genex-dev — GeneX developers

Re: [GeneX-dev] GeneX errors while loading files

[Hrishikesh D. <gen...@ya...>]

Error while loading QTD file, refer to my email a min
back.

System error
error:  	DBD::Pg::db commit failed: commit failed at
/usr/share/perl5/Apache/Session/Store/Postgres.pm line
95.
context:  	
...  	
90:  	
91:  	sub DESTROY {
92:  	my $self = shift;
93:  	
94:  	if ($self->{commit}) {
95:  	$self->{dbh}->commit;
96:  	}
97:  	
98:  	if ($self->{disconnect}) {
...  	
code stack:  
/usr/share/perl5/Apache/Session/Store/Postgres.pm:94
/usr/share/perl5/HTML/Mason/Request.pm:1068
/var/www/genex/mason/autohandler:26
/usr/share/perl5/HTML/Mason/Request.pm:753
/var/www/genex/mason/autohandler:92
--- Hrishikesh Deshmukh <gen...@ya...> wrote:

> Now loading the array design file was successful, i
> have selected dataset 4 (one of your emails dated:
> 27
> April,04 has the details). 
> 
> Second thing which i wanted to do was loading QTD
> file, i selected the quantarray.xml file, the data
> set
> file is 1200-mangle-.txt, the values used were:
> 
> read/write= public
> FESW= Quantarray
> Version= 3.0
> Feature Identifier String= 0.1
> Data start Regex #1= 38
> Data end regex = 5413
> 
> The values 38 and 5413 are the start and stop of the
> actual data in file 1200-mangle.txt
> As suggested in the Howto's i was the user with
> Admin
> priv, AD loading was done by using
> genex_test_curator.
> 
> Here is the error which i get:
> 
> Genex Job Status Page
> 
> Your job is finished. The status is: ERROR
> The error status is: Inappropriate ioctl for device
> 
> Output of the program:
> 
> Must specify --abbrev_name
> USAGE: /usr/local/genex/bin/qtdim-insert.pl
> [OPTIONS]
> file_to_read
> Options:
>     --username=name   : the DB username to login as
>     --password=word   : the DB password to login
> with
>     --name=name       : the name of the
> FeatureExtraction SW program
>     --version=num     : the version of the
> FeatureExtraction SW program
>     --feature_identifier_string=string
>                       : the string that defines how
> which columns to use
>                         to create a feature
> identifier
> from the input
>     --data_start_regex1=regex : regular expression
> indicating where to
>                                 begin reading data
>     --data_start_regex2=regex : in case regex1 is
> not
> sufficient
>     --data_end_regex=regex    : regex indicating
> when
> to stop reading
> 
>   optional parameters:
>     --qtdim_only    : only insert the
> QuantitationType
> info, not anything else
>     --no_db         : only output the .xml and .pm
> files (no DB insert)
>     --ro_groupname  : the read only security group
> NAME
>     --rw_groupname  : the read write security group
> NAME
>     --ro_group_id   : the read only security group
> ID
>     --rw_group_id   : the read write security group
> ID
>     --write_xml     : leave the Table.xml file in
> the
> temp directory
>     --dbname=name   : the name of the DB to use
>     --verbose=n     : Print out lots of diagnostic
> info if 1 and more if 2
>     --debug         : does a rollback instead of a
> commit
>     --help          : print this message
> 
> 
> 
> 
> 
> 
> 
> Thanks,
> Hrishi
> 
> 
> 
> 
> 
> 
> 
> 
> 
> --- Hrishikesh Deshmukh <gen...@ya...> wrote:
> 
> > Hi Jason,
> > 
> > I logged in as genes_test_curator and tried
> loading
> > AD
> > file,here is the "error" which i get:
> > Genex Job Status Page
> > 
> > Your job is finished. The status is: ERROR
> > The error status is: -1
> > 
> > Output of the program:
> > 
> > MAGE creation took: 0 wallclock secs ( 0.20 usr + 
> > 0.01 sys =  0.21 CPU)
> > 24 Reporters to insert
> > In Bio::Genex::ChangeLog::insert_db: pkey = 
> > Inserting Reporters took: 0 wallclock secs ( 0.01
> > usr
> > +  0.00 sys =  0.01 CPU)
> > 24 FeatureReporterMap's to handle
> > Handling FR Maps took: 0 wallclock secs ( 0.00 usr
> +
> > 
> > 0.00 sys =  0.00 CPU)
> > 1 ArrayDesigns to insert
> > Inserting array design: HD_trial_jason_input
> > Found 24 features.
> > In Bio::Genex::ArrayDesign::insert_db: pkey = 
> >   In Bio::Genex::ChangeLog::insert_db: pkey = 
> >   In Bio::Genex::ChangeLog::insert_db: pkey = 
> > Finished
> > 50894
> > 
> > 
> > 
> > 
> > 
> > --- "Jason E. Stewart" <ja...@op...>
> > wrote:
> > 
> > > Hrishikesh Deshmukh <gen...@ya...>
> writes:
> > > 
> > > > for inserting an experiment, here is the error
> > > which i get:
> > > > System error
> > > > error:  Undefined subroutine
> > > &Bio::Genex::ParseDate called at
> > > /usr/local/share/perl/5.8.4/Bio/Genex.pm line
> 190.
> > > >  
> > > > context:  ...   
> > > > 186:   
> > > > 187:  $date .= $args{tz} 
> > > > 188:  if $args{tz}; 
> > > > 189:   
> > > > 190:  return $date 
> > > > 191:  if ParseDate($date); 
> > > > 192:   
> > > > 193:  # we have a bogus date 
> > > > 194:  return undef; 
> > > 
> > > Hi Hrishi,
> > > 
> > > This is odd, because just a few lines above, I
> > > required the Perl
> > > module that provides this method. If you can
> > change
> > > the line to be:
> > > 
> > >   if Date::Manip::ParseDate($date); 
> > > 
> > > run 'sudo make install_modules' and try it
> again.
> > > Perl should be able
> > > to resolve this..
> > > 
> > > > NOW if i use the browsing tab and then insert
> > the
> > > experiment then
> > > > its successful, I filled the date part and
> then
> > i
> > > get an error if i
> > > > don't fill the release date (i.e. today's
> date)
> > > then the error is
> > > > not seen.
> > > 
> > > Correct. The error is caused because you
> attempted
> > > to set a date, and
> > > I have to check that the date given is a real
> > date.
> > > If you don't set
> > > the date, then I don't bother checking. The
> error
> 
=== message truncated ===



		
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Re: [GeneX-dev] GeneX errors while loading files

[Hrishikesh D. <gen...@ya...>]

Now loading the array design file was successful, i
have selected dataset 4 (one of your emails dated: 27
April,04 has the details). 

