Re: [basedb-devel] Tab2Mage exporter plugin

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Hi Jari,

I watched this warning and tried to fix it. But I don't know enough Base 
to understand this warning.
It was there before I worked on the plugin. It's when it wants to 
retrieve LabeledExtract from Hybridization :

    ItemResultList<LabeledExtract> labeledExtracts =
    (ItemResultList<LabeledExtract>) 
    rba.getScan().getHybridization().getCreationEvent().getSources().list(dc);
    for (LabeledExtract labeledExtract :labeledExtracts)
    {

Despite this, it works :)

About, BASE2WSClient.jar, it's a Base2 library. I include it in the lib 
directory because I had a strange error in eclipse without it !?

I realize that my answers are not very clear ^^'

Cheers

Gildas

Le 11/02/2010 15:10, Jari Häkkinen a écrit :
> 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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>>
>>      
>
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