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From: Jian Lu <jl...@vb...> - 2006-02-11 23:56:02
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Hi GUS, I created a new schema name called APP with some new tables. I registered APP to Core.DatabaseInfo and all new tables to Core.TableInfo. When I rebuilt GUS, it seems not recognizing the new schema APP. When talking about extending GUS schema like adding new tables, does it mean all new tables have to fall into existing GUS schema such as DoTS? What should I do in order to support my own schema? Thanks. JL |
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From: Angel P. <an...@ma...> - 2006-02-12 23:54:33
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Did you "touch" the schema VERSION file prior to building? From the wiki: http://www.gusdb.org/wiki/index.php/Installing%20GUS Regenerating the GUS Perl and Java Objects touch $PROJECT_HOME/GUS/Model/schema/VERSION build GUS install -append Jian Lu wrote: > Hi GUS, > > I created a new schema name called APP with some new tables. I > registered APP to Core.DatabaseInfo and all new tables to > Core.TableInfo. When I rebuilt GUS, it seems not recognizing the new > schema APP. > > When talking about extending GUS schema like adding new tables, does > it mean all new tables have to fall into existing GUS schema such as > DoTS? What should I do in order to support my own schema? > > Thanks. > > JL > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log > files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642 > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: Jian Lu <jl...@vb...> - 2006-02-13 00:39:06
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I was using $touch $PROJECT_HOME/GUS/Schema/gus_schema.xml from http://www.gusdb.org/documentation/3.5/developers/html/ch02.html#id856722 I could try what you mentioned here. Thanks. Angel Pizarro wrote: > > Did you "touch" the schema VERSION file prior to building? From the wiki: > > http://www.gusdb.org/wiki/index.php/Installing%20GUS > > > Regenerating the GUS Perl and Java Objects > > touch $PROJECT_HOME/GUS/Model/schema/VERSION > build GUS install -append > > > Jian Lu wrote: > >> Hi GUS, >> >> I created a new schema name called APP with some new tables. I >> registered APP to Core.DatabaseInfo and all new tables to >> Core.TableInfo. When I rebuilt GUS, it seems not recognizing the new >> schema APP. >> >> When talking about extending GUS schema like adding new tables, does >> it mean all new tables have to fall into existing GUS schema such as >> DoTS? What should I do in order to support my own schema? >> >> Thanks. >> >> JL >> >> >> ------------------------------------------------------- >> This SF.net email is sponsored by: Splunk Inc. Do you grep through >> log files >> for problems? Stop! Download the new AJAX search engine that makes >> searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! >> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642 >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
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From: Steve F. <sfi...@pc...> - 2006-02-13 03:15:35
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jian- gus_schema.xml is the right file to touch. we have definitely extended the schema here recently. hopefully someone at cbil who has done so will answer this. if not, please write back, and i'll look into it. steve Jian Lu wrote: > I was using > $touch $PROJECT_HOME/GUS/Schema/gus_schema.xml > > from > http://www.gusdb.org/documentation/3.5/developers/html/ch02.html#id856722 > > I could try what you mentioned here. Thanks. > > Angel Pizarro wrote: >> >> Did you "touch" the schema VERSION file prior to building? From the >> wiki: >> >> http://www.gusdb.org/wiki/index.php/Installing%20GUS >> >> >> Regenerating the GUS Perl and Java Objects >> >> touch $PROJECT_HOME/GUS/Model/schema/VERSION >> build GUS install -append >> >> >> Jian Lu wrote: >> >>> Hi GUS, >>> >>> I created a new schema name called APP with some new tables. I >>> registered APP to Core.DatabaseInfo and all new tables to >>> Core.TableInfo. When I rebuilt GUS, it seems not recognizing the new >>> schema APP. >>> >>> When talking about extending GUS schema like adding new tables, does >>> it mean all new tables have to fall into existing GUS schema such as >>> DoTS? What should I do in order to support my own schema? >>> >>> Thanks. >>> >>> JL >>> >>> >>> ------------------------------------------------------- >>> This SF.net email is sponsored by: Splunk Inc. Do you grep through >>> log files >>> for problems? Stop! Download the new AJAX search engine that makes >>> searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! >>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642 >>> >>> _______________________________________________ >>> Gusdev-gusdev mailing list >>> Gus...@li... >>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log > files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642 > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: Angel P. <an...@ma...> - 2006-02-13 14:02:57
