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PRIDE-Toolsuite / ols-dialog

Java front end to the ontology lookup service (OLS 3.0)
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Failed to contact the OLS (from ProteomeXchange) #9

Closed ovigy closed 5 years ago

ovigy commented 5 years ago

Hello, I'm trying to upload a dataset to PRIDE via ProteomeXchange but the OLS can't be contacted (v3.4.14). I would like to add few annotations that are not proposed in the drop-down lists. I'm online and no firewall problems I guess. Is there any possibility to add those information (checked from the OLS web site) in another way? Thanks for your help. Best regards, Oana

PRIDE_errorOLS

sureshhewabi commented 5 years ago

Dear Oana,

Could you please give more details to replicate this issue?

  1. Your Java version
  2. PX-submission tool version
  3. What is the field you want to add?
  4. What is the value you you want to add(if you know it)?

Best Regards, Suresh

ovigy commented 5 years ago

Dear Suresh,

thanks for your reply:

Please find below the requested information :

  1. Java 8.45

  2. Px-submission-tool 2.4.10

  3. We would like to add few fields

If you can fix the problem, it could be great. Would I need to relaunch the submission tool?

Oana

Le 20/03/2019 à 08:48, sureshhewa a écrit :

Dear Oana,

Could you please give more details to replicate this issue?

  1. Your Java version
  2. PX-submission tool version
  3. What is the field you want to add?
  4. What is the value you you want to add(if you know it)?

Best Regards, Suresh

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/PRIDE-Toolsuite/ols-dialog/issues/9#issuecomment-474722261, or mute the thread https://github.com/notifications/unsubscribe-auth/AHTfqhxamtVw6Bvnj1Baald3JJx30a6cks5vYefCgaJpZM4b-qQS.

-- Oana VIGY

Plate-forme de Protéomique Fonctionnelle (FPP) IGF, CNRS, INSERM, Univ Montpellier 141 rue de la Cardonille 34 094 Montpellier Cedex 5, France

Tel: +33 (0)4 34 35 92 05 Site web : www.fpp.cnrs.fr http://www.fpp.cnrs.fr

sureshhewabi commented 5 years ago

Dear Oana,

I cannot replicate this issue from my side.

Screen Shot 2019-03-20 at 11 06 15

BWT, what is the Operating system you are using? Do you run the tool in a Virtual Environment?

Regards, Suresh

ovigy commented 5 years ago

Dear Suresh,

I'm working on a Windows7 computer.

I just tried on two other computers (Windows 7 and 10) and it works on both. So I will upload the data from a working computer.

Please find below the corresponing error I find in the log file (just see it, that's why I didn't send it first) on my PC.

