gusdev-gusdev — Topics concerning GUS development

[Gusdev-gusdev] uploading P. falciparum data

[Fidel S. <fi...@vb...>]

I tried uploding P. falciparum chromosome data using the GBParser and
ran out of memory in all cases.  setMaximumNumberOfObjects is set to
4000000.  The verbose output files contain the line:
VLD     CBIL::Bio::GenBank::Origin      1
more than 20 million times before an =A8out of memory=A8 message is
output.

Here are some of some of the numbers for some of the files:
bash-2.05$ grep VLD NC_004325.gbk-gbparser.out | grep -c Origin
20479965
bash-2.05$ grep VLD NC_004314.gbk-gbparser.out | grep -c Origin
20356504
bash-2.05$ grep VLD NC_004315.gbk-gbparser.out | grep -c Origin
20335688

Has anyone run into something similar before?  How did the people
working on P. falciparum upload the data into GUS?

Thanks

Fidel

Re: [Gusdev-gusdev] everything works except commit!

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

Michael--

You'll probably need to grant select privileges on the sequence to 
whatever user (or users) login.  This is dependent on your instance of 
GUS, but for example:

grant select on dots.similarity_SQ to DOTS;

would allow the user DOTS to select on this sequence.

--Mike

On Apr 19, 2004, at 2:09 PM, MICHAEL LUCHTAN wrote:

> Michael-
> Just a little bit of sql help left I think.  I took your suggestion 
> below,
> logged in as sysdba executed the commands below.  Now, a regular user
> can't see the table.  I.E. I get the following error message when 
> running
> the plugin:
> DBD::Oracle::db prepare failed: ORA-00942: table or view does not exist
> (DBD ERROR: OCIStmtExecute/Describe) at
> /var/local/gus_home/lib/perl/GUS/Common/Plugin/LoadBlastSimFast.pm line
> 346, <GEN0> line 1651269.
> Which is in reference to the sql statement:
> select dots.similarity_SQ.NEXTVAL from DUAL
>
> Running sqlplus confirms that a regular user will get that error.  
> Running
> sqlplus as sysdba shows that it is there.
>
> How can I grant permission for folks to view /increase this sequence?
>
> Michael Luchtan
> http://www.cs.uga.edu/~luchtan
>
>
> On Mon, 19 Apr 2004, Michael Saffitz wrote:
>
>>
>> Hi Michael,
>>
>> Your sequences are out of sync with the corresponding tables.  You
>> should definitely continue to use the sequences (you'll avoid many
>> problems down the road), but you'll need to alter sequences so that
>> they start with the proper value.  For example, for the similarity
>> table:
>>
>> (Get the maximum value of the primary key:)
>>
>> select max(SIMILARITY_ID) from dots.similarity;
>>
>> You must then drop and recreate the sequence, setting the sequence to
>> start with the value you got in the query above, plus 5 or so to be
>> safe.  Let's say this is 5067:
>>
>> drop sequence dots.similarity_SQ;
>> create sequence dots.similarity_SQ START WITH 5073;
>>
>> Using the count(*) as the primary key generation is not supported and
>> is likely to produced unexpected results.
>>
>> --Mike
>> CBIL DBA
>>
>> On Apr 19, 2004, at 11:58 AM, MICHAEL LUCHTAN wrote:
>>
>>> Hello everyone-
>>> I have been attempting to load blast similarities into GUS with the
>>> plugin
>>> LoadBlastSimFast.pm after already loading some data in with the 
>>> plugin
>>> LoadBlastSimilarityPK.pm (which was slow compared with the Fasst
>>> version).
>>> Well, the first thing that LoadBlastSimFast.pm does is start
>>> complaining
>>> about PrimaryKey uniqueness constraints being violated.  It used some
>>> fancy Oracle SQL that I didn't understand:
>>> select dots.similarity_SQ.NEXTVAL from DUAL
>>> Which by debugging I found out started at one, and increased each 
>>> time
>>> we
>>> tested the plugin, regardless of commit not being turned on.
>>> Naturally this crashed, because
>>> we already had about 3,000 entries in the dots.similarity table and
>>> we already had a sequence_id with value 1.  There
>>> was likewise a problem with the dots.similarityspan table.
>>>
>>> Since I only having a workingman's knowledge of OracleSQL, I switched
>>> it
>>> so that it starts with
>>> select count(*) from dots.similarity
>>> And increases this by one for each entry.  Likewise for
>>> dots.similarityspan.  This seemed to fix the problem, and the plugin
>>> works
>>> great on each file tested, claims to have entered all the correct 
>>> data,
>>> and exits gracefully.  Yet when I run the same command line with
>>> --commit
>>> appended to the end, we start getting these Primary Key constraints
>>> violated errors again.
>>>
>>> Perhaps I do not understand what happens with commit.  I thought that
>>> these kind of errors would be caught with a regular run without 
>>> commit
>>> turned on.
>>> Any help?
>>>
>>>
>>>
>>>
>>> Michael Luchtan
>>> http://www.cs.uga.edu/~luchtan
>>>
>>>
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> This SF.Net email is sponsored by: IBM Linux Tutorials
>>> Free Linux tutorial presented by Daniel Robbins, President and CEO of
>>> GenToo technologies. Learn everything from fundamentals to system
>>> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>>> _______________________________________________
>>> Gusdev-gusdev mailing list
>>> Gus...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by: IBM Linux Tutorials
>> Free Linux tutorial presented by Daniel Robbins, President and CEO of
>> GenToo technologies. Learn everything from fundamentals to system
>> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>

Re: [Gusdev-gusdev] everything works except commit!

[MICHAEL L. <lu...@cs...>]

Michael-
Just a little bit of sql help left I think.  I took your suggestion below,
logged in as sysdba executed the commands below.  Now, a regular user
can't see the table.  I.E. I get the following error message when running
the plugin:
DBD::Oracle::db prepare failed: ORA-00942: table or view does not exist
(DBD ERROR: OCIStmtExecute/Describe) at
/var/local/gus_home/lib/perl/GUS/Common/Plugin/LoadBlastSimFast.pm line
346, <GEN0> line 1651269.
Which is in reference to the sql statement:
select dots.similarity_SQ.NEXTVAL from DUAL

Running sqlplus confirms that a regular user will get that error.  Running
sqlplus as sysdba shows that it is there.

How can I grant permission for folks to view /increase this sequence?

