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From: <jas...@us...> - 2002-10-20 14:43:53
|
Update of /cvsroot/genex/genex-server/Genex/Contact
In directory usw-pr-cvs1:/tmp/cvs-serv11680/Genex/Contact
Modified Files:
Contact.pm
Log Message:
new
Index: Contact.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Contact/Contact.pm,v
retrieving revision 1.33
retrieving revision 1.34
diff -C2 -d -r1.33 -r1.34
*** Contact.pm 15 Oct 2002 14:54:07 -0000 1.33
--- Contact.pm 20 Oct 2002 14:43:19 -0000 1.34
***************
*** 846,853 ****
list context: a list of Bio::Genex::Contact instances
- B<WARNING>: Passing incorrect id values to C<get_objects()> will cause
- a warning from C<Bio::Genex::Contact::initialize()>. Objects will be
- created for other correct id values in the list.
-
=cut
--- 846,849 ----
|
|
From: <jas...@us...> - 2002-10-20 14:43:53
|
Update of /cvsroot/genex/genex-server/Genex/BlastHits
In directory usw-pr-cvs1:/tmp/cvs-serv11680/Genex/BlastHits
Modified Files:
BlastHits.pm
Log Message:
new
Index: BlastHits.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/BlastHits/BlastHits.pm,v
retrieving revision 1.27
retrieving revision 1.28
diff -C2 -d -r1.27 -r1.28
*** BlastHits.pm 15 Oct 2002 14:54:07 -0000 1.27
--- BlastHits.pm 20 Oct 2002 14:43:19 -0000 1.28
***************
*** 754,761 ****
list context: a list of Bio::Genex::BlastHits instances
- B<WARNING>: Passing incorrect id values to C<get_objects()> will cause
- a warning from C<Bio::Genex::BlastHits::initialize()>. Objects will be
- created for other correct id values in the list.
-
=cut
--- 754,757 ----
|
|
From: <jas...@us...> - 2002-10-20 14:43:53
|
Update of /cvsroot/genex/genex-server/Genex/Citation
In directory usw-pr-cvs1:/tmp/cvs-serv11680/Genex/Citation
Modified Files:
Citation.pm
Log Message:
new
Index: Citation.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Citation/Citation.pm,v
retrieving revision 1.33
retrieving revision 1.34
diff -C2 -d -r1.33 -r1.34
*** Citation.pm 15 Oct 2002 14:54:07 -0000 1.33
--- Citation.pm 20 Oct 2002 14:43:19 -0000 1.34
***************
*** 803,810 ****
list context: a list of Bio::Genex::Citation instances
- B<WARNING>: Passing incorrect id values to C<get_objects()> will cause
- a warning from C<Bio::Genex::Citation::initialize()>. Objects will be
- created for other correct id values in the list.
-
=cut
--- 803,806 ----
|
|
From: <jas...@us...> - 2002-10-20 14:43:53
|
Update of /cvsroot/genex/genex-server/Genex/Chromosome
In directory usw-pr-cvs1:/tmp/cvs-serv11680/Genex/Chromosome
Modified Files:
Chromosome.pm
Log Message:
new
Index: Chromosome.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Chromosome/Chromosome.pm,v
retrieving revision 1.37
retrieving revision 1.38
diff -C2 -d -r1.37 -r1.38
*** Chromosome.pm 15 Oct 2002 14:54:07 -0000 1.37
--- Chromosome.pm 20 Oct 2002 14:43:19 -0000 1.38
***************
*** 769,776 ****
list context: a list of Bio::Genex::Chromosome instances
- B<WARNING>: Passing incorrect id values to C<get_objects()> will cause
- a warning from C<Bio::Genex::Chromosome::initialize()>. Objects will be
- created for other correct id values in the list.
-
=cut
--- 769,772 ----
|
|
From: <jas...@us...> - 2002-10-20 14:43:53
|
Update of /cvsroot/genex/genex-server/Genex/Channel
In directory usw-pr-cvs1:/tmp/cvs-serv11680/Genex/Channel
Modified Files:
Channel.pm
Log Message:
new
Index: Channel.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Channel/Channel.pm,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** Channel.pm 15 Oct 2002 14:54:07 -0000 1.5
--- Channel.pm 20 Oct 2002 14:43:19 -0000 1.6
***************
*** 723,730 ****
list context: a list of Bio::Genex::Channel instances
- B<WARNING>: Passing incorrect id values to C<get_objects()> will cause
- a warning from C<Bio::Genex::Channel::initialize()>. Objects will be
- created for other correct id values in the list.
-
=cut
--- 723,726 ----
|
|
From: <jas...@us...> - 2002-10-20 14:43:52
|
Update of /cvsroot/genex/genex-server/Genex/Audit
In directory usw-pr-cvs1:/tmp/cvs-serv11680/Genex/Audit
Modified Files:
Audit.pm
Log Message:
new
Index: Audit.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Audit/Audit.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** Audit.pm 15 Oct 2002 14:54:07 -0000 1.3
--- Audit.pm 20 Oct 2002 14:43:19 -0000 1.4
***************
*** 749,756 ****
list context: a list of Bio::Genex::Audit instances
- B<WARNING>: Passing incorrect id values to C<get_objects()> will cause
- a warning from C<Bio::Genex::Audit::initialize()>. Objects will be
- created for other correct id values in the list.
-
=cut
--- 749,752 ----
|
|
From: <jas...@us...> - 2002-10-20 14:43:52
|
Update of /cvsroot/genex/genex-server/Genex/ArrayDesign
In directory usw-pr-cvs1:/tmp/cvs-serv11680/Genex/ArrayDesign
Modified Files:
ArrayDesign.pm
Log Message:
new
Index: ArrayDesign.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/ArrayDesign/ArrayDesign.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** ArrayDesign.pm 15 Oct 2002 14:54:06 -0000 1.3
--- ArrayDesign.pm 20 Oct 2002 14:43:18 -0000 1.4
***************
*** 868,875 ****
list context: a list of Bio::Genex::ArrayDesign instances
- B<WARNING>: Passing incorrect id values to C<get_objects()> will cause
- a warning from C<Bio::Genex::ArrayDesign::initialize()>. Objects will be
- created for other correct id values in the list.
