From sneumann at ipb-halle.de Tue Apr 1 01:07:36 2008 From: sneumann at ipb-halle.de (Steffen Neumann) Date: Tue, 01 Apr 2008 07:07:36 +0200 Subject: [MOBY-dev] [SPAM_ipb] Eclipse, Maven and JDK In-Reply-To: <52a28ae20803311837m28afe66ag7b7759b4306b5ca1@mail.gmail.com> References: <52a28ae20803311837m28afe66ag7b7759b4306b5ca1@mail.gmail.com> Message-ID: <1207026456.6979.26.camel@samson> On Mon, 2008-03-31 at 18:37 -0700, Wendy Alexander wrote: > Hi all, > > I am having a heck of a time trying to get Eclipse to recognize a JDK so > that it can use the Maven libraries. I have several JDKs installed. In > Eclipse, I set my installed JREs to my JDK directories. I set my path to > include JDK 1.5. I set JAVA_HOME to my JDK directory. I selected JDK > 1.5as my project Jave Library. I added a -vm line to > eclipse.ini directing it to my JDK. Which OS ? On Ubuntu: cat /etc/eclipse/java_home # This file determines the search order the Eclipse Platform uses to find a # compatible JAVA_HOME. This setting may be overridden on a per-user basis by # altering the JAVA_HOME setting in ~/.eclipse/eclipserc. #/usr/lib/jvm/java-7-icedtea /usr/lib/jvm/java-gcj /usr/lib/kaffe/pthreads /usr/lib/jvm/java-6-sun /usr/lib/jvm/java-1.5.0-sun /usr/lib/j2se/1.5 /usr/lib/j2se/1.4 /usr/lib/j2sdk1.5-ibm /usr/lib/j2sdk1.4-ibm /usr/lib/j2sdk1.6-sun /usr/lib/j2sdk1.5-sun /usr/lib/j2sdk1.4-sun -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part URL: From wlalexander at gmail.com Tue Apr 1 11:30:17 2008 From: wlalexander at gmail.com (Wendy Alexander) Date: Tue, 1 Apr 2008 08:30:17 -0700 Subject: [MOBY-dev] [SPAM_ipb] Eclipse, Maven and JDK In-Reply-To: <1207026456.6979.26.camel@samson> References: <52a28ae20803311837m28afe66ag7b7759b4306b5ca1@mail.gmail.com> <1207026456.6979.26.camel@samson> Message-ID: <52a28ae20804010830p6e4e0f33o5f13cdb2f892448c@mail.gmail.com> I'm using Windows. On Mon, Mar 31, 2008 at 10:07 PM, Steffen Neumann wrote: > On Mon, 2008-03-31 at 18:37 -0700, Wendy Alexander wrote: > > Hi all, > > > > I am having a heck of a time trying to get Eclipse to recognize a JDK so > > that it can use the Maven libraries. I have several JDKs installed. In > > Eclipse, I set my installed JREs to my JDK directories. I set my path > to > > include JDK 1.5. I set JAVA_HOME to my JDK directory. I selected JDK > > 1.5as my project Jave Library. I added a -vm line to > > eclipse.ini directing it to my JDK. > > Which OS ? > > On Ubuntu: > > cat /etc/eclipse/java_home > # This file determines the search order the Eclipse Platform uses to find > a > # compatible JAVA_HOME. This setting may be overridden on a per-user basis > by > # altering the JAVA_HOME setting in ~/.eclipse/eclipserc. > > #/usr/lib/jvm/java-7-icedtea > /usr/lib/jvm/java-gcj > /usr/lib/kaffe/pthreads > /usr/lib/jvm/java-6-sun > /usr/lib/jvm/java-1.5.0-sun > /usr/lib/j2se/1.5 > /usr/lib/j2se/1.4 > /usr/lib/j2sdk1.5-ibm > /usr/lib/j2sdk1.4-ibm > /usr/lib/j2sdk1.6-sun > /usr/lib/j2sdk1.5-sun > /usr/lib/j2sdk1.4-sun > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > From wlalexander at gmail.com Wed Apr 2 16:08:46 2008 From: wlalexander at gmail.com (Wendy Alexander) Date: Wed, 2 Apr 2008 13:08:46 -0700 Subject: [MOBY-dev] [SPAM_ipb] Eclipse, Maven and JDK In-Reply-To: <52a28ae20804010830p6e4e0f33o5f13cdb2f892448c@mail.gmail.com> References: <52a28ae20803311837m28afe66ag7b7759b4306b5ca1@mail.gmail.com> <1207026456.6979.26.camel@samson> <52a28ae20804010830p6e4e0f33o5f13cdb2f892448c@mail.gmail.com> Message-ID: <52a28ae20804021308s669a1883j3d7acefa5161e264@mail.gmail.com> Eddie and Mark, you saved the day! Let's hope no one else has this much trouble setting up jMoby on Eclipse! What a nightmare that was! Thanks again! W On Tue, Apr 1, 2008 at 8:30 AM, Wendy Alexander wrote: > I'm using Windows. > > On Mon, Mar 31, 2008 at 10:07 PM, Steffen Neumann > wrote: > > > On Mon, 2008-03-31 at 18:37 -0700, Wendy Alexander wrote: > > > Hi all, > > > > > > I am having a heck of a time trying to get Eclipse to recognize a JDK > > so > > > that it can use the Maven libraries. I have several JDKs installed. > > In > > > Eclipse, I set my installed JREs to my JDK directories. I set my path > > to > > > include JDK 1.5. I set JAVA_HOME to my JDK directory. I selected JDK > > > 1.5as my project Jave Library. I added a -vm line to > > > eclipse.ini directing it to my JDK. > > > > Which OS ? > > > > On Ubuntu: > > > > cat /etc/eclipse/java_home > > # This file determines the search order the Eclipse Platform uses to > > find a > > # compatible JAVA_HOME. This setting may be overridden on a per-user > > basis by > > # altering the JAVA_HOME setting in ~/.eclipse/eclipserc. > > > > #/usr/lib/jvm/java-7-icedtea > > /usr/lib/jvm/java-gcj > > /usr/lib/kaffe/pthreads > > /usr/lib/jvm/java-6-sun > > /usr/lib/jvm/java-1.5.0-sun > > /usr/lib/j2se/1.5 > > /usr/lib/j2se/1.4 > > /usr/lib/j2sdk1.5-ibm > > /usr/lib/j2sdk1.4-ibm > > /usr/lib/j2sdk1.6-sun > > /usr/lib/j2sdk1.5-sun > > /usr/lib/j2sdk1.4-sun > > > > > > _______________________________________________ > > MOBY-dev mailing list > > MOBY-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > > > From Sebastien.Carrere at toulouse.inra.fr Fri Apr 4 10:16:25 2008 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Fri, 04 Apr 2008 16:16:25 +0200 Subject: [MOBY-dev] PlayMOBY: a lightweight framework to deploy BioMOBY web-services in perl Message-ID: <47F63839.7080903@toulouse.inra.fr> Bonjour ? tous, I would like to announce the release of a new BioMOBY tool: http://lipm-bioinfo.toulouse.inra.fr/biomoby/playmoby PlayMOBY is a framework developped in our lab to automatically generate the Perl code and publish BioMOBY web-services. The starting point to deploy a web-service using PlayMOBY is a Mobyle description file (Letondal et al). That's why we provide a perl module (Appli.pm) to produce such a file in the tarball. For more information, please have a look to this section: http://lipm-bioinfo.toulouse.inra.fr/biomoby/playmoby/#synopsis PlayMoby is freely available (CeCill Licence, GNU-GPL compatible). If you are interested in using PlayMOBY and having any problem, do not hesitate to send me an email. Bonne journee, Sebastien Carrere -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From MichaelGerlich at gmx.de Mon Apr 7 06:52:22 2008 From: MichaelGerlich at gmx.de (Michael Gerlich) Date: Mon, 07 Apr 2008 12:52:22 +0200 Subject: [MOBY-dev] Problems with Biomoby Ant Script Message-ID: <20080407105222.61000@gmx.net> Hi there, I'am still having problems getting JMoby to work in Eclipse. First of all, I run Eclipse on OpenSuse 10.3 with updated Java JDK 1.5 Update 15. As written here (http://bioinfo.mpiz-koeln.mpg.de/araws/documentation/help/jmoby-step-by-step/writing-biomoby-web-services/known-errors-and-problems) Eclipse is started from console with parameter -vmargs and -Djava.home=/usr/lib/jvm/java-1.5.0-sun-1.5.0_update15/jre/. Though I'am connected through a proxy, I need to specify proxy settings in net.properties with http_proxy tags (system variables set doesn't seem to affect eclipse or java in any way). Downloading from CVS works fine from Eclipse (even without proxy settings in net.properties), but as soon as I want to call ant scripts (like install), the proxy settings have to be specified or a timeout arises. When running install ant task, after some time, the following shows up: [Local cache] The jMoby is now creating a local cache. Depending [Local cache] on the network speed, it may take several minutes [Local cache] (usually it should be done within about a minute). [Local cache] [Local cache] [You can check the progress in the jMoby.log file.] [Local cache] [Local cache] ===ERROR=== [Local cache] ===ERROR=== [Local cache] Fault details: [Local cache] Fault string: java.net.ConnectException: Die Wartezeit f?r die Verbindung ist abgelaufen [Local cache] Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException [Local cache] Fault actor: null [Local cache] When calling: [Local cache] http://moby.ucalgary.ca/moby/MOBY-Central.pl [Local cache] =========== [Local cache] =========== Retrieving namespaces... BUILD FAILED /home/micge/workspace/moby2/xmls/install.xml:99: Java returned: 1 Total time: 4 minutes 49 seconds Everything before building the cache runs fine, but there is a timeout specified. I don't know what or where to change a thing because the error is caused by the proxy settings (so I guess). Anyone who knows an answer to this? Regards, Michael From groscurt at mpiz-koeln.mpg.de Tue Apr 8 02:41:51 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 08 Apr 2008 08:41:51 +0200 Subject: [MOBY-dev] Problems with Biomoby Ant Script In-Reply-To: <20080407105222.61000@gmx.net> References: <20080407105222.61000@gmx.net> Message-ID: <47FB13AF.7020600@mpiz-koeln.mpg.de> Hi Michael, first of all - please check the page for updates ;-) it has changed so the vmargs parameter are actually not needed to run Eclipse and jmoby correctly. Your error seems simple - http://moby.ucalgary.ca/moby/MOBY-Central.pl was not reachable at the time you tried it ... I recommend just to run the task again - it should work then (at least i can access http://moby.ucalgary.ca/moby/MOBY-Central.pl currently) best andreas Michael Gerlich wrote: > Hi there, > > I'am still having problems getting JMoby to work in Eclipse. > First of all, I run Eclipse on OpenSuse 10.3 with updated Java JDK 1.5 Update 15. > As written here (http://bioinfo.mpiz-koeln.mpg.de/araws/documentation/help/jmoby-step-by-step/writing-biomoby-web-services/known-errors-and-problems) > Eclipse is started from console with parameter -vmargs and -Djava.home=/usr/lib/jvm/java-1.5.0-sun-1.5.0_update15/jre/. > Though I'am connected through a proxy, I need to specify proxy settings in net.properties with http_proxy tags (system variables set doesn't seem to affect eclipse or java in any way). > > Downloading from CVS works fine from Eclipse (even without proxy settings in net.properties), but as soon as I want to call ant scripts (like install), the proxy settings have to be specified or a timeout arises. > > When running install ant task, after some time, the following shows up: > > [Local cache] The jMoby is now creating a local cache. Depending > [Local cache] on the network speed, it may take several minutes > [Local cache] (usually it should be done within about a minute). > [Local cache] > [Local cache] [You can check the progress in the jMoby.log file.] > [Local cache] > [Local cache] ===ERROR=== > [Local cache] ===ERROR=== > [Local cache] Fault details: > [Local cache] Fault string: java.net.ConnectException: Die Wartezeit f?r die Verbindung ist abgelaufen > [Local cache] Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException > [Local cache] Fault actor: null > [Local cache] When calling: > [Local cache] http://moby.ucalgary.ca/moby/MOBY-Central.pl > [Local cache] =========== > [Local cache] =========== > Retrieving namespaces... > > BUILD FAILED > /home/micge/workspace/moby2/xmls/install.xml:99: Java returned: 1 > > Total time: 4 minutes 49 seconds > > Everything before building the cache runs fine, but there is a timeout specified. > I don't know what or where to change a thing because the error is caused by the proxy settings (so I guess). > Anyone who knows an answer to this? > > Regards, > Michael > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From Sebastien.Carrere at toulouse.inra.fr Fri Apr 11 03:17:35 2008 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Fri, 11 Apr 2008 09:17:35 +0200 Subject: [MOBY-dev] Mobycentral down ? Message-ID: <47FF108F.4020006@toulouse.inra.fr> Hi all, I've got the following error when I try to connect to the main registry: ------------------------------------------------ Connection to default MOBY Central died because: DBI connect('mobycentral:localhost:3306','moby',...) failed: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (146) at /opt/coolstack/lib/perl5/site_perl/5.8.8/MOBY/Adaptor/moby/queryapi/mysql.pm line 90 ERROR ERROR ERROR ---------------------------------------------------------------- Sebastien -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From M4o at gmx.de Fri Apr 11 03:40:10 2008 From: M4o at gmx.de (M4o at gmx.de) Date: Fri, 11 Apr 2008 09:40:10 +0200 Subject: [MOBY-dev] Mobycentral down ? In-Reply-To: <47FF108F.4020006@toulouse.inra.fr> References: <47FF108F.4020006@toulouse.inra.fr> Message-ID: <20080411074010.173560@gmx.net> Hi all, yes from Germany the ucalgary.ca- Central also doesn't work. And I have some other points: 1. Will "getDeadServices" Service (http://moby.ucalgary.ca/moby/ValidateService?getDeadServices) come up working again? Cause i use this to filter dead Services from my service list. Or is there an other alternative? Ah working getStatus() or something like that? 2. Is it right that when you call the service.getPrimaryInputs(), there are no LSIDs at the Namespaces anymore (since jmoby 1.0 ?) ? Thanks, Moritz --------------------------------------------------------------------- when i call the findService methode for example... : - DBI connect('mobycentral:localhost:3306','moby',...) failed: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (146) at /opt/coolstack/lib/perl5/site_perl/5.8.8/MOBY/Adaptor/moby/queryapi/mysql.pm line 90 Exception in thread "main" org.biomoby.shared.MobyException: ===ERROR=== Fault details: [stackTrace: null] [hostname: null] Fault string: DBI connect('mobycentral:localhost:3306','moby',...) failed: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (146) at /opt/coolstack/lib/perl5/site_perl/5.8.8/MOBY/Adaptor/moby/queryapi/mysql.pm line 90 Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server Fault actor: null When calling: http://moby.ucalgary.ca/moby/MOBY-Central.pl =========== ---------------------------------------------------------------- -------- Original-Nachricht -------- > Datum: Fri, 11 Apr 2008 09:17:35 +0200 > Von: Sebastien Carrere > An: Core developer announcements > Betreff: [MOBY-dev] Mobycentral down ? > Hi all, > > I've got the following error when I try to connect to the main registry: > > ------------------------------------------------ > Connection to default MOBY Central died because: > DBI connect('mobycentral:localhost:3306','moby',...) failed: Can't > connect to local MySQL server through socket '/tmp/mysql.sock' (146) at > /opt/coolstack/lib/perl5/site_perl/5.8.8/MOBY/Adaptor/moby/queryapi/mysql.pm > line 90 > > ERROR ERROR ERROR > ---------------------------------------------------------------- > > > Sebastien -- Psst! Geheimtipp: Online Games kostenlos spielen bei den GMX Free Games! http://games.entertainment.gmx.net/de/entertainment/games/free From pieter.neerincx at wur.nl Fri Apr 11 06:11:51 2008 From: pieter.neerincx at wur.nl (Pieter Neerincx) Date: Fri, 11 Apr 2008 12:11:51 +0200 Subject: [MOBY-dev] Mobycentral down ? In-Reply-To: <20080411074010.173560@gmx.net> References: <47FF108F.4020006@toulouse.inra.fr> <20080411074010.173560@gmx.net> Message-ID: <96656174-1315-4B6D-871B-2F8F6047AF7A@wur.nl> Hi, Same thing from Wageningen, the Netherlands :(. I hope it's not serious... When the sysadmins try to figure out what's going on could they please also have a look at the MOBY::Client::Central::DUMP() method. Never worked on the Calgary Central as it died with a similar DBI error (unless it was recently fixed, in that case let us know...) Cheers, Pi On 11?Apr?2008, at 9:40 AM, M4o at gmx.de wrote: > Hi all, > > yes from Germany the ucalgary.ca- Central also doesn't work. > > And I have some other points: > > 1. Will "getDeadServices" Service (http://moby.ucalgary.ca/moby/ValidateService?getDeadServices > ) come up working again? Cause i use this to filter dead Services > from my service list. > Or is there an other alternative? Ah working getStatus() or > something like that? > > 2. Is it right that when you call the service.getPrimaryInputs(), > there are no LSIDs at the Namespaces anymore (since jmoby 1.0 ?) ? > > Thanks, > > Moritz > > --------------------------------------------------------------------- > when i call the findService methode for example... : > > - DBI connect('mobycentral:localhost:3306','moby',...) failed: Can't > connect to local MySQL server through socket '/tmp/mysql.sock' (146) > at /opt/coolstack/lib/perl5/site_perl/5.8.8/MOBY/Adaptor/moby/ > queryapi/mysql.pm line 90 > > Exception in thread "main" org.biomoby.shared.MobyException: > ===ERROR=== > Fault details: > [stackTrace: null] > [hostname: null] > Fault string: DBI connect('mobycentral:localhost:3306','moby',...) > failed: Can't connect to local MySQL server through socket '/tmp/ > mysql.sock' (146) at /opt/coolstack/lib/perl5/site_perl/5.8.8/MOBY/ > Adaptor/moby/queryapi/mysql.pm line 90 > > Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server > Fault actor: null > When calling: > http://moby.ucalgary.ca/moby/MOBY-Central.pl > =========== > > ---------------------------------------------------------------- > > > -------- Original-Nachricht -------- >> Datum: Fri, 11 Apr 2008 09:17:35 +0200 >> Von: Sebastien Carrere >> An: Core developer announcements >> Betreff: [MOBY-dev] Mobycentral down ? > >> Hi all, >> >> I've got the following error when I try to connect to the main >> registry: >> >> ------------------------------------------------ >> Connection to default MOBY Central died because: >> DBI connect('mobycentral:localhost:3306','moby',...) failed: Can't >> connect to local MySQL server through socket '/tmp/ >> mysql.sock' (146) at >> /opt/coolstack/lib/perl5/site_perl/5.8.8/MOBY/Adaptor/moby/queryapi/ >> mysql.pm >> line 90 >> >> ERROR ERROR ERROR >> ---------------------------------------------------------------- >> >> >> Sebastien > > -- > Psst! Geheimtipp: Online Games kostenlos spielen bei den GMX Free > Games! > http://games.entertainment.gmx.net/de/entertainment/games/free > _______________________________________________ > 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: +31 (0)317-483 060 fax: +31 (0)317-483 584 mobile: +31 (0)6-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From edward.kawas at gmail.com Fri Apr 11 09:27:27 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 11 Apr 2008 06:27:27 -0700 Subject: [MOBY-dev] Mobycentral down ? In-Reply-To: <96656174-1315-4B6D-871B-2F8F6047AF7A@wur.nl> References: <47FF108F.4020006@toulouse.inra.fr> <20080411074010.173560@gmx.net> <96656174-1315-4B6D-871B-2F8F6047AF7A@wur.nl> Message-ID: <47ff6755.14da600a.27c7.3af5@mx.google.com> Hi Pieter, Dump on mobycentral should work now (once mobycentral is back up and running). This was fixed a while back. 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: April-11-08 3:12 AM To: Core developer announcements Subject: Re: [MOBY-dev] Mobycentral down ? Hi, Same thing from Wageningen, the Netherlands :(. I hope it's not serious... When the sysadmins try to figure out what's going on could they please also have a look at the MOBY::Client::Central::DUMP() method. Never worked on the Calgary Central as it died with a similar DBI error (unless it was recently fixed, in that case let us know...) Cheers, Pi On 11.Apr.2008, at 9:40 AM, M4o at gmx.de wrote: > Hi all, > > yes from Germany the ucalgary.ca- Central also doesn't work. > > And I have some other points: > > 1. Will "getDeadServices" Service (http://moby.ucalgary.ca/moby/ValidateService?getDeadServices > ) come up working again? Cause i use this to filter dead Services > from my service list. > Or is there an other alternative? Ah working getStatus() or > something like that? > > 2. Is it right that when you call the service.getPrimaryInputs(), > there are no LSIDs at the Namespaces anymore (since jmoby 1.0 ?) ? > > Thanks, > > Moritz > > --------------------------------------------------------------------- > when i call the findService methode for example... : > > - DBI connect('mobycentral:localhost:3306','moby',...) failed: Can't > connect to local MySQL server through socket '/tmp/mysql.sock' (146) > at /opt/coolstack/lib/perl5/site_perl/5.8.8/MOBY/Adaptor/moby/ > queryapi/mysql.pm line 90 > > Exception in thread "main" org.biomoby.shared.MobyException: > ===ERROR=== > Fault details: > [stackTrace: null] > [hostname: null] > Fault string: DBI connect('mobycentral:localhost:3306','moby',...) > failed: Can't connect to local MySQL server through socket '/tmp/ > mysql.sock' (146) at /opt/coolstack/lib/perl5/site_perl/5.8.8/MOBY/ > Adaptor/moby/queryapi/mysql.pm line 90 > > Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server > Fault actor: null > When calling: > http://moby.ucalgary.ca/moby/MOBY-Central.pl > =========== > > ---------------------------------------------------------------- > > > -------- Original-Nachricht -------- >> Datum: Fri, 11 Apr 2008 09:17:35 +0200 >> Von: Sebastien Carrere >> An: Core developer announcements >> Betreff: [MOBY-dev] Mobycentral down ? > >> Hi all, >> >> I've got the following error when I try to connect to the main >> registry: >> >> ------------------------------------------------ >> Connection to default MOBY Central died because: >> DBI connect('mobycentral:localhost:3306','moby',...) failed: Can't >> connect to local MySQL server through socket '/tmp/ >> mysql.sock' (146) at >> /opt/coolstack/lib/perl5/site_perl/5.8.8/MOBY/Adaptor/moby/queryapi/ >> mysql.pm >> line 90 >> >> ERROR ERROR ERROR >> ---------------------------------------------------------------- >> >> >> Sebastien > > -- > Psst! Geheimtipp: Online Games kostenlos spielen bei den GMX Free > Games! > http://games.entertainment.gmx.net/de/entertainment/games/free > _______________________________________________ > 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: +31 (0)317-483 060 fax: +31 (0)317-483 584 mobile: +31 (0)6-143 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 Sat Apr 12 12:12:22 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Sat, 12 Apr 2008 18:12:22 +0200 Subject: [MOBY-dev] Mobycentral down ? In-Reply-To: <47ff6755.14da600a.27c7.3af5@mx.google.com> References: <47FF108F.4020006@toulouse.inra.fr> <20080411074010.173560@gmx.net> <96656174-1315-4B6D-871B-2F8F6047AF7A@wur.nl> <47ff6755.14da600a.27c7.3af5@mx.google.com> Message-ID: <6779E917-320E-4253-8C0A-9C92DFA92082@wur.nl> On 11 Apr 2008, at 15:27, Edward Kawas wrote: > Hi Pieter, > > Dump on mobycentral should work now (once mobycentral is back up and > running). This was fixed a while back. Thanks! > > 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: April-11-08 3:12 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Mobycentral down ? > > Hi, > > Same thing from Wageningen, the Netherlands :(. I hope it's not > serious... > > When the sysadmins try to figure out what's going on could they please > also have a look at the MOBY::Client::Central::DUMP() method. Never > worked on the Calgary Central as it died with a similar DBI error > (unless it was recently fixed, in that case let us know...) > > Cheers, > > Pi > > > On 11.Apr.2008, at 9:40 AM, M4o at gmx.de wrote: >> Hi all, >> >> yes from Germany the ucalgary.ca- Central also doesn't work. >> >> And I have some other points: >> >> 1. Will "getDeadServices" Service > (http://moby.ucalgary.ca/moby/ValidateService?getDeadServices >> ) come up working again? Cause i use this to filter dead Services >> from my service list. >> Or is there an other alternative? Ah working getStatus() or >> something like that? >> >> 2. Is it right that when you call the service.getPrimaryInputs(), >> there are no LSIDs at the Namespaces anymore (since jmoby 1.0 ?) ? >> >> Thanks, >> >> Moritz >> >> --------------------------------------------------------------------- >> when i call the findService methode for example... : >> >> - DBI connect('mobycentral:localhost:3306','moby',...) failed: Can't >> connect to local MySQL server through socket '/tmp/mysql.sock' (146) >> at /opt/coolstack/lib/perl5/site_perl/5.8.8/MOBY/Adaptor/moby/ >> queryapi/mysql.pm line 90 >> >> Exception in thread "main" org.biomoby.shared.MobyException: >> ===ERROR=== >> Fault details: >> [stackTrace: null] >> [hostname: null] >> Fault string: DBI connect('mobycentral:localhost:3306','moby',...) >> failed: Can't connect to local MySQL server through socket '/tmp/ >> mysql.sock' (146) at /opt/coolstack/lib/perl5/site_perl/5.8.8/MOBY/ >> Adaptor/moby/queryapi/mysql.pm line 90 >> >> Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server >> Fault actor: null >> When calling: >> http://moby.ucalgary.ca/moby/MOBY-Central.pl >> =========== >> >> ---------------------------------------------------------------- >> >> >> -------- Original-Nachricht -------- >>> Datum: Fri, 11 Apr 2008 09:17:35 +0200 >>> Von: Sebastien