genex-dev — GeneX developers

[GeneX-dev] [ genex-Bugs-958117 ] installer fails to creates /usr/local/genex/bin?

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Bugs item #958117, was opened at 2004-05-21 16:36
Message generated for change (Comment added) made by mangalam
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Category: Installer
Group: None
Status: Open
Resolution: None
Priority: 5
Submitted By: Harry Mangalam (mangalam)
Assigned to: Jason E. Stewart (jason_e_stewart)
Summary: installer fails to creates /usr/local/genex/bin?

Initial Comment:
after running make uninstall, and reconfiguring and installing, 
(make install), new errors have appeared: 
 
cat install-errors.txt 
 
!! System Error: No such file or directory @ line: 286  (cp 
Perl/scripts/scanner-insert.pl /usr/local/genex/bin) 
 
!! System Error: No such file or directory @ line: 286  (cp 
Perl/scripts/software-insert.pl /usr/local/genex/bin) 
 
!! System Error: No such file or directory @ line: 286  (cp 
Perl/scripts/species-insert.pl /usr/local/genex/bin) 
 
!! System Error: No such file or directory @ line: 286  (cp 
Perl/scripts/spotter-insert.pl /usr/local/genex/bin) 
 
!! System Error: No such file or directory @ line: 286  (cp 
Perl/Bio-Genex/html/ExperimentFactors.html /var/www/genex/mason/nologin/docs/perl-api) 
 
!! System Error: No such file or directory @ line: 286  (cp 
Perl/Bio-Genex/html/ExternalDatabase.html /var/www/genex/mason/nologin/docs/perl-api) 
 
It looks like the Install script no longer makes the local genex/bin 
dir? 
 
apologies for not folowing this up to its end - I'm trying to at least 
get the bugs entered. 
hjm 
 

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>Comment By: Harry Mangalam (mangalam)
Date: 2004-05-21 18:25

Message:
Logged In: YES 
user_id=4526

no, not a problem with the creation of ..genex/bin, but the files 
mentioned do not exist. Are they not created or have they been 
removed from the tree? 
 
hjm 
 

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

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[GeneX-dev] [ genex-Bugs-958117 ] installer fails to creates /usr/local/genex/bin?

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Bugs item #958117, was opened at 2004-05-21 16:36
Message generated for change (Tracker Item Submitted) made by Item Submitter
You can respond by visiting: 
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Category: Installer
Group: None
Status: Open
Resolution: None
Priority: 5
Submitted By: Harry Mangalam (mangalam)
Assigned to: Jason E. Stewart (jason_e_stewart)
Summary: installer fails to creates /usr/local/genex/bin?

Initial Comment:
after running make uninstall, and reconfiguring and installing, 
(make install), new errors have appeared: 
 
cat install-errors.txt 
 
!! System Error: No such file or directory @ line: 286  (cp 
Perl/scripts/scanner-insert.pl /usr/local/genex/bin) 
 
!! System Error: No such file or directory @ line: 286  (cp 
Perl/scripts/software-insert.pl /usr/local/genex/bin) 
 
!! System Error: No such file or directory @ line: 286  (cp 
Perl/scripts/species-insert.pl /usr/local/genex/bin) 
 
!! System Error: No such file or directory @ line: 286  (cp 
Perl/scripts/spotter-insert.pl /usr/local/genex/bin) 
 
!! System Error: No such file or directory @ line: 286  (cp 
Perl/Bio-Genex/html/ExperimentFactors.html /var/www/genex/mason/nologin/docs/perl-api) 
 
!! System Error: No such file or directory @ line: 286  (cp 
Perl/Bio-Genex/html/ExternalDatabase.html /var/www/genex/mason/nologin/docs/perl-api) 
 
It looks like the Install script no longer makes the local genex/bin 
dir? 
 
apologies for not folowing this up to its end - I'm trying to at least 
get the bugs entered. 
hjm 
 

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

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

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Bugs item #945670, was opened at 2004-04-30 17:22
Message generated for change (Comment added) made by jason_e_stewart
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Category: Mason GUI
Group: None
Status: Open
Resolution: None
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: 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]]