-
=cut
--- 868,871 ----
|
|
From: <jas...@us...> - 2002-10-20 14:43:51
|
Update of /cvsroot/genex/genex-server/Genex/AM_SuspectSpots In directory usw-pr-cvs1:/tmp/cvs-serv11680/Genex/AM_SuspectSpots Modified Files: AM_SuspectSpots.pm Log Message: new Index: AM_SuspectSpots.pm =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/AM_SuspectSpots/AM_SuspectSpots.pm,v retrieving revision 1.26 retrieving revision 1.27 diff -C2 -d -r1.26 -r1.27 |
|
From: <jas...@us...> - 2002-10-20 14:43:51
|
Update of /cvsroot/genex/genex-server/Genex/AM_Spots
In directory usw-pr-cvs1:/tmp/cvs-serv11680/Genex/AM_Spots
Modified Files:
AM_Spots.pm
Log Message:
new
Index: AM_Spots.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/AM_Spots/AM_Spots.pm,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** AM_Spots.pm 15 Oct 2002 14:54:06 -0000 1.26
--- AM_Spots.pm 20 Oct 2002 14:43:18 -0000 1.27
***************
*** 763,770 ****
list context: a list of Bio::Genex::AM_Spots instances
- B<WARNING>: Passing incorrect id values to C<get_objects()> will cause
- a warning from C<Bio::Genex::AM_Spots::initialize()>. Objects will be
- created for other correct id values in the list.
-
=cut
--- 763,766 ----
|
|
From: <jas...@us...> - 2002-10-20 14:43:51
|
Update of /cvsroot/genex/genex-server/Genex/AM_FactorValues In directory usw-pr-cvs1:/tmp/cvs-serv11680/Genex/AM_FactorValues Modified Files: AM_FactorValues.pm Log Message: new Index: AM_FactorValues.pm =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/AM_FactorValues/AM_FactorValues.pm,v retrieving revision 1.26 retrieving revision 1.27 diff -C2 -d -r1.26 -r1.27 |
|
From: <jas...@us...> - 2002-10-20 14:43:51
|
Update of /cvsroot/genex/genex-server/Genex/Array
In directory usw-pr-cvs1:/tmp/cvs-serv11680/Genex/Array
Modified Files:
Array.pm
Log Message:
new
Index: Array.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Array/Array.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** Array.pm 15 Oct 2002 14:54:06 -0000 1.3
--- Array.pm 20 Oct 2002 14:43:18 -0000 1.4
***************
*** 910,917 ****
list context: a list of Bio::Genex::Array instances
- B<WARNING>: Passing incorrect id values to C<get_objects()> will cause
- a warning from C<Bio::Genex::Array::initialize()>. Objects will be
- created for other correct id values in the list.
-
=cut
--- 910,913 ----
|
|
From: <jas...@us...> - 2002-10-20 14:11:31
|
Update of /cvsroot/genex/genex-server/CyberT-dist In directory usw-pr-cvs1:/tmp/cvs-serv29046/CyberT-dist Modified Files: CyberTDB-6.2.C+E.pl.in CyberTDB-6.2.paired.pl.in CyberTDB-7.0.pl.in Log Message: changed LOCAL_BIN to GENEX_BIN_DIR Index: CyberTDB-6.2.C+E.pl.in =================================================================== RCS file: /cvsroot/genex/genex-server/CyberT-dist/CyberTDB-6.2.C+E.pl.in,v retrieving revision 1.13 retrieving revision 1.14 diff -C2 -d -r1.13 -r1.14 *** CyberTDB-6.2.C+E.pl.in 1 Apr 2001 03:49:19 -0000 1.13 --- CyberTDB-6.2.C+E.pl.in 20 Oct 2002 14:11:23 -0000 1.14 *************** *** 68,72 **** my $R = "%%R%%"; my $MPAGE = "%%MPAGE%%"; ! my $MUNGE4R = "%%LOCAL_BIN%%/munge4R.pl"; my $keycol = 17; # which var are we trying to sort on? # of Labels+C+E + 23 = p_raw (w/ Bayes) --- 68,72 ---- my $R = "%%R%%"; my $MPAGE = "%%MPAGE%%"; ! my $MUNGE4R = "%%GENEX_BIN_DIR%%/munge4R.pl"; my $keycol = 17; # which var are we trying to sort on? # of Labels+C+E + 23 = p_raw (w/ Bayes) Index: CyberTDB-6.2.paired.pl.in =================================================================== RCS file: /cvsroot/genex/genex-server/CyberT-dist/CyberTDB-6.2.paired.pl.in,v retrieving revision 1.13 retrieving revision 1.14 diff -C2 -d -r1.13 -r1.14 *** CyberTDB-6.2.paired.pl.in 1 Apr 2001 03:49:19 -0000 1.13 --- CyberTDB-6.2.paired.pl.in 20 Oct 2002 14:11:24 -0000 1.14 *************** *** 119,123 **** my $R = "%%R%%"; my $MPAGE = "%%MPAGE%%"; ! my $MUNGE4R = "%%LOCAL_BIN%%/munge4R.pl"; my $keycol = 4; # which var are you trying to sort on? # of ratios +4 = t stat (w/ Bayes) --- 119,123 ---- my $R = "%%R%%"; my $MPAGE = "%%MPAGE%%"; ! my $MUNGE4R = "%%GENEX_BIN_DIR%%/munge4R.pl"; my $keycol = 4; # which var are you trying to sort on? # of ratios +4 = t stat (w/ Bayes) Index: CyberTDB-7.0.pl.in =================================================================== RCS file: /cvsroot/genex/genex-server/CyberT-dist/CyberTDB-7.0.pl.in,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -d -r1.7 -r1.8 *** CyberTDB-7.0.pl.in 21 Nov 2001 01:32:59 -0000 1.7 --- CyberTDB-7.0.pl.in 20 Oct 2002 14:11:24 -0000 1.8 *************** *** 48,53 **** my $R = "%%R%% "; my $MPAGE = "%%MPAGE%% "; ! my $MUNGE4R = "%%LOCAL_BIN%%/munge4R.pl "; ! my $CYBERFILTER = "%%LOCAL_BIN%%/cyberfilter.pl "; my $VNCSERVER = "%%VNCSERVER%% "; --- 48,53 ---- my $R = "%%R%% "; my $MPAGE = "%%MPAGE%% "; ! my $MUNGE4R = "%%GENEX_BIN_DIR%%/munge4R.pl "; ! my $CYBERFILTER = "%%GENEX_BIN_DIR%%/cyberfilter.pl "; my $VNCSERVER = "%%VNCSERVER%% "; |
|
From: <jas...@us...> - 2002-10-20 14:04:00
|
Update of /cvsroot/genex/genex-server/DB/xml
In directory usw-pr-cvs1:/tmp/cvs-serv25024/DB/xml
Modified Files:
FeatureExtractionSoftware.xml
Log Message:
* DB/xml/FeatureExtractionSoftware.xml (Repository):
added the data matching regexes needed for the data loader
Index: FeatureExtractionSoftware.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/xml/FeatureExtractionSoftware.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** FeatureExtractionSoftware.xml 15 Oct 2002 14:48:04 -0000 1.1
--- FeatureExtractionSoftware.xml 20 Oct 2002 14:03:57 -0000 1.2
***************
*** 16,19 ****
--- 16,34 ----
comment="This string documents what columns in the data are used
to constructor the feature identifier"/>
+ <column name="data_start_regex1"
+ full_name="Data Start Regular Expression 1"
+ type="varchar(128)"
