genex-cvs-commit Mailing List for GeneX Gene Expression Database (Page 13)

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[Genex-cvs-commit] genex-server/Mason/workspace index.html,1.3,1.4

From: <jas...@us...> - 2003-04-17 04:42:49

Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv17386

Modified Files:
	index.html 
Log Message:
new app


Index: index.html
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/index.html,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** index.html	15 Apr 2003 17:50:13 -0000	1.3
--- index.html	17 Apr 2003 04:42:46 -0000	1.4
***************
*** 19,22 ****
--- 19,23 ----
        <li><a href="group-create.html">group-create.html</a></li>
        <li><a href="contact-insert.html">contact-insert.html</a></li>
+       <li><a href="protocol-insert.html">protocol-insert.html</a></li>
      </ul>
  <%attr>

[Genex-cvs-commit] genex-server/DB/xml AM_SuspectSpots.xml,1.6,NONE

From: <jas...@us...> - 2003-04-17 04:31:53

Update of /cvsroot/genex/genex-server/DB/xml
In directory sc8-pr-cvs1:/tmp/cvs-serv14232

Removed Files:
	AM_SuspectSpots.xml 
Log Message:
old table


--- AM_SuspectSpots.xml DELETED ---

[Genex-cvs-commit] genex-server/Genex/Feature Feature.pm,1.14,1.15

From: <jas...@us...> - 2003-04-16 23:38:05

Update of /cvsroot/genex/genex-server/Genex/Feature
In directory sc8-pr-cvs1:/tmp/cvs-serv17623/Genex/Feature

Modified Files:
	Feature.pm 
Log Message:
new Perl API for Protocol changes


Index: Feature.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Feature/Feature.pm,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15

[Genex-cvs-commit] genex-server/Genex/GenexAdmin GenexAdmin.pm,1.19,1.20

From: <jas...@us...> - 2003-04-16 23:38:05

Update of /cvsroot/genex/genex-server/Genex/GenexAdmin
In directory sc8-pr-cvs1:/tmp/cvs-serv17623/Genex/GenexAdmin

Modified Files:
	GenexAdmin.pm 
Log Message:
new Perl API for Protocol changes


Index: GenexAdmin.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/GenexAdmin/GenexAdmin.pm,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20

[Genex-cvs-commit] genex-server/Genex/FeatureExtractionSoftware FeatureExtractionSoftware.pm,1.6,1.7

From: <jas...@us...> - 2003-04-16 23:38:05

Update of /cvsroot/genex/genex-server/Genex/FeatureExtractionSoftware
In directory sc8-pr-cvs1:/tmp/cvs-serv17623/Genex/FeatureExtractionSoftware

Modified Files:
	FeatureExtractionSoftware.pm 
Log Message:
new Perl API for Protocol changes


Index: FeatureExtractionSoftware.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/FeatureExtractionSoftware/FeatureExtractionSoftware.pm,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** FeatureExtractionSoftware.pm	23 Nov 2002 10:18:15 -0000	1.6
--- FeatureExtractionSoftware.pm	16 Apr 2003 23:23:48 -0000	1.7
***************
*** 88,92 ****
    $TABLE_NAME_VIEW   = q[FeatureExtractionSoftware_view];
    $TABLE_TYPE   = q[DATA];
!   $PKEY_NAME    = q[sw_pk];
  }
  
--- 88,92 ----
    $TABLE_NAME_VIEW   = q[FeatureExtractionSoftware_view];
    $TABLE_TYPE   = q[DATA];
!   $PKEY_NAME    = q[param_pk];
  }
  
***************
*** 125,129 ****
  
    # or specifically
!   my $sw_pk_val = $FeatureExtractionSoftware->sw_pk();
  
    # retreving other DB column attributes
--- 125,129 ----
  
    # or specifically
!   my $param_pk_val = $FeatureExtractionSoftware->param_pk();
  
    # retreving other DB column attributes
***************
*** 421,425 ****
  This method returns the name of the column which is used as the
  primary key for this DB table. This method only exists for data
! table classes, and for Bio::Genex::FeatureExtractionSoftware it returns the value 'sw_pk';
  
  =cut
--- 421,425 ----
  This method returns the name of the column which is used as the
  primary key for this DB table. This method only exists for data
! table classes, and for Bio::Genex::FeatureExtractionSoftware it returns the value 'param_pk';
  
  =cut
***************
*** 513,517 ****
  if ($DEBUG) {
  printf STDERR "%sIn Bio::Genex::FeatureExtractionSoftware::insert_db: pkey = %s\n",
!   ' ' x $::indent, $self->get_attribute('sw_pk');
    $::indent +=2;
  }
--- 513,517 ----
  if ($DEBUG) {
  printf STDERR "%sIn Bio::Genex::FeatureExtractionSoftware::insert_db: pkey = %s\n",
!   ' ' x $::indent, $self->get_attribute('param_pk');
    $::indent +=2;
  }
***************
*** 600,604 ****
                    );
    $pkey = $pkey->[0][0];
!   $values{sw_pk} = $pkey;
    $self->id($pkey);
  
--- 600,604 ----
                    );
    $pkey = $pkey->[0][0];
!   $values{param_pk} = $pkey;
    $self->id($pkey);
  
***************
*** 668,672 ****
    assert_dbh($dbh);
    die "Bio::Genex::FeatureExtractionSoftware::update_db: object not in DB"
!     unless defined $self->id() && defined $self->sw_pk();
  
    # before we can update the values for the object
--- 668,672 ----
    assert_dbh($dbh);
    die "Bio::Genex::FeatureExtractionSoftware::update_db: object not in DB"
!     unless defined $self->id() && defined $self->param_pk();
  
    # before we can update the values for the object
***************
*** 710,714 ****
  
    # execute the UPDATE
!   my $WHERE = 'sw_pk=' . $dbh->quote($self->sw_pk());
    my $table_name = Bio::Genex::FeatureExtractionSoftware->table_or_viewname($dbh);
    my $sql = $dbh->create_update_sql(
--- 710,714 ----
  
    # execute the UPDATE
!   my $WHERE = 'param_pk=' . $dbh->quote($self->param_pk());
    my $table_name = Bio::Genex::FeatureExtractionSoftware->table_or_viewname($dbh);
    my $sql = $dbh->create_update_sql(
***************
*** 991,995 ****
  
    # add primary key to each row
!   push(@{$header},'sw_pk');
  
  
--- 991,995 ----
  
    # add primary key to each row
!   push(@{$header},'param_pk');

[Genex-cvs-commit] genex-server/Genex/GroupLink GroupLink.pm,1.31,1.32

From: <jas...@us...> - 2003-04-16 23:38:05

Update of /cvsroot/genex/genex-server/Genex/GroupLink
In directory sc8-pr-cvs1:/tmp/cvs-serv17623/Genex/GroupLink

Modified Files:
	GroupLink.pm 
Log Message:
new Perl API for Protocol changes


Index: GroupLink.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/GroupLink/GroupLink.pm,v
retrieving revision 1.31
retrieving revision 1.32
diff -C2 -d -r1.31 -r1.32

[Genex-cvs-commit] genex-server/Genex/GroupSec GroupSec.pm,1.38,1.39

From: <jas...@us...> - 2003-04-16 23:38:04

Update of /cvsroot/genex/genex-server/Genex/GroupSec
In directory sc8-pr-cvs1:/tmp/cvs-serv17623/Genex/GroupSec

Modified Files:
	GroupSec.pm 
Log Message:
new Perl API for Protocol changes


Index: GroupSec.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/GroupSec/GroupSec.pm,v
retrieving revision 1.38
retrieving revision 1.39
diff -C2 -d -r1.38 -r1.39

[Genex-cvs-commit] genex-server/Genex/ProtocolStep .cvsignore,NONE,1.1

From: <jas...@us...> - 2003-04-16 23:35:55

Update of /cvsroot/genex/genex-server/Genex/ProtocolStep
In directory sc8-pr-cvs1:/tmp/cvs-serv22596/Genex/ProtocolStep

Added Files:
	.cvsignore 
Log Message:
usual


--- NEW FILE: .cvsignore ---
Makefile
pm_to_blib

[Genex-cvs-commit] genex-server/Genex/ProtocolApplication .cvsignore,NONE,1.1

From: <jas...@us...> - 2003-04-16 23:35:54

Update of /cvsroot/genex/genex-server/Genex/ProtocolApplication
In directory sc8-pr-cvs1:/tmp/cvs-serv22596/Genex/ProtocolApplication

Added Files:
	.cvsignore 
Log Message:
usual


--- NEW FILE: .cvsignore ---
Makefile
pm_to_blib

[Genex-cvs-commit] genex-server/Genex/Procedure .cvsignore,NONE,1.1

From: <jas...@us...> - 2003-04-16 23:35:53

Update of /cvsroot/genex/genex-server/Genex/Procedure
In directory sc8-pr-cvs1:/tmp/cvs-serv22596/Genex/Procedure

Added Files:
	.cvsignore 
Log Message:
usual


--- NEW FILE: .cvsignore ---
Makefile
pm_to_blib

[Genex-cvs-commit] genex-server/Genex/Parameterizable .cvsignore,NONE,1.1

From: <jas...@us...> - 2003-04-16 23:35:53

Update of /cvsroot/genex/genex-server/Genex/Parameterizable
In directory sc8-pr-cvs1:/tmp/cvs-serv22596/Genex/Parameterizable

Added Files:
	.cvsignore 
Log Message:
usual


--- NEW FILE: .cvsignore ---
Makefile
pm_to_blib

[Genex-cvs-commit] genex-server/Genex/ParameterValue .cvsignore,NONE,1.1

From: <jas...@us...> - 2003-04-16 23:35:52

Update of /cvsroot/genex/genex-server/Genex/ParameterValue
In directory sc8-pr-cvs1:/tmp/cvs-serv22596/Genex/ParameterValue

