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find_neuron_term.php
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find_neuron_term.php
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<?php
include ("permission_check.php");
?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<!-- Google Analytics Tracking -->
<?php include_once("analytics.php") ?>
<?php
require_once('class/class.temporary_neuronterm.php');
require_once('class/class.term.php');
require_once('class/class.type.php');
require_once('class/class.synonym.php');
require_once('class/class.evidencepropertyyperel.php');
require_once('class/class.articleevidencerel.php');
require_once('class/class.articleauthorrel.php');
require_once('class/class.article.php');
require_once('class/class.author.php');
require_once('class/class.synonymtyperel.php');
$articleevidencerel = new articleevidencerel($class_articleevidencerel);
$temporary = new temporary_neuronterm();
$term = new term($class_term);
$type_1 = new type($class_type);
$synonym_1 = new synonym($class_synonym);
$evidencepropertyyperel = new evidencepropertyyperel($class_evidence_property_type_rel);
$article = new article($class_article);
$author = new author($class_author);
$articleauthorrel = new articleauthorrel($class_articleauthorrel);
$synonymtyperel = new synonymtyperel($class_synonymtyperel);
$term_last = '';
// Resume searching
if ($_REQUEST['resume_searching_tab'])
{
$resume_searching = $_SESSION['resume_searching'];
$name_temporary_table = $resume_searching;
$_SESSION['name_temporary_table'] = $name_temporary_table;
$temporary->setName_table($name_temporary_table);
}
// Creates the temporary table for the search
if ($_REQUEST['searching'])
{
$ip_address = $_SERVER['REMOTE_ADDR'];
$ip_address = str_replace('.', '_', $ip_address);
$time_t = time();
$name_temporary_table ='search1_'.$ip_address."__".$time_t;
$_SESSION['name_temporary_table'] = $name_temporary_table;
$temporary->setName_table($name_temporary_table);
$temporary->create_temp_table ($name_temporary_table);
$temporary->insert_temporary('all', '');
$temporary_search = 0;
}
// New Request
if($_REQUEST['new'])
{
$ip_address = $_SERVER['REMOTE_ADDR'];
$ip_address = str_replace('.', '_', $ip_address);
$time_t = time();
$name_temporary_table ='search1_'.$ip_address."__".$time_t;
$_SESSION['name_temporary_table'] = $name_temporary_table;
$temporary->setName_table($name_temporary_table);
$temporary->create_temp_table ($name_temporary_table);
$temporary->insert_temporary($_GET["first_neuron"], $_GET["name_neuron"]);
$temporary_search = 0;
}
// update the letter in the temporary table:
$letter = $_REQUEST['letter'];
if ($letter)
{
$name_temporary_table = $_SESSION['name_temporary_table'];
$id_update = $_REQUEST['id'];
// retrieve all neuron terms
$term->retrive_name();
$n_neuron_total_term = $term->getName_neuron();
// keep only those neuron terms that have the first letter = $letter:
$trm_neuron = array();
$n_neuron3 = 0;
for ($i1=0; $i1<$n_neuron_total_term; $i1++)
{
$name_trm_neuron = $term->getName_neuron_array($i1);
if ($letter == 'all')
{
$trm_neuron[$n_neuron3] = $name_trm_neuron;
$n_neuron3 = $n_neuron3 + 1;
}
else if (strtolower($name_trm_neuron[0]) == strtolower($letter))
{
$trm_neuron[$n_neuron3] = $name_trm_neuron;
$n_neuron3 = $n_neuron3 + 1;
}
}
$temporary->setName_table($name_temporary_table);
if ($n_neuron3 > 0)
{
$temporary->update_temporary($letter, $trm_neuron[0], 1, $id_update);
}
else
{
$temporary->update_temporary($letter, '', 1, $id_update);
}
//sort($trm_neuron);
$temporary_search = 0;
}
$neuron5 = $_REQUEST['neuron'];
if ($neuron5)
{
$name_temporary_table = $_SESSION['name_temporary_table'];
$id_update = $_REQUEST['id'];
$temporary->setName_table($name_temporary_table);
$temporary->update_temporary(NULL, $neuron5, 2, $id_update);
$temporary_search = 1;
}
// ADD a new line for a new Author: --------------------------------------------------------------------
if ($_REQUEST['plus'])
{
$name_temporary_table = $_SESSION['name_temporary_table'];
