Update production instance to v0.4.0-beta

[logstar]

The OpenPedCan-api production instance currently runs OpenPedCan-api v0.3.2-beta. The production instance is used by Molecular Targets Platform (MTP) to show TPM boxplots and tables.

The production instance needs to be updated to OpenPedCan-api v0.4.0-beta, in order to use colorblind-friendly colors in boxplots.

The production instance update will take the following steps:

• MTP will be updated to send API request URLs with &includeTumorDesc=primaryOnly appended. This will be implemented, tested, and deployed by @jonkiky. The includeTumorDesc parameter is added in v0.4.0-beta as a required one for all TPM boxplots and tables, which is described in more details in v0.4.0-beta README.md. The extra &includeTumorDesc=primaryOnly in URLs are also compatible with the current v0.3.2-beta version, so MTP will still be functioning properly before the update of OpenPedCan-api production instance to v0.4.0-beta.
• Update production instance database using v0.4.0-beta database dump.
• Update production instance configuration to use the updated database.
• Make a v0.4.0-beta release using the current main branch.
• Update production instance HTTP server using the R HTTP server in v0.4.0-beta release.

cc @chinwallaa @taylordm

[logstar]

The production API and database, https://openpedcan-api-qa.d3b.io/__docs__/, have been updated to v0.4.0-beta, with great help from @blackdenc .

@jonkiky also has updated MTP QA site, https://ppdc-otp-qa.bento-tools.org, to use the updated production API v0.4.0-beta. Following are example QA MTP URLs:

• https://ppdc-otp-qa.bento-tools.org/target/ENSG00000133703
• https://ppdc-otp-qa.bento-tools.org/evidence/ENSG00000134460/EFO_0000621

If there is any question or suggestion, feel free to let me know.

cc @taylordm @chinwallaa @afarrel