XspecT 0.1.3__py3-none-any.whl → 0.2.0__py3-none-any.whl
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- {XspecT-0.1.3.dist-info → XspecT-0.2.0.dist-info}/METADATA +23 -29
- XspecT-0.2.0.dist-info/RECORD +30 -0
- {XspecT-0.1.3.dist-info → XspecT-0.2.0.dist-info}/WHEEL +1 -1
- xspect/definitions.py +42 -0
- xspect/download_filters.py +11 -26
- xspect/fastapi.py +101 -0
- xspect/file_io.py +34 -103
- xspect/main.py +70 -66
- xspect/model_management.py +88 -0
- xspect/models/__init__.py +0 -0
- xspect/models/probabilistic_filter_model.py +277 -0
- xspect/models/probabilistic_filter_svm_model.py +169 -0
- xspect/models/probabilistic_single_filter_model.py +109 -0
- xspect/models/result.py +148 -0
- xspect/pipeline.py +201 -0
- xspect/run.py +38 -0
- xspect/train.py +304 -0
- xspect/train_filter/create_svm.py +6 -183
- xspect/train_filter/extract_and_concatenate.py +117 -121
- xspect/train_filter/html_scrap.py +16 -28
- xspect/train_filter/ncbi_api/download_assemblies.py +7 -8
- xspect/train_filter/ncbi_api/ncbi_assembly_metadata.py +9 -17
- xspect/train_filter/ncbi_api/ncbi_children_tree.py +3 -2
- xspect/train_filter/ncbi_api/ncbi_taxon_metadata.py +7 -5
- XspecT-0.1.3.dist-info/RECORD +0 -49
- xspect/BF_v2.py +0 -637
- xspect/Bootstrap.py +0 -29
- xspect/Classifier.py +0 -142
- xspect/OXA_Table.py +0 -53
- xspect/WebApp.py +0 -724
- xspect/XspecT_mini.py +0 -1363
- xspect/XspecT_trainer.py +0 -611
- xspect/map_kmers.py +0 -155
- xspect/search_filter.py +0 -504
- xspect/static/How-To.png +0 -0
- xspect/static/Logo.png +0 -0
- xspect/static/Logo2.png +0 -0
- xspect/static/Workflow_AspecT.png +0 -0
- xspect/static/Workflow_ClAssT.png +0 -0
- xspect/static/js.js +0 -615
- xspect/static/main.css +0 -280
- xspect/templates/400.html +0 -64
- xspect/templates/401.html +0 -62
- xspect/templates/404.html +0 -62
- xspect/templates/500.html +0 -62
- xspect/templates/about.html +0 -544
- xspect/templates/home.html +0 -51
- xspect/templates/layoutabout.html +0 -87
- xspect/templates/layouthome.html +0 -63
- xspect/templates/layoutspecies.html +0 -468
- xspect/templates/species.html +0 -33
- xspect/train_filter/README_XspecT_Erweiterung.md +0 -119
- xspect/train_filter/get_paths.py +0 -35
- xspect/train_filter/interface_XspecT.py +0 -204
- xspect/train_filter/k_mer_count.py +0 -162
- {XspecT-0.1.3.dist-info → XspecT-0.2.0.dist-info}/LICENSE +0 -0
- {XspecT-0.1.3.dist-info → XspecT-0.2.0.dist-info}/entry_points.txt +0 -0
- {XspecT-0.1.3.dist-info → XspecT-0.2.0.dist-info}/top_level.txt +0 -0
xspect/static/main.css
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/*
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Source:
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https://github.com/CoreyMSchafer/code_snippets/tree/master/Python/Flask_Blog
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*/
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body {
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.download-btn{
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.btn-default {
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left: 0;
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padding: 58px 0 0; /* Height of navbar */
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box-shadow: 0 2px 5px 0 rgb(0 0 0 / 5%), 0 2px 10px 0 rgb(0 0 0 / 5%);
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h1, h2, h3, h4, h5, h6 {
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/*
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*/
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table.dataframe, .dataframe th, .dataframe td {
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}
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tr:nth-child(odd) { background-color:#eee; }
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border-top: 16px solid #fa9c1d; /* Orange */
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<a class="navbar-brand mr-4" href="/about">Home</a>
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28
|
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<button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarToggle" aria-controls="navbarToggle" aria-expanded="false" aria-label="Toggle navigation">
