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  1. Jalview
  2. JAL-2253

Fetch DBRefs from EnsemblGenomes very slow when no entries are found

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      Description

      Load http://www.jalview.org/tutorial/alignment.fa and go to Web Service | Fetch DB References | From EMBL … UNIPROT, then choose EnsemblGenomes. This runs and completes with no return values and no errors, but it is exceptionally slow.

      Console output looks like this:

      Verifying against EnsemblGenomes
      Response code 410 for http://rest.ensemblgenomes.org/info/ping?content-type=application/json
      Error connecting to http://rest.ensembl.org/info/ping.json: null
      Response code 500 for http://rest.ensemblgenomes.org/info/data?content-type=application/json
      Error checking Ensembl data version: null
      Aborting ID retrieval after 0 chunks. Unexpected problem (ENSEMBL Rest API not available.)
      jalview.exceptions.JalviewException: ENSEMBL Rest API not available.
      at jalview.ext.ensembl.EnsemblSeqProxy.fetchSequences(EnsemblSeqProxy.java:407)
      at jalview.ext.ensembl.EnsemblSeqProxy.getSequenceRecords(EnsemblSeqProxy.java:175)
      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/sequence/id/FER_CAPAN?type=genomic&Accept=text/x-fasta
      Response code 400 for http://rest.ensemblgenomes.org/sequence/id/FER1_SOLLC?type=genomic&Accept=text/x-fasta
      Response code 400 for http://rest.ensemblgenomes.org/sequence/id/Q93XJ9_SOLTU?type=genomic&Accept=text/x-fasta
      Response code 410 for http://rest.ensemblgenomes.org/info/ping?content-type=application/json
      Error connecting to http://rest.ensembl.org/info/ping.json: null
      Aborting ID retrieval after 0 chunks. Unexpected problem (ENSEMBL Rest API not available.)
      jalview.exceptions.JalviewException: ENSEMBL Rest API not available.
      at jalview.ext.ensembl.EnsemblSeqProxy.fetchSequences(EnsemblSeqProxy.java:407)
      at jalview.ext.ensembl.EnsemblSeqProxy.getSequenceRecords(EnsemblSeqProxy.java:175)
      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:
              gmungoc Mungo Carstairs
              Reporter:
              kmourao Kira Mourão
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                Created:
                Updated:
                Resolved: