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lib: add support for multi-species, checks and log messages in regula…

lib: add support for multi-species, checks and log messages in regula… #481

GitHub Actions / Surefire tests report failed Jul 26, 2024 in 0s

150 tests run, 78 skipped, 34 failed.

Annotations

Check failure on line 25 in cellbase-core/src/test/java/org/opencb/cellbase/core/config/CellBaseConfigurationTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

CellBaseConfigurationTest.org.opencb.cellbase.core.config.CellBaseConfigurationTest 

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"])
Raw output 
java.io.IOException: 
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"])
	at org.opencb.cellbase.core.config.CellBaseConfigurationTest.setUp(CellBaseConfigurationTest.java:25)
Caused by: com.fasterxml.jackson.databind.exc.UnrecognizedPropertyException: 
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"])
	at org.opencb.cellbase.core.config.CellBaseConfigurationTest.setUp(CellBaseConfigurationTest.java:25)

Check failure on line 58 in cellbase-lib/src/test/java/org/opencb/cellbase/lib/SpeciesUtilsTest.java

See this annotation in the file changed.

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SpeciesUtilsTest.testGetDefaultAssembly 

java.lang.NullPointerException
	at org.opencb.cellbase.lib.SpeciesUtilsTest.testGetDefaultAssembly(SpeciesUtilsTest.java:58)
Raw output 
java.lang.NullPointerException
	at org.opencb.cellbase.lib.SpeciesUtilsTest.testGetDefaultAssembly(SpeciesUtilsTest.java:58)

Check failure on line 35 in cellbase-lib/src/test/java/org/opencb/cellbase/lib/builders/RegulatoryFeatureBuilderTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

RegulatoryFeatureBuilderTest.testParse 

/home/runner/work/cellbase/cellbase/cellbase-lib/target/test-classes/regulation/regulatory_build/regulatoryBuildVersion.json (No such file or directory)
Raw output 
java.io.FileNotFoundException: /home/runner/work/cellbase/cellbase/cellbase-lib/target/test-classes/regulation/regulatory_build/regulatoryBuildVersion.json (No such file or directory)
	at org.opencb.cellbase.lib.builders.RegulatoryFeatureBuilderTest.testParse(RegulatoryFeatureBuilderTest.java:35)

Check failure on line 53 in cellbase-lib/src/test/java/org/opencb/cellbase/lib/builders/RepeatsBuilderTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

RepeatsBuilderTest.testParse 

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"])
Raw output 
java.io.IOException: 
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"])
	at org.opencb.cellbase.lib.builders.RepeatsBuilderTest.testParse(RepeatsBuilderTest.java:53)
Caused by: com.fasterxml.jackson.databind.exc.UnrecognizedPropertyException: 
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"])
	at org.opencb.cellbase.lib.builders.RepeatsBuilderTest.testParse(RepeatsBuilderTest.java:53)

Check failure on line 34 in cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/CellBaseNormalizerSequenceAdaptorTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

CellBaseNormalizerSequenceAdaptorTest.testGenomicSequenceQueryStartOutOfLeftBound 

java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.CellBaseNormalizerSequenceAdaptorTest.<init>(CellBaseNormalizerSequenceAdaptorTest.java:34)
Raw output 
java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.CellBaseNormalizerSequenceAdaptorTest.<init>(CellBaseNormalizerSequenceAdaptorTest.java:34)

Check failure on line 34 in cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/CellBaseNormalizerSequenceAdaptorTest.java

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CellBaseNormalizerSequenceAdaptorTest.testGenomicSequenceChromosomeNotPresent 

java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.CellBaseNormalizerSequenceAdaptorTest.<init>(CellBaseNormalizerSequenceAdaptorTest.java:34)
Raw output 
java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.CellBaseNormalizerSequenceAdaptorTest.<init>(CellBaseNormalizerSequenceAdaptorTest.java:34)

Check failure on line 34 in cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/CellBaseNormalizerSequenceAdaptorTest.java

See this annotation in the file changed.

