gusdev-gusdev — Topics concerning GUS development

[GUSDEV] Problems with post installation setup

[Kamen N. <kan...@gm...>]

Hi everybody,

I'm new to GUS and need some help. I'm trying to start loading data in
e new installation of GUS 3.5 on Oracle 10 but I'm getting an error
message when I run:
                  ga +meta --commit
This is the error I get:
No row in Core.GroupInfo has a name =3D 'group'.  This value was found
in the group=3D property of your .gus.properties file.  Please be sure
it is correct and has been registered in the database at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
878.

I can't register PluginMgr or any other plugin. Here's errors I get:=20

USER ERROR: GUS::PluginMgr::GusApplication has never been registered.
Please use 'ga +create GUS::PluginMgr::GusApplication --commit'
[knikolov@blinky gus]$ ga +create GUS::PluginMgr::GusApplication --commit
=20
USER ERROR: GUS::PluginMgr::GusApplication has never been registered.
Please use 'ga +create GUS::PluginMgr::GusApplication --commit'

If anyone has had similar problems or has any suggestions I would
apreciate any help.

 Thank you,

 Kamen Nikolov

Re: [GUSDEV] GeneticMarker view

[Deborah P. <pi...@pc...>]

Steve Fischer wrote:

> i am not sure i like the idea of stuffing multiple aliases into one row.


I agree but it is a way to keep the data if desired  and is searchable 
and would not require a new table, GeneticMarkerSynonym, as I wanted to 
use the view right away. We have several synonym tables as 
GeneSynonym,MoietySynonym, and ProteinSynonym and a couple others.  I 
would propose an all-purpose table of synonyms  but I thought we were 
very negative about tables with soft-links. At any rate that is a 
discussion for a release.


>
> steve
>
> Deborah Pinney wrote:
>
>> Aaron J. Mackey wrote:
>>
>>> A few notes/thoughts on the proposal:
>>>
>>> Why would a genetic marker be considered a sequence?   I guess you  
>>> instead meant a view of dots.NaFeatureImp?
>>
>>
>>
>>
>> Yes I mistyped in the note, the view definition was  "FROM 
>> DoTS.NAFeatureImp WHERE subclass_view='GeneticMarker' ".
>>
>>>
>>> The relationships between a given set of markers are defined  
>>> genetically (i.e. as linked loci with genetic distances measured in  
>>> centiMorgans) with respect to a single genetic map (which 
>>> corresponds  to a specific set of experimental crosses or an 
>>> observed pedigree).   The same two markers may have different 
>>> distances (or even be  unlinked) in a different map.
>>
>>
>>
>> Not all genetic marker sets are defined strictly genetically. When 
>> location is a physical location on a sequence, this information can 
>> be captured in the dots.nalocation table and a marker can have 
>> multiple locations. When location is defined genetically in the 
>> stricter sense, capturing the information is not as straight forward 
>> but can be done using the same view and nalocation (note that there 
>> is a linkage_group attribute in the proposed view as well as an 
>> external_database_release_id) and a  marker can be represented by 
>> more than one row in the nafeature view.
>>
>>>
>>> A markers phenotype is often only its physical definition: SNP, 
>>> SSLP,  SSCP, RFLP, etc.  Is this what the SO term is supposed to 
>>> capture?   If so, what is the "type" field meant to capture?
>>
>>
>>
>>
>> No, type was intended to capture the kind of marker represented in 
>> the row as the ones you mention as well as markers not necessarily in 
>> SO as blood groups or allozymes. The sequence_ontology_id is there 
>> because all nafeature views have this attribute and of course it can 
>> be used in the case where there is an approrpriate 
>> sequenceontology.term_name.
>>
>>>
>>> As mentioned elsewhere, organism/strain should probably be a single  
>>> foreign key into the taxonomy table.
>>
>>
>>
>> Yes, I agreed with Chris and this was dropped.
>>
>>>
>>> Measures of heterogeneity and penetrance are also specific to a 
>>> given  population study, and are not universally true.  I could 
>>> imagine  these and other attributes of a given study being captured  
>>> independently.  This will be an important area of growth in the 
>>> next  10 years as widescale familial genotyping becomes more prevalent.
>>
>>
>>
>>
>> These are nullable so not required from every study. Perhaps we don't 
>> want these attributes and they can be eliminated. The data I intended 
>> to load don't have these values but this is only one example and 
>> these are values often associated with markers.
>>
>>>
>>>
>>> Markers may have multiple aliases.
>>
>>
>>
>>
>> Yes, this is true. We can decide not to enter a value into this 
>> attribute as it is nullable or we can have a list as the attribute is 
>> a varchar2(1000).
>>
>>>
>>>
>>> Thanks,
>>>
>>> -Aaron
>>>
>>> On Aug 23, 2005, at 12:49 PM, Deborah Pinney wrote:
>>>
>>>> I suggest a new view of dots.NaSequenceImp that would be used to  
>>>> store genetic marker data. Genetic markers are a staple genetic  
>>>> tool but include a large variety of data types, some of which may  
>>>> be covered by other feature views. I am proposing this view for 
>>>> the  variety of genetic marker data that are not specifically 
>>>> stored  elsewhere. Below is a proposed view definition that 
>>>> requires review  and probably modification.
>>>>
>>>> SELECT NA_Feature_ID as na_feature_id,
>>>> NA_SEQUENCE_ID as na_sequence_id,
>>>> SUBCLASS_VIEW as subclass_view,
>>>> NAME as name,
>>>> SEQUENCE_ONTOLOGY_ID as sequence_ontology_id,
>>>> PARENT_ID as parent_id,
>>>> EXTERNAL_DATABASE_RELEASE_ID as external_database_release_id,
>>>> SOURCE_ID as source_id,
>>>> PREDICTION_ALGORITHM_ID as prediction_algorithm_id,
>>>> IS_PREDICTED as is_predicted,
>>>> REVIEW_STATUS_ID as review_status_id,
>>>> STRING1 as alias,
>>>> STRING2 as phenotype,
>>>> STRING3 as type,
>>>> STRING4 as linkage_group,
>>>> STRING5 as centimorgan,
>>>> STRING6 as measure_of_heterogeneity,
>>>> STRING7 as penetrance,
>>>> STRING8 as organism,
>>>> STRING9 as strain,
>>>> STRING12 as product,
>>>> MODIFICATION_DATE as modification_date,
>>>> USER_READ as user_read,
>>>> USER_WRITE as user_write,
>>>> GROUP_READ as group_read,
>>>> GROUP_WRITE as group_write,
>>>> OTHER_READ as other_read,
>>>> OTHER_WRITE as other_write,
>>>> ROW_USER_ID as row_user_id,
>>>> ROW_GROUP_ID as row_group_id,
>>>> ROW_PROJECT_ID as row_project_id,
>>>> ROW_ALG_INVOCATION_ID as row_alg_invocation_id,
>>>> FROM DoTS.NAFeatureImp WHERE subclass_view='GeneticMarker'
>>>>
>>>>
>>>>
>>>> -------------------------------------------------------
>>>> SF.Net email is Sponsored by the Better Software Conference & EXPO
>>>> September 19-22, 2005 * San Francisco, CA * Development Lifecycle  
>>>> Practices
>>>> Agile & Plan-Driven Development * Managing Projects & Teams *  
>>>> Testing & QA
>>>> Security * Process Improvement & Measurement * http://www.sqe.com/ 
>>>> bsce5sf
>>>> _______________________________________________
>>>> Gusdev-gusdev mailing list
>>>> Gus...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>
>>> -- 
>>> Aaron J. Mackey, Ph.D.
>>> Project Manager, ApiDB Bioinformatics Resource Center
>>> Penn Genomics Institute, University of Pennsylvania
>>> email:  am...@pc...
>>> office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI)
>>> fax:    215-746-6697
>>> postal: Penn Genomics Institute
>>>         Goddard Labs 212
>>>         415 S. University Avenue
>>>         Philadelphia, PA  19104-6017
>>>
>>
>>
>>
>> -------------------------------------------------------
>> SF.Net email is Sponsored by the Better Software Conference & EXPO
>> September 19-22, 2005 * San Francisco, CA * Development Lifecycle 
>> Practices
>> Agile & Plan-Driven Development * Managing Projects & Teams * Testing 
>> & QA
>> Security * Process Improvement & Measurement * 
>> http://www.sqe.com/bsce5sf
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

[GUSDEV] Working revisions?

[<hen...@gm...>]

Hi everyone,


I'm trying to use LoadNRDB (rev. 2976)from GUS::Supported::Plugins.
Before starting to use it, I decided to update it to the current
version (rev. 3115). But when trying to update it (w/ 'ga +update ....
--commit'), I got the following message:

"[juca@desterrensis Plugin]$ ga +update
GUS::Supported::Plugin::LoadNRDB --commit

The plugin has an illegal cvs revision: '$Revision$'.  If that doesn't
include a revision number, then the plugin has never been checked into
CVS.  Please do so to give it an intial revision at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line 347."

I saw the the $Id:$ line from the newest revision was empty in
comparison the older revision that I'm using (in rv. 2976 the line was
'$Id: LoadNRDB.pm 2976 2005-06-20 19:26:19Z jldommer $'). Is the
latest (of all GUS) revision working? And if it is, how do I "give it
a initial revision" (if I'm the one who has to do it)?


Thanks,

--=20
Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br

"As soon as you concern yourself with the "good" and "bad" of your fellows,=
=20
you create an opening in your heart for maliciousness to enter. Testing,=20
competing with, and criticizing others weaken and defeat you."

Morihei Ueshiba, O-Sensei (1883-1969)

[GUSDEV] Unsubscribe list

[Poliana M. <pol...@gm...>]

--=20
Poliana G. M. Ojeda

Re: [GUSDEV] GeneticMarker view

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

i am not sure i like the idea of stuffing multiple aliases into one row.

steve

Deborah Pinney wrote:

> Aaron J. Mackey wrote:
>
>> A few notes/thoughts on the proposal:
>>
>> Why would a genetic marker be considered a sequence?   I guess you  
>> instead meant a view of dots.NaFeatureImp?
>
>
>
> Yes I mistyped in the note, the view definition was  "FROM 
> DoTS.NAFeatureImp WHERE subclass_view='GeneticMarker' ".
>
>>
>> The relationships between a given set of markers are defined  
>> genetically (i.e. as linked loci with genetic distances measured in  
>> centiMorgans) with respect to a single genetic map (which 
>> corresponds  to a specific set of experimental crosses or an observed 
>> pedigree).   The same two markers may have different distances (or 
>> even be  unlinked) in a different map.
>
>
> Not all genetic marker sets are defined strictly genetically. When 
> location is a physical location on a sequence, this information can be 
> captured in the dots.nalocation table and a marker can have multiple 
> locations. When location is defined genetically in the stricter sense, 
> capturing the information is not as straight forward but can be done 
> using the same view and nalocation (note that there is a linkage_group 
> attribute in the proposed view as well as an 
> external_database_release_id) and a  marker can be represented by more 
> than one row in the nafeature view.
>
>>
>> A markers phenotype is often only its physical definition: SNP, 
>> SSLP,  SSCP, RFLP, etc.  Is this what the SO term is supposed to 
>> capture?   If so, what is the "type" field meant to capture?
>
>
>
> No, type was intended to capture the kind of marker represented in the 
> row as the ones you mention as well as markers not necessarily in SO 
> as blood groups or allozymes. The sequence_ontology_id is there 
> because all nafeature views have this attribute and of course it can 
> be used in the case where there is an approrpriate 
> sequenceontology.term_name.
>
>>
>> As mentioned elsewhere, organism/strain should probably be a single  
>> foreign key into the taxonomy table.
>
>
> Yes, I agreed with Chris and this was dropped.
>
>>
>> Measures of heterogeneity and penetrance are also specific to a 
>> given  population study, and are not universally true.  I could 
>> imagine  these and other attributes of a given study being captured  
>> independently.  This will be an important area of growth in the next  
>> 10 years as widescale familial genotyping becomes more prevalent.
>
>
>
> These are nullable so not required from every study. Perhaps we don't 
> want these attributes and they can be eliminated. The data I intended 
> to load don't have these values but this is only one example and these 
> are values often associated with markers.
>
>>
>>
>> Markers may have multiple aliases.
>
>
>
> Yes, this is true. We can decide not to enter a value into this 
> attribute as it is nullable or we can have a list as the attribute is 
> a varchar2(1000).
>
>>
>>
>> Thanks,
>>
>> -Aaron
>>
>> On Aug 23, 2005, at 12:49 PM, Deborah Pinney wrote:
>>
>>> I suggest a new view of dots.NaSequenceImp that would be used to  
>>> store genetic marker data. Genetic markers are a staple genetic  
>>> tool but include a large variety of data types, some of which may  
>>> be covered by other feature views. I am proposing this view for the  
>>> variety of genetic marker data that are not specifically stored  
>>> elsewhere. Below is a proposed view definition that requires review  
>>> and probably modification.
>>>
>>> SELECT NA_Feature_ID as na_feature_id,
>>> NA_SEQUENCE_ID as na_sequence_id,
>>> SUBCLASS_VIEW as subclass_view,
>>> NAME as name,
>>> SEQUENCE_ONTOLOGY_ID as sequence_ontology_id,
>>> PARENT_ID as parent_id,
>>> EXTERNAL_DATABASE_RELEASE_ID as external_database_release_id,
>>> SOURCE_ID as source_id,
>>> PREDICTION_ALGORITHM_ID as prediction_algorithm_id,
>>> IS_PREDICTED as is_predicted,
>>> REVIEW_STATUS_ID as review_status_id,
>>> STRING1 as alias,
>>> STRING2 as phenotype,
>>> STRING3 as type,
>>> STRING4 as linkage_group,
>>> STRING5 as centimorgan,
>>> STRING6 as measure_of_heterogeneity,
>>> STRING7 as penetrance,
>>> STRING8 as organism,
>>> STRING9 as strain,
>>> STRING12 as product,
>>> MODIFICATION_DATE as modification_date,
>>> USER_READ as user_read,
>>> USER_WRITE as user_write,
>>> GROUP_READ as group_read,
>>> GROUP_WRITE as group_write,
>>> OTHER_READ as other_read,
>>> OTHER_WRITE as other_write,
>>> ROW_USER_ID as row_user_id,
>>> ROW_GROUP_ID as row_group_id,
>>> ROW_PROJECT_ID as row_project_id,
>>> ROW_ALG_INVOCATION_ID as row_alg_invocation_id,
>>> FROM DoTS.NAFeatureImp WHERE subclass_view='GeneticMarker'
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> SF.Net email is Sponsored by the Better Software Conference & EXPO
>>> September 19-22, 2005 * San Francisco, CA * Development Lifecycle  
>>> Practices
>>> Agile & Plan-Driven Development * Managing Projects & Teams *  
>>> Testing & QA
>>> Security * Process Improvement & Measurement * http://www.sqe.com/ 
>>> bsce5sf
>>> _______________________________________________
>>> Gusdev-gusdev mailing list
>>> Gus...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>
>> -- 
>> Aaron J. Mackey, Ph.D.
>> Project Manager, ApiDB Bioinformatics Resource Center
>> Penn Genomics Institute, University of Pennsylvania
>> email:  am...@pc...
>> office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI)
>> fax:    215-746-6697
>> postal: Penn Genomics Institute
>>         Goddard Labs 212
>>         415 S. University Avenue
>>         Philadelphia, PA  19104-6017
>>
>
>
>
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle 
> Practices
> Agile & Plan-Driven Development * Managing Projects & Teams * Testing 
> & QA
> Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [GUSDEV] GeneticMarker view

