Re: [base] batch importer plugin is available for testing now

2007-03-16 Thread Micha Bayer
Hi,


 Ok, so I made a rookie mistake and forgot to clear the filter ...

Happens to all of us :-)

 However, I never fully got
 through the installation without errors.  I now have the following
 problems:
 
 1)  I don't have an 'import' tab in the detail view of Experiments
(base
 2.1.1).  Does this appear only after the batch importer is correctly
 installed?

Yes it does. 


 2)  I can 'remove' the batch data importer, but it doesn't appear in
the
 trashcan. Is this what Micha was talking about earlier?
 

I take it by remove you mean delete? That's strange - I haven't seen
this behaviour. 

To avoid any ambiguities I would delete it from the database directly
and start afresh. 

Cheers

Micha



 Jeremy
 
 
 
 On 3/15/07, Nicklas Nordborg  [EMAIL PROTECTED]
 mailto:[EMAIL PROTECTED]  wrote:
 
   Jeremy Davis-Turak wrote:
On 3/14/07, Nicklas Nordborg [EMAIL PROTECTED] wrote:
Can someone please give us a hint about how to reproduce this
 behavior?
When I add a new plugin, BASE will complain if I enter an
 incorrect path.
   
Nicklas,
   
 To reproduce this error, I would try creating the definition
with
 the
wrong path.  Then, when this gives you an error, try again
with the
correct path.  That's when I got an error.
 
   I can't reproduce this. If I enter an incorrect path nothing
gets
 added
   to the database and the second attempt with the correct path is
 successful.
 
   
And, if there is an entry already in the database, what is
 stopping you
from using the web interface to edit the plugin definition
and
 enter the
correct path?
   
   
Unfortunately the definition doesn't appear in the web
interface
 after
this error, although clearly it made its way into some of the
 database
tables.
 
   Have you checked that you don't have any filters that prevents
it
 from
   being displayed?
 
   /Nicklas
 
 

-
 
   Take Surveys. Earn Cash. Influence the Future of IT
   Join SourceForge.net's Techsay panel and you'll get the chance
to
 share your
   opinions on IT  business topics through brief surveys-and earn
cash

http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DE
 VDEV

http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVD
EV
 
   ___
   The BASE general discussion mailing list
   basedb-users@lists.sourceforge.net mailto:basedb-
 [EMAIL PROTECTED]
   unsubscribe: send a mail with subject unsubscribe to
   [EMAIL PROTECTED]
 
 

_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

SCRI, Invergowrie, Dundee, DD2 5DA.  
The Scottish Crop Research Institute is a charitable company limited by 
guarantee. 
Registered in Scotland No: SC 29367.
Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.


DISCLAIMER:

This email is from the Scottish Crop Research Institute, but the views 
expressed by the sender are not necessarily the views of SCRI and its 
subsidiaries.  This email and any files transmitted with it are confidential 
to the intended recipient at the e-mail address to which it has been 
addressed.  It may not be disclosed or used by any other than that addressee.
If you are not the intended recipient you are requested to preserve this 
confidentiality and you must not use, disclose, copy, print or rely on this 
e-mail in any way. Please notify [EMAIL PROTECTED] quoting the 
name of the sender and delete the email from your system.

Although SCRI has taken reasonable precautions to ensure no viruses are 
present in this email, neither the Institute nor the sender accepts any 
responsibility for any viruses, and it is your responsibility to scan the email 
and the attachments (if any).


-
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT  business topics through brief surveys-and earn cash
http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV
___
The BASE general discussion mailing list
basedb-users@lists.sourceforge.net
unsubscribe: send a mail with subject unsubscribe to
[EMAIL PROTECTED]


Re: [base] batch importer plugin is available for testing now

2007-03-15 Thread Nicklas Nordborg
Jeremy Davis-Turak wrote:
 On 3/14/07, Nicklas Nordborg [EMAIL PROTECTED] wrote:
 Can someone please give us a hint about how to reproduce this behavior?
 When I add a new plugin, BASE will complain if I enter an incorrect path.
 
 Nicklas,
 
  To reproduce this error, I would try creating the definition with the
 wrong path.  Then, when this gives you an error, try again with the
 correct path.  That's when I got an error.

