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thermo_xcalibur_queue_builder.html
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thermo_xcalibur_queue_builder.html
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<!doctype html>
<html>
<head>
<meta charset="UTF-8">
<title>XCalibur Sequence Generator</title>
<style>
*{
box-sizing: border-box;
font-family: 'Helvetica', sans-serif;
}
html, body{
margin: 0;
height: 100%;
width: 100%;
-webkit-font-smoothing: antialiased;
-moz-osx-font-smoothing: grayscale;
}
input:focus{
outline: 2px solid black
}
input[type="number"]{
width:3em;
}
button{
padding:2px;
}
body.drag_active{
cursor: grabbing;
}
.plate{
background: #e6e6e6;
display: table;
margin:0px auto;
margin-bottom: 70px;
position: relative;
}
.plate::last-child{
margin-bottom: 0px;
}
.plate::before{
content:'sample count: ' attr(data-sample-count);
position: absolute;
bottom: 102%;
right:0;
font-weight: bold;
}
.plate::after{
content: 'well count: ' attr(data-select-well-count);
position: absolute;
left:0;
bottom: 102%;
font-weight: bold;
}
.well{
display: inline-block;
cursor: pointer;
width: 50px;
height: 50px;
margin: 10px;
border-radius: 50px;
background: white;
position: relative;
font-size: 12px;
border:4px solid transparent;
position: relative;
user-select: none;
-webkit-user-select:none;
}
.plate.show_names .well[data-samplename]::after, .well[data-samplename]:hover::after{
content:attr(data-samplename) "\A \A ( " attr(data-inject-count) " )";
position: absolute;
bottom: 30%;
left: 50%;
background: #575757;
color:white;
min-width: 7.8em;
padding: 1px;
line-height: 1em;
font-size: 8px;
text-align: center;
transform: translateX(-50%);
z-index: 50;
white-space: pre-wrap;
word-break: break-all;
webkit-box-shadow: 0px 3px 12px 0px rgba(0,0,0,0.34);
-moz-box-shadow: 0px 3px 12px 0px rgba(0,0,0,0.34);
box-shadow: 0px 3px 12px 0px rgba(0,0,0,0.34);
opacity: 0.9;
}
.well.selected[data-samplename]::after{
background: black !important;
opacity: 1 !important;
}
.well.selected.last[data-samplename]::after{
background: blue !important;
}
.well .indicator{
position: absolute;
top:50%;
left: 50%;
padding: 4px;
text-align: center;
transform: translate(-50%, -50%);
border-radius: 30px;
}
.plate.show_names .well[data-samplename] .indicator{
position: absolute;
top:90%;
font-size: 8px;
}
.well[data-samplename] .indicator{
color: white;
}
.well[data-samplename]:hover::after{
min-width: 12em;
bottom: 100%;
}
.well.selected{
border-color:black;
}
.well.selected.last{
border-color:blue;
}
.well.selected.last .indicator{
color:blue;
}
.well[data-inject-count="1"] .indicator{
background: black;
color:white;
}
.well[data-inject-count="2"] .indicator{
background: red;
color:white;
}
.well[data-inject-count="3"] .indicator{
background: #00ceff;
color:white;
}
.well.multi_inject .indicator{
background: #ff00f5 !important;
color:white;
}
.injection_list{
border-collapse: collapse;
min-width: 300px;
user-select: none;
-webkit-user-select: none;
}
.injection_list:focus{
outline: none;
}
.injection_list.collapsed td{
padding-bottom: 2px;
padding-top: 2px;
}
.injection_list input[type="number"]{
width: 3em;
}
#inj_area{
position: fixed;
height: 100%;
right:0px;
transition: right 0.3s;
top:0;
border-left: 1px solid transparent;
background: #efefef;
width: 450px;
}
#inj_area:focus-within{
background: white;
-webkit-box-shadow: 0px 3px 12px 0px rgba(0,0,0,0.2);
-moz-box-shadow: 0px 3px 12px 0px rgba(0,0,0,0.2);
box-shadow: 0px 3px 12px 0px rgba(0,0,0,0.2);
border-left: 1px solid black;
}
#inj_area:focus{
outline: none;
}
.inj_container{
position: absolute;
height: calc(100% - 140px);
top:140px;
overflow:scroll;
width: 100%;
padding:10px 2px;
}
.control_bar{
position: absolute;
top:0;
width: 100%;
left: 0;
background: #c7c5c5;
height: 140px;
padding: 10px;
font-size: 14px;
overflow: hidden;
}
.control_bar .top_section{
position: absolute;
top:10px;
transition: all 0.3s;
}
.control_bar.show_lower .top_section{
position: absolute;
top:-37px;
}
.control_bar .row{
padding-bottom: 12px;
margin-bottom: 12px;
border-bottom: 1px solid black;
}