+ comment="This string locates the start of the data block in the
+ input file"/>
+ <column name="data_start_regex2"
+ full_name="Data Start Regular Expression 2"
+ type="varchar(128)"
+ comment="This string locates the start of the data block in the
+ input file if the first regex alone is not sufficient"/>
+ <column name="data_end_regex"
+ full_name="Data End Regular Expression"
+ type="varchar(128)"
+ comment="This string locates the end of the data block in the
+ input file."/>
<column name="qd_fk"
full_name="Quantitation Type Dimension"
|
|
From: <jas...@us...> - 2002-10-20 14:03:07
|
Update of /cvsroot/genex/genex-server/DB/xml
In directory usw-pr-cvs1:/tmp/cvs-serv24574/DB/xml
Modified Files:
ExperimentSet.xml
Log Message:
* DB/xml/ExperimentSet.xml (Repository):
renamed submission_date -> creation_date
Index: ExperimentSet.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/xml/ExperimentSet.xml,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** ExperimentSet.xml 29 Aug 2002 13:21:09 -0000 1.5
--- ExperimentSet.xml 20 Oct 2002 14:03:05 -0000 1.6
***************
*** 90,98 ****
type="datetime"
comment=""/>
! <column name="submission_date"
! full_name="Submission Date"
not_null="true"
type="datetime"
! comment=" indicates when XML was uploaded to NCGR"/>
<column name="local_accession"
full_name="Local Accession Number"
--- 90,98 ----
type="datetime"
comment=""/>
! <column name="creation_date"
! full_name="Creation Date"
not_null="true"
type="datetime"
! comment=" indicates when the experiment was created"/>
<column name="local_accession"
full_name="Local Accession Number"
|
|
From: <jas...@us...> - 2002-10-20 14:02:09
|
Update of /cvsroot/genex/genex-server/G2G/mason In directory usw-pr-cvs1:/tmp/cvs-serv24095/G2G/mason Modified Files: .cvsignore Log Message: usual Index: .cvsignore =================================================================== RCS file: /cvsroot/genex/genex-server/G2G/mason/.cvsignore,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** .cvsignore 15 Oct 2002 14:48:58 -0000 1.3 --- .cvsignore 20 Oct 2002 14:02:05 -0000 1.4 *************** *** 1,6 **** --- 1,10 ---- + array-design.html authenticate.html autohandler + bioassay.html + data-loader.html data-sources.html generate_user.html + group-maint.html query.html workspace.html |
|
From: <jas...@us...> - 2002-10-20 14:01:52
|
Update of /cvsroot/genex/genex-server/G2G/mason
In directory usw-pr-cvs1:/tmp/cvs-serv23920/G2G/mason
Modified Files:
workspace.html.in
Log Message:
* G2G/mason/workspace.html.in (Repository):
fixed @local default
commented out session info - seemed to be messing up sub-components
Index: workspace.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/G2G/mason/workspace.html.in,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** workspace.html.in 13 Oct 2002 05:18:54 -0000 1.2
--- workspace.html.in 20 Oct 2002 14:01:48 -0000 1.3
***************
*** 48,55 ****
<%args>
@g2g => ()
! @local => ('%%GENEX_WORKSPACE_URL%%')
$debug => 0
</%args>
<%once>;
</%once>
<%init>;
--- 48,58 ----
<%args>
@g2g => ()
! @local => ('%%DB_NAME%%')
$debug => 0
</%args>
<%once>;
+ use Bio::Genex;
+ use Bio::Genex::Connect;
+ use Bio::Genex::ExperimentSet;
</%once>
<%init>;
***************
*** 57,59 ****
--- 60,71 ----
my $path = $m->current_comp->attr('path');
my $action = $m->current_comp->attr('action');
+
+ # my $session = Bio::Genex::HTMLUtils::get_session_cookie($r);
+ #
+ # my $dbh = Bio::Genex::Connect->new(USER=>$session->{username},
+ # PASSWORD=>$session->{password},
+ # DBNAME=>$session->{dbname},
+ # );
+
+
</%init>
|
|
From: <jas...@us...> - 2002-10-20 13:58:36
|
Update of /cvsroot/genex/genex-server/G2G/mason
In directory usw-pr-cvs1:/tmp/cvs-serv22218/G2G/mason
Modified Files:
index.html
Log Message:
new links
Index: index.html
===================================================================
RCS file: /cvsroot/genex/genex-server/G2G/mason/index.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** index.html 15 Oct 2002 14:48:24 -0000 1.2
--- index.html 20 Oct 2002 13:58:32 -0000 1.3
***************
*** 11,14 ****
--- 11,18 ----
<li><a href="workspace.html">workspace.html</a></li>
<li><a href="generate_user.html">generate_user.html</a></li>
+ <li><a href="group-maint.html">group-maint.html</a></li>
+ <li><a href="data-loader.html">data-loader.html</a></li>
+ <li><a href="array-design.html">array-design.html</a></li>
+ <li><a href="bioassay.html">bioassay.html</a></li>
</ul>
<%attr>
|
|
From: <jas...@us...> - 2002-10-20 13:56:57
|
Update of /cvsroot/genex/genex-server/G2G/mason/workspace-comps In directory usw-pr-cvs1:/tmp/cvs-serv21478/G2G/mason/workspace-comps Removed Files: footer.mason header.mason main.mason nav.mason Log Message: converted components to be substitutable --- footer.mason DELETED --- --- header.mason DELETED --- --- main.mason DELETED --- --- nav.mason DELETED --- |
|
From: <jas...@us...> - 2002-10-20 13:49:36
|
Update of /cvsroot/genex/genex-server/G2G/mason/workspace-comps
In directory usw-pr-cvs1:/tmp/cvs-serv17639/G2G/mason/workspace-comps
Added Files:
footer.mason.in header.mason.in main.mason.in nav.mason.in
Log Message:
converted components to be substitutable
--- NEW FILE: footer.mason.in ---
<thead>
</thead>
<tbody>
<tr align="center">
<td><b>Footer</b></td>
</tr>
</tbody>
<%attr>
</%attr>
<%args>
@g2g => ()
@local => ('%%DB_NAME%%')
$debug => 0
</%args>
<%once>;
</%once>
<%init>;
</%init>
--- NEW FILE: header.mason.in ---
<thead>
</thead>
<tbody>
<tr align="center">
<td><b>Workspace for user: <% $user %></b></td>
<td><b><a href="logout.html">logout</a></b></td>
</tr>
</tbody>
<%attr>
</%attr>
<%args>
@g2g => ()
@local => ('%%DB_NAME%%')
$debug => 0
</%args>
<%once>
</%once>
<%init>;
my $session = Bio::Genex::HTMLUtils::get_session_cookie($r);
my $user = $session->{username};