[Deborah P. <pi...@pc...>]

Aaron J. Mackey wrote:

> A few notes/thoughts on the proposal:
>
> Why would a genetic marker be considered a sequence?   I guess you  
> instead meant a view of dots.NaFeatureImp?


Yes I mistyped in the note, the view definition was  "FROM 
DoTS.NAFeatureImp WHERE subclass_view='GeneticMarker' ".

>
> The relationships between a given set of markers are defined  
> genetically (i.e. as linked loci with genetic distances measured in  
> centiMorgans) with respect to a single genetic map (which corresponds  
> to a specific set of experimental crosses or an observed pedigree).   
> The same two markers may have different distances (or even be  
> unlinked) in a different map.

Not all genetic marker sets are defined strictly genetically. When 
location is a physical location on a sequence, this information can be 
captured in the dots.nalocation table and a marker can have multiple 
locations. When location is defined genetically in the stricter sense, 
capturing the information is not as straight forward but can be done 
using the same view and nalocation (note that there is a linkage_group 
attribute in the proposed view as well as an 
external_database_release_id) and a  marker can be represented by more 
than one row in the nafeature view.

>
> A markers phenotype is often only its physical definition: SNP, SSLP,  
> SSCP, RFLP, etc.  Is this what the SO term is supposed to capture?   
> If so, what is the "type" field meant to capture?


No, type was intended to capture the kind of marker represented in the 
row as the ones you mention as well as markers not necessarily in SO as 
blood groups or allozymes. The sequence_ontology_id is there because all 
nafeature views have this attribute and of course it can be used in the 
case where there is an approrpriate sequenceontology.term_name.

>
> As mentioned elsewhere, organism/strain should probably be a single  
> foreign key into the taxonomy table.

Yes, I agreed with Chris and this was dropped.

>
> Measures of heterogeneity and penetrance are also specific to a given  
> population study, and are not universally true.  I could imagine  
> these and other attributes of a given study being captured  
> independently.  This will be an important area of growth in the next  
> 10 years as widescale familial genotyping becomes more prevalent.


These are nullable so not required from every study. Perhaps we don't 
want these attributes and they can be eliminated. The data I intended to 
load don't have these values but this is only one example and these are 
values often associated with markers.

>
>
> Markers may have multiple aliases.


Yes, this is true. We can decide not to enter a value into this 
attribute as it is nullable or we can have a list as the attribute is a 
varchar2(1000).

>
>
> Thanks,
>
> -Aaron
>
> On Aug 23, 2005, at 12:49 PM, Deborah Pinney wrote:
>
>> I suggest a new view of dots.NaSequenceImp that would be used to  
>> store genetic marker data. Genetic markers are a staple genetic  tool 
>> but include a large variety of data types, some of which may  be 
>> covered by other feature views. I am proposing this view for the  
>> variety of genetic marker data that are not specifically stored  
>> elsewhere. Below is a proposed view definition that requires review  
>> and probably modification.
>>
>> SELECT NA_Feature_ID as na_feature_id,
>> NA_SEQUENCE_ID as na_sequence_id,
>> SUBCLASS_VIEW as subclass_view,
>> NAME as name,
>> SEQUENCE_ONTOLOGY_ID as sequence_ontology_id,
>> PARENT_ID as parent_id,
>> EXTERNAL_DATABASE_RELEASE_ID as external_database_release_id,
>> SOURCE_ID as source_id,
>> PREDICTION_ALGORITHM_ID as prediction_algorithm_id,
>> IS_PREDICTED as is_predicted,
>> REVIEW_STATUS_ID as review_status_id,
>> STRING1 as alias,
>> STRING2 as phenotype,
>> STRING3 as type,
>> STRING4 as linkage_group,
>> STRING5 as centimorgan,
>> STRING6 as measure_of_heterogeneity,
>> STRING7 as penetrance,
>> STRING8 as organism,
>> STRING9 as strain,
>> STRING12 as product,
>> MODIFICATION_DATE as modification_date,
>> USER_READ as user_read,
>> USER_WRITE as user_write,
>> GROUP_READ as group_read,
>> GROUP_WRITE as group_write,
>> OTHER_READ as other_read,
>> OTHER_WRITE as other_write,
>> ROW_USER_ID as row_user_id,
>> ROW_GROUP_ID as row_group_id,
>> ROW_PROJECT_ID as row_project_id,
>> ROW_ALG_INVOCATION_ID as row_alg_invocation_id,
>> FROM DoTS.NAFeatureImp WHERE subclass_view='GeneticMarker'
>>
>>
>>
>> -------------------------------------------------------
>> SF.Net email is Sponsored by the Better Software Conference & EXPO
>> September 19-22, 2005 * San Francisco, CA * Development Lifecycle  
>> Practices
>> Agile & Plan-Driven Development * Managing Projects & Teams *  
>> Testing & QA
>> Security * Process Improvement & Measurement * http://www.sqe.com/ 
>> bsce5sf
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>
> -- 
> Aaron J. Mackey, Ph.D.
> Project Manager, ApiDB Bioinformatics Resource Center
> Penn Genomics Institute, University of Pennsylvania
> email:  am...@pc...
> office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI)
> fax:    215-746-6697
> postal: Penn Genomics Institute
>         Goddard Labs 212
>         415 S. University Avenue
>         Philadelphia, PA  19104-6017
>

Re: [GUSDEV] GeneticMarker view

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

A few notes/thoughts on the proposal:

Why would a genetic marker be considered a sequence?   I guess you  
instead meant a view of dots.NaFeatureImp?

The relationships between a given set of markers are defined  
genetically (i.e. as linked loci with genetic distances measured in  
centiMorgans) with respect to a single genetic map (which corresponds  
to a specific set of experimental crosses or an observed pedigree).   
The same two markers may have different distances (or even be  
unlinked) in a different map.

A markers phenotype is often only its physical definition: SNP, SSLP,  
SSCP, RFLP, etc.  Is this what the SO term is supposed to capture?   
If so, what is the "type" field meant to capture?

As mentioned elsewhere, organism/strain should probably be a single  
foreign key into the taxonomy table.

Measures of heterogeneity and penetrance are also specific to a given  
population study, and are not universally true.  I could imagine  
these and other attributes of a given study being captured  
independently.  This will be an important area of growth in the next  
10 years as widescale familial genotyping becomes more prevalent.

Markers may have multiple aliases.

Thanks,

-Aaron

On Aug 23, 2005, at 12:49 PM, Deborah Pinney wrote:

> I suggest a new view of dots.NaSequenceImp that would be used to  
> store genetic marker data. Genetic markers are a staple genetic  
> tool but include a large variety of data types, some of which may  
> be covered by other feature views. I am proposing this view for the  
> variety of genetic marker data that are not specifically stored  
> elsewhere. Below is a proposed view definition that requires review  
> and probably modification.
>
> SELECT NA_Feature_ID as na_feature_id,
> NA_SEQUENCE_ID as na_sequence_id,
> SUBCLASS_VIEW as subclass_view,
> NAME as name,
> SEQUENCE_ONTOLOGY_ID as sequence_ontology_id,
> PARENT_ID as parent_id,
> EXTERNAL_DATABASE_RELEASE_ID as external_database_release_id,
> SOURCE_ID as source_id,
> PREDICTION_ALGORITHM_ID as prediction_algorithm_id,
> IS_PREDICTED as is_predicted,
> REVIEW_STATUS_ID as review_status_id,
> STRING1 as alias,
> STRING2 as phenotype,
> STRING3 as type,
> STRING4 as linkage_group,
> STRING5 as centimorgan,
> STRING6 as measure_of_heterogeneity,
> STRING7 as penetrance,
> STRING8 as organism,
> STRING9 as strain,
> STRING12 as product,
> MODIFICATION_DATE as modification_date,
> USER_READ as user_read,
> USER_WRITE as user_write,
> GROUP_READ as group_read,
> GROUP_WRITE as group_write,
> OTHER_READ as other_read,
> OTHER_WRITE as other_write,
> ROW_USER_ID as row_user_id,
> ROW_GROUP_ID as row_group_id,
> ROW_PROJECT_ID as row_project_id,
> ROW_ALG_INVOCATION_ID as row_alg_invocation_id,
> FROM DoTS.NAFeatureImp WHERE subclass_view='GeneticMarker'
>
>
>
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle  
> Practices
> Agile & Plan-Driven Development * Managing Projects & Teams *  
> Testing & QA
> Security * Process Improvement & Measurement * http://www.sqe.com/ 
> bsce5sf
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

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

Re: [GUSDEV] GUS plugin InsertGeneOntology missed loading data?

[<jld...@se...>]

Jian,

I've managed to replicate your error, and I'm noticing a pattern with the
missing GO terms and their locations within the file.  I will try to confirm my
suspicions next week.  Sorry this is taking so long, but I think we're making
progress.

Jennifer

Quoting Jian Lu <jl...@vb...>:

> Hi Steve,
> 
> By further investigation of GO data, here is the report:
> 
> Gene Ontology file info:
> !autogenerated-by: DAG-Edit version 1.419 rev 3
> !saved-by:             gocvs
> !date:                 Fri Aug 12 21:00:17 PDT 2005
> !version: $Revision: 3.306 $
> 
> Total unique GO term in component.ontology: 1745
> Total unique GO term in function.ontology: 7902
> Total unique GO term in process.ontology: 10370
> Total unique GO term in three files: 20015 (note: GO:0003673 exists in 
> all three files)
> 
> By comparing our database SRes.GOTERM
> Total loaded by GUS plugin: 19395
> 
> Surprisingly, there are 620 GO terms unloaded!!!
> 
> I have attached a file which lists all unqiue GO terms from three 
> original files with flag 'loaded' and 'missing'.
> 
> Thanks.
> 
> steve wrote:
> 
> > jian-
> >
> > yes, we have used the plugin, but it has been changed a little 
> > recently.  can you do a grep on the file to count how many terms there 
> > are in it?   have you looked carefully at those entries in the file to 
> > see if there is something that distinguishes them?    can you count 
> > how many rows actually are in the database that were put there by that 
> > run of the plugin?
> >
> > thanks for your help,
> > steve
> >
> > Jian Lu wrote:
> >
> >> Hi group,
> >>
> >> I downloaded Gene Ontology version 3.306 
> >> (component.ontology,function.ontology, process.ontology) and ran
> >> GUS::Supported::Plugin::InsertGeneOntology to load them into our GUS 
> >> database.
> >> Here is my command:
> >>
> >> ga GUS::Supported::Plugin::InsertGeneOntology --filePath 
> >> /home/data/ontology --functionExtDbName 'GO Function' 
> >> --processExtDbName 'GO Process' --componentExtDbName 'GO Component' 
> >> --commit
> >>
> >>
> >> Everything looks fine, no errors. It returned a result as "Created 
> >> 19395 entries in GOTerm, 28145 entries in GORelationship, and 16375 
> >> entries in GOSynonym.  Skipped 0 total entries".
> >>
> >> But when I was doing other data checking, I found there are three GO 
> >> terms that have not been loaded, GO:009387, GO:0005331, GO:0009456. 
> >> They do exist on the GO downloaded files.
> >> Has anyone used this plugin to load GO and checked its completeness? 
> >> Please advise. Thanks.
> >>
> >> Jian
> >>
> >>
> >>
> >>
> >> -------------------------------------------------------
> >> SF.Net email is Sponsored by the Better Software Conference & EXPO
> >> September 19-22, 2005 * San Francisco, CA * Development Lifecycle 
> >> Practices
> >> Agile & Plan-Driven Development * Managing Projects & Teams * Testing 
> >> & QA
> >> Security * Process Improvement & Measurement * 
> >> http://www.sqe.com/bsce5sf
> >> _______________________________________________
> >> Gusdev-gusdev mailing list
> >> Gus...@li...
> >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
> 
> 

Re: [GUSDEV] Creating new Schema rules

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

henrique-

i am wondering why you are creating new views.   normally, the gus=20
schema doesn't require that.

what views are you creating and why?

steve

Henrique Juc=E1 wrote:

>Hello everyone,
>
>Is there any nomenclature, or number I should follow for naming a
>rule? How do I access them? I'm creating new views, and I want to
>incorporate the rules that already present in other views. Other thing
>I was wondering was if I replace a view, keeping its current name,=20
>does it lose any rules currently related to it?
>
>
>Thanks in advance,
>
>
>Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br
>
>"As soon as you concern yourself with the "good" and "bad" of your fello=
ws,=20
>you create an opening in your heart for maliciousness to enter. Testing,=
=20
>competing with, and criticizing others weaken and defeat you."
>
>Morihei Ueshiba, O-Sensei (1883-1969)
>
>
>-------------------------------------------------------
>SF.Net email is Sponsored by the Better Software Conference & EXPO
>September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practi=
ces
>Agile & Plan-Driven Development * Managing Projects & Teams * Testing & =
QA
>Security * Process Improvement & Measurement * http://www.sqe.com/bsce5s=
f
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> =20
>

Re: [GUSDEV] Creating new Schema rules

[Michael S. <msa...@pc...>]

Hi Henrique,

I'm not sure what you mean by "rule"-- are you talking about constraints,
triggers, or something else (PostgreSQL has a notion of rules that are
functionally very similar to triggers-- is this what you're referring to?

