Bump webpack-dev-server from 5.1.0 to 5.2.1 in /gemma-web/src/main/webapp #1476
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Always write the ExternalDatabase update first so that it will not be ignored if the write to disk or admin email fails. Do not rethrow an exception when writing the update status to disk fails.
In tests, this ensures that the database is always initialized before any test that uses the SessionFactory runs.
filter categories based on their presence in the BioMaterial factorValues
…yPowerToolsProbesetSummarize Improve usages of the Process API: - use waitFor() with a timeout instead of Thread.sleep() - replace GenericStreamConsumer and GenericParsingConsumer with ProcessBuider and appropriate stream redirections - always specify arguments as an array of strings. - always pipe the standard error and include it in the exception message Replace File with Path. Eliminate native BLAT. It is unused and if we ever want to add it back, it will have to be updated anyway.
Make it clear that a EE set can only contain other EEs. With this change, it becomes impossible to query anything else than an ExpressionExperiment in ExpressionExperimentManipulatingCLI. Perform according simplifications, mainly in the CLI module.
keep default indentation for diff exp trees
Relocate ShellUtils from gemma-cli in gemma-core so that we can use it for quoting and printing command lines.
…ctor Rename ACL config attributes for filtering vectors and composite sequences Make it clearer what is being filtered from the name of the annotation.
…files Mark the test with @DirtiesContext since it alters the FASTQ headers directory. Make some of the implementation methods static so that they are easier to test.
Move utilities to generate a design matrix in DiffExAnalyzerUtils. Move utilities to determine baselines in BaselineSelection. Refactor SearchSettings such that the Highlighter and the issue reporter are passed alongside the settings. Relocate sparse data structures in ubic.gemma.model.util.
Add various typed signatures to prevent misuse. Don't store results and skipDataVectors as an internal state. Drop the overall SlowTest annotation, it's not slow at all!
Cleanup BioAssayValueObject and switch other outlier flags to native booleans.
Do no allow custom MEX to be written to the dataFiles directory. Do not create lock files when writing MEX to a custom directory. Honor the EE last updated when force-writing MEX and tabular single-cell data to the standard location.
Fix autoFlush not being passed in some cases. Fix CELL_IDS format not being written to file. Add more destination options for writing single-cell metadata file.
Tag hotfix
Bumps [webpack-dev-server](https://github.com/webpack/webpack-dev-server) from 5.1.0 to 5.2.1. - [Release notes](https://github.com/webpack/webpack-dev-server/releases) - [Changelog](https://github.com/webpack/webpack-dev-server/blob/master/CHANGELOG.md) - [Commits](webpack/webpack-dev-server@v5.1.0...v5.2.1) --- updated-dependencies: - dependency-name: webpack-dev-server dependency-version: 5.2.1 dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com>
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Bumps webpack-dev-server from 5.1.0 to 5.2.1.
Release notes
Sourced from webpack-dev-server's releases.
Changelog
Sourced from webpack-dev-server's changelog.
Commits
0d22a08chore(release): 5.2.16045b1echore(deps): update (#5444)ffd0b86fix: take the first network found instead of the last one, this restores the ...9ea7b08ci: update dependency-review-action (#5442)5c9378bMerge commit from forkd2575adMerge commit from fork8c1abc9fix: prevent overlay for errors caught by React error boundaries (#5431)5a39c70ci: update codecov/codecov-action to v5 (#5406)55220a8chore(deps-dev): bump the dependencies group across 1 directory with 4 update...09f6f8echore(deps): bump the dependencies group across 1 directory with 2 updates (#...Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting
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