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From: <jas...@us...> - 2002-11-20 21:19:49
|
Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv25788/Mason/workspace
Added Files:
syshandler
Log Message:
new base component
--- NEW FILE: syshandler ---
<% $m->call_next() %>
<%once>
</%once>
<%flags>
inherit => undef
</%flags>
<%init>;
$DEBUG = '';
if ($ARGS{debug}) {
$DEBUG = $m->comp('comps/debug-args.mason','args'=>\%ARGS);
}
</%init>
|
|
From: <jas...@us...> - 2002-11-20 00:24:54
|
Update of /cvsroot/genex/genex-server In directory sc8-pr-cvs1:/tmp/cvs-serv12533 Modified Files: MANIFEST.in Log Message: moved Mason scripts Index: MANIFEST.in =================================================================== RCS file: /cvsroot/genex/genex-server/MANIFEST.in,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** MANIFEST.in 7 Nov 2002 14:51:29 -0000 1.1 --- MANIFEST.in 20 Nov 2002 00:24:51 -0000 1.2 *************** *** 2,40 **** 'apache/genex-2.conf' => '%%APACHE_CONF_DIR%%', ! 'G2G/mason/workspace.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'G2G/mason/add_user_to_group.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'G2G/mason/array-design.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'G2G/mason/authenticate.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'G2G/mason/autohandler' => '%%GENEX_WORKSPACE_DIR%%', ! 'G2G/mason/bioassay.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'G2G/mason/check-cookie.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'G2G/mason/check-login.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'G2G/mason/data-loader.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'G2G/mason/data-sources.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'G2G/mason/experiments.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'G2G/mason/experimentset-create.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'G2G/mason/generate_group.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'G2G/mason/generate_user.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'G2G/mason/group-maint.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'G2G/mason/group-create.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'G2G/mason/index.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'G2G/mason/kill-cookie.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'G2G/mason/logout.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'G2G/mason/query.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'G2G/mason/comps/authenticate.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', ! 'G2G/mason/comps/data-select.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', ! 'G2G/mason/comps/debug-args.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', ! 'G2G/mason/comps/g2g-request.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', ! 'G2G/mason/comps/hiddenlist.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', ! 'G2G/mason/comps/query-checkboxes.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', ! 'G2G/mason/comps/query-drop-down.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', ! 'G2G/mason/comps/query-select.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', ! 'G2G/mason/workspace-comps/footer.mason' => '%%GENEX_WORKSPACE_DIR%%/workspace-comps', ! 'G2G/mason/workspace-comps/header.mason' => '%%GENEX_WORKSPACE_DIR%%/workspace-comps', ! 'G2G/mason/workspace-comps/main.mason' => '%%GENEX_WORKSPACE_DIR%%/workspace-comps', ! 'G2G/mason/workspace-comps/nav.mason' => '%%GENEX_WORKSPACE_DIR%%/workspace-comps', --- 2,40 ---- 'apache/genex-2.conf' => '%%APACHE_CONF_DIR%%', ! 'Mason/workspace/workspace.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'Mason/workspace/add_user_to_group.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'Mason/workspace/array-design.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'Mason/workspace/authenticate.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'Mason/workspace/autohandler' => '%%GENEX_WORKSPACE_DIR%%', ! 'Mason/workspace/bioassay.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'Mason/workspace/check-cookie.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'Mason/workspace/check-login.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'Mason/workspace/data-loader.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'Mason/workspace/data-sources.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'Mason/workspace/experiments.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'Mason/workspace/experimentset-create.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'Mason/workspace/generate_group.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'Mason/workspace/generate_user.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'Mason/workspace/group-maint.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'Mason/workspace/group-create.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'Mason/workspace/index.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'Mason/workspace/kill-cookie.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'Mason/workspace/logout.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'Mason/workspace/query.html' => '%%GENEX_WORKSPACE_DIR%%', ! 'Mason/workspace/comps/authenticate.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', ! 'Mason/workspace/comps/data-select.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', ! 'Mason/workspace/comps/debug-args.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', ! 'Mason/workspace/comps/g2g-request.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', ! 'Mason/workspace/comps/hiddenlist.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', ! 'Mason/workspace/comps/query-checkboxes.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', ! 'Mason/workspace/comps/query-drop-down.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', ! 'Mason/workspace/comps/query-select.mason' => '%%GENEX_WORKSPACE_DIR%%/comps', ! 'Mason/workspace/workspace-comps/footer.mason' => '%%GENEX_WORKSPACE_DIR%%/workspace-comps', ! 'Mason/workspace/workspace-comps/header.mason' => '%%GENEX_WORKSPACE_DIR%%/workspace-comps', ! 'Mason/workspace/workspace-comps/main.mason' => '%%GENEX_WORKSPACE_DIR%%/workspace-comps', ! 'Mason/workspace/workspace-comps/nav.mason' => '%%GENEX_WORKSPACE_DIR%%/workspace-comps', |
|
From: <jas...@us...> - 2002-11-20 00:22:44
|
Update of /cvsroot/genex/genex-server
In directory sc8-pr-cvs1:/tmp/cvs-serv11321
Modified Files:
ChangeLog
Log Message:
usual
Index: ChangeLog
===================================================================
RCS file: /cvsroot/genex/genex-server/ChangeLog,v
retrieving revision 1.108
retrieving revision 1.109
diff -C2 -d -r1.108 -r1.109
*** ChangeLog 18 Nov 2002 04:29:14 -0000 1.108
--- ChangeLog 20 Nov 2002 00:22:41 -0000 1.109
***************
*** 1,2 ****
--- 1,7 ----
+ 2002-11-19 Jason E. Stewart <ja...@op...>
