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lib: improve genome builder by checking files, and fixing sonnar issu… #478

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lib: improve genome builder by checking files, and fixing sonnar issu…

lib: improve genome builder by checking files, and fixing sonnar issu… #478

Triggered via push July 25, 2024 11:01
@jtarragajtarraga
pushed 733cade
TASK-5564
Status Failure
Total duration 3m 37s
Artifacts 1

task.yml

on: push
build  /  Build Java app
55s
build / Build Java app
test  /  Test and push Sonar analysis
2m 23s
test / Test and push Sonar analysis
deploy-docker  /  Push Docker image
deploy-docker / Push Docker image
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34 errors
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"])
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)
RepeatsBuilderTest.testParse: cellbase-lib/src/test/java/org/opencb/cellbase/lib/builders/RepeatsBuilderTest.java#L51
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"])
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
test / Test and push Sonar analysis
There were 33 failed tests

Artifacts

Produced during runtime
Name Size
build-folder Expired
208 MB