forked from pangaea-data-publisher/fuji
-
Notifications
You must be signed in to change notification settings - Fork 4
/
index.php
476 lines (457 loc) · 26.1 KB
/
index.php
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
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
<!doctype html>
<html lang="en">
<head>
<!-- Required meta tags -->
<meta charset="utf-8">
<meta name="keywords" content="FAIR principles, assessment, evaluation, FAIR, research data, quality control, data maturity, metrics, digital objects">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<!-- Bootstrap CSS -->
<link href="https://cdn.jsdelivr.net/npm/[email protected]/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-F3w7mX95PdgyTmZZMECAngseQB83DfGTowi0iMjiWaeVhAn4FJkqJByhZMI3AhiU" crossorigin="anonymous">
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/font/bootstrap-icons.css">
<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/js/bootstrap.bundle.min.js" integrity="sha384-/bQdsTh/da6pkI1MST/rWKFNjaCP5gBSY4sEBT38Q/9RBh9AH40zEOg7Hlq2THRZ" crossorigin="anonymous"></script>
<style>
.loader {
border: 16px solid #f3f3f3; /* Light grey */
border-top: 16px solid #3498db; /* Blue */
border-radius: 50%;
width: 80px;
height: 80px;
animation: spin 2s linear infinite;
display: none;
margin:auto;
}
@keyframes spin {
0% { transform: rotate(0deg); }
100% { transform: rotate(360deg); }
}
</style>
<link rel="icon" type="image/png" href="/icon/fuji_logo_square.png">
<title>F-UJI simple client</title>
</head>
<body style="padding-bottom: 70px;">
<nav class="navbar navbar-expand-lg navbar-light bg-light lead mb-4">
<div class="container-fluid">
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarfuji" aria-controls="navbarfuji" aria-expanded="false" aria-label="Toggle navigation">
<span class="navbar-toggler-icon"></span>
</button>
<a class="navbar-brand" href="#">
<img src="/icon/fuji_logo_square.png" alt="" width="30" height="30" class="d-inline-block align-text-top"> <b>F-UJI simple client</b>
</a>
</div>
</nav>
<?php
if(!isset($_SESSION))
session_start();
set_time_limit(0);
######################## local config ##########################
$fuji_server = 'http://localhost:1071/fuji/api/v1/evaluate';
$fuji_username = 'yourusername';
$fuji_password = 'yourpassword';
#$metric_version = "metrics_v0.5";
$usegithub = true;
################################################################
$fair_basic_terms=['F'=>'Findable','A'=>'Accessible','I'=>'Interoperable','R'=>'Reusable'];
$fair_index=['F'=>0,'A'=>1,'I'=>2,'R'=>3];
$maturity_scale = [0=>'incomplete',1=>'initial',2=>'moderate', 3=>'advanced'];
$status_scale = ['pass'=>'passed', 'fail'=>'not detected'];
$maturity_palette = array(0=>'#fe7d37',1=>'#dfb317',2=>'#97ca00',3=>'#4c1');
$maturity_level_text_array = array(0=>'incomplete',1=>'initial',2=>'managed',3=>'defined');
$input_service_type = 'oai_pmh';
$input_service_url ='';
if (isset($_POST['service_url'])){
$input_service_url = $_POST['service_url'];
if (isset($_POST['service_type'])){
$input_service_type = $_POST['service_type'];
}
}
if(!isset($_POST['use_datacite'])){
$usedatacite=false;
}else{
$usedatacite=true;
}
if (isset($_REQUEST['pid'])){
$input_pid = $_REQUEST['pid'];
}else {
$input_pid =Null;
}
if (isset($_POST['service_url'])){
$input_service_url = $_POST['service_url'];
if (isset($_POST['service_type'])){
$input_service_type = $_POST['service_type'];
}
}
if(isset($_POST['metric_version'])){
$input_metric_version=$_POST['metric_version'];
}else{
$input_metric_version="metrics_v0.7_software";
}
$allowed_service_types = array('oai_pmh'=>'OAI-PMH','ogc_csw'=>'OGC CSW', 'sparql'=>'SPARQL');