Second thing which i wanted to do was loading QTD
file, i selected the quantarray.xml file, the data set
file is 1200-mangle-.txt, the values used were:

read/write= public
FESW= Quantarray
Version= 3.0
Feature Identifier String= 0.1
Data start Regex #1= 38
Data end regex = 5413

The values 38 and 5413 are the start and stop of the
actual data in file 1200-mangle.txt
As suggested in the Howto's i was the user with Admin
priv, AD loading was done by using genex_test_curator.

Here is the error which i get:

Genex Job Status Page

Your job is finished. The status is: ERROR
The error status is: Inappropriate ioctl for device

Output of the program:

Must specify --abbrev_name
USAGE: /usr/local/genex/bin/qtdim-insert.pl [OPTIONS]
file_to_read
Options:
    --username=name   : the DB username to login as
    --password=word   : the DB password to login with
    --name=name       : the name of the
FeatureExtraction SW program
    --version=num     : the version of the
FeatureExtraction SW program
    --feature_identifier_string=string
                      : the string that defines how
which columns to use
                        to create a feature identifier
from the input
    --data_start_regex1=regex : regular expression
indicating where to
                                begin reading data
    --data_start_regex2=regex : in case regex1 is not
sufficient
    --data_end_regex=regex    : regex indicating when
to stop reading

  optional parameters:
    --qtdim_only    : only insert the QuantitationType
info, not anything else
    --no_db         : only output the .xml and .pm
files (no DB insert)
    --ro_groupname  : the read only security group
NAME
    --rw_groupname  : the read write security group
NAME
    --ro_group_id   : the read only security group ID
    --rw_group_id   : the read write security group ID
    --write_xml     : leave the Table.xml file in the
temp directory
    --dbname=name   : the name of the DB to use
    --verbose=n     : Print out lots of diagnostic
info if 1 and more if 2
    --debug         : does a rollback instead of a
commit
    --help          : print this message







Thanks,
Hrishi









--- Hrishikesh Deshmukh <gen...@ya...> wrote:

> Hi Jason,
> 
> I logged in as genes_test_curator and tried loading
> AD
> file,here is the "error" which i get:
> Genex Job Status Page
> 
> Your job is finished. The status is: ERROR
> The error status is: -1
> 
> Output of the program:
> 
> MAGE creation took: 0 wallclock secs ( 0.20 usr + 
> 0.01 sys =  0.21 CPU)
> 24 Reporters to insert
> In Bio::Genex::ChangeLog::insert_db: pkey = 
> Inserting Reporters took: 0 wallclock secs ( 0.01
> usr
> +  0.00 sys =  0.01 CPU)
> 24 FeatureReporterMap's to handle
> Handling FR Maps took: 0 wallclock secs ( 0.00 usr +
> 
> 0.00 sys =  0.00 CPU)
> 1 ArrayDesigns to insert
> Inserting array design: HD_trial_jason_input
> Found 24 features.
> In Bio::Genex::ArrayDesign::insert_db: pkey = 
>   In Bio::Genex::ChangeLog::insert_db: pkey = 
>   In Bio::Genex::ChangeLog::insert_db: pkey = 
> Finished
> 50894
> 
> 
> 
> 
> 
> --- "Jason E. Stewart" <ja...@op...>
> wrote:
> 
> > Hrishikesh Deshmukh <gen...@ya...> writes:
> > 
> > > for inserting an experiment, here is the error
> > which i get:
> > > System error
> > > error:  Undefined subroutine
> > &Bio::Genex::ParseDate called at
> > /usr/local/share/perl/5.8.4/Bio/Genex.pm line 190.
> > >  
> > > context:  ...   
> > > 186:   
> > > 187:  $date .= $args{tz} 
> > > 188:  if $args{tz}; 
> > > 189:   
> > > 190:  return $date 
> > > 191:  if ParseDate($date); 
> > > 192:   
> > > 193:  # we have a bogus date 
> > > 194:  return undef; 
> > 
> > Hi Hrishi,
> > 
> > This is odd, because just a few lines above, I
> > required the Perl
> > module that provides this method. If you can
> change
> > the line to be:
> > 
> >   if Date::Manip::ParseDate($date); 
> > 
> > run 'sudo make install_modules' and try it again.
> > Perl should be able
> > to resolve this..
> > 
> > > NOW if i use the browsing tab and then insert
> the
> > experiment then
> > > its successful, I filled the date part and then
> i
> > get an error if i
> > > don't fill the release date (i.e. today's date)
> > then the error is
> > > not seen.
> > 
> > Correct. The error is caused because you attempted
> > to set a date, and
> > I have to check that the date given is a real
> date.
> > If you don't set
> > the date, then I don't bother checking. The error
> > happens during the
> > check - if it is performed you will always get the
> > same error - if you
> > don't set the date, no check is done, no error
> will
> > happen.
> > 
> > > I went to the url
> > >
> >
>
http://matrix.binf.gmu.edu/genex/mason/login/workspace/edit/experiment-edit.html
> > > and the error is seen if the release date info.
> is
> > filled/given,
> > > leave it blank and it works fine, also for
> > timezone should ET/EastT
> > > should be used, proveide help/desciption.
> > 
> > Sorry, only numeric timezones work. The date entry
> > is a brand new
> > feature - you are most likely the first person to
> > use it. Suggestions
> > for a help message would be appreciated. Also I
> can
> > make the required
> > portions of the date RED and the optional pieces
> > BLACK. TZ is
> > optional. 
> > 
> > > Next thing i did was loading QT dim loader:
> > > Here is the error i get:
> > > System error
> > > error:  DBD::Pg::db commit failed: commit failed
> > at
> > >
> /usr/share/perl5/Apache/Session/Store/Postgres.pm
> > line 95.
> > 
> > Are you logged in as a user with CURATOR
> privelege?
> > Try the same thing
> > logged in as user: 'genex_test_curator' and
> > password: 'test' (the
> > quotes are not part of the username or password).
> > 
> > > SO NOW I AM TRYING TO LOAD ArrayDesign files,
> here
> > is the error:
> > > Genex Job Status Page
> > > Your job is finished. The status is: ERROR
> > > The error status is: 512 
> > > Output of the program:
> > > MAGE creation took:25 wallclock secs (25.41 usr
> + 
> > 0.12 sys = 25.53 CPU)
> > > 1645 Reporters to insert
> > > DBD::Pg::st execute failed: ERROR:  permission
> > denied for relation genex_reporter_view at
> > /usr/local/share/perl/5.8.4/Bio/Genex/Reporter.pm
> > line 903.
> > >
> > >
> >
>
main:/usr/local/genex/bin/array-design-insert.pl:177:Bio::Genex::Reporter::insert_matrix:
> > Couldn't execute insert sql with args: L48-2T3
> > ,clone_name,1128, SQL=[[INSERT INTO
> > GENEX_REPORTER_VIEW (name,rep_type,rep_pk) VALUES
> > (?,?,?)]], DBI=[[ERROR:  permission denied for
> > relation genex_reporter_view]]
> > 
> > ah, it looks as if you are attempting the insert
> as
> > someone with not
> > enough privelege - you need CURATOR privelege to
> > load an
> > ArrayDesign. Did you go to the AD Loader by typing
> > in the URL by hand
> > or by navigating to it using the
> > Workspace/Annotation tab?
> > 
> > > I test thoroughly if i knew excatly what AD file
> > goes with FES and
> > > what dateset, i have tried almost all files for
> AD
> > loading the above
> > > menitioned errors are commonly seen.  
> > 
> > Correct - the DB tables are highly protected so
> > users with
> > insufficient privelege cannot edit things. You
> will
> > get the
> > 'permission denied' error whenever that happens.
> > 
> > In the future I would like to trap these errors
> and
> > display a more
> > useful message.
> > 
> > Cheers,
> > jas.
> > 
> > 
> > 
> >
>
-------------------------------------------------------
> > SF.Net email is sponsored by Shop4tech.com-Lowest
> > price on Blank Media
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> > Save 50% off Retail on Ink & Toner - Free Shipping
> 
=== message truncated ===



