gusdev-gusdev — Topics concerning GUS development

Re: [GUSDEV] About Extending the Schema

[Angel P. <an...@ma...>]

1) I'll update the wiki for to delete the old information.

2) There is no mention of adding the new table definitions to the 
gus_schema.xml file, which should be _the_ canonical version of the 
schema from which perl, ddl and java code should be generated from. This 
guide was probably written while the DBAdmin project was not stable.

We have to make a decision as a community whether we want to continue 
GUS as either a database driven or spec file driven documentation and 
development. Currently it is both, depending on the task. Pretty 
confusing. My vote is for spec-file driven.

-angel


Steve Fischer wrote:

> jian-
>
> gus_schema.xml is the right file to touch.
>
> we have definitely extended the schema here recently.  hopefully 
> someone at cbil who has done so will answer this.  if not, please 
> write back, and i'll look into it.
>
> steve
>
> Jian Lu wrote:
>
>> I was using
>> $touch $PROJECT_HOME/GUS/Schema/gus_schema.xml
>>
>> from 
>> http://www.gusdb.org/documentation/3.5/developers/html/ch02.html#id856722 
>>
>>
>> I could try what you mentioned here. Thanks.
>>
>> Angel Pizarro wrote:
>>
>>>
>>> Did you "touch" the schema VERSION file prior to building? From the 
>>> wiki:
>>>
>>> http://www.gusdb.org/wiki/index.php/Installing%20GUS
>>>
>>>
>>>        Regenerating the GUS Perl and Java Objects
>>>
>>> touch $PROJECT_HOME/GUS/Model/schema/VERSION
>>> build GUS install -append
>>>
>>>
>>> Jian Lu wrote:
>>>
>>>> Hi GUS,
>>>>
>>>> I created a new schema name called APP with some new tables. I 
>>>> registered APP to Core.DatabaseInfo and all new tables to 
>>>> Core.TableInfo. When I rebuilt GUS, it seems not recognizing the 
>>>> new schema APP.
>>>>
>>>> When talking about extending GUS schema like adding new tables, 
>>>> does it mean all new tables have to fall into existing GUS schema 
>>>> such as DoTS? What should I do in order to support my own schema?
>>>>
>>>> Thanks.
>>>>
>>>> JL
>>>>
>>>>
>>>> -------------------------------------------------------
>>>> This SF.net email is sponsored by: Splunk Inc. Do you grep through 
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>>>>
>>>> _______________________________________________
>>>> Gusdev-gusdev mailing list
>>>> Gus...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>
>>
>>
>>
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>

Re: [GUSDEV] About Extending the Schema

[Steve F. <sfi...@pc...>]

jian-

gus_schema.xml is the right file to touch.

we have definitely extended the schema here recently.  hopefully someone 
at cbil who has done so will answer this.  if not, please write back, 
and i'll look into it.

steve

Jian Lu wrote:
> I was using
> $touch $PROJECT_HOME/GUS/Schema/gus_schema.xml
>
> from 
> http://www.gusdb.org/documentation/3.5/developers/html/ch02.html#id856722
>
> I could try what you mentioned here. Thanks.
>
> Angel Pizarro wrote:
>>
>> Did you "touch" the schema VERSION file prior to building? From the 
>> wiki:
>>
>> http://www.gusdb.org/wiki/index.php/Installing%20GUS
>>
>>
>>        Regenerating the GUS Perl and Java Objects
>>
>> touch $PROJECT_HOME/GUS/Model/schema/VERSION
>> build GUS install -append
>>
>>
>> Jian Lu wrote:
>>
>>> Hi GUS,
>>>
>>> I created a new schema name called APP with some new tables. I 
>>> registered APP to Core.DatabaseInfo and all new tables to 
>>> Core.TableInfo. When I rebuilt GUS, it seems not recognizing the new 
>>> schema APP.
>>>
>>> When talking about extending GUS schema like adding new tables, does 
>>> it mean all new tables have to fall into existing GUS schema such as 
>>> DoTS? What should I do in order to support my own schema?
>>>
>>> Thanks.
>>>
>>> JL
>>>
>>>
>>> -------------------------------------------------------
>>> This SF.net email is sponsored by: Splunk Inc. Do you grep through 
>>> log files
>>> for problems?  Stop!  Download the new AJAX search engine that makes
>>> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
>>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642 
>>>
>>> _______________________________________________
>>> Gusdev-gusdev mailing list
>>> Gus...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>
>
>
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Re: [GUSDEV] About Extending the Schema

[Jian Lu <jl...@vb...>]

I was using 

$touch $PROJECT_HOME/GUS/Schema/gus_schema.xml

from 
http://www.gusdb.org/documentation/3.5/developers/html/ch02.html#id856722

I could try what you mentioned here. Thanks.

Angel Pizarro wrote:
>
> Did you "touch" the schema VERSION file prior to building? From the wiki:
>
> http://www.gusdb.org/wiki/index.php/Installing%20GUS
>
>
>        Regenerating the GUS Perl and Java Objects
>
> touch $PROJECT_HOME/GUS/Model/schema/VERSION
> build GUS install -append
>
>
> Jian Lu wrote:
>
>> Hi GUS,
>>
>> I created a new schema name called APP with some new tables. I 
>> registered APP to Core.DatabaseInfo and all new tables to 
>> Core.TableInfo. When I rebuilt GUS, it seems not recognizing the new 
>> schema APP.
>>
>> When talking about extending GUS schema like adding new tables, does 
>> it mean all new tables have to fall into existing GUS schema such as 
>> DoTS? What should I do in order to support my own schema?
>>
>> Thanks.
>>
>> JL
>>
>>
>> -------------------------------------------------------
>> This SF.net email is sponsored by: Splunk Inc. Do you grep through 
>> log files
>> for problems?  Stop!  Download the new AJAX search engine that makes
>> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

Re: [GUSDEV] About Extending the Schema

[Angel P. <an...@ma...>]

Did you "touch" the schema VERSION file prior to building? From the wiki:

http://www.gusdb.org/wiki/index.php/Installing%20GUS


        Regenerating the GUS Perl and Java Objects

touch $PROJECT_HOME/GUS/Model/schema/VERSION
build GUS install -append


Jian Lu wrote:

> Hi GUS,
>
> I created a new schema name called APP with some new tables. I 
> registered APP to Core.DatabaseInfo and all new tables to 
> Core.TableInfo. When I rebuilt GUS, it seems not recognizing the new 
> schema APP.
>
> When talking about extending GUS schema like adding new tables, does 
> it mean all new tables have to fall into existing GUS schema such as 
> DoTS? What should I do in order to support my own schema?
>
> Thanks.
>
> JL
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log 
> files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
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> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

[GUSDEV] About Extending the Schema

[Jian Lu <jl...@vb...>]

Hi GUS,

I created a new schema name called APP with some new tables. I 
registered APP to Core.DatabaseInfo and all new tables to 
Core.TableInfo. When I rebuilt GUS, it seems not recognizing the new 
schema APP.

When talking about extending GUS schema like adding new tables, does it 
mean all new tables have to fall into existing GUS schema such as DoTS? 
What should I do in order to support my own schema?

Thanks.

JL

Re: [GUSDEV] Blast parameters revisited

[<ju...@cs...>]

Chris Stoeckert <sto...@pc...> writes:
>
> AlgorithmInvocation has a comment_string attribute that can be used
> to put your convenient name. AnalysisAlgorithm can be used to tie
> that to Similarity rows through the softlinks table_id, row_id.

Ok, for a set of blast results I can put one row
in Core.AlgorithmInvocation (with the blast parameters)
and Core.AnalysisAlgorithm is the linking table to
multiple lines in DoTS.Similarity.  For this purpose,
one can then just ignore :

    Core.AlgorithmParamKey
    Core.AlgorithmParam
    Core.AlgorithmParamKeyType

I did make it overly complicated.

[...]
> Evidence could
> be use (target = similarity; fact = external database release).

Ok, this could work too.

> We are looking into altering Similarity or adding a table to better
> capture alignments (an attribute to indicate gaps).

Cool;

> We can also
> consider providing a link to external database release as part of
> this if it makes sense.

That's pretty much what I went a head an implemented in
our local installation.

Thanks for taking a look;

Josef



> On Feb 6, 2006, at 12:13 PM, Josef Jurek wrote:
>
> >
> >
> > Any thoughts on this?
> >
> > Does implementing a "SRes.ExternalDatabaseRelease"-like way to group
> > rows in DoTS.Similarity together sound useful to anybody,
> > or do people find the use of Core.AnalysisAlgorithm to accomplish
> > such a thing completely satisfactory?
> >
> > Thanks, Josef
> >
[...]
> >
> > I wrote:
> >>
> >>
> >> In the recent past, some of us needed a way to
> >> distinguish between blast results in DoTS.Similarity by
[...]

Re: [GUSDEV] Blast parameters revisited

[Chris S. <sto...@pc...>]

Hi Josef,
AlgorithmInvocation has a comment_string attribute that can be used  
to put your convenient name. AnalysisAlgorithm can be used to tie  
that to Similarity rows through the softlinks table_id, row_id. Note  
that there is also a record keeping attribute: row_alg_invocation_id  
that could be used as well - this typically stores a record of the  
plugin used to load the data.

The semantics of an ExternalDatabaseRelease have been broadened to  
include data files so that would be OK too if you wanted to record  
details of who, when, where, what etc. in a more structured way. What  
you would want I guess is a linking table that says these  
similarities came from this external database release. Evidence could  
be use (target = similarity; fact = external database release).

We are looking into altering Similarity or adding a table to better  
capture alignments (an attribute to indicate gaps). We can also  
consider providing a link to external database release as part of  
this if it makes sense.

