Hmmm, I don't know if this is related, but having set up BASE, I can get
to http://localhost:8080/base no problem, but as soon as I log in:
HTTP Status 500 -
type Exception report
message
description The server encountered an internal error () that prevented
it from fulfilling this request.
exception
javax.servlet.ServletException: javax.servlet.jsp.JspTagException:
Exception in JSP: /include/menu.jsp:972
969: // Extensions menu
970: JspContext context = ExtensionsControl.createContext(dc,
pageContext);
971: ExtensionsInvoker<MenuItemAction> invoker =
972:
(ExtensionsInvoker<MenuItemAction>)ExtensionsControl.useExtensions(conte
xt,
973:
"net.sf.basedb.clients.web.menu.extensions");
974: ExtensionsControl ec = ExtensionsControl.get(dc);
975: ActionIterator<MenuItemAction> it = invoker.iterate();
Stacktrace:
org.apache.jasper.runtime.PageContextImpl.doHandlePageException(PageCont
extImpl.java:842)
org.apache.jasper.runtime.PageContextImpl.handlePageException(PageContex
tImpl.java:779)
org.apache.jsp.my_005fbase.index_jsp._jspService(index_jsp.java:604)
org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98)
javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.ja
va:328)
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:315)
org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265)
javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(Chara
cterEncodingFilter.java:72)
root cause
org.apache.jasper.JasperException: Exception in JSP:
/include/menu.jsp:972
969: // Extensions menu
970: JspContext context = ExtensionsControl.createContext(dc,
pageContext);
971: ExtensionsInvoker<MenuItemAction> invoker =
972:
(ExtensionsInvoker<MenuItemAction>)ExtensionsControl.useExtensions(conte
xt,
973:
"net.sf.basedb.clients.web.menu.extensions");
974: ExtensionsControl ec = ExtensionsControl.get(dc);
975: ActionIterator<MenuItemAction> it = invoker.iterate();
Stacktrace:
org.apache.jasper.servlet.JspServletWrapper.handleJspException(JspServle
tWrapper.java:467)
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.ja
va:389)
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:315)
org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265)
javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
org.apache.jasper.runtime.JspRuntimeLibrary.include(JspRuntimeLibrary.ja
va:965)
org.apache.jasper.runtime.PageContextImpl.include(PageContextImpl.java:6
05)
net.sf.basedb.clients.web.taglib.Body.doStartTag(Body.java:280)
org.apache.jsp.my_005fbase.index_jsp._jspService(index_jsp.java:223)
org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98)
javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.ja
va:328)
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:315)
org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265)
javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(Chara
cterEncodingFilter.java:72)
root cause
java.lang.NullPointerException
net.sf.basedb.clients.web.extensions.ExtensionsControl.useExtensions(Ext
ensionsControl.java:249)
org.apache.jsp.include.menu_jsp._jspService(menu_jsp.java:2186)
org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98)
javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.ja
va:328)
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:315)
org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265)
javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
org.apache.jasper.runtime.JspRuntimeLibrary.include(JspRuntimeLibrary.ja
va:965)
org.apache.jasper.runtime.PageContextImpl.include(PageContextImpl.java:6
05)
net.sf.basedb.clients.web.taglib.Body.doStartTag(Body.java:280)
org.apache.jsp.my_005fbase.index_jsp._jspService(index_jsp.java:223)
org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98)
javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.ja
va:328)
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:315)
org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265)
javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(Chara
cterEncodingFilter.java:72)
note The full stack trace of the root cause is available in the Apache
Tomcat/5.5.23 logs.
-----Original Message-----
From: michael watson (IAH-C) [mailto:michael.wat...@bbsrc.ac.uk]
Sent: 11 May 2009 12:10
To: BASE ML
Cc: nick...@thep.lu.se
Subject: Re: [base] Installation error messages
Hi Niklas
Thanks for the help - however, how do I actually do this?! :)
The initdb.sh script is a very small script and simply calls java. This
then creates connection url. So what file do I have to edit in order to
add 'characterEncoding=UTF-8' to the connection url?
