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find_pmid.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">
<?php
//include ("access_db.php");
include ("function/scraper_pubmed.php");
require_once('class/class.article.php');
require_once('class/class.author.php');
require_once('class/class.articleauthorrel.php');
require_once('class/class.utils_type.php');
require_once('class/class.utils_author_article.php');
$author_1 = new author($class_author);
$articleauthorrel = new articleauthorrel($class_articleauthorrel);
$article = new article($class_article);
function getSupplemental($sup_id){
$types_array=array();
$index=0;
// retrive the neuron type associated with article using evidence id.
// article to evidence link is found in ArticleEvidenceRel table. All these evidence are further mapped to one or more evidence
// in table EvidenceEvidenceRel(source=evidence2_id and it is evidence_id in ArticleEvidenceRel table)
$query_to_get_type= " SELECT DISTINCT
Typ.id AS type_id,
Typ.nickname,
Typ.name,
'SUPPLEMENTAL' AS status
FROM
EvidencePropertyTypeRel eptr,
Type Typ
WHERE
eptr.Type_id = Typ.id
AND LOCATE('$sup_id', eptr.supplemental_pmids)
UNION
SELECT DISTINCT
t.Type_id AS type_id,
t.name AS nickname,
t.name,
'Onhold' AS status
FROM
Onhold t
WHERE
t.pmid_isbn=$sup_id"
;
//print($query_to_get_type);
$article_type = mysqli_query($GLOBALS['conn'],$query_to_get_type);
if (!$article_type) {
die("<p>Error in Listing Types Table.</p>");
}
while($rows=mysqli_fetch_array($article_type, MYSQLI_ASSOC))
{
$types_array[$index]=new utils_type();
$types_array[$index]->setName($rows['name']);
$types_array[$index]->setNickname($rows['nickname']);
$types_array[$index]->setStatus($rows['status']);
$types_array[$index]->setId($rows['type_id']);
$index++;
}
return $types_array;
}
// Go to the search: --------------------------------------------------------------------------
if ($_REQUEST['search_pmid'])
{
$type_search = $_SESSION['type_search'];
$n_pmid = $_SESSION['n_pmid'];
$pmid = trim($_REQUEST['pubmed_id']);
// Check if the pmid is OK or not: ************
if ($type_search == 'PMID')
{
if ((strlen($pmid) > 10) || (strlen($pmid) < 2))
$error_pmid = 1;
else
{
if (preg_match('[a-z]', $pmid))
$error_pmid = 1;
else
$error_pmid = 0;
}
}
if ($type_search == 'ISBN')
{
if (preg_match('[a-z]', $pmid))
$error_pmid = 1;
else
$error_pmid = 0;
}
// ********************************************
if ($type_search == 'PMID')
$article -> retrive_by_pmid_with_like($pmid, 1);
if ($type_search == 'ISBN')
$article -> retrive_by_pmid_with_like($pmid, 2);
$n_id_article = $article -> getN_id(); // Number of articles founded
}
// -----------------------------------------------------------------------------------------------
else
{
$type_code = $_REQUEST['type_code'];
if ($type_code)
{
$type_search = $type_code;
$_SESSION['type_search'] = $type_search;
}
else
{
$type_search = 'PMID';
$_SESSION['type_search'] = $type_search;
}
$n_pmid = 0;
// Calculate the number of articles or book present in the hippocampone.org
if ($type_search == 'PMID')
$article -> retrive_number_PMID(1);
if ($type_search == 'ISBN')
$article -> retrive_number_PMID(2);
$n_pmid = $article -> getN_pmid();
$_SESSION['n_pmid'] = $n_pmid;
}
?>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<!-- Google Analytics Tracking -->
<?php include_once("analytics.php") ?>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
<?php include ("function/icon.html"); ?>
<title>Find PMID/ISBN</title>
<script type="text/javascript" src="style/resolution.js"></script>
</head>
<body>
<!-- COPY IN ALL PAGES -->
<?php
include ("function/title.php");
include ("function/menu_main.php");
?>
<div class='title_area'>
<font class="font1">Search by PMID/ISBN</font>
</div>
<!-- submenu no tabs
<div class='sub_menu'>
<table width="90%" border="0" cellspacing="0" cellpadding="0">
<tr>
<td width="100%" align="left">
<font class='font1'><em>Find:</em></font>
<a href="search.php?searching=1"><font class="font7">Neuron</font></a> <font class="font7_A">|</font>
