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From: Thomas O. <ot...@fi...> - 2004-03-11 19:54:52
|
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 > |
|
From: Angel P. <an...@pc...> - 2004-03-11 19:46:21
|
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 >> >> >> >> > |
|
From: Thomas O. <ot...@fi...> - 2004-03-11 19:42:51
|
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 > > > |
|
From: Angel P. <an...@pc...> - 2004-03-11 19:38:57
|
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 |
|
From: Steve F. <sfi...@pc...> - 2004-03-11 19:20:53
|
thomas- I don't know the answer to this. I will ask around. steve 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 |
|
From: Thomas O. <ot...@fi...> - 2004-03-11 18:03:34
|
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 |
|
From: Jason H. <jha...@pr...> - 2004-03-10 14:34:19
|
Cool. I'll change it to getDbPlatform in DbiDatabase. I included a setDbPlatform that takes one argument that is used to determine which Db specific class to call. So, what about the Sybase specific stuff? It's really cluttering things in it's present form, and I have no idea how I would make a Sybase.pm. I am making a DefaultDb.pm that has some information about what each of the queries does, and gives some default action when the database engine isn't recognized. So far, all it does is cough up an error message and return undefined, rather than an sql statement. Jason On Mar 10, 2004, at 8:54 AM, Steve Fischer wrote: > sounds good. in the code i am working on now (WDK), I call the method > getDbPlatform(). > > for fetchrow, yes, we'll just use NAME_uc. > > steve > Jason Hackney wrote: > >> Hi Steve, >> >>> I suggested that we factor those queries out of the DbiTable.pm and >>> DbiDatabase.pm files, and place them into an Oracle.pm and >>> PostgreSQL.pm. >>> >>> How did you guys integrate the PostgreSQL specific queries into the >>> object layer? >>> >>> If you haven't done a clean refactoring we can work together on >>> that... >>> >>> steve >>> >> >> It looks like I have a rough first pass refactoring for Oracle and >> PostgreSQL. It still relies on checking the dsn to decide whether to >> use the Oracle of PostgreSQL specific sql outputter I wrote. I >> implemented it as a method for DbiDatabase called getDbSpecSql. This >> method creates a new instance of an GUS::ObjRelP::Oracle or >> ::PostgreSQL class. These classes have methods for giving the correct >> sql statements. This could be done for DbiTable, as well, I just >> don't have it that way right now. >> >> So far it seems to build GUS for PostgreSQL. How many people are >> using Sybase? I ask because some of the places that call for db >> specific sql ask whether you are using Sybase and others don't. >> However, I haven't written anything for Sybase, since I don't really >> see too much of that stuff around. >> >> What is the consensus on the case sensitivity for fetchrow_hashref? >> If it is enough to merely make sure that it is called with either >> 'NAME_lc' or 'NAME_uc' that would be great by me. Anybody have any >> thoughts on this? >> >> Jason > |
|
From: Steve F. <sfi...@pc...> - 2004-03-10 14:03:59
|
sounds good. in the code i am working on now (WDK), I call the method getDbPlatform(). for fetchrow, yes, we'll just use NAME_uc. steve Jason Hackney wrote: > Hi Steve, > >> I suggested that we factor those queries out of the DbiTable.pm and >> DbiDatabase.pm files, and place them into an Oracle.pm and >> PostgreSQL.pm. >> >> How did you guys integrate the PostgreSQL specific queries into the >> object layer? >> >> If you haven't done a clean refactoring we can work together on that... >> >> steve >> > > It looks like I have a rough first pass refactoring for Oracle and > PostgreSQL. It still relies on checking the dsn to decide whether to > use the Oracle of PostgreSQL specific sql outputter I wrote. I > implemented it as a method for DbiDatabase called getDbSpecSql. This > method creates a new instance of an GUS::ObjRelP::Oracle or > ::PostgreSQL class. These classes have methods for giving the correct > sql statements. This could be done for DbiTable, as well, I just don't > have it that way right now. > > So far it seems to build GUS for PostgreSQL. How many people are using > Sybase? I ask because some of the places that call for db specific sql > ask whether you are using Sybase and others don't. However, I haven't > written anything for Sybase, since I don't really see too much of that > stuff around. > > What is the consensus on the case sensitivity for fetchrow_hashref? If > it is enough to merely make sure that it is called with either > 'NAME_lc' or 'NAME_uc' that would be great by me. Anybody have any > thoughts on this? > > Jason |
|
From: Jason H. <jha...@pr...> - 2004-03-09 23:17:00
|
Hi Steve, > I suggested that we factor those queries out of the DbiTable.pm and > DbiDatabase.pm files, and place them into an Oracle.pm and > PostgreSQL.pm. > > How did you guys integrate the PostgreSQL specific queries into the > object layer? > > If you haven't done a clean refactoring we can work together on that... > > steve > It looks like I have a rough first pass refactoring for Oracle and PostgreSQL. It still relies on checking the dsn to decide whether to use the Oracle of PostgreSQL specific sql outputter I wrote. I implemented it as a method for DbiDatabase called getDbSpecSql. This method creates a new instance of an GUS::ObjRelP::Oracle or ::PostgreSQL class. These classes have methods for giving the correct sql statements. This could be done for DbiTable, as well, I just don't have it that way right now. So far it seems to build GUS for PostgreSQL. How many people are using Sybase? I ask because some of the places that call for db specific sql ask whether you are using Sybase and others don't. However, I haven't written anything for Sybase, since I don't really see too much of that stuff around. What is the consensus on the case sensitivity for fetchrow_hashref? If it is enough to merely make sure that it is called with either 'NAME_lc' or 'NAME_uc' that would be great by me. Anybody have any thoughts on this? Jason |
|
