From mwilkinson at mrl.ubc.ca Wed Aug 4 15:49:54 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Wed Aug 4 15:51:13 2004 Subject: [MOBY-dev] MOBY Central registry usage statistics Message-ID: <1091648994.3677.70.camel@myhost.mydomain> Hi all MOBYers! I've compiled the latest stats on MOBY Central's usage. It is striking how quickly it is exploding! Attached is a PDF with a graph of the results. The calls included here includes requests to both the MOBY Central API as well as to the ontology servers (since the latter are still called by someone who has their own registry implementation, like PlaNet does). I'm sure that a lot of the hits are due to the number of new tools coming out that have MOBY embedded in them, like BioTrawler, Taverna, and BlueJay. That's fantastic!! :-) :-) MOBY ON! Mark -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre -------------- next part -------------- A non-text attachment was scrubbed... Name: RegistryUsage.pdf Type: application/pdf Size: 9032 bytes Desc: not available Url : http://biomoby.org/pipermail/moby-dev/attachments/20040804/c62ef2d9/RegistryUsage.pdf From yanwong at ebgm.jussieu.fr Wed Aug 11 06:04:14 2004 From: yanwong at ebgm.jussieu.fr (Yan Wong) Date: Wed Aug 11 06:05:33 2004 Subject: [MOBY-dev] Update for the bioMoby Python API Message-ID: <1092218654.2938.21.camel@prot1.rpbs.jussieu.fr> As my internship is almost finished, I deliver my last update of the bioMoby Python API on the website: http://bioserv.rpbs.jussieu.fr/RPBS/html/an/T0_Software.html in the package you'll find: -the API itself with changes (cf changelog and the howto.pdf) -two little programs: moby2python: It translates by default the whole ontology into a Python package (it helps me to import some bioMoby objects) wx/objectBrowser: A wxPython program that displays the structure of the ontology in a tree view (for more detail consult the doc/howto.pdf). Changes: -MobyMarshal, MobyUnmarshal, serialize deserialize xml objects<-> python objects -ServiceQuery before requires a dictionary, now you can enter parameters directly: before: sq=ServiceQuery({'serviceName':'Service'}) now: sq=ServiceQuery(serviceName='Service') For register/deregister, same thing, no need to enter parameters in a dictionary except for the Service object (as you can either enter a WSDL or the dictionary to build the Service object) The ontology has been integrated as a Python module in the src/ontology directory, thus it is possible to manipulate Moby Objects like any other Python objects (for example make a link between bioPython objects and bioMoby objects). It would be nice if someone could CVS the whole thing as I still don't know if I am still not able to CVS! From mwilkinson at mrl.ubc.ca Wed Aug 11 10:45:58 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Wed Aug 11 10:47:04 2004 Subject: [unclassified] [MOBY-dev] Update for the bioMoby Python API In-Reply-To: <1092218654.2938.21.camel@prot1.rpbs.jussieu.fr> References: <1092218654.2938.21.camel@prot1.rpbs.jussieu.fr> Message-ID: <1092235558.2060.27.camel@myhost.mydomain> Hi Yan! That is great news - thank you for all you efforts! I will pick up the code from your page later today and put it into the CVS if you agree to that. I don't recall if you requested CVS access or not. If you want it, please send a message to: root-l@open-bio.org and tell them you want to be a MOBY developer (c.c. to me please). It usually only takes them a few days to look after such requests. Best wishes! Mark On Wed, 2004-08-11 at 03:04, Yan Wong wrote: > As my internship is almost finished, I deliver my last update of the > bioMoby Python API on the website: > http://bioserv.rpbs.jussieu.fr/RPBS/html/an/T0_Software.html > > in the package you'll find: > -the API itself with changes (cf changelog and the howto.pdf) > -two little programs: > moby2python: It translates by default the whole ontology into a Python > package (it helps me to import some bioMoby objects) > wx/objectBrowser: A wxPython program that displays the structure of > the ontology in a tree view (for more detail consult the doc/howto.pdf). > > Changes: > -MobyMarshal, MobyUnmarshal, serialize deserialize xml objects<-> python > objects > -ServiceQuery before requires a dictionary, now you can enter parameters > directly: > before: > sq=ServiceQuery({'serviceName':'Service'}) > now: > sq=ServiceQuery(serviceName='Service') > > For register/deregister, same thing, no need to enter parameters in a > dictionary except for the Service object (as you can either enter a WSDL > or the dictionary to build the Service object) > > The ontology has been integrated as a Python module in the src/ontology > directory, thus it is possible to manipulate Moby Objects like any other > Python objects (for example make a link between bioPython objects and > bioMoby objects). > > It would be nice if someone could CVS the whole thing as I still don't > know if I am still not able to CVS! > _______________________________________________ > MOBY-dev mailing list > MOBY-dev@biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre From mwilkinson at mrl.ubc.ca Wed Aug 11 10:45:58 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Wed Aug 11 10:47:05 2004 Subject: [unclassified] [MOBY-dev] Update for the bioMoby Python API In-Reply-To: <1092218654.2938.21.camel@prot1.rpbs.jussieu.fr> References: <1092218654.2938.21.camel@prot1.rpbs.jussieu.fr> Message-ID: <1092235558.2060.27.camel@myhost.mydomain> Hi Yan! That is great news - thank you for all you efforts! I will pick up the code from your page later today and put it into the CVS if you agree to that. I don't recall if you requested CVS access or not. If you want it, please send a message to: root-l@open-bio.org and tell them you want to be a MOBY developer (c.c. to me please). It usually only takes them a few days to look after such requests. Best wishes! Mark On Wed, 2004-08-11 at 03:04, Yan Wong wrote: > As my internship is almost finished, I deliver my last update of the > bioMoby Python API on the website: > http://bioserv.rpbs.jussieu.fr/RPBS/html/an/T0_Software.html > > in the package you'll find: > -the API itself with changes (cf changelog and the howto.pdf) > -two little programs: > moby2python: It translates by default the whole ontology into a Python > package (it helps me to import some bioMoby objects) > wx/objectBrowser: A wxPython program that displays the structure of > the ontology in a tree view (for more detail consult the doc/howto.pdf). > > Changes: > -MobyMarshal, MobyUnmarshal, serialize deserialize xml objects<-> python > objects > -ServiceQuery before requires a dictionary, now you can enter parameters > directly: > before: > sq=ServiceQuery({'serviceName':'Service'}) > now: > sq=ServiceQuery(serviceName='Service') > > For register/deregister, same thing, no need to enter parameters in a > dictionary except for the Service object (as you can either enter a WSDL > or the dictionary to build the Service object) > > The ontology has been integrated as a Python module in the src/ontology > directory, thus it is possible to manipulate Moby Objects like any other > Python objects (for example make a link between bioPython objects and > bioMoby objects). > > It would be nice if someone could CVS the whole thing as I still don't > know if I am still not able to CVS! > _______________________________________________ > MOBY-dev mailing list > MOBY-dev@biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre From mwilkinson at mrl.ubc.ca Wed Aug 11 14:12:04 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Wed Aug 11 14:13:16 2004 Subject: [unclassified] [MOBY-dev] Update for the bioMoby Python API In-Reply-To: <1092218654.2938.21.camel@prot1.rpbs.jussieu.fr> References: <1092218654.2938.21.camel@prot1.rpbs.jussieu.fr> Message-ID: <1092247923.1977.111.camel@myhost.mydomain> The python API is now in the CVS in the subdirectory "moby-live/Python". thanks Yan!! Mark On Wed, 2004-08-11 at 03:04, Yan Wong wrote: > As my internship is almost finished, I deliver my last update of the > bioMoby Python API on the website: > http://bioserv.rpbs.jussieu.fr/RPBS/html/an/T0_Software.html > > in the package you'll find: > -the API itself with changes (cf changelog and the howto.pdf) > -two little