[Genex-cvs-commit] genex-server/G2G/mason array-design.html.in,NONE,1.1 bioassay.html.in,NONE,1.1 data-loader.html.in,NONE,1.1 group-maint.html.in,NONE,1.1

[<jas...@us...>]

Update of /cvsroot/genex/genex-server/G2G/mason
In directory usw-pr-cvs1:/tmp/cvs-serv12920/G2G/mason

Added Files:
	array-design.html.in bioassay.html.in data-loader.html.in 
	group-maint.html.in 
Log Message:
new workspace Mason apps


--- NEW FILE: array-design.html.in ---
    <h1 align="center"><% $name %></h1>
    <form action="<% $action %>" 
	  method="post" enctype="multipart/form-data">
      <div align="center">

% if ($submit) {

	<h2><% $data %></h2>

% } else {
	<h2>Read Group</h2>
	<p>Choose the <b>read group</b> that will be givne to create
	the array design files that you load.</p>
 	<table bgcolor="#D8E4F7" border="1" cols="1">
	  <thead  bgcolor="#FFD78F">
	    <tr>
	      <th>Read Group</th>
	    </tr>
	  </thead>
	  <tbody>
 	  <tr>
 	    <td>
		<& comps/query-drop-down.mason, name=>"read_group",
		   array_ref=>\@groups &>
 	    </td>
 	  </tr>
	  </tbody>
	</table>

	<hr noshade size=5>

	<h2>Write Group</h2>
	<p>Choose the <b>write group</b> that will be givne to create
	the array design files that you load.</p>
 	<table bgcolor="#D8E4F7" border="1" cols="1">
	  <thead  bgcolor="#FFD78F">
	    <tr>
	      <th>Write Group</th>
	    </tr>
	  </thead>
	  <tbody>
 	  <tr>
 	    <td>
		<& comps/query-drop-down.mason, name=>"write_group",
		   array_ref=>\@groups &>
 	    </td>
 	  </tr>
	  </tbody>
	</table>

	<hr noshade size=5>

	<h2>Files to Load</h2>
	<p>Choose the array files that you wish to load.</p>
 	<table bgcolor="#D8E4F7" border="1" cols="1">
	  <thead  bgcolor="#FFD78F">
	    <tr>
	      <th>Data Files</th>
	    </tr>
	  </thead>
	  <tbody>
 	  <tr>
 	    <td>
		<& comps/query-select.mason, name=>"data_files",
		   array_ref=>\@data_files &>
 	    </td>
 	  </tr>
	  </tbody>
	</table>

	<hr noshade size=5>

	<input type="submit" name="submit" value="Load Data" size="33">
        <& comps/hiddenlist.mason, name=>'debug', value=>$debug &>
	<hr noshade size=5>

% }
      </div>
    </form>

<%args>
    $debug => 0
    $submit => ''
    $data_files => []
    $read_group => ''
    $write_group => ''
</%args>
<%attr>
  action=>'%%GENEX_WORKSPACE_URL%%/array-design.html'
  name=>'GeneX DB Array Design Loader Page'
  path=>'%%GENEX_WORKSPACE_URL%%/array-design.html'
</%attr>
<%once>
use Bio::Genex;
use Bio::Genex::Connect;
use Bio::Genex::GroupSec;
use Bio::Genex::ArrayDesign;

</%once>
<%init>;
    my $name = $m->current_comp->attr('name');
    my $path = $m->current_comp->attr('path');
    my $action = $m->current_comp->attr('action');

    my $session = Bio::Genex::HTMLUtils::get_session_cookie($r);

    my $dbh = Bio::Genex::Connect->new(USER=>$session->{username},
				    PASSWORD=>$session->{password},
				    DBNAME=>$session->{dbname},
				   );