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

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[GeneX-dev] [ genex-Bugs-956693 ] using oid for pkey is breaking DB insertion code

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Bugs item #956693, was opened at 2004-05-19 06:56
Message generated for change (Tracker Item Submitted) made by Item Submitter
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Category: DB Schema
Group: Genex-2
Status: Open
Resolution: None
Priority: 9
Submitted By: Jason E. Stewart (jason_e_stewart)
Assigned to: Jason E. Stewart (jason_e_stewart)
Summary: using oid for pkey is breaking DB insertion code

Initial Comment:
the change to make oid act as pkey is attempting to
make bogus insert statements. 

SQL=[[INSERT INTO GENEX_ROLE
(role_name_ont_fk,oid,other_table_fk,other_fk) VALUES
('305','641','161','637')]], DBI=[[ERROR:  column "oid"
of relation "genex_role" does not exist]]

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

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[GeneX-dev] [ genex-Bugs-956684 ] update check function is using table not view

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Bugs item #956684, was opened at 2004-05-19 06:42
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Category: DB Schema
Group: Genex-2
Status: Open
Resolution: None
Priority: 9
Submitted By: Jason E. Stewart (jason_e_stewart)
Assigned to: Jason E. Stewart (jason_e_stewart)
Summary: update check function is using table not view

Initial Comment:
create_seq_view_trigger_function() is using the table
name and so any user not in genex_admin gets a
permission denied error

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

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[GeneX-dev] [ genex-Bugs-839473 ] DBD::Pg::st execute failed

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Bugs item #839473, was opened at 2003-11-10 12:55
Message generated for change (Comment added) made by jason_e_stewart
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Category: Mason GUI
Group: None
>Status: Closed
>Resolution: Fixed
Priority: 5
Submitted By: Brandon King (kingb)
Assigned to: Jason E. Stewart (jason_e_stewart)
Summary: DBD::Pg::st execute failed

Initial Comment:
I was trying to upload an array design xml file, that I
created from GPR files when I ran into the /tmp/genex
not writable error... I just created a writable
/tmp/genex directory to bypass it. I then got the
following error after select 'Load Array Designs' from
the GeneX DB Array Design Loader Page:

error:   	DBD::Pg::st execute failed: server closed the
connection unexpectedly at
/usr/share/perl5/Apache/Session/Store/DBI.pm line 65.
context:  	
...  	
61:  	
62:  	$self->{update_sth}->bind_param(1,
$session->{serialized});
63:  	$self->{update_sth}->bind_param(2,
$session->{data}->{_session_id});
64:  	
65:  	$self->{update_sth}->execute;
66:  	
67:  	$self->{update_sth}->finish;
68:  	}
69:  	
...  	
code stack:  
/usr/share/perl5/Apache/Session/Store/DBI.pm:65
/usr/share/perl5/Apache/Session.pm:508
/usr/share/perl5/Apache/Session.pm:462
/usr/share/perl5/HTML/Mason/Request.pm:1050
/var/www/genex/mason/syshandler:1
raw error

DBD::Pg::st execute failed: server closed the
connection unexpectedly at
/usr/share/perl5/Apache/Session/Store/DBI.pm line 65.