+
+ * DB/xml/Software.xml (Repository):
+ removed redundant unique index
+
2002-11-17 Harry Mangalam <hj...@ta...>
* many mods to the INSTALL doc, inclusing breaking some parts out into
|
|
From: <jas...@us...> - 2002-11-20 00:22:18
|
Update of /cvsroot/genex/genex-server/Genex In directory sc8-pr-cvs1:/tmp/cvs-serv11059/Genex Modified Files: ChangeLog Log Message: usual Index: ChangeLog =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/ChangeLog,v retrieving revision 1.119 retrieving revision 1.120 diff -C2 -d -r1.119 -r1.120 *** ChangeLog 15 Nov 2002 21:51:26 -0000 1.119 --- ChangeLog 20 Nov 2002 00:22:15 -0000 1.120 *************** *** 1,3 **** --- 1,26 ---- + 2002-11-19 Jason E. Stewart <ja...@op...> + + * scripts/array-design-insert.pl.in (Message): + added --count + added --reporters_only + renamed --no_reporter to --no_reporters + 2002-11-15 Jason E. Stewart <ja...@op...> + + * scripts/qtdim-insert.pl.in (Repository): + made the data table name based on the command line input instead + of info from the MAGE-ML file + + * scripts/mbad-insert.pl.in (Repository): + use table_or_viewname() for Feature instead of hardcoding + tablename + better error checking on regex's + fixed broken feature identifier string + + * scripts/gendb.pl.in (Repository): + quantarray QT dim fixes + + * scripts/create_genex_class.pl.in (Repository): + insert_matrix() fixes. * Genex.pm.in (Repository): |
|
From: <jas...@us...> - 2002-11-20 00:21:59
|
Update of /cvsroot/genex/genex-server/DB/xml
In directory sc8-pr-cvs1:/tmp/cvs-serv10900/DB/xml
Modified Files:
Software.xml
Log Message:
* DB/xml/Software.xml (Repository):
removed redundant unique index
Index: Software.xml
===================================================================
RCS file: /cvsroot/genex/genex-server/DB/xml/Software.xml,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** Software.xml 13 Apr 2002 23:13:04 -0000 1.5
--- Software.xml 20 Nov 2002 00:21:56 -0000 1.6
***************
*** 63,66 ****
<primary_key column_id="sw_pk"/>
<unique column_ids="name version producer_con_fk"/>
- <unique column_ids="name version"/>
</table>
--- 63,65 ----
|
Update of /cvsroot/genex/genex-server/Mason/workspace/workspace-comps
In directory sc8-pr-cvs1:/tmp/cvs-serv9395/Mason/workspace/workspace-comps
Added Files:
.cvsignore footer.mason.in header.mason.in main.mason.in
nav.mason.in
Log Message:
moved Mason scripts
--- NEW FILE: .cvsignore ---
footer.mason
header.mason
main.mason
nav.mason
--- 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...> - 2002-11-20 00:19:41
|
Update of /cvsroot/genex/genex-server/Mason/workspace/comps
In directory sc8-pr-cvs1:/tmp/cvs-serv9395/Mason/workspace/comps
Added Files:
.cvsignore authenticate.mason.in data-select.mason
debug-args.mason g2g-request.mason hiddenlist.mason
query-checkboxes.mason query-drop-down.mason
query-select.mason
Log Message:
moved Mason scripts
--- NEW FILE: .cvsignore ---
authenticate.mason
--- NEW FILE: authenticate.mason.in ---
<%attr>
name=>'GeneX DB Authentication Checker'
page=>'%%GENEX_WORKSPACE_URL%%/authenticate.html'
</%attr>
<%args>
$caller
</%args>
<%once>;
use Bio::Genex::HTMLUtils;
</%once>
<%init>;
$m->clear_buffer();
# $r is the global variable for the Apache request object
# $m is the global variable for the Mason request object
Bio::Genex::HTMLUtils::call_page($r,
$m->current_comp->attr('page'),
$caller
);
$m->abort(301);
</%init>
--- NEW FILE: data-select.mason ---
<select size="7" multiple="yes" name="<% $name %>">
% foreach (@{$array_ref}) {
% my $pkey = $_->[0];
% my $value = $_->[1];
<option value="<% $pkey %>"><% $value %></option>
% }
</select>
<%args>
$name
$array_ref
</%args>
--- NEW FILE: debug-args.mason ---
<table border="1">
<tr><th>Param Name</th><th>Param Value</th></tr>
% foreach my $arg (keys %params) {
<tr><td><% $arg %></td><td><% $params{$arg} %></td>
% }
</table>
<%args>
$args
</%args>
<%init>
my %params;
foreach my $arg (keys %{$args}) {
if (ref($args->{$arg}) eq 'ARRAY') {
$params{$arg} = join(',', @{$args->{$arg}});
} else {
$params{$arg} = $args->{$arg};
}
}
</%init>
--- NEW FILE: g2g-request.mason ---
<%once>
use Bio::Genex qw(error);
use Bio::Genex::Connect;
use LWP::UserAgent;
my $g2g_sql = <<SQL;
SELECT url FROM G2G
WHERE g2g_pk=?
SQL
my $dbh;
my $ua;
</%once>
<%args>
$request
@g2g
</%args>
<%init>
my %responses;
$dbh = Bio::Genex::Connect->new();
my $sth = $dbh->prepare($g2g_sql);
$dbh->error(sql=>$g2g_sql,
message=>"Couldn't prepare g2g select sql")
if $dbh->err;
my @urls;
foreach my $g2g (@g2g) {
$sth->execute($g2g);
$dbh->error(sql=>$g2g_sql,
sth=>$sth,
message=>"Couldn't exectute g2g select sql for: $g2g")
if $sth->err;
push(@urls,$sth->fetchrow_arrayref->[0]);
}
$sth->finish();
# Create a user agent object
$ua = LWP::UserAgent->new();
$ua->agent("G2G/0.1 " . $ua->agent);
foreach my $url (@urls) {
# Create a request
my $req = HTTP::Request->new(POST=>$url);
$req->content_type('multipart/form-data');
$req->content($request);
# Pass request to the user agent and get a response back
my $res = $ua->request($req);
# Check the outcome of the response
if (!$res->is_success) {
# get the value of the X-G2G-ERROR header
my $error = $res->headers->header('X-G2G-ERROR');
error(message=>"G2G Request Error: $error");
}
$responses{$url} = $res->content();
}
</%init>
<%perl>
return %responses;
</%perl>
--- NEW FILE: hiddenlist.mason ---
% foreach my $val (@values) {
<input type="hidden" name="<% $name %>" value="<% $val %>">
% }
<%args>
$name
$value
</%args>
<%init>
my @values;
if (ref($value) eq 'ARRAY') {
@values = @{$value};
} else {
@values = ($value);
}
</%init>
--- 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>
--- NEW FILE: query-select.mason ---
<select bgcolor="#BFD8D8" size="7" multiple="yes" 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...> - 2002-11-20 00:17:13
|
Update of /cvsroot/genex/genex-server/Mason/workspace/workspace-comps In directory sc8-pr-cvs1:/tmp/cvs-serv7821/Mason/workspace/workspace-comps Log Message: Directory /cvsroot/genex/genex-server/Mason/workspace/workspace-comps added to the repository |
|
From: <jas...@us...> - 2002-11-20 00:16:38
|
Update of /cvsroot/genex/genex-server/Mason/workspace/comps In directory sc8-pr-cvs1:/tmp/cvs-serv7487/Mason/workspace/comps Log Message: Directory /cvsroot/genex/genex-server/Mason/workspace/comps added to the repository |
|
From: <jas...@us...> - 2002-11-20 00:15:15
|
Update of /cvsroot/genex/genex-server/Mason/workspace In directory sc8-pr-cvs1:/tmp/cvs-serv6687/Mason/workspace Log Message: Directory /cvsroot/genex/genex-server/Mason/workspace added to the repository |
|
From: <jas...@us...> - 2002-11-20 00:12:33
|
Update of /cvsroot/genex/genex-server/Mason In directory sc8-pr-cvs1:/tmp/cvs-serv5066/Mason Log Message: Directory /cvsroot/genex/genex-server/Mason added to the repository |
|
From: <jas...@us...> - 2002-11-20 00:12:16
|