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: 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: 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: Jason H. <jha...@pr...> - 2004-03-09 16:09:29
|
Steve- On Mar 9, 2004, at 10:39 AM, Steve Fischer wrote: > Jason- > > Here is a quote from a mail i sent on Feb 13: > <snip> > I know that Laurie was working on porting the queries found in the > object layer, and seems to have succeeded. > > I suggested that we factor those queries out of the DbiTable.pm and > DbiDatabase.pm files, and place them into an Oracle.pm and > PostgreSQL.pm. > > How did you guys integrate the PostgreSQL specific queries into the > object layer? I generally really just plunked them into an 'elsif' where there is an 'if' that asks for getDSN =~/oracle/ Pretty messy. There is one strangely nested if if elsif. That's about it. > If you haven't done a clean refactoring we can work together on that... > I was getting ready to clean some things up. There are changes in DbiTable and DbiDatabase, like you said, there is also a one-line change in DbiRow.pm. I would be happy to help in the code refactoring in any way that I can. I have diffs associated with all of the changes I have made, if you want those. Two of the queries that Laurie wrote don't work, so I rewrote those. Jason > 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: 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 > |
|
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: Steve F. <sfi...@pc...> - 2004-03-09 15:48:38
|
Jason- Here is a quote from a mail i sent on Feb 13: ---------------------------------------------------------------------------------- Porting the Object Layer I just did a quick look in the object layer code (Perl). (we can defer for now on the java object layer since its not in wide use). Only two files seem to use oracle system tables, both in $PROJECT_HOME/GUS/ObjRelP/lib/perl: DbiTable.pm and DbiDatabase.pm. There are about 10 separate sql queries that use the oracle system tables (listed below). A quick fix would be to supply an Oracle.pm and a PostgreSQL.pm which have methods that provide the correct sql for those queries. IF postgres has parallel tables, then this should be trivial. if not...? here are the tables used: all_sequences all_cons_columns all_constraints all_tab_columns all_views ---------------------------------------------------------------------------------- I know that Laurie was working on porting the queries found in the object layer, and seems to have succeeded. I suggested that we factor those queries out of the DbiTable.pm and DbiDatabase.pm files, and place them into an Oracle.pm and PostgreSQL.pm. How did you guys integrate the PostgreSQL specific queries into the object layer? If you haven't done a clean refactoring we can work together on that... 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: Steve F. <sfi...@pc...> - 2004-03-09 15:28:48
|
that sounds good to me. steve Angel Pizarro wrote: > Actually, The Array table is an "ArrayDesign" object in MAGE. Why not > just name it that? > > Angel > Steve Fischer wrote: > >> I think we need to find a name that is appropriate across all >> platforms, and is self-explanatory. we just need to find a prefix >> which captures the full generality of the Array as we are using it. >> >> how about: >> MicroArray >> BioArray >> ExpressionArray >> HybridizationArray >> >> steve >> >> 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: Jason H. <jha...@pr...> - 2004-03-09 15:28:04
|
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 >> |
|
From: Angel P. <an...@pc...> - 2004-03-09 15:22:07
|
Actually, The Array table is an "ArrayDesign" object in MAGE. Why not just name it that? Angel Steve Fischer wrote: > I think we need to find a name that is appropriate across all > platforms, and is self-explanatory. > we just need to find a prefix which captures the full generality of > the Array as we are using it. > > how about: > MicroArray > BioArray > ExpressionArray > HybridizationArray > > steve > > 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: Steve F. <sfi...@pc...> - 2004-03-09 15:18:54
|
I think we need to find a name that is appropriate across all platforms, and is self-explanatory. we just need to find a prefix which captures the full generality of the Array as we are using it. how about: MicroArray BioArray ExpressionArray HybridizationArray steve 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: Steve F. <sfi...@pc...> - 2004-03-09 15:04:27
|
Fantastic!
(don't worry about bothering us. go for it. sorry i didn't get to
your question before *you* did)
steve
Thomas Otto wrote:
> Problem solved - I rebuild all the perl objects with the
> generateGusObjects programm.
>
> Sorry for bothering you,
> Thomas
>
> Thomas Otto wrote:
>
>> Hi,
>>
>> I solved one problem, - I had a little problem with the source_row.pm
>> - I know I shouldn't have, (but I tried something).
>>
>> Anyhow, still doesn't work-
>> Errormessage now:
>> ------------------ entry number 1 -----------------
>> Error: attempting to access a child 'GUS::Model::DoTS::NALocation'
>> of table 'GUS::Model::DoTS::Source' , but that table does not have a
>> child of that type. at
>> /home/oracle/gus_home/lib/perl/GUS/Model/GusRow.pm line 396, <GEN0>
>> line 110.
>>
>> Thomas
>>
>> Thomas Otto wrote:
>>
>>> Hello,
>>>
>>> I have a little problem trying to insert a sequence from Genbank
>>> with the GBParser. (Errormessage and sequence-file (a cutted
>>> version) see below!)
>>>
>>> Looks like, that the table doesn't exists! Do I have to create the
>>> table or is the GBParser not able to insert this type of entries in
>>> general.
>>>
>>> I will continue to resolve the problem, but maybe someone might help
>>> me.
>>>
>>> Thanks a lot,
>>> Thomas
>>>
>>>
>>> Error msg:
>>> Invalid child name: 'GUS::Model::DoTS::AAFeatureComment' at
>>> /home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiTable.pm line
>>> 851
>>> GUS::ObjRelP::DbiTable::addToChildList('GUS::Model::DoTS::Source_Table=HASH(0x8fc9b44)','ARRAY(0x8fee070)','ARRAY(0x8fee0ac)','ARRAY(0x8fee0e8)','ARRAY(0x8fee124)','ARRAY(0x8fee160)','ARRAY(0x8fee19c)','ARRAY(0x8fee1d8)','ARRAY(0x8fee214)',...)