Added Files:
	.cvsignore 
Log Message:
usual


--- NEW FILE: .cvsignore ---
Makefile
pm_to_blib

[Genex-cvs-commit] genex-server/Genex/Hardware .cvsignore,NONE,1.1

From: <jas...@us...> - 2003-04-16 23:35:51

Update of /cvsroot/genex/genex-server/Genex/Hardware
In directory sc8-pr-cvs1:/tmp/cvs-serv22596/Genex/Hardware

Added Files:
	.cvsignore 
Log Message:
usual


--- NEW FILE: .cvsignore ---
Makefile
pm_to_blib

[Genex-cvs-commit] genex-server/Genex/Parameter .cvsignore,NONE,1.1

From: <jas...@us...> - 2003-04-16 23:35:51

Update of /cvsroot/genex/genex-server/Genex/Parameter
In directory sc8-pr-cvs1:/tmp/cvs-serv22596/Genex/Parameter

Added Files:
	.cvsignore 
Log Message:
usual


--- NEW FILE: .cvsignore ---
Makefile
pm_to_blib

[Genex-cvs-commit] genex-server MANIFEST.in,1.7,1.8

From: <jas...@us...> - 2003-04-16 23:30:43

Update of /cvsroot/genex/genex-server
In directory sc8-pr-cvs1:/tmp/cvs-serv21043

Modified Files:
	MANIFEST.in 
Log Message:
new files


Index: MANIFEST.in
===================================================================
RCS file: /cvsroot/genex/genex-server/MANIFEST.in,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** MANIFEST.in	15 Apr 2003 17:50:31 -0000	1.7
--- MANIFEST.in	16 Apr 2003 23:30:38 -0000	1.8
***************
*** 54,57 ****
--- 54,58 ----
  	'Mason/workspace/query.html' => '%%GENEX_WORKSPACE_DIR%%',
  	'Mason/workspace/contact-insert.html' => '%%GENEX_WORKSPACE_DIR%%',
+ 	'Mason/workspace/protocol-insert.html' => '%%GENEX_WORKSPACE_DIR%%',
  
  	'Mason/workspace/comps/authenticate.mason' => '%%GENEX_WORKSPACE_DIR%%/comps',

[Genex-cvs-commit] genex-server .cvsignore,1.11,1.12 ChangeLog,1.124,1.125 TODO,1.21,1.22

From: <jas...@us...> - 2003-04-16 23:30:29

Update of /cvsroot/genex/genex-server
In directory sc8-pr-cvs1:/tmp/cvs-serv20915

Modified Files:
	.cvsignore ChangeLog TODO 
Log Message:
usual


Index: .cvsignore
===================================================================
RCS file: /cvsroot/genex/genex-server/.cvsignore,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** .cvsignore	7 Nov 2002 15:01:08 -0000	1.11
--- .cvsignore	16 Apr 2003 23:30:20 -0000	1.12
***************
*** 1,3 ****
--- 1,4 ----
  .subst_cache
+ Bio
  Config.pm
  MANIFEST

Index: ChangeLog
===================================================================
RCS file: /cvsroot/genex/genex-server/ChangeLog,v
retrieving revision 1.124
retrieving revision 1.125
diff -C2 -d -r1.124 -r1.125
*** ChangeLog	9 Apr 2003 21:13:20 -0000	1.124
--- ChangeLog	16 Apr 2003 23:30:20 -0000	1.125
***************
*** 1,3 ****
--- 1,32 ----
+ 2003-04-16  Jason E. Stewart  <ja...@op...>
+ 
+ 	* DTD/table.dtd (Repository): 
+ 	removed IDREF and IDREFS 
+ 
+ 	* DB/xml/Protocol.xml (Repository): 
+ 	removed not_null on the provider
+ 
+ 	* db.pl (Repository): 
+ 	added fix to get variable substitution on genex email
+ 
+ 	* DB/xml/Software.xml (Repository): 
+ 	now inherits from Parameterizable
+ 
+ 	* DB/xml/Protocol.xml (Repository): 
+ 	New protocol model from ESTap
+ 
+ 	* DB/xml/MeasuredBioAssay.xml (Repository): 
+ 	modified sw pkey
+ 	
+ 	* DB/xml/FeatureExtractionSoftware.xml (Repository): 
+ 	now inherits pkey from Parameterizable
+ 
+ 	* DB/xml/Array.xml (Repository): 
+ 	Spotter ==> Hardware
+ 
  2003-04-09  Jason E. Stewart  <ja...@op...>
+ 
+ 	* DB/scripts/fix-array-mas5.pl (Repository): 
+ 	need to use probe set names for feature names in short files
  
  	* INSTALL (Repository): 

Index: TODO
===================================================================
RCS file: /cvsroot/genex/genex-server/TODO,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** TODO	9 Apr 2003 20:41:55 -0000	1.21
--- TODO	16 Apr 2003 23:30:23 -0000	1.22
***************
*** 1,4 ****
--- 1,9 ----
  TODO
  =======
+ Wed Apr 16 14:57:39 MDT 2003
+ * Make a synonym table for DB table names and column names
+ * start removing all the unnecessary '%%FOO%%' flags and .in files now
+     that we can use $Bio::Genex::Config->{FOO} directly
+ 
  Mon Apr  7 10:20:59 MDT 2003
  * why is quantitationdimension and quantitationdimension_view in the

[Genex-cvs-commit] genex-server/Genex .cvsignore,1.8,1.9 ChangeLog,1.129,1.130

From: <jas...@us...> - 2003-04-16 23:30:01

Update of /cvsroot/genex/genex-server/Genex
In directory sc8-pr-cvs1:/tmp/cvs-serv20730/Genex

Modified Files:
	.cvsignore ChangeLog 
Log Message:
usual


Index: .cvsignore
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/.cvsignore,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** .cvsignore	14 Jan 2001 23:34:09 -0000	1.8
--- .cvsignore	16 Apr 2003 23:29:58 -0000	1.9
***************
*** 2,5 ****
--- 2,6 ----
  .CVS_MAIN
  .subst_cache
+ AM_Spots
  Config.pm
  Genex-0.27.tar.gz

Index: ChangeLog
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/ChangeLog,v
retrieving revision 1.129
retrieving revision 1.130
diff -C2 -d -r1.129 -r1.130
*** ChangeLog	9 Apr 2003 20:42:51 -0000	1.129
--- ChangeLog	16 Apr 2003 23:29:58 -0000	1.130
***************
*** 1,3 ****
--- 1,32 ----
+ 2003-04-16  Jason E. Stewart  <ja...@op...>
+ 
+ 	* XMLUtils/XMLUtils.pm.in (Repository): 
+ 	fixed badly broken algorithm for doing depth-first search on the
+ 	   inheritance graph in xml2sql()
+ 
+ 	* scripts/gendb.pl.in (Repository): 
+ 	commented out broken data insertion after protocol changes
+ 
+ 	* scripts/make_classes.pl (Repository): 
+ 	added new tables, and removed old ones from Protocol changes
+ 
+ 	* scripts/protocol-insert.pl.in (Repository): 
+ 	added ability to add info for a single protocol from the command line
+ 
+ 2003-04-15  Jason E. Stewart  <ja...@op...>
+ 
+ 	* scripts/contact-insert.pl.in (Repository): 
+ 	Updated to take all info from command line
+ 
+ 2003-04-10  Jason E. Stewart  <ja...@op...>
+ 
+ 	* scripts/mbad-insert.pl.in (Repository): 
+ 	users other than genex must use views for insertion
+ 
  2003-04-09  Jason E. Stewart  <ja...@op...>
+ 
+ 	* scripts/user-insert.pl.in (Repository): 
+ 	now ignores 'user already exists' errors from Pg
+ 	must create new connection on error
  
  	* scripts/mbad-insert.pl.in (Repository):

[Genex-cvs-commit] genex-server/Mason/workspace .cvsignore,1.3,1.4

From: <jas...@us...> - 2003-04-16 23:29:44

Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv20661/Mason/workspace

Modified Files:
	.cvsignore 
Log Message:
usual


Index: .cvsignore
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/.cvsignore,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** .cvsignore	25 Nov 2002 21:49:59 -0000	1.3
--- .cvsignore	16 Apr 2003 23:29:41 -0000	1.4
***************
*** 5,8 ****
--- 5,9 ----
  autohandler
  bioassay.html
+ contact-insert.html
  data-loader.html
  data-sources.html

[Genex-cvs-commit] genex-server/Genex/XMLUtils XMLUtils.pm.in,1.30,1.31

From: <jas...@us...> - 2003-04-16 23:29:29

Update of /cvsroot/genex/genex-server/Genex/XMLUtils
In directory sc8-pr-cvs1:/tmp/cvs-serv20560/Genex/XMLUtils

Modified Files:
	XMLUtils.pm.in 
Log Message:
* XMLUtils/XMLUtils.pm.in (Repository): 
fixed badly broken algorithm for doing depth-first search on the
   inheritance graph in xml2sql()



Index: XMLUtils.pm.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/XMLUtils/XMLUtils.pm.in,v
retrieving revision 1.30
retrieving revision 1.31
diff -C2 -d -r1.30 -r1.31
*** XMLUtils.pm.in	12 Jan 2003 22:41:12 -0000	1.30
--- XMLUtils.pm.in	16 Apr 2003 23:29:26 -0000	1.31
***************
*** 386,392 ****
    foreach my $file (@inheritance_tmp) {
      push(@inheritance_set,$docs{$file});
!     foreach my $dep_file (@{$depends{uc($file)}}) {
!       push(@inheritance_set,$docs{$dep_file});
!     }
    }
  