Update of /cvsroot/genex/genex-server/G2G/mason/workspace-comps In directory sc8-pr-cvs1:/tmp/cvs-serv4863/G2G/mason/workspace-comps Removed Files: .cvsignore footer.mason.in header.mason.in main.mason.in nav.mason.in Log Message: moved Mason scripts --- .cvsignore DELETED --- --- footer.mason.in DELETED --- --- header.mason.in DELETED --- --- main.mason.in DELETED --- --- nav.mason.in DELETED --- |
|
From: <jas...@us...> - 2002-11-20 00:12:16
|
Update of /cvsroot/genex/genex-server/G2G/mason/comps In directory sc8-pr-cvs1:/tmp/cvs-serv4863/G2G/mason/comps Removed Files: authenticate.mason.in data-select.mason debug-args.mason g2g-request.mason hiddenlist.mason query-checkboxes.mason query-drop-down.mason query-select.mason Log Message: moved Mason scripts --- authenticate.mason.in DELETED --- --- data-select.mason DELETED --- --- debug-args.mason DELETED --- --- g2g-request.mason DELETED --- --- hiddenlist.mason DELETED --- --- query-checkboxes.mason DELETED --- --- query-drop-down.mason DELETED --- --- query-select.mason DELETED --- |
Update of /cvsroot/genex/genex-server/G2G/mason In directory sc8-pr-cvs1:/tmp/cvs-serv4863/G2G/mason Removed Files: .cvsignore add_user_to_group.html.in array-design.html.in authenticate.html.in autohandler.in bioassay.html.in check-cookie.html check-login.html data-loader.html.in data-sources.html.in experiments.html experimentset-create.html.in generate_group.html.in generate_user.html.in group-create.html.in group-maint.html.in index.html kill-cookie.html logout.html query.html.in user-insert.html.in workspace.html.in Log Message: moved Mason scripts --- .cvsignore DELETED --- --- add_user_to_group.html.in DELETED --- --- array-design.html.in DELETED --- --- authenticate.html.in DELETED --- --- autohandler.in DELETED --- --- bioassay.html.in DELETED --- --- check-cookie.html DELETED --- --- check-login.html DELETED --- --- data-loader.html.in DELETED --- --- data-sources.html.in DELETED --- --- experiments.html DELETED --- --- experimentset-create.html.in DELETED --- --- generate_group.html.in DELETED --- --- generate_user.html.in DELETED --- --- group-create.html.in DELETED --- --- group-maint.html.in DELETED --- --- index.html DELETED --- --- kill-cookie.html DELETED --- --- logout.html DELETED --- --- query.html.in DELETED --- --- user-insert.html.in DELETED --- --- workspace.html.in DELETED --- |
|
From: <jas...@us...> - 2002-11-19 22:33:30
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv28370
Modified Files:
array-design-insert.pl.in
Log Message:
* scripts/array-design-insert.pl.in (Message):
added --reporters_only
renamed --no_reporter to --no_reporters
Index: array-design-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/array-design-insert.pl.in,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** array-design-insert.pl.in 19 Nov 2002 20:44:30 -0000 1.4
--- array-design-insert.pl.in 19 Nov 2002 22:33:25 -0000 1.5
***************
*** 44,48 ****
'ro_group=s',
'rw_group=s',
! 'no_reporter',
'help',
'debug',
--- 44,49 ----
'ro_group=s',
'rw_group=s',
! 'no_reporters',
! 'reporters_only',
'help',
'debug',
***************
*** 60,64 ****
--ro_group : the group with permission to view this design
--rw_group : the group with permission to modify this design
! --no_reporter : do not process reporters
--count=num : print output every num tags
--help : print this message
--- 61,66 ----
--ro_group : the group with permission to view this design
--rw_group : the group with permission to modify this design
! --no_reporters : do not process reporters
! --reporters_only : only process reporters
--count=num : print output every num tags
--help : print this message
***************
*** 77,80 ****
--- 79,85 ----
unless exists $OPTIONS{password};
+ die "--reporters_only and --no_reporters are mutually exclusive\n$USAGE"
+ if exists $OPTIONS{no_reporters} and exists $OPTIONS{reporters_only};
+
# my $PARSER = XML::Xerces::DOMParser->new();
***************
*** 133,137 ****
#
my %REPORTERS;
! unless (exists $OPTIONS{no_reporter}) {
my @mage_reporters = ();
unless (exists $mage->packages->{DesignElement}) {
--- 138,142 ----
#
my %REPORTERS;
! unless (exists $OPTIONS{no_reporters}) {
my @mage_reporters = ();
unless (exists $mage->packages->{DesignElement}) {
***************
*** 158,170 ****
rw_groupname=>$OPTIONS{rw_group},
);
! $REPORTERS{$name} = $rep_db->insert_db(dbh=>$dbh,no_genex_admin=>1);
$dbh->error(@error_args,
message=>"couldn't insert record for reporter: $name")
if $dbh->err;
!
}
$stop = new Benchmark;
$diff = timediff($stop,$start);
print STDERR "Inserting Reporters took:", timestr($diff),"\n";
}
--- 163,177 ----
rw_groupname=>$OPTIONS{rw_group},
);
! my $rep_pk = $rep_db->insert_db(dbh=>$dbh,no_genex_admin=>1);
$dbh->error(@error_args,
message=>"couldn't insert record for reporter: $name")
if $dbh->err;
! $REPORTERS{$name} = $rep_pk
! unless exists $OPTIONS{reporters_only};
}
$stop = new Benchmark;
$diff = timediff($stop,$start);
print STDERR "Inserting Reporters took:", timestr($diff),"\n";
+ exit(0) if $OPTIONS{reporters_only};
}
|
|
From: <tw...@us...> - 2002-11-19 22:16:38
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv21007
Modified Files:
Tag: Rel-1_0_1-branch
analysis_tree_lib.pl test_tree.pl
Log Message:
remove unused subs: analyze_tree(), tile(), tile_pass2()
Index: analysis_tree_lib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/analysis_tree_lib.pl,v
retrieving revision 1.1.2.29
retrieving revision 1.1.2.30
diff -C2 -d -r1.1.2.29 -r1.1.2.30
*** analysis_tree_lib.pl 19 Nov 2002 21:27:32 -0000 1.1.2.29
--- analysis_tree_lib.pl 19 Nov 2002 22:16:35 -0000 1.1.2.30
***************
*** 3,20 ****
use strict;
! my %tree;
! my %parent;
! my %children;
! my %node2g;
! my @generation;
! my %loc;
! my @table;
! my @colors;
! my @m_width;
$::analysis_tree_lib_loaded = 1;
$::analysis_tree_lib_loaded = 1; # quiet compile warnings
-
sub insert_tree
{
--- 3,19 ----
use strict;
! my %tree; # the analysis tree as read in from the db
! my %parent; # key is node, value is node's parent
! my %children; # key is node, value is a list of children nodes
! my %node2g; # key is node, value is a generation
! my @generation;# key is generation, value is a list of nodes in this generation
! my %loc; # key is node, value is a list of row,col
! my @table; # 2D array, indices are [row][col], values are nodes
! my @colors; # 2D array, indices are [row][col], values are HTML colors
! my @m_width; # 1D array, index is node, value is max width of all subsequent generations
$::analysis_tree_lib_loaded = 1;
$::analysis_tree_lib_loaded = 1; # quiet compile warnings
sub insert_tree
{
***************
*** 181,250 ****
}
- sub pass2_old
- {
- my $row;
- my $col;
-
- $row = 0;
- $col = 0;
- my $node;
- my $parent;
- # Layout children of generation $xx, and special case the root.
- # Need to layout children of parent nodes so siblings are together.
