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From: <tw...@cs...> - 2004-03-12 17:04:53
|
Angel,
This sounds good. I am not working on the KEGG tables
at the moment so will that and OMIM to Thomas, but
"I'll be back..." (spoken with thick Austrian accent).
I would be tempted also to ask for
1. test data for the tables and a plugin to load them
if not to query them, (maybe that's the "data migration scripts")
2. an entity-relationship or UML like diagram
as part of the documentation you mention
The one problem I see is that after someone goes through
all the trouble of creating new stuff, the GUS core group
tells them, hey, look over there... Maybe some preliminary
review, but gusdev could be that.
Terry
On Fri, Mar 12, 2004 at 11:20:44AM -0500, Angel Pizarro wrote:
> Thomas and Terry,
> I think that both OMIM and KEGG are good candidates for integration into
> GUS. Here is my advise on how to proceed and get you guys running as
> quick as possible:
>
> 1) Create new schema spaces OMIM and KEGG. Enter this data into
> Core.DatabaseInfo.
> 2) Make the tables as GUS compliant and enter the Core.TableInfo information
> 3) Update the timestamp of $PROJETC_HOME/GUS/Model/schema/VERSION by:
> %> touch $PROJETC_HOME/GUS/Model/schema/VERSION
> 4) rebuild the objects by:
>
> %> build GUS/Model install -append
>
> This should create new objects for these schema spaces for use in plugins
>
> Document your schema and send it to the gusdev list once you have the
> bugs worked and and THEN we can look to see if existing GUS tables
> already fill that role or if these are new tables that should be folded
> into GUS propoer or if these new tables actually do a better job that
> the current GUS tables that holds this data.
> I think this is a good model for further GUS development, and we can
> release these types of development efforts as "contributed" modules of
> code. The contributed modules can be upgraded to "official" after they
> pass a review process and provide data migration scripts.
>
> Any comments?
> Angel
>
> Thomas Otto wrote:
>
> >ftp://ftp.genome.ad.jp/pub/
> >ftp://ftp.genome.ad.jp/pub/kegg/tarfiles
> >from the secound directory I download and parsed the tar files. This
> >suppose to be the files, like the kegg-engine are using them.
> >
> >Thomas
> >
> >Terry Clark wrote:
> >
> >>Thomas,
> >>Could you send a pointer to the KEGG FTP URL you are
> >>accessing and the names (or type of) files that you are using? I
> >>would appreciate this to see how
> >>others are using KEGG.
> >>
> >>OMIM is orthogonal; I just described it and the
> >>parts of KEGG I addressed to explain the material
> >>on my web site.
> >>
> >>Terry
> >>
> >>
> >>On Fri, Mar 12, 2004 at 11:08:29AM -0300, Thomas Otto wrote:
> >>
> >>
> >>>Terry,
> >>>
> >>>first, I parse the information from the files of the ftp-server. I
> >>>do not use the xml stuff.
> >>>
> >>>True, there is a lot of stuff in kegg, but I want to represent it in
> >>>GUS, so...
> >>>
> >>>... I think a link to OMIM makes sense, also to Motif/prosite. For
> >>>me it is important to have all the relations without redundend.
> >>>
> >>>Give me some time, I will see, which parts might help me,
> >>>
> >>>cheers,
> >>>Thomas
> >>>
> >>>
> >>>Terry Clark wrote:
> >>>
> >>>
> >>>
> >>>>Thomas,
> >>>>
> >>>>A few months ago I worked out a preliminary set of tables
> >>>>for *some* KEGG pathway data.
> >>>>(By the way, those reactions are not complete in some of
> >>>>the XML files.) I expect you know, there are two representations
> >>>>in the XML: one with proteins as nodes; the other with reaction
> >>>>products as nodes and proteins as edges. I focused on explicitly
> >>>>representing the latter (the <reaction> tag part of the XML) but
> >>>>have toyed with the idea to do a comprehensive KEGG representation
> >>>>in GUS unless someone else does it first :-)
> >>>>
> >>>>I also have a plugin to load the tables. All I am discussing has
> >>>>been implemented as a site-specific/local extension to GUS. I put
> >>>>the database files (not the plugin - we can talk
> >>>>about that later if you are interested) on the web page
> >>>>
> >>>>http://flora.uchicago.edu/gus/keggschemadraft/
> >>>>
> >>>>One file you might check first at the URL is ** kegg-tables.sql
> >>>>***
> >>>>
> >>>>I am not satisfied with some of the design, and there may be some
> >>>>uninspired things there - caveat emptor. I was waiting for KEGG to
> >>>>fix some problems in the reaction tags,
> >>>>and put together this operational db prototype in the meantime.
> >>>>(For example, check the missing - as of three weeks ago still -
> >>>>reaction tags in the XML for phenylalanine metabolism.)
> >>>>
> >>>>Anyway the files I point to above might be useful to start with
> >>>>rather than from scratch.
> >>>>
> >>>>I also hacked together some table(s) for EnzymeCommission
> >>>>numbers; there might be something in GUS for that, but at
> >>>>the time what I did seemed faster for my needs than otherwise.
> >>>>The OMIM parts there are not related to KEGG but part of a project
> >>>>I am working on.
> >>>>
> >>>>Terry
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>On Thu, Mar 11, 2004 at 04:58:48PM -0300, Thomas Otto wrote:
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>>I think I will all the relation in one table... sort of
> >>>>>EnzymeRelations...
> >>>>>
> >>>>>Thomas
> >>>>>Thomas Otto wrote:
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>>Okay, an example:
> >>>>>>To every enzyme are several reaction associated. i.e. Enzymea,
> >>>>>>has reaction1, ..., reaction n.
> >>>>>>(1) I could be to save the name of the reaction in the table
> >>>>>>EnzymeClassAttribute
> >>>>>>(2) would be, to save nothing of this in the
> >>>>>>EnzymeClassAttribute, but in a table (to create)
> >>>>>>EnzymeReactionRelation.
> >>>>>>
> >>>>>>This will mean a lot of new table, because just for the enzymes
> >>>>>>there are pathways, reaction, compound, substrate, product...
> >>>>>>
> >>>>>>But indeed, I also prefer #2, who is less redundend.
> >>>>>>
> >>>>>>Thanks,
> >>>>>>Thomas
> >>>>>>
> >>>>>>Angel Pizarro wrote:
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>>In the absence of an example of data a definite schema,
> >>>>>>>definitely #2 as the data model of choice. You can always
> >>>>>>>implement materialized view to speed-up/ease queries.
> >>>>>>>
> >>>>>>>Cheers
> >>>>>>>Angel
> >>>>>>>
> >>>>>>>Thomas Otto wrote:
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>>That's what I was thinking about. So I want to know, which
> >>>>>>>>representation of datas you prefer. (1 or 2, it is more a
> >>>>>>>>general question).
> >>>>>>>>
> >>>>>>>>Thomas
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>Angel Pizarro wrote:
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>>OK, I don't see where you are getting EnzymCompoundRelation &
> >>>>>>>>>CompoundClassAttribute from. Our current version of GUS does
> >>>>>>>>>not have these tables. The SRes.EnzymeClass table is also
> >>>>>>>>>looking very wacky to me. Propose a nice structure for this
> >>>>>>>>>and we can put it in the next release of GUS.
> >>>>>>>>>
> >>>>>>>>>Angel
> >>>>>>>>>
> >>>>>>>>>Thomas Otto wrote:
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>>Hello,
> >>>>>>>>>>
> >>>>>>>>>>I am uploading some kegg data in the GUS system...
> >>>>>>>>>>
> >>>>>>>>>>So I looked which tables are existing, and which we are
> >>>>>>>>>>needing i.e. for compound, reactions. Now I am not sure how
> >>>>>>>>>>is the convention to relate the data.
> >>>>>>>>>>
> >>>>>>>>>>Example:
> >>>>>>>>>>The Enzymes are related to the compounds.
> >>>>>>>>>>(1) In EzymeClassAttribute I write the names of the compound
> >>>>>>>>>>related to each enzyme. In CompoundClassAttribute I write
> >>>>>>>>>>also all EC-numbers, related to it.
> >>>>>>>>>>(2) Other possibilty would be to utilize a thrid table
> >>>>>>>>>>EnzymeCompoundRelation, where I put the primkeys of the
> >>>>>>>>>>relations.
> >>>>>>>>>>
> >>>>>>>>>>(1) would be faster, easier to query, but redundend.
> >>>>>>>>>>(2) Cleaner
> >>>>>>>>>>
> >>>>>>>>>>What are you thinking I should use?
