Re: [basedb-devel] Integrating BASE to analysis packages
I have now checked in a foundation for the extension system in the trunk. It should be possible to start developing external extensions in the current state. A simple tutorial can be found at: http://base.thep.lu.se/chrome/site/trunk/html/developerdoc/extensions/extensions.html Note that you have to check out the trunk from our subversion server to be able to work with this. See http://base.thep.lu.se/wiki/DownloadPage There are also some Hello world extension examples to be found at: http://baseplugins.thep.lu.se/wiki/net.sf.basedb.examples.extensions As usual, since this is non-released code, we can't make any guarantee of it's stability. In particular, don't install this in a production environment. Although we don't expect any major changes to the new extensions API, you should be prepared for minor changes to methods, classes, etc. at any time until the final 2.7 release. Currently, there are two extension points, one in the menu and one where the MeV Launcher is in the tree of bioassaysets in the analysis. Suggestions for other extension points can be posted to http://base.thep.lu.se/ticket/933 /Nicklas Nicklas Nordborg wrote: We agree with you, something more general is needed. We have discussed this issue several times and always postponed it, there is so many things to do. There is a very non-informative ticket related to this, http://base.thep.lu.se/ticket/436 but to be honest, to see the connection you need to join us in our coffee room. There is now more information in the ticket referenced above. The terminology has changed. We should should use the term extension instead of plug-in in order to avoid confusion with the existing plug-in system. We have decided to split the implementation in three parts: 1. Create the required infrastructure. This is what ticket 436 is about. 2. Implement a few extension points in the web client. This would cover the place were the Launch MeV button is located and a few other places. This is/will be described in ticket 933: http://base.thep.lu.se/ticket/933 3. Re-implement the Launch MeV functionality as an extension and remove it from the core distribution. This is described in ticket 932: http://base.thep.lu.se/ticket/932 Everything is currently only in the design phase. There are probably lots of details to work out. I'll soon start with some prototype code to see if the general idea works and if something needs to be changed. Comments are welcome. /Nicklas - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] Integrating BASE to analysis packages
Hello, We agree with you, something more general is needed. We have discussed this issue several times and always postponed it, there is so many things to do. There is a very non-informative ticket related to this, http://base.thep.lu.se/ticket/436 but to be honest, to see the connection you need to join us in our coffee room. There is now more information in the ticket referenced above. The terminology has changed. We should should use the term extension instead of plug-in in order to avoid confusion with the existing plug-in system. Looks nice! I'll be on holiday next week, but I'll have a closer look at it after that. Btw. When implementing BASE import, what would be the file format you recommended? MeV format seems tempting as it is a lot simpler compared to BASE format. Cheers, Aleksi - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] Integrating BASE to analysis packages
Aleksi Kallio wrote: Hello all, Hi, Currently BASE has an integration to MeV analysis package, which I believe is something that was a custom job by you (ie. it is a modified version of MeV etc.)? We would be interested in implementing a similar integration into our analysis package Chipster (http://chipster.csc.fi). Chipster would be a nice addition to BASE. Yes, MeV was a custom job, and not too pretty to be honest. We have (internally) discussed to change the MeV implementation. MeV support will be moved out from the core package to become an external plug-in. I have gone through the way MeV is integrated into BASE, and the same approach would work well with Chipster also (and would not need a modified version of the analysis software as with MeV). As adding different analysis packages one by one is a bit of a burden, I would like to suggest that BASE could be modified to allow system manager to configure different Java Web Start based analysis tools to be used. After all, there are quite a few packages out there using Web Start. Of course not only Web Start is required, but the package should also be capable of accepting URL's as arguments and fetch the datafiles pointed by them. Would you consider this as a feasible new feature to implement? We would be willing to contribute this kind of integration, with some help from you core developers! We agree with you, something more general is needed. We have discussed this issue several times and always postponed it, there is so many things to do. There is a very non-informative ticket related to this, http://base.thep.lu.se/ticket/436 but to be honest, to see the connection you need to join us in our coffee room. We are working hard for the next milestone here, so we'd like to pick up this thread after finalization of the milestone (due in two weeks). I hope this is okay with you. And we appreciate your offer to contribute to the project. All the best, Aleksi Cheers, Jari - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] Integrating BASE to analysis packages
Hello all, Currently BASE has an integration to MeV analysis package, which I believe is something that was a custom job by you (ie. it is a modified version of MeV etc.)? We would be interested in implementing a similar integration into our analysis package Chipster (http://chipster.csc.fi). I have gone through the way MeV is integrated into BASE, and the same approach would work well with Chipster also (and would not need a modified version of the analysis software as with MeV). As adding different analysis packages one by one is a bit of a burden, I would like to suggest that BASE could be modified to allow system manager to configure different Java Web Start based analysis tools to be used. After all, there are quite a few packages out there using Web Start. Of course not only Web Start is required, but the package should also be capable of accepting URL's as arguments and fetch the datafiles pointed by them. Would you consider this as a feasible new feature to implement? We would be willing to contribute this kind of integration, with some help from you core developers! All the best, Aleksi - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
