genex-dev — GeneX developers

Re: [GeneX-dev] abbreviations in GeneX schemata

[Tom L. <tw...@vi...>]

Maciej,

Only Jason Steward knows. Last I heard, he was in India. The Genex 
projects are all dead.

If you want an XML schema to analyze, try the NCBI BLAST schema. BLAST 
is an active project.

Best of luck,
Tom


On 02/01/2010 05:52 AM, Maciej Gawinecki wrote:
> Dear authors,
>
> On the page
> http://queens.db.toronto.edu/project/clio/index.php#testschemas
> I found schemata belonging to your project. Since I work on the data
> integration I would like to know what the abbreviation "an" stands for
>
> in the following attributes names:
>
> image_an_params
> image_an_id
> IMAGE_AN_FK
>
> ?
>
> I would be very grateful for your support,
>
> Best regards,
> Maciej
>
>
> ------------------------------------------------------------------------------
> The Planet: dedicated and managed hosting, cloud storage, colocation
> Stay online with enterprise data centers and the best network in the business
> Choose flexible plans and management services without long-term contracts
> Personal 24x7 support from experience hosting pros just a phone call away.
> http://p.sf.net/sfu/theplanet-com
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/genex-dev

-- 
Tom Laudeman
tw...@vi...
(434) 924-2456
http://www.people.virginia.edu/~twl8n/
http://laudeman.com/

[GeneX-dev] abbreviations in GeneX schemata

[Maciej G. <mga...@gm...>]

Dear authors,

On the page
http://queens.db.toronto.edu/project/clio/index.php#testschemas
I found schemata belonging to your project. Since I work on the data 
integration I would like to know what the abbreviation "an" stands for

in the following attributes names:

image_an_params
image_an_id
IMAGE_AN_FK

?

I would be very grateful for your support,

Best regards,
Maciej

Re: [GeneX-dev] OT: Invitation to participate in research project

[Jae K. L. <ja...@vi...>]

Our developers may answer you better, but our open source
development is not based on Java.

---
Jae K. Lee, Ph.D.           
Associate Professor of Biostatistics and Epidemiology 
Director, UVA Bioinformatics Support (BIS) Core 
Department of Public Health Sciences     
Old Medical School, Rm. 3914 (Biostatistics; physical location) 
1335 Hospital Drive, Rm. 3181 (mail delivery)
Hospital West Complex, P.O.Box 800717
University of Virginia School of Medicine
Charlottesville, VA 22908-0717

----- Original Message ----- 
From: "Ben Alex" <ben...@st...>
To: <gen...@li...>
Sent: Monday, June 25, 2007 5:28 AM
Subject: [GeneX-dev] OT: Invitation to participate in research project


> Hello there
> 
> I would greatly appreciate a small amount of your time to assist with
> my doctoral research at The University of Newcastle. The research
> concerns open source licensing and we're seeking developers working on
> Java projects. The research is supervised, ethics-approved, anonymous
> and results will be freely available. Participation will also provide a
> custom licensing report for your project. To learn more, please visit:
> 
>   http://licensing-research.newcastle.edu.au
> 
> Thanks for reading this email, and I hope you'll consider participating.
> 
> Best regards
> Ben Alex
> 
> (My apologies for being off-topic; this list will not be emailed again)
> 
> -------------------------------------------------------------------------
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
> control of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/genex-dev
>

[GeneX-dev] OT: Invitation to participate in research project

[Ben A. <ben...@st...>]

Hello there

I would greatly appreciate a small amount of your time to assist with
my doctoral research at The University of Newcastle. The research
concerns open source licensing and we're seeking developers working on
Java projects. The research is supervised, ethics-approved, anonymous
and results will be freely available. Participation will also provide a
custom licensing report for your project. To learn more, please visit:

   http://licensing-research.newcastle.edu.au

Thanks for reading this email, and I hope you'll consider participating.

Best regards
Ben Alex

(My apologies for being off-topic; this list will not be emailed again)

Re: [GeneX-dev] status

[Harry M. <hj...@ta...>]

Hi there, Pankaj

What happened is that we had some internal personnel problems and have 
been conversing amongst ourselves about how to resolve the problems.  
We've started coding again so we will shortly begin to start posting 
to the list as a communication channel.

Thanks for listening, by the way..

What area are you most interested in helping with?  DB guts?  Mason 
interface?  Loading / pre-processing?