$allowed_metric_versions = array('metrics_v0.7_software'=>'software-agnostic', 'metrics_v0.7_software_cessda'=>'software-CESSDA')
?>
<div class="container">
<h1 class="my-4 display-4 pl-2">FAIR assessment</h1>
<div class="row my-auto">
<div class="col">
<?php
if(!isset($input_pid)){
echo('<div class="lead">
<p>F-UJI is a web service to programatically assess FAIRness of research data objects (aka data sets) based on metrics developed by the <a href="https://www.fairsfair.eu">FAIRsFAIR</a> project.</p>
<p class=" d-none d-lg-block">Please use the form below to enter an identifier (e.g. DOI, URL) of the data set you wish to assess. Optionally you also can enter a metadata service (OAI-PMH, SPARQL, CSW) endpoint URI which F-UJI can use to identify additional information.</p>
</div>');
}
?>
<div class="card bg-light mx-auto" id="assessment_form">
<div class="card-body">
<form class="form mb-3" action="index.php" method="POST">
<div class="row align-items-end">
<div class="col">
<label for="pid" class="col-form-label-sm">Research Data Object (URL/PID):<sup style="color:red">*</sup></label>
<input class="form-control form-control-sm" type="text" value="<?php echo(htmlentities($input_pid));?>" name="pid" id="pid" placeholder="Enter a valid PID or URL of the dataset's landing page (e.g. a DOI)">
</div>
</div>
<div class="row">
<div class="col ms-auto text-end">
<a class="text-decoration-none" data-bs-toggle="collapse" href="#assessment_settings" role="button" aria-expanded="false" aria-controls="collapseExample">
<i class="bi-gear-fill"></i> Settings
</a>
</div>
</div>
<div class="collapse" id="assessment_settings">
<div class="row align-items-end">
<div class="col-8">
<label for="service_url" class="col-form-label-sm">(Optional) Metadata service endpoint:</label>
<input class="form-control form-control-sm" type="text" value="<?php echo(htmlentities($input_service_url));?>" name="service_url" id="service_url" placeholder="(Optional) endpoint serving your metadata in different formats">
</div>
<div class="col-4">
<label for="service_type" class="col-form-label-sm">Metadata service type:</label>
<select class="form-select form-select-sm" name="service_type" id="service_type">
<?php
foreach($allowed_service_types as $sk=> $sv){
if ($sk == $input_service_type)
echo '<option value ="'.$sk.'" selected>'.$sv.'</option>';
else
echo '<option value ="'.$sk.'">'.$sv.'</option>';
}
?>
</select>
</div>
<div class="row align-items-end">
<div class="col-8">
<label for="metric_version" class="col-form-label-sm">Metric version:</label>
<select class="form-select form-select-sm" name="metric_version" id="metric_version">
<?php
foreach($allowed_metric_versions as $mk=> $mv){
if ($mk == $input_metric_version)
echo '<option value ="'.$mk.'" selected>'.$mv.'</option>';
else
echo '<option value ="'.$mk.'">'.$mv.'</option>';
}
?>
</select>
</div>
<div class="col-4">
<?php
$usedatacite_checked = ' checked';
if ($usedatacite == false)
$usedatacite_checked = '';
?>
<input type="checkbox" class="form-check-input" id="use_datacite" name="use_datacite" <?php echo($usedatacite_checked);?>>
<label for="use_datacite" class="form-check-label ">
<small>Use DataCite?</small>
</label>
<img src="../icon/bootstrap/question-circle.svg" alt="help" width="15" height="15" data-toggle="tooltip" title="By default, F-UJI uses content negotiation based on the DOI URL to retrieve DataCite JSON metadata. If you uncheck this option, F-UJI wil try to use the landing page URL instead.">
</div>
</div>
</div>
</div>
<div class="d-flex justify-content-center">
<button type="input" class="btn btn-primary" name="runtest"><i class="bi-caret-right-fill"></i> Start FAIR Assessment</button>