$temporary->setName_table($name_temporary_table);
$temporary->insert_temporary('all', '');
$temporary_search = 0;
}
// REMOVE line -----------------------------------------------------------------------------------------
if ($_REQUEST['remove'])
{
$name_temporary_table = $_SESSION['name_temporary_table'];
$temporary ->setName_table($name_temporary_table);
$id_temp = $_REQUEST['id'];
$temporary->remove($id_temp);
$temporary_search = 1;
}
// Show result --------------------------------------------------------------------------------------------
if ($_REQUEST['see_result'])
{
$name_temporary_table = $_SESSION['name_temporary_table'];
$temporary->setName_table($name_temporary_table);
$temporary_search = 1;
}
if ($temporary_search == 1)
{
$temporary->retrieve_id();
$n_id = $temporary->getN_id();
}
// Clear all ---------------------------------------------
if ($_REQUEST['clear_all'])
{
$name_temporary_table = $_SESSION['name_temporary_table'];
$query = "TRUNCATE $name_temporary_table";
$rs = mysqli_query($GLOBALS['conn'],$query);
// Creates the temporary table:
$temporary->setName_table($name_temporary_table);
$temporary->insert_temporary('all', '');
}
// -------------------------------------------------------
?>
<script type="text/javascript">
// Javascript function *****************************************************************************************************
function letter(link, id_1)
{
var letter=link[link.selectedIndex].value;
var id = id_1;
var destination_page = "find_neuron_term.php";
location.href = destination_page+"?letter="+letter+"&id="+id;
}
function neuron(link, id_1)
{
var neuron=link[link.selectedIndex].value;
var id = id_1;
var destination_page = "find_neuron_term.php";
location.href = destination_page+"?neuron="+neuron+"&id="+id;
}
function term_event(term_parm, term_id)
{
var neuron = term_parm;
var id = term_id;
var destination_page = "find_neuron_term.php";
location.href = destination_page+"?neuron="+neuron+"&id="+id;
}
</script>
<?php include ("function/icon.html"); ?>
<title>Neuron ID</title>
<script type="text/javascript" src="style/resolution.js"></script>
<script src="DataTables-1.9.4/media/js/jquery.js" type="text/javascript"></script>
<script src="DataTables-1.9.4/media/js/jquery.dataTables.js" type="text/javascript"></script>
<link rel="stylesheet" type="text/css" href="DataTables-1.9.4/media/css/demo_table_jui.css"/>
<link rel="stylesheet" type="text/css" href="DataTables-1.9.4/examples/examples_support/themes/smoothness/jquery-ui-1.8.4.custom.css"/>
<script type="text/javascript" charset="utf-8">
$(document).ready(function(){
$('#tab_res').dataTable({
"sPaginationType":"full_numbers",
"bJQueryUI":true,
"oLanguage": {
"sSearch": "Search for keywords inside the table:"
},
"iDisplayLength": 25
});
});
</script>
</head>
<body>
<!-- COPY IN ALL PAGES -->
<?php
include ("function/title.php");
include ("function/menu_main.php");
?>
<div class='title_area'>
<font class="font1">Search Neuron Term for Machine-Readable Definition Identifier</font>
</div>
<div class="table_position_search_page" >
<!-- **************** BODY **************** -->
<?php
//if ($temporary_search == 1)
//{
// if ($n_id == 1)
// print ("<font class='font12'>$n_id Neuron Term has been selected</font>");
// else if ($n_id > 1)
// print ("<font class='font12'> $n_id Neuron Terms have been selected</font>");
// else
// print ("<font class='font12'> 0 Neuron Terms have been selected</font>");
//}
?>
<table border='0' cellspacing='3' cellpadding='0' class='table_search' width='100%'>
<tr>
<td align="center" width="6%" class='table_neuron_page3'>Initial</td>
<td align="center" width="45%" class='table_neuron_page3'>Neuron Term - Selector</td>
<td align="center" width="45%" class='table_neuron_page3'>Neuron Term - Autocomplete</td>
<td align="center" width="2%" class='table_neuron_page3'>+OR</td>
<td align="center" width="2%" class='table_neuron_page3'> - </td>
</tr>
<!-- tr -->
<?php
$temporary->retrieve_id();
$n_search = $temporary->getN_id();
