lib: update regulation download manager, and the configuration file, … #383
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36 errors and 1 warning
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CellBaseConfigurationTest.org.opencb.cellbase.core.config.CellBaseConfigurationTest:
cellbase-core/src/test/java/org/opencb/cellbase/core/config/CellBaseConfigurationTest.java#L25
Configuration file could not be parsed: Unrecognized field "mirbaseReadme" (class org.opencb.cellbase.core.config.DownloadProperties), not marked as ignorable (53 known properties: "miRTarBase", "genomicSuperDups", "revel", "hpoObo", "gwasCatalog", "refSeqFasta", "gerp", "uniprotRelNotes", "lrg", "simpleRepeats", "maneSelect", "windowMasker", "phylop", "refSeqProteinFasta", "cancerHotspot", "disgenet", "docm", "doidObo", "dbsnp", "geneUniprotXref", "disgenetReadme", "refSeqCdna", "intact", "dgidb", "refSeq", "clinvarSummary", "interpro", "dgv", "uniprot", "phastCons", "ensembl", "conservation", "cadd", "ensemblGenomes", "iarctp53", "mondoObo", "hpo", "reactome", "clinvarEfoTerms", "hgnc", "clinvarVariationAllele", "clinvarVariation", "geneExpressionAtlas", "interproRelNotes", "mirbase", "targetScan", "goAnnotation", "docmVersion", "goObo", "pharmGKB", "clinvar", "gnomadConstraints", "pubmed"])
at [Source: (BufferedInputStream); line: 66, column: 5] (through reference chain: org.opencb.cellbase.core.config.CellBaseConfiguration["download"]->org.opencb.cellbase.core.config.DownloadProperties["mirbaseReadme"])
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SpeciesUtilsTest.testGetDefaultAssembly:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/SpeciesUtilsTest.java#L58
java.lang.NullPointerException
at org.opencb.cellbase.lib.SpeciesUtilsTest.testGetDefaultAssembly(SpeciesUtilsTest.java:58)
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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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CellBaseNormalizerSequenceAdaptorTest.testGenomicSequenceQueryStartOutOfLeftBound:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/CellBaseNormalizerSequenceAdaptorTest.java#L34
java.lang.NullPointerException
at org.opencb.cellbase.lib.impl.core.CellBaseNormalizerSequenceAdaptorTest.<init>(CellBaseNormalizerSequenceAdaptorTest.java:34)
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CellBaseNormalizerSequenceAdaptorTest.testGenomicSequenceChromosomeNotPresent:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/CellBaseNormalizerSequenceAdaptorTest.java#L34
java.lang.NullPointerException
at org.opencb.cellbase.lib.impl.core.CellBaseNormalizerSequenceAdaptorTest.<init>(CellBaseNormalizerSequenceAdaptorTest.java:34)
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CellBaseNormalizerSequenceAdaptorTest.testGenomicSequenceQueryEndOutOfRightBound:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/CellBaseNormalizerSequenceAdaptorTest.java#L34
java.lang.NullPointerException
at org.opencb.cellbase.lib.impl.core.CellBaseNormalizerSequenceAdaptorTest.<init>(CellBaseNormalizerSequenceAdaptorTest.java:34)
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CellBaseNormalizerSequenceAdaptorTest.testGenomicSequenceQueryStartEndOutOfRightBound:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/CellBaseNormalizerSequenceAdaptorTest.java#L34
java.lang.NullPointerException
at org.opencb.cellbase.lib.impl.core.CellBaseNormalizerSequenceAdaptorTest.<init>(CellBaseNormalizerSequenceAdaptorTest.java:34)
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ClinicalMongoDBAdaptorTest.parseQueryTest:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/ClinicalMongoDBAdaptorTest.java#L64
java.lang.NullPointerException
at org.opencb.cellbase.lib.impl.core.ClinicalMongoDBAdaptorTest.parseQueryTest(ClinicalMongoDBAdaptorTest.java:64)
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GeneMongoDBAdaptorTest.testQuery:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/GeneMongoDBAdaptorTest.java#L70
java.lang.NullPointerException
at org.opencb.cellbase.lib.impl.core.GeneMongoDBAdaptorTest.testQuery(GeneMongoDBAdaptorTest.java:70)
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GeneMongoDBAdaptorTest.testQueryId:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/GeneMongoDBAdaptorTest.java#L51
java.lang.NullPointerException
at org.opencb.cellbase.lib.impl.core.GeneMongoDBAdaptorTest.testQueryId(GeneMongoDBAdaptorTest.java:51)