> >>>>>>>>>>
> >>>>>>>>>>Thanks,
> >>>>>>>>>>Thomas
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>-------------------------------------------------------
> >>>>>>>>>>This SF.Net email is sponsored by: IBM Linux Tutorials
> >>>>>>>>>>Free Linux tutorial presented by Daniel Robbins, President
> >>>>>>>>>>and CEO of
> >>>>>>>>>>GenToo technologies. Learn everything from fundamentals to
> >>>>>>>>>>system
> >>>>>>>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> >>>>>>>>>>
> >>>>>>>>>>_______________________________________________
> >>>>>>>>>>Gusdev-gusdev mailing list
> >>>>>>>>>>Gus...@li...
> >>>>>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>
> >>>>>>>-------------------------------------------------------
> >>>>>>>This SF.Net email is sponsored by: IBM Linux Tutorials
> >>>>>>>Free Linux tutorial presented by Daniel Robbins, President and
> >>>>>>>CEO of
> >>>>>>>GenToo technologies. Learn everything from fundamentals to system
> >>>>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> >>>>>>>
> >>>>>>>_______________________________________________
> >>>>>>>Gusdev-gusdev mailing list
> >>>>>>>Gus...@li...
> >>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>>-------------------------------------------------------
> >>>>>>This SF.Net email is sponsored by: IBM Linux Tutorials
> >>>>>>Free Linux tutorial presented by Daniel Robbins, President and
> >>>>>>CEO of
> >>>>>>GenToo technologies. Learn everything from fundamentals to system
> >>>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> >>>>>>
> >>>>>>_______________________________________________
> >>>>>>Gusdev-gusdev mailing list
> >>>>>>Gus...@li...
> >>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>
> >>>>>-------------------------------------------------------
> >>>>>This SF.Net email is sponsored by: IBM Linux Tutorials
> >>>>>Free Linux tutorial presented by Daniel Robbins, President and CEO of
> >>>>>GenToo technologies. Learn everything from fundamentals to system
> >>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> >>>>>_______________________________________________
> >>>>>Gusdev-gusdev mailing list
> >>>>>Gus...@li...
> >>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>>
> >>>>>
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>
> >>
> >>
> >>-------------------------------------------------------
> >>This SF.Net email is sponsored by: IBM Linux Tutorials
> >>Free Linux tutorial presented by Daniel Robbins, President and CEO of
> >>GenToo technologies. Learn everything from fundamentals to system
> >>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> >>_______________________________________________
> >>Gusdev-gusdev mailing list
> >>Gus...@li...
> >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>
> >>
> >>
> >
> >
> >
> >
> >-------------------------------------------------------
> >This SF.Net email is sponsored by: IBM Linux Tutorials
> >Free Linux tutorial presented by Daniel Robbins, President and CEO of
> >GenToo technologies. Learn everything from fundamentals to system
> >administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> >_______________________________________________
> >Gusdev-gusdev mailing list
> >Gus...@li...
> >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
|
|
From: Thomas O. <ot...@fi...> - 2004-03-12 17:20:33
|
Hi, I think I give kegg a try... now I have an idea of the relations and first steps. The moment I am done, I will provide a new namespace, ga - module for uploading and the link for the data. Cheers, Thomas Terry Clark wrote: >Angel, > >This sounds good. I am not working on the KEGG tables >at the moment so will that and OMIM to Thomas, but > "I'll be back..." (spoken with thick Austrian accent). > >I would be tempted also to ask for > > 1. test data for the tables and a plugin to load them > if not to query them, (maybe that's the "data migration scripts") > > 2. an entity-relationship or UML like diagram > as part of the documentation you mention > >The one problem I see is that after someone goes through >all the trouble of creating new stuff, the GUS core group >tells them, hey, look over there... Maybe some preliminary >review, but gusdev could be that. > >Terry > > >On Fri, Mar 12, 2004 at 11:20:44AM -0500, Angel Pizarro wrote: > > >>Thomas and Terry, >>I think that both OMIM and KEGG are good candidates for integration into >>GUS. Here is my advise on how to proceed and get you guys running as >>quick as possible: >> >>1) Create new schema spaces OMIM and KEGG. Enter this data into >>Core.DatabaseInfo. >>2) Make the tables as GUS compliant and enter the Core.TableInfo information >>3) Update the timestamp of $PROJETC_HOME/GUS/Model/schema/VERSION by: >>%> touch $PROJETC_HOME/GUS/Model/schema/VERSION >>4) rebuild the objects by: >> >>%> build GUS/Model install -append >> >>This should create new objects for these schema spaces for use in plugins >> >>Document your schema and send it to the gusdev list once you have the >>bugs worked and and THEN we can look to see if existing GUS tables >>already fill that role or if these are new tables that should be folded >>into GUS propoer or if these new tables actually do a better job that >>the current GUS tables that holds this data. >>I think this is a good model for further GUS development, and we can >>release these types of development efforts as "contributed" modules of >>code. The contributed modules can be upgraded to "official" after they >>pass a review process and provide data migration scripts. >> >>Any comments? >>Angel >> >>Thomas Otto wrote: >> >> >> >>>ftp://ftp.genome.ad.jp/pub/ >>>ftp://ftp.genome.ad.jp/pub/kegg/tarfiles >>> >>> >>>from the secound directory I download and parsed the tar files. This >> >> >>>suppose to be the files, like the kegg-engine are using them. >>> >>>Thomas >>> >>>Terry Clark wrote: >>> >>> >>> >>>>Thomas, >>>>Could you send a pointer to the KEGG FTP URL you are >>>>accessing and the names (or type of) files that you are using? I >>>>would appreciate this to see how >>>>others are using KEGG. >>>> >>>>OMIM is orthogonal; I just described it and the >>>>parts of KEGG I addressed to explain the material >>>>on my web site. >>>> >>>>Terry >>>> >>>> >>>>On Fri, Mar 12, 2004 at 11:08:29AM -0300, Thomas Otto wrote: >>>> >>>> >>>> >>>> >>>>>Terry, >>>>> >>>>>first, I parse the information from the files of the ftp-server. I >>>>>do not use the xml stuff. >>>>> >>>>>True, there is a lot of stuff in kegg, but I want to represent it in >>>>>GUS, so... >>>>> >>>>>... I think a link to OMIM makes sense, also to Motif/prosite. For >>>>>me it is important to have all the relations without redundend. >>>>> >>>>>Give me some time, I will see, which parts might help me, >>>>> >>>>>cheers, >>>>>Thomas >>>>> >>>>> >>>>>Terry Clark wrote: >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>>Thomas, >>>>>> >>>>>>A few months ago I worked out a preliminary set of tables >>>>>>for *some* KEGG pathway data. >>>>>>(By the way, those reactions are not complete in some of >>>>>>the XML files.) I expect you know, there are two representations >>>>>>in the XML: one with proteins as nodes; the other with reaction >>>>>>products as nodes and proteins as edges. I focused on explicitly >>>>>>representing the latter (the <reaction> tag part of the XML) but >>>>>>have toyed with the idea to do a comprehensive KEGG representation >>>>>>in GUS unless someone else does it first :-) >>>>>> >>>>>>I also have a plugin to load the tables. All I am discussing has >>>>>>been implemented as a site-specific/local extension to GUS. I put >>>>>>the database files (not the plugin - we can talk >>>>>>about that later if you are interested) on the web page >>>>>> >>>>>>http://flora.uchicago.edu/gus/keggschemadraft/ >>>>>> >>>>>>One file you might check first at the URL is ** kegg-tables.sql >>>>>>*** >>>>>> >>>>>>I am not satisfied with some of the design, and there may be some >>>>>>uninspired things there - caveat emptor. I was waiting for KEGG to >>>>>>fix some problems in the reaction tags, >>>>>>and put together this operational db prototype in the meantime. >>>>>>(For example, check the missing - as of three weeks ago still - >>>>>>reaction tags in the XML for phenylalanine metabolism.) >>>>>> >>>>>>Anyway the files I point to above might be useful to start with >>>>>>rather than from scratch. >>>>>> >>>>>>I also hacked together some table(s) for EnzymeCommission >>>>>>numbers; there might be something in GUS for that, but at >>>>>>the time what I did seemed faster for my needs than otherwise. >>>>>>The OMIM parts there are not related to KEGG but part of a project >>>>>>I am working on. >>>>>> >>>>>>Terry >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>On Thu, Mar 11, 2004 at 04:58:48PM -0300, Thomas Otto wrote: >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>>I think I will all the relation in one table... sort of >>>>>>>EnzymeRelations... >>>>>>> >>>>>>>Thomas >>>>>>>Thomas Otto wrote: >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>>>Okay, an example: >>>>>>>>To every enzyme are several reaction associated. i.e. Enzymea, >>>>>>>>has reaction1, ..., reaction