genex-dev — GeneX developers

Re: [GeneX-dev] Re: One more installation question...

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

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

> Perl/scripts/gendb.pl --db genex --dir /home/acarr/GeneX/genex-server 
> --user genex --pass xxxxx
>
>  .
>  .
>  .
> In Bio::Genex::GroupSecLink::insert_db: pkey =
> Bio::Genex::GroupSec::insert_db: id already defined
> Bio::Genex::UserSec::insert_db: id already defined
> Bio::Genex::UserSec::insert_db: id already defined
> Bio::Genex::GroupSec::insert_db: id already defined
> Bio::Genex::GroupSec::insert_db: id already defined
> Finished
> Finished
> Adding Test Data ...
>         /usr/local/genex/bin/insert-test-data.pl --dbname genex 
> --username genex --password genex13 
> --dir /home/acarr/GeneX/genex-server
> Adding quantarray QuantitationTypeDimension ...
>         /usr/local/genex/bin/qtdim-insert.pl --dbname genex --username 
> genex --password 
> xxxx /home/acarr/GeneX/genex-server/DB/curated_data/quantarray.xml--name=QuantArray 
> --abbrev_name=dqa --version=3.0 --feat="1.2.3.4" 
> --data_start_regex1=^Begin\s+Data --data_start_regex2=^Number 
> --data_end_regex=^End
> main:/usr/local/genex/bin/qtdim-insert.pl:156:Bio::Genex::Connect::insert_mage_qtdim: 
> qtdim argument not provided,

Yes, this is fixed in SVN.

Cheers,
jas.

Re: [GeneX-dev] Patch?

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

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

> Harry,
>
> Thanks for solving the problem I was having.

Ah, ok. So the login problem is fixed, good.

> Do you know if Jason has a version that will install?  Or when one
> will be placed out on the svn?

available on genex2 or from SVN.

Cheers,
jas.

[GeneX-dev] Re: Sept 21 data load trial, mail #3

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

Hi Jason,

As suggested i deleted the file in /tmp and here is error, looks like a 
a relation is not dropped, so the error.

deshmuk@matrix:~$ /usr/local/genex/bin/qtdim-insert.pl --user genex 
--pass yeastecol1 --name=MicroArraySuite --abbrev_name=dmas4 
--version=4.0 --feat="0" --data_start_regex1=^O --data_end_regex=^\s 
/usr/local/genex/uploads/genex_test_curator/qtdim-mas4.xml
Got QT Dimension: MicroArraySuite-4.0
         Got QT : QuantitationType:MicroArraySuite-4.0-1
                 No Channel
         Got QT : QuantitationType:MicroArraySuite-4.0-2
                 No Channel
         Got QT : QuantitationType:MicroArraySuite-4.0-3
                 No Channel
Creating Perl module: Data_MicroArraySuite_4_0
Using target: Data_MicroArraySuite_4_0 => Data_MicroArraySuite_4_0, no 
supporting tables

         Data_MicroArraySuite_4_0: Setting FUNKY primary key
Finished


         Executing Pre-SQL ...



         Creating Data Tables ...

         Creating Data_MicroArraySuite_4_0
NOTICE:  CREATE TABLE / UNIQUE will create implicit index 
"data_microarraysuite_4_0_mba_fk_key" for table "data_microarraysuite_4_0"
DBD::Pg::db do failed: ERROR:  relation "data_microarraysuite_4_0" 
already exists at /usr/local/genex/bin/qtdim-insert.pl line 561.
/usr/local/genex/bin/qtdim-insert.pl: Creating table 
Data_MicroArraySuite_4_0, SQL=[[CREATE TABLE Data_MicroArraySuite_4_0 (
         "mba_fk"        int4 NOT NULL,
         "i_signal"      int4 NOT NULL,
         "i_detection"   int4 NOT NULL,
         "feature_fk"    varchar(32) NOT NULL,
         "i_local_background"    int4 NOT NULL,
         UNIQUE (mba_fk, feature_fk)
)
;
]], DBI=[[ERROR:  relation "data_microarraysuite_4_0" already exists]]

