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test2.php
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test2.php
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<!-- BEGINNING OF DOCUMENT -->
<!DOCTYPE html>
<?php
//header('Content-Type: text/csv');
//header('Content-Disposition: attachment; filename="sample.csv"');
// Hypothes.is API TOKEN: (just a test) 6879-ef-QplA3MslmdVLEuDjP0pQrHmkAxhweWPjAZYOlH_M
// DailyMed group id on Hypothes.is: pGv4X7iV
// List of usernames on the dailymed group that actually have annotations:
/*amrapaliz 66
jonquet 2
liuwenqiangcs 37
lrieswijk 4
micheldumontier 3
rcelebi 98
sandeepayyar19 17
shima 11
Tudorzinho 4
yashvyas 11
Yijia_Zhang 61*/
// DrugCentral DB connection pot
include("conn_dev.php");
// Hypothes.is API wrapper (I also wrapped the DailyMed API call that we use here, in there as well)
require_once('Hypothesis.inc.php');
// Don't time out script if it takes long
set_time_limit(0);
/**
* Find the position of the Xth occurrence of a substring in a string
* @param $haystack
* @param $needle
* @param $number integer > 0
* @return int
*/
function strposX($haystack, $needle, $number){
if($number == '1'){
return strpos($haystack, $needle);
}elseif($number > '1'){
return strpos($haystack, $needle, strposX($haystack, $needle, $number - 1) + strlen($needle));
}else{
return error_log('Error: Value for parameter $number is out of range');
}
}
// Function to calculate the difference between two arrays
function arrayRecursiveDiff($a1, $a2) {
$result = array();
foreach($a1 as $va1) {
$found = false;
foreach($a2 as $va2) {
try{
//echo "va1: ".$va1." va2: ".$va2."<br>";
// if its a single value we need to convert to a singleton array
if (!is_array($va1)){
$va1 = compact($va1);
}
if (!is_array($va2)){
$va2 = compact($va2);
}
$x = array_diff($va1, $va2);
if (empty($x)) {
$found = true;
}
}
catch (Exception $e){
echo "va1: ".$va1." va2: ".$va2.", Exception Line 45: ".$e->getMessage();
}
}
if (!$found) {
$result[] = $va1;
}
}
foreach($a2 as $va2) {
$found = false;
foreach($a1 as $va1) {
try{
//echo "va1: ".$va1." va2: ".$va2."<br>";
// if its a single value we need to convert to a singleton array
if (!is_array($va1)){
$va1 = compact($va1);
}
if (!is_array($va2)){
$va2 = compact($va2);
}
$x = array_diff($va2, $va1);
if (empty($x)) {
$found = true;
}
}
catch (Exception $e){
echo "va1: ".$va1." va2: ".$va2.", Exception Line 63: ".$e->getMessage();
}
}
if (!$found) {
$result[] = $va2;
}
}
return $result;
}
// Function to avoid the "string expected" array found problem
function serialize_array_values($arr){
foreach($arr as $key=>$val){
try{
echo "val: ".$val."<br>";
// if sub-array $val is one value it will not be an array
if (is_array($val)){
sort($val);
}
}
catch (Exception $e){
echo "val: ".$val.", Exception Line 83: ".$e->getMessage();
}
$arr[$key]=serialize($val);
}
return $arr;
}
// Function to avoid the "string expected" array found problem
function serialize_array_values2($arr){
foreach($arr as $key=>$val){
sort($val);
$arr[$key]=json_encode($val);
}
return $arr;
}
function contains($str, $c){
for ($x = 0; $x < strlen($str);$x++){
if ($str[$x] == $c){
return true;
}
}
return false;
}
// Hypothes.is API TOKEN
$token = '6879-2oY7ox3Ka1n2H9x_vimd8sVIZJZWEaDLSprWamIvWlA';
// Hypothes.is and DailyMed PHP Wrapper instances
$hypothesis = new HypothesisAPI();
// Drugname typed in input textbox
$drugname=@$_POST['drugname'];
// Whether the checkbox to indicate drug class has been ticked or not
$isdrugclass=@$_POST['isdrugclass'];
// Just a input validation flag to check if we entered entered anything or if its a single drug or class of drugs