</div>
<input type="hidden" name="action" value="test">
</form>
</div>
</div>
<div class="alert d-none mt-1" role ="alert" id="test_message"></div>
</div>
</div>
<?php
if (isset($input_pid)) {
$ch = curl_init();
$message = new stdClass();
$message->object_identifier = $input_pid;
$message->metadata_service_endpoint = $input_service_url;
$message->metadata_service_type = $input_service_type;
$message->test_debug = true;
$message->use_datacite = $usedatacite;
$message->use_github = $usegithub;
$message->metric_version = $input_metric_version;
$post = json_encode($message);
$username = $fuji_username;
$password = $fuji_password;
curl_setopt($ch, CURLOPT_URL, $fuji_server);
curl_setopt($ch, CURLOPT_HTTPHEADER, array('Content-Type:application/json', 'Allow-Remote-Logging:True'));
curl_setopt($ch, CURLOPT_USERPWD, $username . ":" . $password);
curl_setopt($ch, CURLOPT_POST, 1);
curl_setopt($ch, CURLOPT_POSTFIELDS, $post);
curl_setopt($ch, CURLOPT_RETURNTRANSFER, true);
$server_output = curl_exec($ch);
$response = json_decode($server_output, true);
curl_close($ch);
if(!isset($response)){
print('<div class="alert alert-danger" role="alert">Server not responding </div>');
}
}
$debug_class_list=array('SUCCESS'=>'table-success','WARNING'=>'table-warning','ERROR'=>'table-danger');
$fuji_percent_scores=array(0=>0,1=>0,2=>0,3=>0);
$sections=array();
if(isset($response['results'])){
$metric_version = str_replace('.yaml','',$response['metric_version']);
$software_version = $response['software_version'];
$metric_doi = $response['metric_specification'];
if(is_array($response['results'])){
$total_score = 0;
$earned_score =0;
$percent_score =0;
$pid_url = Null;
$summary = $response['summary'];
foreach ($response['results'] as $result) {
if (str_starts_with($result['metric_identifier'], 'FsF')){
$fair_letter=$result['metric_identifier'][4];
} elseif (str_starts_with($result['metric_identifier'], 'FRSM')){
$fair_letter=$result['metric_identifier'][8];
}
if($result['metric_identifier']=='FsF-F2-01M'){
$metadata= $result['output']['core_metadata_found'];
}
if($result['metric_identifier']=='FsF-F1-02D'){
$pid_url= $result['output']['pid'];
}
$fair_section_regex = '/\-([FAIR][0-9](\.[0-9])?)\-/m';
$fair_section='';
if(preg_match($fair_section_regex,$result['metric_identifier'],$fair_section_match))
$fair_section =$fair_section_match[1];
$fuji_results[$fair_letter][$result['metric_identifier']] = $result;
}
?>
<h2 class="h2 mt-4 mb-3">Assessment Results:</h2>
<h3 class="h3 mb-3">Evaluated Resource:</h3>
<div class="card mb-3">
<h5 class="card-header"><?php
if(isset($metadata['title'])){
if(is_array($metadata['title']))
echo $metadata['title'][0];
else
echo(htmlentities($metadata['title']));
} else {
echo(' ');}?></h5>
<div class="card-body p-2">
<table class="table mt-3 mb-3">
<tr>
<th>FAIR level:
<img src="../icon/bootstrap/question-circle.svg" alt="help" width="15" height="15" data-toggle="tooltip" title="0:incomplete, 1:initial , 2:moderate, 3:advanced">
</th>
<?php
$fair_maturity_color = $maturity_palette[round($summary['maturity']['FAIR'],0)];?>
<td><h4 class="h4 m-0"><span class="badge badge" style="color:white;background-color: <?php echo $fair_maturity_color;?>"><?php print($maturity_scale[round($summary['maturity']['FAIR'],0)]); ?></span></h4></td>
</tr>
<tr><th>Resource PID/URL:</th>
<?php
if(strpos($input_pid,'http') !==false){
?>
<td class="text-break"><a <?php echo('href="'.$input_pid);?>"><?php echo(htmlentities($input_pid));?></a></td>
<?php
} else{
?>
<td class="text-break"><?php echo(htmlentities($input_pid));?></td>
<?php }
?>
</tr>
<tr><th>DataCite support:</th>
<td><?php print($usedatacite ? 'enabled' : 'disabled');?></td>
