Re: [base] Property '' has one or more invalid characters. Only a-z, A-Z, 0-9 and . is allowed.

2009-12-10 Thread michael watson (IAH-C)
Sorry if I seem ungrateful, I'm not :)
Just stressed... 

-Original Message-
From: Olivier Lefevre [mailto:lefev...@yahoo.com] 
Sent: 10 December 2009 15:55
To: BASE ML; michael watson (IAH-C)
Subject: RE: [base] Property '' has one or more invalid characters. Only a-z, 
A-Z, 0-9 and . is allowed.

Well, I agree with you that DC-BASE (and Hibernate!) can be
rather user-unfriendly at times but I am myself only a user.
I reported something that helped me once, no more no less.

Regards,

-- O.L.


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Re: [base] Property '' has one or more invalid characters. Only a-z, A-Z, 0-9 and . is allowed.

2009-12-10 Thread michael watson (IAH-C)
This is really quite a long winded way of doing things.

I just dumped my entire database, removed any record of virus_family in 
anything, dropped and recreated the database and imported everything into a 
clean DB.

And then base goes and inserts virus_family into "Contexts" table and I have 
the same problem.

This is really ridiculous.

Can no-one tell me the constraint (if there is one) that I have to remove to 
stop this from happening?!

I'm beginning to think a complete re-installation would be less work!

-Original Message-
From: Olivier Lefevre [mailto:lefev...@yahoo.com] 
Sent: 10 December 2009 15:28
To: BASE ML; michael watson (IAH-C)
Subject: RE: [base] Property '' has one or more invalid characters. Only a-z, 
A-Z, 0-9 and . is allowed.

> Ah ok, so BASE has built a constraint involving my new column name?

I would think so, although it's been 6 months since I had wade
into that. Suggestion: turn on full query tracing in the log by 
putting all this into your log4j.properties:

# logging queries in BASE
log4j.logger.net.sf.basedb.core=warn
log4j.logger.net.sf.basedb.core.query.ql=debug
log4j.logger.net.sf.basedb.core.query.bind=debug
log4j.logger.org.hibernate.SQL=debug

and then grep the log for "virus_name". Sorry I don't remember
where the log4j.properties file should go.

-- O.L.


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Re: [base] Property '' has one or more invalid characters. Only a-z, A-Z, 0-9 and . is allowed.

2009-12-10 Thread michael watson (IAH-C)
Ah ok, so BASE has built a constraint involving my new column name?

-Original Message-
From: Olivier Lefevre [mailto:lefev...@yahoo.com] 
Sent: 10 December 2009 15:06
To: BASE ML
Subject: Re: [base] Property '' has one or more invalid characters. Only a-z, 
A-Z, 0-9 and . is allowed.

> 'virus_family' has one or more invalid characters.
> Only a-z, A-Z, 0-9 and . is allowed.

I think that message comes from a Hibernate query and refers
to a column name used in constraints; check your constraints.

-- O.L. 

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Re: [base] Property '' has one or more invalid characters. Only a-z, A-Z, 0-9 and . is allowed.

2009-12-10 Thread michael watson (IAH-C)
Hi Nicklas

I would love to use the "Clear Filter" option, but I can't even get onto the 
page that displays that - when I click "View -> Reporters" it shows nothing 
apart from the menu bar and :

'virus_family' has one or more invalid characters. Only a-z, A-Z, 0-9 and . is 
allowed.

Thanks 
Mick

-Original Message-
From: Nicklas Nordborg [mailto:nick...@thep.lu.se] 
Sent: 10 December 2009 14:54
To: BASE ML
Subject: Re: [base] Property '' has one or more invalid characters. Only a-z, 
A-Z, 0-9 and . is allowed.

michael watson (IAH-C) wrote:
> OK, but we put it in accidentally.
> So we are now trying to remove it.
> 
> We have taken it out of extended properties, we have removed the columns from 
> the tables, and we ran the update scripts.
> 
> But we still get:
> 
> 'virus_family' has one or more invalid characters. Only a-z, A-Z, 0-9 and . 
> is allowed.

It is probably in a filter or sorting order for that table. Use the
"clear filter" setting from the "view/presets" dropdown and click on a
different column header to change the sort order. See also ticket
http://base.thep.lu.se/ticket/1014 for some more information.

/Nicklas

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Re: [base] Property '' has one or more invalid characters. Only a-z, A-Z, 0-9 and . is allowed.

2009-12-10 Thread michael watson (IAH-C)
OK, but we put it in accidentally.
So we are now trying to remove it.