</%init>
--- NEW FILE: main.mason.in ---
<thead>
</thead>
<tbody>
<tr>
<th align="left"><b>Experiment</b></th>
<th align="left"><b>Num of PhysicalBioAssays</b></th>
<th align="left"><b>Num of MeasuredBioAssays</b></th>
</tr>
% foreach my $exp (@exps) {
<tr>
<td><% $exp->{name} %></td>
<td><% $exp->{pba_count} %></td>
<td><% $exp->{mba_count} %></td>
</tr>
% }
</tbody>
<%attr>
</%attr>
<%args>
@g2g => ()
@local => ('%%DB_NAME%%')
$debug => 0
</%args>
<%once>;
use Bio::Genex;
use Bio::Genex::HTMLUtils;
use Bio::Genex::Connect;
use Bio::Genex::ExperimentSet;
use Bio::Genex::PhysicalBioAssay;
my @exps;
</%once>
<%init>;
my $session = Bio::Genex::HTMLUtils::get_session_cookie($r);
my $dbh = Bio::Genex::Connect->new(USER=>$session->{username},
PASSWORD=>$session->{password},
DBNAME=>$session->{dbname},
);
$dbh->assert_table_defined('PhysicalBioAssay');
$dbh->assert_table_defined('MeasuredBioAssay');
$dbh->assert_table_defined('ExperimentSet');
my @mba_dbs;
my @pba_dbs;
foreach my $exp (Bio::Genex::ExperimentSet->get_all_objects($dbh)) {
@pba_dbs = Bio::Genex::PhysicalBioAssay->get_all_objects($dbh,
column=>'es_fk',value=>$exp->es_pk);
@mba_dbs = Bio::Genex::MeasuredBioAssay->get_all_objects($dbh,
column=>'es_fk',value=>$exp->es_pk);
push(@exps,{pk=>$exp->es_pk,
name=>$exp->name,
pba_count=>scalar @pba_dbs,
mba_count=>scalar @mba_dbs,
});
}
</%init>
--- NEW FILE: nav.mason.in ---
<thead>
<tr>
<th><b>Navigation Bar</b></th>
</tr>
</thead>
<tbody>
<tr align="center">
<td><b>item1</b></td>
</tr>
<tr align="center">
<td><b>item2</b></td>
</tr>
</tbody>
<%attr>
</%attr>
<%args>
@g2g => ()
@local => ('%%DB_NAME%%')
$debug => 0
</%args>
<%once>;
</%once>
<%init>;
</%init>
|
|
From: <jas...@us...> - 2002-10-20 13:47:07
|
Update of /cvsroot/genex/genex-server/G2G/mason/comps
In directory usw-pr-cvs1:/tmp/cvs-serv13822/G2G/mason/comps
Added Files:
query-checkboxes.mason query-drop-down.mason
Log Message:
new workspace Mason components
--- NEW FILE: query-checkboxes.mason ---
% foreach my $opt (@opts) {
<input type="checkbox" name="<% $name %>" value="<% $opt->{value} %>" <% $opt->{checked} %> >
<label for="<% $opt->{value} %>"><% $opt->{value} %></label><br>
% }
<%args>
$name
$hash_ref
</%args>
<%init>;
my @opts;
foreach my $key (keys %{$hash_ref}) {
my $checked = '';
$checked = 'checked' if $hash_ref->{$key};
push(@opts, {value => $key, checked => $checked});
}
</%init>
--- NEW FILE: query-drop-down.mason ---
<select bgcolor="#BFD8D8" name="<% $name %>">
% foreach my $opt (@opts) {
<option value="<% $opt->{key} %>"><% $opt->{value} %></option>
% }
</select>
<%args>
$name
$array_ref
</%args>
<%init>
my @opts = map {{key => $_->[0], value => $_->[1]}} @{$array_ref};
# we leave a little extra room
my $size = 1 + scalar @opts;
</%init>
|
|
From: <jas...@us...> - 2002-10-20 13:45:15
|
Update of /cvsroot/genex/genex-server/G2G/mason
In directory usw-pr-cvs1:/tmp/cvs-serv12920/G2G/mason
Added Files:
array-design.html.in bioassay.html.in data-loader.html.in
group-maint.html.in
Log Message:
new workspace Mason apps
--- NEW FILE: array-design.html.in ---
<h1 align="center"><% $name %></h1>
<form action="<% $action %>"
method="post" enctype="multipart/form-data">
<div align="center">
% if ($submit) {
<h2><% $data %></h2>
% } else {
<h2>Read Group</h2>
<p>Choose the <b>read group</b> that will be givne to create
the array design files that you load.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>Read Group</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<& comps/query-drop-down.mason, name=>"read_group",
array_ref=>\@groups &>
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<h2>Write Group</h2>
<p>Choose the <b>write group</b> that will be givne to create
the array design files that you load.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>Write Group</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<& comps/query-drop-down.mason, name=>"write_group",
array_ref=>\@groups &>
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<h2>Files to Load</h2>
<p>Choose the array files that you wish to load.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>Data Files</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<& comps/query-select.mason, name=>"data_files",
array_ref=>\@data_files &>
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<input type="submit" name="submit" value="Load Data" size="33">
<& comps/hiddenlist.mason, name=>'debug', value=>$debug &>
<hr noshade size=5>
% }
</div>
</form>
<%args>
$debug => 0
$submit => ''
$data_files => []
$read_group => ''
$write_group => ''
</%args>
<%attr>
action=>'%%GENEX_WORKSPACE_URL%%/array-design.html'
name=>'GeneX DB Array Design Loader Page'
path=>'%%GENEX_WORKSPACE_URL%%/array-design.html'
</%attr>
<%once>
use Bio::Genex;
use Bio::Genex::Connect;
use Bio::Genex::GroupSec;
use Bio::Genex::ArrayDesign;
</%once>
<%init>;
my $name = $m->current_comp->attr('name');
my $path = $m->current_comp->attr('path');
my $action = $m->current_comp->attr('action');
my $session = Bio::Genex::HTMLUtils::get_session_cookie($r);
my $dbh = Bio::Genex::Connect->new(USER=>$session->{username},
PASSWORD=>$session->{password},
DBNAME=>$session->{dbname},
);
$dbh->assert_table_defined('GroupSec');
$dbh->assert_table_defined('ArrayDesign');
my @groups;
my @data_files;
my $data = '';
if ($submit) {
my @files;
if (ref $data_files) {
@files = @{$data_files};
} else {
@files = ($data_files);
}
my $cmd = '%%GENEX_BIN_DIR%%/array-design-insert.pl';
my @args = ("--user=$session->{username}",
"--password=$session->{password}",
"--dbname=$session->{dbname}",
"--ro_group=$read_group",
"--rw_group=$write_group",
);
my @pks;
foreach my $file (@files) {
my @params = ("--file=$file");
my $command = join(' ', $cmd, @args, @params);
my $pk = `$command`;
die $! if $?;
push(@pks,$pk);
}