programs: > moby2python: It translates by default the whole ontology into a Python > package (it helps me to import some bioMoby objects) > wx/objectBrowser: A wxPython program that displays the structure of > the ontology in a tree view (for more detail consult the doc/howto.pdf). > > Changes: > -MobyMarshal, MobyUnmarshal, serialize deserialize xml objects<-> python > objects > -ServiceQuery before requires a dictionary, now you can enter parameters > directly: > before: > sq=ServiceQuery({'serviceName':'Service'}) > now: > sq=ServiceQuery(serviceName='Service') > > For register/deregister, same thing, no need to enter parameters in a > dictionary except for the Service object (as you can either enter a WSDL > or the dictionary to build the Service object) > > The ontology has been integrated as a Python module in the src/ontology > directory, thus it is possible to manipulate Moby Objects like any other > Python objects (for example make a link between bioPython objects and > bioMoby objects). > > It would be nice if someone could CVS the whole thing as I still don't > know if I am still not able to CVS! > _______________________________________________ > MOBY-dev mailing list > MOBY-dev@biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre From mwilkinson at mrl.ubc.ca Wed Aug 11 14:12:04 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Wed Aug 11 14:13:18 2004 Subject: [unclassified] [MOBY-dev] Update for the bioMoby Python API In-Reply-To: <1092218654.2938.21.camel@prot1.rpbs.jussieu.fr> References: <1092218654.2938.21.camel@prot1.rpbs.jussieu.fr> Message-ID: <1092247923.1977.111.camel@myhost.mydomain> The python API is now in the CVS in the subdirectory "moby-live/Python". thanks Yan!! Mark On Wed, 2004-08-11 at 03:04, Yan Wong wrote: > As my internship is almost finished, I deliver my last update of the > bioMoby Python API on the website: > http://bioserv.rpbs.jussieu.fr/RPBS/html/an/T0_Software.html > > in the package you'll find: > -the API itself with changes (cf changelog and the howto.pdf) > -two little programs: > moby2python: It translates by default the whole ontology into a Python > package (it helps me to import some bioMoby objects) > wx/objectBrowser: A wxPython program that displays the structure of > the ontology in a tree view (for more detail consult the doc/howto.pdf). > > Changes: > -MobyMarshal, MobyUnmarshal, serialize deserialize xml objects<-> python > objects > -ServiceQuery before requires a dictionary, now you can enter parameters > directly: > before: > sq=ServiceQuery({'serviceName':'Service'}) > now: > sq=ServiceQuery(serviceName='Service') > > For register/deregister, same thing, no need to enter parameters in a > dictionary except for the Service object (as you can either enter a WSDL > or the dictionary to build the Service object) > > The ontology has been integrated as a Python module in the src/ontology > directory, thus it is possible to manipulate Moby Objects like any other > Python objects (for example make a link between bioPython objects and > bioMoby objects). > > It would be nice if someone could CVS the whole thing as I still don't > know if I am still not able to CVS! > _______________________________________________ > MOBY-dev mailing list > MOBY-dev@biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre From mwilkinson at mrl.ubc.ca Tue Aug 17 20:12:57 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue Aug 17 20:13:51 2004 Subject: [MOBY-dev] small change to the database schema Message-ID: <1092787977.6947.33.camel@myhost.mydomain> the mobycentral.secondary_input columns maximum and minimum are now FLOAT datatypes. If you are running your own installation of MOBY Central you should do a mysql alter table on those two columns. M -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre From mwilkinson at mrl.ubc.ca Wed Aug 4 15:49:54 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Wed, 04 Aug 2004 12:49:54 -0700 Subject: [MOBY-dev] MOBY Central registry usage statistics Message-ID: <1091648994.3677.70.camel@myhost.mydomain> Hi all MOBYers! I've compiled the latest stats on MOBY Central's usage. It