// that we are reporting on
$candisplaystuff = 0;
// Input error flag
$error = 0;
$matchingSETIDs = array();
$setIDToIndicMap = array();
$setIDToUMLSIndicMap = array();
$setIDToSNOMEDIndicMap = array();
$drugnames = array();
$dcids = array();
// If the drugname is specified (textbox is not empty) and the drug class checkbox is not ticked
if(isset($_POST['drugname']) && $drugname <> "" && $isdrugclass == ""){
//do nothing
}
else if(isset($_POST['drugname']) && $drugname <> "" && $isdrugclass == "true"){ // If we are searching for all drugs in a particular drug class
// Different output flag value (we have to display a table with numbers representing indication matches per drug)
$candisplaystuff = 3;
$data = array();
// First get all ATC codes and Struct_IDs for given drug class
// Query string formulation
$getSetIDsQueryStr = "SELECT name, dm_id, dc_id FROM dailymed_comparison WHERE atc LIKE '".$drugname."%'";
//$getStructIDsAndATCCodesQueryStr = "select distinct a.struct_id, b.atc from struct2atc a, cardiovascular_drugs b where a.atc_code like '".$drugname."%' and a.atc_code = b.atc and (b.atc NOT IN (SELECT distinct c.atc FROM dailymed_comparison c WHERE c.atc LIKE 'C%'));";
// Actual query directive to get the Struct_IDs and ATC codes for the given drug class
$getSetIDsQueryResult = pg_query($conn, $getSetIDsQueryStr) or die("Could not execute query");
// If there is at least one atc / set id pair for this drug class in DrugCentrals DB
if (pg_num_rows($getSetIDsQueryResult) > 0){
// Initialise array of SET IDs (drugs) that will match our condition: that they have co-prescribed medication tags in them
//Inaccurate indication codes overall (UMLS)
$umlsCodes = array();
//Inaccurate indication codes overall (DOID)
$doidCodes = array();
// For each drug, check if it has "role" prefixed tags in its annotations and store these to array
while($grow = pg_fetch_array($getSetIDsQueryResult)){
// add name to array
array_push($drugnames, $grow['name']);
// add dcid to array
array_push($dcids, $grow['dc_id']);
// Set the base URL on DailyMed where we are going to search for drug annotations
$dailyMedBaseUrl = "https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=";
// Append the SET ID so we can isolate the actual web page on DailyMed for the given drug
$dailyMedDrugUrl = trim($dailyMedBaseUrl.$grow['dm_id']);
//echo $dailyMedDrugUrl." ";
//echo "<a href='".$dailyMedDrugUrl."'>".$grow['dm_id']."</a><br>";
// Actually get all the Hypothes.is annotations.
// (a) first we pull annotations from the dailymed private group
$pvtGroupAnnotations = $hypothesis->search(array('uri' => $dailyMedDrugUrl, 'group' => 'pGv4X7iV'), $token);
//print_r($pvtGroupAnnotations);
// (b) and then we pull the public annotations
$annotations = $hypothesis->search(array('uri' => $dailyMedDrugUrl), $token);
//print_r($annotations);
// (c) add all private annotations to the public annotations array (collect all indications in one array)
foreach ($pvtGroupAnnotations as $value) {
array_push($annotations, $value);
}
$numAnno = 0;
foreach ($annotations as $value) {
$numAnno++;
}
// Set of inaccurate indication codes (UMLS)
$umlsCodesPerDrug = array();
$umlsCodesPerDrugPrint = array();
// Set of inaccurate indication codes (UMLS)
$doidCodesPerDrug = array();
$doidCodesPerDrugPrint = array();
// Flag to stop when we find an annotation with "role" prefixed tag
$globalDone = false;
// Index for annotations
$globalIndex = 0;
// While we didn't find a "role" prefixed annotation tag and we haven't run out of annotations
//echo "num annos: ".$numAnno."<br>";
while (!$globalDone && ($globalIndex < $numAnno)){
