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Update of /cvsroot/genex/genex-server/DB/html In directory sc8-pr-cvs1:/tmp/cvs-serv15377/DB/html Added Files: Hardware.html Parameter.html ParameterValue.html Parameterizable.html Procedure.html ProtocolApplication.html ProtocolStep.html Log Message: new table html files --- NEW FILE: Hardware.html --- --- NEW FILE: Parameter.html --- --- NEW FILE: ParameterValue.html --- --- NEW FILE: Parameterizable.html --- --- NEW FILE: Procedure.html --- --- NEW FILE: ProtocolApplication.html --- --- NEW FILE: ProtocolStep.html --- |
|
From: <jas...@us...> - 2003-04-16 23:15:17
|
Update of /cvsroot/genex/genex-server/Genex/SampleProtocols In directory sc8-pr-cvs1:/tmp/cvs-serv15140/Genex/SampleProtocols Removed Files: Makefile.PL SampleProtocols.pm Log Message: old tables --- Makefile.PL DELETED --- --- SampleProtocols.pm DELETED --- |
|
From: <jas...@us...> - 2003-04-16 23:15:16
|
Update of /cvsroot/genex/genex-server/Genex/Provider In directory sc8-pr-cvs1:/tmp/cvs-serv15140/Genex/Provider Removed Files: Makefile.PL Provider.pm Log Message: old tables --- Makefile.PL DELETED --- --- Provider.pm DELETED --- |
|
From: <jas...@us...> - 2003-04-16 23:14:09
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv14631/Mason/workspace
Added Files:
protocol-insert.html
Log Message:
new workspace GUI
--- NEW FILE: protocol-insert.html ---
<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 given 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 given 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>Name</h2>
<p>Choose a <b>Name</b> for your protocol. If you use single
quotes, they will be removed, so don't.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>Name</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<input type="text" name="proto_name" size="65" maxlength="128">
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<h2>Protocol Type</h2>
<p>Choose the <b>Protocol Type</b> that describes the type of
protocol.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>Protocol Type</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<& comps/query-drop-down.mason, name=>"protocol_type",
array_ref=>\@protocol_types &>
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<h2>Protocol Description</h2> <p>Describe the protocol. If you
use single quotes, they will be removed, so don't.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>Protocol Description</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<textarea name="proto_desc" rows="5" cols="65"></textarea>
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<h2>URI</h2>
<p> Provide an informational URI for the protocol (if any). If you
use single quotes, they will be removed, so don't.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>URI</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<textarea name="uri" rows="1" cols="65"></textarea>
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<h2>Provider Contact</h2>
<p>Choose the <b>Contact</b> entry who provided the protocol
(if any).</p>
<p>The entry must exist in the DB first, click <a
href="contact-insert.html">here</a> if you need to enter the Contact info, then
return to this page and hit your browsers <b>Reload</b> button.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>Provider Contact</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<& comps/query-drop-down.mason, name=>"provider",
array_ref=>\@contacts &>
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<input type="submit" name="submit" value="Create Protocol" size="33">
<& comps/hiddenlist.mason, name=>'debug', value=>$debug &>
<hr noshade size=5>
% }
</div>
</form>
<%args>
$debug => 0
$submit => ''
$uri => ''
$provider => ''
$read_group => ''
$write_group => ''
$proto_desc => ''
$protocol_type => ''
$proto_name => ''
</%args>
<%attr>
action=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/protocol-insert.html"
name=>'GeneX DB Protocol Creation Page'
path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/protocol-insert.html"
</%attr>
<%once>
use Bio::Genex;
use Bio::Genex::Connect;
use Bio::Genex::Config;
use Bio::Genex::Contact;
use Bio::Genex::GroupSec;
use Bio::Genex::Protocol;
use Bio::Genex::ControlledVocab;
# use Apache::DB ();
</%once>
<%init>;
my $name = $m->current_comp->attr('name');
my $path = $m->current_comp->attr('path');
my $action = $m->current_comp->attr('action');
# Apache::DB->init;
# Apache::DB->handler;
$dbh->assert_table_defined('GroupSec');
$dbh->assert_table_defined('Protocol');
my @groups;
my $no_type = 'NONE';
my @protocol_types = ([$no_type,$no_type]);
my @contacts = ([$no_type,$no_type]);
my $data = '';
if ($submit) {
$proto_name =~ s/\'//;
my $cmd = "$Bio::Genex::Config->{GENEX_BIN_DIR}/protocol-insert.pl";
my @args = ("--user=$session->{username}",
"--password=$session->{password}",
"--dbname=$session->{dbname}",
"--ro_group=$read_group",
"--rw_group=$write_group",
"--name='$proto_name'",
);
if ($proto_desc) {
$proto_desc =~ s/\'//;
push(@args,"--description='$proto_desc'");
}
if ($uri) {
$uri =~ s/\'//;
push(@args,"--uri='$uri'");
}
if ($protocol_type ne $no_type) {
push(@args,"--type=$protocol_type");
}
if ($provider ne $no_type) {
push(@args,"--provider=$provider");
}
my @pks;
my $command = join(' ', $cmd, @args);
my $pk = `$command`;
if ($?) {
$data = <<EOE;
<p><b>ERROR</b></p>
<p>Executing $command</p>
<p>Error output = <$!></p>
EOE
} else {
push(@pks,$pk);
$data = "Protocol, $proto_name, Successfully Created";
}
} else {
my @gs_dbs = Bio::Genex::GroupSec->get_all_objects($dbh);
foreach my $gs_db (@gs_dbs) {
push(@groups,[$gs_db->name,$gs_db->name]);
}
my @con_dbs = Bio::Genex::Contact->get_all_objects($dbh);
foreach my $con_db (@con_dbs) {
push(@contacts,[$con_db->con_pk,'[' . $con_db->contact_person .