Harry




On Sunday 27 February 2005 10:06 pm, Pankaj kaushal wrote:
> hello,
>
> I have been a silent 'listner' to this list for a while, its almost
> dead since the last two months. what happened?
>
> PS: I have some skills with perl and luckily now some time on my
> hands too.
>
> Cheers!
> Pankaj.

-- 
Cheers, Harry
Harry J Mangalam - 949 856 2847 (vox; email for fax) - hj...@ta... 
            <<plain text preferred>>

[GeneX-dev] status

[Pankaj k. <pen...@li...>]

hello,

I have been a silent 'listner' to this list for a while, its almost dead
since the last two months. what happened?

PS: I have some skills with perl and luckily now some time on my hands
too.

Cheers!
Pankaj.
-- 
Always do right. This will gratify some people and astonish the rest.

pub  1024D/94C525E2 2003-02-16
	 Fingerprint=7A60 AE0C C773 2CD2 74E3  29F4 EEFD CD6D 94C5 25E2

Re: [GeneX-dev] Location of specific attribute within the Database...

[Harry M. <hj...@ta...>]

Hi Andrew - sorry for the delay - 
Jason, correct me if I'm in error, but the actual values from the 
arrays are stored in the technology-specific tables that correspond 
to the arrays - ie quantarray data is stored in quantarray_3_0, affy 
data is stored in microarraysuite_cel, etc.  Reporter names are 
stored separately in genex_reporter.

you can peek at the values more easily with a gui like pgaccess or via 
Openoffice, with the ODBC connector for postgres.

hrishi mentioned a schema viewer thingie a while ago from the firebird 
project - ask him about it.  there's another free (?) one from 
theKompany called DataArchitect that seems interesting as well.

hjm


On Tuesday 11 January 2005 11:58 am, dcarr2 wrote:
> Jason or Harry,
>
> A couple questions.
>
> I need to know where and how the actual signal values are stored
> within the postgres genex database.
>
> I am developing a tool to archive the Reporter information, i.e.
> insert the probe sequences, but do not see linkage to the signal
> value.  The probe sequences belong in the genex_reporter table.
>
> Does the rest of the probe information such as interrogation
> position or strandedness belong in the reporter table?
>
> Thanks,
>
> Andrew
>
>
> -------------------------------------------------------
> The SF.Net email is sponsored by: Beat the post-holiday blues
> Get a FREE limited edition SourceForge.net t-shirt from ThinkGeek.
> It's fun and FREE -- well,
> almost....http://www.thinkgeek.com/sfshirt
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/genex-dev

-- 
Cheers, Harry
Harry J Mangalam - 949 856 2847 (vox; email for fax) - hj...@ta... 
            <<plain text preferred>>

[GeneX-dev] Location of specific attribute within the Database...

[dcarr2 <dc...@gm...>]

Jason or Harry,

A couple questions.

I need to know where and how the actual signal values are stored within 
the postgres genex database. 

I am developing a tool to archive the Reporter information, i.e. insert 
the probe sequences, but do not see linkage to the signal value.  The 
probe sequences belong in the genex_reporter table.

Does the rest of the probe information such as interrogation position or 
strandedness belong in the reporter table?

Thanks,

Andrew

Re: [GeneX-dev] General Schema Link Not Up

[<ja...@op...>]

dcarr2 <dc...@gm...> writes:

> Jason or Harry,
>
> The Developer Documents: Schema: Tables Schema Link brings back the
> following error.
>
> ERROR: Page: nologin/docs/table-defs.html not found

Hey Andrew,

Sorry, broken link. The correct link is:

  login/browse/table-defs.html

Cheers,
jas.

[GeneX-dev] General Schema Link Not Up

[dcarr2 <dc...@gm...>]

Jason or Harry,

The Developer Documents: Schema: Tables Schema Link brings back the 
following error.

ERROR: Page: nologin/docs/table-defs.html not found

Is there a current schema available.  I am in the process of working on 
some SQL tools and need to know table names and specific attributes.


If a current schema is not available is there a simple way to create one 
via extraction from postgres, preferably in with a visualization tool?


Thanks,

Andrew

Re: [GeneX-dev] Question

[Hrishikesh D. <hde...@gm...>]

Hi Jason,

I tried as you suggested and no luck.