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1) I'll update the wiki for to delete the old information. 2) There is no mention of adding the new table definitions to the gus_schema.xml file, which should be _the_ canonical version of the schema from which perl, ddl and java code should be generated from. This guide was probably written while the DBAdmin project was not stable. We have to make a decision as a community whether we want to continue GUS as either a database driven or spec file driven documentation and development. Currently it is both, depending on the task. Pretty confusing. My vote is for spec-file driven. -angel Steve Fischer wrote: > jian- > > gus_schema.xml is the right file to touch. > > we have definitely extended the schema here recently. hopefully > someone at cbil who has done so will answer this. if not, please > write back, and i'll look into it. > > steve > > Jian Lu wrote: > >> I was using >> $touch $PROJECT_HOME/GUS/Schema/gus_schema.xml >> >> from >> http://www.gusdb.org/documentation/3.5/developers/html/ch02.html#id856722 >> >> >> I could try what you mentioned here. Thanks. >> >> Angel Pizarro wrote: >> >>> >>> Did you "touch" the schema VERSION file prior to building? From the >>> wiki: >>> >>> http://www.gusdb.org/wiki/index.php/Installing%20GUS >>> >>> >>> Regenerating the GUS Perl and Java Objects >>> >>> touch $PROJECT_HOME/GUS/Model/schema/VERSION >>> build GUS install -append >>> >>> >>> Jian Lu wrote: >>> >>>> Hi GUS, >>>> >>>> I created a new schema name called APP with some new tables. I >>>> registered APP to Core.DatabaseInfo and all new tables to >>>> Core.TableInfo. When I rebuilt GUS, it seems not recognizing the >>>> new schema APP. >>>> >>>> When talking about extending GUS schema like adding new tables, >>>> does it mean all new tables have to fall into existing GUS schema >>>> such as DoTS? What should I do in order to support my own schema? >>>> >>>> Thanks. >>>> >>>> JL >>>> >>>> >>>> ------------------------------------------------------- >>>> This SF.net email is sponsored by: Splunk Inc. Do you grep through >>>> log files >>>> for problems? Stop! Download the new AJAX search engine that makes >>>> searching your log files as easy as surfing the web. DOWNLOAD >>>> SPLUNK! >>>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642 >>>> >>>> _______________________________________________ >>>> Gusdev-gusdev mailing list >>>> Gus...@li... >>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> >>> >> >> >> >> ------------------------------------------------------- >> This SF.net email is sponsored by: Splunk Inc. Do you grep through >> log files >> for problems? Stop! Download the new AJAX search engine that makes >> searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! >> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642 >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
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From: Dhivya A. <dhi...@ya...> - 2006-02-13 17:31:01
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Hi, I'm trying to add a new schema to GUS to add pathway data. I plan to implement the biopax pathway data model on GUS. To do this, can I just add the tables as they are given in Biopax? Or do I need to follow the superclass(imp class)-subclass(view) relationship that is used in GUS? I need to import data into the schema later on which is in BioPax format, so I feel it would be easier to maintain the data model as given in Biopax. But I just wanted to know if it would cause problems since I'll be violating the subclassing relationships followed in GUS. thanks dhivya --------------------------------- Brings words and photos together (easily) with PhotoMail - it's free and works with Yahoo! Mail. |
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From: Angel P. <an...@ma...> - 2006-02-14 20:25:59
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If you want to use GUS objects and write GusApplication plugins for these tables, then you need to convert the BioPax schema. If you want to just query the data (SQL or WDK) and assign your GUS entities to these pathways, you can get away without translating the schema to GUS conventions and adding materialized view relating them (or querying on the fly for the associations). Your answer really depends on the needs of your application and your available coding resources. In either case, I would replicate the BioPax database in a different schema, since translating from DB to DB is slightly easier in a plugin than flat file to DB transformations. Angel Dhivya Aras wrote: > Hi, > > I'm trying to add a new schema to GUS to add pathway data. I plan to > implement the biopax pathway data model on GUS. To do this, can I just > add the tables as they are given in Biopax? Or do I need to follow the > superclass(imp class)-subclass(view) relationship that is used in GUS? > > I need to import data into the schema later on which is in BioPax > format, so I feel it would be easier to maintain the data model as > given in Biopax. But I just wanted to know if it would cause problems > since I'll be violating the subclassing relationships followed in GUS. > > thanks > dhivya > > > ------------------------------------------------------------------------ > Brings words and photos together (easily) with > PhotoMail > <http://us.rd.yahoo.com/mail_us/taglines/PMall/*http://photomail.mail.yahoo.com> > - it's free and works with Yahoo! Mail. -- Angel Pizarro Director, Bioinformatics Facility Institute for Translational Medicine and Therapeutics University of Pennsylvania 806 BRB II/III 421 Curie Blvd. Philadelphia, PA 19104-6160 P: 215-573-3736 F: 215-573-9004 |