// Keep a reference to the current array of tags in this annotation
$current_annotation_tags = $annotations[$globalIndex]->tags;
//echo "num tags in anno ".($globalIndex+1).": ".count($current_annotation_tags)."<br>";
// Flag to stop when we find a tag with "role" as prefix
$done = false;
// Index for tags
$index = 0;
// Iterate through these tags to see if one of them has "role" as prefix
// While we didn't find a "role" prefixed tag and we haven't run out of tags in this annotation
while (!$done && ($index < count($current_annotation_tags))){
//echo substr($current_annotation_tags[$index], 0, 4).", ";
// If the first four or five characters of this tag are "role" or "roles" respectively OR the tag is a "rejected" one OR the tag is "AT" (adjunctive therapy)
$type = "";
if ((substr($current_annotation_tags[$index], 0, 4) == "role") || (substr($current_annotation_tags[$index], 0, 5) == "roles") || ($current_annotation_tags[$index] == "rejected") || ($current_annotation_tags[$index] == "AT")){
if (substr($current_annotation_tags[$index], 0, 4) == "role"){
$type = "role";
}
if (substr($current_annotation_tags[$index], 0, 5) == "roles"){
$type = "roles";
}
if ($current_annotation_tags[$index] == "rejected"){
$type = "rejected";
}
if ($current_annotation_tags[$index] == "AT"){
$type = "AT";
}
// This drug does have role / rejected tags so add it to the list and stop
//$done = true;
//$globalDone = true;
array_push($matchingSETIDs, $grow['dm_id']);
for ($x = 0; $x < count($current_annotation_tags); $x++){
// Get the first four characters of the tag (the annotation protocol dictates that DOID codes
// and UMLS codes start with either "DOID" or "UMLS" respectively)
$firstFourChars = substr($current_annotation_tags[$x], 0, 4);
if ($firstFourChars == "targ"){
//UMLS
$pos = strpos($current_annotation_tags[$x], "target:UMLS_CUI:");
if ($pos === false){
//DOID
$pos = strpos($current_annotation_tags[$x], "target:DOID_");
if ($pos === false){
}
else{
$pos2 = strpos($current_annotation_tags[$x], '_');
array_push($doidCodesPerDrug, substr($current_annotation_tags[$x],$pos2+1));
array_push($doidCodesPerDrugPrint, substr($current_annotation_tags[$x],$pos2+1)."_".$type);
}
}
else{
$pos2 = strposX($current_annotation_tags[$x], ':', 2);
array_push($umlsCodesPerDrug, substr($current_annotation_tags[$x],$pos2+1));
array_push($umlsCodesPerDrugPrint, substr($current_annotation_tags[$x],$pos2+1)."_".$type);
}
}
if ($firstFourChars == "UMLS"){
$pos = strpos($current_annotation_tags[$x], ':');
array_push($umlsCodesPerDrug, substr($current_annotation_tags[$x],$pos+1));
array_push($umlsCodesPerDrugPrint, substr($current_annotation_tags[$x],$pos+1)."_".$type);
}
if ($firstFourChars == "DOID"){
$colon = false;
$colon = contains($current_annotation_tags[$x], ':');
if ($colon){
$pos = strpos($current_annotation_tags[$x], ':');
array_push($doidCodesPerDrug, substr($current_annotation_tags[$x],$pos+1));
array_push($doidCodesPerDrugPrint, substr($current_annotation_tags[$x],$pos+1)."_".$type);
}
else{
$pos = strpos($current_annotation_tags[$x], '_');
array_push($doidCodesPerDrug, substr($current_annotation_tags[$x],$pos+1));
array_push($doidCodesPerDrugPrint, substr($current_annotation_tags[$x],$pos+1)."_".$type);
}
}
}
}
// Next tag
$index++;
}
// Next annotation
$globalIndex++;
}
$umlsCodesPerDrug = array_unique($umlsCodesPerDrug);
$umlsCodesPerDrug = array_values($umlsCodesPerDrug);
$umlsCodesStr = "'" . implode( "','", $umlsCodesPerDrug ) . "'";
//echo "<br>";
//echo $umlsCodesStr."<br>";
$getDCIndicationsQueryStr = "SELECT umls_cui, snomed_conceptid from omop_relationship where struct_id = '".$grow['dc_id']."' and relationship_name = 'indication' and umls_cui in ($umlsCodesStr) ";