		
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[GeneX-dev] re-testing

[<jw...@gm...>]

Hi Jason,
   For the most part I tested everything both logged in as a user and as an administrator. Do the administrator priviliges subsume the curator priviliges? I am not sure that I have a curator-specific persona, but I will ask Harry to create one, it would be good for testing purposes.

 I think that we will have to make the user documents more specific about the curator-specific tasks, from 'this is something the curator should do' to ' this is something the curator will have to do'. 
   I'll get back to you later in the afternoon (my afternoon).
   Cheers,
   Jennifer

Re: [GeneX-dev] GeneX errors while loading files

[Hrishikesh D. <gen...@ya...>]

Hi Jason,

I logged in as genes_test_curator and tried loading AD
file,here is the "error" which i get:
Genex Job Status Page

Your job is finished. The status is: ERROR
The error status is: -1

Output of the program:

MAGE creation took: 0 wallclock secs ( 0.20 usr + 
0.01 sys =  0.21 CPU)
24 Reporters to insert
In Bio::Genex::ChangeLog::insert_db: pkey = 
Inserting Reporters took: 0 wallclock secs ( 0.01 usr
+  0.00 sys =  0.01 CPU)
24 FeatureReporterMap's to handle
Handling FR Maps took: 0 wallclock secs ( 0.00 usr + 
0.00 sys =  0.00 CPU)
1 ArrayDesigns to insert
Inserting array design: HD_trial_jason_input
Found 24 features.
In Bio::Genex::ArrayDesign::insert_db: pkey = 
  In Bio::Genex::ChangeLog::insert_db: pkey = 
  In Bio::Genex::ChangeLog::insert_db: pkey = 
Finished
50894





--- "Jason E. Stewart" <ja...@op...>
wrote:

> Hrishikesh Deshmukh <gen...@ya...> writes:
> 
> > for inserting an experiment, here is the error
> which i get:
> > System error
> > error:  Undefined subroutine
> &Bio::Genex::ParseDate called at
> /usr/local/share/perl/5.8.4/Bio/Genex.pm line 190.
> >  
> > context:  ...   
> > 186:   
> > 187:  $date .= $args{tz} 
> > 188:  if $args{tz}; 
> > 189:   
> > 190:  return $date 
> > 191:  if ParseDate($date); 
> > 192:   
> > 193:  # we have a bogus date 
> > 194:  return undef; 
> 
> Hi Hrishi,
> 
> This is odd, because just a few lines above, I
> required the Perl
> module that provides this method. If you can change
> the line to be:
> 
>   if Date::Manip::ParseDate($date); 
> 
> run 'sudo make install_modules' and try it again.
> Perl should be able
> to resolve this..
> 
> > NOW if i use the browsing tab and then insert the
> experiment then
> > its successful, I filled the date part and then i
> get an error if i
> > don't fill the release date (i.e. today's date)
> then the error is
> > not seen.
> 
> Correct. The error is caused because you attempted
> to set a date, and
> I have to check that the date given is a real date.
> If you don't set
> the date, then I don't bother checking. The error
> happens during the
> check - if it is performed you will always get the
> same error - if you
> don't set the date, no check is done, no error will
> happen.
> 
> > I went to the url
> >
>
http://matrix.binf.gmu.edu/genex/mason/login/workspace/edit/experiment-edit.html
> > and the error is seen if the release date info. is
> filled/given,
> > leave it blank and it works fine, also for
> timezone should ET/EastT
> > should be used, proveide help/desciption.
> 
> Sorry, only numeric timezones work. The date entry
> is a brand new
> feature - you are most likely the first person to
> use it. Suggestions
> for a help message would be appreciated. Also I can
> make the required
> portions of the date RED and the optional pieces
> BLACK. TZ is
> optional. 
> 
> > Next thing i did was loading QT dim loader:
> > Here is the error i get:
> > System error
> > error:  DBD::Pg::db commit failed: commit failed
> at
> > /usr/share/perl5/Apache/Session/Store/Postgres.pm
> line 95.
> 
> Are you logged in as a user with CURATOR privelege?
> Try the same thing
> logged in as user: 'genex_test_curator' and
> password: 'test' (the
> quotes are not part of the username or password).
> 
> > SO NOW I AM TRYING TO LOAD ArrayDesign files, here
> is the error:
> > Genex Job Status Page
> > Your job is finished. The status is: ERROR
> > The error status is: 512 
> > Output of the program:
> > MAGE creation took:25 wallclock secs (25.41 usr + 
> 0.12 sys = 25.53 CPU)
> > 1645 Reporters to insert
> > DBD::Pg::st execute failed: ERROR:  permission
> denied for relation genex_reporter_view at
> /usr/local/share/perl/5.8.4/Bio/Genex/Reporter.pm
> line 903.
> >
> >
>
main:/usr/local/genex/bin/array-design-insert.pl:177:Bio::Genex::Reporter::insert_matrix:
> Couldn't execute insert sql with args: L48-2T3
> ,clone_name,1128, SQL=[[INSERT INTO
> GENEX_REPORTER_VIEW (name,rep_type,rep_pk) VALUES
> (?,?,?)]], DBI=[[ERROR:  permission denied for
> relation genex_reporter_view]]
> 
> ah, it looks as if you are attempting the insert as
> someone with not
> enough privelege - you need CURATOR privelege to
> load an
> ArrayDesign. Did you go to the AD Loader by typing
> in the URL by hand
> or by navigating to it using the
> Workspace/Annotation tab?
> 
> > I test thoroughly if i knew excatly what AD file
> goes with FES and
> > what dateset, i have tried almost all files for AD
> loading the above
> > menitioned errors are commonly seen.  
> 
> Correct - the DB tables are highly protected so
> users with
> insufficient privelege cannot edit things. You will
> get the
> 'permission denied' error whenever that happens.
> 
> In the future I would like to trap these errors and
> display a more
> useful message.
> 
> Cheers,
> jas.
> 
> 
> 
>
-------------------------------------------------------
> SF.Net email is sponsored by Shop4tech.com-Lowest
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> 



		
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[GeneX-dev] Jason Back online

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

Hi Harry, Jennifer,

Sorry for such a long delay.