Michael Luchtan
http://www.cs.uga.edu/~luchtan


On Mon, 19 Apr 2004, Michael Saffitz wrote:

>
> Hi Michael,
>
> Your sequences are out of sync with the corresponding tables.  You
> should definitely continue to use the sequences (you'll avoid many
> problems down the road), but you'll need to alter sequences so that
> they start with the proper value.  For example, for the similarity
> table:
>
> (Get the maximum value of the primary key:)
>
> select max(SIMILARITY_ID) from dots.similarity;
>
> You must then drop and recreate the sequence, setting the sequence to
> start with the value you got in the query above, plus 5 or so to be
> safe.  Let's say this is 5067:
>
> drop sequence dots.similarity_SQ;
> create sequence dots.similarity_SQ START WITH 5073;
>
> Using the count(*) as the primary key generation is not supported and
> is likely to produced unexpected results.
>
> --Mike
> CBIL DBA
>
> On Apr 19, 2004, at 11:58 AM, MICHAEL LUCHTAN wrote:
>
> > Hello everyone-
> > I have been attempting to load blast similarities into GUS with the
> > plugin
> > LoadBlastSimFast.pm after already loading some data in with the plugin
> > LoadBlastSimilarityPK.pm (which was slow compared with the Fasst
> > version).
> > Well, the first thing that LoadBlastSimFast.pm does is start
> > complaining
> > about PrimaryKey uniqueness constraints being violated.  It used some
> > fancy Oracle SQL that I didn't understand:
> > select dots.similarity_SQ.NEXTVAL from DUAL
> > Which by debugging I found out started at one, and increased each time
> > we
> > tested the plugin, regardless of commit not being turned on.
> > Naturally this crashed, because
> > we already had about 3,000 entries in the dots.similarity table and
> > we already had a sequence_id with value 1.  There
> > was likewise a problem with the dots.similarityspan table.
> >
> > Since I only having a workingman's knowledge of OracleSQL, I switched
> > it
> > so that it starts with
> > select count(*) from dots.similarity
> > And increases this by one for each entry.  Likewise for
> > dots.similarityspan.  This seemed to fix the problem, and the plugin
> > works
> > great on each file tested, claims to have entered all the correct data,
> > and exits gracefully.  Yet when I run the same command line with
> > --commit
> > appended to the end, we start getting these Primary Key constraints
> > violated errors again.
> >
> > Perhaps I do not understand what happens with commit.  I thought that
> > these kind of errors would be caught with a regular run without commit
> > turned on.
> > Any help?
> >
> >
> >
> >
> > Michael Luchtan
> > http://www.cs.uga.edu/~luchtan
> >
> >
> >
> >
> >
> > -------------------------------------------------------
> > This SF.Net email is sponsored by: IBM Linux Tutorials
> > Free Linux tutorial presented by Daniel Robbins, President and CEO of
> > GenToo technologies. Learn everything from fundamentals to system
> > administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IBM Linux Tutorials
> Free Linux tutorial presented by Daniel Robbins, President and CEO of
> GenToo technologies. Learn everything from fundamentals to system
> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

Re: [Gusdev-gusdev] everything works except commit!

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

i am not sure about the errors.

but, commit is a basic db term describing "go ahead and *really* update 
the database"

the opposite of commit is rollback.   a transaction (insert or update) 
is either committed or rolled back.

when you run a plugin w/o commit, it runs all the logic, and issues 
commands to insert data, but, at the least minute, oracle rolls back all 
the updates, so the db is not affected.

steve

MICHAEL LUCHTAN wrote:

>And just a clarification, if it is too complicated, don't worry about
>it...
>What exactly does commit do?  Why would it give these errors with commit
>turned on, but not when it is off?
>
>
>Michael Luchtan
>http://www.cs.uga.edu/~luchtan
>
>
>On Mon, 19 Apr 2004, MICHAEL LUCHTAN wrote:
>
>  
>
>>Steve-
>>I will try this.  But some points to consider:
>>1.The previous data was entered using a plugin called
>>LoadBlastSimilaritiesPK.pm, included in the GUS release.
>>2.The "sequences" increments each time regardless of whether commit is
>>turned on.   Maybe not elegant, but I guess this doesn't matter,huh?
>>
>>Thanks,
>>
>>Michael Luchtan
>>http://www.cs.uga.edu/~luchtan
>>
>>
>>On Mon, 19 Apr 2004, Steve Fischer wrote:
>>
>>    
>>
>>>Michael-
>>>
>>>let me try to cobble together an answer.   first, i am the culprit
>>>responsible for that plugin.   but, i think it should be ok.
>>>
>>>about "sequences."    that term refers a database sequence, not a
>>>biological one.   it is a facility supported by oracle (and postgres)
>>>that provides an incremented number.    the plugins and object layer use
>>>such sequences to get the next primary key when inserting a row.
>>>
>>>so, i suspect that your initial data in those tables was added "outside"
>>>the plugin structure.
>>>
>>>i think the thing to do here is:
>>>  1. avoid adding data without using either the plugins/object layer or
>>>using the sequence directly
>>>  2. to correct the out-of-sync sequence, just run it in a loop
>>>advancing it past 3000 or whatever it needs to be.
>>>  3. re-instate the code that uses the sequence
>>>
>>>I would try that first, and then lets see if you still get the
>>>constraint errors.
>>>
>>>steve
>>>
>>>MICHAEL LUCHTAN wrote:
>>>
>>>      
>>>
>>>>Hello everyone-
>>>>I have been attempting to load blast similarities into GUS with the plugin
>>>>LoadBlastSimFast.pm after already loading some data in with the plugin
>>>>LoadBlastSimilarityPK.pm (which was slow compared with the Fasst version).
>>>>Well, the first thing that LoadBlastSimFast.pm does is start complaining
>>>>about PrimaryKey uniqueness constraints being violated.  It used some
>>>>fancy Oracle SQL that I didn't understand:
>>>>select dots.similarity_SQ.NEXTVAL from DUAL
>>>>Which by debugging I found out started at one, and increased each time we
>>>>tested the plugin, regardless of commit not being turned on.  Naturally this crashed, because
>>>>we already had about 3,000 entries in the dots.similarity table and
>>>>we already had a sequence_id with value 1.  There
>>>>was likewise a problem with the dots.similarityspan table.
>>>>
>>>>Since I only having a workingman's knowledge of OracleSQL, I switched it
>>>>so that it starts with
>>>>select count(*) from dots.similarity
>>>>And increases this by one for each entry.  Likewise for
>>>>dots.similarityspan.  This seemed to fix the problem, and the plugin works
>>>>great on each file tested, claims to have entered all the correct data,
>>>>and exits gracefully.  Yet when I run the same command line with --commit
>>>>appended to the end, we start getting these Primary Key constraints
>>>>violated errors again.
>>>>
>>>>Perhaps I do not understand what happens with commit.  I thought that
>>>>these kind of errors would be caught with a regular run without commit
>>>>turned on.
>>>>Any help?
>>>>
>>>>
>>>>
>>>>
>>>>Michael Luchtan
>>>>http://www.cs.uga.edu/~luchtan
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>-------------------------------------------------------
>>>>This SF.Net email is sponsored by: IBM Linux Tutorials
>>>>Free Linux tutorial presented by Daniel Robbins, President and CEO of
>>>>GenToo technologies. Learn everything from fundamentals to system
>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>>>>_______________________________________________
>>>>Gusdev-gusdev mailing list
>>>>Gus...@li...
>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>>
>>>>        
>>>>
>>>
>>>-------------------------------------------------------
>>>This SF.Net email is sponsored by: IBM Linux Tutorials
>>>Free Linux tutorial presented by Daniel Robbins, President and CEO of
>>>GenToo technologies. Learn everything from fundamentals to system
>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>>>_______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>      
>>>
>>
>>-------------------------------------------------------
>>This SF.Net email is sponsored by: IBM Linux Tutorials
>>Free Linux tutorial presented by Daniel Robbins, President and CEO of
>>GenToo technologies. Learn everything from fundamentals to system
>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>>_______________________________________________
>>Gusdev-gusdev mailing list
>>Gus...@li...
>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>    
>>

Re: [Gusdev-gusdev] everything works except commit!