I can't reproduce this. If I enter an incorrect path nothing gets added 
to the database and the second attempt with the correct path is successful.

 
 And, if there is an entry already in the database, what is stopping you
 from using the web interface to edit the plugin definition and enter the
 correct path?

 
 Unfortunately the definition doesn't appear in the web interface after
 this error, although clearly it made its way into some of the database
 tables.

Have you checked that you don't have any filters that prevents it from 
being displayed?

/Nicklas


-
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT  business topics through brief surveys-and earn cash
http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV
___
The BASE general discussion mailing list
basedb-users@lists.sourceforge.net
unsubscribe: send a mail with subject unsubscribe to
[EMAIL PROTECTED]


Re: [base] batch importer plugin is available for testing now

2007-03-15 Thread Jeremy Davis-Turak

Ok, so I made a rookie mistake and forgot to clear the filter ...
The plugin is there, with the correct path.  However, I never fully got
through the installation without errors.  I now have the following problems:

1)  I don't have an 'import' tab in the detail view of Experiments (base
2.1.1).  Does this appear only after the batch importer is correctly
installed?
2)  I can 'remove' the batch data importer, but it doesn't appear in the
trashcan. Is this what Micha was talking about earlier?

Jeremy


On 3/15/07, Nicklas Nordborg [EMAIL PROTECTED] wrote:


Jeremy Davis-Turak wrote:
 On 3/14/07, Nicklas Nordborg [EMAIL PROTECTED] wrote:
 Can someone please give us a hint about how to reproduce this behavior?
 When I add a new plugin, BASE will complain if I enter an incorrect
path.

 Nicklas,

  To reproduce this error, I would try creating the definition with the
 wrong path.  Then, when this gives you an error, try again with the
 correct path.  That's when I got an error.

I can't reproduce this. If I enter an incorrect path nothing gets added
to the database and the second attempt with the correct path is
successful.


 And, if there is an entry already in the database, what is stopping you
 from using the web interface to edit the plugin definition and enter
the
 correct path?


 Unfortunately the definition doesn't appear in the web interface after
 this error, although clearly it made its way into some of the database
 tables.

Have you checked that you don't have any filters that prevents it from
being displayed?

/Nicklas


-
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share
your
opinions on IT  business topics through brief surveys-and earn cash
http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV
___
The BASE general discussion mailing list
basedb-users@lists.sourceforge.net
unsubscribe: send a mail with subject unsubscribe to
[EMAIL PROTECTED]

-
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT  business topics through brief surveys-and earn cash
http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV___
The BASE general discussion mailing list
basedb-users@lists.sourceforge.net
unsubscribe: send a mail with subject unsubscribe to
[EMAIL PROTECTED]


Re: [base] batch importer plugin is available for testing now

2007-03-14 Thread Micha Bayer
Hi,

Yes, I have had this happen too after giving it the wrong path. Sadly
the only way to get rid of the duplicate entry seems to be to delete
directly in the database. You need to find it in the data of the
PluginDefinitions table and delete the entry, but be aware that it will
keep refusing to delete it until all the dependent entries in other
tables have also been deleted.

I am not sure whether this is something that specific to this plugin or
whether it affects all other plugins the same way. Perhaps the dev team
could comment here. 

If it is a general issue we should perhaps add it to Trac as a bug.

Cheers

Micha

==
Dr Micha M Bayer
Bioinformatics Specialist
Genetics Programme
The Scottish Crop Research Institute
Invergowrie
Dundee
DD2 5DA
Scotland, UK
Telephone +44(0)1382 562731 ext. 2309
Fax +44(0)1382 562426
http://www.scri.sari.ac.uk/MichaBayer.htm
=
 

 -Original Message-
 From: [EMAIL PROTECTED] [mailto:basedb-users-
 [EMAIL PROTECTED] On Behalf Of Jeremy Davis-Turak
 Sent: 09 March 2007 19:38
 To: BASE ML
 Subject: Re: [base] batch importer plugin is available for testing now
 
 Hi,
 
 I am trying to install the batch data importer but I get the following
 error:
 Duplicate entry 'sbrn.base.BatchDataImporter' for key 2
 (I tried doing it once but I typed the wrong path; now that I do it
 again I get this error).
 Below is the stack trace.  Please help!
 
 Thanks,
 
 Jeremy
 
 
 Version   BASE 2.1.1 (build #2996; schema #20)
 Web serverApache Tomcat/5.5.17
 Database Dialect  org.hibernate.dialect.MySQLInnoDBDialect
 JDBC Driver   com.mysql.jdbc.Driver (version 3.1)
 Java runtime  Java(TM) 2 Runtime Environment, Standard Edition
 (1.5.0_07-b03), Sun Microsystems Inc.
 Operating system  Linux i386 2.6.18-1.2257.fc5smp
 MemoryTotal: 162.7 MB
 Free: 120.9 MB
 Max: 481.5 MB
 Browser   Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US;
rv:1.8.1.2)
 Gecko/20070219 Firefox/2.0.0.2
 Error message Duplicate entry 'sbrn.base.BatchDataImporter'
for key 2
 Stack trace
 
 ...at HibernateUtil.saveData(HibernateUtil.java:963)
 ...at DbControl.commit(DbControl.java:362)
 ...at

org.apache.jsp.admin.plugindefinitions.index_jsp._jspService(index_jsp.j
av
 a:223)
 ...at
org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97)
 ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
 ...at

org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.ja
va
 :332)
 ...at

org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314)
 ...at
org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264)
 
 ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
 ...at

org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
ti
 onFilterChain.java:252)
 ...at

org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
er
 Chain.java:173)
 ...at

net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(Chara
ct
 erEncodingFilter.java:71)
 ...at

org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
ti
 onFilterChain.java:202)
 ...at

org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
er
 Chain.java:173)
 ...at

org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValv
e.
 java:213)
 ...at

org.apache.catalina.core.StandardContextValve.invoke(StandardContextValv
e.
 java:178)
 ...at

org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java
:1
 26)
 ...at

org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java
:1
 05)
 ...at

org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.
ja
 va:107)
 ...at

org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:1
48
 )
 ...at
 org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:199)
 ...at
org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:282)
 ...at
org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:754)
 ...at

org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:
68
 4)
 ...at

org.apache.jk.common.ChannelSocket$SocketConnection.runIt(ChannelSocket.
ja
 va:876)
 ...at

org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool
.j
 ava:684)
 ...at java.lang.Thread.run(Thread.java:595)
 
 Caused by: java.sql.SQLException
 ...at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2975)
 ...at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600)
 ...at

com.mysql.jdbc.ServerPreparedStatement.serverExecute(ServerPreparedState
me
 nt.java:1125)
 ...at

com.mysql.jdbc.ServerPreparedStatement.executeInternal(ServerPreparedSta
te
 ment.java:677)
 ...at

com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:13
57
 )
 ...at

com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:12
74
 )
 ...at

com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:12

Re: [base] batch importer plugin is available for testing now

2007-03-14 Thread Jeremy Davis-Turak
On 3/14/07, Nicklas Nordborg [EMAIL PROTECTED] wrote:
 Can someone please give us a hint about how to reproduce this behavior?
 When I add a new plugin, BASE will complain if I enter an incorrect path.

Nicklas,

 To reproduce this error, I would try creating the definition with the
wrong path.  Then, when this gives you an error, try again with the
correct path.  That's when I got an error.

 And, if there is an entry already in the database, what is stopping you
 from using the web interface to edit the plugin definition and enter the
 correct path?


Unfortunately the definition doesn't appear in the web interface after
this error, although clearly it made its way into some of the database
tables.

Jeremy

-
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT  business topics through brief surveys-and earn cash
http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV
___
The BASE general discussion mailing list
basedb-users@lists.sourceforge.net
unsubscribe: send a mail with subject unsubscribe to
[EMAIL PROTECTED]


Re: [base] batch importer plugin is available for testing now

2007-02-20 Thread Micha Bayer
Hi Dominic,

Thanks for trying this out.

 I tested the batch import today, on an affy experiment and I got the
ff
 exception:
 
 =
 ===NEW BATCH IMPORT =
 =
 zn =HG-U133A.cdf
 experiment: Experiment[id=5; name=Batch Importer Test]
 file selected: affyMicher.zip
 java.lang.NullPointerException
 at
 sbrn.base.BatchDataImport.unpackZipFile(BatchDataImport.java:135)
 at
sbrn.base.BatchDataImport.importData(BatchDataImport.java:197)
 at sbrn.base.BatchDataImporter.run(BatchDataImporter.java:137)
 at
 net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionReque
 st.java:88)
 at
 net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.ja
 va:420)
 at java.lang.Thread.run(Thread.java:595)
 
 -
 Is this happeneing because of the file format you mentioned in your
read
 me note? The zippped file is in affy format and containes 4 cel file
and
 a cdf file. (5 files in total)

This looks like you are running this as user root. For some reason, user
root does not seem to have a home directory but the code needs to find
the user's home directory so that it can unzip the file there. If you
are logged in as root, then 

homeDir = user.getHomeDirectory();

returns null and this is where the NullPointerException is thrown. I
guess I can catch that and set an appropriate error message. 

Try rerunning this as a non-root user, and if that doesn't work, can you
send me the zip file please so I can try to reproduce the error here. 

I'll also put a note in to the documentation to that extent. 


 Also
 
 --
 7:59:52,287  WARN DbControl:1046 - Found unclosed DbControl during
 finalize; is
 LoggedIn = true; clientId = 0; userId = 1
 java.lang.Throwable: Please check the code to make sure that
 DbControl.close() i
 s always called. Stacktrace of code that created this DbControl:
 at net.sf.basedb.core.DbControl.init(DbControl.java:140)
 at
 net.sf.basedb.core.SessionControl.newDbControl(SessionControl.java:26
 0)
 at sbrn.base.BatchDataImport.init(BatchDataImport.java:109)
 at sbrn.base.BatchDataImporter.run(BatchDataImporter.java:136)
 at
 net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionReque
 st.java:88)
 at
 net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.ja
 va:420)
 at java.lang.Thread.run(Thread.java:595)
 ---
 
 About the above warning, I suggest you close the dbcontrol object in
 your code:
 i.e. finally
 {
 if (dc != null)
 dc.close();
 }

Well spotted -- thanks. I'll get that sorted. 

Cheers

Micha


_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

SCRI, Invergowrie, Dundee, DD2 5DA.  
The Scottish Crop Research Institute is a charitable company limited by 
guarantee. 
Registered in Scotland No: SC 29367.
Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.


DISCLAIMER:

This email is from the Scottish Crop Research Institute, but the views 
expressed by the sender are not necessarily the views of SCRI and its 
subsidiaries.  This email and any files transmitted with it are confidential 
to the intended recipient at the e-mail address to which it has been 
addressed.  It may not be disclosed or used by any other than that addressee.
If you are not the intended recipient you are requested to preserve this 
confidentiality and you must not use, disclose, copy, print or rely on this 
e-mail in any way. Please notify [EMAIL PROTECTED] quoting the 
name of the sender and delete the email from your system.

Although SCRI has taken reasonable precautions to ensure no viruses are 
present in this email, neither the Institute nor the sender accepts any 
responsibility for any viruses, and it is your responsibility to scan the email 
and the attachments (if any).


-
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT  business topics through brief surveys-and earn cash
http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV
___
The BASE general discussion mailing list
basedb-users@lists.sourceforge.net
unsubscribe: send a mail with subject unsubscribe to
[EMAIL PROTECTED]


Re: [base] batch importer plugin is available for testing now

2007-02-20 Thread Nicklas Nordborg
Micha Bayer wrote:
 Hi Dominic,
 
 Thanks for trying this out.
 
 I tested the batch import today, on an affy experiment and I got the
 ff
 exception:
 
 =
 ===NEW BATCH IMPORT =
 =
 zn =HG-U133A.cdf
 experiment: Experiment[id=5; name=Batch Importer Test]
 file selected: affyMicher.zip
 java.lang.NullPointerException
 at
 sbrn.base.BatchDataImport.unpackZipFile(BatchDataImport.java:135)
 at
 sbrn.base.BatchDataImport.importData(BatchDataImport.java:197)
 at sbrn.base.BatchDataImporter.run(BatchDataImporter.java:137)
 at
 net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionReque
 st.java:88)
 at
 net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.ja
 va:420)
 at java.lang.Thread.run(Thread.java:595)

 -
 Is this happeneing because of the file format you mentioned in your
 read
 me note? The zippped file is in affy format and containes 4 cel file
 and
 a cdf file. (5 files in total)
 
 This looks like you are running this as user root. For some reason, user
 root does not seem to have a home directory but the code needs to find
 the user's home directory so that it can unzip the file there. 