Thanks,
Hrishi




Jason E. Stewart wrote:
> Hrishikesh Deshmukh <hde...@gm...> writes:
> 
> 
>>Insertion of qtdim via GUI, there were errors (i believe Jason has
>>fixed this will be installed and tested on genex2) , so tried loading
>>using the command line.
>>
>>Here is the error while i get when i try to load qtdim file using
>>command line:
>>
>>deshmuk@matrix:/$ /usr/local/genex/bin/qtdim-insert.pl --user genex
>>--pass yeastecol1 --name=MicroArraySuite -
>>
>>-abbrev_name=dmas4 --version=4.0 --feat="0" --data_start_regex1=^O
>>--data_end_regex=^\s
>>
>>/usr/local/genex/uploads/genex_test_curator/qtdim-mas4.xml
>>Got QT Dimension: MicroArraySuite-4.0
>>         Got QT : QuantitationType:MicroArraySuite-4.0-1
>>                 No Channel
>>         Got QT : QuantitationType:MicroArraySuite-4.0-2
>>                 No Channel
>>         Got QT : QuantitationType:MicroArraySuite-4.0-3
>>                 No Channel
>>Creating Perl module: Data_MicroArraySuite_4_0
>>Using target: Data_MicroArraySuite_4_0 => Data_MicroArraySuite_4_0, no
>>supporting tables
>>Couldn't open /tmp/Data_MicroArraySuite_4_0.pm for writing at
> 
> 
> For some reason you don't have permission to open the file in
> /tmp. The most obvious reason is that the file already exists there
> and was created by another user, e.g. root. If that is the case,
> remove the file and re-run the program.
> 
> In the new code, I've removed this step so it won't happen again once
> matrix is updated.
> 
> 
>>ONE more question here:
>>
>>>On each install a full test data set is loaded - look at the script
>>>Perl/scripts/insert-test-data.pl to see exactly what it does, but in
>>>brief it uses the very simplistic test files:
>>>
>>>* data file: DB/curated_data/200-short.txt
>>>* AD file: DB/curated_data/200-AD-short.xml
>>>* QT Dim file: DB/curated_data/quantarray.xml
>>
>>Here are the files i am trying to load, but when i am trying to load
>>via command line i am loading qtdim-mas4.xml, shouldn't we be keeping
>>"things" constant when doing an experiment! Just change one variable
>>at a time!
> 
> 
> Sorry, I'm not sure what the problem is. If the issue is that the data
> set installed by the test suite is different than the one recommended
> in the email, that is because we were attempting to install a *real*
> data set, the yeast heat shock data, and we hit a big snag. You need
> the correct QT Dim to load all the HS* files, the quantarray.xml file
> won't work.
> 
> In general you are correct, only change one thing at a time. But I'm
> often answering 12 different questions at once. I ask for your humble
> forgiveness if I sometimes get confusing.
> 
> Cheers,
> jas.

[GeneX-dev] new code installed and tested on genex2

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

Hey All,

My latest code works like a charm on genex2.

Be warned, you must add a new perl module Hash::Case using cpan in
order to install.

You must 'make configure' and then 'make install' because there are
new configuration options.

Please see the new user documentation, QT Dimension, and OntologyEntry
and Data Processing Protocol. I also updated the Data Loading docs.

Comments welcome.

jas.

[GeneX-dev] GAIM sessions with Jason

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

Hey All,

With all the activity going on, there may be issues that require more
direct interaction than email can allow. I am happy to get on Jabber
and have a nice Instant Messaging session with anyone that wants. 

I will make it a point to log on (my user_id is ge...@ja...) at
20:30 every evening (most evenings) and chat with anyone who is
available. If you have something urgent to discuss - email me ahead of
time and that will help me. Scheduling a talk 24 hours in advance is
the best way for me - because I am living with a group of people in an
ashram in India and there are often un-planned conditions which
present challenges for good connectivity.

And thanks for all the activity!

Cheers,
jas.

[GeneX-dev] Re: Sept 21 data load trial, mail #1

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

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

> Step 1: Login
> Logged as genex
>
> Step2: Load Experiment, here is the error i got
>
>
> System error
>
> error:  Couldn't reqire Date::Manip: syntax error at (eval 185) line 1, 
> near "require Date::Manip qw(ParseDate
>
> UnixDate)"

I've changed this so that it shouldn't cause trouble (on my laptop
version). I don't really understand why this is causing problems, but
I guess it has something to do with apache/mod_perl.

Cheers,
jas.

[GeneX-dev] Re: Patch?

