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matthiaskoenig / cy3sbml

cy3sbml: SBML for Cytoscape 3
GNU Lesser General Public License v3.0
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FileNotFoundException due to http->https move of miriam registry breaks all latest cy3sbml versions #241

Closed matthiaskoenig closed 6 years ago

matthiaskoenig commented 6 years ago

The resources cannot be resolved anymore under the http addresses. The FileNotFoundException breaks basically every version of cy3sbml which includes the query of the 

https://www.ebi.ac.uk/miriam/main/export/xml/IdentifiersOrg-Registry.xml

This is a major problem, because none of the cy3sbml versions will startup anymore. No way to fix this. Everyone must update to next release with bugfix.

java.io.FileNotFoundException: /home/mkoenig/CytoscapeConfiguration/cy3sbml/IdentifiersOrg-Registry.xml (No such file or directory)
    at java.io.FileInputStream.open0(Native Method)
    at java.io.FileInputStream.open(FileInputStream.java:195)
    at java.io.FileInputStream.<init>(FileInputStream.java:138)
    at org.cy3sbml.miriam.RegistryUtil.getDataVersionDate(RegistryUtil.java:139)
    at org.cy3sbml.miriam.RegistryUtil.updateMiriamXMLWithNewer(RegistryUtil.java:70)
    at org.cy3sbml.CyActivator$1.run(CyActivator.java:315)
    at java.lang.Thread.run(Thread.java:748)
    at org.cy3sbml.CyActivator.start(CyActivator.java:319)
    at org.apache.felix.framework.util.SecureAction.startActivator(SecureAction.java:645)
    at org.apache.felix.framework.Felix.activateBundle(Felix.java:2146)
    at org.apache.felix.framework.Felix.startBundle(Felix.java:2064)
    at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:955)
    at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:942)
    at org.cytoscape.app.internal.manager.BundleApp.start(BundleApp.java:82)
    at org.cytoscape.app.internal.manager.AppManager$1.onFileCreate(AppManager.java:502)
    at org.cytoscape.app.internal.manager.AppManager$1.onFileChange(AppManager.java:523)
    at org.apache.commons.io.monitor.FileAlterationObserver.doMatch(FileAlterationObserver.java:400)
    at org.apache.commons.io.monitor.FileAlterationObserver.checkAndNotify(FileAlterationObserver.java:334)
    at org.apache.commons.io.monitor.FileAlterationObserver.checkAndNotify(FileAlterationObserver.java:304)
    at org.apache.commons.io.monitor.FileAlterationMonitor.run(FileAlterationMonitor.java:182)
    at java.lang.Thread.run(Thread.java:748)
ERROR (org.cy3sbml.CyActivator) - Could not start server!
java.lang.NullPointerException: null