- $col += int(($m_width[0]/2)+0.5);
- $table[$row][$col] = 0;
- @{$loc{0}} = ($row, $col); # Also put node's location into the %loc hash
- $row+=2;
- my $offset;
- my $siblings;
- for(my $xx=0; $xx<=$#generation; $xx++)
- {
- $col = 0;
- for(my $yy= 0; $yy<=$#{$generation[$xx]}; $yy++)
- {
- $parent = $generation[$xx][$yy];
- for(my $cc=0; $cc<=$#{$children{$parent}}; $cc++)
- {
- $node = $children{$parent}[$cc];
- $siblings = $#{$children{$parent}}+1;
- # old $offset = ((int((($m_width[$parent])))) - $loc{$parent}[1])/$siblings;
- $offset = int(($loc{$parent}[1] - ($m_width[$parent]/2)) + ($m_width[$node]/2));
- # $m_width[$children[$generation[$xx][0]][0]]/2;
- print "node:$node w:$m_width[$parent] l:$loc{$parent}[1] o:$offset\n";
- if ($col==0)
- {
- $col = $offset;
- }
- else
- {
- $col += int((($m_width[$node])/2));
- }
- $table[$row][$col] = $node;
- @{$loc{$node}} = ($row, $col); # Also put node's location into the %loc hash
- # print "$node ($row,$col) (x:$xx,y$yy)\n";
- $col += int((($m_width[$node])/2)+0.5);
- }
- # $col++;
- }
- $row+=2;
- }
- }
-
sub render_at
{
- # analyze_tree(); # reads @tree, created @parent, @children, @generation
# print_tree_info();
# print_children_info();
# print_generation_info();
- #tile(); # creates @table, @loc
- #tile_pass2(); # modifies @table, @loc fixing mis-aligned zeroth row nodes
pass1(); # creates @table, @loc
pass2(); # modifies @table, @loc fixing mis-aligned zeroth row nodes
- write_log("after pass2: $table[0][0]");
tile_color(); # reads @table, creates @colors
- write_log("after tile_color: $table[0][0]");
tile_connect(); # modifies @table adding img tags, reads @loc
- write_log("after tile_connect: $table[0][0]");
my $html = render_html(); # reads @table, @colors
--- 180,193 ----
***************
*** 511,732 ****
$table[$xx-1][$yy] = "<img src=\"../graphics/25a.gif\">";
}
- }
- }
- }
- }
-
- #
- # Starting with highest generation, put children into the current row.
- # Children in this row are added by sibling groups.
- #
- # Add children to this row by looping through parents, and adding all the
- # children of each parent.
- #
- # Once complete, place each parent of this generation based on locations
- # of a given parent's children's positions. ( truncate n/2)
- #
- sub tile
- {
- # @table is a global
- my $row = 0;
- my $col = 0;
- my $gen_max;
- for(my $xx=$#generation; $xx > 0; $xx--)
- {
- $col = 0;
- my $kid_total;
- $kid_total = 0;
- for(my $yy=0; $yy<=$#{$generation[$xx-1]}; $yy++)
- {
- my $num_children = $#{$children{$generation[$xx-1][$yy]}};
- # If there are no children, the $num_children will be -1 since
- # it is an array index. If so, we still have to increment the
- # column for the current generation (children) to leave a blank
- # column below parents without children.
- if ($num_children < 0)
- {
- $kid_total++;
- }
- for(my $nc=0; $nc<=$num_children; $nc++)
- {
- my $node = $children{$generation[$xx-1][$yy]}[$nc];
- my $kid_count = $#{$children{$node}} +1;
- $gen_max = 0; # highest column number of my children; used to align parent above sibling columns
- if ($row >= 2) # only check this after we've layed out at least one generation
- { # remember we increment row by two, leaving room for tile connectors
- for(my $gg=0; $gg<=$#{$table[$row-2]}; $gg++)
- {
- for(my $cc=0; $cc<=$#{$children{$node}}; $cc++)
- {
- if (($table[$row-2][$gg] == $children{$node}[$cc]) && ($gg > $gen_max))
- {
- $gen_max = $gg;
- }
- }
- }
- }
- # How much of the previous row is just my children ($gen_diff)
- # Don't allow negative numbers. The answer is always at least zero.
- my $gen_diff = $gen_max - $kid_total;
- if ($gen_diff < 0)
- {
- $gen_diff = 0;
- }
- $col = $kid_total + int(($gen_diff/2)+0.5); # If $node has children, center above them
- $table[$row][$col] = $node; # Actually write the node into @table
- @{$loc{$node}} = ($row, $col); # Also put node's location into the %loc hash
- # track number of kids for the next iteration
- # at least one for the parent; if there is at least one kid, it lines up
- # with the parent, but if zero kids, then we still need
- # one column below the parent
- if ($kid_count > 0)
- {
- $kid_total += $kid_count;
- }
- else
- {
- $kid_total++;
- }
- # The columns need to account for the children's generation, and we need to at least
- # be beyond the last col of the children's generation.
- if ($kid_total < $gen_max)
- {
- $kid_total = $gen_max + 1;
- }
- }
- }
- $row+=2; # Increment by two in order to leave a blank row for the connector tiles.
- }
- #
- # Fix the root node. We have to repeat most of what happens above,
- # but with some hard coded values.
- #
- my $kid_min = 0;
- $gen_max = 0;
- if ($#table >= 2)
- {
- for(my $gg=0; $gg<=$#{$table[$row-2]}; $gg++)
- {
- for(my $cc=0; $cc<=$#{$children{$tree{root}}}; $cc++)
- {
- if (($table[$row-2][$gg] > 0) && ($kid_min == 0))
- {
- $kid_min = $table[$row-2][$gg];
- }
- if (($table[$row-2][$gg] == $children{$tree{root}}[$cc]) && ($gg > $gen_max))
- {
- $gen_max = $gg;
- }
- }
- }
- }
- else
- {
- $gen_max = 1;
- }
- my $gen_diff = $gen_max - $kid_min;
- $col = $kid_min + int(($gen_diff/2)+0.5); # If $node has children, center above them
- $table[$row][$col] = 0; # root's entry in @table
- @{$loc{0}} = ($row, $col); # root's entry in %loc
- }
-
- #
- # This has correct x and y axis (reversed in @table), unlike most (or all) of the code above.
- # This moves the zeroth row, which can get
- # mis-aligned because there is no subsequent generation.
- # Applying this fix to any row except the zeroth row causes problems.
- #
- sub tile_pass2
- {
- # Instead of looping, just do the zeroth row.
- # for(my $yy=0; $yy<$#table; $yy+=2)
- my $yy = 0;
- {
- for(my $xx=$#{$table[$yy]}; $xx>=0; $xx--)
- {
- if (defined($table[$yy][$xx]))
- {
- # get parent's x coord
- my $parent_node = $parent{$table[$yy][$xx]};
- my $parent_x;
- my $node_x = $xx;
- for(my $zz=0; $zz<=$#{$table[$yy+2]}; $zz++)
- {
- if ($table[$yy+2][$zz] == $parent_node)
- {
- $parent_x = $zz;
- last;
- }
- }
- # loop, moving to x+1 while x+1 < parent_x and as long as x+1 is an empty tile.
- while(($parent_x > $node_x) && (!defined($table[$yy][$node_x+1])))
- {
- # print "$table[$yy][$node_x] p_x: $parent_x n_x: $node_x\n";
- $table[$yy][$node_x+1] = $table[$yy][$node_x];
- $loc{$table[$yy][$node_x]}[1] = $node_x+1;
- undef($table[$yy][$node_x]); # will this work?
- $node_x++;
- }
- }
- }
- }
-
- }
-
- sub analyze_tree
- {
- #
- # who is my parent
- # the number of parent is always one.
- #
- my $node;
- my $curr_node;
- my $xx;
- my $yy;
- #
- # A special case for the root generation info.
- # If we had a situation where the root generation could have
- # multiple nodes, this would need to be changed to take that
- # into account.
