916-refactor-epidata-to-support-ingestion-into-the-LOKI-database

[sudiphzi]

Changes and Information

Please briefly list the changes (main added features, changed items, or corrected bugs) made:

• Refactoring of memilio-epidata, e.g. getCaseData, getDIVIData, getPopulationData and getVaccinationData to allow returning python objects
• Added an argument to the CLI to return datasets

If need be, add additional information and what the reviewer should look out for in particular:

Merge Request - Guideline Checklist

Please check our git workflow. Use the draft feature if the Pull Request is not yet ready to review.

Checks by code author

• Every addressed issue is linked (use the "Closes #ISSUE" keyword below)
• New code adheres to coding guidelines
• No large data files have been added (files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.)
• Tests are added for new functionality and a local test run was successful
• Appropriate documentation for new functionality has been added (Doxygen in the code and Markdown files if necessary)
• Proper attention to licenses, especially no new third-party software with conflicting license has been added
• (For ABM development) Checked benchmark results and ran and posted a local test above from before and after development to ensure performance is monitored.

Checks by code reviewer(s)

• Corresponding issue(s) is/are linked and addressed
• Code is clean of development artifacts (no deactivated or commented code lines, no debugging printouts, etc.)
• Appropriate unit tests have been added, CI passes, code coverage and performance is acceptable (did not decrease)
• No large data files added in the whole history of commits(files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.)
• On merge, add 2-5 lines with the changes (main added features, changed items, or corrected bugs) to the merge-commit-message. This can be taken from the briefly-list-the-changes above (best case) or the separate commit messages (worst case).

Closes #916

[mknaranja]

@sudiphzi @MariamaJ This merge request does not address the issue at all. It is rather reformatting of the original code. Please create corresponding issues and assign pull requests correctly. Please also describe the (necessary) changes.

If development was completed, users have to check the corresponding checkboxes above before review.

Generally: We have an automatted formatter. Formatting by hand should by avoided to not have changes indicated in the pull request were no changes happened.

Furthermore, from clean quality control view, a developer should not be reviewer at the same time (as here).

Thank you.

[MariamaJ]

@mknaranja, I have transferred the task to @sudiphzi and then was assigned to reviewer. But, I will now implement the changes requested and ask you to be the reviewer if that's alright.

[MariamaJ]

And true, this PR now focuses on refactoring the code to ingest it on the LOKI database. I have renamed the issue and PR accordingly.

[patricklnz]

Thanks! I like the general idea of the PR. Only some consistency changes have to be made. If anything seems unclear feel free to contact me :).

[patricklnz]

Looks good!