Hrishi

Jason E. Stewart wrote:
> Hrishikesh Deshmukh <hde...@gm...> writes:
> 
> 
>>I am trying to load data on matrix, so one has to load CDF file and
>>this is taking a looong time, so far:
> 
> 
> Hi Hrishi,
> 
> Big CDF files do take a long time, but not more than 20 minutes or
> so. The Reporters took 824 secs to insert, the Features should take
> about the same. I have seen it get stuck in a loop. I restarted
> postgres ('/etc/init.d/postgresql restart') - which kills the insert -
> and re-ran the program, and the second insert went just fine. 
> 
> Cheers,
> jas.
> 
> 
>>Your job is being run by the system
>>
>>Current run time is 11432 seconds.
>>
>>Output of the program:
>>
>>Found 2065 Blank Features
>>Inserting Reporters took: 824 wallclock secs (102.90 usr + 28.16 sys =
>>131.06 CPU)
>>Found 407536 Reporters, and 407536 Features
>>Parsing CDF took: 58 wallclock secs (56.94 usr +  0.77 sys = 57.71 CPU)
>>Can't ignore signal CHLD, forcing to default.
>>
>>
>>Its still continuing to do!!!
>>Any ideas!
>>
>>Cheers,
>>Hrishi

Re: [GeneX-dev] Question

[<ja...@op...>]

Hrishikesh Deshmukh <hde...@gm...> writes:

> Is it accurate to assume that in order to use genex one needs to have
> ADMIN privileges?!

No, but at the moment if you want to load data matrices, you must ask
an admin to schedule it for you. Once, loaded you can process and
analyze the data without admin privelege.

Although this is not what I intended, it is how the Stanford DB has
worked for many years. 

If you can find a solution to the horrific slowdown's caused by using
INSERT versus the speed-up using COPY and dropping indices (both of
which require admin privelege), I will be *very* happy. I haven't had
the time to investigate further.

> Eagerly waiting for your reply.

Again, *any* ideas how to speed up insertion will be gladly
implemented. 

Cheers,
jas.

Re: [GeneX-dev] Question

[Hrishikesh D. <hde...@gm...>]

Hi Jason,

I am trying to load data on matrix, so one has to load CDF file and this 
is taking a looong time, so far:


Your job is being run by the system

Current run time is 11432 seconds.

Output of the program:

Found 2065 Blank Features
Inserting Reporters took: 824 wallclock secs (102.90 usr + 28.16 sys = 
131.06 CPU)
Found 407536 Reporters, and 407536 Features
Parsing CDF took: 58 wallclock secs (56.94 usr +  0.77 sys = 57.71 CPU)
Can't ignore signal CHLD, forcing to default.


Its still continuing to do!!!
Any ideas!

Cheers,
Hrishi

[GeneX-dev] Re: Check space

[<ja...@op...>]

Hrishikesh Deshmukh <hde...@gm...> writes:

> Harry & Jason: How do i check there is available space in the database
> to upload data?

The database can grow without bounds - only limited by available
diskspace. 

To check diskspace under unix use 'df'.

Cheers,
jas.

Re: [GeneX-dev] Re: Error while loading "bulk" data

[Hrishikesh D. <hde...@gm...>]

How do i drop experiments and along with it the associated files (data 
files...etc.)

Thanks,
Hrishi

Jason E. Stewart wrote:
> Hrishikesh Deshmukh <hde...@gm...> writes:
> 
> 
>>Happy New Year.
> 
> 
> the same.
> 
> 
>>Here is the error which i get when i try to load "bulk" data ~200 .CEL
>>files.My guess is the error is 'coz of this particular file already in
>>the database but i am trying to upload this file in a new experiment!
> 
> 
> MBA's can belong to multiple experiments - you don't need to load the
> same file twice - it can be reused across experiments.
> 
> The MBA table declares that all MBA names must be unique. That creates
> a problem, it would be nice if the loader could do something nice
> insteading of creating an error.
> 
> One thought is to just add a unique 8 character tag to the end of any
> MBA name that conflicts with an existing MBA - or the date or
> something. 
> 
> Or we could just remove the unique name constraint.
> 
> jas.
> 
> 
> -------------------------------------------------------
> The SF.Net email is sponsored by: Beat the post-holiday blues
> Get a FREE limited edition SourceForge.net t-shirt from ThinkGeek.
> It's fun and FREE -- well, almost....http://www.thinkgeek.com/sfshirt
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/genex-dev

[GeneX-dev] Question

[Hrishikesh D. <hde...@gm...>]

Hi All,

Is it accurate to assume that in order to use genex one needs to have 
ADMIN privileges?!
Eagerly waiting for your reply.

