% <ø> (ø)` | | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=elixir-cloud-aai#carryforward-flags-in-the-pull-request-comment) to find out more.

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[JaeAeich]

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[JaeAeich]

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[JaeAeich]

please check #198