is striking how quickly it is exploding! Attached is a PDF with a graph of the results. The calls included here includes requests to both the MOBY Central API as well as to the ontology servers (since the latter are still called by someone who has their own registry implementation, like PlaNet does). I'm sure that a lot of the hits are due to the number of new tools coming out that have MOBY embedded in them, like BioTrawler, Taverna, and BlueJay. That's fantastic!! :-) :-) MOBY ON! Mark -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre -------------- next part -------------- A non-text attachment was scrubbed... Name: RegistryUsage.pdf Type: application/pdf Size: 9032 bytes Desc: not available Url : http://www.biomoby.org/pipermail/moby-dev/attachments/20040804/c62ef2d9/RegistryUsage-0002.pdf From yanwong at ebgm.jussieu.fr Wed Aug 11 06:04:14 2004 From: yanwong at ebgm.jussieu.fr (Yan Wong) Date: 11 Aug 2004 12:04:14 +0200 Subject: [MOBY-dev] Update for the bioMoby Python API Message-ID: <1092218654.2938.21.camel@prot1.rpbs.jussieu.fr> An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://www.biomoby.org/pipermail/moby-dev/attachments/20040811/0f1b1d0f/attachment.pl From mwilkinson at mrl.ubc.ca Wed Aug 11 10:45:58 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Wed, 11 Aug 2004 07:45:58 -0700 Subject: [unclassified] [MOBY-dev] Update for the bioMoby Python API In-Reply-To: <1092218654.2938.21.camel@prot1.rpbs.jussieu.fr> References: <1092218654.2938.21.camel@prot1.rpbs.jussieu.fr> Message-ID: <1092235558.2060.27.camel@myhost.mydomain> Hi Yan! That is great news - thank you for all you efforts! I will pick up the code from your page later today and put it into the CVS if you agree to that. I don't recall if you requested CVS access or not. If you want it, please send a message to: root-l at open-bio.org and tell them you want to be a MOBY developer (c.c. to me please). It usually only takes them a few days to look after such requests. Best wishes! Mark On Wed, 2004-08-11 at 03:04, Yan Wong wrote: > As my internship is almost finished, I deliver my last update of the > bioMoby Python API on the website: > http://bioserv.rpbs.jussieu.fr/RPBS/html/an/T0_Software.html > > in the package you'll find: > -the API itself with changes (cf changelog and the howto.pdf) > -two little programs: > moby2python: It translates by default the whole ontology into a Python > package (it helps me to import some bioMoby objects) > wx/objectBrowser: A wxPython program that displays the structure of > the ontology in a tree view (for more detail consult the doc/howto.pdf). > > Changes: > -MobyMarshal, MobyUnmarshal, serialize deserialize xml objects<-> python > objects > -ServiceQuery before requires a dictionary, now you can enter parameters > directly: > before: > sq=ServiceQuery({'serviceName':'Service'}) > now: > sq=ServiceQuery(serviceName='Service') > > For register/deregister, same thing, no need to enter parameters in a > dictionary except for the Service object (as you can either enter a WSDL > or the dictionary to build the Service object) > > The ontology has been integrated as a Python module in the src/ontology > directory, thus it is possible to manipulate Moby Objects like any other > Python objects (for example make a link between bioPython objects and > bioMoby objects). > > It would be nice if someone could CVS the whole thing as I still don't > know if I am still not able to CVS! > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From mwilkinson at mrl.ubc.ca Wed Aug 11 10:45:58 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Wed, 11 Aug 2004 07:45:58 -0700 Subject: [unclassified] [MOBY-dev] Update for the bioMoby Python API In-Reply-To: <1092218654.2938.21.camel@prot1.rpbs.jussieu.fr> References: <1092218654.2938.21.camel@prot1.rpbs.jussieu.fr> Message-ID: <1092235558.2060.27.camel@myhost.mydomain> Hi Yan! That is great news - thank you for all you efforts! I will pick up the code from your page later today and put it into the CVS if you agree to that. I don't recall if you requested CVS access or not. If you want it, please send a message