QTM fails to run on OS X
arnikz opened this issue · comments
./QTM articles.txt
Solr server has been restarted.
--------------------------------------------
===============
QTLTableMiner++
===============
Input List: [PMC4321030, PMC4266912]
xml file for PMC4321030 not found
Exception in thread "main" java.lang.NullPointerException
at readers.PmcMetaReader.<init>(PmcMetaReader.java:58)
at qtm.QtmMain.main(QtmMain.java:103)
the update code in this branch gives
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(Alerts.java:192)
at sun.security.ssl.SSLSocketImpl.fatal(SSLSocketImpl.java:1949)
at sun.security.ssl.Handshaker.fatalSE(Handshaker.java:302)
at sun.security.ssl.Handshaker.fatalSE(Handshaker.java:296)
at sun.security.ssl.ClientHandshaker.serverCertificate(ClientHandshaker.java:1509)
at sun.security.ssl.ClientHandshaker.processMessage(ClientHandshaker.java:216)
at sun.security.ssl.Handshaker.processLoop(Handshaker.java:979)
at sun.security.ssl.Handshaker.process_record(Handshaker.java:914)
at sun.security.ssl.SSLSocketImpl.readRecord(SSLSocketImpl.java:1062)
at sun.security.ssl.SSLSocketImpl.performInitialHandshake(SSLSocketImpl.java:1375)
at sun.security.ssl.SSLSocketImpl.startHandshake(SSLSocketImpl.java:1403)
at sun.security.ssl.SSLSocketImpl.startHandshake(SSLSocketImpl.java:1387)
at sun.net.www.protocol.https.HttpsClient.afterConnect(HttpsClient.java:559)
at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:185)
at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1513)
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441)
at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:254)
at java.net.URL.openStream(URL.java:1038)
at org.apache.commons.io.FileUtils.copyURLToFile(FileUtils.java:1478)
at readers.PmcMetaReader.pmcDowloadXml(PmcMetaReader.java:528)
at qtm.QtmMain.main(QtmMain.java:94)
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:387)
at sun.security.validator.PKIXValidator.engineValidate(PKIXValidator.java:292)
at sun.security.validator.Validator.validate(Validator.java:260)
at sun.security.ssl.X509TrustManagerImpl.validate(X509TrustManagerImpl.java:324)
at sun.security.ssl.X509TrustManagerImpl.checkTrusted(X509TrustManagerImpl.java:229)
at sun.security.ssl.X509TrustManagerImpl.checkServerTrusted(X509TrustManagerImpl.java:124)
at sun.security.ssl.ClientHandshaker.serverCertificate(ClientHandshaker.java:1491)
... 16 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:146)
at sun.security.provider.certpath.SunCertPathBuilder.engineBuild(SunCertPathBuilder.java:131)
at java.security.cert.CertPathBuilder.build(CertPathBuilder.java:280)
at sun.security.validator.PKIXValidator.doBuild(PKIXValidator.java:382)
... 22 more
PMC4321030.xml
PMC4321030.xml
PMC4321030.xml
Processing article:
PMC4321030
---------------------------------------------
[Fatal Error] :-1:-1: Premature end of file.
org.xml.sax.SAXParseException; Premature end of file.
at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)
at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source)
at readers.PmcMetaReader.read(PmcMetaReader.java:121)
at qtm.QtmMain.main(QtmMain.java:104)
Problem in processing xml file
Exception in thread "main" java.lang.NullPointerException
at qtm.Article.setNumQTLtables(Article.java:63)
at readers.PmcMetaReader.read(PmcMetaReader.java:158)
at qtm.QtmMain.main(QtmMain.java:104
export JAVA_HOME="/Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/"
seems to solve this issue