n. >>>>>>>>(1) I could be to save the name of the reaction in the table >>>>>>>>EnzymeClassAttribute >>>>>>>>(2) would be, to save nothing of this in the >>>>>>>>EnzymeClassAttribute, but in a table (to create) >>>>>>>>EnzymeReactionRelation. >>>>>>>> >>>>>>>>This will mean a lot of new table, because just for the enzymes >>>>>>>>there are pathways, reaction, compound, substrate, product... >>>>>>>> >>>>>>>>But indeed, I also prefer #2, who is less redundend. >>>>>>>> >>>>>>>>Thanks, >>>>>>>>Thomas >>>>>>>> >>>>>>>>Angel Pizarro wrote: >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>>In the absence of an example of data a definite schema, >>>>>>>>>definitely #2 as the data model of choice. You can always >>>>>>>>>implement materialized view to speed-up/ease queries. >>>>>>>>> >>>>>>>>>Cheers >>>>>>>>>Angel >>>>>>>>> >>>>>>>>>Thomas Otto wrote: >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>>That's what I was thinking about. So I want to know, which >>>>>>>>>>representation of datas you prefer. (1 or 2, it is more a >>>>>>>>>>general question). >>>>>>>>>> >>>>>>>>>>Thomas >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>Angel Pizarro wrote: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>>OK, I don't see where you are getting EnzymCompoundRelation & >>>>>>>>>>>CompoundClassAttribute from. Our current version of GUS does >>>>>>>>>>>not have these tables. The SRes.EnzymeClass table is also >>>>>>>>>>>looking very wacky to me. Propose a nice structure for this >>>>>>>>>>>and we can put it in the next release of GUS. >>>>>>>>>>> >>>>>>>>>>>Angel >>>>>>>>>>> >>>>>>>>>>>Thomas Otto wrote: >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>>Hello, >>>>>>>>>>>> >>>>>>>>>>>>I am uploading some kegg data in the GUS system... >>>>>>>>>>>> >>>>>>>>>>>>So I looked which tables are existing, and which we are >>>>>>>>>>>>needing i.e. for compound, reactions. Now I am not sure how >>>>>>>>>>>>is the convention to relate the data. >>>>>>>>>>>> >>>>>>>>>>>>Example: >>>>>>>>>>>>The Enzymes are related to the compounds. >>>>>>>>>>>>(1) In EzymeClassAttribute I write the names of the compound >>>>>>>>>>>>related to each enzyme. In CompoundClassAttribute I write >>>>>>>>>>>>also all EC-numbers, related to it. >>>>>>>>>>>>(2) Other possibilty would be to utilize a thrid table >>>>>>>>>>>>EnzymeCompoundRelation, where I put the primkeys of the >>>>>>>>>>>>relations. >>>>>>>>>>>> >>>>>>>>>>>>(1) would be faster, easier to query, but redundend. >>>>>>>>>>>>(2) Cleaner >>>>>>>>>>>> >>>>>>>>>>>>What are you thinking I should use? >>>>>>>>>>>> >>>>>>>>>>>>Thanks, >>>>>>>>>>>>Thomas >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>>------------------------------------------------------- >>>>>>>>>>>>This SF.Net email is sponsored by: IBM Linux Tutorials >>>>>>>>>>>>Free Linux tutorial presented by Daniel Robbins, President >>>>>>>>>>>>and CEO of >>>>>>>>>>>>GenToo technologies. Learn everything from fundamentals to >>>>>>>>>>>>system >>>>>>>>>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click >>>>>>>>>>>> >>>>>>>>>>>>_______________________________________________ >>>>>>>>>>>>Gusdev-gusdev mailing list >>>>>>>>>>>>Gus...@li... >>>>>>>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>------------------------------------------------------- >>>>>>>>>This SF.Net email is sponsored by: IBM Linux Tutorials >>>>>>>>>Free Linux tutorial presented by Daniel Robbins, President and >>>>>>>>>CEO of >>>>>>>>>GenToo technologies. Learn everything from fundamentals to system >>>>>>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click >>>>>>>>> >>>>>>>>>_______________________________________________ >>>>>>>>>Gusdev-gusdev mailing list >>>>>>>>>Gus...@li... >>>>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>------------------------------------------------------- >>>>>>>>This SF.Net email is sponsored by: IBM Linux Tutorials >>>>>>>>Free Linux tutorial presented by Daniel Robbins, President and >>>>>>>>CEO of >>>>>>>>GenToo technologies. Learn everything from fundamentals to system >>>>>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click >>>>>>>> >>>>>>>>_______________________________________________ >>>>>>>>Gusdev-gusdev mailing list >>>>>>>>Gus...@li... >>>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>------------------------------------------------------- >>>>>>>This SF.Net email is sponsored by: IBM Linux Tutorials >>>>>>>Free Linux tutorial presented by Daniel Robbins, President and CEO of >>>>>>>GenToo technologies. Learn everything from fundamentals to system >>>>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click >>>>>>>_______________________________________________ >>>>>>>Gusdev-gusdev mailing list >>>>>>>Gus...@li... >>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> >>>>------------------------------------------------------- >>>>This SF.Net email is sponsored by: IBM Linux Tutorials >>>>Free Linux tutorial presented by Daniel Robbins, President and CEO of >>>>GenToo technologies. Learn everything from fundamentals to system >>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click >>>>_______________________________________________ >>>>Gusdev-gusdev mailing list >>>>Gus...@li... >>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>> >>>> >>>> >>>> >>>> >>> >>> >>>------------------------------------------------------- >>>This SF.Net email is sponsored by: IBM Linux Tutorials >>>Free Linux tutorial presented by Daniel Robbins, President and CEO of >>>GenToo technologies. Learn everything from fundamentals to system >>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click >>>_______________________________________________ >>>Gusdev-gusdev mailing list >>>Gus...@li... >>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> >>> > > >------------------------------------------------------- >This SF.Net email is sponsored by: IBM Linux Tutorials >Free Linux tutorial presented by Daniel Robbins, President and CEO of >GenToo technologies. Learn everything from fundamentals to system >administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > |
|
From: Steve F. <sfi...@pc...> - 2004-03-12 17:32:03
|
Yes, i agree that we should have a preliminary review. In this case Thomas has provided the create table statements. UML would also be an option. I think the development of the plugin should just be a proof of concept, not a final submission. After final review, then, yes, sample data and a clean plugin would be great. steve Terry Clark wrote: >Angel, > >This sounds good. I am not working on the KEGG tables >at the moment so will that and OMIM to Thomas, but > "I'll be back..." (spoken with thick Austrian accent). > >I would be tempted also to ask for > > 1. test data for the tables and a plugin to load them > if not to query them, (maybe that's the "data migration scripts") > > 2. an entity-relationship or UML like diagram > as part of the documentation you mention > >The one problem I see is that after someone goes through >all the trouble of creating new stuff, the GUS core group >tells them, hey, look over there... Maybe some preliminary >review, but gusdev could be that. > >Terry > > >On Fri, Mar 12, 2004 at 11:20:44AM -0500, Angel Pizarro wrote: > > >>Thomas and Terry, >>I think that both OMIM and KEGG are good candidates for integration into >>GUS. Here is my advise on how to proceed and get you guys running as >>quick as possible: >> >>1) Create new schema spaces OMIM and KEGG. Enter this data into >>Core.DatabaseInfo. >>2) Make the tables as GUS compliant and enter the Core.TableInfo information >>3) Update the timestamp of $PROJETC_HOME/GUS/Model/schema/VERSION by: >>%> touch $PROJETC_HOME/GUS/Model/schema/VERSION >>4) rebuild the objects by: >> >>%> build GUS/Model install -append >> >>This should create new objects for these schema spaces for use in plugins >> >>Document your schema and send it to the gusdev list once you have the >>bugs worked and and THEN we can look to see if existing GUS tables >>already fill that role or if these are new tables that should be folded >>into GUS propoer or if these new tables actually do a better job that >>the current GUS tables that holds this data. >>I think this is a good model for further GUS development, and we can >>release these types of development efforts as "contributed" modules of >>code. The contributed modules can be upgraded to "official" after they >>pass a review process and provide data migration scripts. >> >>Any comments? >>Angel >> >>Thomas Otto wrote: >> >> >> >>>ftp://ftp.genome.ad.jp/pub/ >>>ftp://ftp.genome.ad.jp/pub/kegg/tarfiles >>> >>> >>>from the secound directory I download and parsed the tar files. This >> >> >>>suppose to be the files, like the kegg-engine are using them. >>> >>>Thomas >>> >>>Terry Clark wrote: >>> >>> >>> >>>>Thomas, >>>>Could you send a pointer to the KEGG FTP URL you are >>>>accessing and the names (or type of) files that you are using? I >>>>would appreciate this to see how >>>>others are using KEGG. >>>> >>>>OMIM is orthogonal; I just described it and the >>>>parts of KEGG I addressed to explain the material >>>>on my web site. >>>> >>>>Terry >>>> >>>> >>>>On