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Commit 29249bf0 authored by jlopez's avatar jlopez
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init depot

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Tool.php 0 → 100644
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<?php
/**
* Created by PhpStorm.
* User: jimmy
* Date: 01/02/19
* Time: 13:55
*/
class Tool
{
}
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container.json 0 → 100644
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{
"containers": [
{
"description": "ABySS is a *de novo* sequence assembler",
"documentation": "https://github.com/bcgsc/abyss#abyss",
"install": ["conda install abyss=1.9.0", "ls -l", "pws", "ls -a"],
"name": "abyss",
"version": "1.9.0",
"container": "ubuntu:16.04",
"os": "ubuntu",
"release": "16.04",
"section": "Biotools"
},
{
"description": "C++ API & command-line toolkit for working with BAM data",
"documentation": "https://github.com/pezmaster31/bamtools/wiki",
"install": ["conda install bamtools=2.4.0"],
"name": "bamtools",
"version": "2.4.0",
"container": "ubuntu:16.04",
"os": "ubuntu",
"release": "16.04",
"section": "Biotools2"
},
{
"description": "Bcftools is a program for variant calling and manipulating VCFs and BCFs",
"documentation": "https://samtools.github.io/bcftools/",
"install": ["conda install bcftools=1.5"],
"name": "bcftools",
"version": "1.5",
"container": "ubuntu:16.04",
"os": "ubuntu",
"release": "16.04",
"section": "Biotools"
},
{
"description": "a powerful toolset for genome arithmetic",
"documentation": "http://quinlanlab.org/tutorials/bedtools/bedtools.html",
"install": ["conda install bedtools=2.25.0"],
"name": "bedtools",
"version": "2.25.0",
"container": "ubuntu:18.04",
"os": "ubuntu",
"release": "18.04",
"section": "Biotools"
},
{
"description": "a powerful toolset for genome arithmetic",
"documentation": "http://quinlanlab.org/tutorials/bedtools/bedtools.html",
"install": ["conda install bedtools=2.27.1"],
"name": "bedtools",
"version": "2.27.1",
"container": "ubuntu:16.04",
"os": "ubuntu",
"release": "16.04",
"section": "Biotools"
}
]
}
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css/.DS_Store 0 → 100644
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css/bootstrap-grid.css 0 → 100644
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css/bootstrap-grid.css.map 0 → 100644
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css/bootstrap-grid.min.css 0 → 100644
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css/bootstrap-reboot.css 0 → 100644
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/*!
* Bootstrap Reboot v4.1.3 (https://getbootstrap.com/)
* Copyright 2011-2018 The Bootstrap Authors
* Copyright 2011-2018 Twitter, Inc.
* Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
* Forked from Normalize.css, licensed MIT (https://github.com/necolas/normalize.css/blob/master/LICENSE.md)
*/
*,
*::before,
*::after {
box-sizing: border-box;
}
html {
font-family: sans-serif;
line-height: 1.15;
-webkit-text-size-adjust: 100%;
-ms-text-size-adjust: 100%;
-ms-overflow-style: scrollbar;
-webkit-tap-highlight-color: rgba(0, 0, 0, 0);
}
@-ms-viewport {
width: device-width;
}
article, aside, figcaption, figure, footer, header, hgroup, main, nav, section {
display: block;
}
body {
margin: 0;
font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, "Helvetica Neue", Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol", "Noto Color Emoji";
font-size: 1rem;
font-weight: 400;
line-height: 1.5;
color: #212529;
text-align: left;
background-color: #fff;
}
[tabindex="-1"]:focus {
outline: 0 !important;
}
hr {
box-sizing: content-box;
height: 0;
overflow: visible;
}
h1, h2, h3, h4, h5, h6 {
