Newer
Older
define([
"base/js/namespace",
"base/js/dialog",
"base/js/utils",
"jquery"
],
function(IPython, dialog, utils, $, mc) {
var currentConnection = ''
var selectedPermId = null
var currentSampleIdentifier = null
var currentDownloadPath = null
function show_available_connections (data, conn_table) {
if (!currentDownloadPath) {
currentDownloadPath = data.cwd
}
var table = $('<table>').addClass('table-bordered table-striped table-condensed')
var thead = $('<thead>')
var title_row = $('<tr>')
.append($('<th>')
.text('')
)
.append($('<th>')
.text('Name')
)
.append($('<th>')
.text('URL')
)
title_row.appendTo(thead)
thead.appendTo(table)
data.connections.forEach( function(item, index, arr) {
var conn = $('<input type="radio" name="connection_name">')
.attr("value", item.name)
.attr("url", item.url)
conn.change( function() {
currentConnection = item.name
})
if (item.name === currentConnection) {
conn.prop('checked', true)
}
else {
conn.prop('checked', false)
}
var row = $('<tr>')
.append(
$('<td>').append(conn)
)
.append($('<td>')
.text(item.name)
)
.append($('<td>')
.text(item.url)
)
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
.append($('<td>')
.text(item.status)
)
table.append(row)
})
conn_table.empty().append($('<strong>').text('Please choose a connection')).append(table)
}
function show_datasets_table( data, datasets_table) {
var table = $('<table>').addClass('table-bordered table-striped table-condensed text-nowrap')
var thead = $('<thead>')
var title_row = $('<tr>')
.append($('<th>')
.text('permId')
)
.append($('<th>')
.text('Type')
)
.append($('<th>')
.text('Experiment')
)
.append($('<th>')
.text('Registration Date')
)
.append($('<th>')
.text('Status')
)
.append($('<th>')
.text('Size')
)
title_row.appendTo(thead)
thead.appendTo(table)
data.dataSets.forEach( function(item, index, arr) {
var permId = $('<input type="radio" name="permId">').attr("value", item.permId)
permId.change(function() {
if ($(this).is(':checked')) {
selectedPermId = this.value
}
})
var row = $('<tr>')
.append(
$('<td>').append(permId).append(' ' + item.permId)
)
.append($('<td>')
.text(item.type)
)
.append($('<td>')
.text(item.experiment)
)
.append($('<td>')
.text(item.registrationDate)
)
.append($('<td>')
.text(item.status)
)
.append($('<td>')
.text(item.size)
)
var connectionsUrl = env.notebook.base_url + 'openbis/conn'
var settings = {
url: connectionsUrl,
processData: false,
type: 'GET',
dataType: 'json',
}
var fetchDatasetFromOpenBis = {
help: 'Download a openBIS dataset to your local harddrive',
icon: 'fa-download',
help_index: '',
handler: function (env) {
var conn_table = $('<div id="openbis_connections"/>')
getOpenBisConnections(env, conn_table)
.done(function (data) {
show_available_connections(data, conn_table)
})
.fail(function (data) {
alert(data.status)
})
.always(function () {
showDownloadDialog()
})
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
function showDownloadDialog() {
// This function gets called after loading the openBIS connections
// to make sure we can display the download path provided by the server.