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GeneMongoDBAdaptorTest.testConstraints:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/GeneMongoDBAdaptorTest.java#L124
java.lang.NullPointerException
at org.opencb.cellbase.lib.impl.core.GeneMongoDBAdaptorTest.testConstraints(GeneMongoDBAdaptorTest.java:124)
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GenomeMongoDBAdaptorTest.org.opencb.cellbase.lib.impl.core.GenomeMongoDBAdaptorTest:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/GenomeMongoDBAdaptorTest.java#L50
java.lang.NullPointerException
at org.opencb.cellbase.lib.impl.core.GenomeMongoDBAdaptorTest.<init>(GenomeMongoDBAdaptorTest.java:50)
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MongoDBAdaptorFactoryTest.org.opencb.cellbase.lib.impl.core.MongoDBAdaptorFactoryTest:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/MongoDBAdaptorFactoryTest.java#L36
java.lang.NullPointerException
at org.opencb.cellbase.lib.impl.core.MongoDBAdaptorFactoryTest.<init>(MongoDBAdaptorFactoryTest.java:36)
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PharmacogenomicsMongoDBAdaptorTest.testQuery:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/PharmacogenomicsMongoDBAdaptorTest.java#L73
java.lang.NullPointerException
at org.opencb.cellbase.lib.impl.core.PharmacogenomicsMongoDBAdaptorTest.testQuery(PharmacogenomicsMongoDBAdaptorTest.java:73)
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PharmacogenomicsMongoDBAdaptorTest.testQueryName:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/PharmacogenomicsMongoDBAdaptorTest.java#L55
java.lang.NullPointerException
at org.opencb.cellbase.lib.impl.core.PharmacogenomicsMongoDBAdaptorTest.testQueryName(PharmacogenomicsMongoDBAdaptorTest.java:55)
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ProteinMongoDBAdaptorTest.testQuery:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/ProteinMongoDBAdaptorTest.java#L45
java.lang.NullPointerException
at org.opencb.cellbase.lib.impl.core.ProteinMongoDBAdaptorTest.testQuery(ProteinMongoDBAdaptorTest.java:45)
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TranscriptMongoDBAdaptorTest.testQuery:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/TranscriptMongoDBAdaptorTest.java#L44
java.lang.NullPointerException
at org.opencb.cellbase.lib.impl.core.TranscriptMongoDBAdaptorTest.testQuery(TranscriptMongoDBAdaptorTest.java:44)
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VariantAnnotationCalculatorTest.org.opencb.cellbase.lib.impl.core.VariantAnnotationCalculatorTest:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/VariantAnnotationCalculatorTest.java#L54
java.lang.NullPointerException
at org.opencb.cellbase.lib.impl.core.VariantAnnotationCalculatorTest.<init>(VariantAnnotationCalculatorTest.java:54)
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VariantMongoDBAdaptorTest.testGet:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/VariantMongoDBAdaptorTest.java#L61
java.lang.NullPointerException
at org.opencb.cellbase.lib.impl.core.VariantMongoDBAdaptorTest.<init>(VariantMongoDBAdaptorTest.java:61)
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VariantMongoDBAdaptorTest.testGetFunctionalScoreVariant:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/VariantMongoDBAdaptorTest.java#L61
java.lang.NullPointerException
at org.opencb.cellbase.lib.impl.core.VariantMongoDBAdaptorTest.<init>(VariantMongoDBAdaptorTest.java:61)
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VariantMongoDBAdaptorTest.getPhasedPopulationFrequencyByVariant:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/VariantMongoDBAdaptorTest.java#L61
java.lang.NullPointerException
at org.opencb.cellbase.lib.impl.core.VariantMongoDBAdaptorTest.<init>(VariantMongoDBAdaptorTest.java:61)
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XRefMongoDBAdaptorTest.queryTest:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/XRefMongoDBAdaptorTest.java#L43
java.lang.NullPointerException
at org.opencb.cellbase.lib.impl.core.XRefMongoDBAdaptorTest.queryTest(XRefMongoDBAdaptorTest.java:43)
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IndexManagerTest.testIndexes:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/indexer/IndexManagerTest.java#L39
java.lang.NullPointerException
at org.opencb.cellbase.lib.indexer.IndexManagerTest.<init>(IndexManagerTest.java:39)