[MICHAEL L. <lu...@cs...>]

And just a clarification, if it is too complicated, don't worry about
it...
What exactly does commit do?  Why would it give these errors with commit
turned on, but not when it is off?


Michael Luchtan
http://www.cs.uga.edu/~luchtan


On Mon, 19 Apr 2004, MICHAEL LUCHTAN wrote:

> Steve-
> I will try this.  But some points to consider:
> 1.The previous data was entered using a plugin called
> LoadBlastSimilaritiesPK.pm, included in the GUS release.
> 2.The "sequences" increments each time regardless of whether commit is
> turned on.   Maybe not elegant, but I guess this doesn't matter,huh?
>
> Thanks,
>
> Michael Luchtan
> http://www.cs.uga.edu/~luchtan
>
>
> On Mon, 19 Apr 2004, Steve Fischer wrote:
>
> > Michael-
> >
> > let me try to cobble together an answer.   first, i am the culprit
> > responsible for that plugin.   but, i think it should be ok.
> >
> > about "sequences."    that term refers a database sequence, not a
> > biological one.   it is a facility supported by oracle (and postgres)
> > that provides an incremented number.    the plugins and object layer use
> > such sequences to get the next primary key when inserting a row.
> >
> > so, i suspect that your initial data in those tables was added "outside"
> > the plugin structure.
> >
> > i think the thing to do here is:
> >   1. avoid adding data without using either the plugins/object layer or
> > using the sequence directly
> >   2. to correct the out-of-sync sequence, just run it in a loop
> > advancing it past 3000 or whatever it needs to be.
> >   3. re-instate the code that uses the sequence
> >
> > I would try that first, and then lets see if you still get the
> > constraint errors.
> >
> > steve
> >
> > MICHAEL LUCHTAN wrote:
> >
> > >Hello everyone-
> > >I have been attempting to load blast similarities into GUS with the plugin
> > >LoadBlastSimFast.pm after already loading some data in with the plugin
> > >LoadBlastSimilarityPK.pm (which was slow compared with the Fasst version).
> > >Well, the first thing that LoadBlastSimFast.pm does is start complaining
> > >about PrimaryKey uniqueness constraints being violated.  It used some
> > >fancy Oracle SQL that I didn't understand:
> > >select dots.similarity_SQ.NEXTVAL from DUAL
> > >Which by debugging I found out started at one, and increased each time we
> > >tested the plugin, regardless of commit not being turned on.  Naturally this crashed, because
> > >we already had about 3,000 entries in the dots.similarity table and
> > >we already had a sequence_id with value 1.  There
> > >was likewise a problem with the dots.similarityspan table.
> > >
> > >Since I only having a workingman's knowledge of OracleSQL, I switched it
> > >so that it starts with
> > >select count(*) from dots.similarity
> > >And increases this by one for each entry.  Likewise for
> > >dots.similarityspan.  This seemed to fix the problem, and the plugin works
> > >great on each file tested, claims to have entered all the correct data,
> > >and exits gracefully.  Yet when I run the same command line with --commit
> > >appended to the end, we start getting these Primary Key constraints
> > >violated errors again.
> > >
> > >Perhaps I do not understand what happens with commit.  I thought that
> > >these kind of errors would be caught with a regular run without commit
> > >turned on.
> > >Any help?
> > >
> > >
> > >
> > >
> > >Michael Luchtan
> > >http://www.cs.uga.edu/~luchtan
> > >
> > >
> > >
> > >
> > >
> > >-------------------------------------------------------
> > >This SF.Net email is sponsored by: IBM Linux Tutorials
> > >Free Linux tutorial presented by Daniel Robbins, President and CEO of
> > >GenToo technologies. Learn everything from fundamentals to system
> > >administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> > >_______________________________________________
> > >Gusdev-gusdev mailing list
> > >Gus...@li...
> > >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > >
> > >
> >
> >
> >
> > -------------------------------------------------------
> > This SF.Net email is sponsored by: IBM Linux Tutorials
> > Free Linux tutorial presented by Daniel Robbins, President and CEO of
> > GenToo technologies. Learn everything from fundamentals to system
> > administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IBM Linux Tutorials
> Free Linux tutorial presented by Daniel Robbins, President and CEO of
> GenToo technologies. Learn everything from fundamentals to system
> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

Re: [Gusdev-gusdev] everything works except commit!

[MICHAEL L. <lu...@cs...>]

Steve-
I will try this.  But some points to consider:
1.The previous data was entered using a plugin called
LoadBlastSimilaritiesPK.pm, included in the GUS release.
2.The "sequences" increments each time regardless of whether commit is
turned on.   Maybe not elegant, but I guess this doesn't matter,huh?

Thanks,

Michael Luchtan
http://www.cs.uga.edu/~luchtan


On Mon, 19 Apr 2004, Steve Fischer wrote:

> Michael-
>
> let me try to cobble together an answer.   first, i am the culprit
> responsible for that plugin.   but, i think it should be ok.
>
> about "sequences."    that term refers a database sequence, not a
> biological one.   it is a facility supported by oracle (and postgres)
> that provides an incremented number.    the plugins and object layer use
> such sequences to get the next primary key when inserting a row.
>
> so, i suspect that your initial data in those tables was added "outside"
> the plugin structure.
>
> i think the thing to do here is:
>   1. avoid adding data without using either the plugins/object layer or
> using the sequence directly
>   2. to correct the out-of-sync sequence, just run it in a loop
> advancing it past 3000 or whatever it needs to be.
>   3. re-instate the code that uses the sequence
>
> I would try that first, and then lets see if you still get the
> constraint errors.
>
> steve
>
> MICHAEL LUCHTAN wrote:
>
> >Hello everyone-
> >I have been attempting to load blast similarities into GUS with the plugin
> >LoadBlastSimFast.pm after already loading some data in with the plugin
> >LoadBlastSimilarityPK.pm (which was slow compared with the Fasst version).
> >Well, the first thing that LoadBlastSimFast.pm does is start complaining
> >about PrimaryKey uniqueness constraints being violated.  It used some
> >fancy Oracle SQL that I didn't understand:
> >select dots.similarity_SQ.NEXTVAL from DUAL
> >Which by debugging I found out started at one, and increased each time we
> >tested the plugin, regardless of commit not being turned on.  Naturally this crashed, because
> >we already had about 3,000 entries in the dots.similarity table and
> >we already had a sequence_id with value 1.  There
> >was likewise a problem with the dots.similarityspan table.
> >
> >Since I only having a workingman's knowledge of OracleSQL, I switched it
> >so that it starts with
> >select count(*) from dots.similarity
> >And increases this by one for each entry.  Likewise for
> >dots.similarityspan.  This seemed to fix the problem, and the plugin works
> >great on each file tested, claims to have entered all the correct data,
> >and exits gracefully.  Yet when I run the same command line with --commit
> >appended to the end, we start getting these Primary Key constraints
> >violated errors again.
> >
> >Perhaps I do not understand what happens with commit.  I thought that
> >these kind of errors would be caught with a regular run without commit
> >turned on.
> >Any help?
> >
> >
> >
> >
> >Michael Luchtan
> >http://www.cs.uga.edu/~luchtan
> >
> >
> >
> >
> >
> >-------------------------------------------------------
> >This SF.Net email is sponsored by: IBM Linux Tutorials
> >Free Linux tutorial presented by Daniel Robbins, President and CEO of
> >GenToo technologies. Learn everything from fundamentals to system
> >administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> >_______________________________________________
> >Gusdev-gusdev mailing list
> >Gus...@li...
> >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
> >
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IBM Linux Tutorials
> Free Linux tutorial presented by Daniel Robbins, President and CEO of
> GenToo technologies. Learn everything from fundamentals to system
> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

Re: [Gusdev-gusdev] everything works except commit!