Cheers.
Chris

On Feb 6, 2006, at 12:13 PM, Josef Jurek wrote:

>
>
> Any thoughts on this?
>
> Does implementing a "SRes.ExternalDatabaseRelease"-like way to group
> rows in DoTS.Similarity together sound useful to anybody,
> or do people find the use of Core.AnalysisAlgorithm to accomplish
> such a thing completely satisfactory?
>
> Thanks, Josef
>
>
> Daphne Preuss Laboratory
> Molecular Genetics and Cell Biology
> The University of Chicago
> ju...@cs...
>
> voice: (773) 834-3985
> fax:   (773) 702-6648
>
>
> I wrote:
>>
>>
>> In the recent past, some of us needed a way to
>> distinguish between blast results in DoTS.Similarity by
>> the blast parameters used.  For example, I might
>> blast the same sets of sequences several times
>> with different parameters and put all the results
>> of all these blast searches into DoTS.Similarity.
>>
>> I was of course, able to jury-rig a way to do
>> this, though now with GUS 3.5, an officially
>> sanctioned method has been implemented
>> by using the Core.AnalysisAlgorithm table.
>>
>> Below is a crude entity relationship diagram
>> of how Core.AnalysisAlgorithm fits in with other
>> relevant tables (be sure to view this file with
>> the courier font):
>>
>>                      Core.Algorithm (name)
>>                       |
>>                       |
>>                      Core.AlgorithmImplementation                
>> Core.AlgorithmParamKeyType
>> |                     |                        \               /  
>> (string, float, int, ...)
>> |                     |                         \             /
>> Core.TableInfo       Core.AlgorithmInvocation     
>> Core.AlgorithmParamKey
>> |             \       |                 \       / (description of  
>> parameter)
>> |              \      |                  \     /
>> DoTS.Similarity  Core.AnalysisAlgorithm    Core.AlgorithmParam  
>> (parameters as a string)
>>                                                (individual parameter)
>>
>>
>> And so, to insert into GUS a list of blast parameters such as:
>>
>>    -p blastp -FD -W2 -G 11 -E 1 -e 0.5 -f 11 -M BLOSUM62 -b  
>> 1000000 -v 1000000
>>
>> one would need to:
>>
>>     have a row for every flag in Core.AlgorithmParamKey
>>     have a row for every value after a flag in Core.AlgorithmParam
>>
>> which is very complicated to both insert and query.  I suppose if one
>> wrote a gus plugin which is a wrapper around blast, inserting  
>> parameters
>> in these all of these rows/fields could be easily taken care
>> of, though we at the Preuss lab just are not going to do things
>> that way.  We may get blast data from a collaborator that took
>> days to run on a multi-node cluster and we just want to dump
>> this data into DoTS.Similarity/DoTS.SimilaritySpan and query
>> it.  We can't run this blast search again with a plugin.
>>
>> And again, querying blast results by blast parameter between the
>> same set of sequences looks to be very complex with the
>> above tables.  Imagine writing SQL trying to distinguish between
>> blast results based on these three sets of parameters.
>>
>>    -p blastp -FD -W2 -G 11 -E 1 -e 0.5 -f 11 -M BLOSUM62 -b  
>> 1000000 -v 1000000
>>    -p blastp -FD -W3 -G 11 -E 1 -e 0.5 -f 11 -M BLOSUM62 -b  
>> 1000000 -v 1000000
>>    -p blastp -FD -W2 -G 11 -E 1 -e 0.5 -f 11 -M BLOSUM80 -b  
>> 1000000 -v 1000000
>>
>>
>> Perhaps people on the list can let me know if there are
>> any labs outside of CBIL that are depositing and querying
>> blast search parameters with the above tables.
>>
>>
>> What we at the Preuss lab really need is a simple way
>> to group rows in DoTS.Similarity together, much like the
>> way one groups rows in DoTS.ExternalNASequence together with
>> the table SRes.ExternalDatabaseRelease.  Then a set of blast
>> results could be labeled with a convenient name
>> such as "ME vs Ath, W9" or "Jim's lab, -FF".
>>
>>
>> I will go a head and implement something locally to do
>> this, but I would think such a thing would not only
>> be valuable, but necessary for others too.
>> Does implementing a such a table (perhaps calling it
>> DoTS.SimilaritySet) in the official distribution make
>> sense?
>>
>> Or perhaps I am wrong in my understanding of how
>> the Core.AnalysisAlgorithm table can be used, and
>> there is a simpler way to do this.  If so, I hope
>> someone can enlighten me.
>>
>>
>> Thank you for reading;
>>
>> Josef
>>
>
>
>
>
>
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through  
> log files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD  
> SPLUNK!
> http://sel.as-us.falkag.net/sel? 
> cmd=lnk&kid=103432&bid=230486&dat=121642
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> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [GUSDEV] Blast parameters revisited

[<ju...@cs...>]

Any thoughts on this?

Does implementing a "SRes.ExternalDatabaseRelease"-like way to group
rows in DoTS.Similarity together sound useful to anybody,
or do people find the use of Core.AnalysisAlgorithm to accomplish
such a thing completely satisfactory?

Thanks, Josef


Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...

voice: (773) 834-3985
fax:   (773) 702-6648


I wrote:
> 
> 
> In the recent past, some of us needed a way to
> distinguish between blast results in DoTS.Similarity by
> the blast parameters used.  For example, I might
> blast the same sets of sequences several times
> with different parameters and put all the results
> of all these blast searches into DoTS.Similarity.
> 
> I was of course, able to jury-rig a way to do
> this, though now with GUS 3.5, an officially
> sanctioned method has been implemented
> by using the Core.AnalysisAlgorithm table.
> 
> Below is a crude entity relationship diagram
> of how Core.AnalysisAlgorithm fits in with other
> relevant tables (be sure to view this file with
> the courier font):
> 
>                      Core.Algorithm (name)
>                       |
>                       |
>                      Core.AlgorithmImplementation               Core.AlgorithmParamKeyType
> |                     |                        \               / (string, float, int, ...)
> |                     |                         \             /
> Core.TableInfo       Core.AlgorithmInvocation    Core.AlgorithmParamKey
> |             \       |                 \       / (description of parameter)
> |              \      |                  \     /
> DoTS.Similarity  Core.AnalysisAlgorithm    Core.AlgorithmParam (parameters as a string)
>                                                (individual parameter)
> 
> 
> And so, to insert into GUS a list of blast parameters such as:
> 
>    -p blastp -FD -W2 -G 11 -E 1 -e 0.5 -f 11 -M BLOSUM62 -b 1000000 -v 1000000
> 
> one would need to:
> 
>     have a row for every flag in Core.AlgorithmParamKey
>     have a row for every value after a flag in Core.AlgorithmParam
> 
> which is very complicated to both insert and query.  I suppose if one
> wrote a gus plugin which is a wrapper around blast, inserting parameters
> in these all of these rows/fields could be easily taken care
> of, though we at the Preuss lab just are not going to do things
> that way.  We may get blast data from a collaborator that took
> days to run on a multi-node cluster and we just want to dump
> this data into DoTS.Similarity/DoTS.SimilaritySpan and query
> it.  We can't run this blast search again with a plugin.
> 
> And again, querying blast results by blast parameter between the
> same set of sequences looks to be very complex with the
> above tables.  Imagine writing SQL trying to distinguish between
> blast results based on these three sets of parameters.
> 
>    -p blastp -FD -W2 -G 11 -E 1 -e 0.5 -f 11 -M BLOSUM62 -b 1000000 -v 1000000
>    -p blastp -FD -W3 -G 11 -E 1 -e 0.5 -f 11 -M BLOSUM62 -b 1000000 -v 1000000
>    -p blastp -FD -W2 -G 11 -E 1 -e 0.5 -f 11 -M BLOSUM80 -b 1000000 -v 1000000
> 
> 
> Perhaps people on the list can let me know if there are
> any labs outside of CBIL that are depositing and querying
> blast search parameters with the above tables.
> 
> 
> What we at the Preuss lab really need is a simple way
> to group rows in DoTS.Similarity together, much like the
> way one groups rows in DoTS.ExternalNASequence together with
> the table SRes.ExternalDatabaseRelease.  Then a set of blast
> results could be labeled with a convenient name
> such as "ME vs Ath, W9" or "Jim's lab, -FF".
> 
> 
> I will go a head and implement something locally to do
> this, but I would think such a thing would not only
> be valuable, but necessary for others too.
> Does implementing a such a table (perhaps calling it
> DoTS.SimilaritySet) in the official distribution make
> sense?
> 
> Or perhaps I am wrong in my understanding of how
> the Core.AnalysisAlgorithm table can be used, and
> there is a simpler way to do this.  If so, I hope
> someone can enlighten me.
> 
> 
> Thank you for reading;
> 
> Josef
> 

RE: [GUSDEV] showQuestionSets.do

[Y. T. G. <yg...@pc...>]

That definitely worth checking out first.

Anything with a '.do' suffix you see on the url is a STRUTS action so
you would not find it as a file.
However if you search the struts-config.xml under WEB-INF, you will find
them being bound to a java class.

-Thomas


> -----Original Message-----
> From: gus...@li... 
> [mailto:gus...@li...] On Behalf 
> Of Mark S. Heiges
> Sent: Friday, February 03, 2006 11:35 AM
> To: Federica Viti
> Cc: gus...@li...
> Subject: Re: [GUSDEV] showQuestionSets.do
> 
> 
> I get this error when I've forgotten to rename the web.xml.toy file  
> to web.xml (there's also a footer.tag.toy and header.tag.toy that  
> need to be renamed).
> Could that be it?
> 
> -Mark
> 
> On Feb 3, 2006, at 11:10 AM, Federica Viti wrote:
> 
> > Hi guys, deploying my web application GUSViewToy on tomcat 5.5 I
> > had this
> > error back:
> >
> > HTTP Status 404 - /GUSViewToy/showQuestionSets.do
> >
> > type Status report
> >
> > message /GUSViewToy/showQuestionSets.do
> >
> > description The requested resource (/GUSViewToy/
> > showQuestionSets.do) is
> > not available.
> >
> > My index.jsp file points to showQuestionSets.do, but I 
> can't find it 
> > anywhere in my directories. Can anyone help me?
> > thanks
> > Federica
> >
> >
> >
> >
> > -------------------------------------------------------
> > This SF.net email is sponsored by: Splunk Inc. Do you grep through
> > log files
> > for problems?  Stop!  Download the new AJAX search engine that makes
> > searching your log files as easy as surfing the  web.  DOWNLOAD  
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> > http://sel.as-us.falkag.net/sel? 
> > cmd=lnk&kid=103432&bid=230486&dat=121642
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> 
> 
> 
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dat=121642
_______________________________________________
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Re: [GUSDEV] showQuestionSets.do

[Mark S. H. <mh...@ug...>]

I get this error when I've forgotten to rename the web.xml.toy file  
to web.xml (there's also a footer.tag.toy and header.tag.toy that  
need to be renamed).
Could that be it?

-Mark

On Feb 3, 2006, at 11:10 AM, Federica Viti wrote:

> Hi guys, deploying my web application GUSViewToy on tomcat 5.5 I  
> had this
> error back:
>
> HTTP Status 404 - /GUSViewToy/showQuestionSets.do
>
> type Status report
>
> message /GUSViewToy/showQuestionSets.do
>
> description The requested resource (/GUSViewToy/ 
> showQuestionSets.do) is
> not available.
>
> My index.jsp file points to showQuestionSets.do, but I can't find it
> anywhere in my directories.
> Can anyone help me?
> thanks
> Federica
>
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through  
> log files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD  
> SPLUNK!
> http://sel.as-us.falkag.net/sel? 
> cmd=lnk&kid=103432&bid=230486&dat=121642
> _______________________________________________
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> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

[GUSDEV] showQuestionSets.do

[Federica V. <fed...@bi...>]

Hi guys, deploying my web application GUSViewToy on tomcat 5.5 I had this
error back:

HTTP Status 404 - /GUSViewToy/showQuestionSets.do

type Status report

message /GUSViewToy/showQuestionSets.do

description The requested resource (/GUSViewToy/showQuestionSets.do) is
not available.

My index.jsp file points to showQuestionSets.do, but I can't find it
anywhere in my directories.
Can anyone help me?
thanks
Federica

[GUSDEV] Blast parameters revisited

[Josef J. <ju...@cs...>]

In the recent past, some of us needed a way to
distinguish between blast results in DoTS.Similarity by
the blast parameters used.  For example, I might
blast the same sets of sequences several times
with different parameters and put all the results
of all these blast searches into DoTS.Similarity.

I was of course, able to jury-rig a way to do
this, though now with GUS 3.5, an officially
sanctioned method has been implemented
by using the Core.AnalysisAlgorithm table.