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DataReleaseManagerTest.testAddActiveByDefaultIn:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/managers/DataReleaseManagerTest.java#L35
java.lang.NullPointerException
at org.opencb.cellbase.lib.managers.DataReleaseManagerTest.<init>(DataReleaseManagerTest.java:35)
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DataReleaseManagerTest.testMultipleAddActiveByDefaultIn:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/managers/DataReleaseManagerTest.java#L35
java.lang.NullPointerException
at org.opencb.cellbase.lib.managers.DataReleaseManagerTest.<init>(DataReleaseManagerTest.java:35)
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DataReleaseManagerTest.testAnnotationWithDR0:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/managers/DataReleaseManagerTest.java#L35
java.lang.NullPointerException
at org.opencb.cellbase.lib.managers.DataReleaseManagerTest.<init>(DataReleaseManagerTest.java:35)
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DataReleaseManagerTest.testChangeActiveByDefaultIn:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/managers/DataReleaseManagerTest.java#L35
java.lang.NullPointerException
at org.opencb.cellbase.lib.managers.DataReleaseManagerTest.<init>(DataReleaseManagerTest.java:35)
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DataReleaseManagerTest.failLoading:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/managers/DataReleaseManagerTest.java#L35
java.lang.NullPointerException
at org.opencb.cellbase.lib.managers.DataReleaseManagerTest.<init>(DataReleaseManagerTest.java:35)
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DataReleaseManagerTest.testAnnotationWithInvalidDR_1:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/managers/DataReleaseManagerTest.java#L35
java.lang.NullPointerException
at org.opencb.cellbase.lib.managers.DataReleaseManagerTest.<init>(DataReleaseManagerTest.java:35)
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DataReleaseManagerTest.testCreate:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/managers/DataReleaseManagerTest.java#L35
java.lang.NullPointerException
at org.opencb.cellbase.lib.managers.DataReleaseManagerTest.<init>(DataReleaseManagerTest.java:35)
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DataReleaseManagerTest.testRemoveMultipleAddActiveByDefaultIn:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/managers/DataReleaseManagerTest.java#L35
java.lang.NullPointerException
at org.opencb.cellbase.lib.managers.DataReleaseManagerTest.<init>(DataReleaseManagerTest.java:35)
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DataReleaseManagerTest.testAnnotationWithInvalidDR:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/managers/DataReleaseManagerTest.java#L35
java.lang.NullPointerException
at org.opencb.cellbase.lib.managers.DataReleaseManagerTest.<init>(DataReleaseManagerTest.java:35)
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VariantManagerTest.org.opencb.cellbase.lib.variant.VariantManagerTest:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/variant/VariantManagerTest.java#L49
java.lang.NullPointerException
at org.opencb.cellbase.lib.variant.VariantManagerTest.<init>(VariantManagerTest.java:49)
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HgvsCalculatorTest.org.opencb.cellbase.lib.variant.hgvs.HgvsCalculatorTest:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/variant/hgvs/HgvsCalculatorTest.java#L42
java.lang.NullPointerException
at org.opencb.cellbase.lib.variant.hgvs.HgvsCalculatorTest.<init>(HgvsCalculatorTest.java:42)
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HgvsTranscriptCalculatorTest.org.opencb.cellbase.lib.variant.hgvs.HgvsTranscriptCalculatorTest:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/variant/hgvs/HgvsTranscriptCalculatorTest.java#L60
java.lang.NullPointerException
at org.opencb.cellbase.lib.variant.hgvs.HgvsTranscriptCalculatorTest.<init>(HgvsTranscriptCalculatorTest.java:60)
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test / Test and push Sonar analysis
There were 35 failed tests
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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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Artifacts
Produced during runtime
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build-folder
Expired
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208 MB |
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