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

Jason should know about now - I'll take a closer look this morn and 
see if I can hack something together until Jason can respond.

hjm


On Wednesday 22 September 2004 8:18 am, dcarr2 wrote:
> Harry,
>
> Thanks for solving the problem I was having.
>
> The error you ran across does not currently have a patch that
> Hrishi and I know about.  I did pull this version straight from the
> svn on genex2.
>
> Having talked with Hrishi, his error seems to be different and has
> to do with the data load process and the manner in which the
> current time is brought into the system.
>
> Do you know if Jason has a version that will install?  Or when one
> will be placed out on the svn?
>
> Thanks for all of you assistance.
>
> Andrew

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

[GeneX-dev] Patch?

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

Harry,

Thanks for solving the problem I was having. 

The error you ran across does not currently have a patch that Hrishi and 
I know about.  I did pull this version straight from the svn on genex2.

Having talked with Hrishi, his error seems to be different and has to do 
with the data load process and the manner in which the current time is 
brought into the system. 

Do you know if Jason has a version that will install?  Or when one will 
be placed out on the svn?

Thanks for all of you assistance.

Andrew

[GeneX-dev] Re: One more installation question...

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

Hi Andrew,

The easy answer to this error is that it looks like the password was 
set incorrectly - I dropped the user and db manually, then re-ran the 
install script, giving it the password you wanted and it worked fine.

Unfortunately, I ran into another problem that I think is a result of 
a fix that Jason has already corrected but not put into the svn 
repository.  The symptiom is:

Perl/scripts/gendb.pl --db genex --dir /home/acarr/GeneX/genex-server 
--user genex --pass xxxxx

 .
 .
 .
In Bio::Genex::GroupSecLink::insert_db: pkey =
Bio::Genex::GroupSec::insert_db: id already defined
Bio::Genex::UserSec::insert_db: id already defined
Bio::Genex::UserSec::insert_db: id already defined
Bio::Genex::GroupSec::insert_db: id already defined
Bio::Genex::GroupSec::insert_db: id already defined
Finished
Finished
Adding Test Data ...
        /usr/local/genex/bin/insert-test-data.pl --dbname genex 
--username genex --password genex13 
--dir /home/acarr/GeneX/genex-server
Adding quantarray QuantitationTypeDimension ...
        /usr/local/genex/bin/qtdim-insert.pl --dbname genex --username 
genex --password 
xxxx /home/acarr/GeneX/genex-server/DB/curated_data/quantarray.xml--name=QuantArray 
--abbrev_name=dqa --version=3.0 --feat="1.2.3.4" 
--data_start_regex1=^Begin\s+Data --data_start_regex2=^Number 
--data_end_regex=^End
main:/usr/local/genex/bin/qtdim-insert.pl:156:Bio::Genex::Connect::insert_mage_qtdim: 
qtdim argument not provided,
Died at /usr/local/genex/bin/insert-test-data.pl line 105.
Died at Perl/scripts/gendb.pl line 221.


IS this what Hrishi was kvetching about?  The end of the script is:

 ...
my $array_ref = 
$pkg_ref->{BioAssayData}->quantitationtypedimension_list();
die "Expected an array ref but got " . ref($array_ref)
  unless UNIVERSAL::isa($array_ref, 'ARRAY');

my ($mage_dim) = @{$array_ref};
die "Found no QuantitationTypeDimensions"
  unless defined $mage_dim;

# open up a writeable connection
my $dbh = Bio::Genex::Connect->new(DBNAME=>$OPTIONS{dbname},
                                   USER => $OPTIONS{username},
                                   PASSWORD => $OPTIONS{password},
                                   TRANSACTION => 1,
                                  );

delete @OPTIONS{'username','password','dbname'};
$dbh->insert_mage_qtdim(%OPTIONS,qtdim=>$mage_dim);

...and it appears not to be getting $array_ref

Before I dive deeper, have you patched this already?