to: root-l at open-bio.org and tell them you want to be a MOBY developer (c.c. to me please). It usually only takes them a few days to look after such requests. Best wishes! Mark On Wed, 2004-08-11 at 03:04, Yan Wong wrote: > As my internship is almost finished, I deliver my last update of the > bioMoby Python API on the website: > http://bioserv.rpbs.jussieu.fr/RPBS/html/an/T0_Software.html > > in the package you'll find: > -the API itself with changes (cf changelog and the howto.pdf) > -two little programs: > moby2python: It translates by default the whole ontology into a Python > package (it helps me to import some bioMoby objects) > wx/objectBrowser: A wxPython program that displays the structure of > the ontology in a tree view (for more detail consult the doc/howto.pdf). > > Changes: > -MobyMarshal, MobyUnmarshal, serialize deserialize xml objects<-> python > objects > -ServiceQuery before requires a dictionary, now you can enter parameters > directly: > before: > sq=ServiceQuery({'serviceName':'Service'}) > now: > sq=ServiceQuery(serviceName='Service') > > For register/deregister, same thing, no need to enter parameters in a > dictionary except for the Service object (as you can either enter a WSDL > or the dictionary to build the Service object) > > The ontology has been integrated as a Python module in the src/ontology > directory, thus it is possible to manipulate Moby Objects like any other > Python objects (for example make a link between bioPython objects and > bioMoby objects). > > It would be nice if someone could CVS the whole thing as I still don't > know if I am still not able to CVS! > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From mwilkinson at mrl.ubc.ca Wed Aug 11 14:12:04 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Wed, 11 Aug 2004 11:12:04 -0700 Subject: [unclassified] [MOBY-dev] Update for the bioMoby Python API In-Reply-To: <1092218654.2938.21.camel@prot1.rpbs.jussieu.fr> References: <1092218654.2938.21.camel@prot1.rpbs.jussieu.fr> Message-ID: <1092247923.1977.111.camel@myhost.mydomain> The python API is now in the CVS in the subdirectory "moby-live/Python". thanks Yan!! Mark On Wed, 2004-08-11 at 03:04, Yan Wong wrote: > As my internship is almost finished, I deliver my last update of the > bioMoby Python API on the website: > http://bioserv.rpbs.jussieu.fr/RPBS/html/an/T0_Software.html > > in the package you'll find: > -the API itself with changes (cf changelog and the howto.pdf) > -two little programs: > moby2python: It translates by default the whole ontology into a Python > package (it helps me to import some bioMoby objects) > wx/objectBrowser: A wxPython program that displays the structure of > the ontology in a tree view (for more detail consult the doc/howto.pdf). > > Changes: > -MobyMarshal, MobyUnmarshal, serialize deserialize xml objects<-> python > objects > -ServiceQuery before requires a dictionary, now you can enter parameters > directly: > before: > sq=ServiceQuery({'serviceName':'Service'}) > now: > sq=ServiceQuery(serviceName='Service') > > For register/deregister, same thing, no need to enter parameters in a > dictionary except for the Service object (as you can either enter a WSDL > or the dictionary to build the Service object) > > The ontology has been integrated as a Python module in the src/ontology > directory, thus it is possible to manipulate Moby Objects like any other > Python objects (for example make a link between bioPython objects and > bioMoby objects). > > It would be nice if someone could CVS the whole thing as I still don't > know if I am still not able to CVS! > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From mwilkinson at mrl.ubc.ca Wed Aug 11 14:12:04 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Wed, 11 Aug 2004 11:12:04 -0700 Subject: [unclassified] [MOBY-dev] Update for the bioMoby Python API In-Reply-To: <1092218654.2938.21.camel@prot1.rpbs.jussieu.fr> References: <1092218654.2938.21.camel@prot1.rpbs.jussieu.fr> Message-ID: <1092247923.1977.111.camel@myhost.mydomain> The python API is now in the CVS in the subdirectory "moby-live/Python". thanks Yan!! Mark On