Open AntoniyaAleksandrova opened 2 years ago
Thanks for reporting. Would you have an example or some more details (the command line you use) on how to reproduce the issue?
Yes, of course. Here it is:
$ ./runCESymm.sh -J 1okc --stats=-
Name NumRepeats SymmGroup Refined SymmLevels SymmType RotationAngle ScrewTranslation UnrefinedTMscore UnrefinedRMSD SymmTMscore SymmRMSD RepeatLength CoreLength Length Coverage Repeats
2056 [pool-2-thread-1] ERROR workers.CeSymmWorker - Could not load Structure 1okc
javax.net.ssl.SSLHandshakeException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
at sun.security.ssl.Alert.createSSLException(Alert.java:131) ~[?:?]
at sun.security.ssl.TransportContext.fatal(TransportContext.java:371) ~[?:?]
at sun.security.ssl.TransportContext.fatal(TransportContext.java:314) ~[?:?]
at sun.security.ssl.TransportContext.fatal(TransportContext.java:309) ~[?:?]
at sun.security.ssl.CertificateMessage$T12CertificateConsumer.checkServerCerts(CertificateMessage.java:654) ~[?:?]
at sun.security.ssl.CertificateMessage$T12CertificateConsumer.onCertificate(CertificateMessage.java:473) ~[?:?]
at sun.security.ssl.CertificateMessage$T12CertificateConsumer.consume(CertificateMessage.java:369) ~[?:?]
at sun.security.ssl.SSLHandshake.consume(SSLHandshake.java:396) ~[?:?]
at sun.security.ssl.HandshakeContext.dispatch(HandshakeContext.java:480) ~[?:?]
at sun.security.ssl.HandshakeContext.dispatch(HandshakeContext.java:458) ~[?:?]
at sun.security.ssl.TransportContext.dispatch(TransportContext.java:201) ~[?:?]
at sun.security.ssl.SSLTransport.decode(SSLTransport.java:172) ~[?:?]
at sun.security.ssl.SSLSocketImpl.decode(SSLSocketImpl.java:1500) ~[?:?]
at sun.security.ssl.SSLSocketImpl.readHandshakeRecord(SSLSocketImpl.java:1415) ~[?:?]
at sun.security.ssl.SSLSocketImpl.startHandshake(SSLSocketImpl.java:450) ~[?:?]
at sun.security.ssl.SSLSocketImpl.startHandshake(SSLSocketImpl.java:421) ~[?:?]
at sun.net.www.protocol.https.HttpsClient.afterConnect(HttpsClient.java:580) ~[?:?]
at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:183) ~[?:?]
at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1665) ~[?:?]
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1589) ~[?:?]
at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) ~[?:?]
at java.net.URL.openStream(URL.java:1161) ~[?:?]
at org.biojava.nbio.structure.PDBStatus.getStatus(PDBStatus.java:95) ~[cesymm-2.2.2.jar:2.2.2]
at org.biojava.nbio.structure.io.LocalPDBDirectory.downloadStructure(LocalPDBDirectory.java:520) ~[cesymm-2.2.2.jar:2.2.2]
at org.biojava.nbio.structure.io.LocalPDBDirectory.getInputStream(LocalPDBDirectory.java:370) ~[cesymm-2.2.2.jar:2.2.2]
at org.biojava.nbio.structure.io.LocalPDBDirectory.getStructureById(LocalPDBDirectory.java:348) ~[cesymm-2.2.2.jar:2.2.2]
at org.biojava.nbio.structure.align.util.AtomCache.loadStructureFromBcifByPdbId(AtomCache.java:893) ~[cesymm-2.2.2.jar:2.2.2]
at org.biojava.nbio.structure.align.util.AtomCache.getStructureForPdbId(AtomCache.java:831) ~[cesymm-2.2.2.jar:2.2.2]
at org.biojava.nbio.structure.SubstructureIdentifier.loadStructure(SubstructureIdentifier.java:323) ~[cesymm-2.2.2.jar:2.2.2]
at org.biojava.nbio.structure.align.client.StructureName.loadStructure(StructureName.java:517) ~[cesymm-2.2.2.jar:2.2.2]
at org.biojava.nbio.structure.align.util.AtomCache.getStructure(AtomCache.java:503) ~[cesymm-2.2.2.jar:2.2.2]
at workers.CeSymmWorker.run(CeSymmWorker.java:58) [cesymm-2.2.2.jar:2.2.2]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136) [?:?]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) [?:?]
at java.lang.Thread.run(Thread.java:833) [?:?]