--Mike


On 8/25/05 4:28 PM, "Henrique Juc=E1" <hen...@gm...> wrote:

> Hello everyone,
>=20
> Is there any nomenclature, or number I should follow for naming a
> rule? How do I access them? I'm creating new views, and I want to
> incorporate the rules that already present in other views. Other thing
> I was wondering was if I replace a view, keeping its current name,
> does it lose any rules currently related to it?
>=20
>=20
> Thanks in advance,
>=20
>=20
> Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br
>=20
> "As soon as you concern yourself with the "good" and "bad" of your fellow=
s,
> you create an opening in your heart for maliciousness to enter. Testing,
> competing with, and criticizing others weaken and defeat you."
>=20
> Morihei Ueshiba, O-Sensei (1883-1969)
>=20
>=20
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practic=
es
> Agile & Plan-Driven Development * Managing Projects & Teams * Testing & Q=
A
> Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

[GUSDEV] Creating new Schema rules

[<hen...@gm...>]

Hello everyone,

Is there any nomenclature, or number I should follow for naming a
rule? How do I access them? I'm creating new views, and I want to
incorporate the rules that already present in other views. Other thing
I was wondering was if I replace a view, keeping its current name,=20
does it lose any rules currently related to it?


Thanks in advance,


Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br

"As soon as you concern yourself with the "good" and "bad" of your fellows,=
=20
you create an opening in your heart for maliciousness to enter. Testing,=20
competing with, and criticizing others weaken and defeat you."

Morihei Ueshiba, O-Sensei (1883-1969)

[GUSDEV] SchemaBrowser 2.0 Released

[Michael S. <msa...@pc...>]

From gusdb.org:

The first version of the next generation Schema Browser has been released,
and is available at http://www.gusdb.org/SchemaBrowser. This release
features tables organized by categories, sorting, filtering, and
community-submitted documentation (you must have a Wiki username & password
to submit documentation). Any issues should be filed in the tracker.


--Mike

Re: [GUSDEV] GeneticMarker view

[Deborah P. <pi...@pc...>]

Chris Stoeckert wrote:

You're right about centimorgans, I originally had float and somehow 
dropped it. Also, there is an sres.phenotype table of which I was not 
aware.  Do you know if there is an accepted  phenotype ontology that is 
not mammal centric?  This leads to the question raised by Steve's 
comment that a  foreign key has to be included in the superclass view 
and imp table. Do we want to add phenotype as a foreign key? There 
probably should be a CV for genetic marker type but I haven't seen it 
and SO  terms don't cover them (blood groups for example) so I'm not 
sure that type can be a reference to another table. You're probably 
right about the organism and strain being covered by the taxon_id in the 
NASequence Imp view. Those are probably appropriate for the SeqVariation 
view but not for GeneticMarker and I'll drop them. On second thought, I 
think product should probably be dropped as phenotype is probably the 
correct association and already an attribute. I was trying to anticipate 
a variety of data sets (I'm only dealing with a single example) so I 
included linkage_group but I'm not sure whether this attribute is needed. 

Here is an altered view definition:
SELECT NA_Feature_ID as na_feature_id,
NA_SEQUENCE_ID as na_sequence_id,
SUBCLASS_VIEW as subclass_view,
NAME as name,
SEQUENCE_ONTOLOGY_ID as sequence_ontology_id,
PARENT_ID as parent_id,
EXTERNAL_DATABASE_RELEASE_ID as external_database_release_id,
SOURCE_ID as source_id,
PREDICTION_ALGORITHM_ID as prediction_algorithm_id,
IS_PREDICTED as is_predicted,
REVIEW_STATUS_ID as review_status_id,
STRING1 as alias,
INT1 as phenotype,
STRING3 as type,
STRING4 as linkage_group,
FLOAT1 as centimorgan,
STRING5 as measure_of_heterogeneity,
STRING6 as penetrance,
MODIFICATION_DATE as modification_date,
USER_READ as user_read,
USER_WRITE as user_write,
GROUP_READ as group_read,
GROUP_WRITE as group_write,
OTHER_READ as other_read,
OTHER_WRITE as other_write,
ROW_USER_ID as row_user_id,
ROW_GROUP_ID as row_group_id,
ROW_PROJECT_ID as row_project_id,
ROW_ALG_INVOCATION_ID as row_alg_invocation_id,
FROM DoTS.NAFeatureImp WHERE subclass_view='GeneticMarker'


> Hi Debbie,
> Some of the strings look like they might be numbers (e.g.,  
> centimorgan) or foreign keys to a controlled vocabulary (e.g.,  
> phenotype, type, organism, strain). Since NAFeatures have NASequence  
> which have taxon_id is "organism" really needed? Is product a protein  
> and therefore should be linked to an AA table? In other words, which  
> are the key attributes that should be intregrated with other data in  
> GUS and what can just go into a free text description field?
> Thanks.
> Chris
>
> On Aug 23, 2005, at 12:49 PM, Deborah Pinney wrote:
>
>> I suggest a new view of dots.NaSequenceImp that would be used to  
>> store genetic marker data. Genetic markers are a staple genetic  tool 
>> but include a large variety of data types, some of which may  be 
>> covered by other feature views. I am proposing this view for the  
>> variety of genetic marker data that are not specifically stored  
>> elsewhere. Below is a proposed view definition that requires review  
>> and probably modification.
>>
>> SELECT NA_Feature_ID as na_feature_id,
>> NA_SEQUENCE_ID as na_sequence_id,
>> SUBCLASS_VIEW as subclass_view,
>> NAME as name,
>> SEQUENCE_ONTOLOGY_ID as sequence_ontology_id,
>> PARENT_ID as parent_id,
>> EXTERNAL_DATABASE_RELEASE_ID as external_database_release_id,
>> SOURCE_ID as source_id,
>> PREDICTION_ALGORITHM_ID as prediction_algorithm_id,
>> IS_PREDICTED as is_predicted,
>> REVIEW_STATUS_ID as review_status_id,
>> STRING1 as alias,
>> STRING2 as phenotype,
>> STRING3 as type,
>> STRING4 as linkage_group,
>> STRING5 as centimorgan,
>> STRING6 as measure_of_heterogeneity,
>> STRING7 as penetrance,
>> STRING8 as organism,
>> STRING9 as strain,
>> STRING12 as product,
>> MODIFICATION_DATE as modification_date,
>> USER_READ as user_read,
>> USER_WRITE as user_write,
>> GROUP_READ as group_read,
>> GROUP_WRITE as group_write,
>> OTHER_READ as other_read,
>> OTHER_WRITE as other_write,
>> ROW_USER_ID as row_user_id,
>> ROW_GROUP_ID as row_group_id,
>> ROW_PROJECT_ID as row_project_id,
>> ROW_ALG_INVOCATION_ID as row_alg_invocation_id,
>> FROM DoTS.NAFeatureImp WHERE subclass_view='GeneticMarker'
>>
>>
>>
>> -------------------------------------------------------
>> SF.Net email is Sponsored by the Better Software Conference & EXPO
>> September 19-22, 2005 * San Francisco, CA * Development Lifecycle  
>> Practices
>> Agile & Plan-Driven Development * Managing Projects & Teams *  
>> Testing & QA
>> Security * Process Improvement & Measurement * http://www.sqe.com/ 
>> bsce5sf
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>

Re: [GUSDEV] Build

[Adhemar Z. N. <ad...@cp...>]