Trace begun at
/usr/share/perl5/HTML/Mason/Exceptions.pm line 128
HTML::Mason::Exceptions::rethrow_exception('DBD::Pg::st
execute failed: server closed the connection
unexpectedly at
/usr/share/perl5/Apache/Session/Store/DBI.pm line
65.^J') called at
/usr/share/perl5/Apache/Session/Store/DBI.pm line 65
Apache::Session::Store::DBI::update('Bio::Genex::StorePostgres=HASH(0x958e6bc)',
'Bio::Genex::SessionPostgres=HASH(0x958e6c8)') called
at /usr/share/perl5/Apache/Session.pm line 508
Apache::Session::save('Bio::Genex::SessionPostgres=HASH(0x958e6c8)')
called at /usr/share/perl5/Apache/Session.pm line 462
Apache::Session::DESTROY('Bio::Genex::SessionPostgres=HASH(0x958e6c8)')
called at /usr/share/perl5/HTML/Mason/Request.pm line 1050
eval
{...}('Bio::Genex::SessionPostgres=HASH(0x958e6c8)')
called at /usr/share/perl5/HTML/Mason/Request.pm line 1050
HTML::Mason::Request::comp(undef, undef, 'write_group',
'WoldLab', 'debug', 0, 'submit', 'Load Array Designs',
'data_files',
'/usr/local/genex/uploads/williams-muscleTime.xml',
'read_group', 'WoldLab') called at
/usr/share/perl5/HTML/Mason/Request.pm line 746
HTML::Mason::Request::call_next('HTML::Mason::Request::ApacheHandler=HASH(0x958c6d8)')
called at /var/www/genex/mason/syshandler line 1
HTML::Mason::Commands::__ANON__('write_group',
'WoldLab', 'debug', 0, 'submit', 'Load Array Designs',
'data_files',
'/usr/local/genex/uploads/williams-muscleTime.xml',
'read_group', 'WoldLab') called at
/usr/share/perl5/HTML/Mason/Component.pm line 134
HTML::Mason::Component::run('HTML::Mason::Component::FileBased=HASH(0x94bc07c)',
'write_group', 'WoldLab', 'debug', 0, 'submit', 'Load
Array Designs', 'data_files',
'/usr/local/genex/uploads/williams-muscleTime.xml',
'read_group', 'WoldLab') called at
/usr/share/perl5/HTML/Mason/Request.pm line 1051
eval
{...}('HTML::Mason::Component::FileBased=HASH(0x94bc07c)',
'write_group', 'WoldLab', 'debug', 0, 'submit', 'Load
Array Designs', 'data_files',
'/usr/local/genex/uploads/williams-muscleTime.xml',
'read_group', 'WoldLab') called at
/usr/share/perl5/HTML/Mason/Request.pm line 1050
HTML::Mason::Request::comp(undef, undef, undef,
'write_group', 'WoldLab', 'debug', 0, 'submit', 'Load
Array Designs', 'data_files',
'/usr/local/genex/uploads/williams-muscleTime.xml',
'read_group', 'WoldLab') called at
/usr/share/perl5/HTML/Mason/Request.pm line 331
eval {...}(undef, undef, undef, 'write_group',
'WoldLab', 'debug', 0, 'submit', 'Load Array Designs',
'data_files',
'/usr/local/genex/uploads/williams-muscleTime.xml',
'read_group', 'WoldLab') called at
/usr/share/perl5/HTML/Mason/Request.pm line 331
eval {...}(undef, undef, undef, 'write_group',
'WoldLab', 'debug', 0, 'submit', 'Load Array Designs',
'data_files',
'/usr/local/genex/uploads/williams-muscleTime.xml',
'read_group', 'WoldLab') called at
/usr/share/perl5/HTML/Mason/Request.pm line 290
HTML::Mason::Request::exec('HTML::Mason::Request::ApacheHandler=HASH(0x958c6d8)')
called at /usr/share/perl5/HTML/Mason/ApacheHandler.pm
line 134
eval
{...}('HTML::Mason::Request::ApacheHandler=HASH(0x958c6d8)')
called at /usr/share/perl5/HTML/Mason/ApacheHandler.pm
line 134
HTML::Mason::Request::ApacheHandler::exec('HTML::Mason::Request::ApacheHandler=HASH(0x958c6d8)')
called at /usr/share/perl5/HTML/Mason/ApacheHandler.pm
line 792
HTML::Mason::ApacheHandler::handle_request('HTML::Mason::ApacheHandler=HASH(0x80fc94c)',
'Apache=SCALAR(0x81f6678)') called at
/usr/local/genex/etc/genex-handler.pl line 28
Bio::Genex::ApacheHandler::genex::handler('Apache=SCALAR(0x81f6678)')
called at /dev/null line 0
eval {...}('Apache=SCALAR(0x81f6678)') called at
/dev/null line 0

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

>Comment By: Jason E. Stewart (jason_e_stewart)
Date: 2004-05-19 06:00

Message:
Logged In: YES 
user_id=85550

the timing issue was fixed a long time ago by reading the
mod_perl guide. 

for the curious it has to do with properly handling fork()
under mod_perl

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

Comment By: Jason E. Stewart (jason_e_stewart)
Date: 2003-11-11 03:03

Message:
Logged In: YES 
user_id=85550

Hey Brandon,

This is a wierd timing issue that is hard to solve. 