":" . $con_db->organization . ']']);
}
my @pt_dbs = Bio::Genex::ControlledVocab->get_all_objects($dbh,
column=>'vocab_name',
value=>'PRT_Type',
);
foreach my $pt_db (@pt_dbs) {
push(@protocol_types,[$pt_db->term_string,$pt_db->term_string]);
}
}
</%init>
|
|
From: <jas...@us...> - 2003-04-16 23:12:54
|
Update of /cvsroot/genex/genex-server/DB/html In directory sc8-pr-cvs1:/tmp/cvs-serv14145/DB/html Removed Files: AL_Spots.html ContactOwner.html FeatureExtraction.html Provider.html SampleProtocols.html Scanner.html Security.html SequenceFeature.html Spotter.html TableAdmin.html Log Message: old html table files --- AL_Spots.html DELETED --- --- ContactOwner.html DELETED --- --- FeatureExtraction.html DELETED --- --- Provider.html DELETED --- --- SampleProtocols.html DELETED --- --- Scanner.html DELETED --- --- Security.html DELETED --- --- SequenceFeature.html DELETED --- --- Spotter.html DELETED --- --- TableAdmin.html DELETED --- |
|
From: <jas...@us...> - 2003-04-16 23:12:05
|
Update of /cvsroot/genex/genex-server
In directory sc8-pr-cvs1:/tmp/cvs-serv13809
Modified Files:
db.pl
Log Message:
* db.pl (Repository):
added fix to get variable substitution on genex email
Index: db.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/db.pl,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** db.pl 20 Oct 2002 21:18:51 -0000 1.6
--- db.pl 16 Apr 2003 23:12:01 -0000 1.7
***************
*** 280,284 ****
print STDERR "Couldn't find '$VARS{GENEX_SU_USER}' contact in DB"
unless defined $genex;
! $genex->contact_person_email('$VARS{CONTACT_EMAIL}');
$genex->update_db($dbh);
print STDERR "\n\temail updated for '$VARS{GENEX_SU_USER}' account in DB\n\n";
--- 280,284 ----
print STDERR "Couldn't find '$VARS{GENEX_SU_USER}' contact in DB"
unless defined $genex;
! $genex->contact_person_email($VARS{CONTACT_EMAIL});
$genex->update_db($dbh);
print STDERR "\n\temail updated for '$VARS{GENEX_SU_USER}' account in DB\n\n";
|
|
From: <jas...@us...> - 2003-04-16 21:26:07
|
Update of /cvsroot/genex/genex-server/DB/xml
In directory sc8-pr-cvs1:/tmp/cvs-serv6418
Modified Files:
Software.xml
Log Message:
* DB/xml/Software.xml (Repository):
now inherits from Parameterizable
Index: Software.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/xml/Software.xml,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** Software.xml 23 Nov 2002 07:57:16 -0000 1.7
--- Software.xml 16 Apr 2003 21:26:04 -0000 1.8
***************
*** 1,18 ****
<?xml version="1.0" standalone="no"?>
! <!DOCTYPE table SYSTEM "../../DTD/table.dtd">
! <table name="Software"
type="&data_table;"
! comment=" The Software table describes a variety of software
packages used in the analysis of expression data, e.g. image
analysis software.">
- <column name="sw_pk"
- full_name="Accession Number"
- type="serial"
- comment=""/>
- <column name="name"
- full_name="Name"
- type="varchar(128)"
- not_null="true"
- comment=""/>
<column name="version"
full_name="Version"
--- 1,12 ----
<?xml version="1.0" standalone="no"?>
! <!DOCTYPE table SYSTEM "../../DTD/table.dtd" [
! <!ENTITY table_name "Software">
! ]>
! <table name="&table_name;"
! inherits_from="Parameterizable"
type="&data_table;"
! comment=" The &table_name; table describes a variety of software
packages used in the analysis of expression data, e.g. image
analysis software.">
<column name="version"
full_name="Version"
***************
*** 26,70 ****
comment="controlled vocab"/>
<column name="producer_con_fk"
! full_name="Data Producer"
not_null="true"
! type="varchar(128)"
! comment=" the supplier of the sofware"/>
<foreign_key column_id="producer_con_fk"
foreign_table ="Contact"
foreign_table_pkey ="con_pk"
fkey_type ="&fkey_oto;"/>
! <column name="ro_groupname"
! full_name="Read-Only Group Name"
! not_null="true"
! type="name"
! comment="The group with permission to view this data"/>
! <foreign_key column_id="ro_groupname"
! foreign_table ="GroupSec"
! foreign_table_pkey ="name"
! fkey_type ="&fkey_oto;"/>
! <column name="rw_groupname"
! full_name="Read/Write Group Name"
! not_null="true"
! type="name"
! comment="The group with permission to modify this data"/>
! <foreign_key column_id="rw_groupname"
! foreign_table ="GroupSec"
! foreign_table_pkey ="name"
! fkey_type ="&fkey_oto;"/>
! <column name="audit_fk"
! full_name="Audit"
! not_null="true"
! type="int4"
! comment="The audit entry when this data was last modified, it
! will be null if it is the creation event. We set the
! write_sql attribute to be false so that Postgres doesn't put
! a constraint on this column. It is automatically set by a
! trigger. "/>
! <foreign_key column_id="audit_fk"
! write_sql="false"
! foreign_table ="Audit"
! foreign_table_pkey ="audit_pk"
! fkey_type ="&fkey_oto;"/>
! <primary_key column_id="sw_pk"/>
<unique column_ids="name version producer_con_fk"/>
</table>
--- 20,32 ----
comment="controlled vocab"/>
<column name="producer_con_fk"
! full_name="Protocol Producer"
not_null="true"
! type="int4"
! comment=" the supplier of the protocol"/>
<foreign_key column_id="producer_con_fk"
foreign_table ="Contact"
foreign_table_pkey ="con_pk"
fkey_type ="&fkey_oto;"/>
! <primary_key column_id="param_pk"/>
<unique column_ids="name version producer_con_fk"/>
</table>
|
|
From: <jas...@us...> - 2003-04-16 21:25:15
|
Update of /cvsroot/genex/genex-server/DB/xml
In directory sc8-pr-cvs1:/tmp/cvs-serv6020
Modified Files:
Protocol.xml
Log Message:
* DB/xml/Protocol.xml (Repository):
New protocol model from ESTap
Index: Protocol.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/xml/Protocol.xml,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** Protocol.xml 23 Nov 2002 07:57:16 -0000 1.6
--- Protocol.xml 16 Apr 2003 21:25:12 -0000 1.7
***************
*** 1,26 ****
<?xml version="1.0" standalone="no"?>
! <!DOCTYPE table SYSTEM "../../DTD/table.dtd">
! <table name="Protocol"
type="&data_table;"
! comment=" The Protocol table describes a variety of specific experimental protocols used to perform certain preparations in the experiment, e.g. hybridization, cell culturing, etc. In general, a given protocol may be used by different rsearchers with some variation. Deviations from the standard protocol may be described in comments in the tables which link to Protocol (Sample, PhysicalBioAssay).">
! <column name="prt_pk"
full_name="Accession Number"
- type="serial"
- comment=""/>
- <column name="title"
- full_name="Title"
not_null="true"
! type="varchar(128)"
comment=""/>
! <column name="type"
! full_name="Type"
! not_null="true"
type="varchar(128)"
! comment="controlled vocab"/>
! <column name="text"
! full_name="Text"
! not_null="true"
! type="text"
! comment=""/>
<column name="provider_con_fk"
full_name="Protocol Provider"
--- 1,26 ----
<?xml version="1.0" standalone="no"?>
! <!DOCTYPE table SYSTEM "../../DTD/table.dtd" [