>>> called at /home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiTable.pm
>>> line 844
>>>
>>> GUS::ObjRelP::DbiTable::setChildList('GUS::Model::DoTS::Source_Table=HASH(0x8fc9b44)','ARRAY(0x8fee070)','ARRAY(0x8fee0ac)','ARRAY(0x8fee0e8)','ARRAY(0x8fee124)','ARRAY(0x8fee160)','ARRAY(0x8fee19c)','ARRAY(0x8fee1d8)','ARRAY(0x8fee214)',...)
>>> called at
>>> /home/oracle/gus_home/lib/perl/GUS/Model/DoTS/Source_Table.pm line 16
>>>
>>> GUS::Model::DoTS::Source_Table::setDefaultParams('GUS::Model::DoTS::Source_Table=HASH(0x8fc9b44)')
>>> called at /home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiTable.pm
>>> line 38
>>>
>>> GUS::ObjRelP::DbiTable::new('GUS::Model::DoTS::Source_Table','GUS::Model::DoTS::Source','GUS::ObjRelP::DbiDatabase=HASH(0x8c0e34c)')
>>> called at /home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
>>> line 179
>>>
>>> GUS::ObjRelP::DbiDatabase::getTable('GUS::ObjRelP::DbiDatabase=HASH(0x8c0e34c)','GUS::Model::DoTS::Source')
>>> called
>>> at /home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 30
>>>
>>> GUS::ObjRelP::DbiRow::new('GUS::ObjRelP::DbiRow','GUS::Model::DoTS::Source','HASH(0x8fcb890)','undef','undef')
>>> called at /home/oracle/gus_home/lib/perl/GUS/Model/GusRow.pm line 25
>>>
>>> GUS::Model::GusRow::new('GUS::Model::DoTS::Source','HASH(0x8fcb890)')
>>> called at
>>> /home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 486
>>>
>>> GUS::Common::Plugin::GBParser::buildFeatures('GUS::Common::Plugin::GBParser=HASH(0x856fbac)','CBIL::Bio::GenBank::Entry=HASH(0x8ec70f4)','GUS::Model::DoTS::ExternalNASequence=HASH(0x8f95ea8)')
>>> called at
>>> /home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 251
>>>
>>> GUS::Common::Plugin::GBParser::processEntry('GUS::Common::Plugin::GBParser=HASH(0x856fbac)','CBIL::Bio::GenBank::ArrayStream=HASH(0x8ec7088)')
>>> called at
>>> /home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 185
>>> eval {...} called at
>>> /home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 184
>>>
>>> GUS::Common::Plugin::GBParser::run('GUS::Common::Plugin::GBParser=HASH(0x856fbac)','HASH(0x8e53714)')
>>> called at
>>> /home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 430
>>> eval {...} called at
>>> /home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 427
>>>
>>> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::Common::Plugin::GBParser')
>>> called at
>>> /home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 283
>>>
>>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::Common::Plugin::GBParser')
>>> called at
>>> /home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 192
>>>
>>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','ARRAY(0x80606b0)')
>>> called at /home/oracle/gus_home/bin/ga line 11
>>>
>>> ------------------------------------------------------------------------
>>>
>>> LOCUS ATT8B10 103787 bp DNA linear PLN
>>> 20-MAR-2000
>>> DEFINITION Arabidopsis thaliana DNA chromosome 3, BAC clone T8B10.
>>> ACCESSION AL138646
>>> VERSION AL138646.2 GI:7287982
>>> KEYWORDS .
>>> SOURCE Arabidopsis thaliana (thale cress)
>>> ORGANISM Arabidopsis thaliana
>>> Eukaryota; Viridiplantae; Streptophyta; Embryophyta;
>>> Tracheophyta;
>>> Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots;
>>> rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
>>> REFERENCE 1 (bases 1 to 103787)
>>> AUTHORS Rieger,M., Mueller-Auer,S., Zipp,M., Schaefer,M.,
>>> Mewes,H.W.,
>>> Lemcke,K., Mayer,K.F.X., Quetier,F. and Salanoubat,M.
>>> JOURNAL Unpublished
>>> REFERENCE 2 (bases 1 to 103787)
>>> AUTHORS EU Arabidopsis sequencing,project.