Below is a crude entity relationship diagram
of how Core.AnalysisAlgorithm fits in with other
relevant tables (be sure to view this file with
the courier font):

                     Core.Algorithm (name)
                      |
                      |
                     Core.AlgorithmImplementation               Core.AlgorithmParamKeyType
|                     |                        \               / (string, float, int, ...)
|                     |                         \             /
Core.TableInfo       Core.AlgorithmInvocation    Core.AlgorithmParamKey
|             \       |                 \       / (description of parameter)
|              \      |                  \     /
DoTS.Similarity  Core.AnalysisAlgorithm    Core.AlgorithmParam (parameters as a string)
                                               (individual parameter)


And so, to insert into GUS a list of blast parameters such as:

   -p blastp -FD -W2 -G 11 -E 1 -e 0.5 -f 11 -M BLOSUM62 -b 1000000 -v 1000000

one would need to:

    have a row for every flag in Core.AlgorithmParamKey
    have a row for every value after a flag in Core.AlgorithmParam

which is very complicated to both insert and query.  I suppose if one
wrote a gus plugin which is a wrapper around blast, inserting parameters
in these all of these rows/fields could be easily taken care
of, though we at the Preuss lab just are not going to do things
that way.  We may get blast data from a collaborator that took
days to run on a multi-node cluster and we just want to dump
this data into DoTS.Similarity/DoTS.SimilaritySpan and query
it.  We can't run this blast search again with a plugin.

And again, querying blast results by blast parameter between the
same set of sequences looks to be very complex with the
above tables.  Imagine writing SQL trying to distinguish between
blast results based on these three sets of parameters.

   -p blastp -FD -W2 -G 11 -E 1 -e 0.5 -f 11 -M BLOSUM62 -b 1000000 -v 1000000
   -p blastp -FD -W3 -G 11 -E 1 -e 0.5 -f 11 -M BLOSUM62 -b 1000000 -v 1000000
   -p blastp -FD -W2 -G 11 -E 1 -e 0.5 -f 11 -M BLOSUM80 -b 1000000 -v 1000000


Perhaps people on the list can let me know if there are
any labs outside of CBIL that are depositing and querying
blast search parameters with the above tables.


What we at the Preuss lab really need is a simple way
to group rows in DoTS.Similarity together, much like the
way one groups rows in DoTS.ExternalNASequence together with
the table SRes.ExternalDatabaseRelease.  Then a set of blast
results could be labeled with a convenient name
such as "ME vs Ath, W9" or "Jim's lab, -FF".


I will go a head and implement something locally to do
this, but I would think such a thing would not only
be valuable, but necessary for others too.
Does implementing a such a table (perhaps calling it
DoTS.SimilaritySet) in the official distribution make
sense?

Or perhaps I am wrong in my understanding of how
the Core.AnalysisAlgorithm table can be used, and
there is a simpler way to do this.  If so, I hope
someone can enlighten me.


Thank you for reading;

Josef

[GUSDEV] Go alt_ids

[Ed R. <ero...@ug...>]

We've run into a snag using GO terms for a case where an
analysis app returns an alt_id ( GO:0008722 ) which isn't
loaded into GUS by the InsertGeneOntology plugin.  We need to
get this id into GUS because this is the only id we are
getting back with our data.  We are not being given the main
ID which, in this case, is GO:0043141.

any thoughts?

-ed
-----------------
Ed Robinson
Center for Tropical and Emerging Global Diseases
University of Georgia, Athens, GA 30602
ero...@ug.../(706)542.1447/254.8883

[GUSDEV] Re: [ApiDB] LoadDocumentation Plugin

[Steve F. <sfi...@pc...>]

its not used in any of our pipelines that i know of, nor in the 
installation process.    -steve

Jonathan Schug wrote:

>Hello Folks:
>
>I'm about to upgrade the GUS::Community::Plugin::LoadDocumentation to  
>be more useful (to me at least ;-).  Is this plugin used in any  
>pipelines or in the GUS installation process?  Are there any specific  
>behaviors of the plugin that must be maintained?
>
>Thanks,
>
>Jonathan
>
>
>Jonathan Schug, Ph.D.
>
>Center for Bioinformatics
>Computational Biology and Informatics Lab
>University of Pennsylvania
>
>js...@pc...
>(215) 573-3113 voice
>(215) 573-3111 fax
>
>1413 Blockley Hall, Philadelphia, PA 19014-6021
>
>
>
>_______________________________________________
>ApiDB mailing list
>Ap...@pc...
>https://mail.pcbi.upenn.edu/mailman/listinfo/apidb
>  
>

[GUSDEV] LoadDocumentation Plugin

[Jonathan S. <js...@pc...>]

Hello Folks:

I'm about to upgrade the GUS::Community::Plugin::LoadDocumentation to  
be more useful (to me at least ;-).  Is this plugin used in any  
pipelines or in the GUS installation process?  Are there any specific  
behaviors of the plugin that must be maintained?

Thanks,

Jonathan


Jonathan Schug, Ph.D.

Center for Bioinformatics
Computational Biology and Informatics Lab
University of Pennsylvania

js...@pc...
(215) 573-3113 voice
(215) 573-3111 fax

1413 Blockley Hall, Philadelphia, PA 19014-6021

Re: [GUSDEV] Another error executing ISF

[Aaron J. M. <am...@pc...>]

This is a BioPerl "Unflattener" error; it's unable to automatically  
reconstruct the gene/mRNA/exon logic of some (or all) of the  
annotation in your genbank file.  To get help with this, you should  
post a message to the BioPerl mailing list (bio...@bi...),  
including a snippet of your genbank file.

-Aaron

On Jan 26, 2006, at 11:53 AM, Ricardo Balbi wrote:

> Hi all,
>
>   After making some changes in the gus mapping file to ignore some  
> features of the kinetoplastida database, I followed in the  
> execution of the ISF, however without success.
>
>   Somebody could help me with this error?
>
> thanks in advance,
> Ricardo
>
> ERROR:
>
> ------------- EXCEPTION  -------------
> MSG: structure_type 2 is currently unknown
> STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/local/ 
> bioperl15/Bio/SeqFeature/Tools/Unflattener.pm:1419
> STACK GUS::Supported::Plugin::InsertSequenceFeatures::unflatten / 
> GUS/gus_home/lib/perl/GUS/Supported/Plugin/ 
> InsertSequenceFeatures.pm:353
> STACK  
> GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees /G 
> US/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm: 
> 720
> STACK GUS::Supported::Plugin::InsertSequenceFeatures::run /GUS/ 
> gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm:330
> STACK (eval) /GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm: 
> 549
> STACK GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport /GUS/ 
> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:541
> STACK GUS::PluginMgr::GusApplication::doMajorMode_Run /GUS/gus_home/ 
> lib/perl/GUS/PluginMgr/GusApplication.pm:459
> STACK GUS::PluginMgr::GusApplication::doMajorMode /GUS/gus_home/lib/ 
> perl/GUS/PluginMgr/GusApplication.pm:357
> STACK GUS::PluginMgr::GusApplication::parseAndRun /GUS/gus_home/lib/ 
> perl/GUS/PluginMgr/GusApplication.pm:266
> STACK toplevel /GUS/gus_home/bin/ga:11
>
> --------------------------------------
>
> STACK TRACE:
>  at /usr/local/bioperl15/Bio/Root/Root.pm line 342
>         Bio::Root::Root::throw 
> ('Bio::SeqFeature::Tools::Unflattener=HASH(0xb5e124c)',  
> 'structure_type 2 is currently unknown') called at /usr/local/ 
> bioperl15/Bio/SeqFeature/Tools/Unflattener.pm line 1419
>         Bio::SeqFeature::Tools::Unflattener::unflatten_seq 
> ('Bio::SeqFeature::Tools::Unflattener=HASH(0xb5e124c)', '-seq',  
> 'Bio::Seq::RichSeq=HASH(0xb820b14)', '-use_magic', 1) called at / 
> GUS/gus_home/lib/perl/GUS/Supported/Plugin/ 
> InsertSequenceFeatures.pm line 353
>         GUS::Supported::Plugin::InsertSequenceFeatures::unflatten 
> ('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xa011adc)',  
> 'Bio::Seq::RichSeq=HASH(0xb820b14)') called at /GUS/gus_home/lib/ 
> perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 720
>          
> GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees 
> ('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xa011adc)',  
> 'Bio::Seq::RichSeq=HASH(0xb820b14)', 140, 177) called at /GUS/ 
> gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm  
> line 330
>         GUS::Supported::Plugin::InsertSequenceFeatures::run 
> ('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xa011adc)',  
> 'HASH(0xb047e98)') called at /GUS/gus_home/lib/perl/GUS/PluginMgr/ 
> GusApplication.pm line 549
>         eval {...} called at /GUS/gus_home/lib/perl/GUS/PluginMgr/ 
> GusApplication.pm line 541
>         GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport 
> ('GUS::PluginMgr::GusApplication=HASH(0x9ff0c20)',  
> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at /GUS/ 
> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 459
>         GUS::PluginMgr::GusApplication::doMajorMode_Run 
> ('GUS::PluginMgr::GusApplication=HASH(0x9ff0c20)',  
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/ 
> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357
>         GUS::PluginMgr::GusApplication::doMajorMode 
> ('GUS::PluginMgr::GusApplication=HASH(0x9ff0c20)',  
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/ 
> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266
>         GUS::PluginMgr::GusApplication::parseAndRun 
> ('GUS::PluginMgr::GusApplication=HASH(0x9ff0c20)', 'ARRAY 
> (0xa004738)') called at /GUS/gus_home/bin/ga line 11
>
>
>

--
Dr. Aaron J. Mackey, Ph.D.
Project Manager, ApiDB Bioinformatics Resource Center
Penn Genomics Institute, University of Pennsylvania
email:  am...@pc...
office: 215-898-1205 (Biology, 212 Goddard Labs)
         215-746-7018 (PCBI, 1428 Blockley Hall)
fax:    215-746-6697 (Penn Genomics Institute)
postal: Penn Genomics Institute
         Goddard Labs 212
         415 S. University Avenue
         Philadelphia, PA  19104-6017

[GUSDEV] Another error executing ISF

[Ricardo B. <rb...@gm...>]

Hi all,

  After making some changes in the gus mapping file to ignore some features
of the kinetoplastida database, I followed in the execution of the ISF,
however without success.

  Somebody could help me with this error?

thanks in advance,
Ricardo

ERROR:

------------- EXCEPTION  -------------
MSG: structure_type 2 is currently unknown
STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq
/usr/local/bioperl15/Bio/SeqFeature/Tools/Unflattener.pm:1419
STACK GUS::Supported::Plugin::InsertSequenceFeatures::unflatten
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm:353
STACK GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm:720
STACK GUS::Supported::Plugin::InsertSequenceFeatures::run
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm:330
STACK (eval) /GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:549
STACK GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:541
STACK GUS::PluginMgr::GusApplication::doMajorMode_Run
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:459
STACK GUS::PluginMgr::GusApplication::doMajorMode
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:357
STACK GUS::PluginMgr::GusApplication::parseAndRun
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:266
STACK toplevel /GUS/gus_home/bin/ga:11

--------------------------------------

STACK TRACE:
 at /usr/local/bioperl15/Bio/Root/Root.pm line 342

Bio::Root::Root::throw('Bio::SeqFeature::Tools::Unflattener=3DHASH(0xb5e124=
c)',
'structure_type 2 is currently unknown') called at
/usr/local/bioperl15/Bio/SeqFeature/Tools/Unflattener.pm line 1419

Bio::SeqFeature::Tools::Unflattener::unflatten_seq('Bio::SeqFeature::Tools:=
:Unflattener=3DHASH(0xb5e124c)',
'-seq', 'Bio::Seq::RichSeq=3DHASH(0xb820b14)', '-use_magic', 1) called at
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
353

GUS::Supported::Plugin::InsertSequenceFeatures::unflatten('GUS::Supported::=
Plugin::InsertSequenceFeatures=3DHASH(0xa011adc)',
'Bio::Seq::RichSeq=3DHASH(0xb820b14)') called at
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
720

GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees('GUS::S=
upported::Plugin::InsertSequenceFeatures=3DHASH(0xa011adc)',
'Bio::Seq::RichSeq=3DHASH(0xb820b14)', 140, 177) called at
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
330

GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin=
::InsertSequenceFeatures=3DHASH(0xa011adc)',
'HASH(0xb047e98)') called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 549
        eval {...} called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 541

GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::Gu=
sApplication=3DHASH(0x9ff0c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 459

GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplica=
tion=3DHASH(0x9ff0c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357

GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=
=3DHASH(0x9ff0c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266

GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=
=3DHASH(0x9ff0c20)',
'ARRAY(0xa004738)') called at /GUS/gus_home/bin/ga line 11

[GUSDEV] Inserting blast results

[<fab...@de...>]

Hello all,

 

Having successfully inserted some genbank files with ISF, our next task is
to insert blast results into GUS. To fulfill this requirement I would like
to know what plugin is necessary as well as how it can be used. Until now, I
downloaded some nucleotide genbank and fasta files belonging to the same
organism from NCBI. The genbank file was loaded using ISF. Now I want to use
the Fasta file to run blast and load results into gus too. Is it also
important to load the fasta file content to GUS and keep the relationship
between the source sequence and the blast result from that? If yes, how
could it be done?

 

If someone could help us with these doubts we would be so grateful.

 

Thanks in advance,

 

Fabricio.

Re: [GUSDEV] Re: [Bug 257] The rules had not been created

[<jld...@pc...>]

Ricardo,

The error you received simply means that your mapping file is incomplete.  So,
in your mapping file, under the mRNA feature, you will need to add a qualifier
with the name 'transcript_id' that tells the plugin what to do with transcript
IDs.  There should be examples of qualifiers for you to follow already in the
mapping file.

I hope this helps.

Jennifer

Quoting Ricardo Balbi <rb...@gm...>:

> Hi Angel,
>
>  It is all right now with versioning tables.
>  Now I passed to a next error.
>  It follows below the error that happened.
>
>  I am using the revision 4422
>
>  Do you have any idea ?
>
> ERROR:
> In feature map XML file '/GUS/gus_home/config/genbank2gus.xml' <feature
> name="mRNA"> does not have a <qualifier> for 'transcript_id', which is found
> in the input at /GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapper.pm
> line 106, <GEN30> line 569.
>
> STACK TRACE:
> at /GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapper.pm line 106
>
> GUS::Supported::BioperlFeatMapper::_checkTagExists('GUS::Supported::BioperlFeatMapper=HASH(0xa7d23cc)',
> 'transcript_id') called at
> /GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapper.pm line 30
>
> GUS::Supported::BioperlFeatMapper::sortTags('GUS::Supported::BioperlFeatMapper=HASH(0xa7d23cc)',
> 'db_xref', 'locus_tag', 'product', 'transcript_id') called at
> /GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
> 800
>
> GUS::Supported::Plugin::InsertSequenceFeatures::makeImmediateFeature('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x9756fdc)',
> 'Bio::SeqFeature::Generic=HASH(0xab16364)', 37, 177) called at
> /GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
> 750
>
> GUS::Supported::Plugin::InsertSequenceFeatures::makeFeature('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x9756fdc)',
> 'Bio::SeqFeature::Generic=HASH(0xab16364)', 37, 177) called at
> /GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
> 758
>
> GUS::Supported::Plugin::InsertSequenceFeatures::makeFeature('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x9756fdc)',
> 'Bio::SeqFeature::Generic=HASH(0xabaf3ac)', 37, 177) called at
> /GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
> 727
>
> GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x9756fdc)',
> 'Bio::Seq::RichSeq=HASH(0xa95e35c)', 37, 177) called at
> /GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
> 330
>
> GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x9756fdc)',
> 'HASH(0xa49ac04)') called at
> /GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 549
>    eval {...} called at
> /GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 541
>
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x9538c20)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
> /GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 459
>
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x9538c20)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> /GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357
>
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x9538c20)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> /GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266
>
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x9538c20)',
> 'ARRAY(0x954c728)') called at /GUS/gus_home/bin/ga line 11
>
>
> Ricardo
>
> 2006/1/17, Angel Pizarro <an...@ma...>:
>>
>> Hi Ricardo,
>>
>> The error did not stem from my patch, but rather from another class that
>> failed to add the none-default columns to the version view objects. I
>> have edited a few files, so you will need to revert to current SVN
>> version of the repository for this patch to work:
>> <copy attached file to project home>
>> cd $PROJECT_HOME
>> svn revert GUS/DBAdmin
>> patch -p0 <DBAdmin.diff
>>
>> Then you should be able to rebuild GUS/DBAdmin and run dbaDump schema as
>> before.
>>
>> An example of the output view and rule follows
>> -angel
>>
>>
>> CREATE VIEW DoTSVer.AAFeatureVer AS
>> SELECT AA_FEATURE_ID, AA_SEQUENCE_ID, FEATURE_NAME_ID, PARENT_ID,
>> NA_FEATURE_ID, SUBCLASS_VIEW, SEQUENCE_ONTOLOGY_ID, DESCRIPTION,
>> PFAM_ENTRY_ID, MOTIF_AA_SEQUENCE_ID, REPEAT_TYPE_ID,
>> EXTERNAL_DATABASE_RELEASE_ID, SOURCE_ID, PREDICTION_ALGORITHM_ID,
>> IS_PREDICTED, REVIEW_STATUS_ID , MODIFICATION_DATE, USER_READ,
>> USER_WRITE, GROUP_READ, GROUP_WRITE, OTHER_READ, OTHER_WRITE,
>> ROW_USER_ID, ROW_GROUP_ID, ROW_PROJECT_ID, ROW_ALG_INVOCATION_ID,
>> VERSION_ALG_INVOCATION_ID, VERSION_DATE, VERSION_TRANSACTION_ID FROM
>> DoTSVer.AAFeatureImpVer;
>>
>> CREATE RULE AAFeatureVer_32675 AS ON INSERT TO DoTSVer.AAFeatureVer DO
>> INSTEAD INSERT INTO  DoTSVer.AAFeatureImpVer ( AA_FEATURE_ID,
>> AA_SEQUENCE_ID, FEATURE_NAME_ID, PARENT_ID, NA_FEATURE_ID,
>> SUBCLASS_VIEW, SEQUENCE_ONTOLOGY_ID, DESCRIPTION, PFAM_ENTRY_ID,
>> MOTIF_AA_SEQUENCE_ID, REPEAT_TYPE_ID, EXTERNAL_DATABASE_RELEASE_ID,
>> SOURCE_ID, PREDICTION_ALGORITHM_ID, IS_PREDICTED, REVIEW_STATUS_ID,
>> MODIFICATION_DATE, USER_READ, USER_WRITE, GROUP_READ, GROUP_WRITE,
>> OTHER_READ, OTHER_WRITE, ROW_USER_ID, ROW_GROUP_ID, ROW_PROJECT_ID,
>> ROW_ALG_INVOCATION_ID, VERSION_ALG_INVOCATION_ID, VERSION_DATE,
>> VERSION_TRANSACTION_ID ) VALUES ( new.AA_FEATURE_ID, new.AA_SEQUENCE_ID,
>> new.FEATURE_NAME_ID, new.PARENT_ID, new.NA_FEATURE_ID,
>> new.SUBCLASS_VIEW, new.SEQUENCE_ONTOLOGY_ID, new.DESCRIPTION,
>> new.PFAM_ENTRY_ID, new.MOTIF_AA_SEQUENCE_ID, new.REPEAT_TYPE_ID,
>> new.EXTERNAL_DATABASE_RELEASE_ID, new.SOURCE_ID,
>> new.PREDICTION_ALGORITHM_ID, new.IS_PREDICTED, new.REVIEW_STATUS_ID,
>> new.MODIFICATION_DATE, new.USER_READ, new.USER_WRITE, new.GROUP_READ,
>> new.GROUP_WRITE, new.OTHER_READ, new.OTHER_WRITE, new.ROW_USER_ID,
>> new.ROW_GROUP_ID, new.ROW_PROJECT_ID, new.ROW_ALG_INVOCATION_ID,
>> new.VERSION_ALG_INVOCATION_ID, new.VERSION_DATE,
>> new.VERSION_TRANSACTION_ID );
>>
>> Angel Pizarro wrote:
>>
>> > Yes, I have an idea of what is going on ... sloppy copy-paste coding
>> > on my part :(
>> >
>> > I'll add the other columns to the method and get you another patch.
>> >
>> > -angel
>> >
>>
>>
>>
>> Index: GUS/DBAdmin/src/java/org/gusdb/dbadmin/model/View.java
>> ===================================================================
>> --- GUS/DBAdmin/src/java/org/gusdb/dbadmin/model/View.java      (revision
>> 4068)
>> +++ GUS/DBAdmin/src/java/org/gusdb/dbadmin/model/View.java      (working
>> copy)
>> @@ -48,6 +48,10 @@
>>          return column;
>>      }
>>
>> +    public void setColumns( ArrayList<ColumnPair> colpair) {
>> +        column = colpair;
>> +    }
>> +
>>      public void addColumn( ColumnPair columnPair ) {
>>          if ( !this.column.contains( columnPair ) ) {
>>              this.column.add( columnPair );
>> Index: GUS/DBAdmin/src/java/org/gusdb/dbadmin/writer/PostgresWriter.java
>> ===================================================================
>> --- GUS/DBAdmin/src/java/org/gusdb/dbadmin/writer/PostgresWriter.java
>> (revision 4068)
>> +++ GUS/DBAdmin/src/java/org/gusdb/dbadmin/writer/PostgresWriter.java
>> (working copy)
>> @@ -12,6 +12,7 @@
>> import org.gusdb.dbadmin.model.GusSchema;
>> import org.gusdb.dbadmin.model.GusTable;
>> import org.gusdb.dbadmin.model.GusView;
>> +import org.gusdb.dbadmin.model.VersionView;
>> import org.gusdb.dbadmin.model.Schema;
>> import org.gusdb.dbadmin.model.Sequence;
>> import org.gusdb.dbadmin.model.Table;
>> @@ -105,6 +106,8 @@
>>          super.writeView( view );
>>          if ( view instanceof GusView ) {
>>              writeViewRules( (GusView) view );
>> +        }else if ( view instanceof VersionView ) {
>> +            writeVersionViewRules( (VersionView) view );
>>          }
>>      }
>>
>> @@ -112,8 +115,6 @@
>>       * Since PostgreSQL doesn't support updatable views, this is a hack
>> that
>>       * uses rules to mimick the updatable view functionality.
>>       *
>> -     * TODO: Note that this means version views are now not updatable
>> since they
>> -     * don't have a PK.
>>       *
>>       * @param view DOCUMENT ME!
>>       * @throws IOException DOCUMENT ME!
>> @@ -174,7 +175,47 @@
>>          oStream.flush( );
>>      }
>>
>> +
>>      /**
>> +     * Since PostgreSQL doesn't support updatable views, this is a hack
>> that
>> +     * uses rules to mimick the updatable view functionality.
>> +     *
>> +     * Version views are now not updatable since they
>> +     * don't have a PK, so we limit rules to insertion
>> +     *
>> +     * @param view DOCUMENT ME!
>> +     * @throws IOException DOCUMENT ME!
>> +     */
>> +    private void writeVersionViewRules( VersionView view ) throws
>> IOException {
>> +        oStream.write( "CREATE RULE " + view.getName( ) + "_" +
>> random.nextInt( 100000 ) + " AS ON INSERT TO "
>> +                + view.getSchema( ).getName( ) + "." + view.getName( ) +
>> " DO INSTEAD INSERT INTO  "
>> +                + view.getTable( ).getSchema( ).getName( ) + "." +
>> view.getTable( ).getName( ) + " ( " );
>> +
>> +        boolean first = true;
>> +        for ( ColumnPair columnPair : view.getColumns() ) {
>> +            if ( !first ) {
>> +                oStream.write( ", " );
>> +            }
>> +            oStream.write( columnPair.getTableName( ) );
>> +            first = false;
>> +        }
>> +
>> +        oStream.write( " ) VALUES ( " );
>> +
>> +        first = true;
>> +        for ( ColumnPair columnPair : view.getColumns() ) {
>> +            if ( !first ) {
>> +                oStream.write( ", " );
>> +            }
>> +            oStream.write( "new." + columnPair.getViewName( ) );
>> +            first = false;
>> +        }
>> +
>> +        oStream.write( " );\n\n" );
>> +
>> +    }
>> +
>> +    /**
>>       * DOCUMENT ME!
>>       *
>>       * @param type DOCUMENT ME!
>> Index:
>> GUS/DBAdmin/src/java/org/gusdb/dbadmin/util/GusClassHierarchyConverter.java
>> ===================================================================
>> ---
>> GUS/DBAdmin/src/java/org/gusdb/dbadmin/util/GusClassHierarchyConverter.java
>> (revision 4068)
>> +++
>> GUS/DBAdmin/src/java/org/gusdb/dbadmin/util/GusClassHierarchyConverter.java
>> (working copy)
>> @@ -363,6 +363,9 @@
>>              superClassView.setVersioned( true );
>>              verSql = sql.concat( " " );
>>
>> +           // We need to add the superclass columns to the version view.
>> +           superClassView.getVersionView(
>> ).setColumns((ArrayList<ColumnPair>) superClassView.getColumns().clone());
>> +
>>              for ( Column column : verHousekeepingColumns ) {
>>                  verSql = verSql.concat( ", " + column.getName( ) );
>>                  superClassView.getVersionView( ).addColumn( new
>> ColumnPair( column.getName( ), column.getName( ) ) );
>> @@ -448,7 +451,8 @@
>>          if ( impTable.isVersioned( ) ) {
>>              subClass.setVersioned( true );
>>              verSql = sql.concat( " " );
>> -
>> +           // We need to add the subclass_view's columns
>> +           subClass.getVersionView( ).setColumns((ArrayList<ColumnPair>)
>> subClass.getColumns().clone());
>>              for ( Column column : verHousekeepingColumns ) {
>>                  verSql = verSql.concat( ", " + column.getName( ) );
>>                  subClass.getVersionView( ).addColumn( new ColumnPair(
>> column.getName( ), column.getName( ) ) );
>>
>>
>>
>