! <!ENTITY table_name "Protocol">
! ]>
! <table name="&table_name;"
! inherits_from="Identifiable"
type="&data_table;"
! comment=" The &table_name; table describes a variety of specific
! experimental protocols used to perform certain preparations in
! the experiment, e.g. hybridization, cell culturing, etc. In
! general, a given protocol may be used by different rsearchers
! with some variation. Deviations from the standard protocol may
! be described in comments in the tables which link to Protocol
! (Sample, PhysicalBioAssay).">
! <column name="protocol_pk"
full_name="Accession Number"
not_null="true"
! type="serial"
comment=""/>
! <column name="URI"
! full_name="URI"
type="varchar(128)"
! comment="A URI that contains more information about the
! information in question."/>
<column name="provider_con_fk"
full_name="Protocol Provider"
***************
*** 32,68 ****
foreign_table_pkey ="con_pk"
fkey_type ="&fkey_oto;"/>
! <column name="ro_groupname"
! full_name="Read-Only Group Name"
! not_null="true"
! type="name"
! comment="The group with permission to view this data"/>
! <foreign_key column_id="ro_groupname"
! foreign_table ="GroupSec"
! foreign_table_pkey ="name"
! fkey_type ="&fkey_oto;"/>
! <column name="rw_groupname"
! full_name="Read/Write Group Name"
! not_null="true"
! type="name"
! comment="The group with permission to modify this data"/>
! <foreign_key column_id="rw_groupname"
! foreign_table ="GroupSec"
! foreign_table_pkey ="name"
! fkey_type ="&fkey_oto;"/>
! <column name="audit_fk"
! full_name="Audit"
not_null="true"
! type="int4"
! comment="The audit entry when this data was last modified, it
! will be null if it is the creation event. We set the
! write_sql attribute to be false so that Postgres doesn't put
! a constraint on this column. It is automatically set by a
! trigger. "/>
! <foreign_key column_id="audit_fk"
! write_sql="false"
! foreign_table ="Audit"
! foreign_table_pkey ="audit_pk"
! fkey_type ="&fkey_oto;"/>
! <primary_key column_id="prt_pk"/>
! <unique column_ids="title type"/>
</table>
--- 32,45 ----
foreign_table_pkey ="con_pk"
fkey_type ="&fkey_oto;"/>
! <column name="type"
! full_name="Type"
! type="varchar(128)"
! comment="controlled vocab"/>
! <column name="description"
! full_name="Description"
not_null="true"
! type="text"
! comment=""/>
! <primary_key column_id="protocol_pk"/>
! <unique column_ids="name type provider_con_fk"/>
</table>
|
|
From: <jas...@us...> - 2003-04-16 21:24:26
|
Update of /cvsroot/genex/genex-server/DB/xml
In directory sc8-pr-cvs1:/tmp/cvs-serv5705
Modified Files:
MeasuredBioAssay.xml
Log Message:
* DB/xml/MeasuredBioAssay.xml (Repository):
modified sw pkey
Index: MeasuredBioAssay.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/xml/MeasuredBioAssay.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** MeasuredBioAssay.xml 23 Nov 2002 10:15:05 -0000 1.2
--- MeasuredBioAssay.xml 16 Apr 2003 21:24:22 -0000 1.3
***************
*** 34,38 ****
<foreign_key column_id="sw_fk"
foreign_table ="FeatureExtractionSoftware"
! foreign_table_pkey ="sw_pk"
fkey_type ="&fkey_oto;"/>
<primary_key column_id="mba_pk"/>
--- 34,38 ----
<foreign_key column_id="sw_fk"
foreign_table ="FeatureExtractionSoftware"
! foreign_table_pkey ="param_pk"
fkey_type ="&fkey_oto;"/>
<primary_key column_id="mba_pk"/>
|
|
From: <jas...@us...> - 2003-04-16 21:23:09
|
Update of /cvsroot/genex/genex-server/DB/xml
In directory sc8-pr-cvs1:/tmp/cvs-serv5188
Modified Files:
FeatureExtractionSoftware.xml
Log Message:
* DB/xml/FeatureExtractionSoftware.xml (Repository):
now inherits pkey from Parameterizable
Index: FeatureExtractionSoftware.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/xml/FeatureExtractionSoftware.xml,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** FeatureExtractionSoftware.xml 23 Nov 2002 10:14:35 -0000 1.3
--- FeatureExtractionSoftware.xml 16 Apr 2003 21:23:06 -0000 1.4
***************
*** 1,8 ****
<?xml version="1.0" standalone="no"?>
! <!DOCTYPE table SYSTEM "../../DTD/table.dtd">
! <table name="FeatureExtractionSoftware"
type="&data_table;"
inherits_from="Software"
! comment=" The FeatureExtractionSoftware table holds information
specific to feature extraction software packages">
<column name="feature_identifier_string"
--- 1,10 ----
<?xml version="1.0" standalone="no"?>
! <!DOCTYPE table SYSTEM "../../DTD/table.dtd" [
! <!ENTITY table_name "FeatureExtractionSoftware">
! ]>
! <table name="&table_name;"
type="&data_table;"
inherits_from="Software"
! comment=" The &table_name; table holds information
specific to feature extraction software packages">
<column name="feature_identifier_string"
***************
*** 37,40 ****
foreign_table_pkey ="qd_pk"
fkey_type ="&fkey_oto;"/>
! <primary_key column_id="sw_pk"/>
</table>
--- 39,42 ----
foreign_table_pkey ="qd_pk"
fkey_type ="&fkey_oto;"/>
! <primary_key column_id="param_pk"/>
</table>
|
|
From: <jas...@us...> - 2003-04-16 21:22:31
|
Update of /cvsroot/genex/genex-server/DB/xml
In directory sc8-pr-cvs1:/tmp/cvs-serv4937
Modified Files:
Array.xml
Log Message:
* DB/xml/Array.xml (Repository):
Spotter ==> Hardware
Index: Array.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/xml/Array.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** Array.xml 23 Nov 2002 07:57:16 -0000 1.2
--- Array.xml 16 Apr 2003 21:22:28 -0000 1.3
***************
*** 52,57 ****
type="int4"
comment="The design on which this array is based"/>
! <column name="sptr_fk"
! full_name="Spotter"
type="int4"
comment="spotter hardware used to create layout"/>
--- 52,57 ----
type="int4"
comment="The design on which this array is based"/>
! <column name="spotter_hw_fk"
! full_name="Spotter Hardware"
type="int4"
comment="spotter hardware used to create layout"/>
***************
*** 119,125 ****
foreign_table_pkey ="sw_pk"
fkey_type ="&fkey_oto;"/>
! <foreign_key column_id="sptr_fk"
! foreign_table ="Spotter"
! foreign_table_pkey ="sptr_pk"
fkey_type ="&fkey_oto;"/>
<foreign_key column_id="provider_con_fk"
--- 119,125 ----
foreign_table_pkey ="sw_pk"
fkey_type ="&fkey_oto;"/>
! <foreign_key column_id="spotter_hw_fk"
! foreign_table ="Hardware"
! foreign_table_pkey ="param_pk"
fkey_type ="&fkey_oto;"/>
<foreign_key column_id="provider_con_fk"
|
Update of /cvsroot/genex/genex-server/DB/xml
In directory sc8-pr-cvs1:/tmp/cvs-serv4678
Added Files:
Hardware.xml Parameter.xml ParameterValue.xml
Parameterizable.xml Procedure.xml ProtocolApplication.xml
ProtocolStep.xml
Log Message:
added new table
--- NEW FILE: Hardware.xml ---
<?xml version="1.0" standalone="no"?>
<!DOCTYPE table SYSTEM "../../DTD/table.dtd" [
<!ENTITY table_name "Hardware">
]>
<table name="&table_name;"
inherits_from="Parameterizable"
type="&data_table;"
comment=" The &table_name; table describes the hardware used in experiments.">