>>> TITLE Direct Submission
>>> JOURNAL Submitted (20-MAR-2000) MIPS, at the Max-Planck-Institut
>>> fuer
>>> Biochemie, Am Klopferspitz 18a, D-82152 Martinsried, FRG,
>>> E-mail:
>>> le...@mi...,ma...@mi... Project
>>> Coordinator: Marcel Salanoubat and Francis Quetier,
>>> Groupement
>>> d'Interet Public, Centre National de Sequencage -
>>> GENOSCOPE; 2 rue
>>> Gaston Cremieux, BP191, 91006 Evry Cedex, France;
>>> http://www.genoscope.cns.fr
>>> FEATURES Location/Qualifiers
>>> source 1..103787
>>> /organism="Arabidopsis thaliana"
>>> /mol_type="genomic DNA"
>>> /variety="Columbia"
>>> /db_xref="taxon:3702"
>>> /chromosome="3"
>>> gene 8353..12143
>>> /gene="T8B10_10"
>>> gene complement(join(8353..8556,8641..8947,9034..9209,
>>> 9288..9351,9485..9579,9673..9888,10013..10144,
>>> 10459..10539,10632..12143))
>>> /gene="T8B10_10"
>>> CDS complement(join(8353..8556,8641..8947,9034..9209,
>>> 9288..9351,9485..9579,9673..9888,10013..10144,
>>> 10459..10539,10632..12143))
>>> /gene="T8B10_10"
>>> /note="similarity to arm repeat containing protein
>>> homolog, Arabidopsis thaliana, EMBL:AL133314"
>>> /codon_start=1
>>> /product="Arm repeat containing protein-like"
>>> /protein_id="CAB81821.1"
>>> /db_xref="GI:7287983"
>>> /db_xref="TrEMBL:Q9M224"
>>>
>>> /translation="MSRRVRQRVEDNGKYKVDSPSYTVIGVEDLAPKVQQYVNWTSLP
>>>
>>> YDTVFHLFTRLNYRDRASLASTCRTWRSLGASSFLWSSLDLRAHKFDLSMAASLATRC
>>>
>>> VDLQKIRFRGVDSADAIIHLKARSLLEISGDYCRKITDATLSMIAARHEALESLQLGP
>>>
>>> DFCERITSDAIRVIAFCCPKLKKLRVSGMRDVSSEAIESLAKHCPQLSDLGFLDCLNI
>>>
>>> NEEALGKVVSLRYLSVAGTSNIKWKVALENWEKLPKLIGLDVSRTTIDHIAVSRLLKS
>>>
>>> SQSLKVLCALNCPYLEEDKSYSSNRFKGKVLLAVFTDTFDELASIFADNSKKPKNIFS
>>>
>>> YWRDLIRKDKSIDEIMLWIEWIISHTLLRIAESSNSQGLNDFWLNQGATLLLSLMQSA
>>>
>>> QEDVQERAATGLATFIVVDDENASIDCGRAEAVMRDGGIRLLLELAKSWREGLQSEAA
>>>
>>> KAIANLSVNAKVAKAVAEEGGISVLADLAKSMNRLVAEEAAGGLWNLSVGEEHKNAIA
>>>
>>> QAGGVNALVDLIFRWPHGCDGVLERAAGALANLAADDKCSMEVARAGGVHALVMLARN
>>>
>>> CKYEGAQEQAARALANLAAHGDSNGNNAAVGQEAGALEALVQLTQSPHEGVKQEAAGA
>>>
>>> LWNLAFDDKNRESIAAFGGVEALVALAKSSSNASTGLQERVAGALWGLSVSEANSIAI
>>>
>>> GHEGGIPPLIALVRSEAEDVHETAAGALWNLSFNPGNALRIVEEGGVVALVQLCSSSV
>>>
>>> SKMARFMAALALAYMFDGRMDEYAMIGTSLESTSKSVTLNGARTMALDQIKAFIKTFM
>>>
>>> EHQIFSTGALSSAPSMLAQVSERARIPEAGHLRCSGSEIGRFVTMLRNPCLVLRACAA
>>>
>>> FALLQFTIPESRHAMHHASLMQNAGEARGLRSAAAAASMPREAKIFMKIVLRNLEHQQ
>>> AESPEGMKVSYNRI"
>>> exon complement(8353..8556)
>>> /gene="T8B10_10"
>>> /number=1
>>> intron complement(8557..8640)
>>> /gene="T8B10_10"
>>> /number=1
>>> exon complement(8641..8947)
>>> /gene="T8B10_10"
>>> /number=2
>>> intron complement(8948..9033)
>>> /gene="T8B10_10"
>>> /number=2
>>> exon complement(9034..9209)
>>> /gene="T8B10_10"
>>> /number=3
>>> intron complement(9210..9287)
>>> /gene="T8B10_10"
>>> /number=3
>>> exon complement(9288..9351)
>>> /gene="T8B10_10"
>>> /number=4
>>> intron complement(9352..9484)
>>> /gene="T8B10_10"
>>> /number=4
>>> exon complement(9485..9579)
>>> /gene="T8B10_10"
>>> /number=5
>>> intron complement(9580..9672)
>>> /gene="T8B10_10"
>>> /number=5
>>> exon complement(9673..9888)
>>> /gene="T8B10_10"
>>> /number=6
>>> intron complement(9889..10012)
>>> /gene="T8B10_10"
>>> /number=6
>>> exon complement(10013..10144)
>>> /gene="T8B10_10"
>>> /number=7
>>> intron complement(10145..10458)
>>> /gene="T8B10_10"
>>> /number=7
>>> exon complement(10459..10539)
>>> /gene="T8B10_10"
>>> /number=8
>>> intron complement(10540..10631)
>>> /gene="T8B10_10"
>>> /number=8
>>> exon complement(10632..12143)
>>> /gene="T8B10_10"
>>> /number=9
>>> ORIGIN 1 aagctttgaa gggctaacgg gtgatgcttt ggtgaaggtt
>>> ttttctggtc caggtttgtg
>>> 61 cttattttgc attgcttctc tttgattcac gtctgcataa acatcaaata
>>> attcatttat
>>> 121 gtttgagttg attatgtaga aaaaattatt aggggagatg ctttatgata
>>> agaaaaaaaa
>>> 181 gtggtcttgt ggtatcttaa ggcagaagga aaatatttag tgtcttaatg
>>> agtaatagat
>>> 241 ttatctgtct atccagattt tataactgag ttttagtaac ttccggctca
>>> agcaaaaagg
>>> 301 aagttcgata tgacggacat agaagctctc aaggctatca ccacggagag
>>> cattgatctg
>>> 361 gtatgtactt ttatacctca ccactttttt tttgcagatg attgcttctg
>>> atagctttta
>>>
>>>
>>
>>
>>
>>
>> -------------------------------------------------------
>> 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 13:16:09
|
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 > |
|
From: Thomas O. <ot...@fi...> - 2004-03-09 12:22:37
|
Problem solved - I rebuild all the perl objects with the
generateGusObjects programm.
Sorry for bothering you,
Thomas
Thomas Otto wrote:
> Hi,
>
> I solved one problem, - I had a little problem with the source_row.pm
> - I know I shouldn't have, (but I tried something).