<a href="find_author.php?searching=1"><font class="font7"> Author</font></a><font class="font7_A">|</font>
<font class="font7_B"> PMID/ISBN</font><font class="font7_A">|</font>
</font>
</td>
</tr>
</table>
</div>
-->
<!-- ------------------------ -->
<div class="table_position_search_page">
<table width="95%" border="0" cellspacing="5" cellpadding="0" class='body_table'>
<tr>
<td width="80%">
<!-- **************** BODY **************** -->
<table border="0" cellspacing="3" cellpadding="0" class='table_search'>
<tr>
<td width="100%" align="left">
<?php
if ($type_search == 'PMID')
{
print ("<input type='radio' name='type_search' value='PMID' checked='checked'/>
<font class='font12'>PMID</font> ");
print ("<input type='radio' name='type_search' value='ISBN' onClick=\"javascript:location.href='find_pmid.php?type_code=ISBN'\"/>
<font class='font12'>ISBN</font>");
}
if ($type_search == 'ISBN')
{
print ("<input type='radio' name='type_search' value='PMID' onClick=\"javascript:location.href='find_pmid.php?type_code=PMID'\" />
<font class='font12'>PMID </font>");
print ("<input type='radio' name='type_search' value='ISBN' checked='checked'/>
<font class='font12'>ISBN</font>");
}
?>
</td>
</tr>
<tr>
<td width="100%" align="left">
<?php
if ($type_search == 'PMID')
print ("<font class='font12'>To search one or more publications in <img src='images/Hippocampome_logo.ico' border='0' width='15'/>Hippocampome.org please enter PMID (PubMed identifier) below: </font>");
if ($type_search == 'ISBN')
print ("<font class='font12'>To search one or more books in <img src='images/Hippocampome_logo.ico' border='0' width='15'/>Hippocampome.org please enter ISBN (International Standard Book Number) below: </font>");
?>
</td>
</tr>
<tr>
<td width="100%" align="left">
<?php
if ($type_search == 'PMID')
print ("<font class='font12'>Total number of publications in <img src='images/Hippocampome_logo.ico' border='0' width='15'/>Hippocampome.org: <strong> $n_pmid <strong> </font>");
if ($type_search == 'ISBN')
print ("<font class='font12'>Total number of books in <img src='images/Hippocampome_logo.ico' border='0' width='15'/>Hippocampome.org: <strong> $n_pmid <strong> </font>");
?>
</td>
</tr>
</table>
<form action="find_pmid.php" method="post" style="display:inline">
<table border="0" cellspacing="3" cellpadding="0" class='table_search'>
<tr>
<td width="20%" align="center" class='table_neuron_page1'>
<?php
if ($type_search == 'PMID')
print ("<strong>Enter PMID</strong>");
if ($type_search == 'ISBN')
print ("<strong>Enter ISBN</strong>");
?>
</td>
<td width="30%" align="left">
<input type="text" name='pubmed_id' size='40' />
</td>
<td width="10%" align="center">
<input type="submit" name='search_pmid' value='SEE RESULTS' />
</td>
<td width="40%" align="center">
<?php
if ($pmid)
{
if ($error_pmid == 1)
print ("<font class='font12'>PMID is not valid!</font>");
else
print ("<font class='font12'>Result for: $pmid </font> <font class='font14'> ( $n_id_article result(s) )</font>");
}
?>
</td>
</tr>
</table>
</form>
<?php
if ( ($n_id_article != 0) && ($error_pmid == 0) )
{
print ("<table border='0' class='table_result' id='tab_res' width='100%'>");
print ("<thead><tr>
<td align='center' width='20%' class='table_neuron_page1'> <strong>Authors</strong> </td>
<td align='center' width='40%' class='table_neuron_page1'> <strong>Title </strong></td>
<td align='center' width='10%' class='table_neuron_page1'> <strong>Journal/Book</strong> </td>
<td align='center' width='5%' class='table_neuron_page1'> <strong>Year </strong></td>
<td align='center' width='5%' class='table_neuron_page1'> <strong>PMID</strong></td>
<td align='center' width='20%' class='table_neuron_page1'> <strong>Types</strong></td>
</tr></thead><tbody>");
$aut_art_typ_utils = new utils_author_article();
for ($i1=0; $i1<$n_id_article; $i1++)
{
$id_article = $article -> getID_array($i1);
$article -> retrive_by_id($id_article);
$title = $article -> getTitle();
$journal = $article -> getPublication();
$year = $article -> getYearSansMonth();
$PMID1 = $article -> getPmid_isbn();