Wed, 2004-08-11 at 03:04, Yan Wong wrote: > As my internship is almost finished, I deliver my last update of the > bioMoby Python API on the website: > http://bioserv.rpbs.jussieu.fr/RPBS/html/an/T0_Software.html > > in the package you'll find: > -the API itself with changes (cf changelog and the howto.pdf) > -two little programs: > moby2python: It translates by default the whole ontology into a Python > package (it helps me to import some bioMoby objects) > wx/objectBrowser: A wxPython program that displays the structure of > the ontology in a tree view (for more detail consult the doc/howto.pdf). > > Changes: > -MobyMarshal, MobyUnmarshal, serialize deserialize xml objects<-> python > objects > -ServiceQuery before requires a dictionary, now you can enter parameters > directly: > before: > sq=ServiceQuery({'serviceName':'Service'}) > now: > sq=ServiceQuery(serviceName='Service') > > For register/deregister, same thing, no need to enter parameters in a > dictionary except for the Service object (as you can either enter a WSDL > or the dictionary to build the Service object) > > The ontology has been integrated as a Python module in the src/ontology > directory, thus it is possible to manipulate Moby Objects like any other > Python objects (for example make a link between bioPython objects and > bioMoby objects). > > It would be nice if someone could CVS the whole thing as I still don't > know if I am still not able to CVS! > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From mwilkinson at mrl.ubc.ca Tue Aug 17 20:12:57 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue, 17 Aug 2004 17:12:57 -0700 Subject: [MOBY-dev] small change to the database schema Message-ID: <1092787977.6947.33.camel@myhost.mydomain> the mobycentral.secondary_input columns maximum and minimum are now FLOAT datatypes. If you are running your own installation of MOBY Central you should do a mysql alter table on those two columns. M -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From mwilkinson at mrl.ubc.ca Wed Aug 4 19:49:54 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Wed, 04 Aug 2004 12:49:54 -0700 Subject: [MOBY-dev] MOBY Central registry usage statistics Message-ID: <1091648994.3677.70.camel@myhost.mydomain> Hi all MOBYers! I've compiled the latest stats on MOBY Central's usage. It is striking how quickly it is exploding! Attached is a PDF with a graph of the results. The calls included here includes requests to both the MOBY Central API as well as to the ontology servers (since the latter are still called by someone who has their own registry implementation, like PlaNet does). I'm sure that a lot of the hits are due to the number of new tools coming out that have MOBY embedded in them, like BioTrawler, Taverna, and BlueJay. That's fantastic!! :-) :-) MOBY ON! Mark -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre -------------- next part -------------- A non-text attachment was scrubbed... Name: RegistryUsage.pdf Type: application/pdf Size: 9032 bytes Desc: not available URL: From yanwong at ebgm.jussieu.fr Wed Aug 11 10:04:14 2004 From: yanwong at ebgm.jussieu.fr (Yan Wong) Date: 11 Aug 2004 12:04:14 +0200 Subject: [MOBY-dev] Update for the bioMoby Python API Message-ID: <1092218654.2938.21.camel@prot1.rpbs.jussieu.fr> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From mwilkinson at mrl.ubc.ca Wed Aug 11 14:45:58 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Wed, 11 Aug 2004 07:45:58 -0700 Subject: [unclassified] [MOBY-dev] Update for the bioMoby Python API In-Reply-To: <1092218654.2938.21.camel@prot1.rpbs.jussieu.fr> References: <1092218654.2938.21.camel@prot1.rpbs.jussieu.fr> Message-ID: <1092235558.2060.27.camel@myhost.mydomain> Hi Yan! That is great news - thank you for all you efforts! I will pick up the code from your page later today and put it into the CVS if you agree to that. I don't recall if you requested CVS access or not. If you want it, please send a message to: root-l at open-bio.org and tell them you want to be a MOBY developer (c.c. to me please). It usually only takes them a few days to look after such requests. Best wishes! Mark