From markw at illuminae.com Tue Nov 3 12:18:37 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 03 Nov 2009 09:18:37 -0800 Subject: [MOBY-dev] What's up with Moby-2 --> SADI Message-ID: Hi all! About every month or so, someone writes to me to ask what's up with Moby-2. Here's the update: We've finished our first pass at the specification and reference implementation of SADI - Semantic Automated Discovery and Integration. The manuscript describing the overall architecture will be presented at the IEEE Semantic Web Services meeting in Singapore in December, but the text of that paper is here: http://sadiframework.org/documentation/SADI_SWSIP09_personal.pdf The project website is: http://sadiframework.org and from there you can get to our first prototype client. Other clients are coming soon, including the SADI-Taverna plugin. The SADI equivalent to MoSeS is almost finished, and is available on CPAN - it does a pretty good job of auto-writing SADI services already, and it will get better soon! See the SADI homepage for the link. The meta-map of possible service connections is here: http://biordf.net/cardioSHARE/images/predicates.png You can already do some pretty cool SPARQL queries in our prototype interface! And finally, we are putting out a press release this week to announce that we have just received almost $1M in funding from CANARIE to deploy SADI services over Canadian (and international) bioinformatics resources, as well as provide training in semantic web and semantic web service provision. We wont be starting the training component until late next year, but if you are interested please follow our progress on the SADI homepage. That's all the news! Cheers! Mark From klee at mpiz-koeln.mpg.de Fri Nov 27 09:08:12 2009 From: klee at mpiz-koeln.mpg.de (Kathrin Klee) Date: Fri, 27 Nov 2009 15:08:12 +0100 Subject: [MOBY-dev] Compiling datatypes Message-ID: <4B0FDD4C.801@mpiz-koeln.mpg.de> Hello everybody, I'm quite new in the BioMoby field and have a problem in compiling datatypes via the dashboard. Whenever I try to process datatypes or skeletons the same fallowing error occurs: compile-datatypes: [javac] Compiling 587 source files to /home/pcb/klee/workspace/jMoby/build/others/datatypes [javac] /home/pcb/klee/workspace/jMoby/generated/datatypes/org/biomoby/shared/datatypes/GCP_Contact.java:95: getMoby_affiliation() in org.biomoby.shared.datatypes.GCP_Contact cannot override getMoby_affiliation() in org.biomoby.shared.datatypes.GCP_Person; attempting to use incompatible return type [javac] found : org.biomoby.shared.datatypes.GCP_Organization [javac] required: org.biomoby.shared.datatypes.GCP_LegalEntity[] [javac] public GCP_Organization getMoby_affiliation() { [javac] ^ [javac] 1 error I did not work on this datatype at all and I do not have any error messages within my biomoby datatype classes. Did anyone had similar problems or knows what is causing such problems? Thanks a lot in advance. Regards Kathrin -- -------------------------------------------------- Kathrin Klee Bioinformatician Max Planck Institute for Plant Breeding Research Plant Computational Biology Carl-von-Linne Weg 10 50829 Koeln Germany +49 (0)221 / 5062 - 449 -------------------------------------------------- From martin.senger at gmail.com Sun Nov 29 16:52:02 2009 From: martin.senger at gmail.com (Martin Senger) Date: Sun, 29 Nov 2009 21:52:02 +0000 Subject: [MOBY-dev] Compiling datatypes In-Reply-To: <4B0FDD4C.801@mpiz-koeln.mpg.de> References: <4B0FDD4C.801@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0911291352j1571fc4fy9ef07cefc265f2dd@mail.gmail.com> Hi, Which moby registry are you using? Probably the default one? Anyway, your local cache may have some incompatible (meaning older) datatypes. The first step would be to remove the whole cache and let it fill again (from the Dashboard or by the command-line programs). Sorry for this vague answer, but I am now travelling and I cannot check it on my computer. Perhaps Eddie can be more specific (he works now with moby much much more than I do :-)). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From edward.kawas at gmail.com Sun Nov 29 20:13:59 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Sun, 29 Nov 2009 17:13:59 -0800 Subject: [MOBY-dev] Compiling datatypes In-Reply-To: <4d93f07c0911291352j1571fc4fy9ef07cefc265f2dd@mail.gmail.com> References: <4B0FDD4C.801@mpiz-koeln.mpg.de> <4d93f07c0911291352j1571fc4fy9ef07cefc265f2dd@mail.gmail.com> Message-ID: <4b131c58.9413f30a.3e62.2600@mx.google.com> Hmm, I tried to replicate the problem, but I was having problems on Friday downloading the jmoby dependencies and couldn't build anything. I will try again Monday. As an aside, I vaguely remember someone having similar issues when using java 1.6. Is this what you are using? 