Fri, Mar 12, 2004 at 11:08:29AM -0300, Thomas Otto wrote: >>>> >>>> >>>> >>>> >>>>>Terry, >>>>> >>>>>first, I parse the information from the files of the ftp-server. I >>>>>do not use the xml stuff. >>>>> >>>>>True, there is a lot of stuff in kegg, but I want to represent it in >>>>>GUS, so... >>>>> >>>>>... I think a link to OMIM makes sense, also to Motif/prosite. For >>>>>me it is important to have all the relations without redundend. >>>>> >>>>>Give me some time, I will see, which parts might help me, >>>>> >>>>>cheers, >>>>>Thomas >>>>> >>>>> >>>>>Terry Clark wrote: >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>>Thomas, >>>>>> >>>>>>A few months ago I worked out a preliminary set of tables >>>>>>for *some* KEGG pathway data. >>>>>>(By the way, those reactions are not complete in some of >>>>>>the XML files.) I expect you know, there are two representations >>>>>>in the XML: one with proteins as nodes; the other with reaction >>>>>>products as nodes and proteins as edges. I focused on explicitly >>>>>>representing the latter (the <reaction> tag part of the XML) but >>>>>>have toyed with the idea to do a comprehensive KEGG representation >>>>>>in GUS unless someone else does it first :-) >>>>>> >>>>>>I also have a plugin to load the tables. All I am discussing has >>>>>>been implemented as a site-specific/local extension to GUS. I put >>>>>>the database files (not the plugin - we can talk >>>>>>about that later if you are interested) on the web page >>>>>> >>>>>>http://flora.uchicago.edu/gus/keggschemadraft/ >>>>>> >>>>>>One file you might check first at the URL is ** kegg-tables.sql >>>>>>*** >>>>>> >>>>>>I am not satisfied with some of the design, and there may be some >>>>>>uninspired things there - caveat emptor. I was waiting for KEGG to >>>>>>fix some problems in the reaction tags, >>>>>>and put together this operational db prototype in the meantime. >>>>>>(For example, check the missing - as of three weeks ago still - >>>>>>reaction tags in the XML for phenylalanine metabolism.) >>>>>> >>>>>>Anyway the files I point to above might be useful to start with >>>>>>rather than from scratch. >>>>>> >>>>>>I also hacked together some table(s) for EnzymeCommission >>>>>>numbers; there might be something in GUS for that, but at >>>>>>the time what I did seemed faster for my needs than otherwise. >>>>>>The OMIM parts there are not related to KEGG but part of a project >>>>>>I am working on. >>>>>> >>>>>>Terry >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>On Thu, Mar 11, 2004 at 04:58:48PM -0300, Thomas Otto wrote: >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>>I think I will all the relation in one table... sort of >>>>>>>EnzymeRelations... >>>>>>> >>>>>>>Thomas >>>>>>>Thomas Otto wrote: >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>>>Okay, an example: >>>>>>>>To every enzyme are several reaction associated. i.e. Enzymea, >>>>>>>>has reaction1, ..., reaction n. >>>>>>>>(1) I could be to save the name of the reaction in the table >>>>>>>>EnzymeClassAttribute >>>>>>>>(2) would be, to save nothing of this in the >>>>>>>>EnzymeClassAttribute, but in a table (to create) >>>>>>>>EnzymeReactionRelation. >>>>>>>> >>>>>>>>This will mean a lot of new table, because just for the enzymes >>>>>>>>there are pathways, reaction, compound, substrate, product... >>>>>>>> >>>>>>>>But indeed, I also prefer #2, who is less redundend. >>>>>>>> >>>>>>>>Thanks, >>>>>>>>Thomas >>>>>>>> >>>>>>>>Angel Pizarro wrote: >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>>In the absence of an example of data a definite schema, >>>>>>>>>definitely #2 as the data model of choice. You can always >>>>>>>>>implement materialized view to speed-up/ease queries. >>>>>>>>> >>>>>>>>>Cheers >>>>>>>>>Angel >>>>>>>>> >>>>>>>>>Thomas Otto wrote: >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>>That's what I was thinking about. So I want to know, which >>>>>>>>>>representation of datas you prefer. (1 or 2, it is more a >>>>>>>>>>general question). >>>>>>>>>> >>>>>>>>>>Thomas >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>Angel Pizarro wrote: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>>OK, I don't see where you are getting EnzymCompoundRelation & >>>>>>>>>>>CompoundClassAttribute from. Our current version of GUS does >>>>>>>>>>>not have these tables. The SRes.EnzymeClass table is also >>>>>>>>>>>looking very wacky to me. Propose a nice structure for this >>>>>>>>>>>and we can put it in the next release of GUS. >>>>>>>>>>> >>>>>>>>>>>Angel >>>>>>>>>>> >>>>>>>>>>>Thomas Otto wrote: >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>>Hello, >>>>>>>>>>>> >>>>>>>>>>>>I am uploading some kegg data in the GUS system... >>>>>>>>>>>> >>>>>>>>>>>>So I looked which tables are existing, and which we are >>>>>>>>>>>>needing i.e. for compound, reactions. Now I am not sure how >>>>>>>>>>>>is the convention to relate the data. >>>>>>>>>>>> >>>>>>>>>>>>Example: >>>>>>>>>>>>The Enzymes are related to the compounds. >>>>>>>>>>>>(1) In EzymeClassAttribute I write the names of the compound >>>>>>>>>>>>related to each enzyme. In CompoundClassAttribute I write >>>>>>>>>>>>also all EC-numbers, related to it. >>>>>>>>>>>>(2) Other possibilty would be to utilize a thrid table >>>>>>>>>>>>EnzymeCompoundRelation, where I put the primkeys of the >>>>>>>>>>>>relations. >>>>>>>>>>>> >>>>>>>>>>>>(1) would be faster, easier to query, but redundend. >>>>>>>>>>>>(2) Cleaner >>>>>>>>>>>> >>>>>>>>>>>>What are you thinking I should use? >>>>>>>>>>>> >>>>>>>>>>>>Thanks, >>>>>>>>>>>>Thomas >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>>------------------------------------------------------- >>>>>>>>>>>>This SF.Net email is sponsored by: IBM Linux Tutorials >>>>>>>>>>>>Free Linux tutorial presented by Daniel Robbins, President >>>>>>>>>>>>and CEO of >>>>>>>>>>>>GenToo technologies. Learn everything from fundamentals to >>>>>>>>>>>>system >>>>>>>>>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click >>>>>>>>>>>> >>>>>>>>>>>>_______________________________________________ >>>>>>>>>>>>Gusdev-gusdev mailing list >>>>>>>>>>>>Gus...@li... >>>>>>>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>------------------------------------------------------- >>>>>>>>>This SF.Net email is sponsored by: IBM Linux Tutorials >>>>>>>>>Free Linux tutorial presented by Daniel Robbins, President and >>>>>>>>>CEO of >>>>>>>>>GenToo technologies. Learn everything from fundamentals to system >>>>>>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click >>>>>>>>> >>>>>>>>>_______________________________________________ >>>>>>>>>Gusdev-gusdev mailing list >>>>>>>>>Gus...@li... >>>>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>------------------------------------------------------- >>>>>>>>This SF.Net email is sponsored by: IBM Linux Tutorials >>>>>>>>Free Linux tutorial presented by Daniel Robbins, President and >>>>>>>>CEO of >>>>>>>>GenToo technologies. Learn everything from fundamentals to system >>>>>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click >>>>>>>> >>>>>>>>_______________________________________________ >>>>>>>>Gusdev-gusdev mailing list >>>>>>>>Gus...@li... >>>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>------------------------------------------------------- >>>>>>>This SF.Net email is sponsored by: IBM Linux Tutorials >>>>>>>Free Linux tutorial presented by Daniel Robbins, President and CEO of >>>>>>>GenToo technologies. Learn everything from fundamentals to system >>>>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click >>>>>>>_______________________________________________ >>>>>>>Gusdev-gusdev mailing list >>>>>>>Gus...@li... >>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> >>>>------------------------------------------------------- >>>>This SF.Net email is sponsored by: IBM Linux Tutorials >>>>Free Linux tutorial presented by Daniel Robbins, President and CEO of >>>>GenToo technologies. Learn everything from fundamentals to system >>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click >>>>_______________________________________________ >>>>Gusdev-gusdev mailing list >>>>Gus...@li... >>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>> >>>> >>>> >>>> >>>> >>> >>> >>>------------------------------------------------------- >>>This SF.Net email is sponsored by: IBM Linux Tutorials >>>Free Linux tutorial presented by Daniel Robbins, President and CEO of >>>GenToo technologies. Learn everything from fundamentals to system >>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click >>>_______________________________________________ >>>Gusdev-gusdev mailing list >>>Gus...@li... >>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> >>> > > >------------------------------------------------------- >This SF.Net email is sponsored by: IBM Linux Tutorials >Free Linux tutorial presented by Daniel Robbins, President and CEO of >GenToo technologies. Learn everything from fundamentals to system >administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
|
From: Thomas O. <ot...@fi...> - 2004-04-12 14:40:03
|
Hi,
I will try to change the GBParser to upload AA-sequences.
