Add regression tests, along with necessary dependency and deployment configuration

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#29 · Created  · Last updated

Merged pull request

Merged in regression-tests (pull request #29)

  • 52a2ea7
  • Author:
  • Closed by:
  • 2021-11-24

Description

This PR adds regression testing to the integration test system. Currently this PR targets the integration-tests branch, but it should not be merged until after PR #28.

Regression testing is configured by changing a dependency version in the POM which determines the reference data artifact (stored in the encyclopedia-maven-repo) that's compared to the results of the current build.

Results of the build (when integration/regression tests are enabled by -DskipITs=false) are packaged and deployed to the maven repository from builds that execute the deploy goal; currently this is only done automatically for tagged versions. When results change due to development of the program it's possible to deploy results from any commit using the custom: deploy-maven-artifacts pipeline. Care must be taken when deploying updated reference data artifacts and/or when changing the reference data dependency version.

Documentation is also available on the repository wiki: https://bitbucket.org/searleb/encyclopedia/wiki/Bitbucket_Pipelines

Commits in this PR:

  • Basic regression test to compare peptides from current version to cached version

  • When copy-and-paste goes wrong

  • Added metadata checks for pi0 to regression tests

  • Clean up checks for peptide matches. Relax RT requirement.

  • Pull report generation into setUp method

  • Added failure messages to assertions

  • Improve RT range overlap assertion.

  • Move jobData setUp to setUp

  • tempReport is now setup and teardown per report

  • Pull proportion constants out.

  • Return false for non-overlapping retention times.

  • Successfully filter out non Chromatogram entries

  • Clean up and initial changes towards deploying reference data.

  • Implement copying of files to target/ directory in preparation for packaging and deployment.

  • Switch to passing around resource URLs as strings instead of LibraryFile instances and begin fleshing out copying of combined results for deployment.

  • Update remaining test methods for deploying combined results.

  • Improve debugging when issues arise. Copy individual xcordia results to reference data folder.

  • Add profile and assembly descriptor for building and attaching a reference-data JAR with the results from IT/regression test searches.

  • Update profile to add reference-data dependency when running ITs.

  • Force installation of Percolator-required library before running Bitbucket builds.

  • Remove sudo from installation command.

  • Add deployment repository configuration to allow deploying build artifacts and (importantly) regression reference data.

  • Ignore test failures when manually triggering deployment to Maven.

 

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