app: update the CellBase loader for variation data according to the l… #487
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Build Java app
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35 errors
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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 "disgenet" (class org.opencb.cellbase.core.config.DownloadProperties), not marked as ignorable (45 known properties: "miRTarBase", "intact", "dgidb", "genomicSuperDups", "revel", "refSeq", "interpro", "dgv", "hpoObo", "hgmd", "uniprot", "interproRelNotes", "cancerGeneCensus", "phastCons", "ensembl", "cadd", "uniprotRelNotes", "ensemblGenomes", "lrg", "mondoObo", "simpleRepeats", "maneSelect", "reactome", "windowMasker", "phylop", "targetScan", "cancerHotspot", "hgnc", "doidObo", "dbsnp", "pharmGKB", "mmSplice", "geneUniprotXref", "geneExpressionAtlas", "spliceAi", "gwasCatalog", "clinvar", "gerp", "cosmic", "mirbase", "gnomadConstraints", "goObo", "goAnnotation", "hpo", "pubmed"])
at [Source: (BufferedInputStream); line: 139, column: 5] (through reference chain: org.opencb.cellbase.core.config.CellBaseConfiguration["download"]->org.opencb.cellbase.core.config.DownloadProperties["disgenet"])
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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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RegulatoryFeatureBuilderTest.testParse:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/builders/RegulatoryFeatureBuilderTest.java#L35
/home/runner/work/cellbase/cellbase/cellbase-lib/target/test-classes/regulation/regulatory_build/regulatoryBuildVersion.json (No such file or directory)
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RepeatsBuilderTest.testParse:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/builders/RepeatsBuilderTest.java#L53
Configuration file could not be parsed: Unrecognized field "disgenet" (class org.opencb.cellbase.core.config.DownloadProperties), not marked as ignorable (45 known properties: "miRTarBase", "intact", "dgidb", "genomicSuperDups", "revel", "refSeq", "interpro", "dgv", "hpoObo", "hgmd", "uniprot", "interproRelNotes", "cancerGeneCensus", "phastCons", "ensembl", "cadd", "uniprotRelNotes", "ensemblGenomes", "lrg", "mondoObo", "simpleRepeats", "maneSelect", "reactome", "windowMasker", "phylop", "targetScan", "cancerHotspot", "hgnc", "doidObo", "dbsnp", "pharmGKB", "mmSplice", "geneUniprotXref", "geneExpressionAtlas", "spliceAi", "gwasCatalog", "clinvar", "gerp", "cosmic", "mirbase", "gnomadConstraints", "goObo", "goAnnotation", "hpo", "pubmed"])
at [Source: (BufferedInputStream); line: 126, column: 5] (through reference chain: org.opencb.cellbase.core.config.CellBaseConfiguration["download"]->org.opencb.cellbase.core.config.DownloadProperties["disgenet"])
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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#L55
java.lang.NullPointerException
at org.opencb.cellbase.lib.impl.core.ClinicalMongoDBAdaptorTest.parseQueryTest(ClinicalMongoDBAdaptorTest.java:55)
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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#L63
java.lang.NullPointerException
at org.opencb.cellbase.lib.impl.core.PharmacogenomicsMongoDBAdaptorTest.testQuery(PharmacogenomicsMongoDBAdaptorTest.java:63)
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PharmacogenomicsMongoDBAdaptorTest.testQueryName:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/PharmacogenomicsMongoDBAdaptorTest.java#L45
java.lang.NullPointerException
at org.opencb.cellbase.lib.impl.core.PharmacogenomicsMongoDBAdaptorTest.testQueryName(PharmacogenomicsMongoDBAdaptorTest.java:45)
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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#L54
java.lang.NullPointerException
at org.opencb.cellbase.lib.impl.core.VariantMongoDBAdaptorTest.<init>(VariantMongoDBAdaptorTest.java:54)
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VariantMongoDBAdaptorTest.testGetFunctionalScoreVariant:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/VariantMongoDBAdaptorTest.java#L54
java.lang.NullPointerException
at org.opencb.cellbase.lib.impl.core.VariantMongoDBAdaptorTest.<init>(VariantMongoDBAdaptorTest.java:54)
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VariantMongoDBAdaptorTest.getPhasedPopulationFrequencyByVariant:
cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/VariantMongoDBAdaptorTest.java#L54
java.lang.NullPointerException
at org.opencb.cellbase.lib.impl.core.VariantMongoDBAdaptorTest.<init>(VariantMongoDBAdaptorTest.java:54)
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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#L35
java.lang.NullPointerException
at org.opencb.cellbase.lib.indexer.IndexManagerTest.<init>(IndexManagerTest.java:35)
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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.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.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.testAnnotation:
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#L36
java.lang.NullPointerException
at org.opencb.cellbase.lib.variant.hgvs.HgvsCalculatorTest.<init>(HgvsCalculatorTest.java:36)
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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#L54
java.lang.NullPointerException
at org.opencb.cellbase.lib.variant.hgvs.HgvsTranscriptCalculatorTest.<init>(HgvsTranscriptCalculatorTest.java:54)
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test / Test and push Sonar analysis
There were 34 failed tests
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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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