From d.navarro at bmb.sdu.dk Mon Apr 1 10:33:16 2002 From: d.navarro at bmb.sdu.dk (Danny Navarro) Date: Sat Mar 5 14:43:12 2005 Subject: [Biopython-dev] biopython in ZOPE In-Reply-To: <20020401091050.36306.qmail@web10806.mail.yahoo.com> References: <20020401091050.36306.qmail@web10806.mail.yahoo.com> Message-ID: <1017675196.18960.12.camel@boli> > It would be nice if we could use some bioperl stuff, they are quite mature and > have lots of functionality. How to do that best in ZOPE, im not sure. > ActiveState had some ZOPE-perl stuff, but it dosnt look very active now. Hi Florian, I totally agree with that. The new modules incorporated in the 1.0 realease are really impressive. But I like more Python... I started to learn programming with Perl but when I discovered Python I didn't have any doubt about getting deep into it. I am not going to discuss here why but what I mean is that I feel more comfortable working with Python than with Perl. It'll be easier, at least to me, to wrap biopython modules in Zope than the the bioperl ones. But if anybody wants to do it, it should be possible. In theory you could use pyperl to embed Perl code in Python and zoperl to access to the Zope API. But as you said it doesn't seem to be maintained anymore and I don't know if the Zope Perl scripts work properly. http://www.zope.org/Wikis/zope-perl/ http://lists.zope.org/pipermail/zope-perl/ I think the easiest way to incorporate the bioperl functionality is first try to implement biopython modules in Zope classes. After that then we could try to access bioperl and biojava through bioCORBA. But I haven't tried bioCORBA yet and I can't assess the feasibility of this. Danny From katel at worldpath.net Mon Apr 1 18:17:54 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:12 2005 Subject: [Biopython-dev] Last chance to claim Dispatch bug fix References: <002e01c1d6bb$2a40c200$08fea8c0@pcklindner> <20020328210341.E440@krusty.stanford.edu> Message-ID: <003401c1d9d3$755f6f00$08fea8c0@pcklindner> I posted a description of my fix. So I have a grren light to proceed? Cayte ----- Original Message ----- From: "Jeffrey Chang" To: "Cayte" Cc: Sent: Thursday, March 28, 2002 9:03 PM Subject: Re: [Biopython-dev] Last chance to claim Dispatch bug fix > Hi Cayte, > > Could you please describe your fixes in a little more detail? For > example, I'm not sure what you're planning on doing with _consumer in > ParserSupport, or what problem it's trying to solve. Also, for > _consumer, are you referring to the member variable of the > EventGenerator or SGMLStrippingConsumer, or something else? > From jchang at smi.stanford.edu Mon Apr 1 20:10:17 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:12 2005 Subject: [Biopython-dev] Last chance to claim Dispatch bug fix In-Reply-To: <003401c1d9d3$755f6f00$08fea8c0@pcklindner> References: <002e01c1d6bb$2a40c200$08fea8c0@pcklindner> <20020328210341.E440@krusty.stanford.edu> <003401c1d9d3$755f6f00$08fea8c0@pcklindner> Message-ID: <20020401171017.A382@krusty.stanford.edu> Please don't do that. If I understand correctly, you are having problems with Martel.Parser._parse_elements because it is checking to see if a class is an instance of Dispatch.Dispatcher. You are using a ParserSupport._EventGenerator object that is decorating a _consumer member that is a Dispatcher. Since _EventGenerator is not a Dispatcher, the check in _parse_elements fails. You want it to succeed because your _consumer can handle the Dispatcher calls. Thus, you would like to patch _EventGenerator to expose the _consumer member via a function call, and patch _parse_elements to call that function to see whether the decorated object is a Dispatcher. I don't think this is the right approach to solve the problem, because it makes too many changes to the APIs to both _EventGenerator and _parse_elements. This might be acceptable if it's a common enough case, but I'm not convinced that it is. The problem with adding new APIs is that they're hard to get rid of. If you add a method to get the decorated object of _EventGenerator, future implementations and subclasses of this object will have to also implement this method, even if it's not a decorator. Plus, if you add another check in _parse_elements, that method will have to do multiple checks forever. In addition, any other method that checks to see whether an object is a Dispatcher will have to do that check too. It gets messy and bug-prone really fast. Instead, you should create your own subclass of _EventGenerator that also inherits from Dispatcher, so that you conform to the API that _parse_elements is expecting. Jeff On Mon, Apr 01, 2002 at 03:17:54PM -0800, Cayte wrote: > I posted a description of my fix. So I have a grren light to proceed? > Cayte > ----- Original Message ----- > From: "Jeffrey Chang" > To: "Cayte" > Cc: > Sent: Thursday, March 28, 2002 9:03 PM > Subject: Re: [Biopython-dev] Last chance to claim Dispatch bug fix > > > > Hi Cayte, > > > > Could you please describe your fixes in a little more detail? For > > example, I'm not sure what you're planning on doing with _consumer in > > ParserSupport, or what problem it's trying to solve. Also, for > > _consumer, are you referring to the member variable of the > > EventGenerator or SGMLStrippingConsumer, or something else? > > > From katel at worldpath.net Mon Apr 1 23:39:44 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:12 2005 Subject: [Biopython-dev] Last chance to claim Dispatch bug fix References: <002e01c1d6bb$2a40c200$08fea8c0@pcklindner> <20020328210341.E440@krusty.stanford.edu> <003401c1d9d3$755f6f00$08fea8c0@pcklindner> <20020401171017.A382@krusty.stanford.edu> Message-ID: <005a01c1da00$6b9d2340$08fea8c0@pcklindner> I agree that changing the interface can cause a mess but so can multiple inheritance. Maybe someone, ( Andrew? ) has a better idea. If not I'll consider multiple inheritance. Cayte From biopython-bugs at bioperl.org Wed Apr 3 04:01:34 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:12 2005 Subject: [Biopython-dev] Notification: incoming/62 Message-ID: <200204030901.g3391YkO030061@pw600a.bioperl.org> JitterBug notification new message incoming/62 Message summary for PR#62 From: Subject: TONER CARTRIDGES Date: Wed, 03 Apr 2002 00:08:36 -0480 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From vertex@golfmail.net Wed Apr 3 04:01:33 2002 Received: from yahoo.com ([211.185.173.1]) by pw600a.bioperl.org (8.12.2/8.12.2) with SMTP id g3391CkO030056 for ; Wed, 3 Apr 2002 04:01:14 -0500 Received: from 167.8.9.24 ([167.8.9.24]) by da001d2020.lax-ca.osd.concentric.net with QMQP; Mon, 1 Apr 2002 13:06:12 -0000 Reply-To: Message-ID: From: Subject: TONER CARTRIDGES Date: Wed, 03 Apr 2002 00:08:36 -0480 MiME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_00T7_69W80Z1A.A1111E22" X-Priority: 3 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2002 15:48:32 0800 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From info@expatsh.com Thu Apr 11 03:50:20 2002 Received: from 550e ([61.171.91.111]) by pw600a.bioperl.org (8.12.2/8.12.2) with SMTP id g3B7o9kO025751 for ; Thu, 11 Apr 2002 03:50:17 -0400 x-esmtp: 0 0 1 Message-ID: <752956-22002441174832963@expatsh.com> X-EM-Version: 6, 0, 1, 0 X-EM-Registration: #00F06206106618006920 X-Priority: 3 Reply-To: info@expatsh.com To: "Shanghai" From: "" Subject: Rutgers EMBA Information Session - 18 April 2002 Date: Thu, 11 Apr 2002 15:48:32 +0800 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_84815C5ABAF209EF376268C8" X-SMTPExp-Version: 1, 0, 2, 13 X-SMTPExp-Registration: 00B0320C107602006905 ------=_NextPart_84815C5ABAF209EF376268C8 Content-type: text/plain; charset="US-ASCII" SHANGHAI INFORMATION SESSION Thursday, April 18, 2002. at 8F, Shui On Plaza, 333 Huai Hai Zhong Lu 6.30pm - 8.30pm The Information Session on 18 April will answer the questions you may have about the Rutgers International Executive MBA program. *AACSB fully accredited MBA without having to leave Shanghai, nor drop your career, nor lose your current income *The same quality curriculum, textbooks, learning materials, professors available in the US, also made available to you in Shanghai *World-class professors with industry, publishing, and consulting experience *A conveniently designed class schedule that fully accommodates your work schedule so you can complete your International Executive MBA within 14 months (primarily 2 weekends & 2 evenings per month) By including you in this reception, we also want to demonstrate our sincerity in encouraging you to actively pursue the achievement of your MBA career objective To confirm your attendance please e-mail: rutgers@online.sh.cn with the following Registration Details: Attendee's Name, Company Name, Position in Company, Years of Managerial Experience, contact telephone number and e-mail address. To forward us these details via e-mail, please click Here or Telephone 6293 2628 and Fax 6293 2740 Please Click Here if you Do Not wish to Receive These E-Mails ------=_NextPart_84815C5ABAF209EF376268C8 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable Rutgers Information Session
=20 =20 <= /tr>=20 =20
<= div align=3D"center">=20