Re: [GUSDEV] Re: [Bug 257] The rules had not been created

[Ricardo B. <rb...@gm...>]

Hi Angel,

  It is all right now with versioning tables.
  Now I passed to a next error.
  It follows below the error that happened.

  I am using the revision 4422

  Do you have any idea ?

ERROR:
In feature map XML file '/GUS/gus_home/config/genbank2gus.xml' <feature
name=3D"mRNA"> does not have a <qualifier> for 'transcript_id', which is fo=
und
in the input at /GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapper.pm
line 106, <GEN30> line 569.

STACK TRACE:
 at /GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapper.pm line 106

GUS::Supported::BioperlFeatMapper::_checkTagExists('GUS::Supported::Bioperl=
FeatMapper=3DHASH(0xa7d23cc)',
'transcript_id') called at
/GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapper.pm line 30

GUS::Supported::BioperlFeatMapper::sortTags('GUS::Supported::BioperlFeatMap=
per=3DHASH(0xa7d23cc)',
'db_xref', 'locus_tag', 'product', 'transcript_id') called at
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
800

GUS::Supported::Plugin::InsertSequenceFeatures::makeImmediateFeature('GUS::=
Supported::Plugin::InsertSequenceFeatures=3DHASH(0x9756fdc)',
'Bio::SeqFeature::Generic=3DHASH(0xab16364)', 37, 177) called at
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
750

GUS::Supported::Plugin::InsertSequenceFeatures::makeFeature('GUS::Supported=
::Plugin::InsertSequenceFeatures=3DHASH(0x9756fdc)',
'Bio::SeqFeature::Generic=3DHASH(0xab16364)', 37, 177) called at
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
758

GUS::Supported::Plugin::InsertSequenceFeatures::makeFeature('GUS::Supported=
::Plugin::InsertSequenceFeatures=3DHASH(0x9756fdc)',
'Bio::SeqFeature::Generic=3DHASH(0xabaf3ac)', 37, 177) called at
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
727

GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees('GUS::S=
upported::Plugin::InsertSequenceFeatures=3DHASH(0x9756fdc)',
'Bio::Seq::RichSeq=3DHASH(0xa95e35c)', 37, 177) called at
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
330

GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin=
::InsertSequenceFeatures=3DHASH(0x9756fdc)',
'HASH(0xa49ac04)') called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 549
    eval {...} called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 541

GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::Gu=
sApplication=3DHASH(0x9538c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 459

GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplica=
tion=3DHASH(0x9538c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357

GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=
=3DHASH(0x9538c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266

GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=
=3DHASH(0x9538c20)',
'ARRAY(0x954c728)') called at /GUS/gus_home/bin/ga line 11


Ricardo

2006/1/17, Angel Pizarro <an...@ma...>:
>
> Hi Ricardo,
>
> The error did not stem from my patch, but rather from another class that
> failed to add the none-default columns to the version view objects. I
> have edited a few files, so you will need to revert to current SVN
> version of the repository for this patch to work:
> <copy attached file to project home>
> cd $PROJECT_HOME
> svn revert GUS/DBAdmin
> patch -p0 <DBAdmin.diff
>
> Then you should be able to rebuild GUS/DBAdmin and run dbaDump schema as
> before.
>
> An example of the output view and rule follows
> -angel
>
>
> CREATE VIEW DoTSVer.AAFeatureVer AS
> SELECT AA_FEATURE_ID, AA_SEQUENCE_ID, FEATURE_NAME_ID, PARENT_ID,
> NA_FEATURE_ID, SUBCLASS_VIEW, SEQUENCE_ONTOLOGY_ID, DESCRIPTION,
> PFAM_ENTRY_ID, MOTIF_AA_SEQUENCE_ID, REPEAT_TYPE_ID,
> EXTERNAL_DATABASE_RELEASE_ID, SOURCE_ID, PREDICTION_ALGORITHM_ID,
> IS_PREDICTED, REVIEW_STATUS_ID , MODIFICATION_DATE, USER_READ,
> USER_WRITE, GROUP_READ, GROUP_WRITE, OTHER_READ, OTHER_WRITE,
> ROW_USER_ID, ROW_GROUP_ID, ROW_PROJECT_ID, ROW_ALG_INVOCATION_ID,
> VERSION_ALG_INVOCATION_ID, VERSION_DATE, VERSION_TRANSACTION_ID FROM
> DoTSVer.AAFeatureImpVer;
>
> CREATE RULE AAFeatureVer_32675 AS ON INSERT TO DoTSVer.AAFeatureVer DO
> INSTEAD INSERT INTO  DoTSVer.AAFeatureImpVer ( AA_FEATURE_ID,
> AA_SEQUENCE_ID, FEATURE_NAME_ID, PARENT_ID, NA_FEATURE_ID,
> SUBCLASS_VIEW, SEQUENCE_ONTOLOGY_ID, DESCRIPTION, PFAM_ENTRY_ID,
> MOTIF_AA_SEQUENCE_ID, REPEAT_TYPE_ID, EXTERNAL_DATABASE_RELEASE_ID,
> SOURCE_ID, PREDICTION_ALGORITHM_ID, IS_PREDICTED, REVIEW_STATUS_ID,
> MODIFICATION_DATE, USER_READ, USER_WRITE, GROUP_READ, GROUP_WRITE,
> OTHER_READ, OTHER_WRITE, ROW_USER_ID, ROW_GROUP_ID, ROW_PROJECT_ID,
> ROW_ALG_INVOCATION_ID, VERSION_ALG_INVOCATION_ID, VERSION_DATE,
> VERSION_TRANSACTION_ID ) VALUES ( new.AA_FEATURE_ID, new.AA_SEQUENCE_ID,
> new.FEATURE_NAME_ID, new.PARENT_ID, new.NA_FEATURE_ID,
> new.SUBCLASS_VIEW, new.SEQUENCE_ONTOLOGY_ID, new.DESCRIPTION,
> new.PFAM_ENTRY_ID, new.MOTIF_AA_SEQUENCE_ID, new.REPEAT_TYPE_ID,
> new.EXTERNAL_DATABASE_RELEASE_ID, new.SOURCE_ID,
> new.PREDICTION_ALGORITHM_ID, new.IS_PREDICTED, new.REVIEW_STATUS_ID,
> new.MODIFICATION_DATE, new.USER_READ, new.USER_WRITE, new.GROUP_READ,
> new.GROUP_WRITE, new.OTHER_READ, new.OTHER_WRITE, new.ROW_USER_ID,
> new.ROW_GROUP_ID, new.ROW_PROJECT_ID, new.ROW_ALG_INVOCATION_ID,
> new.VERSION_ALG_INVOCATION_ID, new.VERSION_DATE,
> new.VERSION_TRANSACTION_ID );
>
> Angel Pizarro wrote:
>
> > Yes, I have an idea of what is going on ... sloppy copy-paste coding
> > on my part :(
> >
> > I'll add the other columns to the method and get you another patch.
> >
> > -angel
> >
>
>
>
> Index: GUS/DBAdmin/src/java/org/gusdb/dbadmin/model/View.java
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> --- GUS/DBAdmin/src/java/org/gusdb/dbadmin/model/View.java      (revision
> 4068)
> +++ GUS/DBAdmin/src/java/org/gusdb/dbadmin/model/View.java      (working
> copy)
> @@ -48,6 +48,10 @@
>          return column;
>      }
>
> +    public void setColumns( ArrayList<ColumnPair> colpair) {
> +        column =3D colpair;
> +    }
> +
>      public void addColumn( ColumnPair columnPair ) {
>          if ( !this.column.contains( columnPair ) ) {
>              this.column.add( columnPair );
> Index: GUS/DBAdmin/src/java/org/gusdb/dbadmin/writer/PostgresWriter.java
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> --- GUS/DBAdmin/src/java/org/gusdb/dbadmin/writer/PostgresWriter.java
> (revision 4068)
> +++ GUS/DBAdmin/src/java/org/gusdb/dbadmin/writer/PostgresWriter.java
> (working copy)
> @@ -12,6 +12,7 @@
> import org.gusdb.dbadmin.model.GusSchema;
> import org.gusdb.dbadmin.model.GusTable;
> import org.gusdb.dbadmin.model.GusView;
> +import org.gusdb.dbadmin.model.VersionView;
> import org.gusdb.dbadmin.model.Schema;
> import org.gusdb.dbadmin.model.Sequence;
> import org.gusdb.dbadmin.model.Table;
> @@ -105,6 +106,8 @@
>          super.writeView( view );
>          if ( view instanceof GusView ) {
>              writeViewRules( (GusView) view );
> +        }else if ( view instanceof VersionView ) {
> +            writeVersionViewRules( (VersionView) view );
>          }
>      }
>
> @@ -112,8 +115,6 @@
>       * Since PostgreSQL doesn't support updatable views, this is a hack
> that
>       * uses rules to mimick the updatable view functionality.
>       *
> -     * TODO: Note that this means version views are now not updatable
> since they
> -     * don't have a PK.
>       *
>       * @param view DOCUMENT ME!
>       * @throws IOException DOCUMENT ME!
> @@ -174,7 +175,47 @@
>          oStream.flush( );
>      }
>
> +
>      /**
> +     * Since PostgreSQL doesn't support updatable views, this is a hack
> that
> +     * uses rules to mimick the updatable view functionality.
> +     *
> +     * Version views are now not updatable since they
> +     * don't have a PK, so we limit rules to insertion
> +     *
> +     * @param view DOCUMENT ME!
> +     * @throws IOException DOCUMENT ME!
> +     */
> +    private void writeVersionViewRules( VersionView view ) throws
> IOException {
> +        oStream.write( "CREATE RULE " + view.getName( ) + "_" +
> random.nextInt( 100000 ) + " AS ON INSERT TO "
> +                + view.getSchema( ).getName( ) + "." + view.getName( ) +
> " DO INSTEAD INSERT INTO  "
> +                + view.getTable( ).getSchema( ).getName( ) + "." +
> view.getTable( ).getName( ) + " ( " );
> +
> +        boolean first =3D true;
> +        for ( ColumnPair columnPair : view.getColumns() ) {
> +            if ( !first ) {
> +                oStream.write( ", " );
> +            }
> +            oStream.write( columnPair.getTableName( ) );
> +            first =3D false;
> +        }
> +
> +        oStream.write( " ) VALUES ( " );
> +
> +        first =3D true;
> +        for ( ColumnPair columnPair : view.getColumns() ) {
> +            if ( !first ) {
> +                oStream.write( ", " );
> +            }
> +            oStream.write( "new." + columnPair.getViewName( ) );
> +            first =3D false;
> +        }
> +
> +        oStream.write( " );\n\n" );
> +
> +    }
> +
> +    /**
>       * DOCUMENT ME!
>       *
>       * @param type DOCUMENT ME!
> Index:
> GUS/DBAdmin/src/java/org/gusdb/dbadmin/util/GusClassHierarchyConverter.ja=
va
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> ---
> GUS/DBAdmin/src/java/org/gusdb/dbadmin/util/GusClassHierarchyConverter.ja=
va
> (revision 4068)
> +++
> GUS/DBAdmin/src/java/org/gusdb/dbadmin/util/GusClassHierarchyConverter.ja=
va
> (working copy)
> @@ -363,6 +363,9 @@
>              superClassView.setVersioned( true );
>              verSql =3D sql.concat( " " );
>
> +           // We need to add the superclass columns to the version view.
> +           superClassView.getVersionView(
> ).setColumns((ArrayList<ColumnPair>) superClassView.getColumns().clone())=
;
> +
>              for ( Column column : verHousekeepingColumns ) {
>                  verSql =3D verSql.concat( ", " + column.getName( ) );
>                  superClassView.getVersionView( ).addColumn( new
> ColumnPair( column.getName( ), column.getName( ) ) );
> @@ -448,7 +451,8 @@
>          if ( impTable.isVersioned( ) ) {
>              subClass.setVersioned( true );
>              verSql =3D sql.concat( " " );
> -
> +           // We need to add the subclass_view's columns
> +           subClass.getVersionView( ).setColumns((ArrayList<ColumnPair>)
> subClass.getColumns().clone());
>              for ( Column column : verHousekeepingColumns ) {
>                  verSql =3D verSql.concat( ", " + column.getName( ) );
>                  subClass.getVersionView( ).addColumn( new ColumnPair(
> column.getName( ), column.getName( ) ) );
>
>
>