hjm


On Tuesday 21 September 2004 1:49 pm, you wrote:
> Harry,
>
> The password is: xxxx
>
> Andrew
>
> ----- Original Message -----
> From: Harry Mangalam <hj...@ta...>
> Date: Tuesday, September 21, 2004 4:40 pm
> Subject: Re: One more installation question...
>
> > I'll plink at it.
> >
> > What password did you set for postgres user genex?
> >
> > hjm
> >
> > On Tuesday 21 September 2004 1:13 pm, you wrote:
> > > Harry,
> > >
> > > Thanks for the new INSTALL....
> > >
> > >
> > > I used it to double check what I had done in configuring the
> > > pg_hba.conf file.  What I have done matches what is in the
> > > install doc and I am still getting the same error with a the
> > > password authentication problem in postgres.
> > >
> > >
> > > This time the template1 gave the error...
> > >
> > > ___________________________________________
> > > DBI connect('dbname=template1','genex',...) failed: FATAL:
> > > Password authentication failed for user "genex" at
> > > /usr/local/share/perl/5.8.4/Class/ObjectTemplate/DB/Connect.pm
> > > line 210 Couldn't connect to template1: FATAL:  Password
> > > authentication failed for user "genex" at
> > > /usr/local/share/perl/5.8.4/Class/ObjectTemplate/DB/Connect.pm
> > > line 215. Died at Perl/scripts/gendb.pl line 121.
> > >
> > >   FATAL ERROR
> > >
> > > I got an error when I ran the DB installer.
> > >
> > >
> > > !! System Error:  @ line: 371  (su -c '/usr/bin/perl
> > > /home/acarr/GeneX/genex-server/Perl/scripts/db.pl' postgres)
> > >
> > >   FATAL ERROR
> > >
> > > I got an error when I ran the DB installer.
> >
> > --
> > Cheers, Harry
> > Harry J Mangalam - 949 856 2847 (vox; email for fax) -
> > hj...@ta...
> >            <<plain text preferred>>

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

[GeneX-dev] Sept 21 data load trial, mail #3

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

Insertion of qtdim via GUI, there were errors (i believe Jason has fixed 
this will be installed and tested on genex2) , so tried loading using 
the command line.

Here is the error while i get when i try to load qtdim file using 
command line:

deshmuk@matrix:/$ /usr/local/genex/bin/qtdim-insert.pl --user genex 
--pass yeastecol1 --name=MicroArraySuite -

-abbrev_name=dmas4 --version=4.0 --feat="0" --data_start_regex1=^O 
--data_end_regex=^\s

/usr/local/genex/uploads/genex_test_curator/qtdim-mas4.xml
Got QT Dimension: MicroArraySuite-4.0
         Got QT : QuantitationType:MicroArraySuite-4.0-1
                 No Channel
         Got QT : QuantitationType:MicroArraySuite-4.0-2
                 No Channel
         Got QT : QuantitationType:MicroArraySuite-4.0-3
                 No Channel
Creating Perl module: Data_MicroArraySuite_4_0
Using target: Data_MicroArraySuite_4_0 => Data_MicroArraySuite_4_0, no 
supporting tables
Couldn't open /tmp/Data_MicroArraySuite_4_0.pm for writing at

/usr/local/share/perl/5.8.4/Class/ObjectTemplate/DB/Create.pm line 162.

ONE more question here:
On each install a full test data set is loaded - look at the script
Perl/scripts/insert-test-data.pl to see exactly what it does, but in
brief it uses the very simplistic test files:

* data file: DB/curated_data/200-short.txt
* AD file: DB/curated_data/200-AD-short.xml
* QT Dim file: DB/curated_data/quantarray.xml

Here are the files i am trying to load, but when i am trying to load via 
command line i am loading qtdim-mas4.xml, shouldn't we be keeping 
"things" constant when doing an experiment! Just change one variable at 
a time!

Hrishi

[GeneX-dev] Sept 21 data load trial, mail # 2

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

INTERESTING OBSERVATION!!!

I logged in as hrishi and genex_test_curator and it shows i am logged in 
as genex!!!!


Insertion of Biomaterial, there were no errors.


Inserion of array design, there were no errors.Genex Job Status Page
Your job is finished. The status is: SUCCESS

Output of the program:

MAGE creation took: 1 wallclock secs ( 0.47 usr +  0.00 sys =  0.47 CPU)
24 Reporters to insert
In Bio::Genex::ChangeLog::insert_db: pkey =
Inserting Reporters took: 0 wallclock secs ( 0.00 usr +  0.01 sys = 
0.01 CPU)
24 FeatureReporterMap's to handle
Handling FR Maps took: 0 wallclock secs ( 0.01 usr +  0.00 sys =  0.01 CPU)
1 ArrayDesigns to insert
Inserting array design: Sept21_trial
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
47849