- #
- foreach my $node (keys(%tree))
- {
- if ($node !~ m/\d+/)
- {
- next; # only do numeric nodes. We now have $tree{"root"}
- }
- if ($tree{$node}[1] == -1)
- {
- # parent and children need to be hashes due to
- # sparse data
- $parent{$node} = -1; # we can only have one parent
- $node2g{$node} = 0; # my generation zero
- push(@{$generation[$node2g{$node}]}, $node); # add self to my generation's list
- last;
- }
- }
- #
- # The %node2g hash really depends on the parent node having been resolved.
- # The %generation hash depends on node2g.
- # Therefore, we must run through the %tree hash in sorted ascending node order.
- #
- foreach my $parent (sort(keys(%tree)))
- {
- if ($parent == -1)
- {
- next;
- }
- foreach my $node (sort(keys(%tree)))
- {
- if ($node !~ m/\d+/)
- {
- next; # only do numeric nodes. We now have $tree{"root"}
- }
- if ($tree{$node}[1] == $parent)
- {
- $parent{$node} = $parent; # we can only have one parent
- push(@{$children{$parent}}, $node); # add self to parent's children list
- $node2g{$node} = $node2g{$parent{$node}} + 1; # my generation is my parent's generation +1
- push(@{$generation[$node2g{$node}]}, $node); # add self to my generation's list
}
}
--- 454,457 ----
Index: test_tree.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/test_tree.pl,v
retrieving revision 1.1.2.3
retrieving revision 1.1.2.4
diff -C2 -d -r1.1.2.3 -r1.1.2.4
*** test_tree.pl 19 Nov 2002 21:27:31 -0000 1.1.2.3
--- test_tree.pl 19 Nov 2002 22:16:35 -0000 1.1.2.4
***************
*** 10,24 ****
my $dbh = new_connection();
read_db($dbh,100);
- # analyze_tree();
print_tree_info();
print_children_info();
print_generation_info();
- # tile(); # creates @table
- # tile_pass2(); # modifies @table fixing mis-aligned zeroth row nodes
-
pass1(); # creates @table
pass2(); # modifies @table fixing mis-aligned zeroth row nodes
tile_color(); # reads @table, creates @colors
#tile_connect(); # modifies @table adding img tags
my $html = render_html(); # reads @table, @colors
--- 10,22 ----
my $dbh = new_connection();
read_db($dbh,100);
print_tree_info();
print_children_info();
print_generation_info();
pass1(); # creates @table
pass2(); # modifies @table fixing mis-aligned zeroth row nodes
tile_color(); # reads @table, creates @colors
+ # if you uncomment tile_connect() it will do the connecting tile parts,
+ # and they print as i on the ascii rendering.
#tile_connect(); # modifies @table adding img tags
my $html = render_html(); # reads @table, @colors
|
|
From: <tw...@us...> - 2002-11-19 21:27:35
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv32266
Modified Files:
Tag: Rel-1_0_1-branch
test_tree.pl analysis_tree_lib.pl
Log Message:
Build %children, %parent, %node2g, and %generation in a single pass
reading from the db. analyze_tree() no longer used. That saves a couple of
passes through the tree data.
Index: test_tree.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/test_tree.pl,v
retrieving revision 1.1.2.2
retrieving revision 1.1.2.3
diff -C2 -d -r1.1.2.2 -r1.1.2.3
*** test_tree.pl 19 Nov 2002 20:40:34 -0000 1.1.2.2
--- test_tree.pl 19 Nov 2002 21:27:31 -0000 1.1.2.3
***************
*** 10,14 ****
my $dbh = new_connection();
read_db($dbh,100);
! analyze_tree();
print_tree_info();
print_children_info();
--- 10,14 ----
my $dbh = new_connection();
read_db($dbh,100);
! # analyze_tree();
print_tree_info();
print_children_info();
Index: analysis_tree_lib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/analysis_tree_lib.pl,v
retrieving revision 1.1.2.28
retrieving revision 1.1.2.29
diff -C2 -d -r1.1.2.28 -r1.1.2.29
*** analysis_tree_lib.pl 19 Nov 2002 20:40:34 -0000 1.1.2.28
--- analysis_tree_lib.pl 19 Nov 2002 21:27:32 -0000 1.1.2.29
***************
*** 233,237 ****
sub render_at
{
! analyze_tree(); # reads @tree, created @parent, @children, @generation
# print_tree_info();
# print_children_info();
--- 233,237 ----
sub render_at
{
! # analyze_tree(); # reads @tree, created @parent, @children, @generation
# print_tree_info();
# print_children_info();
***************
*** 323,336 ****
while(( my $tree_name, my $node_pk, my $an_name, my $parent_key, my $an_fk) = $sth->fetchrow_array())
{
if ($parent_key == -1)
{
$tree{root} = $node_pk;
$tree{tree_name} = $tree_name;
}
! push(@{$tree{$node_pk}}, $an_name);
! push(@{$tree{$node_pk}}, $parent_key);
! push(@{$tree{$node_pk}}, $an_fk);
! push(@{$tree{$node_pk}}, $tree_pk);
! write_log("pk:$node_pk n:$an_name p:$parent_key a:$an_fk t:$tree_pk");
}
# I know... %tree is a package global, and we're returning it.
--- 323,346 ----
while(( my $tree_name, my $node_pk, my $an_name, my $parent_key, my $an_fk) = $sth->fetchrow_array())
{
+ push(@{$tree{$node_pk}}, $an_name);
+ push(@{$tree{$node_pk}}, $parent_key);
+ push(@{$tree{$node_pk}}, $an_fk);
+ push(@{$tree{$node_pk}}, $tree_pk);
if ($parent_key == -1)
{
$tree{root} = $node_pk;
$tree{tree_name} = $tree_name;
+ $parent{$node_pk} = -1; # we can only have one parent
+ $node2g{$node_pk} = 0; # my generation zero
+ push(@{$generation[$node2g{$node_pk}]}, $node_pk); # add self to my generation's list
}
! else
! {
! $parent{$node_pk} = $parent_key;
! push(@{$children{$parent_key}}, $node_pk);
! $node2g{$node_pk} = $node2g{$parent{$node_pk}} + 1; # nodes must be processed in order
! push(@{$generation[$node2g{$node_pk}]}, $node_pk); # ditto
! }
! # write_log("pk:$node_pk n:$an_name p:$parent_key a:$an_fk t:$tree_pk");
}
# I know... %tree is a package global, and we're returning it.
|
|
From: <jas...@us...> - 2002-11-19 20:44:33
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv14468
Modified Files:
array-design-insert.pl.in
Log Message:
* scripts/array-design-insert.pl.in (Message):
added --count
Index: array-design-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/array-design-insert.pl.in,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** array-design-insert.pl.in 20 Oct 2002 14:49:56 -0000 1.3
--- array-design-insert.pl.in 19 Nov 2002 20:44:30 -0000 1.4
***************
*** 38,41 ****
--- 38,42 ----
$OPTIONS{rw_group} = '%%GENEX_SUPERUSER_GROUP%%';
my $rc = GetOptions(\%OPTIONS,
+ 'count=i',
'dbname=s',
'username=s',
***************
*** 60,63 ****
--- 61,65 ----
--rw_group : the group with permission to modify this design
--no_reporter : do not process reporters
+ --count=num : print output every num tags
--help : print this message
EOU
***************
*** 116,120 ****
my $start = new Benchmark;
! my $reader = Bio::MAGE::XMLReader->new();
my $mage = $reader->read($OPTIONS{file});
--- 118,126 ----
my $start = new Benchmark;
! my @args;
! if (exists $OPTIONS{count}) {
! push(@args,count=>$OPTIONS{count});
! }
! my $reader = Bio::MAGE::XMLReader->new(@args);
my $mage = $reader->read($OPTIONS{file});
|
|
From: <tw...@us...> - 2002-11-19 20:40:37
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv10840
Modified Files:
Tag: Rel-1_0_1-branch
analysis_tree_lib.pl test_tree.pl
Log Message:
Generation builing depends on crawling the tree in order.