[GUSDEV] parentList definitions in table object layer

[Mark S. H. <mh...@ug...>]

My GUS3.5 DoTS::TranslatedAAFeature_Table has two entries for  
TranslatedAASequence its parentList:

['GUS::Model::DoTS::TranslatedAASequence','aa_sequence_id','aa_sequence_ 
id'],
['GUS::Model::DoTS::TranslatedAASequence','motif_aa_sequence_id','aa_seq 
uence_id']

(there are also many other parent tables defined)

I'm having problems with this definition (while running the  
DoTS::DotsBuild::Plugin::UpdateDotsAssembliesWithCap4 plugin). When a  
new TranslatedAAFeature (taf) is being created as a child of  
TranslatedAASequence (tas) the tas.aa_sequence_id is being passed to  
taf.motif_aa_sequence_id instead of the non-nullable taf.aa_sequence_id

The end result is the error "cannot insert NULL into  
("DOTS"."AAFEATUREIMP"."AA_SEQUENCE_ID")"

If I swap the order of the two TAS parents (or delete the problem  
one) then the TAF child is created fine.

My old GUS3.0  DoTS::TranslatedAAFeature_Table has only one parent  
link to TranslatedAASequence. Why does my GUS3.5 table object define  
multiple parents? (There are multiple parentList entries for other  
tables as well but so far I've only had problems with this one.) Are  
my table constraints mucked up or is there some other problem?


-M

Re: [GUSDEV] Re: [Bug 257] The rules had not been created

[Angel P. <an...@ma...>]

Hi Ricardo,

The error did not stem from my patch, but rather from another class that 
failed to add the none-default columns to the version view objects. I 
have edited a few files, so you will need to revert to current SVN 
version of the repository for this patch to work:
<copy attached file to project home>
cd $PROJECT_HOME
svn revert GUS/DBAdmin
patch -p0 <DBAdmin.diff

Then you should be able to rebuild GUS/DBAdmin and run dbaDump schema as 
before.

An example of the output view and rule follows
-angel


CREATE VIEW DoTSVer.AAFeatureVer AS
SELECT AA_FEATURE_ID, AA_SEQUENCE_ID, FEATURE_NAME_ID, PARENT_ID, 
NA_FEATURE_ID, SUBCLASS_VIEW, SEQUENCE_ONTOLOGY_ID, DESCRIPTION, 
PFAM_ENTRY_ID, MOTIF_AA_SEQUENCE_ID, REPEAT_TYPE_ID, 
EXTERNAL_DATABASE_RELEASE_ID, SOURCE_ID, PREDICTION_ALGORITHM_ID, 
IS_PREDICTED, REVIEW_STATUS_ID , MODIFICATION_DATE, USER_READ, 
USER_WRITE, GROUP_READ, GROUP_WRITE, OTHER_READ, OTHER_WRITE, 
ROW_USER_ID, ROW_GROUP_ID, ROW_PROJECT_ID, ROW_ALG_INVOCATION_ID, 
VERSION_ALG_INVOCATION_ID, VERSION_DATE, VERSION_TRANSACTION_ID FROM 
DoTSVer.AAFeatureImpVer;

CREATE RULE AAFeatureVer_32675 AS ON INSERT TO DoTSVer.AAFeatureVer DO 
INSTEAD INSERT INTO  DoTSVer.AAFeatureImpVer ( AA_FEATURE_ID, 
AA_SEQUENCE_ID, FEATURE_NAME_ID, PARENT_ID, NA_FEATURE_ID, 
SUBCLASS_VIEW, SEQUENCE_ONTOLOGY_ID, DESCRIPTION, PFAM_ENTRY_ID, 
MOTIF_AA_SEQUENCE_ID, REPEAT_TYPE_ID, EXTERNAL_DATABASE_RELEASE_ID, 
SOURCE_ID, PREDICTION_ALGORITHM_ID, IS_PREDICTED, REVIEW_STATUS_ID, 
MODIFICATION_DATE, USER_READ, USER_WRITE, GROUP_READ, GROUP_WRITE, 
OTHER_READ, OTHER_WRITE, ROW_USER_ID, ROW_GROUP_ID, ROW_PROJECT_ID, 
ROW_ALG_INVOCATION_ID, VERSION_ALG_INVOCATION_ID, VERSION_DATE, 
VERSION_TRANSACTION_ID ) VALUES ( new.AA_FEATURE_ID, new.AA_SEQUENCE_ID, 
new.FEATURE_NAME_ID, new.PARENT_ID, new.NA_FEATURE_ID, 
new.SUBCLASS_VIEW, new.SEQUENCE_ONTOLOGY_ID, new.DESCRIPTION, 
new.PFAM_ENTRY_ID, new.MOTIF_AA_SEQUENCE_ID, new.REPEAT_TYPE_ID, 
new.EXTERNAL_DATABASE_RELEASE_ID, new.SOURCE_ID, 
new.PREDICTION_ALGORITHM_ID, new.IS_PREDICTED, new.REVIEW_STATUS_ID, 
new.MODIFICATION_DATE, new.USER_READ, new.USER_WRITE, new.GROUP_READ, 
new.GROUP_WRITE, new.OTHER_READ, new.OTHER_WRITE, new.ROW_USER_ID, 
new.ROW_GROUP_ID, new.ROW_PROJECT_ID, new.ROW_ALG_INVOCATION_ID, 
new.VERSION_ALG_INVOCATION_ID, new.VERSION_DATE, 
new.VERSION_TRANSACTION_ID );

Angel Pizarro wrote:

> Yes, I have an idea of what is going on ... sloppy copy-paste coding 
> on my part :(
>
> I'll add the other columns to the method and get you another patch.
>
> -angel
>

Re: [GUSDEV] Re: [Bug 257] The rules had not been created

[Angel P. <an...@ma...>]

Yes, I have an idea of what is going on ... sloppy copy-paste coding on 
my part :(

I'll add the other columns to the method and get you another patch.

