[base] Can't find getting started guide

2009-09-15 Thread Daniel Octavio Palenzuela Gardon 
Hi,

Iam new in BASE and I wanted to start from getting_started guide that outlines 
the first steps with BASE 2. I tried next link 
http://base.thep.lu.se/chrome/site/doc/user/getting_started.html  but 
unfortunately, this page is not found in the web. Can someone help me to find 
started guide for BASE2?.



Many thanks

Daniel
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[base] Can't export data to Tmev

2009-09-23 Thread Daniel Octavio Palenzuela Gardon 
Hi all,

We installed Tmev pluging in BASE and we are trying to export data to Mev but 
we receive below error. Could someone give us a  help to solve this problem.??
Regards
Daniel

Error:

Permission denied: Not allowed to read Directory[id=501; name=raw data]
Show
Permission denied: Not allowed to read Directory[id=501; name=raw data]
 net.sf.basedb.core.PermissionDeniedException: Permission denied: Not allowed 
to read Directory[id=501; name=raw data]
...at net.sf.basedb.core.BasicItem.checkPermission(BasicItem.java:110)
...at net.sf.basedb.core.DbControl.getItem(DbControl.java:824)
...at net.sf.basedb.core.DbControl.loadItem(DbControl.java:709)
...at net.sf.basedb.core.Directory.getById(Directory.java:197)
...at net.sf.basedb.core.Directory.getByPath(Directory.java:217)
...at net.sf.basedb.core.File.getByPath(File.java:180)
...at 
net.sf.basedb.core.plugin.AbstractExporterPlugin.pathCanBeUsed(AbstractExporterPlugin.java:363)
...at 
net.sf.basedb.mev.plugin.TdmsExporterPlugin.configure(TdmsExporterPlugin.java:163)
...at 
net.sf.basedb.core.PluginConfigurationRequest.invoke(PluginConfigurationRequest.java:114)
...at org.apache.jsp.common.plugin.index_jsp._jspService(index_jsp.java:493)
...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:70)
...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:293)
...at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:849)
...at 
org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:583)
...at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:454)
...at java.lang.Thread.run(Unknown Source)

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developing skills, take BlackBerry mobile applications to market and stay 
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Re: [base] Can't export data to Tmev

2009-09-24 Thread Daniel Octavio Palenzuela Gardon 
I have logged as postgres the default administrator of BASE, which suppose to 
have full access. Do I have to create a new user??

Regards
Daniel


Daniel Octavio Palenzuela Gardon wrote:
> Hi all,
>
>
>
> We installed Tmev pluging in BASE and we are trying to export data to
> Mev but we receive below error. Could someone give us a  help to solve
> this problem.??

It seems like the logged in user doesn't have permission to access the
"raw data" directory.

/Nicklas

From: Daniel Octavio Palenzuela Gardon
Sent: Wednesday, September 23, 2009 12:33 PM
To: 'basedb-users@lists.sourceforge.net'
Subject: Can't export data to Tmev

Hi all,

We installed Tmev pluging in BASE and we are trying to export data to Mev but 
we receive below error. Could someone give us a  help to solve this problem.??
Regards
Daniel

Error:

Permission denied: Not allowed to read Directory[id=501; name=raw data]
Show
Permission denied: Not allowed to read Directory[id=501; name=raw data]
 net.sf.basedb.core.PermissionDeniedException: Permission denied: Not allowed 
to read Directory[id=501; name=raw data]
...at net.sf.basedb.core.BasicItem.checkPermission(BasicItem.java:110)
...at net.sf.basedb.core.DbControl.getItem(DbControl.java:824)
...at net.sf.basedb.core.DbControl.loadItem(DbControl.java:709)
...at net.sf.basedb.core.Directory.getById(Directory.java:197)
...at net.sf.basedb.core.Directory.getByPath(Directory.java:217)
...at net.sf.basedb.core.File.getByPath(File.java:180)
...at 
net.sf.basedb.core.plugin.AbstractExporterPlugin.pathCanBeUsed(AbstractExporterPlugin.java:363)
...at 
net.sf.basedb.mev.plugin.TdmsExporterPlugin.configure(TdmsExporterPlugin.java:163)
...at 
net.sf.basedb.core.PluginConfigurationRequest.invoke(PluginConfigurationRequest.java:114)
...at org.apache.jsp.common.plugin.index_jsp._jspService(index_jsp.java:493)
...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:70)
...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:293)
...at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:849)
...at 
org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:583)
...at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:454)
...at java.lang.Thread.run(Unknown Source)

--
Come build with us! The BlackBerry® Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay 
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Re: [base] Can't export data to Tmev

2009-09-26 Thread Daniel Octavio Palenzuela Gardon 
During the installation of Tmev there is a step to create a plugin by clicking 
the 'New' button on the 'Administrate -> Plugins -> Definitions' page. After 
this step we cannot see any new Mev plugin in Definition page. Where we can 
find TDMS exporter plugin to verify its permissions options?.

By other side, when we try to launch Mev in the "Tools" column when viewing 
bioassay sets of an experiment, there is a file with extension ...TDMS.TXT that 
it`s suppose to be save in raw data, but when we do browse, there isn't any 
file with this extension in raw data folder.

Regards
Daniel





Daniel Octavio Palenzuela Gardon wrote:
> I have logged as postgres the default administrator of BASE, which
> suppose to have full access. Do I have to create a new user??
>

No, you don't need another user. The root user should have full access.
Are you sure that you are using the correct account? Have you modified
the permissions for the TDMS exporter plug-in? It should be using the
'no permissions' option.

From: Daniel Octavio Palenzuela Gardon
Sent: Thursday, September 24, 2009 4:59 PM
To: 'basedb-users@lists.sourceforge.net'
Subject: RE: Can't export data to Tmev

I have logged as postgres the default administrator of BASE, which suppose to 
have full access. Do I have to create a new user??

Regards
Daniel


Daniel Octavio Palenzuela Gardon wrote:
> Hi all,
>
>
>
> We installed Tmev pluging in BASE and we are trying to export data to
> Mev but we receive below error. Could someone give us a  help to solve
> this problem.??

It seems like the logged in user doesn't have permission to access the
"raw data" directory.

/Nicklas

From: Daniel Octavio Palenzuela Gardon
Sent: Wednesday, September 23, 2009 12:33 PM
To: 'basedb-users@lists.sourceforge.net'
Subject: Can't export data to Tmev

Hi all,

We installed Tmev pluging in BASE and we are trying to export data to Mev but 
we receive below error. Could someone give us a  help to solve this problem.??
Regards
Daniel

Error:

Permission denied: Not allowed to read Directory[id=501; name=raw data]
Show
Permission denied: Not allowed to read Directory[id=501; name=raw data]
 net.sf.basedb.core.PermissionDeniedException: Permission denied: Not allowed 
to read Directory[id=501; name=raw data]
...at net.sf.basedb.core.BasicItem.checkPermission(BasicItem.java:110)
...at net.sf.basedb.core.DbControl.getItem(DbControl.java:824)
...at net.sf.basedb.core.DbControl.loadItem(DbControl.java:709)
...at net.sf.basedb.core.Directory.getById(Directory.java:197)
...at net.sf.basedb.core.Directory.getByPath(Directory.java:217)
...at net.sf.basedb.core.File.getByPath(File.java:180)
...at 
net.sf.basedb.core.plugin.AbstractExporterPlugin.pathCanBeUsed(AbstractExporterPlugin.java:363)
...at 
net.sf.basedb.mev.plugin.TdmsExporterPlugin.configure(TdmsExporterPlugin.java:163)
...at 
net.sf.basedb.core.PluginConfigurationRequest.invoke(PluginConfigurationRequest.java:114)
...at org.apache.jsp.common.plugin.index_jsp._jspService(index_jsp.java:493)
...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:70)
...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:293)
...at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:849)
...at 
org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:583)
...at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:454)
...at java.lang.Thread.run(Unknown Source)

-

Re: [base] Can't export data to Tmev

2009-09-28 Thread Daniel Octavio Palenzuela Gardon 
Dear Niklas

The filters were checked in both case and nor Mev plugin is created neither 
file TDMS.TXT is saved.
Do you have any other suggestion to solve this problem??
Regards
Daniel


Daniel Octavio Palenzuela Gardon wrote:
> During the installation of Tmev there is a step to create a plugin by
> clicking the 'New' button on the 'Administrate -> Plugins ->
> Definitions' page. After this step we cannot see any new Mev plugin in
> Definition page. Where we can find TDMS exporter plugin to verify its
> permissions options?.

Please make sure that you remove all filters from the list page. Search
for 'MeV%' in the name column.


> By other side, when we try to launch Mev in the "Tools" column when
> viewing bioassay sets of an experiment, there is a file with extension
> ...TDMS.TXT that it`s suppose to be save in raw data, but when we do
> browse, there isn't any file with this extension in raw data folder.

Again... check your filters
--
Come build with us! The BlackBerry® Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay 
ahead of the curve. Join us from November 9-12, 2009. Register now!
http://p.sf.net/sfu/devconf___
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basedb-users@lists.sourceforge.net
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Re: [base] can't export data to Mev

2009-09-29 Thread Daniel Octavio Palenzuela Gardon 
Dear Jari
We checked the directory we assigned for experiment (template/raw data). No Mev 
files appears here, neither in home directory. Yesterday I sent Tomcat's log 
file with error that perhaps explain why the Mev files are not saved.
Any help will be highly appreciated
Regards
Daniel


Nicklas Nordborg wrote:
> Daniel Octavio Palenzuela Gardon wrote:
>> By other side, when we try to launch Mev in the "Tools" column when
>> viewing bioassay sets of an experiment, there is a file with extension
>> ...TDMS.TXT that it`s suppose to be save in raw data, but when we do
>> browse, there isn't any file with this extension in raw data folder.
>
> Again... check your filters.

And remember, the MeV generated file ends up in the directory you
assigned for your experiment when the experiment was created. If you did
not set a directory for your experiment, the files end up in your hone
directory.


Cheers,

Jari
--
Come build with us! The BlackBerry® Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay 
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The BASE general discussion mailing list
basedb-users@lists.sourceforge.net
unsubscribe: send a mail with subject "unsubscribe" to
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