$data = "@pks";
} else {
my @gs_dbs = Bio::Genex::GroupSec->get_all_objects($dbh);
foreach my $gs_db (@gs_dbs) {
push(@groups,[$gs_db->name,$gs_db->name]);
}
my @files = glob('%%GENEX_UPLOAD_DIR%%/*.xml');
foreach my $name (@files) {
my $short_name = $name;
$short_name =~ s|.*/||;
push(@data_files,[$name,$short_name]);
}
}
</%init>
--- NEW FILE: bioassay.html.in ---
<h1 align="center"><% $name %></h1>
<form action="<% $action %>"
method="post" enctype="multipart/form-data">
<div align="center">
<h2>BioAssays in DB</h2>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>BioAssays</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<& comps/query-select.mason, name=>"bioassays",
array_ref=>\@bioassays &>
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<input type="submit" name="submit" value="Load Data" size="33">
<& comps/hiddenlist.mason, name=>'debug', value=>$debug &>
<hr noshade size=5>
</div>
</form>
<%args>
$debug => 0
$submit => ''
$data_files => []
$read_group => ''
$write_group => ''
</%args>
<%attr>
action=>'%%GENEX_WORKSPACE_URL%%/array-design.html'
name=>'GeneX DB Array Design Loader Page'
path=>'%%GENEX_WORKSPACE_URL%%/array-design.html'
</%attr>
<%once>
use Bio::Genex;
use Bio::Genex::Connect;
use Bio::Genex::GroupSec;
use Bio::Genex::MeasuredBioAssay;
</%once>
<%init>;
my $name = $m->current_comp->attr('name');
my $path = $m->current_comp->attr('path');
my $action = $m->current_comp->attr('action');
my $session = Bio::Genex::HTMLUtils::get_session_cookie($r);
my $dbh = Bio::Genex::Connect->new(USER=>$session->{username},
PASSWORD=>$session->{password},
DBNAME=>$session->{dbname},
);
$dbh->assert_table_defined('MeasuredBioAssay');
my @bioassays;
my @data_files;
my $data = '';
my @mba_dbs = Bio::Genex::MeasuredBioAssay->get_all_objects($dbh);
foreach my $mba_db (@mba_dbs) {
push(@bioassays,[$mba_db->mba_pk,$mba_db->name]);
}
</%init>
--- NEW FILE: data-loader.html.in ---
<h1 align="center"><% $name %></h1>
<form action="<% $action %>"
method="post" enctype="multipart/form-data">
<div align="center">
% if ($submit) {
<h2><% $data %></h2>
% } 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">
<thead bgcolor="#FFD78F">
<tr>
<th>Read Group</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<& comps/query-drop-down.mason, name=>"read_group",
array_ref=>\@groups &>
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<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">
<thead bgcolor="#FFD78F">
<tr>
<th>Write Group</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<& comps/query-drop-down.mason, name=>"write_group",
array_ref=>\@groups &>
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<h2>Array Designs</h2>
<p>Choose the Array Design file from the DB from which the
arrays you wish to load have been created.</p>
<table bgcolor="#FFFFFF" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>Array Designs</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<& comps/query-drop-down.mason, name=>"ad_pk",
array_ref=>\@array_designs &>
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<h2>Experiment Sets</h2>
<p>Choose the ExperimentSet to which you wish to add the
arrays.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>Experiment Sets</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<& comps/query-drop-down.mason, name=>"es_pk",
array_ref=>\@experiment_sets &>
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<h2>Feature Extraction Software</h2>
<p>Choose the feature extraction software package that was
used to create the array files that you wish to load.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>Feature Extraction Software</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<& comps/query-drop-down.mason, name=>"fe_sw_pk",
array_ref=>\@feature_extractions &>
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<h2>Files to Load</h2>
<p>Choose the array files that you wish to load.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>Data Files</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<& comps/query-select.mason, name=>"data_files",
array_ref=>\@data_files &>
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<input type="submit" name="submit" value="Load Data" size="33">
<& comps/hiddenlist.mason, name=>'debug', value=>$debug &>
<hr noshade size=5>
% }
</div>
</form>
<%args>
$debug => 0
$submit => ''
$data_files => []
$read_group => ''
$write_group => ''
$es_pk => ''
$ad_pk => ''
$fe_sw_pk => ''
</%args>
<%attr>
action=>'%%GENEX_WORKSPACE_URL%%/data-loader.html'
name=>'GeneX DB Data Loader Page'
path=>'%%GENEX_WORKSPACE_URL%%/data-loader.html'
</%attr>
<%once>
use Bio::Genex;
use Bio::Genex::Connect;
use Bio::Genex::ArrayDesign;
use Bio::Genex::ExperimentSet;
use Bio::Genex::FeatureExtractionSoftware;
</%once>
<%init>
my $name = $m->current_comp->attr('name');
my $path = $m->current_comp->attr('path');
my $action = $m->current_comp->attr('action');
my $session = Bio::Genex::HTMLUtils::get_session_cookie($r);
my $dbh = Bio::Genex::Connect->new(USER=>$session->{username},
PASSWORD=>$session->{password},
DBNAME=>$session->{dbname},
);
$dbh->assert_table_defined('ExperimentSet');
$dbh->assert_table_defined('ArrayDesign');
$dbh->assert_table_defined('FeatureExtractionSoftware');
my @groups;
my @data_files;
my @feature_extractions;
my @experiment_sets;
my @array_designs;
my $data = '';
if ($submit) {
my @files;
if (ref $data_files) {
@files = @{$data_files};
} else {
@files = ($data_files);
}
my $cmd = '%%GENEX_BIN_DIR%%/mbad-insert.pl';
my @args = ("--user=$session->{username}",
"--password=$session->{password}",
"--dbname=$session->{dbname}",
"--ro_group=$read_group",
"--rw_group=$write_group",
"--es_pk=$es_pk",
"--ad_pk=$ad_pk",
# "--fe_sw_pk=$fe_sw_pk",
"--fe_sw_pk=3",
);
my @pks;
foreach my $file (@files) {
my @params = ($file);
