From jeff at bioinformatics.org Thu Jan 4 19:01:32 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:40 2006 Subject: [Pipet Devel] progress Message-ID: <3A550EDC.47621773@bioinformatics.org> Hi guys! Happy New Year and all that. It's pretty darn quiet around here. I was wondering if Jean-Marc and Brad got to take a look at the Overflow errors Jarl was getting. Cheers. Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein -- From valj01 at gel.usherb.ca Fri Jan 5 01:59:25 2001 From: valj01 at gel.usherb.ca (Jean-Marc Valin) Date: Fri Feb 10 19:20:41 2006 Subject: [Pipet Devel] progress References: <3A550EDC.47621773@bioinformatics.org> Message-ID: <3A5570CD.4B10DC6E@gel.usherb.ca> > It's pretty darn quiet around here. I was wondering if Jean-Marc and Brad got > to take a look at the Overflow errors Jarl was getting. Sorry, what errors? I probably missed that one. Yes, I've been pretty quiet lately and will be for the next 2 weeks. I'm starting a new job next Monday at "Locus Dialog" and still need to finish writing my master thesis. The next Piper-related stuff on my list has to do with Overflow internals, like allow feedback loops with the links. So that's the status for me. Happy New Year everyone! Jean-Marc -- Jean-Marc Valin Universite de Sherbrooke - Genie Electrique valj01@gel.usherb.ca From jarl at casema.net Sat Jan 6 08:29:56 2001 From: jarl at casema.net (jarl van katwijk) Date: Fri Feb 10 19:20:41 2006 Subject: [Pipet Devel] progress References: <3A550EDC.47621773@bioinformatics.org> <3A5570CD.4B10DC6E@gel.usherb.ca> Message-ID: <3A571DD4.4A2DBB8@casema.net> > Hi devel people, > > It's pretty darn quiet around here. Thanx Jeff for bringing this one up ;) I'm the time I was waiting for the feedback on the currect status, I worked on the security code of the BL. I'm doing some experimenting with various availeble libraries like SESAME and AKENTI, two (OSS) distributed authorisation libs. Sesame looks most promising, but the code is such a mess I still aint got it compiled. More on this later.. > > to take a look at the Overflow errors Jarl was getting. > > Sorry, what errors? I probably missed that one. Jean Marc, I had this little icq conversation with you about this one, remember? OK, it's about this: I more-or-less finished the pilot goals a few weeks ago, I hooked all 4 layers together. Since then the cvs code is able to let you create a network in the UIL and commit the structure via the DL\BL to the PL, which SEEMS to execute it. My knowlegde about the Overflow nodes is too limited to judge whether it's going ok, or what is going wrong. That is what we need you for, to do some testing. And give me the feedback I need to fix the bugs that probably are still there. > Yes, I've been pretty quiet > lately and will be for the next 2 weeks. I'm starting a new job next Monday at > "Locus Dialog" and still need to finish writing my master thesis. The next > Piper-related stuff on my list has to do with Overflow internals, like allow > feedback loops with the links. So that's the status for me. You can spend some time looking at the lastest Piper code soon? If we fix the last issues we can put some working code online ;) bye, jarl From jeff at bioinformatics.org Sat Jan 6 04:45:39 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:41 2006 Subject: [Pipet Devel] progress References: <3A550EDC.47621773@bioinformatics.org> <3A5570CD.4B10DC6E@gel.usherb.ca> <3A571DD4.4A2DBB8@casema.net> Message-ID: <3A56E943.D2BE8C7@bioinformatics.org> jarl van katwijk wrote: > > Since then the cvs code is [...] BTW, we just fixed anonymous CVS. So, Jean-Marc, you can checkout Piper with the following command (in case you don't want to use your account): cvs -d:pserver:anonymous@bioinformatics.org:/cvsroot checkout piper Daily snapshots are also kept in... ftp://bioinformatics.org/pub/piper/CVS Overflow is in there too! :-) Cheers. Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein -- From chapmanb at arches.uga.edu Tue Jan 9 17:34:18 2001 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Fri Feb 10 19:20:41 2006 Subject: [Pipet Devel] progress In-Reply-To: <3A571DD4.4A2DBB8@casema.net> References: <3A550EDC.47621773@bioinformatics.org> <3A5570CD.4B10DC6E@gel.usherb.ca> <3A571DD4.4A2DBB8@casema.net> Message-ID: <14939.37354.916572.642407@taxus.athen1.ga.home.com> Hey all! Sorry I haven't had time to get gack with you all and try out the brand spanking new CVS stuff before now. Anyways, I just took a look at the CVS version and have some feedback (as requested :-). I hope this stuff helps. In general, things look very nice -- it is great to see everything working together. Here are the comments from the buffer I kept while looking at things: * I made a small fix to the PID storing code (in the dl python part) because if you don't have the PID directory already created, python would complain. * There seem to be some lingering problems from Jeff's new UI structure. The things that I noticed that used to work before and no longer do now are: o deleting nodes (with shift-click) o adding containers o moving around components once they are added >From the python tracebacks, it looks like these are all due to differences between Jeff's new code and how things are supposed to look. * There are a bunch of Overflow messages that get spit out. They don't seem to cause any problems, but I can't explain 'em, either. * The code for submitting to the BL seems to work fine. Good work with your python, Jarl :-) I'm glad I commented enough so you could make sense of the part that needed to be filled in. Note that right now sometimes there will be a python traceback if you click on submit. This is expected, and it will make sense if you read the error message (at least it makes sense to me :-) -- the reason for the message is this: Right now, the way the submission works is that the node that is selected (the one with the box around it) is the "sink" or pull node that the results all will pull from. If you don't have a node selected then the DL will raise an error (rightly so!). This is a CORBA error and is passed to the UI without a problem, so eventually the UI could catch it and display an error box or something. But right now the text warning is all you get :-). Other than that the submission seems to work -- now Jarl and Jean-Marc just need to work on submitting the XML to the PL for processing... You should just be able to feed into UIDocument::run() (unless things are changed) but from there I don't know what your guys plans are :-). * Right now the ./piper script seems to require that the bin directory is on the users path -- do you want that requirement? Well that's it that I noticed. I hope this helps some with things -- I'm really happy to see all the work going on with the code! Brad From jeff at bioinformatics.org Wed Jan 10 02:41:01 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:41 2006 