|
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|
-
<span class="navbar-toggler-icon"></span>
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</button>
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<div class="collapse navbar-collapse" id="navbarToggle">
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-
<div class="navbar-nav mr-auto">
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<a class="nav-item nav-link" href="/species">XspecT</a>
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<a class="nav-item nav-link" href="/about">About</a>
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|
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</div>
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</div>
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</div>
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</nav>
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</header>
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-
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<!-- variable content -->
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|
-
<main role="main" class="container">
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|
-
<div class="row">
|
|
44
|
-
<div class="col-md-11">
|
|
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|
-
<h4>Error 400: Bad Request</h4>
|
|
46
|
-
<h2> This Tool uses a file reader that is not supported by all browsers.</h2>
|
|
47
|
-
<h2> Find supported browsers <a href="https://caniuse.com/#feat=filereader">here</a>.</h2>
|
|
48
|
-
|
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|
-
<p> </p>
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<p> Back to <a href="/">home</a>.</p>
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</div>
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-
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</div>
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</main>
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-
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<!-- Optional JavaScript -->
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<!-- jQuery first, then Popper.js, then Bootstrap JS -->
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<script src="https://code.jquery.com/jquery-3.2.1.slim.min.js" integrity="sha384-KJ3o2DKtIkvYIK3UENzmM7KCkRr/rE9/Qpg6aAZGJwFDMVNA/GpGFF93hXpG5KkN" crossorigin="anonymous"></script>
|
|
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|
-
<script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js" integrity="sha384-ApNbgh9B+Y1QKtv3Rn7W3mgPxhU9K/ScQsAP7hUibX39j7fakFPskvXusvfa0b4Q" crossorigin="anonymous"></script>
|
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<script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js" integrity="sha384-JZR6Spejh4U02d8jOt6vLEHfe/JQGiRRSQQxSfFWpi1MquVdAyjUar5+76PVCmYl" crossorigin="anonymous"></script>
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-
</body>
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</html>
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xspect/templates/401.html
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@@ -1,62 +0,0 @@
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-
<!DOCTYPE html>
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2
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<html lang="en">
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3
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<head>
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4
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-
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5
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<!-- Required meta tags -->
|
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7
|
-
<meta charset="utf-8">
|
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-
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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9
|
-
|
|
10
|
-
<!-- Bootstrap CSS -->
|
|
11
|
-
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css" integrity="sha384-Gn5384xqQ1aoWXA+058RXPxPg6fy4IWvTNh0E263XmFcJlSAwiGgFAW/dAiS6JXm" crossorigin="anonymous">