[GeneX-dev] Sept 21 data load trial, mail #1

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

Data loading trial on Sept 21:

Step 1: Login
Logged as genex

Step2: Load Experiment, here is the error i got


System error

error:  Couldn't reqire Date::Manip: syntax error at (eval 185) line 1, 
near "require Date::Manip qw(ParseDate

UnixDate)"

context:  ...
170:  my %args = @_;
171:
172:  # eval "require Date::Manip";
173:  eval "require Date::Manip qw(ParseDate UnixDate)";
174:  die "Couldn't reqire Date::Manip: $@"
175:  if $@;
176:
177:  # if none of the arguments are set, we return false
178:  return 0
...

code stack:  /usr/local/share/perl/5.8.4/Bio/Genex.pm:174
/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

[GeneX-dev] [ genex-Bugs-1031756 ] test Array and ArrayManufacture must have name

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

Bugs item #1031756, was opened at 2004-09-21 02:03
Message generated for change (Tracker Item Submitted) made by Item Submitter
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=116453&aid=1031756&group_id=16453

Category: Installer
Group: Genex-2
Status: Open
Resolution: None
Priority: 5
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Jason E. Stewart (jason_e_stewart)
Summary: test Array and ArrayManufacture must have name

Initial Comment:
The test data is inserting nameless Array and
ArrayManufacture which  make them dificult to select
from the drop-down menus

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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=116453&aid=1031756&group_id=16453

[GeneX-dev] Re: New cpan error in loading Apache::Subprocess

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

I agree - it looks like it's broken - missing all the files that are 
supposed to go with it.  I copied over my installed copy into 
the /usr/local/lib/perl/5.8.4/Apache/SubProcess.pm, so things should 
go OK from there - give it a try.

Jason, is this your take as well?

hjm


On Thursday 16 September 2004 10:55 am, you wrote:
> Harry,
>
> The Apache::SubProcess will not load properly using cpan.
>
> It does get further than it used to.  It is not finding any of the
> required http*.h files it needs to compile.
>
> Below I have given you the first two errors of quite a long list.
> Having explored the apache_inc.h file none of the referenced
> headers are found and are not on the system.
>
> Am I missing a package?
>
> Andrew
>
>
>
> _______________________________________________________
> In file included
> from
> /usr/lib/perl5/auto/Apache/include/modules/perl/mod_perl.h:162,
> from SubProcess.xs:1:
> /usr/lib/perl5/auto/Apache/include/modules/perl/apache_inc.h:120:20
>: httpd.h: No such file or directory
> /usr/lib/perl5/auto/Apache/include/modules/perl/apache_inc.h:121:26
>: http_config.h: No such fileor directory

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

[GeneX-dev] Re: Uninstall

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

make uninstall


On Tuesday 14 September 2004 8:12 am, dc...@gm... wrote:
> Genex Developers,
>
> Is there and uninstall process/program for Genex?
>
>
> Thanks,
> Andrew

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

[GeneX-dev] Uninstall

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

Genex Developers,

Is there and uninstall process/program for Genex?


Thanks,
Andrew

[GeneX-dev] Re: Files for AD,FES and data set

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

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

> Do you have three files one each for array design, data set and
> feature extraction software which have worked for you when you tried
> loading the same.

Hi Hrishi,

On each install a full test data set is loaded - look at the script
Perl/scripts/insert-test-data.pl to see exactly what it does, but in
brief it uses the very simplistic test files:

* data file: DB/curated_data/200-short.txt
* AD file: DB/curated_data/200-AD-short.xml
* QT Dim file: DB/curated_data/quantarray.xml

You can see from the script that a number of QT Dim files get loaded. 

Also, this set *should* be working but I will have to test on genex2
before I can guarantee it:

* data file: DB/curated_data/HS_120_1.txt
* AD file: DB/curated_data/YE6100.xml (you have to gunzip the .gz file)
* QT Dim file: DB/curated_data/qtdim-mas5.xml

I'll send you another email after I test these as well.

Cheers,
jas.

[GeneX-dev] Files for AD,FES and data set

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

Hi Jason,

Do you have three files one each for array design, data set and feature 
extraction software which have worked for you when you tried loading the 
same.

Thanks,
Hrishi

Re: [GeneX-dev] svn repository

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

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

> Yes, it is.  The apache2 server quits every once in a while.  I just restarted 
> it and added a restart in the crontab.