    $dbh->assert_table_defined('GroupSec');
    $dbh->assert_table_defined('ArrayDesign');

    my @groups;
    my @data_files;
    my $data = '';
    if ($submit) {
      my @files;
      if (ref $data_files) {
	@files = @{$data_files};
      } else {
	@files = ($data_files);
      }

      my $cmd = '%%GENEX_BIN_DIR%%/array-design-insert.pl';
      my @args = ("--user=$session->{username}",
		  "--password=$session->{password}",
		  "--dbname=$session->{dbname}",
		  "--ro_group=$read_group",
		  "--rw_group=$write_group",
		 );
      my @pks;
      foreach my $file (@files) {
	my @params = ("--file=$file");
	my $command = join(' ', $cmd, @args, @params);
	my $pk = `$command`;
	die $! if $?;
	push(@pks,$pk);
      }
      $data = "@pks";
    } else {
      my @gs_dbs = Bio::Genex::GroupSec->get_all_objects($dbh);
      foreach my $gs_db (@gs_dbs) {
	push(@groups,[$gs_db->name,$gs_db->name]);
      }

      my @files = glob('%%GENEX_UPLOAD_DIR%%/*.xml');
      foreach my $name (@files) {
	my $short_name = $name;
	$short_name =~ s|.*/||;
	push(@data_files,[$name,$short_name]);
      }
    }

</%init>

--- NEW FILE: bioassay.html.in ---
    <h1 align="center"><% $name %></h1>
    <form action="<% $action %>" 
	  method="post" enctype="multipart/form-data">
      <div align="center">

	<h2>BioAssays in DB</h2>
 	<table bgcolor="#D8E4F7" border="1" cols="1">
	  <thead  bgcolor="#FFD78F">
	    <tr>
	      <th>BioAssays</th>
	    </tr>
	  </thead>
	  <tbody>
 	  <tr>
 	    <td>
		<& comps/query-select.mason, name=>"bioassays",
		   array_ref=>\@bioassays &>
 	    </td>
 	  </tr>
	  </tbody>
	</table>

	<hr noshade size=5>

	<input type="submit" name="submit" value="Load Data" size="33">
        <& comps/hiddenlist.mason, name=>'debug', value=>$debug &>
	<hr noshade size=5>

      </div>
    </form>

<%args>
    $debug => 0
    $submit => ''
    $data_files => []
    $read_group => ''
    $write_group => ''
</%args>
<%attr>
  action=>'%%GENEX_WORKSPACE_URL%%/array-design.html'
  name=>'GeneX DB Array Design Loader Page'
  path=>'%%GENEX_WORKSPACE_URL%%/array-design.html'
</%attr>
<%once>
use Bio::Genex;
use Bio::Genex::Connect;
use Bio::Genex::GroupSec;
use Bio::Genex::MeasuredBioAssay;

</%once>
<%init>;
    my $name = $m->current_comp->attr('name');
    my $path = $m->current_comp->attr('path');
    my $action = $m->current_comp->attr('action');

    my $session = Bio::Genex::HTMLUtils::get_session_cookie($r);

    my $dbh = Bio::Genex::Connect->new(USER=>$session->{username},
				    PASSWORD=>$session->{password},
				    DBNAME=>$session->{dbname},
				   );


    $dbh->assert_table_defined('MeasuredBioAssay');

    my @bioassays;
    my @data_files;
    my $data = '';

      my @mba_dbs = Bio::Genex::MeasuredBioAssay->get_all_objects($dbh);
      foreach my $mba_db (@mba_dbs) {
	push(@bioassays,[$mba_db->mba_pk,$mba_db->name]);
      }


</%init>

--- NEW FILE: data-loader.html.in ---
    <h1 align="center"><% $name %></h1>
    <form action="<% $action %>" 
	  method="post" enctype="multipart/form-data">
      <div align="center">

% if ($submit) {

	<h2><% $data %></h2>

% } else {
	<h2>Read Group</h2>
	<p>Choose the <b>read group</b> that will be givne to create
	the array design files that you load.</p>
 	<table bgcolor="#D8E4F7" border="1" cols="1">
	  <thead  bgcolor="#FFD78F">
	    <tr>
	      <th>Read Group</th>
	    </tr>
	  </thead>
	  <tbody>
 	  <tr>
 	    <td>
		<& comps/query-drop-down.mason, name=>"read_group",
		   array_ref=>\@groups &>
 	    </td>
 	  </tr>
	  </tbody>
	</table>