Thanks,
Hrishi

[GeneX-dev] Check space

[Hrishikesh D. <hde...@gm...>]

Hi All,

Harry & Jason: How do i check there is available space in the database 
to upload data?

Eagerly waiting for your reply.

Thanks,
Hrishi

[GeneX-dev] Re: Errors loading "bulk" data

[Hrishikesh D. <hde...@gm...>]

Hi Jason,

I am attempting everything on genex2, my guess is that its running 
earlier version of 1725, so it may not be up-to-date!!!
If you want i can update but i need step by step instructions, i have 
written to Harry to send the same, if you can send me the inst. i will 
update genex2.

For the same experiment name i cannot add already loaded files(wanted to 
check if we could add redundancy), cannot load new files and cannot load 
replicates.

Here is the error which i get.

Your job is finished. The status is: ERROR

The error status is: 2304
Output of the program:

Using Software: MAS-CEL
Using Experiment: Jan05-ADENO-Batch1
Using ArrayDesign: www.affymetrix.com/ArrayDesign/HG_U95Av2-AD
Dropping data indices
DBD::Pg::db do failed: ERROR:  constraint 
"microarraysuite_cel_feature_fk_fkey" does not exist at 
/usr/local/genex/bin/mbad-insert.pl line 170.
/usr/local/genex/bin/mbad-insert.pl: Couldn't drop indices, SQL=[[alter 
table MICROARRAYSUITE_CEL drop constraint 
MICROARRAYSUITE_CEL_feature_fk_fkey;
alter table MICROARRAYSUITE_CEL drop constraint 
MICROARRAYSUITE_CEL_mba_fk_fkey;
alter table MICROARRAYSUITE_CEL drop constraint 
MICROARRAYSUITE_CEL_mba_fk_key;
]], DBI=[[ERROR:  constraint "microarraysuite_cel_feature_fk_fkey" does 
not exist]]

Thanks,
Hrishi





Jason E. Stewart wrote:
> Hrishikesh Deshmukh <hde...@gm...> writes:
> 
> 
>>Hi Jason,
>>
>>Here is the error which i get when i try to use MBAD loader for
>>loading data being genex_test and genex_test_curator. This should not
>>happen since use of MBAD should be a simple "user" job.
>>
>>ERROR: ACCESS DENIED: You must be a Genex ADMIN in order to use the
>>MBAD Data Loader
> 
> 
> From the data loading howto:
> 
>  Then there are the required tasks for data loading.
> 
> [snip]
> 
>    2. The data files are loaded into the DB - requires ADMIN privelege. Required.
> 
>       The output data matrices produced by scanning the chips are
>       loaded into the DB using the the MBA Data Loader GUI. This will
>       create a single MeasuredBioAssay and PhysicalBioAssay for each
>       file loaded.
> 
> This was originally a user task. Due to unforeseen performance issues
> we had to use performance tweaks that require ADMIN privelege. Until
> someone (else) fixes those, you have to be an admin, sorry.
> 
> jas.

[GeneX-dev] Re: Error while loading "bulk" data

[<ja...@op...>]

Hrishikesh Deshmukh <hde...@gm...> writes:

> Happy New Year.

the same.

> Here is the error which i get when i try to load "bulk" data ~200 .CEL
> files.My guess is the error is 'coz of this particular file already in
> the database but i am trying to upload this file in a new experiment!

MBA's can belong to multiple experiments - you don't need to load the
same file twice - it can be reused across experiments.

The MBA table declares that all MBA names must be unique. That creates
a problem, it would be nice if the loader could do something nice
insteading of creating an error.

One thought is to just add a unique 8 character tag to the end of any
MBA name that conflicts with an existing MBA - or the date or
something. 

Or we could just remove the unique name constraint.

jas.

[GeneX-dev] Errors loading "bulk" data

[Hrishikesh D. <hde...@gm...>]

Hi Jason,

Here is the error which i get when i try to load replicates,i have 
double checked and this data doesn't exist in the database.
I assume that somewhere the file name is used as a part of primary key, 
but how much of the file name is used to form the primary key?!