I'm back in India now with a reliable internet connection. 

My connection is of the pay-as-you-use-it type, so I will be
attempting to offload chores that require me to be online (if
possible).

I'm going over all the email reports, but it may take a day or two
before I've gone through all of them. If there is anything urgent,
please let me know in a private email, and I'll prioritize that work.

I should be in good email contact for the next week (no travels, no
major interruptions). I'll be sure to post any interruption I know of
before it happens. So if you send an email to me and don't recieve an
email back within 24 hours - something has happened.

Cheers,
jas.

Re: [GeneX-dev] GeneX errors while loading files

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

Hrishikesh Deshmukh <gen...@ya...> writes:

> for inserting an experiment, here is the error which i get:
> System error
> error:  Undefined subroutine &Bio::Genex::ParseDate called at /usr/local/share/perl/5.8.4/Bio/Genex.pm line 190.
>  
> context:  ...   
> 186:   
> 187:  $date .= $args{tz} 
> 188:  if $args{tz}; 
> 189:   
> 190:  return $date 
> 191:  if ParseDate($date); 
> 192:   
> 193:  # we have a bogus date 
> 194:  return undef; 

Hi Hrishi,

This is odd, because just a few lines above, I required the Perl
module that provides this method. If you can change the line to be:

  if Date::Manip::ParseDate($date); 

run 'sudo make install_modules' and try it again. Perl should be able
to resolve this..

> NOW if i use the browsing tab and then insert the experiment then
> its successful, I filled the date part and then i get an error if i
> don't fill the release date (i.e. today's date) then the error is
> not seen.

Correct. The error is caused because you attempted to set a date, and
I have to check that the date given is a real date. If you don't set
the date, then I don't bother checking. The error happens during the
check - if it is performed you will always get the same error - if you
don't set the date, no check is done, no error will happen.

> I went to the url
> http://matrix.binf.gmu.edu/genex/mason/login/workspace/edit/experiment-edit.html
> and the error is seen if the release date info. is filled/given,
> leave it blank and it works fine, also for timezone should ET/EastT
> should be used, proveide help/desciption.

Sorry, only numeric timezones work. The date entry is a brand new
feature - you are most likely the first person to use it. Suggestions
for a help message would be appreciated. Also I can make the required
portions of the date RED and the optional pieces BLACK. TZ is
optional. 

> Next thing i did was loading QT dim loader:
> Here is the error i get:
> System error
> error:  DBD::Pg::db commit failed: commit failed at
> /usr/share/perl5/Apache/Session/Store/Postgres.pm line 95.

Are you logged in as a user with CURATOR privelege? Try the same thing
logged in as user: 'genex_test_curator' and password: 'test' (the
quotes are not part of the username or password).

> SO NOW I AM TRYING TO LOAD ArrayDesign files, here is the error:
> Genex Job Status Page
> Your job is finished. The status is: ERROR
> The error status is: 512 
> Output of the program:
> MAGE creation took:25 wallclock secs (25.41 usr +  0.12 sys = 25.53 CPU)
> 1645 Reporters to insert
> DBD::Pg::st execute failed: ERROR:  permission denied for relation genex_reporter_view at /usr/local/share/perl/5.8.4/Bio/Genex/Reporter.pm line 903.
>
> main:/usr/local/genex/bin/array-design-insert.pl:177:Bio::Genex::Reporter::insert_matrix: Couldn't execute insert sql with args: L48-2T3 ,clone_name,1128, SQL=[[INSERT INTO GENEX_REPORTER_VIEW (name,rep_type,rep_pk) VALUES (?,?,?)]], DBI=[[ERROR:  permission denied for relation genex_reporter_view]]

ah, it looks as if you are attempting the insert as someone with not
enough privelege - you need CURATOR privelege to load an
ArrayDesign. Did you go to the AD Loader by typing in the URL by hand
or by navigating to it using the Workspace/Annotation tab?

> I test thoroughly if i knew excatly what AD file goes with FES and
> what dateset, i have tried almost all files for AD loading the above
> menitioned errors are commonly seen.  

Correct - the DB tables are highly protected so users with
insufficient privelege cannot edit things. You will get the
'permission denied' error whenever that happens.

In the future I would like to trap these errors and display a more
useful message.

Cheers,
jas.

Re: [GeneX-dev] Plug OpenOffice.org into PostgreSQL

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

Harry J Mangalam <hj...@ta...> writes:

> No need to use ODBC soon.  OOo has developed its own native PostgreSQL driver.  
> I'll test it and if it works OK, I'll write it up for the GeneX docs.
>
> http://software.newsforge.com/software/04/07/22/160206.shtml?tid=93&tid=72

Ok. Is there any big win over the ODBC driver? Less configuration,
easier data access? I wasn't able to tell from the article.

Cheers,
jas.

[GeneX-dev] Re: Updating wellerlab1 genex

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

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

> Changing permissions on Genex trees..
>
> key 'APACHE_CONF_DIR' does not exist at Install line 406
> make: *** [install] Error 255

Hi Hrishi,

Sorry for the ***long*** delay - I am back in India now with a
reliable internet connection.

Did you run 'make configure' before running 'make install'?

Cheers,
jas.

Re: [GeneX-dev] Test: Browsers and Add User

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

Harry Mangalam <hj...@ta...> writes:

> jw...@gm... wrote:
>> Test: login and add user with different browsers
>> Action: login using IE and Mozilla (1.7.2)
>> Consequence: when Hrishi logged in the screen briefly showed his
>> account
> information, including password using either Mozilla or IE, logging in as
> either himself or Jennifer. Jennifer could not replicate this behavior
> when logging in from her own machine.
>
> I could not replicate this with  Mozilla 1.6, 1.7 or Konqueror.
> Hrishi could do this on Moz and IE on windows, I assume?  or on Mac?
> Or Moz on Linux and IE on win?
>
> Did he turn on debugging?  Can he turn it off? (under Admin -> Edit ->
> User preferences
>
>
>> Hrishi is seeing DeBugging whether or not he has selected it as a
> preference.Jennifer can turn it on and off by clicking preferences.
>
> This would explain why he can see the login info.

For some reason which I do not comprehend the debugging info will
persist for a few pages after it has been switched off. If you
logout/login twice it will be gone. 

Please repeat and see if this is the case, i.e. you don't see
debugging info for a user that has never activated it before, and that
after activatin/deactivation of debugging the info *does* go away
after a few pages or after two logout/login attempts.

If people think it worthwhile - I can remove the password from the
debugging output.