--- 386,393 ----
    foreach my $file (@inheritance_tmp) {
      push(@inheritance_set,$docs{$file});
! 
!     # add any dependent tables to the queue
!     push(@inheritance_tmp,@{$depends{uc($file)}})
!       if exists $depends{uc($file)};
    }

[Genex-cvs-commit] genex-server/Mason/workspace data-loader.html.in,1.3,1.4

From: <jas...@us...> - 2003-04-16 23:28:11

Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv20104/Mason/workspace

Modified Files:
	data-loader.html.in 
Log Message:
typo


Index: data-loader.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/data-loader.html.in,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** data-loader.html.in	24 Nov 2002 01:59:15 -0000	1.3
--- data-loader.html.in	16 Apr 2003 23:28:04 -0000	1.4
***************
*** 10,14 ****
  % } else {
  	<h2>Read Group</h2>
! 	<p>Choose the <b>read group</b> that will be givne to create
  	the array design files that you load.</p>
   	<table bgcolor="#D8E4F7" border="1" cols="1">
--- 10,14 ----
  % } else {
  	<h2>Read Group</h2>
! 	<p>Choose the <b>read group</b> that will be given to create
  	the array design files that you load.</p>
   	<table bgcolor="#D8E4F7" border="1" cols="1">
***************
*** 31,35 ****
  
  	<h2>Write Group</h2>
! 	<p>Choose the <b>write group</b> that will be givne to create
  	the array design files that you load.</p>
   	<table bgcolor="#D8E4F7" border="1" cols="1">
--- 31,35 ----
  
  	<h2>Write Group</h2>
! 	<p>Choose the <b>write group</b> that will be given to create
  	the array design files that you load.</p>
   	<table bgcolor="#D8E4F7" border="1" cols="1">

[Genex-cvs-commit] genex-server/Genex/t Array.t,1.2,1.3 FeatureExtractionSoftware.t,1.3,1.4 Protocol.t,1.7,1.8 Sample.t,1.9,1.10 Software.t,1.8,1.9

From: <jas...@us...> - 2003-04-16 23:27:43

Update of /cvsroot/genex/genex-server/Genex/t
In directory sc8-pr-cvs1:/tmp/cvs-serv19835/Genex/t

Modified Files:
	Array.t FeatureExtractionSoftware.t Protocol.t Sample.t 
	Software.t 
Log Message:
new column names from protocol changes


Index: Array.t
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/Array.t,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** Array.t	7 Nov 2002 14:49:32 -0000	1.2
--- Array.t	16 Apr 2003 23:27:40 -0000	1.3
***************
*** 56,62 ****
  result ($obj->ad_fk() == 555);
  
! # testing the sptr_fk attribute method
! $obj->sptr_fk(555);
! result ($obj->sptr_fk() == 555);
  
  # testing the sw_fk attribute method
--- 56,62 ----
  result ($obj->ad_fk() == 555);
  
! # testing the spotter_hw_fk attribute method
! $obj->spotter_hw_fk(555);
! result ($obj->spotter_hw_fk() == 555);
  
  # testing the sw_fk attribute method
***************
*** 140,146 ****
  result ($obj->sw_obj() == 555);
  
! # testing the sptr_obj attribute method
! $obj->sptr_obj(555);
! result ($obj->sptr_obj() == 555);
  
  # testing the provider_con_obj attribute method
--- 140,146 ----
  result ($obj->sw_obj() == 555);
  
! # testing the spotter_hw_obj attribute method
! $obj->spotter_hw_obj(555);
! result ($obj->spotter_hw_obj() == 555);
  
  # testing the provider_con_obj attribute method

Index: FeatureExtractionSoftware.t
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/FeatureExtractionSoftware.t,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** FeatureExtractionSoftware.t	23 Nov 2002 10:23:36 -0000	1.3
--- FeatureExtractionSoftware.t	16 Apr 2003 23:27:40 -0000	1.4
***************
*** 7,11 ****
  # (It may become useful if the test is moved to ./t subdirectory.)
  
! BEGIN { $| = 1; print "1..25\n"; }
  END {print "not ok 1\n" unless $loaded;}
  use Carp;
--- 7,11 ----
  # (It may become useful if the test is moved to ./t subdirectory.)
  
! BEGIN { $| = 1; print "1..27\n"; }
  END {print "not ok 1\n" unless $loaded;}
  use Carp;
***************
*** 77,81 ****
  
  # testing the pkey_name method
! result($obj->pkey_name() eq 'sw_pk');
  
  
--- 77,81 ----
  
  # testing the pkey_name method
! result($obj->pkey_name() eq 'param_pk');
  
  
***************
*** 138,141 ****
--- 138,147 ----
  # testing superclass Bio::Genex::Software
  result($obj->isa(q[Bio::Genex::Software]));
+ 
+ # testing superclass Bio::Genex::Parameterizable
+ result($obj->isa(q[Bio::Genex::Parameterizable]));
+ 
+ # testing superclass Bio::Genex::Identifiable
+ result($obj->isa(q[Bio::Genex::Identifiable]));
  
  # testing the column_names method

Index: Protocol.t
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/Protocol.t,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** Protocol.t	18 Sep 2002 20:45:49 -0000	1.7
--- Protocol.t	16 Apr 2003 23:27:40 -0000	1.8
***************
*** 7,11 ****
  # (It may become useful if the test is moved to ./t subdirectory.)
  
! BEGIN { $| = 1; print "1..37\n"; }
  END {print "not ok 1\n" unless $loaded;}
  use Carp;
--- 7,11 ----
  # (It may become useful if the test is moved to ./t subdirectory.)
  
! BEGIN { $| = 1; print "1..25\n"; }
  END {print "not ok 1\n" unless $loaded;}
  use Carp;
***************
*** 32,50 ****
  my $obj = Bio::Genex::Protocol->new();
  
! # testing the prt_pk attribute method
! $obj->prt_pk(555);
! result ($obj->prt_pk() == 555);
! 
! # testing the title attribute method
! $obj->title(555);
! result ($obj->title() == 555);
! 
! # testing the type attribute method
! $obj->type(555);
! result ($obj->type() == 555);
  
! # testing the text attribute method
! $obj->text(555);
! result ($obj->text() == 555);
  
  # testing the provider_con_fk attribute method
--- 32,42 ----
  my $obj = Bio::Genex::Protocol->new();
  
! # testing the protocol_pk attribute method
! $obj->protocol_pk(555);
! result ($obj->protocol_pk() == 555);
  
! # testing the URI attribute method
! $obj->URI(555);
! result ($obj->URI() == 555);
  
  # testing the provider_con_fk attribute method
***************
*** 52,66 ****
  result ($obj->provider_con_fk() == 555);
  
! # testing the ro_groupname attribute method
! $obj->ro_groupname(555);
! result ($obj->ro_groupname() == 555);
! 
! # testing the rw_groupname attribute method
! $obj->rw_groupname(555);
! result ($obj->rw_groupname() == 555);
  
! # testing the audit_fk attribute method
! $obj->audit_fk(555);
! result ($obj->audit_fk() == 555);
  
  # testing the provider_con_obj attribute method
--- 44,54 ----
  result ($obj->provider_con_fk() == 555);
  
! # testing the type attribute method
! $obj->type(555);
! result ($obj->type() == 555);
  
! # testing the description attribute method
! $obj->description(555);
! result ($obj->description() == 555);
  
  # testing the provider_con_obj attribute method
***************
*** 68,91 ****
  result ($obj->provider_con_obj() == 555);
  
- # testing the ro_groupname_obj attribute method
- $obj->ro_groupname_obj(555);
- result ($obj->ro_groupname_obj() == 555);
- 
- # testing the rw_groupname_obj attribute method
- $obj->rw_groupname_obj(555);
- result ($obj->rw_groupname_obj() == 555);
- 
- # testing the audit_obj attribute method
- $obj->audit_obj(555);
- result ($obj->audit_obj() == 555);
- 
- # testing the sampleprotocols_obj attribute method
- $obj->sampleprotocols_obj(555);
- result ($obj->sampleprotocols_obj() == 555);
- 
- # testing the sampleprotocols_fk attribute method
- $obj->sampleprotocols_fk(555);
- result ($obj->sampleprotocols_fk() == 555);
- 
  # testing the fetched attribute method
  $obj->fetched(555);
--- 56,59 ----
***************
*** 109,113 ****
  
  # testing the pkey_name method
! result($obj->pkey_name() eq 'prt_pk');
  
  
--- 77,81 ----
  
  # testing the pkey_name method
! result($obj->pkey_name() eq 'protocol_pk');
  
  
***************
*** 167,170 ****
--- 135,141 ----
                 ));
  }
+ 
+ # testing superclass Bio::Genex::Identifiable
+ result($obj->isa(q[Bio::Genex::Identifiable]));
  
  # testing the column_names method

Index: Sample.t
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/Sample.t,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** Sample.t	7 Nov 2002 14:49:32 -0000	1.9
--- Sample.t	16 Apr 2003 23:27:40 -0000	1.10
***************
*** 7,11 ****
  # (It may become useful if the test is moved to ./t subdirectory.)
  
! BEGIN { $| = 1; print "1..68\n"; }
  END {print "not ok 1\n" unless $loaded;}
  use Carp;
--- 7,11 ----
  # (It may become useful if the test is moved to ./t subdirectory.)
  