Carrere >>> An: Core developer announcements >>> Betreff: [MOBY-dev] Mobycentral down ? >> >>> Hi all, >>> >>> I've got the following error when I try to connect to the main >>> registry: >>> >>> ------------------------------------------------ >>> Connection to default MOBY Central died because: >>> DBI connect('mobycentral:localhost:3306','moby',...) failed: >>> Can't >>> connect to local MySQL server through socket '/tmp/ >>> mysql.sock' (146) at >>> /opt/coolstack/lib/perl5/site_perl/5.8.8/MOBY/Adaptor/moby/queryapi/ >>> mysql.pm >>> line 90 >>> >>> ERROR ERROR ERROR >>> ---------------------------------------------------------------- >>> >>> >>> Sebastien >> >> -- >> Psst! Geheimtipp: Online Games kostenlos spielen bei den GMX Free >> Games! >> http://games.entertainment.gmx.net/de/entertainment/games/free >> _______________________________________________ >> 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: +31 (0)317-483 060 > fax: +31 (0)317-483 584 > mobile: +31 (0)6-143 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: +31 (0)317-483 060 fax: +31 (0)317-483 584 mobile: +31 (0)6-143 66 783 e-mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------- From groscurt at mpiz-koeln.mpg.de Mon Apr 14 07:16:53 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 14 Apr 2008 13:16:53 +0200 Subject: [MOBY-dev] RDFAgent and local MobyCentral In-Reply-To: <6779E917-320E-4253-8C0A-9C92DFA92082@wur.nl> References: <47FF108F.4020006@toulouse.inra.fr> <20080411074010.173560@gmx.net> <96656174-1315-4B6D-871B-2F8F6047AF7A@wur.nl> <47ff6755.14da600a.27c7.3af5@mx.google.com> <6779E917-320E-4253-8C0A-9C92DFA92082@wur.nl> Message-ID: <48033D25.7070703@mpiz-koeln.mpg.de> Hi, I've set up a local MobyCentral and installed the RDF agent. When I call the RDFagent (or when i try to get the Ontologies via dashboard), it always breaks for the Datatypes with the message (found in the error log of apache): (or the rdfagent breaks during a find servicecall respectively): HTTP::Message content not bytes at /usr/local/lib/site_perl/SOAP/Transport/HTTP.pm line 424 Premature end of script headers: MOBY-Central.pl Apparently the connection works and I cant find problems in the apache logs. I think the problem could be in the MOBY-Central.pl - what value do i have to enter for 'dispatch_to(...)' ? the path to the MOBY perl installation. I checked out moby from the cvs and run MOBY-Server/MakeFile.PL to install moby into /usr/local/perl. So MOBY can be found under /usr/local/perl/lib/site_perl - is this what i have to enter ? Thanks andreas From edward.kawas at gmail.com Mon Apr 14 08:54:11 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 14 Apr 2008 05:54:11 -0700 Subject: [MOBY-dev] RDFAgent and local MobyCentral In-Reply-To: <48033D25.7070703@mpiz-koeln.mpg.de> References: <47FF108F.4020006@toulouse.inra.fr> <20080411074010.173560@gmx.net> <96656174-1315-4B6D-871B-2F8F6047AF7A@wur.nl> <47ff6755.14da600a.27c7.3af5@mx.google.com> <6779E917-320E-4253-8C0A-9C92DFA92082@wur.nl> <48033D25.7070703@mpiz-koeln.mpg.de> Message-ID: <480353fb.1abd600a.4785.2768@mx.google.com> Hi Andreas, You shouldn't have to change anything in the dispatcher file. You should try running the agent from the command line and seeing what errors are outputted. For the ontologies, do the other ones work? If so, try deleting the cache and try again. 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: April-14-08 4:17 AM To: Core developer announcements Subject: [MOBY-dev] RDFAgent and local MobyCentral Hi, I've set up a local MobyCentral and installed the RDF agent. When I call the RDFagent (or when i try to get the Ontologies via dashboard), it always breaks for the Datatypes with the message (found in the error log of apache): (or the rdfagent breaks during a find servicecall respectively): HTTP::Message content not bytes at /usr/local/lib/site_perl/SOAP/Transport/HTTP.pm line 424 Premature end of script headers: MOBY-Central.pl Apparently the connection works and I cant find problems in the apache logs. I think the problem could be in the MOBY-Central.pl - what value do i have to enter for 'dispatch_to(...)' ? the path to the MOBY perl installation. I checked out moby from the cvs and run MOBY-Server/MakeFile.PL to install moby into /usr/local/perl. So MOBY can be found under /usr/local/perl/lib/site_perl - is this what i have to enter ? Thanks 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 Mon Apr 14 10:45:32 2008 From: MichaelGerlich at gmx.de (Michael Gerlich) Date: Mon, 14 Apr 2008 16:45:32 +0200 Subject: [MOBY-dev] Mobycentral down ? In-Reply-To: References: <694746.46545.qm@web57412.mail.re1.yahoo.com> Message-ID: <40032716AC524238B1F7EE46611A8D71@Galaxy> Hi all, after finally getting Dashboard to work, I wanted to write some little "nonsense" services to get used to the Biomoby world. I tried to register them in the testing registry because they would obviously be misplaced in the central registry. After this weekend and the problems that occured with the registries , I still get errors from the testing registry. Will this be fixed or what would be the appropriate procedure for me to try out such nonsense (but for me useful) services. Regards, Michael From edward.kawas at gmail.com Mon Apr 14 12:08:59 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 14 Apr 2008 09:08:59 -0700 Subject: [MOBY-dev] Mobycentral down ? In-Reply-To: <40032716AC524238B1F7EE46611A8D71@Galaxy> References: <694746.46545.qm@web57412.mail.re1.yahoo.com> <40032716AC524238B1F7EE46611A8D71@Galaxy> Message-ID: <480381a7.23f8720a.7db3.fffff7c3@mx.google.com> What errors are you getting from the testing registry? Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Michael Gerlich Sent: April-14-08 7:46 AM To: moby-dev at lists.open-bio.org Subject: Re: [MOBY-dev] Mobycentral down ? Hi all, after finally getting Dashboard to work, I wanted to write some little "nonsense" services to get used to the Biomoby world. I tried to register them in the testing registry because they would obviously be misplaced in the central registry. After this weekend and the problems that occured with the registries , I still get errors from the testing registry. Will this be fixed or what would be the appropriate procedure for me to try out such nonsense (but for me useful) services. Regards, Michael _______________________________________________ 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 Mon Apr 14 12:46:42 2008 From: MichaelGerlich at gmx.de (Michael Gerlich) Date: Mon, 14 Apr 2008 18:46:42 +0200 Subject: [MOBY-dev] Mobycentral down ? In-Reply-To: <480381a7.23f8720a.7db3.fffff7c3@mx.google.com> References: <694746.46545.qm@web57412.mail.re1.yahoo.com> <40032716AC524238B1F7EE46611A8D71@Galaxy> <480381a7.23f8720a.7db3.fffff7c3@mx.google.com> Message-ID: <000001c89e4f$1e7e2e50$5b7a8af0$@de> When I start Dashboard with testing registry (as chosen from the last run), Java Socket Connect exceptions occur. But if I change to central registry, everything works fine and all lists are loaded. When I try to change back to testing, all the list stay empty, reloading doesn't change anything and no error messages appear at all. I hope this will help. Regards, Michael From edward.kawas at gmail.com Mon Apr 14 13:18:05 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 14 Apr 2008 10:18:05 -0700 Subject: [MOBY-dev] Mobycentral down ? In-Reply-To: <000001c89e4f$1e7e2e50$5b7a8af0$@de> References: <694746.46545.qm@web57412.mail.re1.yahoo.com> <40032716AC524238B1F7EE46611A8D71@Galaxy> <480381a7.23f8720a.7db3.fffff7c3@mx.google.com> <000001c89e4f$1e7e2e50$5b7a8af0$@de> Message-ID: <480391d7.0f98600a.4452.084c@mx.google.com> When I start up dashboard, and then select the test registry, it works fine for me. What endpoint pops up when you select the testing registry? Is it http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl? Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Michael Gerlich Sent: April-14-08 9:47 AM To: 'Core developer announcements' Subject: Re: [MOBY-dev] Mobycentral down ? When I start Dashboard with testing registry (as chosen from the last run), Java Socket Connect exceptions occur. But if I change to central registry, everything works fine and all lists are loaded. When I try to change back to testing, all the list stay empty, reloading doesn't change anything and no error messages appear at all. I hope this will help. Regards, Michael _______________________________________________ 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 Mon Apr 14 13:39:04 2008 From: MichaelGerlich at gmx.de (Michael Gerlich) Date: Mon, 14 Apr 2008 19:39:04 +0200 Subject: [MOBY-dev] Mobycentral down ? In-Reply-To: <480391d7.0f98600a.4452.084c@mx.google.com> References: <694746.46545.qm@web57412.mail.re1.yahoo.com> <40032716AC524238B1F7EE46611A8D71@Galaxy> <480381a7.23f8720a.7db3.fffff7c3@mx.google.com> <000001c89e4f$1e7e2e50$5b7a8af0$@de> <480391d7.0f98600a.4452.084c@mx.google.com> Message-ID: <000001c89e56$6f2d6080$4d882180$@de> Yes, that's it. Guess I should have a look into my connection configs if you say testing registry is up working again. Michael From jmrodriguez at cnio.es Tue Apr 15 04:50:47 2008 From: jmrodriguez at cnio.es (Jose Manuel rodriguez) Date: Tue, 15 Apr 2008 10:50:47 +0200 Subject: [MOBY-dev] Problems installing MOBY-Client libraries Message-ID: <48046C67.3080704@cnio.es> Hello, I have downloaded the latest code using anonymous CVS and I am trying to install the MOBY-Client libraries but I have found some bugs: 1) The version 0.8.2.2 of WSRF::Lite is already installed in the machine but MOBY does not found. 2) (and most important) The installed package says me "the following files are missing in your kit" (lib/MOBY/...). Below I have attached the piece of messages. Best Regards, Jos? Manuel. -------------------------- root at terril:/opt/moby-live/Perl/MOBY-Client# perl Makefile.PL *** Module::AutoInstall version 1.03 *** Checking for Perl dependencies... [Core Features] - Test::More ...loaded. (0.78) - Test::Pod ...loaded. (1.26) - SOAP::Lite ...loaded. (0.67 >= 0.60) - XML::LibXML ...loaded. (1.66) - LWP::UserAgent ...loaded. (2.033) - CGI ...loaded. (3.15) - HTTP::Request::Common ...loaded. (1.26) - URI::Escape ...loaded. (3.28) - RDF::Core ...loaded. (0.51 >= 0.51) - HTML::Entities ...loaded. (1.35) - WSRF::Lite ...missing. (would need 0.8.2.2) - XML::DOM ...loaded. (1.44) - DateTime::Format::Epoch ...loaded. (0.10) - DateTime::Format::W3CDTF ...loaded. (0.04) - HTTP::Daemon ...loaded. (1.36) - HTTP::Daemon::SSL ...loaded. (1.02) - MIME::Base64 ...loaded. (3.07) - Digest::SHA1 ...loaded. (2.11) - Crypt::OpenSSL::RSA ...loaded. (0.25) - XML::CanonicalizeXML ...loaded. (0.03 >= 0.02) - Sys::Hostname::Long ...loaded. (1.4) - Crypt::OpenSSL::X509 ...loaded. (0.6) ==> Auto-install the 1 mandatory module(s) from CPAN? [y] CPAN: File::HomeDir loaded ok (v0.56) *** Dependencies will be installed the next time you type 'make'. *** Module::AutoInstall configuration finished. Checking if your kit is complete... Warning: the following files are missing in your kit: lib/MOBY/Async/LSAE.pm lib/MOBY/Async/Service.pm lib/MOBY/Async/SimpleServer.pm lib/MOBY/Async/WSRF.pm lib/MOBY/Client/Central.pm lib/MOBY/Client/CollectionArticle.pm lib/MOBY/Client/Exception/MobyException.pm lib/MOBY/Client/Exception/MobyExceptionCodes.pm lib/MOBY/Client/OntologyServer.pm lib/MOBY/Client/Registration.pm lib/MOBY/Client/SecondaryArticle.pm lib/MOBY/Client/Service.pm lib/MOBY/Client/ServiceInstance.pm lib/MOBY/Client/SimpleArticle.pm lib/MOBY/Client/SimpleInput.pm lib/MOBY/CommonSubs.pm lib/MOBY/CrossReference.pm lib/MOBY/MobyXMLConstants.pm lib/MOBY/RDF/Parsers/DatatypeParser.pm lib/MOBY/RDF/Parsers/NamespaceParser.pm lib/MOBY/RDF/Parsers/ServiceTypeParser.pm lib/MOBY/RDF/Predicates/DC_PROTEGE.pm lib/MOBY/RDF/Predicates/FETA.pm lib/MOBY/RDF/Predicates/MOBY_PREDICATES.pm lib/MOBY/RDF/Predicates/OMG_LSID.pm lib/MOBY/RDF/Predicates/OWL.pm lib/MOBY/RDF/Predicates/RDF.pm lib/MOBY/RDF/Predicates/RDFS.pm lib/MOBY/RDF/Utils.pm Please inform the author. Warning: prerequisite WSRF::Lite 0.8.2.2 not found. We have. Writing Makefile for MOBY::Client ------------------------------- -- Jos? Manuel Rodr?guez Carrasco e-mail: jmrodriguez at cnio.es Tlfn: (+34) 91 732 80 00 ext: 2256 Fax: (+34) 91 224 69 76 Bioinformatic Unit Spanish National Cancer Center (CNIO) http://www.cnio.es Zip Code: 28029 Address: C/. Melchor Fernandez Almagro n? 3, Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From edward.kawas at gmail.com Tue Apr 15 09:38:48 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 15 Apr 2008 06:38:48 -0700 Subject: [MOBY-dev] Problems installing MOBY-Client libraries In-Reply-To: <48046C67.3080704@cnio.es> References: <48046C67.3080704@cnio.es> Message-ID: <4804aff3.20d7720a.1a88.ffffe7b4@mx.google.com> Hi Jose Manuel, Sorry for not posting this on the list or somewhere for others to read, but to install the MOBY-Client libraries, you have to options: Download the module from cpan: http://search.cpan.org/dist/MOBY-Client Or build it from the cvs (instructions taken from moby-live/Perl/README): To install just the *client* Perl MOBY libraries on your system, type the following (from within MOBY-Client/): perl populate_libs.pl perl Makefile.PL make make test make install The script populate_libs.pl goes through the MOBY-Server directory and extracts those modules required just for Client side MOBY. If you install from the cvs, then make sure *not* to the commit MOBY-Client/lib directory. So unfortunately our computers are not able to determine if some modules are installed or not and WSRF is one of those modules. If you are sure that your computer has the module, then just tell the makefile not to install dependencies. Hope this helps, Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jose Manuel rodriguez Sent: April-15-08 1:51 AM To: moby-dev at lists.open-bio.org; moby-dev-bounces at lists.open-bio.org Subject: [MOBY-dev] Problems installing MOBY-Client libraries Hello, I have downloaded the latest code using anonymous CVS and I am trying to install the MOBY-Client libraries but I have found some bugs: 1) The version 0.8.2.2 of WSRF::Lite is already installed in the machine but MOBY does not found. 2) (and most important) The installed package says me "the following files are missing in your kit" (lib/MOBY/...). Below I have attached the piece of messages. Best Regards, Jos? Manuel. -------------------------- root at terril:/opt/moby-live/Perl/MOBY-Client# perl Makefile.PL *** Module::AutoInstall version 1.03 *** Checking for Perl dependencies... [Core Features] - Test::More ...loaded. (0.78) - Test::Pod ...loaded. (1.26) - SOAP::Lite ...loaded. (0.67 >= 0.60) - XML::LibXML ...loaded. (1.66) - LWP::UserAgent ...loaded. (2.033) - CGI ...loaded. (3.15) - HTTP::Request::Common ...loaded. (1.26) - URI::Escape ...loaded. (3.28) - RDF::Core ...loaded. (0.51 >= 0.51) - HTML::Entities ...loaded. (1.35) - WSRF::Lite ...missing. (would need 0.8.2.2) - XML::DOM ...loaded. (1.44) - DateTime::Format::Epoch ...loaded. (0.10) - DateTime::Format::W3CDTF ...loaded. (0.04) - HTTP::Daemon ...loaded. (1.36) - HTTP::Daemon::SSL ...loaded. (1.02) - MIME::Base64 ...loaded. (3.07) - Digest::SHA1 ...loaded. (2.11) - Crypt::OpenSSL::RSA ...loaded. (0.25) - XML::CanonicalizeXML ...loaded. (0.03 >= 0.02) - Sys::Hostname::Long ...loaded. (1.4) - Crypt::OpenSSL::X509 ...loaded. (0.6) ==> Auto-install the 1 mandatory module(s) from CPAN? [y] CPAN: File::HomeDir loaded ok (v0.56) *** Dependencies will be installed the next time you type 'make'. *** Module::AutoInstall configuration finished. Checking if your kit is complete... Warning: the following files are missing in your kit: lib/MOBY/Async/LSAE.pm lib/MOBY/Async/Service.pm lib/MOBY/Async/SimpleServer.pm lib/MOBY/Async/WSRF.pm lib/MOBY/Client/Central.pm lib/MOBY/Client/CollectionArticle.pm lib/MOBY/Client/Exception/MobyException.pm lib/MOBY/Client/Exception/MobyExceptionCodes.pm lib/MOBY/Client/OntologyServer.pm lib/MOBY/Client/Registration.pm lib/MOBY/Client/SecondaryArticle.pm lib/MOBY/Client/Service.pm lib/MOBY/Client/ServiceInstance.pm lib/MOBY/Client/SimpleArticle.pm lib/MOBY/Client/SimpleInput.pm lib/MOBY/CommonSubs.pm lib/MOBY/CrossReference.pm lib/MOBY/MobyXMLConstants.pm lib/MOBY/RDF/Parsers/DatatypeParser.pm lib/MOBY/RDF/Parsers/NamespaceParser.pm lib/MOBY/RDF/Parsers/ServiceTypeParser.pm lib/MOBY/RDF/Predicates/DC_PROTEGE.pm