// retrieve tha list of authors: -----------------------------------------------
$articleauthorrel -> retrive_author_position($id_article);
$n_author = $articleauthorrel -> getN_author_id();
for ($ii3=0; $ii3<$n_author; $ii3++)
$auth_pos[$ii3] = $articleauthorrel -> getAuthor_position_array($ii3);
sort ($auth_pos);
for ($ii3=0; $ii3<$n_author; $ii3++)
{
$articleauthorrel -> retrive_author_id($id_article, $auth_pos[$ii3]);
$id_author = $articleauthorrel -> getAuthor_id_array(0);
$author_1 -> retrive_by_id($id_author);
$name_a = $author_1 -> getName_author_array(0);
$name_authors[$ii3] = $name_a;
}
$name_authors1 = NULL;
for ($ii3=0; $ii3<$n_author; $ii3++)
$name_authors1 = $name_authors1.", ".$name_authors[$ii3];
$name_authors1[0]='';
// -----------------------------------------------------------------------------
if ($type_search == 'PMID')
{
$value_link ='PMID: '.$PMID1;
$link2 = "<a href='http://www.ncbi.nlm.nih.gov/pubmed?term=$value_link' target='_blank'>";
}
if ($type_search == 'ISBN')
{
$link2 = "<a href='$link_isbn$PMID1' target='_blank'>";
}
print ("<tr>
<td align='left' width='20%' class='table_neuron_page4'>$name_authors1.</td>
<td align='left' width='40%' class='table_neuron_page4'>$title </td>
<td align='left' width='10%' class='table_neuron_page4'>$journal.</td>
<td align='left' width='5%' class='table_neuron_page4'>$year </td>
<td align='left' width='5%' class='table_neuron_page4'>$link2 <font class='font13'><strong>$PMID1</strong></font> </a> </td>
<td align='left' width='20%' class='table_neuron_page4'>");
// Get the Types using Article ID
$type_id_array = $aut_art_typ_utils -> getArticleTypesArray($id_article);
$count=0;
for ($j=0; $j < sizeof($type_id_array) ; $j++)
{
$type_name=$type_id_array[$j]->getName();
$type_nickname=$type_id_array[$j]->getNickname();
$type_status =$type_id_array[$j]->getStatus();
$type_id = $type_id_array[$j]->getId();
if($type_status!=NULL&&$type_status!='frozen')
{
$count++;
if($type_status=='SUPPLEMENTAL')
print("$count) <a href='neuron_page.php?id=$type_id' target='_blank' title='".$type_name."'>$type_nickname (Suppl)</a><br/>");
if($type_status=='Onhold')
print("$count) $type_nickname (On-hold)<br/>");
else
print("$count) <a href='neuron_page.php?id=$type_id' target='_blank' title='".$type_name."'>$type_nickname</a><br/>");
}
}
if ($count==0)
{
print("(to be determined)");
}
print("</td></tr>");
} // end $i1
print ("</tbody></table>");
}
// for supplement id without articles
else if($pmid!=""){
$n_id_article=1;
$sup_types=getSupplemental($pmid);
if(count($sup_types)!=0){
print ("<table border='0' class='table_result' id='tab_res' width='100%'>");
print ("<thead><tr>
<td align='center' width='20%' class='table_neuron_page1'> <strong>Authors</strong> </td>
<td align='center' width='40%' class='table_neuron_page1'> <strong>Title </strong></td>
<td align='center' width='10%' class='table_neuron_page1'> <strong>Journal/Book</strong> </td>
<td align='center' width='5%' class='table_neuron_page1'> <strong>Year </strong></td>
<td align='center' width='5%' class='table_neuron_page1'> <strong>PMID</strong></td>
<td align='center' width='20%' class='table_neuron_page1'> <strong>Types</strong></td>
</tr></thead><tbody>");
$value_link ='PMID: '.$pmid;
$link2 = "<a href='http://www.ncbi.nlm.nih.gov/pubmed?term=$value_link' target='_blank'>";
print ("<tr>
<td align='left' width='20%' class='table_neuron_page4'></td>
<td align='left' width='40%' class='table_neuron_page4'></td>
<td align='left' width='10%' class='table_neuron_page4'></td>
<td align='left' width='5%' class='table_neuron_page4'></td>
<td align='left' width='5%' class='table_neuron_page4'>$link2 <font class='font13'><strong>$pmid</strong></font> </a> </td>
<td align='left' width='20%' class='table_neuron_page4'>");
$count=0;
for ($j=0; $j < sizeof($sup_types) ; $j++)
{
$type_name=$sup_types[$j]->getName();
$type_nickname=$sup_types[$j]->getNickname();
$type_status =$sup_types[$j]->getStatus();
$type_id = $sup_types[$j]->getId();
if($type_status!=NULL&&$type_status!='frozen')
{
