Details
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Type: Bug
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Status: Being documented
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Priority: Major
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Resolution: Unresolved
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Affects Version/s: 2.10.1
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Fix Version/s: None
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Component/s: data retrieval services
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Labels:
Description
Whilst trying to resolve EnsemblGenomes IDs for sequences I saw this:
Response code 400 for http://rest.ensemblgenomes.org/overlap/id/KMI50280?content-type=text/x-gff3&feature=gene&feature=transcript&feature=exon&feature=cds&feature=variation
Exception in thread "Thread-104"
java.lang.Error: Implementation error. Null FileParse in copy constructor
at jalview.io.FileParse.<init>(FileParse.java:128)
at jalview.io.AlignFile.<init>(AlignFile.java:154)
at jalview.io.AlignFile.<init>(AlignFile.java:140)
at jalview.io.FeaturesFile.<init>(FeaturesFile.java:112)
at jalview.ext.ensembl.EnsemblFeatures.getSequenceRecords(EnsemblFeatures.java:88)
at jalview.ext.ensembl.EnsemblFeatures.getSequenceRecords(EnsemblFeatures.java:158)
at jalview.ext.ensembl.EnsemblSeqProxy.addFeaturesAndProduct(EnsemblSeqProxy.java:234)
at jalview.ext.ensembl.EnsemblSeqProxy.getSequenceRecords(EnsemblSeqProxy.java:199)
at jalview.ext.ensembl.EnsemblGene.getSequenceRecords(EnsemblGene.java:140)
at jalview.ws.DBRefFetcher.run(DBRefFetcher.java:418)
at java.lang.Thread.run(Thread.java:745)
Response code 400 for http://rest.ensemblgenomes.org/overlap/id/KMI50280?content-type=text/x-gff3&feature=gene&feature=transcript&feature=exon&feature=cds&feature=variation
Exception in thread "Thread-104"
java.lang.Error: Implementation error. Null FileParse in copy constructor
at jalview.io.FileParse.<init>(FileParse.java:128)
at jalview.io.AlignFile.<init>(AlignFile.java:154)
at jalview.io.AlignFile.<init>(AlignFile.java:140)
at jalview.io.FeaturesFile.<init>(FeaturesFile.java:112)
at jalview.ext.ensembl.EnsemblFeatures.getSequenceRecords(EnsemblFeatures.java:88)
at jalview.ext.ensembl.EnsemblFeatures.getSequenceRecords(EnsemblFeatures.java:158)
at jalview.ext.ensembl.EnsemblSeqProxy.addFeaturesAndProduct(EnsemblSeqProxy.java:234)
at jalview.ext.ensembl.EnsemblSeqProxy.getSequenceRecords(EnsemblSeqProxy.java:199)
at jalview.ext.ensembl.EnsemblGene.getSequenceRecords(EnsemblGene.java:140)
at jalview.ws.DBRefFetcher.run(DBRefFetcher.java:418)
at java.lang.Thread.run(Thread.java:745)