|
|
12
|
-
|
|
13
|
-
<!-- Costum stuff from css file -->
|
|
14
|
-
<link rel="stylesheet" type="text/css" href="{{ url_for('static', filename='main.css') }}">
|
|
15
|
-
|
|
16
|
-
|
|
17
|
-
<meta charset="UTF-8">
|
|
18
|
-
<title> Clonetye Assignment </title>
|
|
19
|
-
<link rel="icon" href="data:,">
|
|
20
|
-
</head>
|
|
21
|
-
<body>
|
|
22
|
-
|
|
23
|
-
<!-- Sidebar -->
|
|
24
|
-
<header class="site-header">
|
|
25
|
-
<nav class="navbar navbar-expand-md navbar-dark bg-steel fixed-top">
|
|
26
|
-
<div class="container">
|
|
27
|
-
<a class="navbar-brand mr-4" href="/about">Home</a>
|
|
28
|
-
<button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarToggle" aria-controls="navbarToggle" aria-expanded="false" aria-label="Toggle navigation">
|
|
29
|
-
<span class="navbar-toggler-icon"></span>
|
|
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|
-
</button>
|
|
31
|
-
<div class="collapse navbar-collapse" id="navbarToggle">
|
|
32
|
-
<div class="navbar-nav mr-auto">
|
|
33
|
-
<a class="nav-item nav-link" href="/species">XspecT</a>
|
|
34
|
-
<a class="nav-item nav-link" href="/about">About</a>
|
|
35
|
-
</div>
|
|
36
|
-
</div>
|
|
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|
-
</div>
|
|
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|
-
</nav>
|
|
39
|
-
</header>
|
|
40
|
-
|
|
41
|
-
<!-- variable content -->
|
|
42
|
-
<main role="main" class="container">
|
|
43
|
-
<div class="row">
|
|
44
|
-
<div class="col-md-11">
|
|
45
|
-
<h4>Error 401: Unauthorized</h4>
|
|
46
|
-
<h2> You have no access to this page.</h2>
|
|
47
|
-
<p> </p>
|
|
48
|
-
<p> Back to <a href="/">home</a>.</p>
|
|
49
|
-
</div>
|
|
50
|
-
|
|
51
|
-
</div>
|
|
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|
-
</main>
|
|
53
|
-
|
|
54
|
-
|
|
55
|
-
<!-- Optional JavaScript -->
|
|
56
|
-
<!-- jQuery first, then Popper.js, then Bootstrap JS -->
|
|
57
|
-
<script src="https://code.jquery.com/jquery-3.2.1.slim.min.js" integrity="sha384-KJ3o2DKtIkvYIK3UENzmM7KCkRr/rE9/Qpg6aAZGJwFDMVNA/GpGFF93hXpG5KkN" crossorigin="anonymous"></script>
|
|
58
|
-
<script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js" integrity="sha384-ApNbgh9B+Y1QKtv3Rn7W3mgPxhU9K/ScQsAP7hUibX39j7fakFPskvXusvfa0b4Q" crossorigin="anonymous"></script>
|
|
59
|
-
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js" integrity="sha384-JZR6Spejh4U02d8jOt6vLEHfe/JQGiRRSQQxSfFWpi1MquVdAyjUar5+76PVCmYl" crossorigin="anonymous"></script>
|
|
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|
-
|
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-
</body>
|
|
62
|
-
</html>
|
xspect/templates/404.html
DELETED
|
@@ -1,62 +0,0 @@
|
|
|
1
|
-
<!DOCTYPE html>
|
|
2
|
-
<html lang="en">
|
|
3
|
-
<head>
|
|
4
|
-
|
|
5
|
-
|
|
6
|
-
<!-- Required meta tags -->
|
|
7
|
-
<meta charset="utf-8">
|
|
8
|
-
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
|
|
9
|
-
|
|
10
|
-
<!-- Bootstrap CSS -->
|
|
11
|
-
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css" integrity="sha384-Gn5384xqQ1aoWXA+058RXPxPg6fy4IWvTNh0E263XmFcJlSAwiGgFAW/dAiS6JXm" crossorigin="anonymous">
|
|
12
|
-
|
|
13
|
-
<!-- Costum stuff from css file -->
|
|
14
|
-
<link rel="stylesheet" type="text/css" href="{{ url_for('static', filename='main.css') }}">
|
|
15
|
-
|
|
16
|
-
|
|
17
|
-
<meta charset="UTF-8">
|
|
18
|
-
<title> Clonetye Assignment </title>
|
|
19
|
-
<link rel="icon" href="data:,">
|
|
20
|
-
</head>
|
|
21
|
-
<body>
|
|
22
|
-
|
|
23
|
-
<!-- Sidebar -->
|
|
24
|
-
<header class="site-header">
|
|
25
|
-
<nav class="navbar navbar-expand-md navbar-dark bg-steel fixed-top">
|
|
26
|
-
<div class="container">
|
|
27
|
-
<a class="navbar-brand mr-4" href="/about">Home</a>
|
|
28
|
-
<button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarToggle" aria-controls="navbarToggle" aria-expanded="false" aria-label="Toggle navigation">
|
|
29
|
-
<span class="navbar-toggler-icon"></span>
|
|
30
|
-
</button>
|
|
31
|
-
<div class="collapse navbar-collapse" id="navbarToggle">
|
|
32
|
-
<div class="navbar-nav mr-auto">
|
|
33
|
-
<a class="nav-item nav-link" href="/species">XspecT</a>