Caused by: sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
at sun.security.validator.PKIXValidator.doBuild(PKIXValidator.java:439) ~[?:?]
at sun.security.validator.PKIXValidator.engineValidate(PKIXValidator.java:306) ~[?:?]
at sun.security.validator.Validator.validate(Validator.java:264) ~[?:?]
at sun.security.ssl.X509TrustManagerImpl.checkTrusted(X509TrustManagerImpl.java:231) ~[?:?]
at sun.security.ssl.X509TrustManagerImpl.checkServerTrusted(X509TrustManagerImpl.java:132) ~[?:?]
at sun.security.ssl.CertificateMessage$T12CertificateConsumer.checkServerCerts(CertificateMessage.java:638) ~[?:?]
... 30 more
Caused by: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
at sun.security.provider.certpath.SunCertPathBuilder.build(SunCertPathBuilder.java:141) ~[?:?]
at sun.security.provider.certpath.SunCertPathBuilder.engineBuild(SunCertPathBuilder.java:126) ~[?:?]
at java.security.cert.CertPathBuilder.build(CertPathBuilder.java:297) ~[?:?]
at sun.security.validator.PKIXValidator.doBuild(PKIXValidator.java:434) ~[?:?]
at sun.security.validator.PKIXValidator.engineValidate(PKIXValidator.java:306) ~[?:?]
at sun.security.validator.Validator.validate(Validator.java:264) ~[?:?]
at sun.security.ssl.X509TrustManagerImpl.checkTrusted(X509TrustManagerImpl.java:231) ~[?:?]
at sun.security.ssl.X509TrustManagerImpl.checkServerTrusted(X509TrustManagerImpl.java:132) ~[?:?]
at sun.security.ssl.CertificateMessage$T12CertificateConsumer.checkServerCerts(CertificateMessage.java:638) ~[?:?]
... 30 more
And here is the example with a locally downloaded structure:
$ ./runCESymm.sh -J 1okc.pdb --stats=-
Name NumRepeats SymmGroup Refined SymmLevels SymmType RotationAngle ScrewTranslation UnrefinedTMscore UnrefinedRMSD SymmTMscore SymmRMSD RepeatLength CoreLength Length Coverage Repeats
1702 [pool-2-thread-1] ERROR org.biojava.nbio.structure.chem.DownloadChemCompProvider - Could not download https://files.rcsb.org/ligands/download/ASP.cif OR store locally to /var/folders/s0/64fs4yt56yq1x9szt115jtjj40rjv4/T/chemcomp/ASP.cif.gz Error =PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
1995 [pool-2-thread-1] ERROR org.biojava.nbio.structure.chem.DownloadChemCompProvider - Could not download https://files.rcsb.org/ligands/download/GLN.cif OR store locally to /var/folders/s0/64fs4yt56yq1x9szt115jtjj40rjv4/T/chemcomp/GLN.cif.gz Error =PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
2186 [pool-2-thread-1] ERROR org.biojava.nbio.structure.chem.DownloadChemCompProvider - Could not download https://files.rcsb.org/ligands/download/ALA.cif OR store locally to /var/folders/s0/64fs4yt56yq1x9szt115jtjj40rjv4/T/chemcomp/ALA.cif.gz Error =PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
2378 [pool-2-thread-1] ERROR org.biojava.nbio.structure.chem.DownloadChemCompProvider - Could not download https://files.rcsb.org/ligands/download/UNK.cif OR store locally to /var/folders/s0/64fs4yt56yq1x9szt115jtjj40rjv4/T/chemcomp/UNK.cif.gz Error =PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
2795 [pool-2-thread-1] ERROR org.biojava.nbio.structure.chem.DownloadChemCompProvider - Could not download https://files.rcsb.org/ligands/download/SER.cif OR store locally to /var/folders/s0/64fs4yt56yq1x9szt115jtjj40rjv4/T/chemcomp/SER.cif.gz Error =PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
2978 [pool-2-thread-1] ERROR org.biojava.nbio.structure.chem.DownloadChemCompProvider - Could not download https://files.rcsb.org/ligands/download/PHE.cif OR store locally to /var/folders/s0/64fs4yt56yq1x9szt115jtjj40rjv4/T/chemcomp/PHE.cif.gz Error =PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
3156 [pool-2-thread-1] ERROR org.biojava.nbio.structure.chem.DownloadChemCompProvider - Could not download https://files.rcsb.org/ligands/download/LEU.cif OR store locally to /var/folders/s0/64fs4yt56yq1x9szt115jtjj40rjv4/T/chemcomp/LEU.cif.gz Error =PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