SHANGHAI INFORMATION SESSIO= N
Thursday,=20 April 18, 2002=2E

at=20 8F, Shui On Plaza, 333 Huai Hai Zhong Lu

6=2E30pm=20 - 8=2E30pm

=
=
=20

The Information Session on 18 Apri= l will answer=20 the questions you may have about the Rutgers International Executive MBA p= rogram=2E=20

*AACSB=20 fully accredited MBA without having to leave Shanghai, nor drop your caree= r, nor=20 lose your current income

*The=20 same quality curriculum, textbooks, learning materials, professors availab= le in=20 the US, also made available to you in Shanghai

*World-class=20 professors with industry, publishing, and consulting experience=

*A=20 conveniently designed class schedule that fully accommodates your work sch= edule=20 so you can complete your International Executive MBA within 14 months (pri= marily=20 2 weekends & 2 evenings per month)

=20 By including you in this reception, we also want to demonstrate our sincer= ity=20 in encouraging you to actively pursue the achievement of your MBA career o= bjective

To=20 confirm your attendance please e-mail: rutgers@online=2Esh=2Ecn=20 with the following Registration Details:

=20 Attendee's Name, Company Name, Position in Company,

=

=20 Years of Managerial Experience, contact telephone number and e-mail addres= s=2E
=20

To=20 forward us these details via e-mail, please click Here=20 or Telephone 6293 2628 and Fax 6293 2740