my $command = join(' ', $cmd, @args, @params);
my $pk = `$command`;
die $! if $?;
push(@pks,$pk);
}
$data = "@pks";
} else {
my @gs_dbs = Bio::Genex::GroupSec->get_all_objects($dbh);
foreach my $gs_db (@gs_dbs) {
push(@groups,[$gs_db->name,$gs_db->name]);
}
my @ad_dbs = Bio::Genex::ArrayDesign->get_all_objects($dbh);
foreach my $ad_db (@ad_dbs) {
push(@array_designs,[$ad_db->ad_pk,$ad_db->name]);
}
my @exp_dbs = Bio::Genex::ExperimentSet->get_all_objects($dbh);
foreach my $exp_db (@exp_dbs) {
push(@experiment_sets,[$exp_db->es_pk,$exp_db->name]);
}
my @fe_dbs = Bio::Genex::FeatureExtractionSoftware->get_all_objects($dbh);
foreach my $fe_db (@fe_dbs) {
push(@feature_extractions,[$fe_db->fesw_pk,$fe_db->name . ':' . $fe_db->version]);
}
my @files = glob('%%GENEX_UPLOAD_DIR%%/*.txt');
foreach my $name (@files) {
my $short_name = $name;
$short_name =~ s|.*/||;
push(@data_files,[$name,$short_name]);
}
}
</%init>
--- NEW FILE: group-maint.html.in ---
% if (($response_page eq "NEW")) {
<center>
<h1>Group Member Assicoation Modification</h1>
<form action="<% $action %>"><br></br>
<br></br>
<table cellpadding="2" cellspacing="2" border="0"
style="text-align: left; margin-left: auto; margin-right: auto;"
title="Select the group to work with"
summary="Choose Group">
<tbody>
<tr>
<td valign="top">Which Group would you like to add or
remove members?<br></br>
</td>
<td valign="top">
<& comps/query-drop-down.mason, name=>"groupname",
array_ref=>\@groupnames &>
<td valign="top">
</tr>
</tbody>
</table>
<br></br>
<br></br>
<input name="submitted" type="hidden" value="true"></input>
<input type="submit" name="submit" value="Modify This Group"></input>
<br></br>
</form>
</center>
% } else { # session is initialized
<center>
<h1>Group Member Assicoation Modification</h1>
<form action="<% $action %>"><br></br>
<input type="hidden" name="groupname" value="<% $groupname %>"></input>
<input type="hidden" name="modified" value=1></input>
% if ($response_page eq "DONE"){
<div style="text-align: center;">
<h1>Genex User-associations Updated</h1>
% }
<br></br>
% if ($response_page eq "BadGroup"){
<h3><font color="red">You chose an invalid group to
associate this user with</font>
</h3>
% }
<b>Check/Uncheck the Users you wish to be associated with/dissociated from this group.</b>
<table cellpadding="5" cellspacing="2" border="0"
style="text-align: left; margin-left: auto; margin-right: auto;"
title="Enter the following information for your group"
summary="information about the group">
<caption>
<br></br>
</caption>
<tbody>
<tr>
<td valign="top">Group <i><% $groupname %></i><br></br>
currently has the following members, shown here: <br></br>
</td>
<td valign="top">
<& comps/query-checkboxes.mason,
name=>"new_affiliations",
hash_ref=>\%affiliations &>
</td>
</tr>
</tbody>
</table>
<br></br>
<input name="submitted" type="hidden" value="true"></input>
<input type="submit" name="submit" value="Modify This Group"></input>
</div>
</form>
</center>
% }
<%attr>
action=>'%%GENEX_WORKSPACE_URL%%/user_group_add.html'
name=>'Associate Genex User With Group'
path=>'%%GENEX_WORKSPACE_URL%%/user_group_add.html'
</%attr>
<%args>
$groupname => ""
$submitted => ""
$modified => 0
$debug => 0
$new_affiliations => []
</%args>
<%once>;
use Bio::Genex;
use Bio::Genex::Connect;
use Bio::Genex::GroupSec;
use Bio::Genex::UserSec;
use Bio::Genex::GroupLink;
use Bio::Genex::HTMLUtils;
</%once>
<%init>;
my $name = $m->current_comp->attr('name');
my $path = $m->current_comp->attr('path');
my $action = $m->current_comp->attr('action');
my $session = Bio::Genex::HTMLUtils::get_session_cookie($r);
my $dbh = Bio::Genex::Connect->new(USER=>$session->{username},
PASSWORD=>$session->{password},
DBNAME=>$session->{dbname},
);
$dbh->assert_table_defined('UserSec');
$dbh->assert_table_defined('GroupSec');
$dbh->assert_table_defined('GroupLink');
my $response_page;
my %affiliations;
# get list of all valid users and groups for various purposes
my @groupnames; # holds the names of all groups that exist
my %users;
my %groups;
my @allgroups = Bio::Genex::GroupSec->get_all_objects($dbh); #returns objects
my %my_groups = map {$_->groupname=>1}
Bio::Genex::GroupLink->get_all_objects($dbh,
column=>'username',
value=>$session->{username}
);
foreach (@allgroups){
push(@groupnames, [$_->name,$_->name])
if $my_groups{$_->rw_groupname};
$groups{$_->name} = $_;
}
my $entered;
if ($submitted ne "true") { # this is a fresh load of the page
$response_page="NEW";
} elsif ($groupname && !(grep { $_->[0] eq $groupname } @groupnames)) {
$response_page="BadGroup";
} else {
my @old_users = map {$_->username}
Bio::Genex::GroupLink->get_all_objects($dbh,
column=>'groupname',
value=>$groupname
);
my @allusers = Bio::Genex::UserSec->get_all_objects($dbh);
%users = map {$_->username=>$_} @allusers;
%affiliations = map {$_->username=>0} @allusers;
foreach my $groupname (@old_users) {
$affiliations{$groupname}++;
}
if ($modified) {
# Bug in mason, a single checkbox comes back as a string
# not as an array ref with a single string
my %new_affiliations;
if (ref $new_affiliations) {
%new_affiliations = map {$_=>1} @{$new_affiliations};
} else {
%new_affiliations = ($new_affiliations=>1);
}
foreach my $username (keys %new_affiliations){
next if $affiliations{$username};
$entered = "yes";
my $gl_db = Bio::Genex::GroupLink->new(groupname_obj=>$groups{$groupname},
username_obj=>$users{$username},
);
$gl_db->insert_db($dbh);
}
foreach my $username (@old_users){
next if exists $new_affiliations{$username};
$dbh->do("DELETE FROM GroupLink
WHERE username='$username' AND groupname='$groupname'");
$affiliations{$username} = 0;
}
$response_page="DONE";
}
}
</%init>
|
Update of /cvsroot/genex/genex-server/DB/html
In directory usw-pr-cvs1:/tmp/cvs-serv10895/DB/html
Added Files:
FeatureExtractionSoftware.html G2G.html MeasuredBioAssay.html