Whenever this happens, simply refresh the page, and you will
get the correct status output. I want to fix this
eventually, but since it is harmless once you know what to
do, it's going to have to wait

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

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[GeneX-dev] [ genex-Bugs-848096 ] mason-edit-class.pl: support for tables without pkeys

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Bugs item #848096, was opened at 2003-11-24 00:30
Message generated for change (Settings changed) made by jason_e_stewart
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Category: Mason GUI
Group: Genex-2
>Status: Closed
>Resolution: Fixed
Priority: 5
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Jason E. Stewart (jason_e_stewart)
Summary: mason-edit-class.pl: support for tables without pkeys

Initial Comment:
mason-edit-class.pl: support for tables without pkeys, use unique  cols

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

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[GeneX-dev] [ genex-Bugs-950864 ] obj2table.mason should show MTO fkey name, not table name

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Bugs item #950864, was opened at 2004-05-09 11:06
Message generated for change (Settings changed) made by jason_e_stewart
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Category: Mason GUI
Group: Genex-2
>Status: Closed
>Resolution: Fixed
Priority: 7
Submitted By: Jason E. Stewart (jason_e_stewart)
Assigned to: Jason E. Stewart (jason_e_stewart)
Summary: obj2table.mason should show MTO fkey name, not table name

Initial Comment:
In the MTO fkey columns, it is showing the table name -
when it has multiple fkeys from the same table, it is
impossible to determine which column is to which fkey.

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

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[GeneX-dev] [ genex-Bugs-955104 ] objs2table.mason: OTM fkeys should fetch count only

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Bugs item #955104, was opened at 2004-05-17 00:35
Message generated for change (Settings changed) made by jason_e_stewart
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Category: Mason GUI
Group: Genex-2
>Status: Closed
>Resolution: Fixed
Priority: 7
Submitted By: Jason E. Stewart (jason_e_stewart)
Assigned to: Jason E. Stewart (jason_e_stewart)
Summary: objs2table.mason: OTM fkeys should fetch count only

Initial Comment:
currently this component is doing a full DB lookup for
all rows in all OTM fkeys. With an empty DB this is
doable, but later it will be slow and useless.

Instead, all that is needed is the number of rows to be
fetched. This can be done simply after fixing
get_all_objects() to return a row count in a scalar
context.

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

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[GeneX-dev] [ genex-Bugs-956626 ] insert_db() automatic changelog entry insertion broken

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Bugs item #956626, was opened at 2004-05-19 04:46
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Category: Bio::Genex Perl API
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: insert_db() automatic changelog entry insertion broken

Initial Comment:
the $UNIQUE_WHERE variable has been removed, and so all
the changelog's are useless.

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

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[GeneX-dev] [ genex-Bugs-956619 ] gendb.pl: split test data loading into seperate script

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Bugs item #956619, was opened at 2004-05-19 04:24
Message generated for change (Settings changed) made by jason_e_stewart
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Category: Installer
Group: Genex-2
>Status: Closed
>Resolution: Fixed
Priority: 9
Submitted By: Jason E. Stewart (jason_e_stewart)
Assigned to: Jason E. Stewart (jason_e_stewart)
Summary: gendb.pl: split test data loading into seperate script

Initial Comment:
gendb.pl is getting big and unwieldy, the test data
part should be split out.

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

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[GeneX-dev] [ genex-Bugs-956619 ] gendb.pl: split test data loading into seperate script

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Bugs item #956619, was opened at 2004-05-19 04:24
Message generated for change (Tracker Item Submitted) made by Item Submitter
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Category: Installer
Group: Genex-2
Status: Open
Resolution: None
Priority: 9
Submitted By: Jason E. Stewart (jason_e_stewart)
Assigned to: Jason E. Stewart (jason_e_stewart)
Summary: gendb.pl: split test data loading into seperate script

Initial Comment:
gendb.pl is getting big and unwieldy, the test data
part should be split out.