<column name="model"
full_name="Model"
type="varchar(128)"
comment=""/>
<column name="make"
full_name="Make"
type="varchar(128)"
comment=""/>
<column name="type"
full_name="Type"
not_null="true"
type="varchar(128)"
comment="controlled vocab"/>
<column name="model_description"
full_name="Model Description"
not_null="true"
type="varchar(128)"
comment=""/>
<column name="producer_con_fk"
full_name="Protocol Producer"
not_null="true"
type="int4"
comment=" the supplier of the protocol"/>
<foreign_key column_id="producer_con_fk"
foreign_table ="Contact"
foreign_table_pkey ="con_pk"
fkey_type ="&fkey_oto;"/>
<primary_key column_id="param_pk"/>
<unique column_ids="model make producer_con_fk"/>
</table>
--- NEW FILE: Parameter.xml ---
<?xml version="1.0" standalone="no"?>
<!DOCTYPE table SYSTEM "../../DTD/table.dtd" [
<!ENTITY table_name "Parameter">
]>
<table name="&table_name;"
type="&data_table;"
inherits_from="Identifiable"
comment=" The &table_name; table describes the individual
parameters of a protocol, software, or hardware.">
<column name="default_value"
full_name="Default Value"
type="varchar(128)"
comment="The value to use if none is specified by the application"/>
<column name="parameter_pk"
full_name="Accession Number"
type="serial"
comment=""/>
<column name="type"
full_name="Type"
type="varchar(128)"
comment="controlled vocab"/>
<column name="proc_fk"
full_name="Procedure"
not_null="true"
type="int4"
comment="the procedure this parameter applies to"/>
<foreign_key column_id="proc_fk"
foreign_table ="Procedure"
foreign_table_pkey ="proc_pk"
fkey_type ="&fkey_oto;"/>
<primary_key column_id="parameter_pk"/>
</table>
--- NEW FILE: ParameterValue.xml ---
<?xml version="1.0" standalone="no"?>
<!DOCTYPE table SYSTEM "../../DTD/table.dtd" [
<!ENTITY table_name "ParameterValue">
]>
<table name="&table_name;"
type="&data_table;"
comment=" The &table_name; table contains the values for
parameters used in any step.">
<column name="param_value_pk"
full_name="Accession Number"
not_null="true"
type="serial"
comment=""/>
<column name="value"
full_name="Value"
type="varchar(128)"
comment="The value of the parameter"/>
<column name="proto_step_fk"
full_name="Protocol Step"
not_null="true"
type="int4"
comment="the protocol step this parameter value applies to"/>
<foreign_key column_id="proto_step_fk"
foreign_table ="ProtocolStep"
foreign_table_pkey ="proto_step_pk"
fkey_type ="&fkey_oto;"/>
<column name="parameter_fk"
full_name="Parameter"
not_null="true"
type="int4"
comment="the procedure parameter this parameter value applies to"/>
<foreign_key column_id="proto_step_fk"
foreign_table ="ProtocolStep"
foreign_table_pkey ="proto_step_pk"
fkey_type ="&fkey_oto;"/>
<primary_key column_id="param_value_pk"/>
</table>
--- NEW FILE: Parameterizable.xml ---
<?xml version="1.0" standalone="no"?>
<!DOCTYPE table SYSTEM "../../DTD/table.dtd" [
<!ENTITY table_name "Parameterizable">
]>
<table name="&table_name;"
inherits_from="Identifiable"
type="&data_table;"
comment="The &table_name; table is an abstract table that other
tables inherit from. It specifies that things can have parameters">
<column name="param_pk"
full_name="Accession Number"
type="serial"
comment=""/>
<column name="URI"
full_name="URI"
type="varchar(128)"
comment="A URI that contains more information about the
information in question."/>
<column name="provider_con_fk"
full_name="Protocol Provider"
type="int4"
comment=" the supplier of the protocol"/>
<foreign_key column_id="provider_con_fk"
foreign_table ="Contact"
foreign_table_pkey ="con_pk"
fkey_type ="&fkey_oto;"/>
<primary_key column_id="param_pk"/>
</table>
--- NEW FILE: Procedure.xml ---
<?xml version="1.0" standalone="no"?>
<!DOCTYPE table SYSTEM "../../DTD/table.dtd" [
<!ENTITY table_name "Procedure">
]>
<table name="&table_name;"
inherits_from="Identifiable"
type="&data_table;"
comment=" The &table_name; table contains individual components
that can be sequenced together to create protocols">
<column name="proc_pk"
full_name="Accession Number"
not_null="true"
type="serial"
comment=""/>
<column name="type"
full_name="Type"
type="varchar(128)"
comment="controlled vocab"/>
<column name="description"
full_name="Description"
not_null="true"
type="text"
comment=""/>
<primary_key column_id="proc_pk"/>
</table>
--- NEW FILE: ProtocolApplication.xml ---
<?xml version="1.0" standalone="no"?>
<!DOCTYPE table SYSTEM "../../DTD/table.dtd" [
<!ENTITY table_name "ProtocolApplication">
]>
<table name="&table_name;"
inherits_from="Identifiable"
type="&data_table;"
comment=" The &table_name; table describes the concrete use in
time by a person of a protocol.">
<column name="proto_app_pk"
full_name="Accession Number"
type="serial"
comment=""/>
<column name="activity_date"
full_name="Activity Date"
not_null="true"
type="datetime"
comment=" the date when the protocol was performed"/>
<column name="performer_con_fk"
full_name="Protocol Performer"
not_null="true"
type="int4"
comment=" the person who performed the protocol"/>
<foreign_key column_id="performer_con_fk"
foreign_table ="Contact"
foreign_table_pkey ="con_pk"
fkey_type ="&fkey_oto;"/>
<column name="protocol_fk"
full_name="Protocol"
not_null="true"
type="int4"
comment="The protocol that was performed"/>
<foreign_key column_id="protocol_fk"
foreign_table ="Protocol"
foreign_table_pkey ="protocol_pk"
fkey_type ="&fkey_oto;"/>
<primary_key column_id="proto_app_pk"/>
</table>
--- NEW FILE: ProtocolStep.xml ---
<?xml version="1.0" standalone="no"?>
<!DOCTYPE table SYSTEM "../../DTD/table.dtd" [
<!ENTITY table_name "ProtocolStep">
]>
<table name="&table_name;"
type="&data_table;"
comment=" The &table_name; table contains the steps for protocols.">
<column name="proto_step_pk"
full_name="Accession Number"
not_null="true"
type="serial"
comment=""/>
<column name="order"
full_name="Order"
type="int4"
comment="The order of this step in the protocol"/>
<column name="protocol_fk"
full_name="Protocol"
not_null="true"
type="int4"
comment="the protocol this step applies to"/>
<foreign_key column_id="protocol_fk"
foreign_table ="Protocol"
foreign_table_pkey ="protocol_pk"
fkey_type ="&fkey_oto;"/>
<column name="proc_fk"
full_name="Procedure"
not_null="true"
type="int4"
comment="the procedure this step applies to"/>
<foreign_key column_id="proc_fk"
foreign_table ="Procedure"
foreign_table_pkey ="proc_pk"
fkey_type ="&fkey_oto;"/>
<primary_key column_id="proto_step_pk"/>
</table>
|
|
From: <jas...@us...> - 2003-04-16 21:21:15
|
Update of /cvsroot/genex/genex-server/DB/xml In directory sc8-pr-cvs1:/tmp/cvs-serv4449 Removed Files: AM_Spots.xml Provider.xml SampleProtocols.xml Scanner.xml Spotter.xml Log Message: removed old tables --- AM_Spots.xml DELETED --- --- Provider.xml DELETED --- --- SampleProtocols.xml DELETED --- --- Scanner.xml DELETED --- --- Spotter.xml DELETED --- |