Good deal thanks for that harry.

Cheers,
jas.

Re: [GeneX-dev] svn repository

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

Yes, it is.  The apache2 server quits every once in a while.  I just restarted 
it and added a restart in the crontab.

hjm


On Monday 30 August 2004 7:55 pm, Diane Trout wrote:
> Hi,
>
> I was wondering if http://genex2.binf.gmu.edu:8080 is still the genex
> subversion repository?
>
> as of 2004 Aug 30 19:55 there's no one answering at that port.
>
> thanks,
> diane

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

[GeneX-dev] svn repository

[Diane T. <di...@ca...>]

Hi,

I was wondering if http://genex2.binf.gmu.edu:8080 is still the genex
subversion repository?

as of 2004 Aug 30 19:55 there's no one answering at that port.

thanks,
diane

[GeneX-dev] Re: QTD upload

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

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

> Ok, i will work with Harry and Jennifer to diagnose the problem.  

Hey Hrishi,

Sorry if my email was unclear. I have already fixed the bug you found
- so please don't waste any of your time trying to solve it. 

My only intent behind the email was that for *future* bugs, you could
more easily recognize at what *level* the problem is happening -
i.e. whether it was something within your control (like choosing the
wrong file, or not providing all the required parameters) or whether
it was something out of your control (a programming error).

> I am trying to use me the data sets which are in
> ,genex-server./DB/curated_data, can you please send me/upload them
> on to genex2 (let me know the path and file names) 3 files i.e. 1)
> Test Data, 2) Array Design 3) FE software. I will take these files
> and do testing.

There is already a complete installation on genex2. It lives in
~jasons (i.e. /home/jasons). The type of diagnosing you could do can
easily be done on matrix though. I'm not suggesting that you go in and
modify the code (although you are welcome to), I'm suggesting reading
the code to understand what it does and to see if you can figure out
where it has gone wrong.

Cheers,
jas.

[GeneX-dev] Re: QTD upload

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

Hi Jason,

Ok, i will work with Harry and Jennifer to diagnose the problem.
I am trying to use me the data sets which are in 
,genex-server./DB/curated_data, can you please send me/upload them on to 
genex2 (let me know the path and file names) 3 files i.e. 1) Test Data, 
2) Array Design 3) FE software. I will take these files and do testing.

Thanks,
Hrishi


Jason E. Stewart wrote:

> Hrishikesh Deshmukh <hde...@gm...> writes:
> 
> 
>>Hi All,
>>
>>Here is the error which i get when i try to load a QTD file, login as
>>hrishi (admin,user) and
>>
>>genex_test_curator.
>>
>>The "values" for the fields on the form are:
>>public,public,quantarray,3.0, 38, 5413, quantarray.xml
>>38, 5413 are the rows from data file 1200-mangle.txt, 38 being the
>>start and 5413 end of data.
>>
>>Is the "values" which i am using a problem!!!
>>I have already i think filed this as a bug.
> 
> 
> Yes, you filed it as a bug already.
> 
> It would be good for you and Harry and Jennifer to be able to diagnose
> certain levels of problems from the error output. Let me see if I can
> give you enough information to help you diagnose things better
> yourselves - that way you can get further without needing to wait for
> a response from me.
> 
> First, genex needs better error messages. Please help me with
> suggestions on how to do this.
> 
> Second, in the mean time we need to do more testing and bug fixes, so
> we have to deal with many error messages that already exist. So here
> is a short piece describing this particular error in hopes of
> educating you all a bit to get more information from the existing
> messages. 
> 
> The majority of the Mason GUI applications (especially all of the
> load-* apps) simply collect user input and then run a command line
> perl script to actually do the real work. The error that you see for
> this bug is the following:
> 
>   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
> 
>   [snip]
>   
> This is a big clue. ALL of my command line perl scripts will give
> output like this when you get an error. This is called a USAGE
> line. So whenever you see a GUI that gives this kind of error, you
> know the trouble was not in the GUI, but in the command line script. 
> 
> The first piece tells you what the error is:
> 
>   Must specify --abbrev_name
> 
> and the rest is supposed to tell you how you should *really* have run
> the program - the USAGE.
> 
> So what this error tells me is that the QT Dim loader (Mason GUI)
> called the qtdim-insert.pl perl script but didn't supply one of the
> required parameters --abrev_name. So no matter what input you give the
> GUI it is still going to give insufficient information to the perl
> script. To know this you would have to:
> 1) realize what perl script is being called. You get this from the
>    USAGE line:
> 
>   USAGE: /usr/local/genex/bin/qtdim-insert.pl [OPTIONS] file_to_read
> 
> 2) Check the perl script and see what the required parameters are. My
>    USAGE output is *supposed* to tell you that. But many of my script
>    still use the old-style USAGE commands that have to be updated
>    manually whenever I add new parameters - this can lead to an
>    out-of-synch problem (which this script suffered from). So you have
>    to read the top of the script to see that --abbrev_name is checked
>    and if it didn't exist the program would exit with an error.
> 
> 3) Check the Mason GUI code and see how it was calling the script. In
>    this case you could see that under no circumstance was
>    --abbrev_name ever given.
> 
> None of this tells you how to *fix* the bug, but it does tell you that
> you matter what input you give the GUI, it would still cause the same
> error. 
> 
> I hope this was helpful and informative.
> jas.