Sorting the keys of %tree fixes this, but the better fix
is to build %parent, %children %node2g and %generation inside read_db()
as each record is read. Records are already ordered by node_pk.
Index: analysis_tree_lib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/analysis_tree_lib.pl,v
retrieving revision 1.1.2.27
retrieving revision 1.1.2.28
diff -C2 -d -r1.1.2.27 -r1.1.2.28
*** analysis_tree_lib.pl 12 Nov 2002 22:34:36 -0000 1.1.2.27
--- analysis_tree_lib.pl 19 Nov 2002 20:40:34 -0000 1.1.2.28
***************
*** 675,679 ****
my $yy;
#
! # Hard code the root generation info.
# If we had a situation where the root generation could have
# multiple nodes, this would need to be changed to take that
--- 675,679 ----
my $yy;
#
! # A special case for the root generation info.
# If we had a situation where the root generation could have
# multiple nodes, this would need to be changed to take that
***************
*** 696,703 ****
}
}
! #$node2g{0} = 0;
! #push(@{$generation[$node2g{0}]}, 0);
! #$parent{0} = 0;
! foreach my $parent (keys(%tree))
{
if ($parent == -1)
--- 696,705 ----
}
}
! #
! # The %node2g hash really depends on the parent node having been resolved.
! # The %generation hash depends on node2g.
! # Therefore, we must run through the %tree hash in sorted ascending node order.
! #
! foreach my $parent (sort(keys(%tree)))
{
if ($parent == -1)
***************
*** 705,709 ****
next;
}
! foreach my $node (keys(%tree))
{
if ($node !~ m/\d+/)
--- 707,711 ----
next;
}
! foreach my $node (sort(keys(%tree)))
{
if ($node !~ m/\d+/)
Index: test_tree.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/test_tree.pl,v
retrieving revision 1.1.2.1
retrieving revision 1.1.2.2
diff -C2 -d -r1.1.2.1 -r1.1.2.2
*** test_tree.pl 8 Nov 2002 21:22:53 -0000 1.1.2.1
--- test_tree.pl 19 Nov 2002 20:40:34 -0000 1.1.2.2
***************
*** 9,13 ****
{
my $dbh = new_connection();
! read_db($dbh,1);
analyze_tree();
print_tree_info();
--- 9,13 ----
{
my $dbh = new_connection();
! read_db($dbh,100);
analyze_tree();
print_tree_info();
|
|
From: <tw...@us...> - 2002-11-19 20:18:19
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv1237
Modified Files:
Tag: Rel-1_0_1-branch
load_data1.pl
Added Files:
Tag: Rel-1_0_1-branch
get_data2.pl
Log Message:
single sql query (as opposed to the Perl looped multi query and a hash) data extraction working.
--- NEW FILE: get_data2.pl ---
#!/usr/bin/perl
use strict;
use CGI;
use CGI::Carp qw(fatalsToBrowser);
require "sessionlib.pl";
main:
{
my $q = new CGI;
my $dbh = new_connection(); # sessionlib.pl
# Build a list of am_pk's to analyze, grouped by ec_pk
my %ana = build_ana_hash($dbh, $q);
# Check to make sure we are allowed to read all the ec_pk's and am_pk's
# Check to make sure all the hybs are using the same chip
# my $al_fk = check_chip_type(\%ana);
# Write a labels file.
# Write the data file.
write_data_file($dbh, \%ana);
print "Content-type: text/html\n\n<html><body>get_data2.pl</body></html>\n";
$dbh->disconnect();
}
sub build_ana_hash
{
my $dbh = $_[0];
my $q = $_[1];
my %ch = $q->Vars();
my %ana; # hash of lists. hash keyed by ec_pk. list of am_pk's
#
# am_pk_n are checkboxes for hybridizations
# ec_pk_n are the matching ec_pk's
#
foreach my $key (keys (%ch))
{
if ($key =~ m/am_pk_(\d+)/)
{
my $ch_key = "ec_pk_$1";
push(@{$ana{$ch{$ch_key}}}, $ch{$key});
# write_log("$ch{$ch_key} is $ch{$key}");
}
}
return %ana;
}
sub write_lables_file
{
my $dbh = $_[0];
my %ana = %{$_[1]};
}
sub write_data_file
{
my $dbh = $_[0];
my %ana = %{$_[1]};
my @am_pk_list;
# generate the SQL
my $sql_template = "
select al_spots.spot_identifier,<signal_name>
from
<signal_select>,
(select spot_identifier,als_pk from al_spots) as al_spots
where
<join>";
# build the ordered list of am_pk's
foreach my $ec_pk (keys(%ana))
{
foreach my $am_pk (@{$ana{$ec_pk}})
{
push(@am_pk_list,$am_pk);
# write_log("pushing $am_pk");
}
}
my $signal_name;
my $signal_select;
my $join;
my $j_tween = "";
my $s_tween = "";
for(my $xx=0; $xx<=$#am_pk_list; $xx++)
{
my $am_pk = $am_pk_list[$xx];
$signal_name = "am_fk_$am_pk.signal";
$signal_select = "(select signal,usf_fk from am_spots_mas5 where am_fk=$am_pk) as am_fk_$am_pk";
$join = "am_fk_$am_pk.usf_fk=al_spots.als_pk";
if ($xx > 0)
{
$s_tween = ", \n";
$j_tween = " and \n"
}
$sql_template =~ s/<signal_name>/$s_tween $signal_name<signal_name>/;
$sql_template =~ s/<signal_select>/$s_tween $signal_select<signal_select>/;
$sql_template =~ s/<join>/$j_tween $join<join>/;
}
$sql_template =~ s/<.*?>//g;
# write_log("$sql_template");
my $sth = $dbh->prepare($sql_template) || die "gd prep: $sql_template\n$DBI::errstr\n";
$sth->execute();
my @data; # a single record
open(OUT, "> /var/genres/twl8n/demo.dat") || die "Can't open demo.dat\n";
while( @data = $sth->fetchrow_array())
{
my $tab = ""; # no tab for first column;
foreach my $col (@data)
{
print OUT "$tab$col";
$tab = "\t";
}
print OUT "\n";
}
close(OUT);