Hi Michael,<br /><br />Thanks for the tip. I'm a newbie on oracle also.
Now I created the tablespace. The build ran perfectly.<br /><br
/>Regards,<br /><br />Adhemar<br /><br />&gt; <br />&gt; Hi Adhemar,<br
/>&gt; <br />&gt; Can you confirm that the GUSDB tablespace does exist?=20
Perhaps by logging<br />&gt; into your instance as the GUS user and
doing:<br />&gt; <br />&gt; create table test ( test_id number) tablespac=
e
gusdb;<br />&gt; <br />&gt;&gt; [InstallSchema] INFO: Validating Database=
:
'null'<br />&gt; <br />&gt; This is normal-- don't worry about that
&quot;null&quot; in there.<br />&gt; <br />&gt; Thanks,<br />&gt; <br
/>&gt; --Mike<br />&gt; <br />&gt; <br />&gt; On 8/23/05 4:16 PM,
&quot;Adhemar Zerlotini Neto&quot; <adhemar @cpqrr.fiocruz.br=3D""><br
/>&gt; wrote:<br />&gt; <br />&gt;&gt;<br />&gt;&gt; Hi Everybody,<br
/>&gt;&gt;<br />&gt;&gt; I=B4m a newbie using GUS. I=B4m trying to instal=
l the
3.5 version on Oracle<br />&gt;&gt; 10g<br />&gt;&gt; and I=B4m having so=
me
problems with the build script.<br />&gt;&gt;<br />&gt;&gt; I tried to us=
e
the build script serveral times from the scratch. Here is<br />&gt;&gt;
the<br />&gt;&gt; output of the last try:<br />&gt;&gt;<br />&gt;&gt;
[oracle@gus install]$<br />&gt;&gt; build GUS install -append
-installDBSchema<br />&gt;&gt;     [mkdir] Created dir:<br />&gt;&gt;
/usr/local/GUS/project_home/install/classes<br />&gt;&gt;     [javac]
Compiling 1<br />&gt;&gt; source file to
/usr/local/GUS/project_home/install/classes<br />&gt;&gt;
[WritePropertyFiles] Aug 23, 2005 9:37:09 AM<br />&gt;&gt;
org.gusdb.install.WritePropertyFileTask initialize<br />&gt;&gt;
[WritePropertyFiles] INFO: Creating configuration directory<br
/>&gt;&gt;<br />&gt;&gt; [copy] Copying 1 file to
/usr/local/GUS/gus_home/config<br />&gt;&gt;     [copy]<br />&gt;&gt;
Copying 1 file to /usr/local/GUS/gus_home/config<br />&gt;&gt;     [echo]
.<br />&gt;&gt;      [echo] Installing CBIL/Bio<br />&gt;&gt;     [mkdir]
Created dir:<br />&gt;&gt; /usr/local/GUS/gus_home/bin<br />&gt;&gt;    =20
[copy] Copying 5 files to<br />&gt;&gt; /usr/local/GUS/gus_home/bin<br
/>&gt;&gt;     [mkdir] Created dir:<br />&gt;&gt;
/usr/local/GUS/gus_home/lib/perl/CBIL/Bio<br />&gt;&gt;      [copy]
Copying 66<br />&gt;&gt; files to
/usr/local/GUS/gus_home/lib/perl/CBIL/Bio<br />&gt;&gt;     [mkdir]<br
/>&gt;&gt; Created dir: /usr/local/GUS/gus_home/test/CBIL/Bio<br
/>&gt;&gt;      [copy]<br />&gt;&gt; Copying 4 files to
/usr/local/GUS/gus_home/test/CBIL/Bio<br />&gt;&gt;    [mkdir]<br
/>&gt;&gt; Created dir: /usr/local/GUS/gus_home/data/CBIL/Bio<br
/>&gt;&gt;     [copy]<br />&gt;&gt; Copying 9 files to
/usr/local/GUS/gus_home/data/CBIL/Bio<br />&gt;&gt;  [echo]<br />&gt;&gt;
.<br />&gt;&gt;      [echo] Installing CBIL/CSP<br />&gt;&gt;      [copy]
Copying 1 file to<br />&gt;&gt; /usr/local/GUS/gus_home/bin<br />&gt;&gt;=
=20
   [mkdir] Created dir:<br />&gt;&gt;
/usr/local/GUS/gus_home/lib/perl/CBIL/CSP<br />&gt;&gt;     [copy] Copyin=
g
11<br />&gt;&gt; files to /usr/local/GUS/gus_home/lib/perl/CBIL/CSP<br
/>&gt;&gt;     [mkdir]<br />&gt;&gt; Created dir:
/usr/local/GUS/gus_home/lib/java<br />&gt;&gt;      [copy] Copying 2<br
/>&gt;&gt; files to /usr/local/GUS/gus_home/lib/java<br />&gt;&gt;   =20
[mkdir] Created dir:<br />&gt;&gt; /usr/local/GUS/gus_home/doc/CBIL/CSP<b=
r
/>&gt;&gt;      [copy] Copying 10 files to<br />&gt;&gt;
/usr/local/GUS/gus_home/doc/CBIL/CSP<br />&gt;&gt;     [mkdir] Created
dir:<br />&gt;&gt; /usr/local/GUS/project_home/CBIL/CSP/classes<br
/>&gt;&gt;    [javac] Compiling 27<br />&gt;&gt; source files to
/usr/local/GUS/project_home/CBIL/CSP/classes<br />&gt;&gt;<br />&gt;&gt;
[javac] Note:<br />&gt;&gt;
/usr/local/GUS/project_home/CBIL/CSP/src/java/edu/cbil/csp/dialog/Action.=
java<br
/>&gt;&gt; uses or overrides a deprecated API.<br />&gt;&gt;     [javac]
Note: Recompile with<br />&gt;&gt; -Xlint:deprecation for details.<br
/>&gt;&gt;     [javac] Note: Some input files<br />&gt;&gt; use unchecked
or unsafe operations.<br />&gt;&gt;     [javac] Note: Recompile with<br
/>&gt;&gt; -Xlint:unchecked for details.<br />&gt;&gt;       [jar]
Building jar:<br />&gt;&gt;
/usr/local/GUS/gus_home/lib/java/CBIL-CSP.jar<br />&gt;&gt;     [echo]
.<br />&gt;&gt;<br />&gt;&gt; [echo] Installing CBIL/Util<br />&gt;&gt;  =
=20
 [mkdir] Created dir:<br />&gt;&gt;
/usr/local/GUS/gus_home/lib/perl/CBIL/Util<br />&gt;&gt;     [copy]
Copying 8<br />&gt;&gt; files to
/usr/local/GUS/gus_home/lib/perl/CBIL/Util<br />&gt;&gt;     [mkdir]<br
/>&gt;&gt; Created dir: /usr/local/GUS/gus_home/doc/CBIL/Util<br
/>&gt;&gt;      [copy]<br />&gt;&gt; Copying 1 file to
/usr/local/GUS/gus_home/doc/CBIL/Util<br />&gt;&gt;      [echo]<br
/>&gt;&gt; .<br />&gt;&gt;      [echo] Installing CBIL/HQ<br />&gt;&gt;  =
=20
  [copy] Copying 1 file to<br />&gt;&gt; /usr/local/GUS/gus_home/bin<br
/>&gt;&gt;     [mkdir] Created dir:<br />&gt;&gt;
/usr/local/GUS/gus_home/lib/perl/CBIL/HQ<br />&gt;&gt;      [copy] Copyin=
g
3 files<br />&gt;&gt; to /usr/local/GUS/gus_home/lib/perl/CBIL/HQ<br
/>&gt;&gt;      [echo] .<br />&gt;&gt;<br />&gt;&gt; [echo] Installing
CBIL/ObjectMapper<br />&gt;&gt;     [mkdir] Created dir:<br />&gt;&gt;
/usr/local/GUS/gus_home/lib/perl/CBIL/ObjectMapper<br />&gt;&gt;=20
[copy]<br />&gt;&gt; Copying 7 files to
/usr/local/GUS/gus_home/lib/perl/CBIL/ObjectMapper<br />&gt;&gt;    =20
[copy] Copying 1 file to /usr/local/GUS/gus_home/config<br />&gt;&gt;<br
/>&gt;&gt; [mkdir] Created dir:
/usr/local/GUS/gus_home/doc/CBIL/ObjectMapper<br />&gt;&gt;     [copy]
Copying 1 file to<br />&gt;&gt;
/usr/local/GUS/gus_home/doc/CBIL/ObjectMapper<br />&gt;&gt;    [concat] N=
o
existing<br />&gt;&gt; files and no nested text, doing nothing<br
/>&gt;&gt;      [echo] .<br />&gt;&gt;<br />&gt;&gt; [echo] Installing
GUS/Supported<br />&gt;&gt;      [copy] Copying 1 file to<br />&gt;&gt;
/usr/local/GUS/gus_home/bin<br />&gt;&gt;     [mkdir] Created dir:<br
/>&gt;&gt; /usr/local/GUS/gus_home/lib/perl/GUS/Supported<br />&gt;&gt;  =
=20
  [copy] Copying 2<br />&gt;&gt; files to
/usr/local/GUS/gus_home/lib/perl/GUS/Supported<br />&gt;&gt;   =20
[mkdir]<br />&gt;&gt; Created dir:
/usr/local/GUS/gus_home/lib/perl/GUS/Supported/Plugin<br />&gt;&gt;    =20
[copy] Copying 19 files to<br />&gt;&gt;
/usr/local/GUS/gus_home/lib/perl/GUS/Supported/Plugin<br />&gt;&gt;   =20
[copy]<br />&gt;&gt; Copying 2 files to /usr/local/GUS/gus_home/config<br
/>&gt;&gt;    [mkdir] Created<br />&gt;&gt; dir:
/usr/local/GUS/gus_home/doc/GUS/Supported<br />&gt;&gt;   [copy] Copying
5<br />&gt;&gt; files to /usr/local/GUS/gus_home/doc/GUS/Supported<br
/>&gt;&gt;      [echo] .<br />&gt;&gt;     [echo] Installing
GUS/Community<br />&gt;&gt;      [copy] Copying 4 files to<br />&gt;&gt;
/usr/local/GUS/gus_home/bin<br />&gt;&gt;     [mkdir] Created dir:<br
/>&gt;&gt; /usr/local/GUS/gus_home/lib/perl/GUS/Community<br />&gt;&gt;  =
=20
  [copy] Copying 10<br />&gt;&gt; files to
/usr/local/GUS/gus_home/lib/perl/GUS/Community<br />&gt;&gt;     [copy]<b=
r
/>&gt;&gt; Copying 2 files to /usr/local/GUS/gus_home/lib/java<br
/>&gt;&gt;    [mkdir]<br />&gt;&gt; Created dir:
/usr/local/GUS/gus_home/lib/perl/GUS/Community/Plugin<br />&gt;&gt;    =20
[copy] Copying 41 files to<br />&gt;&gt;
/usr/local/GUS/gus_home/lib/perl/GUS/Community/Plugin<br />&gt;&gt;   =20
[copy]<br />&gt;&gt; Copying 10 files to /usr/local/GUS/gus_home/config<b=
r
/>&gt;&gt;    [mkdir]<br />&gt;&gt; Created dir:
/usr/local/GUS/gus_home/doc/GUS/Community<br />&gt;&gt;   [copy]<br
/>&gt;&gt; Copying 7 files to /usr/local/GUS/gus_home/doc/GUS/Community<b=
r
/>&gt;&gt;<br />&gt;&gt; [echo] .<br />&gt;&gt;     [echo] Installing
GUS/DBAdmin<br />&gt;&gt;      [copy] Copying<br />&gt;&gt; 8 files to
/usr/local/GUS/gus_home/bin<br />&gt;&gt;     [mkdir] Created dir:<br
/>&gt;&gt; /usr/local/GUS/gus_home/lib/perl/GUS/DBAdmin<br />&gt;&gt;    =
=20
[copy] Copying 6<br />&gt;&gt; files to
/usr/local/GUS/gus_home/lib/perl/GUS/DBAdmin<br />&gt;&gt;     [copy]<br
/>&gt;&gt; Copying 5 files to /usr/local/GUS/gus_home/lib/java<br
/>&gt;&gt;    [mkdir]<br />&gt;&gt; Created dir:
/usr/local/GUS/project_home/GUS/DBAdmin/classes<br />&gt;&gt;<br
/>&gt;&gt; [javac] Compiling 46 source files to<br />&gt;&gt;
/usr/local/GUS/project_home/GUS/DBAdmin/classes<br />&gt;&gt;     [javac]
Note:<br />&gt;&gt; Some input files use unchecked or unsafe
operations.<br />&gt;&gt;    [javac]<br />&gt;&gt; Note: Recompile with
-Xlint:unchecked for details.<br />&gt;&gt;      [jar]<br />&gt;&gt;
Building jar: /usr/local/GUS/gus_home/lib/java/GUS-DBAdmin.jar<br
/>&gt;&gt;<br />&gt;&gt; [echo] .<br />&gt;&gt;      [echo] Installing
GUS/GOPredict<br />&gt;&gt;      [copy]<br />&gt;&gt; Copying 3 files to
/usr/local/GUS/gus_home/bin<br />&gt;&gt;     [mkdir] Created<br
/>&gt;&gt; dir: /usr/local/GUS/gus_home/lib/perl/GUS/GOPredict<br
/>&gt;&gt;      [copy]<br />&gt;&gt; Copying 20 files to
/usr/local/GUS/gus_home/lib/perl/GUS/GOPredict<br />&gt;&gt;  [mkdir]
Created dir:<br />&gt;&gt;
/usr/local/GUS/gus_home/lib/perl/GUS/GOPredict/Plugin<br />&gt;&gt;   =20
[copy]<br />&gt;&gt; Copying 8 files to<br />&gt;&gt;
/usr/local/GUS/gus_home/lib/perl/GUS/GOPredict/Plugin<br />&gt;&gt;  =20
[mkdir]<br />&gt;&gt; Created dir:
/usr/local/GUS/gus_home/doc/GUS/GOPredict<br />&gt;&gt;   [copy]<br
/>&gt;&gt; Copying 1 file to /usr/local/GUS/gus_home/doc/GUS/GOPredict<br
/>&gt;&gt;<br />&gt;&gt; [mkdir] Created dir:
/usr/local/GUS/project_home/GUS/GOPredict/classes<br />&gt;&gt;   =20
[javac] Compiling 10 source files to<br />&gt;&gt;
/usr/local/GUS/project_home/GUS/GOPredict/classes<br />&gt;&gt;   =20
[javac] Note:<br />&gt;&gt; Some input files use unchecked or unsafe
operations.<br />&gt;&gt;    [javac]<br />&gt;&gt; Note: Recompile with
-Xlint:unchecked for details.<br />&gt;&gt;      [jar]<br />&gt;&gt;
Building jar: /usr/local/GUS/gus_home/lib/java/GUS-GOPredict.jar<br
/>&gt;&gt;<br />&gt;&gt; [echo] .<br />&gt;&gt;      [echo] Installing
GUS/Schema<br />&gt;&gt;     [mkdir] Created<br />&gt;&gt; dir:
/usr/local/GUS/project_home/GUS/Schema/classes<br />&gt;&gt;   =20
[javac]<br />&gt;&gt; Compiling 1 source file to<br />&gt;&gt;
/usr/local/GUS/project_home/GUS/Schema/classes<br />&gt;&gt;     [javac]
Note:<br />&gt;&gt;
/usr/local/GUS/project_home/GUS/Schema/src/java/org/gusdb/schema/InstallS=
chema<br
/>&gt;&gt; Task.java<br />&gt;&gt; uses unchecked or unsafe operations.<b=
r
/>&gt;&gt;     [javac] Note: Recompile with<br />&gt;&gt; -Xlint:unchecke=
d
for details.<br />&gt;&gt;       [jar] Building jar:<br />&gt;&gt;
/usr/local/GUS/gus_home/lib/java/GUS-Schema.jar<br />&gt;&gt;
[InstallSchema] Aug<br />&gt;&gt; 23, 2005 9:37:23 AM
org.gusdb.schema.InstallSchemaTask execute<br />&gt;&gt; [InstallSchema]
INFO: Reading database from<br />&gt;&gt;
/usr/local/GUS/project_home/GUS/Schema/gus_schema.xml<br />&gt;&gt;
[InstallSchema]<br />&gt;&gt; Aug 23, 2005 9:37:23 AM
org.gusdb.dbadmin.reader.SchemaReader doRead<br />&gt;&gt; [InstallSchema=
]
INFO: Reading Database<br />&gt;&gt; [InstallSchema] Aug 23, 2005<br
/>&gt;&gt; 9:37:27 AM org.gusdb.dbadmin.model.Database
resolveReferences<br />&gt;&gt; [InstallSchema] INFO: Resolving Database
References<br />&gt;&gt; [InstallSchema]<br />&gt;&gt; Aug 23, 2005
9:37:28 AM org.gusdb.dbadmin.util.DatabaseValidator<br />&gt;&gt;
validate<br />&gt;&gt; [InstallSchema] INFO: Validating Database:
'null'<br />&gt;&gt; [InstallSchema] Aug 23, 2005 9:37:28 AM<br />&gt;&gt=
;
org.gusdb.schema.InstallSchemaTask setTablespace<br />&gt;&gt;
[InstallSchema]<br />&gt;&gt; INFO: Setting tablespaces to gusdb<br
/>&gt;&gt; [InstallSchema] Aug 23, 2005<br />&gt;&gt; 9:37:28 AM
org.gusdb.dbadmin.util.DatabaseValidator validate<br />&gt;&gt;
[InstallSchema] INFO: Validating Database: 'null'<br />&gt;&gt;
[InstallSchema]<br />&gt;&gt; Aug 23, 2005 9:37:28 AM
org.gusdb.dbadmin.writer.SchemaWriter write<br />&gt;&gt; [InstallSchema]
INFO: Writing Database<br />&gt;&gt; [InstallSchema] Aug 23, 2005<br
/>&gt;&gt; 9:37:29 AM org.gusdb.dbadmin.util.DatabaseValidator validate<b=
r
/>&gt;&gt; [InstallSchema] INFO: Validating Database: 'null'<br />&gt;&gt=
;
[InstallSchema]<br />&gt;&gt; Aug 23, 2005 9:37:29 AM
org.gusdb.dbadmin.writer.SchemaWriter write<br />&gt;&gt; [InstallSchema]
INFO: Writing Database<br />&gt;&gt;<br />&gt;&gt; BUILD FAILED<br
/>&gt;&gt; /usr/local/GUS/project_home/install/build.xml:28: The followin=
g
error<br />&gt;&gt; occurred while executing this line:<br />&gt;&gt;
/usr/local/GUS/project_home/GUS/build.xml:92: java.io.IOException:
Error<br />&gt;&gt; executing SQL: '<br />&gt;&gt; ALTER USER RAD QUOTA
UNLIMITED ON gusdb' Error:<br />&gt;&gt; ORA-00959: tablespace 'GUSDB'
does not exist<br />&gt;&gt;<br />&gt;&gt;<br />&gt;&gt; Total<br
/>&gt;&gt; time: 22 seconds<br />&gt;&gt;<br />&gt;&gt;<br />&gt;&gt; The
user GUS<br />&gt;&gt; uses to connect has all sysdba privileges but the
related to rule, rule<br />&gt;&gt; set and evaluation context.<br
/>&gt;&gt;<br />&gt;&gt; I believe that somehow the build<br />&gt;&gt;
script can't not connect to the gusdb tablespace sometimes. And there's<b=
r
/>&gt;&gt; another strange thing with the DatabaseValidator at some lines
like<br />&gt;&gt; this:<br />&gt;&gt;<br />&gt;&gt;
org.gusdb.dbadmin.util.DatabaseValidator<br />&gt;&gt; validate<br
/>&gt;&gt;<br />&gt;&gt; [InstallSchema] INFO: Validating Database:
'null'<br />&gt;&gt;<br />&gt;&gt; Can anyone give me a tip?<br
/>&gt;&gt;<br />&gt;&gt; Thanks<br />&gt;&gt;<br />&gt;&gt; Adhemar
Zerlotini Neto<br />&gt;&gt; Centro de Pesquisas Ren=E9 Rachou - FIOCRUZ<=
br
/>&gt;&gt; Av. Augusto de Lima 1715<br />&gt;&gt; BH MG 30190-002,
Brazil<br />&gt;&gt; Phone: +55-31-3349-7785<br />&gt;&gt;
------------------------------------------------------- SF.Net email is<b=
r
/>&gt;&gt; Sponsored by the Better Software Conference  EXPO September
19-22, 2005<br />&gt;&gt; * San<br />&gt;&gt; Francisco, CA * Development
Lifecycle Practices Agile  Plan-Driven<br />&gt;&gt; Development<br
/>&gt;&gt; * Managing Projects  Teams * Testing  QA Security * Process
Improvement<br />&gt;&gt; Measurement * http://www.sqe.com/bsce5sf<br
/>&gt;&gt; _______________________________________________ Gusdev-gusdev
mailing<br />&gt;&gt; list<br />&gt;&gt;
Gus...@li...<br />&gt;&gt;
https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev<br />&gt; <br
/>&gt; <br />&gt; <br />&gt; --<br />&gt; Centro de Pesquisas Ren=E9
Rachou/CPqRR - A FIOCRUZ em Minas Gerais.<br />&gt; Rene Rachou Research
Center/CPqRR - The Oswaldo Cruz Foundation in the<br />&gt; State of Mina=
s
Gerais-Brazil.<br />&gt; http://www.cpqrr.fiocruz.br<br />&gt; <br />&gt;
<br /><br /><br />Adhemar Zerlotini Neto<br />Centro de Pesquisas Ren=E9
Rachou - FIOCRUZ<br />Av. Augusto de Lima 1715<br />BH MG 30190-002,
Brazil<br />Phone: +55-31-3349-7785</adhemar>