|
|
34
|
-
<a class="nav-item nav-link" href="/about">About</a>
|
|
35
|
-
</div>
|
|
36
|
-
</div>
|
|
37
|
-
</div>
|
|
38
|
-
</nav>
|
|
39
|
-
</header>
|
|
40
|
-
|
|
41
|
-
<!-- variable content -->
|
|
42
|
-
<main role="main" class="container">
|
|
43
|
-
<div class="row">
|
|
44
|
-
<div class="col-md-11">
|
|
45
|
-
<h4>Error 404</h4>
|
|
46
|
-
<h2> This page does not exist.</h2>
|
|
47
|
-
<p> </p>
|
|
48
|
-
<p> Back to <a href="/home">home</a>.</p>
|
|
49
|
-
</div>
|
|
50
|
-
|
|
51
|
-
</div>
|
|
52
|
-
</main>
|
|
53
|
-
|
|
54
|
-
|
|
55
|
-
<!-- Optional JavaScript -->
|
|
56
|
-
<!-- jQuery first, then Popper.js, then Bootstrap JS -->
|
|
57
|
-
<script src="https://code.jquery.com/jquery-3.2.1.slim.min.js" integrity="sha384-KJ3o2DKtIkvYIK3UENzmM7KCkRr/rE9/Qpg6aAZGJwFDMVNA/GpGFF93hXpG5KkN" crossorigin="anonymous"></script>
|
|
58
|
-
<script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js" integrity="sha384-ApNbgh9B+Y1QKtv3Rn7W3mgPxhU9K/ScQsAP7hUibX39j7fakFPskvXusvfa0b4Q" crossorigin="anonymous"></script>
|
|
59
|
-
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js" integrity="sha384-JZR6Spejh4U02d8jOt6vLEHfe/JQGiRRSQQxSfFWpi1MquVdAyjUar5+76PVCmYl" crossorigin="anonymous"></script>
|
|
60
|
-
|
|
61
|
-
</body>
|
|
62
|
-
</html>
|
xspect/templates/500.html
DELETED
|
@@ -1,62 +0,0 @@
|
|
|
1
|
-
<!DOCTYPE html>
|
|
2
|
-
<html lang="en">
|
|
3
|
-
<head>
|
|
4
|
-
|
|
5
|
-
|
|
6
|
-
<!-- Required meta tags -->
|
|
7
|
-
<meta charset="utf-8">
|
|
8
|
-
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
|
|
9
|
-
|
|
10
|
-
<!-- Bootstrap CSS -->
|
|
11
|
-
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css" integrity="sha384-Gn5384xqQ1aoWXA+058RXPxPg6fy4IWvTNh0E263XmFcJlSAwiGgFAW/dAiS6JXm" crossorigin="anonymous">
|
|
12
|
-
|
|
13
|
-
<!-- Costum stuff from css file -->
|
|
14
|
-
<link rel="stylesheet" type="text/css" href="{{ url_for('static', filename='main.css') }}">
|
|
15
|
-
|
|
16
|
-
|
|
17
|
-
<meta charset="UTF-8">
|
|
18
|
-
<title> Clonetye Assignment </title>
|
|
19
|
-
<link rel="icon" href="data:,">
|
|
20
|
-
</head>
|
|
21
|
-
<body>
|
|
22
|
-
|
|
23
|
-
<!-- Sidebar -->
|
|
24
|
-
<header class="site-header">
|
|
25
|
-
<nav class="navbar navbar-expand-md navbar-dark bg-steel fixed-top">
|
|
26
|
-
<div class="container">
|
|
27
|
-
<a class="navbar-brand mr-4" href="/about">Home</a>
|
|
28
|
-
<button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarToggle" aria-controls="navbarToggle" aria-expanded="false" aria-label="Toggle navigation">
|
|
29
|
-
<span class="navbar-toggler-icon"></span>
|
|
30
|
-
</button>
|
|
31
|
-
<div class="collapse navbar-collapse" id="navbarToggle">
|
|
32
|
-
<div class="navbar-nav mr-auto">
|
|
33
|
-
<a class="nav-item nav-link" href="/species">XspecT</a>
|
|
34
|
-
<a class="nav-item nav-link" href="/about">About</a>
|
|
35
|
-
</div>
|
|
36
|
-
</div>
|
|
37
|
-
</div>
|
|
38
|
-
</nav>
|
|
39
|
-
</header>
|
|
40
|
-
|
|
41
|
-
<!-- variable content -->
|
|
42
|
-
<main role="main" class="container">
|
|
43
|
-
<div class="row">
|
|
44
|
-
<div class="col-md-11">
|
|
45
|
-
<h4>Error 500: Internal Server Error</h4>
|
|
46
|
-
<h2> The server was unable to deal with your request, data has been logged for bug fixing.</h2>
|
|
47
|
-
<p> </p>
|
|
48
|
-
<p> Back to <a href="/home">home</a>.</p>
|
|
49
|
-
</div>
|
|
50
|
-
|
|
51
|
-
</div>
|
|
52
|
-
</main>
|
|
53
|
-
|
|
54
|
-
|
|
55
|
-
<!-- Optional JavaScript -->
|
|
56
|
-
<!-- jQuery first, then Popper.js, then Bootstrap JS -->
|
|
57
|
-
<script src="https://code.jquery.com/jquery-3.2.1.slim.min.js" integrity="sha384-KJ3o2DKtIkvYIK3UENzmM7KCkRr/rE9/Qpg6aAZGJwFDMVNA/GpGFF93hXpG5KkN" crossorigin="anonymous"></script>
|
|
58
|
-
<script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js" integrity="sha384-ApNbgh9B+Y1QKtv3Rn7W3mgPxhU9K/ScQsAP7hUibX39j7fakFPskvXusvfa0b4Q" crossorigin="anonymous"></script>
|
|
59
|
-
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js" integrity="sha384-JZR6Spejh4U02d8jOt6vLEHfe/JQGiRRSQQxSfFWpi1MquVdAyjUar5+76PVCmYl" crossorigin="anonymous"></script>
|
|
60
|
-
|
|
61
|
-
</body>
|
|
62
|
-
</html>
|