// show DataSets for Sample identifier/permid
var sample = $("<div>")
sample.append($('<strong>').text('Sample identfier/permId: '))
sample.css('margin-top', '10px')
var sampleIdentifier = $('<input type="text" name="sampleIdentifier" size=40 placeholder="sample identifier">')
.val(currentSampleIdentifier)
var show_datasets_btn = $('<button type="button" class="btn-info btn-xs">show datasets</button>')
var datasets_table = $('<div id="dataset_table">')
.addClass("output output_scroll")
.css('max-height', '10em')
show_datasets_btn.click(function () {
var connection_name = $('input[name="connection_name"]:checked').val()
currentConnection = connection_name
currentSampleIdentifier = sampleIdentifier.val()
if (!connection_name) {
alert('Please choose a connection')
return false
}
if (!currentSampleIdentifier) {
alert('Please specify a sample identifier/permId')
return false
}
var settings = {
url: env.notebook.base_url + 'openbis/sample/' + connection_name + '/' + encodeURIComponent(currentSampleIdentifier),
processData: false,
type: 'GET',
dataType: 'json',
contentType: 'application/json'
.done(function(data) {
show_datasets_table(data, datasets_table)
})
.fail(function(data) {
alert('Error:' + data.statusText)
})
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
})
sample.append(sampleIdentifier).append(show_datasets_btn).append(datasets_table)
// dataSetPermId only
var dataset = $('<p>')
.css('margin-top', '10px')
.append($('<b>').text('... or enter DataSet permId directly: '))
var datasetPermId = $('<input type="text" name="datasetPermId" size=40 placeholder="dataset permId">')
dataset.append(datasetPermId)
// download path
var downloadPath =$('<input type="text" name="downloadPath" size=100>')
.val(currentDownloadPath)
var path = $('<div>')
.append($('<strong>').text('download data to path: '))
.append(downloadPath)
var download_dialog_box = $('<div/>')
download_dialog_box.append(conn_table).append(sample).append(dataset).append(path)
function downloadDataset(permId, path) {
var notebook = IPython.notebook
var connection_name = $('input[name="connection_name"]:checked').val()
var connection_url = $('input[name="connection_name"]:checked').attr('url')
var downloadUrl = env.notebook.base_url + 'openbis/dataset/'
+ connection_name + '/' + permId + '/' + encodeURIComponent(path)
// get the canvas for user feedback
var container = $('#notebook-container')
var settings = {
url: downloadUrl,
processData: false,
type: 'GET',
dataType: 'json',
contentType: 'application/json'
}
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
// download the dataset files
utils.ajax(settings)
.done(function (data) {
// display feedback to user
var feedback = '<div class="openbis-feedback alert alert-success alert-dismissible" role="alert">' +
'<button type="button" class="close" data-dismiss="alert" aria-label="Close">' +
'<span aria-hidden="true">×</span></button>' +
data.statusText +
'</div>'
// display feedback
$('.openbis-feedback').remove()
container.prepend(feedback)
// write statusText from returned data to notebooks metadata
if (typeof notebook.metadata.openbis_connections === 'undefined') {
notebook.metadata.openbis_connections = {}
}
if (typeof notebook.metadata.openbis_connections[connection_url] === 'undefined') {
notebook.metadata.openbis_connections[connection_url] = {}
}
// store metadata about the downloaded files into the notebook-metadata
if (data.permId) {
notebook.metadata.openbis_connections[connection_url][data.permId] = {
"permId": data.permId,
"path": data.path,
"dataStore": data.dataStore,
"location": data.location,
"size": data.size,
"status": data.statusText
}
}
currentDownloadPath = path
})
.fail(function (data) {
// display feedback to user
var feedback =
'<div class="openbis-feedback alert alert-danger alert-dismissible" role="alert">' +
'<button type="button" class="close" data-dismiss="alert" aria-label="Close"><span aria-hidden="true">×</span></button>' +
'<strong>Error: </strong>Dataset was not downloaded.<div>' + data.statusText + '</div></div>'
// display feedback
$('.openbis-feedback').remove()
container.prepend(feedback)
})
function onDownloadClick() {
connection_name = $('input[name="connection_name"]:checked').val()
if (typeof connection_name === "undefined") {
alert('please choose a connection')
return false
}
if (!selectedPermId) {
selectedPermId = datasetPermId.val()
}
if (!selectedPermId) {
alert('please select a dataset or provide a permId')
return false
}
downloadDataset(selectedPermId, downloadPath.val())
}
dialog.modal({
body: download_dialog_box,