Many thanks
Mick
-----Original Message-----
From: Nicklas Nordborg [mailto:nick...@thep.lu.se]
Sent: 08 May 2009 19:01
To: BASE ML
Subject: Re: [base] Installation error messages
It doesn't seem related to the Java version. If I remember correctly
there has been users with similar problems before and I think the
problem was a mismatch of the character encoding used by the MySQL
server and the character encoding used by the JDBC driver.
I recommend that you use the UTF-8 character set since from BASE 2.9
this is required for BASE to work. I can see that you connection url is
missing an encoding. Try adding 'characterEncoding=UTF-8' to it and see
if it helps.
/Nicklas
michael watson (IAH-C) wrote:
> Dear List
>
>
>
> I'm trying to install BASE 2.8.4 on a new server.
>
>
>
> We have Java 1.6 but I think it is the Red Hat OpenJDK version. We
also
> have MySQL 5.0.45
>
>
>
> Any clues appreciated!
>
>
>
> When I run initdb.sh I get:
>
>
>
> --System information-----------------------------
>
> BASE : 2.8.4
>
> Database :
>
jdbc:mysql://localhost/base2?useCursorFetch=true&defaultFetchSize=100&us
eServerPrepStmts=true
>
> Dialect : org.hibernate.dialect.MySQLInnoDBDialect
>
> JDBC : com.mysql.jdbc.Driver; version 5.1
>
> Java : OpenJDK Runtime Environment; 1.6.0-b09; Sun Microsystems
Inc.
>
> OS : Linux; amd64; 2.6.18-92.el5
>
> -------------------------------------------------
>
> Building database..........
>
> Database built successfully.
>
> Initialising database...
>
> --Creating quota types...
>
> --Creating quota...
>
> --Creating roles...
>
> --Creating users...
>
> --Creating groups...
>
> --Creating keys...
>
> --Creating protocol types...
>
> --Creating hardware types...
>
> --Creating hardware...
>
> --Creating software types...
>
> --Creating software...
>
> --Creating directories...
>
> --Creating file types...
>
> --Creating MIME types...
>
> --Creating plate geometries...
>
> --Creating plate mappings...
>
> --Creating labels...
>
> --Creating annotation types...
>
> --Creating clients...
>
> --Creating news...
>
> --Creating plugin definitions...
>
> --Creating example plugin configurations...
>
> --Creating formulas...
>
> --Creating job agents...
>
> --Creating data file types...
>
> --Creating platforms...
>
> Database initialised successfully.
>
> Updating database...
>
> Database updated successfully.
>
> Installing web application...
>
>
>
> net.sf.basedb.core.BaseException: could not insert:
> [net.sf.basedb.core.data.HelpData]
>
> at
> net.sf.basedb.plugins.HelpImporter.doImport(HelpImporter.java:395)
>
> at
>
net.sf.basedb.plugins.HelpImporter.installHelpTexts(HelpImporter.java:47
8)
>
> at
> net.sf.basedb.install.Webclient.installHelpTexts(Webclient.java:196)
>
> at net.sf.basedb.install.Webclient.install(Webclient.java:155)
>
> at net.sf.basedb.install.InitDB.main(InitDB.java:81)
>
> Caused by: net.sf.basedb.core.BaseException: could not insert:
> [net.sf.basedb.core.data.HelpData]
>
> at
> net.sf.basedb.core.HibernateUtil.saveData(HibernateUtil.java:1065)
>
> at net.sf.basedb.core.DbControl.commit(DbControl.java:381)
>
> at
> net.sf.basedb.plugins.HelpImporter.doImport(HelpImporter.java:386)
>
> ... 4 more
>
> Caused by: org.hibernate.exception.GenericJDBCException: could not
> insert: [net.sf.basedb.core.data.HelpData]
>
> at
>
org.hibernate.exception.SQLStateConverter.handledNonSpecificException(SQ
LStateConverter.java:103)
>
> at
>
org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java
:91)
>
> at
>
org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.