$umlsCodesPerDrugPrint = array_unique($umlsCodesPerDrugPrint);
$umlsCodesPerDrugPrint = array_values($umlsCodesPerDrugPrint);
//echo $getDCIndicationsQueryStr."<br>";
//echo "<br>";
$getDCIndicationsQueryResult = pg_query($conn, $getDCIndicationsQueryStr) or die("Could not execute query");
$snomedCodesDC = array();
$umlsCodesDC = array();
if (pg_num_rows($getDCIndicationsQueryResult) > 0){
while($grow2 = pg_fetch_array($getDCIndicationsQueryResult)){
array_push($snomedCodesDC, $grow2['snomed_conceptid']);
array_push($umlsCodesDC, $grow2['umls_cui']);
}
}
$setIDToNameMap[$grow['dm_id']] = $grow['name'];
$setIDToDCIDMap[$grow['dm_id']] = $grow['dc_id'];
$setIDToUMLSIndicMap[$grow['dm_id']] = implode(", ",$umlsCodesDC);
$setIDToSNOMEDIndicMap[$grow['dm_id']] = implode(", ",$snomedCodesDC);
$setIDToIndicMap[$grow['dm_id']] = implode(", ",$umlsCodesPerDrugPrint);
}
$matchingSETIDs = array_unique($matchingSETIDs);
$matchingSETIDs = array_values($matchingSETIDs);
// Now print our results to HTML page
}
}
?>
<!-- DISPLAY TABLE OF RESULTS -->
<html lang="en">
<head>
<meta charset="utf-8" />
<title>DrugCentral vs DailyMed: indication codes comparison</title>
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta content="width=device-width, initial-scale=1" name="viewport" />
<meta content="" name="description" />
<meta content="" name="author" />
<link href="http://fonts.googleapis.com/css?family=Open+Sans:400,300,600,700&subset=all" rel="stylesheet" type="text/css" />
<link href="css/font-awesome/css/font-awesome.min.css" rel="stylesheet" type="text/css" />
<link href="css/simple-line-icons/simple-line-icons.min.css" rel="stylesheet" type="text/css" />
<link href="css/bootstrap.min.css" rel="stylesheet" type="text/css" />
<link href="css/layout.css" rel="stylesheet" type="text/css" />
<link rel="stylesheet" href="dist.css"></link>
<link rel="stylesheet" href="//code.jquery.com/ui/1.12.1/themes/base/jquery-ui.css">
<link rel="stylesheet" href="/resources/demos/style.css">
<script src="https://code.jquery.com/jquery-1.12.4.js"></script>
<script src="https://code.jquery.com/ui/1.12.1/jquery-ui.js"></script>
<script type="text/javascript" src="js/jquery/asidebar.jquery.js"></script>
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css">
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"></script>
<style>
.container{
margin-top: 100px;
margin: auto;
}
h1{
/*margin-top: 100px;*/
text-align: center;
color: #747f8c;
}
@import url('http://fonts.googleapis.com/css?family=Roboto+Condensed');
.back {
width: 33%;
height: 100px;
background-color: #eeeeee;
border: 10px;
border-color: #ffffff;
border-style: solid;
box-sizing: border-box;
-webkit-box-sizing: border-box;
-moz-box-sizing: border-box;
counter-increment: bc;
padding: 0px 5px 5px 5px;
}
.back:before {
content: counter(bc) "_";
position: absolute;
padding: 10px;
}
@media screen and (max-width: 1260px) {
.back {
width: 50%;
}
}
@media screen and (max-width: 840px) {
.back
{ width: 100%;
}
}
.button_base {
font-size: 18px;
margin:auto!important;
border-radius: 10px;
width: 218px;
height: 50px;
text-align: center;
box-sizing: border-box;
-webkit-box-sizing: border-box;
-moz-box-sizing: border-box;
-webkit-user-select: none;
cursor: default;
}
.button_base:hover {
cursor: pointer;
}
.b01_simple_rollover {
color: #ffffff;
border: #747f8c solid 1px;
background-color: #51ede4;
}
.b01_simple_rollover:hover {
color: #747f8c;
background-color: #ffffff;
}
.formcontainer{
float: left;
width:150px;
}
p {
font-size: 14pt;
padding-left: 0.5cm;
}
input[type=submit]{
text-align: center;
font-weight: bold;
}