.control_bar .row:last-child{
border-bottom:none;
}
.control_bar > div:last-child{
border-bottom: none;
}
.control_bar input{
margin-right: 25px;
}
.row button{
margin-right: 8px;
}
.timepoint{
font-weight: bold;
padding: 3px;
}
#seq_start_time:focus{
color:blue;
outline: none;
}
#seq_start_time:hover{
background: #e6e6e6;
cursor: pointer;
}
.inj_container table{
width: 100%;
}
th, td{
padding:8px;
padding-right: 10px;
min-width: 30px;
max-width: 60px;
}
td.sample_name{
min-width: 200px;
max-width: 300px;
color: white;
word-break: break-all;
}
th{
padding-bottom: 15px;
border-bottom: 2px solid black;
vertical-align: center;
}
td{
padding-bottom:10px;
vertical-align: top;
border-bottom: 1px solid #d8d8d8;
font-size: 14px;
}
tr.selected {
color: #1830b7;
background: #f2f2f2;
}
tr.selected .index{
color: #1830b7;
}
tr.selected input {
color: #1830b7;
}
td.index{
font-size: 11px;
min-width: 2em !important;
width: 2em;
padding: 4px;
padding-top: 5px !important;;
color:gray;
}
.well_selector{
background: #cecece;
cursor: pointer;
display: table;
position: fixed;
z-index: 100;
border:1px solid #454545;
pointer-events: none;
visibility: hidden;
}
.well_selector.visible{
visibility: visible;
pointer-events: all;
}
.well_option{
display: inline-block;
width: 30px;
height: 30px;
line-height: 30px;
text-align: center;
background: white;
position: relative;
font-size: 15px;
color: #a5a5a5;
}
.well_option.selected{
background: #cc282e;
color: white;
}
.well_option:hover{
color: black;
font-weight: bold;
background: #c9c9c9;
}
.well_option:active{
background: #646464;
color: white;
}
.well_selector_input{
display: inline-block;
width: 40px;
height: 16px;
cursor: pointer;
}
.well_selector_input:hover{
background: #e5e5e5;
outline: 5px solid #e5e5e5;
font-weight: bold;
}
#DRAG_ROW{
pointer-events: none;
position: fixed;
-webkit-box-shadow: 0px 3px 12px 0px rgba(0,0,0,0.4);
-moz-box-shadow: 0px 3px 12px 0px rgba(0,0,0,0.4);
box-shadow: 0px 3px 12px 0px rgba(0,0,0,0.4);
background: white;
opacity: 0.8;
}
.injection.moving td{
opacity: 0 !important;
}
.injection.moving{
background: white;
}
#plate_area{
position: fixed;
top:0;
height: 100%;
width: calc(100% - 450px);
left:calc(50% - 225px);
transform: translateX(-50%);
}
#plate_container{
position: absolute;
top:150px;
left: 0;
padding: 40px;
overflow: scroll;
width: 100%;
height: calc(100% - 150px);
}
#sample_name_input{
width: 24em;
}
#help_section{
position: fixed;
overflow: scroll;
z-index: 1000;
width: 100%;
height: 100%;
top:0;
left: 0;
background: #dbdbdb;
font-size: 13px;
opacity: 0.95;
padding: 40px;
opacity: 0;
pointer-events: none;
}
#help_section.visible{
opacity:1;
pointer-events: all;
}
#help_section li{
padding: 5px;
}
#copytext{
position: fixed;
top:-1000px;
}
#exp_edit_panel{
position: fixed;
display: none;
top:10px;
left: 220px;
font-size: 13px;
font-weight: bold;
background: white;
border: 1px solid black;
text-align: right;
width: 700px;
padding: 10px;
}
#exp_id_selector{
width: 10em;
}
#exp_edit_panel.visible{
display: block;
webkit-box-shadow: 0px 3px 12px 0px rgba(0,0,0,0.2);
-moz-box-shadow: 0px 3px 12px 0px rgba(0,0,0,0.2);
box-shadow: 0px 3px 12px 0px rgba(0,0,0,0.2);
}
#exp_edit_input{
display: inline-block;
background: #e3e3e3;
width: calc(100% - 23em);
padding: 3px;
border-radius: 3px;
font-weight: bold;
font-size: 13px;
word-break: break-all;
}
#exp_edit_input:hover{
color: #2c2ccc;
cursor: pointer;
}
#exp_edit_panel input{
width: calc(100% - 14em);
padding: 0.2em;
}
#exp_edit_panel div{
margin-bottom: 4px;
}
#help_bttn{
position: fixed;
top:0;
left: 100%;
width: 70px;
height: 70px;
background: red;
z-index: 1002;
transform:translate(-50%, -50%) rotateZ(45deg);
cursor: pointer;
user-select: none;
-webkit-user-select:none;
}
#help_bttn::after {
position: absolute;
content: "?";
top: 62%;
left: 42%;
color: white;
font-size: 26px;
font-weight: bold;
transform: rotateZ(-45deg);
}
#help_bttn:hover::before{
position: absolute;
content: "toggle help manual";
word-break: keep-all;
top: 141%;
left: -77%;
color: white;
padding: 4px;
background: black;
font-size: 12px;
transform: rotateZ(-45deg);