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

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[GeneX-dev] Beta Release Test Plan

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

Hey All,

Here's a draft of a plan for testing genex before making a release.

1) Test that fresh install runs without errors - i.e. 
  - make uninstall
  - make configure
  - make install

2) Test Mason components
  - which should be tested?

3) Test automateable perl scripts
  - which should be tested?

4) Test 'make test' on all API modules runs w/o errors
  - Bio-Genex
  - Bio-MAGE
  - Class-ObjectTemplate
  - Class-ObjectTemplate-DB

5) All required docs up-to-date
  - which are required?

6) External data analysis
  - should OO.o be included in beta?

7) Other? WWW site?

For part 1) perhaps we should attempt some optional installation
parameters as well, such as: alternate installation locations for the
three different directories (html, cgi, bin), tcp/ip support, others?

For part 3), this can be automated - and most of it is tested in
gendb.pl at installation time already.

For part 4) only Bio-Genex and Class-ObjectTemplate-DB change, and I
run 'make test' on them whenever I remember (although I've been rather
bad with Class-ObjectTemplate-DB and not written any useful regression
tests in a long time).

For part 5) we should look at the SF task tracker and prioritize the
documents: all 7,8, and 9 get included in the beta, and 5 and 6 for
the full release.

That leaves part 2). We should test:
- insert DB User
- change password
- set user preferences
- all required docs available
- Full data load path:
  * insert Experiment (user)
  * insert Biomaterial (user)
  * load ArrayDesign (curator)
  * insert ArrayManufacture (user)
  * insert Array (user)
  * load MBA Data (user) - also adds MBA and PBA
  * add Image to PBA (user)
  * copy MBA Data to Scratch (user)
  * run processing protocol on Scratch data
  * add scratch view (curator)???
  * add processing protocol (curator)???
  * annotate BiomaterialCharacteristics (user)???
- export DBA/MBA data to tab file
- other???

If this is totally wackoo, let me know - but we need some checklist so
that we can get a beta release out the door REAL SOON!!!

Cheers,
jas.

[GeneX-dev] [ genex-Bugs-953958 ] Errors on make install

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Bugs item #953958, was opened at 2004-05-14 07:24
Message generated for change (Settings changed) made by jason_e_stewart
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Category: Installer
Group: Genex-2
>Status: Closed
>Resolution: Fixed
Priority: 7
Submitted By: Jason E. Stewart (jason_e_stewart)
Assigned to: Harry Mangalam (mangalam)
Summary: Errors on make install 

Initial Comment:
Array-model.txt was removed but the entry in the
MANIFEST.in is still there

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

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[GeneX-dev] [ genex-Bugs-955931 ] navbar is too cramped

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Bugs item #955931, was opened at 2004-05-18 07:43
Message generated for change (Comment added) made by jason_e_stewart
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Category: Mason GUI
Group: Genex-2
>Status: Closed
>Resolution: Fixed
Priority: 7
Submitted By: Jason E. Stewart (jason_e_stewart)
Assigned to: Jason E. Stewart (jason_e_stewart)
Summary: navbar is too cramped

Initial Comment:
since changing to login/nologin layout, the navbar is
totally cramped

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>Comment By: Jason E. Stewart (jason_e_stewart)
Date: 2004-05-18 07:53

Message:
Logged In: YES 
user_id=85550

actually - that is bullshit. The tigris.css #leftcol section
is set at 14em, I had a bogus width="20%" that was
over-riding that.

