From Pieter.Neerincx at wur.nl Mon Feb 4 14:26:37 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Mon, 4 Feb 2008 20:26:37 +0100 Subject: [MOBY-dev] IO::Template missing for MOSES::MOBY In-Reply-To: References: <20080131104248.4E82E2DEA19@marz.stanford.edu> Message-ID: <148D36BB-BECF-4B43-967C-639832792372@wur.nl> Hi Eddie, I'm trying to install MOSES::MOBY in our main production environment using CPAN :), but it wants IO::Template. This one is new for me, not available on CPAN and Google won't tell me where to get it either. Is this a very obscure module or maybe a typo in the prerequisites? Cheers, Pi From edward.kawas at gmail.com Mon Feb 4 14:53:10 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 4 Feb 2008 11:53:10 -0800 Subject: [MOBY-dev] IO::Template missing for MOSES::MOBY In-Reply-To: <148D36BB-BECF-4B43-967C-639832792372@wur.nl> References: <20080131104248.4E82E2DEA19@marz.stanford.edu> <148D36BB-BECF-4B43-967C-639832792372@wur.nl> Message-ID: <47a76d27.15588c0a.27b2.2e6d@mx.google.com> Hi Pieter, The module is at http://search.cpan.org/dist/Template-Toolkit/. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter Neerincx Sent: February-04-08 11:27 AM To: Core developer announcements Subject: [MOBY-dev] IO::Template missing for MOSES::MOBY Hi Eddie, I'm trying to install MOSES::MOBY in our main production environment using CPAN :), but it wants IO::Template. This one is new for me, not available on CPAN and Google won't tell me where to get it either. Is this a very obscure module or maybe a typo in the prerequisites? Cheers, Pi _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From Pieter.Neerincx at wur.nl Mon Feb 4 17:01:23 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Mon, 04 Feb 2008 23:01:23 +0100 Subject: [MOBY-dev] IO::Template missing for MOSES::MOBY In-Reply-To: <47a76d27.15588c0a.27b2.2e6d@mx.google.com> References: <20080131104248.4E82E2DEA19@marz.stanford.edu> <148D36BB-BECF-4B43-967C-639832792372@wur.nl> <47a76d27.15588c0a.27b2.2e6d@mx.google.com> Message-ID: <20CCF5A5-969D-47AC-A793-A2F4C81A0F78@wur.nl> Ok, thanks! Somehow CPAN doesn't mangage to figure out the dependancy... and I don't find IO::Template in there either. Shouldn't the requirement be Template instead of IO::Template? Cheers, Pi On 04 Feb 2008, at 20:53, Edward Kawas wrote: > Hi Pieter, > > The module is at http://search.cpan.org/dist/Template-Toolkit/. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter > Neerincx > Sent: February-04-08 11:27 AM > To: Core developer announcements > Subject: [MOBY-dev] IO::Template missing for MOSES::MOBY > > Hi Eddie, > > I'm trying to install MOSES::MOBY in our main production environment > using CPAN :), but it wants IO::Template. This one is new for me, not > available on CPAN and Google won't tell me where to get it either. Is > this a very obscure module or maybe a typo in the prerequisites? > > Cheers, > > Pi > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------- From edward.kawas at gmail.com Mon Feb 4 17:36:42 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 4 Feb 2008 14:36:42 -0800 Subject: [MOBY-dev] IO::Template missing for MOSES::MOBY In-Reply-To: <20CCF5A5-969D-47AC-A793-A2F4C81A0F78@wur.nl> References: <20080131104248.4E82E2DEA19@marz.stanford.edu> <148D36BB-BECF-4B43-967C-639832792372@wur.nl> <47a76d27.15588c0a.27b2.2e6d@mx.google.com> <20CCF5A5-969D-47AC-A793-A2F4C81A0F78@wur.nl> Message-ID: <47a7937c.01538c0a.5153.32b8@mx.google.com> I will look into this as you might be right. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter Neerincx Sent: February-04-08 2:01 PM To: Core developer announcements Subject: Re: [MOBY-dev] IO::Template missing for MOSES::MOBY Ok, thanks! Somehow CPAN doesn't mangage to figure out the dependancy... and I don't find IO::Template in there either. Shouldn't the requirement be Template instead of IO::Template? Cheers, Pi On 04 Feb 2008, at 20:53, Edward Kawas wrote: > Hi Pieter, > > The module is at http://search.cpan.org/dist/Template-Toolkit/. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter > Neerincx > Sent: February-04-08 11:27 AM > To: Core developer announcements > Subject: [MOBY-dev] IO::Template missing for MOSES::MOBY > > Hi Eddie, > > I'm trying to install MOSES::MOBY in our main production environment > using CPAN :), but it wants IO::Template. This one is new for me, not > available on CPAN and Google won't tell me where to get it either. Is > this a very obscure module or maybe a typo in the prerequisites? > > Cheers, > > Pi > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------- _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Mon Feb 4 17:56:31 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 4 Feb 2008 14:56:31 -0800 Subject: [MOBY-dev] IO::Template missing for MOSES::MOBY In-Reply-To: <148D36BB-BECF-4B43-967C-639832792372@wur.nl> References: <20080131104248.4E82E2DEA19@marz.stanford.edu> <148D36BB-BECF-4B43-967C-639832792372@wur.nl> Message-ID: <47a79821.0e578c0a.0282.ffffb68e@mx.google.com> Hmm, I don't want to beat this dead horse any more than I should, but I am looking at the MOSES::MOBY module and I cant find IO::Template in it anywere. Where did you get this error from? Also, the makefile has 'Template' in it already... Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter Neerincx Sent: February-04-08 11:27 AM To: Core developer announcements Subject: [MOBY-dev] IO::Template missing for MOSES::MOBY Hi Eddie, I'm trying to install MOSES::MOBY in our main production environment using CPAN :), but it wants IO::Template. This one is new for me, not available on CPAN and Google won't tell me where to get it either. Is this a very obscure module or maybe a typo in the prerequisites? Cheers, Pi _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Mon Feb 4 18:41:17 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 4 Feb 2008 15:41:17 -0800 Subject: [MOBY-dev] cvs perl folder - potential changes Message-ID: <47a7a29f.22528c0a.1300.5fb7@mx.google.com> Hi, I have been working on a MOBY cpan module that is hopefully going to simplify the registry installation portion of mobycentral. I am writing to the list to see who would be upset with me if I were to re-arrange the moby-live/Perl/ folder in the cvs. Currently, the moby-live/Perl/ folder looks like: Perl/ |--> Accessories/ |--> docs/ |--> MOBY/ |--> scripts/ |--> t/ Some files ... I would like to do the following: Move Perl/MOBY to Perl/lib/MOBY Perl/scripts to Perl/share/[cgi|config|db|scripts] Create a Perl/bin/scripts directory, and a Perl/inc directory. Replace the Makefile.PL with my new Makefile.PL. One reason that I wish to do this is to reduce the chance of code forking (http://en.wikipedia.org/wiki/Fork_(software_development) ) in the future with the cvs release and cpan releases. In addition, the new folder layout is what is used when creating the cpan release module for MOBY. Anyone object? I will wait for comments/concerns/etc all this week and next week during the hackathon, I will hopefully carry out these changes. Thanks, Eddie From markw at illuminae.com Mon Feb 4 22:38:57 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 04 Feb 2008 19:38:57 -0800 Subject: [MOBY-dev] cvs perl folder - potential changes In-Reply-To: <47a7a29f.22528c0a.1300.5fb7@mx.google.com> References: <47a7a29f.22528c0a.1300.5fb7@mx.google.com> Message-ID: Sounds good to me! On Mon, 04 Feb 2008 15:41:17 -0800, Edward Kawas wrote: > I would like to do the following: > > Move > Perl/MOBY to Perl/lib/MOBY > Perl/scripts to Perl/share/[cgi|config|db|scripts] > > Create a Perl/bin/scripts directory, and a Perl/inc directory. > > Replace the Makefile.PL with my new Makefile.PL. From Pieter.Neerincx at wur.nl Tue Feb 5 05:54:09 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Tue, 5 Feb 2008 11:54:09 +0100 Subject: [MOBY-dev] cvs perl folder - potential changes In-Reply-To: References: <47a7a29f.22528c0a.1300.5fb7@mx.google.com> Message-ID: Yep, same here. Looking forward to test the Moby Central CPAN module! Just one request: could you make a copy of the "old" cvs Perl folder first and put that on the website as a "release". I'm running a course over the next weeks involving BioMoby service development, so it would be nice to have a "backup" of the 1.0 Moby code. Cheers, Pi On 5-feb-2008, at 4:38, Mark Wilkinson wrote: > Sounds good to me! > > > On Mon, 04 Feb 2008 15:41:17 -0800, Edward Kawas > wrote: > > > >> I would like to do the following: >> >> Move >> Perl/MOBY to Perl/lib/MOBY >> Perl/scripts to Perl/share/[cgi|config|db|scripts] >> >> Create a Perl/bin/scripts directory, and a Perl/inc directory. >> >> Replace the Makefile.PL with my new Makefile.PL. > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From Pieter.Neerincx at wur.nl Tue Feb 5 06:01:55 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Tue, 5 Feb 2008 12:01:55 +0100 Subject: [MOBY-dev] IO::Template missing for MOSES::MOBY In-Reply-To: <47a79821.0e578c0a.0282.ffffb68e@mx.google.com> References: <20080131104248.4E82E2DEA19@marz.stanford.edu> <148D36BB-BECF-4B43-967C-639832792372@wur.nl> <47a79821.0e578c0a.0282.ffffb68e@mx.google.com> Message-ID: <237435F5-3D96-4B8F-AAC8-B1F498548A6A@wur.nl> Hi Eddie, Must be an "undead" zombie than :(. This is what I get: CPAN.pm: Going to build E/EK/EKAWAS/MOSES-MOBY-0.84.tar.gz Cannot determine perl version info from lib/MOSES/MOBY.pm *** Module::AutoInstall version 1.03 *** Checking for Perl dependencies... [Core Features] - Test::More ...loaded. (0.62 >= 0.42) - ExtUtils::MakeMaker ...loaded. (6.17 >= 6.11) - Carp ...loaded. (1.01) - File::Spec ...loaded. (3.19 >= 0.80) - SOAP::Lite ...loaded. (0.69 >= 0.69) - XML::LibXML ...loaded. (1.66 >= 1.62) - Log::Log4perl ...loaded. (1.14 >= 1.12) - Template ...loaded. (2.19 >= 1.11) - Config::Simple ...loaded. (4.58 >= 4.58) - IO::Stringy ...loaded. (2.110 >= 2.11) - Unicode::String ...loaded. (2.09 >= 2.09) - File::HomeDir ...loaded. (0.69 >= 0.65) - File::ShareDir ...loaded. (0.05 >= 0.05) - Class::Inspector ...loaded. (1.18 >= 1.17) - Params::Util ...loaded. (0.31 >= 0.28) - IO::Prompt ...missing. (would need 0.99) ==> Auto-install the 1 mandatory module(s) from CPAN? [y] n ==> The module(s) are mandatory! Really skip? [n] y *** Module::AutoInstall configuration finished. Checking if your kit is complete... Looks good Warning: prerequisite IO::Prompt 0.99 not found. We have 0.099004. Writing Makefile for MOSES::MOBY ---- Unsatisfied dependencies detected during [E/EK/EKAWAS/MOSES- MOBY-0.84.tar.gz] ----- IO::Template Shall I follow them and prepend them to the queue of modules we are processing right now? [yes] If I answer yes it can't find IO::Template on CPAN. Notice that the version number of IO::Prompt is messed up. I tried to stick to 0.99.2 as suggested by your documentation to prevent the documented bogus errors, but apparently we already have 0.99.4 on the production machine... It's probably not a MOSES::MOBY bug, but an erroneous dependancy in IO::... (If I tell CPAN to try to install IO::Prompt I get the same error) Cheers, Pi On 4-feb-2008, at 23:56, Edward Kawas wrote: > Hmm, I don't want to beat this dead horse any more than I should, > but I am > looking at the MOSES::MOBY module and I cant find IO::Template in it > anywere. Where did you get this error from? Also, the makefile has > 'Template' in it already... > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter > Neerincx > Sent: February-04-08 11:27 AM > To: Core developer announcements > Subject: [MOBY-dev] IO::Template missing for MOSES::MOBY > > Hi Eddie, > > I'm trying to install MOSES::MOBY in our main production environment > using CPAN :), but it wants IO::Template. This one is new for me, not > available on CPAN and Google won't tell me where to get it either. Is > this a very obscure module or maybe a typo in the prerequisites? > > Cheers, > > Pi > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From markw at illuminae.com Tue Feb 5 08:52:30 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 05 Feb 2008 05:52:30 -0800 Subject: [MOBY-dev] cvs perl folder - potential changes In-Reply-To: References: <47a7a29f.22528c0a.1300.5fb7@mx.google.com> Message-ID: The 1.0 Perl code was released a few days ago to correspond with the publication. (see homepage). I'm waiting for the Java crew to release their bit. M On Tue, 05 Feb 2008 02:54:09 -0800, Pieter Neerincx wrote: > Yep, same here. Looking forward to test the Moby Central CPAN module! > Just one request: could you make a copy of the "old" cvs Perl folder > first and put that on the website as a "release". I'm running a course > over the next weeks involving BioMoby service development, so it would > be nice to have a "backup" of the 1.0 Moby code. > > Cheers, > > Pi > > On 5-feb-2008, at 4:38, Mark Wilkinson wrote: > >> Sounds good to me! >> >> >> On Mon, 04 Feb 2008 15:41:17 -0800, Edward Kawas >> wrote: >> >> >> >>> I would like to do the following: >>> >>> Move >>> Perl/MOBY to Perl/lib/MOBY >>> Perl/scripts to Perl/share/[cgi|config|db|scripts] >>> >>> Create a Perl/bin/scripts directory, and a Perl/inc directory. >>> >>> Replace the Makefile.PL with my new Makefile.PL. >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 039 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------ > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Tue Feb 5 09:21:25 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 5 Feb 2008 06:21:25 -0800 Subject: [MOBY-dev] IO::Template missing for MOSES::MOBY In-Reply-To: <237435F5-3D96-4B8F-AAC8-B1F498548A6A@wur.nl> References: <20080131104248.4E82E2DEA19@marz.stanford.edu> <148D36BB-BECF-4B43-967C-639832792372@wur.nl> <47a79821.0e578c0a.0282.ffffb68e@mx.google.com> <237435F5-3D96-4B8F-AAC8-B1F498548A6A@wur.nl> Message-ID: <47a870e9.02578c0a.1362.ffffe220@mx.google.com> I don't know what to say... I have never seen that error before. Do you get the same error if you download the module yourself from cpan? Also, using IO::Prompt 0.99.4 might lead to some problems, so I highly recommend that you use the previous version of that module 0.99.2. Also, I have never been able to install IO::Prompt using command line cpan ... That module is a pain in the butt! Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter Neerincx Sent: February-05-08 3:02 AM To: Core developer announcements Subject: Re: [MOBY-dev] IO::Template missing for MOSES::MOBY Hi Eddie, Must be an "undead" zombie than :(. This is what I get: CPAN.pm: Going to build E/EK/EKAWAS/MOSES-MOBY-0.84.tar.gz Cannot determine perl version info from lib/MOSES/MOBY.pm *** Module::AutoInstall version 1.03 *** Checking for Perl dependencies... [Core Features] - Test::More ...loaded. (0.62 >= 0.42) - ExtUtils::MakeMaker ...loaded. (6.17 >= 6.11) - Carp ...loaded. (1.01) - File::Spec ...loaded. (3.19 >= 0.80) - SOAP::Lite ...loaded. (0.69 >= 0.69) - XML::LibXML ...loaded. (1.66 >= 1.62) - Log::Log4perl ...loaded. (1.14 >= 1.12) - Template ...loaded. (2.19 >= 1.11) - Config::Simple ...loaded. (4.58 >= 4.58) - IO::Stringy ...loaded. (2.110 >= 2.11) - Unicode::String ...loaded. (2.09 >= 2.09) - File::HomeDir ...loaded. (0.69 >= 0.65) - File::ShareDir ...loaded. (0.05 >= 0.05) - Class::Inspector ...loaded. (1.18 >= 1.17) - Params::Util ...loaded. (0.31 >= 0.28) - IO::Prompt ...missing. (would need 0.99) ==> Auto-install the 1 mandatory module(s) from CPAN? [y] n ==> The module(s) are mandatory! Really skip? [n] y *** Module::AutoInstall configuration finished. Checking if your kit is complete... Looks good Warning: prerequisite IO::Prompt 0.99 not found. We have 0.099004. Writing Makefile for MOSES::MOBY ---- Unsatisfied dependencies detected during [E/EK/EKAWAS/MOSES- MOBY-0.84.tar.gz] ----- IO::Template Shall I follow them and prepend them to the queue of modules we are processing right now? [yes] If I answer yes it can't find IO::Template on CPAN. Notice that the version number of IO::Prompt is messed up. I tried to stick to 0.99.2 as suggested by your documentation to prevent the documented bogus errors, but apparently we already have 0.99.4 on the production machine... It's probably not a MOSES::MOBY bug, but an erroneous dependancy in IO::... (If I tell CPAN to try to install IO::Prompt I get the same error) Cheers, Pi On 4-feb-2008, at 23:56, Edward Kawas wrote: > Hmm, I don't want to beat this dead horse any more than I should, > but I am > looking at the MOSES::MOBY module and I cant find IO::Template in it > anywere. Where did you get this error from? Also, the makefile has > 'Template' in it already... > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter > Neerincx > Sent: February-04-08 11:27 AM > To: Core developer announcements > Subject: [MOBY-dev] IO::Template missing for MOSES::MOBY > > Hi Eddie, > > I'm trying to install MOSES::MOBY in our main production environment > using CPAN :), but it wants IO::Template. This one is new for me, not > available on CPAN and Google won't tell me where to get it either. Is > this a very obscure module or maybe a typo in the prerequisites? > > Cheers, > > Pi > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From Pieter.Neerincx at wur.nl Tue Feb 5 09:33:31 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Tue, 5 Feb 2008 15:33:31 +0100 Subject: [MOBY-dev] cvs perl folder - potential changes In-Reply-To: References: <47a7a29f.22528c0a.1300.5fb7@mx.google.com> Message-ID: <5F8AF1F8-8541-4187-ACA8-A2EFBC73EB41@wur.nl> Ok, thanks! On 5-feb-2008, at 14:52, Mark Wilkinson wrote: > The 1.0 Perl code was released a few days ago to correspond with > the publication. > (see homepage). I'm waiting for the Java crew to release their bit. > > M > > > On Tue, 05 Feb 2008 02:54:09 -0800, Pieter Neerincx > wrote: > >> Yep, same here. Looking forward to test the Moby Central CPAN >> module! Just one request: could you make a copy of the "old" cvs >> Perl folder first and put that on the website as a "release". I'm >> running a course over the next weeks involving BioMoby service >> development, so it would be nice to have a "backup" of the 1.0 >> Moby code. >> >> Cheers, >> >> Pi >> >> On 5-feb-2008, at 4:38, Mark Wilkinson wrote: >> >>> Sounds good to me! >>> >>> >>> On Mon, 04 Feb 2008 15:41:17 -0800, Edward Kawas >>> wrote: >>> >>> >>> >>>> I would like to do the following: >>>> >>>> Move >>>> Perl/MOBY to Perl/lib/MOBY >>>> Perl/scripts to Perl/share/[cgi|config|db|scripts] >>>> >>>> Create a Perl/bin/scripts directory, and a Perl/inc directory. >>>> >>>> Replace the Makefile.PL with my new Makefile.PL. >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >> >> ------------------------------------------------------------- >> Wageningen University and Research centre (WUR) >> Laboratory of Bioinformatics >> Transitorium (building 312) room 1034 >> >> Dreijenlaan 3 >> 6703 HA Wageningen >> The Netherlands >> >> phone: 0317-483 039 >> fax: 0317-483 584 >> mobile: 06-143 66 783 >> mail: pieter.neerincx at wur.nl >> skype: pieter.online >> ------------------------------------------------------------ >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From markw at illuminae.com Wed Feb 6 16:49:02 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 06 Feb 2008 13:49:02 -0800 Subject: [MOBY-dev] The beginnings of the new Moby homepage Message-ID: Hi all, I've spent the day working on the new Joomla site that we're considering using as the new Moby homepage. I also wanted to get it running in time for the hackathon as a place to store notes and updates etc. http://biomoby.org/JOOMLA/ It's still basically empty, and the menu buttons are not all well-thought-out yet. Does anyone on the list know Joomla well? I'm starting to get the hang of it, but I'm still quite a beginner! Mark From groscurt at mpiz-koeln.mpg.de Thu Feb 7 09:39:09 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 7 Feb 2008 15:39:09 +0100 Subject: [MOBY-dev] http://biomoby.org/jmoby-jars/jars-archive/ gone ? In-Reply-To: References: Message-ID: <200802071539.09914.groscurt@mpiz-koeln.mpg.de> where are the libs gone ... ?! ant task gather fails because of a 404 andreas -- Andreas Groscurth Bioinformatics Developer Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-449 From gss at ncgr.org Thu Feb 7 12:05:09 2008 From: gss at ncgr.org (Gary Schiltz) Date: Thu, 07 Feb 2008 10:05:09 -0700 Subject: [MOBY-dev] The beginnings of the new Moby homepage In-Reply-To: References: Message-ID: <47AB3A45.2090108@ncgr.org> Mark, Would you care to say a few words about why you want to switch to Joomla from WordPress? Just curious... // Gary On 2/6/2008 2:49 PM, Mark Wilkinson wrote: > Hi all, > > I've spent the day working on the new Joomla site that we're considering > using as the new Moby homepage. I also wanted to get it running in time > for the hackathon as a place to store notes and updates etc. > > http://biomoby.org/JOOMLA/ > > It's still basically empty, and the menu buttons are not all > well-thought-out yet. Does anyone on the list know Joomla well? I'm > starting to get the hang of it, but I'm still quite a beginner! > > Mark From martin.senger at gmail.com Thu Feb 7 12:29:30 2008 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 7 Feb 2008 17:29:30 +0000 Subject: [MOBY-dev] http://biomoby.org/jmoby-jars/jars-archive/ gone ? In-Reply-To: <200802071539.09914.groscurt@mpiz-koeln.mpg.de> References: <200802071539.09914.groscurt@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0802070929qa7584a5y9796be5dcc00432b@mail.gmail.com> > where are the libs gone ... ?! I am getting the same message - but I do not know (yet). I will check it. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Thu Feb 7 14:11:00 2008 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 7 Feb 2008 19:11:00 +0000 Subject: [MOBY-dev] http://biomoby.org/jmoby-jars/jars-archive/ gone ? In-Reply-To: <200802071539.09914.groscurt@mpiz-koeln.mpg.de> References: <200802071539.09914.groscurt@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0802071111v2803896aof0bef0f6b21be37a@mail.gmail.com> Andreas, where are the libs gone ... ?! > > ant task gather fails because of a 404 > Is it better now? Because suddenly I cannot reproduce the error... Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From serr at ac.uma.es Mon Feb 11 03:10:20 2008 From: serr at ac.uma.es (Sergio Ramirez Ramirez) Date: Mon, 11 Feb 2008 09:10:20 +0100 Subject: [MOBY-dev] INB Proposal for Mirroring - RFC In-Reply-To: <938F7558-E5E8-4073-B08C-A37437E46543@wur.nl> References: <938F7558-E5E8-4073-B08C-A37437E46543@wur.nl> Message-ID: <47B002EC.1020307@ac.uma.es> Hello to all the mobiers, In this link http://chirimoyo.ac.uma.es/proposals/BioMOBY_Mirroring.pdf you can find the INB proposal for mirroring services. It describes the new functions and the changes needed in the functions that already exist in the API of BioMOBY. The proposal also includes different options for managing the mirrors using RDF files. We would appreciate comments and suggestions, in particular how to deal with the RDF data. We have implemented the described functionality in the MOBYCentral perl code. This code will be made available, and in a few days we will provide a new link with a small tutorial about how to use the client side library. Best regards, Sergio. Pieter Neerincx wrote: > Hi, > > I searched my mail archive and the website, but I can not find this > RFC.... Was it that long ago? Anyway, can someone please send us > pointer where to find this RFC? > > Thanks, > > Pi > > On 22-jan-2008, at 0:58, Mark Wilkinson wrote: > >> Hi everyone, >> >> Has anyone else looked at the INB proposal for mirroring of services? >> I think it's really nice, personally! I had a couple of small >> questions and concerns, but it really doesn't seem like an overly >> disruptive change, and apparently they already have it working at >> INB, so the codebase to support it already exists. >> >> I think we should vote on the issue soon, as the INB folks have been >> very, VERY patient! >> >> M >> >> >> >> -- >> -- >> Mark Wilkinson >> Assistant Professor, Dept. Medical Genetics >> University of British Columbia >> PI Bioinformatics >> iCAPTURE Centre, St. Paul's Hospital >> Tel: 604 682 2344 x62129 >> Fax: 604 806 9274 >> >> ***CONFIDENTIALITY NOTICE*** >> This electronic message is intended only for the use of the addressee >> and may contain information that is privileged and confidential. Any >> dissemination, distribution or copying of this communication by >> unauthorized individuals is strictly prohibited. If you have received >> this communication in error, please notify the sender immediately by >> reply e-mail and delete the original and all copies from your system. >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 039 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------ > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Sergio Ram?rez Ram?rez Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 "Short-term decisions tend to fail in the long-term." Frank Herbert, God Emperor of Dune From sylvie.huchet at enst-bretagne.fr Tue Feb 12 09:38:31 2008 From: sylvie.huchet at enst-bretagne.fr (Sylvie Huchet) Date: Tue, 12 Feb 2008 15:38:31 +0100 Subject: [MOBY-dev] createInstanceFromDOM Message-ID: <47B1AF67.4040604@enst-bretagne.fr> Hi, I would like to create a biomoby instance from a file that contains data. The data file is an XML file that comply (or should comply) with biomoby format. I thought that if the file contained a data type that is not a biomoby data type (doesn't belong to the object ontology), the createInstanceFromDOM method would throw an exception, but that is not the case. A NullPointerException is thrown by an inner method (MobyDatacomposite constructor). Should I use another method to check that the data type present in the data file is correct or is it a problem with createInstanceFromDOM that should throw an exception ? Thanks, and Best regards, Sylvie. -------------- next part -------------- A non-text attachment was scrubbed... Name: sylvie.huchet.vcf Type: text/x-vcard Size: 215 bytes Desc: not available URL: From gordonp at ucalgary.ca Tue Feb 12 20:03:23 2008 From: gordonp at ucalgary.ca (gordonp at ucalgary.ca) Date: Tue, 12 Feb 2008 18:03:23 -0700 (MST) Subject: [MOBY-dev] createInstanceFromDOM In-Reply-To: <47B1AF67.4040604@enst-bretagne.fr> References: <47B1AF67.4040604@enst-bretagne.fr> Message-ID: <41259.122.26.202.49.1202864603.squirrel@122.26.202.49> Hi Sylvie, If you send me the example XML, that will help me determine the issue. It should be able to parse the data, even if the datatypes are not in the ontology. Regards, Paul If you could send the example file to me, it would > Hi, > > I would like to create a biomoby instance from a file that contains data. > > The data file is an XML file that comply (or should comply) with biomoby > format. > I thought that if the file contained a data type that is not a biomoby > data type > (doesn't belong to the object ontology), the createInstanceFromDOM method > would > throw an exception, but that is not the case. A NullPointerException is > thrown > by an inner method (MobyDatacomposite constructor). > > Should I use another method to check that the data type present in the > data file > is correct or is it a problem with createInstanceFromDOM that should throw > an > exception ? > > Thanks, and > Best regards, > Sylvie. > > > !DSPAM:60005,47b1bec010950204642575! > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > !DSPAM:60005,47b1bec010950204642575! > From markw at illuminae.com Tue Feb 12 21:54:27 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 12 Feb 2008 18:54:27 -0800 Subject: [MOBY-dev] Decisions from the BioHackathon Message-ID: Hi all, Since we have a quorum of the RFC committee here at the Open BioHackathon, we've managed to make quite a few decisions, and we're now in the process of coding them. Here are the decisions in a nutshell: 1) The RFC from INB regarding mirroring of services was accepted with a few changes. We'll get a copy of the revised proposal from Oswaldo in the next few days. Apparently they have already coded support for these changes at INB so it will quickly get into the codebase. 2) Moby will *immediately* start supporting document-literal services. These services will be identified using the "Category" tag in the service registration/discovery XML. Two new categories will be "doc-literal" and "doc-literal-async". Until we get better support for document-literal services in Perl it is likely that these will not be available to Perl clients, but apparently it's no problem in Java. Some considerations that arise from this are: (a) you must now remove the XML header from your data if you're using document-literal, and therefore (b) clients and services need to specify the appropriate character encoding (e.g. UTF-8) in the SOAP XML header. 3) Sending data by reference: we have decided to allow the sending of data by reference rather than as the content of an object. We'll write-up the formal specification of how to do this soon, but briefly the idea is that we will use the xlink XML attribute in a Moby Object XML <.... xlink=''/>. When that tag is present, it is assumed that the content of that node is available at the URI in that reference. During service registration a provider will indicate the various transport protocols they provide for creating references (e.g. http, ftp) and this will be discoverable during a registry query. If you don't indicate a protocol, then you are saying that you do not support pass-by-reference, and therefore all existing services are supported. When accessing a service, you indicate to the service provider that you want data to be passed by reference by adding an attribute in the mobyData block . The service provider then has the option of providing you references for any data they wish. The xlink attribute can appear at any level in your Moby object, such that some data may be passed in the object itself, while other data from the same object may be passed by reference. 4) Validating services: Moby will have several levels of validation: (1) ping, (2) does the service crash when accesed with sample data? (3) does the service output the correct object type? (4) does the service output data that validates against XPath and/or REGEX. The sample input data will be in the service provider's RDF, and there will be several new predicates added to the RDF (I'll provide the OWL file shortly that defines how these predicates are to be used): unit_test, example_input, valid_xpath, valid_regex, valid_output_xml. The validation of output XML will be canonicalized (i.e. xmldiff, not byte-identity) Hackers - please correct me if I have mis-represented anything. I'm working from Eddie's scribbled notes ;-) Hopefully we'll find time to document these changes between our hacking sessions :-) Cheers all! Greetings from Tokyo! Mark From sylvie.huchet at enst-bretagne.fr Wed Feb 13 03:05:14 2008 From: sylvie.huchet at enst-bretagne.fr (Sylvie Huchet) Date: Wed, 13 Feb 2008 09:05:14 +0100 Subject: [MOBY-dev] createInstanceFromDOM In-Reply-To: <41259.122.26.202.49.1202864603.squirrel@122.26.202.49> References: <47B1AF67.4040604@enst-bretagne.fr> <41259.122.26.202.49.1202864603.squirrel@122.26.202.49> Message-ID: <47B2A4BA.3020202@enst-bretagne.fr> Hi Paul, Below is the XML file containing the parameters I want to send to a Biomoby service. With this XML file, I created a DOM object that I use to create a MobyContentInstance (this mobycontentInstance should then be used to fill the data field of a mobyRequest). As the simple parameter contains data of a wrong type, I thought I could catch a MOBYException during the MobycontentInstance constructor call. But the inner MobyDatacomposite constructor throws a NullPointerException. Thanks for hour help, Sylvie. 