[Genex-cvs-commit] genex-server/Mason/workspace sample-protocols.html.in,NONE,1.1 physicalbioassay-insert.html.in,NONE,1.1

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

Update of /cvsroot/genex/genex-server/Mason/workspace
In directory sc8-pr-cvs1:/tmp/cvs-serv10973

Added Files:
	sample-protocols.html.in physicalbioassay-insert.html.in 
Log Message:
new

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

% if ($error) {

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

% } elsif ($submit) {

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

% } elsif ($sample_fk) {

  <h2>Associating Protocol Application Events with Sample <% $sample_name %></h2>

      <table bgcolor="#D8E4F7" width="444" border="1">
	<theader>
	  <th colspan="100"><b>Protocol Application Entries</b></th>
	</theader>
	<& comps/objs2table.mason, objects=>\@protocol_app_dbs,
	check=>1, check_header=>'Include', check_name=>'include_protocol'
	&>
</table>

	<input type="submit" name="submit" 
	       value="Add Protocols to Sample" size="33">
        <& comps/hiddenlist.mason, name=>'debug', value=>$debug &>
        <& comps/hiddenlist.mason, name=>'sample_fk', value=>$sample_fk &>
	<hr noshade size=5>

% } else {

  <h2>Choose a Sample</h2>
	    <p>In order to associate <b>Protocol Applications</b> with
	      a <b>Sample</b>, your must first choose the <b>Sample</b>
	      entry which is being applied</p>

	    <p>Then you will have the opportunity to associate the
	      <b>Protocol Applications</b> events events for this
	      <b>Sample</b></p>

	  <& comps/fkey-menu.mason,
	  class=>'Sample',
	  script=>'sample-insert.html',
	  cgi_param_name=>'sample_fk',
	  array_ref=>\@samples,
	  entry_name=>$cur_class &>

	<hr noshade size=5>

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

% }
      </div>
    </form>

<%args>
    $debug => 0
    $submit => ''
    $sample => ''

    $sample_fk => ''
    $include_protocol => ''
</%args>
<%attr>
  action=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/sample-protocols.html"
  name=>'GeneX DB Sample Protocols Page'
  path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/sample-protocols.html"
</%attr>
<%once>
use lib qw(%%GENEX_EXTRALIBS%%);

use Bio::Genex;
use Bio::Genex::Config;
use Bio::Genex::Sample;
use Bio::Genex::ProtocolApplication;
use Bio::Genex::ProtocolApplicationLink;
use Bio::Genex::Protocol;
# 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');
    my $cur_class = 'Sample';
    my $other_class = 'ProtocolStepApplication';

# Apache::DB->init;
# Apache::DB->handler;

    my $no_type = 'NONE';
    my $data = '';
    my $error;
    my @samples;
    my @protocol_app_dbs;
    my $sample_name;
    my $sample_db;
    if ($sample) {
      $sample_db = Bio::Genex::Sample->new(dbh=>$dbh,id=>$sample_fk);
      $sample_name = $sample_db->name;

      @protocol_app_dbs = Bio::Genex::ProtocolApplication->get_all_objects($dbh);

    } elsif ($submit) {
      my @pks;
      my @protocol_pks = ref($include_protocol) eq 'ARRAY' ? @{$include_protocol}
                                                           : $include_protocol;
      foreach my $proto_pk (@protocol_pks) {
	my $proto_db =
	  Bio::Genex::ProtocolApplicationLink->new(proto_app_fk=>$proto_pk,
						   other_fk=>$sample_fk,
						  );
	my $pk = $proto_db->insert_db($dbh);
	unless (defined $pk) {
	  $error = 1;
	  $data = <<EOE;
<p>Inserting Protocol Application: $proto_pk, Sample: $sample_fk</p>
<p>Error output = &lt;$DBI::errstr&gt;</p>
EOE
	  goto ERROR;
	}
	push(@pks,$pk);
      }
      $data = "Protocols Successfully Added with primary keys: " . join(' ', @pks);
    } else {
      my @samp_dbs = Bio::Genex::Sample->get_all_objects($dbh);
      foreach my $samp_db (@samp_dbs) {
	push(@samples,[$samp_db->smp_pk,
		       $samp_db->name,
		      ]);
      }
    }
ERROR : {
  $data = qq[<font color="red"><h2>ERROR</h2><b>$data</b></font>]
    if $error;
}
</%init>