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: Sunday, November 29, 2009 1:52 PM To: Core developer announcements Subject: Re: [MOBY-dev] Compiling datatypes Hi, Which moby registry are you using? Probably the default one? Anyway, your local cache may have some incompatible (meaning older) datatypes. The first step would be to remove the whole cache and let it fill again (from the Dashboard or by the command-line programs). Sorry for this vague answer, but I am now travelling and I cannot check it on my computer. Perhaps Eddie can be more specific (he works now with moby much much more than I do :-)). 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 Mon Nov 30 00:19:22 2009 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 30 Nov 2009 05:19:22 +0000 Subject: [MOBY-dev] Compiling datatypes In-Reply-To: <4b131c58.9413f30a.3e62.2600@mx.google.com> References: <4B0FDD4C.801@mpiz-koeln.mpg.de> <4d93f07c0911291352j1571fc4fy9ef07cefc265f2dd@mail.gmail.com> <4b131c58.9413f30a.3e62.2600@mx.google.com> Message-ID: <4d93f07c0911292119hf254873neb0d656c3cb90ead@mail.gmail.com> > > but I was having problems on Friday > downloading the jmoby dependencies and couldn't build anything. I have fixed the dependency problem yesterday. There is an updated xmls/project.pom. Thanks for looking for the datatypes problem... Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From edward.kawas at gmail.com Mon Nov 30 10:13:39 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 30 Nov 2009 07:13:39 -0800 Subject: [MOBY-dev] Compiling datatypes In-Reply-To: <4d93f07c0911291352j1571fc4fy9ef07cefc265f2dd@mail.gmail.com> References: <4B0FDD4C.801@mpiz-koeln.mpg.de> <4d93f07c0911291352j1571fc4fy9ef07cefc265f2dd@mail.gmail.com> Message-ID: <4b13e124.171bf30a.6a3b.33d3@mx.google.com> Okay, I just removed my .m2/ folder (maven dependencies), ant clean, followed by ant jar-datatypes and I had no problems. So perhaps, like Martin said, you may want to clear your cache (ant clean should do it) and try again. If that doesn't help, and you are using java 6, maybe check for an upgrade to the java 6 update that you have. 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: Sunday, November 29, 2009 1:52 PM To: Core developer announcements Subject: Re: [MOBY-dev] Compiling datatypes Hi, Which moby registry are you using? Probably the default one? Anyway, your local cache may have some incompatible (meaning older) datatypes. The first step would be to remove the whole cache and let it fill again (from the Dashboard or by the command-line programs). Sorry for this vague answer, but I am now travelling and I cannot check it on my computer. Perhaps Eddie can be more specific (he works now with moby much much more than I do :-)). 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 markw at illuminae.com Tue Nov 3 17:18:37 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 03 Nov 2009 09:18:37 -0800 Subject: [MOBY-dev] What's up with Moby-2 --> SADI Message-ID: Hi all! About every month or so, someone writes to me to ask what's up with Moby-2. Here's the update: We've finished our first pass at the specification and reference implementation of SADI - Semantic Automated Discovery and Integration. The manuscript describing the overall architecture will be presented at the IEEE Semantic Web Services meeting in Singapore in December, but the text of that paper is here: http://sadiframework.org/documentation/SADI_SWSIP09_personal.pdf The project website is: http://sadiframework.org and from there you can get to our first prototype client. Other clients are coming soon, including the SADI-Taverna plugin. The SADI equivalent to MoSeS is almost finished, and is available on CPAN - it does a pretty good job of auto-writing SADI services already, and it will get better soon! See the SADI homepage for the link. The meta-map of possible service connections is here: http://biordf.net/cardioSHARE/images/predicates.png You can already do some pretty cool SPARQL queries in our prototype interface! And finally, we are putting out a press release this week to announce that we have just received almost $1M in funding from CANARIE to deploy SADI services over Canadian (and international) bioinformatics resources, as well as provide training in semantic web and semantic web service provision. We wont be starting the training component until late next year, but if you are interested please follow our progress on the SADI homepage. That's all the news! Cheers! Mark From klee at mpiz-koeln.mpg.de Fri Nov 27 14:08:12 2009 From: klee at mpiz-koeln.mpg.de (Kathrin Klee) Date: Fri, 27 Nov 2009 15:08:12 +0100 Subject: [MOBY-dev] Compiling datatypes Message-ID: <4B0FDD4C.801@mpiz-koeln.mpg.de> Hello everybody, I'm quite new in the BioMoby field and have a problem in compiling datatypes via the dashboard. Whenever I try to process datatypes or skeletons the same fallowing error occurs: compile-datatypes: [javac] Compiling 587 source files to /home/pcb/klee/workspace/jMoby/build/others/datatypes [javac] /home/pcb/klee/workspace/jMoby/generated/datatypes/org/biomoby/shared/datatypes/GCP_Contact.java:95: getMoby_affiliation() in org.biomoby.shared.datatypes.GCP_Contact cannot override getMoby_affiliation() in org.biomoby.shared.datatypes.GCP_Person; attempting to use incompatible return type [javac] found : org.biomoby.shared.datatypes.GCP_Organization [javac] required: org.biomoby.shared.datatypes.GCP_LegalEntity[] [javac] public GCP_Organization getMoby_affiliation() { [javac] ^ [javac] 1 error I did not work on this datatype at all and I do not have any error messages within my biomoby datatype classes. Did anyone had similar problems or knows what is causing such problems? Thanks a lot in advance. Regards Kathrin -- -------------------------------------------------- Kathrin Klee Bioinformatician Max Planck Institute for Plant Breeding Research Plant Computational Biology Carl-von-Linne Weg 10 50829 Koeln Germany +49 (0)221 / 5062 - 449 -------------------------------------------------- From martin.senger at gmail.com Sun Nov 29 21:52:02 2009 From: martin.senger at gmail.com (Martin Senger) Date: Sun, 29 Nov 2009 21:52:02 +0000 Subject: [MOBY-dev] Compiling datatypes In-Reply-To: <4B0FDD4C.801@mpiz-koeln.mpg.de> References: <4B0FDD4C.801@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0911291352j1571fc4fy9ef07cefc265f2dd@mail.gmail.com> Hi, Which moby registry are you using? Probably the default one? Anyway, your local cache may have some incompatible (meaning older) datatypes. The first step would be to remove the whole cache and let it fill again (from the Dashboard or by the command-line programs). Sorry for this vague answer, but I am now travelling and I cannot check it on my computer. Perhaps Eddie can be more specific (he works now with moby much much more than I do :-)). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From edward.kawas at gmail.com Mon Nov 30 01:13:59 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Sun, 29 Nov 2009 17:13:59 -0800 Subject: [MOBY-dev] Compiling datatypes In-Reply-To: <4d93f07c0911291352j1571fc4fy9ef07cefc265f2dd@mail.gmail.com> References: <4B0FDD4C.801@mpiz-koeln.mpg.de> <4d93f07c0911291352j1571fc4fy9ef07cefc265f2dd@mail.gmail.com> Message-ID: <4b131c58.9413f30a.3e62.2600@mx.google.com> Hmm, I tried to replicate the problem, but I was having problems on Friday downloading the jmoby dependencies and couldn't build anything. I will try again Monday. As an aside, I vaguely remember someone having similar issues when using java 1.6. Is this what you are using? 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: Sunday, November 29, 2009 1:52 PM To: Core developer announcements Subject: Re: [MOBY-dev] Compiling datatypes Hi, Which moby registry are you using? Probably the default one? Anyway, your local cache may have some incompatible (meaning older) datatypes. The first step would be to remove the whole cache and let it fill again (from the Dashboard or by the command-line programs). Sorry for this vague answer, but I am now travelling and I cannot check it on my computer. Perhaps Eddie can be more specific (he works now with moby much much more than I do :-)). 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 Mon Nov 30 05:19:22 2009 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 30 Nov 2009 05:19:22 +0000 Subject: [MOBY-dev] Compiling datatypes In-Reply-To: <4b131c58.9413f30a.3e62.2600@mx.google.com> References: <4B0FDD4C.801@mpiz-koeln.mpg.de> <4d93f07c0911291352j1571fc4fy9ef07cefc265f2dd@mail.gmail.com> <4b131c58.9413f30a.3e62.2600@mx.google.com> Message-ID: <4d93f07c0911292119hf254873neb0d656c3cb90ead@mail.gmail.com> > > but I was having problems on Friday > downloading the jmoby dependencies and couldn't build anything. I have fixed the dependency problem yesterday. There is an updated xmls/project.pom. Thanks for looking for the datatypes problem... Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From edward.kawas at gmail.com Mon Nov 30 15:13:39 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 30 Nov 2009 07:13:39 -0800 Subject: [MOBY-dev] Compiling datatypes In-Reply-To: <4d93f07c0911291352j1571fc4fy9ef07cefc265f2dd@mail.gmail.com> References: <4B0FDD4C.801@mpiz-koeln.mpg.de> <4d93f07c0911291352j1571fc4fy9ef07cefc265f2dd@mail.gmail.com> Message-ID: <4b13e124.171bf30a.6a3b.33d3@mx.google.com> Okay, I just removed my .m2/ folder (maven dependencies), ant clean, followed by ant jar-datatypes and I had no problems. So perhaps, like Martin said, you may want to clear your cache (ant clean should do it) and try again. If that doesn't help, and you are using java 6, maybe check for an upgrade to the java 6 update that you have. 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: Sunday, November 29, 2009 1:52 PM To: Core developer announcements Subject: Re: [MOBY-dev] Compiling datatypes Hi, Which moby registry are you using? Probably the default one? Anyway, your local cache may have some incompatible (meaning older) datatypes. The first step would be to remove the whole cache and let it fill again (from the Dashboard or by the command-line programs). Sorry for this vague answer, but I am now travelling and I cannot check it on my computer. Perhaps Eddie can be more specific (he works now with moby much much more than I do :-)). 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