</tr>
<tr><th>GitHub support:</th>
<td><?php print($usegithub ? 'enabled' : 'disabled');?></td>
</tr>
<tr><th>Metric Version:</th>
<td><?php echo(htmlentities($metric_version));?></td>
</tr>
<tr><th>Metric Specification:</th>
<td><a href="<?php echo(htmlentities($metric_doi));?>"><?php echo(htmlentities($metric_doi));?></a></td>
</tr>
<tr><th>Software version:</th>
<td><?php echo(htmlentities($software_version));?></td>
</tr>
</table>
</div>
</div>
<h3>Summary:</h3>
<div class="card-group">
<div class="card mb-3">
<div class="my-auto mx-auto p-3" style="max-width: 250px">
<span class="display-2 text-nowrap"><?php print($summary['score_percent']['FAIR']) ?>%</span>
</div>
</div>
<div class="card mb-3">
<table class="table table-bordered table-responsive">
<tr><th></th><th class="d-sm-none d-md-block">Score earned:</th><th>Fair level:</th></tr>
<?php
foreach(array('F','A','I','R') as $fairid){
?>
<tr>
<th><?php echo($fair_basic_terms[$fairid].': ');?></th>
<td style="min-width: 110px" class="d-sm-none d-md-block"><?php
print($summary['score_earned'][$fairid]);
print(' of ');
print($summary['score_total'][$fairid]);
?>
</td>
<td>
<?php
if(isset($summary['maturity'])){
$principle_maturity_color = $maturity_palette[$summary['maturity'][$fairid]];
?>
<h4 class="h4 m-0"><span class="badge badge" style="color:white;background-color: <?php echo $principle_maturity_color;?>"><?php print($maturity_scale[$summary['maturity'][$fairid]]); ?></span></h4></td>
<?php
}
?>
</td>
</tr>
<?php
}
?>
</table>
</div>
</div>
<?php
print('<h3>Report:</h3>');
foreach($fuji_results as $fair_index=>$fuji_fairsection){
print('<h4 class="h-4 mb-3 mt-3 fst-italic">'.$fair_basic_terms[$fair_index].'</h4>');
print('<div class="accordion" id="accordion_'.$fair_index.'">');
$test_index=0;
foreach($fuji_fairsection as $fuji_res){
$test_index++;
print('<div class="class="accordion-item mb-3">');
print('<h2 class="accordion-header lead border border-1 mt-1" id="head_'.$fuji_res['metric_identifier'].'">');
print('<button class="accordion-button collapsed" data-bs-toggle="collapse"
data-bs-target="#body_'.$fair_index.'_'.$test_index.'" aria-expanded="false"
aria-controls="body_'.$fair_index.'_'.$test_index.'">');
print('<h5 class="h-5 text-muted" style="width:90%">');
print($fuji_res['metric_identifier'].' - '.$fuji_res['metric_name']);
print('</h5>');
if($fuji_res['maturity'] >= 1)
print('<img style="margin-left:auto; width:30px; float:right" src="/icon/passed_'.$fuji_res['maturity'].'.png">');
elseif(!is_int($fuji_res['maturity'])){
if($fuji_res['test_status']=='pass')
print('<img style="margin-left:auto; width:30px; float:right" src="/icon/passed.png">');
else
print('<img style="margin-left:auto; width:30px; float:right" src="/icon/unknown.png">');
}
else
print('<img style="margin-left:auto; width:30px; float:right" src="/icon/unknown.png">');
print('</button></h2>');
print('<div class="accordion-collapse collapse" aria-labelledby="head_'.$fair_index.'_'.$test_index.'" id="body_'.$fair_index.'_'.$test_index.'" data-parent="#accordion_'.$fair_index.'">');
print('<div class="accordion-body border rounded-1 border-1">');
if (!is_int($fuji_res['maturity'])){
$maturity_key = array_search($fuji_res['maturity'],$maturity_scale_old);
if($maturity_key!==False) {
$fuji_res['maturity'] = $maturity_key;
$scaled_maturity = $maturity_scale[$maturity_key];
$maturity_color = $maturity_palette[$maturity_key];
}else {
$scaled_maturity = $fuji_res['maturity'];
$maturity_color = 'grey';
}
}else{
$scaled_maturity = $maturity_scale[$fuji_res['maturity']];
$maturity_color = $maturity_palette[$fuji_res['maturity']];
}
print('<div class="row mb-2">