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

Comment By: Jason E. Stewart (jason_e_stewart)
Date: 2004-05-18 07:49

Message:
Logged In: YES 
user_id=85550

needed to add a width="85%" to the main section <td> tag

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

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[GeneX-dev] [ genex-Bugs-955931 ] navbar is too cramped

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

Bugs item #955931, was opened at 2004-05-18 07:43
Message generated for change (Comment added) made by jason_e_stewart
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Category: Mason GUI
Group: Genex-2
Status: Open
Resolution: None
Priority: 7
Submitted By: Jason E. Stewart (jason_e_stewart)
Assigned to: Jason E. Stewart (jason_e_stewart)
Summary: navbar is too cramped

Initial Comment:
since changing to login/nologin layout, the navbar is
totally cramped

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

>Comment By: Jason E. Stewart (jason_e_stewart)
Date: 2004-05-18 07:49

Message:
Logged In: YES 
user_id=85550

needed to add a width="85%" to the main section <td> tag

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

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[GeneX-dev] [ genex-Bugs-955931 ] navbar is too cramped

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

Bugs item #955931, was opened at 2004-05-18 07:43
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=955931&group_id=16453

Category: Mason GUI
Group: Genex-2
Status: Open
Resolution: None
Priority: 7
Submitted By: Jason E. Stewart (jason_e_stewart)
Assigned to: Jason E. Stewart (jason_e_stewart)
Summary: navbar is too cramped

Initial Comment:
since changing to login/nologin layout, the navbar is
totally cramped

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

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[GeneX-dev] [ genex-Bugs-955651 ] user-insert.pl broken

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Bugs item #955651, was opened at 2004-05-18 00:59
Message generated for change (Settings changed) made by jason_e_stewart
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Category: Mason GUI
Group: Genex-2
>Status: Closed
>Resolution: Fixed
Priority: 9
Submitted By: Jason E. Stewart (jason_e_stewart)
Assigned to: Jason E. Stewart (jason_e_stewart)
Summary: user-insert.pl broken

Initial Comment:
Global symbol "$p" requires explicit package name at
/usr/local/genex2/bin/user-insert.pl line 132.

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

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[GeneX-dev] [ genex-Bugs-955651 ] user-insert.pl broken

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

Bugs item #955651, was opened at 2004-05-18 00:59
Message generated for change (Tracker Item Submitted) made by Item Submitter
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Category: Mason GUI
Group: Genex-2
Status: Open
Resolution: None
Priority: 9
Submitted By: Jason E. Stewart (jason_e_stewart)
Assigned to: Jason E. Stewart (jason_e_stewart)
Summary: user-insert.pl broken

Initial Comment:
Global symbol "$p" requires explicit package name at
/usr/local/genex2/bin/user-insert.pl line 132.

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

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[GeneX-dev] [ genex-Bugs-951918 ] linking table entries getting inserted multiple times

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

Bugs item #951918, was opened at 2004-05-11 08:10
Message generated for change (Comment added) made by jason_e_stewart
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Category: Bio::Genex Perl API
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: linking table entries getting inserted multiple times

Initial Comment:
There is no checking mechanism to see if a linking
table entry is in the DB, so they will get inserted
multiple times (especially if there is no unique index
on the table).

A quick fix is to simply check if dbh() is set. 

A more interesting fix is to add support for oids -
that way even linking table entries would have pkeys.
This would fix support for applications like
mason-edit-app.pl

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

>Comment By: Jason E. Stewart (jason_e_stewart)
Date: 2004-05-17 23:17

Message:
Logged In: YES 
user_id=85550

dbh() checking has been implemented for non-pkey tables

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

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[GeneX-dev] Schema changes in SVN

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

Hey All,

All my changes are now committed to SVN. This includes:
* Image support
* ControlledVocab renamed to OntologyEntry, and all OE's are now
  referenced as fkeys (before they were referenced only by name, so
  there was non integrity checks). Also, all MAGE compatibility
  changes were made
* API documentation updated and enhanced (I couldn't remember my own
  code). 

According to the SF bug-tracking system, these were the final DB
Schema changes with priority 7,8, or 9. 

Celebration!!!