3409 [pool-2-thread-1] ERROR org.biojava.nbio.structure.chem.DownloadChemCompProvider - Could not download https://files.rcsb.org/ligands/download/LYS.cif OR store locally to /var/folders/s0/64fs4yt56yq1x9szt115jtjj40rjv4/T/chemcomp/LYS.cif.gz Error =PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
3589 [pool-2-thread-1] ERROR org.biojava.nbio.structure.chem.DownloadChemCompProvider - Could not download https://files.rcsb.org/ligands/download/GLY.cif OR store locally to /var/folders/s0/64fs4yt56yq1x9szt115jtjj40rjv4/T/chemcomp/GLY.cif.gz Error =PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
3779 [pool-2-thread-1] ERROR org.biojava.nbio.structure.chem.DownloadChemCompProvider - Could not download https://files.rcsb.org/ligands/download/VAL.cif OR store locally to /var/folders/s0/64fs4yt56yq1x9szt115jtjj40rjv4/T/chemcomp/VAL.cif.gz Error =PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
3964 [pool-2-thread-1] ERROR org.biojava.nbio.structure.chem.DownloadChemCompProvider - Could not download https://files.rcsb.org/ligands/download/ILE.cif OR store locally to /var/folders/s0/64fs4yt56yq1x9szt115jtjj40rjv4/T/chemcomp/ILE.cif.gz Error =PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
4154 [pool-2-thread-1] ERROR org.biojava.nbio.structure.chem.DownloadChemCompProvider - Could not download https://files.rcsb.org/ligands/download/THR.cif OR store locally to /var/folders/s0/64fs4yt56yq1x9szt115jtjj40rjv4/T/chemcomp/THR.cif.gz Error =PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
4451 [pool-2-thread-1] ERROR org.biojava.nbio.structure.chem.DownloadChemCompProvider - Could not download https://files.rcsb.org/ligands/download/PRO.cif OR store locally to /var/folders/s0/64fs4yt56yq1x9szt115jtjj40rjv4/T/chemcomp/PRO.cif.gz Error =PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
4823 [pool-2-thread-1] ERROR org.biojava.nbio.structure.chem.DownloadChemCompProvider - Could not download https://files.rcsb.org/ligands/download/GLU.cif OR store locally to /var/folders/s0/64fs4yt56yq1x9szt115jtjj40rjv4/T/chemcomp/GLU.cif.gz Error =PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
5368 [pool-2-thread-1] ERROR org.biojava.nbio.structure.chem.DownloadChemCompProvider - Could not download https://files.rcsb.org/ligands/download/ARG.cif OR store locally to /var/folders/s0/64fs4yt56yq1x9szt115jtjj40rjv4/T/chemcomp/ARG.cif.gz Error =PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
5690 [pool-2-thread-1] ERROR org.biojava.nbio.structure.chem.DownloadChemCompProvider - Could not download https://files.rcsb.org/ligands/download/HIS.cif OR store locally to /var/folders/s0/64fs4yt56yq1x9szt115jtjj40rjv4/T/chemcomp/HIS.cif.gz Error =PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
6191 [pool-2-thread-1] ERROR org.biojava.nbio.structure.chem.DownloadChemCompProvider - Could not download https://files.rcsb.org/ligands/download/TYR.cif OR store locally to /var/folders/s0/64fs4yt56yq1x9szt115jtjj40rjv4/T/chemcomp/TYR.cif.gz Error =PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
6552 [pool-2-thread-1] ERROR org.biojava.nbio.structure.chem.DownloadChemCompProvider - Could not download https://files.rcsb.org/ligands/download/CYS.cif OR store locally to /var/folders/s0/64fs4yt56yq1x9szt115jtjj40rjv4/T/chemcomp/CYS.cif.gz Error =PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
6918 [pool-2-thread-1] ERROR org.biojava.nbio.structure.chem.DownloadChemCompProvider - Could not download https://files.rcsb.org/ligands/download/TRP.cif OR store locally to /var/folders/s0/64fs4yt56yq1x9szt115jtjj40rjv4/T/chemcomp/TRP.cif.gz Error =PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