<div class="col-md-2"><b>FAIR level:</b></div>
<div class="col-md-8">'.$fuji_res['maturity'].' of 3 </div>');
print('<div class ="col-md-2 text-right">
<span class="badge badge" style="color:white;background-color: '.$maturity_color.'">'.$scaled_maturity.'</span>
</div>');
print('</div>');
print('<div class="row mb-2"><div class="col-md-2"><b>Score:</b></div><div class="col-md-10">');
print($fuji_res['score']['earned'].' of '.$fuji_res['score']['total']);
print('</div></div>');
print('<div class="row mb-2"><div class="col-md-2"><b>Output:</b></div><div class="col-md-10">');
print('<pre><code>'.htmlspecialchars(json_encode($fuji_res['output'], JSON_PRETTY_PRINT)).'</code></pre>');
print('</div></div>');
print('<div class="row mb-3"><div class="col-md-2"><b>Metric tests:</b></div><div class="col-md-10">');
print('<table class="table w-100"><tr><th>Test:</th><th>Test name:</th><th>Score:</th><th>Maturity:</th></th><th>Result:</th></tr>');
foreach($fuji_res['metric_tests'] as $test_key=>$metric_test){
if(preg_match('/-[0-9]{1}([a-z]{1})$/',$test_key,$tm)){
$mstyle=' style="font-size:smaller"';
$test_key = ' '.$tm[1];
}else{
$mstyle='';
}
print('<tr'.$mstyle.'><th scope="row">'.$test_key.'</th><td>'.$metric_test['metric_test_name'].'</td><td>');
if($metric_test['metric_test_score']['earned'] !=0){
print($metric_test['metric_test_score']['earned']);
}
print('</td><td>');
if($metric_test['metric_test_status']=='pass'){
print($metric_test['metric_test_maturity']);
}
print('</td><td>');
if($metric_test['metric_test_status']=='pass')
print('<img class="mx-auto d-block" style="width:30px;" src="/icon/passed.png">');
else
print('<img class="mx-auto d-block" style="width:30px;" src="/icon/unknown.png">');
print('</td></tr>');
}
print('</table>');
print('</div></div>');
print('<div class="row"><div class="col-md-2"><b>Debug messages:</b></div><div class="col-md-10">');
print('<table class="table table-sm w-100 table-striped table-bordered"><tr><th>Level:</th><th>Message:</th></tr>');
foreach($fuji_res['test_debug'] as $debug_message){
if(preg_match('/([A-Z]+):\s+(.*+)/',$debug_message,$debug_regex_result)) {
if(array_key_exists($debug_regex_result[1],$debug_class_list)){
$debug_class=' class="debug_'.$debug_regex_result[1].' '.$debug_class_list[$debug_regex_result[1]].'"';
}
else
$debug_class='';
print('<tr'.$debug_class.'><th scope="row">'.$debug_regex_result[1].'</th><td>'.$debug_regex_result[2].'</td></tr>');
}
}
print('</table>');
print('</div></div>');
print('</div></div>');
print('</div>');
}
print('</div>');
}
}
}elseif(isset($response['status'])){
if ($response['status']==401) {
print('<div id="fuji_error" class="alert alert-danger">');
print('<b>Authorisation failed</b>');
print('</div>');
}
elseif ($response['status']==500) {
print('<div id="fuji_error" class="alert alert-danger">');
print('<b>'.$response['title'].'</b>');
print('<br>');
print($response['detail']);
print('<br> If this error persists please report at: <a href="https://github.com/pangaea-data-publisher/fuji/issues">
https://github.com/pangaea-data-publisher/fuji/issues</a>');
print('</div>');
}else{
print('<div id="fuji_error" class="alert alert-danger">');
print('<b>Response code: </b>'.$response['status']);
print('</div>');
}
}
?>
<div class="navbar">
<div class="container text-center justify-content-center">
<div class="justify-content-center">
F-UJI is a result of the <a href="https://www.fairsfair.eu">FAIRsFAIR</a> “Fostering FAIR Data Practices In Europe”
project which received funding from the European Union’s Horizon 2020 project call H2020-INFRAEOSC-2018-2020 (grant agreement 831558).
</div>
</div>
</div>
</body>
</html>