Subject: [Pipet Devel] progress References: <3A550EDC.47621773@bioinformatics.org> <3A5570CD.4B10DC6E@gel.usherb.ca> <3A571DD4.4A2DBB8@casema.net> <14939.37354.916572.642407@taxus.athen1.ga.home.com> Message-ID: <3A5C120D.8A7E07D8@bioinformatics.org> Hi Brad! It's good to hear from you. I hope your break is going well. Brad Chapman wrote: > > * There seem to be some lingering problems from Jeff's new UI > structure. The things that I noticed that used to work before and no > longer do now are: > > o deleting nodes (with shift-click) > o adding containers I haven't tried these since committing the new code. > o moving around components once they are added Hmm. That's one I didn't notice. > >From the python tracebacks, it looks like these are all due to > differences between Jeff's new code and how things are supposed to > look. Do you mean name changes? Thanks for the bug report. I'll go fix 'er up right away :-) Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein -- From jarl at planetX.bastards.nl Wed Jan 10 04:46:46 2001 From: jarl at planetX.bastards.nl (jarl) Date: Fri Feb 10 19:20:41 2006 Subject: [Pipet Devel] progress In-Reply-To: <14939.37354.916572.642407@taxus.athen1.ga.home.com>; from chapmanb@arches.uga.edu on Tue, Jan 09, 2001 at 05:34:18PM -0500 References: <3A550EDC.47621773@bioinformatics.org> <3A5570CD.4B10DC6E@gel.usherb.ca> <3A571DD4.4A2DBB8@casema.net> <14939.37354.916572.642407@taxus.athen1.ga.home.com> Message-ID: <20010110104646.A17040@planetx.bastards.nl> Thnx Brad for this feedback, > >From the python tracebacks, it looks like these are all due to > differences between Jeff's new code and how things are supposed to > look. What do you mean by this Brad? Has the Overflow API\formatting changed ? > * There are a bunch of Overflow messages that get spit out. They don't > seem to cause any problems, but I can't explain 'em, either. JeanMarc, already had a look? > Other than that the submission seems to work -- now Jarl and Jean-Marc > just need to work on submitting the XML to the PL for > processing... You should just be able to feed into UIDocument::run() The submitted networks are passed on the Document::run() already. Try comitting the hello.n and it will be executed by the PL. But when I try to do something more complex, Overflow start complaining about things not being ok. My problem here is that I dont understand how Overflow needs the node structurized. jarl From chapmanb at arches.uga.edu Wed Jan 10 22:19:14 2001 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Fri Feb 10 19:20:41 2006 Subject: [Pipet Devel] progress In-Reply-To: <20010110104646.A17040@planetx.bastards.nl> References: <3A550EDC.47621773@bioinformatics.org> <3A5570CD.4B10DC6E@gel.usherb.ca> <3A571DD4.4A2DBB8@casema.net> <14939.37354.916572.642407@taxus.athen1.ga.home.com> <20010110104646.A17040@planetx.bastards.nl> Message-ID: <14941.9778.814900.72806@taxus.athen1.ga.home.com> Hey Jarl! me: > > From the python tracebacks, it looks like these are all due to > > differences between Jeff's new code and how things are supposed to > > look. Jarl: > What do you mean by this Brad? Has the Overflow API\formatting changed ? No API has changed, but Jeff made a lot of changes to the organization of the Pied UI code, and it just looks like not all of the functionality that the old organization had working got propogated to the new code. me: > > Other than that the submission seems to work -- now Jarl and Jean-Marc > > just need to work on submitting the XML to the PL for > > processing... You should just be able to feed into > > UIDocument::run() Jarl > The submitted networks are passed on the Document::run() already. It does? Is this code in CVS? I was basing the fact that it didn't do anything on reading the Representation_upload() code in messaging_db.c, and it doesn't look like it does anything more than return a valid URI. Am I looking in the wrong place? Or maybe I had just drunk too much beer before looking at the code? :-) > Try comitting the hello.n and it will be executed by the PL. But > when I try to do something more complex, Overflow start complaining > about things not being ok. My problem here is that I dont understand > how Overflow needs the node structurized. The XML that the DL creates should, to the best of my understanding, be what Overflow needs (after all, I actually create it using Overflow libraries -- I didn't spend all that time wrapping them for nothing :-). If there are problems, it could be due to mistakes I made in understanding or coding. In my mind, the DL should do a lot of checking so that "bad" XML representations (at least, as far as the DL is able to tell that they are bad) don't get sent at all to the BL and send back an error to the UI. If you are referring to how to structure Overflow nodes together to make it do useful work, this is probably best explained by Jean-Marc. I played with Overflow quite a bit in the past, which helped me learn what little I do know, but he is definately the expert :-). Brad From valj01 at gel.usherb.ca Wed Jan 10 22:37:10 2001 From: valj01 at gel.usherb.ca (Jean-Marc Valin) Date: Fri Feb 10 19:20:41 2006 Subject: [Pipet Devel] progress References: <3A550EDC.47621773@bioinformatics.org> <3A5570CD.4B10DC6E@gel.usherb.ca> <3A571DD4.4A2DBB8@casema.net> <14939.37354.916572.642407@taxus.athen1.ga.home.com> <20010110104646.A17040@planetx.bastards.nl> <14941.9778.814900.72806@taxus.athen1.ga.home.com> Message-ID: <3A5D2A66.4049BBBB@gel.usherb.ca> > > Try comitting the hello.n and it will be executed by the PL. But > > when I try to do something more complex, Overflow start complaining > > about things not being ok. My problem here is that I dont understand > > how Overflow needs the node structurized. What does Overflow say exactly? > > The XML that the DL creates should, to the best of my understanding, > be what Overflow needs (after all, I actually create it using Overflow > libraries -- I didn't spend all that time wrapping them for nothing > :-). If there are problems, it could be due to mistakes I made in > understanding or coding. In my mind, the DL should do a lot of > checking so that "bad" XML representations (at least, as far as the DL > is able to tell that they are bad) don't get sent at all to the BL and > send back an error to the UI. It's not that much that the XML would be bad in itself, but the fact that there could be a missing connexion or something like that. An incomplete Overflow network is OK as far as the Overflow libs are concerned... as long as you don't try to run it. Normally, Overflow shouldn't crash because of those errors, but hey, there's still some error handling to complete... Could you send me an XML file that causes problem with Overflow, so I can tell you if the problem is with the Overflow libs or the GUI? > If you are referring to how to structure Overflow nodes together to > make it do useful work, this