lib/MOBY/RDF/Predicates/FETA.pm lib/MOBY/RDF/Predicates/MOBY_PREDICATES.pm lib/MOBY/RDF/Predicates/OMG_LSID.pm lib/MOBY/RDF/Predicates/OWL.pm lib/MOBY/RDF/Predicates/RDF.pm lib/MOBY/RDF/Predicates/RDFS.pm lib/MOBY/RDF/Utils.pm Please inform the author. Warning: prerequisite WSRF::Lite 0.8.2.2 not found. We have. Writing Makefile for MOBY::Client ------------------------------- -- Jos? Manuel Rodr?guez Carrasco e-mail: jmrodriguez at cnio.es Tlfn: (+34) 91 732 80 00 ext: 2256 Fax: (+34) 91 224 69 76 Bioinformatic Unit Spanish National Cancer Center (CNIO) http://www.cnio.es Zip Code: 28029 Address: C/. Melchor Fernandez Almagro n? 3, Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. _______________________________________________ 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 Apr 15 15:05:41 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 15 Apr 2008 12:05:41 -0700 Subject: [MOBY-dev] tools for registering items into mobycentral Message-ID: <4804fc92.1bbc720a.5a00.ffff9710@mx.google.com> A long time ago, I created some java applets that aided in the registration of datatypes, namespaces, services, and service types into mobycentral. They were a good first crack at things, but had many flaws. Recently, I have removed them and replaced them with pure javascript versions located at: http://bioinfo.icapture.ubc.ca:8090/MobyRegistrationPages. The new version is lacking documentation, but doc is in the works. I am posting the url for people to try and to provide feedback for me to improve them. Right now, there are some style sheet issues, but the pages are functional. I know that they work in the most recent version of Opera and firefox. They should also work in Internet explorer and Safari. Let me know if you find any errors and if/how you think I could improve the look and feel of the pages. I am by no means an expert in creating UIs or in html/javascript so your suggestions are welcomed! Thanks, Eddie From serr at ac.uma.es Wed Apr 16 03:33:00 2008 From: serr at ac.uma.es (Sergio Ramirez Ramirez) Date: Wed, 16 Apr 2008 09:33:00 +0200 Subject: [MOBY-dev] tools for registering items into mobycentral In-Reply-To: <4804fc92.1bbc720a.5a00.ffff9710@mx.google.com> References: <4804fc92.1bbc720a.5a00.ffff9710@mx.google.com> Message-ID: <4805ABAC.9060408@ac.uma.es> Hi Eddi, Sorry but I have problems trying to access the url. Is the server online? Kind Regards, Sergio Edward Kawas wrote: > A long time ago, I created some java applets that aided in the registration > of datatypes, namespaces, services, and service types into mobycentral. They > were a good first crack at things, but had many flaws. > > Recently, I have removed them and replaced them with pure javascript > versions located at: > http://bioinfo.icapture.ubc.ca:8090/MobyRegistrationPages. > > The new version is lacking documentation, but doc is in the works. I am > posting the url for people to try and to provide feedback for me to improve > them. Right now, there are some style sheet issues, but the pages are > functional. I know that they work in the most recent version of Opera and > firefox. They should also work in Internet explorer and Safari. > > Let me know if you find any errors and if/how you think I could improve the > look and feel of the pages. I am by no means an expert in creating UIs or in > html/javascript so your suggestions are welcomed! > > Thanks, > > Eddie > > _______________________________________________ > 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 edward.kawas at gmail.com Wed Apr 16 09:06:05 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 16 Apr 2008 06:06:05 -0700 Subject: [MOBY-dev] tools for registering items into mobycentral In-Reply-To: <4805ABAC.9060408@ac.uma.es> References: <4804fc92.1bbc720a.5a00.ffff9710@mx.google.com> <4805ABAC.9060408@ac.uma.es> Message-ID: <4805f9cb.1bd6720a.1b8e.ffffab85@mx.google.com> The server is online; you might be having problems because the url is on port 8090. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sergio Ramirez Ramirez Sent: April-16-08 12:33 AM To: Core developer announcements Subject: Re: [MOBY-dev] tools for registering items into mobycentral Hi Eddi, Sorry but I have problems trying to access the url. Is the server online? Kind Regards, Sergio Edward Kawas wrote: > A long time ago, I created some java applets that aided in the registration > of datatypes, namespaces, services, and service types into mobycentral. They > were a good first crack at things, but had many flaws. > > Recently, I have removed them and replaced them with pure javascript > versions located at: > http://bioinfo.icapture.ubc.ca:8090/MobyRegistrationPages. > > The new version is lacking documentation, but doc is in the works. I am > posting the url for people to try and to provide feedback for me to improve > them. Right now, there are some style sheet issues, but the pages are > functional. I know that they work in the most recent version of Opera and > firefox. They should also work in Internet explorer and Safari. > > Let me know if you find any errors and if/how you think I could improve the > look and feel of the pages. I am by no means an expert in creating UIs or in > html/javascript so your suggestions are welcomed! > > Thanks, > > Eddie > > _______________________________________________ > 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 _______________________________________________ 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 Wed Apr 16 09:32:42 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 16 Apr 2008 15:32:42 +0200 Subject: [MOBY-dev] tools for registering items into mobycentral In-Reply-To: <4805f9cb.1bd6720a.1b8e.ffffab85@mx.google.com> References: <4804fc92.1bbc720a.5a00.ffff9710@mx.google.com> <4805ABAC.9060408@ac.uma.es> <4805f9cb.1bd6720a.1b8e.ffffab85@mx.google.com> Message-ID: <4805FFFA.3080803@mpiz-koeln.mpg.de> cant connect either Edward Kawas wrote: > The server is online; you might be having problems because the url is on > port 8090. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sergio Ramirez > Ramirez > Sent: April-16-08 12:33 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] tools for registering items into mobycentral > > Hi Eddi, > > Sorry but I have problems trying to access the url. > Is the server online? > > Kind Regards, > Sergio > > Edward Kawas wrote: > >> A long time ago, I created some java applets that aided in the >> > registration > >> of datatypes, namespaces, services, and service types into mobycentral. >> > They > >> were a good first crack at things, but had many flaws. >> >> Recently, I have removed them and replaced them with pure javascript >> versions located at: >> http://bioinfo.icapture.ubc.ca:8090/MobyRegistrationPages. >> >> The new version is lacking documentation, but doc is in the works. I am >> posting the url for people to try and to provide feedback for me to >> > improve > >> them. Right now, there are some style sheet issues, but the pages are >> functional. I know that they work in the most recent version of Opera and >> firefox. They should also work in Internet explorer and Safari. >> >> Let me know if you find any errors and if/how you think I could improve >> > the > >> look and feel of the pages. I am by no means an expert in creating UIs or >> > in > >> html/javascript so your suggestions are welcomed! >> >> Thanks, >> >> Eddie >> >> _______________________________________________ >> 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 Wed Apr 16 09:33:35 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 16 Apr 2008 06:33:35 -0700 Subject: [MOBY-dev] tools for registering items into mobycentral In-Reply-To: <4805FFFA.3080803@mpiz-koeln.mpg.de> References: <4804fc92.1bbc720a.5a00.ffff9710@mx.google.com> <4805ABAC.9060408@ac.uma.es> <4805f9cb.1bd6720a.1b8e.ffffab85@mx.google.com> <4805FFFA.3080803@mpiz-koeln.mpg.de> Message-ID: <4806003d.1dba720a.210c.ffffb164@mx.google.com> Oops, the server was down. Sorry. I just assumed that the problem was with the port number. It should be up now. 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: April-16-08 6:33 AM To: Core developer announcements Subject: Re: [MOBY-dev] tools for registering items into mobycentral cant connect either Edward Kawas wrote: > The server is online; you might be having problems because the url is on > port 8090. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sergio Ramirez > Ramirez > Sent: April-16-08 12:33 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] tools for registering items into mobycentral > > Hi Eddi, > > Sorry but I have problems trying to access the url. > Is the server online? > > Kind Regards, > Sergio > > Edward Kawas wrote: > >> A long time ago, I created some java applets that aided in the >> > registration > >> of datatypes, namespaces, services, and service types into mobycentral. >> > They > >> were a good first crack at things, but had many flaws. >> >> Recently, I have removed them and replaced them with pure javascript >> versions located at: >> http://bioinfo.icapture.ubc.ca:8090/MobyRegistrationPages. >> >> The new version is lacking documentation, but doc is in the works. I am >> posting the url for people to try and to provide feedback for me to >> > improve > >> them. Right now, there are some style sheet issues, but the pages are >> functional. I know that they work in the most recent version of Opera and >> firefox. They should also work in Internet explorer and Safari. >> >> Let me know if you find any errors and if/how you think I could improve >> > the > >> look and feel of the pages. I am by no means an expert in creating UIs or >> > in > >> html/javascript so your suggestions are welcomed! >> >> Thanks, >> >> Eddie >> >> _______________________________________________ >> 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 From edward.kawas at gmail.com Wed Apr 16 09:43:11 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 16 Apr 2008 06:43:11 -0700 Subject: [MOBY-dev] Mobycentral down ? In-Reply-To: <20080411074010.173560@gmx.net> References: <47FF108F.4020006@toulouse.inra.fr> <20080411074010.173560@gmx.net> Message-ID: <4806027e.23f8720a.7db3.fffffb68@mx.google.com> The getDeadServices is back and running. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of M4o at gmx.de Sent: April-11-08 12:40 AM To: Core developer announcements Subject: Re: [MOBY-dev] Mobycentral down ? Hi all, yes from Germany the ucalgary.ca- Central also doesn't work. And I have some other points: 1. Will "getDeadServices" Service (http://moby.ucalgary.ca/moby/ValidateService?getDeadServices) come up working again? Cause i use this to filter dead Services from my service list. Or is there an other alternative? Ah working getStatus() or something like that? 2. Is it right that when you call the service.getPrimaryInputs(), there are no LSIDs at the Namespaces anymore (since jmoby 1.0 ?) ? Thanks, Moritz --------------------------------------------------------------------- when i call the findService methode for example... : - DBI connect('mobycentral:localhost:3306','moby',...) failed: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (146) at /opt/coolstack/lib/perl5/site_perl/5.8.8/MOBY/Adaptor/moby/queryapi/mysql.pm line 90 Exception in thread "main" org.biomoby.shared.MobyException: ===ERROR=== Fault details: [stackTrace: null] [hostname: null] Fault string: DBI connect('mobycentral:localhost:3306','moby',...) failed: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (146) at /opt/coolstack/lib/perl5/site_perl/5.8.8/MOBY/Adaptor/moby/queryapi/mysql.pm line 90 Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server Fault actor: null When calling: http://moby.ucalgary.ca/moby/MOBY-Central.pl =========== ---------------------------------------------------------------- -------- Original-Nachricht -------- > Datum: Fri, 11 Apr 2008 09:17:35 +0200 > Von: Sebastien Carrere > An: Core developer announcements > Betreff: [MOBY-dev] Mobycentral down ? > Hi all, > > I've got the following error when I try to connect to the main registry: > > ------------------------------------------------ > Connection to default MOBY Central died because: > DBI connect('mobycentral:localhost:3306','moby',...) failed: Can't > connect to local MySQL server through socket '/tmp/mysql.sock' (146) at > /opt/coolstack/lib/perl5/site_perl/5.8.8/MOBY/Adaptor/moby/queryapi/mysql.pm > line 90 > > ERROR ERROR ERROR > ---------------------------------------------------------------- > > > Sebastien -- Psst! Geheimtipp: Online Games kostenlos spielen bei den GMX Free Games! http://games.entertainment.gmx.net/de/entertainment/games/free _______________________________________________ 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 Wed Apr 16 11:09:15 2008 From: pieter.neerincx at wur.nl (Pieter Neerincx) Date: Wed, 16 Apr 2008 17:09:15 +0200 Subject: [MOBY-dev] BioMOBY namespace and attributes In-Reply-To: <4806027e.23f8720a.7db3.fffffb68@mx.google.com> References: <47FF108F.4020006@toulouse.inra.fr> <20080411074010.173560@gmx.net> <4806027e.23f8720a.7db3.fffffb68@mx.google.com> Message-ID: Hi, I'm having trouble with an XML parser in combination with a recent version of CommonSubs.pm and was wondering what the official rules are for applying the BioMOBY namespace (I'm talking about the xmlns thingy not the namespace atribute in BioMOBY objects). Therefore I have have the following questions: 1. Is the BioMOBY namespace required for BioMOBY object nodes? 2. Is the BioMOBY namespace required for the id, namespace and articleName attributes of BioMOBY object nodes? 3. Is the BioMOBY namespace required for the other attributes in BioMOBY XML? (for example the queryID attribute of the mobyData node.) With xmlns:moby='http://www.biomoby.org/moby' and xmlns='http://www.biomoby.org/moby' for the default namespace defined somewhere higher up the tree are the following Object objects legal?: A. < Object namespace='' id='' articleName=''/> legal:yes/no B. legal:yes/no C. < Object moby:namespace='' moby:id='' moby:articleName=''/> legal:yes/no D. legal:yes/no The problem I have is that the default namespace only applies to element names, but not to attribute names as per XML spec. Therefore A and B are equivalents as are C and D, but moby:articleName is not the same attribute as articleName without the moby namespace prefix.... Cheers, Pi From markw at illuminae.com Wed Apr 16 12:58:35 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 16 Apr 2008 09:58:35 -0700 Subject: [MOBY-dev] Significant but "invisible" change to MOBY Central configuration Message-ID: Hi all, I just thought I should give everyone a heads-up about a change I made to MOBY Central a couple of days ago, since it will cause *slightly* different behaviour than what you might be used to. the Config.pm file used to create a new instance of dbConfig.pm every time it was called. dbConfig in turn calls the mobycentral.config text file and reads-in the configuration fields. As a result, it was always possible to re-configure MOBY Central's calls to the back-end database simply by editing mobycentral.config without having to restart Apache. THIS IS NO LONGER THE CASE! It turns out that dbConfig was opening and closing the mobycentral.config file sometimes several thousand times over a matter of seconds under high server load! Clearly this is not a Good Thing :-) so I have re-coded Config.pm to store the contents of mobycentral.config as a Class variable. As such, it is read ONCE upon Apache startup (under mod_perl) and this stored copy is then available to every child Apache process. As such, from now on whenever you edit the mobycentral.config file you will need to restart Apache. I hope this doesn't cause anyone too much headache! Mark -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research Providence Heart + Lung Institute University of British Columbia - St. Paul's Hospital Vancouver, BC, Canada From markw at illuminae.com Wed Apr 16 12:53:18 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 16 Apr 2008 09:53:18 -0700 Subject: [MOBY-dev] BioMOBY namespace and attributes In-Reply-To: References: <47FF108F.4020006@toulouse.inra.fr> <20080411074010.173560@gmx.net> <4806027e.23f8720a.7db3.fffffb68@mx.google.com> Message-ID: I think the honest answer would be "we have never really made a decision". My understanding of the spec is as follows: articleName is the same as moby:articleName so