Details
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Type: Bug
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Status: Closed
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Priority: Minor
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Resolution: Fixed
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Affects Version/s: 2.10.0, 2.10.0b1, 2.10.2
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Fix Version/s: 2.10.3
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Component/s: data retrieval services
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Labels:
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)
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)