# fetch and write data to a file
}
# This is the unfinished Perl alg. version, as opposed to the SQL version above.
sub write_data_file_perl
{
my $dbh = $_[0];
my %ana = %{$_[1]};
my $al_fk = $_[2];
my %data; # key is probe_set_id as a string, list of signals
# get data
foreach my $ec_pk (keys(%ana))
{
foreach my $am_pk (@{$ana{$ec_pk}})
{
# select spot_identifier,signal from am_spots_mas5, al_spots where am_spots_mas5.usf_fk=als_pk and am_fk=$am_pk;
# push(@{$data{$spot_identifier}}, $signal);
}
}
# sanity check on the number of elements (columns) for each key of %data
#write each record to disk
my $data_max = 0;
foreach my $probe_id (keys(%data))
{
print OUT "$probe_id";
foreach my $signal (@{$data{$probe_id}})
{
print OUT "\t$signal";
}
print OUT "\n";
}
# do the usual file_info bookkeeping
}
Index: load_data1.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/load_data1.pl,v
retrieving revision 1.1.2.1
retrieving revision 1.1.2.2
diff -C2 -d -r1.1.2.1 -r1.1.2.2
*** load_data1.pl 24 Oct 2002 18:26:53 -0000 1.1.2.1
--- load_data1.pl 19 Nov 2002 20:18:15 -0000 1.1.2.2
***************
*** 45,49 ****
if ($file =~ m/.*\.$ext/i)
{
! write_log("$ext trying $file");
$ok_flag = 1;
$ch{file_list} .= "$file\t";
--- 45,49 ----
if ($file =~ m/.*\.$ext/i)
{
! # write_log("$ext trying $file");
$ok_flag = 1;
$ch{file_list} .= "$file\t";
***************
*** 110,114 ****
my $cl_safe_cdp = $vars{CHIP_DATA_PATH};
$cl_safe_cdp =~ s/ /\\ /g;
! write_log("csc: $cl_safe_cdp");
my @flist = `find $cl_safe_cdp -iname "$order_number*\.RPT"`;
chomp(@flist);
--- 110,114 ----
my $cl_safe_cdp = $vars{CHIP_DATA_PATH};
$cl_safe_cdp =~ s/ /\\ /g;
! # write_log("csc: $cl_safe_cdp");
my @flist = `find $cl_safe_cdp -iname "$order_number*\.RPT"`;
chomp(@flist);
|
Update of /cvsroot/genex/genex-server/site/webtools
In directory sc8-pr-cvs1:/tmp/cvs-serv11423
Modified Files:
Tag: Rel-1_0_1-branch
choose_order_curator.html choose_order_curator.pl sql_lib.pl
choose_order.pl
Log Message:
Added phone number, moved related query to sql_lib.pl
Index: choose_order_curator.html
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/choose_order_curator.html,v
retrieving revision 1.1.2.1
retrieving revision 1.1.2.2
diff -C2 -d -r1.1.2.1 -r1.1.2.2
*** choose_order_curator.html 24 Oct 2002 18:26:53 -0000 1.1.2.1
--- choose_order_curator.html 18 Nov 2002 21:20:53 -0000 1.1.2.2
***************
*** 22,26 ****
<div align="right">Owner:</div>
</td>
! <td width="30%"> {contact_fname} {contact_lname} ( {login} )</td>
<td width="40%"> </td>
<td width="40%"><input type=submit name="submit" value="Update"></td>
--- 22,26 ----
<div align="right">Owner:</div>
</td>
! <td width="30%"> {contact_fname} {contact_lname} ( {login} ) {contact_phone}</td>
<td width="40%"> </td>
<td width="40%"><input type=submit name="submit" value="Update"></td>
Index: choose_order_curator.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/choose_order_curator.pl,v
retrieving revision 1.1.2.1
retrieving revision 1.1.2.2
diff -C2 -d -r1.1.2.1 -r1.1.2.2
*** choose_order_curator.pl 24 Oct 2002 18:26:53 -0000 1.1.2.1
--- choose_order_curator.pl 18 Nov 2002 21:20:53 -0000 1.1.2.2
***************
*** 52,56 ****
my $sample_sql = "select timestamp, exp_condition.name as ec_name, abbrev_name, study.study_name, study.sty_pk from sample,exp_condition,study where study.sty_pk=exp_condition.sty_fk and exp_condition.ec_pk=sample.ec_fk and smp_pk=?";
my $sc_sql = "select count(smp_pk) from sample where oi_fk=?";
- my $owner_sql = "select usersec.login,contact.contact_fname,contact.contact_lname,usersec.us_pk from order_info,groupref,usersec,contact where order_info.oi_pk=? and groupref.ref_fk=oi_pk and contact.con_pk=groupref.us_fk and groupref.us_fk=usersec.us_pk";
my $am_sql = "select hybridization_name,smp_pk,am_pk,al_fk from arraymeasurement,sample,order_info where oi_pk=? and order_info.oi_pk=sample.oi_fk and arraymeasurement.smp_fk=sample.smp_pk order by smp_pk,am_pk";
my $al_sql = "select arraylayout.name as al_name from arraylayout where al_pk=?";
--- 52,55 ----
***************
*** 61,65 ****
my $sample_sth = $dbh->prepare($sample_sql);
my $sc_sth = $dbh->prepare($sc_sql);
! my $owner_sth = $dbh->prepare($owner_sql);
my $am_sth = $dbh->prepare($am_sql);
my $al_sth = $dbh->prepare($al_sql);
--- 60,64 ----
my $sample_sth = $dbh->prepare($sample_sql);
my $sc_sth = $dbh->prepare($sc_sql);
! my $owner_sth = getq("order_owner_info", $dbh);
my $am_sth = $dbh->prepare($am_sql);
my $al_sth = $dbh->prepare($al_sql);
***************
*** 79,84 ****
($o_hr->{number_of_samples}) = $sc_sth->fetchrow_array();
! $owner_sth->execute($o_hr->{oi_pk}) || die "$owner_sql\n$DBI::errstr\n";
! ($o_hr->{login}, $o_hr->{contact_fname}, $o_hr->{contact_lname}, $o_hr->{us_pk}) = $owner_sth->fetchrow_array();
my $loop_instance = $loop_template;
--- 78,83 ----
($o_hr->{number_of_samples}) = $sc_sth->fetchrow_array();
! $owner_sth->execute($o_hr->{oi_pk}) || die "Query order_owner_info execute failed. $DBI::errstr\n";
! ($o_hr->{login},$o_hr->{contact_fname},$o_hr->{contact_lname},$o_hr->{contact_phone},$o_hr->{us_pk}) = $owner_sth->fetchrow_array();
my $loop_instance = $loop_template;
***************
*** 109,112 ****
--- 108,116 ----
}
$temp = verify_exp($dbh, $o_hr->{us_pk}, $s_hr->{sty_pk}, 16, $s_hr->{ec_name}, $s_hr->{abbrev_name});
+ if ($o_hr->{message} !~ m/^$temp|m$temp/)
+ {
+ $o_hr->{message} .= $temp;
+ }
+ $temp = verify_hyb($dbh, $s_hr->{am_pk});
if ($o_hr->{message} !~ m/^$temp|m$temp/)
{
Index: sql_lib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/sql_lib.pl,v
retrieving revision 1.1.2.8
retrieving revision 1.1.2.9
diff -C2 -d -r1.1.2.8 -r1.1.2.9
*** sql_lib.pl 18 Nov 2002 19:10:35 -0000 1.1.2.8
--- sql_lib.pl 18 Nov 2002 21:20:53 -0000 1.1.2.9
***************
*** 97,100 ****
--- 97,120 ----
$sql = "select count(smp_pk) from sample where oi_fk=? and (ec_fk is null or ec_fk='')";
}
+ elsif ($q_name eq "order_owner_info")
+ {
+ $sql = "
+ SELECT
+ usersec.login,
+ contact.contact_fname,
+ contact.contact_lname,
+ contact.contact_phone,
+ usersec.us_pk
+ FROM
+ order_info,
+ groupref,
+ usersec,
+ contact
+ WHERE
+ order_info.oi_pk=? AND
+ groupref.ref_fk=oi_pk AND
+ contact.con_pk=groupref.us_fk AND
+ groupref.us_fk=usersec.us_pk";
+ }
if (defined($sql))
Index: choose_order.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/site/webtools/Attic/choose_order.pl,v