The easiest way might be to change a bit the GBParser...
A question: If I have an entry with
source 1..47
/organism="Oryctolagus cuniculus"
/isolate="COF12"
/db_xref="taxon:9986"
/chromosome="1"
/map="1q14-q21"
/clone="22"
/transgenic
/note="Chagas disease"
I just create a view sourceAA or AAsource on AAFeartureimp, with the
rows like organism...
Does that sounds logic?
Next question: Might it be important to have also the NA - sequence of
the AA in the schema?
Cheers,
Thomas
|
|
From: Thomas O. <ot...@fi...> - 2004-04-12 17:46:22
|
Hi, I thought a little bit about the stuff. If the NA genbank entry is available, namely the most information will be in GUS with the GBParser module. So the GBAAParser could maybe write some information in the dots.protein, dots.rna table and so one. I will think on this. Cheers, Thomas Thomas Otto wrote: > Hi, > > I will try to change the GBParser to upload AA-sequences. > > The easiest way might be to change a bit the GBParser... > > A question: If I have an entry with > source 1..47 > /organism="Oryctolagus cuniculus" > /isolate="COF12" > /db_xref="taxon:9986" > /chromosome="1" > /map="1q14-q21" > /clone="22" > /transgenic > /note="Chagas disease" > I just create a view sourceAA or AAsource on AAFeartureimp, with the > rows like organism... > Does that sounds logic? > > Next question: Might it be important to have also the NA - sequence of > the AA in the schema? > > Cheers, > Thomas > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: IBM Linux Tutorials > Free Linux tutorial presented by Daniel Robbins, President and CEO of > GenToo technologies. Learn everything from fundamentals to system > administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
|
From: Deborah F. P. <pi...@pc...> - 2004-03-15 15:37:34
|
There is a set of tables in the current schema that were designed to
accomodate interaction data of unspecified type. This includes
dots.Interaction,dots.InteractionLnteractionLOE. dots.InteractionLOE,
dots.InteractionType, dots.EffectorActionType, and maybe dots.rowset and
sots.rowsetmember. Data from KEGG was migrated to these table from a set
of Pathway tables that existed in a previous version of the GUS schema. It
might be a good idea to look at these tables to see if they can accomodate
the data you want to insert.
Debbie
On Fri, 12 Mar 2004, Angel Pizarro wrote:
> Thomas and Terry,
> I think that both OMIM and KEGG are good candidates for integration into
> GUS. Here is my advise on how to proceed and get you guys running as
> quick as possible:
>
> 1) Create new schema spaces OMIM and KEGG. Enter this data into
> Core.DatabaseInfo.
> 2) Make the tables as GUS compliant and enter the Core.TableInfo information
> 3) Update the timestamp of $PROJETC_HOME/GUS/Model/schema/VERSION by:
> %> touch $PROJETC_HOME/GUS/Model/schema/VERSION
> 4) rebuild the objects by:
>
> %> build GUS/Model install -append
>
> This should create new objects for these schema spaces for use in plugins
>
> Document your schema and send it to the gusdev list once you have the
> bugs worked and and THEN we can look to see if existing GUS tables
> already fill that role or if these are new tables that should be folded
> into GUS propoer or if these new tables actually do a better job that
> the current GUS tables that holds this data.
> I think this is a good model for further GUS development, and we can
> release these types of development efforts as "contributed" modules of
> code. The contributed modules can be upgraded to "official" after they
> pass a review process and provide data migration scripts.
>
> Any comments?
> Angel
>
> Thomas Otto wrote:
>
> > ftp://ftp.genome.ad.jp/pub/
> > ftp://ftp.genome.ad.jp/pub/kegg/tarfiles
> > from the secound directory I download and parsed the tar files. This
> > suppose to be the files, like the kegg-engine are using them.
> >
> > Thomas
> >
> > Terry Clark wrote:
> >
> >> Thomas,
> >> Could you send a pointer to the KEGG FTP URL you are
> >> accessing and the names (or type of) files that you are using? I
> >> would appreciate this to see how
> >> others are using KEGG.
> >>
> >> OMIM is orthogonal; I just described it and the
> >> parts of KEGG I addressed to explain the material
> >> on my web site.
> >>
> >> Terry
> >>
> >>
> >> On Fri, Mar 12, 2004 at 11:08:29AM -0300, Thomas Otto wrote:
> >>
> >>
> >>> Terry,
> >>>
> >>> first, I parse the information from the files of the ftp-server. I
> >>> do not use the xml stuff.
> >>>
> >>> True, there is a lot of stuff in kegg, but I want to represent it in
> >>> GUS, so...
> >>>
> >>> ... I think a link to OMIM makes sense, also to Motif/prosite. For
> >>> me it is important to have all the relations without redundend.
> >>>
> >>> Give me some time, I will see, which parts might help me,
> >>>
> >>> cheers,
> >>> Thomas
> >>>
> >>>
> >>> Terry Clark wrote:
> >>>
> >>>
> >>>
> >>>> Thomas,
> >>>>
> >>>> A few months ago I worked out a preliminary set of tables
> >>>> for *some* KEGG pathway data.
> >>>> (By the way, those reactions are not complete in some of
> >>>> the XML files.) I expect you know, there are two representations
> >>>> in the XML: one with proteins as nodes; the other with reaction
> >>>> products as nodes and proteins as edges. I focused on explicitly
> >>>> representing the latter (the <reaction> tag part of the XML) but
> >>>> have toyed with the idea to do a comprehensive KEGG representation
> >>>> in GUS unless someone else does it first :-)
> >>>>
> >>>> I also have a plugin to load the tables. All I am discussing has
> >>>> been implemented as a site-specific/local extension to GUS. I put
> >>>> the database files (not the plugin - we can talk
> >>>> about that later if you are interested) on the web page
> >>>>
> >>>> http://flora.uchicago.edu/gus/keggschemadraft/
> >>>>
> >>>> One file you might check first at the URL is ** kegg-tables.sql
> >>>> ***
> >>>>
> >>>> I am not satisfied with some of the design, and there may be some
> >>>> uninspired things there - caveat emptor. I was waiting for KEGG to
> >>>> fix some problems in the reaction tags,
> >>>> and put together this operational db prototype in the meantime.
> >>>> (For example, check the missing - as of three weeks ago still -
> >>>> reaction tags in the XML for phenylalanine metabolism.)
> >>>>
> >>>> Anyway the files I point to above might be useful to start with
> >>>> rather than from scratch.
> >>>>
> >>>> I also hacked together some table(s) for EnzymeCommission
> >>>> numbers; there might be something in GUS for that, but at
> >>>> the time what I did seemed faster for my needs than otherwise.
> >>>> The OMIM parts there are not related to KEGG but part of a project
> >>>> I am working on.
> >>>>
> >>>> Terry
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> On Thu, Mar 11, 2004 at 04:58:48PM -0300, Thomas Otto wrote:
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>> I think I will all the relation in one table... sort of
> >>>>> EnzymeRelations...
> >>>>>
> >>>>> Thomas
> >>>>> Thomas Otto wrote:
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>> Okay, an example:
> >>>>>> To every enzyme are several reaction associated. i.e. Enzymea,
> >>>>>> has reaction1, ..., reaction n.
> >>>>>> (1) I could be to save the name of the reaction in the table
> >>>>>> EnzymeClassAttribute
> >>>>>> (2) would be, to save nothing of this in the
> >>>>>> EnzymeClassAttribute, but in a table (to create)
> >>>>>> EnzymeReactionRelation.
> >>>>>>
> >>>>>> This will mean a lot of new table, because just for the enzymes
> >>>>>> there are pathways, reaction, compound, substrate, product...
> >>>>>>
> >>>>>> But indeed, I also prefer #2, who is less redundend.
