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Add other TRS entry types to getToolId so other entry types can be aggregated #6028

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Merged
merged 2 commits into from
Oct 28, 2024
Merged

Add other TRS entry types to getToolId so other entry types can be aggregated #6028

merged 2 commits into from
Oct 28, 2024

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kathy-t
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@kathy-t kathy-t commented Oct 25, 2024 •
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Description
Another follow-up to https://ucsc-cgl.atlassian.net/browse/SEAB-6467 and #6022, this time it's failing on the metrics-aggregator side when aggregating notebooks because it's calling a dockstore-common function that doesn't take into account other TRS entry types here.

This PR is set to the release branch...if it's too late, I can put it to develop. It just means that aggregation of other entry types that are not tools and workflows would fail from the metrics-aggregator side. We're only ingesting metrics for workflows from Terra right now, so maybe that's okay.

Review Instructions
See dockstore/dockstore-support#500

Issue
https://ucsc-cgl.atlassian.net/browse/SEAB-6467

Security and Privacy

If there are any concerns that require extra attention from the security team, highlight them here and check the box when complete.

  • Security and Privacy assessed

e.g. Does this change...

  • Any user data we collect, or data location?
  • Access control, authentication or authorization?
  • Encryption features?

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.

@kathy-t kathy-t self-assigned this Oct 25, 2024
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codecov bot commented Oct 25, 2024 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 74.45%. Comparing base (c845950) to head (2a94302).

Additional details and impacted files 
@@                     Coverage Diff                     @@
##             release/1.16.0-beta.3    #6028      +/-   ##
===========================================================
+ Coverage                    74.43%   74.45%   +0.01%     
- Complexity                    5493     5495       +2     
===========================================================
  Files                          381      381              
  Lines                        19788    19786       -2     
  Branches                      2044     2043       -1     
===========================================================
+ Hits                         14730    14731       +1     
+ Misses                        4076     4075       -1     
+ Partials                       982      980       -2
Flag Coverage Δ
bitbuckettests 26.66% <0.00%> (+<0.01%) ⬆️
hoverflytests 27.94% <0.00%> (+<0.01%) ⬆️
integrationtests 56.70% <0.00%> (+<0.01%) ⬆️
languageparsingtests 11.05% <0.00%> (+<0.01%) ⬆️
localstacktests 21.57% <100.00%> (+<0.01%) ⬆️
toolintegrationtests 30.03% <0.00%> (+<0.01%) ⬆️
unit-tests_and_non-confidential-tests 25.79% <100.00%> (+<0.01%) ⬆️
workflowintegrationtests 38.05% <0.00%> (+<0.01%) ⬆️

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Quality Gate Passed Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
100.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

coverbeck
coverbeck approved these changes Oct 25, 2024
View reviewed changes
dockstore-common/generated/src/main/resources/pom.xml
@@ -19,7 +19,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>io.dockstore</groupId>
<artifactId>dockstore-common</artifactId>
<version>1.16.0-beta.6</version>
<version>1.16.0-SNAPSHOT</version>
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Hmm, not sure this should be changed. Maybe it should though, I'm a little unclear.

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I think it should be. In the wiki, it says to reset the generated files after pushing the new tag:

reset generated files if the branch you're working on is going to be merged (like in hubflow release finish)
./mvnw clean install -DskipTests

The build also fails if I don't update the generated files

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Yeah, to confirm, I think tagged builds will get a "real" version.
All other generated pom files will get a snapshot version.
That said, for this change to show up in a "normal" PR, I think that means a step was skipped somewhere

denis-yuen
denis-yuen approved these changes Oct 28, 2024
View reviewed changes
dockstore-common/generated/src/main/resources/pom.xml
@@ -19,7 +19,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>io.dockstore</groupId>
<artifactId>dockstore-common</artifactId>
<version>1.16.0-beta.6</version>
<version>1.16.0-SNAPSHOT</version>
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Yeah, to confirm, I think tagged builds will get a "real" version.
All other generated pom files will get a snapshot version.
That said, for this change to show up in a "normal" PR, I think that means a step was skipped somewhere

@kathy-t kathy-t merged commit 818443d into release/1.16.0-beta.3 Oct 28, 2024
18 of 19 checks passed
@kathy-t kathy-t deleted the seab-6467/trs-id-fix branch October 28, 2024 18:02
@kathy-t kathy-t mentioned this pull request Oct 28, 2024
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@coverbeck coverbeck coverbeck approved these changes

@denis-yuen denis-yuen denis-yuen approved these changes

@svonworl svonworl svonworl approved these changes

@hyunnaye hyunnaye Awaiting requested review from hyunnaye

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@kathy-t @coverbeck @denis-yuen @svonworl
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