Update of /cvsroot/genex/genex-www/genex-2 In directory sc8-pr-cvs1:/tmp/cvs-serv2286 Added Files: Hardware.html Parameter.html ParameterValue.html Parameterizable.html Procedure.html ProtocolApplication.html ProtocolStep.html Log Message: added new tables for new protocol model --- NEW FILE: Hardware.html --- --- NEW FILE: Parameter.html --- --- NEW FILE: ParameterValue.html --- --- NEW FILE: Parameterizable.html --- --- NEW FILE: Procedure.html --- --- NEW FILE: ProtocolApplication.html --- --- NEW FILE: ProtocolStep.html --- |
|
From: <jas...@us...> - 2003-04-16 21:15:31
|
Update of /cvsroot/genex/genex-www/genex-2 In directory sc8-pr-cvs1:/tmp/cvs-serv1973 Removed Files: AL_Spots.html ArrayLayout.html ArrayMeasurement.html ContactOwner.html FeatureExtraction.html Provider.html SampleProtocols.html Scanner.html Security.html SequenceFeature.html Spotter.html TableAdmin.html Log Message: removed old tables --- AL_Spots.html DELETED --- --- ArrayLayout.html DELETED --- --- ArrayMeasurement.html DELETED --- --- ContactOwner.html DELETED --- --- FeatureExtraction.html DELETED --- --- Provider.html DELETED --- --- SampleProtocols.html DELETED --- --- Scanner.html DELETED --- --- Security.html DELETED --- --- SequenceFeature.html DELETED --- --- Spotter.html DELETED --- --- TableAdmin.html DELETED --- |
|
From: <jas...@us...> - 2003-04-15 17:50:35
|
Update of /cvsroot/genex/genex-server In directory sc8-pr-cvs1:/tmp/cvs-serv14793 Modified Files: MANIFEST.in Log Message: added new files Index: MANIFEST.in =================================================================== RCS file: /cvsroot/genex/genex-server/MANIFEST.in,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** MANIFEST.in 20 Dec 2002 05:35:04 -0000 1.6 --- MANIFEST.in 15 Apr 2003 17:50:31 -0000 1.7 *************** *** 53,56 **** --- 53,57 ---- 'Mason/workspace/logout.html' => '%%GENEX_WORKSPACE_DIR%%', 'Mason/workspace/query.html' => '%%GENEX_WORKSPACE_DIR%%', + 'Mason/workspace/contact-insert.html' => '%%GENEX_WORKSPACE_DIR%%', 'Mason/workspace/comps/authenticate.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', *************** *** 74,77 **** --- 75,79 ---- 'Genex/scripts/cv-check.pl' => '%%GENEX_BIN_DIR%%', 'Genex/scripts/cv-insert.pl' => '%%GENEX_BIN_DIR%%', + 'Genex/scripts/contact-insert.pl' => '%%GENEX_BIN_DIR%%', 'Genex/scripts/externaldb-insert.pl' => '%%GENEX_BIN_DIR%%', 'Genex/scripts/generate_group.pl' => '%%GENEX_BIN_DIR%%', |
|
From: <jas...@us...> - 2003-04-15 17:50:22
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv14653/Mason/workspace
Modified Files:
index.html
Log Message:
new page
Index: index.html
===================================================================
RCS file: /cvsroot/genex/genex-server/Mason/workspace/index.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** index.html 20 Nov 2002 22:28:26 -0000 1.2
--- index.html 15 Apr 2003 17:50:13 -0000 1.3
***************
*** 18,21 ****
--- 18,22 ----
href="experimentset-create.html">experimentset-create.html</a></li>
<li><a href="group-create.html">group-create.html</a></li>
+ <li><a href="contact-insert.html">contact-insert.html</a></li>
</ul>
<%attr>
|
|
From: <jas...@us...> - 2003-04-15 17:47:33
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv13376/Mason/workspace
Added Files:
contact-insert.html.in
Log Message:
new page for adding contact info
--- NEW FILE: contact-insert.html.in ---
% if (($response_page eq "NEW") || ($response_page eq "badUP") || ($response_page eq "badORG")) {
<center>
<h1>Create New Genex Contact</h1>
<form action="<% $action %>"><br>
<br>
% if ($response_page eq "badUP"){
<h3><font color="red">Your information was incomplete. You must supply:
<ul>
<li>Your new Contact's Name or Organization
</ul>
</font></h3>
% }
<center>
<table cellpadding="2" cellspacing="2" border="0"
style="width: 70%; text-align: left; margin-left: auto; margin-right: auto;"
title="enter the following information for your contact"
summary="information about the new genex contact">
<caption><br>
</caption> <tbody>
<tr>
<td valign="top">Contact:<br>
<br>
</td>
<td valign="top"><br>
<br>
</td>
<td valign="top"><br>
<br>
</td>
<td valign="top"><br>
<br>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Name (required unless organization is specified)<br>
<br>
</td>
<td valign="top"><input type="text" name="contact_person" width="30" value="<% $contact_person %>"></td>
<td valign="top"><br>
<br>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Phone<br>
<br>
</td>
<td valign="top"><input type="text" name="contact_person_phone" width="30" value="<% $contact_person_phone %>"></td>
<td valign="top"><br>
<br>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Email<br>
<br>
</td>
<td valign="top"><input type="text" name="contact_person_email" width="30" value="<% $contact_person_email %>"></td>
<td valign="top"><br>
<br>
</td>
</tr>
<tr>
<td valign="top">Organization:<br>
</td>
<td valign="top"><br>
<br>
</td>
<td valign="top"><br>
<br>
</td>
<td valign="top"><br>
<br>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Name (required unless contact person is specified)<br>
<br>
</td>
<td valign="top"><input name="organization" type="text" width="30" value="<% $organization %>">
</td>
<td valign="top"><br>
<br>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Phone<br>
<br>
</td>
<td valign="top"><input name="org_phone" type="text" width="30" value="<% $org_phone %>">
</td>
<td valign="top"><br>
<br>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Toll-free<br>
<br>
</td>
<td valign="top"><input name="org_toll_free_phone" type="text" value="<% $org_toll_free_phone %>" width="30"></td>
<td valign="top"><br>
<br>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Fax<br>
<br>
</td>
<td valign="top"><input name="org_fax" type="text" width="30" value="<% $org_fax %>">
</td>
<td valign="top"><br>
<br>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Email<br>
</td>
<td valign="top"><input name="org_email" type="text" width="30" value="<% $org_email %>">
</td>
<td valign="top"><br>
<br>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">URL<br>
<br>
</td>
<td valign="top"><input name="url" type="text" width="30" value="<% $url %>"></td>
<td valign="top"><br>
<br>
</td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top">Mailing Address<br>
</td>
<td valign="top" colspan="2"><textarea width="40" height="7" name="org_mail_address"><% $org_mail_address %></textarea></td>
</tr>
<tr>
<td valign="top"><br>
<br>
</td>
<td valign="top"><br>
<br>
</td>
<td valign="top"><br>
<br>
</td>
<td valign="top"><br>
<br>
</td>
</tr>
</tbody>
</table>
</center>
<hr noshade size=5>
<h2>Contact Type</h2>