Re: [GUSDEV] GeneticMarker view

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

just a reminder that foreign keys have to go into the Imp table, and 
therefore into the superclass...
steve

Chris Stoeckert wrote:

> Hi Debbie,
> Some of the strings look like they might be numbers (e.g.,  
> centimorgan) or foreign keys to a controlled vocabulary (e.g.,  
> phenotype, type, organism, strain). Since NAFeatures have NASequence  
> which have taxon_id is "organism" really needed? Is product a protein  
> and therefore should be linked to an AA table? In other words, which  
> are the key attributes that should be intregrated with other data in  
> GUS and what can just go into a free text description field?
> Thanks.
> Chris
>
> On Aug 23, 2005, at 12:49 PM, Deborah Pinney wrote:
>
>> I suggest a new view of dots.NaSequenceImp that would be used to  
>> store genetic marker data. Genetic markers are a staple genetic  tool 
>> but include a large variety of data types, some of which may  be 
>> covered by other feature views. I am proposing this view for the  
>> variety of genetic marker data that are not specifically stored  
>> elsewhere. Below is a proposed view definition that requires review  
>> and probably modification.
>>
>> SELECT NA_Feature_ID as na_feature_id,
>> NA_SEQUENCE_ID as na_sequence_id,
>> SUBCLASS_VIEW as subclass_view,
>> NAME as name,
>> SEQUENCE_ONTOLOGY_ID as sequence_ontology_id,
>> PARENT_ID as parent_id,
>> EXTERNAL_DATABASE_RELEASE_ID as external_database_release_id,
>> SOURCE_ID as source_id,
>> PREDICTION_ALGORITHM_ID as prediction_algorithm_id,
>> IS_PREDICTED as is_predicted,
>> REVIEW_STATUS_ID as review_status_id,
>> STRING1 as alias,
>> STRING2 as phenotype,
>> STRING3 as type,
>> STRING4 as linkage_group,
>> STRING5 as centimorgan,
>> STRING6 as measure_of_heterogeneity,
>> STRING7 as penetrance,
>> STRING8 as organism,
>> STRING9 as strain,
>> STRING12 as product,
>> MODIFICATION_DATE as modification_date,
>> USER_READ as user_read,
>> USER_WRITE as user_write,
>> GROUP_READ as group_read,
>> GROUP_WRITE as group_write,
>> OTHER_READ as other_read,
>> OTHER_WRITE as other_write,
>> ROW_USER_ID as row_user_id,
>> ROW_GROUP_ID as row_group_id,
>> ROW_PROJECT_ID as row_project_id,
>> ROW_ALG_INVOCATION_ID as row_alg_invocation_id,
>> FROM DoTS.NAFeatureImp WHERE subclass_view='GeneticMarker'
>>
>>
>>
>> -------------------------------------------------------
>> SF.Net email is Sponsored by the Better Software Conference & EXPO
>> September 19-22, 2005 * San Francisco, CA * Development Lifecycle  
>> Practices
>> Agile & Plan-Driven Development * Managing Projects & Teams *  
>> Testing & QA
>> Security * Process Improvement & Measurement * http://www.sqe.com/ 
>> bsce5sf
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>
>
>
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle 
> Practices
> Agile & Plan-Driven Development * Managing Projects & Teams * Testing 
> & QA
> Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [GUSDEV] GeneticMarker view

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

Hi Debbie,
Some of the strings look like they might be numbers (e.g.,  
centimorgan) or foreign keys to a controlled vocabulary (e.g.,  
phenotype, type, organism, strain). Since NAFeatures have NASequence  
which have taxon_id is "organism" really needed? Is product a protein  
and therefore should be linked to an AA table? In other words, which  
are the key attributes that should be intregrated with other data in  
GUS and what can just go into a free text description field?
Thanks.
Chris

On Aug 23, 2005, at 12:49 PM, Deborah Pinney wrote:

> I suggest a new view of dots.NaSequenceImp that would be used to  
> store genetic marker data. Genetic markers are a staple genetic  
> tool but include a large variety of data types, some of which may  
> be covered by other feature views. I am proposing this view for the  
> variety of genetic marker data that are not specifically stored  
> elsewhere. Below is a proposed view definition that requires review  
> and probably modification.
>
> SELECT NA_Feature_ID as na_feature_id,
> NA_SEQUENCE_ID as na_sequence_id,
> SUBCLASS_VIEW as subclass_view,
> NAME as name,
> SEQUENCE_ONTOLOGY_ID as sequence_ontology_id,
> PARENT_ID as parent_id,
> EXTERNAL_DATABASE_RELEASE_ID as external_database_release_id,
> SOURCE_ID as source_id,
> PREDICTION_ALGORITHM_ID as prediction_algorithm_id,
> IS_PREDICTED as is_predicted,
> REVIEW_STATUS_ID as review_status_id,
> STRING1 as alias,
> STRING2 as phenotype,
> STRING3 as type,
> STRING4 as linkage_group,
> STRING5 as centimorgan,
> STRING6 as measure_of_heterogeneity,
> STRING7 as penetrance,
> STRING8 as organism,
> STRING9 as strain,
> STRING12 as product,
> MODIFICATION_DATE as modification_date,
> USER_READ as user_read,
> USER_WRITE as user_write,
> GROUP_READ as group_read,
> GROUP_WRITE as group_write,
> OTHER_READ as other_read,
> OTHER_WRITE as other_write,
> ROW_USER_ID as row_user_id,
> ROW_GROUP_ID as row_group_id,
> ROW_PROJECT_ID as row_project_id,
> ROW_ALG_INVOCATION_ID as row_alg_invocation_id,
> FROM DoTS.NAFeatureImp WHERE subclass_view='GeneticMarker'
>
>
>
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle  
> Practices
> Agile & Plan-Driven Development * Managing Projects & Teams *  
> Testing & QA
> Security * Process Improvement & Measurement * http://www.sqe.com/ 
> bsce5sf
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

Re: [GUSDEV] Build

[Michael S. <msa...@pc...>]

Hi Adhemar,

Can you confirm that the GUSDB tablespace does exist?  Perhaps by logging
into your instance as the GUS user and doing:

create table test ( test_id number) tablespace gusdb;

> [InstallSchema] INFO: Validating Database: 'null'

This is normal-- don't worry about that "null" in there.

Thanks,

--Mike


On 8/23/05 4:16 PM, "Adhemar Zerlotini Neto" <ad...@cp...>
wrote:

>=20
> Hi Everybody,
>=20
> I=B4m a newbie using GUS. I=B4m trying to install the 3.5 version on Oracle 1=
0g
> and I=B4m having some problems with the build script.
>=20
> I tried to use the build script serveral times from the scratch. Here is =
the
> output of the last try:
>=20
> [oracle@gus install]$
> build GUS install -append -installDBSchema
>     [mkdir] Created dir:
> /usr/local/GUS/project_home/install/classes
>     [javac] Compiling 1
> source file to /usr/local/GUS/project_home/install/classes
> [WritePropertyFiles] Aug 23, 2005 9:37:09 AM
> org.gusdb.install.WritePropertyFileTask initialize
> [WritePropertyFiles] INFO: Creating configuration directory
>    =20
> [copy] Copying 1 file to /usr/local/GUS/gus_home/config
>     [copy]
> Copying 1 file to /usr/local/GUS/gus_home/config
>     [echo] .
>      [echo] Installing CBIL/Bio
>     [mkdir] Created dir:
> /usr/local/GUS/gus_home/bin
>      [copy] Copying 5 files to
> /usr/local/GUS/gus_home/bin
>     [mkdir] Created dir:
> /usr/local/GUS/gus_home/lib/perl/CBIL/Bio
>      [copy] Copying 66
> files to /usr/local/GUS/gus_home/lib/perl/CBIL/Bio
>     [mkdir]
> Created dir: /usr/local/GUS/gus_home/test/CBIL/Bio
>      [copy]
> Copying 4 files to /usr/local/GUS/gus_home/test/CBIL/Bio
>    [mkdir]
> Created dir: /usr/local/GUS/gus_home/data/CBIL/Bio
>     [copy]
> Copying 9 files to /usr/local/GUS/gus_home/data/CBIL/Bio
>  [echo]
> .
>      [echo] Installing CBIL/CSP
>      [copy] Copying 1 file to
> /usr/local/GUS/gus_home/bin
>     [mkdir] Created dir:
> /usr/local/GUS/gus_home/lib/perl/CBIL/CSP
>     [copy] Copying 11
> files to /usr/local/GUS/gus_home/lib/perl/CBIL/CSP
>     [mkdir]
> Created dir: /usr/local/GUS/gus_home/lib/java
>      [copy] Copying 2
> files to /usr/local/GUS/gus_home/lib/java
>     [mkdir] Created dir:
> /usr/local/GUS/gus_home/doc/CBIL/CSP
>      [copy] Copying 10 files to
> /usr/local/GUS/gus_home/doc/CBIL/CSP
>     [mkdir] Created dir:
> /usr/local/GUS/project_home/CBIL/CSP/classes
>    [javac] Compiling 27
> source files to /usr/local/GUS/project_home/CBIL/CSP/classes
>   =20
> [javac] Note:
> /usr/local/GUS/project_home/CBIL/CSP/src/java/edu/cbil/csp/dialog/Action.=
java
> uses or overrides a deprecated API.
>     [javac] Note: Recompile with
> -Xlint:deprecation for details.
>     [javac] Note: Some input files
> use unchecked or unsafe operations.
>     [javac] Note: Recompile with
> -Xlint:unchecked for details.
>       [jar] Building jar:
> /usr/local/GUS/gus_home/lib/java/CBIL-CSP.jar
>     [echo] .
>    =20
> [echo] Installing CBIL/Util
>     [mkdir] Created dir:
> /usr/local/GUS/gus_home/lib/perl/CBIL/Util
>     [copy] Copying 8
> files to /usr/local/GUS/gus_home/lib/perl/CBIL/Util
>     [mkdir]
> Created dir: /usr/local/GUS/gus_home/doc/CBIL/Util
>      [copy]
> Copying 1 file to /usr/local/GUS/gus_home/doc/CBIL/Util
>      [echo]
> .
>      [echo] Installing CBIL/HQ
>      [copy] Copying 1 file to
> /usr/local/GUS/gus_home/bin
>     [mkdir] Created dir:
> /usr/local/GUS/gus_home/lib/perl/CBIL/HQ
>      [copy] Copying 3 files
> to /usr/local/GUS/gus_home/lib/perl/CBIL/HQ
>      [echo] .
>    =20
> [echo] Installing CBIL/ObjectMapper
>     [mkdir] Created dir:
> /usr/local/GUS/gus_home/lib/perl/CBIL/ObjectMapper
>  [copy]
> Copying 7 files to /usr/local/GUS/gus_home/lib/perl/CBIL/ObjectMapper
>      [copy] Copying 1 file to /usr/local/GUS/gus_home/config
>   =20
> [mkdir] Created dir: /usr/local/GUS/gus_home/doc/CBIL/ObjectMapper
>     [copy] Copying 1 file to
> /usr/local/GUS/gus_home/doc/CBIL/ObjectMapper
>    [concat] No existing
> files and no nested text, doing nothing
>      [echo] .
>    =20
> [echo] Installing GUS/Supported
>      [copy] Copying 1 file to
> /usr/local/GUS/gus_home/bin
>     [mkdir] Created dir:
> /usr/local/GUS/gus_home/lib/perl/GUS/Supported
>      [copy] Copying 2
> files to /usr/local/GUS/gus_home/lib/perl/GUS/Supported
>     [mkdir]
> Created dir: /usr/local/GUS/gus_home/lib/perl/GUS/Supported/Plugin
>      [copy] Copying 19 files to
> /usr/local/GUS/gus_home/lib/perl/GUS/Supported/Plugin
>     [copy]
> Copying 2 files to /usr/local/GUS/gus_home/config
>    [mkdir] Created
> dir: /usr/local/GUS/gus_home/doc/GUS/Supported
>   [copy] Copying 5
> files to /usr/local/GUS/gus_home/doc/GUS/Supported
>      [echo] .
>     [echo] Installing GUS/Community
>      [copy] Copying 4 files to
> /usr/local/GUS/gus_home/bin
>     [mkdir] Created dir:
> /usr/local/GUS/gus_home/lib/perl/GUS/Community
>      [copy] Copying 10
> files to /usr/local/GUS/gus_home/lib/perl/GUS/Community
>     [copy]
> Copying 2 files to /usr/local/GUS/gus_home/lib/java
>    [mkdir]
> Created dir: /usr/local/GUS/gus_home/lib/perl/GUS/Community/Plugin
>      [copy] Copying 41 files to
> /usr/local/GUS/gus_home/lib/perl/GUS/Community/Plugin
>     [copy]
> Copying 10 files to /usr/local/GUS/gus_home/config
>    [mkdir]
> Created dir: /usr/local/GUS/gus_home/doc/GUS/Community
>   [copy]
> Copying 7 files to /usr/local/GUS/gus_home/doc/GUS/Community
>    =20
> [echo] .
>     [echo] Installing GUS/DBAdmin
>      [copy] Copying
> 8 files to /usr/local/GUS/gus_home/bin
>     [mkdir] Created dir:
> /usr/local/GUS/gus_home/lib/perl/GUS/DBAdmin
>      [copy] Copying 6
> files to /usr/local/GUS/gus_home/lib/perl/GUS/DBAdmin
>     [copy]
> Copying 5 files to /usr/local/GUS/gus_home/lib/java
>    [mkdir]
> Created dir: /usr/local/GUS/project_home/GUS/DBAdmin/classes
>   =20
> [javac] Compiling 46 source files to
> /usr/local/GUS/project_home/GUS/DBAdmin/classes
>     [javac] Note:
> Some input files use unchecked or unsafe operations.
>    [javac]
> Note: Recompile with -Xlint:unchecked for details.
>      [jar]
> Building jar: /usr/local/GUS/gus_home/lib/java/GUS-DBAdmin.jar
>    =20
> [echo] .
>      [echo] Installing GUS/GOPredict
>      [copy]
> Copying 3 files to /usr/local/GUS/gus_home/bin
>     [mkdir] Created
> dir: /usr/local/GUS/gus_home/lib/perl/GUS/GOPredict
>      [copy]
> Copying 20 files to /usr/local/GUS/gus_home/lib/perl/GUS/GOPredict
>  [mkdir] Created dir:
> /usr/local/GUS/gus_home/lib/perl/GUS/GOPredict/Plugin
>     [copy]
> Copying 8 files to
> /usr/local/GUS/gus_home/lib/perl/GUS/GOPredict/Plugin
>    [mkdir]
> Created dir: /usr/local/GUS/gus_home/doc/GUS/GOPredict
>   [copy]
> Copying 1 file to /usr/local/GUS/gus_home/doc/GUS/GOPredict
>   =20
> [mkdir] Created dir: /usr/local/GUS/project_home/GUS/GOPredict/classes
>     [javac] Compiling 10 source files to
> /usr/local/GUS/project_home/GUS/GOPredict/classes
>     [javac] Note:
> Some input files use unchecked or unsafe operations.
>    [javac]
> Note: Recompile with -Xlint:unchecked for details.
>      [jar]
> Building jar: /usr/local/GUS/gus_home/lib/java/GUS-GOPredict.jar
>    =20
> [echo] .
>      [echo] Installing GUS/Schema
>     [mkdir] Created
> dir: /usr/local/GUS/project_home/GUS/Schema/classes
>     [javac]
> Compiling 1 source file to
> /usr/local/GUS/project_home/GUS/Schema/classes
>     [javac] Note:
> /usr/local/GUS/project_home/GUS/Schema/src/java/org/gusdb/schema/InstallS=
chema
> Task.java
> uses unchecked or unsafe operations.
>     [javac] Note: Recompile with
> -Xlint:unchecked for details.
>       [jar] Building jar:
> /usr/local/GUS/gus_home/lib/java/GUS-Schema.jar
> [InstallSchema] Aug
> 23, 2005 9:37:23 AM org.gusdb.schema.InstallSchemaTask execute
> [InstallSchema] INFO: Reading database from
> /usr/local/GUS/project_home/GUS/Schema/gus_schema.xml
> [InstallSchema]
> Aug 23, 2005 9:37:23 AM org.gusdb.dbadmin.reader.SchemaReader doRead
> [InstallSchema] INFO: Reading Database
> [InstallSchema] Aug 23, 2005
> 9:37:27 AM org.gusdb.dbadmin.model.Database resolveReferences
> [InstallSchema] INFO: Resolving Database References
> [InstallSchema]
> Aug 23, 2005 9:37:28 AM org.gusdb.dbadmin.util.DatabaseValidator
> validate
> [InstallSchema] INFO: Validating Database: 'null'
> [InstallSchema] Aug 23, 2005 9:37:28 AM
> org.gusdb.schema.InstallSchemaTask setTablespace
> [InstallSchema]
> INFO: Setting tablespaces to gusdb
> [InstallSchema] Aug 23, 2005
> 9:37:28 AM org.gusdb.dbadmin.util.DatabaseValidator validate
> [InstallSchema] INFO: Validating Database: 'null'
> [InstallSchema]
> Aug 23, 2005 9:37:28 AM org.gusdb.dbadmin.writer.SchemaWriter write
> [InstallSchema] INFO: Writing Database
> [InstallSchema] Aug 23, 2005
> 9:37:29 AM org.gusdb.dbadmin.util.DatabaseValidator validate
> [InstallSchema] INFO: Validating Database: 'null'
> [InstallSchema]
> Aug 23, 2005 9:37:29 AM org.gusdb.dbadmin.writer.SchemaWriter write
> [InstallSchema] INFO: Writing Database
> =20
> BUILD FAILED
> /usr/local/GUS/project_home/install/build.xml:28: The following error
> occurred while executing this line:
> /usr/local/GUS/project_home/GUS/build.xml:92: java.io.IOException: Error
> executing SQL: '
> ALTER USER RAD QUOTA UNLIMITED ON gusdb' Error:
> ORA-00959: tablespace 'GUSDB' does not exist
> =20
> =20
> Total
> time: 22 seconds
>=20
>=20
> The user GUS
> uses to connect has all sysdba privileges but the related to rule, rule
> set and evaluation context.
>=20
> I believe that somehow the build
> script can't not connect to the gusdb tablespace sometimes. And there's
> another strange thing with the DatabaseValidator at some lines like
> this:
>=20
> org.gusdb.dbadmin.util.DatabaseValidator
> validate
>=20
> [InstallSchema] INFO: Validating Database: 'null'
>=20
> Can anyone give me a tip?
>=20
> Thanks=20
>=20
> Adhemar Zerlotini Neto
> Centro de Pesquisas Ren=E9 Rachou - FIOCRUZ
> Av. Augusto de Lima 1715
> BH MG 30190-002, Brazil
> Phone: +55-31-3349-7785
> ------------------------------------------------------- SF.Net email is
> Sponsored by the Better Software Conference  EXPO September 19-22, 2005 *=
 San
> Francisco, CA * Development Lifecycle Practices Agile  Plan-Driven Develo=
pment
> * Managing Projects  Teams * Testing  QA Security * Process Improvement
> Measurement * http://www.sqe.com/bsce5sf
> _______________________________________________ Gusdev-gusdev mailing lis=
t
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

[GUSDEV] Build

[Adhemar Z. N. <ad...@cp...>]