! BEGIN { $| = 1; print "1..64\n"; }
  END {print "not ok 1\n" unless $loaded;}
  use Carp;
***************
*** 191,202 ****
  $obj->samplelink_fk(555);
  result ($obj->samplelink_fk() == 555);
- 
- # testing the sampleprotocols_obj attribute method
- $obj->sampleprotocols_obj(555);
- result ($obj->sampleprotocols_obj() == 555);
- 
- # testing the sampleprotocols_fk attribute method
- $obj->sampleprotocols_fk(555);
- result ($obj->sampleprotocols_fk() == 555);
  
  # testing the fetched attribute method
--- 191,194 ----

Index: Software.t
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/Software.t,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** Software.t	18 Sep 2002 20:45:49 -0000	1.8
--- Software.t	16 Apr 2003 23:27:40 -0000	1.9
***************
*** 7,11 ****
  # (It may become useful if the test is moved to ./t subdirectory.)
  
! BEGIN { $| = 1; print "1..36\n"; }
  END {print "not ok 1\n" unless $loaded;}
  use Carp;
--- 7,11 ----
  # (It may become useful if the test is moved to ./t subdirectory.)
  
! BEGIN { $| = 1; print "1..27\n"; }
  END {print "not ok 1\n" unless $loaded;}
  use Carp;
***************
*** 48,59 ****
  my $obj = Bio::Genex::Software->new();
  
- # testing the sw_pk attribute method
- $obj->sw_pk(555);
- result ($obj->sw_pk() == 555);
- 
- # testing the name attribute method
- $obj->name(555);
- result ($obj->name() == 555);
- 
  # testing the version attribute method
  $obj->version(555);
--- 48,51 ----
***************
*** 68,99 ****
  result ($obj->producer_con_fk() == 555);
  
- # testing the ro_groupname attribute method
- $obj->ro_groupname(555);
- result ($obj->ro_groupname() == 555);
- 
- # testing the rw_groupname attribute method
- $obj->rw_groupname(555);
- result ($obj->rw_groupname() == 555);
- 
- # testing the audit_fk attribute method
- $obj->audit_fk(555);
- result ($obj->audit_fk() == 555);
- 
  # testing the producer_con_obj attribute method
  $obj->producer_con_obj(555);
  result ($obj->producer_con_obj() == 555);
  
- # testing the ro_groupname_obj attribute method
- $obj->ro_groupname_obj(555);
- result ($obj->ro_groupname_obj() == 555);
- 
- # testing the rw_groupname_obj attribute method
- $obj->rw_groupname_obj(555);
- result ($obj->rw_groupname_obj() == 555);
- 
- # testing the audit_obj attribute method
- $obj->audit_obj(555);
- result ($obj->audit_obj() == 555);
- 
  # testing the fetched attribute method
  $obj->fetched(555);
--- 60,67 ----
***************
*** 117,121 ****
  
  # testing the pkey_name method
! result($obj->pkey_name() eq 'sw_pk');
  
  
--- 85,89 ----
  
  # testing the pkey_name method
! result($obj->pkey_name() eq 'param_pk');
  
  
***************
*** 175,178 ****
--- 143,152 ----
                 ));
  }
+ 
+ # testing superclass Bio::Genex::Parameterizable
+ result($obj->isa(q[Bio::Genex::Parameterizable]));
+ 
+ # testing superclass Bio::Genex::Identifiable
+ result($obj->isa(q[Bio::Genex::Identifiable]));
  
  # testing the column_names method

[Genex-cvs-commit] genex-server/Genex/t Hardware.t,NONE,1.1 Parameter.t,NONE,1.1 ParameterValue.t,NONE,1.1 Parameterizable.t,NONE,1.1 Procedure.t,NONE,1.1 ProtocolApplication.t,NONE,1.1 ProtocolStep.t,NONE,1.1

From: <jas...@us...> - 2003-04-16 23:27:18

Update of /cvsroot/genex/genex-server/Genex/t
In directory sc8-pr-cvs1:/tmp/cvs-serv19684/Genex/t

Added Files:
	Hardware.t Parameter.t ParameterValue.t Parameterizable.t 
	Procedure.t ProtocolApplication.t ProtocolStep.t 
Log Message:
new tables, new tests


--- NEW FILE: Hardware.t ---
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl Hardware.t'

######################### We start with some black magic to print on failure.

# Change 1..1 below to 1..last_test_to_print .
# (It may become useful if the test is moved to ./t subdirectory.)

BEGIN { $| = 1; print "1..26\n"; }
END {print "not ok 1\n" unless $loaded;}
use Carp;
use lib 't';

# use blib;
use TestDB qw(result);
use vars qw($i $loaded);
use Bio::Genex::Hardware;
use Bio::Genex qw(is_object);
use Bio::Genex::Fkey qw(:FKEY);
$loaded = 1;
$i = 1;
result($i);

######################### End of black magic.

# Insert your test code below (better if it prints "ok 13"
# (correspondingly "not ok 13") depending on the success of chunk 13
# of the test code):



my $obj = Bio::Genex::Hardware->new();

# testing the model attribute method
$obj->model(555);
result ($obj->model() == 555);

# testing the make attribute method
$obj->make(555);
result ($obj->make() == 555);

# testing the type attribute method
$obj->type(555);
result ($obj->type() == 555);

# testing the model_description attribute method
$obj->model_description(555);
result ($obj->model_description() == 555);

# testing the producer_con_fk attribute method
$obj->producer_con_fk(555);
result ($obj->producer_con_fk() == 555);

# testing the producer_con_obj attribute method
$obj->producer_con_obj(555);
result ($obj->producer_con_obj() == 555);

# testing the fetched attribute method
$obj->fetched(555);
result ($obj->fetched() == 555);

# testing the fetch_all attribute method
$obj->fetch_all(555);
result ($obj->fetch_all() == 555);

# testing the fetched_attr attribute method
$obj->fetched_attr(555);
result ($obj->fetched_attr() == 555);

# testing the id attribute method
$obj->id(555);
result ($obj->id() == 555);

# testing the dbh attribute method
$obj->dbh(555);
result ($obj->dbh() == 555);

# testing the pkey_name method
result($obj->pkey_name() eq 'param_pk');


# testing the tablename method
result($obj->tablename() eq q[Hardware]);

# testing the table_type method
result($obj->table_type() eq q[DATA]);

# test $LIMIT
result(!defined $Bio::Genex::Hardware::LIMIT);

# test $USE_CACHE
result(defined $Bio::Genex::Hardware::USE_CACHE);

# testing the column2name method
result(ref($obj->column2name) eq 'HASH' and
       scalar keys %{$obj->column2name} >=
       scalar keys %{$Bio::Genex::Hardware::COLUMN2NAME});

# testing the name2column method
result(ref($obj->name2column) eq 'HASH' and
       scalar keys %{$obj->name2column} >=
       scalar keys %{$Bio::Genex::Hardware::NAME2COLUMN});

# testing the fkeys method
result(ref($obj->fkeys) eq 'HASH' and
       scalar keys %{$obj->fkeys} >=
       scalar keys %{$Bio::Genex::Hardware::FKEYS});

# testing the fkey_obj2raw method
result(ref($obj->fkey_obj2raw) eq 'HASH' and
       scalar keys %{$obj->fkey_obj2raw} >=
       scalar keys %{$Bio::Genex::Hardware::FKEY_OBJ2RAW});

# testing each fkey
foreach my $fkey (values %{$Bio::Genex::Hardware::FKEYS}) {
  result($fkey->isa('Bio::Genex::Fkey')
         && $fkey->fkey_name()
         && $fkey->pkey_name()
         && $fkey->table_name()
         && grep {$fkey->fkey_type eq $_}
               (FKEY_OTM,
                FKEY_OTM_LT,
                FKEY_OTM_LINK,
                FKEY_LINK,
                FKEY_OTO,
                FKEY_LT,
                FKEY_MTO,
                FKEY_OTM_OO,
                FKEY_OTM_LT_OO,
                FKEY_OTM_LINK_OO,
                FKEY_LINK_OO,
                FKEY_OTO_OO,
                FKEY_LT_OO,
                FKEY_MTO_OO,
               ));
}

# testing superclass Bio::Genex::Parameterizable
result($obj->isa(q[Bio::Genex::Parameterizable]));

# testing superclass Bio::Genex::Identifiable
result($obj->isa(q[Bio::Genex::Identifiable]));

# testing the column_names method
result(ref($obj->column_names) eq 'ARRAY' and
       scalar @{$obj->column_names} >=
       scalar @{$Bio::Genex::Hardware::COLUMN_NAMES});

# testing the unique_columns method
result(ref($obj->unique_columns) eq 'ARRAY' and
       scalar @{$obj->unique_columns} >=
       scalar @{$Bio::Genex::Hardware::UNIQUE_COLUMNS});


--- NEW FILE: Parameter.t ---
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl Parameter.t'

######################### We start with some black magic to print on failure.

# Change 1..1 below to 1..last_test_to_print .
# (It may become useful if the test is moved to ./t subdirectory.)

BEGIN { $| = 1; print "1..24\n"; }
END {print "not ok 1\n" unless $loaded;}
use Carp;
use lib 't';

# use blib;
use TestDB qw(result);
use vars qw($i $loaded);
use Bio::Genex::Parameter;
use Bio::Genex qw(is_object);
use Bio::Genex::Fkey qw(:FKEY);
$loaded = 1;
$i = 1;
result($i);

######################### End of black magic.