We have taken it out of extended properties, we have removed the columns from 
the tables, and we ran the update scripts.

But we still get:

'virus_family' has one or more invalid characters. Only a-z, A-Z, 0-9 and . is 
allowed.

When we try and list reporters.

So somewhere we don't know about, virus_family is stored in the BASE2 database 
- is there some documentation that says where?

-Original Message-
From: Nicklas Nordborg [mailto:nick...@thep.lu.se] 
Sent: 10 December 2009 14:38
To: BASE ML
Subject: Re: [base] Property '' has one or more invalid characters. Only a-z, 
A-Z, 0-9 and . is allowed.

michael watson (IAH-C) wrote:
> Hello
> 
>  
> 
> I am running BASE 2.8.4 (sorry, I know it is old)
> 
>  
> 
> I have added extended properties to my database.
> 
>  
> 
> I added these after the database had been used, so what I have are some
> extra columns with no data in them in the reporter table
> 
>  
> 
> This is the XML I used:
> 
>  
> 
>  
> name="virus_family"
> 
> title="VirusFamily"
> 
> description="The virus family from
> which the reporter is derived"
> 
> column="virus_family"
> 
> type="string"
> 
> length="65535"
> 
> />
> 
>  
> 
> The update scripts ran fine.
> 
>  
> 
> When I view reporters, the column is there, but when I sort on the
> column, I get the error:
> 
>  
> 
> Property '' has one or more invalid characters. Only a-z, A-Z, 0-9 and .
> is allowed.


virus_family is not allowed as a name since it has an underscore in the
name.

/Nicklas

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[base] Property '' has one or more invalid characters. Only a-z, A-Z, 0-9 and . is allowed.

2009-12-10 Thread michael watson (IAH-C)
Hello

I am running BASE 2.8.4 (sorry, I know it is old)

I have added extended properties to my database.

I added these after the database had been used, so what I have are some extra 
columns with no data in them in the reporter table

This is the XML I used:



The update scripts ran fine.

When I view reporters, the column is there, but when I sort on the column, I 
get the error:

Property '' has one or more invalid characters. Only a-z, A-Z, 0-9 and . is 
allowed.

What's up here?

Mick

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.
The information contained in this message may be confidential or legally 
privileged and is intended solely for the addressee. If you have received this 
message in error please delete it & notify the originator immediately.  
Unauthorised use, disclosure, copying or alteration of this message is 
forbidden & may be unlawful.  The contents of this e-mail are the views of the 
sender and do not necessarily represent the views of the Institute.   This 
email, and associated attachments, has been checked locally for viruses but we 
can accept no responsibility once it has left our systems.  Communications on 
Institute computers are monitored to secure the effective operation of the 
systems and for other lawful purposes.

The Institute for Animal Health is a company limited by guarantee, registered 
in England no. 559784.
The Institute is also a registered charity, Charity Commissioners Reference No. 
228824

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Re: [base] scrollable result sets are not enabled

2009-12-10 Thread michael watson (IAH-C)
Restarted Catalina and Apache and it now seems to be working.

Ideally I'd like to stop this happening again in future though "restart the 
system" fixes I associate more with Microsoft than apache stuff!

-Original Message-
From: Nicklas Nordborg [mailto:nick...@thep.lu.se] 
Sent: 10 December 2009 09:02
To: BASE ML
Subject: Re: [base] scrollable result sets are not enabled

michael watson (IAH-C) wrote:
> Hi Nicklas
> 
> Thanks for replying :)
> 
> The server itself is unchanged, so this has probably come about due to some 
> kind of user input...

It seems like the log file doesn't contain much information. It's kind
of strange since I has expected that the source of the error would be
from the database. As it is now, it seems to stop somewhere in Hibernate
before even a query is executed. And since you also say that you get the
same error on every page it seems unlikely that it should have anything
to do with user input. It it more likely some kind of configuration
issue, though I don't know what it could be.

