Re: [basedb-devel] Tab2Mage exporter plugin
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 :
ItemResultListLabeledExtract labeledExtracts =
(ItemResultListLabeledExtract)
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.ItemResultListcapture#213 of
? extends net.sf.basedb.core.MeasuredBioMaterial
[javac] required:
net.sf.basedb.core.ItemResultListnet.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
Re: [basedb-devel] Tab2Mage exporter plugin
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.ItemResultListcapture#213 of ? extends net.sf.basedb.core.MeasuredBioMaterial [javac] required: net.sf.basedb.core.ItemResultListnet.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 -- The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel -- The Planet: dedicated and managed hosting, cloud
Re: [basedb-devel] Tab2Mage exporter plugin
On 2010-02-05 10:07, Gildas Le Corguillé wrote: 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. It appeared in BASE 2.5. We usually try to add a note in the javadoc for the api: http://base.thep.lu.se/chrome/site/latest/api/net/sf/basedb/core/RawBioAssay.html#getFileSet() Our policy for the Required BASE version for plug-ins is to specify the version that was used when testing. Even if it theoretically can be compiled against an older BASE version we really don't know if it works with that version. And since we don't have any resources to test with older BASE versions this usually means that all plug-ins will require the BASE version that was the current at the time the plug-in was released. If you, for example, tested your changes with BASE 2.14 it would mean that the new requirement is BASE 2.14. /Nicklas -- The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