# Insert your test code below (better if it prints "ok 13"
# (correspondingly "not ok 13") depending on the success of chunk 13
# of the test code):



my $obj = Bio::Genex::Parameter->new();

# testing the default_value attribute method
$obj->default_value(555);
result ($obj->default_value() == 555);

# testing the parameter_pk attribute method
$obj->parameter_pk(555);
result ($obj->parameter_pk() == 555);

# testing the type attribute method
$obj->type(555);
result ($obj->type() == 555);

# testing the proc_fk attribute method
$obj->proc_fk(555);
result ($obj->proc_fk() == 555);

# testing the proc_obj attribute method
$obj->proc_obj(555);
result ($obj->proc_obj() == 555);

# testing the fetched attribute method
$obj->fetched(555);
result ($obj->fetched() == 555);

# testing the fetch_all attribute method
$obj->fetch_all(555);
result ($obj->fetch_all() == 555);

# testing the fetched_attr attribute method
$obj->fetched_attr(555);
result ($obj->fetched_attr() == 555);

# testing the id attribute method
$obj->id(555);
result ($obj->id() == 555);

# testing the dbh attribute method
$obj->dbh(555);
result ($obj->dbh() == 555);

# testing the pkey_name method
result($obj->pkey_name() eq 'parameter_pk');


# testing the tablename method
result($obj->tablename() eq q[Parameter]);

# testing the table_type method
result($obj->table_type() eq q[DATA]);

# test $LIMIT
result(!defined $Bio::Genex::Parameter::LIMIT);

# test $USE_CACHE
result(defined $Bio::Genex::Parameter::USE_CACHE);

# testing the column2name method
result(ref($obj->column2name) eq 'HASH' and
       scalar keys %{$obj->column2name} >=
       scalar keys %{$Bio::Genex::Parameter::COLUMN2NAME});

# testing the name2column method
result(ref($obj->name2column) eq 'HASH' and
       scalar keys %{$obj->name2column} >=
       scalar keys %{$Bio::Genex::Parameter::NAME2COLUMN});

# testing the fkeys method
result(ref($obj->fkeys) eq 'HASH' and
       scalar keys %{$obj->fkeys} >=
       scalar keys %{$Bio::Genex::Parameter::FKEYS});

# testing the fkey_obj2raw method
result(ref($obj->fkey_obj2raw) eq 'HASH' and
       scalar keys %{$obj->fkey_obj2raw} >=
       scalar keys %{$Bio::Genex::Parameter::FKEY_OBJ2RAW});

# testing each fkey
foreach my $fkey (values %{$Bio::Genex::Parameter::FKEYS}) {
  result($fkey->isa('Bio::Genex::Fkey')
         && $fkey->fkey_name()
         && $fkey->pkey_name()
         && $fkey->table_name()
         && grep {$fkey->fkey_type eq $_}
               (FKEY_OTM,
                FKEY_OTM_LT,
                FKEY_OTM_LINK,
                FKEY_LINK,
                FKEY_OTO,
                FKEY_LT,
                FKEY_MTO,
                FKEY_OTM_OO,
                FKEY_OTM_LT_OO,
                FKEY_OTM_LINK_OO,
                FKEY_LINK_OO,
                FKEY_OTO_OO,
                FKEY_LT_OO,
                FKEY_MTO_OO,
               ));
}

# testing superclass Bio::Genex::Identifiable
result($obj->isa(q[Bio::Genex::Identifiable]));

# testing the column_names method
result(ref($obj->column_names) eq 'ARRAY' and
       scalar @{$obj->column_names} >=
       scalar @{$Bio::Genex::Parameter::COLUMN_NAMES});

# testing the unique_columns method
result(ref($obj->unique_columns) eq 'ARRAY' and
       scalar @{$obj->unique_columns} >=
       scalar @{$Bio::Genex::Parameter::UNIQUE_COLUMNS});


--- NEW FILE: ParameterValue.t ---
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl ParameterValue.t'

######################### We start with some black magic to print on failure.

# Change 1..1 below to 1..last_test_to_print .
# (It may become useful if the test is moved to ./t subdirectory.)

BEGIN { $| = 1; print "1..25\n"; }
END {print "not ok 1\n" unless $loaded;}
use Carp;
use lib 't';

# use blib;
use TestDB qw(result);
use vars qw($i $loaded);
use Bio::Genex::ParameterValue;
use Bio::Genex qw(is_object);
use Bio::Genex::Fkey qw(:FKEY);
$loaded = 1;
$i = 1;
result($i);

######################### End of black magic.

# Insert your test code below (better if it prints "ok 13"
# (correspondingly "not ok 13") depending on the success of chunk 13
# of the test code):



my $obj = Bio::Genex::ParameterValue->new();

# testing the param_value_pk attribute method
$obj->param_value_pk(555);
result ($obj->param_value_pk() == 555);

# testing the value attribute method
$obj->value(555);
result ($obj->value() == 555);

# testing the proto_step_fk attribute method
$obj->proto_step_fk(555);
result ($obj->proto_step_fk() == 555);

# testing the parameter_fk attribute method
$obj->parameter_fk(555);
result ($obj->parameter_fk() == 555);

# testing the proto_step_obj attribute method
$obj->proto_step_obj(555);
result ($obj->proto_step_obj() == 555);

# testing the proto_step_obj attribute method
$obj->proto_step_obj(555);
result ($obj->proto_step_obj() == 555);

# testing the fetched attribute method
$obj->fetched(555);
result ($obj->fetched() == 555);

# testing the fetch_all attribute method
$obj->fetch_all(555);
result ($obj->fetch_all() == 555);

# testing the fetched_attr attribute method
$obj->fetched_attr(555);
result ($obj->fetched_attr() == 555);

# testing the id attribute method
$obj->id(555);
result ($obj->id() == 555);

# testing the dbh attribute method
$obj->dbh(555);
result ($obj->dbh() == 555);

# testing the pkey_name method
result($obj->pkey_name() eq 'param_value_pk');


# testing the tablename method
result($obj->tablename() eq q[ParameterValue]);

# testing the table_type method
result($obj->table_type() eq q[DATA]);

# test $LIMIT
result(!defined $Bio::Genex::ParameterValue::LIMIT);

# test $USE_CACHE
result(defined $Bio::Genex::ParameterValue::USE_CACHE);

# testing the column2name method
result(ref($obj->column2name) eq 'HASH' and
       scalar keys %{$obj->column2name} >=
       scalar keys %{$Bio::Genex::ParameterValue::COLUMN2NAME});

# testing the name2column method
result(ref($obj->name2column) eq 'HASH' and
       scalar keys %{$obj->name2column} >=
       scalar keys %{$Bio::Genex::ParameterValue::NAME2COLUMN});

# testing the fkeys method
result(ref($obj->fkeys) eq 'HASH' and
       scalar keys %{$obj->fkeys} >=
       scalar keys %{$Bio::Genex::ParameterValue::FKEYS});

# testing the fkey_obj2raw method
result(ref($obj->fkey_obj2raw) eq 'HASH' and
       scalar keys %{$obj->fkey_obj2raw} >=
       scalar keys %{$Bio::Genex::ParameterValue::FKEY_OBJ2RAW});

# testing each fkey
foreach my $fkey (values %{$Bio::Genex::ParameterValue::FKEYS}) {
  result($fkey->isa('Bio::Genex::Fkey')
         && $fkey->fkey_name()
         && $fkey->pkey_name()
         && $fkey->table_name()
         && grep {$fkey->fkey_type eq $_}
               (FKEY_OTM,
                FKEY_OTM_LT,
                FKEY_OTM_LINK,
                FKEY_LINK,
                FKEY_OTO,
                FKEY_LT,
                FKEY_MTO,
                FKEY_OTM_OO,
                FKEY_OTM_LT_OO,
                FKEY_OTM_LINK_OO,
                FKEY_LINK_OO,
                FKEY_OTO_OO,
                FKEY_LT_OO,
                FKEY_MTO_OO,
               ));
}

# testing the column_names method
result(ref($obj->column_names) eq 'ARRAY' and
       scalar @{$obj->column_names} >=
       scalar @{$Bio::Genex::ParameterValue::COLUMN_NAMES});

# testing the unique_columns method
result(ref($obj->unique_columns) eq 'ARRAY' and
       scalar @{$obj->unique_columns} >=
       scalar @{$Bio::Genex::ParameterValue::UNIQUE_COLUMNS});


--- NEW FILE: Parameterizable.t ---
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl Parameterizable.t'

######################### We start with some black magic to print on failure.

# Change 1..1 below to 1..last_test_to_print .
# (It may become useful if the test is moved to ./t subdirectory.)

BEGIN { $| = 1; print "1..23\n"; }
END {print "not ok 1\n" unless $loaded;}
use Carp;
use lib 't';

# use blib;
use TestDB qw(result);
use vars qw($i $loaded);
use Bio::Genex::Parameterizable;
use Bio::Genex qw(is_object);
use Bio::Genex::Fkey qw(:FKEY);
$loaded = 1;
$i = 1;
result($i);

######################### End of black magic.