=20
------=_NextPart_84815C5ABAF209EF376268C8-- From biopython-bugs at bioperl.org Fri Apr 12 01:52:48 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:12 2005 Subject: [Biopython-dev] Notification: incoming/64 Message-ID: <200204120552.g3C5qmkO006491@pw600a.bioperl.org> JitterBug notification new message incoming/64 Message summary for PR#64 From: "=?gb2312?q?=F4=E4=B4=E4.com_"?= Subject: =?gb2312?q?=F4=E4=B4=E4=D6=AE=C3=C0?= Date: Fri, 12 Apr 2002 13:53:38 0800 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From fcuimailmaster@elong.com Fri Apr 12 01:52:44 2002 Received: from www ([218.63.91.21]) by pw600a.bioperl.org (8.12.2/8.12.2) with SMTP id g3C5qekO006487 for ; Fri, 12 Apr 2002 01:52:42 -0400 Message-Id: <200204120552.g3C5qekO006487@pw600a.bioperl.org> From: "=?gb2312?q?=F4=E4=B4=E4.com_"?= Reply-To: fcuimailmaster@elong.com Subject: =?gb2312?q?=F4=E4=B4=E4=D6=AE=C3=C0?= Date: Fri, 12 Apr 2002 13:53:38 +0800 MIME-Version: 1.0 Content-Type: multipart/related; boundary="319a192c-4e1a-11d6-a76e-00e04c4a956b" This is a multi-part message in MIME format --319a192c-4e1a-11d6-a76e-00e04c4a956b Content-Type: text/html; charset=gb2312 Content-Transfer-Encoding: quoted-printable email-1.gif
--319a192c-4e1a-11d6-a76e-00e04c4a956b-- From biopython-bugs at bioperl.org Fri Apr 12 01:54:13 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:12 2005 Subject: [Biopython-dev] Notification: incoming/65 Message-ID: <200204120554.g3C5sDkO006514@pw600a.bioperl.org> JitterBug notification new message incoming/65 Message summary for PR#65 From: "=?gb2312?q?=F4=E4=B4=E4.com_"?= Subject: =?gb2312?q?=F4=E4=B4=E4=D6=AE=C3=C0?= Date: Fri, 12 Apr 2002 13:55:07 0800 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From fcuimailmaster@elong.com Fri Apr 12 01:54:13 2002 Received: from www ([218.63.91.21]) by pw600a.bioperl.org (8.12.2/8.12.2) with SMTP id g3C5s9kO006504 for ; Fri, 12 Apr 2002 01:54:11 -0400 Message-Id: <200204120554.g3C5s9kO006504@pw600a.bioperl.org> From: "=?gb2312?q?=F4=E4=B4=E4.com_"?= Reply-To: fcuimailmaster@elong.com Subject: =?gb2312?q?=F4=E4=B4=E4=D6=AE=C3=C0?= Date: Fri, 12 Apr 2002 13:55:07 +0800 MIME-Version: 1.0 Content-Type: multipart/related; boundary="319a1aee-4e1a-11d6-a76e-00e04c4a956b" This is a multi-part message in MIME format --319a1aee-4e1a-11d6-a76e-00e04c4a956b Content-Type: text/html; charset=gb2312 Content-Transfer-Encoding: quoted-printable email-1.gif
--319a1aee-4e1a-11d6-a76e-00e04c4a956b-- From diego at conysis.com Tue Apr 16 07:55:28 2002 From: diego at conysis.com (Diego Brouard) Date: Sat Mar 5 14:43:12 2005 Subject: [Biopython-dev] debian packages of BioPython Message-ID: <20020416115528.GA24175@valhalla.id-agora.net> Hi all, and thanks for your efforts. First, I'll present me. I'm a Biologist who works as Programmer in Python, so, I felt quite comfortable when I began reading about this proyect. Anyway, I'm afraid I does not have time to work in development ( I hope in the future, I will ), but I have packaged biopython, the Debian way. You can download ( and test ) these unofficial Debian Packages from http://www.conysis.com/~diego/debian I hope also that in one or two months, they will become "Official Packages", as I will become "Official Developer". And yes!, these packages are from version 1.00a3, don't worry, this weekend I promise to upload the new version'packages. Two more things: following the Debian Policy, you'll find 2 packages: python-bio ( I have to name the binary packages this way ) and, python-bio-doc ( which has the doc :) ) Diego. From chapmanb at arches.uga.edu Wed Apr 17 10:42:29 2002 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:12 2005 Subject: [Biopython-dev] debian packages of BioPython In-Reply-To: <20020416115528.GA24175@valhalla.id-agora.net> References: <20020416115528.GA24175@valhalla.id-agora.net> Message-ID: <20020417104229.A24523@ci350185-a.athen1.ga.home.com> Hi Diego; > First, I'll present me. I'm a Biologist who works as Programmer in > Python, so, I felt quite comfortable when I began reading about this > proyect. Great! Nice to have you aboard! > I have packaged biopython, the Debian way. Thanks! This is great to here. I don't use Debian myself, but am very appreciative of getting Biopython packaged for native package systems. I've added you to the CONTRIB file (as an extra encouragement to keep packaging :-). If you'd like to add Debian directions for installation to the Biopython docs, just send 'em my way, and I'll be more than happy to add them. Thanks again! Brad From katel at worldpath.net Fri Apr 19 18:35:48 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:12 2005 Subject: [Biopython-dev] biopython in ZOPE Message-ID: <002f01c1e7f2$8f2bd180$08fea8c0@pcklindner> >I think the easiest way to incorporate the bioperl functionality is >first try to implement biopython modules in Zope classes. Do you mean ZClasses? I'm slogging through the Book of ZOPE. ZOPE has a lot of ways to do the same thing. The online book has template object language but one of the examples doesn't work on my machine. Its the compoundingInterestRate problem in Chapter4 Using Basic Zope Objects. The parameter passing to python causes an error. I've tried various changes and experiments but can't get it to complete. I like the ZClasses better and find them easier to understand Cayte From katel at worldpath.net Fri Apr 19 22:10:37 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:12 2005 Subject: [Biopython-dev] ZCatalog Message-ID: <004301c1e810$912498a0$08fea8c0@pcklindner> Looks like the ZOPE ZCatalog may mesh nicely with the indexxes built by the format parsers. Cayte From katel at worldpath.net Sun Apr 21 19:18:38 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:12 2005 Subject: [Biopython-dev] Zope Message-ID: <000b01c1e98a$df52f8c0$08fea8c0@pcklindner> Next week I'll be writing experimental Zope apps to hopefully integrate with some biopython stuff. I'd like to check it into a collaboration area where it is available to other developers but not part of the download. Do we have any mechanism of this type? Maybe we needone. Cayte From katel at worldpath.net Wed Apr 24 22:45:12 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:12 2005 Subject: [Biopython-dev] Zope Products Message-ID: <004001c1ec03$3a1e3600$8872bbd1@pcklindner> Zope Products are a snazzy way of packaging related classes, form and files. The Book of Zope suggests using ZClass for prototyping and later migrating to ZProducts when you reach a consensus. Cayte From katel at worldpath.net Fri Apr 26 18:54:17 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:12 2005 Subject: [Biopython-dev] Zope lesson Message-ID: <001201c1ed75$4d912940$fc72bbd1@pcklindner> I finally got a template to call python. Getting it to work depends on a subtle distinction between dtml methods and documents. Methods rely on acquisition( zope lingo for its namespace inheritance mechanism ). So next I can explore templates as another possibility. Cayte