java:43)
>
> at
>
org.hibernate.id.insert.AbstractReturningDelegate.performInsert(Abstract
ReturningDelegate.java:40)
>
> at
>
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEn
tityPersister.java:2158)
>
> at
>
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEn
tityPersister.java:2638)
>
> at
>
org.hibernate.action.EntityIdentityInsertAction.execute(EntityIdentityIn
sertAction.java:48)
>
> at
org.hibernate.engine.ActionQueue.execute(ActionQueue.java:250)
>
> at
>
org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate
(AbstractSaveEventListener.java:298)
>
> at
>
org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSa
veEventListener.java:181)
>
> at
>
org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(Ab
stractSaveEventListener.java:107)
>
> at
>
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGenerat
edOrRequestedId(DefaultSaveOrUpdateEventListener.java:187)
>
> at
>
org.hibernate.event.def.DefaultSaveEventListener.saveWithGeneratedOrRequ
estedId(DefaultSaveEventListener.java:33)
>
> at
>
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransie
nt(DefaultSaveOrUpdateEventListener.java:172)
>
> at
>
org.hibernate.event.def.DefaultSaveEventListener.performSaveOrUpdate(Def
aultSaveEventListener.java:27)
>
> at
>
org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(
DefaultSaveOrUpdateEventListener.java:70)
>
> at
org.hibernate.impl.SessionImpl.fireSave(SessionImpl.java:535)
>
> at org.hibernate.impl.SessionImpl.save(SessionImpl.java:523)
>
> at org.hibernate.impl.SessionImpl.save(SessionImpl.java:519)
>
> at
> net.sf.basedb.core.HibernateUtil.saveData(HibernateUtil.java:1056)
>
> ... 6 more
>
> Caused by: java.sql.SQLException: Incorrect string value:
'\xD7</lbl...'
> for column 'description' at row 1
>
> at
com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1055)
>
> at
com.mysql.jdbc.SQLError.createSQLException(SQLError.java:956)
>
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3491)
>
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3423)
>
> at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1936)
>
> at
>
com.mysql.jdbc.ServerPreparedStatement.serverExecute(ServerPreparedState
ment.java:1328)
>
> at
>
com.mysql.jdbc.ServerPreparedStatement.executeInternal(ServerPreparedSta
tement.java:838)
>
> at
>
com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:20
19)
>
> at
>
com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:19
37)
>
> at
>
com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:19
22)
>
> at
>
com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeUpdate(NewProx
yPreparedStatement.java:105)
>
> at
>
org.hibernate.id.IdentityGenerator$GetGeneratedKeysDelegate.executeAndEx
tract(IdentityGenerator.java:73)
>
> at
>
org.hibernate.id.insert.AbstractReturningDelegate.performInsert(Abstract
ReturningDelegate.java:33)
>
> ... 22 more
>
>
>
> Head of Bioinformatics
> Institute for Animal Health
> Compton
> Berks
> RG20 7NN
> 01635 578411
>
> * *
>
> *Please consider the environment and don't print this e-mail unless
you
> really need to.*
>
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> privileged and is intended solely for the addressee. If you have
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>
>
>
>
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>
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------------------------------------------------------------------------
>
> _______________________________________________
> The BASE general discussion mailing list
> basedb-users@lists.sourceforge.net
> unsubscribe: send a mail with subject "unsubscribe" to
> basedb-users-requ...@lists.sourceforge.net
------------------------------------------------------------------------
------
The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
production scanning environment may not be a perfect world - but thanks
to
Kodak, there's a perfect scanner to get the job done! With the NEW KODAK
i700
Series Scanner you'll get full speed at 300 dpi even with all image
processing features enabled. http://p.sf.net/sfu/kodak-com
_______________________________________________
The BASE general discussion mailing list
basedb-users@lists.sourceforge.net
unsubscribe: send a mail with subject "unsubscribe" to
basedb-users-requ...@lists.sourceforge.net
------------------------------------------------------------------------
------
The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
production scanning environment may not be a perfect world - but thanks
to
Kodak, there's a perfect scanner to get the job done! With the NEW KODAK
i700
Series Scanner you'll get full speed at 300 dpi even with all image
processing features enabled. http://p.sf.net/sfu/kodak-com
_______________________________________________
The BASE general discussion mailing list
basedb-users@lists.sourceforge.net
unsubscribe: send a mail with subject "unsubscribe" to
basedb-users-requ...@lists.sourceforge.net
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