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lib: check pharmacogenomics collection in the target data release bef… #332

lib: check pharmacogenomics collection in the target data release bef…

lib: check pharmacogenomics collection in the target data release bef… #332

Triggered via push January 10, 2024 12:16
Status Failure
Total duration 10m 51s
Artifacts 1

task.yml

on: push
test  /  Test and push Sonar analysis
6m 6s
test / Test and push Sonar analysis
deploy-docker  /  Push Docker image
deploy-docker / Push Docker image
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3 errors
PharmacogenomicsMongoDBAdaptorTest.testQueryName: cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/PharmacogenomicsMongoDBAdaptorTest.java#L62
com.fasterxml.jackson.databind.exc.InvalidFormatException: Cannot deserialize value of type `java.lang.Integer` from String "DataRelease{release=1, date='20231011090804', activeByDefaultIn=[v5.8], collections={genome_info=genome_info__v1, genome_sequence=genome_sequence__v1, gene=gene__v1, refseq=refseq__v1, conservation=conservation__v1, regulatory_region=regulatory_region__v1, protein=protein__v1, protein_functional_prediction=protein_functional_prediction__v1, variation=variation__v1, variation_functional_score=variation_functional_score__v1, repeats=repeats__v1, ontology=ontology__v1, missense_variation_functional]...[rvation=conservation__v1, regulatory_region=regulatory_region__v1, protein=protein__v1, protein_functional_prediction=protein_functional_prediction__v1, variation=variation__v1, variation_functional_score=variation_functional_score__v1, repeats=repeats__v1, ontology=ontology__v1, missense_variation_functional_score=missense_variation_functional_score__v1, splice_score=splice_score__v1, clinical_variants=clinical_variants__v1, pharmacogenomics=pharmacogenomics__v1, pubmed=pubmed__v1}, sources=[]}": not a valid Integer value at [Source: UNKNOWN; line: -1, column: -1] (through reference chain: org.opencb.cellbase.core.api.PharmaChemicalQuery["dataRelease"])
IndexManagerTest.testIndexes: cellbase-lib/src/test/java/org/opencb/cellbase/lib/indexer/IndexManagerTest.java#L46
Command failed with error 73 (InvalidNamespace): 'Fully qualified namespace is too long. Namespace: cellbase_hsapiens_grch38_v5_8.gene__vDataRelease{release=1, date='20231011090804', activeByDefaultIn=[v5.8], collections={genome_info=genome_info__v1, genome_sequence=genome_sequence__v1, gene=gene__v1, refseq=refseq__v1, conservation=conservation__v1, regulatory_region=regulatory_region__v1, protein=protein__v1, protein_functional_prediction=protein_functional_prediction__v1, variation=variation__v1, variation_functional_score=variation_functional_score__v1, repeats=repeats__v1, ontology=ontology__v1, missense_variation_functional_score=missense_variation_functional_score__v1, splice_score=splice_score__v1, clinical_variants=clinical_variants__v1, pharmacogenomics=pharmacogenomics__v1, pubmed=pubmed__v1}, sources=[]} Max: 255' on server localhost:27017. The full response is {"ok": 0.0, "errmsg": "Fully qualified namespace is too long. Namespace: cellbase_hsapiens_grch38_v5_8.gene__vDataRelease{release=1, date='20231011090804', activeByDefaultIn=[v5.8], collections={genome_info=genome_info__v1, genome_sequence=genome_sequence__v1, gene=gene__v1, refseq=refseq__v1, conservation=conservation__v1, regulatory_region=regulatory_region__v1, protein=protein__v1, protein_functional_prediction=protein_functional_prediction__v1, variation=variation__v1, variation_functional_score=variation_functional_score__v1, repeats=repeats__v1, ontology=ontology__v1, missense_variation_functional_score=missense_variation_functional_score__v1, splice_score=splice_score__v1, clinical_variants=clinical_variants__v1, pharmacogenomics=pharmacogenomics__v1, pubmed=pubmed__v1}, sources=[]} Max: 255", "code": 73, "codeName": "InvalidNamespace", "$clusterTime": {"clusterTime": {"$timestamp": {"t": 1704889344, "i": 1}}, "signature": {"hash": {"$binary": {"base64": "WIbmYiNgn5e20IAueCgpTIHYb64=", "subType": "00"}}, "keyId": 7276163942227902466}}, "operationTime": {"$timestamp": {"t": 1704889344, "i": 1}}}
test / Test and push Sonar analysis
There were 2 failed tests

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