8 6 Alpha1 AAGAAG Alpha2 AAGAAG Beta1 AAGGGG Beta2 AAGGGG Gamma1 AGGAAG Gamma2 AGGAAG Delta GGAGGA Epsilon GGAAAG no 100 1000 no 1.0 1 gordonp at ucalgary.ca a ?crit : > Hi Sylvie, > > If you send me the example XML, that will help me determine the issue. > It should be able to parse the data, even if the datatypes are not in the > ontology. > > Regards, > > Paul > > If you could send the example file to me, it would > > >>Hi, >> >>I would like to create a biomoby instance from a file that contains data. >> >>The data file is an XML file that comply (or should comply) with biomoby >>format. >>I thought that if the file contained a data type that is not a biomoby >>data type >>(doesn't belong to the object ontology), the createInstanceFromDOM method >>would >>throw an exception, but that is not the case. A NullPointerException is >>thrown >>by an inner method (MobyDatacomposite constructor). >> >>Should I use another method to check that the data type present in the >>data file >>is correct or is it a problem with createInstanceFromDOM that should throw >>an >>exception ? >> >>Thanks, and >>Best regards, >>Sylvie. >> >> >>!DSPAM:60005,47b1bec010950204642575! >>_______________________________________________ >>MOBY-dev mailing list >>MOBY-dev at lists.open-bio.org >>http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> >>!DSPAM:60005,47b1bec010950204642575! >> > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > -------------- next part -------------- A non-text attachment was scrubbed... Name: sylvie.huchet.vcf Type: text/x-vcard Size: 215 bytes Desc: not available URL: From gordonp at ucalgary.ca Wed Feb 13 04:33:09 2008 From: gordonp at ucalgary.ca (gordonp at ucalgary.ca) Date: Wed, 13 Feb 2008 02:33:09 -0700 (MST) Subject: [MOBY-dev] createInstanceFromDOM In-Reply-To: <47B2A4BA.3020202@enst-bretagne.fr> References: <47B1AF67.4040604@enst-bretagne.fr> <41259.122.26.202.49.1202864603.squirrel@122.26.202.49> <47B2A4BA.3020202@enst-bretagne.fr> Message-ID: <53820.122.26.202.49.1202895189.squirrel@122.26.202.49> Hi Sylvie, I've fixed it to throw an explanatory MobyException. Regards, Paul > Hi Paul, > > Below is the XML file containing the parameters I want to send to a > Biomoby service. > With this XML file, I created a DOM object that I use to create a > MobyContentInstance (this mobycontentInstance should then be used to fill > the > data field of a mobyRequest). > As the simple parameter contains data of a wrong type, I thought I could > catch a > MOBYException during the MobycontentInstance constructor call. But the > inner > MobyDatacomposite constructor throws a NullPointerException. > > Thanks for hour help, > Sylvie. > > > > > > > > moby:id="" > moby:namespace=""> > moby:articleName="content">8 > 6 > Alpha1 AAGAAG > Alpha2 AAGAAG > Beta1 AAGGGG > Beta2 AAGGGG > Gamma1 AGGAAG > Gamma2 AGGAAG > Delta GGAGGA > Epsilon GGAAAG > > > > > no > > > 100 > > > 1000 > > > no > > > 1.0 > > > 1 > > > > > > gordonp at ucalgary.ca a ?crit : >> Hi Sylvie, >> >> If you send me the example XML, that will help me determine the issue. >> It should be able to parse the data, even if the datatypes are not in >> the >> ontology. >> >> Regards, >> >> Paul >> >> If you could send the example file to me, it would >> >> >>>Hi, >>> >>>I would like to create a biomoby instance from a file that contains >>> data. >>> >>>The data file is an XML file that comply (or should comply) with >>> biomoby >>>format. >>>I thought that if the file contained a data type that is not a biomoby >>>data type >>>(doesn't belong to the object ontology), the createInstanceFromDOM >>> method >>>would >>>throw an exception, but that is not the case. A NullPointerException is >>>thrown >>>by an inner method (MobyDatacomposite constructor). >>> >>>Should I use another method to check that the data type present in the >>>data file >>>is correct or is it a problem with createInstanceFromDOM that should >>> throw >>>an >>>exception ? >>> >>>Thanks, and >>>Best regards, >>>Sylvie. >>> >>> >>> >>>_______________________________________________ >>>MOBY-dev mailing list >>>MOBY-dev at lists.open-bio.org >>>http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >>> >>>!DSPAM:60005,47b1bec010950204642575! >>> >> >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> > > > !DSPAM:60005,47b2a29c109502586129532! > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > !DSPAM:60005,47b2a29c109502586129532! > From martin.senger at gmail.com Wed Feb 13 09:20:51 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 13 Feb 2008 23:20:51 +0900 Subject: [MOBY-dev] changes in jMoby may cause some disruptions Message-ID: <4d93f07c0802130620i7219d706g68f06cfeb2f22047@mail.gmail.com> Dear moby developers, Some jMoby developers are this week in a Biohackathlon meeting. We are rearranging jMoby modules (not that much the code itself but the way how the jMoby is built, etc.). This may cause a day or two disruptions. Sorry for any inconvenience. We will inform the list when we are done. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From sylvie.huchet at enst-bretagne.fr Wed Feb 13 09:36:16 2008 From: sylvie.huchet at enst-bretagne.fr (Sylvie Huchet) Date: Wed, 13 Feb 2008 15:36:16 +0100 Subject: [MOBY-dev] createInstanceFromDOM In-Reply-To: <53820.122.26.202.49.1202895189.squirrel@122.26.202.49> References: <47B1AF67.4040604@enst-bretagne.fr> <41259.122.26.202.49.1202864603.squirrel@122.26.202.49> <47B2A4BA.3020202@enst-bretagne.fr> <53820.122.26.202.49.1202895189.squirrel@122.26.202.49> Message-ID: <47B30060.8080607@enst-bretagne.fr> Thanks Paul, Now it works. Sylvie. gordonp at ucalgary.ca a ?crit : > Hi Sylvie, > > I've fixed it to throw an explanatory MobyException. > > Regards, > > Paul > > >>Hi Paul, >> >>Below is the XML file containing the parameters I want to send to a >>Biomoby service. >>With this XML file, I created a DOM object that I use to create a >>MobyContentInstance (this mobycontentInstance should then be used to fill >>the >>data field of a mobyRequest). >>As the simple parameter contains data of a wrong type, I thought I could >>catch a >>MOBYException during the MobycontentInstance constructor call. But the >>inner >>MobyDatacomposite constructor throws a NullPointerException. >> >>Thanks for hour help, >>Sylvie. >> >> >> >> >> >> >> >> >moby:id="" >>moby:namespace=""> >> >moby:articleName="content">8 >> 6 >>Alpha1 AAGAAG >>Alpha2 AAGAAG >>Beta1 AAGGGG >>Beta2 AAGGGG >>Gamma1 AGGAAG >>Gamma2 AGGAAG >>Delta GGAGGA >>Epsilon GGAAAG >> >> >> >> >> no >> >> >> 100 >> >> >> 1000 >> >> >> no >> >> >> 1.0 >> >> >> 1 >> >> >> >> >> >>gordonp at ucalgary.ca a ?crit : >> >>>Hi Sylvie, >>> >>> If you send me the example XML, that will help me determine the issue. >>>It should be able to parse the data, even if the datatypes are not in >>>the >>>ontology. >>> >>>Regards, >>> >>>Paul >>> >>>If you could send the example file to me, it would >>> >>> >>> >>>>Hi, >>>> >>>>I would like to create a biomoby instance from a file that contains >>>>data. >>>> >>>>The data file is an XML file that comply (or should comply) with >>>>biomoby >>>>format. >>>>I thought that if the file contained a data type that is not a biomoby >>>>data type >>>>(doesn't belong to the object ontology), the createInstanceFromDOM >>>>method >>>>would >>>>throw an exception, but that is not the case. A NullPointerException is >>>>thrown >>>>by an inner method (MobyDatacomposite constructor). >>>> >>>>Should I use another method to check that the data type present in the >>>>data file >>>>is correct or is it a problem with createInstanceFromDOM that should >>>>throw >>>>an >>>>exception ? >>>> >>>>Thanks, and >>>>Best regards, >>>>Sylvie. >>>> >>>> >>>> >>>>_______________________________________________ >>>>MOBY-dev mailing list >>>>MOBY-dev at lists.open-bio.org >>>>http://lists.open-bio.org/mailman/listinfo/moby-dev >>>> >>>> >>>>!DSPAM:60005,47b1bec010950204642575! >>>> >>> >>> >>> >>>_______________________________________________ >>>MOBY-dev mailing list >>>MOBY-dev at lists.open-bio.org >>>http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >>> >> >> >>!DSPAM:60005,47b2a29c109502586129532! >>_______________________________________________ >>MOBY-dev mailing list >>MOBY-dev at lists.open-bio.org >>http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> >>!DSPAM:60005,47b2a29c109502586129532! >> > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > -------------- next part -------------- A non-text attachment was scrubbed... Name: sylvie.huchet.vcf Type: text/x-vcard Size: 215 bytes Desc: not available URL: From dmitry.repchevski at bsc.es Wed Feb 13 11:56:25 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 13 Feb 2008 17:56:25 +0100 Subject: [MOBY-dev] Decisions from the BioHackathon In-Reply-To: References: Message-ID: <47B32139.1070605@bsc.es> Hello, As a java developer I'm completely happy with document-literal services. Should I understand that from this moment all *new* services should be preferably document-literal ones? > Some considerations that > arise from this are: (a) you must now remove the XML header from your > data if you're using document-literal, and therefore (b) clients and > services need to specify the appropriate character encoding (e.g. UTF-8) > in the SOAP XML header. > Could someone explain this please? Now Moby passes the Moby part (xml) as a String SOAP parameter. What changes if I pass this string using "document-literal" encoding? The service still needs to parse the "moby" XML. Cheers, Dmitry From edward.kawas at gmail.com Wed Feb 13 18:11:13 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 13 Feb 2008 15:11:13 -0800 Subject: [MOBY-dev] people hosting perl registries Message-ID: <47b37924.1e078e0a.4939.fffffb01@mx.google.com> This morning I discovered a bug in the caching code for Namespace RDF and promptly fixed it. If you are hosting a pure Perl based registry and you are aware of clients that use RDF with your registry, I would advise you to think about updating the core codebase. The problem is that the RDF served by the registry for namespaces never updates regardless of whether or not namespaces have been added/removed from the registry. If you need any other information, please let me know! Eddie From johan at ac.uma.es Fri Feb 15 07:14:26 2008 From: johan at ac.uma.es (Johan Karlsson) Date: Fri, 15 Feb 2008 13:14:26 +0100 Subject: [MOBY-dev] Decisions from the BioHackathon In-Reply-To: References: Message-ID: <47B58222.1000404@ac.uma.es> Mark Wilkinson wrote: > 1) The RFC from INB regarding mirroring of services was accepted with > a few changes. We'll get a copy of the revised proposal from Oswaldo > in the next few days. Apparently they have already coded support for > these changes at INB so it will quickly get into the codebase. Dear all, We are working on an updated version of the proposal which we plan to have ready in a week. Kind regards, Johan -- Johan Karlsson Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.10 29071 M?laga (Spain) +34 95 213 7236 From johan at ac.uma.es Fri Feb 15 07:14:26 2008 From: johan at ac.uma.es (Johan Karlsson) Date: Fri, 15 Feb 2008 13:14:26 +0100 Subject: [MOBY-dev] Decisions from the BioHackathon In-Reply-To: References: Message-ID: <47B58222.1000404@ac.uma.es> Mark Wilkinson wrote: > 1) The RFC from INB regarding mirroring of services was accepted with > a few changes. We'll get a copy of the revised proposal from Oswaldo > in the next few days. Apparently they have already coded support for > these changes at INB so it will quickly get into the codebase. Dear all, We are working on an updated version of the proposal which we plan to have ready in a week. Kind regards, Johan -- Johan Karlsson Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.10 29071 M?laga (Spain) +34 95 213 7236 From martin.senger at gmail.com Sun Feb 17 19:20:39 2008 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 18 Feb 2008 08:20:39 +0800 Subject: [MOBY-dev] Decisions from the BioHackathon In-Reply-To: <47B32139.1070605@bsc.es> References: <47B32139.1070605@bsc.es> Message-ID: <4d93f07c0802171620m145495f9vd6b1d98811415193@mail.gmail.com> > Could someone explain this please? > What do you want to explain? I guess that if there is anything to explain more than Mark did we may be wrong, after all, and actually it could be you who can explain us where we got it wrong :-) > Now Moby passes the Moby part (xml) as a String SOAP parameter. What > changes if I pass this string using "document-literal" encoding? My (a bit vague) understanding of the document/literal style is that the message payload becomes an integral part of the whole SOAP message. Therefore, the payload itself cannot start with " Hi, Eclipse / ant is complaining about the it says 'Reference dependency.classpath not found' ... this could be the problem why the task 'generate-datatypes' fails. I remember Martin talking something about this dependency.classpaths and runtime.classpaths or so... do I need to define it somewhere ?! best andreas From groscurt at mpiz-koeln.mpg.de Mon Feb 18 03:57:22 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 18 Feb 2008 09:57:22 +0100 Subject: [MOBY-dev] current problems with JMoby In-Reply-To: <4d93f07c0802171620m145495f9vd6b1d98811415193@mail.gmail.com> References: <47B32139.1070605@bsc.es> <4d93f07c0802171620m145495f9vd6b1d98811415193@mail.gmail.com> Message-ID: <47B94872.9000004@mpiz-koeln.mpg.de> Hi, I currently have a look in our new jmoby building process to find out if everything works, which is not the case ;-) The following things make me think or needs to be fixed: 1. In some ant tasks the jmoby-others.jar is still mentioned... did we agree to delete that (and as far as i see, it is not created at all in the 'jars' task) 2. The overview of the different ant tasks in Eclipse is weird (it shows the tasks and the build file which they come from) - 'bindist-mobysync' comes from 'seahawkBuild', 'install' from 'null' and 'jar-rdfagent' from 'qt'.... so this is not quite right at all.... anyone an idea why this is coming from what ? 3. Generating the datatypes failes (neither in dashboard nor via the 'generate-datatype' task). It complaines generate-datatypes: [Data Types] java.lang.NoClassDefFoundError: org/tulsoft/tools/BaseCmdLine [Data Types] Exception in thread "main" the class should be in alltools.jar, shouldnt it ? in my maven repository there is the alltools-2.1.1.jar. But neither in dashboard nor via the console the task generate-datatypes work. Any hints, comments, suggestions :-) Best andreas From groscurt at mpiz-koeln.mpg.de Mon Feb 18 04:29:01 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 18 Feb 2008 10:29:01 +0100 Subject: [MOBY-dev] Happy error world Message-ID: <200802181029.01615.groscurt@mpiz-koeln.mpg.de> Hiho, debugging the new building system the something part (maybe all these errors occur becaus i miss something....) I checked out moby fresh from cvs and after 'boostrap' I started "install". BUILD FAILED /home/pcb/groscurt/workspace/Moby/xmls/maven.xml:91: Unable to resolve artifact: Missing: ---------- 1) javax.jws:jsr181-api:jar:1.0-MR1 Try downloading the file manually from the project website. Then, install it using the command: mvn install:install-file -DgroupId=javax.jws -DartifactId=jsr181-api -Dversion=1.0-MR1 -Dpackaging=jar -Dfile=/path/to/file Alternatively, if you host your own repository you can deploy the file there: mvn deploy:deploy-file -DgroupId=javax.jws -DartifactId=jsr181-api -Dversion=1.0-MR1 -Dpackaging=jar -Dfile=/path/to/file -Durl=[url] -DrepositoryId=[id] Path to dependency: 1) org.biomoby:jmoby:jar:1.0.0 2) javax.jws:jsr181-api:jar:1.0-MR1 2) com.sun.xml.ws:jaxws-tools:jar:2.1.3 Try downloading the file manually from the project website. Then, install it using the command: mvn install:install-file -DgroupId=com.sun.xml.ws -DartifactId=jaxws-tools -Dversion=2.1.3 -Dpackaging=jar -Dfile=/path/to/file Alternatively, if you host your own repository you can deploy the file there: mvn deploy:deploy-file -DgroupId=com.sun.xml.ws -DartifactId=jaxws-tools -Dversion=2.1.3 -Dpackaging=jar -Dfile=/path/to/file -Durl=[url] -DrepositoryId=[id] Path to dependency: 1) org.biomoby:jmoby:jar:1.0.0 2) com.sun.xml.ws:jaxws-tools:jar:2.1.3 ---------- 2 required artifacts are missing. for artifact: org.biomoby:jmoby:jar:1.0.0 from the specified remote repositories: central (http://repo1.maven.org/maven2), java.net-m2 (http://download.java.net/maven/2), java.net (https://maven-repository.dev.java.net/repository/), hpl.hp.repository (http://jena.hpl.hp.com/repo/), bio.maven.repository (http://biomoby.org/m2repo/) Would be great to help me out here :) Best andreas PS: more probably to come ;-) -- Andreas Groscurth Bioinformatics Developer Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-449 From martin.senger at gmail.com Mon Feb 18 04:56:22 2008 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 18 Feb 2008 17:56:22 +0800 Subject: [MOBY-dev] dependency.classpath not found In-Reply-To: <47B94B85.6080800@mpiz-koeln.mpg.de> References: <47B94B85.6080800@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0802180156u4996a316waaacf1989cf9e7fd@mail.gmail.com> > it says 'Reference dependency.classpath not found' ... this could be the > problem why the task 'generate-datatypes' fails. > > I remember Martin talking something about this dependency.classpaths and > runtime.classpaths or so... do I need to define it somewhere ?! > No, you don't. Let me fix it. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From dmitry.repchevski at bsc.es Mon Feb 18 04:57:45 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Mon, 18 Feb 2008 10:57:45 +0100 Subject: [MOBY-dev] Decisions from the BioHackathon In-Reply-To: <4d93f07c0802171620m145495f9vd6b1d98811415193@mail.gmail.com> References: <4d93f07c0802171620m145495f9vd6b1d98811415193@mail.gmail.com> Message-ID: <47B95699.8080707@bsc.es> Hello Martin, > My (a bit vague) understanding of the document/literal style is that the > message payload becomes an integral part of the whole SOAP message. > Therefore, the payload itself cannot start with If I understand you correct, the proposal is to use the MobyMessage itself as a payload and not the String as it is now. COOL!!! This could makes happy. So actually the Java method would looks like: MobyMessage runMyService(MobeMessage msg); So, actually we are moving to XML Schema message representation (which is EXACTLY that my API does). In this case WSDL would have XML Schema for the message (which would be the same for ANY "doc-literal" service when MobyObject would be represented as XML ANY type, but this is the problem of representing an ontology object in XML schema and, IMHO, we can do nothing with it.). Here is the possible WSDL with MobyMessage XML Schema: ********************************************************************************************* ********************************************************************************************* This WSDL is AUTOMATICALLY generated for the Service: ********************************************************************************************* package es.bsc.inb.ejb.moby; import javax.jws.WebService; import javax.ejb.Stateless; import org.biomoby.shared.jaxb.messages.MobyMessage; @Stateless() @WebService() public class MobyDocWebService { public MobyMessage runMyService(MobyMessage msg) { return msg; } } ********************************************************************************************* Cheers, Dmitry From martin.senger at gmail.com Mon Feb 18 04:59:17 2008 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 18 Feb 2008 17:59:17 +0800 Subject: [MOBY-dev] current problems with JMoby In-Reply-To: <47B94872.9000004@mpiz-koeln.mpg.de> References: <47B32139.1070605@bsc.es> <4d93f07c0802171620m145495f9vd6b1d98811415193@mail.gmail.com> <47B94872.9000004@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0802180159p26e2fb82p44422993a56fa1bd@mail.gmail.com> > 1. In some ant tasks the jmoby-others.jar is still mentioned... did we > agree to delete that (and as far as i see, it is not created at all in > the 'jars' task) I will fix this. > 2. The overview of the different ant tasks in Eclipse is weird (it shows > the tasks and the build file which they come from) - 'bindist-mobysync' > comes from 'seahawkBuild', 'install' from 'null' and 'jar-rdfagent' from > 'qt'.... so this is not quite right at all.... anyone an idea why this > is coming from what ? I suggest you to try to fix it. You are our Mr. Eclipese :-) > 3. Generating the datatypes failes (neither in dashboard nor via the > 'generate-datatype' task). It complaines > My fix - I will do it. Thanks for going through the testing. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Mon Feb 18 05:00:59 2008 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 18 Feb 2008 18:00:59 +0800 Subject: [MOBY-dev] Happy error world In-Reply-To: <200802181029.01615.groscurt@mpiz-koeln.mpg.de> References: <200802181029.01615.groscurt@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0802180200s54222c2eh3351e7cb0c5fcd4@mail.gmail.com> > BUILD FAILED > /home/pcb/groscurt/workspace/Moby/xmls/maven.xml:91: Unable to resolve > artifact: Missing: > ---------- > 1) javax.jws:jsr181-api:jar:1.0-MR1 I thought that we had fixed this. I will look at it. What version of java are you using? Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Mon Feb 18 05:09:31 2008 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 18 Feb 2008 18:09:31 +0800 Subject: [MOBY-dev] Decisions from the BioHackathon In-Reply-To: <47B95699.8080707@bsc.es> References: <4d93f07c0802171620m145495f9vd6b1d98811415193@mail.gmail.com> <47B95699.8080707@bsc.es> Message-ID: <4d93f07c0802180209t6932d6feu9e8011ae5b87ad7a@mail.gmail.com> > If I understand you correct, the proposal is to use the MobyMessage > itself as a payload and not the String as it is now. What is the "MobyMessage"? Never heard this term. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From groscurt at mpiz-koeln.mpg.de Mon Feb 18 05:12:04 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 18 Feb 2008 11:12:04 +0100 Subject: [MOBY-dev] Happy error world In-Reply-To: <4d93f07c0802180200s54222c2eh3351e7cb0c5fcd4@mail.gmail.com> References: <200802181029.01615.groscurt@mpiz-koeln.mpg.de> <4d93f07c0802180200s54222c2eh3351e7cb0c5fcd4@mail.gmail.com> Message-ID: <200802181112.05047.groscurt@mpiz-koeln.mpg.de> On Monday 18 February 2008 11:00, Martin Senger wrote: > > BUILD FAILED > > /home/pcb/groscurt/workspace/Moby/xmls/maven.xml:91: Unable to resolve > > artifact: Missing: > > ---------- > > 1) javax.jws:jsr181-api:jar:1.0-MR1 > > I thought that we had fixed this. I will look at it. What version of java > are you using? > > Martin Version i use: java version "1.5.0_06" Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_06-b05) Java HotSpot(TM) 64-Bit Server VM (build 1.5.0_06-b05, mixed mode) thanks martin -- Andreas Groscurth Bioinformatics Developer Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-449 From Pieter.Neerincx at wur.nl Mon Feb 18 05:40:46 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Mon, 18 Feb 2008 11:40:46 +0100 Subject: [MOBY-dev] Decisions from the BioHackathon In-Reply-To: References: Message-ID: <3BD9524C-096C-43E0-8C67-3C14E496129B@wur.nl> Hi All, This is very good news*4! Looks like it's been a fruitful event :). Cheers, Pi On 13 Feb 2008, at 03:54, Mark Wilkinson wrote: > Hi all, > > Since we have a quorum of the RFC committee here at the Open > BioHackathon, we've managed to make quite a few decisions, and > we're now in the process of coding them. > > Here are the decisions in a nutshell: > > 1) The RFC from INB regarding mirroring of services was accepted > with a few changes. We'll get a copy of the revised proposal from > Oswaldo in the next few days. Apparently they have already coded > support for these changes at INB so it will quickly get into the > codebase. > > 2) Moby will *immediately* start supporting document-literal > services. These services will be identified using the "Category" > tag in the service registration/discovery XML. Two new categories > will be "doc-literal" and "doc-literal-async". Until we get better > support for document-literal services in Perl it is likely that > these will not be available to Perl clients, but apparently it's no > problem in Java. Some considerations that arise from this are: > (a) you must now remove the XML header from your data if you're > using document-literal, and therefore (b) clients and services need > to specify the appropriate character encoding (e.g. UTF-8) in the > SOAP XML header. > > 3) Sending data by reference: we have decided to allow the > sending of data by reference rather than as the content of an > object. We'll write-up the formal specification of how to do this > soon, but briefly the idea is that we will use the xlink XML > attribute in a Moby Object XML <.... xlink=''/>. When that tag is > present, it is assumed that the content of that node is available > at the URI in that reference. During service registration a > provider will indicate the various transport protocols they provide > for creating references (e.g. http, ftp) and this will be > discoverable during a registry query. If you don't indicate a > protocol, then you are saying that you do not support pass-by- > reference, and therefore all existing services are supported. When > accessing a service, you indicate to the service provider that you > want data to be passed by reference by adding an attribute in the > mobyData block . The service > provider then has the option of providing you references for any > data they wish. The xlink attribute can appear at any level in > your Moby object, such that some data may be passed in the object > itself, while other data from the same object may be passed by > reference. > > 4) Validating services: Moby will have several levels of > validation: (1) ping, (2) does the service crash when accesed with > sample data? (3) does the service output the correct object > type? (4) does the service output data that validates against > XPath and/or REGEX. The sample input data will be in the service > provider's RDF, and there will be several new predicates added to > the RDF (I'll provide the OWL file shortly that defines how these > predicates are to be used): unit_test, example_input, valid_xpath, > valid_regex, valid_output_xml. The validation of output XML will > be canonicalized (i.e. xmldiff, not byte-identity) > > > Hackers - please correct me if I have mis-represented anything. > I'm working from Eddie's scribbled notes ;-) > > Hopefully we'll find time to document these changes between our > hacking sessions :-) > > Cheers all! Greetings from Tokyo! > > Mark > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------- From dmitry.repchevski at bsc.es Mon Feb 18 06:15:21 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Mon, 18 Feb 2008 12:15:21 +0100 Subject: [MOBY-dev] Decisions from the BioHackathon In-Reply-To: <4d93f07c0802180209t6932d6feu9e8011ae5b87ad7a@mail.gmail.com> References: <4d93f07c0802180209t6932d6feu9e8011ae5b87ad7a@mail.gmail.com> Message-ID: <47B968C9.9060400@bsc.es> > > What is the "MobyMessage"? Never heard this term. > Martin It's my own java Moby API... Actually it's a little more when JAXB annotated classes for Moby messages... Since it's based on XML Schema (JAXB) it perfectly integrates into latest standard Java API. You can read more at http://inb.bsc.es/java/index.html. I'm continuously improving it... Cheers, Dmitry From dmitry.repchevski at bsc.es Tue Feb 19 06:03:10 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 19 Feb 2008 12:03:10 +0100 Subject: [MOBY-dev] document/literal services Message-ID: <47BAB76E.90904@bsc.es> Hello all, I'm still trying to figure out what is the decision was made about support of document/literal services. Q1. Does it mean that we can use Moby message as a payload? Hope so... Q2. Which parameter style to use (wrapped/unwrapped)? IMHO having only one parameter IN and one OUT, Unwrapped is better. Yours sincerely, Dmitry From groscurt at mpiz-koeln.mpg.de Tue Feb 19 09:53:55 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 19 Feb 2008 15:53:55 +0100 Subject: [MOBY-dev] JMoby.... In-Reply-To: <47BAB76E.90904@bsc.es> References: <47BAB76E.90904@bsc.es> Message-ID: <47BAED83.2010801@mpiz-koeln.mpg.de> Hiho, I dont know whether Martin fixed it or its just working mostly now... With a new checkout eclipse is able to set up a project and getting the libraries and starting dashboard.... this didnt work last time. Also the simple client is working, but MoSeS not - still got the generate-datatypes: [Data Types] java.lang.NoClassDefFoundError: org/tulsoft/tools/BaseCmdLine [Data Types] Exception in thread "main" Also Eclipse complains about 'Reference dependency.classpath not found - but besides that the building process works now (windows & eclipse) best and thanks andreas From edward.kawas at gmail.com Tue Feb 19 10:03:02 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 19 Feb 2008 07:03:02 -0800 Subject: [MOBY-dev] JMoby.... In-Reply-To: <47BAED83.2010801@mpiz-koeln.mpg.de> References: <47BAB76E.90904@bsc.es> <47BAED83.2010801@mpiz-koeln.mpg.de> Message-ID: <47baefa9.1cef600a.2d62.2f6a@mx.google.com> Hi Andreas, I can confirm that at the very least, ant bootstrap, ant compile, ant dashboard, and ant generate-datatypes work on windows from the command line. When I try to generate service skeletons in dashboard, I get the following: generate-services: [Service(s)] Using filter for authorities: '^arexdb.org$' [Service(s)] Generating services into 'c:\moby-live\Java\generated\skeletons'... [Service(s)] Reading service names... [Service(s)] getGOCollection (arexdb.org) [Service(s)] getAREXGFPImageCollection (arexdb.org) [Service(s)] Generated 2 service skeletons. BUILD FAILED c:\moby-live\Java\xmls\maven.xml:85: java.lang.NullPointerException Also, when I generate datatypes from within dashboard, I also get the null pointer exception mentioned above. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth Sent: February-19-08 6:54 AM To: Core developer announcements Subject: [MOBY-dev] JMoby.... Hiho, I dont know whether Martin fixed it or its just working mostly now... With a new checkout eclipse is able to set up a project and getting the libraries and starting dashboard.... this didnt work last time. Also the simple client is working, but MoSeS not - still got the generate-datatypes: [Data Types] java.lang.NoClassDefFoundError: org/tulsoft/tools/BaseCmdLine [Data Types] Exception in thread "main" Also Eclipse complains about 'Reference dependency.classpath not found - but besides that the building process works now (windows & eclipse) best and thanks andreas _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From dmitry.repchevski at bsc.es Tue Feb 19 10:23:41 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 19 Feb 2008 16:23:41 +0100 Subject: [MOBY-dev] JMoby.... In-Reply-To: <47BAED83.2010801@mpiz-koeln.mpg.de> References: <47BAED83.2010801@mpiz-koeln.mpg.de> Message-ID: <47BAF47D.5000104@bsc.es> Hello Andreas, Thank you for reply, but actually I do not use Eclipse, neither JMoby... Could we once and forever clarify the difference between specification and implementation. I have my own (not JMoby) API that could allow me to use a standard JAX-WS web-services if BioMoby team follows the standard. On the server side it could look like: ***************************** package es.bsc.inb.ejb.moby; import javax.jws.