build: upgrade FOCA to 0.13.0

[jvkersch]

Description

Updates FOCA to the latest version, which is 0.13.0 at the time this PR was opened.

Fixes #49

Type of change

Please delete options that are not relevant.

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation update

Checklist:

• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
• I have not reduced the existing code coverage
• I have added docstrings following the Python style guidelines of this project to all new modules, classes, methods and functions are documented with docstrings following; I have updated any previously existing docstrings, if applicable
• I have updated any sections of the app's documentation that are affected by the proposed changes, if applicable

Summary by Sourcery

This pull request updates the FOCA library to version 0.13.0, refactors the code to use the new configuration syntax, and adjusts the test cases accordingly to ensure compatibility and functionality.

• Bug Fixes:
  • Updated FOCA to version 0.13.0 to fix compatibility issues.
• Enhancements:
  • Refactored test cases to use the updated FOCA configuration syntax.
• Tests:
  • Modified test cases to align with the new FOCA configuration structure.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request updates the FOCA library to version 0.13.0. The primary change involves updating the way the FOCA configuration is accessed within the application code and tests. Specifically, the configuration is now accessed using app.config.foca instead of app.config['FOCA']. This update addresses issue #49 and ensures compatibility with the latest version of FOCA.

File-Level Changes

Files	Changes
tests/ga4gh/drs/test_server.py tests/ga4gh/drs/endpoints/test_service_info.py tests/ga4gh/drs/endpoints/test_register_objects.py	Updated FOCA configuration access in multiple test files to use app.config.foca instead of app.config['FOCA'].
drs_filer/ga4gh/drs/endpoints/register_objects.py drs_filer/ga4gh/drs/server.py drs_filer/ga4gh/drs/endpoints/service_info.py	Updated FOCA configuration access in multiple endpoint and server files to use current_app.config.foca instead of current_app.config['FOCA'].

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[sourcery-ai]

Hey @jvkersch - I've reviewed your changes and found some issues that need to be addressed.

Blocking issues:

• Avoid using eval for security reasons. (link)

Here's what I looked at during the review

• 🟡 General issues: 5 issues found
• 🔴 Security: 1 blocking issue
• 🟢 Testing: all looks good
• 🟢 Complexity: all looks good

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[sourcery-ai]

🚨 issue (security): Avoid using eval for security reasons.

Using eval can introduce security vulnerabilities. Consider using a safer alternative like ast.literal_eval if the input is expected to be a valid Python literal structure.

[jvkersch]

Flagged as #54.

[jvkersch]

I can address #54 right after this PR, but I prefer not mixing maintenance changes and behavioral changes.

[kushagra189]

Only one minor comment. We have made some repetitive usages but we can take that up in a separate refactor as well.

[jvkersch]

Thanks @kushagra189, I've done that particular refactor in the module where there were a lot of repeated usages of that object. There was another instance where Sourcery suggested a refactor but that was not applicable (the repeated code was spread out over multiple functions).

The only open issue is the use of eval (#54). I would suggest merging this PR as-is and tackling that issue separately.

[kushagra189]

Thanks @jvkersch , LGTM.