>
> Anyhow, still doesn't work-
> Errormessage now:
> ------------------ entry number 1 -----------------
> Error: attempting to access a child 'GUS::Model::DoTS::NALocation' of
> table 'GUS::Model::DoTS::Source' , but that table does not have a
> child of that type. at
> /home/oracle/gus_home/lib/perl/GUS/Model/GusRow.pm line 396, <GEN0>
> line 110.
>
> Thomas
>
> Thomas Otto wrote:
>
>> Hello,
>>
>> I have a little problem trying to insert a sequence from Genbank with
>> the GBParser. (Errormessage and sequence-file (a cutted version) see
>> below!)
>>
>> Looks like, that the table doesn't exists! Do I have to create the
>> table or is the GBParser not able to insert this type of entries in
>> general.
>>
>> I will continue to resolve the problem, but maybe someone might help me.
>>
>> Thanks a lot,
>> Thomas
>>
>>
>> Error msg:
>> Invalid child name: 'GUS::Model::DoTS::AAFeatureComment' at
>> /home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiTable.pm line
>> 851
>> GUS::ObjRelP::DbiTable::addToChildList('GUS::Model::DoTS::Source_Table=HASH(0x8fc9b44)','ARRAY(0x8fee070)','ARRAY(0x8fee0ac)','ARRAY(0x8fee0e8)','ARRAY(0x8fee124)','ARRAY(0x8fee160)','ARRAY(0x8fee19c)','ARRAY(0x8fee1d8)','ARRAY(0x8fee214)',...)
>> called at /home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiTable.pm line
>> 844
>>
>> GUS::ObjRelP::DbiTable::setChildList('GUS::Model::DoTS::Source_Table=HASH(0x8fc9b44)','ARRAY(0x8fee070)','ARRAY(0x8fee0ac)','ARRAY(0x8fee0e8)','ARRAY(0x8fee124)','ARRAY(0x8fee160)','ARRAY(0x8fee19c)','ARRAY(0x8fee1d8)','ARRAY(0x8fee214)',...)
>> called at
>> /home/oracle/gus_home/lib/perl/GUS/Model/DoTS/Source_Table.pm line 16
>>
>> GUS::Model::DoTS::Source_Table::setDefaultParams('GUS::Model::DoTS::Source_Table=HASH(0x8fc9b44)')
>> called at /home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiTable.pm line 38
>>
>> GUS::ObjRelP::DbiTable::new('GUS::Model::DoTS::Source_Table','GUS::Model::DoTS::Source','GUS::ObjRelP::DbiDatabase=HASH(0x8c0e34c)')
>> called at /home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
>> line 179
>>
>> GUS::ObjRelP::DbiDatabase::getTable('GUS::ObjRelP::DbiDatabase=HASH(0x8c0e34c)','GUS::Model::DoTS::Source')
>> called
>> at /home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 30
>>
>> GUS::ObjRelP::DbiRow::new('GUS::ObjRelP::DbiRow','GUS::Model::DoTS::Source','HASH(0x8fcb890)','undef','undef')
>> called at /home/oracle/gus_home/lib/perl/GUS/Model/GusRow.pm line 25
>>
>> GUS::Model::GusRow::new('GUS::Model::DoTS::Source','HASH(0x8fcb890)')
>> called at
>> /home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 486
>>
>> GUS::Common::Plugin::GBParser::buildFeatures('GUS::Common::Plugin::GBParser=HASH(0x856fbac)','CBIL::Bio::GenBank::Entry=HASH(0x8ec70f4)','GUS::Model::DoTS::ExternalNASequence=HASH(0x8f95ea8)')
>> called at
>> /home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 251
>>
>> GUS::Common::Plugin::GBParser::processEntry('GUS::Common::Plugin::GBParser=HASH(0x856fbac)','CBIL::Bio::GenBank::ArrayStream=HASH(0x8ec7088)')
>> called at
>> /home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 185
>> eval {...} called at
>> /home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 184
>>
>> GUS::Common::Plugin::GBParser::run('GUS::Common::Plugin::GBParser=HASH(0x856fbac)','HASH(0x8e53714)')
>> called at
>> /home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 430
>> eval {...} called at
>> /home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 427
>>
>> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::Common::Plugin::GBParser')
>> called at
>> /home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 283
>>
>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::Common::Plugin::GBParser')
>> called at
>> /home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 192
>>
>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','ARRAY(0x80606b0)')
>> called at /home/oracle/gus_home/bin/ga line 11
>>
>> ------------------------------------------------------------------------
>>
>> LOCUS ATT8B10 103787 bp DNA linear PLN
>> 20-MAR-2000
>> DEFINITION Arabidopsis thaliana DNA chromosome 3, BAC clone T8B10.
>> ACCESSION AL138646
>> VERSION AL138646.2 GI:7287982
>> KEYWORDS .
>> SOURCE Arabidopsis thaliana (thale cress)
>> ORGANISM Arabidopsis thaliana
>> Eukaryota; Viridiplantae; Streptophyta; Embryophyta;
>> Tracheophyta;
>> Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots;
>> rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
>> REFERENCE 1 (bases 1 to 103787)
>> AUTHORS Rieger,M., Mueller-Auer,S., Zipp,M., Schaefer,M., Mewes,H.W.,
>> Lemcke,K., Mayer,K.F.X., Quetier,F. and Salanoubat,M.
>> JOURNAL Unpublished
>> REFERENCE 2 (bases 1 to 103787)
>> AUTHORS EU Arabidopsis sequencing,project.