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

Hi Michael,

Your sequences are out of sync with the corresponding tables.  You 
should definitely continue to use the sequences (you'll avoid many 
problems down the road), but you'll need to alter sequences so that 
they start with the proper value.  For example, for the similarity 
table:

(Get the maximum value of the primary key:)

select max(SIMILARITY_ID) from dots.similarity;

You must then drop and recreate the sequence, setting the sequence to 
start with the value you got in the query above, plus 5 or so to be 
safe.  Let's say this is 5067:

drop sequence dots.similarity_SQ;
create sequence dots.similarity_SQ START WITH 5073;

Using the count(*) as the primary key generation is not supported and 
is likely to produced unexpected results.

--Mike
CBIL DBA

On Apr 19, 2004, at 11:58 AM, MICHAEL LUCHTAN wrote:

> Hello everyone-
> I have been attempting to load blast similarities into GUS with the 
> plugin
> LoadBlastSimFast.pm after already loading some data in with the plugin
> LoadBlastSimilarityPK.pm (which was slow compared with the Fasst 
> version).
> Well, the first thing that LoadBlastSimFast.pm does is start 
> complaining
> about PrimaryKey uniqueness constraints being violated.  It used some
> fancy Oracle SQL that I didn't understand:
> select dots.similarity_SQ.NEXTVAL from DUAL
> Which by debugging I found out started at one, and increased each time 
> we
> tested the plugin, regardless of commit not being turned on.  
> Naturally this crashed, because
> we already had about 3,000 entries in the dots.similarity table and
> we already had a sequence_id with value 1.  There
> was likewise a problem with the dots.similarityspan table.
>
> Since I only having a workingman's knowledge of OracleSQL, I switched 
> it
> so that it starts with
> select count(*) from dots.similarity
> And increases this by one for each entry.  Likewise for
> dots.similarityspan.  This seemed to fix the problem, and the plugin 
> works
> great on each file tested, claims to have entered all the correct data,
> and exits gracefully.  Yet when I run the same command line with 
> --commit
> appended to the end, we start getting these Primary Key constraints
> violated errors again.
>
> Perhaps I do not understand what happens with commit.  I thought that
> these kind of errors would be caught with a regular run without commit
> turned on.
> Any help?
>
>
>
>
> Michael Luchtan
> http://www.cs.uga.edu/~luchtan
>
>
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IBM Linux Tutorials
> Free Linux tutorial presented by Daniel Robbins, President and CEO of
> GenToo technologies. Learn everything from fundamentals to system
> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [Gusdev-gusdev] everything works except commit!

[MICHAEL L. <lu...@cs...>]

Hello Sucheta-
No. the plugin will not work with the raw blast output.  You must parse it
using a script such as parseBlastFilesForSimilarity.pl
which puts it in the format:
Cutoff parameters:
        P value: 1e-05
        Length: 10
        Percent Identity: 20

>383609 (96 subjects)
  Sum: 384224:3658:0.:16:2169:14:2163:2:3583:1525:2039:0:
   HSP1: 384224:905:1236:2247:3658:0.:16:2136:14:2135:0:
   HSP2: 384224:620:803:1336:2695:2.8e-282:884:2169:892:2163:0:
  Sum: 384422:3445:0.:1:2193:1:2163:2:2258:1076:1337:0:
   HSP1: 384422:800:986:1652:3445:0.:616:2193:586:2163:0:
   HSP2: 384422:276:351:606:1201:0.:1:575:1:576:0:
  Sum: 383758:3124:0.:3:2203:5:2163:4:4205:1809:2322:0:
   HSP1: 383758:773:977:1701:3124:0.:570:2180:555:2150:0:
   HSP2: 383758:601:794:1569:1928:0.:718:2203:692:2163:0:
   HSP3: 383758:259:314:494:1191:0.:3:473:5:481:0:
   HSP4: 383758:176:237:441:708:0.:310:718:298:700:0:
  Sum: 385607:3061:0.:8:2231:14:2163:3:2833:1143:1528:0:
   HSP1: 385607:728:940:1653:3061:0.:600:2192:577:2147:0:
   HSP2: 385607:248:332:568:1046:0.:8:550:14:549:0:
   HSP3: 385607:167:256:612:353:3.2e-134:1654:2231:1613:2163:0:
  Sum: 388168:2786:0.:5:2223:9:2163:5:2775:1226:1578:0:
   HSP1: 388168:659:831:1446:2786:0.:821:2200:770:2150:0:
   HSP2: 388168:243:295:473:1114:0.:5:459:9:453:0:
   HSP3: 388168:133:169:326:538:0.:290:607:287:588:0:
   HSP4: 388168:113:186:376:445:4.8e-179:641:996:572:932:0:
   HSP5: 388168:78:97:154:317:0.:2073:2223:2026:2163:0:
.
.
.
.


Michael Luchtan
http://www.cs.uga.edu/~luchtan


On Mon, 19 Apr 2004, Sucheta Tripathy wrote:

> Hi Michael,
>
> I have not worked with the plugin yet, but just curious to know what input
> file type did you provide? Is it the raw blast output?
>
> Thanks
>
> Sucheta
>
> > Hello everyone-
> > I have been attempting to load blast similarities into GUS with the plugin
> > LoadBlastSimFast.pm after already loading some data in with the plugin
> > LoadBlastSimilarityPK.pm (which was slow compared with the Fasst version).
> > Well, the first thing that LoadBlastSimFast.pm does is start complaining
> > about PrimaryKey uniqueness constraints being violated.  It used some
> > fancy Oracle SQL that I didn't understand:
> > select dots.similarity_SQ.NEXTVAL from DUAL
> > Which by debugging I found out started at one, and increased each time we
> > tested the plugin, regardless of commit not being turned on.  Naturally
> > this crashed, because
> > we already had about 3,000 entries in the dots.similarity table and
> > we already had a sequence_id with value 1.  There
> > was likewise a problem with the dots.similarityspan table.
> >
> > Since I only having a workingman's knowledge of OracleSQL, I switched it
> > so that it starts with
> > select count(*) from dots.similarity
> > And increases this by one for each entry.  Likewise for
> > dots.similarityspan.  This seemed to fix the problem, and the plugin works
> > great on each file tested, claims to have entered all the correct data,
> > and exits gracefully.  Yet when I run the same command line with --commit
> > appended to the end, we start getting these Primary Key constraints
> > violated errors again.
> >
> > Perhaps I do not understand what happens with commit.  I thought that
> > these kind of errors would be caught with a regular run without commit
> > turned on.
> > Any help?
> >
> >
> >
> >
> > Michael Luchtan
> > http://www.cs.uga.edu/~luchtan
> >
> >
> >
> >
> >
> > -------------------------------------------------------
> > This SF.Net email is sponsored by: IBM Linux Tutorials
> > Free Linux tutorial presented by Daniel Robbins, President and CEO of
> > GenToo technologies. Learn everything from fundamentals to system
> > administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
>
>
> --
> Sucheta Tripathy
> Virginia Bioinformatics Institute Phase-I
> Washington street.
> Virginia Tech.
> Blacksburg,VA 24061-0447
> phone:(540)231-8138
> Fax:  (540) 231-2606
>

Re: [Gusdev-gusdev] everything works except commit!