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CellBaseNormalizerSequenceAdaptorTest.testGenomicSequenceQueryEndOutOfRightBound 

java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.CellBaseNormalizerSequenceAdaptorTest.<init>(CellBaseNormalizerSequenceAdaptorTest.java:34)
Raw output 
java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.CellBaseNormalizerSequenceAdaptorTest.<init>(CellBaseNormalizerSequenceAdaptorTest.java:34)

Check failure on line 34 in cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/CellBaseNormalizerSequenceAdaptorTest.java

See this annotation in the file changed.

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CellBaseNormalizerSequenceAdaptorTest.testGenomicSequenceQueryStartEndOutOfRightBound 

java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.CellBaseNormalizerSequenceAdaptorTest.<init>(CellBaseNormalizerSequenceAdaptorTest.java:34)
Raw output 
java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.CellBaseNormalizerSequenceAdaptorTest.<init>(CellBaseNormalizerSequenceAdaptorTest.java:34)

Check failure on line 55 in cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/ClinicalMongoDBAdaptorTest.java

See this annotation in the file changed.

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ClinicalMongoDBAdaptorTest.parseQueryTest 

java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.ClinicalMongoDBAdaptorTest.parseQueryTest(ClinicalMongoDBAdaptorTest.java:55)
Raw output 
java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.ClinicalMongoDBAdaptorTest.parseQueryTest(ClinicalMongoDBAdaptorTest.java:55)

Check failure on line 70 in cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/GeneMongoDBAdaptorTest.java

See this annotation in the file changed.

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GeneMongoDBAdaptorTest.testQuery 

java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.GeneMongoDBAdaptorTest.testQuery(GeneMongoDBAdaptorTest.java:70)
Raw output 
java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.GeneMongoDBAdaptorTest.testQuery(GeneMongoDBAdaptorTest.java:70)

Check failure on line 51 in cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/GeneMongoDBAdaptorTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

GeneMongoDBAdaptorTest.testQueryId 

java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.GeneMongoDBAdaptorTest.testQueryId(GeneMongoDBAdaptorTest.java:51)
Raw output 
java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.GeneMongoDBAdaptorTest.testQueryId(GeneMongoDBAdaptorTest.java:51)

Check failure on line 124 in cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/GeneMongoDBAdaptorTest.java

See this annotation in the file changed.

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GeneMongoDBAdaptorTest.testConstraints 

java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.GeneMongoDBAdaptorTest.testConstraints(GeneMongoDBAdaptorTest.java:124)
Raw output 
java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.GeneMongoDBAdaptorTest.testConstraints(GeneMongoDBAdaptorTest.java:124)

Check failure on line 50 in cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/GenomeMongoDBAdaptorTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

GenomeMongoDBAdaptorTest.org.opencb.cellbase.lib.impl.core.GenomeMongoDBAdaptorTest 

java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.GenomeMongoDBAdaptorTest.<init>(GenomeMongoDBAdaptorTest.java:50)
Raw output 
java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.GenomeMongoDBAdaptorTest.<init>(GenomeMongoDBAdaptorTest.java:50)

Check failure on line 36 in cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/MongoDBAdaptorFactoryTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

MongoDBAdaptorFactoryTest.org.opencb.cellbase.lib.impl.core.MongoDBAdaptorFactoryTest 

java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.MongoDBAdaptorFactoryTest.<init>(MongoDBAdaptorFactoryTest.java:36)
Raw output 
java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.MongoDBAdaptorFactoryTest.<init>(MongoDBAdaptorFactoryTest.java:36)

Check failure on line 63 in cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/PharmacogenomicsMongoDBAdaptorTest.java

See this annotation in the file changed.

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PharmacogenomicsMongoDBAdaptorTest.testQuery 

java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.PharmacogenomicsMongoDBAdaptorTest.testQuery(PharmacogenomicsMongoDBAdaptorTest.java:63)
Raw output 
java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.PharmacogenomicsMongoDBAdaptorTest.testQuery(PharmacogenomicsMongoDBAdaptorTest.java:63)

Check failure on line 45 in cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/PharmacogenomicsMongoDBAdaptorTest.java

See this annotation in the file changed.