> >>>>>>
> >>>>>> Thanks,
> >>>>>> Thomas
> >>>>>>
> >>>>>> Angel Pizarro wrote:
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>> In the absence of an example of data a definite schema,
> >>>>>>> definitely #2 as the data model of choice. You can always
> >>>>>>> implement materialized view to speed-up/ease queries.
> >>>>>>>
> >>>>>>> Cheers
> >>>>>>> Angel
> >>>>>>>
> >>>>>>> Thomas Otto wrote:
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>> That's what I was thinking about. So I want to know, which
> >>>>>>>> representation of datas you prefer. (1 or 2, it is more a
> >>>>>>>> general question).
> >>>>>>>>
> >>>>>>>> Thomas
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> Angel Pizarro wrote:
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>> OK, I don't see where you are getting EnzymCompoundRelation &
> >>>>>>>>> CompoundClassAttribute from. Our current version of GUS does
> >>>>>>>>> not have these tables. The SRes.EnzymeClass table is also
> >>>>>>>>> looking very wacky to me. Propose a nice structure for this
> >>>>>>>>> and we can put it in the next release of GUS.
> >>>>>>>>>
> >>>>>>>>> Angel
> >>>>>>>>>
> >>>>>>>>> Thomas Otto wrote:
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>> Hello,
> >>>>>>>>>>
> >>>>>>>>>> I am uploading some kegg data in the GUS system...
> >>>>>>>>>>
> >>>>>>>>>> So I looked which tables are existing, and which we are
> >>>>>>>>>> needing i.e. for compound, reactions. Now I am not sure how
> >>>>>>>>>> is the convention to relate the data.
> >>>>>>>>>>
> >>>>>>>>>> Example:
> >>>>>>>>>> The Enzymes are related to the compounds.
> >>>>>>>>>> (1) In EzymeClassAttribute I write the names of the compound
> >>>>>>>>>> related to each enzyme. In CompoundClassAttribute I write
> >>>>>>>>>> also all EC-numbers, related to it.
> >>>>>>>>>> (2) Other possibilty would be to utilize a thrid table
> >>>>>>>>>> EnzymeCompoundRelation, where I put the primkeys of the
> >>>>>>>>>> relations.
> >>>>>>>>>>
> >>>>>>>>>> (1) would be faster, easier to query, but redundend.
> >>>>>>>>>> (2) Cleaner
> >>>>>>>>>>
> >>>>>>>>>> What are you thinking I should use?
> >>>>>>>>>>
> >>>>>>>>>> Thanks,
> >>>>>>>>>> Thomas
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> -------------------------------------------------------
> >>>>>>>>>> This SF.Net email is sponsored by: IBM Linux Tutorials
> >>>>>>>>>> Free Linux tutorial presented by Daniel Robbins, President
> >>>>>>>>>> and CEO of
> >>>>>>>>>> GenToo technologies. Learn everything from fundamentals to
> >>>>>>>>>> system
> >>>>>>>>>> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> >>>>>>>>>>
> >>>>>>>>>> _______________________________________________
> >>>>>>>>>> Gusdev-gusdev mailing list
> >>>>>>>>>> Gus...@li...
> >>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>
> >>>>>>> -------------------------------------------------------
> >>>>>>> This SF.Net email is sponsored by: IBM Linux Tutorials
> >>>>>>> Free Linux tutorial presented by Daniel Robbins, President and
> >>>>>>> CEO of
> >>>>>>> GenToo technologies. Learn everything from fundamentals to system
> >>>>>>> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> >>>>>>>
> >>>>>>> _______________________________________________
> >>>>>>> Gusdev-gusdev mailing list
> >>>>>>> Gus...@li...
> >>>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>> -------------------------------------------------------
> >>>>>> This SF.Net email is sponsored by: IBM Linux Tutorials
> >>>>>> Free Linux tutorial presented by Daniel Robbins, President and
> >>>>>> CEO of
> >>>>>> GenToo technologies. Learn everything from fundamentals to system
> >>>>>> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> Gusdev-gusdev mailing list
> >>>>>> Gus...@li...
> >>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>
> >>>>> -------------------------------------------------------
> >>>>> This SF.Net email is sponsored by: IBM Linux Tutorials
> >>>>> Free Linux tutorial presented by Daniel Robbins, President and CEO of
> >>>>> GenToo technologies. Learn everything from fundamentals to system
> >>>>> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> >>>>> _______________________________________________
> >>>>> Gusdev-gusdev mailing list
> >>>>> Gus...@li...
> >>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>>
> >>>>>
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>
> >>
> >>
> >> -------------------------------------------------------
> >> This SF.Net email is sponsored by: IBM Linux Tutorials
> >> Free Linux tutorial presented by Daniel Robbins, President and CEO of
> >> GenToo technologies. Learn everything from fundamentals to system
> >> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> >> _______________________________________________
> >> Gusdev-gusdev mailing list
> >> Gus...@li...
> >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>
> >>
> >>
> >
> >
> >
> >
> > -------------------------------------------------------
> > This SF.Net email is sponsored by: IBM Linux Tutorials
> > Free Linux tutorial presented by Daniel Robbins, President and CEO of
> > GenToo technologies. Learn everything from fundamentals to system
> > administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IBM Linux Tutorials
> Free Linux tutorial presented by Daniel Robbins, President and CEO of
> GenToo technologies. Learn everything from fundamentals to system
> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
|
|
From: Steve F. <sfi...@pc...> - 2004-03-09 16:03:06
|
To test things out, i would turn to the User Guides available from the gusdb.org site. They will tell you what data to load initially (but maybe you've already done that). You could tinker with the GUS::Common::Plugin::SubmitRow for a start. steve Jason Hackney wrote: > Hi Chris, > > Well, I wouldn't be so fast to do that just yet. As of this morning, I > have rebuilt Pg 7.3, and reinstalled GUS. Everything builds fine, > including the array and associated tables, as far as I can tell. I can > register plugins using ga. That's about it, so far. What I think would > be useful would be some examples of Perl modules built using Oracle, > just so I can make sure that everything is kosher. Anyone want to > volunteer a couple of modules they have built, so I can compare and > contrast? So far, so good, though. > > Cheers, > Jason > > On Mar 9, 2004, at 8:06 AM, Chris Stoeckert wrote: > >> Hi Jason, >> Great to hear of your progress. Sounds like we will need to change >> the table name for Array in RAD. >> >> Any suggestions? "Array_" "ArrayP" (for ArraryPostgreSQL) >> >> Chris >> >> On Mar 8, 2004, at 7:04 PM, Jason Hackney wrote: >> >>> Hi all, >>> >>> I am working with Laurie Kramer to port the GUS platform to >>> PostgreSQL. Most things work, or are pretty trivial to get working >>> (more on that later). The only real issue I have run into is >>> PostgreSQL uses array as a reserved word (it's a datatype), and you >>> can't make a table called array. This is as of PostgreSQL 7.4 (and >>> is a keyword according to SQL99). PostgreSQL 7.3 doesn't reserve >>> this word, but is a bit gimpy on sub-selects, if necessary we can >>> downgrade, but this will be an issue in the future, as 7.3 departs >>> and 7.4 takes over for it. >>> >>> Cheers, >>> Jason >>> >>> Jason A. Hackney >>> Graduate Student >>> Princeton University >>> >>> >>> >>> ------------------------------------------------------- >>> This SF.Net email is sponsored by: IBM Linux Tutorials >>> Free Linux tutorial presented by Daniel Robbins, President and CEO of >>> GenToo technologies. Learn everything from fundamentals to system >>> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click >>> _______________________________________________ >>> Gusdev-gusdev mailing list >>> Gus...@li... >>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: IBM Linux Tutorials > Free Linux tutorial presented by Daniel Robbins, President and CEO of > GenToo technologies. Learn everything from fundamentals to system > administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
|
From: Jason H. <jha...@pr...> - 2004-03-09 16:25:14
|