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

Michael-

let me try to cobble together an answer.   first, i am the culprit 
responsible for that plugin.   but, i think it should be ok.

about "sequences."    that term refers a database sequence, not a 
biological one.   it is a facility supported by oracle (and postgres) 
that provides an incremented number.    the plugins and object layer use 
such sequences to get the next primary key when inserting a row.

so, i suspect that your initial data in those tables was added "outside" 
the plugin structure.

i think the thing to do here is:
  1. avoid adding data without using either the plugins/object layer or 
using the sequence directly
  2. to correct the out-of-sync sequence, just run it in a loop 
advancing it past 3000 or whatever it needs to be.
  3. re-instate the code that uses the sequence

I would try that first, and then lets see if you still get the 
constraint errors.

steve

MICHAEL LUCHTAN wrote:

>Hello everyone-
>I have been attempting to load blast similarities into GUS with the plugin
>LoadBlastSimFast.pm after already loading some data in with the plugin
>LoadBlastSimilarityPK.pm (which was slow compared with the Fasst version).
>Well, the first thing that LoadBlastSimFast.pm does is start complaining
>about PrimaryKey uniqueness constraints being violated.  It used some
>fancy Oracle SQL that I didn't understand:
>select dots.similarity_SQ.NEXTVAL from DUAL
>Which by debugging I found out started at one, and increased each time we
>tested the plugin, regardless of commit not being turned on.  Naturally this crashed, because
>we already had about 3,000 entries in the dots.similarity table and
>we already had a sequence_id with value 1.  There
>was likewise a problem with the dots.similarityspan table.
>
>Since I only having a workingman's knowledge of OracleSQL, I switched it
>so that it starts with
>select count(*) from dots.similarity
>And increases this by one for each entry.  Likewise for
>dots.similarityspan.  This seemed to fix the problem, and the plugin works
>great on each file tested, claims to have entered all the correct data,
>and exits gracefully.  Yet when I run the same command line with --commit
>appended to the end, we start getting these Primary Key constraints
>violated errors again.
>
>Perhaps I do not understand what happens with commit.  I thought that
>these kind of errors would be caught with a regular run without commit
>turned on.
>Any help?
>
>
>
>
>Michael Luchtan
>http://www.cs.uga.edu/~luchtan
>
>
>
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by: IBM Linux Tutorials
>Free Linux tutorial presented by Daniel Robbins, President and CEO of
>GenToo technologies. Learn everything from fundamentals to system
>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

[Gusdev-gusdev] everything works except commit!

[MICHAEL L. <lu...@cs...>]

Hello everyone-
I have been attempting to load blast similarities into GUS with the plugin
LoadBlastSimFast.pm after already loading some data in with the plugin
LoadBlastSimilarityPK.pm (which was slow compared with the Fasst version).
Well, the first thing that LoadBlastSimFast.pm does is start complaining
about PrimaryKey uniqueness constraints being violated.  It used some
fancy Oracle SQL that I didn't understand:
select dots.similarity_SQ.NEXTVAL from DUAL
Which by debugging I found out started at one, and increased each time we
tested the plugin, regardless of commit not being turned on.  Naturally this crashed, because
we already had about 3,000 entries in the dots.similarity table and
we already had a sequence_id with value 1.  There
was likewise a problem with the dots.similarityspan table.

Since I only having a workingman's knowledge of OracleSQL, I switched it
so that it starts with
select count(*) from dots.similarity
And increases this by one for each entry.  Likewise for
dots.similarityspan.  This seemed to fix the problem, and the plugin works
great on each file tested, claims to have entered all the correct data,
and exits gracefully.  Yet when I run the same command line with --commit
appended to the end, we start getting these Primary Key constraints
violated errors again.

Perhaps I do not understand what happens with commit.  I thought that
these kind of errors would be caught with a regular run without commit
turned on.
Any help?




Michael Luchtan
http://www.cs.uga.edu/~luchtan

Re: [Gusdev-gusdev] Problem installing GUS: "Package Table Name is not in the form of xxxxxx.model.Schema"

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

Dear Madhura-

I have not seen this message before.  Two things to try:

  1. I am seeing mention in the error message of ORACLE_HOME not set.   
Have you set it?   (I just looked through the documentation and it seems 
that we don't mention that this is necessary.  I suspect that is because 
we just recently added the Java Object Layer as a default part of the 
build, and it needs ORACLE_HOME.  I'll add that to the docs).

Here is what my ORACLE_HOME looks like:

[sfischer@cottus ~]$ echo $ORACLE_HOME
/files/oracle/9.2.0.1.0
[sfischer@cottus ~]$ ls $ORACLE_HOME
Apache/      demo/             jar/     ldap/     oem_webstage/  
precomp/   sqlplus/
assistants/  doc/              javavm/  lib/      olap/          
rdbms/     syndication/
BC4J/        ds/               jdbc/    md/       oracore/       
relnotes/  sysman/
bin/         hs/               jdk/     network/  ord/           
root.sh*   ultrasearch/
classes/     install/          jlib/    oci/      otrace/        
slax/      weboamlib/
ctx/         install.platform  JRE@     ocommon/  owm/           
soap/      wwg/
dbs/         inventory/        jsp/     ocs4j/    plsql/         
sqlj/      xdk/

Here is what I have in my .cshrc rile (it configures the environment for 
my shell.  I use tsch):
[sfischer@cottus ~]$ grep ORACLE .cshrc
setenv ORACLE_HOME /files/oracle/9.2.0.1.0
setenv LD_LIBRARY_PATH $ORACLE_HOME/lib
setenv PATH $ORACLE_HOME/bin:$PATH


2. If that doesn't fix it, then it might help if we improve the error 
message.  Change line 90 of 
$PROJECT_HOME/GUS/ObjRelP/lib/perl/Generator/RowGenerator.pm 

from:
    die "Error:  Package Table Name is not in the form of 
xxxxxx.model.Schema.Name";

to:
    die "Error:  Package Table Name '$packageTableName' is not in the 
form of org.gusdb.model.SCHEMA.NAME";



    die "Error:  Package Table Name '$packageTableName' is not in the 
form of org.gusdb.model.SCHEMA.NAME";