# Insert your test code below (better if it prints "ok 13"
# (correspondingly "not ok 13") depending on the success of chunk 13
# of the test code):



my $obj = Bio::Genex::Parameterizable->new();

# testing the param_pk attribute method
$obj->param_pk(555);
result ($obj->param_pk() == 555);

# testing the URI attribute method
$obj->URI(555);
result ($obj->URI() == 555);

# testing the provider_con_fk attribute method
$obj->provider_con_fk(555);
result ($obj->provider_con_fk() == 555);

# testing the provider_con_obj attribute method
$obj->provider_con_obj(555);
result ($obj->provider_con_obj() == 555);

# testing the fetched attribute method
$obj->fetched(555);
result ($obj->fetched() == 555);

# testing the fetch_all attribute method
$obj->fetch_all(555);
result ($obj->fetch_all() == 555);

# testing the fetched_attr attribute method
$obj->fetched_attr(555);
result ($obj->fetched_attr() == 555);

# testing the id attribute method
$obj->id(555);
result ($obj->id() == 555);

# testing the dbh attribute method
$obj->dbh(555);
result ($obj->dbh() == 555);

# testing the pkey_name method
result($obj->pkey_name() eq 'param_pk');


# testing the tablename method
result($obj->tablename() eq q[Parameterizable]);

# testing the table_type method
result($obj->table_type() eq q[DATA]);

# test $LIMIT
result(!defined $Bio::Genex::Parameterizable::LIMIT);

# test $USE_CACHE
result(defined $Bio::Genex::Parameterizable::USE_CACHE);

# testing the column2name method
result(ref($obj->column2name) eq 'HASH' and
       scalar keys %{$obj->column2name} >=
       scalar keys %{$Bio::Genex::Parameterizable::COLUMN2NAME});

# testing the name2column method
result(ref($obj->name2column) eq 'HASH' and
       scalar keys %{$obj->name2column} >=
       scalar keys %{$Bio::Genex::Parameterizable::NAME2COLUMN});

# testing the fkeys method
result(ref($obj->fkeys) eq 'HASH' and
       scalar keys %{$obj->fkeys} >=
       scalar keys %{$Bio::Genex::Parameterizable::FKEYS});

# testing the fkey_obj2raw method
result(ref($obj->fkey_obj2raw) eq 'HASH' and
       scalar keys %{$obj->fkey_obj2raw} >=
       scalar keys %{$Bio::Genex::Parameterizable::FKEY_OBJ2RAW});

# testing each fkey
foreach my $fkey (values %{$Bio::Genex::Parameterizable::FKEYS}) {
  result($fkey->isa('Bio::Genex::Fkey')
         && $fkey->fkey_name()
         && $fkey->pkey_name()
         && $fkey->table_name()
         && grep {$fkey->fkey_type eq $_}
               (FKEY_OTM,
                FKEY_OTM_LT,
                FKEY_OTM_LINK,
                FKEY_LINK,
                FKEY_OTO,
                FKEY_LT,
                FKEY_MTO,
                FKEY_OTM_OO,
                FKEY_OTM_LT_OO,
                FKEY_OTM_LINK_OO,
                FKEY_LINK_OO,
                FKEY_OTO_OO,
                FKEY_LT_OO,
                FKEY_MTO_OO,
               ));
}

# testing superclass Bio::Genex::Identifiable
result($obj->isa(q[Bio::Genex::Identifiable]));

# testing the column_names method
result(ref($obj->column_names) eq 'ARRAY' and
       scalar @{$obj->column_names} >=
       scalar @{$Bio::Genex::Parameterizable::COLUMN_NAMES});

# testing the unique_columns method
result(ref($obj->unique_columns) eq 'ARRAY' and
       scalar @{$obj->unique_columns} >=
       scalar @{$Bio::Genex::Parameterizable::UNIQUE_COLUMNS});


--- NEW FILE: Procedure.t ---
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl Procedure.t'

######################### We start with some black magic to print on failure.

# Change 1..1 below to 1..last_test_to_print .
# (It may become useful if the test is moved to ./t subdirectory.)

BEGIN { $| = 1; print "1..21\n"; }
END {print "not ok 1\n" unless $loaded;}
use Carp;
use lib 't';

# use blib;
use TestDB qw(result);
use vars qw($i $loaded);
use Bio::Genex::Procedure;
use Bio::Genex qw(is_object);
use Bio::Genex::Fkey qw(:FKEY);
$loaded = 1;
$i = 1;
result($i);

######################### End of black magic.

# Insert your test code below (better if it prints "ok 13"
# (correspondingly "not ok 13") depending on the success of chunk 13
# of the test code):



my $obj = Bio::Genex::Procedure->new();

# testing the proc_pk attribute method
$obj->proc_pk(555);
result ($obj->proc_pk() == 555);

# testing the type attribute method
$obj->type(555);
result ($obj->type() == 555);

# testing the description attribute method
$obj->description(555);
result ($obj->description() == 555);

# testing the fetched attribute method
$obj->fetched(555);
result ($obj->fetched() == 555);

# testing the fetch_all attribute method
$obj->fetch_all(555);
result ($obj->fetch_all() == 555);

# testing the fetched_attr attribute method
$obj->fetched_attr(555);
result ($obj->fetched_attr() == 555);

# testing the id attribute method
$obj->id(555);
result ($obj->id() == 555);

# testing the dbh attribute method
$obj->dbh(555);
result ($obj->dbh() == 555);

# testing the pkey_name method
result($obj->pkey_name() eq 'proc_pk');


# testing the tablename method
result($obj->tablename() eq q[Procedure]);

# testing the table_type method
result($obj->table_type() eq q[DATA]);

# test $LIMIT
result(!defined $Bio::Genex::Procedure::LIMIT);

# test $USE_CACHE
result(defined $Bio::Genex::Procedure::USE_CACHE);

# testing the column2name method
result(ref($obj->column2name) eq 'HASH' and
       scalar keys %{$obj->column2name} >=
       scalar keys %{$Bio::Genex::Procedure::COLUMN2NAME});

# testing the name2column method
result(ref($obj->name2column) eq 'HASH' and
       scalar keys %{$obj->name2column} >=
       scalar keys %{$Bio::Genex::Procedure::NAME2COLUMN});

# testing the fkeys method
result(ref($obj->fkeys) eq 'HASH' and
       scalar keys %{$obj->fkeys} >=
       scalar keys %{$Bio::Genex::Procedure::FKEYS});

# testing the fkey_obj2raw method
result(ref($obj->fkey_obj2raw) eq 'HASH' and
       scalar keys %{$obj->fkey_obj2raw} >=
       scalar keys %{$Bio::Genex::Procedure::FKEY_OBJ2RAW});

# testing each fkey
foreach my $fkey (values %{$Bio::Genex::Procedure::FKEYS}) {
  result($fkey->isa('Bio::Genex::Fkey')
         && $fkey->fkey_name()
         && $fkey->pkey_name()
         && $fkey->table_name()
         && grep {$fkey->fkey_type eq $_}
               (FKEY_OTM,
                FKEY_OTM_LT,
                FKEY_OTM_LINK,
                FKEY_LINK,
                FKEY_OTO,
                FKEY_LT,
                FKEY_MTO,
                FKEY_OTM_OO,
                FKEY_OTM_LT_OO,
                FKEY_OTM_LINK_OO,
                FKEY_LINK_OO,
                FKEY_OTO_OO,
                FKEY_LT_OO,
                FKEY_MTO_OO,
               ));
}

# testing superclass Bio::Genex::Identifiable
result($obj->isa(q[Bio::Genex::Identifiable]));

# testing the column_names method
result(ref($obj->column_names) eq 'ARRAY' and
       scalar @{$obj->column_names} >=
       scalar @{$Bio::Genex::Procedure::COLUMN_NAMES});

# testing the unique_columns method
result(ref($obj->unique_columns) eq 'ARRAY' and
       scalar @{$obj->unique_columns} >=
       scalar @{$Bio::Genex::Procedure::UNIQUE_COLUMNS});


--- NEW FILE: ProtocolApplication.t ---
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl ProtocolApplication.t'

######################### We start with some black magic to print on failure.

# Change 1..1 below to 1..last_test_to_print .
# (It may become useful if the test is moved to ./t subdirectory.)

BEGIN { $| = 1; print "1..26\n"; }
END {print "not ok 1\n" unless $loaded;}
use Carp;
use lib 't';

# use blib;
use TestDB qw(result);
use vars qw($i $loaded);
use Bio::Genex::ProtocolApplication;
use Bio::Genex qw(is_object);
use Bio::Genex::Fkey qw(:FKEY);
$loaded = 1;
$i = 1;
result($i);

######################### End of black magic.

# Insert your test code below (better if it prints "ok 13"
# (correspondingly "not ok 13") depending on the success of chunk 13
# of the test code):



my $obj = Bio::Genex::ProtocolApplication->new();

# testing the proto_app_pk attribute method
$obj->proto_app_pk(555);
result ($obj->proto_app_pk() == 555);

# testing the activity_date attribute method
$obj->activity_date(555);
result ($obj->activity_date() == 555);

# testing the performer_con_fk attribute method
$obj->performer_con_fk(555);
result ($obj->performer_con_fk() == 555);

# testing the protocol_fk attribute method
$obj->protocol_fk(555);
result ($obj->protocol_fk() == 555);

# testing the performer_con_obj attribute method
$obj->performer_con_obj(555);
result ($obj->performer_con_obj() == 555);

# testing the protocol_obj attribute method
$obj->protocol_obj(555);
result ($obj->protocol_obj() == 555);

# testing the fetched attribute method
$obj->fetched(555);
result ($obj->fetched() == 555);

# testing the fetch_all attribute method
$obj->fetch_all(555);
result ($obj->fetch_all() == 555);

# testing the fetched_attr attribute method
$obj->fetched_attr(555);
result ($obj->fetched_attr() == 555);

# testing the id attribute method
$obj->id(555);
result ($obj->id() == 555);

# testing the dbh attribute method
$obj->dbh(555);
result ($obj->dbh() == 555);

# testing the pkey_name method
result($obj->pkey_name() eq 'proto_app_pk');


# testing the tablename method
result($obj->tablename() eq q[ProtocolApplication]);

# testing the table_type method
result($obj->table_type() eq q[DATA]);

# test $LIMIT
result(!defined $Bio::Genex::ProtocolApplication::LIMIT);

# test $USE_CACHE
result(defined $Bio::Genex::ProtocolApplication::USE_CACHE);

# testing the column2name method
result(ref($obj->column2name) eq 'HASH' and
       scalar keys %{$obj->column2name} >=
       scalar keys %{$Bio::Genex::ProtocolApplication::COLUMN2NAME});

# testing the name2column method
result(ref($obj->name2column) eq 'HASH' and
       scalar keys %{$obj->name2column} >=
       scalar keys %{$Bio::Genex::ProtocolApplication::NAME2COLUMN});