long as the default (xmlns="...") namespace and the moby namespace (xmlns:moby="...") are the same. I'm not certain if Moby Central or the Moby server software currently adds a defaut namespace, but it would be a good idea to do so. I could go through the code and make sure... would that help? M On Wed, 16 Apr 2008 08:09:15 -0700, Pieter Neerincx wrote: > Hi, > > I'm having trouble with an XML parser in combination with a recent > version of CommonSubs.pm and was wondering what the official rules are > for applying the BioMOBY namespace (I'm talking about the xmlns thingy > not the namespace atribute in BioMOBY objects). Therefore I have have > the following questions: > > 1. Is the BioMOBY namespace required for BioMOBY object nodes? > 2. Is the BioMOBY namespace required for the id, namespace and > articleName attributes of BioMOBY object nodes? > 3. Is the BioMOBY namespace required for the other attributes in BioMOBY > XML? (for example the queryID attribute of the mobyData node.) > > With xmlns:moby='http://www.biomoby.org/moby' and > xmlns='http://www.biomoby.org/moby' for the default namespace defined > somewhere higher up the tree are the following Object objects legal?: > > A. < Object namespace='' id='' articleName=''/> > legal:yes/no > B. > legal:yes/no > C. < Object moby:namespace='' moby:id='' moby:articleName=''/> > legal:yes/no > D. > legal:yes/no > > The problem I have is that the default namespace only applies to element > names, but not to attribute names as per XML spec. Therefore A and B are > equivalents as are C and D, but moby:articleName is not the same > attribute as articleName without the moby namespace prefix.... > > Cheers, > > Pi > > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research Providence Heart + Lung Institute University of British Columbia - St. Paul's Hospital Vancouver, BC, Canada From pieter.neerincx at wur.nl Wed Apr 16 13:45:09 2008 From: pieter.neerincx at wur.nl (Pieter Neerincx) Date: Wed, 16 Apr 2008 19:45:09 +0200 Subject: [MOBY-dev] BioMOBY namespace and attributes In-Reply-To: References: <47FF108F.4020006@toulouse.inra.fr> <20080411074010.173560@gmx.net> <4806027e.23f8720a.7db3.fffffb68@mx.google.com> Message-ID: <993F12BF-8836-460A-8FEB-A3D300C4E954@wur.nl> Hi Mark, On 16?Apr?2008, at 6:53 PM, Mark Wilkinson wrote: > I think the honest answer would be "we have never really made a > decision". > > My understanding of the spec is as follows: > > articleName is the same as moby:articleName so long as the default > (xmlns="...") namespace and the moby namespace (xmlns:moby="...") > are the same. That's what I expected :), but previously I never encountered moby:articleName, so my code is only looking for the attributes without the namespace prefix. Since the attributes with and without the namespace prefix are not the same for an XML parser (like XML::LibXML for those in the Perl world), my code doesn't find the ones with the namespace. I'll just have to change my code to look for both cases. I can imagine people are reluctant to put the moby namespace prefix on each and every attribute name as it makes the XML rather fat. Usually you can leave them out, but I can also imagine that for a generic attribute name like "id" it is sometimes necessary to stick a namespace onto them to put them in the right context. It would have been handy if the XML specification would allow the declaration of a default namespace for attribute names too... but a.f.a.i.k. that's not possible. > I'm not certain if Moby Central or the Moby server software > currently adds a defaut namespace, but it would be a good idea to do > so. Yes, it does, which is good for the element names, but the default namespace has no effect on the attribute names. > I could go through the code and make sure... would that help? Not necessary yet, but if I run into problems with the BioMOBY code and can't fix it in CVS I'll let you know... Thanks, Pi > M > > > > > On Wed, 16 Apr 2008 08:09:15 -0700, Pieter Neerincx > wrote: > >> Hi, >> >> I'm having trouble with an XML parser in combination with a recent >> version of CommonSubs.pm and was wondering what the official rules >> are for applying the BioMOBY namespace (I'm talking about the xmlns >> thingy not the namespace atribute in BioMOBY objects). Therefore I >> have have the following questions: >> >> 1. Is the BioMOBY namespace required for BioMOBY object nodes? >> 2. Is the BioMOBY namespace required for the id, namespace and >> articleName attributes of BioMOBY object nodes? >> 3. Is the BioMOBY namespace required for the other attributes in >> BioMOBY XML? (for example the queryID attribute of the mobyData >> node.) >> >> With xmlns:moby='http://www.biomoby.org/moby' and xmlns='http://www.biomoby.org/moby' >> for the default namespace defined somewhere higher up the tree >> are the following Object objects legal?: >> >> A. < Object namespace='' id='' articleName=''/> >> legal:yes/no >> B. >> legal:yes/no >> C. < Object moby:namespace='' moby:id='' moby:articleName=''/> >> legal:yes/no >> D. >> legal:yes/no >> >> The problem I have is that the default namespace only applies to >> element names, but not to attribute names as per XML spec. >> Therefore A and B are equivalents as are C and D, but >> moby:articleName is not the same attribute as articleName without >> the moby namespace prefix.... >> >> Cheers, >> >> Pi >> >> >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > > > -- > Mark D Wilkinson, PI Bioinformatics > Assistant Professor, Medical Genetics > The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary > Research > Providence Heart + Lung Institute > University of British Columbia - St. Paul's Hospital > Vancouver, BC, Canada > > _______________________________________________ > 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: +31 (0)317-483 060 fax: +31 (0)317-483 584 mobile: +31 (0)6-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From markw at illuminae.com Fri Apr 18 11:45:14 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 18 Apr 2008 08:45:14 -0700 Subject: [MOBY-dev] Important observations about MOBY Central CPU usage Message-ID: Hi all, this is info for people who host MOBY Central's: Since I made the changes to MOBY Central last week we have noticed that CPU usage has dropped from average 38% utilization down to an average 6.5% utilization, and has never raeched 100% in the past week. This is likely important information for anyone hosting a registry! As far as I am aware, the only file you need to update is: MOBY::Config.pm best wishes everyone! Mark -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research Providence Heart + Lung Institute University of British Columbia - St. Paul's Hospital Vancouver, BC, Canada From groscurt at mpiz-koeln.mpg.de Mon Apr 21 04:53:37 2008 From: groscurt at mpiz-koeln.mpg.de (groscurt) Date: Mon, 21 Apr 2008 10:53:37 +0200 Subject: [MOBY-dev] maven-ant-tasks-2.0.8.jar unavailable In-Reply-To: Message-ID: Hiho, the ant install task of jmoby fails because http://apache.hoxt.com/maven/binaries/maven-ant-tasks-2.0.8.jar is not available (anymore?) so the jar can not be found anymore on the url. There is a only a newer version maven-ant-tasks-2.0.9.jar... so somehow jmoby needs to fetch the most current version or the jar has to be placed somewhere else Best andreas From dmitry.repchevski at bsc.es Mon Apr 21 05:36:51 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Mon, 21 Apr 2008 11:36:51 +0200 Subject: [MOBY-dev] BioMOBY namespace and attributes In-Reply-To: <993F12BF-8836-460A-8FEB-A3D300C4E954@wur.nl> References: <993F12BF-8836-460A-8FEB-A3D300C4E954@wur.nl> Message-ID: <480C6033.2000907@bsc.es> Hello Pieter, This is the old discussion... Here was my suggestion we discussed in INB and how my library works: > 1. All Elements must be in biomoby namespace > ("http://www.biomoby.org/moby"). > 2. The name of prefix MUST have no matter (because of XML specification). > 3. All attributes of Moby Message (those that belongs to "special" > Moby structures like, Simple, Collection...) MUST be in biomoby > namespace. > 4. All attributes of Moby Primitive types MUST NOT have any defined > namespace. > 5. All attributes that belongs to the Ontology (