lib: improve repeat downloader by updating versions from config file,… #366
task.yml
on: push
build
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Build Java app
2m 37s
deploy-docker
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Push Docker image
Annotations
2 errors and 2 warnings
RepeatsBuilderTest.testParse:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/builders/RepeatsBuilderTest.java#L53
expected: <[{"id": null, "chromosome": "1", "start": 10758, "end": 10997, "period": 76, "consensusSize": 76, "copyNumber": 3.2, "percentageMatch": 0.95, "score": 434.0, "sequence": "GGCGCAGGCGCAGAGAGGCGCGCCGCGCCGGCGCAGGCGCAGAGACACATGCTAGCGCGTCCAGGGGTGGAGGCGT", "source": "trf"}, {"id": "7822", "chromosome": "1", "start": 10001, "end": 20818, "period": null, "consensusSize": null, "copyNumber": 2.0, "percentageMatch": 0.983054, "score": null, "sequence": null, "source": "genomicSuperDup"}, {"id": null, "chromosome": "1", "start": 10628, "end": 10800, "period": 29, "consensusSize": 29, "copyNumber": 6.0, "percentageMatch": 1.0, "score": 346.0, "sequence": "AGGCGCGCCGCGCCGGCGCAGGCGCAGAG", "source": "trf"}, {"id": "chr1.4", "chromosome": "1", "start": 10628, "end": 10802, "period": null, "consensusSize": null, "copyNumber": null, "percentageMatch": null, "score": null, "sequence": null, "source": "windowMasker"}, {"id": "1", "chromosome": "1", "start": 10170, "end": 37148, "period": null, "consensusSize": null, "copyNumber": 2.0, "percentageMatch": 0.989999, "score": null, "sequence": null, "source": "genomicSuperDup"}, {"id": null, "chromosome": "1", "start": 11226, "end": 11447, "period": 117, "consensusSize": 121, "copyNumber": 1.9, "percentageMatch": 0.8, "score": 273.0, "sequence": "CGCCCCCTGCTGGCGACTAGGGCAACTGCAGGGTCCTCTTGCTCAAGGTGAGTGGCAGACGCCCACCTGCTGGCAGCCGGGGACACTGCAGGGCCCTCTTGCTTACTGTATAGTGGTGGCA", "source": "trf"}, {"id": "11764", "chromosome": "1", "start": 10001, "end": 87112, "period": null, "consensusSize": null, "copyNumber": 2.0, "percentageMatch": 0.992918, "score": null, "sequence": null, "source": "genomicSuperDup"}, {"id": "chr1.1", "chromosome": "1", "start": 10001, "end": 10470, "period": null, "consensusSize": null, "copyNumber": null, "percentageMatch": null, "score": null, "sequence": null, "source": "windowMasker"}, {"id": null, "chromosome": "1", "start": 10001, "end": 10468, "period": 6, "consensusSize": 6, "copyNumber": 77.2, "percentageMatch": 0.95, "score": 789.0, "sequence": "TAACCC", "source": "trf"}, {"id": "3851", "chromosome": "1", "start": 10001, "end": 19844, "period": null, "consensusSize": null, "copyNumber": 2.0, "percentageMatch": 0.982898, "score": null, "sequence": null, "source": "genomicSuperDup"}, {"id": "chr1.3", "chromosome": "1", "start": 10587, "end": 10610, "period": null, "consensusSize": null, "copyNumber": null, "percentageMatch": null, "score": null, "sequence": null, "source": "windowMasker"}, {"id": "chr1.2", "chromosome": "1", "start": 10560, "end": 10582, "period": null, "consensusSize": null, "copyNumber": null, "percentageMatch": null, "score": null, "sequence": null, "source": "windowMasker"}]> but was: <[{"id": null, "chromosome": "1", "start": 10758, "end": 10997, "period": 76, "consensusSize": 76, "copyNumber": 3.2, "percentageMatch": 0.95, "score": 434.0, "sequence": "GGCGCAGGCGCAGAGAGGCGCGCCGCGCCGGCGCAGGCGCAGAGACACATGCTAGCGCGTCCAGGGGTGGAGGCGT", "source": "trf"}, {"id": "7822", "chromosome": "1", "start": 10001, "end": 20818, "period": null, "consensusSize": null, "copyNumber": 2.0, "percentageMatch": 0.983054, "score": null, "sequence": null, "source": "genomicSuperDup"}, {"id": null, "chromosome": "1", "start": 10628, "end": 10800, "period": 29, "consensusSize": 29, "copyNumber": 6.0, "percentageMatch": 1.0, "score": 346.0, "sequence": "AGGCGCGCCGCGCCGGCGCAGGCGCAGAG", "source": "trf"}, {"id": "1", "chromosome": "1", "start": 10170, "end": 37148, "period": null, "consensusSize": null, "copyNumber": 2.0, "percentageMatch": 0.989999, "score": null, "sequence": null, "source": "genomicSuperDup"}, {"id": null, "chromosome": "1", "start": 11226, "end": 11447, "period": 117, "consensusSize": 121, "copyNumber": 1.9, "percentageMatch": 0.8, "score": 273.0, "sequence": "CGCCCCCTGCTGGCGACTAGGGCAACTGCAGGGTCCTCTTGCTCAAGGTGAGTGGCAGACGCCCACCTGCTGGCAGCCGGGGACACTGCAGGGCCCTCTTGCTTACTGTATAGTGGTGGCA", "source": "trf"}, {"id": "11764", "chromosome": "1", "start": 10001, "end": 87112, "period": null, "consensusSize": null, "copyNumber": 2.0, "percentageMatch": 0.992918, "score": null, "sequence": null, "source": "genomicSuperDup"}, {"id": null, "chromosome": "1", "start": 10001, "end": 10468, "period": 6, "consensusSize": 6, "copyNumber": 77.2, "percentageMatch": 0.95, "score": 789.0, "sequence": "TAACCC", "source": "trf"}, {"id": "3851", "chromosome": "1", "start": 10001, "end": 19844, "period": null, "consensusSize": null, "copyNumber": 2.0, "percentageMatch": 0.982898, "score": null, "sequence": null, "source": "genomicSuperDup"}]>
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test / Test and push Sonar analysis
There were 1 failed tests
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build / Build Java app
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/setup-java@v3, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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test / Test and push Sonar analysis
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/setup-java@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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build-folder
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232 MB |
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