Code changes and documentation for end-to-end demo

jeff-cohere commented 6 months ago

This PR has everything that was needed to get the DTS prototype to successfully demonstrate a JGI Data Portal -> KBase file transfer, including the generation and transmittal of a manifest.

In particular:

error handling and logging were greatly improved in order to debug lots of configuration and permissions issues
materials for a static documentation website now live in the docs/ folder, and a GitHub Action auto-publishes docs for merged PRs
DTS now performs Globus re-authentication flows where needed to access files on Guest Collections, per Globus's REST API recommendations
a Dockerfile and deployment instructions were created that allow DTS to be deployed within Spin (and presumably other Docker/Kubernetes environments)

Closes #31

github-actions[bot] commented 6 months ago

PR Preview Action v1.4.7 :---: :rocket: Deployed preview to https://kbase.github.io/dts/pr-preview/pr-52/ on branch gh-pages at 2024-03-07 19:07 UTC

jeff-cohere commented 6 months ago

Sorry about the large PR, AJ. :-) A lot of it is documentation, though, so maybe that's positive? :-)

codecov[bot] commented 6 months ago

Codecov Report

Attention: Patch coverage is 42.89773% with 201 lines in your changes are missing coverage. Please review.

Project coverage is 56.96%. Comparing base (1e2d60d) to head (fe4d930).

Files	Patch %	Lines
tasks/tasks.go	38.13%	61 Missing and 12 partials :warning:
endpoints/globus/endpoint.go	48.83%	59 Missing and 7 partials :warning:
main.go	0.00%	25 Missing :warning:
services/prototype.go	33.33%	17 Missing and 1 partial :warning:
databases/jdp/jamo.go	56.75%	12 Missing and 4 partials :warning:
databases/kbase/database.go	0.00%	2 Missing :warning:
endpoints/local/endpoint.go	0.00%	1 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #52 +/- ## ========================================== - Coverage 61.44% 56.96% -4.49% ========================================== Files 12 16 +4 Lines 2023 2384 +361 ========================================== + Hits 1243 1358 +115 - Misses 604 845 +241 - Partials 176 181 +5 ```

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

kbase / dts

Code changes and documentation for end-to-end demo #52

Codecov Report