>> TITLE Direct Submission
>> JOURNAL Submitted (20-MAR-2000) MIPS, at the Max-Planck-Institut fuer
>> Biochemie, Am Klopferspitz 18a, D-82152 Martinsried, FRG,
>> E-mail:
>> le...@mi...,ma...@mi... Project
>> Coordinator: Marcel Salanoubat and Francis Quetier,
>> Groupement
>> d'Interet Public, Centre National de Sequencage -
>> GENOSCOPE; 2 rue
>> Gaston Cremieux, BP191, 91006 Evry Cedex, France;
>> http://www.genoscope.cns.fr
>> FEATURES Location/Qualifiers
>> source 1..103787
>> /organism="Arabidopsis thaliana"
>> /mol_type="genomic DNA"
>> /variety="Columbia"
>> /db_xref="taxon:3702"
>> /chromosome="3"
>> gene 8353..12143
>> /gene="T8B10_10"
>> gene complement(join(8353..8556,8641..8947,9034..9209,
>> 9288..9351,9485..9579,9673..9888,10013..10144,
>> 10459..10539,10632..12143))
>> /gene="T8B10_10"
>> CDS complement(join(8353..8556,8641..8947,9034..9209,
>> 9288..9351,9485..9579,9673..9888,10013..10144,
>> 10459..10539,10632..12143))
>> /gene="T8B10_10"
>> /note="similarity to arm repeat containing protein
>> homolog, Arabidopsis thaliana, EMBL:AL133314"
>> /codon_start=1
>> /product="Arm repeat containing protein-like"
>> /protein_id="CAB81821.1"
>> /db_xref="GI:7287983"
>> /db_xref="TrEMBL:Q9M224"
>>
>> /translation="MSRRVRQRVEDNGKYKVDSPSYTVIGVEDLAPKVQQYVNWTSLP
>>
>> YDTVFHLFTRLNYRDRASLASTCRTWRSLGASSFLWSSLDLRAHKFDLSMAASLATRC
>>
>> VDLQKIRFRGVDSADAIIHLKARSLLEISGDYCRKITDATLSMIAARHEALESLQLGP
>>
>> DFCERITSDAIRVIAFCCPKLKKLRVSGMRDVSSEAIESLAKHCPQLSDLGFLDCLNI
>>
>> NEEALGKVVSLRYLSVAGTSNIKWKVALENWEKLPKLIGLDVSRTTIDHIAVSRLLKS
>>
>> SQSLKVLCALNCPYLEEDKSYSSNRFKGKVLLAVFTDTFDELASIFADNSKKPKNIFS
>>
>> YWRDLIRKDKSIDEIMLWIEWIISHTLLRIAESSNSQGLNDFWLNQGATLLLSLMQSA
>>
>> QEDVQERAATGLATFIVVDDENASIDCGRAEAVMRDGGIRLLLELAKSWREGLQSEAA
>>
>> KAIANLSVNAKVAKAVAEEGGISVLADLAKSMNRLVAEEAAGGLWNLSVGEEHKNAIA
>>
>> QAGGVNALVDLIFRWPHGCDGVLERAAGALANLAADDKCSMEVARAGGVHALVMLARN
>>
>> CKYEGAQEQAARALANLAAHGDSNGNNAAVGQEAGALEALVQLTQSPHEGVKQEAAGA
>>
>> LWNLAFDDKNRESIAAFGGVEALVALAKSSSNASTGLQERVAGALWGLSVSEANSIAI
>>
>> GHEGGIPPLIALVRSEAEDVHETAAGALWNLSFNPGNALRIVEEGGVVALVQLCSSSV
>>
>> SKMARFMAALALAYMFDGRMDEYAMIGTSLESTSKSVTLNGARTMALDQIKAFIKTFM
>>
>> EHQIFSTGALSSAPSMLAQVSERARIPEAGHLRCSGSEIGRFVTMLRNPCLVLRACAA
>>
>> FALLQFTIPESRHAMHHASLMQNAGEARGLRSAAAAASMPREAKIFMKIVLRNLEHQQ
>> AESPEGMKVSYNRI"
>> exon complement(8353..8556)
>> /gene="T8B10_10"
>> /number=1
>> intron complement(8557..8640)
>> /gene="T8B10_10"
>> /number=1
>> exon complement(8641..8947)
>> /gene="T8B10_10"
>> /number=2
>> intron complement(8948..9033)
>> /gene="T8B10_10"
>> /number=2
>> exon complement(9034..9209)
>> /gene="T8B10_10"
>> /number=3
>> intron complement(9210..9287)
>> /gene="T8B10_10"
>> /number=3
>> exon complement(9288..9351)
>> /gene="T8B10_10"
>> /number=4
>> intron complement(9352..9484)
>> /gene="T8B10_10"
>> /number=4
>> exon complement(9485..9579)
>> /gene="T8B10_10"
>> /number=5
>> intron complement(9580..9672)
>> /gene="T8B10_10"
>> /number=5
>> exon complement(9673..9888)
>> /gene="T8B10_10"
>> /number=6
>> intron complement(9889..10012)
>> /gene="T8B10_10"
>> /number=6
>> exon complement(10013..10144)
>> /gene="T8B10_10"
>> /number=7
>> intron complement(10145..10458)
>> /gene="T8B10_10"
>> /number=7
>> exon complement(10459..10539)
>> /gene="T8B10_10"
>> /number=8
>> intron complement(10540..10631)
>> /gene="T8B10_10"
>> /number=8
>> exon complement(10632..12143)
>> /gene="T8B10_10"
>> /number=9
>> ORIGIN 1 aagctttgaa gggctaacgg gtgatgcttt ggtgaaggtt
>> ttttctggtc caggtttgtg
>> 61 cttattttgc attgcttctc tttgattcac gtctgcataa acatcaaata
>> attcatttat
>> 121 gtttgagttg attatgtaga aaaaattatt aggggagatg ctttatgata
>> agaaaaaaaa
>> 181 gtggtcttgt ggtatcttaa ggcagaagga aaatatttag tgtcttaatg
>> agtaatagat
>> 241 ttatctgtct atccagattt tataactgag ttttagtaac ttccggctca
>> agcaaaaagg
>> 301 aagttcgata tgacggacat agaagctctc aaggctatca ccacggagag
>> cattgatctg
>> 361 gtatgtactt ttatacctca ccactttttt tttgcagatg attgcttctg
>> atagctttta
>>
>>
>
>
>
>
> -------------------------------------------------------
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>
|
|
From: Jason H. <jha...@pr...> - 2004-03-09 00:13:03
|
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 |
|
From: Thomas O. <ot...@fi...> - 2004-03-08 20:37:10
|
Hi,
I solved one problem, - I had a little problem with the source_row.pm -
I know I shouldn't have, (but I tried something).