Madhura Sharangpani wrote:

> Hi
>  
> I am trying to install GUS on my client machine that remotely accesses
> Oracle 9i located on the server. After creating all required 
> table-spaces, users
> etc, when I am running the build system for the 3rd time (as specified 
> in Fidel and
> Sucheta's installation guide), I get the following error:
>  
> .........
>  
>      [echo] Installing GUS/ObjRelJ
>      [echo] starting target: javaGeneratedModel
>    [delete] Deleting 2 files from 
> /afs/ir/users/s/m/smadhura/RA/Projects/GUS/Mod
> el/src/java/org/gusdb/model/DoTS
>    [delete] Deleting 1 files from 
> /afs/ir/users/s/m/smadhura/RA/Projects/GUS/Mod
> el/src/java/org/gusdb/model/SRes
>      [echo] generating java objects
>      [exec] Reading properties from 
> /afs/ir/users/s/m/smadhura/.gus.properties
>      [exec] ORACLE_HOME environment variable not set!
>      [exec] Generating objects for 917 java tables and views
>      [exec] generating java object for DoTS::GOAssociation
>      [exec] (Caching all real table names)
>      [exec] ORACLE_HOME environment variable not set!
>      [exec] ORACLE_HOME environment variable not set!
>      [exec] (Caching all parents)
>      [exec] Error:  Package Table Name is not in the form of 
> xxxxxx.model.Schema
> .Name at 
> /afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/ObjRelP/Generator/RowGen
> erator.pm line 90.
>  
> BUILD FAILED
> /afs/ir/users/s/m/smadhura/RA/Projects/install/build.xml:26: Following 
> error occ
> ured while executing this line
> /afs/ir/users/s/m/smadhura/RA/Projects/GUS/build.xml:114: exec returned: 2
>  
> I am not able to understand why this error is occuring.
>  
> Can someone please help?
>  
> Thanks!
>  
> Madhura
>  

[Gusdev-gusdev] Re: KEGG data (fwd)

[Trish W. <wh...@pc...>]

Forwarding some mail regarding KEGG data that did not make it to the list.

Trish

---------- Forwarded message ----------
Hi Thomas,

Attached is the basic flow of data entry in order to represent the 
reaction below. Let me know if/what questions you may have on this. 

Sincerely,
Trish

========
Attachment

Mapping KEGG Data into GUS

Case Study:
Map the pathway C00103 <=> C00668 (alpha-D-glucose 1-phosphate =
alpha-D-glucose 6-phosphate) which involves the enzyme 5.4.2.2
(phosphoglucomutase)

Information Needed:
-GenBank Accession for the Enzymes in the Pathway of interest
In order to be able to point to a row in DoTs.ExternalAASequence, the 
following
tables need to be loaded DoTS.ExternalNASequence <-na_sequence_id->
DoTS.RNAFeature <-na_feature_id-> DoTS.TranslatedAAFeature, this can then 
be
joined to DoTS.ExternalAASequence using aa_sequence_id

-Table that holds information on small molecules

Tables Involved:
Dots::Pathway
DoTS::PathwayInteraction
DoTS::Interaction
DoTS::InteractionType
DoTS::EffectorActionType
DoTS::RowSet
DoTS::RowSetMember
SRes::ReviewStatus

Flow of Data Entry:
NOTE:  this pathway will need to be represented as 2 interactions
NOTE:  Need to find/create tables to store compounds, look in EcoCyc 
and/or
BioComp, Adam Arkin, cheminformatics info

-insert into dots.pathway (name, description) values ('RN00010' , 
'Glycolysis /
Gluconeogenesis');
RESULT: $pathway_id

-insert into dots.interactiontype (name, description) values ('term from
controlled vocabulary' , 'definition of term');
RESULT: $interaction_id

-insert into dots.effectoractiontype (name, description,
external_database_release_id, source_id) values ('phosphorylation' , 
'residue
modification' , 'ADD ext_db_rel_id for PSI Ontology' , 'MI:0170');
RESULT: $effector_action_type_id

For Interaction 1 and 2
-insert into dots.rowset ();
RESULT: $row_set_id1
-insert into dots.rowsetmember (row_set_id, table_id, row_id) values
('$row_set_id1', 'table_id of DoTS.ExternalAASequence' , 'PK of row of
interest'); --> this represents the enzyme (effector)

For Interaction 1
-insert into dots.rowset ();
RESULT: $row_set_id2
-insert into dots.rowsetmember (row_set_id, table_id, row_id) values
('$row_set_id2',  'table_id for table with small molecules/compounds' ,
'Primary key of row of interest in the table with small 
molecules/compounds');
--> this represents the molecule (target)

For interaction 2
-insert into dots.rowset ();
RESULT: $row_set_id3
-insert into dots.rowsetmember (row_set_id, table_id, row_id) values
('$row_set_id' , 'table_id for table with small molecules/compounds' , 
'Primary
key of row of interest in the table with small molecules/compounds'); --> 
this
represents the molecule (target)

-insert into dots.interaction (interaction_type_id, 
effector_action_type_id,
effector_row_set_id, target_row_set_id, has_direction, direction_is_known)
values ($interaction_type_id, $effector_action_type_id, $row_set_id1,
$row_set_id2, 'integer to represent direction', '1');
RESULT: $interaction_id

-insert into dots.pathwayinteraction (pathway_id, interaction_id) values
($pathway_id, $interaction_id);
========

> To understand the talbe, maybe it would be easier to do an example:
> So how would you save in the table this reaction, of Pathway Map0010 
> (http://www.genome.ad.jp/dbget-bin/get_pathway?org_name=rn&mapno=00010):
> 
> D-Glucose 1-phosphate (C00103) <--- reaction alpha-D-Glucose 1-phosphate 1,6-phosphomutase (envolving enzyme 5.4.2.2 <http://www.genome.ad.jp/dbget-bin/www_bget?enzyme+5.4.2.2>         5.4.2.5 <http://www.genome.ad.jp/dbget-bin/www_bget?enzyme+5.4.2.5>
> 
> ) --->  C00668 
> <http://www.genome.ad.jp/dbget-bin/get_linkdb?compound+C00668>  
> alpha-D-Glucose 6-phosphate
> 
> Maybe this helps me to understand the table.
> 
> Thanks,
> Thomas
 

[Gusdev-gusdev] Problem installing GUS: "Package Table Name is not in the form of xxxxxx.model.Schema"

[Madhura S. <sma...@st...>]

Hi

I am trying to install GUS on my client machine that remotely accesses
Oracle 9i located on the server. After creating all required =
table-spaces, users
etc, when I am running the build system for the 3rd time (as specified =
in Fidel and
Sucheta's installation guide), I get the following error:

.........