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From: Michael S. <m...@sa...> - 2006-02-13 22:03:10
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Comments inline... read all the way to the bottom for my thoughts on the original issue. Angel Pizarro wrote: > 1) I'll update the wiki for to delete the old information. > > 2) There is no mention of adding the new table definitions to the > gus_schema.xml file, which should be _the_ canonical version of the > schema from which perl, ddl and java code should be generated from. This > guide was probably written while the DBAdmin project was not stable. > No, the guide was written after DBAdmin stabilized, but the thought was that end users (who the guide was written for) weren't likely to be modifying this file (more likely, they'd directly add their tables to the DB and want objects generated). The XML file is quite large, with many references and dependencies, and was never really intended to be edited by hand, another reason there is no documentation for doing so (I never really did this either beyond simply precision changes). > We have to make a decision as a community whether we want to continue > GUS as either a database driven or spec file driven documentation and > development. Currently it is both, depending on the task. I disagree with this. I maintain that as of 3.5, GUS is spec file driven. Either way, that'd be my vote too. (More below) Pretty > confusing. My vote is for spec-file driven. > > -angel > > > Steve Fischer wrote: > >> jian- >> >> gus_schema.xml is the right file to touch. >> >> we have definitely extended the schema here recently. hopefully >> someone at cbil who has done so will answer this. if not, please >> write back, and i'll look into it. >> I *think* you may have to add the new schema to the gus_config file. New objects don't need to be in XML, but they do need to be in the metadata tables (databaseinfo and tableinfo) and I think in the config file as well. The system doesn't really support adding new schemas in a good way... you may also have to add the schemas to the build.xml file ( there's an open issue for resolving this). --Mike >> steve >> >> Jian Lu wrote: >> >>> I was using >>> $touch $PROJECT_HOME/GUS/Schema/gus_schema.xml >>> >>> from >>> http://www.gusdb.org/documentation/3.5/developers/html/ch02.html#id856722 >>> >>> >>> I could try what you mentioned here. Thanks. >>> >>> Angel Pizarro wrote: >>> >>>> >>>> Did you "touch" the schema VERSION file prior to building? From the >>>> wiki: >>>> >>>> http://www.gusdb.org/wiki/index.php/Installing%20GUS >>>> >>>> >>>> Regenerating the GUS Perl and Java Objects >>>> >>>> touch $PROJECT_HOME/GUS/Model/schema/VERSION >>>> build GUS install -append >>>> >>>> >>>> Jian Lu wrote: >>>> >>>>> Hi GUS, >>>>> >>>>> I created a new schema name called APP with some new tables. I >>>>> registered APP to Core.DatabaseInfo and all new tables to >>>>> Core.TableInfo. When I rebuilt GUS, it seems not recognizing the >>>>> new schema APP. >>>>> >>>>> When talking about extending GUS schema like adding new tables, >>>>> does it mean all new tables have to fall into existing GUS schema >>>>> such as DoTS? What should I do in order to support my own schema? >>>>> >>>>> Thanks. >>>>> >>>>> JL >>>>> >>>>> >>>>> ------------------------------------------------------- >>>>> This SF.net email is sponsored by: Splunk Inc. Do you grep through >>>>> log files >>>>> for problems? Stop! Download the new AJAX search engine that makes >>>>> searching your log files as easy as surfing the web. DOWNLOAD >>>>> SPLUNK! >>>>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642 >>>>> >>>>> _______________________________________________ >>>>> Gusdev-gusdev mailing list >>>>> Gus...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>> >>>> >>> >>> >>> >>> ------------------------------------------------------- >>> This SF.net email is sponsored by: Splunk Inc. Do you grep through >>> log files >>> for problems? Stop! Download the new AJAX search engine that makes >>> searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! >>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642 >>> _______________________________________________ >>> Gusdev-gusdev mailing list >>> Gus...@li... >>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log > files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642 > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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