A user is not required to have a home directory. The home directory may 
be null for any user. To solve this the plugin could for example ask for 
a directory where the file should be unzipped (use a PathParameterType 
object for this). The default value of this directory could then be set 
to the user's home directory or maybe even better, the same directory 
where the zipped file is located.

/Nicklas

  If you
 are logged in as root, then 
 
 homeDir = user.getHomeDirectory();
 
 returns null and this is where the NullPointerException is thrown. I
 guess I can catch that and set an appropriate error message. 
 
 Try rerunning this as a non-root user, and if that doesn't work, can you
 send me the zip file please so I can try to reproduce the error here. 
 
 I'll also put a note in to the documentation to that extent. 
 
 
 Also

 --
 7:59:52,287  WARN DbControl:1046 - Found unclosed DbControl during
 finalize; is
 LoggedIn = true; clientId = 0; userId = 1
 java.lang.Throwable: Please check the code to make sure that
 DbControl.close() i
 s always called. Stacktrace of code that created this DbControl:
 at net.sf.basedb.core.DbControl.init(DbControl.java:140)
 at
 net.sf.basedb.core.SessionControl.newDbControl(SessionControl.java:26
 0)
 at sbrn.base.BatchDataImport.init(BatchDataImport.java:109)
 at sbrn.base.BatchDataImporter.run(BatchDataImporter.java:136)
 at
 net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionReque
 st.java:88)
 at
 net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.ja
 va:420)
 at java.lang.Thread.run(Thread.java:595)
 ---

 About the above warning, I suggest you close the dbcontrol object in
 your code:
 i.e. finally
 {
 if (dc != null)
 dc.close();
 }
 
 Well spotted -- thanks. I'll get that sorted. 
 
 Cheers
 
 Micha
 
 
 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
 
 SCRI, Invergowrie, Dundee, DD2 5DA.  
 The Scottish Crop Research Institute is a charitable company limited by 
 guarantee. 
 Registered in Scotland No: SC 29367.
 Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.
 
 
 DISCLAIMER:
 
 This email is from the Scottish Crop Research Institute, but the views 
 expressed by the sender are not necessarily the views of SCRI and its 
 subsidiaries.  This email and any files transmitted with it are confidential 
 to the intended recipient at the e-mail address to which it has been 
 addressed.  It may not be disclosed or used by any other than that addressee.
 If you are not the intended recipient you are requested to preserve this 
 confidentiality and you must not use, disclose, copy, print or rely on this 
 e-mail in any way. Please notify [EMAIL PROTECTED] quoting the 
 name of the sender and delete the email from your system.
 
 Although SCRI has taken reasonable precautions to ensure no viruses are 
 present in this email, neither the Institute nor the sender accepts any 
 responsibility for any viruses, and it is your responsibility to scan the 
 email 
 and the attachments (if any).
 
 
 -
 Take Surveys. Earn Cash. Influence the Future of IT
 Join SourceForge.net's Techsay panel and you'll get the chance to share your
 opinions on IT  business topics through brief surveys-and earn cash
 http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV
 ___
 The BASE general discussion mailing list
 basedb-users@lists.sourceforge.net
 unsubscribe: send a mail with 

Re: [base] batch importer plugin is available for testing now

2007-02-19 Thread Dominic Oyeniran
Hi Micha,

Nice work.
I tested the batch import today, on an affy experiment and I got the ff 
exception:

=
===NEW BATCH IMPORT =
=
zn =HG-U133A.cdf
experiment: Experiment[id=5; name=Batch Importer Test]
file selected: affyMicher.zip
java.lang.NullPointerException
at sbrn.base.BatchDataImport.unpackZipFile(BatchDataImport.java:135)
at sbrn.base.BatchDataImport.importData(BatchDataImport.java:197)
at sbrn.base.BatchDataImporter.run(BatchDataImporter.java:137)
at 
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionReque
st.java:88)
at 
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.ja
va:420)
at java.lang.Thread.run(Thread.java:595)

