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error on entrez-organism - this has been fixed

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error on entrez-organism - this has been fixed

Julie Sullivan-2
If you've gotten an error on entrez-organism, this is a bug in Java but
has been fixed. I would recommend switching to Java 8 but the bug has
been patched in Java 7 too.

http://stackoverflow.com/questions/6851461/java-why-does-ssl-handshake-give-could-not-generate-dh-keypair-exception

Below is the full stacktrace. As to why this has started happening now,
I assume the NCBI has changed something as they switch to HTTPS.

BUILD FAILED
/data/tools/intermine/prod/intermine/imbuild/integrate.xml:54: The
following error occurred while executing this line:
/data/tools/intermine/prod/intermine/bio/sources/entrez-organism/build.xml:18:
exception while retrieving organisms
        at
org.intermine.bio.dataconversion.EntrezOrganismRetriever.execute(EntrezOrganismRetriever.java:127)
        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
        at org.apache.tools.ant.Task.perform(Task.java:348)
        at org.apache.tools.ant.Target.execute(Target.java:390)
        at org.apache.tools.ant.Target.performTasks(Target.java:411)
        at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
        at
org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
        at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
        at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:442)
        at org.intermine.task.Integrate.performAction(Integrate.java:219)
        at org.intermine.task.Integrate.performAction(Integrate.java:131)
        at org.intermine.task.Integrate.execute(Integrate.java:123)
        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
        at org.apache.tools.ant.Task.perform(Task.java:348)
        at org.apache.tools.ant.Target.execute(Target.java:390)
        at org.apache.tools.ant.Target.performTasks(Target.java:411)
        at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
        at org.apache.tools.ant.Project.executeTarget(Project.java:1368)
        at
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
        at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
        at org.apache.tools.ant.Main.runBuild(Main.java:809)
        at org.apache.tools.ant.Main.startAnt(Main.java:217)
        at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
        at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
Caused by: javax.net.ssl.SSLException: java.lang.RuntimeException: Could
not generate DH keypair
        at com.sun.net.ssl.internal.ssl.Alerts.getSSLException(Alerts.java:190)
        at
com.sun.net.ssl.internal.ssl.SSLSocketImpl.fatal(SSLSocketImpl.java:1731)
        at
com.sun.net.ssl.internal.ssl.SSLSocketImpl.fatal(SSLSocketImpl.java:1692)
        at
com.sun.net.ssl.internal.ssl.SSLSocketImpl.handleException(SSLSocketImpl.java:1675)
        at
com.sun.net.ssl.internal.ssl.SSLSocketImpl.startHandshake(SSLSocketImpl.java:1204)
        at
com.sun.net.ssl.internal.ssl.SSLSocketImpl.startHandshake(SSLSocketImpl.java:1181)
        at
sun.net.www.protocol.https.HttpsClient.afterConnect(HttpsClient.java:434)
        at
sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:166)
        at
sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1172)
        at
sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:234)
        at org.apache.xerces.impl.XMLEntityManager.setupCurrentEntity(Unknown
Source)
        at org.apache.xerces.impl.XMLEntityManager.startEntity(Unknown Source)
        at org.apache.xerces.impl.XMLEntityManager.startDTDEntity(Unknown Source)
        at org.apache.xerces.impl.XMLDTDScannerImpl.setInputSource(Unknown Source)
        at
org.apache.xerces.impl.XMLDocumentScannerImpl$DTDDispatcher.dispatch(Unknown
Source)
        at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown
Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
        at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
        at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
        at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
        at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
        at org.intermine.util.SAXParser.parse(SAXParser.java:59)
        at
org.intermine.bio.dataconversion.EntrezOrganismRetriever.execute(EntrezOrganismRetriever.java:115)
        ... 31 more
Caused by: java.lang.RuntimeException: Could not generate DH keypair
        at com.sun.net.ssl.internal.ssl.DHCrypt.<init>(DHCrypt.java:106)
        at
com.sun.net.ssl.internal.ssl.ClientHandshaker.serverKeyExchange(ClientHandshaker.java:556)
        at
com.sun.net.ssl.internal.ssl.ClientHandshaker.processMessage(ClientHandshaker.java:183)
        at com.sun.net.ssl.internal.ssl.Handshaker.processLoop(Handshaker.java:593)
        at
com.sun.net.ssl.internal.ssl.Handshaker.process_record(Handshaker.java:529)
        at
com.sun.net.ssl.internal.ssl.SSLSocketImpl.readRecord(SSLSocketImpl.java:925)
        at
com.sun.net.ssl.internal.ssl.SSLSocketImpl.performInitialHandshake(SSLSocketImpl.java:1170)
        at
com.sun.net.ssl.internal.ssl.SSLSocketImpl.startHandshake(SSLSocketImpl.java:1197)
        ... 50 more
Caused by: java.security.InvalidAlgorithmParameterException: Prime size
must be multiple of 64, and can only range from 512 to 1024 (inclusive)
        at com.sun.crypto.provider.DHKeyPairGenerator.initialize(DashoA13*..)
        at
java.security.KeyPairGenerator$Delegate.initialize(KeyPairGenerator.java:627)
        at com.sun.net.ssl.internal.ssl.DHCrypt.<init>(DHCrypt.java:100)
        ... 57 more

Total time: 19 seconds
Mon Aug 29 19:12:43 PDT 2016

finished


ERROR: 256
failed with exit code 0: ant -v -Drelease=prod2 -Dsource=entrez-organism

---------

Let me know if this doesn't fix your problems!

Julie
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