QuantitationTypeDimension.html Reporter.html Sessions.html
Log Message:
new
--- NEW FILE: FeatureExtractionSoftware.html ---
<html><head><META http-equiv="Content-Type" content="text/html; charset=UTF-8"><title>
GeneX-2.0 DB: FeatureExtractionSoftware Table
</title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
GeneX-2.0 DB: FeatureExtractionSoftware Table
</th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The FeatureExtractionSoftware table holds information specific to feature extraction software packages</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>data_end_regex</td><td>Data End Regular Expression</td><td>varchar(128)</td><td>false</td><td>This string locates the end of the data block in the input file.</td></tr><tr bgcolor="#D8E4F7"><td>data_start_regex1</td><td>Data Start Regular Expression 1</td><td>varchar(128)</td><td>false</td><td>This string locates the start of the data block in the input file</td></tr><tr bgcolor="#D8E4F7"><td>data_start_regex2</td><td>Data Start Regular Expression 2</td><td>varchar(128)</td><td>false</td><td>This string locates the start of the data block in the input file if the first regex alone is not sufficient</td></tr><tr bgcolor="#D8E4F7"><td>feature_identifier_string</td><td>Feature Identifier String</td><td>varchar(128)</td><td>true</td><td>This string documents what columns in the data are used to constructor the feature identifier</td></tr><tr bgcolor="#D8E4F7"><td>fesw_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>qd_fk</td><td>Quantitation Type Dimension</td><td>int4</td><td>true</td><td>The quantitation dimension that this software package outputs its data as</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>fesw_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>qd_fk</td><td><a href="QuantitationTypeDimension.html">QuantitationTypeDimension</a></td><td>qd_pk</td><td>ONE_TO_ONE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
--- NEW FILE: G2G.html ---
<html><head><META http-equiv="Content-Type" content="text/html; charset=UTF-8"><title>
GeneX-2.0 DB: G2G Table
</title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
GeneX-2.0 DB: G2G Table
</th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th>The G2G table supports distributed queries amongst Genex DB's</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>URL</td><td>URL</td><td>character(128)</td><td>true</td><td></td></tr><tr bgcolor="#D8E4F7"><td>g2g_pk</td><td>Accession Number</td><td>serial</td><td>true</td><td></td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>g2g_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
--- NEW FILE: MeasuredBioAssay.html ---
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GeneX-2.0 DB: MeasuredBioAssay Table
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GeneX-2.0 DB: MeasuredBioAssay Table
</th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th>The MeasuredBioAssay table holds the meta-data associated with a data matrix stored in a MeasuredBioAssayData table</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>description</td><td>Description</td><td>text</td><td>false</td><td> a more verbose description of the purpose of this MeasuredBioAssay</td></tr><tr bgcolor="#D8E4F7"><td>es_fk</td><td>Primary Experiment Set</td><td>int4</td><td>true</td><td> the primary experiment in which the MeasuredBioAssay was taken (the ExperimentSet in which it was submitted)</td></tr><tr bgcolor="#D8E4F7"><td>fesw_fk</td><td>Feature Extraction Software</td><td>int4</td><td>true</td><td>The feature extraction software used to extract the numerical data from the image</td></tr><tr bgcolor="#D8E4F7"><td>mba_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>mba_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>es_fk</td><td><a href="ExperimentSet.html">ExperimentSet</a></td><td>es_pk</td><td>MANY_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>fesw_fk</td><td><a href="FeatureExtractionSoftware.html">FeatureExtractionSoftware</a></td><td>fesw_pk</td><td>ONE_TO_ONE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
--- NEW FILE: QuantitationTypeDimension.html ---
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GeneX-2.0 DB: QuantitationTypeDimension Table
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GeneX-2.0 DB: QuantitationTypeDimension Table
</th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The QuantitationTypeDimension table stores the ordered lists of QuantitationTypes that define the spot tables</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>data_table_name</td><td>Data Table Name</td><td>varchar(128)</td><td>true</td><td>Every QuantitationTypeDimension stores its data in its own unique data table</td></tr><tr bgcolor="#D8E4F7"><td>qd_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>qd_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
--- NEW FILE: Reporter.html ---
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GeneX-2.0 DB: Reporter Table
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GeneX-2.0 DB: Reporter Table