>> Add User Error: The Admin Tools menu under the Admin Tab only shows
>
>   up when you log in as genex (Hrishi and Jennifer both tried logging
>
> in from different machines and browsers and as various personas).
>
> I logged in as genex, gave myself a login as hjm, added myself to the
> superuser group and can see the whole Admin services. Did you try
> loggin in as jwwadmin?

The nav bar box only appears when the user is logged in has ADMIN
privelege.

Cheers,
jas.

Re: [GeneX-dev] Test: Change User Preferences

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

jw...@gm... writes:

> Menu: Select data browsing, Browse, Browse by Table, GeneX_Group_Sec
> table. Something is indicated although it is not really clear
> what. However, the bottom half of the screen now shows Debugging on.

Currently the debugging only shows CGI parameters passed to Mason. I
could provide much more, but this was already present and required
little additional work on my part.

> Comment: what other types of preferences would be reasonable to
> provide? I don=92t know the capabilities so I can=92t offer suggestions
> at the moment.

Here are some thoughts:
* in browse mode - what columns to show/not to show
* for annotation - what default read/write groups to use
* for annotation - limit entries in fkey drop-down menus using certain
  criteria (the fkey menus will become horrifically long unless we do
  this).=20
* color selection for all pages.

Just a few of the ideas I've considered.
jas.

Re: [GeneX-dev] Test: add DB User, Group

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

jw...@gm... writes:

> Action: Return to Admin Tab, select Associate Group =96 User. Only the
> groups public, superuser and jwwadmin are shown, although others
> exist. The new group that was added does not appear.

Hey Jennifer,

One problem is what read/write group did you give to the new group?
The groups in the drop-down menu are filtered to show only those
groups which the current user has permission to modify. If the group
does not show up in the list, that means you don't have permission to
modify it.

Now, if you are logged in as someone with admin privelege it shouldn't
matter what the write permissions are - you should still be allowed to
modify it anyway. If that doesn't work let me know it is a bug.

Cheers,
jas.

[GeneX-dev] Jason Back online

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

Hi Harry, Jennifer,

Sorry for such a long delay.

I'm back in India now with a reliable internet connection. 

My connection is of the pay-as-you-use-it type, so I will be
attempting to offload chores that require me to be online (if
possible).

I'm going over all the email reports, but it may take a day or two
before I've gone through all of them. If there is anything urgent,
please let me know in a private email, and I'll prioritize that work.

I should be in good email contact for the next week (no travels, no
major interruptions). I'll be sure to post any interruption I know of
before it happens. So if you send an email to me and don't recieve an
email back within 24 hours - something has happened.

Cheers,
jas.

Re: [GeneX-dev] missing file in Installation

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

Harry J Mangalam <hj...@ta...> writes:

> In refreshing the installation on matrix, the only error in the whole thing  
> was:
>
> !! System Error: No such file or directory @ line: 286  (cp 
> Mason/login/workspace/comps/exp-analyze.mason /var/www/genex/mason/login/workspace/comps)
>
> Since the source file itself is missing, this looks like an error in
> the MANIFEST file - right?
>
> Otherwise it looks like a clean install and all dependencies are
> still current relative to Deb unstable and the INSTALL doc.

Hi Harry,

Correct - that is the error you will get if the MANIFEST lists a file
that has been removed. 

My bad. If you could remove the offending line from the file - I would
be grateful.

Cheers,
jas.

[GeneX-dev] Test: Documentation availability Quantitation Type Dimension HOWTO

[<jw...@gm...>]

Test: Documentation Availability
Action: Under Documentation Tab find the Quantitation Type Dimension HOWTO cited in the Load Data HOWTO Document
Result: can not be seen, nor did a file search through the system reveal an obvious candidate.

End: JWW

[GeneX-dev] Draft 1 User Guide to loading data

[<jw...@gm...>]

The following arises from reading existing documentation that is availabl=
e with the GeneX distribution and follow-up conversations with Jason Stew=
art=2E It may not be accurate=2E I welcome suggestions and comments on st=
yle as well as content=2C I usually begin in verbose mode and drivel down=
hill from there=2E
Begin=3A

Loading Intensity Data files into GeneX=2C or what the heck is going on=3F=
 =

=85=85Guide for Users

Before you upload data you will need=3A

1=2EArray Design		2=2EQT Dimension		3=2EData file
What is the name of each 	What bits do I want to keep	Where are the bits
 location			and what do they mean	I want to store in 								this particu=
lar data file=2E
Why=3F
When you run a microarray experiment=2C you are making use of the microar=
ray design output of a synthesis/software system like GenePix=2C and the =
signal detection/data extraction design of a detector/software system lik=
e Quantarray=2E Some providers integrate both=2C like Affymetrix=2E The m=
icroarray design coordinates information about the physical entity at a l=
ocation on a chip (e=2Eg=2E the DNA on a spot) and what it is supposed to=
 be interrogating (e=2Eg=2E the gene)=2E The signal detection system coll=
ects all the output=2C usually as an image=2C and the associated data ext=
raction software presents an intensity value for a particular wavelength =
of light at a particular location (the spot value) and may also automatic=
ally compute values such as ratios=2E The data extraction software usuall=
y replicates some of the information from the array design such as the pr=
obe name and a gene identifier=2E To interpret the data from your microar=
ray experiment you need to associate both of these types of information w=
ith the data set=2E

1=2E The Array Design should be provided by the array manufacturer=2E Aff=
ymetrix provides the =2Ecdf and =2Egif files=2C GenePix provides a text f=
ile whose contents will depend on the designer of the custom array=2E  Th=
ere are three levels of information that may possibly be provided in such=
 a file=2E The most basic and absolutely required is the Feature level=2C=
 which gives the spot location as a column each for the s and y coordinat=
es=2C or sometimes as a subarray with its own row and column identifier w=
hich requires another two columns=2C and the name assigned to the attache=
d DNA=2E Since two things cannot exist at the same place at the same time=
=2C the combination of the location and the name will be unique=2C even i=
f the name itself is not=2E A second level of information is called the R=
eporter although it is more properly the BioSequence information=2C the n=
ucleotide sequence of the probe resident at a location=2E For oligonucleo=
tide-based and PCR-product based probes this sequence should be complete =
and unambiguous=3B in some cases on cDNA arrays the precise sequence of a=
n insert has not been determined=2E The third level of information is abo=
ut the Composite Sequence=2C referring to the expected target (mRNA or ge=
ne)=2E Some platforms=2C such as the Affymetrix GeneChip=2C use a set of =
oligonucleotides to measure the presence of a target=3B this set comprise=
s a composite sequence and the user may extract the intensity for each me=
mber of the set or a single weighted value across the set=2E There is inc=
reasing uncertainty at each level=3A something with a particular name has=
 been attached at a given location unless the chemistry has failed altoge=
ther=3B the attached entity has particular physical/chemical characterist=
ics unless reagents have been contaminated or the synthesis device was mi=
saligned=3B the attached entity provides information about a particular g=
ene if no competing sequences exist in the target pool=2E Only rigorous q=
uality control and empirical validation allow the investigator to make an=
 interpretation at the third level as if it were a direct measurement at =
the first level=2E