}
#toggle_ctrl_bar{
position: absolute;
right: 0px;
top:102px;
width: 30px;
height: 30px;
line-height: 30px;
background: #c7c7c7;
text-align: center;
user-select: none;
-webkit-user-select:none;
cursor: pointer;
}
#toggle_ctrl_bar:hover::after{
color:red;
}
#toggle_ctrl_bar::after{
content:'▲'
}
#toggle_ctrl_bar.on::after{
content:'▼'
}
#toggle_ctrl_bar:hover::before{
position: absolute;
content: "toggle injection time";
word-break: keep-all;
bottom: 105%;
width: 100px;
right: 50%;
color: white;
padding: 4px;
background: black;
font-size: 12px;
line-height: 12px;
}
#status_bar{
font-weight: lighter;
letter-spacing: 0.5px;
color:white;
padding:1em;
font-size: 14px;
width: 100%;
margin-bottom: 0.5em;
position: fixed;
top:-50px;
-webkit-transition: top 0.2s;
transition: top 0.2s;
z-index: 100000;
}
#status_bar.show{
top:0px;
}
#status_bar.success{
background: #4aa24a;
}
#status_bar.error{
background: #af4949;
}
@media print{
#inj_area{
display: none;
}
#plate_area{
left: 0;
width:100%;
position: absolute;
transform: none;
display: block;
height: auto;
overflow: visible;
}
#exp_edit_panel{
display: none;
}
#help_bttn{
display: none;
}
#plate_container{
top:0;
display: block;
width: 100%;
height: auto;
overflow: visible;
}
.plate{
page-break-inside: avoid;
break-inside:avoid;
}
.plate::before {
page-break-inside: avoid;
break-inside:avoid;
}
.plate::after{
display: none;
}
.well{
width: 45px;
height: 45px;
margin: 5px;
}
.well::after{
font-size: 5px !important;
}
#plate_area .control_bar{
display: none;
}
#exp_edit_panel{
display: none !important;
}
}
</style>
</head>
<body>
<div id = "plate_area" tabindex="0">
<div class = "control_bar">
<div class = "row">
experiment: <select id = "exp_id_selector" style="margin-right: 10px"></select>
<span id="exp_edit_input" data-id="0">asparagine/20200725/krall/UC13glucose-MCF10A-cells</span>
<button id = "clone_exp_bttn">clone</button>
</div>
<div class = "row">
sample name: <input id = "sample_name_input" type="text" placeholder="{D}-sample-{2*# + 1}" style="margin-right:0" maxlength="70">
<button id = "add_sample_bttn" style="margin-right: 20px">add</button>
dynamic selection: <input id="move_select_post_add" type="checkbox" checked>
show sample names:<input id="show_sample_names" type="checkbox" style="margin-right:0">
</div>
insert mode:
<select id = "ins_mode_input" style="margin-right: 20px">
<option>replace</option>
<option>before</option>
<option>after</option>
</select>
search: <input id = "search_input" type="text" placeholder="gLucxosee">
insert: <input id = "insert_input" type="text" placeholder="glucose" style="margin-right:0">
<button id = "insert_bttn" style="margin-right:25px">insert</button>
</div>
<div id = "plate_container"></div>
</div>
<div id = "exp_edit_panel">
<div>project: <input id = "pi" type="text"></div>
<div>date: <input id = "di" type="text"></div>
<div>experimentor lastname: <input id = "eli" type="text"></div>
<div>experiment title: <input id = "eti" type="text"></div>
<div>output folder path: <input id = "ofpi" type="text"></div>
<div>method file path: <input id = "mfpi" type="text"></div>
</div>
<div id = "inj_area" tabindex="0">
<div class = "control_bar" style="user-select: none; -webkit-user-select:none">
<div class = "top_section">
<div class = "row">
insert mode:
<select id = "inj_mode_input" style="margin-right: 20px">
<option>end</option>
<option>start</option>
<option>before selection</option>
<option>after selection</option>
</select>
count: <span id = "inj_count" style="font-weight: bold;"></span>
</div>
<div class = "row">
<button id = "set_epxid_bttn">set experiment id</button> : <input id = "exp_id_input" type = "number" min = "0" max = "99" value="0">
<button id = "set_vol_bttn">set volume</button> : <input id = "vol_input" type = "number" min = "1" max = "20" value="10">
</div>
<div class="row">
<button id="select_all_bttn">select all</button> <button id="clr_select_bttn">clear selection</button> <button id="delete_bttn">delete selection</button> <button id="download_bttn">download selection</button>
</div>
<div class="row">
