Hi Iry, I know i am not really helpful here but just to make you aware that rc7 was never officially released and we recommend that people work with our latest official release: rc6
a On Thu, Jan 24, 2013 at 7:03 PM, Iry Witham <[email protected]> wrote: > I have been working on this for some time with little success. I have > finally gotten the portal to display in my browser. However, I have the > following issues: > > 1. I can no longer launch martconfigurator or martrunner. I get the > following errors: > > Starting MartConfigurator please wait .... Exception in thread "main" > java.lang.NoClassDefFoundError: > org.biomart.configurator.test.MartConfigurator Caused by: > java.lang.ClassNotFoundException: > org.biomart.configurator.test.MartConfigurator at > java.net.URLClassLoader.findClass(URLClassLoader.java:421) at > java.lang.ClassLoader.loadClass(ClassLoader.java:652) at > sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:346) at > java.lang.ClassLoader.loadClass(ClassLoader.java:618) Could not find the > main class: org.biomart.configurator.test.MartConfigurator. Program will > exit. biomart@g1-biomart:~/biomart_0_8/release-0_8-candidate_6> > ./scripts/martrunner.sh Starting MartRunner please wait .... Exception in > thread "main" java.lang.NoClassDefFoundError: > org.biomart.runner.view.cli.MartRunner Caused by: > java.lang.ClassNotFoundException: org.biomart.runner.view.cli.MartRunner at > java.net.URLClassLoader.findClass(URLClassLoader.java:421) at > java.lang.ClassLoader.loadClass(ClassLoader.java:652) at > sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:346) at > java.lang.ClassLoader.loadClass(ClassLoader.java:618) Could not find the > main class: org.biomart.runner.view.cli.MartRunner. Program will exit. > > The dist/logs/stdouterr.2013_01_24.log shows the following: > > Starting server > 2013-01-24 13:17:19,024 INFO [main:Log.java:164]: Loading resources from > org/biomart/configurator/resources/messages > 2013-01-24 13:17:19,027 INFO [main:Log.java:164]: Done loading resources > 2013-01-24 13:17:19,201 INFO [main:Log.java:164]: Loading resources from > org/biomart/configurator/resources/messages > 2013-01-24 13:17:19,202 INFO [main:Log.java:164]: Done loading resources > 2013-01-24 13:17:20,441 INFO [main:Log.java:164]: Initialize source schema > 2013-01-24 13:17:20,503 INFO [main:Log.java:164]: done synchronize > 2013-01-24 13:17:20,563 INFO [main:Log.java:164]: Registered processor TSV > 2013-01-24 13:17:20,564 INFO [main:Log.java:164]: Registered processor > TSVX > 2013-01-24 13:17:20,565 INFO [main:Log.java:164]: Registered processor > SPARQLXML > 2013-01-24 13:17:20,565 INFO [main:Log.java:164]: Registered processor CSV > 2013-01-24 13:17:20,566 INFO [main:Log.java:164]: Registered processor > JSON > 2013-01-24 13:17:20,567 INFO [main:Log.java:164]: Adding to classpath: > /local/biomart/biomart_0_8/release-0_8-candidate_6/dist/plugins/sequence/lib/sequence-processor.jar > 2013-01-24 13:17:20,568 INFO [main:Log.java:164]: Added to classpath > file:/local/biomart/biomart_0_8/release-0_8-candidate_6/dist/plugins/sequence/lib/sequence-processor.jar > 2013-01-24 13:17:20,636 INFO [main:Log.java:164]: Registered processor > Sequence > 2013-01-24 13:17:20,956 INFO [main:Log.java:164]: Populating default > BioMart OAuth consumer: key=0e60157a903b15d9c6b96f7aaab0680b > 2013-01-24 13:17:20,958 INFO [main:Log.java:164]: Using Mock backend > 2013-01-24 13:17:20,961 INFO [main:Log.java:164]: Loading OAuth consumer: > BioMart > 2013-01-24 13:17:20,961 INFO [main:Log.java:164]: Added to classpath > file:/local/biomart/biomart_0_8/release-0_8-candidate_6/dist/web/etc/labels/ > Jan 24, 2013 1:17:20 PM > com.sun.xml.ws.transport.http.servlet.WSServletContextListener > contextInitialized > INFO: WSSERVLET12: JAX-WS context listener initializing > Jan 24, 2013 1:17:22 PM com.sun.xml.ws.server.MonitorBase createRoot > INFO: Metro monitoring rootname successfully set to: null > Jan 24, 2013 1:17:22 PM > com.sun.xml.ws.transport.http.servlet.WSServletDelegate <init> > INFO: WSSERVLET14: JAX-WS servlet initializing > Jan 24, 2013 1:17:22 PM com.sun.jersey.api.core.PackagesResourceConfig init > INFO: Scanning for root resource and provider classes in the packages: > org.biomart.api > org.codehaus.jackson.jaxrs > Jan 24, 2013 1:17:23 PM com.sun.jersey.api.core.ScanningResourceConfig > logClasses > INFO: Root resource classes found: > class org.biomart.api.rest.ViewerResource > class org.biomart.api.rest.UserResource > class org.biomart.api.rest.SPARQLResource > class org.biomart.api.rest.FileResource > class org.biomart.api.rest.PortalResource > class org.biomart.api.rest.QueryResource > class org.biomart.api.rest.ChartResource > Jan 24, 2013 1:17:23 PM com.sun.jersey.api.core.ScanningResourceConfig > logClasses > INFO: Provider classes found: > class org.codehaus.jackson.jaxrs.JsonParseExceptionMapper > class org.codehaus.jackson.jaxrs.JacksonJaxbJsonProvider > class org.biomart.api.rest.exceptions.FunctionalExceptionMapper > class org.codehaus.jackson.jaxrs.JsonMappingExceptionMapper > class org.biomart.api.rest.exceptions.BioMartApiExceptionMapper > class org.codehaus.jackson.jaxrs.JacksonJsonProvider > class org.biomart.api.rest.exceptions.TechnicalExceptionMapper > class org.biomart.api.rest.exceptions.NullPointerExceptionMapper > Jan 24, 2013 1:17:23 PM > com.sun.jersey.server.impl.application.WebApplicationImpl _initiate > INFO: Initiating Jersey application, version 'Jersey: 1.4-SNAPSHOT > 09/07/2010 08:23 PM' > Jan 24, 2013 1:17:24 PM > com.sun.jersey.guice.spi.container.GuiceComponentProviderFactory > getComponentProvider > INFO: Binding org.biomart.api.rest.PortalResource to > GuiceInstantiatedComponentProvider > Jan 24, 2013 1:17:24 PM > com.sun.jersey.guice.spi.container.GuiceComponentProviderFactory > getComponentProvider > INFO: Binding org.biomart.api.rest.QueryResource to > GuiceInstantiatedComponentProvider > Jan 24, 2013 1:17:24 PM > com.sun.jersey.guice.spi.container.GuiceComponentProviderFactory > getComponentProvider > INFO: Binding org.biomart.api.rest.SPARQLResource to > GuiceInstantiatedComponentProvider > Jan 24, 2013 1:17:24 PM > com.sun.jersey.guice.spi.container.GuiceComponentProviderFactory > getComponentProvider > INFO: Binding org.biomart.api.rest.UserResource to > GuiceInstantiatedComponentProvider > 2013-01-24 13:17:24,431 INFO [main:Log.java:164]: Loading OAuth consumer: > BioMart > Server started at : http://g1-biomart.jax.org:8080/ > Exception in thread "main" java.lang.InternalError: Can't connect to X11 > window server using 'localhost:10.0' as the value of the DISPLAY variable. > at sun.awt.X11GraphicsEnvironment.initDisplay(Native Method) > at > sun.awt.X11GraphicsEnvironment.access$100(X11GraphicsEnvironment.java:52) > at sun.awt.X11GraphicsEnvironment$1.run(X11GraphicsEnvironment.java:155) > at java.security.AccessController.doPrivileged(AccessController.java:202) > at sun.awt.X11GraphicsEnvironment.<clinit>(X11GraphicsEnvironment.java:131) > at java.lang.J9VMInternals.initializeImpl(Native Method) > at java.lang.J9VMInternals.initialize(J9VMInternals.java:200) > at java.lang.Class.forNameImpl(Native Method) > at java.lang.Class.forName(Class.java:136) > at > java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnvironment.java:68) > at sun.awt.X11.XToolkit.<clinit>(XToolkit.java:89) > at java.lang.J9VMInternals.initializeImpl(Native Method) > at java.lang.J9VMInternals.initialize(J9VMInternals.java:200) > at java.lang.Class.forNameImpl(Native Method) > at java.lang.Class.forName(Class.java:136) > at java.awt.Toolkit$2.run(Toolkit.java:846) > at java.security.AccessController.doPrivileged(AccessController.java:202) > at java.awt.Toolkit.getDefaultToolkit(Toolkit.java:838) > at java.awt.Desktop.isDesktopSupported(Desktop.java:163) > at org.biomart.start.Main.start(Main.java:173) > at org.biomart.start.Main.main(Main.java:195) > > 2. I am not at all formiluar with OpenId and would like to disable it > since this will be internal/private data for the immediate future. I will > be setting up LDAP/AD authentication. > > 3. My data does not appear to be available. I have configured both of > the biomart.properties files as follows: > > locale.name = en > locale.plurals = true > ################################################## > # HTTP SETTINGS > ################################################## > http.host = my_server > http.port = 8080 > # Only if public URL different from host+port above > http.url = http://my_server:8080/ > > ################################################## > # HTTPS SETTINGS > ################################################## > #https.port = 9043 > # Only if public URL different from host+port above > #https.url = https://localhost:9043 > > #ssl.keystore = etc/keystore > #ssl.password = OBF:19iy19j019j219j419j619j8 > #ssl.truststore = etc/keystore > #ssl.trustpassword = OBF:19iy19j019j219j419j619j8 > > # Set to false if x509 certificate verification is required > x509.trustall = true > > ################################################## > # SITE SETTINGS > ################################################## > #site.includes = > /local/biomart/biomart_0_8/release-0_8-candidate_6/web/includes > > ################################################## > # SESSIONS SETTINGS > ################################################## > # Timeout in seconds > session.timeout = 1200 > > session.connection = memory:// > > # It is recommended that you change the session backend to either JDBC > or Voldemort. > # > # See documentation for more details > # > # e.g. > session.connection = > jdbc:mysql://my_server:3306/g1biomart?user=biomart&password=G14TJ! > # OR > # session.connection = voldemort:// > > # Make sure you set an unique workername to each BioMart server instance > (defaults to biomart1) > #session.workername = biomart1 > > ################################################## > # OAUTH SETTINGS > ################################################## > oauth.consumer.key = 0e60157a903b15d9c6b96f7aaab0680b > oauth.consumer.secret = > OBF:1k8e1j1m19q51i6o1iz819q71idt1i6m1ikw1j8t1jfy1jkh1t331sw21ju61jri1shm1jd81ing1jrk1ju61iky1jg21shw1ju81jrk1svw1t331jn11jdc1j691ini1i9c1igd19q71j1m1i9a19q91iz81k5s > # If this is true, OAuth communication has to be secured > oauth.forcehttps = true > > ################################################## > # BIOMART APPLICATION SETTINGS > ################################################## > biomart.debug = false > biomart.registry.file = > /local/biomart/biomart_0_8/release-0_8-candidate_6/registry/G1Biomart.xml > biomart.registry.key.file = > /local/biomart/biomart_0_8/release-0_8-candidate_6/registry/.G1Biomart > biomart.sidebar = true > > ################################################## > # DATA STORAGE SETTINGS > ################################################## > datastore.engine = mock > datastore.url = none > > Thanks in advance, > > Iry > > The information in this email, including attachments, may be confidential > and is intended solely for the addressee(s). If you believe you received > this email by mistake, please notify the sender by return email as soon as > possible. > > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users > >
_______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