*; import javax.ejb.Stateless; import javax.jws.soap.SOAPBinding; import org.biomoby.shared.jaxb.messages.MobyMessage; @Stateless() @WebService() @SOAPBinding(style=SOAPBinding.Style.DOCUMENT, use=SOAPBinding.Use.LITERAL, parameterStyle=SOAPBinding.ParameterStyle.BARE) public class MobyDocWebService { @WebResult(name="result") public MobyMessage runMyService(@WebParam(name="request", mode = WebParam.Mode.IN) MobyMessage msg) { return msg; } } ***************************** This is the STANDARD JAX-WS endpoint. You can deploy it on ANY JEE5 Application server. The application server will generate and deploy the service automatically. Here is generated (by JBoss) wsdl: ***************************** ***************************** Having this you do not need even my API on the client side (you could generate it using the tool for your language) Well you still need an ontology which couldn't (?) be injected in wsdl... My API generates JAXB annotated ontology classes that JAX-WS automatically marshal/unmarshall. This is IF we would use Document/Literal encoding and not just a hack when we pass the XML String and have to parse it manually. Using Moby Message (the Moby XML that we pass as a string now) as a payload would allow us in future to explore the full power of SOAP (streaming, compression, WS-Addresing for TRULY asynchronous services through callbacks and so on). This is the question I'm asking: Are we going to use the same ugly hack (passing the XML string) for the document/literal or, finally, move on to the standard, interoperable Web Services? Best regards, Dmitry P.S. I'm afraid that JMoby has a hard time to support this... / / From groscurt at mpiz-koeln.mpg.de Tue Feb 19 10:37:01 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 19 Feb 2008 16:37:01 +0100 Subject: [MOBY-dev] JMoby.... In-Reply-To: <47BAF47D.5000104@bsc.es> References: <47BAED83.2010801@mpiz-koeln.mpg.de> <47BAF47D.5000104@bsc.es> Message-ID: <47BAF79D.6020508@mpiz-koeln.mpg.de> Dmitry Repchevsky wrote: > Hello Andreas, > > Thank you for reply, but actually I do not use Eclipse, neither JMoby... > Could we once and forever clarify the difference between specification > and implementation. aehh... what ? i didnt actually reply to your message... my email was about the new building process Martin setup up for JavaMoby... nothing to do with your implementation or what you wrote. I guess this is also important - but my mail was in no case any answer for your mail ;-) andreas From dmitry.repchevski at bsc.es Tue Feb 19 10:39:27 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 19 Feb 2008 16:39:27 +0100 Subject: [MOBY-dev] JMoby.... In-Reply-To: <47BAF79D.6020508@mpiz-koeln.mpg.de> References: <47BAF79D.6020508@mpiz-koeln.mpg.de> Message-ID: <47BAF82F.3070702@bsc.es> Oops... Sorry, it was in my thread, so I supposed it was a typical "look in the jmoby" style... Again, sorry for the tone... Dmitry From martin.senger at gmail.com Tue Feb 19 19:55:24 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 20 Feb 2008 08:55:24 +0800 Subject: [MOBY-dev] JMoby.... In-Reply-To: <47BAF47D.5000104@bsc.es> References: <47BAED83.2010801@mpiz-koeln.mpg.de> <47BAF47D.5000104@bsc.es> Message-ID: <4d93f07c0802191655x5825fd7sadb76247a5b01b32@mail.gmail.com> My dear Dmitry, Could we once and forever clarify the difference between specification > and implementation. Could we please once and forever clarify what is polite and what is not? Your emails are sometimes a bit aggressive (as are mine, probably) up to the point that they decrease motivation to respond to them. Just my 2c's. Regarding your comment, I am almost sure that the difference between specification and implementation is clear enough. It may not be the case about two years ago but today I do not see any discrepancies. What do you wish to clarify? > I have my own (not JMoby) API that could allow me to use a standard > JAX-WS web-services if BioMoby team follows the standard. > Between BioMoby developers, we usually save the word "API" to indicate the API defining an access to the BioMoby registry and to the BioMoby services. In other words, we usually refer to this API as to a language-independent interface, while "Java API" (or "jMoby API") is used only for Java developers - if they are interested to use it. It is, of course, up to them how they realize their access to the BioMoby entities. Regarding standards, we do our best in the changing world of standards. As you have been informed, during the last meeting we made steps to accept also the document/literal style and we are working on its implementation. But any good clients will need to support, now and in the future, both protocols, RPC/encoded and document/literal styles - we cannot afford to tell the service providers "please throw out your running services and start again". Therefore, if you are using only standard web-services style, your code is not smart enough to be worth to look at (see? - this is my bit of aggressivity :-)). Regarding other standard - the XML Schema (of the messages between client and services, not between clients and registry) - and the WSDL derived from the schema, I believe that you are not fully aware of the fact that there is no way to express the current BioMoby payload in the XML Schema (unless you change the schema with every request). Take it or leave it. Having said that does not mean that I am personally happy with it but c'est la vie. For BioMoby the future probably is in the RDF orientation and not to try go back to the compliancy with the XML Schema (Mark's words in my poor interpretation). But it would help people (like you) to understand why BioMoby payload cannot be fully expressed in an XML Schema if we document it. I believe that during the last meeting we agreed that the reasons why XML cannot be created will be documented soon (on the new BioMoby pages that are being created as we speak). Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Wed Feb 20 03:06:51 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 20 Feb 2008 16:06:51 +0800 Subject: [MOBY-dev] dependency.classpath not found In-Reply-To: <4d93f07c0802180156u4996a316waaacf1989cf9e7fd@mail.gmail.com> References: <47B94B85.6080800@mpiz-koeln.mpg.de> <4d93f07c0802180156u4996a316waaacf1989cf9e7fd@mail.gmail.com> Message-ID: <4d93f07c0802200006t6555bf54w3efc4049e1526bb9@mail.gmail.com> > it says 'Reference dependency.classpath not found' ... this could be the > > problem why the task 'generate-datatypes' fails. > > > Fixed (I believe :-)). Please make 'cvs update -dP'. Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Wed Feb 20 05:08:55 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 20 Feb 2008 18:08:55 +0800 Subject: [MOBY-dev] Happy error world In-Reply-To: <200802181029.01615.groscurt@mpiz-koeln.mpg.de> References: <200802181029.01615.groscurt@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0802200208m3e17fa2fu1d308d86d7b303a2@mail.gmail.com> Andreas, BUILD FAILED > /home/pcb/groscurt/workspace/Moby/xmls/maven.xml:91: Unable to resolve > artifact: Missing: > ---------- > 1) javax.jws:jsr181-api:jar:1.0-MR1 > I am afraid that I cannot reproduce your error. It simply works on my machine. Please try again: 1) Remove the two mentioned/problematic directories from your local maven repository. On the unix machine, they are: ~/.m2/repository/com/sun/xml/ws/jaxws-tools/2.1.3, and ~/.m2/repository/javax/jws/jsr181-api (under windows they are in the similar structure in your 'Documents and settings/...' directory). 2) Run: ant clean compile. I am correctly getting this (indicating that the just removed dependencies are downloaded again): initmaven: [artifact:dependencies] Downloading: javax.jws/poms/jsr181-api-1.0-MR1.pomfrom java.net [artifact:dependencies] Transferring 0K from java.net [artifact:dependencies] Downloading: com.sun.xml.ws/poms/jaxws-tools-2.1.3.pom from java.net [artifact:dependencies] Transferring 2K from java.net [artifact:dependencies] Downloading: javax.jws/jars/jsr181-api-1.0-MR1.jarfrom java.net [artifact:dependencies] Transferring 8K from java.net [artifact:dependencies] Downloading: com.sun.xml.ws/jars/jaxws-tools-2.1.3.jar from java.net [artifact:dependencies] Transferring 497K from java.net Do you still have the error? If not, try it in Eclipse... PS: more probably to come ;-) Have they came? Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From dmitry.repchevski at bsc.es Wed Feb 20 05:56:40 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 20 Feb 2008 11:56:40 +0100 Subject: [MOBY-dev] JMoby.... In-Reply-To: <4d93f07c0802191655x5825fd7sadb76247a5b01b32@mail.gmail.com> References: <4d93f07c0802191655x5825fd7sadb76247a5b01b32@mail.gmail.com> Message-ID: <47BC0768.50905@bsc.es> Dear Martin, Thank you for the reply. > Your emails are sometimes a bit aggressive (as are mine, probably) up to the > point that they decrease motivation to respond to them. I do not intend to offend anyone, but sometimes a provocative style is the only way I can get the response, unfortunately. (I've been asked several times the same question, but got the answer only to the last post, so subconscious I somehow decided that this is the way to get answered... sorry). As an example I would like to repeat the question I asked several times and still have no answer: Q: BioMoby doesn't use WSDL file to access the Web Services, so is there any specification about parameter names (example part name="request")? Ignoring the WSDL without explicit accordance in it makes virtually all BioMoby requests wrong and rejected by all modern Java webservices stacks (even it works in AXIS). It is as easy as to put "request parameter name must be 'request' and response must be named 'response'" into the "specification". ... sorry for the aggressiveness again ;-). > ...we usually refer to this API as to a language-independent > interface, while "Java API" (or "jMoby API") is used only for Java > developers - if they are interested to use it. Well there are two definition of API - specification and implementation, usually (in my experience) the API means concrete implementation of the specification, i accept that this could be different... Thank you to clarify this. > As you have been informed, during the last meeting we made steps to accept also > the document/literal style and we are working on its implementation. But any > good clients will need to support, now and in the future, both protocols, > RPC/encoded and document/literal styles - we cannot afford to tell the > service providers "please throw out your running services and start again". > Therefore, if you are using only standard web-services style, your code is > not smart enough to be worth to look at (see? - this is my bit of > aggressivity :-)). This is the case. My own implementation API (or package or how should I call it in BioMoby terms) is compatible both with rpc/encoded AND document/literal styles. :-) Strange I see nothing aggressive here... Maybe because I'm Russian :-) > Regarding other standard - the XML Schema (of the messages between client > and services, not between clients and registry) - and the WSDL derived from > the schema, I believe that you are not fully aware of the fact that there is > no way to express the current BioMoby payload in the XML Schema (unless you > change the schema with every request). Take it or leave it. Completely wrong! (oops, sorry :-)) I have WORKING implementation of it if you look in this thread. As I said it is impossible to put the ONTOLOGY in WSDL 1.1 (while it IS possible in WSDL 2.0), but to make XML Schema for Moby Messages is possible and what I am trying to explain for the last three months. Again my solution by now is to keep two parts separately - Moby Messages - a set of JAXB annotated classes that comply to "Moby Message" XML Schema and could be put into the WSDL Schema and Datatypes - a set of JAXB annotated classes that comply the "Ontology" XML Schema. The last one couldn't be put into WSDL 1.1, but are processed by JAX-WS automatically. > For BioMoby the future probably is in the RDF orientation and not to > try go back to the compliancy with the XML Schema (Mark's words in my poor > interpretation). But it would help people (like you) to understand why > BioMoby payload cannot be fully expressed in an XML Schema if we document > it. I believe that during the last meeting we agreed that the reasons why > XML cannot be created will be documented soon (on the new BioMoby pages that > are being created as we speak). I think there is a misunderstanding. The ontology itself can not be described by XML Schema (That's why OWL/RDF exist), but the serialization format CAN. Of course the problem is that in the WSDL schema there will be In place of concrete datatype, so it's up to the web-service protocol correctly marshall/unmarshall it. JAX-WS can do this. In my implementation if JAX-WS find some unknown type it substitutes it by special object "AnyMobyObject" keeping the total structure intact (so it can have some AminoAcidSequence object as an attribute for example). It is possible to make an implementation that in this case consult RDF or Biomoby Cental to dynamically generate the class, bu I see no reason in it, because there is no need in object when service/client has no idea about, but with "AnyMobyObject" they still can get all the properties. Well to be fair one reason is to cast this object to the known one... Yours sincerely, Dmitry From groscurt at mpiz-koeln.mpg.de Thu Feb 21 10:16:37 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 21 Feb 2008 16:16:37 +0100 Subject: [MOBY-dev] ready to release jMoby 1.0.0? In-Reply-To: <4d93f07c0802201630i6d0e958fxc16be9c568345ee6@mail.gmail.com> References: <4d93f07c0802200238p73f4e45bq7dd40a0085803c4c@mail.gmail.com> <47BC0471.7030507@mpiz-koeln.mpg.de> <47bc83c3.1498600a.5725.ffffc7b6@mx.google.com> <4d93f07c0802201630i6d0e958fxc16be9c568345ee6@mail.gmail.com> Message-ID: <47BD95D5.7030105@mpiz-koeln.mpg.de> Hi, you also have my OK. Somehow everything works although Eclipse / dashboard make some weird things. If I use the generate-datatypes task from eclipse or from console everything is fine. Calling it from Dashboard will generate all datatypes but when its finished it throws the NullPointerException C:\workspace\moby\xmls\maven.xml:85: java.lang.NullPointerException but even with that Nullpointer I do have all datatypes in the Eclipse project. calling the generate-services does fine via the ant tasks in eclipse or the console... calling it from dashboard will generate the skeleton but then fails because it always starts with generate-datatypes and breaks because of the NullPointer... The same tasks in Eclipse without Dashboard work fine... so have you any clue what the Nullpointer is about ? its in the maven.xml the line but in fact... when one knows what to do... it works ;-) so my ok btw - I commited the changed mobysync build file. best andreas Martin Senger wrote: > > I updated the agents build file and tested it some what. I > committed it. > > You have my 'A OK!' > > > Thanks! > > > For the doc, you mentioned that you were updating them > and that we should too. Have you committed your changes to the doc > yet? > > > Yes, I have. > > Cheers, > Martin > > -- > Martin Senger > email: martin.senger at gmail.com > m.senger at cgiar.org > skype: martinsenger From groscurt at mpiz-koeln.mpg.de Thu Feb 21 10:46:02 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 21 Feb 2008 16:46:02 +0100 Subject: [MOBY-dev] BioMoby goes openoffice ? In-Reply-To: <47BD95D5.7030105@mpiz-koeln.mpg.de> References: <4d93f07c0802200238p73f4e45bq7dd40a0085803c4c@mail.gmail.com> <47BC0471.7030507@mpiz-koeln.mpg.de> <47bc83c3.1498600a.5725.ffffc7b6@mx.google.com> <4d93f07c0802201630i6d0e958fxc16be9c568345ee6@mail.gmail.com> <47BD95D5.7030105@mpiz-koeln.mpg.de> Message-ID: <47BD9CBA.7000000@mpiz-koeln.mpg.de> Hi, I'm wondering... why does maven downloads several libs from openoffice ? I do have the feeling that since the maven dependencies we have lots more libs than before ? can someone explain that to me ? cheers andreas From edward.kawas at gmail.com Thu Feb 21 14:44:28 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 21 Feb 2008 11:44:28 -0800 Subject: [MOBY-dev] BioMoby goes openoffice ? In-Reply-To: <47BD9CBA.7000000@mpiz-koeln.mpg.de> References: <4d93f07c0802200238p73f4e45bq7dd40a0085803c4c@mail.gmail.com> <47BC0471.7030507@mpiz-koeln.mpg.de> <47bc83c3.1498600a.5725.ffffc7b6@mx.google.com> <4d93f07c0802201630i6d0e958fxc16be9c568345ee6@mail.gmail.com> <47BD95D5.7030105@mpiz-koeln.mpg.de> <47BD9CBA.7000000@mpiz-koeln.mpg.de> Message-ID: <47bdd4a6.1cef600a.361e.ffff939a@mx.google.com> Hi Andreas, I believe that seahawk uses the open office libs. Paul can confirm. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth Sent: February-21-08 7:46 AM To: Core developer announcements Subject: [MOBY-dev] BioMoby goes openoffice ? Hi, I'm wondering... why does maven downloads several libs from openoffice ? I do have the feeling that since the maven dependencies we have lots more libs than before ? can someone explain that to me ? cheers andreas _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Mon Feb 25 09:56:09 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 25 Feb 2008 07:56:09 -0700 Subject: [MOBY-dev] BioMoby goes openoffice ? In-Reply-To: <47bdd4a6.1cef600a.361e.ffff939a@mx.google.com> References: <4d93f07c0802200238p73f4e45bq7dd40a0085803c4c@mail.gmail.com> <47BC0471.7030507@mpiz-koeln.mpg.de> <47bc83c3.1498600a.5725.ffffc7b6@mx.google.com> <4d93f07c0802201630i6d0e958fxc16be9c568345ee6@mail.gmail.com> <47BD95D5.7030105@mpiz-koeln.mpg.de> <47BD9CBA.7000000@mpiz-koeln.mpg.de> <47bdd4a6.1cef600a.361e.ffff939a@mx.google.com> Message-ID: <47C2D709.2050602@ucalgary.ca> Yup, Seahawk can import Word, Excel, etc. files via an OpenOffice connectivity bridge (the actual conversion is done on our server, but several libs are needed for the connection). Edward Kawas wrote: > Hi Andreas, > > I believe that seahawk uses the open office libs. Paul can confirm. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth > Sent: February-21-08 7:46 AM > To: Core developer announcements > Subject: [MOBY-dev] BioMoby goes openoffice ? > > Hi, > > I'm wondering... why does maven downloads several libs from openoffice ? > I do have the feeling that since the maven dependencies we have lots > more libs than before ? > > can someone explain that to me ? > > cheers > andreas > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,47bdd28b109502142110999! > > > > From martin.senger at gmail.com Mon Feb 25 23:57:19 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 26 Feb 2008 12:57:19 +0800 Subject: [MOBY-dev] getting RDF resources in the compressed format Message-ID: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> Eddie, Paul, Mark et al, Because of the new implementation of the registry cache (written by Eddie) that uses RDF, the RDF resources will be more used (also from the Dashboard). To get them fast is, therefore, a priority. I remember that when the new method (to get URLs of the registry resources) was added to the BioMoby API we had discussed how to deliver these resources in a compressed format, as well. Has anybody remember how it was proposed to work? Because we definitely need to compress it now. Thanks, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From gordonp at ucalgary.ca Tue Feb 26 18:45:39 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 26 Feb 2008 16:45:39 -0700 Subject: [MOBY-dev] getting RDF resources in the compressed format In-Reply-To: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> References: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> Message-ID: <47C4A4A3.1050601@ucalgary.ca> I believe the solution we agreed upon was that if the client sends an "Accept-encoding" HTTP header with x-gzip, we'd have the server send gzip'ed if it finds it. I use this mechanism all the time for sending big HTML files... Martin Senger wrote: > Eddie, Paul, Mark et al, > > Because of the new implementation of the registry cache (written by Eddie) > that uses RDF, the RDF resources will be more used (also from the > Dashboard). To get them fast is, therefore, a priority. > > I remember that when the new method (to get URLs of the registry resources) > was added to the BioMoby API we had discussed how to deliver these resources > in a compressed format, as well. Has anybody remember how it was proposed to > work? Because we definitely need to compress it now. > > Thanks, > Martin > > From martin.senger at gmail.com Tue Feb 26 19:34:31 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 27 Feb 2008 08:34:31 +0800 Subject: [MOBY-dev] getting RDF resources in the compressed format In-Reply-To: <47C4A4A3.1050601@ucalgary.ca> References: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> <47C4A4A3.1050601@ucalgary.ca> Message-ID: <4d93f07c0802261634u5aade00ak988ebfbff38d308a@mail.gmail.com> Many thanks, Paul. I believe the solution we agreed upon was that if the client sends an > "Accept-encoding" HTTP header with x-gzip Yes, that was what I vaguely remembered but was not sure about details. [BTW, is there a way to search the whole biomoby email archive?] How does client know what was sent from the server? Is is in the HTTP Content-type header? If so, what mime-type should be there? Eddie, it would be nice to have this feature implemented on the registry site (so other registry providers can copy it, as well). Would you consider it please? Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Tue Feb 26 19:53:35 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 27 Feb 2008 08:53:35 +0800 Subject: [MOBY-dev] a space in the data type name Message-ID: <4d93f07c0802261653k3f2001a8gfdf1f16f2cd6b15e@mail.gmail.com> Recently, a new data type ' RNAStructAlignmentML' was registered. It starts with a space. I think that the registry should reject it. In the BioMoby registry API, we have rules for article names ("Article names for each contained object type may not contain spaces or other special characters") but not for the data type names. But they should be driven what is allowed for the XML element names. Is it possible to change the name, and perhaps to add a more strict checking when an entity is being registered please? Thanks, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Tue Feb 26 20:17:04 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 27 Feb 2008 09:17:04 +0800 Subject: [MOBY-dev] a space in the data type name In-Reply-To: <4d93f07c0802261653k3f2001a8gfdf1f16f2cd6b15e@mail.gmail.com> References: <4d93f07c0802261653k3f2001a8gfdf1f16f2cd6b15e@mail.gmail.com> Message-ID: <4d93f07c0802261717j71ee1dadkd3a8e658e3ae4f47@mail.gmail.com> ...[cont.] and the same for ' AlignmentML', ' SequenceML' data types I believe. (Actually the SequenceML is there twice, once with a space and once without). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From markw at illuminae.com Wed Feb 27 01:25:54 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 26 Feb 2008 22:25:54 -0800 Subject: [MOBY-dev] a space in the data type name In-Reply-To: <4d93f07c0802261717j71ee1dadkd3a8e658e3ae4f47@mail.gmail.com> References: <4d93f07c0802261653k3f2001a8gfdf1f16f2cd6b15e@mail.gmail.com> <4d93f07c0802261717j71ee1dadkd3a8e658e3ae4f47@mail.gmail.com> Message-ID: Absolutely! I'll fix this in the registry right away. I wonder if I should manually repair the DB entries, or if I should ask the individuals who registered the objects to re-register them? Probably best to at least warn them... M On Tue, 26 Feb 2008 17:17:04 -0800, Martin Senger wrote: > ...[cont.] and the same for ' AlignmentML', ' SequenceML' data types I > believe. (Actually the SequenceML is there twice, once with a space and > once > without). > > Cheers, > Martin > From edward.kawas at gmail.com Wed Feb 27 13:09:12 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 27 Feb 2008 10:09:12 -0800 Subject: [MOBY-dev] getting RDF resources in the compressed format In-Reply-To: <4d93f07c0802261634u5aade00ak988ebfbff38d308a@mail.gmail.com> References: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> <47C4A4A3.1050601@ucalgary.ca> <4d93f07c0802261634u5aade00ak988ebfbff38d308a@mail.gmail.com> Message-ID: <47c5a763.0f98600a.4716.ffffa8be@mx.google.com> Okay, I set up mod_deflate on my local linux installation and tried it out. Some results: Service instance RDF: Original size: 7052579bytes Compressed size: 305092bytes Savings: ~96% Object RDF: Original size: 2864668 bytes Compressed size: 219478 bytes Savings: ~92% I know that it is obvious that we will get big savings by compressing text files ... The question was how to implement this ... Here is what I did: 1. enabled mod_deflate for apache This differs from installation to installation, but for me, running ubuntu, all I had to do was create 2 sym links in /etc/apache2/mods-enabled/ for the files deflate.conf and deflate.load in /etc/apache2/mods-available. 2. edit the conf file Again this differs, but what I did was edit deflate.conf and put the following inside: # mime types to compress AddOutputFilterByType DEFLATE text/html text/plain text/xml # support for older browsers BrowserMatch ^Mozilla/4 gzip-only-text/html BrowserMatch ^Mozilla/4\.0[678] no-gzip BrowserMatch \bMSIE !no-gzip !gzip-only-text/html BrowserMatch \bMSI[E] !no-gzip !gzip-only-text/html 3. I restarted apache More doc available at http://httpd.apache.org/docs/2.0/mod/mod_deflate.html Now when a request comes in with the header 'Accept-Encoding: gzip' apache compresses the RDF. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger Sent: February-26-08 4:35 PM To: Core developer announcements Subject: Re: [MOBY-dev] getting RDF resources in the compressed format Many thanks, Paul. I believe the solution we agreed upon was that if the client sends an > "Accept-encoding" HTTP header with x-gzip Yes, that was what I vaguely remembered but was not sure about details. [BTW, is there a way to search the whole biomoby email archive?] How does client know what was sent from the server? Is is in the HTTP Content-type header? If so, what mime-type should be there? Eddie, it would be nice to have this feature implemented on the registry site (so other registry providers can copy it, as well). Would you consider it please? Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Wed Feb 27 13:28:36 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 27 Feb 2008 11:28:36 -0700 Subject: [MOBY-dev] getting RDF resources in the compressed format In-Reply-To: <47c5a763.0f98600a.4716.ffffa8be@mx.google.com> References: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> <47C4A4A3.1050601@ucalgary.ca> <4d93f07c0802261634u5aade00ak988ebfbff38d308a@mail.gmail.com> <47c5a763.0f98600a.4716.ffffa8be@mx.google.com> Message-ID: <47C5ABD4.7060309@ucalgary.ca> The question is whether URL.openStream() sends such a header. Probably not, in which case CentralXXXImpl will need to use Apache httpclient or something similar instead... Edward Kawas wrote: > Okay, > > I set up mod_deflate on my local linux installation and tried it out. > > Some results: > Service instance RDF: > Original size: 7052579bytes > Compressed size: 305092bytes > Savings: ~96% > Object RDF: > Original size: 2864668 bytes > Compressed size: 219478 bytes > Savings: ~92% > > I know that it is obvious that we will get big savings by compressing text > files ... The question was how to implement this ... > > Here is what I did: > 1. enabled mod_deflate for apache > This differs from installation to installation, but for me, running > ubuntu, all I had to do was create 2 sym links in /etc/apache2/mods-enabled/ > for the files deflate.conf and deflate.load in /etc/apache2/mods-available. > 2. edit the conf file > Again this differs, but what I did was edit deflate.conf and put the > following inside: > > > # mime types to compress > AddOutputFilterByType DEFLATE text/html text/plain text/xml > # support for older browsers > BrowserMatch ^Mozilla/4 gzip-only-text/html > BrowserMatch ^Mozilla/4\.0[678] no-gzip > BrowserMatch \bMSIE !no-gzip !gzip-only-text/html > BrowserMatch \bMSI[E] !no-gzip !gzip-only-text/html > > > > 3. I restarted apache > > More doc available at http://httpd.apache.org/docs/2.0/mod/mod_deflate.html > > Now when a request comes in with the header 'Accept-Encoding: gzip' apache > compresses the RDF. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger > Sent: February-26-08 4:35 PM > To: Core developer announcements > Subject: Re: [MOBY-dev] getting RDF resources in the compressed format > > Many thanks, Paul. > > I believe the solution we agreed upon was that if the client sends an > >> "Accept-encoding" HTTP header with x-gzip >> > > > Yes, that was what I vaguely remembered but was not sure about details. > [BTW, is there a way to search the whole biomoby email archive?] > > How does client know what was sent from the server? Is is in the HTTP > Content-type header? If so, what mime-type should be there? > > Eddie, it would be nice to have this feature implemented on the registry > site (so other registry providers can copy it, as well). Would you consider > it please? > > Cheers, > Martin > > > From edward.kawas at gmail.com Wed Feb 27 14:11:46 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 27 Feb 2008 11:11:46 -0800 Subject: [MOBY-dev] getting RDF resources in the compressed format In-Reply-To: <47C5ABD4.7060309@ucalgary.ca> References: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> <47C4A4A3.1050601@ucalgary.ca> <4d93f07c0802261634u5aade00ak988ebfbff38d308a@mail.gmail.com> <47c5a763.0f98600a.4716.ffffa8be@mx.google.com> <47C5ABD4.7060309@ucalgary.ca> Message-ID: <47c5b60f.1def600a.5a28.1b48@mx.google.com> No, we can still use java libraries (I am doing this with the java RDF parsers): public static InputStream getBufferedInputStream(URL url) throws MobyException { try { HttpURLConnection urlConnection = null; urlConnection = (HttpURLConnection) url.openConnection(); urlConnection.setRequestProperty("User-Agent", "jmoby-extended/1.0"); urlConnection.setRequestProperty("Accept-Encoding", "gzip, deflate"); urlConnection.setDefaultUseCaches(false); urlConnection.setUseCaches(false); BufferedInputStream is = null; if (("gzip").equalsIgnoreCase(urlConnection.getContentEncoding())) { // handle gzip encoded content is = new BufferedInputStream(new GZIPInputStream(urlConnection.getInputStream())); } else { is = new BufferedInputStream(urlConnection.getInputStream()); } return is; } catch (IOException e) { throw new MobyException("Error creating input stream:",e.getCause()); } } Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Paul Gordon Sent: February-27-08 10:29 AM To: Core developer announcements Subject: Re: [MOBY-dev] getting RDF resources in the compressed format The question is whether URL.openStream() sends such a header. Probably not, in which case CentralXXXImpl will need to use Apache httpclient or something similar instead... Edward Kawas wrote: > Okay, > > I set up mod_deflate on my local linux installation and tried it out. > > Some results: > Service instance RDF: > Original size: 7052579bytes > Compressed size: 305092bytes > Savings: ~96% > Object RDF: > Original size: 2864668 bytes > Compressed size: 219478 bytes > Savings: ~92% > > I know that it is obvious that we will get big savings by compressing text > files ... The question was how to implement this ... > > Here is what I did: > 1. enabled mod_deflate for apache > This differs from installation to installation, but for me, running > ubuntu, all I had to do was create 2 sym links in /etc/apache2/mods-enabled/ > for the files deflate.conf and deflate.load in /etc/apache2/mods-available. > 2. edit the conf file > Again this differs, but what I did was edit deflate.conf and put the > following inside: > > > # mime types to compress > AddOutputFilterByType DEFLATE text/html text/plain text/xml > # support for older browsers > BrowserMatch ^Mozilla/4 gzip-only-text/html > BrowserMatch ^Mozilla/4\.0[678] no-gzip > BrowserMatch \bMSIE !no-gzip !gzip-only-text/html > BrowserMatch \bMSI[E] !no-gzip !gzip-only-text/html > > > > 3. I restarted apache > > More doc available at http://httpd.apache.org/docs/2.0/mod/mod_deflate.html > > Now when a request comes in with the header 'Accept-Encoding: gzip' apache > compresses the RDF. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger > Sent: February-26-08 4:35 PM > To: Core developer announcements > Subject: Re: [MOBY-dev] getting RDF resources in the compressed format > > Many thanks, Paul. > > I believe the solution we agreed upon was that if the client sends an > >> "Accept-encoding" HTTP header with x-gzip >> > > > Yes, that was what I vaguely remembered but was not sure about details. > [BTW, is there a way to search the whole biomoby email archive?] > > How does client know what was sent from the server? Is is in the HTTP > Content-type header? If so, what mime-type should be there? > > Eddie, it would be nice to have this feature implemented on the registry > site (so other registry providers can copy it, as well). Would you consider > it please? > > Cheers, > Martin > > > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From martin.senger at gmail.com Wed Feb 27 19:05:42 2008 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 28 Feb 2008 08:05:42 +0800 Subject: [MOBY-dev] getting RDF resources in the compressed format In-Reply-To: <47c5b60f.1def600a.5a28.1b48@mx.google.com> References: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> <47C4A4A3.1050601@ucalgary.ca> <4d93f07c0802261634u5aade00ak988ebfbff38d308a@mail.gmail.com> <47c5a763.0f98600a.4716.ffffa8be@mx.google.com> <47C5ABD4.7060309@ucalgary.ca> <47c5b60f.1def600a.5a28.1b48@mx.google.com> Message-ID: <4d93f07c0802271605qd460892q2dc2a4c69679a5a2@mail.gmail.com> Eddie, Thanks for making it happen. Today's questions are: 1) Is the compressing working on your laptop or already on the default BioMoby registry. If the former, when the latter is planned? 2) Are you considering to update registry documentation (so other sites, like IRRI, can benefit immediately from your investigation)? Regarding the implementation in the Java library, I am going to add it to CentralXXX classes this week (I am with Paul, I prefer Apache httpclient). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From edward.kawas at gmail.com Wed Feb 27 19:47:56 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 27 Feb 2008 16:47:56 -0800 Subject: [MOBY-dev] getting RDF resources in the compressed format In-Reply-To: <4d93f07c0802271605qd460892q2dc2a4c69679a5a2@mail.gmail.com> References: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> <47C4A4A3.1050601@ucalgary.ca> <4d93f07c0802261634u5aade00ak988ebfbff38d308a@mail.gmail.com> <47c5a763.0f98600a.4716.ffffa8be@mx.google.com> <47C5ABD4.7060309@ucalgary.ca> <47c5b60f.1def600a.5a28.1b48@mx.google.com> <4d93f07c0802271605qd460892q2dc2a4c69679a5a2@mail.gmail.com> Message-ID: <47c604e1.1498600a.5266.ffff8ff9@mx.google.com> Hi Martin, 1) It's working on my notebook and Mark is trying to make it work on the test registry. 2) I will update the docs, regarding what has to be done. Basically, you have to enable mod_deflate on apache and enable compression for text/xml and application/xml. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger Sent: February-27-08 4:06 PM To: Core developer announcements Subject: Re: [MOBY-dev] getting RDF resources in the compressed format Eddie, Thanks for making it happen. Today's questions are: 1) Is the compressing working on your laptop or already on the default BioMoby registry. If the former, when the latter is planned? 2) Are you considering to update registry documentation (so other sites, like IRRI, can benefit immediately from your investigation)? Regarding the implementation in the Java library, I am going to add it to CentralXXX classes this week (I am with Paul, I prefer Apache httpclient). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From martin.senger at gmail.com Wed Feb 27 21:09:48 2008 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 28 Feb 2008 10:09:48 +0800 Subject: [MOBY-dev] getting RDF resources in the compressed format In-Reply-To: <47c604e1.1498600a.5266.ffff8ff9@mx.google.com> References: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> <47C4A4A3.1050601@ucalgary.ca> <4d93f07c0802261634u5aade00ak988ebfbff38d308a@mail.gmail.com> <47c5a763.0f98600a.4716.ffffa8be@mx.google.com> <47C5ABD4.7060309@ucalgary.ca> <47c5b60f.1def600a.5a28.1b48@mx.google.com> <4d93f07c0802271605qd460892q2dc2a4c69679a5a2@mail.gmail.com> <47c604e1.1498600a.5266.ffff8ff9@mx.google.com> Message-ID: <4d93f07c0802271809l2eab744ema30e350f1603f704@mail.gmail.com> > 1) It's working on my notebook and Mark is trying to make it work on the > test registry. It's great! When do you, or does Mark, plan to make it available also from the Calgary registry? Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From edward.kawas at gmail.com Wed Feb 27 21:26:37 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 27 Feb 2008 18:26:37 -0800 Subject: [MOBY-dev] getting RDF resources in the compressed format In-Reply-To: <4d93f07c0802271809l2eab744ema30e350f1603f704@mail.gmail.com> References: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> <47C4A4A3.1050601@ucalgary.ca> <4d93f07c0802261634u5aade00ak988ebfbff38d308a@mail.gmail.com> <47c5a763.0f98600a.4716.ffffa8be@mx.google.com> <47C5ABD4.7060309@ucalgary.ca> <47c5b60f.1def600a.5a28.1b48@mx.google.com> <4d93f07c0802271605qd460892q2dc2a4c69679a5a2@mail.gmail.com> <47c604e1.1498600a.5266.ffff8ff9@mx.google.com> <4d93f07c0802271809l2eab744ema30e350f1603f704@mail.gmail.com> Message-ID: <47c61c02.1abd600a.0ce4.ffff929e@mx.google.com> I believe Mark actually had big problems doing it on the test registry (in fact he is still trying!). I am not sure why ... on my linux installation it was super simple ;-) I am sure that once Mark does the test registry, the Calgary one will follow quickly. I cant actually wait!!!! Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger Sent: February-27-08 6:10 PM To: Core developer announcements Subject: Re: [MOBY-dev] getting RDF resources in the compressed format > 1) It's working on my notebook and Mark is trying to make it work on the > test registry. It's great! When do you, or does Mark, plan to make it available also from the Calgary registry? Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From groscurt at mpiz-koeln.mpg.de Thu Feb 28 03:47:27 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 28 Feb 2008 09:47:27 +0100 Subject: [MOBY-dev] Dashboard as standalone In-Reply-To: <47c61c02.1abd600a.0ce4.ffff929e@mx.google.com> References: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> <47C4A4A3.1050601@ucalgary.ca> <4d93f07c0802261634u5aade00ak988ebfbff38d308a@mail.gmail.com> <47c5a763.0f98600a.4716.ffffa8be@mx.google.com> <47C5ABD4.7060309@ucalgary.ca> <47c5b60f.1def600a.5a28.1b48@mx.google.com> <4d93f07c0802271605qd460892q2dc2a4c69679a5a2@mail.gmail.com> <47c604e1.1498600a.5266.ffff8ff9@mx.google.com> <4d93f07c0802271809l2eab744ema30e350f1603f704@mail.gmail.com> <47c61c02.1abd600a.0ce4.ffff929e@mx.google.com> Message-ID: <47C6751F.8040000@mpiz-koeln.mpg.de> Hi, I just saw that in the docs it is written, that maybe there is a installanywhere version of dashboard. Any progress there or is it off the table ? I would love to have a standalone version of dashboard (somehow - even just the jar) - is this planned or is there some docs about how to create that ? best andreas From gordonp at ucalgary.ca Thu Feb 28 09:53:10 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 28 Feb 2008 07:53:10 -0700 Subject: [MOBY-dev] Dashboard as standalone In-Reply-To: <47C6751F.8040000@mpiz-koeln.mpg.de> References: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> <47C4A4A3.1050601@ucalgary.ca> <4d93f07c0802261634u5aade00ak988ebfbff38d308a@mail.gmail.com> <47c5a763.0f98600a.4716.ffffa8be@mx.google.com> <47C5ABD4.7060309@ucalgary.ca> <47c5b60f.1def600a.5a28.1b48@mx.google.com> <4d93f07c0802271605qd460892q2dc2a4c69679a5a2@mail.gmail.com> <47c604e1.1498600a.5266.ffff8ff9@mx.google.com> <4d93f07c0802271809l2eab744ema30e350f1603f704@mail.gmail.com> <47c61c02.1abd600a.0ce4.ffff929e@mx.google.com> <47C6751F.8040000@mpiz-koeln.mpg.de> Message-ID: <47C6CAD6.2010501@ucalgary.ca> We have an InstallAnywhere license for our lab, in case no one else manages to do it... Andreas Groscurth wrote: > Hi, > > I just saw that in the docs it is written, that maybe there is a > installanywhere version of dashboard. Any progress there or is it off > the table ? > > I would love to have a standalone version of dashboard (somehow - even > just the jar) - is this planned or is there some docs about how to > create that ? > > best > andreas > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,47c6725f10950272424736! > > > From martin.senger at gmail.com Thu Feb 28 10:03:51 2008 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 28 Feb 2008 23:03:51 +0800 Subject: [MOBY-dev] Dashboard as standalone In-Reply-To: <47C6CAD6.2010501@ucalgary.ca> References: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> <47c5a763.0f98600a.4716.ffffa8be@mx.google.com> <47C5ABD4.7060309@ucalgary.ca> <47c5b60f.1def600a.5a28.1b48@mx.google.com> <4d93f07c0802271605qd460892q2dc2a4c69679a5a2@mail.gmail.com> <47c604e1.1498600a.5266.ffff8ff9@mx.google.com> <4d93f07c0802271809l2eab744ema30e350f1603f704@mail.gmail.com> <47c61c02.1abd600a.0ce4.ffff929e@mx.google.com> <47C6751F.8040000@mpiz-koeln.mpg.de> <47C6CAD6.2010501@ucalgary.ca> Message-ID: <4d93f07c0802280703t4a44be88w6570e66e25b1b118@mail.gmail.com> I may have installAnywhere at IRRI. But I am waiting for the new way how to fill the local cache (using the RDF resources) - it is practically done (we are just waiting only for compressing RDF files from the default registry). When this is done, I will make the long-delayed fixes to dashboard and then try installAnywhere. Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Thu Feb 28 10:16:10 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 28 Feb 2008 16:16:10 +0100 Subject: [MOBY-dev] Dashboard as standalone In-Reply-To: <4d93f07c0802280703t4a44be88w6570e66e25b1b118@mail.gmail.com> References: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> <47c5a763.0f98600a.4716.ffffa8be@mx.google.com> <47C5ABD4.7060309@ucalgary.ca> <47c5b60f.1def600a.5a28.1b48@mx.google.com> <4d93f07c0802271605qd460892q2dc2a4c69679a5a2@mail.gmail.com> <47c604e1.1498600a.5266.ffff8ff9@mx.google.com> <4d93f07c0802271809l2eab744ema30e350f1603f704@mail.gmail.com> <47c61c02.1abd600a.0ce4.ffff929e@mx.google.com> <47C6751F.8040000@mpiz-koeln.mpg.de> <47C6CAD6.2010501@ucalgary.ca> <4d93f07c0802280703t4a44be88w6570e66e25b1b118@mail.gmail.com> Message-ID: <47C6D03A.6090804@mpiz-koeln.mpg.de> Yeah - thanks Martin Martin Senger wrote: > I may have installAnywhere at IRRI. But I am waiting for the new way how to > fill the local cache (using the RDF resources) - it is practically done (we > are just waiting only for compressing RDF files from the default registry). > When this is done, I will make the long-delayed fixes to dashboard and then > try installAnywhere. > > Martin > > From edward.kawas at gmail.com Thu Feb 28 11:35:02 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 28 Feb 2008 08:35:02 -0800 Subject: [MOBY-dev] getting RDF resources in the compressed format In-Reply-To: <4d93f07c0802271809l2eab744ema30e350f1603f704@mail.gmail.com> References: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> <47C4A4A3.1050601@ucalgary.ca> <4d93f07c0802261634u5aade00ak988ebfbff38d308a@mail.gmail.com> <47c5a763.0f98600a.4716.ffffa8be@mx.google.com> <47C5ABD4.7060309@ucalgary.ca> <47c5b60f.1def600a.5a28.1b48@mx.google.com> <4d93f07c0802271605qd460892q2dc2a4c69679a5a2@mail.gmail.com> <47c604e1.1498600a.5266.ffff8ff9@mx.google.com> <4d93f07c0802271809l2eab744ema30e350f1603f704@mail.gmail.com> Message-ID: <47c6e2dd.081b600a.52df.ffff896e@mx.google.com> The Calgary registry now returns gzipped RDF if requested. For those wishing to do this with your own personal registry, I added a bit of documentation on the RegistryScripts documentation page. This file can be accessed from the link 'Setting up a custom MOBY Central' on the biomoby.org homepage or: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/RegistrySc ripts.html [although, you might have to wait a few hours for the content to become available on the web, but the cvs is up to date!]. Thanks Mark! Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger Sent: February-27-08 6:10 PM To: Core developer announcements Subject: Re: [MOBY-dev] getting RDF resources in the compressed format > 1) It's working on my notebook and Mark is trying to make it work on the > test registry. It's great! When do you, or does Mark, plan to make it available also from the Calgary registry? Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From sneumann at ipb-halle.de Fri Feb 29 04:32:40 2008 From: sneumann at ipb-halle.de (Neumann, Steffen) Date: Fri, 29 Feb 2008 10:32:40 +0100 Subject: [MOBY-dev] Current CVS ant works, eclipse woes Message-ID: <1204277560.31184.306.camel@lathan.ipb-sub.ipb-halle.de> Hi moby hackers, (Hi Andreas ;-) I am just trying the current jmoby CVS snapshot, and share the experience, and maybe they'll make it into Andreas' "known-errors-and-problems". The command line ant targets work fine: ant bootstrap ant initeclipse ant bootstrap ant compile ant dashboard But in eclipse I get errors upon build: 29.02.08 10:20:53 CET: Reading /moby/pom.xml 29.02.08 10:21:00 CET: [WARN] Artifact javax.servlet:servlet-api:jar:2.5:provided retains local scope 'provided' overriding broader scope 'compile' given by a dependency. If this is not intended, modify or remove the local scope. 29.02.08 10:21:05 CET: [INFO] artifact org.jvnet.staxex:stax-ex: checking for updates from java.net 29.02.08 10:21:10 CET: [INFO] artifact org.jvnet.staxex:stax-ex: checking for updates from bio.maven.repository 29.02.08 10:21:12 CET: [INFO] artifact org.jvnet.staxex:stax-ex: checking for updates from java.net-m2 29.02.08 10:21:14 CET: [INFO] artifact org.jvnet.staxex:stax-ex: checking for updates from hpl.hp.repository 29.02.08 10:21:14 CET: [INFO] artifact org.jvnet.staxex:stax-ex: checking for updates from central 29.02.08 10:21:15 CET: [WARN] Artifact junit:junit:jar:4.4:test retains local scope 'test' overriding broader scope 'compile' given by a dependency. If this is not intended, modify or remove the local scope. 29.02.08 10:21:16 CET: Reading /moby/src/samples/pom.xml 29.02.08 10:21:17 CET: [WARN] Unable to get resource from repository central (http://repo1.maven.org/maven2) 29.02.08 10:21:17 CET: Project build error Cannot find parent: org.biomoby:jmoby for project: org.biomoby:jmoby-plugins:jar:1.0.0 29.02.08 10:21:17 CET: Reading /moby/src/main/pom.xml 29.02.08 10:21:18 CET: [WARN] Unable to get resource from repository central (http://repo1.maven.org/maven2) 29.02.08 10:21:18 CET: Project build error Cannot find parent: org.biomoby:jmoby for project: org.biomoby:jmoby-core:jar:1.0.0 29.02.08 10:25:27 CET: Reading /moby/pom.xml 29.02.08 10:25:28 CET: Reading /moby/src/samples/pom.xml 29.02.08 10:25:29 CET: [WARN] Unable to get resource from repository central (http://repo1.maven.org/maven2) 29.02.08 10:25:29 CET: Project build error Cannot find parent: org.biomoby:jmoby for project: org.biomoby:jmoby-plugins:jar:1.0.0 29.02.08 10:25:29 CET: Reading /moby/src/main/pom.xml 29.02.08 10:25:29 CET: [WARN] Unable to get resource from repository central (http://repo1.maven.org/maven2) 29.02.08 10:25:29 CET: Project build error Cannot find parent: org.biomoby:jmoby for project: org.biomoby:jmoby-core:jar:1.0.0 Severity and Description Path Resource Location Creation Time Id Project build error Cannot find parent: org.biomoby:jmoby for project: org.biomoby:jmoby-core:jar:1.0.0 moby/src/main pom.xml line 1 1204277129754 135628 Project build error Cannot find parent: org.biomoby:jmoby for project: org.biomoby:jmoby-plugins:jar:1.0.0 moby/src/samples pom.xml line 1 1204277129072 135627 The project was not built since its build path is incomplete. Cannot find the class file for org.biomoby.shared.MobyService. Fix the build path then try building this project moby Unknown 1204277127536 135626 The type org.biomoby.shared.MobyService cannot be resolved. It is indirectly referenced from required .class files moby/src/main/org/biomoby/client Taverna.java line 98 1204277127533 135625 This is linux / Sun JDK-1.5 / eclipse-3.2 Any ideas ? Further info needed ? Yours, Steffen -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 191 bytes Desc: This is a digitally signed message part URL: From groscurt at mpiz-koeln.mpg.de Fri Feb 29 05:44:09 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 29 Feb 2008 11:44:09 +0100 Subject: [MOBY-dev] Testing registry problems In-Reply-To: <1204277560.31184.306.camel@lathan.ipb-sub.ipb-halle.de> References: <1204277560.31184.306.camel@lathan.ipb-sub.ipb-halle.de> Message-ID: <47C7E1F9.5010106@mpiz-koeln.mpg.de> hiho, we getting constant ===ERROR=== Fault details: [string: null] [HttpErrorCode: null] Fault string: (0)null Fault code: {http://xml.apache.org/axis/}HTTP Fault actor: null When calling: http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl =========== while loading the ontologies in dashboard from the test registry - URL is accessible via browser. ? best andreas From groscurt at mpiz-koeln.mpg.de Fri Feb 29 05:51:21 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 29 Feb 2008 11:51:21 +0100 Subject: [MOBY-dev] warning on start of dashboard In-Reply-To: <1204277560.31184.306.camel@lathan.ipb-sub.ipb-halle.de> References: <1204277560.31184.306.camel@lathan.ipb-sub.ipb-halle.de> Message-ID: <200802291151.22060.groscurt@mpiz-koeln.mpg.de> hiho. starting dashboard from console gives me Warning: Reference moses.build.classpath has not been set at runtime, but was found during build file parsing, attempting to resolve. Future versions of Ant may support referencing ids defined in non-executed targets. dashboard works - but warning is there :-) Best andreas From edward.kawas at gmail.com Fri Feb 29 08:56:18 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 29 Feb 2008 05:56:18 -0800 Subject: [MOBY-dev] Testing registry problems In-Reply-To: <47C7E1F9.5010106@mpiz-koeln.mpg.de> References: <1204277560.31184.306.camel@lathan.ipb-sub.ipb-halle.de> <47C7E1F9.5010106@mpiz-koeln.mpg.de> Message-ID: <47c80f05.1fba720a.6278.31fd@mx.google.com> The test registry is down because apache is not working at the moment. Mark is trying to fix it. Sorry! Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth Sent: February-29-08 2:44 AM To: Core developer announcements Subject: [MOBY-dev] Testing registry problems hiho, we getting constant ===ERROR=== Fault details: [string: null] [HttpErrorCode: null] Fault string: (0)null Fault code: {http://xml.apache.org/axis/}HTTP Fault actor: null When calling: http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl =========== while loading the ontologies in dashboard from the test registry - URL is accessible via browser. ? best andreas _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From MichaelGerlich at gmx.de Thu Feb 28 15:07:24 2008 From: MichaelGerlich at gmx.de (Michael Gerlich) Date: Thu, 28 Feb 2008 21:07:24 +0100 Subject: [MOBY-dev] Dashboard can't connect to Registries Message-ID: <000601c87a45$892f2700$9b8d7500$@de> Hi there, First of all thanks for your tutorials about setting up Biomoby with Eclipse and for the newly created Known errors site at http://bioinfo.mpiz-koeln.mpg.de/araws/documentation/help/jmoby-step-by-step /writing-biomoby-web-services/known-errors-and-problems, they helped me a lot and I finally have successful Builds with the Ant Scripts (using JDK 1.5). But there are some things I still have problems with. 1) Eclipse keeps reporting that it misses required libraries, even though the initeclipse script says Build successful. Are these errors some kind of artifacts or should I check the ant scripts or checkout JMoby again? micge at linux-vm:~/eclipse> ./eclipse -vmargs -Djava.home=/usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/ ZoneInfo: /usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/lib/zi/ZoneInfoMappings (Datei oder Verzeichnis nicht gefunden) ZoneInfo: /usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/lib/zi/ZoneInfoMappings (Datei oder Verzeichnis nicht gefunden) ZoneInfo: /usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/lib/zi/ZoneInfoMappings (Datei oder Verzeichnis nicht gefunden) ZoneInfo: /usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/lib/zi/ZoneInfoMappings (Datei oder Verzeichnis nicht gefunden) ZoneInfo: /usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/lib/zi/ZoneInfoMappings (Datei oder Verzeichnis nicht gefunden) Severity and Description Project 'moby' is missing required library: 'lib/activation.jar' Project 'moby' is missing required library: 'lib/adenine.jar' Project 'moby' is missing required library: 'lib/alltools2.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-antlr.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-apache-bcel.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-apache-bsf.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-apache-log4j.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-apache-oro.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-apache-regexp.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-apache-resolver.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-commons-logging.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-commons-net.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-contrib.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-icontract.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-jai.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-javamail.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-jdepend.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-jmf.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-jsch.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-junit.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-launcher.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-netrexx.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-nodeps.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-starteam.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-stylebook.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-swing.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-trax.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-vaj.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-weblogic.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-xalan1.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-xslp.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/xercesImpl.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/xml-apis.jar' Project 'moby' is missing required library: 'lib/axis-ant.jar' Project 'moby' is missing required library: 'lib/axis.jar' Project 'moby' is missing required library: 'lib/castor-0.9.5.jar' Project 'moby' is missing required library: 'lib/commons-codec-1.3.jar' Project 'moby' is missing required library: 'lib/commons-collections-2.1.jar' Project 'moby' is missing required library: 'lib/commons-dbcp-1.1.jar' Project 'moby' is missing required library: 'lib/commons-discovery-0.2.jar' Project 'moby' is missing required library: 'lib/commons-httpclient-3.0-rc2.jar' Project 'moby' is missing required library: 'lib/commons-io-1.0.jar' Project 'moby' is missing required library: 'lib/commons-lang-2.1.jar' Project 'moby' is missing required library: 'lib/commons-logging-1.0.4.jar' Project 'moby' is missing required library: 'lib/commons-pool-1.1.jar' Project 'moby' is missing required library: 'lib/concurrent.jar' Project 'moby' is missing required library: 'lib/dnsjava-1.3.2.jar' Project 'moby' is missing required library: 'lib/icis-pedigree.jar' Project 'moby' is missing required library: 'lib/icu4j.jar' Project 'moby' is missing required library: 'lib/jakarta-oro-2.0.5.jar' Project 'moby' is missing required library: 'lib/jaxen-core.jar' Project 'moby' is missing required library: 'lib/jaxen-jdom.jar' Project 'moby' is missing required library: 'lib/jaxrpc.jar' Project 'moby' is missing required library: 'lib/jcalendar.jar' Project 'moby' is missing required library: 'lib/jdom.jar' Project 'moby' is missing required library: 'lib/jena.jar' Project 'moby' is missing required library: 'lib/jfcunit.jar' Project 'moby' is missing required library: 'lib/jodconverter-2.2.0.jar' Project 'moby' is missing required library: 'lib/junit.jar' Project 'moby' is missing required library: 'lib/log4j-1.2.12.jar' Project 'moby' is missing required library: 'lib/lsid-client-1.1.2.jar' Project 'moby' is missing required library: 'lib/lsid-server-1.1.2.jar' Project 'moby' is missing required library: 'lib/mail.jar' Project 'moby' is missing required library: 'lib/mailapi_1_3_1.jar' Project 'moby' is missing required library: 'lib/mysql-connector-java-3.1.7-bin.jar' Project 'moby' is missing required library: 'lib/rdf-api-2001-01-19.jar' Project 'moby' is missing required library: 'lib/saaj.jar' Project 'moby' is missing required library: 'lib/saxpath.jar' Project 'moby' is missing required library: 'lib/servlet.jar' Project 'moby' is missing required library: 'lib/taverna.jar' Project 'moby' is missing required library: 'lib/wsdl4j-1.5.1.jar' Project 'moby' is missing required library: 'lib/xalan.jar' Project 'moby' is missing required library: 'lib/xercesImpl.jar' Project 'moby' is missing required library: 'lib/xercesSamples.jar' Project 'moby' is missing required library: 'lib/xml-apis.jar' Project 'moby' is missing required library: 'lib/xmlParserAPIs.jar' Project build error Cannot find parent: org.biomoby:jmoby for project: org.biomoby:jmoby-core:jar:1.0.0 moby/src/main pom.xml line 1 1204224268317 133440 Project build error Cannot find parent: org.biomoby:jmoby for project: org.biomoby:jmoby-plugins:jar:1.0.0 moby/src/samples pom.xml line 1 1204224267905 133439 The project cannot be built until build path errors are resolved moby 2) I'am behind a proxy server, so I had to edit proxy settings in net.properties of JDK 1.5 (http_proxy environment variable is set, but without effect to Java). With this, all the ant scripts work without any problems, but when I run Dashboard, all I got are empty lists and the following messages: Inside Eclipse: --------------- Buildfile: /home/micge/workspace/moby/build.xml checkmaven: initmaven: init: config: compile: moses-init: samples-init: dashboard-init: dashboard-config: dashboard: [Dashboard] libxcb: WARNING! Program tries to unlock a connection without having acquired [Dashboard] a lock first, which indicates a programming error. [Dashboard] There will be no further warnings about this issue. [Dashboard] libxcb: WARNING! Program tries to lock an already locked connection, [Dashboard] which indicates a programming error. [Dashboard] There will be no further warnings about this issue. [Dashboard] 192616 [Thread-6] WARN CentralDigestCachedImpl - Error with Services RDF [Dashboard] org.biomoby.shared.MobyException: ===ERROR=== [Dashboard] Fault details: [Dashboard] Fault string: java.net.ConnectException: Connection timed out [Dashboard] Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException [Dashboard] Fault actor: null [Dashboard] When calling: [Dashboard] http://moby.ucalgary.ca/moby/MOBY-Central.pl [Dashboard] =========== [Dashboard] at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:230) [Dashboard] at org.biomoby.client.CentralImpl.getResourceRefs(CentralImpl.java:1772) [Dashboard] at org.biomoby.client.CentralImpl.getResource(CentralImpl.java:1807) [Dashboard] at org.biomoby.client.CentralDigestCachedImpl.getResourceAsString(CentralDigest CachedImpl.java:216) [Dashboard] at org.biomoby.client.CentralDigestCachedImpl.fillServicesCache(CentralDigestCa chedImpl.java:243) [Dashboard] at org.biomoby.client.CentralDigestCachedImpl.getServices(CentralDigestCachedIm pl.java:709) [Dashboard] at org.biomoby.service.dashboard.RegistryModel.getServices(RegistryModel.java:5 61) [Dashboard] at org.biomoby.service.dashboard.ServicesTree$4.construct(ServicesTree.java:121 ) [Dashboard] at org.biomoby.service.dashboard.SwingWorker$2.run(SwingWorker.java:117) [Dashboard] at java.lang.Thread.run(Thread.java:595) [Dashboard] Caused by: java.net.ConnectException: Connection timed out [Dashboard] at org.apache.axis.AxisFault.makeFault(AxisFault.java:101) [Dashboard] at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:154) [Dashboard] at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java: 32) [Dashboard] at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118) [Dashboard] at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83) [Dashboard] at org.apache.axis.client.AxisClient.invoke(AxisClient.java:165) [Dashboard] at org.apache.axis.client.Call.invokeEngine(Call.java:2784) [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2767) [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2443) [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2366) [Dashboard] at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:226) [Dashboard] ... 9 more [Dashboard] Caused by: java.net.ConnectException: Connection timed out [Dashboard] at java.net.PlainSocketImpl.socketConnect(Native Method) [Dashboard] at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333) [Dashboard] at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195) [Dashboard] at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182) [Dashboard] at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366) [Dashboard] at java.net.Socket.connect(Socket.java:520) [Dashboard] at java.net.Socket.connect(Socket.java:470) [Dashboard] at java.net.Socket.(Socket.java:367) [Dashboard] at java.net.Socket.(Socket.java:180) [Dashboard] at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFact ory.java:149) [Dashboard] at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFact ory.java:120) [Dashboard] at org.apache.axis.transport.http.HTTPSender.getSocket(HTTPSender.java:191) [Dashboard] at org.apache.axis.transport.http.HTTPSender.writeToSocket(HTTPSender.java:404) [Dashboard] at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:138) [Dashboard] ... 18 more [Dashboard] 193461 [Thread-7] WARN CentralDigestCachedImpl - Error with Services RDF [Dashboard] org.biomoby.shared.MobyException: ===ERROR=== [Dashboard] Fault details: [Dashboard] Fault string: java.net.ConnectException: Connection timed out [Dashboard] Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException [Dashboard] Fault actor: null [Dashboard] When calling: [Dashboard] http://moby.ucalgary.ca/moby/MOBY-Central.pl [Dashboard] =========== [Dashboard] at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:230) [Dashboard] at org.biomoby.client.CentralImpl.getResourceRefs(CentralImpl.java:1772) [Dashboard] at org.biomoby.client.CentralImpl.getResource(CentralImpl.java:1807) [Dashboard] at org.biomoby.client.CentralDigestCachedImpl.getResourceAsString(CentralDigest CachedImpl.java:216) [Dashboard] at org.biomoby.client.CentralDigestCachedImpl.fillServicesCache(CentralDigestCa chedImpl.java:243) [Dashboard] at org.biomoby.client.CentralDigestCachedImpl.getServices(CentralDigestCachedIm pl.java:709) [Dashboard] at org.biomoby.service.dashboard.RegistryModel.getServices(RegistryModel.java:5 61) [Dashboard] at org.biomoby.service.dashboard.ServicesTree$4.construct(ServicesTree.java:121 ) [Dashboard] at org.biomoby.service.dashboard.SwingWorker$2.run(SwingWorker.java:117) [Dashboard] at java.lang.Thread.run(Thread.java:595) [Dashboard] Caused by: java.net.ConnectException: Connection timed out [Dashboard] at org.apache.axis.AxisFault.makeFault(AxisFault.java:101) [Dashboard] at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:154) [Dashboard] at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java: 32) [Dashboard] at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118) [Dashboard] at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83) [Dashboard] at org.apache.axis.client.AxisClient.invoke(AxisClient.java:165) [Dashboard] at org.apache.axis.client.Call.invokeEngine(Call.java:2784) [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2767) [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2443) [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2366) [Dashboard] at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:226) [Dashboard] ... 9 more [Dashboard] Caused by: java.net.ConnectException: Connection timed out [Dashboard] at java.net.PlainSocketImpl.socketConnect(Native Method) [Dashboard] at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333) [Dashboard] at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195) [Dashboard] at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182) [Dashboard] at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366) [Dashboard] at java.net.Socket.connect(Socket.java:520) [Dashboard] at java.net.Socket.connect(Socket.java:470) [Dashboard] at java.net.Socket.(Socket.java:367) [Dashboard] at java.net.Socket.(Socket.java:180) [Dashboard] at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFact ory.java:149) [Dashboard] at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFact ory.java:120) [Dashboard] at org.apache.axis.transport.http.HTTPSender.getSocket(HTTPSender.java:191) [Dashboard] at org.apache.axis.transport.http.HTTPSender.writeToSocket(HTTPSender.java:404) [Dashboard] at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:138) [Dashboard] ... 