Forgot this in my previous post.
I have committed the code to the repository. Building Tab2MageExporter
causes a few warnings of which all but is complaining about use of
deprecated BASE2Core calls. There is one warning about unchecked cast:
src/uk/ac/ebi/nugo/plugins/ta2mageexport/Tab2MageValidator.java:216:
warning: [unchecked] unchecked cast
[javac] found : net.sf.basedb.core.ItemResultList<capture#213 of
? extends net.sf.basedb.core.MeasuredBioMaterial>
[javac] required:
net.sf.basedb.core.ItemResultList<net.sf.basedb.core.LabeledExtract>
[javac]
rba.getScan().getHybridization().getCreationEvent().getSources().list(dc);
But that is probably okay?
Also, the patch you provided has a reference to a file
Tab2MageExporter/lib/BASE2WSClient.jar that is not in the repository.
The file is not required for a successful compile of the
Tab2MageExporter. Maybe it is a stray file in your working copy?
Cheers,
Jari
On 2/9/10 2:29 PM, Gildas Le Corguillé wrote:
> Hi,
>
> I join you my patch for Tab2MageExporter. Is it what you expected in
> your email ?
>
> Until now, I've never participated to an open project. Thus don't be
> affraid if you see my name everywhere, it's because I wanted to sign and
> assume what I changed if there were troubles with my updates.
>
> I might have to make modifications later (bugs) or adapt this current
> script for a MAGE-TAB exporter because Tab2Mage format don't allow
> pooling like Base does :
> - Base : n samples in 1 sample
> - Tab2Mage : n sampels in 1 extract
> It will depend of my free times among my own projects.
>
> Excerpt from ChangeLog.txt :
>
> version 1.01 : 08/02/2010 - lecorguille
> - Fix a problem with pooling which was not supported ... for me
> - Modification : Filenames are use instead of RawBioAssays' names
> for File[raw] column in the Hybridization section
> - Add the possibility to have several Files[raw] per RawBioAssay (ex
> : one cy3 and one cy5)
> - Add a scan column in the Hybridization section
> - Add a BioSourceDescription column in the Hybridization section
> - Fix a problem with protocols in the Hybridization section
>
>
> Cheers
>
> Gildas
>
>
>
> Le 05/02/2010 11:27, Jari Häkkinen a écrit :
>> Hi Gildas,
>>
>> Great to see work done on the Tab2Mage exporter. The original author has
>> left for other tasks and the Tab2Mage code is currently without a
>> maintainer but lives under the GPL2 license so it is free to modify and
>> improve.
>>
>> You can submit your patches to me and I make sure that they are
>> committed to the repository. If you checked out the source from
>> subversion then you can simply create a patch diff. Excerpt from
>> http://base.thep.lu.se/wiki/DeveloperInformation:
>>
>> ... send an email to the developers list containing your log message and
>> the output of svn diff (from the top of your Subversion working copy) ...
>>
>> Send the patch to me.
>>
>> For the new method usage we simply increase the BASE version requirement
>> on the plug-in. I'll find out when the new method appeared in BASE.
>> Changing the Tab2Mage plugin will not affect already installed servers
>> but rather new users of the Tab2Mage plugin. Of course, users wanting to
>> use your new features must of course upgrade their BASE if it is
>> obsolete.
>>
>>
>> Cheers,
>>
>> Jari
>>
>>
>> On 2/5/10 10:07 AM, Gildas Le Corguillé wrote:
>>> Dear colleagues,
>>>
>>> I had a problem with Tab2Mage exporter plugin about polling.
>>> Then to know if it was my fault or its fault, I downloaded the sources
>>> to study the pooling implications.
>>>
>>> And finally, I tried to fix what I thought be a bug.
>>>
>>> Now Tab2Mage_exporter :
>>> - supports pooling
>>> - creates a scan column in the output file
>>> - uses the filemane name in the "File[raw]" column instead of the
>>> RawBioAssay name
>>> - supports several files per RawBioAssay
>>>
>>>
>>> I hope I didn't add bug !?
>>> And now, what is your policy about submiting an update ? Must I contact
>>> the original author ?
>>>
>>> For the last point, I had to use the method RawBioAssay.setFileSet().
>>> Which is implement in a newer BASE2Core than Tab2Mage_exporter
>>> previously used.
>>> But I don't know from which version of Base, this method appear ? Then
>>> if we propose my update, old version of base will show troubles.
>>>
>>> Thank you for your attention
>>>
>>> Best regards
>>>
>>> Gildas
>>>
>>>
>>>
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