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@denis-yuen denis-yuen commented Sep 27, 2024

Description
Add dockstore_absolute_path to files endpoint and descriptors
Add dockstore_self_url to descriptors

Review Instructions
Load up a test DB and try the following urls

http://hostname:4200/api/ga4gh/trs/v2/tools/%23workflow%2Fgithub.com%2Fbroadinstitute%2Fwarp%2FOptimus/versions/develop/WDL/files will have list the files and have dockstore_absolute_path for each file in the list

http://hostname:4200/api/ga4gh/trs/v2/tools/%23workflow%2Fgithub.com%2Fbroadinstitute%2Fwarp%2FOptimus/versions/develop/WDL/descriptor will show the json for one file and have both dockstore_absolute_path and dockstore_self_url

Issue
https://ucsc-cgl.atlassian.net/browse/SEAB-6699

Security and Privacy

None

  • Security and Privacy assessed

Please make sure that you've checked the following before submitting your pull request. Thanks!

  • Check that you pass the basic style checks and unit tests by running mvn clean install
  • Ensure that the PR targets the correct branch. Check the milestone or fix version of the ticket.
  • Follow the existing JPA patterns for queries, using named parameters, to avoid SQL injection
  • If you are changing dependencies, check the Snyk status check or the dashboard to ensure you are not introducing new high/critical vulnerabilities
  • Assume that inputs to the API can be malicious, and sanitize and/or check for Denial of Service type values, e.g., massive sizes
  • Do not serve user-uploaded binary images through the Dockstore API
  • Ensure that endpoints that only allow privileged access enforce that with the @RolesAllowed annotation
  • Do not create cookies, although this may change in the future
  • If this PR is for a user-facing feature, create and link a documentation ticket for this feature (usually in the same milestone as the linked issue). Style points if you create a documentation PR directly and link that instead.

@denis-yuen denis-yuen self-assigned this Sep 27, 2024
@denis-yuen denis-yuen changed the title WIP WIP trs extensions Sep 30, 2024
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codecov bot commented Sep 30, 2024

Codecov Report

Attention: Patch coverage is 90.90909% with 2 lines in your changes missing coverage. Please review.

Project coverage is 74.47%. Comparing base (5fed68d) to head (fed6bcf).
Report is 3 commits behind head on develop.

Files with missing lines Patch % Lines
.../java/io/openapi/api/impl/ToolsApiServiceImpl.java 88.88% 0 Missing and 2 partials ⚠️
Additional details and impacted files
@@              Coverage Diff              @@
##             develop    #6005      +/-   ##
=============================================
+ Coverage      74.45%   74.47%   +0.02%     
- Complexity      5495     5497       +2     
=============================================
  Files            381      381              
  Lines          19786    19802      +16     
  Branches        2043     2044       +1     
=============================================
+ Hits           14731    14747      +16     
  Misses          4075     4075              
  Partials         980      980              
Flag Coverage Δ
bitbuckettests 26.68% <45.45%> (+0.02%) ⬆️
hoverflytests 27.92% <0.00%> (-0.03%) ⬇️
integrationtests 56.74% <90.90%> (+0.03%) ⬆️
languageparsingtests 11.07% <36.36%> (+0.02%) ⬆️
localstacktests 21.55% <0.00%> (-0.02%) ⬇️
toolintegrationtests 30.06% <59.09%> (+0.03%) ⬆️
unit-tests_and_non-confidential-tests 25.79% <22.72%> (+<0.01%) ⬆️
workflowintegrationtests 38.09% <72.72%> (+0.03%) ⬆️

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@denis-yuen denis-yuen changed the title WIP trs extensions trs extensions to facilitate toil development Oct 31, 2024
@denis-yuen
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denis-yuen commented Oct 31, 2024

Note will need to make a tag on our fork of the TRS repository on PR approval and update PR to match

@denis-yuen denis-yuen requested review from a team, coverbeck, david4096, hyunnaye and kathy-t and removed request for a team October 31, 2024 20:57
@denis-yuen denis-yuen requested a review from coverbeck November 4, 2024 18:23
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sonarqubecloud bot commented Nov 6, 2024

@denis-yuen denis-yuen merged commit d8e12f9 into develop Nov 6, 2024
7 checks passed
@denis-yuen denis-yuen deleted the feature/extra_trs_fields branch November 6, 2024 20:48
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5 participants