     [echo] Installing GUS/ObjRelJ
     [echo] starting target: javaGeneratedModel
   [delete] Deleting 2 files from =
/afs/ir/users/s/m/smadhura/RA/Projects/GUS/Mod
el/src/java/org/gusdb/model/DoTS
   [delete] Deleting 1 files from =
/afs/ir/users/s/m/smadhura/RA/Projects/GUS/Mod
el/src/java/org/gusdb/model/SRes
     [echo] generating java objects
     [exec] Reading properties from =
/afs/ir/users/s/m/smadhura/.gus.properties
     [exec] ORACLE_HOME environment variable not set!
     [exec] Generating objects for 917 java tables and views
     [exec] generating java object for DoTS::GOAssociation
     [exec] (Caching all real table names)
     [exec] ORACLE_HOME environment variable not set!
     [exec] ORACLE_HOME environment variable not set!
     [exec] (Caching all parents)
     [exec] Error:  Package Table Name is not in the form of =
xxxxxx.model.Schema
.Name at =
/afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/ObjRelP/Generator/RowGen
erator.pm line 90.

BUILD FAILED
/afs/ir/users/s/m/smadhura/RA/Projects/install/build.xml:26: Following =
error occ
ured while executing this line
/afs/ir/users/s/m/smadhura/RA/Projects/GUS/build.xml:114: exec returned: =
2


I am not able to understand why this error is occuring.

Can someone please help?

Thanks!

Madhura

[Gusdev-gusdev] Re: wdk cvs

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

michael-

we have made alot of progress in the new WDK.   The Model of the 
Model-View-Controller has met its first deliverable milestone.   We 
expect the View development to kick in in the next few weeks.   So, I 
would estimate 4-6 weeks for a starting system.

steve

MICHAEL LUCHTAN wrote:

>Hello-
>I've noticed a number of recent (more than 6 months) changes in the
>sanger cvs.  Is this workable?  Is it updates to the wdk-classic or a
>completely new design?
>Is it in a state where you need folks debugging?  Is it working in some
>sense?
>I'm not too crazy about the way wdk-classic is working out, so I might be
>interested in getting in on the ground floor (or closer to it) of the
>supported wdk.
>
>Michael Luchtan
>http://www.cs.uga.edu/~luchtan
>
>  
>

[Gusdev-gusdev] wdk cvs

[MICHAEL L. <lu...@cs...>]

Hello-
I've noticed a number of recent (more than 6 months) changes in the
sanger cvs.  Is this workable?  Is it updates to the wdk-classic or a
completely new design?
Is it in a state where you need folks debugging?  Is it working in some
sense?
I'm not too crazy about the way wdk-classic is working out, so I might be
interested in getting in on the ground floor (or closer to it) of the
supported wdk.

Michael Luchtan
http://www.cs.uga.edu/~luchtan

Re: [Gusdev-gusdev] KEEG to GUS

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

thomas-

there is definite interest in incorporating KEGG data into GUS.   I am 
hoping we can work with you and the folks at PSU (Sanger) to develop a 
GUS compliant schema for this.

steve

Thomas Otto wrote:

> Hi,
>                                                                                                     
>
> I think it is time to discuss a bit about the stuff in did so far 
> concerning Kegg to Gus.
>                                                                                                     
>
> The principle idea was to put the datas in a relations database. The 
> visualization of the pathway will not be changed.
>                                                                                                     
>
> So we did the schema for the oracle, under the namespace CLASS. Some 
> tables already exist, like pathway, OMIM, enzymeclass... (but we kept 
> it in a package). Still Trish and I are talking about the tail of the 
> pathway-table (interaction and so). Shouldn't be too difficult to 
> parse the information from the tables for the compounds, reactions and 
> enzymes to the interaction tables.
>                                                                                                     
>
> Some might say this approve is a little bit static, but at least it a 
> base of informations.
>                                                                                                     
>
> We also wrote a parser (a bit beta stage, but coming soon) to upload 
> the data in the tables. The data itself can be downloaded at 
> ftp://ftp.genome.ad.jp/pub/kegg. Further we are working on a 
> classification for protein and functions.
>                                                                                                     
>
> To use the pathways locally, we wrote some scripts to surf through the 
> pathway, the enzyme, compounds and so one, looks like under kegg, just 
> in perl (do we need this in C?), so a bit slower and not complete so 
> far (i.e. structure information). If there is interest, I will install 
> it on a webserver. (If you want to be a betatester :-))
>                                                                                                     
>
> Maybe it would be useful to talk first about the tableschema before to 
> get from alpha stage to the beta with the programms.
> We hope to get some new ideas.
>                                                                                                     
>
> Cheers,
> Thomas
>                                                                                                     
>
> PS: All stuff is in beta stage (I couldn't use the dumpSchema.pl :-(), 
> so please tell me the bugs, thanks.
>

[Gusdev-gusdev] KEEG to GUS

[Thomas O. <ot...@fi...>]

Hi,
                                                                                                     
 
I think it is time to discuss a bit about the stuff in did so far 
concerning Kegg to Gus.
                                                                                                     
 
The principle idea was to put the datas in a relations database. The 
visualization of the pathway will not be changed.
                                                                                                     
 
So we did the schema for the oracle, under the namespace CLASS. Some 
tables already exist, like pathway, OMIM, enzymeclass... (but we kept it 
in a package). Still Trish and I are talking about the tail of the 
pathway-table (interaction and so). Shouldn't be too difficult to parse 
the information from the tables for the compounds, reactions and enzymes 
to the interaction tables.
                                                                                                     
 
Some might say this approve is a little bit static, but at least it a 
base of informations.
                                                                                                     
 
We also wrote a parser (a bit beta stage, but coming soon) to upload the 
data in the tables. The data itself can be downloaded at 
ftp://ftp.genome.ad.jp/pub/kegg. Further we are working on a 
classification for protein and functions.
                                                                                                     
 
To use the pathways locally, we wrote some scripts to surf through the 
pathway, the enzyme, compounds and so one, looks like under kegg, just 
in perl (do we need this in C?), so a bit slower and not complete so far 
(i.e. structure information). If there is interest, I will install it on 
a webserver. (If you want to be a betatester :-))
                                                                                                     
 
Maybe it would be useful to talk first about the tableschema before to 
get from alpha stage to the beta with the programms.
We hope to get some new ideas.
                                                                                                     
 
Cheers,
Thomas
                                                                                                     
 
PS: All stuff is in beta stage (I couldn't use the dumpSchema.pl :-(), 
so please tell me the bugs, thanks.

Re: [Gusdev-gusdev] GBAAParser

[Thomas O. <ot...@fi...>]

Hi,

I thought a little bit about the stuff. If the NA genbank entry is 
available, namely the most information will be in GUS with the GBParser 
module.
So the GBAAParser could maybe write some information in the 
dots.protein, dots.rna table and so one.

I will think on this.

Cheers,
Thomas
Thomas Otto wrote:

> Hi,
>
> I will try to change the GBParser to upload AA-sequences.
>
> The easiest way might be to change a bit the GBParser...
>
> A question: If I have an entry with
>  source          1..47
>                     /organism="Oryctolagus cuniculus"
>                     /isolate="COF12"
>                     /db_xref="taxon:9986"
>                     /chromosome="1"
>                     /map="1q14-q21"
>                     /clone="22"
>                     /transgenic
>                     /note="Chagas disease"
> I just create a view sourceAA or AAsource on AAFeartureimp, with the 
> rows like organism...
> Does that sounds logic?
>
> Next question: Might it be important to have also the NA - sequence of 
> the AA in the schema?
>
> Cheers,
> Thomas
>
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IBM Linux Tutorials
> Free Linux tutorial presented by Daniel Robbins, President and CEO of
> GenToo technologies. Learn everything from fundamentals to system
> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

[Gusdev-gusdev] GBAAParser

[Thomas O. <ot...@fi...>]

Hi,

I will try to change the GBParser to upload AA-sequences.