</th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The Reporter table describes the genetic elements that are used as probes in gene expression experiments (e.g. the cDNA elements that are immobilized on a glass slide). They can be cloned genes, ESTs, etc.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td>Audit</td><td>int4</td><td>true</td><td>The audit entry when this data was last modified</td></tr><tr bgcolor="#D8E4F7"><td>chromosome</td><td>Chromosome Location</td><td>varchar(128)</td><td>false</td><td> the chromosome on which the Reporter resides</td></tr><tr bgcolor="#D8E4F7"><td>clone_name</td><td>Clone Name</td><td>varchar(128)</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>clone_provider_con_fk</td><td>Clone Provider Contact</td><td>int4</td><td>false</td><td> useful for tracking where the sequence feature came from if the clone was provided by another source ??an untested feature at best, shouldn't this be handled ??by the smp_fk</td></tr><tr bgcolor="#D8E4F7"><td>description</td><td>Description</td><td>varchar(128)</td><td>false</td><td> a short description of the Reporter</td></tr><tr bgcolor="#D8E4F7"><td>end_position</td><td>End Position</td><td>int4</td><td>false</td><td> the location with respect to the origin of the chromosome</td></tr><tr bgcolor="#D8E4F7"><td>other_name</td><td>Other Name</td><td>varchar(128)</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>other_type</td><td>Other Type</td><td>varchar(128)</td><td>false</td><td> an alternative name by which the entity is known ??doesn't this want to be a restricted vocab</td></tr><tr bgcolor="#D8E4F7"><td>plate_column</td><td>Plate Column</td><td>varchar(128)</td><td>false</td><td> column reference to indentify the well on the plate this sequence feature came from.</td></tr><tr bgcolor="#D8E4F7"><td>plate_identifier</td><td>Plate</td><td>varchar(128)</td><td>false</td><td> Used to identify a source plate for this sequence feature This could be a reference to the spotting plate, or it could refer to the original clone library plate.</td></tr><tr bgcolor="#D8E4F7"><td>plate_row</td><td>Plate Row</td><td>varchar(128)</td><td>false</td><td> Row reference to indentify the well on the plate this sequence feature came from.</td></tr><tr bgcolor="#D8E4F7"><td>provider_con_fk</td><td>Provider Contact</td><td>int4</td><td>false</td><td> the researcher that provided the reporter info</td></tr><tr bgcolor="#D8E4F7"><td>rep_name</td><td>Sequence Feature Name</td><td>varchar(128)</td><td>true</td><td> an identifier such as EST or ORF name, by which the entity is known in the lab using it is expression experiments</td></tr><tr bgcolor="#D8E4F7"><td>rep_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>rep_type</td><td>Sequence Feature Type</td><td>varchar(128)</td><td>true</td><td>conrolled vocab</td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td>Read-Only Group Name</td><td>name</td><td>true</td><td>The group with permission to view this data</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td>Read/Write Group Name</td><td>name</td><td>true</td><td>The group with permission to modify this data</td></tr><tr bgcolor="#D8E4F7"><td>sequence</td><td>Sequence</td><td>text</td><td>false</td><td> may be used when dealing with ESTs that have not been submitted to a public database (won't be used for public version, but may be useful for local installations)</td></tr><tr bgcolor="#D8E4F7"><td>smp_fk</td><td>Sample</td><td>int4</td><td>false</td><td> sample information for the Reporter this may be useful for identifying the state of the organism from which the sequence feature was obtained</td></tr><tr bgcolor="#D8E4F7"><td>spc_fk</td><td>Species</td><td>int4</td><td>false</td><td> the species to which the Reporter belongs</td></tr><tr bgcolor="#D8E4F7"><td>start_position</td><td>Start Position</td><td>int4</td><td>false</td><td> the location with respect to the origin of the chromosome</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>rep_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td><a href="Audit.html">Audit</a></td><td>audit_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>clone_provider_con_fk</td><td><a href="Contact.html">Contact</a></td><td>con_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>provider_con_fk</td><td><a href="Contact.html">Contact</a></td><td>con_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>smp_fk</td><td><a href="Sample.html">Sample</a></td><td>smp_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>spc_fk</td><td><a href="Species.html">Species</a></td><td>spc_pk</td><td>MANY_TO_ONE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>rep_name provider_con_fk spc_fk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
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GeneX-2.0 DB: Sessions Table
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GeneX-2.0 DB: Sessions Table
</th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th>The Session table supports storing WWW session data to the DB</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>a_session</td><td>Session Data</td><td>text</td><td>false</td><td>the encrypted session data</td></tr><tr bgcolor="#D8E4F7"><td>id</td><td>Session Number</td><td>character(32)</td><td>true</td><td></td></tr><tr bgcolor="#D8E4F7"><td>modification_time</td><td>Modification Time</td><td>datetime</td><td>true</td><td>the encrypted session data</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
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From: <jas...@us...> - 2002-10-20 13:39:05
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Update of /cvsroot/genex/genex-server/affyloader In directory usw-pr-cvs1:/tmp/cvs-serv10150/affyloader Removed Files: loadamspots.pl.in Log Message: cruft --- loadamspots.pl.in DELETED --- |
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From: <jas...@us...> - 2002-10-20 13:30:41
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Update of /cvsroot/genex/genex-server/Genex/QuantitationDimension In directory usw-pr-cvs1:/tmp/cvs-serv5580/Genex/QuantitationDimension Removed Files: .cvsignore Log Message: cruft --- .cvsignore DELETED --- |
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From: <jas...@us...> - 2002-10-20 13:30:41
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Update of /cvsroot/genex/genex-server/Genex/SequenceFeature In directory usw-pr-cvs1:/tmp/cvs-serv5580/Genex/SequenceFeature Removed Files: .cvsignore Log Message: cruft --- .cvsignore DELETED --- |