Thanks,
Hrishi


Your job is finished. The status is: ERROR

The error status is: 2304
Output of the program:

Using Software: MAS-CEL
Using Experiment: Replicates
Using ArrayDesign: www.affymetrix.com/ArrayDesign/HG_U95Av2-AD
Dropping data indices
DBD::Pg::db do failed: ERROR:  constraint 
"microarraysuite_cel_feature_fk_fkey" does not exist at 
/usr/local/genex/bin/mbad-insert.pl line 170.
/usr/local/genex/bin/mbad-insert.pl: Couldn't drop indices, SQL=[[alter 
table MICROARRAYSUITE_CEL drop constraint 
MICROARRAYSUITE_CEL_feature_fk_fkey;
alter table MICROARRAYSUITE_CEL drop constraint 
MICROARRAYSUITE_CEL_mba_fk_fkey;
alter table MICROARRAYSUITE_CEL drop constraint 
MICROARRAYSUITE_CEL_mba_fk_key;
]], DBI=[[ERROR:  constraint "microarraysuite_cel_feature_fk_fkey" does 
not exist]]

[GeneX-dev] Open-Source Affy. Client-Sever System

[Hrishikesh D. <hde...@gm...>]

FYI:

http://hc.ims.u-tokyo.ac.jp/JSBi/journal/GIW03/GIW03SS04/GIW03SS04.html

Thanks,
Hrishi

[GeneX-dev] Error while loading "bulk" data

[Hrishikesh D. <hde...@gm...>]

Hi Jason,

Happy New Year.

Here is the error which i get when i try to load "bulk" data ~200 .CEL 
files.My guess is the error is 'coz of this particular file already in 
the database but i am trying to upload this file in a new experiment!

Hrishi


Your job is finished. The status is: ERROR

The error status is: 65280
Output of the program:

Using Software: MAS-CEL
Using Experiment: Dec06-LUNG-Bulk-Complete
Using ArrayDesign: www.affymetrix.com/ArrayDesign/HG_U95Av2-AD
Dropping data indices
Pre-fetching Feature Data
Handled 10000 lines
Handled 20000 lines
Handled 30000 lines
Handled 40000 lines
Handled 50000 lines
Handled 60000 lines
Handled 70000 lines
Handled 80000 lines
Handled 90000 lines
Handled 100000 lines
Handled 110000 lines
Handled 120000 lines
Handled 130000 lines
Handled 140000 lines
Handled 150000 lines
Handled 160000 lines
Handled 170000 lines
Handled 180000 lines
Handled 190000 lines
Handled 200000 lines
Handled 210000 lines
Handled 220000 lines
Handled 230000 lines
Handled 240000 lines
Handled 250000 lines
Handled 260000 lines
Handled 270000 lines
Handled 280000 lines
Handled 290000 lines
Handled 300000 lines
Handled 310000 lines
Handled 320000 lines
Handled 330000 lines
Handled 340000 lines
Handled 350000 lines
Handled 360000 lines
Handled 370000 lines
Handled 380000 lines
Handled 390000 lines
Handled 400000 lines
Handled 410000 lines
Copying data for MBA: CL2001031606AA.CEL into MICROARRAYSUITE_CEL
Pre-fetching Feature Data
Handled 10000 lines
Handled 20000 lines
Handled 30000 lines
Handled 40000 lines
Handled 50000 lines
Handled 60000 lines
Handled 70000 lines
Handled 80000 lines
Handled 90000 lines
Handled 100000 lines
Handled 110000 lines
Handled 120000 lines
Handled 130000 lines
Handled 140000 lines
Handled 150000 lines
Handled 160000 lines
Handled 170000 lines
Handled 180000 lines
Handled 190000 lines
Handled 200000 lines
Handled 210000 lines
Handled 220000 lines
Handled 230000 lines
Handled 240000 lines
Handled 250000 lines
Handled 260000 lines
Handled 270000 lines
Handled 280000 lines
Handled 290000 lines
Handled 300000 lines
Handled 310000 lines
Handled 320000 lines
Handled 330000 lines
Handled 340000 lines
Handled 350000 lines
Handled 360000 lines
Handled 370000 lines
Handled 380000 lines
Handled 390000 lines
Handled 400000 lines
Handled 410000 lines
Copying data for MBA: CL2001031607AA.CEL into MICROARRAYSUITE_CEL
DBD::Pg::st execute failed: ERROR:  duplicate key violates unique 
constraint "genex_measured_bioassay_name_key" at 
/usr/local/share/perl/5.8.3/Bio/Genex/MeasuredBioAssay.pm line 1126.
Bio::Genex::MeasuredBioAssay::insert_db: SQL=[[INSERT INTO 
GENEX_MEASURED_BIOASSAY (ro_gs_fk,name,rw_gs_fk,fe_sw_fk,mba_pk) VALUES 
('671','CL2001031608AA.CEL','679','827','2871919')]], DBI=[[ERROR: 
duplicate key violates unique constraint 
"genex_measured_bioassay_name_key"]] at 
/usr/local/share/perl/5.8.3/Bio/Genex/MeasuredBioAssay.pm line 1130.
/usr/local/genex/bin/mbad-insert.pl: Couldn't insert MeasuredBioAssay: 
CL2001031608AA.CEL, DBI=[[ERROR:  duplicate key violates unique 
constraint "genex_measured_bioassay_name_key"]]
DBD::Pg::db do failed: execute on disconnected handle at 
/usr/local/genex/bin/mbad-insert.pl line 401.