title: 'Download openBIS DataSet',
buttons: {
'Cancel': {},
'Download': {
class: 'btn-primary btn-large',
click: onDownloadClick,
},
notebook: env.notebook,
keyboard_manager: env.notebook.keyboard_manager
})
}
}
}
var uploadDatasetsToOpenBis = {
help: 'upload Notebook and Data to openBIS',
icon: 'fa-cloud-upload',
help_index: '',
handler: function (env) {
var conn_table = $('<div id="openbis_connections"/>')
getOpenBisConnections(env, conn_table)
.done(function (data) {
show_available_connections(data, conn_table)
})
.fail(function (data) {
alert(data.status)
})
var ds_name = $('<input type="text" name="ds_name" size=40 placeholder="name">')
var ds_description = $('<input type="text" name="ds_description" size=40 placeholder="description">')
var ds_type = $('<input type="text" name="ds_type" size=40 placeholder="type">')
var sampleIdentifier = $('<input type="text" name="sampleIdentifier" size=40 placeholder="sample identifier">')
.val(currentSampleIdentifier)
var ds_files = $('<input type="text" name="files" size=40 placeholder="filenames">')
var inputs = $('<div>')
.css('margin-top', '10px')
.append($('<p>').text('Name: ').append(ds_name))
.append($('<p>').text('Description: ').append(ds_description))
.append($('<p>').text('Type: ').append(ds_type))
.append($('<p>').text('Sample: ').append(sampleIdentifier))
.append($('<p>').text('Files: ').append(ds_files))
var uploadDialogBox = $('<div/>').append(conn_table).append(inputs)
// get the canvas for user feedback
var container = $('#notebook-container')
function onOk () {
var connection_name = $('input[name="connection_name"]:checked').val()
var uploadUrl = env.notebook.base_url + 'openbis/dataset/' + connection_name
var filepath = window.location.pathname.match(re)[1]
files.push(filepath)
if (ds_files.val()) {
files.push(ds_files.val())
}
var dataSetInfo = {
"name" : ds_name.val(),
"description" : ds_description.val(),
"type" : ds_type.val(),
"files" : files,
"sampleIdentifier": sampleIdentifier.val()
}
console.log(dataSetInfo);
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
contentType: 'application/json',
success: function (data) {
// display feedback to user
var feedback = '<div class="openbis-feedback alert alert-success alert-dismissible" role="alert">' +
'<button type="button" class="close" data-dismiss="alert" aria-label="Close">' +
'<span aria-hidden="true">×</span></button>' +
data.statusText +
'</div>'
// display feedback
$('.openbis-feedback').remove()
container.prepend(feedback)
// write statusText from returned data to notebooks metadata
if ( typeof notebook.metadata.openbis === 'undefined') {
notebook.metadata.openbis = {}
}
if ( typeof notebook.metadata.openbis.permIds === 'undefined' ) {
notebook.metadata.openbis.permIds = {}
}
if ( data.permId ) {
notebook.metadata.openbis.permIds[data.permId] = data.statusText
}
},
error: function (data) {
// display feedback to user
var feedback =
'<div class="openbis-feedback alert alert-danger alert-dismissible" role="alert">' +
'<button type="button" class="close" data-dismiss="alert" aria-label="Close"><span aria-hidden="true">×</span></button>' +
'<strong>Warning!</strong> Something went wrong.<div>' + data.statusText + '</div></div>'
// display feedback
$('.openbis-feedback').remove()
container.prepend(feedback)
}
}
// display preloader during commit and push
var preloader = '<img class="openbis-feedback" src="https://cdnjs.cloudflare.com/ajax/libs/slick-carousel/1.5.8/ajax-loader.gif">'
container.prepend(preloader)
$('.openbis-feedback').remove()
// commit and push
utils.ajax(settings)
}
if (IPython.notebook.dirty === true) {
dialog.modal({
body: 'Please save the notebook before uploading it to openBIS.',
title: 'Save notebook first',
buttons: {
'Back': {}
},
notebook: env.notebook,
keyboard_manager: env.notebook.keyboard_manager
})
}
else {
dialog.modal({
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
title: 'Upload openBIS DataSet',
buttons: {
'Cancel': {},
'Upload': {
class: 'btn-primary btn-large',
click: onOk
}
},
notebook: env.notebook,
keyboard_manager: env.notebook.keyboard_manager
})
}
}
}
function _onLoad () {
// register new action
var download_datasets = IPython.keyboard_manager.actions.register(
fetchDatasetFromOpenBis, 'openbis-dataset-download', 'jupyter-openBIS')
var upload_datasets = IPython.keyboard_manager.actions.register(
uploadDatasetsToOpenBis, 'openbis-dataset-upload', 'jupyter-openBIS')
// add button for new action
IPython.toolbar.add_buttons_group([download_datasets, upload_datasets])
}
return {load_ipython_extension: _onLoad}
})