18 more BUILD SUCCESSFUL >From Dashboard (after one minute) -------------- ===Error=== Fault details: Fault string: java.net.ConnectException: Connection timed out Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException Fault actor: null when calling: http://moby.uralgary.ca/moby/MOBY-Central.pl Is this a problem with the proxy settings I made in net.properties or is it inside Dashboard? Regards, Michael From hao.chen at uni-bielefeld.de Wed Feb 20 11:01:33 2008 From: hao.chen at uni-bielefeld.de (wasser) Date: Wed, 20 Feb 2008 16:01:33 -0000 Subject: [MOBY-dev] can not generate service skeleton Message-ID: <1203522403.11381.6.camel@andreas.dhcp.studentenwerk-bielefeld.de> hi, everyone I got this error just from yesterday and Moses generator works very good before. Now every time I try to generate new service , I got an error message which tells me that compile failed. It seems that ant doesn't work correctly. Have somebody the same problem? regards h.chen From Pieter.Neerincx at wur.nl Mon Feb 4 19:26:37 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Mon, 4 Feb 2008 20:26:37 +0100 Subject: [MOBY-dev] IO::Template missing for MOSES::MOBY In-Reply-To: References: <20080131104248.4E82E2DEA19@marz.stanford.edu> Message-ID: <148D36BB-BECF-4B43-967C-639832792372@wur.nl> Hi Eddie, I'm trying to install MOSES::MOBY in our main production environment using CPAN :), but it wants IO::Template. This one is new for me, not available on CPAN and Google won't tell me where to get it either. Is this a very obscure module or maybe a typo in the prerequisites? Cheers, Pi From edward.kawas at gmail.com Mon Feb 4 19:53:10 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 4 Feb 2008 11:53:10 -0800 Subject: [MOBY-dev] IO::Template missing for MOSES::MOBY In-Reply-To: <148D36BB-BECF-4B43-967C-639832792372@wur.nl> References: <20080131104248.4E82E2DEA19@marz.stanford.edu> <148D36BB-BECF-4B43-967C-639832792372@wur.nl> Message-ID: <47a76d27.15588c0a.27b2.2e6d@mx.google.com> Hi Pieter, The module is at http://search.cpan.org/dist/Template-Toolkit/. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter Neerincx Sent: February-04-08 11:27 AM To: Core developer announcements Subject: [MOBY-dev] IO::Template missing for MOSES::MOBY Hi Eddie, I'm trying to install MOSES::MOBY in our main production environment using CPAN :), but it wants IO::Template. This one is new for me, not available on CPAN and Google won't tell me where to get it either. Is this a very obscure module or maybe a typo in the prerequisites? Cheers, Pi _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From Pieter.Neerincx at wur.nl Mon Feb 4 22:01:23 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Mon, 04 Feb 2008 23:01:23 +0100 Subject: [MOBY-dev] IO::Template missing for MOSES::MOBY In-Reply-To: <47a76d27.15588c0a.27b2.2e6d@mx.google.com> References: <20080131104248.4E82E2DEA19@marz.stanford.edu> <148D36BB-BECF-4B43-967C-639832792372@wur.nl> <47a76d27.15588c0a.27b2.2e6d@mx.google.com> Message-ID: <20CCF5A5-969D-47AC-A793-A2F4C81A0F78@wur.nl> Ok, thanks! Somehow CPAN doesn't mangage to figure out the dependancy... and I don't find IO::Template in there either. Shouldn't the requirement be Template instead of IO::Template? Cheers, Pi On 04 Feb 2008, at 20:53, Edward Kawas wrote: > Hi Pieter, > > The module is at http://search.cpan.org/dist/Template-Toolkit/. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter > Neerincx > Sent: February-04-08 11:27 AM > To: Core developer announcements > Subject: [MOBY-dev] IO::Template missing for MOSES::MOBY > > Hi Eddie, > > I'm trying to install MOSES::MOBY in our main production environment > using CPAN :), but it wants IO::Template. This one is new for me, not > available on CPAN and Google won't tell me where to get it either. Is > this a very obscure module or maybe a typo in the prerequisites? > > Cheers, > > Pi > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------- From edward.kawas at gmail.com Mon Feb 4 22:36:42 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 4 Feb 2008 14:36:42 -0800 Subject: [MOBY-dev] IO::Template missing for MOSES::MOBY In-Reply-To: <20CCF5A5-969D-47AC-A793-A2F4C81A0F78@wur.nl> References: <20080131104248.4E82E2DEA19@marz.stanford.edu> <148D36BB-BECF-4B43-967C-639832792372@wur.nl> <47a76d27.15588c0a.27b2.2e6d@mx.google.com> <20CCF5A5-969D-47AC-A793-A2F4C81A0F78@wur.nl> Message-ID: <47a7937c.01538c0a.5153.32b8@mx.google.com> I will look into this as you might be right. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter Neerincx Sent: February-04-08 2:01 PM To: Core developer announcements Subject: Re: [MOBY-dev] IO::Template missing for MOSES::MOBY Ok, thanks! Somehow CPAN doesn't mangage to figure out the dependancy... and I don't find IO::Template in there either. Shouldn't the requirement be Template instead of IO::Template? Cheers, Pi On 04 Feb 2008, at 20:53, Edward Kawas wrote: > Hi Pieter, > > The module is at http://search.cpan.org/dist/Template-Toolkit/. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter > Neerincx > Sent: February-04-08 11:27 AM > To: Core developer announcements > Subject: [MOBY-dev] IO::Template missing for MOSES::MOBY > > Hi Eddie, > > I'm trying to install MOSES::MOBY in our main production environment > using CPAN :), but it wants IO::Template. This one is new for me, not > available on CPAN and Google won't tell me where to get it either. Is > this a very obscure module or maybe a typo in the prerequisites? > > Cheers, > > Pi > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------- _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Mon Feb 4 22:56:31 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 4 Feb 2008 14:56:31 -0800 Subject: [MOBY-dev] IO::Template missing for MOSES::MOBY In-Reply-To: <148D36BB-BECF-4B43-967C-639832792372@wur.nl> References: <20080131104248.4E82E2DEA19@marz.stanford.edu> <148D36BB-BECF-4B43-967C-639832792372@wur.nl> Message-ID: <47a79821.0e578c0a.0282.ffffb68e@mx.google.com> Hmm, I don't want to beat this dead horse any more than I should, but I am looking at the MOSES::MOBY module and I cant find IO::Template in it anywere. Where did you get this error from? Also, the makefile has 'Template' in it already... Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter Neerincx Sent: February-04-08 11:27 AM To: Core developer announcements Subject: [MOBY-dev] IO::Template missing for MOSES::MOBY Hi Eddie, I'm trying to install MOSES::MOBY in our main production environment using CPAN :), but it wants IO::Template. This one is new for me, not available on CPAN and Google won't tell me where to get it either. Is this a very obscure module or maybe a typo in the prerequisites? Cheers, Pi _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Mon Feb 4 23:41:17 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 4 Feb 2008 15:41:17 -0800 Subject: [MOBY-dev] cvs perl folder - potential changes Message-ID: <47a7a29f.22528c0a.1300.5fb7@mx.google.com> Hi, I have been working on a MOBY cpan module that is hopefully going to simplify the registry installation portion of mobycentral. I am writing to the list to see who would be upset with me if I were to re-arrange the moby-live/Perl/ folder in the cvs. Currently, the moby-live/Perl/ folder looks like: Perl/ |--> Accessories/ |--> docs/ |--> MOBY/ |--> scripts/ |--> t/ Some files ... I would like to do the following: Move Perl/MOBY to Perl/lib/MOBY Perl/scripts to Perl/share/[cgi|config|db|scripts] Create a Perl/bin/scripts directory, and a Perl/inc directory. Replace the Makefile.PL with my new Makefile.PL. One reason that I wish to do this is to reduce the chance of code forking (http://en.wikipedia.org/wiki/Fork_(software_development) ) in the future with the cvs release and cpan releases. In addition, the new folder layout is what is used when creating the cpan release module for MOBY. Anyone object? I will wait for comments/concerns/etc all this week and next week during the hackathon, I will hopefully carry out these changes. Thanks, Eddie From markw at illuminae.com Tue Feb 5 03:38:57 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 04 Feb 2008 19:38:57 -0800 Subject: [MOBY-dev] cvs perl folder - potential changes In-Reply-To: <47a7a29f.22528c0a.1300.5fb7@mx.google.com> References: <47a7a29f.22528c0a.1300.5fb7@mx.google.com> Message-ID: Sounds good to me! On Mon, 04 Feb 2008 15:41:17 -0800, Edward Kawas wrote: > I would like to do the following: > > Move > Perl/MOBY to Perl/lib/MOBY > Perl/scripts to Perl/share/[cgi|config|db|scripts] > > Create a Perl/bin/scripts directory, and a Perl/inc directory. > > Replace the Makefile.PL with my new Makefile.PL. From Pieter.Neerincx at wur.nl Tue Feb 5 10:54:09 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Tue, 5 Feb 2008 11:54:09 +0100 Subject: [MOBY-dev] cvs perl folder - potential changes In-Reply-To: References: <47a7a29f.22528c0a.1300.5fb7@mx.google.com> Message-ID: Yep, same here. Looking forward to test the Moby Central CPAN module! Just one request: could you make a copy of the "old" cvs Perl folder first and put that on the website as a "release". I'm running a course over the next weeks involving BioMoby service development, so it would be nice to have a "backup" of the 1.0 Moby code. Cheers, Pi On 5-feb-2008, at 4:38, Mark Wilkinson wrote: > Sounds good to me! > > > On Mon, 04 Feb 2008 15:41:17 -0800, Edward Kawas > wrote: > > > >> I would like to do the following: >> >> Move >> Perl/MOBY to Perl/lib/MOBY >> Perl/scripts to Perl/share/[cgi|config|db|scripts] >> >> Create a Perl/bin/scripts directory, and a Perl/inc directory. >> >> Replace the Makefile.PL with my new Makefile.PL. > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From Pieter.Neerincx at wur.nl Tue Feb 5 11:01:55 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Tue, 5 Feb 2008 12:01:55 +0100 Subject: [MOBY-dev] IO::Template missing for MOSES::MOBY In-Reply-To: <47a79821.0e578c0a.0282.ffffb68e@mx.google.com> References: <20080131104248.4E82E2DEA19@marz.stanford.edu> <148D36BB-BECF-4B43-967C-639832792372@wur.nl> <47a79821.0e578c0a.0282.ffffb68e@mx.google.com> Message-ID: <237435F5-3D96-4B8F-AAC8-B1F498548A6A@wur.nl> Hi Eddie, Must be an "undead" zombie than :(. This is what I get: CPAN.pm: Going to build E/EK/EKAWAS/MOSES-MOBY-0.84.tar.gz Cannot determine perl version info from lib/MOSES/MOBY.pm *** Module::AutoInstall version 1.03 *** Checking for Perl dependencies... [Core Features] - Test::More ...loaded. (0.62 >= 0.42) - ExtUtils::MakeMaker ...loaded. (6.17 >= 6.11) - Carp ...loaded. (1.01) - File::Spec ...loaded. (3.19 >= 0.80) - SOAP::Lite ...loaded. (0.69 >= 0.69) - XML::LibXML ...loaded. (1.66 >= 1.62) - Log::Log4perl ...loaded. (1.14 >= 1.12) - Template ...loaded. (2.19 >= 1.11) - Config::Simple ...loaded. (4.58 >= 4.58) - IO::Stringy ...loaded. (2.110 >= 2.11) - Unicode::String ...loaded. (2.09 >= 2.09) - File::HomeDir ...loaded. (0.69 >= 0.65) - File::ShareDir ...loaded. (0.05 >= 0.05) - Class::Inspector ...loaded. (1.18 >= 1.17) - Params::Util ...loaded. (0.31 >= 0.28) - IO::Prompt ...missing. (would need 0.99) ==> Auto-install the 1 mandatory module(s) from CPAN? [y] n ==> The module(s) are mandatory! Really skip? [n] y *** Module::AutoInstall configuration finished. Checking if your kit is complete... Looks good Warning: prerequisite IO::Prompt 0.99 not found. We have 0.099004. Writing Makefile for MOSES::MOBY ---- Unsatisfied dependencies detected during [E/EK/EKAWAS/MOSES- MOBY-0.84.tar.gz] ----- IO::Template Shall I follow them and prepend them to the queue of modules we are processing right now? [yes] If I answer yes it can't find IO::Template on CPAN. Notice that the version number of IO::Prompt is messed up. I tried to stick to 0.99.2 as suggested by your documentation to prevent the documented bogus errors, but apparently we already have 0.99.4 on the production machine... It's probably not a MOSES::MOBY bug, but an erroneous dependancy in IO::... (If I tell CPAN to try to install IO::Prompt I get the same error) Cheers, Pi On 4-feb-2008, at 23:56, Edward Kawas wrote: > Hmm, I don't want to beat this dead horse any more than I should, > but I am > looking at the MOSES::MOBY module and I cant find IO::Template in it > anywere. Where did you get this error from? Also, the makefile has > 'Template' in it already... > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter > Neerincx > Sent: February-04-08 11:27 AM > To: Core developer announcements > Subject: [MOBY-dev] IO::Template missing for MOSES::MOBY > > Hi Eddie, > > I'm trying to install MOSES::MOBY in our main production environment > using CPAN :), but it wants IO::Template. This one is new for me, not > available on CPAN and Google won't tell me where to get it either. Is > this a very obscure module or maybe a typo in the prerequisites? > > Cheers, > > Pi > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From markw at illuminae.com Tue Feb 5 13:52:30 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 05 Feb 2008 05:52:30 -0800 Subject: [MOBY-dev] cvs perl folder - potential changes In-Reply-To: References: <47a7a29f.22528c0a.1300.5fb7@mx.google.com> Message-ID: The 1.0 Perl code was released a few days ago to correspond with the publication. (see homepage). I'm waiting for the Java crew to release their bit. M On Tue, 05 Feb 2008 02:54:09 -0800, Pieter Neerincx wrote: > Yep, same here. Looking forward to test the Moby Central CPAN module! > Just one request: could you make a copy of the "old" cvs Perl folder > first and put that on the website as a "release". I'm running a course > over the next weeks involving BioMoby service development, so it would > be nice to have a "backup" of the 1.0 Moby code. > > Cheers, > > Pi > > On 5-feb-2008, at 4:38, Mark Wilkinson wrote: > >> Sounds good to me! >> >> >> On Mon, 04 Feb 2008 15:41:17 -0800, Edward Kawas >> wrote: >> >> >> >>> I would like to do the following: >>> >>> Move >>> Perl/MOBY to Perl/lib/MOBY >>> Perl/scripts to Perl/share/[cgi|config|db|scripts] >>> >>> Create a Perl/bin/scripts directory, and a Perl/inc directory. >>> >>> Replace the Makefile.PL with my new Makefile.PL. >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 039 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------ > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Tue Feb 5 14:21:25 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 5 Feb 2008 06:21:25 -0800 Subject: [MOBY-dev] IO::Template missing for MOSES::MOBY In-Reply-To: <237435F5-3D96-4B8F-AAC8-B1F498548A6A@wur.nl> References: <20080131104248.4E82E2DEA19@marz.stanford.edu> <148D36BB-BECF-4B43-967C-639832792372@wur.nl> <47a79821.0e578c0a.0282.ffffb68e@mx.google.com> <237435F5-3D96-4B8F-AAC8-B1F498548A6A@wur.nl> Message-ID: <47a870e9.02578c0a.1362.ffffe220@mx.google.com> I don't know what to say... I have never seen that error before. Do you get the same error if you download the module yourself from cpan? Also, using IO::Prompt 0.99.4 might lead to some problems, so I highly recommend that you use the previous version of that module 0.99.2. Also, I have never been able to install IO::Prompt using command line cpan ... That module is a pain in the butt! Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter Neerincx Sent: February-05-08 3:02 AM To: Core developer announcements Subject: Re: [MOBY-dev] IO::Template missing for MOSES::MOBY Hi Eddie, Must be an "undead" zombie than :(. This is what I get: CPAN.pm: Going to build E/EK/EKAWAS/MOSES-MOBY-0.84.tar.gz Cannot determine perl version info from lib/MOSES/MOBY.pm *** Module::AutoInstall version 1.03 *** Checking for Perl dependencies... [Core Features] - Test::More ...loaded. (0.62 >= 0.42) - ExtUtils::MakeMaker ...loaded. (6.17 >= 6.11) - Carp ...loaded. (1.01) - File::Spec ...loaded. (3.19 >= 0.80) - SOAP::Lite ...loaded. (0.69 >= 0.69) - XML::LibXML ...loaded. (1.66 >= 1.62) - Log::Log4perl ...loaded. (1.14 >= 1.12) - Template ...loaded. (2.19 >= 1.11) - Config::Simple ...loaded. (4.58 >= 4.58) - IO::Stringy ...loaded. (2.110 >= 2.11) - Unicode::String ...loaded. (2.09 >= 2.09) - File::HomeDir ...loaded. (0.69 >= 0.65) - File::ShareDir ...loaded. (0.05 >= 0.05) - Class::Inspector ...loaded. (1.18 >= 1.17) - Params::Util ...loaded. (0.31 >= 0.28) - IO::Prompt ...missing. (would need 0.99) ==> Auto-install the 1 mandatory module(s) from CPAN? [y] n ==> The module(s) are mandatory! Really skip? [n] y *** Module::AutoInstall configuration finished. Checking if your kit is complete... Looks good Warning: prerequisite IO::Prompt 0.99 not found. We have 0.099004. Writing Makefile for MOSES::MOBY ---- Unsatisfied dependencies detected during [E/EK/EKAWAS/MOSES- MOBY-0.84.tar.gz] ----- IO::Template Shall I follow them and prepend them to the queue of modules we are processing right now? [yes] If I answer yes it can't find IO::Template on CPAN. Notice that the version number of IO::Prompt is messed up. I tried to stick to 0.99.2 as suggested by your documentation to prevent the documented bogus errors, but apparently we already have 0.99.4 on the production machine... It's probably not a MOSES::MOBY bug, but an erroneous dependancy in IO::... (If I tell CPAN to try to install IO::Prompt I get the same error) Cheers, Pi On 4-feb-2008, at 23:56, Edward Kawas wrote: > Hmm, I don't want to beat this dead horse any more than I should, > but I am > looking at the MOSES::MOBY module and I cant find IO::Template in it > anywere. Where did you get this error from? Also, the makefile has > 'Template' in it already... > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter > Neerincx > Sent: February-04-08 11:27 AM > To: Core developer announcements > Subject: [MOBY-dev] IO::Template missing for MOSES::MOBY > > Hi Eddie, > > I'm trying to install MOSES::MOBY in our main production environment > using CPAN :), but it wants IO::Template. This one is new for me, not > available on CPAN and Google won't tell me where to get it either. Is > this a very obscure module or maybe a typo in the prerequisites? > > Cheers, > > Pi > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From Pieter.Neerincx at wur.nl Tue Feb 5 14:33:31 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Tue, 5 Feb 2008 15:33:31 +0100 Subject: [MOBY-dev] cvs perl folder - potential changes In-Reply-To: References: <47a7a29f.22528c0a.1300.5fb7@mx.google.com> Message-ID: <5F8AF1F8-8541-4187-ACA8-A2EFBC73EB41@wur.nl> Ok, thanks! On 5-feb-2008, at 14:52, Mark Wilkinson wrote: > The 1.0 Perl code was released a few days ago to correspond with > the publication. > (see homepage). I'm waiting for the Java crew to release their bit. > > M > > > On Tue, 05 Feb 2008 02:54:09 -0800, Pieter Neerincx > wrote: > >> Yep, same here. Looking forward to test the Moby Central CPAN >> module! Just one request: could you make a copy of the "old" cvs >> Perl folder first and put that on the website as a "release". I'm >> running a course over the next weeks involving BioMoby service >> development, so it would be nice to have a "backup" of the 1.0 >> Moby code. >> >> Cheers, >> >> Pi >> >> On 5-feb-2008, at 4:38, Mark Wilkinson wrote: >> >>> Sounds good to me! >>> >>> >>> On Mon, 04 Feb 2008 15:41:17 -0800, Edward Kawas >>> wrote: >>> >>> >>> >>>> I would like to do the following: >>>> >>>> Move >>>> Perl/MOBY to Perl/lib/MOBY >>>> Perl/scripts to Perl/share/[cgi|config|db|scripts] >>>> >>>> Create a Perl/bin/scripts directory, and a Perl/inc directory. >>>> >>>> Replace the Makefile.PL with my new Makefile.PL. >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >> >> ------------------------------------------------------------- >> Wageningen University and Research centre (WUR) >> Laboratory of Bioinformatics >> Transitorium (building 312) room 1034 >> >> Dreijenlaan 3 >> 6703 HA Wageningen >> The Netherlands >> >> phone: 0317-483 039 >> fax: 0317-483 584 >> mobile: 06-143 66 783 >> mail: pieter.neerincx at wur.nl >> skype: pieter.online >> ------------------------------------------------------------ >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From markw at illuminae.com Wed Feb 6 21:49:02 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 06 Feb 2008 13:49:02 -0800 Subject: [MOBY-dev] The beginnings of the new Moby homepage Message-ID: Hi all, I've spent the day working on the new Joomla site that we're considering using as the new Moby homepage. I also wanted to get it running in time for the hackathon as a place to store notes and updates etc. http://biomoby.org/JOOMLA/ It's still basically empty, and the menu buttons are not all well-thought-out yet. Does anyone on the list know Joomla well? I'm starting to get the hang of it, but I'm still quite a beginner! Mark From groscurt at mpiz-koeln.mpg.de Thu Feb 7 14:39:09 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 7 Feb 2008 15:39:09 +0100 Subject: [MOBY-dev] http://biomoby.org/jmoby-jars/jars-archive/ gone ? In-Reply-To: References: Message-ID: <200802071539.09914.groscurt@mpiz-koeln.mpg.de> where are the libs gone ... ?! ant task gather fails because of a 404 andreas -- Andreas Groscurth Bioinformatics Developer Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-449 From gss at ncgr.org Thu Feb 7 17:05:09 2008 From: gss at ncgr.org (Gary Schiltz) Date: Thu, 07 Feb 2008 10:05:09 -0700 Subject: [MOBY-dev] The beginnings of the new Moby homepage In-Reply-To: References: Message-ID: <47AB3A45.2090108@ncgr.org> Mark, Would you care to say a few words about why you want to switch to Joomla from WordPress? Just curious... // Gary On 2/6/2008 2:49 PM, Mark Wilkinson wrote: > Hi all, > > I've spent the day working on the new Joomla site that we're considering > using as the new Moby homepage. I also wanted to get it running in time > for the hackathon as a place to store notes and updates etc. > > http://biomoby.org/JOOMLA/ > > It's still basically empty, and the menu buttons are not all > well-thought-out yet. Does anyone on the list know Joomla well? I'm > starting to get the hang of it, but I'm still quite a beginner! > > Mark From martin.senger at gmail.com Thu Feb 7 17:29:30 2008 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 7 Feb 2008 17:29:30 +0000 Subject: [MOBY-dev] http://biomoby.org/jmoby-jars/jars-archive/ gone ? In-Reply-To: <200802071539.09914.groscurt@mpiz-koeln.mpg.de> References: <200802071539.09914.groscurt@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0802070929qa7584a5y9796be5dcc00432b@mail.gmail.com> > where are the libs gone ... ?! I am getting the same message - but I do not know (yet). I will check it. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Thu Feb 7 19:11:00 2008 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 7 Feb 2008 19:11:00 +0000 Subject: [MOBY-dev] http://biomoby.org/jmoby-jars/jars-archive/ gone ? In-Reply-To: <200802071539.09914.groscurt@mpiz-koeln.mpg.de> References: <200802071539.09914.groscurt@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0802071111v2803896aof0bef0f6b21be37a@mail.gmail.com> Andreas, where are the libs gone ... ?! > > ant task gather fails because of a 404 > Is it better now? Because suddenly I cannot reproduce the error... Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From serr at ac.uma.es Mon Feb 11 08:10:20 2008 From: serr at ac.uma.es (Sergio Ramirez Ramirez) Date: Mon, 11 Feb 2008 09:10:20 +0100 Subject: [MOBY-dev] INB Proposal for Mirroring - RFC In-Reply-To: <938F7558-E5E8-4073-B08C-A37437E46543@wur.nl> References: <938F7558-E5E8-4073-B08C-A37437E46543@wur.nl> Message-ID: <47B002EC.1020307@ac.uma.es> Hello to all the mobiers, In this link http://chirimoyo.ac.uma.es/proposals/BioMOBY_Mirroring.pdf you can find the INB proposal for mirroring services. It describes the new functions and the changes needed in the functions that already exist in the API of BioMOBY. The proposal also includes different options for managing the mirrors using RDF files. We would appreciate comments and suggestions, in particular how to deal with the RDF data. We have implemented the described functionality in the MOBYCentral perl code. This code will be made available, and in a few days we will provide a new link with a small tutorial about how to use the client side library. Best regards, Sergio. Pieter Neerincx wrote: > Hi, > > I searched my mail archive and the website, but I can not find this > RFC.... Was it that long ago? Anyway, can someone please send us > pointer where to find this RFC? > > Thanks, > > Pi > > On 22-jan-2008, at 0:58, Mark Wilkinson wrote: > >> Hi everyone, >> >> Has anyone else looked at the INB proposal for mirroring of services? >> I think it's really nice, personally! I had a couple of small >> questions and concerns, but it really doesn't seem like an overly >> disruptive change, and apparently they already have it working at >> INB, so the codebase to support it already exists. >> >> I think we should vote on the issue soon, as the INB folks have been >> very, VERY patient! >> >> M >> >> >> >> -- >> -- >> Mark Wilkinson >> Assistant Professor, Dept. Medical Genetics >> University of British Columbia >> PI Bioinformatics >> iCAPTURE Centre, St. Paul's Hospital >> Tel: 604 682 2344 x62129 >> Fax: 604 806 9274 >> >> ***CONFIDENTIALITY NOTICE*** >> This electronic message is intended only for the use of the addressee >> and may contain information that is privileged and confidential. Any >> dissemination, distribution or copying of this communication by >> unauthorized individuals is strictly prohibited. If you have received >> this communication in error, please notify the sender immediately by >> reply e-mail and delete the original and all copies from your system. >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 039 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------ > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Sergio Ram?rez Ram?rez Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 "Short-term decisions tend to fail in the long-term." Frank Herbert, God Emperor of Dune From sylvie.huchet at enst-bretagne.fr Tue Feb 12 14:38:31 2008 From: sylvie.huchet at enst-bretagne.fr (Sylvie Huchet) Date: Tue, 12 Feb 2008 15:38:31 +0100 Subject: [MOBY-dev] createInstanceFromDOM Message-ID: <47B1AF67.4040604@enst-bretagne.fr> Hi, I would like to create a biomoby instance from a file that contains data. The data file is an XML file that comply (or should comply) with biomoby format. I thought that if the file contained a data type that is not a biomoby data type (doesn't belong to the object ontology), the createInstanceFromDOM method would throw an exception, but that is not the case. A NullPointerException is thrown by an inner method (MobyDatacomposite constructor). Should I use another method to check that the data type present in the data file is correct or is it a problem with createInstanceFromDOM that should throw an exception ? Thanks, and Best regards, Sylvie. -------------- next part -------------- A non-text attachment was scrubbed... Name: sylvie.huchet.vcf Type: text/x-vcard Size: 215 bytes Desc: not available URL: From gordonp at ucalgary.ca Wed Feb 13 01:03:23 2008 From: gordonp at ucalgary.ca (gordonp at ucalgary.ca) Date: Tue, 12 Feb 2008 18:03:23 -0700 (MST) Subject: [MOBY-dev] createInstanceFromDOM In-Reply-To: <47B1AF67.4040604@enst-bretagne.fr> References: <47B1AF67.4040604@enst-bretagne.fr> Message-ID: <41259.122.26.202.49.1202864603.squirrel@122.26.202.49> Hi Sylvie, If you send me the example XML, that will help me determine the issue. It should be able to parse the data, even if the datatypes are not in the ontology. Regards, Paul If you could send the example file to me, it would > Hi, > > I would like to create a biomoby instance from a file that contains data. > > The data file is an XML file that comply (or should comply) with biomoby > format. > I thought that if the file contained a data type that is not a biomoby > data type > (doesn't belong to the object ontology), the createInstanceFromDOM method > would > throw an exception, but that is not the case. A NullPointerException is > thrown > by an inner method (MobyDatacomposite constructor). > > Should I use another method to check that the data type present in the > data file > is correct or is it a problem with createInstanceFromDOM that should throw > an > exception ? > > Thanks, and > Best regards, > Sylvie. > > > !DSPAM:60005,47b1bec010950204642575! > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > !DSPAM:60005,47b1bec010950204642575! > From markw at illuminae.com Wed Feb 13 02:54:27 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 12 Feb 2008 18:54:27 -0800 Subject: [MOBY-dev] Decisions from the BioHackathon Message-ID: Hi all, Since we have a quorum of the RFC committee here at the Open BioHackathon, we've managed to make quite a few decisions, and we're now in the process of coding them. Here are the decisions in a nutshell: 1) The RFC from INB regarding mirroring of services was accepted with a few changes. We'll get a copy of the revised proposal from Oswaldo in the next few days. Apparently they have already coded support for these changes at INB so it will quickly get into the codebase. 2) Moby will *immediately* start supporting document-literal services. These services will be identified using the "Category" tag in the service registration/discovery XML. Two new categories will be "doc-literal" and "doc-literal-async". Until we get better support for document-literal services in Perl it is likely that these will not be available to Perl clients, but apparently it's no problem in Java. Some considerations that arise from this are: (a) you must now remove the XML header from your data if you're using document-literal, and therefore (b) clients and services need to specify the appropriate character encoding (e.g. UTF-8) in the SOAP XML header. 3) Sending data by reference: we have decided to allow the sending of data by reference rather than as the content of an object. We'll write-up the formal specification of how to do this soon, but briefly the idea is that we will use the xlink XML attribute in a Moby Object XML <.... xlink=''/>. When that tag is present, it is assumed that the content of that node is available at the URI in that reference. During service registration a provider will indicate the various transport protocols they provide for creating references (e.g. http, ftp) and this will be discoverable during a registry query. If you don't indicate a protocol, then you are saying that you do not support pass-by-reference, and therefore all existing services are supported. When accessing a service, you indicate to the service provider that you want data to be passed by reference by adding an attribute in the mobyData block . The service provider then has the option of providing you references for any data they wish. The xlink attribute can appear at any level in your Moby object, such that some data may be passed in the object itself, while other data from the same object may be passed by reference. 4) Validating services: Moby will have several levels of validation: (1) ping, (2) does the service crash when accesed with sample data? (3) does the service output the correct object type? (4) does the service output data that validates against XPath and/or REGEX. The sample input data will be in the service provider's RDF, and there will be several new predicates added to the RDF (I'll provide the OWL file shortly that defines how these predicates are to be used): unit_test, example_input, valid_xpath, valid_regex, valid_output_xml. The validation of output XML will be canonicalized (i.e. xmldiff, not byte-identity) Hackers - please correct me if I have mis-represented anything. I'm working from Eddie's scribbled notes ;-) Hopefully we'll find time to document these changes between our hacking sessions :-) Cheers all! Greetings from Tokyo! Mark From sylvie.huchet at enst-bretagne.fr Wed Feb 13 08:05:14 2008 From: sylvie.huchet at enst-bretagne.fr (Sylvie Huchet) Date: Wed, 13 Feb 2008 09:05:14 +0100 Subject: [MOBY-dev] createInstanceFromDOM In-Reply-To: <41259.122.26.202.49.1202864603.squirrel@122.26.202.49> References: <47B1AF67.4040604@enst-bretagne.fr> <41259.122.26.202.49.1202864603.squirrel@122.26.202.49> Message-ID: <47B2A4BA.3020202@enst-bretagne.fr> Hi Paul, Below is the XML file containing the parameters I want to send to a Biomoby service. With this XML file, I created a DOM object that I use to create a MobyContentInstance (this mobycontentInstance should then be used to fill the data field of a mobyRequest). As the simple parameter contains data of a wrong type, I thought I could catch a MOBYException during the MobycontentInstance constructor call. But the inner MobyDatacomposite constructor throws a NullPointerException. Thanks for hour help, Sylvie. 