Hi Jari, That sounds perfectly reasonable when you put it like this, but I was put off going down that route by a post to the list from Nicklas (http://www.mail-archive.com/basedb-users@lists.sourceforge.net/msg00228.html) where he says that it is best to not use a plugin to do this because of interface issues (whatever they are).
Personally, I think a plugin would be far better than what I have done -- if I was to persist with my solution I would have to modify the BASE source every time a new version comes out. I also think that batch import *is* a high priority thing for most users, whether they have a pile of legacy data or not. Most biologists I know would probably rather spend a solid period doing labwork, and then process a whole bunch of experiments in a oner. I also think it is a nonsense to have a human doing boring, repetitive stuff -- computers are there to do that. Why waste your time on something that a for loop can do. So perhaps the dev team should reconsider this. I am just talking to my boss about code ownership issues but I can probably offer up my stuff one way or another, and people can then either cannibalise it and turn it into a plugin, or adopt it (or a modified version) into the core etc etc -- happy with any solution that makes others benefit from my blood sweat and tears shed ..... :-) Cheers Micha ================================== Dr Micha M Bayer Bioinformatics Specialist Genetics Programme The Scottish Crop Research Institute Invergowrie Dundee DD2 5DA Scotland, UK Telephone +44(0)1382 562731 ext. 2309 Fax +44(0)1382 562426 http://www.scri.sari.ac.uk/MichaBayer.htm ============================= > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:basedb-users- > [EMAIL PROTECTED] On Behalf Of Jari Häkkinen > Sent: 29 November 2006 14:14 > To: BASE ML > Subject: Re: [base] Offline files > > Hi all, > > Just a thought, I think the best choice to trigger a large import like > this is to create a plug-in instead of adding extra tabs to the file > browser. The plug-in should start by requesting the zip file/directory > to import. If the zip file is not already uploaded the user will have an > opportunity to upload it. After choosing the zip file/directory the > plug-in could start its import and creation of necessary items. > > The above is fairly straightforward already today and the new code would > start at import/creation of necessary items. > > This will yield very little (or no) changes to the core and the plug-in > should probably be started from the experiment listing page. This will > of course change the experiment list jsp (a import tab is needed). > > In my naive view this will only affect a jsp and a new plug-in is needed. > > > Jari > > dominic oyeniran wrote: > > > > > > > > -----Original Message----- > > From: [EMAIL PROTECTED] > > [mailto:[EMAIL PROTECTED] On Behalf Of Micha > Bayer > > > > Hi Micha, > > > > > >> I have just finished writing one. The user uploads a zip file, a new > > directory is created in the user's raw data directory (with >the same > name > > as the zip file) and the files are then unzipped in there. They are then > > imported one by one as new > >> RawBioAssay objects and at the end a new Experiment is created that has > all > > these hanging off it. At the moment it only > >> works for non-Affy data though. > > > > > >> To do this I had to hack the BASE source (plugin wasn't possible as far > as > > I can tell), and I am always reluctant to do that > >> sort of thing because of versioning/upgrade issues (i.e. having to > repeat > > this every time a new version is out). I have > >> modified >the JSP page that controls the menus and inserted a new item > > there, and added a couple of JSP pages myself that >provide the UI for > all > > this. > > > >> I did some more detailed testing yesterday and things worked fine but > it's > > all still pretty raw and probably full of bugs. I am > >> happy to share the code with others though, or even make it a full > > contribution to BASE if people are happy with it (perhaps >after it has > been > > gone over by some of the BASE team). I also think the exception handling > > needs more work probably. > > > > > > Base 2 has plans to have tab2mage import (importing experiments and > > associated files) see Ticket #338 on base2 trac > > http://base.thep.lu.se/ticket/338 system, and your zip file loader would > > certaily help to in importing experiments from repositories and doing > other > > interesting stuff. We have this on our do list and would certainly > > appreciate if you can share the code with us to help in this process. > > > > Also, do you have plans to extend the functionality to non-affy data > too? > > > > Thanks and hope to read from you. > > > > Dominic > > ************ > > > > > > > > ------------------------------------------------------------------------ > - > > 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 > > > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > > _______________________________________________ > > The BASE general discussion mailing list > > basedb-users@lists.sourceforge.net > > unsubscribe: send a mail with subject "unsubscribe" to > > [EMAIL PROTECTED] > > > > -- > Jari Häkkinen, PhD > Complex Systems Division mailto:[EMAIL PROTECTED] > Department of Theoretical Physics phone: +46 (0)46 2229347 > Lund University fax: +46 (0)46 2229686 > Sölvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se > > > ------------------------------------------------------------------------- > 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 > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 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. 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