I've already looked at the user guides. I've also loaded many of the plugins just to make sure that they will load. There is one issue here. When a gus module returns dbi results as a hash, the hash keys are all lowercase. This is because of PostgreSQL's insane attempts to be case insensitive by forcing one implicit (lower) case unless _everything_ is enclosed by quotes. I don't know how this is done by Oracle. This required changing two lines of GusApplication.pm to allow me to load things at all. On Mar 9, 2004, at 10:53 AM, Steve Fischer wrote: > To test things out, i would turn to the User Guides available from the > gusdb.org site. They will tell you what data to load initially (but > maybe you've already done that). > > You could tinker with the GUS::Common::Plugin::SubmitRow for a start. > > steve > > Jason Hackney wrote: > >> Hi Chris, >> >> Well, I wouldn't be so fast to do that just yet. As of this morning, >> I have rebuilt Pg 7.3, and reinstalled GUS. Everything builds fine, >> including the array and associated tables, as far as I can tell. I >> can register plugins using ga. That's about it, so far. What I think >> would be useful would be some examples of Perl modules built using >> Oracle, just so I can make sure that everything is kosher. Anyone >> want to volunteer a couple of modules they have built, so I can >> compare and contrast? So far, so good, though. >> >> Cheers, >> Jason >> >> On Mar 9, 2004, at 8:06 AM, Chris Stoeckert wrote: >> >>> Hi Jason, >>> Great to hear of your progress. Sounds like we will need to change >>> the table name for Array in RAD. >>> >>> Any suggestions? "Array_" "ArrayP" (for ArraryPostgreSQL) >>> >>> Chris >>> >>> On Mar 8, 2004, at 7:04 PM, Jason Hackney wrote: >>> >>>> Hi all, >>>> >>>> I am working with Laurie Kramer to port the GUS platform to >>>> PostgreSQL. Most things work, or are pretty trivial to get working >>>> (more on that later). The only real issue I have run into is >>>> PostgreSQL uses array as a reserved word (it's a datatype), and you >>>> can't make a table called array. This is as of PostgreSQL 7.4 (and >>>> is a keyword according to SQL99). PostgreSQL 7.3 doesn't reserve >>>> this word, but is a bit gimpy on sub-selects, if necessary we can >>>> downgrade, but this will be an issue in the future, as 7.3 departs >>>> and 7.4 takes over for it. >>>> >>>> Cheers, >>>> Jason >>>> >>>> Jason A. Hackney >>>> Graduate Student >>>> Princeton University >>>> >>>> >>>> >>>> ------------------------------------------------------- >>>> This SF.Net email is sponsored by: IBM Linux Tutorials >>>> Free Linux tutorial presented by Daniel Robbins, President and CEO >>>> of >>>> GenToo technologies. Learn everything from fundamentals to system >>>> administration.http://ads.osdn.com/? >>>> ad_id=1470&alloc_id=3638&op=click >>>> _______________________________________________ >>>> Gusdev-gusdev mailing list >>>> Gus...@li... >>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>> >> >> >> >> ------------------------------------------------------- >> This SF.Net email is sponsored by: IBM Linux Tutorials >> Free Linux tutorial presented by Daniel Robbins, President and CEO of >> GenToo technologies. Learn everything from fundamentals to system >> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
|
From: Angel P. <an...@pc...> - 2004-03-09 17:16:48
|
Ugh, I was hoping this issue did not rear it's ugly head. Oracle by
default returns hashes with keys as uppercase. The Perl DBI
fetchrow_hashref() method does take and argument "NAME_lc" to force
lowercase & 'NAME_uc' to force uppercase hash keys. Usually people like
lowercase keys and have mostly used the 'NAME_lc" option throughout the
code when they have a DBI handle (or at least I always did) .
But you will notice that if you use the
GUS::PluginMgr::Plugin->sql_get_as_hash_refs($sql) to run sql the method
returns an array of hashes with lowercase keys.
My point is that I don't think this is as big an issue as first appears.
From GusApplication, There are five lines that are affected:
[angel@pythia perl]$ grep -n fetchrow_hashref GusApplication.pm
553: while (my $alg_h = $sh->fetchrow_hashref) {
565: while (my $imp_h = $imp_sh->fetchrow_hashref) {
582: while (my $par_h = $par_sh->fetchrow_hashref) {
597: while (my $inv_h = $inv_sh->fetchrow_hashref) {
606: while (my $val_h = $val_sh->fetchrow_hashref) {
Changing all of these to $st->fetchrow_hasref("NAME_uc") will fix all of
the code in GusApplication.
For individual plugins, it is a simple replacement to change any
fetchrow_hashref that do not already have the NAME_* option to bring
back whatever the default one is for the code.
Angel
Jason Hackney wrote:
> I've already looked at the user guides. I've also loaded many of the
> plugins just to make sure that they will load. There is one issue
> here. When a gus module returns dbi results as a hash, the hash keys
> are all lowercase. This is because of PostgreSQL's insane attempts to
> be case insensitive by forcing one implicit (lower) case unless
> _everything_ is enclosed by quotes. I don't know how this is done by
> Oracle. This required changing two lines of GusApplication.pm to
> allow me to load things at all.
>
> On Mar 9, 2004, at 10:53 AM, Steve Fischer wrote:
>
>> To test things out, i would turn to the User Guides available from
>> the gusdb.org site. They will tell you what data to load initially
>> (but maybe you've already done that).
>>
>> You could tinker with the GUS::Common::Plugin::SubmitRow for a start.
>>
>> steve
>>
>> Jason Hackney wrote:
>>
>>> Hi Chris,
>>>
>>> Well, I wouldn't be so fast to do that just yet. As of this
>>> morning, I have rebuilt Pg 7.3, and reinstalled GUS. Everything
>>> builds fine, including the array and associated tables, as far as I
>>> can tell. I can register plugins using ga. That's about it, so far.
>>> What I think would be useful would be some examples of Perl modules
>>> built using Oracle, just so I can make sure that everything is
>>> kosher. Anyone want to volunteer a couple of modules they have
>>> built, so I can compare and contrast? So far, so good, though.
>>>
>>> Cheers,
>>> Jason
>>>
>>> On Mar 9, 2004, at 8:06 AM, Chris Stoeckert wrote:
>>>
>>>> Hi Jason,
>>>> Great to hear of your progress. Sounds like we will need to change
>>>> the table name for Array in RAD.
>>>>
>>>> Any suggestions? "Array_" "ArrayP" (for ArraryPostgreSQL)
>>>>
>>>> Chris
>>>>
>>>> On Mar 8, 2004, at 7:04 PM, Jason Hackney wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> I am working with Laurie Kramer to port the GUS platform to
>>>>> PostgreSQL. Most things work, or are pretty trivial to get
>>>>> working (more on that later). The only real issue I have run into
>>>>> is PostgreSQL uses array as a reserved word (it's a datatype),
>>>>> and you can't make a table called array. This is as of PostgreSQL
>>>>> 7.4 (and is a keyword according to SQL99). PostgreSQL 7.3 doesn't
>>>>> reserve this word, but is a bit gimpy on sub-selects, if
>>>>> necessary we can downgrade, but this will be an issue in the
>>>>> future, as 7.3 departs and 7.4 takes over for it.
>>>>>
>>>>> Cheers,
>>>>> Jason
>>>>>
>>>>> Jason A. Hackney
>>>>> Graduate Student
>>>>> Princeton University
>>>>>
>>>>>
>>>>>
>>>>> -------------------------------------------------------
>>>>> This SF.Net email is sponsored by: IBM Linux Tutorials
>>>>> Free Linux tutorial presented by Daniel Robbins, President and
>>>>> CEO of
>>>>> GenToo technologies. Learn everything from fundamentals to system
>>>>> administration.http://ads.osdn.com/?
>>>>> ad_id=1470&alloc_id=3638&op=click
>>>>> _______________________________________________
>>>>> Gusdev-gusdev mailing list
>>>>> Gus...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> This SF.Net email is sponsored by: IBM Linux Tutorials
>>> Free Linux tutorial presented by Daniel Robbins, President and CEO of
>>> GenToo technologies. Learn everything from fundamentals to system
>>> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>>> _______________________________________________
>>> Gusdev-gusdev mailing list
>>> Gus...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IBM Linux Tutorials
> Free Linux tutorial presented by Daniel Robbins, President and CEO of
> GenToo technologies. Learn everything from fundamentals to system
> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
|
|
From: Steve F. <sfi...@pc...> - 2004-03-09 17:29:19
|
Here are all the calls in the code base to fetchrow_hashref that do not
use explicit casing:
DoTS/DotsBuild/plugin/perl/AssignLibraryDistributionToAssemblies.pm:
while (my $row = $updateStmt->fetchrow_hashref()) {
DoTS/DotsBuild/plugin/perl/NewLibDist.pm: while (my $row =
$updateStmt->fetchrow_hashref()) {
GUS/Model/lib/perl/DoTS/Evidence.pm.man: while (my $row =
$sth->fetchrow_hashref()){
GUS/Model/lib/perl/DoTS/Evidence.pm: while (my $row =
$sth->fetchrow_hashref()){
GUS/PluginMgr/lib/perl/GusApplication.pm: while (my $alg_h =
$sh->fetchrow_hashref) {
GUS/PluginMgr/lib/perl/GusApplication.pm: while (my $imp_h =
$imp_sh->fetchrow_hashref) {
GUS/PluginMgr/lib/perl/GusApplication.pm: while (my $par_h =
$par_sh->fetchrow_hashref) {
GUS/PluginMgr/lib/perl/GusApplication.pm: while (my $inv_h =
$inv_sh->fetchrow_hashref) {
GUS/PluginMgr/lib/perl/GusApplication.pm: while (my $val_h =
$val_sh->fetchrow_hashref) {
GUS/PluginMgr/lib/perl/Plugin.pm: while (my $row = $sh->fetchrow_hashref) {
steve
Angel Pizarro wrote:
> Ugh, I was hoping this issue did not rear it's ugly head. Oracle by
> default returns hashes with keys as uppercase. The Perl DBI
> fetchrow_hashref() method does take and argument "NAME_lc" to force
> lowercase & 'NAME_uc' to force uppercase hash keys. Usually people
> like lowercase keys and have mostly used the 'NAME_lc" option
> throughout the code when they have a DBI handle (or at least I always
> did) .