-angel

Ricardo Balbi wrote:

> Angel,
>   I followed all the steps that you indicated me. 
>   I saved the PostgresWriter.diff file that you sent in $PROJECT_HOME.
>   I executed the commands
>     1. patch - p0 < PostgresWriter.diff
>     2. build GUS/DBAdmin install - append
>     3. dbaDumpSchema - sourceType xml - source 
> GusSchema/Definition/config/gus_schema.xml - targetType postgres - 
> target gus.pg.ddl,
>   that generated the gus.pg.ddl file with all the creation of the 
> database. 
>   However, the rules of table versioning had not been created 
> correctly because only some common fields  are involved in the rules 
> (modification_date, user_read, user_write, group_read, group_write, 
> other_read, other_write, row_user_id, row_group_id, row_project_id, 
> row_alg_invocation_id, version_alg_invocation_id, version_date, 
> version_transaction_id). 
>   If the other fields will no be created, errors in the execution of 
> ISF plugin occur when trying to insert null fields. 
>  
>   It follows the example of three bred rules:
>
> CREATE RULE AAFeatureVer_5159 AS ON INSERT TO DoTSVer.AAFeatureVer DO 
> INSTEAD INSERT INTO  DoTSVer.AAFeatureImpVer ( MODIFICATION_DATE, 
> USER_READ, USER_WRITE, GROUP_READ, GROUP_WRITE, OTHER_READ, 
> OTHER_WRITE, ROW_USER_ID, ROW_GROUP_ID, ROW_PROJECT_ID, 
> ROW_ALG_INVOCATION_ID, VERSION_ALG_INVOCATION_ID, VERSION_DATE, 
> VERSION_TRANSACTION_ID ) VALUES ( new.MODIFICATION_DATE, 
> new.USER_READ, new.USER_WRITE, new.GROUP_READ, new.GROUP_WRITE, 
> new.OTHER_READ, new.OTHER_WRITE, new.ROW_USER_ID, new.ROW_GROUP_ID, 
> new.ROW_PROJECT_ID, new.ROW_ALG_INVOCATION_ID, 
> new.VERSION_ALG_INVOCATION_ID, new.VERSION_DATE, 
> new.VERSION_TRANSACTION_ID );
>
> CREATE RULE AffymetrixCELVer_10403 AS ON INSERT TO 
> RADVer.AffymetrixCELVer DO INSTEAD INSERT INTO  
> RADVer.ElementResultImpVer ( MODIFICATION_DATE, USER_READ, USER_WRITE, 
> GROUP_READ, GROUP_WRITE, OTHER_READ, OTHER_WRITE, ROW_USER_ID, 
> ROW_GROUP_ID, ROW_PROJECT_ID, ROW_ALG_INVOCATION_ID, 
> VERSION_ALG_INVOCATION_ID, VERSION_DATE, VERSION_TRANSACTION_ID ) 
> VALUES ( new.MODIFICATION_DATE, new.USER_READ, new.USER_WRITE, 
> new.GROUP_READ, new.GROUP_WRITE, new.OTHER_READ, new.OTHER_WRITE, 
> new.ROW_USER_ID, new.ROW_GROUP_ID, new.ROW_PROJECT_ID, 
> new.ROW_ALG_INVOCATION_ID, new.VERSION_ALG_INVOCATION_ID, 
> new.VERSION_DATE, new.VERSION_TRANSACTION_ID );
>
> CREATE RULE BioSourceVer_45682 AS ON INSERT TO StudyVer.BioSourceVer 
> DO INSTEAD INSERT INTO  StudyVer.BioMaterialImpVer ( 
> MODIFICATION_DATE, USER_READ, USER_WRITE, GROUP_READ, GROUP_WRITE, 
> OTHER_READ, OTHER_WRITE, ROW_USER_ID, ROW_GROUP_ID, ROW_PROJECT_ID, 
> ROW_ALG_INVOCATION_ID, VERSION_ALG_INVOCATION_ID, VERSION_DATE, 
> VERSION_TRANSACTION_ID ) VALUES ( new.MODIFICATION_DATE, 
> new.USER_READ, new.USER_WRITE, new.GROUP_READ, new.GROUP_WRITE, 
> new.OTHER_READ, new.OTHER_WRITE, new.ROW_USER_ID, new.ROW_GROUP_ID, 
> new.ROW_PROJECT_ID, new.ROW_ALG_INVOCATION_ID, 
> new.VERSION_ALG_INVOCATION_ID, new.VERSION_DATE, 
> new.VERSION_TRANSACTION_ID );
>
>   Do you have any idea why this is happening ?
>
> Thanks in advance,
> Ricardo
>
> 2006/1/10, Angel Pizarro <an...@ma... 
> <mailto:an...@ma...>>:
>
>     Hi Ricardo,
>     I imagine that Mike has not had a chance to get to this, so I took a
>     stab at fixing this problem. Could you test out the attached
>     patch? Copy
>     the file to $PROJECT_HOME then:
>
>     cd $PROJECT_HOME
>     patch -p0 <PostgresWriter.diff
>
>     Then rebuild the GUS/DBAdmin project and redump the schema from
>     the XML
>     schema file:
>
>     build GUS/DBAdmin install -append
>     dbaDumpSchema -sourceType xml -source
>     GusSchema/Definition/config/gus_schema.xml -targetType postgres
>     -target
>     gus.pg.ddl
>
>     That should produce the proper PostgreSQL ddl from which you can grep
>     the version views and test the loads. If your tests are
>     successful, I'll
>     commit the file and post the patch on the bug.
>
>     -angel
>
>     Ricardo Balbi wrote:
>
>     > Mike / Steve,
>     >   We would like to know if you already had created the rules of the
>     > version tables.
>     >   We believe that with these rules we will go to obtain the loads,
>     > using the ISF.
>     >   In case that you have some position, you he could inform to
>     me, please.
>     >
>     > thanks in advance,
>     > Ricardo
>     >
>     > 2006/1/3, bug...@pc...
>     <mailto:bug...@pc...>
>     > <mailto:bug...@pc...
>     <mailto:bug...@pc...>>
>     > <bug...@pc...
>     <mailto:bug...@pc...>
>     <mailto:bug...@pc...
>     <mailto:bug...@pc...>>>:
>     >
>     >     https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=257
>     <https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=257>
>     >     <https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=257>
>     >
>     >
>     >     msa...@pc... <mailto:msa...@pc...>
>     <mailto:msa...@pc... <mailto:msa...@pc...>>
>     changed:
>     >
>     >                What    |Removed                     |Added
>     >    
>     ----------------------------------------------------------------------------
>     >                  Status|RESOLVED                    |REOPENED
>     >              Resolution|INVALID                     |
>     >
>     >
>     >
>     >
>     >     ------- Comment #4 from msa...@pc...
>     <mailto:msa...@pc...>
>     >     <mailto:msa...@pc...
>     <mailto:msa...@pc...>>  2006-01-03 12:05 -------
>     >     version table rules are indeed not being created.  this
>     should be
>     >     relatively
>     >     straight forward to fix.
>     >
>     >
>     >     --
>     >     Configure bugmail:
>     >     https://www.cbil.upenn.edu/tracker/userprefs.cgi?tab=email
>     >     ------- You are receiving this mail because: -------
>     >     You reported the bug, or are watching the reporter.
>     >
>     >
>
>
>     --
>
>     Angel Pizarro
>     Director, Bioinformatics Facility
>     Institute for Translational Medicine and Therapeutics
>     University of Pennsylvania
>     806 BRB II/III
>     421 Curie Blvd.
>     Philadelphia, PA 19104-6160
>
>     P: 215-573-3736
>     F: 215-573-9004
>
>
>
>     Index:
>     GUS/DBAdmin/src/java/org/gusdb/dbadmin/writer/PostgresWriter.java
>     ===================================================================
>     ---
>     GUS/DBAdmin/src/java/org/gusdb/dbadmin/writer/PostgresWriter.java  
>     (revision 4068)
>     +++
>     GUS/DBAdmin/src/java/org/gusdb/dbadmin/writer/PostgresWriter.java  
>     (working copy)
>     @@ -12,6 +12,7 @@
>     import org.gusdb.dbadmin.model.GusSchema;
>     import org.gusdb.dbadmin.model.GusTable;
>     import org.gusdb.dbadmin.model.GusView ;
>     +import org.gusdb.dbadmin.model.VersionView;
>     import org.gusdb.dbadmin.model.Schema;
>     import org.gusdb.dbadmin.model.Sequence;
>     import org.gusdb.dbadmin.model.Table;
>     @@ -105,6 +106,8 @@
>              super.writeView ( view );
>              if ( view instanceof GusView ) {
>                  writeViewRules( (GusView) view );
>     +        }else if ( view instanceof VersionView ) {
>     +            writeVersionViewRules( (VersionView) view );
>              }
>          }
>
>     @@ -112,8 +115,6 @@
>           * Since PostgreSQL doesn't support updatable views, this is
>     a hack that
>           * uses rules to mimick the updatable view functionality.
>           *
>     -     * TODO: Note that this means version views are now not
>     updatable since they
>     -     * don't have a PK.
>           *
>           * @param view DOCUMENT ME!
>           * @throws IOException DOCUMENT ME!
>     @@ -174,7 +175,47 @@
>              oStream.flush( );
>          }
>
>     +
>          /**
>     +     * Since PostgreSQL doesn't support updatable views, this is
>     a hack that
>     +     * uses rules to mimick the updatable view functionality.
>     +     *
>     +     * Version views are now not updatable since they
>     +     * don't have a PK, so we limit rules to insertion
>     +     *
>     +     * @param view DOCUMENT ME!
>     +     * @throws IOException DOCUMENT ME!
>     +     */
>     +    private void writeVersionViewRules( VersionView view ) throws
>     IOException {
>     +        oStream.write( "CREATE RULE " + view.getName( ) + "_" +
>     random.nextInt( 100000 ) + " AS ON INSERT TO "
>     +                + view.getSchema( ).getName( ) + "." +
>     view.getName( ) + " DO INSTEAD INSERT INTO  "
>     +                + view.getTable( ).getSchema( ).getName( ) + "."
>     + view.getTable( ).getName( ) + " ( " );
>     +
>     +        boolean first = true;
>     +        for ( ColumnPair columnPair : view.getColumns() ) {
>     +            if ( !first ) {
>     +                oStream.write( ", " );
>     +            }
>     +            oStream.write( columnPair.getTableName( ) );
>     +            first = false;
>     +        }
>     +
>     +        oStream.write( " ) VALUES ( " );
>     +
>     +        first = true;
>     +        for ( ColumnPair columnPair : view.getColumns() ) {
>     +            if ( !first ) {
>     +                oStream.write( ", " );
>     +            }
>     +            oStream.write( "new." + columnPair.getViewName( ) );
>     +            first = false;
>     +        }
>     +
>     +        oStream.write( " );\n\n" );
>     +
>     +    }
>     +
>     +    /**
>           * DOCUMENT ME!
>           *
>           * @param type DOCUMENT ME!
>
>
>

Re: [GUSDEV] Re: [Bug 257] The rules had not been created

[Ricardo B. <rb...@gm...>]

Angel,
  I followed all the steps that you indicated me.
  I saved the PostgresWriter.diff file that you sent in $PROJECT_HOME.
  I executed the commands
    1. patch - p0 < PostgresWriter.diff
    2. build GUS/DBAdmin install - append
    3. dbaDumpSchema - sourceType xml - source
GusSchema/Definition/config/gus_schema.xml - targetType postgres - target
gus.pg.ddl,
  that generated the gus.pg.ddl file with all the creation of the database.

  However, the rules of table versioning had not been created correctly
because only some common fields  are involved in the rules
(modification_date, user_read, user_write, group_read, group_write,
other_read, other_write, row_user_id, row_group_id, row_project_id,
row_alg_invocation_id, version_alg_invocation_id, version_date,
version_transaction_id).
  If the other fields will no be created, errors in the execution of ISF
plugin occur when trying to insert null fields.

