java 21 updates and license inventory#181
Merged
Merged
Conversation
|
You are seeing this message because GitHub Code Scanning has recently been set up for this repository, or this pull request contains the workflow file for the Code Scanning tool. What Enabling Code Scanning Means:
For more information about GitHub Code Scanning, check out the documentation. |
denis-yuen
changed the title
denis-yuen
commented
Jun 9, 2026
|
|
||
| - name: Autobuild | ||
| uses: github/codeql-action/autobuild@v2 | ||
| uses: github/codeql-action/autobuild@v4 |
Member
Author
There was a problem hiding this comment.
code ql was only running on the javascript stuff
| @Test | ||
| public void successfulResponseOfComplexWorkflow() throws IOException { | ||
| LanguageParsingRequest request = new LanguageParsingRequest(); | ||
| request.setBranch("dockstore-test"); |
Member
Author
There was a problem hiding this comment.
The old workflow fails when being checked by the newer womtool
| <groupId>com.github.spotbugs</groupId> | ||
| <artifactId>spotbugs-maven-plugin</artifactId> | ||
| <version>4.0.4</version> | ||
| <version>4.9.8.3</version> |
Member
Author
There was a problem hiding this comment.
These changes needed mostly for Java 21 compatibility
| @@ -0,0 +1,193 @@ | |||
|
|
|||
| Lists of 191 third-party dependencies. | |||
Member
Author
There was a problem hiding this comment.
This is for the security spreadsheet
denis-yuen
requested review from
a team,
nolunwa-ucsc and
svonworl
and removed request for
a team
svonworl
approved these changes
Jun 11, 2026
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Description
Adding a license and third party inventory file, generated from the Java build
Getting it working required an update to Java 21 which had to be done eventually since the runtime depreciation would occur June 30, 2027. That dragged in issues with Scala, spotbugs, etc.
Nextflow lambda not updated or included since it is not in use yet
I actually recommend deploying after substantial testing
i.e. may be a post 1.20 thing
Issue
https://ucsc-cgl.atlassian.net/browse/SEAB-7611 (click-through comments for how this looks in the spreadsheet)
Security
None, should be substantial upgrade dependency-wise
Please make sure that you've checked the following before submitting your pull request. Thanks!