>
> But you will notice that if you use the
> GUS::PluginMgr::Plugin->sql_get_as_hash_refs($sql) to run sql the
> method returns an array of hashes with lowercase keys.
>
> My point is that I don't think this is as big an issue as first appears.
>
>> From GusApplication, There are five lines that are affected:
>
> [angel@pythia perl]$ grep -n fetchrow_hashref GusApplication.pm
> 553: while (my $alg_h = $sh->fetchrow_hashref) {
> 565: while (my $imp_h = $imp_sh->fetchrow_hashref) {
> 582: while (my $par_h = $par_sh->fetchrow_hashref) {
> 597: while (my $inv_h = $inv_sh->fetchrow_hashref) {
> 606: while (my $val_h = $val_sh->fetchrow_hashref) {
>
> Changing all of these to $st->fetchrow_hasref("NAME_uc") will fix all
> of the code in GusApplication.
>
> For individual plugins, it is a simple replacement to change any
> fetchrow_hashref that do not already have the NAME_* option to bring
> back whatever the default one is for the code.
>
> Angel
>
> Jason Hackney wrote:
>
>> I've already looked at the user guides. I've also loaded many of the
>> plugins just to make sure that they will load. There is one issue
>> here. When a gus module returns dbi results as a hash, the hash keys
>> are all lowercase. This is because of PostgreSQL's insane attempts
>> to be case insensitive by forcing one implicit (lower) case unless
>> _everything_ is enclosed by quotes. I don't know how this is done by
>> Oracle. This required changing two lines of GusApplication.pm to
>> allow me to load things at all.
>>
>> On Mar 9, 2004, at 10:53 AM, Steve Fischer wrote:
>>
>>> To test things out, i would turn to the User Guides available from
>>> the gusdb.org site. They will tell you what data to load
>>> initially (but maybe you've already done that).
>>>
>>> You could tinker with the GUS::Common::Plugin::SubmitRow for a start.
>>>
>>> steve
>>>
>>> Jason Hackney wrote:
>>>
>>>> Hi Chris,
>>>>
>>>> Well, I wouldn't be so fast to do that just yet. As of this
>>>> morning, I have rebuilt Pg 7.3, and reinstalled GUS. Everything
>>>> builds fine, including the array and associated tables, as far as
>>>> I can tell. I can register plugins using ga. That's about it, so
>>>> far. What I think would be useful would be some examples of Perl
>>>> modules built using Oracle, just so I can make sure that
>>>> everything is kosher. Anyone want to volunteer a couple of modules
>>>> they have built, so I can compare and contrast? So far, so good,
>>>> though.
>>>>
>>>> Cheers,
>>>> Jason
>>>>
>>>> On Mar 9, 2004, at 8:06 AM, Chris Stoeckert wrote:
>>>>
>>>>> Hi Jason,
>>>>> Great to hear of your progress. Sounds like we will need to
>>>>> change the table name for Array in RAD.
>>>>>
>>>>> Any suggestions? "Array_" "ArrayP" (for ArraryPostgreSQL)
>>>>>
>>>>> Chris
>>>>>
>>>>> On Mar 8, 2004, at 7:04 PM, Jason Hackney wrote:
>>>>>
>>>>>> Hi all,
>>>>>>
>>>>>> I am working with Laurie Kramer to port the GUS platform to
>>>>>> PostgreSQL. Most things work, or are pretty trivial to get
>>>>>> working (more on that later). The only real issue I have run
>>>>>> into is PostgreSQL uses array as a reserved word (it's a
>>>>>> datatype), and you can't make a table called array. This is as
>>>>>> of PostgreSQL 7.4 (and is a keyword according to SQL99).
>>>>>> PostgreSQL 7.3 doesn't reserve this word, but is a bit gimpy on
>>>>>> sub-selects, if necessary we can downgrade, but this will be an
>>>>>> issue in the future, as 7.3 departs and 7.4 takes over for it.
>>>>>>
>>>>>> Cheers,
>>>>>> Jason
>>>>>>
>>>>>> Jason A. Hackney
>>>>>> Graduate Student
>>>>>> Princeton University
>>>>>>
>>>>>>
>>>>>>
>>>>>> -------------------------------------------------------
>>>>>> This SF.Net email is sponsored by: IBM Linux Tutorials
>>>>>> Free Linux tutorial presented by Daniel Robbins, President and
>>>>>> CEO of
>>>>>> GenToo technologies. Learn everything from fundamentals to system
>>>>>> administration.http://ads.osdn.com/?
>>>>>> ad_id=1470&alloc_id=3638&op=click
>>>>>> _______________________________________________
>>>>>> Gusdev-gusdev mailing list
>>>>>> Gus...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>>
>>>>
>>>>
>>>>
>>>> -------------------------------------------------------
>>>> This SF.Net email is sponsored by: IBM Linux Tutorials
>>>> Free Linux tutorial presented by Daniel Robbins, President and CEO of
>>>> GenToo technologies. Learn everything from fundamentals to system
>>>> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>>>> _______________________________________________
>>>> Gusdev-gusdev mailing list
>>>> Gus...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>
>>>
>>
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by: IBM Linux Tutorials
>> Free Linux tutorial presented by Daniel Robbins, President and CEO of
>> GenToo technologies. Learn everything from fundamentals to system
>> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
|
|
From: Chris S. <sto...@pc...> - 2004-03-09 16:05:32
|
OK. I like the idea of changing the name from Array to ArrayDesign. Your getting going in Pg 7.3 gives us time to plan this transition gracefully. Chris On Mar 9, 2004, at 10:18 AM, Jason Hackney wrote: > Hi Chris, > > Well, I wouldn't be so fast to do that just yet. As of this morning, I > have rebuilt Pg 7.3, and reinstalled GUS. Everything builds fine, > including the array and associated tables, as far as I can tell. I can > register plugins using ga. That's about it, so far. What I think would > be useful would be some examples of Perl modules built using Oracle, > just so I can make sure that everything is kosher. Anyone want to > volunteer a couple of modules they have built, so I can compare and > contrast? So far, so good, though. > > Cheers, > Jason > > On Mar 9, 2004, at 8:06 AM, Chris Stoeckert wrote: > >> Hi Jason, >> Great to hear of your progress. Sounds like we will need to change >> the table name for Array in RAD. >> >> Any suggestions? "Array_" "ArrayP" (for ArraryPostgreSQL) >> >> Chris >> >> On Mar 8, 2004, at 7:04 PM, Jason Hackney wrote: >> >>> Hi all, >>> >>> I am working with Laurie Kramer to port the GUS platform to >>> PostgreSQL. Most things work, or are pretty trivial to get working >>> (more on that later). The only real issue I have run into is >>> PostgreSQL uses array as a reserved word (it's a datatype), and you >>> can't make a table called array. This is as of PostgreSQL 7.4 (and >>> is a keyword according to SQL99). PostgreSQL 7.3 doesn't reserve >>> this word, but is a bit gimpy on sub-selects, if necessary we can >>> downgrade, but this will be an issue in the future, as 7.3 departs >>> and 7.4 takes over for it. >>> >>> Cheers, >>> Jason >>> >>> Jason A. Hackney >>> Graduate Student >>> Princeton University >>> >>> >>> >>> ------------------------------------------------------- >>> This SF.Net email is sponsored by: IBM Linux Tutorials >>> Free Linux tutorial presented by Daniel Robbins, President and CEO of >>> GenToo technologies. Learn everything from fundamentals to system >>> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click >>> _______________________________________________ >>> Gusdev-gusdev mailing list >>> Gus...@li... >>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: IBM Linux Tutorials > Free Linux tutorial presented by Daniel Robbins, President and CEO of > GenToo technologies. Learn everything from fundamentals to system > administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
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