Details
-
Type: Bug
-
Status: Closed
-
Priority: Major
-
Resolution: Duplicate
-
Affects Version/s: 2.11.1.6
-
Fix Version/s: 2.11.1.7
-
Component/s: None
-
Labels:None
-
Environment:linux , ubuntu 20.04
jalview installed using jalview-2_11_1_4-linux_x64-java_8.sh
Description
When try to fetch PFAM using File/Fetch I am getting:
Jalview Version: 2.11.1.6
Jalview Installation: Source git-commit:a7e71732f [releases/Release_2_11_1_Branch]
Build Date: 10:31:23 06 January 2022
Java version: 1.8.0_242
amd64 Linux 5.11.0-44-generic
Install4j version: 8.0.11
Install4j template version: 2.11.1.4_Fa87edcab_C930bcaf01
Launcher version: 1.8.3-1.2.9_JVL
LookAndFeel: Metal (javax.swing.plaf.metal.MetalLookAndFeel)
Getdown appdir: /home/petr/opt/jalview
Java home: /home/petr/opt/jalview/jre
java.io.IOException: Failed to read data from source: CANNOT ACCESS DATA AT URL 'https://pfam.xfam.org/family/PF03760/alignment/seed/gzipped' (sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target)
at jalview.io.FileParse.<init>(FileParse.java:514)
at jalview.io.AppletFormatAdapter.readFile(AppletFormatAdapter.java:180)
at jalview.io.FormatAdapter.readFile(FormatAdapter.java:235)
at jalview.ws.dbsources.Xfam.getSequenceRecords(Xfam.java:71)
at jalview.gui.SequenceFetcher.fetchSingleAccession(SequenceFetcher.java:915)
at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:700)
at java.lang.Thread.run(Thread.java:748)
Failed to read alignment using the 'Stockholm' reader.
java.io.IOException: Failed to read data from source: CANNOT ACCESS DATA AT URL 'https://pfam.xfam.org/family/PF03760/alignment/seed/gzipped' (sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target)
I testes regular installation using linux installer(2.11.1.6) and also conda installer ( 2.11.1.5)
when tried to download https://pfam.xfam.org/family/PF03760/alignment/seed/gzipped, it return correct gziped file
Jalview Version: 2.11.1.6
Jalview Installation: Source git-commit:a7e71732f [releases/Release_2_11_1_Branch]
Build Date: 10:31:23 06 January 2022
Java version: 1.8.0_242
amd64 Linux 5.11.0-44-generic
Install4j version: 8.0.11
Install4j template version: 2.11.1.4_Fa87edcab_C930bcaf01
Launcher version: 1.8.3-1.2.9_JVL
LookAndFeel: Metal (javax.swing.plaf.metal.MetalLookAndFeel)
Getdown appdir: /home/petr/opt/jalview
Java home: /home/petr/opt/jalview/jre
java.io.IOException: Failed to read data from source: CANNOT ACCESS DATA AT URL 'https://pfam.xfam.org/family/PF03760/alignment/seed/gzipped' (sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target)
at jalview.io.FileParse.<init>(FileParse.java:514)
at jalview.io.AppletFormatAdapter.readFile(AppletFormatAdapter.java:180)
at jalview.io.FormatAdapter.readFile(FormatAdapter.java:235)
at jalview.ws.dbsources.Xfam.getSequenceRecords(Xfam.java:71)
at jalview.gui.SequenceFetcher.fetchSingleAccession(SequenceFetcher.java:915)
at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:700)
at java.lang.Thread.run(Thread.java:748)
Failed to read alignment using the 'Stockholm' reader.
java.io.IOException: Failed to read data from source: CANNOT ACCESS DATA AT URL 'https://pfam.xfam.org/family/PF03760/alignment/seed/gzipped' (sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target)
I testes regular installation using linux installer(2.11.1.6) and also conda installer ( 2.11.1.5)
when tried to download https://pfam.xfam.org/family/PF03760/alignment/seed/gzipped, it return correct gziped file
Attachments
Issue Links
- depends on
-
JAL-3937 PFAM services have a new certificate that JRE cacerts does not cover
- Closed