-
Is this happeneing because of the file format you mentioned in your read 
me note? The zippped file is in affy format and containes 4 cel file and 
a cdf file. (5 files in total)
Also

--
7:59:52,287  WARN DbControl:1046 - Found unclosed DbControl during 
finalize; is
LoggedIn = true; clientId = 0; userId = 1
java.lang.Throwable: Please check the code to make sure that 
DbControl.close() i
s always called. Stacktrace of code that created this DbControl:
at net.sf.basedb.core.DbControl.init(DbControl.java:140)
at 
net.sf.basedb.core.SessionControl.newDbControl(SessionControl.java:26
0)
at sbrn.base.BatchDataImport.init(BatchDataImport.java:109)
at sbrn.base.BatchDataImporter.run(BatchDataImporter.java:136)
at 
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionReque
st.java:88)
at 
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.ja
va:420)
at java.lang.Thread.run(Thread.java:595)
---

About the above warning, I suggest you close the dbcontrol object in 
your code:
i.e. finally
{
if (dc != null)
dc.close();
}   

Regards,

Dominic

-
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT  business topics through brief surveys-and earn cash
http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV
___
The BASE general discussion mailing list
basedb-users@lists.sourceforge.net
unsubscribe: send a mail with subject unsubscribe to
[EMAIL PROTECTED]


[base] batch importer plugin is available for testing now

2007-02-15 Thread Micha Bayer
Hi,

An early, alpha-quality version of the batch data import plugin is now
available at 

http://lev.thep.lu.se/trac/baseplugins/wiki/BatchDataImporter

This version has been through the first round of bug fixes but has then
not been tested by anyone other than myself locally, so please feel free
to test it. Any feedback on bugs would be greatly appreciated -- I'll
try and fix them as quickly as poss but help from others in
maintaining/extending this plugin would also be appreciated. 

The plugin takes a zip file with multiple data files in the same format,
unzips this, and then creates a new RawBioAssay object for each data
file. It is invoked from the Import tab in the Experiment (detail) view
and the raw bioassays created are then appended to this experiment.
Instructions for use and installation as well as links to the source
code and the plugin jar are provided on the plugin home page (see
above). 

It does currently not create any other objects (Annotations etc) so
clearly there is lots of scope for extensions. My time on BASE things is
rather limited though, and if there is anyone out there who wants to
help extend this, please get in touch with myself and/or Jari. The code
is in the BASE plugins SVN repo so the potential for easy collaboration
is there anyway. 

Cheers

Micha

==
Dr Micha M Bayer
Bioinformatics Specialist
Genetics Programme
The Scottish Crop Research Institute
Invergowrie
Dundee
DD2 5DA
Scotland, UK
Telephone +44(0)1382 562731 ext. 2309
Fax +44(0)1382 562426
http://www.scri.sari.ac.uk/MichaBayer.htm
=
 

_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

SCRI, Invergowrie, Dundee, DD2 5DA.  
The Scottish Crop Research Institute is a charitable company limited by 
guarantee. 
Registered in Scotland No: SC 29367.
Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.


DISCLAIMER:

This email is from the Scottish Crop Research Institute, but the views 
expressed by the sender are not necessarily the views of SCRI and its 
subsidiaries.  This email and any files transmitted with it are confidential 
to the intended recipient at the e-mail address to which it has been 
addressed.  It may not be disclosed or used by any other than that addressee.
If you are not the intended recipient you are requested to preserve this 
confidentiality and you must not use, disclose, copy, print or rely on this 
e-mail in any way. Please notify [EMAIL PROTECTED] quoting the 
name of the sender and delete the email from your system.

Although SCRI has taken reasonable precautions to ensure no viruses are 
present in this email, neither the Institute nor the sender accepts any 
responsibility for any viruses, and it is your responsibility to scan the email 
and the attachments (if any).


-
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT  business topics through brief surveys-and earn cash
http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV
___
The BASE general discussion mailing list
basedb-users@lists.sourceforge.net
unsubscribe: send a mail with subject unsubscribe to
[EMAIL PROTECTED]