for ($i=0; $i<$n_search; $i++)
{
print("<tr><td align='center' width='6%' class='table_neuron_page1'>");
$id = $temporary->getID_array($i);
print("<select name='letter1' size='1' class='select1' onChange='letter(this, $id)'>");
$temporary->retrieve_letter_from_id($id);
$letter_t = $temporary->getLetter();
if ($letter_t)
{
if ($letter_t == 'all')
$letter_t = 'all';
print("<OPTION VALUE='$letter_t'> $letter_t </OPTION>");
}
print(" <OPTION VALUE='A'> A </OPTION>
<OPTION VALUE='B'> B </OPTION>
<OPTION VALUE='C'> C </OPTION>
<OPTION VALUE='D'> D </OPTION>
<OPTION VALUE='E'> E </OPTION>
<OPTION VALUE='F'> F </OPTION>
<OPTION VALUE='G'> G </OPTION>
<OPTION VALUE='H'> H </OPTION>
<OPTION VALUE='I'> I </OPTION>
<OPTION VALUE='J'> J </OPTION>
<OPTION VALUE='K'> K </OPTION>
<OPTION VALUE='L'> L </OPTION>
<OPTION VALUE='M'> M </OPTION>
<OPTION VALUE='N'> N </OPTION>
<OPTION VALUE='O'> O </OPTION>
<OPTION VALUE='P'> P </OPTION>
<OPTION VALUE='Q'> Q </OPTION>
<OPTION VALUE='R'> R </OPTION>
<OPTION VALUE='S'> S </OPTION>
<OPTION VALUE='T'> T </OPTION>
<OPTION VALUE='U'> U </OPTION>
<OPTION VALUE='V'> V </OPTION>
<OPTION VALUE='W'> W </OPTION>
<OPTION VALUE='X'> X </OPTION>
<OPTION VALUE='Y'> Y </OPTION>
<OPTION VALUE='Z'> Z </OPTION>
<OPTION VALUE='all'> all </OPTION>
</select></td>"
);
// retrieve all terms from table 'Term'
$term->retrive_name();
$n_neuron_total_term = $term->getName_neuron();
// keep only the neuron terms from table 'Term' that have the first letter = $letter_t:
$trm_neuron = array();
$n_neuron3 = 0;
for ($i1=0; $i1<$n_neuron_total_term; $i1++)
{
$name_trm_neuron = $term->getName_neuron_array($i1);
if ($letter_t == 'all')
{
$trm_neuron[$n_neuron3] = $name_trm_neuron;
$n_neuron3 = $n_neuron3 + 1;
}
else if (strtolower($name_trm_neuron[0]) == strtolower($letter_t))
{
$trm_neuron[$n_neuron3] = $name_trm_neuron;
$n_neuron3 = $n_neuron3 + 1;
}
}
//sort($trm_neuron);
$temporary->retrieve_neuron_from_id($id);
$name_neuron_right = $temporary->getNeuron();
$term_last = $temporary->getNeuron();
$result = $trm_neuron;
$total = $n_neuron3;
// Selector
print("<td align='left' width='45%'class='table_neuron_page1'>");
print("<select name='neuron1' size='1' class='select1' value='$term_last' onChange='neuron(this,$id)' style='width:450px'>");
$temp_neuron = htmlspecialchars($name_neuron_right,ENT_QUOTES);
echo"<option value='".$temp_neuron."'>".stripslashes($name_neuron_right)."</option>";
print("<OPTION VALUE='' disabled></OPTION>");
if ($total == 0)
{
print("<OPTION VALUE=''>-</OPTION>");
}
else
{
for ($k1=0; $k1<$total; $k1++)
{
$temp_neuron = htmlspecialchars($result[$k1],ENT_QUOTES);
echo"<option value='".$temp_neuron."'>".$result[$k1]."</option>";
}
}
print("</select>");
print("</td>");
// Autocomplete
print("<td align='left' width='45%' class='table_neuron_page1'>");
print("<datalist id='term_list'>");
for ($k1=0; $k1<$total; $k1++)
{
$temp_neuron = htmlspecialchars($result[$k1],ENT_QUOTES);
echo"<option value='".$temp_neuron."'>".$result[$k1]."</option>";
}
print("</datalist>");
print("<input type='text' list='term_list' name='neuron1' class='select1' value='$term_last' onChange='term_event(value,$id)' style='width:450px' autocomplete='on' autofocus>");
print("</td>");
// AND term controls i.e. the plus and minus sign buttons
print("<td align='center' width='2%'>
<form action='find_neuron_term.php' method='post' style='display:inline'>
<input type='submit' name='plus' value=' + ' class='more_button'></form></td>"
);
if ($i > 0)
print("</td><td align='center' width='2%'>
<form action='find_neuron_term.php' method='post' style='display:inline'>
<input type='submit' name='remove' value=' - ' class='more_button'>
<input type='hidden' name='id' value='$id'></form></td>"
);
else
print("</td><td align='center' width='2%'></td>");
} //END for ($i=0; $i<$n_search; $i++)
?>
</tr>
</table>
<div align="left" >
<table width='100%'>
<tr>
<td width='6%'>
<form action="find_neuron_term.php" method="post" style='display:inline'>