2019-03-20 09:09:33,524 ERROR [AWT-EventQueue-0] u.a.e.p.t.o.d.t.i.GetOntologiesTask [GetOntologiesTask.java:96] Error when trying to access OLS: 2019-03-20 09:09:33,531 ERROR [AWT-EventQueue-0] u.a.e.p.t.o.d.t.AbstractTask [AbstractTask.java:294] uk.ac.ebi.pride.toolsuite.ols.dialog.task.impl.GetOntologiesTask@7f0e8608 failed on : org.springframework.web.client.ResourceAccessException: I/O error on GET request for "https://www.ebi.ac.uk/ols/api/ontologies?page=0&size=100": sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target; nested exception is javax.net.ssl.SSLHandshakeException: sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target org.springframework.web.client.ResourceAccessException: I/O error on GET request for "https://www.ebi.ac.uk/ols/api/ontologies?page=0&size=100": sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target; nested exception is javax.net.ssl.SSLHandshakeException: sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target     at org.springframework.web.client.RestTemplate.doExecute(RestTemplate.java:607)     at org.springframework.web.client.RestTemplate.execute(RestTemplate.java:572)     at org.springframework.web.client.RestTemplate.getForObject(RestTemplate.java:280)     at uk.ac.ebi.pride.utilities.ols.web.service.client.OLSClient.getOntologyQuery(OLSClient.java:425)     at uk.ac.ebi.pride.utilities.ols.web.service.client.OLSClient.getOntologies(OLSClient.java:260)     at uk.ac.ebi.pride.toolsuite.ols.dialog.task.impl.GetOntologiesTask.doInBackground(GetOntologiesTask.java:48)     at javax.swing.SwingWorker$1.call(Unknown Source)     at java.util.concurrent.FutureTask.run(Unknown Source)     at javax.swing.SwingWorker.run(Unknown Source)     at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)     at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)     at java.lang.Thread.run(Unknown Source) Caused by: javax.net.ssl.SSLHandshakeException: 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.ssl.Alerts.getSSLException(Unknown Source)     at sun.security.ssl.SSLSocketImpl.fatal(Unknown Source)     at sun.security.ssl.Handshaker.fatalSE(Unknown Source)     at sun.security.ssl.Handshaker.fatalSE(Unknown Source)     at sun.security.ssl.ClientHandshaker.serverCertificate(Unknown Source)     at sun.security.ssl.ClientHandshaker.processMessage(Unknown Source)     at sun.security.ssl.Handshaker.processLoop(Unknown Source)     at sun.security.ssl.Handshaker.process_record(Unknown Source)     at sun.security.ssl.SSLSocketImpl.readRecord(Unknown Source)     at sun.security.ssl.SSLSocketImpl.performInitialHandshake(Unknown Source)     at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source)     at sun.security.ssl.SSLSocketImpl.startHandshake(Unknown Source)     at sun.net.www.protocol.https.HttpsClient.afterConnect(Unknown Source)     at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source)     at sun.net.www.protocol.https.HttpsURLConnectionImpl.connect(Unknown Source)     at org.springframework.http.client.SimpleBufferingClientHttpRequest.executeInternal(SimpleBufferingClientHttpRequest.java:80)     at org.springframework.http.client.AbstractBufferingClientHttpRequest.executeInternal(AbstractBufferingClientHttpRequest.java:48)     at org.springframework.http.client.AbstractClientHttpRequest.execute(AbstractClientHttpRequest.java:53)     at org.springframework.web.client.RestTemplate.doExecute(RestTemplate.java:596)     ... 11 common frames omitted 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(Unknown Source)     at sun.security.validator.PKIXValidator.engineValidate(Unknown Source)     at sun.security.validator.Validator.validate(Unknown Source)     at sun.security.ssl.X509TrustManagerImpl.validate(Unknown Source)     at sun.security.ssl.X509TrustManagerImpl.checkTrusted(Unknown Source)     at sun.security.ssl.X509TrustManagerImpl.checkServerTrusted(Unknown Source)     ... 26 common frames omitted Caused by: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target     at sun.security.provider.certpath.SunCertPathBuilder.build(Unknown Source)     at sun.security.provider.certpath.SunCertPathBuilder.engineBuild(Unknown Source)     at java.security.cert.CertPathBuilder.build(Unknown Source)     ... 32 common frames omitted

Best regards,

Oana

Le 20/03/2019 à 10:13, sureshhewa a écrit :

Dear Oana,

I cannot replicate this issue from my side.

Screen Shot 2019-03-20 at 11 06 15 https://user-images.githubusercontent.com/5387193/54672452-b7f6d180-4b00-11e9-8b89-a6125ca0d67a.png

BWT, what is the Operating system you are using? Do you run the tool in a Virtual Environment?

Regards, Suresh

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/PRIDE-Toolsuite/ols-dialog/issues/9#issuecomment-474747148, or mute the thread https://github.com/notifications/unsubscribe-auth/AHTfqpj6fFxz2I24dOuiPrgnEoQU4_T3ks5vYfu-gaJpZM4b-qQS.

-- Oana VIGY

Plate-forme de Protéomique Fonctionnelle (FPP) IGF, CNRS, INSERM, Univ Montpellier 141 rue de la Cardonille 34 094 Montpellier Cedex 5, France

Tel: +33 (0)4 34 35 92 05 Site web : www.fpp.cnrs.fr http://www.fpp.cnrs.fr