margin-top: 0;
margin-bottom: 0.5rem;
}
p {
margin-top: 0;
margin-bottom: 1rem;
}
abbr[title],
abbr[data-original-title] {
text-decoration: underline;
-webkit-text-decoration: underline dotted;
text-decoration: underline dotted;
cursor: help;
border-bottom: 0;
}
address {
margin-bottom: 1rem;
font-style: normal;
line-height: inherit;
}
ol,
ul,
dl {
margin-top: 0;
margin-bottom: 1rem;
}
ol ol,
ul ul,
ol ul,
ul ol {
margin-bottom: 0;
}
dt {
font-weight: 700;
}
dd {
margin-bottom: .5rem;
margin-left: 0;
}
blockquote {
margin: 0 0 1rem;
}
dfn {
font-style: italic;
}
b,
strong {
font-weight: bolder;
}
small {
font-size: 80%;
}
sub,
sup {
position: relative;
font-size: 75%;
line-height: 0;
vertical-align: baseline;
}
sub {
bottom: -.25em;
}
sup {
top: -.5em;
}
a {
color: #007bff;
text-decoration: none;
background-color: transparent;
-webkit-text-decoration-skip: objects;
}
a:hover {
color: #0056b3;
text-decoration: underline;
}
a:not([href]):not([tabindex]) {
color: inherit;
text-decoration: none;
}
a:not([href]):not([tabindex]):hover, a:not([href]):not([tabindex]):focus {
color: inherit;
text-decoration: none;
}
a:not([href]):not([tabindex]):focus {
outline: 0;
}
pre,
code,
kbd,
samp {
font-family: SFMono-Regular, Menlo, Monaco, Consolas, "Liberation Mono", "Courier New", monospace;
font-size: 1em;
}
pre {
margin-top: 0;
margin-bottom: 1rem;
overflow: auto;
-ms-overflow-style: scrollbar;
}
figure {
margin: 0 0 1rem;
}
img {
vertical-align: middle;
border-style: none;
}
svg {
overflow: hidden;
vertical-align: middle;
}
table {
border-collapse: collapse;
}
caption {
padding-top: 0.75rem;
padding-bottom: 0.75rem;
color: #6c757d;
text-align: left;
caption-side: bottom;
}
th {
text-align: inherit;
}
label {
display: inline-block;
margin-bottom: 0.5rem;
}
button {
border-radius: 0;
}
button:focus {
outline: 1px dotted;
outline: 5px auto -webkit-focus-ring-color;
}
input,
button,
select,
optgroup,
textarea {
margin: 0;
font-family: inherit;
font-size: inherit;
line-height: inherit;
}
button,
input {
overflow: visible;
}
button,
select {
text-transform: none;
}
button,
html [type="button"],
[type="reset"],
[type="submit"] {
-webkit-appearance: button;
}
button::-moz-focus-inner,
[type="button"]::-moz-focus-inner,
[type="reset"]::-moz-focus-inner,
[type="submit"]::-moz-focus-inner {
padding: 0;
border-style: none;
}
input[type="radio"],
input[type="checkbox"] {
box-sizing: border-box;
padding: 0;
}
input[type="date"],
input[type="time"],
input[type="datetime-local"],
input[type="month"] {
-webkit-appearance: listbox;
}
textarea {
overflow: auto;
resize: vertical;
}
fieldset {
min-width: 0;
padding: 0;
margin: 0;
border: 0;
}
legend {
display: block;
width: 100%;
max-width: 100%;
padding: 0;
margin-bottom: .5rem;
font-size: 1.5rem;
line-height: inherit;
color: inherit;
white-space: normal;
}
progress {
vertical-align: baseline;
}
[type="number"]::-webkit-inner-spin-button,
[type="number"]::-webkit-outer-spin-button {
height: auto;
}
[type="search"] {
outline-offset: -2px;
-webkit-appearance: none;
}
[type="search"]::-webkit-search-cancel-button,
[type="search"]::-webkit-search-decoration {
-webkit-appearance: none;
}
::-webkit-file-upload-button {
font: inherit;
-webkit-appearance: button;
}
output {
display: inline-block;
}
summary {
display: list-item;
cursor: pointer;
}
template {
display: none;
}
[hidden] {
display: none !important;
}
/*# sourceMappingURL=bootstrap-reboot.css.map */
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css/bootstrap-reboot.min.css 0 → 100644
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/*!
* Bootstrap Reboot v4.1.3 (https://getbootstrap.com/)
* Copyright 2011-2018 The Bootstrap Authors
* Copyright 2011-2018 Twitter, Inc.
* Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
* Forked from Normalize.css, licensed MIT (https://github.com/necolas/normalize.css/blob/master/LICENSE.md)
*/*,::after,::before{box-sizing:border-box}html{font-family:sans-serif;line-height:1.15;-webkit-text-size-adjust:100%;-ms-text-size-adjust:100%;-ms-overflow-style:scrollbar;-webkit-tap-highlight-color:transparent}@-ms-viewport{width:device-width}article,aside,figcaption,figure,footer,header,hgroup,main,nav,section{display:block}body{margin:0;font-family:-apple-system,BlinkMacSystemFont,"Segoe UI",Roboto,"Helvetica Neue",Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol","Noto Color Emoji";font-size:1rem;font-weight:400;line-height:1.5;color:#212529;text-align:left;background-color:#fff}[tabindex="-1"]:focus{outline:0!important}hr{box-sizing:content-box;height:0;overflow:visible}h1,h2,h3,h4,h5,h6{margin-top:0;margin-bottom:.5rem}p{margin-top:0;margin-bottom:1rem}abbr[data-original-title],abbr[title]{text-decoration:underline;-webkit-text-decoration:underline dotted;text-decoration:underline dotted;cursor:help;border-bottom:0}address{margin-bottom:1rem;font-style:normal;line-height:inherit}dl,ol,ul{margin-top:0;margin-bottom:1rem}ol ol,ol ul,ul ol,ul ul{margin-bottom:0}dt{font-weight:700}dd{margin-bottom:.5rem;margin-left:0}blockquote{margin:0 0 1rem}dfn{font-style:italic}b,strong{font-weight:bolder}small{font-size:80%}sub,sup{position:relative;font-size:75%;line-height:0;vertical-align:baseline}sub{bottom:-.25em}sup{top:-.5em}a{color:#007bff;text-decoration:none;background-color:transparent;-webkit-text-decoration-skip:objects}a:hover{color:#0056b3;text-decoration:underline}a:not([href]):not([tabindex]){color:inherit;text-decoration:none}a:not([href]):not([tabindex]):focus,a:not([href]):not([tabindex]):hover{color:inherit;text-decoration:none}a:not([href]):not([tabindex]):focus{outline:0}code,kbd,pre,samp{font-family:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace;font-size:1em}pre{margin-top:0;margin-bottom:1rem;overflow:auto;-ms-overflow-style:scrollbar}figure{margin:0 0 1rem}img{vertical-align:middle;border-style:none}svg{overflow:hidden;vertical-align:middle}table{border-collapse:collapse}caption{padding-top:.75rem;padding-bottom:.75rem;color:#6c757d;text-align:left;caption-side:bottom}th{text-align:inherit}label{display:inline-block;margin-bottom:.5rem}button{border-radius:0}button:focus{outline:1px dotted;outline:5px auto -webkit-focus-ring-color}button,input,optgroup,select,textarea{margin:0;font-family:inherit;font-size:inherit;line-height:inherit}button,input{overflow:visible}button,select{text-transform:none}[type=reset],[type=submit],button,html [type=button]{-webkit-appearance:button}[type=button]::-moz-focus-inner,[type=reset]::-moz-focus-inner,[type=submit]::-moz-focus-inner,button::-moz-focus-inner{padding:0;border-style:none}input[type=checkbox],input[type=radio]{box-sizing:border-box;padding:0}input[type=date],input[type=datetime-local],input[type=month],input[type=time]{-webkit-appearance:listbox}textarea{overflow:auto;resize:vertical}fieldset{min-width:0;padding:0;margin:0;border:0}legend{display:block;width:100%;max-width:100%;padding:0;margin-bottom:.5rem;font-size:1.5rem;line-height:inherit;color:inherit;white-space:normal}progress{vertical-align:baseline}[type=number]::-webkit-inner-spin-button,[type=number]::-webkit-outer-spin-button{height:auto}[type=search]{outline-offset:-2px;-webkit-appearance:none}[type=search]::-webkit-search-cancel-button,[type=search]::-webkit-search-decoration{-webkit-appearance:none}::-webkit-file-upload-button{font:inherit;-webkit-appearance:button}output{display:inline-block}summary{display:list-item;cursor:pointer}template{display:none}[hidden]{display:none!important}
/*# sourceMappingURL=bootstrap-reboot.min.css.map */
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css/style.css 0 → 100644
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/* change the background color */
.navbar-custom {
background-color: #34495e;
}
/* change the brand and text color */
.navbar-custom .navbar-brand,
.navbar-custom .navbar-text {
color: rgba(255,255,255,.8);
padding: 0.8rem 1rem;