8 6 Alpha1 AAGAAG Alpha2 AAGAAG Beta1 AAGGGG Beta2 AAGGGG Gamma1 AGGAAG Gamma2 AGGAAG Delta GGAGGA Epsilon GGAAAG no 100 1000 no 1.0 1 gordonp at ucalgary.ca a ?crit : > Hi Sylvie, > > If you send me the example XML, that will help me determine the issue. > It should be able to parse the data, even if the datatypes are not in the > ontology. > > Regards, > > Paul > > If you could send the example file to me, it would > > >>Hi, >> >>I would like to create a biomoby instance from a file that contains data. >> >>The data file is an XML file that comply (or should comply) with biomoby >>format. >>I thought that if the file contained a data type that is not a biomoby >>data type >>(doesn't belong to the object ontology), the createInstanceFromDOM method >>would >>throw an exception, but that is not the case. A NullPointerException is >>thrown >>by an inner method (MobyDatacomposite constructor). >> >>Should I use another method to check that the data type present in the >>data file >>is correct or is it a problem with createInstanceFromDOM that should throw >>an >>exception ? >> >>Thanks, and >>Best regards, >>Sylvie. >> >> >>!DSPAM:60005,47b1bec010950204642575! >>_______________________________________________ >>MOBY-dev mailing list >>MOBY-dev at lists.open-bio.org >>http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> >>!DSPAM:60005,47b1bec010950204642575! >> > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > -------------- next part -------------- A non-text attachment was scrubbed... Name: sylvie.huchet.vcf Type: text/x-vcard Size: 215 bytes Desc: not available URL: From gordonp at ucalgary.ca Wed Feb 13 09:33:09 2008 From: gordonp at ucalgary.ca (gordonp at ucalgary.ca) Date: Wed, 13 Feb 2008 02:33:09 -0700 (MST) Subject: [MOBY-dev] createInstanceFromDOM In-Reply-To: <47B2A4BA.3020202@enst-bretagne.fr> References: <47B1AF67.4040604@enst-bretagne.fr> <41259.122.26.202.49.1202864603.squirrel@122.26.202.49> <47B2A4BA.3020202@enst-bretagne.fr> Message-ID: <53820.122.26.202.49.1202895189.squirrel@122.26.202.49> Hi Sylvie, I've fixed it to throw an explanatory MobyException. Regards, Paul > Hi Paul, > > Below is the XML file containing the parameters I want to send to a > Biomoby service. > With this XML file, I created a DOM object that I use to create a > MobyContentInstance (this mobycontentInstance should then be used to fill > the > data field of a mobyRequest). > As the simple parameter contains data of a wrong type, I thought I could > catch a > MOBYException during the MobycontentInstance constructor call. But the > inner > MobyDatacomposite constructor throws a NullPointerException. > > Thanks for hour help, > Sylvie. > > > > > > > > moby:id="" > moby:namespace=""> > moby:articleName="content">8 > 6 > Alpha1 AAGAAG > Alpha2 AAGAAG > Beta1 AAGGGG > Beta2 AAGGGG > Gamma1 AGGAAG > Gamma2 AGGAAG > Delta GGAGGA > Epsilon GGAAAG > > > > > no > > > 100 > > > 1000 > > > no > > > 1.0 > > > 1 > > > > > > gordonp at ucalgary.ca a ?crit : >> Hi Sylvie, >> >> If you send me the example XML, that will help me determine the issue. >> It should be able to parse the data, even if the datatypes are not in >> the >> ontology. >> >> Regards, >> >> Paul >> >> If you could send the example file to me, it would >> >> >>>Hi, >>> >>>I would like to create a biomoby instance from a file that contains >>> data. >>> >>>The data file is an XML file that comply (or should comply) with >>> biomoby >>>format. >>>I thought that if the file contained a data type that is not a biomoby >>>data type >>>(doesn't belong to the object ontology), the createInstanceFromDOM >>> method >>>would >>>throw an exception, but that is not the case. A NullPointerException is >>>thrown >>>by an inner method (MobyDatacomposite constructor). >>> >>>Should I use another method to check that the data type present in the >>>data file >>>is correct or is it a problem with createInstanceFromDOM that should >>> throw >>>an >>>exception ? >>> >>>Thanks, and >>>Best regards, >>>Sylvie. >>> >>> >>> >>>_______________________________________________ >>>MOBY-dev mailing list >>>MOBY-dev at lists.open-bio.org >>>http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >>> >>>!DSPAM:60005,47b1bec010950204642575! >>> >> >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> > > > !DSPAM:60005,47b2a29c109502586129532! > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > !DSPAM:60005,47b2a29c109502586129532! > From martin.senger at gmail.com Wed Feb 13 14:20:51 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 13 Feb 2008 23:20:51 +0900 Subject: [MOBY-dev] changes in jMoby may cause some disruptions Message-ID: <4d93f07c0802130620i7219d706g68f06cfeb2f22047@mail.gmail.com> Dear moby developers, Some jMoby developers are this week in a Biohackathlon meeting. We are rearranging jMoby modules (not that much the code itself but the way how the jMoby is built, etc.). This may cause a day or two disruptions. Sorry for any inconvenience. We will inform the list when we are done. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From sylvie.huchet at enst-bretagne.fr Wed Feb 13 14:36:16 2008 From: sylvie.huchet at enst-bretagne.fr (Sylvie Huchet) Date: Wed, 13 Feb 2008 15:36:16 +0100 Subject: [MOBY-dev] createInstanceFromDOM In-Reply-To: <53820.122.26.202.49.1202895189.squirrel@122.26.202.49> References: <47B1AF67.4040604@enst-bretagne.fr> <41259.122.26.202.49.1202864603.squirrel@122.26.202.49> <47B2A4BA.3020202@enst-bretagne.fr> <53820.122.26.202.49.1202895189.squirrel@122.26.202.49> Message-ID: <47B30060.8080607@enst-bretagne.fr> Thanks Paul, Now it works. Sylvie. gordonp at ucalgary.ca a ?crit : > Hi Sylvie, > > I've fixed it to throw an explanatory MobyException. > > Regards, > > Paul > > >>Hi Paul, >> >>Below is the XML file containing the parameters I want to send to a >>Biomoby service. >>With this XML file, I created a DOM object that I use to create a >>MobyContentInstance (this mobycontentInstance should then be used to fill >>the >>data field of a mobyRequest). >>As the simple parameter contains data of a wrong type, I thought I could >>catch a >>MOBYException during the MobycontentInstance constructor call. But the >>inner >>MobyDatacomposite constructor throws a NullPointerException. >> >>Thanks for hour help, >>Sylvie. >> >> >> >> >> >> >> >> >moby:id="" >>moby:namespace=""> >> >moby:articleName="content">8 >> 6 >>Alpha1 AAGAAG >>Alpha2 AAGAAG >>Beta1 AAGGGG >>Beta2 AAGGGG >>Gamma1 AGGAAG >>Gamma2 AGGAAG >>Delta GGAGGA >>Epsilon GGAAAG >> >> >> >> >> no >> >> >> 100 >> >> >> 1000 >> >> >> no >> >> >> 1.0 >> >> >> 1 >> >> >> >> >> >>gordonp at ucalgary.ca a ?crit : >> >>>Hi Sylvie, >>> >>> If you send me the example XML, that will help me determine the issue. >>>It should be able to parse the data, even if the datatypes are not in >>>the >>>ontology. >>> >>>Regards, >>> >>>Paul >>> >>>If you could send the example file to me, it would >>> >>> >>> >>>>Hi, >>>> >>>>I would like to create a biomoby instance from a file that contains >>>>data. >>>> >>>>The data file is an XML file that comply (or should comply) with >>>>biomoby >>>>format. >>>>I thought that if the file contained a data type that is not a biomoby >>>>data type >>>>(doesn't belong to the object ontology), the createInstanceFromDOM >>>>method >>>>would >>>>throw an exception, but that is not the case. A NullPointerException is >>>>thrown >>>>by an inner method (MobyDatacomposite constructor). >>>> >>>>Should I use another method to check that the data type present in the >>>>data file >>>>is correct or is it a problem with createInstanceFromDOM that should >>>>throw >>>>an >>>>exception ? >>>> >>>>Thanks, and >>>>Best regards, >>>>Sylvie. >>>> >>>> >>>> >>>>_______________________________________________ >>>>MOBY-dev mailing list >>>>MOBY-dev at lists.open-bio.org >>>>http://lists.open-bio.org/mailman/listinfo/moby-dev >>>> >>>> >>>>!DSPAM:60005,47b1bec010950204642575! >>>> >>> >>> >>> >>>_______________________________________________ >>>MOBY-dev mailing list >>>MOBY-dev at lists.open-bio.org >>>http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >>> >> >> >>!DSPAM:60005,47b2a29c109502586129532! >>_______________________________________________ >>MOBY-dev mailing list >>MOBY-dev at lists.open-bio.org >>http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> >>!DSPAM:60005,47b2a29c109502586129532! >> > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > -------------- next part -------------- A non-text attachment was scrubbed... Name: sylvie.huchet.vcf Type: text/x-vcard Size: 215 bytes Desc: not available URL: From dmitry.repchevski at bsc.es Wed Feb 13 16:56:25 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 13 Feb 2008 17:56:25 +0100 Subject: [MOBY-dev] Decisions from the BioHackathon In-Reply-To: References: Message-ID: <47B32139.1070605@bsc.es> Hello, As a java developer I'm completely happy with document-literal services. Should I understand that from this moment all *new* services should be preferably document-literal ones? > Some considerations that > arise from this are: (a) you must now remove the XML header from your > data if you're using document-literal, and therefore (b) clients and > services need to specify the appropriate character encoding (e.g. UTF-8) > in the SOAP XML header. > Could someone explain this please? Now Moby passes the Moby part (xml) as a String SOAP parameter. What changes if I pass this string using "document-literal" encoding? The service still needs to parse the "moby" XML. Cheers, Dmitry From edward.kawas at gmail.com Wed Feb 13 23:11:13 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 13 Feb 2008 15:11:13 -0800 Subject: [MOBY-dev] people hosting perl registries Message-ID: <47b37924.1e078e0a.4939.fffffb01@mx.google.com> This morning I discovered a bug in the caching code for Namespace RDF and promptly fixed it. If you are hosting a pure Perl based registry and you are aware of clients that use RDF with your registry, I would advise you to think about updating the core codebase. The problem is that the RDF served by the registry for namespaces never updates regardless of whether or not namespaces have been added/removed from the registry. If you need any other information, please let me know! Eddie From johan at ac.uma.es Fri Feb 15 12:14:26 2008 From: johan at ac.uma.es (Johan Karlsson) Date: Fri, 15 Feb 2008 13:14:26 +0100 Subject: [MOBY-dev] Decisions from the BioHackathon In-Reply-To: References: Message-ID: <47B58222.1000404@ac.uma.es> Mark Wilkinson wrote: > 1) The RFC from INB regarding mirroring of services was accepted with > a few changes. We'll get a copy of the revised proposal from Oswaldo > in the next few days. Apparently they have already coded support for > these changes at INB so it will quickly get into the codebase. Dear all, We are working on an updated version of the proposal which we plan to have ready in a week. Kind regards, Johan -- Johan Karlsson Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.10 29071 M?laga (Spain) +34 95 213 7236 From johan at ac.uma.es Fri Feb 15 12:14:26 2008 From: johan at ac.uma.es (Johan Karlsson) Date: Fri, 15 Feb 2008 13:14:26 +0100 Subject: [MOBY-dev] Decisions from the BioHackathon In-Reply-To: References: Message-ID: <47B58222.1000404@ac.uma.es> Mark Wilkinson wrote: > 1) The RFC from INB regarding mirroring of services was accepted with > a few changes. We'll get a copy of the revised proposal from Oswaldo > in the next few days. Apparently they have already coded support for > these changes at INB so it will quickly get into the codebase. Dear all, We are working on an updated version of the proposal which we plan to have ready in a week. Kind regards, Johan -- Johan Karlsson Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.10 29071 M?laga (Spain) +34 95 213 7236 From martin.senger at gmail.com Mon Feb 18 00:20:39 2008 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 18 Feb 2008 08:20:39 +0800 Subject: [MOBY-dev] Decisions from the BioHackathon In-Reply-To: <47B32139.1070605@bsc.es> References: <47B32139.1070605@bsc.es> Message-ID: <4d93f07c0802171620m145495f9vd6b1d98811415193@mail.gmail.com> > Could someone explain this please? > What do you want to explain? I guess that if there is anything to explain more than Mark did we may be wrong, after all, and actually it could be you who can explain us where we got it wrong :-) > Now Moby passes the Moby part (xml) as a String SOAP parameter. What > changes if I pass this string using "document-literal" encoding? My (a bit vague) understanding of the document/literal style is that the message payload becomes an integral part of the whole SOAP message. Therefore, the payload itself cannot start with " Hi, Eclipse / ant is complaining about the it says 'Reference dependency.classpath not found' ... this could be the problem why the task 'generate-datatypes' fails. I remember Martin talking something about this dependency.classpaths and runtime.classpaths or so... do I need to define it somewhere ?! best andreas From groscurt at mpiz-koeln.mpg.de Mon Feb 18 08:57:22 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 18 Feb 2008 09:57:22 +0100 Subject: [MOBY-dev] current problems with JMoby In-Reply-To: <4d93f07c0802171620m145495f9vd6b1d98811415193@mail.gmail.com> References: <47B32139.1070605@bsc.es> <4d93f07c0802171620m145495f9vd6b1d98811415193@mail.gmail.com> Message-ID: <47B94872.9000004@mpiz-koeln.mpg.de> Hi, I currently have a look in our new jmoby building process to find out if everything works, which is not the case ;-) The following things make me think or needs to be fixed: 1. In some ant tasks the jmoby-others.jar is still mentioned... did we agree to delete that (and as far as i see, it is not created at all in the 'jars' task) 2. The overview of the different ant tasks in Eclipse is weird (it shows the tasks and the build file which they come from) - 'bindist-mobysync' comes from 'seahawkBuild', 'install' from 'null' and 'jar-rdfagent' from 'qt'.... so this is not quite right at all.... anyone an idea why this is coming from what ? 3. Generating the datatypes failes (neither in dashboard nor via the 'generate-datatype' task). It complaines generate-datatypes: [Data Types] java.lang.NoClassDefFoundError: org/tulsoft/tools/BaseCmdLine [Data Types] Exception in thread "main" the class should be in alltools.jar, shouldnt it ? in my maven repository there is the alltools-2.1.1.jar. But neither in dashboard nor via the console the task generate-datatypes work. Any hints, comments, suggestions :-) Best andreas From groscurt at mpiz-koeln.mpg.de Mon Feb 18 09:29:01 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 18 Feb 2008 10:29:01 +0100 Subject: [MOBY-dev] Happy error world Message-ID: <200802181029.01615.groscurt@mpiz-koeln.mpg.de> Hiho, debugging the new building system the something part (maybe all these errors occur becaus i miss something....) I checked out moby fresh from cvs and after 'boostrap' I started "install". BUILD FAILED /home/pcb/groscurt/workspace/Moby/xmls/maven.xml:91: Unable to resolve artifact: Missing: ---------- 1) javax.jws:jsr181-api:jar:1.0-MR1 Try downloading the file manually from the project website. Then, install it using the command: mvn install:install-file -DgroupId=javax.jws -DartifactId=jsr181-api -Dversion=1.0-MR1 -Dpackaging=jar -Dfile=/path/to/file Alternatively, if you host your own repository you can deploy the file there: mvn deploy:deploy-file -DgroupId=javax.jws -DartifactId=jsr181-api -Dversion=1.0-MR1 -Dpackaging=jar -Dfile=/path/to/file -Durl=[url] -DrepositoryId=[id] Path to dependency: 1) org.biomoby:jmoby:jar:1.0.0 2) javax.jws:jsr181-api:jar:1.0-MR1 2) com.sun.xml.ws:jaxws-tools:jar:2.1.3 Try downloading the file manually from the project website. Then, install it using the command: mvn install:install-file -DgroupId=com.sun.xml.ws -DartifactId=jaxws-tools -Dversion=2.1.3 -Dpackaging=jar -Dfile=/path/to/file Alternatively, if you host your own repository you can deploy the file there: mvn deploy:deploy-file -DgroupId=com.sun.xml.ws -DartifactId=jaxws-tools -Dversion=2.1.3 -Dpackaging=jar -Dfile=/path/to/file -Durl=[url] -DrepositoryId=[id] Path to dependency: 1) org.biomoby:jmoby:jar:1.0.0 2) com.sun.xml.ws:jaxws-tools:jar:2.1.3 ---------- 2 required artifacts are missing. for artifact: org.biomoby:jmoby:jar:1.0.0 from the specified remote repositories: central (http://repo1.maven.org/maven2), java.net-m2 (http://download.java.net/maven/2), java.net (https://maven-repository.dev.java.net/repository/), hpl.hp.repository (http://jena.hpl.hp.com/repo/), bio.maven.repository (http://biomoby.org/m2repo/) Would be great to help me out here :) Best andreas PS: more probably to come ;-) -- Andreas Groscurth Bioinformatics Developer Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-449 From martin.senger at gmail.com Mon Feb 18 09:56:22 2008 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 18 Feb 2008 17:56:22 +0800 Subject: [MOBY-dev] dependency.classpath not found In-Reply-To: <47B94B85.6080800@mpiz-koeln.mpg.de> References: <47B94B85.6080800@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0802180156u4996a316waaacf1989cf9e7fd@mail.gmail.com> > it says 'Reference dependency.classpath not found' ... this could be the > problem why the task 'generate-datatypes' fails. > > I remember Martin talking something about this dependency.classpaths and > runtime.classpaths or so... do I need to define it somewhere ?! > No, you don't. Let me fix it. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From dmitry.repchevski at bsc.es Mon Feb 18 09:57:45 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Mon, 18 Feb 2008 10:57:45 +0100 Subject: [MOBY-dev] Decisions from the BioHackathon In-Reply-To: <4d93f07c0802171620m145495f9vd6b1d98811415193@mail.gmail.com> References: <4d93f07c0802171620m145495f9vd6b1d98811415193@mail.gmail.com> Message-ID: <47B95699.8080707@bsc.es> Hello Martin, > My (a bit vague) understanding of the document/literal style is that the > message payload becomes an integral part of the whole SOAP message. > Therefore, the payload itself cannot start with If I understand you correct, the proposal is to use the MobyMessage itself as a payload and not the String as it is now. COOL!!! This could makes happy. So actually the Java method would looks like: MobyMessage runMyService(MobeMessage msg); So, actually we are moving to XML Schema message representation (which is EXACTLY that my API does). In this case WSDL would have XML Schema for the message (which would be the same for ANY "doc-literal" service when MobyObject would be represented as XML ANY type, but this is the problem of representing an ontology object in XML schema and, IMHO, we can do nothing with it.). Here is the possible WSDL with MobyMessage XML Schema: ********************************************************************************************* ********************************************************************************************* This WSDL is AUTOMATICALLY generated for the Service: ********************************************************************************************* package es.bsc.inb.ejb.moby; import javax.jws.WebService; import javax.ejb.Stateless; import org.biomoby.shared.jaxb.messages.MobyMessage; @Stateless() @WebService() public class MobyDocWebService { public MobyMessage runMyService(MobyMessage msg) { return msg; } } ********************************************************************************************* Cheers, Dmitry From martin.senger at gmail.com Mon Feb 18 09:59:17 2008 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 18 Feb 2008 17:59:17 +0800 Subject: [MOBY-dev] current problems with JMoby In-Reply-To: <47B94872.9000004@mpiz-koeln.mpg.de> References: <47B32139.1070605@bsc.es> <4d93f07c0802171620m145495f9vd6b1d98811415193@mail.gmail.com> <47B94872.9000004@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0802180159p26e2fb82p44422993a56fa1bd@mail.gmail.com> > 1. In some ant tasks the jmoby-others.jar is still mentioned... did we > agree to delete that (and as far as i see, it is not created at all in > the 'jars' task) I will fix this. > 2. The overview of the different ant tasks in Eclipse is weird (it shows > the tasks and the build file which they come from) - 'bindist-mobysync' > comes from 'seahawkBuild', 'install' from 'null' and 'jar-rdfagent' from > 'qt'.... so this is not quite right at all.... anyone an idea why this > is coming from what ? I suggest you to try to fix it. You are our Mr. Eclipese :-) > 3. Generating the datatypes failes (neither in dashboard nor via the > 'generate-datatype' task). It complaines > My fix - I will do it. Thanks for going through the testing. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Mon Feb 18 10:00:59 2008 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 18 Feb 2008 18:00:59 +0800 Subject: [MOBY-dev] Happy error world In-Reply-To: <200802181029.01615.groscurt@mpiz-koeln.mpg.de> References: <200802181029.01615.groscurt@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0802180200s54222c2eh3351e7cb0c5fcd4@mail.gmail.com> > BUILD FAILED > /home/pcb/groscurt/workspace/Moby/xmls/maven.xml:91: Unable to resolve > artifact: Missing: > ---------- > 1) javax.jws:jsr181-api:jar:1.0-MR1 I thought that we had fixed this. I will look at it. What version of java are you using? Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Mon Feb 18 10:09:31 2008 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 18 Feb 2008 18:09:31 +0800 Subject: [MOBY-dev] Decisions from the BioHackathon In-Reply-To: <47B95699.8080707@bsc.es> References: <4d93f07c0802171620m145495f9vd6b1d98811415193@mail.gmail.com> <47B95699.8080707@bsc.es> Message-ID: <4d93f07c0802180209t6932d6feu9e8011ae5b87ad7a@mail.gmail.com> > If I understand you correct, the proposal is to use the MobyMessage > itself as a payload and not the String as it is now. What is the "MobyMessage"? Never heard this term. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From groscurt at mpiz-koeln.mpg.de Mon Feb 18 10:12:04 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 18 Feb 2008 11:12:04 +0100 Subject: [MOBY-dev] Happy error world In-Reply-To: <4d93f07c0802180200s54222c2eh3351e7cb0c5fcd4@mail.gmail.com> References: <200802181029.01615.groscurt@mpiz-koeln.mpg.de> <4d93f07c0802180200s54222c2eh3351e7cb0c5fcd4@mail.gmail.com> Message-ID: <200802181112.05047.groscurt@mpiz-koeln.mpg.de> On Monday 18 February 2008 11:00, Martin Senger wrote: > > BUILD FAILED > > /home/pcb/groscurt/workspace/Moby/xmls/maven.xml:91: Unable to resolve > > artifact: Missing: > > ---------- > > 1) javax.jws:jsr181-api:jar:1.0-MR1 > > I thought that we had fixed this. I will look at it. What version of java > are you using? > > Martin Version i use: java version "1.5.0_06" Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_06-b05) Java HotSpot(TM) 64-Bit Server VM (build 1.5.0_06-b05, mixed mode) thanks martin -- Andreas Groscurth Bioinformatics Developer Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-449 From Pieter.Neerincx at wur.nl Mon Feb 18 10:40:46 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Mon, 18 Feb 2008 11:40:46 +0100 Subject: [MOBY-dev] Decisions from the BioHackathon In-Reply-To: References: Message-ID: <3BD9524C-096C-43E0-8C67-3C14E496129B@wur.nl> Hi All, This is very good news*4! Looks like it's been a fruitful event :). Cheers, Pi On 13 Feb 2008, at 03:54, Mark Wilkinson wrote: > Hi all, > > Since we have a quorum of the RFC committee here at the Open > BioHackathon, we've managed to make quite a few decisions, and > we're now in the process of coding them. > > Here are the decisions in a nutshell: > > 1) The RFC from INB regarding mirroring of services was accepted > with a few changes. We'll get a copy of the revised proposal from > Oswaldo in the next few days. Apparently they have already coded > support for these changes at INB so it will quickly get into the > codebase. > > 2) Moby will *immediately* start supporting document-literal > services. These services will be identified using the "Category" > tag in the service registration/discovery XML. Two new categories > will be "doc-literal" and "doc-literal-async". Until we get better > support for document-literal services in Perl it is likely that > these will not be available to Perl clients, but apparently it's no > problem in Java. Some considerations that arise from this are: > (a) you must now remove the XML header from your data if you're > using document-literal, and therefore (b) clients and services need > to specify the appropriate character encoding (e.g. UTF-8) in the > SOAP XML header. > > 3) Sending data by reference: we have decided to allow the > sending of data by reference rather than as the content of an > object. We'll write-up the formal specification of how to do this > soon, but briefly the idea is that we will use the xlink XML > attribute in a Moby Object XML <.... xlink=''/>. When that tag is > present, it is assumed that the content of that node is available > at the URI in that reference. During service registration a > provider will indicate the various transport protocols they provide > for creating references (e.g. http, ftp) and this will be > discoverable during a registry query. If you don't indicate a > protocol, then you are saying that you do not support pass-by- > reference, and therefore all existing services are supported. When > accessing a service, you indicate to the service provider that you > want data to be passed by reference by adding an attribute in the > mobyData block . The service > provider then has the option of providing you references for any > data they wish. The xlink attribute can appear at any level in > your Moby object, such that some data may be passed in the object > itself, while other data from the same object may be passed by > reference. > > 4) Validating services: Moby will have several levels of > validation: (1) ping, (2) does the service crash when accesed with > sample data? (3) does the service output the correct object > type? (4) does the service output data that validates against > XPath and/or REGEX. The sample input data will be in the service > provider's RDF, and there will be several new predicates added to > the RDF (I'll provide the OWL file shortly that defines how these > predicates are to be used): unit_test, example_input, valid_xpath, > valid_regex, valid_output_xml. The validation of output XML will > be canonicalized (i.e. xmldiff, not byte-identity) > > > Hackers - please correct me if I have mis-represented anything. > I'm working from Eddie's scribbled notes ;-) > > Hopefully we'll find time to document these changes between our > hacking sessions :-) > > Cheers all! Greetings from Tokyo! > > Mark > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------- From dmitry.repchevski at bsc.es Mon Feb 18 11:15:21 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Mon, 18 Feb 2008 12:15:21 +0100 Subject: [MOBY-dev] Decisions from the BioHackathon In-Reply-To: <4d93f07c0802180209t6932d6feu9e8011ae5b87ad7a@mail.gmail.com> References: <4d93f07c0802180209t6932d6feu9e8011ae5b87ad7a@mail.gmail.com> Message-ID: <47B968C9.9060400@bsc.es> > > What is the "MobyMessage"? Never heard this term. > Martin It's my own java Moby API... Actually it's a little more when JAXB annotated classes for Moby messages... Since it's based on XML Schema (JAXB) it perfectly integrates into latest standard Java API. You can read more at http://inb.bsc.es/java/index.html. I'm continuously improving it... Cheers, Dmitry From dmitry.repchevski at bsc.es Tue Feb 19 11:03:10 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 19 Feb 2008 12:03:10 +0100 Subject: [MOBY-dev] document/literal services Message-ID: <47BAB76E.90904@bsc.es> Hello all, I'm still trying to figure out what is the decision was made about support of document/literal services. Q1. Does it mean that we can use Moby message as a payload? Hope so... Q2. Which parameter style to use (wrapped/unwrapped)? IMHO having only one parameter IN and one OUT, Unwrapped is better. Yours sincerely, Dmitry From groscurt at mpiz-koeln.mpg.de Tue Feb 19 14:53:55 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 19 Feb 2008 15:53:55 +0100 Subject: [MOBY-dev] JMoby.... In-Reply-To: <47BAB76E.90904@bsc.es> References: <47BAB76E.90904@bsc.es> Message-ID: <47BAED83.2010801@mpiz-koeln.mpg.de> Hiho, I dont know whether Martin fixed it or its just working mostly now... With a new checkout eclipse is able to set up a project and getting the libraries and starting dashboard.... this didnt work last time. Also the simple client is working, but MoSeS not - still got the generate-datatypes: [Data Types] java.lang.NoClassDefFoundError: org/tulsoft/tools/BaseCmdLine [Data Types] Exception in thread "main" Also Eclipse complains about 'Reference dependency.classpath not found - but besides that the building process works now (windows & eclipse) best and thanks andreas From edward.kawas at gmail.com Tue Feb 19 15:03:02 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 19 Feb 2008 07:03:02 -0800 Subject: [MOBY-dev] JMoby.... In-Reply-To: <47BAED83.2010801@mpiz-koeln.mpg.de> References: <47BAB76E.90904@bsc.es> <47BAED83.2010801@mpiz-koeln.mpg.de> Message-ID: <47baefa9.1cef600a.2d62.2f6a@mx.google.com> Hi Andreas, I can confirm that at the very least, ant bootstrap, ant compile, ant dashboard, and ant generate-datatypes work on windows from the command line. When I try to generate service skeletons in dashboard, I get the following: generate-services: [Service(s)] Using filter for authorities: '^arexdb.org$' [Service(s)] Generating services into 'c:\moby-live\Java\generated\skeletons'... [Service(s)] Reading service names... [Service(s)] getGOCollection (arexdb.org) [Service(s)] getAREXGFPImageCollection (arexdb.org) [Service(s)] Generated 2 service skeletons. BUILD FAILED c:\moby-live\Java\xmls\maven.xml:85: java.lang.NullPointerException Also, when I generate datatypes from within dashboard, I also get the null pointer exception mentioned above. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth Sent: February-19-08 6:54 AM To: Core developer announcements Subject: [MOBY-dev] JMoby.... Hiho, I dont know whether Martin fixed it or its just working mostly now... With a new checkout eclipse is able to set up a project and getting the libraries and starting dashboard.... this didnt work last time. Also the simple client is working, but MoSeS not - still got the generate-datatypes: [Data Types] java.lang.NoClassDefFoundError: org/tulsoft/tools/BaseCmdLine [Data Types] Exception in thread "main" Also Eclipse complains about 'Reference dependency.classpath not found - but besides that the building process works now (windows & eclipse) best and thanks andreas _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From dmitry.repchevski at bsc.es Tue Feb 19 15:23:41 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 19 Feb 2008 16:23:41 +0100 Subject: [MOBY-dev] JMoby.... In-Reply-To: <47BAED83.2010801@mpiz-koeln.mpg.de> References: <47BAED83.2010801@mpiz-koeln.mpg.de> Message-ID: <47BAF47D.5000104@bsc.es> Hello Andreas, Thank you for reply, but actually I do not use Eclipse, neither JMoby... Could we once and forever clarify the difference between specification and implementation. I have my own (not JMoby) API that could allow me to use a standard JAX-WS web-services if BioMoby team follows the standard. On the server side it could look like: ***************************** package es.bsc.inb.ejb.moby; import javax.jws.