is probably best explained by > Jean-Marc. I played with Overflow quite a bit in the past, which > helped me learn what little I do know, but he is definately the expert > :-). What do you mean by "how to structure Overflow nodes together"? Jean-Marc -- Jean-Marc Valin Universite de Sherbrooke - Genie Electrique valj01@gel.usherb.ca From jarl at casema.net Thu Jan 11 06:51:01 2001 From: jarl at casema.net (jarl van katwijk) Date: Fri Feb 10 19:20:41 2006 Subject: [Pipet Devel] progress References: <3A550EDC.47621773@bioinformatics.org> <3A5570CD.4B10DC6E@gel.usherb.ca> <3A571DD4.4A2DBB8@casema.net> <14939.37354.916572.642407@taxus.athen1.ga.home.com> <20010110104646.A17040@planetx.bastards.nl> <14941.9778.814900.72806@taxus.athen1.ga.home.com> Message-ID: <3A5D9E25.A75A38C4@casema.net> > > What do you mean by this Brad? Has the Overflow API\formatting changed ? > > No API has changed, but Jeff made a lot of changes to the organization > of the Pied UI code, and it just looks like not all of the > functionality that the old organization had working got propogated to > the new code. Jeff, you know about this? > > > The submitted networks are passed on the Document::run() already. > > It does? Is this code in CVS? I was basing the fact that it didn't do > anything on reading the Representation_upload() code in > messaging_db.c, and it doesn't look like it does anything more than > return a valid URI. Am I looking in the wrong place? Or maybe I had > just drunk too much beer before looking at the code? :-) The code is in plugins/plugin_sensor_DL.c. The code you were looking at is old and should be cleaned ;) If you want to have a look at the BL->PL code, it's in plugins/plugin_sensor_PL.c. OK, I can imaging this to be unclear, I'll make a picture of the setup later today. > > Try comitting the hello.n and it will be executed by the PL. But > > when I try to do something more complex, Overflow start complaining > > about things not being ok. My problem here is that I dont understand > > how Overflow needs the node structurized. > > The XML that the DL creates should, to the best of my understanding, > be what Overflow needs Ic. So all I have to do now is to understand the structure of the Overflow networks: what needs to be there, what types of nodes can be at the beginning of a network, which ones at the end, etc. Is there such a document around? jarl From jarl at planetx.bastards.nl Thu Jan 11 03:47:02 2001 From: jarl at planetx.bastards.nl (jarl) Date: Fri Feb 10 19:20:41 2006 Subject: [Pipet Devel] progress In-Reply-To: <3A5D2A66.4049BBBB@gel.usherb.ca>; from valj01@gel.usherb.ca on Wed, Jan 10, 2001 at 10:37:10PM -0500 References: <3A550EDC.47621773@bioinformatics.org> <3A5570CD.4B10DC6E@gel.usherb.ca> <3A571DD4.4A2DBB8@casema.net> <14939.37354.916572.642407@taxus.athen1.ga.home.com> <20010110104646.A17040@planetx.bastards.nl> <14941.9778.814900.72806@taxus.athen1.ga.home.com> <3A5D2A66.4049BBBB@gel.usherb.ca> Message-ID: <20010111094702.A14010@planetx.bastards.nl> > > > Try comitting the hello.n and it will be executed by the PL. But > > > when I try to do something more complex, Overflow start complaining > > > about things not being ok. My problem here is that I dont understand > > > how Overflow needs the node structurized. > > What does Overflow say exactly? This aint a question I can answer, I think you dont understand my problem yet. It's like asking me to reproduce a chinees sentence so that somebody can translate it for me. The way Overflow handles networks is like chinees to me :) So I'll ask you again: spend 1 or 2 hours compiling Piper, and playing with it. Maybe you find that all is working fine (by all I mean creating->uploading->executing networks), but probably there're bug you can point me at. There's simply too much noise for me to get a clear picture of what's working right and what it not. > > If you are referring to how to structure Overflow nodes together to > > make it do useful work, this is probably best explained by > > Jean-Marc. I played with Overflow quite a bit in the past, which > > helped me learn what little I do know, but he is definately the expert > > :-). > > What do you mean by "how to structure Overflow nodes together"? What type of nodes are allowed to be used as a 'start' of a network, which ones should be one the end, and what other 'rules' are there for a Overflow network? jarl From jeff at bioinformatics.org Thu Jan 11 09:09:13 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:41 2006 Subject: [Pipet Devel] progress References: <3A550EDC.47621773@bioinformatics.org> <3A5570CD.4B10DC6E@gel.usherb.ca> <3A571DD4.4A2DBB8@casema.net> <14939.37354.916572.642407@taxus.athen1.ga.home.com> <20010110104646.A17040@planetx.bastards.nl> <14941.9778.814900.72806@taxus.athen1.ga.home.com> <3A5D9E25.A75A38C4@casema.net> Message-ID: <3A5DBE89.8707F17B@bioinformatics.org> jarl van katwijk wrote: > > > No API has changed, but Jeff made a lot of changes to the organization > > of the Pied UI code, and it just looks like not all of the > > functionality that the old organization had working got propogated to > > the new code. > > Jeff, you know about this? I do now. Brad pointed out a few bugs that I have in the "new and improved Pied". Like Brad, I've been doing a ton of bioinformatics programming in Python recently, and that has take up my vacation time. I'll try to nail down those bugs by this weekend. Cheers. Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein -- From jarl at casema.net Sun Jan 14 22:32:11 2001 From: jarl at casema.net (jarl van katwijk) Date: Fri Feb 10 19:20:41 2006 Subject: [Pipet Devel] BL work References: <3A550EDC.47621773@bioinformatics.org> <3A5570CD.4B10DC6E@gel.usherb.ca> <3A571DD4.4A2DBB8@casema.net> Message-ID: <3A626F3B.74D8DECB@casema.net> Hi people, this weekend I started on something that will take my buzy for a while. I'm migrating current (procedural) BL code to OOP classes. done a structure for the classes, and I'm at 10% of the work to rewrite the code, already got a few sources compiling with the new classes. did this because the old code wasn't really designed for what the BL needs to do now. doing this rewrite now will spare much time later ;) bye, jarl From bizzaro at mercury.capeonramp.com Sun Jan 14 19:01:19 2001 From: bizzaro at mercury.capeonramp.com (bizzaro) Date: Fri Feb 10 19:20:41 2006 Subject: [Pipet Devel] BL work Message-ID: <200101141901.AA113705182@mercury.capeonramp.com> >this weekend I started on something that will take my buzy for a while. I'm migrating >current (procedural) BL code to OOP classes. done a structure for the classes, and I'm >at 10% of the work to rewrite the code, already got a few sources compiling with the >new classes. did this because the old code wasn't really designed for what the >BL needs to do now. doing this rewrite now will spare much time later ;) That's good to hear. As