7361 [pool-2-thread-1] ERROR org.biojava.nbio.structure.chem.DownloadChemCompProvider - Could not download https://files.rcsb.org/ligands/download/ASN.cif OR store locally to /var/folders/s0/64fs4yt56yq1x9szt115jtjj40rjv4/T/chemcomp/ASN.cif.gz Error =PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
7655 [pool-2-thread-1] ERROR org.biojava.nbio.structure.chem.DownloadChemCompProvider - Could not download https://files.rcsb.org/ligands/download/MET.cif OR store locally to /var/folders/s0/64fs4yt56yq1x9szt115jtjj40rjv4/T/chemcomp/MET.cif.gz Error =PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
8158 [pool-2-thread-1] ERROR org.biojava.nbio.structure.chem.DownloadChemCompProvider - Could not download https://files.rcsb.org/ligands/download/CXT.cif OR store locally to /var/folders/s0/64fs4yt56yq1x9szt115jtjj40rjv4/T/chemcomp/CXT.cif.gz Error =PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
8327 [pool-2-thread-1] ERROR org.biojava.nbio.structure.chem.DownloadChemCompProvider - Could not download https://files.rcsb.org/ligands/download/CDL.cif OR store locally to /var/folders/s0/64fs4yt56yq1x9szt115jtjj40rjv4/T/chemcomp/CDL.cif.gz Error =PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
8510 [pool-2-thread-1] ERROR org.biojava.nbio.structure.chem.DownloadChemCompProvider - Could not download https://files.rcsb.org/ligands/download/LDM.cif OR store locally to /var/folders/s0/64fs4yt56yq1x9szt115jtjj40rjv4/T/chemcomp/LDM.cif.gz Error =PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
9553 [pool-2-thread-1] ERROR org.biojava.nbio.structure.chem.DownloadChemCompProvider - Could not download https://files.rcsb.org/ligands/download/PC1.cif OR store locally to /var/folders/s0/64fs4yt56yq1x9szt115jtjj40rjv4/T/chemcomp/PC1.cif.gz Error =PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
9729 [pool-2-thread-1] ERROR org.biojava.nbio.structure.chem.DownloadChemCompProvider - Could not download https://files.rcsb.org/ligands/download/HOH.cif OR store locally to /var/folders/s0/64fs4yt56yq1x9szt115jtjj40rjv4/T/chemcomp/HOH.cif.gz Error =PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
1okc.pdb 3 C3 true 1 CLOSED 119.99 0.00 0.81 2.31 0.78 2.25 83 249 291 0.86 1OKC.A_4-92;1OKC.A_110-195;1OKC.A_207-292
To confirm the version:
$ ./runCESymm.sh --version
CE-Symm 2.2.2
That's interesting. It looks like your java doesn't like the security certificates from rcsb.org for some reason.
Could you also provide what's the output of command java -version
? And what is your OS?
Sure. I ran this on masOSCatalina, where I have:
$ java --version
java 17 2021-09-14 LTS
Java(TM) SE Runtime Environment (build 17+35-LTS-2724)
Java HotSpot(TM) 64-Bit Server VM (build 17+35-LTS-2724, mixed mode, sharing)
I just retested this on a Linux machine with CentOs 7 and java openjdk version "1.8.0_322", where it worked without errors. Is it something about my java version on my Mac then? I believe it worked just fine with the previous version of CE-Symm, while that was viable.
I've tried this in Mac OS Monterey, with java 18 (openjdk version "18" 2022-03-22) and it works fine for me. That is with cesymm version 2.2.3-SNAPSHOT (building from current master HEAD).
I'd recommend 2 things:
brew update && brew upgrade
)I updated to the version of java you are using and the result is the same, unfortunately. However, I have what I need right now in terms of functionality, so I am happy to proceed. Thanks.
Thank you for releasing updates, I really appreciate it. By the way, I've noticed that the latest release of CE-Symm (version 2.2.2 from February 2022) is having issues retrieving a structure from the PDB databank and when provided with a downloaded structure, is unable to retrieve the cif files for the amino acids. I imagine this is all due to the recent changes in the PDB databank but I was wondering if you have any notion of when this issue might be fixed.