Details
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Type:
Bug
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Status: Closed
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Priority:
Major
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Resolution: Fixed
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Affects Version/s: 2.11.4.0, 2.11.4.1
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Fix Version/s: 2.11.5.0
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Component/s: data retrieval services
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Labels:None
Description
Jalview throws an exception when trying to access URLs from web servers that do not provide content and encoding headers. This results in a 'Cannot Access URL' or 'File format not recognized' dialog, and a buried Null pointer exception report.
ERROR - Error whilst trying to read https://www.compbio.dundee.ac.uk/jpred4/results/jp_9qjIzLs/jp_9qjIzLs.align
java.io.IOException: Failed to read data from source: CANNOT ACCESS DATA AT URL 'https://www.compbio.dundee.ac.uk/jpred4/results/jp_9qjIzLs/jp_9qjIzLs.align' (null)
at jalview.io.FileParse.parse(FileParse.java:586) ~[jalview.jar:2.11.5.0-test]
at jalview.io.FileParse.<init>(FileParse.java:439) ~[jalview.jar:2.11.5.0-test]
at jalview.io.IdentifyFile.identify(IdentifyFile.java:115) ~[jalview.jar:2.11.5.0-test]
at jalview.io.IdentifyFile.identify(IdentifyFile.java:92) ~[jalview.jar:2.11.5.0-test]
at jalview.gui.Desktop.lambda$inputURLMenuItem_actionPerformed$2(Desktop.java:1601) ~[jalview.jar:2.11.5.0-test]
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) [?:1.8.0_372]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) [?:1.8.0_372]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [?:1.8.0_372]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [?:1.8.0_372]
at java.lang.Thread.run(Thread.java:750) [?:1.8.0_372]
ERROR - File at URL 'https://www.compbio.dundee.ac.uk/jpred4/results/jp_9qjIzLs/jp_9qjIzLs.align' format not recognised
jalview.io.FileFormatException: UNIDENTIFIED FILE PARSING ERROR
at jalview.io.IdentifyFile.identify(IdentifyFile.java:141) ~[jalview.jar:2.11.5.0-test]
at jalview.io.IdentifyFile.identify(IdentifyFile.java:92) ~[jalview.jar:2.11.5.0-test]
at jalview.gui.Desktop.lambda$inputURLMenuItem_actionPerformed$2(Desktop.java:1601) ~[jalview.jar:2.11.5.0-test]
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) [?:1.8.0_372]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) [?:1.8.0_372]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [?:1.8.0_372]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [?:1.8.0_372]
at java.lang.Thread.run(Thread.java:750) [?:1.8.0_372]
ERROR - Error whilst trying to read https://www.compbio.dundee.ac.uk/jpred4/results/jp_9qjIzLs/jp_9qjIzLs.align
java.io.IOException: Failed to read data from source: CANNOT ACCESS DATA AT URL 'https://www.compbio.dundee.ac.uk/jpred4/results/jp_9qjIzLs/jp_9qjIzLs.align' (null)
at jalview.io.FileParse.parse(FileParse.java:586) ~[jalview.jar:2.11.5.0-test]
at jalview.io.FileParse.<init>(FileParse.java:439) ~[jalview.jar:2.11.5.0-test]
at jalview.io.IdentifyFile.identify(IdentifyFile.java:115) ~[jalview.jar:2.11.5.0-test]
at jalview.io.IdentifyFile.identify(IdentifyFile.java:92) ~[jalview.jar:2.11.5.0-test]
at jalview.gui.Desktop.lambda$inputURLMenuItem_actionPerformed$2(Desktop.java:1601) ~[jalview.jar:2.11.5.0-test]
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) [?:1.8.0_372]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) [?:1.8.0_372]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [?:1.8.0_372]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [?:1.8.0_372]
at java.lang.Thread.run(Thread.java:750) [?:1.8.0_372]
ERROR - File at URL 'https://www.compbio.dundee.ac.uk/jpred4/results/jp_9qjIzLs/jp_9qjIzLs.align' format not recognised
jalview.io.FileFormatException: UNIDENTIFIED FILE PARSING ERROR
at jalview.io.IdentifyFile.identify(IdentifyFile.java:141) ~[jalview.jar:2.11.5.0-test]
at jalview.io.IdentifyFile.identify(IdentifyFile.java:92) ~[jalview.jar:2.11.5.0-test]
at jalview.gui.Desktop.lambda$inputURLMenuItem_actionPerformed$2(Desktop.java:1601) ~[jalview.jar:2.11.5.0-test]
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) [?:1.8.0_372]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) [?:1.8.0_372]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [?:1.8.0_372]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [?:1.8.0_372]
at java.lang.Thread.run(Thread.java:750) [?:1.8.0_372]