<p>Choose the type of contact you are creating.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>Contact Type</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<& comps/query-drop-down.mason, name=>"contact_type",
array_ref=>\@types &>
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<h2>Read Group</h2>
<p>Choose the <b>read group</b> that will be given to the
contact entry you create.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>Read Group</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<& comps/query-drop-down.mason, name=>"read_group",
array_ref=>\@groups &>
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<h2>Write Group</h2>
<p>Choose the <b>write group</b> that will be given to contact
entry you create.</p>
<table bgcolor="#D8E4F7" border="1" cols="1">
<thead bgcolor="#FFD78F">
<tr>
<th>Write Group</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<& comps/query-drop-down.mason, name=>"write_group",
array_ref=>\@groups &>
</td>
</tr>
</tbody>
</table>
<hr noshade size=5>
<br>
<input name="submitted" type="hidden" value="true">
<input type="submit" name="submit" value="Create This Contact"><br>
<br>
<br>
</center>
% }
% if ($response_page eq "DONE"){
<div style="text-align: center;">
<h1>Genex Contact Created</h1>
% } elsif (!($response_page eq "NEW")){
<b>Contact Creation Failed.</b>
<pre><% $response %></pre>
<b> Hit the back button and try again.</b>
% }
<%attr>
action=>'%%GENEX_WORKSPACE_URL%%/contact-insert.html'
name=>'Create New Genex Contact'
path=>'%%GENEX_WORKSPACE_URL%%/contact-insert.html'
</%attr>
<%args>
$contact_type => ""
$read_group => ""
$write_group => ""
$organization => ""
$org_phone => ""
$org_toll_free_phone => ""
$org_fax => ""
$org_email => ""
$org_mail_address => ""
$url => ""
$contact_person => ""
$contact_person_phone => ""
$contact_person_email => ""
$submitted => ""
$debug => 0
</%args>
<%once>;
</%once>
<%init>;
my $VERSION = '$Id: contact-insert.html.in,v 1.1 2003/04/15 17:47:28 jason_e_stewart Exp $ ';
use Carp;
use Getopt::Long;
use File::Basename;
%%GENEX_EXTRALIBS%%
use Bio::Genex;
use Bio::Genex::Connect;
use Bio::Genex::Config;
use Bio::Genex::GroupSec;
use Bio::Genex::ControlledVocab;
my $action = $m->current_comp->attr('action');
my $response_page;
my $response;
my $commandline;
my @all;
my @groups;
my @types;
my @gs_dbs = Bio::Genex::GroupSec->get_all_objects($dbh);
foreach my $gs_db (@gs_dbs) {
push(@groups,[$gs_db->name,$gs_db->name]);
}
my @ct_dbs = Bio::Genex::ControlledVocab->get_all_objects($dbh,column=>'vocab_name',value=>'ContactType');
foreach my $ct_db (@ct_dbs) {
push(@types,[$ct_db->cv_pk,$ct_db->term_string]);
}
unless ($submitted eq "true"){ # first time only, never clicked the button
$response_page="NEW";
} else {
if (!$contact_person and ! $organization){
$response_page="badUP";
} else {
$commandline = "$Bio::Genex::Config->{GENEX_BIN_DIR}/contact-insert.pl ";
my @args;
push(@args,"--ro_groupname='$read_group'",
"--rw_groupname='$write_group'",
"--username='$session->{username}'",
"--password='$session->{password}'",
"--dbname='$session->{dbname}'");
push(@args,"--organization='$organization'")
if $organization;
push(@args,"--contact_person='$contact_person'")
if $contact_person;
push(@args,"--contact_person_phone='$contact_person_phone'")
if $contact_person_phone;
push(@args,"--contact_person_email='$contact_person_email'")
if $contact_person_email;
push(@args,"--org_email='$org_email'")
if $org_email;
push(@args,"--org_mail_address='$org_mail_address'")
if $org_mail_address;
push(@args,"--org_phone='$org_phone'")
if $org_phone;
push(@args,"--org_toll_free_phone='$org_toll_free_phone'")
if $org_toll_free_phone;
push(@args,"--org_fax='$org_fax'")
if $org_fax;
push(@args,"--url='$url'")
if $url;
$commandline .= join(' ', @args);
open (IN, "$commandline |") || die "cant start script $!\n";
push @all, "result:\n";
while ($response = <IN>){
push @all, $response;
chomp $response;
last if ($response eq "Finished");
}
if ($response eq "Finished"){
$response_page="DONE";
} else {
$response_page="badOPTS";
}
}
}
</%init>
|
|
From: <jas...@us...> - 2003-04-15 17:46:44
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv13011/Genex/scripts
Modified Files:
contact-insert.pl.in
Log Message:
* scripts/contact-insert.pl.in (Repository):
Updated to take all info from command line
Index: contact-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/contact-insert.pl.in,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** contact-insert.pl.in 22 Mar 2002 06:15:59 -0000 1.9
--- contact-insert.pl.in 15 Apr 2003 17:46:37 -0000 1.10
***************
*** 1,11 ****
%%START_PERL%%
! # author: Jason E. Stewart (je...@nc... || ja...@op...)
! # Copyright 2001 Jason E. Stewart
! # Copyright 2000-2001 NCGR
#
my $VERSION = '$Id$ ';
use strict;
! # use blib;
use Carp;
use Getopt::Long;
--- 1,16 ----
%%START_PERL%%
! #
! # contact-insert.pl:
! # script for inserting a new contact into GeneX
! #
! # author: Jason E. Stewart (ja...@op...)
! #
! # Copyright 2002-3 OpenInformatics
#
my $VERSION = '$Id$ ';
+
use strict;
! #use blib;
use Carp;
use Getopt::Long;
***************
*** 13,185 ****
%%GENEX_EXTRALIBS%%
! use XML::DOM;
! use Bio::Genex qw(error);
! use Bio::Genex::DBUtils;
! use Bio::Genex::XMLUtils qw(assert_element);
! use Bio::Genex::GenexAdmin;
my %OPTIONS;
! $OPTIONS{dbname} = $Bio::Genex::DBNAME;
my $rc = GetOptions(\%OPTIONS,
! 'file=s',
! 'name=s',
! 'dbname=s',
! 'update'
);
my $USAGE = <<"EOU";
! usage: $0 --file=file_name [options]
! options: --update
! --dbname=dbname
! --name=email_address
! EOU
!
! die "Bad option: $rc\n$USAGE" unless $rc;
! die "Must specify --file\n$USAGE" unless defined $OPTIONS{file};
!
!
! unless (exists $OPTIONS{name}) {
! select(STDOUT);
! $| = 1;
! DB_INSTALLED_BY: while (1) {
! print STDOUT <<"EOT";
! You didn\'t identify yourself with the --name option.
! I need to know your FULL EMAIL address so that I can store it in the
! GenexAdmin table in case trouble with this update is encountered.
! EOT
! print STDOUT "[$OPTIONS{name}] ? ";
! my $tmp;
! $tmp = <>;
! $tmp =~ s/\s//g;
! if (!$tmp) {
! last DB_INSTALLED_BY;
! } elsif ($tmp =~ /@/) {
! $OPTIONS{name} = $tmp;
! last DB_INSTALLED_BY;
! } else {
! print STDERR <<"EOE";
! #### ERROR ####
! I need a full, email address such as "genex\@your.place.com"
! Please try again.
- EOE
- }
- }
- }
- my $PARSER = XML::DOM::Parser->new();
! my $DOC = $PARSER->parsefile($OPTIONS{file});
! my @contact_list = $DOC->getElementsByTagName('contact');
my @error_args = (caller=>$0);
! # open up a writeable connection
! my $dbh = Bio::Genex::Connect->new(USER=>$SU_USERNAME,
! PASSWORD=>$SU_PASSWORD,
! DBNAME=>$OPTIONS{dbname},
! TRANSACTION=>1
! );
! error(@error_args,
! message=>"Couldn't login to DB: $DBI::errstr",
! );
!
! my $curr_table = 'Contact';
! my $timeformat = '%r %A %B %d %Y';
!