*; import javax.ejb.Stateless; import javax.jws.soap.SOAPBinding; import org.biomoby.shared.jaxb.messages.MobyMessage; @Stateless() @WebService() @SOAPBinding(style=SOAPBinding.Style.DOCUMENT, use=SOAPBinding.Use.LITERAL, parameterStyle=SOAPBinding.ParameterStyle.BARE) public class MobyDocWebService { @WebResult(name="result") public MobyMessage runMyService(@WebParam(name="request", mode = WebParam.Mode.IN) MobyMessage msg) { return msg; } } ***************************** This is the STANDARD JAX-WS endpoint. You can deploy it on ANY JEE5 Application server. The application server will generate and deploy the service automatically. Here is generated (by JBoss) wsdl: ***************************** ***************************** Having this you do not need even my API on the client side (you could generate it using the tool for your language) Well you still need an ontology which couldn't (?) be injected in wsdl... My API generates JAXB annotated ontology classes that JAX-WS automatically marshal/unmarshall. This is IF we would use Document/Literal encoding and not just a hack when we pass the XML String and have to parse it manually. Using Moby Message (the Moby XML that we pass as a string now) as a payload would allow us in future to explore the full power of SOAP (streaming, compression, WS-Addresing for TRULY asynchronous services through callbacks and so on). This is the question I'm asking: Are we going to use the same ugly hack (passing the XML string) for the document/literal or, finally, move on to the standard, interoperable Web Services? Best regards, Dmitry P.S. I'm afraid that JMoby has a hard time to support this... / / From groscurt at mpiz-koeln.mpg.de Tue Feb 19 15:37:01 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 19 Feb 2008 16:37:01 +0100 Subject: [MOBY-dev] JMoby.... In-Reply-To: <47BAF47D.5000104@bsc.es> References: <47BAED83.2010801@mpiz-koeln.mpg.de> <47BAF47D.5000104@bsc.es> Message-ID: <47BAF79D.6020508@mpiz-koeln.mpg.de> Dmitry Repchevsky wrote: > Hello Andreas, > > Thank you for reply, but actually I do not use Eclipse, neither JMoby... > Could we once and forever clarify the difference between specification > and implementation. aehh... what ? i didnt actually reply to your message... my email was about the new building process Martin setup up for JavaMoby... nothing to do with your implementation or what you wrote. I guess this is also important - but my mail was in no case any answer for your mail ;-) andreas From dmitry.repchevski at bsc.es Tue Feb 19 15:39:27 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 19 Feb 2008 16:39:27 +0100 Subject: [MOBY-dev] JMoby.... In-Reply-To: <47BAF79D.6020508@mpiz-koeln.mpg.de> References: <47BAF79D.6020508@mpiz-koeln.mpg.de> Message-ID: <47BAF82F.3070702@bsc.es> Oops... Sorry, it was in my thread, so I supposed it was a typical "look in the jmoby" style... Again, sorry for the tone... Dmitry From martin.senger at gmail.com Wed Feb 20 00:55:24 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 20 Feb 2008 08:55:24 +0800 Subject: [MOBY-dev] JMoby.... In-Reply-To: <47BAF47D.5000104@bsc.es> References: <47BAED83.2010801@mpiz-koeln.mpg.de> <47BAF47D.5000104@bsc.es> Message-ID: <4d93f07c0802191655x5825fd7sadb76247a5b01b32@mail.gmail.com> My dear Dmitry, Could we once and forever clarify the difference between specification > and implementation. Could we please once and forever clarify what is polite and what is not? Your emails are sometimes a bit aggressive (as are mine, probably) up to the point that they decrease motivation to respond to them. Just my 2c's. Regarding your comment, I am almost sure that the difference between specification and implementation is clear enough. It may not be the case about two years ago but today I do not see any discrepancies. What do you wish to clarify? > I have my own (not JMoby) API that could allow me to use a standard > JAX-WS web-services if BioMoby team follows the standard. > Between BioMoby developers, we usually save the word "API" to indicate the API defining an access to the BioMoby registry and to the BioMoby services. In other words, we usually refer to this API as to a language-independent interface, while "Java API" (or "jMoby API") is used only for Java developers - if they are interested to use it. It is, of course, up to them how they realize their access to the BioMoby entities. Regarding standards, we do our best in the changing world of standards. As you have been informed, during the last meeting we made steps to accept also the document/literal style and we are working on its implementation. But any good clients will need to support, now and in the future, both protocols, RPC/encoded and document/literal styles - we cannot afford to tell the service providers "please throw out your running services and start again". Therefore, if you are using only standard web-services style, your code is not smart enough to be worth to look at (see? - this is my bit of aggressivity :-)). Regarding other standard - the XML Schema (of the messages between client and services, not between clients and registry) - and the WSDL derived from the schema, I believe that you are not fully aware of the fact that there is no way to express the current BioMoby payload in the XML Schema (unless you change the schema with every request). Take it or leave it. Having said that does not mean that I am personally happy with it but c'est la vie. For BioMoby the future probably is in the RDF orientation and not to try go back to the compliancy with the XML Schema (Mark's words in my poor interpretation). But it would help people (like you) to understand why BioMoby payload cannot be fully expressed in an XML Schema if we document it. I believe that during the last meeting we agreed that the reasons why XML cannot be created will be documented soon (on the new BioMoby pages that are being created as we speak). Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Wed Feb 20 08:06:51 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 20 Feb 2008 16:06:51 +0800 Subject: [MOBY-dev] dependency.classpath not found In-Reply-To: <4d93f07c0802180156u4996a316waaacf1989cf9e7fd@mail.gmail.com> References: <47B94B85.6080800@mpiz-koeln.mpg.de> <4d93f07c0802180156u4996a316waaacf1989cf9e7fd@mail.gmail.com> Message-ID: <4d93f07c0802200006t6555bf54w3efc4049e1526bb9@mail.gmail.com> > it says 'Reference dependency.classpath not found' ... this could be the > > problem why the task 'generate-datatypes' fails. > > > Fixed (I believe :-)). Please make 'cvs update -dP'. Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Wed Feb 20 10:08:55 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 20 Feb 2008 18:08:55 +0800 Subject: [MOBY-dev] Happy error world In-Reply-To: <200802181029.01615.groscurt@mpiz-koeln.mpg.de> References: <200802181029.01615.groscurt@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0802200208m3e17fa2fu1d308d86d7b303a2@mail.gmail.com> Andreas, BUILD FAILED > /home/pcb/groscurt/workspace/Moby/xmls/maven.xml:91: Unable to resolve > artifact: Missing: > ---------- > 1) javax.jws:jsr181-api:jar:1.0-MR1 > I am afraid that I cannot reproduce your error. It simply works on my machine. Please try again: 1) Remove the two mentioned/problematic directories from your local maven repository. On the unix machine, they are: ~/.m2/repository/com/sun/xml/ws/jaxws-tools/2.1.3, and ~/.m2/repository/javax/jws/jsr181-api (under windows they are in the similar structure in your 'Documents and settings/...' directory). 2) Run: ant clean compile. I am correctly getting this (indicating that the just removed dependencies are downloaded again): initmaven: [artifact:dependencies] Downloading: javax.jws/poms/jsr181-api-1.0-MR1.pomfrom java.net [artifact:dependencies] Transferring 0K from java.net [artifact:dependencies] Downloading: com.sun.xml.ws/poms/jaxws-tools-2.1.3.pom from java.net [artifact:dependencies] Transferring 2K from java.net [artifact:dependencies] Downloading: javax.jws/jars/jsr181-api-1.0-MR1.jarfrom java.net [artifact:dependencies] Transferring 8K from java.net [artifact:dependencies] Downloading: com.sun.xml.ws/jars/jaxws-tools-2.1.3.jar from java.net [artifact:dependencies] Transferring 497K from java.net Do you still have the error? If not, try it in Eclipse... PS: more probably to come ;-) Have they came? Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From dmitry.repchevski at bsc.es Wed Feb 20 10:56:40 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 20 Feb 2008 11:56:40 +0100 Subject: [MOBY-dev] JMoby.... In-Reply-To: <4d93f07c0802191655x5825fd7sadb76247a5b01b32@mail.gmail.com> References: <4d93f07c0802191655x5825fd7sadb76247a5b01b32@mail.gmail.com> Message-ID: <47BC0768.50905@bsc.es> Dear Martin, Thank you for the reply. > Your emails are sometimes a bit aggressive (as are mine, probably) up to the > point that they decrease motivation to respond to them. I do not intend to offend anyone, but sometimes a provocative style is the only way I can get the response, unfortunately. (I've been asked several times the same question, but got the answer only to the last post, so subconscious I somehow decided that this is the way to get answered... sorry). As an example I would like to repeat the question I asked several times and still have no answer: Q: BioMoby doesn't use WSDL file to access the Web Services, so is there any specification about parameter names (example part name="request")? Ignoring the WSDL without explicit accordance in it makes virtually all BioMoby requests wrong and rejected by all modern Java webservices stacks (even it works in AXIS). It is as easy as to put "request parameter name must be 'request' and response must be named 'response'" into the "specification". ... sorry for the aggressiveness again ;-). > ...we usually refer to this API as to a language-independent > interface, while "Java API" (or "jMoby API") is used only for Java > developers - if they are interested to use it. Well there are two definition of API - specification and implementation, usually (in my experience) the API means concrete implementation of the specification, i accept that this could be different... Thank you to clarify this. > As you have been informed, during the last meeting we made steps to accept also > the document/literal style and we are working on its implementation. But any > good clients will need to support, now and in the future, both protocols, > RPC/encoded and document/literal styles - we cannot afford to tell the > service providers "please throw out your running services and start again". > Therefore, if you are using only standard web-services style, your code is > not smart enough to be worth to look at (see? - this is my bit of > aggressivity :-)). This is the case. My own implementation API (or package or how should I call it in BioMoby terms) is compatible both with rpc/encoded AND document/literal styles. :-) Strange I see nothing aggressive here... Maybe because I'm Russian :-) > Regarding other standard - the XML Schema (of the messages between client > and services, not between clients and registry) - and the WSDL derived from > the schema, I believe that you are not fully aware of the fact that there is > no way to express the current BioMoby payload in the XML Schema (unless you > change the schema with every request). Take it or leave it. Completely wrong! (oops, sorry :-)) I have WORKING implementation of it if you look in this thread. As I said it is impossible to put the ONTOLOGY in WSDL 1.1 (while it IS possible in WSDL 2.0), but to make XML Schema for Moby Messages is possible and what I am trying to explain for the last three months. Again my solution by now is to keep two parts separately - Moby Messages - a set of JAXB annotated classes that comply to "Moby Message" XML Schema and could be put into the WSDL Schema and Datatypes - a set of JAXB annotated classes that comply the "Ontology" XML Schema. The last one couldn't be put into WSDL 1.1, but are processed by JAX-WS automatically. > For BioMoby the future probably is in the RDF orientation and not to > try go back to the compliancy with the XML Schema (Mark's words in my poor > interpretation). But it would help people (like you) to understand why > BioMoby payload cannot be fully expressed in an XML Schema if we document > it. I believe that during the last meeting we agreed that the reasons why > XML cannot be created will be documented soon (on the new BioMoby pages that > are being created as we speak). I think there is a misunderstanding. The ontology itself can not be described by XML Schema (That's why OWL/RDF exist), but the serialization format CAN. Of course the problem is that in the WSDL schema there will be In place of concrete datatype, so it's up to the web-service protocol correctly marshall/unmarshall it. JAX-WS can do this. In my implementation if JAX-WS find some unknown type it substitutes it by special object "AnyMobyObject" keeping the total structure intact (so it can have some AminoAcidSequence object as an attribute for example). It is possible to make an implementation that in this case consult RDF or Biomoby Cental to dynamically generate the class, bu I see no reason in it, because there is no need in object when service/client has no idea about, but with "AnyMobyObject" they still can get all the properties. Well to be fair one reason is to cast this object to the known one... Yours sincerely, Dmitry From groscurt at mpiz-koeln.mpg.de Thu Feb 21 15:16:37 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 21 Feb 2008 16:16:37 +0100 Subject: [MOBY-dev] ready to release jMoby 1.0.0? In-Reply-To: <4d93f07c0802201630i6d0e958fxc16be9c568345ee6@mail.gmail.com> References: <4d93f07c0802200238p73f4e45bq7dd40a0085803c4c@mail.gmail.com> <47BC0471.7030507@mpiz-koeln.mpg.de> <47bc83c3.1498600a.5725.ffffc7b6@mx.google.com> <4d93f07c0802201630i6d0e958fxc16be9c568345ee6@mail.gmail.com> Message-ID: <47BD95D5.7030105@mpiz-koeln.mpg.de> Hi, you also have my OK. Somehow everything works although Eclipse / dashboard make some weird things. If I use the generate-datatypes task from eclipse or from console everything is fine. Calling it from Dashboard will generate all datatypes but when its finished it throws the NullPointerException C:\workspace\moby\xmls\maven.xml:85: java.lang.NullPointerException but even with that Nullpointer I do have all datatypes in the Eclipse project. calling the generate-services does fine via the ant tasks in eclipse or the console... calling it from dashboard will generate the skeleton but then fails because it always starts with generate-datatypes and breaks because of the NullPointer... The same tasks in Eclipse without Dashboard work fine... so have you any clue what the Nullpointer is about ? its in the maven.xml the line but in fact... when one knows what to do... it works ;-) so my ok btw - I commited the changed mobysync build file. best andreas Martin Senger wrote: > > I updated the agents build file and tested it some what. I > committed it. > > You have my 'A OK!' > > > Thanks! > > > For the doc, you mentioned that you were updating them > and that we should too. Have you committed your changes to the doc > yet? > > > Yes, I have. > > Cheers, > Martin > > -- > Martin Senger > email: martin.senger at gmail.com > m.senger at cgiar.org > skype: martinsenger From groscurt at mpiz-koeln.mpg.de Thu Feb 21 15:46:02 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 21 Feb 2008 16:46:02 +0100 Subject: [MOBY-dev] BioMoby goes openoffice ? In-Reply-To: <47BD95D5.7030105@mpiz-koeln.mpg.de> References: <4d93f07c0802200238p73f4e45bq7dd40a0085803c4c@mail.gmail.com> <47BC0471.7030507@mpiz-koeln.mpg.de> <47bc83c3.1498600a.5725.ffffc7b6@mx.google.com> <4d93f07c0802201630i6d0e958fxc16be9c568345ee6@mail.gmail.com> <47BD95D5.7030105@mpiz-koeln.mpg.de> Message-ID: <47BD9CBA.7000000@mpiz-koeln.mpg.de> Hi, I'm wondering... why does maven downloads several libs from openoffice ? I do have the feeling that since the maven dependencies we have lots more libs than before ? can someone explain that to me ? cheers andreas From edward.kawas at gmail.com Thu Feb 21 19:44:28 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 21 Feb 2008 11:44:28 -0800 Subject: [MOBY-dev] BioMoby goes openoffice ? In-Reply-To: <47BD9CBA.7000000@mpiz-koeln.mpg.de> References: <4d93f07c0802200238p73f4e45bq7dd40a0085803c4c@mail.gmail.com> <47BC0471.7030507@mpiz-koeln.mpg.de> <47bc83c3.1498600a.5725.ffffc7b6@mx.google.com> <4d93f07c0802201630i6d0e958fxc16be9c568345ee6@mail.gmail.com> <47BD95D5.7030105@mpiz-koeln.mpg.de> <47BD9CBA.7000000@mpiz-koeln.mpg.de> Message-ID: <47bdd4a6.1cef600a.361e.ffff939a@mx.google.com> Hi Andreas, I believe that seahawk uses the open office libs. Paul can confirm. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth Sent: February-21-08 7:46 AM To: Core developer announcements Subject: [MOBY-dev] BioMoby goes openoffice ? Hi, I'm wondering... why does maven downloads several libs from openoffice ? I do have the feeling that since the maven dependencies we have lots more libs than before ? can someone explain that to me ? cheers andreas _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Mon Feb 25 14:56:09 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 25 Feb 2008 07:56:09 -0700 Subject: [MOBY-dev] BioMoby goes openoffice ? In-Reply-To: <47bdd4a6.1cef600a.361e.ffff939a@mx.google.com> References: <4d93f07c0802200238p73f4e45bq7dd40a0085803c4c@mail.gmail.com> <47BC0471.7030507@mpiz-koeln.mpg.de> <47bc83c3.1498600a.5725.ffffc7b6@mx.google.com> <4d93f07c0802201630i6d0e958fxc16be9c568345ee6@mail.gmail.com> <47BD95D5.7030105@mpiz-koeln.mpg.de> <47BD9CBA.7000000@mpiz-koeln.mpg.de> <47bdd4a6.1cef600a.361e.ffff939a@mx.google.com> Message-ID: <47C2D709.2050602@ucalgary.ca> Yup, Seahawk can import Word, Excel, etc. files via an OpenOffice connectivity bridge (the actual conversion is done on our server, but several libs are needed for the connection). Edward Kawas wrote: > Hi Andreas, > > I believe that seahawk uses the open office libs. Paul can confirm. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth > Sent: February-21-08 7:46 AM > To: Core developer announcements > Subject: [MOBY-dev] BioMoby goes openoffice ? > > Hi, > > I'm wondering... why does maven downloads several libs from openoffice ? > I do have the feeling that since the maven dependencies we have lots > more libs than before ? > > can someone explain that to me ? > > cheers > andreas > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,47bdd28b109502142110999! > > > > From martin.senger at gmail.com Tue Feb 26 04:57:19 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 26 Feb 2008 12:57:19 +0800 Subject: [MOBY-dev] getting RDF resources in the compressed format Message-ID: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> Eddie, Paul, Mark et al, Because of the new implementation of the registry cache (written by Eddie) that uses RDF, the RDF resources will be more used (also from the Dashboard). To get them fast is, therefore, a priority. I remember that when the new method (to get URLs of the registry resources) was added to the BioMoby API we had discussed how to deliver these resources in a compressed format, as well. Has anybody remember how it was proposed to work? Because we definitely need to compress it now. Thanks, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From gordonp at ucalgary.ca Tue Feb 26 23:45:39 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 26 Feb 2008 16:45:39 -0700 Subject: [MOBY-dev] getting RDF resources in the compressed format In-Reply-To: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> References: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> Message-ID: <47C4A4A3.1050601@ucalgary.ca> I believe the solution we agreed upon was that if the client sends an "Accept-encoding" HTTP header with x-gzip, we'd have the server send gzip'ed if it finds it. I use this mechanism all the time for sending big HTML files... Martin Senger wrote: > Eddie, Paul, Mark et al, > > Because of the new implementation of the registry cache (written by Eddie) > that uses RDF, the RDF resources will be more used (also from the > Dashboard). To get them fast is, therefore, a priority. > > I remember that when the new method (to get URLs of the registry resources) > was added to the BioMoby API we had discussed how to deliver these resources > in a compressed format, as well. Has anybody remember how it was proposed to > work? Because we definitely need to compress it now. > > Thanks, > Martin > > From martin.senger at gmail.com Wed Feb 27 00:34:31 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 27 Feb 2008 08:34:31 +0800 Subject: [MOBY-dev] getting RDF resources in the compressed format In-Reply-To: <47C4A4A3.1050601@ucalgary.ca> References: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> <47C4A4A3.1050601@ucalgary.ca> Message-ID: <4d93f07c0802261634u5aade00ak988ebfbff38d308a@mail.gmail.com> Many thanks, Paul. I believe the solution we agreed upon was that if the client sends an > "Accept-encoding" HTTP header with x-gzip Yes, that was what I vaguely remembered but was not sure about details. [BTW, is there a way to search the whole biomoby email archive?] How does client know what was sent from the server? Is is in the HTTP Content-type header? If so, what mime-type should be there? Eddie, it would be nice to have this feature implemented on the registry site (so other registry providers can copy it, as well). Would you consider it please? Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Wed Feb 27 00:53:35 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 27 Feb 2008 08:53:35 +0800 Subject: [MOBY-dev] a space in the data type name Message-ID: <4d93f07c0802261653k3f2001a8gfdf1f16f2cd6b15e@mail.gmail.com> Recently, a new data type ' RNAStructAlignmentML' was registered. It starts with a space. I think that the registry should reject it. In the BioMoby registry API, we have rules for article names ("Article names for each contained object type may not contain spaces or other special characters") but not for the data type names. But they should be driven what is allowed for the XML element names. Is it possible to change the name, and perhaps to add a more strict checking when an entity is being registered please? Thanks, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Wed Feb 27 01:17:04 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 27 Feb 2008 09:17:04 +0800 Subject: [MOBY-dev] a space in the data type name In-Reply-To: <4d93f07c0802261653k3f2001a8gfdf1f16f2cd6b15e@mail.gmail.com> References: <4d93f07c0802261653k3f2001a8gfdf1f16f2cd6b15e@mail.gmail.com> Message-ID: <4d93f07c0802261717j71ee1dadkd3a8e658e3ae4f47@mail.gmail.com> ...[cont.] and the same for ' AlignmentML', ' SequenceML' data types I believe. (Actually the SequenceML is there twice, once with a space and once without). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From markw at illuminae.com Wed Feb 27 06:25:54 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 26 Feb 2008 22:25:54 -0800 Subject: [MOBY-dev] a space in the data type name In-Reply-To: <4d93f07c0802261717j71ee1dadkd3a8e658e3ae4f47@mail.gmail.com> References: <4d93f07c0802261653k3f2001a8gfdf1f16f2cd6b15e@mail.gmail.com> <4d93f07c0802261717j71ee1dadkd3a8e658e3ae4f47@mail.gmail.com> Message-ID: Absolutely! I'll fix this in the registry right away. I wonder if I should manually repair the DB entries, or if I should ask the individuals who registered the objects to re-register them? Probably best to at least warn them... M On Tue, 26 Feb 2008 17:17:04 -0800, Martin Senger wrote: > ...[cont.] and the same for ' AlignmentML', ' SequenceML' data types I > believe. (Actually the SequenceML is there twice, once with a space and > once > without). > > Cheers, > Martin > From edward.kawas at gmail.com Wed Feb 27 18:09:12 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 27 Feb 2008 10:09:12 -0800 Subject: [MOBY-dev] getting RDF resources in the compressed format In-Reply-To: <4d93f07c0802261634u5aade00ak988ebfbff38d308a@mail.gmail.com> References: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> <47C4A4A3.1050601@ucalgary.ca> <4d93f07c0802261634u5aade00ak988ebfbff38d308a@mail.gmail.com> Message-ID: <47c5a763.0f98600a.4716.ffffa8be@mx.google.com> Okay, I set up mod_deflate on my local linux installation and tried it out. Some results: Service instance RDF: Original size: 7052579bytes Compressed size: 305092bytes Savings: ~96% Object RDF: Original size: 2864668 bytes Compressed size: 219478 bytes Savings: ~92% I know that it is obvious that we will get big savings by compressing text files ... The question was how to implement this ... Here is what I did: 1. enabled mod_deflate for apache This differs from installation to installation, but for me, running ubuntu, all I had to do was create 2 sym links in /etc/apache2/mods-enabled/ for the files deflate.conf and deflate.load in /etc/apache2/mods-available. 2. edit the conf file Again this differs, but what I did was edit deflate.conf and put the following inside: # mime types to compress AddOutputFilterByType DEFLATE text/html text/plain text/xml # support for older browsers BrowserMatch ^Mozilla/4 gzip-only-text/html BrowserMatch ^Mozilla/4\.0[678] no-gzip BrowserMatch \bMSIE !no-gzip !gzip-only-text/html BrowserMatch \bMSI[E] !no-gzip !gzip-only-text/html 3. I restarted apache More doc available at http://httpd.apache.org/docs/2.0/mod/mod_deflate.html Now when a request comes in with the header 'Accept-Encoding: gzip' apache compresses the RDF. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger Sent: February-26-08 4:35 PM To: Core developer announcements Subject: Re: [MOBY-dev] getting RDF resources in the compressed format Many thanks, Paul. I believe the solution we agreed upon was that if the client sends an > "Accept-encoding" HTTP header with x-gzip Yes, that was what I vaguely remembered but was not sure about details. [BTW, is there a way to search the whole biomoby email archive?] How does client know what was sent from the server? Is is in the HTTP Content-type header? If so, what mime-type should be there? Eddie, it would be nice to have this feature implemented on the registry site (so other registry providers can copy it, as well). Would you consider it please? Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Wed Feb 27 18:28:36 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 27 Feb 2008 11:28:36 -0700 Subject: [MOBY-dev] getting RDF resources in the compressed format In-Reply-To: <47c5a763.0f98600a.4716.ffffa8be@mx.google.com> References: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> <47C4A4A3.1050601@ucalgary.ca> <4d93f07c0802261634u5aade00ak988ebfbff38d308a@mail.gmail.com> <47c5a763.0f98600a.4716.ffffa8be@mx.google.com> Message-ID: <47C5ABD4.7060309@ucalgary.ca> The question is whether URL.openStream() sends such a header. Probably not, in which case CentralXXXImpl will need to use Apache httpclient or something similar instead... Edward Kawas wrote: > Okay, > > I set up mod_deflate on my local linux installation and tried it out. > > Some results: > Service instance RDF: > Original size: 7052579bytes > Compressed size: 305092bytes > Savings: ~96% > Object RDF: > Original size: 2864668 bytes > Compressed size: 219478 bytes > Savings: ~92% > > I know that it is obvious that we will get big savings by compressing text > files ... The question was how to implement this ... > > Here is what I did: > 1. enabled mod_deflate for apache > This differs from installation to installation, but for me, running > ubuntu, all I had to do was create 2 sym links in /etc/apache2/mods-enabled/ > for the files deflate.conf and deflate.load in /etc/apache2/mods-available. > 2. edit the conf file > Again this differs, but what I did was edit deflate.conf and put the > following inside: > > > # mime types to compress > AddOutputFilterByType DEFLATE text/html text/plain text/xml > # support for older browsers > BrowserMatch ^Mozilla/4 gzip-only-text/html > BrowserMatch ^Mozilla/4\.0[678] no-gzip > BrowserMatch \bMSIE !no-gzip !gzip-only-text/html > BrowserMatch \bMSI[E] !no-gzip !gzip-only-text/html > > > > 3. I restarted apache > > More doc available at http://httpd.apache.org/docs/2.0/mod/mod_deflate.html > > Now when a request comes in with the header 'Accept-Encoding: gzip' apache > compresses the RDF. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger > Sent: February-26-08 4:35 PM > To: Core developer announcements > Subject: Re: [MOBY-dev] getting RDF resources in the compressed format > > Many thanks, Paul. > > I believe the solution we agreed upon was that if the client sends an > >> "Accept-encoding" HTTP header with x-gzip >> > > > Yes, that was what I vaguely remembered but was not sure about details. > [BTW, is there a way to search the whole biomoby email archive?] > > How does client know what was sent from the server? Is is in the HTTP > Content-type header? If so, what mime-type should be there? > > Eddie, it would be nice to have this feature implemented on the registry > site (so other registry providers can copy it, as well). Would you consider > it please? > > Cheers, > Martin > > > From edward.kawas at gmail.com Wed Feb 27 19:11:46 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 27 Feb 2008 11:11:46 -0800 Subject: [MOBY-dev] getting RDF resources in the compressed format In-Reply-To: <47C5ABD4.7060309@ucalgary.ca> References: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> <47C4A4A3.1050601@ucalgary.ca> <4d93f07c0802261634u5aade00ak988ebfbff38d308a@mail.gmail.com> <47c5a763.0f98600a.4716.ffffa8be@mx.google.com> <47C5ABD4.7060309@ucalgary.ca> Message-ID: <47c5b60f.1def600a.5a28.1b48@mx.google.com> No, we can still use java libraries (I am doing this with the java RDF parsers): public static InputStream getBufferedInputStream(URL url) throws MobyException { try { HttpURLConnection urlConnection = null; urlConnection = (HttpURLConnection) url.openConnection(); urlConnection.setRequestProperty("User-Agent", "jmoby-extended/1.0"); urlConnection.setRequestProperty("Accept-Encoding", "gzip, deflate"); urlConnection.setDefaultUseCaches(false); urlConnection.setUseCaches(false); BufferedInputStream is = null; if (("gzip").equalsIgnoreCase(urlConnection.getContentEncoding())) { // handle gzip encoded content is = new BufferedInputStream(new GZIPInputStream(urlConnection.getInputStream())); } else { is = new BufferedInputStream(urlConnection.getInputStream()); } return is; } catch (IOException e) { throw new MobyException("Error creating input stream:",e.getCause()); } } Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Paul Gordon Sent: February-27-08 10:29 AM To: Core developer announcements Subject: Re: [MOBY-dev] getting RDF resources in the compressed format The question is whether URL.openStream() sends such a header. Probably not, in which case CentralXXXImpl will need to use Apache httpclient or something similar instead... Edward Kawas wrote: > Okay, > > I set up mod_deflate on my local linux installation and tried it out. > > Some results: > Service instance RDF: > Original size: 7052579bytes > Compressed size: 305092bytes > Savings: ~96% > Object RDF: > Original size: 2864668 bytes > Compressed size: 219478 bytes > Savings: ~92% > > I know that it is obvious that we will get big savings by compressing text > files ... The question was how to implement this ... > > Here is what I did: > 1. enabled mod_deflate for apache > This differs from installation to installation, but for me, running > ubuntu, all I had to do was create 2 sym links in /etc/apache2/mods-enabled/ > for the files deflate.conf and deflate.load in /etc/apache2/mods-available. > 2. edit the conf file > Again this differs, but what I did was edit deflate.conf and put the > following inside: > > > # mime types to compress > AddOutputFilterByType DEFLATE text/html text/plain text/xml > # support for older browsers > BrowserMatch ^Mozilla/4 gzip-only-text/html > BrowserMatch ^Mozilla/4\.0[678] no-gzip > BrowserMatch \bMSIE !no-gzip !gzip-only-text/html > BrowserMatch \bMSI[E] !no-gzip !gzip-only-text/html > > > > 3. I restarted apache > > More doc available at http://httpd.apache.org/docs/2.0/mod/mod_deflate.html > > Now when a request comes in with the header 'Accept-Encoding: gzip' apache > compresses the RDF. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger > Sent: February-26-08 4:35 PM > To: Core developer announcements > Subject: Re: [MOBY-dev] getting RDF resources in the compressed format > > Many thanks, Paul. > > I believe the solution we agreed upon was that if the client sends an > >> "Accept-encoding" HTTP header with x-gzip >> > > > Yes, that was what I vaguely remembered but was not sure about details. > [BTW, is there a way to search the whole biomoby email archive?] > > How does client know what was sent from the server? Is is in the HTTP > Content-type header? If so, what mime-type should be there? > > Eddie, it would be nice to have this feature implemented on the registry > site (so other registry providers can copy it, as well). Would you consider > it please? > > Cheers, > Martin > > > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From martin.senger at gmail.com Thu Feb 28 00:05:42 2008 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 28 Feb 2008 08:05:42 +0800 Subject: [MOBY-dev] getting RDF resources in the compressed format In-Reply-To: <47c5b60f.1def600a.5a28.1b48@mx.google.com> References: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> <47C4A4A3.1050601@ucalgary.ca> <4d93f07c0802261634u5aade00ak988ebfbff38d308a@mail.gmail.com> <47c5a763.0f98600a.4716.ffffa8be@mx.google.com> <47C5ABD4.7060309@ucalgary.ca> <47c5b60f.1def600a.5a28.1b48@mx.google.com> Message-ID: <4d93f07c0802271605qd460892q2dc2a4c69679a5a2@mail.gmail.com> Eddie, Thanks for making it happen. Today's questions are: 1) Is the compressing working on your laptop or already on the default BioMoby registry. If the former, when the latter is planned? 2) Are you considering to update registry documentation (so other sites, like IRRI, can benefit immediately from your investigation)? Regarding the implementation in the Java library, I am going to add it to CentralXXX classes this week (I am with Paul, I prefer Apache httpclient). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From edward.kawas at gmail.com Thu Feb 28 00:47:56 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 27 Feb 2008 16:47:56 -0800 Subject: [MOBY-dev] getting RDF resources in the compressed format In-Reply-To: <4d93f07c0802271605qd460892q2dc2a4c69679a5a2@mail.gmail.com> References: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> <47C4A4A3.1050601@ucalgary.ca> <4d93f07c0802261634u5aade00ak988ebfbff38d308a@mail.gmail.com> <47c5a763.0f98600a.4716.ffffa8be@mx.google.com> <47C5ABD4.7060309@ucalgary.ca> <47c5b60f.1def600a.5a28.1b48@mx.google.com> <4d93f07c0802271605qd460892q2dc2a4c69679a5a2@mail.gmail.com> Message-ID: <47c604e1.1498600a.5266.ffff8ff9@mx.google.com> Hi Martin, 1) It's working on my notebook and Mark is trying to make it work on the test registry. 2) I will update the docs, regarding what has to be done. Basically, you have to enable mod_deflate on apache and enable compression for text/xml and application/xml. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger Sent: February-27-08 4:06 PM To: Core developer announcements Subject: Re: [MOBY-dev] getting RDF resources in the compressed format Eddie, Thanks for making it happen. Today's questions are: 1) Is the compressing working on your laptop or already on the default BioMoby registry. If the former, when the latter is planned? 2) Are you considering to update registry documentation (so other sites, like IRRI, can benefit immediately from your investigation)? Regarding the implementation in the Java library, I am going to add it to CentralXXX classes this week (I am with Paul, I prefer Apache httpclient). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From martin.senger at gmail.com Thu Feb 28 02:09:48 2008 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 28 Feb 2008 10:09:48 +0800 Subject: [MOBY-dev] getting RDF resources in the compressed format In-Reply-To: <47c604e1.1498600a.5266.ffff8ff9@mx.google.com> References: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> <47C4A4A3.1050601@ucalgary.ca> <4d93f07c0802261634u5aade00ak988ebfbff38d308a@mail.gmail.com> <47c5a763.0f98600a.4716.ffffa8be@mx.google.com> <47C5ABD4.7060309@ucalgary.ca> <47c5b60f.1def600a.5a28.1b48@mx.google.com> <4d93f07c0802271605qd460892q2dc2a4c69679a5a2@mail.gmail.com> <47c604e1.1498600a.5266.ffff8ff9@mx.google.com> Message-ID: <4d93f07c0802271809l2eab744ema30e350f1603f704@mail.gmail.com> > 1) It's working on my notebook and Mark is trying to make it work on the > test registry. It's great! When do you, or does Mark, plan to make it available also from the Calgary registry? Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From edward.kawas at gmail.com Thu Feb 28 02:26:37 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 27 Feb 2008 18:26:37 -0800 Subject: [MOBY-dev] getting RDF resources in the compressed format In-Reply-To: <4d93f07c0802271809l2eab744ema30e350f1603f704@mail.gmail.com> References: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> <47C4A4A3.1050601@ucalgary.ca> <4d93f07c0802261634u5aade00ak988ebfbff38d308a@mail.gmail.com> <47c5a763.0f98600a.4716.ffffa8be@mx.google.com> <47C5ABD4.7060309@ucalgary.ca> <47c5b60f.1def600a.5a28.1b48@mx.google.com> <4d93f07c0802271605qd460892q2dc2a4c69679a5a2@mail.gmail.com> <47c604e1.1498600a.5266.ffff8ff9@mx.google.com> <4d93f07c0802271809l2eab744ema30e350f1603f704@mail.gmail.com> Message-ID: <47c61c02.1abd600a.0ce4.ffff929e@mx.google.com> I believe Mark actually had big problems doing it on the test registry (in fact he is still trying!). I am not sure why ... on my linux installation it was super simple ;-) I am sure that once Mark does the test registry, the Calgary one will follow quickly. I cant actually wait!!!! Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger Sent: February-27-08 6:10 PM To: Core developer announcements Subject: Re: [MOBY-dev] getting RDF resources in the compressed format > 1) It's working on my notebook and Mark is trying to make it work on the > test registry. It's great! When do you, or does Mark, plan to make it available also from the Calgary registry? Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From groscurt at mpiz-koeln.mpg.de Thu Feb 28 08:47:27 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 28 Feb 2008 09:47:27 +0100 Subject: [MOBY-dev] Dashboard as standalone In-Reply-To: <47c61c02.1abd600a.0ce4.ffff929e@mx.google.com> References: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> <47C4A4A3.1050601@ucalgary.ca> <4d93f07c0802261634u5aade00ak988ebfbff38d308a@mail.gmail.com> <47c5a763.0f98600a.4716.ffffa8be@mx.google.com> <47C5ABD4.7060309@ucalgary.ca> <47c5b60f.1def600a.5a28.1b48@mx.google.com> <4d93f07c0802271605qd460892q2dc2a4c69679a5a2@mail.gmail.com> <47c604e1.1498600a.5266.ffff8ff9@mx.google.com> <4d93f07c0802271809l2eab744ema30e350f1603f704@mail.gmail.com> <47c61c02.1abd600a.0ce4.ffff929e@mx.google.com> Message-ID: <47C6751F.8040000@mpiz-koeln.mpg.de> Hi, I just saw that in the docs it is written, that maybe there is a installanywhere version of dashboard. Any progress there or is it off the table ? I would love to have a standalone version of dashboard (somehow - even just the jar) - is this planned or is there some docs about how to create that ? best andreas From gordonp at ucalgary.ca Thu Feb 28 14:53:10 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 28 Feb 2008 07:53:10 -0700 Subject: [MOBY-dev] Dashboard as standalone In-Reply-To: <47C6751F.8040000@mpiz-koeln.mpg.de> References: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> <47C4A4A3.1050601@ucalgary.ca> <4d93f07c0802261634u5aade00ak988ebfbff38d308a@mail.gmail.com> <47c5a763.0f98600a.4716.ffffa8be@mx.google.com> <47C5ABD4.7060309@ucalgary.ca> <47c5b60f.1def600a.5a28.1b48@mx.google.com> <4d93f07c0802271605qd460892q2dc2a4c69679a5a2@mail.gmail.com> <47c604e1.1498600a.5266.ffff8ff9@mx.google.com> <4d93f07c0802271809l2eab744ema30e350f1603f704@mail.gmail.com> <47c61c02.1abd600a.0ce4.ffff929e@mx.google.com> <47C6751F.8040000@mpiz-koeln.mpg.de> Message-ID: <47C6CAD6.2010501@ucalgary.ca> We have an InstallAnywhere license for our lab, in case no one else manages to do it... Andreas Groscurth wrote: > Hi, > > I just saw that in the docs it is written, that maybe there is a > installanywhere version of dashboard. Any progress there or is it off > the table ? > > I would love to have a standalone version of dashboard (somehow - even > just the jar) - is this planned or is there some docs about how to > create that ? > > best > andreas > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,47c6725f10950272424736! > > > From martin.senger at gmail.com Thu Feb 28 15:03:51 2008 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 28 Feb 2008 23:03:51 +0800 Subject: [MOBY-dev] Dashboard as standalone In-Reply-To: <47C6CAD6.2010501@ucalgary.ca> References: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> <47c5a763.0f98600a.4716.ffffa8be@mx.google.com> <47C5ABD4.7060309@ucalgary.ca> <47c5b60f.1def600a.5a28.1b48@mx.google.com> <4d93f07c0802271605qd460892q2dc2a4c69679a5a2@mail.gmail.com> <47c604e1.1498600a.5266.ffff8ff9@mx.google.com> <4d93f07c0802271809l2eab744ema30e350f1603f704@mail.gmail.com> <47c61c02.1abd600a.0ce4.ffff929e@mx.google.com> <47C6751F.8040000@mpiz-koeln.mpg.de> <47C6CAD6.2010501@ucalgary.ca> Message-ID: <4d93f07c0802280703t4a44be88w6570e66e25b1b118@mail.gmail.com> I may have installAnywhere at IRRI. But I am waiting for the new way how to fill the local cache (using the RDF resources) - it is practically done (we are just waiting only for compressing RDF files from the default registry). When this is done, I will make the long-delayed fixes to dashboard and then try installAnywhere. Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Thu Feb 28 15:16:10 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 28 Feb 2008 16:16:10 +0100 Subject: [MOBY-dev] Dashboard as standalone In-Reply-To: <4d93f07c0802280703t4a44be88w6570e66e25b1b118@mail.gmail.com> References: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> <47c5a763.0f98600a.4716.ffffa8be@mx.google.com> <47C5ABD4.7060309@ucalgary.ca> <47c5b60f.1def600a.5a28.1b48@mx.google.com> <4d93f07c0802271605qd460892q2dc2a4c69679a5a2@mail.gmail.com> <47c604e1.1498600a.5266.ffff8ff9@mx.google.com> <4d93f07c0802271809l2eab744ema30e350f1603f704@mail.gmail.com> <47c61c02.1abd600a.0ce4.ffff929e@mx.google.com> <47C6751F.8040000@mpiz-koeln.mpg.de> <47C6CAD6.2010501@ucalgary.ca> <4d93f07c0802280703t4a44be88w6570e66e25b1b118@mail.gmail.com> Message-ID: <47C6D03A.6090804@mpiz-koeln.mpg.de> Yeah - thanks Martin Martin Senger wrote: > I may have installAnywhere at IRRI. But I am waiting for the new way how to > fill the local cache (using the RDF resources) - it is practically done (we > are just waiting only for compressing RDF files from the default registry). > When this is done, I will make the long-delayed fixes to dashboard and then > try installAnywhere. > > Martin > > From edward.kawas at gmail.com Thu Feb 28 16:35:02 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 28 Feb 2008 08:35:02 -0800 Subject: [MOBY-dev] getting RDF resources in the compressed format In-Reply-To: <4d93f07c0802271809l2eab744ema30e350f1603f704@mail.gmail.com> References: <4d93f07c0802252057q42579fe6qc999c8d6f17082dc@mail.gmail.com> <47C4A4A3.1050601@ucalgary.ca> <4d93f07c0802261634u5aade00ak988ebfbff38d308a@mail.gmail.com> <47c5a763.0f98600a.4716.ffffa8be@mx.google.com> <47C5ABD4.7060309@ucalgary.ca> <47c5b60f.1def600a.5a28.1b48@mx.google.com> <4d93f07c0802271605qd460892q2dc2a4c69679a5a2@mail.gmail.com> <47c604e1.1498600a.5266.ffff8ff9@mx.google.com> <4d93f07c0802271809l2eab744ema30e350f1603f704@mail.gmail.com> Message-ID: <47c6e2dd.081b600a.52df.ffff896e@mx.google.com> The Calgary registry now returns gzipped RDF if requested. For those wishing to do this with your own personal registry, I added a bit of documentation on the RegistryScripts documentation page. This file can be accessed from the link 'Setting up a custom MOBY Central' on the biomoby.org homepage or: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/RegistrySc ripts.html [although, you might have to wait a few hours for the content to become available on the web, but the cvs is up to date!]. Thanks Mark! Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger Sent: February-27-08 6:10 PM To: Core developer announcements Subject: Re: [MOBY-dev] getting RDF resources in the compressed format > 1) It's working on my notebook and Mark is trying to make it work on the > test registry. It's great! When do you, or does Mark, plan to make it available also from the Calgary registry? Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From sneumann at ipb-halle.de Fri Feb 29 09:32:40 2008 From: sneumann at ipb-halle.de (Neumann, Steffen) Date: Fri, 29 Feb 2008 10:32:40 +0100 Subject: [MOBY-dev] Current CVS ant works, eclipse woes Message-ID: <1204277560.31184.306.camel@lathan.ipb-sub.ipb-halle.de> Hi moby hackers, (Hi Andreas ;-) I am just trying the current jmoby CVS snapshot, and share the experience, and maybe they'll make it into Andreas' "known-errors-and-problems". The command line ant targets work fine: ant bootstrap ant initeclipse ant bootstrap ant compile ant dashboard But in eclipse I get errors upon build: 29.02.08 10:20:53 CET: Reading /moby/pom.xml 29.02.08 10:21:00 CET: [WARN] Artifact javax.servlet:servlet-api:jar:2.5:provided retains local scope 'provided' overriding broader scope 'compile' given by a dependency. If this is not intended, modify or remove the local scope. 29.02.08 10:21:05 CET: [INFO] artifact org.jvnet.staxex:stax-ex: checking for updates from java.net 29.02.08 10:21:10 CET: [INFO] artifact org.jvnet.staxex:stax-ex: checking for updates from bio.maven.repository 29.02.08 10:21:12 CET: [INFO] artifact org.jvnet.staxex:stax-ex: checking for updates from java.net-m2 29.02.08 10:21:14 CET: [INFO] artifact org.jvnet.staxex:stax-ex: checking for updates from hpl.hp.repository 29.02.08 10:21:14 CET: [INFO] artifact org.jvnet.staxex:stax-ex: checking for updates from central 29.02.08 10:21:15 CET: [WARN] Artifact junit:junit:jar:4.4:test retains local scope 'test' overriding broader scope 'compile' given by a dependency. If this is not intended, modify or remove the local scope. 29.02.08 10:21:16 CET: Reading /moby/src/samples/pom.xml 29.02.08 10:21:17 CET: [WARN] Unable to get resource from repository central (http://repo1.maven.org/maven2) 29.02.08 10:21:17 CET: Project build error Cannot find parent: org.biomoby:jmoby for project: org.biomoby:jmoby-plugins:jar:1.0.0 29.02.08 10:21:17 CET: Reading /moby/src/main/pom.xml 29.02.08 10:21:18 CET: [WARN] Unable to get resource from repository central (http://repo1.maven.org/maven2) 29.02.08 10:21:18 CET: Project build error Cannot find parent: org.biomoby:jmoby for project: org.biomoby:jmoby-core:jar:1.0.0 29.02.08 10:25:27 CET: Reading /moby/pom.xml 29.02.08 10:25:28 CET: Reading /moby/src/samples/pom.xml 29.02.08 10:25:29 CET: [WARN] Unable to get resource from repository central (http://repo1.maven.org/maven2) 29.02.08 10:25:29 CET: Project build error Cannot find parent: org.biomoby:jmoby for project: org.biomoby:jmoby-plugins:jar:1.0.0 29.02.08 10:25:29 CET: Reading /moby/src/main/pom.xml 29.02.08 10:25:29 CET: [WARN] Unable to get resource from repository central (http://repo1.maven.org/maven2) 29.02.08 10:25:29 CET: Project build error Cannot find parent: org.biomoby:jmoby for project: org.biomoby:jmoby-core:jar:1.0.0 Severity and Description Path Resource Location Creation Time Id Project build error Cannot find parent: org.biomoby:jmoby for project: org.biomoby:jmoby-core:jar:1.0.0 moby/src/main pom.xml line 1 1204277129754 135628 Project build error Cannot find parent: org.biomoby:jmoby for project: org.biomoby:jmoby-plugins:jar:1.0.0 moby/src/samples pom.xml line 1 1204277129072 135627 The project was not built since its build path is incomplete. Cannot find the class file for org.biomoby.shared.MobyService. Fix the build path then try building this project moby Unknown 1204277127536 135626 The type org.biomoby.shared.MobyService cannot be resolved. It is indirectly referenced from required .class files moby/src/main/org/biomoby/client Taverna.java line 98 1204277127533 135625 This is linux / Sun JDK-1.5 / eclipse-3.2 Any ideas ? Further info needed ? Yours, Steffen -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 191 bytes Desc: This is a digitally signed message part URL: From groscurt at mpiz-koeln.mpg.de Fri Feb 29 10:44:09 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 29 Feb 2008 11:44:09 +0100 Subject: [MOBY-dev] Testing registry problems In-Reply-To: <1204277560.31184.306.camel@lathan.ipb-sub.ipb-halle.de> References: <1204277560.31184.306.camel@lathan.ipb-sub.ipb-halle.de> Message-ID: <47C7E1F9.5010106@mpiz-koeln.mpg.de> hiho, we getting constant ===ERROR=== Fault details: [string: null] [HttpErrorCode: null] Fault string: (0)null Fault code: {http://xml.apache.org/axis/}HTTP Fault actor: null When calling: http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl =========== while loading the ontologies in dashboard from the test registry - URL is accessible via browser. ? best andreas From groscurt at mpiz-koeln.mpg.de Fri Feb 29 10:51:21 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 29 Feb 2008 11:51:21 +0100 Subject: [MOBY-dev] warning on start of dashboard In-Reply-To: <1204277560.31184.306.camel@lathan.ipb-sub.ipb-halle.de> References: <1204277560.31184.306.camel@lathan.ipb-sub.ipb-halle.de> Message-ID: <200802291151.22060.groscurt@mpiz-koeln.mpg.de> hiho. starting dashboard from console gives me Warning: Reference moses.build.classpath has not been set at runtime, but was found during build file parsing, attempting to resolve. Future versions of Ant may support referencing ids defined in non-executed targets. dashboard works - but warning is there :-) Best andreas From edward.kawas at gmail.com Fri Feb 29 13:56:18 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 29 Feb 2008 05:56:18 -0800 Subject: [MOBY-dev] Testing registry problems In-Reply-To: <47C7E1F9.5010106@mpiz-koeln.mpg.de> References: <1204277560.31184.306.camel@lathan.ipb-sub.ipb-halle.de> <47C7E1F9.5010106@mpiz-koeln.mpg.de> Message-ID: <47c80f05.1fba720a.6278.31fd@mx.google.com> The test registry is down because apache is not working at the moment. Mark is trying to fix it. Sorry! Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth Sent: February-29-08 2:44 AM To: Core developer announcements Subject: [MOBY-dev] Testing registry problems hiho, we getting constant ===ERROR=== Fault details: [string: null] [HttpErrorCode: null] Fault string: (0)null Fault code: {http://xml.apache.org/axis/}HTTP Fault actor: null When calling: http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl =========== while loading the ontologies in dashboard from the test registry - URL is accessible via browser. ? best andreas _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From MichaelGerlich at gmx.de Thu Feb 28 20:07:24 2008 From: MichaelGerlich at gmx.de (Michael Gerlich) Date: Thu, 28 Feb 2008 21:07:24 +0100 Subject: [MOBY-dev] Dashboard can't connect to Registries Message-ID: <000601c87a45$892f2700$9b8d7500$@de> Hi there, First of all thanks for your tutorials about setting up Biomoby with Eclipse and for the newly created Known errors site at http://bioinfo.mpiz-koeln.mpg.de/araws/documentation/help/jmoby-step-by-step /writing-biomoby-web-services/known-errors-and-problems, they helped me a lot and I finally have successful Builds with the Ant Scripts (using JDK 1.5). But there are some things I still have problems with. 1) Eclipse keeps reporting that it misses required libraries, even though the initeclipse script says Build successful. Are these errors some kind of artifacts or should I check the ant scripts or checkout JMoby again? micge at linux-vm:~/eclipse> ./eclipse -vmargs -Djava.home=/usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/ ZoneInfo: /usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/lib/zi/ZoneInfoMappings (Datei oder Verzeichnis nicht gefunden) ZoneInfo: /usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/lib/zi/ZoneInfoMappings (Datei oder Verzeichnis nicht gefunden) ZoneInfo: /usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/lib/zi/ZoneInfoMappings (Datei oder Verzeichnis nicht gefunden) ZoneInfo: /usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/lib/zi/ZoneInfoMappings (Datei oder Verzeichnis nicht gefunden) ZoneInfo: /usr/lib/jvm/java-1.5.0-sun-1.5.0_update14/lib/zi/ZoneInfoMappings (Datei oder Verzeichnis nicht gefunden) Severity and Description Project 'moby' is missing required library: 'lib/activation.jar' Project 'moby' is missing required library: 'lib/adenine.jar' Project 'moby' is missing required library: 'lib/alltools2.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-antlr.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-apache-bcel.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-apache-bsf.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-apache-log4j.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-apache-oro.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-apache-regexp.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-apache-resolver.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-commons-logging.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-commons-net.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-contrib.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-icontract.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-jai.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-javamail.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-jdepend.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-jmf.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-jsch.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-junit.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-launcher.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-netrexx.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-nodeps.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-starteam.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-stylebook.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-swing.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-trax.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-vaj.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-weblogic.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-xalan1.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant-xslp.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/ant.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/xercesImpl.jar' Project 'moby' is missing required library: 'lib/ant_home/lib/xml-apis.jar' Project 'moby' is missing required library: 'lib/axis-ant.jar' Project 'moby' is missing required library: 'lib/axis.jar' Project 'moby' is missing required library: 'lib/castor-0.9.5.jar' Project 'moby' is missing required library: 'lib/commons-codec-1.3.jar' Project 'moby' is missing required library: 'lib/commons-collections-2.1.jar' Project 'moby' is missing required library: 'lib/commons-dbcp-1.1.jar' Project 'moby' is missing required library: 'lib/commons-discovery-0.2.jar' Project 'moby' is missing required library: 'lib/commons-httpclient-3.0-rc2.jar' Project 'moby' is missing required library: 'lib/commons-io-1.0.jar' Project 'moby' is missing required library: 'lib/commons-lang-2.1.jar' Project 'moby' is missing required library: 'lib/commons-logging-1.0.4.jar' Project 'moby' is missing required library: 'lib/commons-pool-1.1.jar' Project 'moby' is missing required library: 'lib/concurrent.jar' Project 'moby' is missing required library: 'lib/dnsjava-1.3.2.jar' Project 'moby' is missing required library: 'lib/icis-pedigree.jar' Project 'moby' is missing required library: 'lib/icu4j.jar' Project 'moby' is missing required library: 'lib/jakarta-oro-2.0.5.jar' Project 'moby' is missing required library: 'lib/jaxen-core.jar' Project 'moby' is missing required library: 'lib/jaxen-jdom.jar' Project 'moby' is missing required library: 'lib/jaxrpc.jar' Project 'moby' is missing required library: 'lib/jcalendar.jar' Project 'moby' is missing required library: 'lib/jdom.jar' Project 'moby' is missing required library: 'lib/jena.jar' Project 'moby' is missing required library: 'lib/jfcunit.jar' Project 'moby' is missing required library: 'lib/jodconverter-2.2.0.jar' Project 'moby' is missing required library: 'lib/junit.jar' Project 'moby' is missing required library: 'lib/log4j-1.2.12.jar' Project 'moby' is missing required library: 'lib/lsid-client-1.1.2.jar' Project 'moby' is missing required library: 'lib/lsid-server-1.1.2.jar' Project 'moby' is missing required library: 'lib/mail.jar' Project 'moby' is missing required library: 'lib/mailapi_1_3_1.jar' Project 'moby' is missing required library: 'lib/mysql-connector-java-3.1.7-bin.jar' Project 'moby' is missing required library: 'lib/rdf-api-2001-01-19.jar' Project 'moby' is missing required library: 'lib/saaj.jar' Project 'moby' is missing required library: 'lib/saxpath.jar' Project 'moby' is missing required library: 'lib/servlet.jar' Project 'moby' is missing required library: 'lib/taverna.jar' Project 'moby' is missing required library: 'lib/wsdl4j-1.5.1.jar' Project 'moby' is missing required library: 'lib/xalan.jar' Project 'moby' is missing required library: 'lib/xercesImpl.jar' Project 'moby' is missing required library: 'lib/xercesSamples.jar' Project 'moby' is missing required library: 'lib/xml-apis.jar' Project 'moby' is missing required library: 'lib/xmlParserAPIs.jar' Project build error Cannot find parent: org.biomoby:jmoby for project: org.biomoby:jmoby-core:jar:1.0.0 moby/src/main pom.xml line 1 1204224268317 133440 Project build error Cannot find parent: org.biomoby:jmoby for project: org.biomoby:jmoby-plugins:jar:1.0.0 moby/src/samples pom.xml line 1 1204224267905 133439 The project cannot be built until build path errors are resolved moby 2) I'am behind a proxy server, so I had to edit proxy settings in net.properties of JDK 1.5 (http_proxy environment variable is set, but without effect to Java). With this, all the ant scripts work without any problems, but when I run Dashboard, all I got are empty lists and the following messages: Inside Eclipse: --------------- Buildfile: /home/micge/workspace/moby/build.xml checkmaven: initmaven: init: config: compile: moses-init: samples-init: dashboard-init: dashboard-config: dashboard: [Dashboard] libxcb: WARNING! Program tries to unlock a connection without having acquired [Dashboard] a lock first, which indicates a programming error. [Dashboard] There will be no further warnings about this issue. [Dashboard] libxcb: WARNING! Program tries to lock an already locked connection, [Dashboard] which indicates a programming error. [Dashboard] There will be no further warnings about this issue. [Dashboard] 192616 [Thread-6] WARN CentralDigestCachedImpl - Error with Services RDF [Dashboard] org.biomoby.shared.MobyException: ===ERROR=== [Dashboard] Fault details: [Dashboard] Fault string: java.net.ConnectException: Connection timed out [Dashboard] Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException [Dashboard] Fault actor: null [Dashboard] When calling: [Dashboard] http://moby.ucalgary.ca/moby/MOBY-Central.pl [Dashboard] =========== [Dashboard] at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:230) [Dashboard] at org.biomoby.client.CentralImpl.getResourceRefs(CentralImpl.java:1772) [Dashboard] at org.biomoby.client.CentralImpl.getResource(CentralImpl.java:1807) [Dashboard] at org.biomoby.client.CentralDigestCachedImpl.getResourceAsString(CentralDigest CachedImpl.java:216) [Dashboard] at org.biomoby.client.CentralDigestCachedImpl.fillServicesCache(CentralDigestCa chedImpl.java:243) [Dashboard] at org.biomoby.client.CentralDigestCachedImpl.getServices(CentralDigestCachedIm pl.java:709) [Dashboard] at org.biomoby.service.dashboard.RegistryModel.getServices(RegistryModel.java:5 61) [Dashboard] at org.biomoby.service.dashboard.ServicesTree$4.construct(ServicesTree.java:121 ) [Dashboard] at org.biomoby.service.dashboard.SwingWorker$2.run(SwingWorker.java:117) [Dashboard] at java.lang.Thread.run(Thread.java:595) [Dashboard] Caused by: java.net.ConnectException: Connection timed out [Dashboard] at org.apache.axis.AxisFault.makeFault(AxisFault.java:101) [Dashboard] at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:154) [Dashboard] at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java: 32) [Dashboard] at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118) [Dashboard] at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83) [Dashboard] at org.apache.axis.client.AxisClient.invoke(AxisClient.java:165) [Dashboard] at org.apache.axis.client.Call.invokeEngine(Call.java:2784) [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2767) [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2443) [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2366) [Dashboard] at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:226) [Dashboard] ... 9 more [Dashboard] Caused by: java.net.ConnectException: Connection timed out [Dashboard] at java.net.PlainSocketImpl.socketConnect(Native Method) [Dashboard] at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333) [Dashboard] at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195) [Dashboard] at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182) [Dashboard] at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366) [Dashboard] at java.net.Socket.connect(Socket.java:520) [Dashboard] at java.net.Socket.connect(Socket.java:470) [Dashboard] at java.net.Socket.(Socket.java:367) [Dashboard] at java.net.Socket.(Socket.java:180) [Dashboard] at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFact ory.java:149) [Dashboard] at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFact ory.java:120) [Dashboard] at org.apache.axis.transport.http.HTTPSender.getSocket(HTTPSender.java:191) [Dashboard] at org.apache.axis.transport.http.HTTPSender.writeToSocket(HTTPSender.java:404) [Dashboard] at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:138) [Dashboard] ... 18 more [Dashboard] 193461 [Thread-7] WARN CentralDigestCachedImpl - Error with Services RDF [Dashboard] org.biomoby.shared.MobyException: ===ERROR=== [Dashboard] Fault details: [Dashboard] Fault string: java.net.ConnectException: Connection timed out [Dashboard] Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException [Dashboard] Fault actor: null [Dashboard] When calling: [Dashboard] http://moby.ucalgary.ca/moby/MOBY-Central.pl [Dashboard] =========== [Dashboard] at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:230) [Dashboard] at org.biomoby.client.CentralImpl.getResourceRefs(CentralImpl.java:1772) [Dashboard] at org.biomoby.client.CentralImpl.getResource(CentralImpl.java:1807) [Dashboard] at org.biomoby.client.CentralDigestCachedImpl.getResourceAsString(CentralDigest CachedImpl.java:216) [Dashboard] at org.biomoby.client.CentralDigestCachedImpl.fillServicesCache(CentralDigestCa chedImpl.java:243) [Dashboard] at org.biomoby.client.CentralDigestCachedImpl.getServices(CentralDigestCachedIm pl.java:709) [Dashboard] at org.biomoby.service.dashboard.RegistryModel.getServices(RegistryModel.java:5 61) [Dashboard] at org.biomoby.service.dashboard.ServicesTree$4.construct(ServicesTree.java:121 ) [Dashboard] at org.biomoby.service.dashboard.SwingWorker$2.run(SwingWorker.java:117) [Dashboard] at java.lang.Thread.run(Thread.java:595) [Dashboard] Caused by: java.net.ConnectException: Connection timed out [Dashboard] at org.apache.axis.AxisFault.makeFault(AxisFault.java:101) [Dashboard] at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:154) [Dashboard] at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java: 32) [Dashboard] at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118) [Dashboard] at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83) [Dashboard] at org.apache.axis.client.AxisClient.invoke(AxisClient.java:165) [Dashboard] at org.apache.axis.client.Call.invokeEngine(Call.java:2784) [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2767) [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2443) [Dashboard] at org.apache.axis.client.Call.invoke(Call.java:2366) [Dashboard] at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:226) [Dashboard] ... 9 more [Dashboard] Caused by: java.net.ConnectException: Connection timed out [Dashboard] at java.net.PlainSocketImpl.socketConnect(Native Method) [Dashboard] at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333) [Dashboard] at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195) [Dashboard] at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182) [Dashboard] at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366) [Dashboard] at java.net.Socket.connect(Socket.java:520) [Dashboard] at java.net.Socket.connect(Socket.java:470) [Dashboard] at java.net.Socket.(Socket.java:367) [Dashboard] at java.net.Socket.(Socket.java:180) [Dashboard] at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFact ory.java:149) [Dashboard] at org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFact ory.java:120) [Dashboard] at org.apache.axis.transport.http.HTTPSender.getSocket(HTTPSender.java:191) [Dashboard] at org.apache.axis.transport.http.HTTPSender.writeToSocket(HTTPSender.java:404) [Dashboard] at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:138) [Dashboard] ... 18 more BUILD SUCCESSFUL >From Dashboard (after one minute) -------------- ===Error=== Fault details: Fault string: java.net.ConnectException: Connection timed out Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException Fault actor: null when calling: http://moby.uralgary.ca/moby/MOBY-Central.pl Is this a problem with the proxy settings I made in net.properties or is it inside Dashboard? Regards, Michael From hao.chen at uni-bielefeld.de Wed Feb 20 16:01:33 2008 From: hao.chen at uni-bielefeld.de (wasser) Date: Wed, 20 Feb 2008 16:01:33 -0000 Subject: [MOBY-dev] can not generate service skeleton Message-ID: <1203522403.11381.6.camel@andreas.dhcp.studentenwerk-bielefeld.de> hi, everyone I got this error just from yesterday and Moses generator works very good before. Now every time I try to generate new service , I got an error message which tells me that compile failed. It seems that ant doesn't work correctly. Have somebody the same problem? regards h.chen