$count++;
if($type_status=='SUPPLEMENTAL')
print("$count) <a href='neuron_page.php?id=$type_id' target='_blank' title='".$type_name."'>$type_nickname (Suppl)</a><br/>");
else if($type_status=='Onhold')
print("$count) $type_nickname (On-hold)<br/>");
}
}
if ($count==0)
{
print("(to be determined)");
}
}
}
// Send an email ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
if ( ($n_id_article == 0) && ($error_pmid == 0) )
{
print ("<form action='send_email.php' method='post' style='display:inline'> ");
if ($pmid != NULL)
{
if ($type_search == 'PMID')
$res=scraper_pubmed($pmid);
if ($type_search == 'ISBN');
//if ($res[0] == '1')
//{
// $res[0] = "Insert the title";
// $author_3 = "Insert the authors";
// $res[2] = "Insert the publication";
//}
//else
// $author_3 = $res[1].". et al.";
$res[0] = "";
$author_3 = "";
$res[2] = "";
print ("<table border='0' cellspacing='2' cellpadding='0' class='table_result'>");
print ("<tr>");
print ("
<td width='10%' ></td>
<td width='80%' align='center' bgcolor='#CBDFE1'>
<font class='font2'>
This publication is not yet
in the Hippocampome. <br> To add it to the pipeline, please complete the information below.<br>
Include your e-mail address, if you would like an update on its status.
</font>
</td>
<td width='10%' ></td>
");
print ("</tr>");
print ("</table>");
print ("<table border='0' cellspacing='2' cellpadding='0' class='table_result'>");
print ("<tr>");
print ("
<td width='10%' ></td>
<td width='20%' class='table_neuron_page4' align='right'> $type_search </td>
<td width='60%' align='left' class='table_neuron_page4'>
<input type='text' name='pmid_send' value='$pmid' size='20'>
</td>
<td width='10%'></td>
");
print ("</tr>");
print ("<tr>");
print ("
<td width='10%'></td>
<td width='20%' class='table_neuron_page4' align='right'> TITLE </td>
<td width='60%' align='left' class='table_neuron_page4'>
<input type='text' name='title_send' value='$res[0]' size='70'>
</td>
<td width='10%'></td>
");
print ("</tr>");
print ("<tr>");
print ("
<td width='10%'></td>
<td width='20%' align='right' class='table_neuron_page4'> AUTHOR </td>
<td width='60%' align='left' class='table_neuron_page4'>
<input type='text' name='author_send' value='$author_3' size='30'>
</td>
<td width='10%'></td>
");
print ("</tr>");
print ("<tr>");
print ("
<td width='10%'></td>
<td width='20%' align='right' class='table_neuron_page4'> PUBLICATION </td>
<td width='60%' align='left' class='table_neuron_page4'>
<input type='text' name='publication_send' value='$res[2]' size='50'>
</td>
<td width='10%'></td>
");
print ("</tr>");
print ("</table>");
print ("<table border='0' cellspacing='2' cellpadding='0' class='table_result'>");
print ("<tr>");
print ("
<td width='10%'></td>
<td width='20%' align='right' class='table_neuron_page4'> YOUR NAME </td>
<td width='60%' align='left' class='table_neuron_page4'>
<input type='text' name='name_send' value='' size='50'>
</td>
<td width='10%'></td>
");
print ("</tr>");
print ("</table>");
print ("<table border='0' cellspacing='2' cellpadding='0' class='table_result'>");
print ("<tr>");
print ("
<td width='10%'></td>
<td width='20%' align='right' class='table_neuron_page4'> YOUR INSTITUTE </td>
<td width='60%' align='left' class='table_neuron_page4'>
<input type='text' name='institute_send' value='' size='50'>
</td>
<td width='10%'></td>
");
print ("</tr>");
print ("</table>");
print ("<table border='0' cellspacing='2' cellpadding='0' class='table_result'>");
print ("<tr>");
print ("
<td width='10%'></td>
<td width='20%' align='right' class='table_neuron_page4'> YOUR EMAIL* </td>
<td width='60%' align='left' class='table_neuron_page4'>
<input type='text' name='email_send' value='' size='50'>
</td>
<td width='10%'></td>
");
print ("</tr>");
print ("</table>");
print ("<br>
<table border='0' cellspacing='2' cellpadding='0' class='table_result'>
<tr>
<td width='100%' align='center'>
<input type='submit' name='send_email' value=' SEND '>
</form>
</td>
</tr>
</table>
<br><br>
");
}
} // END ELSE (send an email)
?>
</td>
</tr>
</table>
</body>
</html>