! print STDERR scalar @contact_list, " Contacts to insert\n";
! foreach my $con_node (@contact_list) {
! # assert_element($con_node,'contact');
! # my $type = $con_node->getAttribute('type');
! # error("Couldn't find type for node: " . $con_node->toString())
! # unless $type ne '';
! my $name = $con_node->getAttribute('contact_person') ne '' ?
! $con_node->getAttribute('contact_person') :
! $con_node->getAttribute('organization');
! $dbh->error(@error_args,
! no_errstr=>1,
! message=>"Couldn't find name for node: " . $con_node->toString()
! )
! unless $name ne '';
! my $column_map = $con_node->getAttributes();
! my @attr_nodes = @{$column_map->getValues()};
! my %attributes = map {$_->getName, $_->getValue} @attr_nodes;
! if ($OPTIONS{update}) {
! # print STDERR "Updating contact for $type, $name\n";
! print STDERR "Updating contact for $name\n";
- my $WHERE = '(contact_person=' .
- $dbh->quote($name) . ' OR organization=' . $dbh->quote($name);
- my $sql = $dbh->create_select_sql(
- FROM=>[$curr_table],
- COLUMNS=>['con_pk'],
- WHERE=>"$WHERE"
- );
- my $con_pk = $dbh->selectall_arrayref($sql);
- $dbh->error(@error_args,
- message=>"couldn't SELECT contact for node: " . $con_node->toString(),
- sql=>$sql,
- )
- if $dbh->err;
- # extract the value from the array of arrays
- $con_pk = $con_pk->[0][0];
- $dbh->error(@error_args,
- no_errstr=>1,
- message=>"couldn't get contact for node: " . $con_node->toString(),
- sql=>$sql,
- )
- unless $con_pk;
! foreach my $key (keys %attributes) {
! $sql = "UPDATE $curr_table set $key=? WHERE con_pk=$con_pk";
! my $sth = $dbh->prepare($sql);
! $dbh->error(@error_args,
! message=>"couldn't prepare update SQL",
! sql=>$sql,
! )
! if $dbh->err;
! $sth->execute($attributes{$key});
! $dbh->error(@error_args,
! message=>"couldn't execute update SQL for <$key>=<$attributes{$key}>",
! sql=>$sql,
! sth=>$sth,
! )
! if $dbh->err;
! }
! } else {
! print STDERR "Inserting contact for $name\n";
! my $sql = $dbh->create_insert_sql($curr_table,\%attributes);
! $dbh->do($sql);
! $dbh->error(@error_args,
! message=>"couldn't insert record for node: " . $con_node->toString(),
! sql=>$sql,
! )
! if $dbh->err;
! }
}
-
- my $ga_db = Bio::Genex::GenexAdmin->new();
- # $ga_db->install_date(timestamp);
- $ga_db->installed_by($OPTIONS{name});
- $ga_db->description('upgraded using $0, Users affected: ' . join(', ', @contact_list));
- $ga_db->insert_db();
-
- $dbh->error(@error_args,
- message=>"Couldn't insert GenexAdmin record: DBI=<$DBI::errstr>")
- if $dbh->err;
-
- $dbh->commit();
- # $dbh->rollback();
$dbh->disconnect();
exit(0);
--- 18,163 ----
%%GENEX_EXTRALIBS%%
! use Bio::Genex;
! use Bio::Genex::Config;
! use Bio::Genex::Connect;
! use Bio::Genex::Contact;
! use Bio::Genex::ContactType;
my %OPTIONS;
! $OPTIONS{dbname} = $Bio::Genex::Config->{DB_NAME};
my $rc = GetOptions(\%OPTIONS,
! 'username=s', # Clients username
! 'password=s', # clients password
! 'new_user=s', # new genex user username
! 'new_pass=s', # new genex user password
! 'new_pass2=s',# retype
! 'dbname=s', # name of the database
! 'debug', # dedbug mode?
! 'no_group', # don't unclude group info
! 'organization=s',
! 'contact_person=s',
! 'contact_person_phone=s',
! 'contact_person_email=s',
! 'org_phone=s',
! 'org_email=s',
! 'org_mail_address=s',
! 'org_toll_free_phone=s',
! 'org_fax=s',
! 'url=s',
! 'ro_groupname=s',
! 'rw_groupname=s',
!
);
my $USAGE = <<"EOU";
! usage: $0 [required params] [options]
! require params:
! --username=name : name of user to login to DB as
! --password=word : password to use for DB login
! one of the following must be specified:
! --contact_person=name : contact full name
! --organization=name : contact organization
! options:
! --dbname=name : name of DB to use (defaults to $Bio::Genex::Config->{DB_NAME})
! --ro_groupname=name : name of RO group (defaults to $Bio::Genex::Config->{GENEX_PUBLIC_GROUP})
! --rw_groupname=name : name of RW group (defaults to $Bio::Genex::Config->{GENEX_SUPERUSER_GROUP})
! --contact_person_phone=name : contact phone
! --contact_person_email=name : contact email
! --org_phone=name : contact organization\'s phone
! --org_email=name : contact organization\'s phone
! --org_mail_address=name : contact organization\'s address
! --org_toll_free_phone=name : contact organization\'s toll free phone
! --org_fax=name : contact organization\'s fax
! --url=name : contact url
! --debug : rollback instead of commit
! --help : this message
! EOU
! die "Bad option\n$USAGE" unless $rc;
! die "$USAGE" if exists $OPTIONS{help};
! die "Must specify --organization or --contact_person\n$USAGE"
! unless exists $OPTIONS{contact_person} or exists $OPTIONS{organization};
! die "Must specify --username\n$USAGE"
! unless exists $OPTIONS{username};
! die "Must specify --password\n$USAGE"
! unless exists $OPTIONS{password};
! $OPTIONS{ro_groupname} = $Bio::Genex::Config->{GENEX_PUBLIC_GROUP}
! unless $OPTIONS{ro_groupname};
! $OPTIONS{rw_groupname} = $Bio::Genex::Config->{GENEX_SUPERUSER_GROUP}
! unless $OPTIONS{rw_groupname};
! my @args = (USER=>$OPTIONS{username},
! PASSWORD=>$OPTIONS{password},
! DBNAME=>$OPTIONS{dbname},
! TRANSACTION=>1,
! );
! my $dbh = Bio::Genex::Connect->new(@args);
! die "Couldn't login to DB: Bad username or password"
! unless defined $dbh;
my @error_args = (caller=>$0);
! my ($ro_group_db) = Bio::Genex::GroupSec->get_objects($dbh,
! $OPTIONS{ro_groupname});
! $dbh->error(@error_args,
! msg=>"Group $OPTIONS{ro_groupname} doesn't exist in DB",
! ) unless defined $ro_group_db;
! my ($rw_group_db) = Bio::Genex::GroupSec->get_objects($dbh,
! $OPTIONS{rw_groupname});
! $dbh->error(@error_args,
! msg=>"Group $OPTIONS{rw_groupname} doesn't exist in DB",
! ) unless defined $rw_group_db;
! # the user controls his own contact info
! my $c = Bio::Genex::Contact->new(ro_groupname_obj=>$ro_group_db,
! rw_groupname_obj=>$rw_group_db
! );
! $c->contact_person($OPTIONS{contact_person})
! if exists $OPTIONS{contact_person};
! $c->organization($OPTIONS{organization})
! if exists $OPTIONS{organization};
! $c->contact_person_phone($OPTIONS{contact_person_phone})
! if exists $OPTIONS{contact_person_phone};
! $c->contact_person_email($OPTIONS{contact_person_email})
! if exists $OPTIONS{contact_person_email};
! $c->org_phone($OPTIONS{org_phone})
