Details
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Type: Bug
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Status: Closed
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Priority: Blocker
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Resolution: Fixed
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Affects Version/s: 2.11.4.0
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Fix Version/s: 2.11.4.0
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Component/s: data retrieval services
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Labels:
Description
noticed whilst reviewing JAL-3018 and JAL-3982 - Ensembl fetch completely fails for Jalview Test/2.11.4.0rc2.
Errors are
java.lang.IllegalStateException: connect in progress
at java.base/sun.net.www.protocol.http.HttpURLConnection.setRequestMethod(HttpURLConnection.java:568)
at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.setRequestMethod(HttpsURLConnectionImpl.java:370)
at jalview.ext.ensembl.EnsemblRestClient.tryConnection(EnsemblRestClient.java:354)
at jalview.ext.ensembl.EnsemblRestClient.getJSON(EnsemblRestClient.java:299)
at jalview.ext.ensembl.EnsemblRestClient.getJSON(EnsemblRestClient.java:514)
at jalview.ext.ensembl.EnsemblLookup.getResult(EnsemblLookup.java:221)
at jalview.ext.ensembl.EnsemblLookup.getGeneId(EnsemblLookup.java:142)
at jalview.ext.ensembl.EnsemblLookup.getGeneId(EnsemblLookup.java:129)
at jalview.ext.ensembl.EnsemblGene.getGeneIds(EnsemblGene.java:253)
at jalview.ext.ensembl.EnsemblGene.getSequenceRecords(EnsemblGene.java:142)
at jalview.gui.SequenceFetcher.fetchMultipleAccessions(SequenceFetcher.java:746)
at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:594)
at java.base/java.lang.Thread.run(Thread.java:829)
Errors are
java.lang.IllegalStateException: connect in progress
at java.base/sun.net.www.protocol.http.HttpURLConnection.setRequestMethod(HttpURLConnection.java:568)
at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.setRequestMethod(HttpsURLConnectionImpl.java:370)
at jalview.ext.ensembl.EnsemblRestClient.tryConnection(EnsemblRestClient.java:354)
at jalview.ext.ensembl.EnsemblRestClient.getJSON(EnsemblRestClient.java:299)
at jalview.ext.ensembl.EnsemblRestClient.getJSON(EnsemblRestClient.java:514)
at jalview.ext.ensembl.EnsemblLookup.getResult(EnsemblLookup.java:221)
at jalview.ext.ensembl.EnsemblLookup.getGeneId(EnsemblLookup.java:142)
at jalview.ext.ensembl.EnsemblLookup.getGeneId(EnsemblLookup.java:129)
at jalview.ext.ensembl.EnsemblGene.getGeneIds(EnsemblGene.java:253)
at jalview.ext.ensembl.EnsemblGene.getSequenceRecords(EnsemblGene.java:142)
at jalview.gui.SequenceFetcher.fetchMultipleAccessions(SequenceFetcher.java:746)
at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:594)
at java.base/java.lang.Thread.run(Thread.java:829)