On Wed, 2004-08-11 at 03:04, Yan Wong wrote: > As my internship is almost finished, I deliver my last update of the > bioMoby Python API on the website: > http://bioserv.rpbs.jussieu.fr/RPBS/html/an/T0_Software.html > > in the package you'll find: > -the API itself with changes (cf changelog and the howto.pdf) > -two little programs: > moby2python: It translates by default the whole ontology into a Python > package (it helps me to import some bioMoby objects) > wx/objectBrowser: A wxPython program that displays the structure of > the ontology in a tree view (for more detail consult the doc/howto.pdf). > > Changes: > -MobyMarshal, MobyUnmarshal, serialize deserialize xml objects<-> python > objects > -ServiceQuery before requires a dictionary, now you can enter parameters > directly: > before: > sq=ServiceQuery({'serviceName':'Service'}) > now: > sq=ServiceQuery(serviceName='Service') > > For register/deregister, same thing, no need to enter parameters in a > dictionary except for the Service object (as you can either enter a WSDL > or the dictionary to build the Service object) > > The ontology has been integrated as a Python module in the src/ontology > directory, thus it is possible to manipulate Moby Objects like any other > Python objects (for example make a link between bioPython objects and > bioMoby objects). > > It would be nice if someone could CVS the whole thing as I still don't > know if I am still not able to CVS! > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From mwilkinson at mrl.ubc.ca Wed Aug 11 14:45:58 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Wed, 11 Aug 2004 07:45:58 -0700 Subject: [unclassified] [MOBY-dev] Update for the bioMoby Python API In-Reply-To: <1092218654.2938.21.camel@prot1.rpbs.jussieu.fr> References: <1092218654.2938.21.camel@prot1.rpbs.jussieu.fr> Message-ID: <1092235558.2060.27.camel@myhost.mydomain> Hi Yan! That is great news - thank you for all you efforts! I will pick up the code from your page later today and put it into the CVS if you agree to that. I don't recall if you requested CVS access or not. If you want it, please send a message to: root-l at open-bio.org and tell them you want to be a MOBY developer (c.c. to me please). It usually only takes them a few days to look after such requests. Best wishes! Mark On Wed, 2004-08-11 at 03:04, Yan Wong wrote: > As my internship is almost finished, I deliver my last update of the > bioMoby Python API on the website: > http://bioserv.rpbs.jussieu.fr/RPBS/html/an/T0_Software.html > > in the package you'll find: > -the API itself with changes (cf changelog and the howto.pdf) > -two little programs: > moby2python: It translates by default the whole ontology into a Python > package (it helps me to import some bioMoby objects) > wx/objectBrowser: A wxPython program that displays the structure of > the ontology in a tree view (for more detail consult the doc/howto.pdf). > > Changes: > -MobyMarshal, MobyUnmarshal, serialize deserialize xml objects<-> python > objects > -ServiceQuery before requires a dictionary, now you can enter parameters > directly: > before: > sq=ServiceQuery({'serviceName':'Service'}) > now: > sq=ServiceQuery(serviceName='Service') > > For register/deregister, same thing, no need to enter parameters in a > dictionary except for the Service object (as you can either enter a WSDL > or the dictionary to build the Service object) > > The ontology has been integrated as a Python module in the src/ontology > directory, thus it is possible to manipulate Moby Objects like any other > Python objects (for example make a link between bioPython objects and > bioMoby objects). > > It would be nice if someone could CVS the whole thing as I still don't > know if I am still not able to CVS! > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From mwilkinson at mrl.ubc.ca Wed Aug 11 18:12:04 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Wed, 11 Aug 2004 11:12:04 -0700 Subject: [unclassified] [MOBY-dev] Update for the bioMoby Python API In-Reply-To: <1092218654.2938.21.camel@prot1.rpbs.jussieu.fr> References: <1092218654.2938.21.camel@prot1.rpbs.jussieu.fr> Message-ID: <1092247923.1977.111.camel@myhost.mydomain> The python API is now in the CVS in the subdirectory "moby-live/Python". thanks Yan!! Mark On Wed, 2004-08-11 at 03:04, Yan Wong wrote: > As my internship is almost finished, I deliver my last update of the > bioMoby Python API on the website: > http://bioserv.rpbs.jussieu.fr/RPBS/html/an/T0_Software.html > > in the package you'll find: > -the API itself with changes (cf changelog and the howto.pdf) > -two little programs: > moby2python: It translates by default the whole ontology into a Python > package (it helps me to import some bioMoby objects) > wx/objectBrowser: A wxPython program that displays the structure of > the ontology in a tree view (for more detail consult the doc/howto.pdf). > > Changes: > -MobyMarshal, MobyUnmarshal, serialize deserialize xml objects<-> python > objects > -ServiceQuery before requires a dictionary, now you can enter parameters > directly: > before: > sq=ServiceQuery({'serviceName':'Service'}) > now: > sq=ServiceQuery(serviceName='Service') > > For register/deregister, same thing, no need to enter parameters in a > dictionary except for the Service object (as you can either enter a WSDL > or the dictionary to build the Service object) > > The ontology has been integrated as a Python module in the src/ontology > directory, thus it is possible to manipulate Moby Objects like any other > Python objects (for example make a link between bioPython objects and > bioMoby objects). > > It would be nice if someone could CVS the whole thing as I still don't > know if I am still not able to CVS! > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From mwilkinson at mrl.ubc.ca Wed Aug 11 18:12:04 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Wed, 11 Aug 2004 11:12:04 -0700 Subject: [unclassified] [MOBY-dev] Update for the bioMoby Python API In-Reply-To: <1092218654.2938.21.camel@prot1.rpbs.jussieu.fr> References: <1092218654.2938.21.camel@prot1.rpbs.jussieu.fr> Message-ID: <1092247923.1977.111.camel@myhost.mydomain> The python API is now in the CVS in the subdirectory "moby-live/Python". thanks Yan!! Mark On Wed, 2004-08-11 at 03:04, Yan Wong wrote: > As my internship is almost finished, I deliver my last update of the > bioMoby Python API on the website: > http://bioserv.rpbs.jussieu.fr/RPBS/html/an/T0_Software.html > > in the package you'll find: > -the API itself with changes (cf changelog and the howto.pdf) > -two little programs: > moby2python: It translates by default the whole ontology into a Python > package (it helps me to import some bioMoby objects) > wx/objectBrowser: A wxPython program that displays the structure of > the ontology in a tree view (for more detail consult the doc/howto.pdf). > > Changes: > -MobyMarshal, MobyUnmarshal, serialize deserialize xml objects<-> python > objects > -ServiceQuery before requires a dictionary, now you can enter parameters > directly: > before: > sq=ServiceQuery({'serviceName':'Service'}) > now: > sq=ServiceQuery(serviceName='Service') > > For register/deregister, same thing, no need to enter parameters in a > dictionary except for the Service object (as you can either enter a WSDL > or the dictionary to build the Service object) > > The ontology has been integrated as a Python module in the src/ontology > directory, thus it is possible to manipulate Moby Objects like any other > Python objects (for example make a link between bioPython objects and > bioMoby objects). > > It would be nice if someone could CVS the whole thing as I still don't > know if I am still not able to CVS! > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From mwilkinson at mrl.ubc.ca Wed Aug 18 00:12:57 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue, 17 Aug 2004 17:12:57 -0700 Subject: [MOBY-dev] small change to the database schema Message-ID: <1092787977.6947.33.camel@myhost.mydomain> the mobycentral.secondary_input columns maximum and minimum are now FLOAT datatypes. If you are running your own installation of MOBY Central you should do a mysql alter table on those two columns. M -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre