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{%extends "base.html"%}
{%from "flash_messages.html" import flash_all_messages%}
{%from "upload_progress_indicator.html" import upload_progress_indicator%}
{%block title%}Upload R/qtl2 Bundle{%endblock%}
{%block contents%}
{%macro rqtl2_file_help()%}
<span class="form-text text-muted">
<p>
Provide a valid R/qtl2 zip file here. In particular, ensure your zip bundle
contains exactly one control file and the corresponding files mentioned in
the control file.
</p>
<p>
The control file can be either a YAML or JSON file. <em>ALL</em> other data
files in the zip bundle should be CSV files.
</p>
<p>See the
<a href="https://kbroman.org/qtl2/assets/vignettes/input_files.html"
target="_blank">
R/qtl2 file format specifications
</a>
for more details.
</p>
</span>
{%endmacro%}
{{upload_progress_indicator()}}
<div id="resumable-file-display-template"
class="panel panel-info"
style="display: none">
<div class="panel-heading"></div>
<div class="panel-body"></div>
</div>
<h2 class="heading">Upload R/qtl2 Bundle</h2>
<div id="resumable-drop-area"
style="display:none;background:#eeeeee;min-height:12em;border-radius:0.5em;padding:1em;">
<p>
<a id="resumable-browse-button" href="#"
class="btn btn-info">Browse</a>
</p>
<p class="form-text text-muted">
You can drag and drop your file here, or click the browse button.
Click on the file to remove it.
</p>
{{rqtl2_file_help()}}
<div id="resumable-selected-files"
style="display:flex;flex-direction:row;flex-wrap: wrap;justify-content:space-around;gap:10px 20px;"></div>
<div id="resumable-class-buttons" style="text-align: right;">
<button id="resumable-upload-button"
class="btn btn-primary"
style="display: none">start upload</button>
<button id="resumable-cancel-upload-button"
class="btn btn-danger"
style="display: none">cancel upload</button>
</div>
<div id="resumable-progress-bar" class="progress" style="display: none">
<div class="progress-bar"
role="progress-bar"
aria-valuenow="60"
aria-valuemin="0"
aria-valuemax="100"
style="width: 0%;">
Uploading: 60%
</div>
</div>
</div>
<form id="frm-upload-rqtl2-bundle"
action="{{url_for('upload.rqtl2.upload_rqtl2_bundle',
species_id=species.SpeciesId,
population_id=population.InbredSetId)}}"
method="POST"
enctype="multipart/form-data"
data-resumable-target="{{url_for(
'upload.rqtl2.upload_rqtl2_bundle_chunked_post',
species_id=species.SpeciesId,
population_id=population.InbredSetId)}}">
<input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
<input type="hidden" name="population_id"
value="{{population.InbredSetId}}" />
{{flash_all_messages()}}
<div class="form-group">
<legend class="heading">file upload</legend>
<label for="file-rqtl2-bundle" class="form-label">R/qtl2 bundle</label>
<input type="file" id="file-rqtl2-bundle" name="rqtl2_bundle_file"
accept="application/zip, .zip"
required="required"
class="form-control" />
{{rqtl2_file_help()}}
</div>
<button type="submit"
class="btn btn-primary"
data-toggle="modal"
data-target="#upload-progress-indicator">upload R/qtl2 bundle</button>
</form>
{%endblock%}
{%block javascript%}
<script src="{{url_for('base.node_modules',
filename='resumablejs/resumable.js')}}"></script>
<script type="text/javascript" src="/static/js/upload_progress.js"></script>
<script type="text/javascript">
function readBinaryFile(file) {
return new Promise((resolve, reject) => {
var _reader = new FileReader();
_reader.onload = (event) => {resolve(_reader.result);};
_reader.readAsArrayBuffer(file);
});
}
function computeFileChecksum(file) {
return readBinaryFile(file)
.then((content) => {
