MetGENE/combineStudies.php at main · metabolomicsworkbench/MetGENE · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
<!DOCTYPE html>
<html xmlns='http://www.w3.org/1999/xhtml' xml:lang='en' lang='en'>
<head><title>MetGENE: Combined Studies</title>

<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<?php
  $curDirPath = dirname(htmlentities($_SERVER['PHP_SELF']));
  $METGENE_BASE_DIR_NAME = $curDirPath;

    echo "<link rel=\"apple-touch-icon\" sizes=\"180x180\" href=\"".$METGENE_BASE_DIR_NAME."/images/apple-touch-icon.png\">";
    echo "<link rel=\"apple-touch-icon\" sizes=\"180x180\" href=\"".$METGENE_BASE_DIR_NAME."/images/apple-touch-icon.png\">";
    echo "<link rel=\"icon\" type=\"image/png\" sizes=\"32x32\" href=\"".$METGENE_BASE_DIR_NAME."/images/favicon-32x32.png\">";
    echo "<link rel=\"icon\" type=\"image/png\" sizes=\"16x16\" href=\"".$METGENE_BASE_DIR_NAME."/images/favicon-16x16.png\">";
    echo "<link rel=\"manifest\" href=\"".$METGENE_BASE_DIR_NAME."/site.webmanifest\">";

?>
<?php     include($_SERVER['DOCUMENT_ROOT'].$METGENE_BASE_DIR_NAME."/nav.php");?>


</head>
<style type='text/css' media='screen, projection, print'>
.btn
{
    background-color: rgb(7, 55, 99);
    color: white;
    border: none;
    cursor: pointer;
    padding: 2px 12px 3px 12px;
    text-decoration: none;

}

table th, td {word-wrap:break-word;white-space: pre-line;border-bottom: 1px solid #dddddd;}
table tbody tr:nth-of-type(even) {
    background-color: #f3f3f3;
}


</style>
<body>


<div id="constrain">
<div class="constrain">
<h3>Combined studies for the selected metabolites</h3>
<br>
<?php
function CallAPI($method, $url, $data = false)
{
    $curl = curl_init();

    switch ($method)
    {
        case "POST":
            curl_setopt($curl, CURLOPT_POST, 1);

            if ($data)
                curl_setopt($curl, CURLOPT_POSTFIELDS, $data);
            break;
        case "PUT":
            curl_setopt($curl, CURLOPT_PUT, 1);
            break;
        default:
            if ($data)
                $url = sprintf("%s?%s", $url, http_build_query($data));
    }

    // Optional Authentication:
    curl_setopt($curl, CURLOPT_HTTPAUTH, CURLAUTH_BASIC);
    curl_setopt($curl, CURLOPT_USERPWD, "username:password");

    curl_setopt($curl, CURLOPT_URL, $url);
    curl_setopt($curl, CURLOPT_RETURNTRANSFER, 1);

    $result = curl_exec($curl);

    curl_close($curl);

    return $result;
}

//Retrieve the string, which was sent via the POST parameter "user"
$map1 = isset($_GET['metabolites']) ? $_GET['metabolites'] : '';


//Decode the JSON string and convert it into a PHP associative array.
$string = explode(',', $map1);

$compound_arr = [];
$all_studies_arr = array();

foreach ($string as &$value) {
 $split_str = explode(':',$value);
  $curr_comp = $split_str[0];
  $curr_comp = str_replace("___", ":",$curr_comp);
//  echo $curr_comp;
  // remove all characters except alphanumeric and + and -
  $compName = preg_replace("/[^a-zA-Z0-9\s\-\+\:\_]/", "", $curr_comp);
//  $compQry = encodeURIComponent($compName);
// if there is a space replace with plus
  $compQry = str_replace("+","%2b",$compName);
  $compId = str_replace(" ","+",$compQry);

//  echo $compName." ";
//  echo "<br>";
// convert the string to URL

  $compURL = "<a href=\"https://www.metabolomicsworkbench.org/databases/refmet/refmet_details.php?REFMET_NAME=".$compId."\">".$compName."</a>";
//  echo $compURL;
//  echo "<br>";
//  array_push($compound_arr, $compId);
    array_push($compound_arr, $compURL);


 $studiesStr = $split_str[1];
  $studies = explode(" ", $studiesStr);


/* Iterate through all elements and save all unique values in the result array */
  for ($i = 0; $i < count($studies); $i++) {
      if (!in_array($studies[$i], $all_studies_arr)) {
          //          $curr_study = preg_replace("/[^a-zA-Z0-9]+/", "", $studies[$i]);
          $curr_study = preg_replace("/[^A-Z0-9]/", "", $studies[$i]);
	  $mw_rest_url = "https://www.metabolomicsworkbench.org/rest/study/study_id/".$curr_study."/summary/";
          $mw_res = callAPI("GET", $mw_rest_url, true);

          $decoded_json = json_decode($mw_res, true);
          $curr_study_title = $decoded_json['study_title'];
          $curr_study_url = "<a href=\"https://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=".$curr_study."\" title=\"".$curr_study_title."\" target=\"_blank\">".$curr_study."</a>";
          array_push($all_studies_arr, $curr_study_url);

      }
  }

/* Unset array */
  unset($studies);

}
$unique_studies_arr = array_unique($all_studies_arr);
//unset($unique_studies_arr[0]);

//print_r($compound_arr);
//print_r($unique_studies_arr);
$compStr = implode(',', $compound_arr);

$allStudiesStr = implode(', ',$unique_studies_arr);

//echo $compStr;
echo "<table id='Table1' class='styled-table'>";
echo "<tr>";
echo "<td>".$compStr."</td>"."<td>".$allStudiesStr."</td>";

echo "</tr>";
echo "</table>";


?>
<p><button id="json">TO JSON</button> <button id="csv">TO CSV</button> </p>


</div>

</div>
<script src="https://code.jquery.com/jquery-3.6.0.min.js"></script>
<?php echo "<script src=\"".$METGENE_BASE_DIR_NAME."/src/tableHTMLExport.js\"></script>"; ?>
<script>
  $('#json').on('click',function(){
    $("#Table1").tableHTMLExport({type:'json',filename:'combinedStudies.json'});
  })
  $('#csv').on('click',function(){
    $("#Table1").tableHTMLExport({type:'csv',filename:'combinedStudies.csv'});
  })
  </script>

<?php include($_SERVER['DOCUMENT_ROOT'].$METGENE_BASE_DIR_NAME."/footer.php");?>
</body>
</html>