retrieving revision 1.1.2.2
retrieving revision 1.1.2.3
diff -C2 -d -r1.1.2.2 -r1.1.2.3
*** choose_order.pl 18 Nov 2002 19:09:25 -0000 1.1.2.2
--- choose_order.pl 18 Nov 2002 21:20:53 -0000 1.1.2.3
***************
*** 88,96 ****
my $hyb_sth = $dbh->prepare($hyb_sql);
- # if (($sth->rows() == 0) &&
- # $message !~ m/^20m|m20m/)
- # {
- # $message .= "20m";
- # }
my $temp = verify_order($dbh, $oi_pk);
if ($message !~ m/^$temp|m$temp/)
--- 88,91 ----
|
|
From: <jas...@pr...> - 2002-11-18 19:48:56
|
Update of /cvsroot/genex/genex-server/G2G/mason In directory sc8-pr-cvs1:/tmp/cvs-serv2346 Modified Files: .cvsignore Log Message: usual Index: .cvsignore =================================================================== RCS file: /cvsroot/genex/genex-server/G2G/mason/.cvsignore,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -d -r1.5 -r1.6 *** .cvsignore 7 Nov 2002 14:59:19 -0000 1.5 --- .cvsignore 18 Nov 2002 19:48:53 -0000 1.6 *************** *** 12,14 **** --- 12,15 ---- group-maint.html query.html + user-insert.html workspace.html |
|
From: <jas...@pr...> - 2002-11-18 19:48:43
|
Update of /cvsroot/genex/genex-server/G2G/mason
In directory sc8-pr-cvs1:/tmp/cvs-serv2271
Modified Files:
group-maint.html.in
Log Message:
wrong app name
Index: group-maint.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/G2G/mason/group-maint.html.in,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** group-maint.html.in 7 Nov 2002 14:40:10 -0000 1.2
--- group-maint.html.in 18 Nov 2002 19:48:40 -0000 1.3
***************
*** 79,85 ****
<%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>
--- 79,85 ----
<%attr>
! action=>'%%GENEX_WORKSPACE_URL%%/group_maint.html'
name=>'Associate Genex User With Group'
! path=>'%%GENEX_WORKSPACE_URL%%/group_maint.html'
</%attr>
<%args>
|
|
From: <man...@pr...> - 2002-11-18 04:43:02
|
Update of /cvsroot/genex/genex-server/rcluster-1.0/lib/r
In directory sc8-pr-cvs1:/tmp/cvs-serv29996
Modified Files:
permcluster.r
Added Files:
ChangeLog
Log Message:
updated permcluster, added a Changelog to the rcluster/lib/r dir
--- NEW FILE: ChangeLog ---
2002-11-17 Harry Mangalam <hj...@ta...>
* committed Karen's changes to permcluster.r
Index: permcluster.r
===================================================================
RCS file: /cvsroot/genex/genex-server/rcluster-1.0/lib/r/permcluster.r,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** permcluster.r 20 Jan 2002 01:00:10 -0000 1.4
--- permcluster.r 18 Nov 2002 04:42:58 -0000 1.5
***************
*** 1,670 ****
! ######################################################################
! # Copyright 2000-2001
! # National Center for Genome Resources
! # All rights reserved
! # file permcluster.r, written by Karen Schlauch
! ######################################################################
! # Version $Id$
! #####################################################################################################
! ## Main program call
! ## This program does a breadth-first search of the clustering tree generated by Murtagh's
[...1313 lines suppressed...]
! {sumxy<-sumxy+(x[i]*y[i])
! sumx<-sumx+x[i]^2
! sumy<-sumy+y[i]^2
! diffxy<-diffxy+abs(x[i]-y[i])}
! tmpcosxy<-sumxy/(sqrt(sumx)*sqrt(sumy))
! cosxy<-1-tmpcosxy
! return(cosxy)}
!
!
!
!
!
!
!
!
!
!
!
!
!
|
|
From: <man...@pr...> - 2002-11-18 04:29:18
|
Update of /cvsroot/genex/genex-server
In directory sc8-pr-cvs1:/tmp/cvs-serv23215
Modified Files:
ChangeLog INSTALL
Added Files:
GeneSpring.notes
Log Message:
added GeneSpring.notes, updated INSTALL doc
--- NEW FILE: GeneSpring.notes ---
GeneSpring Notes:
For both Windows and Linux/Unix GeneSpring clients to connect to the GeneX DB, the GeneX/Postgresql server will need the JDBC driver installed. This can be installed and configured automatically for Debian systems by installing the
libpgjava deb pkg.
For Windows, to connect GeneSpring to GeneX, you will in addition need:
- the ODBC driver installed and configured on Windows
- the JDBC driver installed and configured on Windows
- the ODBC postgresql driver installed on the GeneX server. This can be automatically installed and configured by installing the debian 'libiodbc2' 'unixodbc', and 'odbc-postgresql' pkgs.
For Linux/Unix, to connect GeneSpring to GeneX, you will need:
- the JDBC driver installed so that your Java VM can find and use it (typically, it is installed in the <java_root>/jre/lib/ext/ directory.
- GeneSpring configured to use the JDBC driver appropriately. This is done by specifying it in GeneSpring -> Edit -> Preferences -> Database -> JDBC driver : [org.postgresql.Driver]. Alternatively, you can enter it direclty in the GeneSpring preference file: <genespring_home>/data/GeneSpring\ Preferences
- additionally, you should use the suppplied JVM or Sun's JRE 1.4.1_01.
- you dhould upgrade to the latest GeneSpring jar by using the upgrade utility within GeneSpring or downloading the latest demo which has the identical new jar. ja...@si... was very helpful in assisting with some of this debugging.
Index: ChangeLog
===================================================================
RCS file: /cvsroot/genex/genex-server/ChangeLog,v
retrieving revision 1.107
retrieving revision 1.108
diff -C2 -d -r1.107 -r1.108
*** ChangeLog 15 Nov 2002 22:05:41 -0000 1.107
--- ChangeLog 18 Nov 2002 04:29:14 -0000 1.108
***************
*** 1,2 ****
--- 1,11 ----
+ 2002-11-17 Harry Mangalam <hj...@ta...>
+ * many mods to the INSTALL doc, inclusing breaking some parts out into
+ separate files for smoothing the doc path (Using.CPAN, Porting.txt).
+ * Added GeneSpring.notes as a starter doc as to how to configure
+ the GeneX server to be able to server requests to GeneSpring and also
+ how to configure the Windows and *nix clients to access the server using
+ ODBC and JDBC.
+
+
2002-11-15 Jason E. Stewart <ja...@op...>
Index: INSTALL
===================================================================
RCS file: /cvsroot/genex/genex-server/INSTALL,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -d -r1.23 -r1.24
*** INSTALL 14 Nov 2002 04:32:40 -0000 1.23
--- INSTALL 18 Nov 2002 04:29:14 -0000 1.24
***************
*** 62,65 ****
--- 62,73 ----
apache-dev libapache-mod-perl libdevel-symdump-perl
+ for genespring/odbc connectivity
+ libiodbc2 unixodbc odbc-postgresql
+
+ for jdbc (to service direct jdbc calls)
+ libpgjava
+
+ for guis:
+ pgaccess unixodbc-bin
Required Utilities
|