for me, I have been spending some time doing some unrelated programming in Python. But that's not a bad thing, since I've got my Python gears greased now. I hope to finally dive back into Pied/Piper this week. Cheers. Jeff From jeff at bioinformatics.org Mon Jan 22 15:20:29 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:41 2006 Subject: [Pipet Devel] progress References: <3A550EDC.47621773@bioinformatics.org> <3A5570CD.4B10DC6E@gel.usherb.ca> <3A571DD4.4A2DBB8@casema.net> <14939.37354.916572.642407@taxus.athen1.ga.home.com> Message-ID: <3A6C960D.AA302C7C@bioinformatics.org> Brad Chapman wrote: > > * There seem to be some lingering problems from Jeff's new UI > structure. The things that I noticed that used to work before and no > longer do now are: > > o deleting nodes (with shift-click) > o adding containers > o moving around components once they are added Brad, I don't get an error for moving around components. Do you get a traceback? If so, could you send it to me. Also, what version of Gtk/Gnome are you using? Cheers. Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein -- From chapmanb at arches.uga.edu Wed Jan 24 05:48:25 2001 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Fri Feb 10 19:20:41 2006 Subject: [Pipet Devel] progress In-Reply-To: <3A6C960D.AA302C7C@bioinformatics.org> References: <3A550EDC.47621773@bioinformatics.org> <3A5570CD.4B10DC6E@gel.usherb.ca> <3A571DD4.4A2DBB8@casema.net> <14939.37354.916572.642407@taxus.athen1.ga.home.com> <3A6C960D.AA302C7C@bioinformatics.org> Message-ID: <14958.45817.622826.703008@taxus.athen1.ga.home.com> Hi Jeff! Sorry to be so slow -- my ISP has been dead for the past couple of days. me: > > * There seem to be some lingering problems from Jeff's new UI > > structure. The things that I noticed that used to work before and no > > longer do now are: > > > > o deleting nodes (with shift-click) > > o adding containers > > o moving around components once they are added > > Brad, I don't get an error for moving around components. Do you get a > traceback? If so, could you send it to me. Also, what version of Gtk/Gnome > are you using? Ooops, I don't know why I wrote components -- I meant "composite", as in just the composite node types. Here is the traceback I get, if you can't duplicate this over there: Traceback (most recent call last): File "/usr/local/lib/python2.0/site-packages/gtk.py", line 125, in __call__ ret = apply(self.func, a) File "/home/chapmanb/test/piper/piper/uil/pied/modules/network.py", line 371, in node_event self.node_motion_notify(event, node) File "/home/chapmanb/test/piper/piper/uil/pied/modules/network.py", line 447, in node_motion_notify self.node_move(node, move_x, move_y) File "/home/chapmanb/test/piper/piper/uil/pied/modules/network.py", line 513, in node_move if (node.windowlet.shown == 1): AttributeError: 'PiedNode' instance has no attribute 'windowlet' This is with gtk-1.2.8, gnomelibs-1.2.4, py-gnome-1.0.53 and py-gtk-0.6.6. I haven't really been following py-gtk development very much -- do I need to upgrade or do you see this problem too? Brad From jeff at bioinformatics.org Fri Jan 26 20:42:57 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:41 2006 Subject: [Pipet Devel] piper developers meeting Message-ID: <3A7227A1.1FB21391@bioinformatics.org> Jarl, a few months back you mentioned that you genuinely want the Piper developers to meet. I was wondering about your thoughts on the subject now. I ask because there will be a bioinformatics conference in Denmark in July. Brad and I attended this conference last year when it was in California. I'm likely to attend this year, and suspect that Brad will (Brad?). We *COULD* have a Piper Developers Meeting around that time, allowing Brad and I to kill two birds with one stone. And it would be fairly convenient for you (a hop across the Baltic). What do you think? Would you like to meet sooner than July? Jean-Marc, how about you? Would you be able to go to Denmark? Maybe a meeting in Montreal would be better? Cheers. Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein -- From jarl at casema.net Sat Jan 27 12:40:37 2001 From: jarl at casema.net (jarl van katwijk) Date: Fri Feb 10 19:20:41 2006 Subject: [Pipet Devel] piper developers meeting References: <3A7227A1.1FB21391@bioinformatics.org> Message-ID: <3A730815.4D0383A6@casema.net> > Hi Jeff, I currently have my email\isp swithed, maybe you got an earlier email about this. Anyways, my new email is jarl@xs4all.nl and I now have an adsl connection ;) So I'll catch up with the piper emails this weekend. Also I hope to have a compiling version on the new OOP BL, work on that is going smoothly, but I exspect much troubles near the end. > Jarl, a few months back you mentioned that you genuinely want the Piper > developers to meet. I was wondering about your thoughts on the subject now. I still want that to happen. There's still so much work to do, a meeting can clearify the direction on which wwe'll gonna work. > I ask because there will be a bioinformatics conference in Denmark in July. > Brad and I attended this conference last year when it was in California. I'm > likely to attend this year, and suspect that Brad will (Brad?). We *COULD* > have a Piper Developers Meeting around that time, allowing Brad and I to kill > two birds with one stone. And it would be fairly convenient for you (a hop > across the Baltic). That would be nice indead. The conference wouldn't be of much interest to me, but Denmark would be nice to see once. Is it in Kopenhagen? > > > What do you think? Would you like to meet sooner than July? I think it will be July sooner as we want it to come ;) bye, jarl From jeff at bioinformatics.org Sun Jan 28 06:30:48 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:41 2006 Subject: [Pipet Devel] piper developers meeting References: <3A7227A1.1FB21391@bioinformatics.org> <3A730815.4D0383A6@casema.net> Message-ID: <3A7402E8.8B64D4D8@bioinformatics.org> Hi Jarl! jarl van katwijk wrote: > > I currently have my email\isp swithed, maybe you got an earlier email about this. > Anyways, my new email is jarl@xs4all.nl and I now have an adsl connection ;) If you need to change your mailing list subscriptions, you can via http://bioinformatics.org/mailman/listinfo/ > So I'll catch up with the piper emails this weekend. Also I hope to have a > compiling version on the new OOP BL, work on that is going smoothly, but I > exspect much troubles near the end. Okay. > > Jarl, a few months back you mentioned that you genuinely want the Piper > > developers to meet. I was wondering about your thoughts on the subject now. > > I still want that to happen. There's still so much work to do, a meeting can > clearify the direction on which wwe'll gonna work. Right, I agree. [conference] > That would be nice indead. The conference wouldn't be of much interest to me, but > Denmark would be nice to see once. Is it in Kopenhagen? Kopenhagen, indeed. > > What do you think? Would you like to meet sooner than July? > > I think it will be July sooner as we want it to come ;) So, July is soon enough for you. Okay, then the only question is, will Jean-Marc and Brad come? I suppose if Brad is going to the bioinformatics conference, then it wouldn't be difficult for us to get him to go. But I think it is critical that at least you, Jean-Marc and I be there. It won't work otherwise. Jean-Marc? Brad? Cheers. Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein -- From jarl at casema.net Sun Jan 28 10:59:43 2001 From: jarl at casema.net (jarl van katwijk) Date: Fri Feb 10 19:20:42 2006 Subject: [Pipet Devel] piper developers meeting References: <3A7227A1.1FB21391@bioinformatics.org> <3A730815.4D0383A6@casema.net> <3A7402E8.8B64D4D8@bioinformatics.org> Message-ID: <3A7441EF.8070705@casema.net> > > >> I currently have my email\isp swithed, maybe you got an earlier email about this. >> Anyways, my new email is jarl@xs4all.nl and I now have an adsl connection ;) > > > If you need to change your mailing list subscriptions, you can via > > http://bioinformatics.org/mailman/listinfo/ > I can change all sort of setting, but not my email address on that interface. Should I desubscribe my old one and subscribe the new or is there a better method? From jeff at bioinformatics.org Sun Jan 28 08:20:17 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:42 2006 Subject: [Pipet Devel] piper developers meeting References: <3A7227A1.1FB21391@bioinformatics.org> <3A730815.4D0383A6@casema.net> <3A7402E8.8B64D4D8@bioinformatics.org> <3A7441EF.8070705@casema.net> Message-ID: <3A741C91.7F34F940@bioinformatics.org> jarl van katwijk wrote: > > I can change all sort of setting, but not my email address on that > interface. Should I desubscribe my old one and subscribe the new or is > there a better method? Yes, that's probably the best thing to do. I forgot that you can't change your e-mail address. Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein -- From chapmanb at arches.uga.edu Sun Jan 28 09:00:33 2001 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Fri Feb 10 19:20:42 2006 Subject: [Pipet Devel] piper developers meeting In-Reply-To: <3A7402E8.8B64D4D8@bioinformatics.org> References: <3A7227A1.1FB21391@bioinformatics.org> <3A730815.4D0383A6@casema.net> <3A7402E8.8B64D4D8@bioinformatics.org> Message-ID: <14964.9729.6498.217819@taxus.athen1.ga.home.com> [proposed Piper meeting in July in Copenhagen to coincide with ISMB 2001] Jeff: > Okay, then the only question is, will Jean-Marc and Brad come? > > Brad? As of right now, I'm planning on being at ISMB (http://ismb01.cbs.dtu.dk/, in case Jarl or Jean-Marc is interested in why we'd want to go to Denmark). It probably depends on two factors for me, whether or not there is a Bioinformatics Open Source Conference, and whether or not I can finish enough research to present a poster. Right now I'm hopeful for both of these, so I think I'll be there. Of course, you guys should schedule to make things easiest for yourselves first -- you are the main developers on this! Brad From jarl at yournews.nl Mon Jan 29 05:08:36 2001 From: jarl at yournews.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:42 2006 Subject: [Pipet Devel] Piper HOWTO References: <3A7227A1.1FB21391@bioinformatics.org> <3A730815.4D0383A6@casema.net> <3A7402E8.8B64D4D8@bioinformatics.org> <3A7441EF.8070705@casema.net> Message-ID: <3A754124.C9538CFF@yournews.nl> Hi there, I think it's time 4 us to write a little HOWTO for using Piper. What do you people feel about this, too early? Or too late ;) Jeff: It seems exspecially the GUI needs a doc, I myself dont understant it fully, so probably new users wont do so too. So Jeff, can you start such a doc? I'll write a BL chapter, and Jean-Marc can copy-paste-extend some of his Overflow doc's into this HOWTO. I remember somebody asking me to write some about BL-in-a-multi-machine-environment (Jeff?), I'll add that to this HOWTO too once it's there. The BL code I mean, because ATM the BL aint capable of BL-BL communication yet. I finally got hold of a copy of 'kapi', which I want to use for BL-BL comms. bye, jarl From jeff at bioinformatics.org Mon Jan 29 06:09:36 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:42 2006 Subject: [Pipet Devel] Piper HOWTO References: <3A7227A1.1FB21391@bioinformatics.org> <3A730815.4D0383A6@casema.net> <3A7402E8.8B64D4D8@bioinformatics.org> <3A7441EF.8070705@casema.net> <3A754124.C9538CFF@yournews.nl> Message-ID: <3A754F70.5EC7BD66@bioinformatics.org> Jarl van Katwijk wrote: > > I think it's time 4 us to write a little HOWTO for using Piper. What do you people feel > about this, too early? Or too late ;) I think it is time. > Jeff: It seems exspecially the GUI needs a doc, I myself dont understant it fully, so > probably new users wont do so too. So Jeff, can you start such a doc? I wrote a teeny HOWTO in the README file in the pied directory. Of course, something to consider is the fact that Pied/Piper might not always be the user's UI. But, we do need to write the HOWTO with *SOME* UI in mind, so it might as well be Pied/Piper. Would you like me to begin the HOWTO? > I remember somebody asking me to write some about BL-in-a-multi-machine-environment > (Jeff?) Uh-yup, dat waz me. Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein -- From jeff at bioinformatics.org Mon Jan 29 06:21:26 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:42 2006 Subject: [Pipet Devel] Piper HOWTO References: <3A7227A1.1FB21391@bioinformatics.org> <3A730815.4D0383A6@casema.net> <3A7402E8.8B64D4D8@bioinformatics.org> <3A7441EF.8070705@casema.net> <3A754124.C9538CFF@yournews.nl> Message-ID: <3A755236.68D9AA03@bioinformatics.org> Jarl van Katwijk wrote: > > I finally got hold of a copy of > 'kapi', which I want to use for BL-BL comms. Kapi? Did you mention that before? Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein -- From jarl at yournews.nl Mon Jan 29 06:13:56 2001 From: jarl at yournews.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:42 2006 Subject: [Pipet Devel] Piper HOWTO References: <3A7227A1.1FB21391@bioinformatics.org> <3A730815.4D0383A6@casema.net> <3A7402E8.8B64D4D8@bioinformatics.org> <3A7441EF.8070705@casema.net> <3A754124.C9538CFF@yournews.nl> <3A754F70.5EC7BD66@bioinformatics.org> Message-ID: <3A755074.C9F96CB1@yournews.nl> > > > Jeff: It seems exspecially the GUI needs a doc, I myself dont understant it fully, so > > probably new users wont do so too. So Jeff, can you start such a doc? > > I wrote a teeny HOWTO in the README file in the pied directory. > > Of course, something to consider is the fact that Pied/Piper might not always > be the user's UI. But, we do need to write the HOWTO with *SOME* UI in mind, > so it might as well be Pied/Piper. Ic, forgot. Ok, once you got the Pied HOWTO, I'll copy your framework and start a Piper HOWTO. This Piper howto wont be very usefull for some time, because there isn't much to configure right now. But good thing to start these docs so we wont have to write a huge one later. > > Would you like me to begin the HOWTO? Please do! Jarl From jarl at yournews.nl Mon Jan 29 06:19:31 2001 From: jarl at yournews.