	<hr noshade size=5>

	<h2>Write Group</h2>
	<p>Choose the <b>write group</b> that will be givne to create
	the array design files that you load.</p>
 	<table bgcolor="#D8E4F7" border="1" cols="1">
	  <thead  bgcolor="#FFD78F">
	    <tr>
	      <th>Write Group</th>
	    </tr>
	  </thead>
	  <tbody>
 	  <tr>
 	    <td>
		<& comps/query-drop-down.mason, name=>"write_group",
		   array_ref=>\@groups &>
 	    </td>
 	  </tr>
	  </tbody>
	</table>

	<hr noshade size=5>

	<h2>Array Designs</h2>
      <p>Choose the Array Design file from the DB from which the
      arrays you wish to load have been created.</p>
 	<table bgcolor="#FFFFFF" border="1" cols="1">
	  <thead  bgcolor="#FFD78F">
	    <tr>
	      <th>Array Designs</th>
	    </tr>
	  </thead>
	  <tbody>
 	  <tr>
 	    <td>
		<& comps/query-drop-down.mason, name=>"ad_pk",
		   array_ref=>\@array_designs &>
 	    </td>
 	  </tr>
	  </tbody>
	</table>

	<hr noshade size=5>

	<h2>Experiment Sets</h2>
	<p>Choose the ExperimentSet to which you wish to add the
	  arrays.</p>
 	<table bgcolor="#D8E4F7" border="1" cols="1">
	  <thead  bgcolor="#FFD78F">
	    <tr>
	      <th>Experiment Sets</th>
	    </tr>
	  </thead>
	  <tbody>
 	  <tr>
 	    <td>
		<& comps/query-drop-down.mason, name=>"es_pk",
		   array_ref=>\@experiment_sets &>
 	    </td>
 	  </tr>
	  </tbody>
	</table>

	<hr noshade size=5>

	<h2>Feature Extraction Software</h2>
	<p>Choose the feature extraction software package that was
	used to create the array files that you wish to load.</p>
 	<table bgcolor="#D8E4F7" border="1" cols="1">
	  <thead  bgcolor="#FFD78F">
	    <tr>
	      <th>Feature Extraction Software</th>
	    </tr>
	  </thead>
	  <tbody>
 	  <tr>
 	    <td>
		<& comps/query-drop-down.mason, name=>"fe_sw_pk",
		   array_ref=>\@feature_extractions &>
 	    </td>
 	  </tr>
	  </tbody>
	</table>

	<hr noshade size=5>

	<h2>Files to Load</h2>
	<p>Choose the array files that you wish to load.</p>
 	<table bgcolor="#D8E4F7" border="1" cols="1">
	  <thead  bgcolor="#FFD78F">
	    <tr>
	      <th>Data Files</th>
	    </tr>
	  </thead>
	  <tbody>
 	  <tr>
 	    <td>
		<& comps/query-select.mason, name=>"data_files",
		   array_ref=>\@data_files &>
 	    </td>
 	  </tr>
	  </tbody>
	</table>

	<hr noshade size=5>

	<input type="submit" name="submit" value="Load Data" size="33">
        <& comps/hiddenlist.mason, name=>'debug', value=>$debug &>
	<hr noshade size=5>

% }

      </div>
    </form>

<%args>
 $debug => 0
    $submit => ''
    $data_files => []
    $read_group => ''
    $write_group => ''
    $es_pk => ''
    $ad_pk => ''
    $fe_sw_pk => ''
</%args>
<%attr>
  action=>'%%GENEX_WORKSPACE_URL%%/data-loader.html'
  name=>'GeneX DB Data Loader Page'
  path=>'%%GENEX_WORKSPACE_URL%%/data-loader.html'
</%attr>
<%once>
use Bio::Genex;
use Bio::Genex::Connect;
use Bio::Genex::ArrayDesign;
use Bio::Genex::ExperimentSet;
use Bio::Genex::FeatureExtractionSoftware;

</%once>
<%init>
my $name = $m->current_comp->attr('name');
my $path = $m->current_comp->attr('path');
my $action = $m->current_comp->attr('action');

    my $session = Bio::Genex::HTMLUtils::get_session_cookie($r);

    my $dbh = Bio::Genex::Connect->new(USER=>$session->{username},
				    PASSWORD=>$session->{password},
				    DBNAME=>$session->{dbname},
				   );