/Nicklas

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Re: [base] scrollable result sets are not enabled

2009-12-10 Thread michael watson (IAH-C)
:374)
at 
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:342)
at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:267)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at 
org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:630)
at 
org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:436)
at 
org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:374)
at 
org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:302)
at 
org.apache.jasper.runtime.PageContextImpl.doForward(PageContextImpl.java:696)
at 
org.apache.jasper.runtime.PageContextImpl.forward(PageContextImpl.java:667)
at 
org.apache.jsp.lims.arraydesigns.index_jsp._jspService(index_jsp.java:400)
at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
at 
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:374)
at 
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:342)
at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:267)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at 
net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:72)
at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at 
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
at 
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
at 
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:128)
at 
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
at 
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
at 
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:286)
at 
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:845)
at 
org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:583)
at 
org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:447)
at java.lang.Thread.run(Thread.java:636)
08-Dec-2009 22:49:05 org.apache.catalina.core.StandardHostValve custom
SEVERE: Exception Processing ErrorPage[exceptionType=java.lang.Throwable, 
location=/exception/exception.jsp]
java.lang.IllegalStateException
at org.apache.coyote.Response.reset(Response.java:297)
at org.apache.catalina.connector.Response.reset(Response.java:658)
at org.apache.catalina.connector.Response.reset(Response.java:925)
at 
org.apache.catalina.core.StandardHostValve.custom(StandardHostValve.java:417)
at 
org.apache.catalina.core.StandardHostValve.throwable(StandardHostValve.java:271)
at 
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:142)
at 
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
at 
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
at 
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:286)
at 
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:845)
at 
org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:583)
at 
org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:447)
at java.lang.Thread.run(Thread.java:636)

-Original Message-
From: Nicklas Nordborg [mailto:nick...@thep.lu.se] 
Sent: 10 December 2009 08:24
To: BASE ML
Subject: Re: [base] scrollable result sets are not enabled

michael watson (IAH-C) wrote:
> Just logged into my BASE server as root (version 2.8.4) and I can't "see" 
> anything - no users, no array designs, nothing.
> 
> All I see is at the top of each page a red bar that says:
> 
> scrollable result sets are not enabled


Can you check Tomcat's log file for a complete stack trace? The error
message you see in the browser is probably just a secondary error that

[base] scrollable result sets are not enabled

2009-12-08 Thread michael watson (IAH-C)
Just logged into my BASE server as root (version 2.8.4) and I can't "see" 
anything - no users, no array designs, nothing.

All I see is at the top of each page a red bar that says:

scrollable result sets are not enabled

Erm... huh?

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Re: [base] File path derivations

2009-11-03 Thread michael watson (IAH-C)
Maybe I can say something here, though Tory may want to add some more.

We decided not to go with a full plug-in for BASE simply because BASE 2 
plug-ins are so difficult to develop, and we needed to get something up and 
running quickly.  Sorry, I hope this comes across as constructive criticism 
rather...


From: Jari Häkkinen [j...@thep.lu.se]
Sent: 03 November 2009 13:35
To: BASE ML
Subject: Re: [base] File path derivations

Offord, Victoria wrote:
> I gather that the 2009 is the year and the 02 refers to the date the
> file was uploaded. How are the other numbers/values created as I
> wanted to add folders/directories from a program I am running which
> creates reults files for the data stored in BASE and wanted to keep
> them in line with the setup.

Why not store the files in BASE? Manual transform creator (1( might
help? Or using the same scheme as the MeV plug-in (2) that allows users
to stores data in BASE from within MeV?


(1)http://base.thep.lu.se/chrome/site/latest/html/appendix/appendix.coreplugins.html#coreplugins.analyze

(2)http://baseplugins.thep.lu.se/wiki/net.sf.basedb.mev


Jari

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[base] File already exists but I can't see it - and I am root

2009-05-22 Thread michael watson (IAH-C)
Hi

 

I'm just getting to grips with my newly installed BASE (2.8.4 (build
#4603; schema #63).

 

After messing around with reporter map and reporter configurations,
using the same file that I uploaded once, the file then disappeared from
view.  It's not in the view -> files section and I can't select it in
anything.

 

Yet when I try and upload it again, I get an error - file with that name
already exists.

 

Wut?

 

Thanks for the help

 

Mick

 

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.

The information contained in this message may be confidential or legally
privileged and is intended solely for the addressee. If you have
received this message in error please delete it & notify the originator
immediately.  Unauthorised use, disclosure, copying or alteration of
this message is forbidden & may be unlawful.  The contents of this
e-mail are the views of the sender and do not necessarily represent the
views of the Institute.   This email, and associated attachments, has
been checked locally for viruses but we can accept no responsibility
once it has left our systems.  Communications on Institute computers are
monitored to secure the effective operation of the systems and for other
lawful purposes.

 

The Institute for Animal Health is a company limited by guarantee,
registered in England no. 559784.  

The Institute is also a registered charity, Charity Commissioners
Reference No. 228824

 

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Re: [base] Installation error messages

2009-05-15 Thread michael watson (IAH-C)
ethodError:
javax.servlet.ServletContext.getContextPath()Ljava/lang/String;
at
net.sf.basedb.clients.web.servlet.ExtensionsServlet.init(ExtensionsServl
et.java:78)
at javax.servlet.GenericServlet.init(GenericServlet.java:212)
at
org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.jav
a:1139)
at
org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:966)
at
org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.j
ava:3956)
at
org.apache.catalina.core.StandardContext.start(StandardContext.java:4230
)
at
org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.ja
va:760)
at
org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:740)
at
org.apache.catalina.core.StandardHost.addChild(StandardHost.java:544)
at
org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:9
20)
at
org.apache.catalina.startup.HostConfig.deployDirectories(HostConfig.java
:883)
at
org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:492)
at
org.apache.catalina.startup.HostConfig.start(HostConfig.java:1138)
at
org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:31
1)
at
org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSu
pport.java:120)
at
org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1022)
at
org.apache.catalina.core.StandardHost.start(StandardHost.java:736)
at
org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1014)
at
org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443)
at
org.apache.catalina.core.StandardService.start(StandardService.java:448)
at
org.apache.catalina.core.StandardServer.start(StandardServer.java:700)
at org.apache.catalina.startup.Catalina.start(Catalina.java:552)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.jav
a:57)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:43)
at java.lang.reflect.Method.invoke(Method.java:616)
at
org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295)
at
org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433)
15-May-2009 14:55:51 org.apache.catalina.core.ApplicationContext log
INFO: ContextListener: contextInitialized()
15-May-2009 14:55:51 org.apache.catalina.core.ApplicationContext log
INFO: SessionListener: contextInitialized()
15-May-2009 14:55:51 org.apache.coyote.http11.Http11BaseProtocol start
INFO: Starting Coyote HTTP/1.1 on http-8080
15-May-2009 14:55:51 org.apache.jk.common.ChannelSocket init
INFO: JK: ajp13 listening on /0.0.0.0:8009
15-May-2009 14:55:51 org.apache.jk.server.JkMain start
INFO: Jk running ID=0 time=0/13  config=null
15-May-2009 14:55:51 org.apache.catalina.storeconfig.StoreLoader load
INFO: Find registry server-registry.xml at classpath resource
15-May-2009 14:55:51 org.apache.catalina.startup.Catalina start
INFO: Server startup in 7631 ms

-Original Message-
From: Nicklas Nordborg [mailto:nick...@thep.lu.se] 
Sent: 15 May 2009 13:58
To: BASE ML
Subject: Re: [base] Installation error messages

This is the same stacktrace as you sent before. If you clean up the log
file and
restart your server do you see anything in the log file that is related
to the
start up that happens before you even try to load the login page in a
web browser?
If not, enable the info-level logging as described in the previous mail
and restart
Tomcat again.

/Nicklas

michael watson (IAH-C) wrote:
> This from my Catalina.out file:
> 
> 13:44:51,875 ERROR [jsp]:723 - Servlet.service() for servlet jsp threw
> exception
> java.lang.NullPointerException
>   at
>
net.sf.basedb.clients.web.extensions.ExtensionsControl.useExtensions(Ext
> ensionsControl.java:249)
>   at
> org.apache.jsp.include.menu_jsp._jspService(menu_jsp.java:2186)
>   at
> org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98)
>   at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
>   at
>
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.ja
> va:328)
>   at
>
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:315)
>   at
> org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265)
>   at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
>   at
>
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
> tionFilterChain.java:269)
>   at
>
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
> erChain.java:188)
>   at
>
org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatc
> her.java:691)
>   at
&

Re: [base] Installation error messages

2009-05-15 Thread michael watson (IAH-C)
erWorkerThread.java:81)
at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool
.java:685)
at java.lang.Thread.run(Thread.java:636)
15-May-2009 13:44:51 org.apache.catalina.core.StandardHostValve custom
SEVERE: Exception Processing
ErrorPage[exceptionType=java.lang.Throwable,
location=/exception/exception.jsp]
org.apache.jasper.JasperException: Exception in JSP:
/exception/exception.jsp:146

143:}
144:
145: 
146: 
147:" 
148:style="width:90%;" messagestyle="height: 450px;">
149:


Stacktrace:
at
org.apache.jasper.servlet.JspServletWrapper.handleJspException(JspServle
tWrapper.java:467)
at
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.ja
va:371)
at
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:315)
at
org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:269)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:188)
at
org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatc
her.java:691)
at
org.apache.catalina.core.ApplicationDispatcher.processRequest(Applicatio
nDispatcher.java:471)
at
org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDisp
atcher.java:403)
at
org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispat
cher.java:301)
at
org.apache.catalina.core.StandardHostValve.custom(StandardHostValve.java
:364)
at
org.apache.catalina.core.StandardHostValve.throwable(StandardHostValve.j
ava:213)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java
:135)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java
:117)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.
java:108)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:1
51)
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:87
0)
at
org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.proc
essConnection(Http11BaseProtocol.java:665)
at
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint
.java:528)
at
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollow
erWorkerThread.java:81)
at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool
.java:685)
at java.lang.Thread.run(Thread.java:636)

-Original Message-
From: Nicklas Nordborg [mailto:nick...@thep.lu.se] 
Sent: 15 May 2009 13:29
To: BASE ML
Subject: Re: [base] Installation error messages

This is most likely a secondary problem that is caused by some other
problem
when the server is started. Can you check the log file in Tomcat to see
if there
are more information. If you can't find anything you can try to enable
INFO-level
logging in BASE by setting the following property in the
log4j.properties file.
This file is found in WEB-INF/classes. This is the property you should
set:

log4j.logger.net.sf.basedb=info

/Nicklas

michael watson (IAH-C) wrote:
> 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 invoker = 
> 972:
>
(ExtensionsInvoker)ExtensionsControl.useExtensions(conte
> xt, 
> 973:
> "net.sf.basedb.clients.web.menu.extensions");
> 974:ExtensionsControl ec = ExtensionsControl.get(dc);
> 975:ActionIterator it = invoker.iterate();
> 
> 


--
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unlimited royalty-free distribution of the report engine 
for externally facing server and web deployment. 
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--
C

Re: [base] Installation error messages

2009-05-15 Thread michael watson (IAH-C)
----
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)
> 
>

Re: [base] Installation error messages

2009-05-11 Thread michael watson (IAH-C)
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.EntityIden

Re: [base] Installation error messages

2009-05-11 Thread michael watson (IAH-C)
Trying to keep our test and production servers in sync :)

-Original Message-
From: Jari Häkkinen [mailto:j...@thep.lu.se] 
Sent: 08 May 2009 22:10
To: BASE ML
Subject: Re: [base] Installation error messages

And why not use the latest BASE 2.11?


Jari


Nicklas Nordborg wrote:
> 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&useServerPrepStmts=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:478)
>>
>> 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(SQLStateConverter.java:103)
>>
>> at 
>> org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:91)
>>
>> at 
>> org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43

[base] Installation error messages

2009-05-08 Thread michael watson (IAH-C)
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--
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Re: [base] BASE on 64-bit machine

2009-02-02 Thread michael watson (IAH-C)
Hi

This is a new installation, so if the only problem is a possible
migration problem, then we shall proceed with 64 bit

Thanks
Michael

-Original Message-
From: Nicklas Nordborg [mailto:nick...@thep.lu.se] 
Sent: 02 February 2009 11:10
To: BASE ML
Subject: Re: [base] BASE on 64-bit machine

michael watson (IAH-C) wrote:
> Dear All
> 
> Quick question with a quick answer I expect - our sys admin is
> recommending an upgrade to 64 bit version of Red Hat Enterprise 5.  
> 
> Are there are known problems with running BASE off a 64-bit server?  

If you are upgrading an existing 32-bit system and also want to run the
64-bit version of MySQL, you probably need to check how to upgrade the
database files. The binary file format used by MySQL may be different on
a 64-bit version.

/Nicklas


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[base] BASE on 64-bit machine

2009-02-02 Thread michael watson (IAH-C)
Dear All

Quick question with a quick answer I expect - our sys admin is
recommending an upgrade to 64 bit version of Red Hat Enterprise 5.  

Are there are known problems with running BASE off a 64-bit server?  

Thanks
Mick

 

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[base] Which import plugins are available in BASE?

2008-06-17 Thread michael watson (IAH-C)
Hi

Lets assume I have a huge load of array data I want to import into BASE.
Is this possible?  Having read the docs, I see there are some "import
plugins" but it doesn't say which kind they are.

Can someone tell me which import plugins are available, in whichever
version of BASE?

Thanks
Mick

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[base] Virtual Machine with BASE installed?

2007-10-05 Thread michael watson (IAH-C)
Hi 

Just wondering if anyone has a Virtual Machine with BASE installed on
it?

Thanks
Mick

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