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PharmacogenomicsMongoDBAdaptorTest.testQueryName 

java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.PharmacogenomicsMongoDBAdaptorTest.testQueryName(PharmacogenomicsMongoDBAdaptorTest.java:45)
Raw output 
java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.PharmacogenomicsMongoDBAdaptorTest.testQueryName(PharmacogenomicsMongoDBAdaptorTest.java:45)

Check failure on line 45 in cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/ProteinMongoDBAdaptorTest.java

See this annotation in the file changed.

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ProteinMongoDBAdaptorTest.testQuery 

java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.ProteinMongoDBAdaptorTest.testQuery(ProteinMongoDBAdaptorTest.java:45)
Raw output 
java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.ProteinMongoDBAdaptorTest.testQuery(ProteinMongoDBAdaptorTest.java:45)

Check failure on line 44 in cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/TranscriptMongoDBAdaptorTest.java

See this annotation in the file changed.

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TranscriptMongoDBAdaptorTest.testQuery 

java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.TranscriptMongoDBAdaptorTest.testQuery(TranscriptMongoDBAdaptorTest.java:44)
Raw output 
java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.TranscriptMongoDBAdaptorTest.testQuery(TranscriptMongoDBAdaptorTest.java:44)

Check failure on line 54 in cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/VariantAnnotationCalculatorTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

VariantAnnotationCalculatorTest.org.opencb.cellbase.lib.impl.core.VariantAnnotationCalculatorTest 

java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.VariantAnnotationCalculatorTest.<init>(VariantAnnotationCalculatorTest.java:54)
Raw output 
java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.VariantAnnotationCalculatorTest.<init>(VariantAnnotationCalculatorTest.java:54)

Check failure on line 54 in cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/VariantMongoDBAdaptorTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

VariantMongoDBAdaptorTest.testGet 

java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.VariantMongoDBAdaptorTest.<init>(VariantMongoDBAdaptorTest.java:54)
Raw output 
java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.VariantMongoDBAdaptorTest.<init>(VariantMongoDBAdaptorTest.java:54)

Check failure on line 54 in cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/VariantMongoDBAdaptorTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

VariantMongoDBAdaptorTest.testGetFunctionalScoreVariant 

java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.VariantMongoDBAdaptorTest.<init>(VariantMongoDBAdaptorTest.java:54)
Raw output 
java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.VariantMongoDBAdaptorTest.<init>(VariantMongoDBAdaptorTest.java:54)

Check failure on line 54 in cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/VariantMongoDBAdaptorTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

VariantMongoDBAdaptorTest.getPhasedPopulationFrequencyByVariant 

java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.VariantMongoDBAdaptorTest.<init>(VariantMongoDBAdaptorTest.java:54)
Raw output 
java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.VariantMongoDBAdaptorTest.<init>(VariantMongoDBAdaptorTest.java:54)

Check failure on line 43 in cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/XRefMongoDBAdaptorTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

XRefMongoDBAdaptorTest.queryTest 

java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.XRefMongoDBAdaptorTest.queryTest(XRefMongoDBAdaptorTest.java:43)
Raw output 
java.lang.NullPointerException
	at org.opencb.cellbase.lib.impl.core.XRefMongoDBAdaptorTest.queryTest(XRefMongoDBAdaptorTest.java:43)

Check failure on line 35 in cellbase-lib/src/test/java/org/opencb/cellbase/lib/indexer/IndexManagerTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report

IndexManagerTest.testIndexes 

java.lang.NullPointerException
	at org.opencb.cellbase.lib.indexer.IndexManagerTest.<init>(IndexManagerTest.java:35)
Raw output 
java.lang.NullPointerException
	at org.opencb.cellbase.lib.indexer.IndexManagerTest.<init>(IndexManagerTest.java:35)

Check failure on line 35 in cellbase-lib/src/test/java/org/opencb/cellbase/lib/managers/DataReleaseManagerTest.java

See this annotation in the file changed.

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DataReleaseManagerTest.testAddActiveByDefaultIn 

java.lang.NullPointerException
	at org.opencb.cellbase.lib.managers.DataReleaseManagerTest.<init>(DataReleaseManagerTest.java:35)
Raw output 
java.lang.NullPointerException
	at org.opencb.cellbase.lib.managers.DataReleaseManagerTest.<init>(DataReleaseManagerTest.java:35)
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