     $dbh->assert_table_defined('ExperimentSet');
     $dbh->assert_table_defined('ArrayDesign');
     $dbh->assert_table_defined('FeatureExtractionSoftware');

    my @groups;
    my @data_files;
    my @feature_extractions;
    my @experiment_sets;
    my @array_designs;
    my $data = '';
    if ($submit) {
      my @files;
      if (ref $data_files) {
	@files = @{$data_files};
      } else {
	@files = ($data_files);
      }

      my $cmd = '%%GENEX_BIN_DIR%%/mbad-insert.pl';
      my @args = ("--user=$session->{username}",
		  "--password=$session->{password}",
		  "--dbname=$session->{dbname}",
		  "--ro_group=$read_group",
		  "--rw_group=$write_group",
		  "--es_pk=$es_pk",
		  "--ad_pk=$ad_pk",
# 		  "--fe_sw_pk=$fe_sw_pk",
		  "--fe_sw_pk=3",
		 );
      my @pks;

      foreach my $file (@files) {
	my @params = ($file);
	my $command = join(' ', $cmd, @args, @params);
	my $pk = `$command`;
	die $! if $?;
	push(@pks,$pk);
      }

      $data = "@pks";
    } else {
      my @gs_dbs = Bio::Genex::GroupSec->get_all_objects($dbh);
      foreach my $gs_db (@gs_dbs) {
	push(@groups,[$gs_db->name,$gs_db->name]);
      }

      my @ad_dbs = Bio::Genex::ArrayDesign->get_all_objects($dbh);
      foreach my $ad_db (@ad_dbs) {
	push(@array_designs,[$ad_db->ad_pk,$ad_db->name]);
      }

      my @exp_dbs = Bio::Genex::ExperimentSet->get_all_objects($dbh);
      foreach my $exp_db (@exp_dbs) {
	push(@experiment_sets,[$exp_db->es_pk,$exp_db->name]);
      }

      my @fe_dbs = Bio::Genex::FeatureExtractionSoftware->get_all_objects($dbh);
      foreach my $fe_db (@fe_dbs) {
	push(@feature_extractions,[$fe_db->fesw_pk,$fe_db->name . ':' . $fe_db->version]);
      }

      my @files = glob('%%GENEX_UPLOAD_DIR%%/*.txt');
      foreach my $name (@files) {
	my $short_name = $name;
	$short_name =~ s|.*/||;
	push(@data_files,[$name,$short_name]);
      }
    }
</%init>

--- NEW FILE: group-maint.html.in ---
% if (($response_page eq "NEW")) { 
  <center>
    <h1>Group Member Assicoation Modification</h1>
    <form action="<% $action %>"><br></br>
      <br></br>
      <table cellpadding="2" cellspacing="2" border="0"
	     style="text-align: left; margin-left: auto; margin-right: auto;"
	     title="Select the group to work with"
	     summary="Choose Group">
	<tbody>
	  <tr>
	    <td valign="top">Which Group would you like to add or
              remove members?<br></br>
	    </td>
	    <td valign="top">
	      <& comps/query-drop-down.mason, name=>"groupname",
	      array_ref=>\@groupnames &>
              <td valign="top">
	  </tr>
	</tbody>
      </table>
      <br></br>
      <br></br>
      <input name="submitted" type="hidden" value="true"></input>
      <input type="submit" name="submit" value="Modify This Group"></input>
      <br></br>
    </form>
  </center>
% } else {  # session is initialized
  <center>
    <h1>Group Member Assicoation Modification</h1>
    <form action="<% $action %>"><br></br>
      <input type="hidden" name="groupname" value="<% $groupname %>"></input>
      <input type="hidden" name="modified" value=1></input>

% if ($response_page eq "DONE"){
      <div style="text-align: center;">
	<h1>Genex User-associations Updated</h1>
% }

	<br></br>

% if ($response_page eq "BadGroup"){
	<h3><font color="red">You chose an invalid group to 
	    associate this user with</font>
	</h3>
% }