<br />Hi Everybody,<br /><br />I=B4m a newbie using GUS. I=B4m trying to
install the 3.5 version on Oracle 10g and I=B4m having some problems with
the build script.<br /><br />I tried to use the build script serveral
times from the scratch. Here is the output of the last try:<br /><br
/><font size=3D"1" style=3D"font-family: courier new,courier,monospace;">=
<font
size=3D"1">[oracle@gus install]$<br />build GUS install -append
-installDBSchema<br />    [mkdir] Created dir:<br
/>/usr/local/GUS/project_home/install/classes<br />    [javac] Compiling
1<br />source file to /usr/local/GUS/project_home/install/classes<br
/>[WritePropertyFiles] Aug 23, 2005 9:37:09 AM<br
/>org.gusdb.install.WritePropertyFileTask initialize<br
/>[WritePropertyFiles] INFO: Creating configuration directory<br />    <b=
r
/>[copy] Copying 1 file to /usr/local/GUS/gus_home/config<br />   =20
[copy]<br />Copying 1 file to /usr/local/GUS/gus_home/config<br />   =20
[echo] .<br />     [echo] Installing CBIL/Bio<br />    [mkdir] Created
dir:<br />/usr/local/GUS/gus_home/bin<br />     [copy] Copying 5 files
to<br />/usr/local/GUS/gus_home/bin<br />    [mkdir] Created dir:<br
/>/usr/local/GUS/gus_home/lib/perl/CBIL/Bio<br />     [copy] Copying 66<b=
r
/>files to /usr/local/GUS/gus_home/lib/perl/CBIL/Bio<br />    [mkdir]<br
/>Created dir: /usr/local/GUS/gus_home/test/CBIL/Bio<br />     [copy]<br
/>Copying 4 files to /usr/local/GUS/gus_home/test/CBIL/Bio<br />  =20
[mkdir]<br />Created dir: /usr/local/GUS/gus_home/data/CBIL/Bio<br />   =20
[copy]<br />Copying 9 files to /usr/local/GUS/gus_home/data/CBIL/Bio<br /=
>
    [echo]<br />.<br />     [echo] Installing CBIL/CSP<br />     [copy]
Copying 1 file to<br />/usr/local/GUS/gus_home/bin<br />    [mkdir]
Created dir:<br />/usr/local/GUS/gus_home/lib/perl/CBIL/CSP<br />   =20
[copy] Copying 11<br />files to
/usr/local/GUS/gus_home/lib/perl/CBIL/CSP<br />    [mkdir]<br />Created
dir: /usr/local/GUS/gus_home/lib/java<br />     [copy] Copying 2<br
/>files to /usr/local/GUS/gus_home/lib/java<br />    [mkdir] Created
dir:<br />/usr/local/GUS/gus_home/doc/CBIL/CSP<br />     [copy] Copying 1=
0
files to<br />/usr/local/GUS/gus_home/doc/CBIL/CSP<br />    [mkdir]
Created dir:<br />/usr/local/GUS/project_home/CBIL/CSP/classes<br />  =20
[javac] Compiling 27<br />source files to
/usr/local/GUS/project_home/CBIL/CSP/classes<br />   <br />[javac]
Note:<br
/>/usr/local/GUS/project_home/CBIL/CSP/src/java/edu/cbil/csp/dialog/Actio=
n.java<br
/>uses or overrides a deprecated API.<br />    [javac] Note: Recompile
with<br />-Xlint:deprecation for details.<br />    [javac] Note: Some
input files<br />use unchecked or unsafe operations.<br />    [javac]
Note: Recompile with<br />-Xlint:unchecked for details.<br />      [jar]
Building jar:<br />/usr/local/GUS/gus_home/lib/java/CBIL-CSP.jar<br />   =
=20
[echo] .<br />    <br />[echo] Installing CBIL/Util<br />    [mkdir]
Created dir:<br />/usr/local/GUS/gus_home/lib/perl/CBIL/Util<br />   =20
[copy] Copying 8<br />files to
/usr/local/GUS/gus_home/lib/perl/CBIL/Util<br />    [mkdir]<br />Created
dir: /usr/local/GUS/gus_home/doc/CBIL/Util<br />     [copy]<br />Copying =
1
file to /usr/local/GUS/gus_home/doc/CBIL/Util<br />     [echo]<br />.<br
/>     [echo] Installing CBIL/HQ<br />     [copy] Copying 1 file to<br
/>/usr/local/GUS/gus_home/bin<br />    [mkdir] Created dir:<br
/>/usr/local/GUS/gus_home/lib/perl/CBIL/HQ<br />     [copy] Copying 3
files<br />to /usr/local/GUS/gus_home/lib/perl/CBIL/HQ<br />     [echo]
.<br />    <br />[echo] Installing CBIL/ObjectMapper<br />    [mkdir]
Created dir:<br />/usr/local/GUS/gus_home/lib/perl/CBIL/ObjectMapper<br /=
>
    [copy]<br />Copying 7 files to
/usr/local/GUS/gus_home/lib/perl/CBIL/ObjectMapper<br />     [copy]
Copying 1 file to /usr/local/GUS/gus_home/config<br />   <br />[mkdir]
Created dir: /usr/local/GUS/gus_home/doc/CBIL/ObjectMapper<br />   =20
[copy] Copying 1 file to<br
/>/usr/local/GUS/gus_home/doc/CBIL/ObjectMapper<br />   [concat] No
existing<br />files and no nested text, doing nothing<br />     [echo]
.<br />    <br />[echo] Installing GUS/Supported<br />     [copy] Copying
1 file to<br />/usr/local/GUS/gus_home/bin<br />    [mkdir] Created
dir:<br />/usr/local/GUS/gus_home/lib/perl/GUS/Supported<br />     [copy]
Copying 2<br />files to /usr/local/GUS/gus_home/lib/perl/GUS/Supported<br
/>    [mkdir]<br />Created dir:
/usr/local/GUS/gus_home/lib/perl/GUS/Supported/Plugin<br />     [copy]
Copying 19 files to<br
/>/usr/local/GUS/gus_home/lib/perl/GUS/Supported/Plugin<br />   =20
[copy]<br />Copying 2 files to /usr/local/GUS/gus_home/config<br />  =20
[mkdir] Created<br />dir: /usr/local/GUS/gus_home/doc/GUS/Supported<br />=
=20
   [copy] Copying 5<br />files to
/usr/local/GUS/gus_home/doc/GUS/Supported<br />     [echo] .<br />   =20
[echo] Installing GUS/Community<br />     [copy] Copying 4 files to<br
/>/usr/local/GUS/gus_home/bin<br />    [mkdir] Created dir:<br
/>/usr/local/GUS/gus_home/lib/perl/GUS/Community<br />     [copy] Copying
10<br />files to /usr/local/GUS/gus_home/lib/perl/GUS/Community<br />   =20
[copy]<br />Copying 2 files to /usr/local/GUS/gus_home/lib/java<br />  =20
[mkdir]<br />Created dir:
/usr/local/GUS/gus_home/lib/perl/GUS/Community/Plugin<br />     [copy]
Copying 41 files to<br
/>/usr/local/GUS/gus_home/lib/perl/GUS/Community/Plugin<br />   =20
[copy]<br />Copying 10 files to /usr/local/GUS/gus_home/config<br />  =20
[mkdir]<br />Created dir: /usr/local/GUS/gus_home/doc/GUS/Community<br />=
=20
   [copy]<br />Copying 7 files to
/usr/local/GUS/gus_home/doc/GUS/Community<br />    <br />[echo] .<br />  =
=20
 [echo] Installing GUS/DBAdmin<br />     [copy] Copying<br />8 files to
/usr/local/GUS/gus_home/bin<br />    [mkdir] Created dir:<br
/>/usr/local/GUS/gus_home/lib/perl/GUS/DBAdmin<br />     [copy] Copying
6<br />files to /usr/local/GUS/gus_home/lib/perl/GUS/DBAdmin<br />   =20
[copy]<br />Copying 5 files to /usr/local/GUS/gus_home/lib/java<br />  =20
[mkdir]<br />Created dir:
/usr/local/GUS/project_home/GUS/DBAdmin/classes<br />   <br />[javac]
Compiling 46 source files to<br
/>/usr/local/GUS/project_home/GUS/DBAdmin/classes<br />    [javac]
Note:<br />Some input files use unchecked or unsafe operations.<br />  =20
[javac]<br />Note: Recompile with -Xlint:unchecked for details.<br />    =
=20
[jar]<br />Building jar:
/usr/local/GUS/gus_home/lib/java/GUS-DBAdmin.jar<br />    <br />[echo]
.<br />     [echo] Installing GUS/GOPredict<br />     [copy]<br />Copying
3 files to /usr/local/GUS/gus_home/bin<br />    [mkdir] Created<br />dir:
/usr/local/GUS/gus_home/lib/perl/GUS/GOPredict<br />     [copy]<br
/>Copying 20 files to /usr/local/GUS/gus_home/lib/perl/GUS/GOPredict<br /=
>
   [mkdir] Created dir:<br
/>/usr/local/GUS/gus_home/lib/perl/GUS/GOPredict/Plugin<br />   =20
[copy]<br />Copying 8 files to<br
/>/usr/local/GUS/gus_home/lib/perl/GUS/GOPredict/Plugin<br />  =20
[mkdir]<br />Created dir: /usr/local/GUS/gus_home/doc/GUS/GOPredict<br />=
=20
   [copy]<br />Copying 1 file to
/usr/local/GUS/gus_home/doc/GUS/GOPredict<br />   <br />[mkdir] Created
dir: /usr/local/GUS/project_home/GUS/GOPredict/classes<br />    [javac]
Compiling 10 source files to<br
/>/usr/local/GUS/project_home/GUS/GOPredict/classes<br />    [javac]
Note:<br />Some input files use unchecked or unsafe operations.<br />  =20
[javac]<br />Note: Recompile with -Xlint:unchecked for details.<br />    =
=20
[jar]<br />Building jar:
/usr/local/GUS/gus_home/lib/java/GUS-GOPredict.jar<br />    <br />[echo]
.<br />     [echo] Installing GUS/Schema<br />    [mkdir] Created<br
/>dir: /usr/local/GUS/project_home/GUS/Schema/classes<br />    [javac]<br
/>Compiling 1 source file to<br
/>/usr/local/GUS/project_home/GUS/Schema/classes<br />    [javac] Note:<b=
r
/>/usr/local/GUS/project_home/GUS/Schema/src/java/org/gusdb/schema/Instal=
lSchemaTask.java<br
/>uses unchecked or unsafe operations.<br />    [javac] Note: Recompile
with<br />-Xlint:unchecked for details.<br />      [jar] Building jar:<br
/>/usr/local/GUS/gus_home/lib/java/GUS-Schema.jar<br />[InstallSchema]
Aug<br />23, 2005 9:37:23 AM org.gusdb.schema.InstallSchemaTask execute<b=
r
/>[InstallSchema] INFO: Reading database from<br
/>/usr/local/GUS/project_home/GUS/Schema/gus_schema.xml<br
/>[InstallSchema]<br />Aug 23, 2005 9:37:23 AM
org.gusdb.dbadmin.reader.SchemaReader doRead<br />[InstallSchema] INFO:
Reading Database<br />[InstallSchema] Aug 23, 2005<br />9:37:27 AM
org.gusdb.dbadmin.model.Database resolveReferences<br />[InstallSchema]
INFO: Resolving Database References<br />[InstallSchema]<br />Aug 23, 200=
5
9:37:28 AM org.gusdb.dbadmin.util.DatabaseValidator<br />validate<br
/>[InstallSchema] INFO: Validating Database: 'null'<br />[InstallSchema]
Aug 23, 2005 9:37:28 AM<br />org.gusdb.schema.InstallSchemaTask
setTablespace<br />[InstallSchema]<br />INFO: Setting tablespaces to
gusdb<br />[InstallSchema] Aug 23, 2005<br />9:37:28 AM
org.gusdb.dbadmin.util.DatabaseValidator validate<br />[InstallSchema]
INFO: Validating Database: 'null'<br />[InstallSchema]<br />Aug 23, 2005
9:37:28 AM org.gusdb.dbadmin.writer.SchemaWriter write<br
/>[InstallSchema] INFO: Writing Database<br />[InstallSchema] Aug 23,
2005<br />9:37:29 AM org.gusdb.dbadmin.util.DatabaseValidator validate<br
/>[InstallSchema] INFO: Validating Database: 'null'<br
/>[InstallSchema]<br />Aug 23, 2005 9:37:29 AM
org.gusdb.dbadmin.writer.SchemaWriter write<br />[InstallSchema] INFO:
Writing Database<br /> <br />BUILD FAILED<br
/>/usr/local/GUS/project_home/install/build.xml:28: The following error<b=
r
/>occurred while executing this line:<br
/>/usr/local/GUS/project_home/GUS/build.xml:92: java.io.IOException:
Error<br />executing SQL: '<br />ALTER USER RAD QUOTA UNLIMITED ON gusdb'
Error:<br />ORA-00959: tablespace 'GUSDB' does not exist<br /> <br /> <br
/>Total<br />time: 22 seconds</font><br /></font><br /><br />The user
GUS<br />uses to connect has all sysdba privileges but the related to
rule, rule<br />set and evaluation context. <br /><br />I believe that
somehow the build<br />script can't not connect to the gusdb tablespace
sometimes. And there's<br />another strange thing with the
DatabaseValidator at some lines like<br />this:<br /><br /><font size=3D"=
1"
style=3D"font-family: courier
new,courier,monospace;">org.gusdb.dbadmin.util.DatabaseValidator<br
/>validate<br /><br />[InstallSchema] INFO: Validating Database:
'null'</font><br /><br />Can anyone give me a tip?<br /><br />Thanks <br
/><br />Adhemar Zerlotini Neto<br />Centro de Pesquisas Ren=E9 Rachou -
FIOCRUZ<br />Av. Augusto de Lima 1715<br />BH MG 30190-002, Brazil<br
/>Phone: +55-31-3349-7785

[GUSDEV] GeneticMarker view

[Deborah P. <pi...@pc...>]

I suggest a new view of dots.NaSequenceImp that would be used to store genetic marker data. Genetic markers are a staple 
genetic tool but include a large variety of data types, some of which may be covered by other feature views. I am proposing this view 
for the variety of genetic marker data that are not specifically stored elsewhere. Below is a proposed view definition that requires 
review and probably modification.  


SELECT NA_Feature_ID as na_feature_id,
NA_SEQUENCE_ID as na_sequence_id,
SUBCLASS_VIEW as subclass_view,
NAME as name,
SEQUENCE_ONTOLOGY_ID as sequence_ontology_id,
PARENT_ID as parent_id,
EXTERNAL_DATABASE_RELEASE_ID as external_database_release_id,
SOURCE_ID as source_id,
PREDICTION_ALGORITHM_ID as prediction_algorithm_id,
IS_PREDICTED as is_predicted,
REVIEW_STATUS_ID as review_status_id,
STRING1 as alias,
STRING2 as phenotype,
STRING3 as type,
STRING4 as linkage_group,
STRING5 as centimorgan,
STRING6 as measure_of_heterogeneity,
STRING7 as penetrance,
STRING8 as organism,
STRING9 as strain,
STRING12 as product,
MODIFICATION_DATE as modification_date,
USER_READ as user_read,
USER_WRITE as user_write,
GROUP_READ as group_read,
GROUP_WRITE as group_write,
OTHER_READ as other_read,
OTHER_WRITE as other_write,
ROW_USER_ID as row_user_id,
ROW_GROUP_ID as row_group_id,
ROW_PROJECT_ID as row_project_id,
ROW_ALG_INVOCATION_ID as row_alg_invocation_id,
FROM DoTS.NAFeatureImp WHERE subclass_view='GeneticMarker'

Re: [GUSDEV] Gus Release Schedule

[Michael S. <msa...@pc...>]

Yes, I agree--  for all types of issues the bug should not be closed until
it has been fully resolved, i.e. a change has been made in code.  For schema
issues, the flow I anticipate is:

1) An issue is opened, and automatically assigned to the owner of the
relevant schema.

2) The issue is investigated, with the schema owner ultimately accepting the
change or rejecting it.  If the change is accepted, the issue should be
reassigned to me with a comment indicating acceptance.

3) I'll implement the change, and when complete, mark the issue as closed.

Note, when I say that I'll implement the change, I mean updated the schema
XML file to reflect it.

8/29 works for me as well.

--Mike


On 8/19/05 5:36 PM, "Chris Stoeckert" <sto...@pc...> wrote:

> Mike,
>> When all issues from the report have been closed, the product is
>> ready for
>> release.
>> 
>> Comments/Suggestions?
> 
> I think we need some clarification of this. For schema, it doesn't
> seem right to mark a bug as resolved until the change has been made.
> Also, the schema owners need to meet and go over the upcoming patch
> schema changes, have you administer the accepted ones, and then close
> them as resolved. Let's pick a date for this. How about August 29th?
> 
> Thanks,
> Chris
> 
>   

Re: [GUSDEV] Gus Release Schedule

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

Mike,
> When all issues from the report have been closed, the product is  
> ready for
> release.
>
> Comments/Suggestions?