Anyhow, still doesn't work-
Errormessage now:
------------------ entry number 1 -----------------
Error: attempting to access a child 'GUS::Model::DoTS::NALocation' of
table 'GUS::Model::DoTS::Source' , but that table does not have a child
of that type. at /home/oracle/gus_home/lib/perl/GUS/Model/GusRow.pm line
396, <GEN0> line 110.
Thomas
Thomas Otto wrote:
> Hello,
>
> I have a little problem trying to insert a sequence from Genbank with
> the GBParser. (Errormessage and sequence-file (a cutted version) see
> below!)
>
> Looks like, that the table doesn't exists! Do I have to create the
> table or is the GBParser not able to insert this type of entries in
> general.
>
> I will continue to resolve the problem, but maybe someone might help me.
>
> Thanks a lot,
> Thomas
>
>
> Error msg:
> Invalid child name: 'GUS::Model::DoTS::AAFeatureComment' at
> /home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiTable.pm line 851
> GUS::ObjRelP::DbiTable::addToChildList('GUS::Model::DoTS::Source_Table=HASH(0x8fc9b44)','ARRAY(0x8fee070)','ARRAY(0x8fee0ac)','ARRAY(0x8fee0e8)','ARRAY(0x8fee124)','ARRAY(0x8fee160)','ARRAY(0x8fee19c)','ARRAY(0x8fee1d8)','ARRAY(0x8fee214)',...)
> called at /home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiTable.pm line 844
>
> GUS::ObjRelP::DbiTable::setChildList('GUS::Model::DoTS::Source_Table=HASH(0x8fc9b44)','ARRAY(0x8fee070)','ARRAY(0x8fee0ac)','ARRAY(0x8fee0e8)','ARRAY(0x8fee124)','ARRAY(0x8fee160)','ARRAY(0x8fee19c)','ARRAY(0x8fee1d8)','ARRAY(0x8fee214)',...)
> called at
> /home/oracle/gus_home/lib/perl/GUS/Model/DoTS/Source_Table.pm line 16
>
> GUS::Model::DoTS::Source_Table::setDefaultParams('GUS::Model::DoTS::Source_Table=HASH(0x8fc9b44)')
> called at /home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiTable.pm line 38
>
> GUS::ObjRelP::DbiTable::new('GUS::Model::DoTS::Source_Table','GUS::Model::DoTS::Source','GUS::ObjRelP::DbiDatabase=HASH(0x8c0e34c)')
> called at /home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
> line 179
>
> GUS::ObjRelP::DbiDatabase::getTable('GUS::ObjRelP::DbiDatabase=HASH(0x8c0e34c)','GUS::Model::DoTS::Source')
> called
> at /home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 30
>
> GUS::ObjRelP::DbiRow::new('GUS::ObjRelP::DbiRow','GUS::Model::DoTS::Source','HASH(0x8fcb890)','undef','undef')
> called at /home/oracle/gus_home/lib/perl/GUS/Model/GusRow.pm line 25
>
> GUS::Model::GusRow::new('GUS::Model::DoTS::Source','HASH(0x8fcb890)')
> called at /home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm
> line 486
>
> GUS::Common::Plugin::GBParser::buildFeatures('GUS::Common::Plugin::GBParser=HASH(0x856fbac)','CBIL::Bio::GenBank::Entry=HASH(0x8ec70f4)','GUS::Model::DoTS::ExternalNASequence=HASH(0x8f95ea8)')
> called at /home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm
> line 251
>
> GUS::Common::Plugin::GBParser::processEntry('GUS::Common::Plugin::GBParser=HASH(0x856fbac)','CBIL::Bio::GenBank::ArrayStream=HASH(0x8ec7088)')
> called at /home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm
> line 185
> eval {...} called at
> /home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 184
>
> GUS::Common::Plugin::GBParser::run('GUS::Common::Plugin::GBParser=HASH(0x856fbac)','HASH(0x8e53714)')
> called at
> /home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 430
> eval {...} called at
> /home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 427
>
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::Common::Plugin::GBParser')
> called at
> /home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 283
>
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::Common::Plugin::GBParser')
> called at
> /home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 192
>
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','ARRAY(0x80606b0)')
> called at /home/oracle/gus_home/bin/ga line 11
>
>------------------------------------------------------------------------
>
>LOCUS ATT8B10 103787 bp DNA linear PLN 20-MAR-2000
>DEFINITION Arabidopsis thaliana DNA chromosome 3, BAC clone T8B10.
>ACCESSION AL138646
>VERSION AL138646.2 GI:7287982
>KEYWORDS .
>SOURCE Arabidopsis thaliana (thale cress)
> ORGANISM Arabidopsis thaliana
> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
> Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots;
> rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
>REFERENCE 1 (bases 1 to 103787)
> AUTHORS Rieger,M., Mueller-Auer,S., Zipp,M., Schaefer,M., Mewes,H.W.,
> Lemcke,K., Mayer,K.F.X., Quetier,F. and Salanoubat,M.
> JOURNAL Unpublished
>REFERENCE 2 (bases 1 to 103787)
> AUTHORS EU Arabidopsis sequencing,project.