min per inj:<input id = "min_per_inj_input" type="number" value="30" min="0" max="99"> start:<span class = "timepoint" id = "seq_start_time" tabindex="1" style="margin-right: 20px;">Fri 11:30pm</span> end:<span class = "timepoint" id = "seq_end_time">Sat 10:00am</span>
</div>
</div>
</div>
<div class="inj_container"></div>
</div>
<div id = "help_bttn"></div>
<div id = "toggle_ctrl_bar" ></div>
<div id = "help_section">
<h1>General Help</h1>
<ul>
<li>White wells contain no samples. Once a well has a sample it will be filled with a color. Replicate samples have the same color. To view the sample name either hover over a well or click the show sample names checkbox. Either of these actions will bring up text above the well which indicates the sample name and the number of injections from that well in parentheses. Any well that has been added to the injection list will have a colored dot underneath its location text. Black = 1 injection. Red = 2 injections. Blue = 3 injections. Pink = > 3 injections.</li>
<li>Click on wells to toggle their selection. Dragging the mouse over an unselected well will cause it to be selected. To cancel all well selections use the escape key. The last selected well is shown in blue and is the target of any copy/paste operations.</li>
<li>The sample name input field supports "smart expressions" that consist of special characters. Use {D} to insert the current date as a string. Use {#} to denote the index of the sample/replciate. This character supports mathematical operations such as {2*# + 5}, {10 - #*2}. When evaluated, the final number inserted into the sample name will be the result of the original index altered by the function.</li>
<li>Use the input fields below the sample name entry to edit sample names. You can replace any text or insert new text before or after any search term. These changes will apply to all sample names even if they are not selected. Any changes made to sample names on the plate will automatically be reflected in the sample names of the corresponding injections.</li>
<li>The dynamic selection option, which is enabled by default, causes the selection on a plate to auto-migrate right and downard anytime samples are added or injected.</li>
<li>When injecting samples, the new injections will be assigned the experiment id that is currently displayed in the top bar.</li>
<li>Use the top left drop down menu to select a different experiment. To edit the currently selected experiment click the top experiment info bar to reveal an edit form. To copy the currently selected experiment and add it as an option at the end of the list click the clone button to the right of the experiment info bar. </li>
<li>Once added injections can be deleted, dragged to a new position, or edited. Click on the well position inside an injection to bring up a well selector. Use the top bar above the injections to alter either their injection volumes or their experiment id.</li>
</ul>
<h1>Keyboard Shortcuts</h1>
<ul>
<li><b>esc:</b> clear selection</li>
<li><b>delete/backspace:</b> delete selected samples or injections</li>
<li><b>click + Shift:</b> select all items between closest selected item and clicked item. Works on wells and injections.</li>
<li><b>Shift + A:</b> select all injections</li>
<li><b>Shift + (+):</b> duplicate selected injections</li>
<li><b>Shift + (Enter):</b> inject samples from selected wells</li>
<li><b>Shift + (delete):</b> delete injections from selected wells</li>
<li><b>Shift + T:</b> toggle dynamic selection</li>
<li><b>Ctrl + c:</b> copy the sample name from the most recently selected well in blue</li>
<li><b>Ctrl + v:</b> paste text into most recently selected well in blue. Multiple lines in the paste text will result in each line used as the name for a new sample.</li>
<li></li>
<li><b>Enter (while sample name has focus):</b> add new sample to selected wells</li>
<li><b>Enter (while insert text has focus):</b> alter the names of all selected samples according to the set pattern</li>
</ul>
</div>
<input id="copytext" type="text">
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