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  1. Jalview
  2. JAL-2354

EnsembGenomes retrieval fails with exception

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    Details

    • Type: Bug
    • Status: Being documented
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: 2.10.1
    • Fix Version/s: None
    • 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)


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            Assignee:
            jprocter James Procter
            Reporter:
            jprocter James Procter
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              Dates

              Created:
              Updated: