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