	<b>Check/Uncheck the Users you wish to be associated with/dissociated from this group.</b>
	<table cellpadding="5" cellspacing="2" border="0"
	       style="text-align: left; margin-left: auto; margin-right: auto;"
	       title="Enter the following information for your group"
	       summary="information about the group">
	  <caption>
	    <br></br>
	  </caption>  
	  <tbody>
	    <tr>
	      <td valign="top">Group <i><% $groupname %></i><br></br>
		currently has the following members, shown here: <br></br>
	      </td>
	      <td valign="top">
		<& comps/query-checkboxes.mason, 
		name=>"new_affiliations",
		hash_ref=>\%affiliations &>
	      </td>
	    </tr>
	  </tbody>
	</table>
	<br></br>
	<input name="submitted" type="hidden" value="true"></input>
	<input type="submit" name="submit" value="Modify This Group"></input>
      </div>
    </form>
  </center>
% }

<%attr>
  action=>'%%GENEX_WORKSPACE_URL%%/user_group_add.html'
  name=>'Associate Genex User With Group'
  path=>'%%GENEX_WORKSPACE_URL%%/user_group_add.html'
</%attr>
<%args>
  $groupname => ""
  $submitted => ""
  $modified => 0
  $debug => 0
  $new_affiliations => []
</%args>
<%once>;
use Bio::Genex;
use Bio::Genex::Connect;
use Bio::Genex::GroupSec;
use Bio::Genex::UserSec;
use Bio::Genex::GroupLink;
use Bio::Genex::HTMLUtils;

</%once>
<%init>;
my $name = $m->current_comp->attr('name');
my $path = $m->current_comp->attr('path');
my $action = $m->current_comp->attr('action');

my $session = Bio::Genex::HTMLUtils::get_session_cookie($r);

my $dbh = Bio::Genex::Connect->new(USER=>$session->{username},
				   PASSWORD=>$session->{password},
				   DBNAME=>$session->{dbname},
				  );


$dbh->assert_table_defined('UserSec');
$dbh->assert_table_defined('GroupSec');
$dbh->assert_table_defined('GroupLink');

my $response_page;
my %affiliations;

# get list of all valid users and groups for various purposes
my @groupnames;  # holds the names of all groups that exist
my %users;
my %groups;

my @allgroups = Bio::Genex::GroupSec->get_all_objects($dbh); #returns objects

my %my_groups = map {$_->groupname=>1}
  Bio::Genex::GroupLink->get_all_objects($dbh,
					 column=>'username',
					 value=>$session->{username}
					);
foreach (@allgroups){
  push(@groupnames, [$_->name,$_->name])
    if $my_groups{$_->rw_groupname};
  $groups{$_->name} = $_;
}

my $entered;

if ($submitted ne "true") {  # this is a fresh load of the page
  $response_page="NEW";
} elsif ($groupname && !(grep { $_->[0] eq $groupname } @groupnames)) {
  $response_page="BadGroup";
} else {

  my @old_users = map {$_->username}
    Bio::Genex::GroupLink->get_all_objects($dbh,
					   column=>'groupname',
					   value=>$groupname
					  );

  my @allusers = Bio::Genex::UserSec->get_all_objects($dbh);
  %users = map {$_->username=>$_} @allusers;

  %affiliations = map {$_->username=>0} @allusers;
  foreach my $groupname (@old_users) {
    $affiliations{$groupname}++;
  }

  if ($modified) {

    # Bug in mason, a single checkbox comes back as a string
    # not as an array ref with a single string
    my %new_affiliations;
    if (ref $new_affiliations) {
      %new_affiliations = map {$_=>1} @{$new_affiliations};
    } else {
      %new_affiliations = ($new_affiliations=>1);
    }

    foreach my $username (keys %new_affiliations){
      next if $affiliations{$username};
      $entered = "yes";
      my $gl_db = Bio::Genex::GroupLink->new(groupname_obj=>$groups{$groupname},
					     username_obj=>$users{$username},
					    );
      $gl_db->insert_db($dbh);
    }

    foreach my $username (@old_users){
      next if exists $new_affiliations{$username};
      $dbh->do("DELETE FROM GroupLink
                WHERE username='$username' AND groupname='$groupname'");
      $affiliations{$username} = 0;
    }
    $response_page="DONE";
  }
}

</%init>