[GeneX-dev] [ genex-Bugs-948987 ] Need date component for annotation apps

[SourceForge.net <no...@so...>]

Bugs item #948987, was opened at 2004-05-06 02:13
Message generated for change (Settings changed) made by jason_e_stewart
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=116453&aid=948987&group_id=16453

Category: Mason GUI
Group: Genex-2
>Status: Closed
>Resolution: Fixed
Priority: 8
Submitted By: Jason E. Stewart (jason_e_stewart)
Assigned to: Jason E. Stewart (jason_e_stewart)
>Summary: Need date component for annotation apps

Initial Comment:
Users don't know how add dates

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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=116453&aid=948987&group_id=16453

[GeneX-dev] [ genex-Bugs-945670 ] mason errors when exporting data

[SourceForge.net <no...@so...>]

Bugs item #945670, was opened at 2004-04-30 17:22
Message generated for change (Settings changed) made by jason_e_stewart
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=116453&aid=945670&group_id=16453

Category: Mason GUI
Group: None
>Status: Closed
>Resolution: Fixed
Priority: 8
Submitted By: Harry Mangalam (mangalam)
Assigned to: Jason E. Stewart (jason_e_stewart)
Summary: mason errors when exporting data

Initial Comment:
repeated errors when trying to view data on genex2 - 

from:
http://genex2.binf.gmu.edu/genex/mason/login/workspace/workspace.html
logged in as test/test

try to export anything, get a mason errror:
 	could not find component for path 'class-from-tablename'

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

>Comment By: Jason E. Stewart (jason_e_stewart)
Date: 2005-01-06 02:33

Message:
Logged In: YES 
user_id=85550

Seems that this bug has been fixed

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

Comment By: Jason E. Stewart (jason_e_stewart)
Date: 2004-05-20 04:00

Message:
Logged In: YES 
user_id=85550

this problem is fixed but there is a new error:

column 'type' doesn't exist: 

HTML::Mason::Commands:/var/www/genex2/mason/login/workspace/comps/exp-analyze.mason:85:Class::ObjectTemplate::DB::Base::get_all_objects:
Bio::Genex::Protocol::get_all_objects: Couldn't execute
select, SQL=[[SELECT * FROM GENEX_PROTOCOL_VIEW WHERE type =
? ]], DBI=[[ERROR: column "type" does not exist]]

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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=116453&aid=945670&group_id=16453

[GeneX-dev] [ genex-Bugs-945413 ] table browser is not caching table names properly

[SourceForge.net <no...@so...>]

Bugs item #945413, was opened at 2004-04-30 10:40
Message generated for change (Comment added) made by jason_e_stewart
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=116453&aid=945413&group_id=16453

Category: Mason GUI
Group: Genex-2
Status: Open
Resolution: None
>Priority: 5
Submitted By: Jason E. Stewart (jason_e_stewart)
Assigned to: Jason E. Stewart (jason_e_stewart)
Summary: table browser is not caching table names properly

Initial Comment:
Loading either of the browse table pages is
*really*slow. We're supposed to be caching the TableDef
entries so that we don't need to reload them.

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

>Comment By: Jason E. Stewart (jason_e_stewart)
Date: 2005-01-06 02:27

Message:
Logged In: YES 
user_id=85550

Downgrading priority - list-tables.mason uses
TableDef::get_all_objects() and doesn't cache the results. 

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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=116453&aid=945413&group_id=16453