.table td {
text-align: center;
}
.table th {
text-align: center;
}
table, td, th {
border: 1px solid #ddd;
text-align: left;
}
table {
border-collapse: collapse;
width: 100%;
}
th, td {
padding: 15px;
}
</style>
<h1 style="margin-top:100px;">DrugCentral vs DailyMed: indication codes comparison</h1>
</head>
<body>
<br><br>
<section>
<div id="formcontainer">
<form action="test2.php" method="post">
<div align="center">
<div style="color: #747f8c; font-size: 20px;"> Drug name or class: </div> <br> <input type="text" id="drugname" name="drugname">
</div>
<br>
<div align="center">
<input type="checkbox" name="isdrugclass" value="true">Class<br>
</div>
<br>
<div align="center">
<input class="back button_base b01_simple_rollover" type="submit" value="View Report">
</div>
<br><br>
</form>
</div>
<?php if ($candisplaystuff == 2) { ?>
<h1><?php echo $drugname." (".$atc.")"; ?></h1>
<div class="container">
<table class="table table-hover" style="table-layout:fixed">
<thead>
<tr bgcolor="#51ede4">
<th>DrugCentral ID</th>
<th>Indication Name</th>
<th>UMLS Code</th>
<th>DOID Code</th>
<th>SNOMED Code</th>
<th>SNOMED Name</th>
</tr>
</thead>
<tbody>
<?php while($grow = pg_fetch_array($getIndicationCodesQueryResult)) { ?>
<tr>
<td><?php echo $grow['struct_id']; ?></td>
<td><?php echo $grow['concept_name']; ?></td>
<td><?php echo $grow['umls_cui']; ?></td>
<td><?php echo str_replace("DOID", "", $grow['doid']); ?></td>
<td><?php echo $grow['snomed_conceptid']; ?></td>
<td><?php echo $grow['snomed_full_name']; ?></td>
</tr>
<?php } ?>
</tbody>
</table>
<br><br>
<table class="table table-hover" style="table-layout:fixed">
<thead>
<tr bgcolor="#51ede4">
<th>DailyMed ID</th>
<th>Indication Name</th>
<th>UMLS Code</th>
<th>DOID Code</th>
<th>SNOMED Code</th>
<th>SNOMED Name</th>
</tr>
</thead>
<tbody>
<?php for($x = 0; $x < count($result); $x++) { ?>
<tr>
<td><?php echo $dailyMedIndications[$x][0]; ?></td>
<td><?php echo $dailyMedIndications[$x][1]; ?></td>
<td><?php echo $dailyMedIndications[$x][2]; ?></td>
<td><?php echo $dailyMedIndications[$x][3]; ?></td>
<td><?php echo $dailyMedIndications[$x][4]; ?></td>
<td><?php echo $dailyMedIndications[$x][5]; ?></td>
</tr>
<?php } ?>
</tbody>
</table>
</div>
<?php }
else{
if ($candisplaystuff == 1){
echo '<script language="javascript">';
echo 'alert("Please type in a drug name")';
echo '</script>';
exit;
}
else if ($candisplaystuff == 999){
echo '<script language="javascript">';
echo 'alert("Could not find information for this drug or class.")';
echo '</script>';
exit;
}
else if ($candisplaystuff == 3){ ?>
<h1><?php echo "Drug Class: ".$drugname; ?></h1>
<div class="container">
<table class="table table-hover" style="table-layout:fixed">
<thead>
<tr bgcolor="#51ede4">
<th>#</th>
<th>DrugCentral Link</th>
<th>IDS Annotations Link</th>
<th>Inaccurate Indications (IIs)</th>
<th>IIs On DrugCentral (SNOMED)</th>
<th>IIs On DrugCentral (UMLS)</th>
</tr>
</thead>
<tbody>
<?php for($x = 0; $x < count($matchingSETIDs); $x++) { ?>
<tr>
<td><?php echo $x+1; ?></td>
<td><?php echo "<a href='http://drugcentral.org/drugcard/".$setIDToDCIDMap[$matchingSETIDs[$x]]."'>".$setIDToNameMap[$matchingSETIDs[$x]]."</a>"; ?></td>
<td><?php echo "<a href='https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=".$matchingSETIDs[$x]."'>".$setIDToNameMap[$matchingSETIDs[$x]]."</a>"; ?></td>
<td><?php echo $setIDToIndicMap[$matchingSETIDs[$x]]; ?></td>
<td><?php echo $setIDToSNOMEDIndicMap[$matchingSETIDs[$x]]; ?></td>
<td><?php echo $setIDToUMLSIndicMap[$matchingSETIDs[$x]]; ?></td>
</tr>
<?php } ?>
</tbody>
</table>
</div>
<?php }
} ?>
</section>
</body>
</html>
<!-- END OF DOCUMENT -->