# testing the fkeys method
result(ref($obj->fkeys) eq 'HASH' and
       scalar keys %{$obj->fkeys} >=
       scalar keys %{$Bio::Genex::ProtocolApplication::FKEYS});

# testing the fkey_obj2raw method
result(ref($obj->fkey_obj2raw) eq 'HASH' and
       scalar keys %{$obj->fkey_obj2raw} >=
       scalar keys %{$Bio::Genex::ProtocolApplication::FKEY_OBJ2RAW});

# testing each fkey
foreach my $fkey (values %{$Bio::Genex::ProtocolApplication::FKEYS}) {
  result($fkey->isa('Bio::Genex::Fkey')
         && $fkey->fkey_name()
         && $fkey->pkey_name()
         && $fkey->table_name()
         && grep {$fkey->fkey_type eq $_}
               (FKEY_OTM,
                FKEY_OTM_LT,
                FKEY_OTM_LINK,
                FKEY_LINK,
                FKEY_OTO,
                FKEY_LT,
                FKEY_MTO,
                FKEY_OTM_OO,
                FKEY_OTM_LT_OO,
                FKEY_OTM_LINK_OO,
                FKEY_LINK_OO,
                FKEY_OTO_OO,
                FKEY_LT_OO,
                FKEY_MTO_OO,
               ));
}

# testing superclass Bio::Genex::Identifiable
result($obj->isa(q[Bio::Genex::Identifiable]));

# testing the column_names method
result(ref($obj->column_names) eq 'ARRAY' and
       scalar @{$obj->column_names} >=
       scalar @{$Bio::Genex::ProtocolApplication::COLUMN_NAMES});

# testing the unique_columns method
result(ref($obj->unique_columns) eq 'ARRAY' and
       scalar @{$obj->unique_columns} >=
       scalar @{$Bio::Genex::ProtocolApplication::UNIQUE_COLUMNS});


--- NEW FILE: ProtocolStep.t ---
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl ProtocolStep.t'

######################### We start with some black magic to print on failure.

# Change 1..1 below to 1..last_test_to_print .
# (It may become useful if the test is moved to ./t subdirectory.)

BEGIN { $| = 1; print "1..25\n"; }
END {print "not ok 1\n" unless $loaded;}
use Carp;
use lib 't';

# use blib;
use TestDB qw(result);
use vars qw($i $loaded);
use Bio::Genex::ProtocolStep;
use Bio::Genex qw(is_object);
use Bio::Genex::Fkey qw(:FKEY);
$loaded = 1;
$i = 1;
result($i);

######################### End of black magic.

# Insert your test code below (better if it prints "ok 13"
# (correspondingly "not ok 13") depending on the success of chunk 13
# of the test code):



my $obj = Bio::Genex::ProtocolStep->new();

# testing the proto_step_pk attribute method
$obj->proto_step_pk(555);
result ($obj->proto_step_pk() == 555);

# testing the order attribute method
$obj->order(555);
result ($obj->order() == 555);

# testing the protocol_fk attribute method
$obj->protocol_fk(555);
result ($obj->protocol_fk() == 555);

# testing the proc_fk attribute method
$obj->proc_fk(555);
result ($obj->proc_fk() == 555);

# testing the protocol_obj attribute method
$obj->protocol_obj(555);
result ($obj->protocol_obj() == 555);

# testing the proc_obj attribute method
$obj->proc_obj(555);
result ($obj->proc_obj() == 555);

# testing the fetched attribute method
$obj->fetched(555);
result ($obj->fetched() == 555);

# testing the fetch_all attribute method
$obj->fetch_all(555);
result ($obj->fetch_all() == 555);

# testing the fetched_attr attribute method
$obj->fetched_attr(555);
result ($obj->fetched_attr() == 555);

# testing the id attribute method
$obj->id(555);
result ($obj->id() == 555);

# testing the dbh attribute method
$obj->dbh(555);
result ($obj->dbh() == 555);

# testing the pkey_name method
result($obj->pkey_name() eq 'proto_step_pk');


# testing the tablename method
result($obj->tablename() eq q[ProtocolStep]);

# testing the table_type method
result($obj->table_type() eq q[DATA]);

# test $LIMIT
result(!defined $Bio::Genex::ProtocolStep::LIMIT);

# test $USE_CACHE
result(defined $Bio::Genex::ProtocolStep::USE_CACHE);

# testing the column2name method
result(ref($obj->column2name) eq 'HASH' and
       scalar keys %{$obj->column2name} >=
       scalar keys %{$Bio::Genex::ProtocolStep::COLUMN2NAME});

# testing the name2column method
result(ref($obj->name2column) eq 'HASH' and
       scalar keys %{$obj->name2column} >=
       scalar keys %{$Bio::Genex::ProtocolStep::NAME2COLUMN});

# testing the fkeys method
result(ref($obj->fkeys) eq 'HASH' and
       scalar keys %{$obj->fkeys} >=
       scalar keys %{$Bio::Genex::ProtocolStep::FKEYS});

# testing the fkey_obj2raw method
result(ref($obj->fkey_obj2raw) eq 'HASH' and
       scalar keys %{$obj->fkey_obj2raw} >=
       scalar keys %{$Bio::Genex::ProtocolStep::FKEY_OBJ2RAW});

# testing each fkey
foreach my $fkey (values %{$Bio::Genex::ProtocolStep::FKEYS}) {
  result($fkey->isa('Bio::Genex::Fkey')
         && $fkey->fkey_name()
         && $fkey->pkey_name()
         && $fkey->table_name()
         && grep {$fkey->fkey_type eq $_}
               (FKEY_OTM,
                FKEY_OTM_LT,
                FKEY_OTM_LINK,
                FKEY_LINK,
                FKEY_OTO,
                FKEY_LT,
                FKEY_MTO,
                FKEY_OTM_OO,
                FKEY_OTM_LT_OO,
                FKEY_OTM_LINK_OO,
                FKEY_LINK_OO,
                FKEY_OTO_OO,
                FKEY_LT_OO,
                FKEY_MTO_OO,
               ));
}

# testing the column_names method
result(ref($obj->column_names) eq 'ARRAY' and
       scalar @{$obj->column_names} >=
       scalar @{$Bio::Genex::ProtocolStep::COLUMN_NAMES});

# testing the unique_columns method
result(ref($obj->unique_columns) eq 'ARRAY' and
       scalar @{$obj->unique_columns} >=
       scalar @{$Bio::Genex::ProtocolStep::UNIQUE_COLUMNS});

[Genex-cvs-commit] genex-server/Genex/t Chromosome-pre.xml,1.2,1.3 Contact-pre.xml,1.2,1.3 ContactType-pre.xml,1.2,1.3 GroupLink-pre.xml,1.2,1.3 GroupSec-pre.xml,1.2,1.3 Software-pre.xml,1.2,1.3 Species-pre.xml,1.1,1.2 Spotter-pre.xml,1.2,1.3 UserSec-pre.xml,1.2,1.3

From: <jas...@us...> - 2003-04-16 23:26:49

Update of /cvsroot/genex/genex-server/Genex/t
In directory sc8-pr-cvs1:/tmp/cvs-serv19530/Genex/t

Modified Files:
	Chromosome-pre.xml Contact-pre.xml ContactType-pre.xml 
	GroupLink-pre.xml GroupSec-pre.xml Software-pre.xml 
	Species-pre.xml Spotter-pre.xml UserSec-pre.xml 
Log Message:
Xerces is now picking up a bug in the DOCTYPE name that has existed
for a long time


Index: Chromosome-pre.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/Chromosome-pre.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** Chromosome-pre.xml	22 Mar 2002 06:19:33 -0000	1.2
--- Chromosome-pre.xml	16 Apr 2003 23:26:46 -0000	1.3
***************
*** 1,4 ****
  <?xml version="1.0" standalone="no"?>
! <!DOCTYPE table SYSTEM "../../DTD/tests.dtd">
  <tests>
  <test>
--- 1,4 ----
  <?xml version="1.0" standalone="no"?>
! <!DOCTYPE tests SYSTEM "../../DTD/tests.dtd">
  <tests>
  <test>

Index: Contact-pre.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/Contact-pre.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** Contact-pre.xml	22 Mar 2002 06:19:33 -0000	1.2
--- Contact-pre.xml	16 Apr 2003 23:26:46 -0000	1.3
***************
*** 1,4 ****
  <?xml version="1.0" standalone="no"?>
! <!DOCTYPE table SYSTEM "../../DTD/tests.dtd">
    <tests>
      <test>
--- 1,4 ----
  <?xml version="1.0" standalone="no"?>
! <!DOCTYPE tests SYSTEM "../../DTD/tests.dtd">
    <tests>
      <test>

Index: ContactType-pre.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/ContactType-pre.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** ContactType-pre.xml	22 Mar 2002 06:19:33 -0000	1.2
--- ContactType-pre.xml	16 Apr 2003 23:26:46 -0000	1.3
***************
*** 1,4 ****
  <?xml version="1.0" standalone="no"?>
! <!DOCTYPE table SYSTEM "../../DTD/tests.dtd">
    <tests>
      <test>
--- 1,4 ----
  <?xml version="1.0" standalone="no"?>
! <!DOCTYPE tests SYSTEM "../../DTD/tests.dtd">
    <tests>
      <test>

Index: GroupLink-pre.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/GroupLink-pre.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** GroupLink-pre.xml	22 Mar 2002 06:19:33 -0000	1.2
--- GroupLink-pre.xml	16 Apr 2003 23:26:46 -0000	1.3
***************
*** 1,4 ****
  <?xml version="1.0" standalone="no"?>
! <!DOCTYPE table SYSTEM "../../DTD/tests.dtd">
    <tests>
      <test>
--- 1,4 ----
  <?xml version="1.0" standalone="no"?>
! <!DOCTYPE tests SYSTEM "../../DTD/tests.dtd">
    <tests>
      <test>