[GeneX-dev] r1449

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

Hey All,

I've just added a bunch of code changes - and one (very minor) schema
changed to svn.

The Makefile now has a 'make update' target which will add all new
files and modules but leave the DB untouched - that is all data added
will be preserved, it only fixes bugs and adds new stuff.

Again, 'make update' will not affect your DB.

It fixes the bugs reported by Hrishi and others, as well as continuing
to add more support for running external apps from within Genex. There
is even some beginning documentation for how to hook up apps to Genex.

Cheers,
jas.

[GeneX-dev] Re: QTD upload

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

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

> Hi All,
>
> Here is the error which i get when i try to load a QTD file, login as
> hrishi (admin,user) and
>
> genex_test_curator.
>
> The "values" for the fields on the form are:
> public,public,quantarray,3.0, 38, 5413, quantarray.xml
> 38, 5413 are the rows from data file 1200-mangle.txt, 38 being the
> start and 5413 end of data.
>
> Is the "values" which i am using a problem!!!
> I have already i think filed this as a bug.

Yes, you filed it as a bug already.

It would be good for you and Harry and Jennifer to be able to diagnose
certain levels of problems from the error output. Let me see if I can
give you enough information to help you diagnose things better
yourselves - that way you can get further without needing to wait for
a response from me.

First, genex needs better error messages. Please help me with
suggestions on how to do this.

Second, in the mean time we need to do more testing and bug fixes, so
we have to deal with many error messages that already exist. So here
is a short piece describing this particular error in hopes of
educating you all a bit to get more information from the existing
messages. 

The majority of the Mason GUI applications (especially all of the
load-* apps) simply collect user input and then run a command line
perl script to actually do the real work. The error that you see for
this bug is the following:

  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

  [snip]
  
This is a big clue. ALL of my command line perl scripts will give
output like this when you get an error. This is called a USAGE
line. So whenever you see a GUI that gives this kind of error, you
know the trouble was not in the GUI, but in the command line script. 

The first piece tells you what the error is:

  Must specify --abbrev_name

and the rest is supposed to tell you how you should *really* have run
the program - the USAGE.

So what this error tells me is that the QT Dim loader (Mason GUI)
called the qtdim-insert.pl perl script but didn't supply one of the
required parameters --abrev_name. So no matter what input you give the
GUI it is still going to give insufficient information to the perl
script. To know this you would have to:
1) realize what perl script is being called. You get this from the
   USAGE line:

  USAGE: /usr/local/genex/bin/qtdim-insert.pl [OPTIONS] file_to_read

2) Check the perl script and see what the required parameters are. My
   USAGE output is *supposed* to tell you that. But many of my script
   still use the old-style USAGE commands that have to be updated
   manually whenever I add new parameters - this can lead to an
   out-of-synch problem (which this script suffered from). So you have
   to read the top of the script to see that --abbrev_name is checked
   and if it didn't exist the program would exit with an error.

3) Check the Mason GUI code and see how it was calling the script. In
   this case you could see that under no circumstance was
   --abbrev_name ever given.

None of this tells you how to *fix* the bug, but it does tell you that
you matter what input you give the GUI, it would still cause the same
error. 

I hope this was helpful and informative.
jas.