You must be able to associate an Array Design with your experiment=2E Mos=
t users will rely on a programmer or the Curator to properly extract a us=
able Array Design and insert it into the database=2E Instructions are giv=
en in the GeneX Documentation=2C Array Design Creation HOWTO and sample p=
rograms and files are provided for guidance=2E This need only be done onc=
e for each build of an array or chip=2E When a separate array design file=
 is not available from the manufacturer it is often possible to extract t=
he minimally needed information from the output of the signal detection s=
oftware (e=2Eg=2E the Quantarray file)=2E =


An experiment involves hybridizing labeled target to a microarray of some=
 particular design=2E After washing the microarray is inserted into a dev=
ice that can excite the reporter (if necessary) and measure=2C at the req=
uired resolution=2C the signal output of whatever reporter molecule was a=
ttached to the target (usually 32P or one or more fluorescent dyes)=2E Th=
e instrument collects the output signal as an image=2E While the image ca=
n be stored it is not useful data in this form=2C so software is used to =
extract the signal intensity at each spot and output it as a unique row i=
n an output file=2E We refer to this software program as the Feature Extr=
action Software=2E It is possible to store the original image of the enti=
re array=2C unextracted (usually as a 16-but =2Etif file=2C but Affymetri=
x also outputs the proprietary =2Ecdf file)=2E Thus it is possible to re-=
extract the signal from each spot using some other image analysis program=
 or parameter settings than was part of the original platform=2E For this=
 reason the GeneX form requires that the user provide information about t=
he version and name of the feature extraction software used to produce a =
particular data set=2E

2=2E The Quantitation Type Dimension represents the categories of informa=
tion the investigator wants to retain from the extracted data file=2E The=
 output of a scanner=2C or reader=2C is the product of some software pack=
age=2C such as QuantArray 3=2E0=2E There are usually two major parts to t=
hese data files=2E At the top=2C or =3Fheader=3F section=2C you usually s=
ee some rows of general information=2C perhaps an experiment title and da=
te and other high-level data=2E There might also be information about ins=
trument settings=2E Farther down will be the data matrix=2C which can hav=
e a row for every probe or CompositeProbe and from a few to very many col=
umns=2E Typically a given row of data for a spot has columns that give sp=
ot identifiers like the x and y position=2C the name for the probe and pe=
rhaps associated information like a LocusLink identifier or GenBank acces=
sion number=2C and then numbers indicating signal intensity values follow=
ed by various manipulations of those values=2C which we refer to collecti=
vely as derived data=2E The intensities are generally given for each wave=
length or channel measured (e=2Eg=2E for the Cy3 and Cy5 emission optima)=
 for both the foreground  (or spot) and the background=2E Derived values =
are potentially limitless but nearly always include values such as backgr=
ound subtracted signal=2C and signal ratios as well as statistical measur=
es in profusion=2E Not only will each system have a different way of doin=
g the calculations and presenting the results=2C but many are user-config=
urable=2C so that exactly what is calculated and the order in which infor=
mation is presented will differ between users or over time for one user o=
f the same system=2E The GeneX database has to be told which of these val=
ues you want to store and the meaning of those values=2E Thus it is neces=
sary that you sit down before you do the experiment and familiarize yours=
elf with the output=2C and make sure that you know what parts of it you w=
ish to store and what they mean (i=2Ee=2E how they are derived)=2E It is =
possible to request more output data than you intend to store=2C of cours=
e=2C but it is necessary that you describe for the GeneX database exactly=
 what parts you want to store=2E This information is what goes into the Q=
uantitation Type Dimension file=2E This will be produced by a programmer =
or curator to your specification=2E The instructions are given in the Gen=
eX Documentation Tab as QT Dimension Creation HOWTO=2E

Why not have a completely simple and generic QTD=3F After all=2C you woul=
d expect to get a probe=5Fid=2C Channel 1 signal=2C Channel 1 background =
from any system that exists=2C with the logical additional categories for=
 multi-channel systems=2E It is true that background-subtracted signal an=
d measures such as variance can be reproduced if the original data exists=
=2C but it is often more convenient to retain values that have already be=
en computed=2E Because many derived values are unique to particular syste=
m=2C the QT Dimension will in fact most often be linked to a Feature Extr=
action Software package and a particular user=2E For all columns you must=
 specify the type and format of data (the location as x=2Cy for example) =
and for derived data types a definition that defines relationships=2C inc=
luding those among other columns=3A so the =91signal ratio=92 is more pre=
cisely defined as =5BChannel 1 signal - Channel 1 background=5D divided b=
y =5BChannel 2 signal - Channel 2 background=5D=2E Without this level of =
detail a new user (or the same user six months later) will not be clear a=
s to whether or not the background was subtracted when the ratio was made=
 and which channel was used as the numerator and which the denominator=2E=
 Since producing these files require advance planning and the assistance =
of the Curator it is recommended that a single useful format be determine=
d and used consistently by a user or lab for one platform=2E

3=2E Data file output organization can change fairly quickly=2C sometimes=
 with every software upgrade=2E This means that the information included =
in the header may take fewer lines or more lines this month than last=2E =
It also means that for programs that are not user-configurable the positi=
on of particular columns (Ch1 signal and Ch1 background=2C for instance) =
may alter=2E Thus=2C the investigator must inspect the spot intensity out=
put file and at data upload describe for the GeneX system at what row the=
 actual data starts and where it ends=2C as well as the relative position=
 of the columns described by the QTD file=2E =


Preparing to upload data=3A Ahead of time arrange with the Curator to pro=
vide an Array Design file and a Quantitation Type Dimension file to the G=
eneX system=2E Know what version of feature extraction software you will =
use and any important parameter settings=2E When you are ready to upload =
data check the data file and know what columns represent the values the Q=
TD expects to store=2E Know at what row in the file the actual data begin=
s=2C and where it ends=2E =

From here you can follow the simple instructions in the Data Loading HOWT=
O (see Documentation Tab)=2E =


End=3A JWW

Re: [GeneX-dev] Test: Browsers and Add User

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

jw...@gm... wrote:
> Test: login and add user with different browsers
> Action: login using IE and Mozilla (1.7.2)
> Consequence: when Hrishi logged in the screen briefly showed his account 
information, including password using either Mozilla or IE, logging in as
either himself or Jennifer. Jennifer could not replicate this behavior
when logging in from her own machine.

I could not replicate this with  Mozilla 1.6, 1.7 or Konqueror.  Hrishi could do 
this on Moz and IE on windows, I assume?  or on Mac?  Or Moz on Linux and IE on win?

Did he turn on debugging?  Can he turn it off? (under Admin -> Edit -> User 
preferences


> Hrishi is seeing DeBugging whether or not he has selected it as a 
preference.Jennifer can turn it on and off by clicking preferences.