> TITLE Direct Submission
> JOURNAL Submitted (20-MAR-2000) MIPS, at the Max-Planck-Institut fuer
> Biochemie, Am Klopferspitz 18a, D-82152 Martinsried, FRG, E-mail:
> le...@mi...,ma...@mi... Project
> Coordinator: Marcel Salanoubat and Francis Quetier, Groupement
> d'Interet Public, Centre National de Sequencage - GENOSCOPE; 2 rue
> Gaston Cremieux, BP191, 91006 Evry Cedex, France;
> http://www.genoscope.cns.fr
>FEATURES Location/Qualifiers
> source 1..103787
> /organism="Arabidopsis thaliana"
> /mol_type="genomic DNA"
> /variety="Columbia"
> /db_xref="taxon:3702"
> /chromosome="3"
> gene 8353..12143
> /gene="T8B10_10"
> gene complement(join(8353..8556,8641..8947,9034..9209,
> 9288..9351,9485..9579,9673..9888,10013..10144,
> 10459..10539,10632..12143))
> /gene="T8B10_10"
> CDS complement(join(8353..8556,8641..8947,9034..9209,
> 9288..9351,9485..9579,9673..9888,10013..10144,
> 10459..10539,10632..12143))
> /gene="T8B10_10"
> /note="similarity to arm repeat containing protein
> homolog, Arabidopsis thaliana, EMBL:AL133314"
> /codon_start=1
> /product="Arm repeat containing protein-like"
> /protein_id="CAB81821.1"
> /db_xref="GI:7287983"
> /db_xref="TrEMBL:Q9M224"
> /translation="MSRRVRQRVEDNGKYKVDSPSYTVIGVEDLAPKVQQYVNWTSLP
> YDTVFHLFTRLNYRDRASLASTCRTWRSLGASSFLWSSLDLRAHKFDLSMAASLATRC
> VDLQKIRFRGVDSADAIIHLKARSLLEISGDYCRKITDATLSMIAARHEALESLQLGP
> DFCERITSDAIRVIAFCCPKLKKLRVSGMRDVSSEAIESLAKHCPQLSDLGFLDCLNI
> NEEALGKVVSLRYLSVAGTSNIKWKVALENWEKLPKLIGLDVSRTTIDHIAVSRLLKS
> SQSLKVLCALNCPYLEEDKSYSSNRFKGKVLLAVFTDTFDELASIFADNSKKPKNIFS
> YWRDLIRKDKSIDEIMLWIEWIISHTLLRIAESSNSQGLNDFWLNQGATLLLSLMQSA
> QEDVQERAATGLATFIVVDDENASIDCGRAEAVMRDGGIRLLLELAKSWREGLQSEAA
> KAIANLSVNAKVAKAVAEEGGISVLADLAKSMNRLVAEEAAGGLWNLSVGEEHKNAIA
> QAGGVNALVDLIFRWPHGCDGVLERAAGALANLAADDKCSMEVARAGGVHALVMLARN
> CKYEGAQEQAARALANLAAHGDSNGNNAAVGQEAGALEALVQLTQSPHEGVKQEAAGA
> LWNLAFDDKNRESIAAFGGVEALVALAKSSSNASTGLQERVAGALWGLSVSEANSIAI
> GHEGGIPPLIALVRSEAEDVHETAAGALWNLSFNPGNALRIVEEGGVVALVQLCSSSV
> SKMARFMAALALAYMFDGRMDEYAMIGTSLESTSKSVTLNGARTMALDQIKAFIKTFM
> EHQIFSTGALSSAPSMLAQVSERARIPEAGHLRCSGSEIGRFVTMLRNPCLVLRACAA
> FALLQFTIPESRHAMHHASLMQNAGEARGLRSAAAAASMPREAKIFMKIVLRNLEHQQ
> AESPEGMKVSYNRI"
> exon complement(8353..8556)
> /gene="T8B10_10"
> /number=1
> intron complement(8557..8640)
> /gene="T8B10_10"
> /number=1
> exon complement(8641..8947)
> /gene="T8B10_10"
> /number=2
> intron complement(8948..9033)
> /gene="T8B10_10"
> /number=2
> exon complement(9034..9209)
> /gene="T8B10_10"
> /number=3
> intron complement(9210..9287)
> /gene="T8B10_10"
> /number=3
> exon complement(9288..9351)
> /gene="T8B10_10"
> /number=4
> intron complement(9352..9484)
> /gene="T8B10_10"
> /number=4
> exon complement(9485..9579)
> /gene="T8B10_10"
> /number=5
> intron complement(9580..9672)
> /gene="T8B10_10"
> /number=5
> exon complement(9673..9888)
> /gene="T8B10_10"
> /number=6
> intron complement(9889..10012)
> /gene="T8B10_10"
> /number=6
> exon complement(10013..10144)
> /gene="T8B10_10"
> /number=7
> intron complement(10145..10458)
> /gene="T8B10_10"
> /number=7
> exon complement(10459..10539)
> /gene="T8B10_10"
> /number=8
> intron complement(10540..10631)
> /gene="T8B10_10"
> /number=8
> exon complement(10632..12143)
> /gene="T8B10_10"
> /number=9
>ORIGIN
> 1 aagctttgaa gggctaacgg gtgatgcttt ggtgaaggtt ttttctggtc caggtttgtg
> 61 cttattttgc attgcttctc tttgattcac gtctgcataa acatcaaata attcatttat
> 121 gtttgagttg attatgtaga aaaaattatt aggggagatg ctttatgata agaaaaaaaa
> 181 gtggtcttgt ggtatcttaa ggcagaagga aaatatttag tgtcttaatg agtaatagat
> 241 ttatctgtct atccagattt tataactgag ttttagtaac ttccggctca agcaaaaagg
> 301 aagttcgata tgacggacat agaagctctc aaggctatca ccacggagag cattgatctg
> 361 gtatgtactt ttatacctca ccactttttt tttgcagatg attgcttctg atagctttta
>
>
|
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