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