}
/* change the link color and add padding for height */
.navbar-custom .navbar-nav .nav-link {
color: rgba(255,255,255,.5);
padding: 1rem 1rem;
}
/* change the color of active or hovered links */
.navbar-custom .nav-item.active .nav-link,
.navbar-custom .nav-item:hover .nav-link {
color: #ffffff;
background-color: #2c3e50; /* add background-color to active links */
}
.custom-checkbox {
min-height: 1rem;
padding-left: 0;
margin-right: 0;
cursor: pointer;
}
.custom-checkbox .custom-control-indicator {
content: "";
display: inline-block;
position: relative;
width: 30px;
height: 10px;
background-color: #e74c3c;
border-radius: 15px;
margin-right: 10px;
-webkit-transition: background .3s ease;
transition: background .3s ease;
vertical-align: middle;
margin: 0 16px;
box-shadow: none;
}
.custom-checkbox .custom-control-indicator:after {
content: "";
position: absolute;
display: inline-block;
width: 18px;
height: 18px;
background-color: #c0392b;
border-radius: 21px;
box-shadow: 0 1px 3px 1px rgba(0, 0, 0, 0.4);
left: -2px;
top: -4px;
-webkit-transition: left .3s ease, background .3s ease, box-shadow .1s ease;
transition: left .3s ease, background .3s ease, box-shadow .1s ease;
}
.custom-checkbox .custom-control-input:checked ~ .custom-control-indicator {
background-color: #2ecc71;
background-image: none;
box-shadow: none !important;
}
.custom-checkbox .custom-control-input:checked ~ .custom-control-indicator:after {
background-color: #27ae60;
left: 15px;
}
.custom-checkbox .custom-control-input:focus ~ .custom-control-indicator {
box-shadow: none !important;
}
.badge-bio {
background-color: #8e44ad;
color: #fff;
}
dao/DBquery.php 0 → 100644
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<?php
/**
* Created by PhpStorm.
* User: jimmy
* Date: 29/01/19
* Time: 16:38
*/
require_once(__DIR__.'/../conf/Conf.php');
class DBquery
{
var $dbh = NULL;
public function __construct() {
$this->openConnection();
}
/**
* For open a database connection
**/
public function openConnection() {
$this->dbh = mysqli_connect(Conf::$DB_HOSTNAME, conf::$DB_USERNAME, Conf::$DB_PP, Conf::$DB_NAME);
if(!$this->dbh){
die('Could not connect: ' . mysqli_error($this->dbh));
}
if (mysqli_connect_errno()) {
printf("Echec connection : %s\n", mysqli_connect_error());
exit();
}
}
/**
* Escapes special characters in a string for use in an SQL statement
* @param string $value
* @return string
*/
public function escape($value) {
return mysqli_real_escape_string($this->dbh, $value);
}
public function getDistribs() {
$sql = "SELECT * FROM `Distrib` ORDER BY `Distrib`.`name` ASC;";
$result = mysqli_query($this->dbh, $sql);
$results = array();
while($row = mysqli_fetch_assoc($result)){
array_push($results,array($row['name'], $row['version'], $row['manager']));
}
return $results;
}
public function getManagers() {
$sql = "SELECT * FROM `Manager` ORDER BY `Manager`.`name` ASC;";
$result = mysqli_query($this->dbh, $sql);
$results = array();
while($row = mysqli_fetch_assoc($result)){
array_push($results,array($row['name'], $row['value']));
}
return $results;
}
public function getSectionParent() {
$sql = "SELECT * FROM `Section` WHERE `Section`.`parent` IS NULL ORDER BY `Section`.`arrangement` ASC;";
$result = mysqli_query($this->dbh, $sql);
$results = array();
while($row = mysqli_fetch_assoc($result)){
array_push($results,array($row['name'], $row['active'], $row['color']));
}
return $results;
}
public function getSectionWhithParent($parent) {
$sql = "SELECT * FROM `Section` WHERE `Section`.`parent` = '$parent' ORDER BY `Section`.`arrangement` ASC;";
$result = mysqli_query($this->dbh, $sql);
$results = array();
while($row = mysqli_fetch_assoc($result)){
array_push($results,array($row['name'], $row['active'], $row['color']));
}
return $results;
}
public function getSection() {
$sql = "SELECT * FROM `Section` ORDER BY `Section`.`arrangement` ASC;";
$result = mysqli_query($this->dbh, $sql);
$results = array();
while($row = mysqli_fetch_assoc($result)){
array_push($results,array($row['name'], $row['active'], $row['color'], $row['parent']));
}
return $results;
}
public function getPackages($distrib, $filter, $patternName, $patternDescription, $limit) {