I suggest:
1) Harry and I test the system for a few days to find any major pieces
   that I may have overlooked, and then update matrix. 
2) Once matrix is update, declare a schema freeze => only priority 9
   schema bugs will be modified, and this will require a script which
   guarantees that a DB upgrade will *not* harm any data in the DB.
3) We decide on a test plan, and follow through with it logging bugs
   as we go.
4) Only priority 9 feature requests will be fixed for the beta
   release, and only priority 8 and 9 bugs will be fixed for the beta
   release. 
5) Make a beta release.
6) Re-evaluate all bugs/feature requests and move all important ones
   to 7,8, or 9.
7) fix all high-priority bugs/features
8) test
9) release Genex-2.0!!!
10) celebrate 2 long years!!!!!!

Cheers,
jas.

[GeneX-dev] [ genex-Bugs-952015 ] admin users cannot see data in views if not in ro_gs_fk

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

Bugs item #952015, was opened at 2004-05-11 10:36
Message generated for change (Settings changed) made by jason_e_stewart
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Category: DB Schema
Group: Genex-2
Status: Open
Resolution: None
>Priority: 6
Submitted By: Jason E. Stewart (jason_e_stewart)
Assigned to: Jason E. Stewart (jason_e_stewart)
Summary: admin users cannot see data in views if not in ro_gs_fk

Initial Comment:
admin users should be able to see all data, even when
looking through a view - this is probably important for
using scratch views.

There should be a function is_admin() that returns true
if the user is in the genex_admin group. Then we can
make the sec view sql where clause be:

   WHERE is_genex_admin() or ...



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

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[GeneX-dev] [ genex-Bugs-955360 ] post_process() support for ArrayManufacture + OntologyEntry

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

Bugs item #955360, was opened at 2004-05-17 11:24
Message generated for change (Tracker Item Submitted) made by Item Submitter
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Category: Mason GUI
Group: Genex-2
Status: Open
Resolution: None
Priority: 6
Submitted By: Jason E. Stewart (jason_e_stewart)
Assigned to: Jason E. Stewart (jason_e_stewart)
Summary: post_process() support for ArrayManufacture + OntologyEntry

Initial Comment:
These table need more descriptive entries for table
browsing

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

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Re: [GeneX-dev] WWW links to Genex

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

Tom Laudeman <tw...@vi...> writes:

> Jason, Todd,
>
> We're chaning our name to Gene Expression Open Source System or GEOSS
> to avoid confusion.

Hey Tom, Todd,

That's probably a good idea. A lot of the pages that I found had
either Genex-lite and UVa Genex or they had Genex and UVa Genex, but
they didn't have Genex-lite and Genex listed together. So I pointed
them to all three projects.

> Jason, I've got a description of Genex-Lite from Todd. If you send
> me one for GeneX 2, I'll add that (and a link) to our "background"
> page.

Ok, I'll do that, Thanks!
jas.

Re: [GeneX-dev] WWW links to Genex

[Todd F. P. <tf...@nc...>]

Tom, yer the man!

Todd

On Mon, 17 May 2004, Tom Laudeman wrote:

> Jason, Todd,
>
> We're chaning our name to Gene Expression Open Source System
> or GEOSS to avoid confusion.
>
> Jason, I've got a description of Genex-Lite from Todd. If
> you send me one for GeneX 2, I'll add that (and a link) to
> our "background" page.
>
> Cheers!
> Tom
>
>
>
>
> Todd F. Peterson wrote:
> > We still do have a version at NCGR.
> >
> > Todd
> >
> > On Mon, 17 May 2004, Jason E. Stewart wrote:
> >
> >
> >>Hey All,
> >>
> >>I did a google search on genex and found a number of pages that are
> >>still referring to the project as part of NCGR. So I wrote to about
> >>five of the webmasters and let them know of the SF site. They have all
> >>written back thanking me for the update, and have said they have
> >>already or the will update their pages.
> >>
> >>Cheers,
> >>jas.
> >>
> >>
> >>-------------------------------------------------------
> >>This SF.Net email is sponsored by: SourceForge.net Broadband
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> >>_______________________________________________
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> >>
> >
> >
> >
> >
> > -------------------------------------------------------
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> > _______________________________________________
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> >
>
> --
> Tom Laudeman
> mailto:tw...@vi...
> (434) 924-2456
> http://www.people.virginia.edu/~twl8n/
> http://laudeman.com/
>
>