The easiest way might be to change a bit the GBParser...

A question: If I have an entry with
  source          1..47
                     /organism="Oryctolagus cuniculus"
                     /isolate="COF12"
                     /db_xref="taxon:9986"
                     /chromosome="1"
                     /map="1q14-q21"
                     /clone="22"
                     /transgenic
                     /note="Chagas disease"
I just create a view sourceAA or AAsource on AAFeartureimp, with the 
rows like organism...
Does that sounds logic?

Next question: Might it be important to have also the NA - sequence of 
the AA in the schema?

Cheers,
Thomas

[Gusdev-gusdev] Anybody using Oracle 8i or earlier?

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

folks-

as you probably know we are moving ahead with making GUS compatible with 
PostgreSQL.   We have discovered that our code is relying on an Oracle 
specific syntax for outer joins (using the '+' symbol).   Apparently 
Oracle adopted the ANSI standard for outer joins with release 9i.

if we move our code ahead to use that syntax any of you who are using 
Oracle 8i will have a problem (or need to upgrade).

Will this affect any of you?

Steve

Re: [Gusdev-gusdev] a NEW table?

[Bindu G. <bi...@pc...>]

hi Michael -
this table is in the plasmodb schema.

SQL> desc plasmodb_41.seq_browser_feats
  Name            Null?    Type
  ----------------------------------------- -------- 
----------------------------
  SEQ_TAXON_NAME          NOT NULL VARCHAR2(30)
  SEQ_SOURCE_ID           NOT NULL VARCHAR2(30)
  START_MIN           NOT NULL NUMBER(12)
  END_MAX           NOT NULL NUMBER(12)
  STRAND               VARCHAR2(1)
  FEAT_TABLE_NAME         NOT NULL VARCHAR2(30)
  FEAT_ROW_ID           NOT NULL NUMBER(12)
  FEAT_SOURCE_ID             VARCHAR2(50)
  FEAT_PREDICTION_ALGORITHM          VARCHAR2(50)
  SPAN_ORDER_NUM          NOT NULL NUMBER(12)

Bindu


On Apr 5, 2004, at 10:48 PM, Michael Saffitz wrote:

>
> Michael,
>
> To the best of my knowledge, SEQ_BROWSER_FEATS is not part of GUS-- 
> it's a table specific to one of CBIL's projects (PlasmoDB).
>
> I'm not familiar with the image tool, and don't know why you're coming 
> across dependancies on this table.  Perhaps someone else on the list 
> can shed light on that.
>
> --Mike
> CBIL DBA
>
> On Apr 5, 2004, at 3:24 PM, MICHAEL LUCHTAN wrote:
>
>> Hello-
>> I am trying to get the image tool for sequence retrieval working, but
>> unfortunately I have encountered a new table, which seems to be 
>> required.
>> Has anyone ever heard of a table called:
>>
>> seq_browser_feats
>>
>> It is certainly not in the schema browser.  Is this a part of gus?  
>> Or is
>> it getting phased out?
>>
>>
>> Michael Luchtan
>> http://www.cs.uga.edu/~luchtan
>>
>>
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by: IBM Linux Tutorials
>> Free Linux tutorial presented by Daniel Robbins, President and CEO of
>> GenToo technologies. Learn everything from fundamentals to system
>> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [Gusdev-gusdev] a NEW table?

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

Michael,

To the best of my knowledge, SEQ_BROWSER_FEATS is not part of GUS-- 
it's a table specific to one of CBIL's projects (PlasmoDB).

I'm not familiar with the image tool, and don't know why you're coming 
across dependancies on this table.  Perhaps someone else on the list 
can shed light on that.

--Mike
CBIL DBA

On Apr 5, 2004, at 3:24 PM, MICHAEL LUCHTAN wrote:

> Hello-
> I am trying to get the image tool for sequence retrieval working, but
> unfortunately I have encountered a new table, which seems to be 
> required.
> Has anyone ever heard of a table called:
>
> seq_browser_feats
>
> It is certainly not in the schema browser.  Is this a part of gus?  Or 
> is
> it getting phased out?
>
>
> Michael Luchtan
> http://www.cs.uga.edu/~luchtan
>
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IBM Linux Tutorials
> Free Linux tutorial presented by Daniel Robbins, President and CEO of
> GenToo technologies. Learn everything from fundamentals to system
> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

[Gusdev-gusdev] a NEW table?

[MICHAEL L. <lu...@cs...>]

Hello-
I am trying to get the image tool for sequence retrieval working, but
unfortunately I have encountered a new table, which seems to be required.
Has anyone ever heard of a table called:

seq_browser_feats

It is certainly not in the schema browser.  Is this a part of gus?  Or is
it getting phased out?


Michael Luchtan
http://www.cs.uga.edu/~luchtan

Re: [Gusdev-gusdev] data type change

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

Hi Joan,

This is done.

As an aside to the rest of the list, we've been discussing using the 
list to request, discuss, and track GUS schema changes, in an effort to 
ensure that the schema changes are seen as broadly as possible.  This 
would be a change from using the SourceForge-provided trackers, which 
tend to be slow and inconsistent, and perhaps overkill for our needs.  
Any strong feelings about this one way or another?

Mike
CBIL DBA

On Apr 1, 2004, at 2:40 PM, Joan Mazzarelli wrote:

> Hi Mike,
>
> I would like to request a change in sres.SequenceOntology table.
> Since so_id's are of the form, SO:0000204, the type for the so_id 
> attribute needs to be changed from  number(10) to varchar2(32).
> Currently, there are no rows in the sres.SequenceOntology table.
>
> Joan
>
>
>
> -- 
> Joan Mazzarelli, Ph.D.
> Computational Biology and Informatics Laboratory
> Center for Bioinformatics
> University of Pennsylvania
> 1429 Blockley Hall
> 423 Guardian Drive
> Philadelphia, PA 19104
> ma...@pc...
> Ph:215-573-4413 FAX:215-573-3111
>
>
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IBM Linux Tutorials
> Free Linux tutorial presented by Daniel Robbins, President and CEO of
> GenToo technologies. Learn everything from fundamentals to system
> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

[Gusdev-gusdev] data type change

[Joan M. <ma...@pc...>]

Hi Mike,

I would like to request a change in sres.SequenceOntology table.
Since so_id's are of the form, SO:0000204, the type for the so_id 
attribute needs to be changed from  number(10) to varchar2(32).
Currently, there are no rows in the sres.SequenceOntology table.

Joan



-- 
Joan Mazzarelli, Ph.D.
Computational Biology and Informatics Laboratory
Center for Bioinformatics
University of Pennsylvania
1429 Blockley Hall
423 Guardian Drive
Philadelphia, PA 19104
ma...@pc...
Ph:215-573-4413 FAX:215-573-3111