This would explain why he can see the login info.


> Add User Error: The Admin Tools menu under the Admin Tab only shows

  up when you log in as genex (Hrishi and Jennifer both tried logging

in from different machines and browsers and as various personas).

I logged in as genex, gave myself a login as hjm, added myself to the superuser 
group and can see the whole Admin services. Did you try loggin in as jwwadmin?

hjm


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

[GeneX-dev] Test: Browsers and Add User

[<jw...@gm...>]

Test: login and add user with different browsers
Action: login using IE and Mozilla (1.7.2)
Consequence: when Hrishi logged in the screen briefly showed his account information, including password using either Mozilla or IE, logging in as either himself or Jennifer. Jennifer could not replicate this behavior when logging in from her own machine. 
Hrishi is seeing DeBugging whether or not he has selected it as a preference.Jennifer can turn it on and off by clicking preferences.
Add User Error: The Admin Tools menu under the Admin Tab only shows up when you log in as genex (Hrishi and Jennifer both tried logging in from different machines and browsers and as various personas).

End JWW

Re: [GeneX-dev] Test: add DB User, Group

[Hrishikesh D. <gen...@ya...>]

Hi Harry,
 
How do i update my system to present day status of genex.
 
Thanks,
Hrishi

Harry Mangalam <hj...@ta...> wrote:
The Insert User thingie is on the left hand sidebar named
Insert
- DB User

at the very bottom, and (with some wonkiness) it works for me.

hjm

jw...@gm... wrote:
> Test: Add a DB User and DB Group
> Error: Can’t find User heading in Admin, not all Groups visible 
in table can be selected in Associate Groups-Users.
> Actions:
> Log in as admin
> Tab Select Admin
> Sidebar Select Insert ?User? can’t be found
> Sidebar Select Insert Group
> Actions: A new group was named and successfully saved. It was possible
to navigate to Tab Browse, and show that the new group showed up in the
GeneX_Group_Sec table.
> Action: Return to Admin Tab, select Associate Group – User. Only the 
groups public, superuser and jwwadmin are shown, although others exist.
The new group that was added does not appear.
> 
> Repeating the process logged in as a user did not alter the above phenotype.
> 
> End JWW 
> 
> 

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


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Re: [GeneX-dev] Test: add DB User, Group

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

The Insert User thingie is on the left hand sidebar named
Insert
  -  DB User

at the very bottom, and (with some wonkiness) it works for me.

hjm

jw...@gm... wrote:
> Test: Add a DB User and DB Group
> Error: Can=92t find User heading in Admin, not all Groups visible=20
in table can be selected in Associate Groups-Users.
> Actions:
>    Log in as admin
>    Tab Select Admin
>    Sidebar Select Insert ?User? can=92t be found
>    Sidebar Select Insert Group
> Actions: A new group was named and successfully saved. It was possible
to navigate to Tab Browse, and show that the new group showed up in the
GeneX_Group_Sec table.
> Action: Return to Admin Tab, select Associate Group =96 User. Only the =

groups public, superuser and jwwadmin are shown, although others exist.
The new group that was added does not appear.
>=20
> Repeating the process logged in as a user did not alter the above pheno=
type.
>=20
> End JWW=20
>=20
>=20

--=20
Cheers, Harry
Harry J Mangalam - 949 856 2847 (vox; email for fax) - hj...@ta...
             <<plain text preferred>>

[GeneX-dev] Test: Change User Preferences

[<jw...@gm...>]

Test=3A Change User Preferences
Error=3A none=2C see comment at end
Actions=3A Log in as admin
Tab=3A Select Admin
Menu=3A Select Edit Select User Preferences
Actions=3A Click box to add Mason Debugging=2C save
Followup=3A =

Tab=3A Browse
Menu=3A Select data browsing=2C Browse=2C Browse by Table=2C GeneX=5FGrou=
p=5FSec table=2E Something is indicated although it is not really clear w=
hat=2E However=2C the bottom half of the screen now shows Debugging on=2E=


Comment=3A what other types of preferences would be reasonable to provide=
=3F I don=92t know the capabilities so I can=92t offer suggestions at the=
 moment=2E

End JWW

[GeneX-dev] Test: Edit Group

[<jw...@gm...>]

Test: Edit Group
Error: permission denied to assign curator as Read/Write access for a group.
Actions:
   Log in as admin
   Tab Select Admin
   Edit Group 
Actions: Select the Weller Lab just added. Under the drop-down lists for both Read and Read/Write permissions all groups shown in the GeneX_Group_Sec table are displayed as well as NONE. Select Curator for the READ/Write group. The same error appears if jwwadmin is selected (which is what I am logged in as), or entering public for both.

Message appears:
ERROR: 
Updating GroupSec: 1139
Error output = [ERROR: Permission denied: not in rw_gs_fk]



End JWW   

[GeneX-dev] Test: add DB User, Group

[<jw...@gm...>]

Test=3A Add a DB User and DB Group
Error=3A Can=92t find User heading in Admin=2C not all Groups visible in =
table can be selected in Associate Groups-Users=2E
Actions=3A
   Log in as admin
   Tab Select Admin
   Sidebar Select Insert =3FUser=3F can=92t be found
   Sidebar Select Insert Group
Actions=3A A new group was named and successfully saved=2E It was possibl=
e to navigate to Tab Browse=2C and show that the new group showed up in t=
he GeneX=5FGroup=5FSec table=2E
Action=3A Return to Admin Tab=2C select Associate Group =96 User=2E Only =
the groups public=2C superuser and jwwadmin are shown=2C although others =
exist=2E The new group that was added does not appear=2E

Repeating the process logged in as a user did not alter the above phenoty=
pe=2E

End JWW =

[GeneX-dev] Login GUI link error part 2

[<jw...@gm...>]

I'm not sure where I got the original link, both Hrishi and I had it bookmarked. It is certainly something that seems reasonable to try if you end up at the matrix mason index page. 

The other thing you have to be aware of is that even though you get the error message screen, you are in fact logged in, and since closing the browser window does not log you off, you will stay logged in.

Anyway since the screen looks right,  it isn't necessarily clear to a casual user what has gone wrong.

Maybe this isn't a 'bug' but it does seem user-relevant.