Index: GroupSec-pre.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/GroupSec-pre.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** GroupSec-pre.xml	22 Mar 2002 06:19:33 -0000	1.2
--- GroupSec-pre.xml	16 Apr 2003 23:26:46 -0000	1.3
***************
*** 1,4 ****
  <?xml version="1.0" standalone="no"?>
! <!DOCTYPE table SYSTEM "../../DTD/tests.dtd">
    <tests>
      <test>
--- 1,4 ----
  <?xml version="1.0" standalone="no"?>
! <!DOCTYPE tests SYSTEM "../../DTD/tests.dtd">
    <tests>
      <test>

Index: Software-pre.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/Software-pre.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** Software-pre.xml	22 Mar 2002 06:19:33 -0000	1.2
--- Software-pre.xml	16 Apr 2003 23:26:46 -0000	1.3
***************
*** 1,4 ****
  <?xml version="1.0" standalone="no"?>
! <!DOCTYPE table SYSTEM "../../DTD/tests.dtd">
    <tests>
      <test>
--- 1,4 ----
  <?xml version="1.0" standalone="no"?>
! <!DOCTYPE tests SYSTEM "../../DTD/tests.dtd">
    <tests>
      <test>

Index: Species-pre.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/Species-pre.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** Species-pre.xml	22 Mar 2002 02:00:39 -0000	1.1
--- Species-pre.xml	16 Apr 2003 23:26:46 -0000	1.2
***************
*** 1,4 ****
  <?xml version="1.0" standalone="no"?>
! <!DOCTYPE table SYSTEM "../../DTD/tests.dtd">
    <tests>
      <test>
--- 1,4 ----
  <?xml version="1.0" standalone="no"?>
! <!DOCTYPE tests SYSTEM "../../DTD/tests.dtd">
    <tests>
      <test>

Index: Spotter-pre.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/Spotter-pre.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** Spotter-pre.xml	22 Mar 2002 06:19:33 -0000	1.2
--- Spotter-pre.xml	16 Apr 2003 23:26:46 -0000	1.3
***************
*** 1,4 ****
  <?xml version="1.0" standalone="no"?>
! <!DOCTYPE table SYSTEM "../../DTD/tests.dtd">
    <tests>
      <test>
--- 1,4 ----
  <?xml version="1.0" standalone="no"?>
! <!DOCTYPE tests SYSTEM "../../DTD/tests.dtd">
    <tests>
      <test>

Index: UserSec-pre.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/t/UserSec-pre.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** UserSec-pre.xml	22 Mar 2002 06:19:33 -0000	1.2
--- UserSec-pre.xml	16 Apr 2003 23:26:46 -0000	1.3
***************
*** 1,4 ****
  <?xml version="1.0" standalone="no"?>
! <!DOCTYPE table SYSTEM "../../DTD/tests.dtd">
    <tests>
      <test>
--- 1,4 ----
  <?xml version="1.0" standalone="no"?>
! <!DOCTYPE tests SYSTEM "../../DTD/tests.dtd">
    <tests>
      <test>

[Genex-cvs-commit] genex-server/Genex/scripts gendb.pl.in,1.9,1.10

From: <jas...@us...> - 2003-04-16 23:25:51

Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv19148/Genex/scripts

Modified Files:
	gendb.pl.in 
Log Message:
* scripts/gendb.pl.in (Repository): 
commented out broken data insertion after protocol changes



Index: gendb.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/gendb.pl.in,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** gendb.pl.in	24 Nov 2002 02:08:41 -0000	1.9
--- gendb.pl.in	16 Apr 2003 23:25:48 -0000	1.10
***************
*** 124,127 ****
--- 124,129 ----
  }
  
+ if (0) {
+ 
  unless (exists $OPTIONS{no_spotter}) {
    $cmd = "$SCRIPTS_DIR/spotter-insert.pl";
***************
*** 159,166 ****
  }
  
! unless (exists $OPTIONS{no_species}) {
!   $cmd = "$SCRIPTS_DIR/species-insert.pl";
!   my @params = ('--file'=>"$OPTIONS{dir}/DB/curated_data/species.xml");
!   print STDERR "Adding species ...\n";
    printf STDERR "\t$cmd %s\n", join(' ', @args, @params);
  
--- 161,168 ----
  }
  
! unless (exists $OPTIONS{no_protocols}) {
!   $cmd = "$SCRIPTS_DIR/protocol-insert.pl";
!   my @params = ('--file'=>"$OPTIONS{dir}/DB/curated_data/protocols.xml");
!   print STDERR "Adding protocols ...\n";
    printf STDERR "\t$cmd %s\n", join(' ', @args, @params);
  
***************
*** 171,178 ****
  }
  
! unless (exists $OPTIONS{no_protocols}) {
!   $cmd = "$SCRIPTS_DIR/protocol-insert.pl";
!   my @params = ('--file'=>"$OPTIONS{dir}/DB/curated_data/protocols.xml");
!   print STDERR "Adding protocols ...\n";
    printf STDERR "\t$cmd %s\n", join(' ', @args, @params);
  
--- 173,182 ----
  }
  
! }
! 
! unless (exists $OPTIONS{no_species}) {
!   $cmd = "$SCRIPTS_DIR/species-insert.pl";
!   my @params = ('--file'=>"$OPTIONS{dir}/DB/curated_data/species.xml");
!   print STDERR "Adding species ...\n";
    printf STDERR "\t$cmd %s\n", join(' ', @args, @params);
  
***************
*** 205,209 ****
  		'--data_end_regex=^End',
  	       );
!   print STDERR "Adding example QuantitationTypeDimension ...\n";
    printf STDERR "\t$cmd %s\n", join(' ', @args, @params);
  
--- 209,229 ----
  		'--data_end_regex=^End',
  	       );
!   print STDERR "Adding quantarray QuantitationTypeDimension ...\n";
!   printf STDERR "\t$cmd %s\n", join(' ', @args, @params);
! 
!   system($cmd, @args, @params);
!   die $! if $?;
! 
! 
!   $cmd = "$SCRIPTS_DIR/qtdim-insert.pl";
!   my @params = ("$OPTIONS{dir}/DB/curated_data/qtdim-mas5.xml",
! 		'--name=MicroArraySuite',
! 		'--version=5.0',
! 		'--feat="0"',
! 		'--data_start_regex1=^Expression\\s+Analysis',
! 		'--data_start_regex2=^\\tAnalysis',
! 		'--data_end_regex=^$', #'
! 	       );
!   print STDERR "Adding mas5 QuantitationTypeDimension ...\n";
    printf STDERR "\t$cmd %s\n", join(' ', @args, @params);

[Genex-cvs-commit] genex-server/Genex/scripts make_classes.pl,1.28,1.29

From: <jas...@us...> - 2003-04-16 23:25:22

Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv18924/Genex/scripts

Modified Files:
	make_classes.pl 
Log Message:
* scripts/make_classes.pl (Repository): 
added new tables, and removed old ones from Protocol changes



Index: make_classes.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/make_classes.pl,v
retrieving revision 1.28
retrieving revision 1.29
diff -C2 -d -r1.28 -r1.29
*** make_classes.pl	23 Nov 2002 10:24:55 -0000	1.28
--- make_classes.pl	16 Apr 2003 23:25:19 -0000	1.29
***************
*** 76,83 ****
  		  'SF_ExternalDBLink']},
         {target=>'Sample',
! 	support=>['SampleProtocols',
! 		  'SampleLink']},
!        {target=>'Protocol',
! 	support=>['SampleProtocols']},
         {target=>'GroupSec',
  	support=>['GroupLink']},
--- 76,80 ----
  		  'SF_ExternalDBLink']},
         {target=>'Sample',
! 	support=>['SampleLink']},
         {target=>'GroupSec',
  	support=>['GroupLink']},
***************
*** 96,99 ****
--- 93,104 ----
         # simple classes with no supporting tables
         {target=>'Array'},
+        {target=>'Parameter'},
+        {target=>'ParameterValue'},
+        {target=>'ProtocolStep'},
+        {target=>'Protocol'},
+        {target=>'ProtocolApplication'},
+        {target=>'Procedure'},
+        {target=>'Parameterizable'},
+        {target=>'Hardware'},
         {target=>'MeasuredBioAssay'},
         {target=>'Channel'},
***************
*** 108,113 ****
         {target=>'Citation'},
         {target=>'Software'},
!        {target=>'Scanner'},
!        {target=>'Spotter'},
         {target=>'ExternalDatabase'},
         {target=>'BlastHits'},
--- 113,118 ----
         {target=>'Citation'},
         {target=>'Software'},
! #       {target=>'Scanner'},
! #       {target=>'Spotter'},
         {target=>'ExternalDatabase'},
         {target=>'BlastHits'},
***************
*** 120,124 ****
         {target=>'HotSpots',linking=>1},
         {target=>'Treatment_AMs',linking=>1},
!        {target=>'SampleProtocols',linking=>1},
         {target=>'SF_ExternalDBLink',linking=>1},
         {target=>'TL_FactorValues',linking=>1},
--- 125,129 ----
         {target=>'HotSpots',linking=>1},
         {target=>'Treatment_AMs',linking=>1},
! #        {target=>'SampleProtocols',linking=>1},
         {target=>'SF_ExternalDBLink',linking=>1},
         {target=>'TL_FactorValues',linking=>1},
***************
*** 126,130 ****
  
         # view classes
!        {target=>'Provider'},
         
         # controlled vocabular classes
--- 131,135 ----
  
         # view classes
! #       {target=>'Provider'},
         
         # controlled vocabular classes

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