return window.crypto.subtle.digest(
"SHA-256", new Uint8Array(content));
}).then((digest) => {
return Uint8ArrayToHex(new Uint8Array(digest))
});
}
function Uint8ArrayToHex(arr) {
var toHex = (val) => {
_hex = val.toString(16);
if(_hex.length < 2) {
return "0" + val;
}
return _hex;
};
_hexstr = ""
arr.forEach((val) => {_hexstr += toHex(val)});
return _hexstr
}
var r = Resumable({
target: $("#frm-upload-rqtl2-bundle").attr("data-resumable-target"),
fileType: ["zip"],
maxFiles: 1,
forceChunkSize: true,
generateUniqueIdentifier: (file, event) => {
return computeFileChecksum(file).then((checksum) => {
var _relativePath = (file.webkitRelativePath
|| file.relativePath
|| file.fileName
|| file.name);
return checksum + "-" + _relativePath.replace(
/[^a-zA-Z0-9_-]/img, "");
});
}
});
if(r.support) {
//Hide form and display drag&drop UI
$("#frm-upload-rqtl2-bundle").css("display", "none");
$("#resumable-drop-area").css("display", "block");
// Define UI elements for browse and drag&drop
r.assignDrop(document.getElementById("resumable-drop-area"));
r.assignBrowse(document.getElementById("resumable-browse-button"));
// Event handlers
function display_files(files) {
displayArea = $("#resumable-selected-files")
displayArea.empty();
files.forEach((file) => {
var displayElement = $(
"#resumable-file-display-template").clone();
displayElement.removeAttr("id");
displayElement.css("display", "");
displayElement.find(".panel-heading").text(file.fileName);
list = $("<ul></ul>");
list.append($("<li><strong>Name</strong>: "
+ (file.name
|| file.fileName
|| file.relativePath
|| file.webkitRelativePath)
+ "</li>"));
list.append($("<li><strong>Size</strong>: "
+ (file.size / (1024*1024)).toFixed(2)
+ " MB</li>"));
list.append($("<li><strong>Unique Identifier</strong>: "
+ file.uniqueIdentifier + "</li>"));
list.append($("<li><strong>Mime</strong>: "
+ file.file.type
+ "</li>"));
displayElement.find(".panel-body").append(list);
displayElement.appendTo("#resumable-selected-files");
});
}
r.on("filesAdded", function(files) {
display_files(files);
$("#resumable-upload-button").css("display", "");
$("#resumable-upload-button").on("click", (event) => {
r.upload();
});
});
r.on("uploadStart", (event) => {
$("#resumable-upload-button").css("display", "none");
$("#resumable-cancel-upload-button").css("display", "");
$("#resumable-cancel-upload-button").on("click", (event) => {
r.files.forEach((file) => {
if(file.isUploading()) {
file.abort();
}
});
$("#resumable-cancel-upload-button").css("display", "none");
$("#resumable-upload-button").on("click", (event) => {
r.files.forEach((file) => {file.retry();});
});
$("#resumable-upload-button").css("display", "");
});
});
r.on("progress", () => {
var progress = (r.progress() * 100).toFixed(2);
var pbar = $("#resumable-progress-bar > .progress-bar");
$("#resumable-progress-bar").css("display", "");
pbar.css("width", progress+"%");
pbar.attr("aria-valuenow", progress);
pbar.text("Uploading: " + progress + "%");
})
r.on("fileSuccess", (file, message) => {
if(message != "OK") {
var uri = (window.location.protocol
+ "//"
+ window.location.host
+ message);
window.location.replace(uri);
}
});
} else {
setup_upload_handlers(
"frm-upload-rqtl2-bundle", make_data_uploader(
function (form) {
var formdata = new FormData();
formdata.append(
"species_id",
form.querySelector('input[name="species_id"]').value);
formdata.append(
"population_id",
form.querySelector('input[name="population_id"]').value);
formdata.append(
"rqtl2_bundle_file",
form.querySelector("#file-rqtl2-bundle").files[0]);
return formdata;
}));
}
</script>
{%endblock%}
|