<input type='submit' name='clear_all' value='RESET' />
</form>
</td>
<td width='45%' style='width:450px'>
<form action="find_neuron_term.php" method="post" style='display:inline'>
<input type='submit' name='see_result' value='SEE RESULTS' />
</form>
</td>
<td width='45%' style='width:450px'>
<form action='find_neuron_term.php' method='post' style='display:inline'>
<input type='submit' name='see_result' value='SET SELECTOR' />
</form>
</td>
<td width='4%' style='width:300px'>
</td>
</tr>
</table>
<?php
if ($_REQUEST['see_result'])
{
print("<table border='0' class='table_result' id='tab_res' width='100%'>");
print("<thead><tr>
<th style='display:none;' align='center' width=' 5%' class='table_neuron_page1'> <strong>Rank</strong></th></font>
<th align='center' width='15%' class='table_neuron_page1'> <strong>Term</strong></th></font>
<th align='center' width='15%' class='table_neuron_page1'> <strong>Concept</strong></th></font>
<th align='center' width='10%' class='table_neuron_page1'> <strong>Resource</strong></th></font>
<th align='center' width='55%' class='table_neuron_page1'> <strong>Definition</strong></th></font>
</tr></thead><tbody>"
);
$temporary->retrieve_id();
$n_id = $temporary->getN_id();
for ($j1=0; $j1<$n_id; $j1++)
{
$name_trm_neur[$j1] = $temporary->getNeuron_array($j1);
$name_neuron = $name_trm_neur[$j1];
$term->retrive_name();
$n_total_name = $term->getName_neuron();
for ($i2=0; $i2<$n_total_name; $i2++)
{
if ($name_neuron == $term->getName_neuron_array($i2))
{
$term->retrive_id_by_name($name_neuron);
$n_term_id = $term->getN_id();
$concept_title='';
$terms_concept = '';
$parents_concept = '';
for ($k3=0; $k3<$n_term_id; $k3++)
{
$id_term = $term->getID_array($k3);
$term->retrive_by_id($id_term);
$term_parent = $term->getParent();
$term_concept = $term->getConcept();
//$term_term = $term->getTerm();
$term_term = $name_neuron; // overide database term with selector term
$term_resource_rank = $term->getResourceRank();
$term_resource = $term->getResource();
$term_portal = $term->getPortal();
$term_repository = $term->getRepository();
$term_unique_id = $term->getUniqueID();
$term_definition_link = $term->getDefinitionLink();
$term_definition = $term->getDefinition();
$term_protein_gene = $term->getProteinGene();
$term_human_rat = $term->getHumanRat();
$term_term_display = '';
$term_concept_display = '';
if ($k3 == 0) {
$term_term_display = $term_term;
$term_concept_display = $term_concept;
}
print(" <tr>
<td style='display:none;' align='center' width=' 5%' class='table_neuron_page4'>$term_resource_rank</td>
<td align='center' width='15%' class='table_neuron_page4'>$term_term_display</td>
<td id='concept' align='center' width='15%' class='table_neuron_page4' title=''>$term_concept_display</td>
<td align='center' width='10%' class='table_neuron_page4'><a href='$term_definition_link' target='_blank'><font class='font13'>$term_resource</font></a></td>
<td align='left' width='55%' class='table_neuron_page4'>$term_definition</td>
</tr>"
);
}
$terms_concept = $term->retrive_term_concept($term_concept);
$value = '';
$allTerms = '';
if (!empty($terms_concept)) {
foreach ($terms_concept as $value) {
$allTerms .= $value.",".$allTerms;
}
}
$allTerms = trim(implode(',',array_unique(explode(',', $allTerms))), ",");
$allTerms = 'Synonym(s):\r\n '.str_replace(",",'\r\n ',$allTerms);
$parents_concept = $term->retrive_parent_concept($term_concept);
$value = '';
$allParents = '';
if (!empty($parents_concept)) {
foreach ($parents_concept as $value) {
$allParents .= $value.",".$allParents;
}
}
$allParents = trim(implode(',',array_unique(explode(',', $allParents))), ",");
$allParents = 'Term Source(s):\r\n '.str_replace(",",'\r\n ',$allParents);
$concept_title = $allParents.'\r\n'.$allTerms;
?>
<script language="javascript">
$('#concept').attr('title', '<?php echo $concept_title;?>');
</script>
<?php
}
} //END for ($i2=0; $i2<$n_total_name; $i2++)
} //END for ($j1=0; $j1<$n_id; $j1++)
print("</tbody></table>");
}
?>
<br /><br />
</div>
</div>
</body>
</html>