Add TCGA expanded TPM boxplots

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Description

Added TCGA expanded TPM boxplots.

Resolved #72.

Notes for reviewers:

• 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 tcga-tpm-boxplot branch, i.e., version v0.6.0-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 tcga-tpm-boxplot branch needs to be evaluated locally.

Type of change

Changed

• Changed the interface of get_gene_tpm_tbl function:
  • Added a required parameter tcga_sample_group.
• Changed the interface of get_tpm_endpoint_tbl function:
  • Added a required parameter tcga_sample_group.
• Updated db/db.Dockerfile PostgreSQL docker image to version 12.13.

Added

• Added OpenPedCan-analysis TCGA TPM data to the database.
• Added the following TCGA expanded TPM boxplot and summary table endpoints:
  • /tpm/gene-disease-tcga/plot
  • /tpm/gene-disease-tcga/json
  • /tpm/gene-disease-tcga-gtex/plot
  • /tpm/gene-disease-tcga-gtex/json
  • /tpm/gene-all-cancer-tcga/plot
  • /tpm/gene-all-cancer-tcga/json
  • /tpm/gene-all-cancer-tcga-gtex/plot
  • /tpm/gene-all-cancer-tcga-gtex/json
• Added tests in tests/r_test_scripts/test_endpoint_http.R to test the added TCGA expanded TPM boxplot and summary table endpoints.

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
✔ | 885       | tests/r_test_scripts/test_endpoint_http.R [3180.9 s]

══ Results ═══════════════════════════════
Duration: 3180.9 s

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 885 ]
Done running run_tests.sh

For more details about testing environment, options, and resources, see 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
• [NA] New and existing unit tests pass locally with my changes
• [x] 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 😉

cc @chinwallaa

[logstar]

@kelseykeith - Thank you very much for reviewing the PR. I will merge this PR to the main branch soon, which would also deploy it to the QA site.