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

% if ($error) {

	<% $data %>

% } elsif ($submit) {

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

% } else {

      <& comps/ro_rw_group.mason, type=>$cur_class &>

	<hr noshade size=5>

	<& comps/value-input.mason, 
	value_name=>"Name",
	cgi_param_name=>"pba_name",
	entry_name=>$cur_class &>

	<hr noshade size=5>

	  <& comps/fkey-menu.mason,
	  class=>"ExperimentSet",
	  script=>"experimentset-create.html",
	  cgi_param_name=>"es_fk",
	  array_ref=>\@experiments,
	  entry_name=>$cur_class &>

	<hr noshade size=5>

	  <& comps/fkey-menu.mason,
	  class=>"Array",
	  script=>"array-insert.html",
	  cgi_param_name=>"array_fk",
	  array_ref=>\@arrays,
	  entry_name=>$cur_class &>

	<hr noshade size=5>

	    <& comps/textarea-input.mason,
	    cgi_param_name=>"pba_desc",
	    entry_name=>$cur_class, 
	    value_name=>"Physical BioAssay Description",
	    &>

	<hr noshade size=5>

		<& comps/contacts.mason, type=>"$cur_class" &>

	<hr noshade size=5>

	<input type="submit" name="submit" value="Create Physical BioAssay" size="33">
        <& comps/hiddenlist.mason, name=>"debug", value=>$debug &>
	<hr noshade size=5>

% }
      </div>
    </form>

<%args>
    $debug => 0
    $submit => ''

    $provider => ''
    $read_group => ''
    $write_group => ''

    $pba_desc => ''
    $es_fk => ''
    $array_fk => ''
    $pba_name => ''
</%args>
<%attr>
  action=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/physicalbioassay-insert.html"
  name=>'GeneX DB Physical BioAssay Creation Page'
  path=>"$Bio::Genex::Config->{GENEX_WORKSPACE_URL}/physicalbioassay-insert.html"
</%attr>
<%once>
use lib qw(%%GENEX_EXTRALIBS%%);

use Bio::Genex;
use Bio::Genex::Connect;
use Bio::Genex::Config;
use Bio::Genex::Contact;
use Bio::Genex::GroupSec;
use Bio::Genex::PhysicalBioAssay;
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');
my $error;

# Apache::DB->init;
# Apache::DB->handler;

my $data = '';
my $cur_class = 'PhysicalBioAssay';
$dbh->assert_table_defined($cur_class);

my @experiments;
my @arrays;

if ($submit) {
  # handle required arguments
  unless ($es_fk) {
    $error = 1;
    $data = <<EOE;
<p>Required argument <b>es_fk</b> not provided</p>
EOE
    goto ERROR;
  }
  unless ($array_fk) {
    $error = 1;
    $data = <<EOE;
<p>Required argument <b>array_fk</b> not provided</p>
EOE
    goto ERROR;
  }
  unless ($pba_name) {
    $error = 1;
    $data = <<EOE;
<p>Required argument <b>pba_name</b> not provided</p>
EOE
    goto ERROR;
  }


  my @pks;
  my $pba_db = Bio::Genex::PhysicalBioAssay->new();

  $pba_db->name($pba_name);
  $pba_db->ro_groupname($read_group);
  $pba_db->rw_groupname($write_group);
  $pba_db->es_fk($es_fk);
  $pba_db->array_fk($array_fk);

  if ($provider) {
    $pba_db->provider_con_fk($provider);
  }
  if ($pba_desc) {
    $pba_desc =~ s/\'//;
    $pba_db->description($pba_desc);
  }

  my $pk = $pba_db->insert_db($dbh);
  unless (defined $pk) {
    $error = 1;
    $data = <<EOE;
<p>DBI Error while Inserting $cur_class</p>
<p>Error output = &lt;$DBI::errstr&gt;</p>
EOE
    goto ERROR;
  } else {
    $data = "$cur_class, $pba_name, Successfully Created with pkey: $pk";
  }
} else {
  my @exp_dbs = Bio::Genex::ExperimentSet->get_all_objects($dbh);
  foreach my $exp_db (@exp_dbs) {
    push(@experiments,[$exp_db->es_pk,
		       $exp_db->name,
		      ]);
  }
  my @array_dbs = Bio::Genex::Array->get_all_objects($dbh);
  foreach my $array_db (@array_dbs) {
    push(@arrays,[$array_db->array_pk,
		  $array_db->name,
		 ]);
  }
}

ERROR : {
  $data = qq[<font color="red"><h2>ERROR</h2><b>$data</b></font>]
    if $error;
}
</%init>