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:42 2006 Subject: [Pipet Devel] Piper HOWTO References: <3A7227A1.1FB21391@bioinformatics.org> <3A730815.4D0383A6@casema.net> <3A7402E8.8B64D4D8@bioinformatics.org> <3A7441EF.8070705@casema.net> <3A754124.C9538CFF@yournews.nl> <3A755236.68D9AA03@bioinformatics.org> Message-ID: <3A7551C3.1B444F96@yournews.nl> > > > I finally got hold of a copy of > > 'kapi', which I want to use for BL-BL comms. > > Kapi? Did you mention that before? No likely, but I mentioned I wanted to implement BL-BL comms by KQML. Like to avoid writing that myself, kapi might do the trick. But the code is very old (1994), seems to be unsupported since then, and has much hooks to the SunOS api's. Trying to get it to compile under linux now. jarl From jeff at bioinformatics.org Mon Jan 29 07:28:42 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:42 2006 Subject: [Pipet Devel] Piper HOWTO References: <3A7227A1.1FB21391@bioinformatics.org> <3A730815.4D0383A6@casema.net> <3A7402E8.8B64D4D8@bioinformatics.org> <3A7441EF.8070705@casema.net> <3A754124.C9538CFF@yournews.nl> <3A754F70.5EC7BD66@bioinformatics.org> <3A755074.C9F96CB1@yournews.nl> Message-ID: <3A7561FA.8ED344A6@bioinformatics.org> Jarl van Katwijk wrote: > > > Would you like me to begin the HOWTO? > > Please do! Here we go again: Wiki, LaTeX, text, ...? :-) Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein -- From jeff at bioinformatics.org Mon Jan 29 07:30:35 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:42 2006 Subject: [Pipet Devel] Piper HOWTO References: <3A7227A1.1FB21391@bioinformatics.org> <3A730815.4D0383A6@casema.net> <3A7402E8.8B64D4D8@bioinformatics.org> <3A7441EF.8070705@casema.net> <3A754124.C9538CFF@yournews.nl> <3A755236.68D9AA03@bioinformatics.org> <3A7551C3.1B444F96@yournews.nl> Message-ID: <3A75626B.C73B5CF6@bioinformatics.org> Jarl van Katwijk wrote: > > No likely, but I mentioned I wanted to implement BL-BL comms by KQML. Like to > avoid writing that myself, kapi might do the trick. But the code is very old > (1994), seems to be unsupported since then, and has much hooks to the > SunOS api's. Trying to get it to compile under linux now. Will kapi become a prerequisit/requirement for Piper? If so, what do we do about it being so old and unsupported? Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein -- From jarl at yournews.nl Mon Jan 29 07:43:40 2001 From: jarl at yournews.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:42 2006 Subject: [Pipet Devel] Piper HOWTO References: <3A7227A1.1FB21391@bioinformatics.org> <3A730815.4D0383A6@casema.net> <3A7402E8.8B64D4D8@bioinformatics.org> <3A7441EF.8070705@casema.net> <3A754124.C9538CFF@yournews.nl> <3A755236.68D9AA03@bioinformatics.org> <3A7551C3.1B444F96@yournews.nl> <3A75626B.C73B5CF6@bioinformatics.org> Message-ID: <3A75657B.830B1DA6@yournews.nl> > Will kapi become a prerequisit/requirement for Piper? If so, what do we do > about it being so old and unsupported? It will be fully intergrated into the BL and wont be a seperate library anymore. The code will be merged with BL plugin code and packed with Piper. (it's only 248kb) I just got it compiling, which too some hacking because the original is SunOS only. A copy of the licence is here http://co4.inrialpes.fr/docs/co4-1.0a/co4-Appendix-2.html. This is the 2.6e licence, I only could find version 2.6b. The reason I try to get KQML functional is that it is a standard, and that's always A Good Thing, maybe other systems can act as 'the other BL' in BL->BL communications... jarl From jeff at bioinformatics.org Mon Jan 29 08:14:40 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:42 2006 Subject: [Pipet Devel] Piper HOWTO References: <3A7227A1.1FB21391@bioinformatics.org> <3A730815.4D0383A6@casema.net> <3A7402E8.8B64D4D8@bioinformatics.org> <3A7441EF.8070705@casema.net> <3A754124.C9538CFF@yournews.nl> <3A755236.68D9AA03@bioinformatics.org> <3A7551C3.1B444F96@yournews.nl> <3A75626B.C73B5CF6@bioinformatics.org> <3A75657B.830B1DA6@yournews.nl> Message-ID: <3A756CBF.918CC527@bioinformatics.org> Jarl van Katwijk wrote: > > A copy of the licence is here > http://co4.inrialpes.fr/docs/co4-1.0a/co4-Appendix-2.html. This is the 2.6e > licence, I only could find version 2.6b. This is a "non-commercial only" license. It's not L/GPL. It says that you can make a derivitative work (which is I guess what you're doing), but that you have to let them know. I don't know what they will allow for the licensing of our derivative. We should (1) contact them (if there is anyone to contact), (2) tell them what we want to do with the library, and (3) ask if we can relicense the derivative under the L/GPL or ask if they really don't care what we do. Otherwise, we'll probably have to distribute the library separately. That's the only legal alternative. Cheers. Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein -- From jeff at bioinformatics.org Mon Jan 29 08:21:23 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:42 2006 Subject: [Pipet Devel] kapi (was: Piper HOWTO) References: <3A7227A1.1FB21391@bioinformatics.org> <3A730815.4D0383A6@casema.net> <3A7402E8.8B64D4D8@bioinformatics.org> <3A7441EF.8070705@casema.net> <3A754124.C9538CFF@yournews.nl> <3A755236.68D9AA03@bioinformatics.org> <3A7551C3.1B444F96@yournews.nl> <3A75626B.C73B5CF6@bioinformatics.org> <3A75657B.830B1DA6@yournews.nl> <3A756CBF.918CC527@bioinformatics.org> Message-ID: <3A756E53.BFB46EE7@bioinformatics.org> "J.W. Bizzaro" wrote: > > Otherwise, we'll probably have to distribute the library separately. That's > the only legal alternative. Wouldn't there be a need for a "Linux Kapi", which is what you're working on? Question: If kapi/KQML is a standard, why is kapi so old and undeveloped? Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein -- From jarl at yournews.nl Mon Jan 29 08:26:58 2001 From: jarl at yournews.