! if exists $OPTIONS{org_phone};
! $c->org_email($OPTIONS{org_email})
! if exists $OPTIONS{org_email};
! $c->org_mail_address($OPTIONS{org_mail_address})
! if exists $OPTIONS{org_mail_address};
! $c->org_toll_free_phone($OPTIONS{org_toll_free_phone})
! if exists $OPTIONS{org_toll_free_phone};
! $c->org_fax($OPTIONS{org_fax})
! if exists $OPTIONS{org_fax};
! $c->url($OPTIONS{url})
! if exists $OPTIONS{url};
! my $ct = Bio::Genex::ContactType->new(con_obj=>$c,
! type=>'user'
! );
! print "Adding contact info\n";
! $ct->insert_db($dbh);
! $dbh->error(@error_args,
! message=>"Couldn't insert contact",
! ) if $dbh->err;
! print "Finished\n";
! if ($OPTIONS{debug}) {
! $dbh->rollback();
! } else {
! $dbh->commit();
}
$dbh->disconnect();
exit(0);
|
|
From: <jas...@us...> - 2003-04-10 08:02:23
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv31934
Modified Files:
mbad-insert.pl.in
Log Message:
* scripts/mbad-insert.pl.in (Repository):
users other than genex must use views for insertion
Index: mbad-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/mbad-insert.pl.in,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** mbad-insert.pl.in 9 Apr 2003 19:51:20 -0000 1.11
--- mbad-insert.pl.in 10 Apr 2003 08:02:18 -0000 1.12
***************
*** 111,114 ****
--- 111,115 ----
my $data_table = $qt_dim_db->data_table_name();
+ $data_table .= '_view' unless $OPTIONS{username} eq 'genex';
print STDERR "Using data table: $data_table\n" if $OPTIONS{debug};
|
|
From: <jas...@us...> - 2003-04-09 21:54:51
|
Update of /cvsroot/genex/genex-server/DB/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv29964
Modified Files:
fix-array-mas5.pl
Log Message:
* DB/scripts/fix-array-mas5.pl (Repository):
need to use probe set names for feature names in short files
Index: fix-array-mas5.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/scripts/fix-array-mas5.pl,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** fix-array-mas5.pl 7 Apr 2003 19:07:31 -0000 1.2
--- fix-array-mas5.pl 9 Apr 2003 21:54:45 -0000 1.3
***************
*** 106,109 ****
--- 106,110 ----
if (exists $OPTIONS{short}) {
+ # short files use probe set names not line numbers
@INDICES = qw(0 0);
$data_start_regexp = qr/^\s+/;
***************
*** 146,152 ****
my @data = split /\t/;
my ($num,$name) = @data[@INDICES];
-
- # we create the line number for short files
- $num = $count if exists $OPTIONS{short};
# commence error checking
--- 147,150 ----
|
|
From: <jas...@us...> - 2003-04-09 21:41:23
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv24736
Modified Files:
user-insert.pl.in
Log Message:
finish => disconnect, doh.
Index: user-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/user-insert.pl.in,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** user-insert.pl.in 9 Apr 2003 21:40:06 -0000 1.7
--- user-insert.pl.in 9 Apr 2003 21:41:18 -0000 1.8
***************
*** 121,125 ****
# permissions for this DB. We need to reconnect to start a new
# transaction
! $dbh->finish();
$dbh = Bio::Genex::Connect->new(@args);
} else {
--- 121,125 ----
# permissions for this DB. We need to reconnect to start a new
# transaction
! $dbh->disconnect();
$dbh = Bio::Genex::Connect->new(@args);
} else {
|
|
From: <jas...@us...> - 2003-04-09 21:40:17
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv24333
Modified Files:
user-insert.pl.in
Log Message:
* scripts/user-insert.pl.in (Repository):
must create new connection on error
Index: user-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/user-insert.pl.in,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** user-insert.pl.in 9 Apr 2003 21:35:59 -0000 1.6
--- user-insert.pl.in 9 Apr 2003 21:40:06 -0000 1.7
***************
*** 103,112 ****
unless $OPTIONS{rw_groupname};
! my $dbh = Bio::Genex::Connect->new(
! USER=>$OPTIONS{username},
! PASSWORD=>$OPTIONS{password},
! DBNAME=>$OPTIONS{dbname},
! TRANSACTION=>1,
! );
die "Couldn't login to DB: Bad username or password"
unless defined $dbh;
--- 103,112 ----
unless $OPTIONS{rw_groupname};
! my @args = (USER=>$OPTIONS{username},
! PASSWORD=>$OPTIONS{password},
! DBNAME=>$OPTIONS{dbname},
! TRANSACTION=>1,
! );
! my $dbh = Bio::Genex::Connect->new(@args);
die "Couldn't login to DB: Bad username or password"
unless defined $dbh;
***************
*** 117,123 ****
$dbh->do($sql);
if ($dbh->err) {
! # if the user already exists in Postgres, we still want to set
! # permissions for this DB
! unless ($dbh->errstr =~ /already exists/) {
$dbh->error(@error_args,
sql=>$sql,
--- 117,127 ----
$dbh->do($sql);
if ($dbh->err) {
! if ($dbh->errstr =~ /already exists/) {
! # if the user already exists in Postgres, we still want to set
! # permissions for this DB. We need to reconnect to start a new
! # transaction
! $dbh->finish();
! $dbh = Bio::Genex::Connect->new(@args);
! } else {
$dbh->error(@error_args,
sql=>$sql,
|
|
From: <jas...@us...> - 2003-04-09 21:39:11
|
Update of /cvsroot/genex/genex-server
In directory sc8-pr-cvs1:/tmp/cvs-serv13129
Modified Files:
Configure
Log Message:
* Configure (Repository):
exchanged one more hard-coded 'genex' for $GENEX_DIR
Index: Configure
===================================================================
RCS file: /cvsroot/genex/genex-server/Configure,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** Configure 9 Apr 2003 20:40:09 -0000 1.15
--- Configure 9 Apr 2003 21:12:56 -0000 1.16
***************
*** 1385,1389 ****
unless (defined $DB_NAME) {
spacer();
! $DB_NAME = $DEFAULT_VARS{DB_NAME} || 'genex';
my @sources;
--- 1385,1389 ----
unless (defined $DB_NAME) {
spacer();
! $DB_NAME = $DEFAULT_VARS{DB_NAME} || $GENEX_DIR;
my @sources;
|
|
From: <jas...@us...> - 2003-04-09 21:39:10
|
Update of /cvsroot/genex/genex-server In directory sc8-pr-cvs1:/tmp/cvs-serv13285 Modified Files: ChangeLog Log Message: new Index: ChangeLog =================================================================== RCS file: /cvsroot/genex/genex-server/ChangeLog,v retrieving revision 1.123 retrieving revision 1.124 diff -C2 -d -r1.123 -r1.124 *** ChangeLog 9 Apr 2003 20:41:54 -0000 1.123 --- ChangeLog 9 Apr 2003 21:13:20 -0000 1.124 *************** *** 6,9 **** --- 6,10 ---- * Configure (Repository): ensured that everything was based off GENEX_DIR + exchanged one more hard-coded 'genex' for $GENEX_DIR 2003-04-07 Jason E. Stewart <ja...@op...> |
