Update API database using OpenPedCan-analysis v11 TPM data release

[logstar]

Description

Updated API database using OpenPedCan-analysis v11 TPM data release.

Resolved #76.

Notes for reviewers:

• This PR intends to merge v11-tpm branch to v10-dge branch. Therefore, it is recommended to review https://github.com/PediatricOpenTargets/OpenPedCan-api/pull/65 before reviewing this PR, because https://github.com/PediatricOpenTargets/OpenPedCan-api/pull/65 intends to merge v10-dge branch to main branch. After https://github.com/PediatricOpenTargets/OpenPedCan-api/pull/65 is approved and merged, the base branch of this PR can be changed to main branch.
• Most of the changed files are test output files under tests/results, tests/http_response_output_files, and tests/plots. The test output files only need to be reviewed by their content, e.g., whether a plot looks as expected or not.
• The v11-tpm branch, i.e., version v0.5.3-beta, has been deployed to the DEV site, https://openpedcan-api-dev.d3b.io/__docs__/. If the DEV site has been deployed with another branch at a later point, the v11-tpm branch needs to be evaluated locally.

Type of change

Non-breaking change. Database update.

How Has This Been Tested?

Terminal returns for testing DEV host:

$ API_HOST=dev ./tests/run_tests.sh
API base URL: https://openpedcan-api-dev.d3b.io
✔ |  OK F W S | Context
✔ | 453       | tests/r_test_scripts/test_endpoint_http.R [1757.5 s]

══ Results ════════════════════════
Duration: 1757.5 s

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 453 ]

For more details about testing environment, options, and resources, see https://github.com/PediatricOpenTargets/OpenPedCan-api/blob/98632b538a0416fe0f27d0ad8ebd117d2969466c/README.md.

Checklist

• [x] My code follows the style guidelines of this project
• [x] I have performed a self-review of my own code
• [x] I have commented my code, particularly in hard-to-understand areas
• [x] I have made corresponding changes to the documentation
• [x] My changes generate no new warnings
• [x] I have added tests that prove my fix is effective or that my feature works
• [x] New and existing unit tests pass locally with my changes
• [NA] Any dependent changes have been merged and published in downstream modules
• [x] I have checked my code and corrected any misspellings
• [ ] I have emojis in my PR and commits 😉

[kelseykeith]

Code and Results Review

This looks good!

• API code runs correctly when I reconstruct the database and run the test server independently
• Code is pulling from the v11 data.
• Results from the API call match data in OpenPedCan-analysis tables.
• Both tables and plots subset samples correctly based on the subgroup asked for.

Since this PR was for updated TPMs and v10 differential gene expression table is still being used, I did not review the differential gene expression result tables. Did look at the plots however and they looked good.

[logstar]

@kelseykeith - Thank you for reviewing the TPM boxplot PRs. I will merge this PR soon.