  It follows the example of three bred rules:

CREATE RULE AAFeatureVer_5159 AS ON INSERT TO DoTSVer.AAFeatureVer DO
INSTEAD INSERT INTO  DoTSVer.AAFeatureImpVer ( MODIFICATION_DATE, USER_READ=
,
USER_WRITE, GROUP_READ, GROUP_WRITE, OTHER_READ, OTHER_WRITE, ROW_USER_ID,
ROW_GROUP_ID, ROW_PROJECT_ID, ROW_ALG_INVOCATION_ID,
VERSION_ALG_INVOCATION_ID, VERSION_DATE, VERSION_TRANSACTION_ID ) VALUES (
new.MODIFICATION_DATE, new.USER_READ, new.USER_WRITE, new.GROUP_READ,
new.GROUP_WRITE, new.OTHER_READ, new.OTHER_WRITE, new.ROW_USER_ID,
new.ROW_GROUP_ID, new.ROW_PROJECT_ID, new.ROW_ALG_INVOCATION_ID,
new.VERSION_ALG_INVOCATION_ID, new.VERSION_DATE, new.VERSION_TRANSACTION_ID=
);

CREATE RULE AffymetrixCELVer_10403 AS ON INSERT TO
RADVer.AffymetrixCELVerDO INSTEAD INSERT INTO
RADVer.ElementResultImpVer ( MODIFICATION_DATE, USER_READ, USER_WRITE,
GROUP_READ, GROUP_WRITE, OTHER_READ, OTHER_WRITE, ROW_USER_ID, ROW_GROUP_ID=
,
ROW_PROJECT_ID, ROW_ALG_INVOCATION_ID, VERSION_ALG_INVOCATION_ID,
VERSION_DATE, VERSION_TRANSACTION_ID ) VALUES ( new.MODIFICATION_DATE,
new.USER_READ, new.USER_WRITE, new.GROUP_READ, new.GROUP_WRITE,
new.OTHER_READ, new.OTHER_WRITE, new.ROW_USER_ID, new.ROW_GROUP_ID,
new.ROW_PROJECT_ID, new.ROW_ALG_INVOCATION_ID, new.VERSION_ALG_INVOCATION_I=
D,
new.VERSION_DATE, new.VERSION_TRANSACTION_ID );

CREATE RULE BioSourceVer_45682 AS ON INSERT TO StudyVer.BioSourceVer DO
INSTEAD INSERT INTO  StudyVer.BioMaterialImpVer ( MODIFICATION_DATE,
USER_READ, USER_WRITE, GROUP_READ, GROUP_WRITE, OTHER_READ, OTHER_WRITE,
ROW_USER_ID, ROW_GROUP_ID, ROW_PROJECT_ID, ROW_ALG_INVOCATION_ID,
VERSION_ALG_INVOCATION_ID, VERSION_DATE, VERSION_TRANSACTION_ID ) VALUES (
new.MODIFICATION_DATE, new.USER_READ, new.USER_WRITE, new.GROUP_READ,
new.GROUP_WRITE, new.OTHER_READ, new.OTHER_WRITE, new.ROW_USER_ID,
new.ROW_GROUP_ID, new.ROW_PROJECT_ID, new.ROW_ALG_INVOCATION_ID,
new.VERSION_ALG_INVOCATION_ID, new.VERSION_DATE, new.VERSION_TRANSACTION_ID=
);

  Do you have any idea why this is happening ?

Thanks in advance,
Ricardo

2006/1/10, Angel Pizarro <an...@ma...>:
>
> Hi Ricardo,
> I imagine that Mike has not had a chance to get to this, so I took a
> stab at fixing this problem. Could you test out the attached patch? Copy
> the file to $PROJECT_HOME then:
>
> cd $PROJECT_HOME
> patch -p0 <PostgresWriter.diff
>
> Then rebuild the GUS/DBAdmin project and redump the schema from the XML
> schema file:
>
> build GUS/DBAdmin install -append
> dbaDumpSchema -sourceType xml -source
> GusSchema/Definition/config/gus_schema.xml -targetType postgres -target
> gus.pg.ddl
>
> That should produce the proper PostgreSQL ddl from which you can grep
> the version views and test the loads. If your tests are successful, I'll
> commit the file and post the patch on the bug.
>
> -angel
>
> Ricardo Balbi wrote:
>
> > Mike / Steve,
> >   We would like to know if you already had created the rules of the
> > version tables.
> >   We believe that with these rules we will go to obtain the loads,
> > using the ISF.
> >   In case that you have some position, you he could inform to me,
> please.
> >
> > thanks in advance,
> > Ricardo
> >
> > 2006/1/3, bug...@pc...
> > <mailto:bug...@pc...>
> > <bug...@pc... <mailto:bug...@pc...
> >>:
> >
> >     https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=3D257
> >     <https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=3D257>
> >
> >
> >     msa...@pc... <mailto:msa...@pc...> changed:
> >
> >                What    |Removed                     |Added
> >
> -------------------------------------------------------------------------=
---
> >                  Status|RESOLVED                    |REOPENED
> >              Resolution|INVALID                     |
> >
> >
> >
> >
> >     ------- Comment #4 from msa...@pc...
> >     <mailto:msa...@pc...>  2006-01-03 12:05 -------
> >     version table rules are indeed not being created.  this should be
> >     relatively
> >     straight forward to fix.
> >
> >
> >     --
> >     Configure bugmail:
> >     https://www.cbil.upenn.edu/tracker/userprefs.cgi?tab=3Demail
> >     ------- You are receiving this mail because: -------
> >     You reported the bug, or are watching the reporter.
> >
> >
>
>
> --
>
> Angel Pizarro
> Director, Bioinformatics Facility
> Institute for Translational Medicine and Therapeutics
> University of Pennsylvania
> 806 BRB II/III
> 421 Curie Blvd.
> Philadelphia, PA 19104-6160
>
> P: 215-573-3736
> F: 215-573-9004
>
>
>
> Index: GUS/DBAdmin/src/java/org/gusdb/dbadmin/writer/PostgresWriter.java
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> --- GUS/DBAdmin/src/java/org/gusdb/dbadmin/writer/PostgresWriter.java
> (revision 4068)
> +++ GUS/DBAdmin/src/java/org/gusdb/dbadmin/writer/PostgresWriter.java
> (working copy)
> @@ -12,6 +12,7 @@
> import org.gusdb.dbadmin.model.GusSchema;
> import org.gusdb.dbadmin.model.GusTable;
> import org.gusdb.dbadmin.model.GusView;
> +import org.gusdb.dbadmin.model.VersionView;
> import org.gusdb.dbadmin.model.Schema;
> import org.gusdb.dbadmin.model.Sequence;
> import org.gusdb.dbadmin.model.Table;
> @@ -105,6 +106,8 @@
>          super.writeView( view );
>          if ( view instanceof GusView ) {
>              writeViewRules( (GusView) view );
> +        }else if ( view instanceof VersionView ) {
> +            writeVersionViewRules( (VersionView) view );
>          }
>      }
>
> @@ -112,8 +115,6 @@
>       * Since PostgreSQL doesn't support updatable views, this is a hack
> that
>       * uses rules to mimick the updatable view functionality.
>       *
> -     * TODO: Note that this means version views are now not updatable
> since they
> -     * don't have a PK.
>       *
>       * @param view DOCUMENT ME!
>       * @throws IOException DOCUMENT ME!
> @@ -174,7 +175,47 @@
>          oStream.flush( );
>      }
>
> +
>      /**
> +     * Since PostgreSQL doesn't support updatable views, this is a hack
> that
> +     * uses rules to mimick the updatable view functionality.
> +     *
> +     * Version views are now not updatable since they
> +     * don't have a PK, so we limit rules to insertion
> +     *
> +     * @param view DOCUMENT ME!
> +     * @throws IOException DOCUMENT ME!
> +     */
> +    private void writeVersionViewRules( VersionView view ) throws
> IOException {
> +        oStream.write( "CREATE RULE " + view.getName( ) + "_" +
> random.nextInt( 100000 ) + " AS ON INSERT TO "
> +                + view.getSchema( ).getName( ) + "." + view.getName( ) +
> " DO INSTEAD INSERT INTO  "
> +                + view.getTable( ).getSchema( ).getName( ) + "." +
> view.getTable( ).getName( ) + " ( " );
> +
> +        boolean first =3D true;
> +        for ( ColumnPair columnPair : view.getColumns() ) {
> +            if ( !first ) {
> +                oStream.write( ", " );
> +            }
> +            oStream.write( columnPair.getTableName( ) );
> +            first =3D false;
> +        }
> +
> +        oStream.write( " ) VALUES ( " );
> +
> +        first =3D true;
> +        for ( ColumnPair columnPair : view.getColumns() ) {
> +            if ( !first ) {
> +                oStream.write( ", " );
> +            }
> +            oStream.write( "new." + columnPair.getViewName( ) );
> +            first =3D false;
> +        }
> +
> +        oStream.write( " );\n\n" );
> +
> +    }
> +
> +    /**
>       * DOCUMENT ME!
>       *
>       * @param type DOCUMENT ME!
>
>
>

Re: [GUSDEV] Re: [Bug 257] The rules had not been created

[Angel P. <an...@ma...>]

Hi Ricardo,
I imagine that Mike has not had a chance to get to this, so I took a 
stab at fixing this problem. Could you test out the attached patch? Copy 
the file to $PROJECT_HOME then:

cd $PROJECT_HOME
patch -p0 <PostgresWriter.diff

Then rebuild the GUS/DBAdmin project and redump the schema from the XML 
schema file:

build GUS/DBAdmin install -append
dbaDumpSchema -sourceType xml -source  
GusSchema/Definition/config/gus_schema.xml -targetType postgres -target 
gus.pg.ddl

That should produce the proper PostgreSQL ddl from which you can grep 
the version views and test the loads. If your tests are successful, I'll 
commit the file and post the patch on the bug.

-angel

Ricardo Balbi wrote:

> Mike / Steve,
>   We would like to know if you already had created the rules of the 
> version tables. 
>   We believe that with these rules we will go to obtain the loads, 
> using the ISF. 
>   In case that you have some position, you he could inform to me, please.
>
> thanks in advance,
> Ricardo
>
> 2006/1/3, bug...@pc... 
> <mailto:bug...@pc...> 
> <bug...@pc... <mailto:bug...@pc...>>:
>
>     https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=257
>     <https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=257>
>
>
>     msa...@pc... <mailto:msa...@pc...> changed:
>
>                What    |Removed                     |Added
>     ----------------------------------------------------------------------------
>                  Status|RESOLVED                    |REOPENED
>              Resolution|INVALID                     |
>
>
>
>
>     ------- Comment #4 from msa...@pc...
>     <mailto:msa...@pc...>  2006-01-03 12:05 -------
>     version table rules are indeed not being created.  this should be
>     relatively
>     straight forward to fix.
>
>
>     --
>     Configure bugmail:
>     https://www.cbil.upenn.edu/tracker/userprefs.cgi?tab=email
>     ------- You are receiving this mail because: -------
>     You reported the bug, or are watching the reporter.
>
>


-- 

Angel Pizarro
Director, Bioinformatics Facility
Institute for Translational Medicine and Therapeutics
University of Pennsylvania
806 BRB II/III
421 Curie Blvd.
Philadelphia, PA 19104-6160

P: 215-573-3736
F: 215-573-9004