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:42 2006 Subject: [Pipet Devel] kapi (was: Piper HOWTO) References: <3A7227A1.1FB21391@bioinformatics.org> <3A730815.4D0383A6@casema.net> <3A7402E8.8B64D4D8@bioinformatics.org> <3A7441EF.8070705@casema.net> <3A754124.C9538CFF@yournews.nl> <3A755236.68D9AA03@bioinformatics.org> <3A7551C3.1B444F96@yournews.nl> <3A75626B.C73B5CF6@bioinformatics.org> <3A75657B.830B1DA6@yournews.nl> <3A756CBF.918CC527@bioinformatics.org> <3A756E53.BFB46EE7@bioinformatics.org> Message-ID: <3A756FA2.E0C82FFC@yournews.nl> > > Otherwise, we'll probably have to distribute the library separately. That's > > the only legal alternative. > > Wouldn't there be a need for a "Linux Kapi", which is what you're working on? I'll put the Linux version online when it's ok. > > Question: If kapi/KQML is a standard, why is kapi so old and undeveloped? This is the only implementation in C, the other (alive) projects are all Java. Or commecial ones. > We should (1) contact them (if there is anyone to contact), (2) tell them what > we want to do with the library, and (3) ask if we can relicense the derivative > under the L/GPL or ask if they really don't care what we do. I think there wont be anyone to contact anymore. I send an email to the contact person some weeks ago if I could get a copy of the most recent version, but got no reply at all. I'll try again right now and also ask about these legal issues. > Otherwise, we'll probably have to distribute the library separately. That's > the only legal alternative. Arf. That would suck, because I already dislike the large number of dependancies that need to be installed for Piper. bye, jarl From jeff at bioinformatics.org Mon Jan 29 08:41:08 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:42 2006 Subject: [Pipet Devel] kapi (was: Piper HOWTO) References: <3A7227A1.1FB21391@bioinformatics.org> <3A730815.4D0383A6@casema.net> <3A7402E8.8B64D4D8@bioinformatics.org> <3A7441EF.8070705@casema.net> <3A754124.C9538CFF@yournews.nl> <3A755236.68D9AA03@bioinformatics.org> <3A7551C3.1B444F96@yournews.nl> <3A75626B.C73B5CF6@bioinformatics.org> <3A75657B.830B1DA6@yournews.nl> <3A756CBF.918CC527@bioinformatics.org> <3A756E53.BFB46EE7@bioinformatics.org> <3A756FA2.E0C82FFC@yournews.nl> Message-ID: <3A7572F4.C549E09C@bioinformatics.org> Jarl van Katwijk wrote: > > > Otherwise, we'll probably have to distribute the library separately. That's > > the only legal alternative. > Arf. That would suck, because I already dislike the large number of dependancies > that need to be installed for Piper. Yeah, it would suck. Would *COULD* include it with Piper, but we would need to write an exception to our own license (a modification of the L/GPL), and we would have to say that Piper has a mixed license, which I think would suck equally. Let me know if you have any luck contacting the authors. If you don't, I'll give it a try. I may have to contact Lockheed or whoever by phone, but if I reach the legal department, I'M *POSITIVE* that they *WON'T* let us have it or change the license (lawyers). Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein -- From jeff at bioinformatics.org Mon Jan 29 08:45:36 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:42 2006 Subject: [Pipet Devel] kapi (was: Piper HOWTO) References: <3A7227A1.1FB21391@bioinformatics.org> <3A730815.4D0383A6@casema.net> <3A7402E8.8B64D4D8@bioinformatics.org> <3A7441EF.8070705@casema.net> <3A754124.C9538CFF@yournews.nl> <3A755236.68D9AA03@bioinformatics.org> <3A7551C3.1B444F96@yournews.nl> <3A75626B.C73B5CF6@bioinformatics.org> <3A75657B.830B1DA6@yournews.nl> <3A756CBF.918CC527@bioinformatics.org> <3A756E53.BFB46EE7@bioinformatics.org> <3A756FA2.E0C82FFC@yournews.nl> <3A7572F4.C549E09C@bioinformatics.org> Message-ID: <3A757400.217CF2BF@bioinformatics.org> You could also make a C++ version that is "inspired by" (not derived directly from) kapi. How hard would it be to do that? Are you *SURE* there is no GNU C or C++ version out there somewhere? Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein -- From jarl at yournews.nl Mon Jan 29 08:48:09 2001 From: jarl at yournews.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:42 2006 Subject: [Pipet Devel] kapi (was: Piper HOWTO) References: <3A7227A1.1FB21391@bioinformatics.org> <3A730815.4D0383A6@casema.net> <3A7402E8.8B64D4D8@bioinformatics.org> <3A7441EF.8070705@casema.net> <3A754124.C9538CFF@yournews.nl> <3A755236.68D9AA03@bioinformatics.org> <3A7551C3.1B444F96@yournews.nl> <3A75626B.C73B5CF6@bioinformatics.org> <3A75657B.830B1DA6@yournews.nl> <3A756CBF.918CC527@bioinformatics.org> <3A756E53.BFB46EE7@bioinformatics.org> <3A756FA2.E0C82FFC@yournews.nl> <3A7572F4.C549E09C@bioinformatics.org> <3A757400.217CF2BF@bioinformatics.org> Message-ID: <3A757499.4EF8B61A@yournews.nl> > You could also make a C++ version that is "inspired by" (not derived directly > from) kapi. How hard would it be to do that? Hmm.. I need to port the code so it compiles with gcc, recode all variable types to glib ones, probably replace the network code, rename all stuff to be very standard (strip 'kapi' naming prefixes) and port to C++. I even might need to put the code into classes. Wont be much original lines left after that. ;) > > Are you *SURE* there is no GNU C or C++ version out there somewhere? > Nope. Been searching various times for 6months now, and even this old version of kapi I found was darn hard to find. From jeff at bioinformatics.org Mon Jan 29 09:06:25 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:42 2006 Subject: [Pipet Devel] KQML Software Message-ID: <3A7578E1.505A760C@bioinformatics.org> http://www.csee.umbc.edu/kqml/software/ Jeff From jeff at bioinformatics.org Mon Jan 29 09:07:40 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:42 2006 Subject: [Pipet Devel] Magenta Message-ID: <3A75792C.978C090F@bioinformatics.org> Jarl, have you seen this? http://logic.stanford.edu/software/magenta/ Jeff From jarl at yournews.nl Mon Jan 29 09:10:17 2001 From: jarl at yournews.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:42 2006 Subject: [Pipet Devel] Magenta References: <3A75792C.978C090F@bioinformatics.org> Message-ID: <3A7579C9.BB92EF21@yournews.nl> "J.W. Bizzaro" wrote: > Jarl, have you seen this? > > http://logic.stanford.edu/software/magenta/ > Yes, seen it, and searched for the C++ sources. And then for a contact person. Sounds very nice this C++ lib, but seems even more dead as Kapi. From jeff at bioinformatics.org Mon Jan 29 09:31:19 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:42 2006 Subject: [Pipet Devel] Magenta References: <3A75792C.978C090F@bioinformatics.org> <3A7579C9.BB92EF21@yournews.nl> Message-ID: <3A757EB7.98B11BE4@bioinformatics.org> Jarl van Katwijk wrote: > > Yes, seen it, and searched for the C++ sources. And then for a contact > person. Sounds very nice this C++ lib, but seems even more dead as Kapi. Yeah, the site says they disabled downloading and are phasing out support. Have you been able to find the sources? I have no idea what the license is. Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein -- From jarl at yournews.nl Mon Jan 29 09:39:22 2001 From: jarl at yournews.nl (Jarl van Katwijk) Date: Fri Feb 10 19:20:42 2006 Subject: [Pipet Devel] Magenta References: <3A75792C.978C090F@bioinformatics.org> <3A7579C9.BB92EF21@yournews.nl> <3A757EB7.98B11BE4@bioinformatics.org> Message-ID: <3A75809A.34C19FE0@yournews.nl> > > Yes, seen it, and searched for the C++ sources. And then for a contact > > person. Sounds very nice this C++ lib, but seems even more dead as Kapi. > > Yeah, the site says they disabled downloading and are phasing out support. > > Have you been able to find the sources? I have no idea what the license is. > No, didn't found any source. I just looked again btw. I got Kapi running now under linux. Doesn't do it's job though, I don't know yet if that is because of miss configuration or sunos-linux differences. jarl From jarl at casema.net Mon Jan 29 15:19:35 2001 From: jarl at casema.net (jarl van katwijk) Date: Fri Feb 10 19:20:42 2006 Subject: [Pipet Devel] Piper HOWTO References: <3A7227A1.1FB21391@bioinformatics.org> <3A730815.4D0383A6@casema.net> <3A7402E8.8B64D4D8@bioinformatics.org> <3A7441EF.8070705@casema.net> <3A754124.C9538CFF@yournews.nl> <3A754F70.5EC7BD66@bioinformatics.org> <3A755074.C9F96CB1@yournews.nl> <3A7561FA.8ED344A6@bioinformatics.org> Message-ID: <3A75D057.63B68499@casema.net> > > > > > Would you like me to begin the HOWTO? > > > > Please do! > > Here we go again: Wiki, LaTeX, text, ...? :-) uhh... start with wiki. jarl From valj01 at gel.usherb.ca Mon Jan 29 20:25:55 2001 From: valj01 at gel.usherb.ca (Jean-Marc Valin) Date: Fri Feb 10 19:20:42 2006 Subject: [Pipet Devel] Piper HOWTO References: <3A7227A1.1FB21391@bioinformatics.org> <3A730815.4D0383A6@casema.net> <3A7402E8.8B64D4D8@bioinformatics.org> <3A7441EF.8070705@casema.net> <3A754124.C9538CFF@yournews.nl> <3A755236.68D9AA03@bioinformatics.org> <3A7551C3.1B444F96@yournews.nl> <3A75626B.C73B5CF6@bioinformatics.org> <3A75657B.830B1DA6@yournews.nl> <3A756CBF.918CC527@bioinformatics.org> Message-ID: <3A761823.2C092A08@gel.usherb.ca> > > A copy of the licence is here > > http://co4.inrialpes.fr/docs/co4-1.0a/co4-Appendix-2.html. This is the 2.6e > > licence, I only could find version 2.6b. > > This is a "non-commercial only" license. It's not L/GPL. It says that you > can make a derivitative work (which is I guess what you're doing), but that > you have to let them know. I don't know what they will allow for the > licensing of our derivative. > > We should (1) contact them (if there is anyone to contact), (2) tell them what > we want to do with the library, and (3) ask if we can relicense the derivative > under the L/GPL or ask if they really don't care what we do. Good idea... > > Otherwise, we'll probably have to distribute the library separately. That's > the only legal alternative. No, that's not even an option... because then Pipers users wouldn't be allowed to use Piper commercially (as it would imply using the library commercially). This license is NOT compatible with the L(GPL), so it would be illegal to redistribute Piper if it links with this library (whether or not the library is separated from Piper). I'm no lawyer, but I've looked closely at the GPL a couple times. Jean-Marc -- Jean-Marc Valin Universite de Sherbrooke - Genie Electrique valj01@gel.usherb.ca From valj01 at gel.usherb.ca Mon Jan 29 20:28:20 2001 From: valj01 at gel.usherb.ca (Jean-Marc Valin) Date: Fri Feb 10 19:20:42 2006 Subject: [Pipet Devel] Piper HOWTO References: <3A7227A1.1FB21391@bioinformatics.org> <3A730815.4D0383A6@casema.net> <3A7402E8.8B64D4D8@bioinformatics.org> <3A7441EF.8070705@casema.net> <3A754124.C9538CFF@yournews.nl> <3A754F70.5EC7BD66@bioinformatics.org> <3A755074.C9F96CB1@yournews.nl> <3A7561FA.8ED344A6@bioinformatics.org> Message-ID: <3A7618B4.829FDCBA@gel.usherb.ca> > > > Would you like me to begin the HOWTO? > > > > Please do! > > Here we go again: Wiki, LaTeX, text, ...? :-) I'm voting for LaTeX, as it can be easily converted to almost any other doc type: HTML, PS, PDF, RTF, ... Jean-Marc -- Jean-Marc Valin Universite de Sherbrooke - Genie Electrique valj01@gel.usherb.ca From jeff at bioinformatics.org Tue Jan 30 01:05:48 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:42 2006 Subject: [Pipet Devel] Re: kapi (was: Piper HOWTO) References: <3A7227A1.1FB21391@bioinformatics.org> <3A730815.4D0383A6@casema.net> <3A7402E8.8B64D4D8@bioinformatics.org> <3A7441EF.8070705@casema.net> <3A754124.C9538CFF@yournews.nl> <3A755236.68D9AA03@bioinformatics.org> <3A7551C3.1B444F96@yournews.nl> <3A75626B.C73B5CF6@bioinformatics.org> <3A75657B.830B1DA6@yournews.nl> <3A756CBF.918CC527@bioinformatics.org> <3A761823.2C092A08@gel.usherb.ca> Message-ID: <3A7659BC.806BD179@bioinformatics.org> Jean-Marc Valin wrote: > > > Otherwise, we'll probably have to distribute the library separately. That's > > the only legal alternative. > > No, that's not even an option... because then Pipers users wouldn't be allowed > to use Piper commercially (as it would imply using the library commercially). > This license is NOT compatible with the L(GPL), so it would be illegal to > redistribute Piper if it links with this library (whether or not the library is > separated from Piper). I'm no lawyer, but I've looked closely at the GPL a > couple times. You're right. Using kapi as a separate, but required, library only solves the problem for non-commercial users. However, it makes the commercial use of Piper illegal (the L/GPL cannot be mixed with commercial licenses). Unless, of course, we ammend the L/GPL and used a mixed license. I don't want to do that, though. We're in a tight spot here. Cheers. Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "All those scientists--they're all alike! They say they're working for us, but what they really want is to rule the world!" -- Angry Villager, Young Frankenstein -- From jarl at casema.net Tue Jan 30 05:52:25 2001 From: jarl at casema.net (jarl van katwijk) Date: Fri Feb 10 19:20:42 2006 Subject: [Pipet Devel] Re: kapi (was: Piper HOWTO) References: <3A7227A1.1FB21391@bioinformatics.org> <3A730815.4D0383A6@casema.net> <3A7402E8.8B64D4D8@bioinformatics.org> <3A7441EF.8070705@casema.net> <3A754124.C9538CFF@yournews.nl> <3A755236.68D9AA03@bioinformatics.org> <3A7551C3.1B444F96@yournews.nl> <3A75626B.C73B5CF6@bioinformatics.org> <3A75657B.830B1DA6@yournews.nl> <3A756CBF.918CC527@bioinformatics.org> <3A761823.2C092A08@gel.usherb.ca> <3A7659BC.806BD179@bioinformatics.org> Message-ID: <3A769CE9.969BF076@casema.net> > You're right. Using kapi as a separate, but required, library only solves the > problem for non-commercial users. However, it makes the commercial use of > Piper illegal (the L/GPL cannot be mixed with commercial licenses). Unless, > of course, we ammend the L/GPL and used a mixed license. I don't want to do > that, though. > > We're in a tight spot here. > I didn't got any reply on my requests to the Kapi contact persons yet. So the plan is if there comes a positive reply that we can re-licence the code I'll clean up the code and hook it into the BL. If not, we'll code our own kqml implementation from scratch based on this example code. Some extra we get by using kqml is that it has a (sub-) system included called ANS that handles localisation on nodes. So I can handle the 'central localisation server' we got in mind for Piper. any more obstacles? jarl