I think we need some clarification of this. For schema, it doesn't  
seem right to mark a bug as resolved until the change has been made.  
Also, the schema owners need to meet and go over the upcoming patch  
schema changes, have you administer the accepted ones, and then close  
them as resolved. Let's pick a date for this. How about August 29th?

Thanks,
Chris

  

Re: [GUSDEV] GUS plugin InsertGeneOntology missed loading data?

[steve <sfi...@pc...>]

a quick report on the status of this.   jennifer made progress, being 
able to reproduce the problem here at cbil.  today is a vacation day for 
her, so i expect she'll be able to make more progress on monday. 

steve

jld...@se... wrote:

>I'm looking into the issue, and will let you know what I find as soon as possible.
>
>Jennifer
>
>Quoting Jian Lu <jl...@vb...>:
>
>  
>
>>Steve,
>>
>>After further investigation of GO files and comparison of the database, 
>>here is the report:
>>
>>GO file information:
>>!autogenerated-by:     DAG-Edit version 1.419 rev 3
>>!saved-by:             gocvs
>>!date:                 Fri Aug 12 21:00:17 PDT 2005
>>!version: $Revision: 3.306 $
>>
>>unique GO terms in component.ontology: 1745
>>unique GO terms in function.ontology: 7902
>>unique GO terms in process.ontology: 10370
>>unique GO terms in all three files: 20015
>>
>>total loaded GO terms: 19395
>>total missing GO terms: 620
>>
>>
>>steve wrote:
>>
>>    
>>
>>>jian-
>>>
>>>yes, we have used the plugin, but it has been changed a little 
>>>recently.  can you do a grep on the file to count how many terms there 
>>>are in it?   have you looked carefully at those entries in the file to 
>>>see if there is something that distinguishes them?    can you count 
>>>how many rows actually are in the database that were put there by that 
>>>run of the plugin?
>>>
>>>thanks for your help,
>>>steve
>>>
>>>Jian Lu wrote:
>>>
>>>      
>>>
>>>>Hi group,
>>>>
>>>>I downloaded Gene Ontology version 3.306 
>>>>(component.ontology,function.ontology, process.ontology) and ran
>>>>GUS::Supported::Plugin::InsertGeneOntology to load them into our GUS 
>>>>database.
>>>>Here is my command:
>>>>
>>>>ga GUS::Supported::Plugin::InsertGeneOntology --filePath 
>>>>/home/data/ontology --functionExtDbName 'GO Function' 
>>>>--processExtDbName 'GO Process' --componentExtDbName 'GO Component' 
>>>>--commit
>>>>
>>>>
>>>>Everything looks fine, no errors. It returned a result as "Created 
>>>>19395 entries in GOTerm, 28145 entries in GORelationship, and 16375 
>>>>entries in GOSynonym.  Skipped 0 total entries".
>>>>
>>>>But when I was doing other data checking, I found there are three GO 
>>>>terms that have not been loaded, GO:009387, GO:0005331, GO:0009456. 
>>>>They do exist on the GO downloaded files.
>>>>Has anyone used this plugin to load GO and checked its completeness? 
>>>>Please advise. Thanks.
>>>>
>>>>Jian
>>>>
>>>>
>>>>
>>>>
>>>>-------------------------------------------------------
>>>>SF.Net email is Sponsored by the Better Software Conference & EXPO
>>>>September 19-22, 2005 * San Francisco, CA * Development Lifecycle 
>>>>Practices
>>>>Agile & Plan-Driven Development * Managing Projects & Teams * Testing 
>>>>& QA
>>>>Security * Process Improvement & Measurement * 
>>>>http://www.sqe.com/bsce5sf
>>>>_______________________________________________
>>>>Gusdev-gusdev mailing list
>>>>Gus...@li...
>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>        
>>>>
>>    
>>
>
>
>
>
>-------------------------------------------------------
>SF.Net email is Sponsored by the Better Software Conference & EXPO
>September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices
>Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA
>Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

Re: [GUSDEV] GUS plugin InsertGeneOntology missed loading data?

[Michael S. <msa...@pc...>]

Has a bug been filed for this?  If not, please do so.

--Mike



On 8/18/05 5:25 PM, "jld...@se..." <jld...@se...>
wrote:

> I'm looking into the issue, and will let you know what I find as soon as
> possible.
> 
> Jennifer
> 
> Quoting Jian Lu <jl...@vb...>:
> 
>> Steve,
>> 
>> After further investigation of GO files and comparison of the database,
>> here is the report:
>> 
>> GO file information:
>> !autogenerated-by:     DAG-Edit version 1.419 rev 3
>> !saved-by:             gocvs
>> !date:                 Fri Aug 12 21:00:17 PDT 2005
>> !version: $Revision: 3.306 $
>> 
>> unique GO terms in component.ontology: 1745
>> unique GO terms in function.ontology: 7902
>> unique GO terms in process.ontology: 10370
>> unique GO terms in all three files: 20015
>> 
>> total loaded GO terms: 19395
>> total missing GO terms: 620
>> 
>> 
>> steve wrote:
>> 
>>> jian-
>>> 
>>> yes, we have used the plugin, but it has been changed a little
>>> recently.  can you do a grep on the file to count how many terms there
>>> are in it?   have you looked carefully at those entries in the file to
>>> see if there is something that distinguishes them?    can you count
>>> how many rows actually are in the database that were put there by that
>>> run of the plugin?
>>> 
>>> thanks for your help,
>>> steve
>>> 
>>> Jian Lu wrote:
>>> 
>>>> Hi group,
>>>> 
>>>> I downloaded Gene Ontology version 3.306
>>>> (component.ontology,function.ontology, process.ontology) and ran
>>>> GUS::Supported::Plugin::InsertGeneOntology to load them into our GUS
>>>> database.
>>>> Here is my command:
>>>> 
>>>> ga GUS::Supported::Plugin::InsertGeneOntology --filePath
>>>> /home/data/ontology --functionExtDbName 'GO Function'
>>>> --processExtDbName 'GO Process' --componentExtDbName 'GO Component'
>>>> --commit
>>>> 
>>>> 
>>>> Everything looks fine, no errors. It returned a result as "Created
>>>> 19395 entries in GOTerm, 28145 entries in GORelationship, and 16375
>>>> entries in GOSynonym.  Skipped 0 total entries".
>>>> 
>>>> But when I was doing other data checking, I found there are three GO
>>>> terms that have not been loaded, GO:009387, GO:0005331, GO:0009456.
>>>> They do exist on the GO downloaded files.
>>>> Has anyone used this plugin to load GO and checked its completeness?
>>>> Please advise. Thanks.
>>>> 
>>>> Jian
>>>> 
>>>> 
>>>> 
>>>> 
>>>> -------------------------------------------------------
>>>> SF.Net email is Sponsored by the Better Software Conference & EXPO
>>>> September 19-22, 2005 * San Francisco, CA * Development Lifecycle
>>>> Practices
>>>> Agile & Plan-Driven Development * Managing Projects & Teams * Testing
>>>> & QA
>>>> Security * Process Improvement & Measurement *
>>>> http://www.sqe.com/bsce5sf
>>>> _______________________________________________
>>>> Gusdev-gusdev mailing list
>>>> Gus...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>> 
>> 
>> 
> 
> 
> 
> 
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices
> Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA
> Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [GUSDEV] GUS plugin InsertGeneOntology missed loading data?

[Michael S. <msa...@pc...>]

Has a bug been filed for this?  If not, please do so.

--Mike


On 8/18/05 5:25 PM, "jld...@se..." <jld...@se...>
wrote:

> I'm looking into the issue, and will let you know what I find as soon as
> possible.
> 
> Jennifer
> 
> Quoting Jian Lu <jl...@vb...>:
> 
>> Steve,
>> 
>> After further investigation of GO files and comparison of the database,
>> here is the report:
>> 
>> GO file information:
>> !autogenerated-by:     DAG-Edit version 1.419 rev 3
>> !saved-by:             gocvs
>> !date:                 Fri Aug 12 21:00:17 PDT 2005
>> !version: $Revision: 3.306 $
>> 
>> unique GO terms in component.ontology: 1745
>> unique GO terms in function.ontology: 7902
>> unique GO terms in process.ontology: 10370
>> unique GO terms in all three files: 20015
>> 
>> total loaded GO terms: 19395
>> total missing GO terms: 620
>> 
>> 
>> steve wrote:
>> 
>>> jian-
>>> 
>>> yes, we have used the plugin, but it has been changed a little
>>> recently.  can you do a grep on the file to count how many terms there
>>> are in it?   have you looked carefully at those entries in the file to
>>> see if there is something that distinguishes them?    can you count
>>> how many rows actually are in the database that were put there by that
>>> run of the plugin?
>>> 
>>> thanks for your help,
>>> steve
>>> 
>>> Jian Lu wrote:
>>> 
>>>> Hi group,
>>>> 
>>>> I downloaded Gene Ontology version 3.306
>>>> (component.ontology,function.ontology, process.ontology) and ran
>>>> GUS::Supported::Plugin::InsertGeneOntology to load them into our GUS
>>>> database.
>>>> Here is my command:
>>>> 
>>>> ga GUS::Supported::Plugin::InsertGeneOntology --filePath
>>>> /home/data/ontology --functionExtDbName 'GO Function'
>>>> --processExtDbName 'GO Process' --componentExtDbName 'GO Component'
>>>> --commit
>>>> 
>>>> 
>>>> Everything looks fine, no errors. It returned a result as "Created
>>>> 19395 entries in GOTerm, 28145 entries in GORelationship, and 16375
>>>> entries in GOSynonym.  Skipped 0 total entries".
>>>> 
>>>> But when I was doing other data checking, I found there are three GO
>>>> terms that have not been loaded, GO:009387, GO:0005331, GO:0009456.
>>>> They do exist on the GO downloaded files.
>>>> Has anyone used this plugin to load GO and checked its completeness?
>>>> Please advise. Thanks.
>>>> 
>>>> Jian
>>>> 
>>>> 
>>>> 
>>>> 
>>>> -------------------------------------------------------
>>>> SF.Net email is Sponsored by the Better Software Conference & EXPO
>>>> September 19-22, 2005 * San Francisco, CA * Development Lifecycle
>>>> Practices
>>>> Agile & Plan-Driven Development * Managing Projects & Teams * Testing
>>>> & QA
>>>> Security * Process Improvement & Measurement *
>>>> http://www.sqe.com/bsce5sf
>>>> _______________________________________________
>>>> Gusdev-gusdev mailing list
>>>> Gus...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>> 
>> 
>> 
> 
> 
> 
> 
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices
> Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA
> Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
> _______________________________________________
> Gusdev-gusdev mailing list
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> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [GUSDEV] GUS plugin InsertGeneOntology missed loading data?

[<jld...@se...>]

I'm looking into the issue, and will let you know what I find as soon as possible.

Jennifer

Quoting Jian Lu <jl...@vb...>:

> Steve,
> 
> After further investigation of GO files and comparison of the database, 
> here is the report:
> 
> GO file information:
> !autogenerated-by:     DAG-Edit version 1.419 rev 3
> !saved-by:             gocvs
> !date:                 Fri Aug 12 21:00:17 PDT 2005
> !version: $Revision: 3.306 $
> 
> unique GO terms in component.ontology: 1745
> unique GO terms in function.ontology: 7902
> unique GO terms in process.ontology: 10370
> unique GO terms in all three files: 20015
> 
> total loaded GO terms: 19395
> total missing GO terms: 620
> 
> 
> steve wrote:
> 
> > jian-
> >
> > yes, we have used the plugin, but it has been changed a little 
> > recently.  can you do a grep on the file to count how many terms there 
> > are in it?   have you looked carefully at those entries in the file to 
> > see if there is something that distinguishes them?    can you count 
> > how many rows actually are in the database that were put there by that 
> > run of the plugin?
> >
> > thanks for your help,
> > steve
> >
> > Jian Lu wrote:
> >
> >> Hi group,
> >>
> >> I downloaded Gene Ontology version 3.306 
> >> (component.ontology,function.ontology, process.ontology) and ran
> >> GUS::Supported::Plugin::InsertGeneOntology to load them into our GUS 
> >> database.
> >> Here is my command:
> >>
> >> ga GUS::Supported::Plugin::InsertGeneOntology --filePath 
> >> /home/data/ontology --functionExtDbName 'GO Function' 
> >> --processExtDbName 'GO Process' --componentExtDbName 'GO Component' 
> >> --commit
> >>
> >>
> >> Everything looks fine, no errors. It returned a result as "Created 
> >> 19395 entries in GOTerm, 28145 entries in GORelationship, and 16375 
> >> entries in GOSynonym.  Skipped 0 total entries".
> >>
> >> But when I was doing other data checking, I found there are three GO 
> >> terms that have not been loaded, GO:009387, GO:0005331, GO:0009456. 
> >> They do exist on the GO downloaded files.
> >> Has anyone used this plugin to load GO and checked its completeness? 
> >> Please advise. Thanks.
> >>
> >> Jian
> >>
> >>
> >>
> >>
> >> -------------------------------------------------------
> >> SF.Net email is Sponsored by the Better Software Conference & EXPO
> >> September 19-22, 2005 * San Francisco, CA * Development Lifecycle 
> >> Practices
> >> Agile & Plan-Driven Development * Managing Projects & Teams * Testing 
> >> & QA
> >> Security * Process Improvement & Measurement * 
> >> http://www.sqe.com/bsce5sf
> >> _______________________________________________
> >> Gusdev-gusdev mailing list
> >> Gus...@li...
> >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
> 
>