End JWW



----- Original Message -----
From: Harry Mangalam <hj...@ta...>
Date: Wednesday, August 11, 2004 2:43 pm
Subject: Re: [GeneX-dev] Login GUI link error

> The URL:
> http://matrix.binf.gmu.edu/genex/mason/login/workspace/workspace.html
> 
> is the one that is supposed to be used.  Where did you see/get 
> this one:
> 
> http://matrix.binf.gmu.edu/genex/mason/workspace/workspace.html
> 
> This is the reason I postedthat maybe we should put a referer link at
> 
> http://host/genex/index.html
> 
> Otherwise it can be  difficult to find the right starting URL.
> 
> hjm
> 
> 
> jw...@gm... wrote:
> > Task: Login GUI
> > Error: link to workspace in new browser window.
> > Actions:
> >>From a new browser window
> > Use this URL to log in:
> > 
> http://matrix.binf.gmu.edu/genex/mason/authenticate.html?caller=http://matrix.binf.gmu.edu/genex/mason/workspace/workspace.html> Result: the login screen appears. 
> > Enter name and password.
> > The URL that appears is to:
> > http://matrix.binf.gmu.edu/genex/mason/workspace/workspace.html
> > And this gives a error (can?t find page)
> > 
> > If the login screen URL is modified:
> > 
> http://matrix.binf.gmu.edu/genex/mason/login/workspace/workspace.html> 
> > Result: you find that you are logged in and at the workspace screen.
> > 
> > If you logout you are taken to the login screen at 
> > 
> http://matrix.binf.gmu.edu/genex/mason/authenticate.html?caller=http://matrix.binf.gmu.edu/genex/mason/login/workspace/workspace.html 
> > 
> > and this time after filling in name and password you are taken 
> to the workspace at 
> > 
> http://matrix.binf.gmu.edu/genex/mason/login/workspace/workspace.html 
> > 
> > 
> > 
> > End JWW
> 
> -- 
> Cheers, Harry
> Harry J Mangalam - 949 856 2847 (vox; email for fax) - hj...@ta...
>             <<plain text preferred>>
> 

[GeneX-dev] GeneX errors while loading files

[Hrishikesh D. <gen...@ya...>]

Here is what i did:
First i copied the data files from harry's /home/harry/genex/genex-server/DB/curated_data to /usr/local/genex/uplaods/hrishi
then used the url http://matrix.binf.gmu.edu/genex/mason/login/workspace/edit/experiment-edit.html
for inserting an experiment, here is the error which i get:
System error
error:  Undefined subroutine &Bio::Genex::ParseDate called at /usr/local/share/perl/5.8.4/Bio/Genex.pm line 190.
 
context:  ...   
186:   
187:  $date .= $args{tz} 
188:  if $args{tz}; 
189:   
190:  return $date 
191:  if ParseDate($date); 
192:   
193:  # we have a bogus date 
194:  return undef; 
...   
 
code stack:  /usr/local/share/perl/5.8.4/Bio/Genex.pm:190
/var/www/genex/mason/login/workspace/edit/experiment-edit.html:374
/usr/share/perl5/HTML/Mason/Request.pm:753
/var/www/genex/mason/login/workspace/edit/experiment-edit.html:224
/var/www/genex/mason/login/workspace/autohandler:2
/usr/share/perl5/HTML/Mason/Request.pm:753
/usr/local/genex/mason/obj/login/workspace/autohandler:28
/var/www/genex/mason/login/autohandler:39
/usr/share/perl5/HTML/Mason/Request.pm:753
/var/www/genex/mason/login/autohandler:118
/var/www/genex/mason/autohandler:26
/usr/share/perl5/HTML/Mason/Request.pm:753
/var/www/genex/mason/autohandler:92
 
raw error

NOW if i use the browsing tab and then insert the experiment then its successful, 
GeneX DB Experiment Edit Page 
Experiment Successfully Added for entry: 1116:hd_test  
I filled the date part and then i get an error if i don't fill the release date (i.e. today's date) then the error is not seen.
I went to the url http://matrix.binf.gmu.edu/genex/mason/login/workspace/edit/experiment-edit.html and the error is seen if the release date info. is filled/given, leave it blank and it works fine, also for timezone should ET/EastT should be used, proveide help/desciption.

Inser biomaterial works, url used: http://matrix.binf.gmu.edu/genex/mason/login/workspace/edit/biomaterial-edit.html

Next thing i did was loading QT dim loader:
Here is the error i get:
System error
error:  DBD::Pg::db commit failed: commit failed at /usr/share/perl5/Apache/Session/Store/Postgres.pm line 95.
 
context:  ...   
90:   
91:  sub DESTROY { 
92:  my $self = shift; 
93:   
94:  if ($self->{commit}) { 
95:  $self->{dbh}->commit; 
96:  } 
97:   
98:  if ($self->{disconnect}) { 
...   
 
code stack:  /usr/share/perl5/Apache/Session/Store/Postgres.pm:94
/usr/share/perl5/HTML/Mason/Request.pm:1068
/var/www/genex/mason/autohandler:26
/usr/share/perl5/HTML/Mason/Request.pm:753
/var/www/genex/mason/autohandler:92
 
raw error
SO NOW I AM TRYING TO LOAD ArrayDesign files, here is the error:
Genex Job Status Page
Your job is finished. The status is: ERROR
The error status is: 512 
Output of the program:
MAGE creation took:25 wallclock secs (25.41 usr +  0.12 sys = 25.53 CPU)
1645 Reporters to insert
DBD::Pg::st execute failed: ERROR:  permission denied for relation genex_reporter_view at /usr/local/share/perl/5.8.4/Bio/Genex/Reporter.pm line 903.
main:/usr/local/genex/bin/array-design-insert.pl:177:Bio::Genex::Reporter::insert_matrix: Couldn't execute insert sql with args: L48-2T3 ,clone_name,1128, SQL=[[INSERT INTO GENEX_REPORTER_VIEW (name,rep_type,rep_pk) VALUES (?,?,?)]], DBI=[[ERROR:  permission denied for relation genex_reporter_view]]
 
 
Created MAGE-ML from 1200-mangle-AD.txt file and here is the error which iget:
Genex Job Status Page
Your job is finished. The status is: ERROR
The error status is: 512 
Output of the program:
MAGE creation took:90 wallclock secs (89.14 usr +  0.40 sys = 89.54 CPU)
5308 Reporters to insert
DBD::Pg::st execute failed: ERROR:  permission denied for relation genex_reporter_view at /usr/local/share/perl/5.8.4/Bio/Genex/Reporter.pm line 903.
main:/usr/local/genex/bin/array-design-insert.pl:177:Bio::Genex::Reporter::insert_matrix: Couldn't execute insert sql with args: reporter00000,clone_name,1134, SQL=[[INSERT INTO GENEX_REPORTER_VIEW (name,rep_type,rep_pk) VALUES (?,?,?)]], DBI=[[ERROR:  permission denied for relation genex_reporter_view]]
 
 
I test thoroughly if i knew excatly what AD file goes with FES and what dateset, i have tried almost all files for AD loading the above menitioned errors are commonly seen.
Hrishi
 



		
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[GeneX-dev] Plug OpenOffice.org into PostgreSQL

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

No need to use ODBC soon.  OOo has developed its own native PostgreSQL driver.  
I'll test it and if it works OK, I'll write it up for the GeneX docs.

http://software.newsforge.com/software/04/07/22/160206.shtml?tid=93&tid=72
-- 
Cheers, Harry
Harry J Mangalam - 949 856 2847 (v&f) - hj...@ta... 
            <<plain text preferred>>