diff --git a/jupyter-openbis-extension/static/dialog.js b/jupyter-openbis-extension/static/dialog.js
index a64f341490772260ca96fd9c9507025176b2afac..b122f0c2304ddc05a4aaf286b124c6d02806a49b 100644
--- a/jupyter-openbis-extension/static/dialog.js
+++ b/jupyter-openbis-extension/static/dialog.js
@@ -6,7 +6,6 @@ define([
],
function(IPython, dialog, utils, $, mc) {
var currentConnection = ''
- var selectedPermId = null
var currentSampleIdentifier = null
var currentDownloadPath = null
var ds_type = document.createElement("SELECT")
@@ -23,9 +22,12 @@ define([
var thead = table.createTHead()
var thead_row = thead.insertRow(0)
var titles = ['', 'Name', 'URL', 'Status']
- titles.forEach( function(item, index) {
- thead_row.insertCell().textContent = item
- })
+ for (title of titles) {
+ thead_row.insertCell().textContent = title
+ }
+ //titles.forEach( function(item, index) {
+ // thead_row.insertCell().textContent = item
+ //})
tbody = table.createTBody()
data.connections.forEach( function(item, index, arr) {
@@ -74,95 +76,36 @@ define([
function show_datasets_table( data, datasets_table) {
var table = document.createElement("TABLE")
+ table.className = "table-bordered table-striped table-condensed text-nowrap"
var thead = table.createTHead()
var t_row = thead.insertRow()
- var titles = ['permId', 'Type', 'Experiment', 'Registration Date', 'Status', 'Size']
+ var titles = ['', 'permId', 'Type', 'Experiment', 'Registration Date', 'Status', 'Size']
titles.forEach( function(title) {
t_row.insertCell().textContent = title
})
+ var tbody = table.createTBody()
+
+ for (dataSet of data.dataSets) {
- //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 = document.createElement("INPUT")
- permId.type = "radio"
+ permId.type = "checkbox"
permId.name = "permId"
- permId.value = item.permId
-
- //var permId = $('<input type="radio" name="permId">').attr("value", item.permId)
- permId.onchange = function() {
- if (this.checked) {
- selectedPermId = this.value
- }
- }
- //permId.change(function() {
- // if ($(this).is(':checked')) {
- // selectedPermId = this.value
- // }
- //})
+ permId.value = dataSet.permId
- var tbody = table.createTBody()
var row = tbody.insertRow()
row.insertCell().appendChild(permId)
- row.insertCell().textContent = item.type
- row.insertCell().textContent = item.experiment
- row.insertCell().textContent = item.registrationDate
- row.insertCell().textContent = item.status
- row.insertCell().textContent = item.size
-
- //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)
- // )
- //table.append(row)
- })
+ row.insertCell().textContent = dataSet.permId
+ row.insertCell().textContent = dataSet.type
+ row.insertCell().textContent = dataSet.experiment
+ row.insertCell().textContent = dataSet.registrationDate
+ row.insertCell().textContent = dataSet.status
+ row.insertCell().textContent = dataSet.size
+ }
while (datasets_table.firstChild) {
datasets_table.removeChild(datasets_table.firstChild);
}
datasets_table.appendChild(table)
-
- //datasets_table.innerHTML = ''
- //datasets_table.innerHTML = table
- //datasets_table.empty().append(table)
-
}
function getOpenBisConnections(env, conn_table) {
@@ -177,6 +120,26 @@ define([
return utils.ajax(settings)
}
+ function createFeedback(type, content) {
+ var close = document.createElement("BUTTON")
+ close.className = "close"
+ close.setAttribute("data-dismiss", "alert")
+ close.setAttribute("aria-label", "Close")
+ var x = document.createElement("SPAN")
+ x.setAttribute("aria-hidden", true)
+ x.innerHTML = "×"
+ close.appendChild(x)
+
+ var feedbackBox = document.createElement( "DIV" )
+ feedbackBox.className = "openbis-feedback alert alert-dismissible alert-" + type
+ feedbackBox.setAttribute("role","alert")
+ feedbackBox.innerHTML = content
+ feedbackBox.prepend(close)
+
+ var nb_container = document.getElementById('notebook-container')
+ nb_container.prepend(feedbackBox)
+ }
+
var fetchDatasetFromOpenBis = {
help: 'Download a openBIS dataset to your local harddrive',
icon: 'fa-download',
@@ -201,11 +164,11 @@ define([
// to make sure we can display the download path provided by the server.
// show DataSets for Sample identifier/permid
- var sample = document.createElement("DIV")
+ var showDataSets = document.createElement("DIV")
var title = document.createElement("STRONG")
title.textContent = "Sample identfier/permId: "
- sample.appendChild(title)
- sample.style.marginTop = '10px'
+ showDataSets.appendChild(title)
+ showDataSets.style.marginTop = '10px'
var sampleIdentifier = document.createElement("INPUT")
sampleIdentifier.type = "text"
@@ -237,40 +200,63 @@ define([
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'
- //}
var url = env.notebook.base_url + 'openbis/sample/' + connection_name + '/' + encodeURIComponent(currentSampleIdentifier)
- var xhttp = new XMLHttpRequest()
- xhttp.onreadystatechange = function() {
- var data = JSON.parse(this.responseText)
- //if (this.readyState == 4 && this.status == 200) {
- if (this.status == 200) {
- show_datasets_table(data, datasets_table)
- }
- else {
- alert("Error:" + data.statusText)
- }
- };
- xhttp.open("GET", url, true);
- xhttp.send();
-
- //utils.ajax(settings)
- // .done(function(data) {
+ fetch(url)
+ .then( function(response) {
+ if (response.ok) {
+ response.json()
+ .then( function(data) {
+ show_datasets_table(data, datasets_table)
+ })
+ }
+ else {
+ response.json()
+ .then( function(error) {
+ console.log(error.reason)
+ alert("Error: " + error.reason)
+ })
+ }
+ })
+ .catch( function(error) {
+ console.error('A serious network problem occured:', error)
+ })
+ //.then( function(response) {
+ // if (response.ok) {
+ // return response.json()
+ // }
+ // //throw new Error('Error fetching datasets.');
+ // response.text().then( function(errorMsg) {
+ // throw new Error(errorMsg);
+ // })
+ //})
+ //.then( function(data) {
+ // show_datasets_table(data, datasets_table)
+ //})
+ //.catch( function(error) {
+ // console.error(error)
+ // alert("Error: " + error.message )
+ //})
+
+ //var xhttp = new XMLHttpRequest()
+ //xhttp.onreadystatechange = function() {
+ // //var data = JSON.parse(this.responseText)
+ // //if (this.readyState == 4 && this.status == 200) {
+ // if (this.readyState === 4 && this.status >= 200 && this.status < 300) {
+ // var data = JSON.parse(this.response)
// show_datasets_table(data, datasets_table)
- // })
- // .fail(function(data) {
- // alert('Error:' + data.statusText)
- // })
+ // }
+ // else if (this.readyState === 4 && this.status >= 400) {
+ // alert("Error:" + this.statusText)
+ // }
+ //};
+ //xhttp.open("GET", url, true);
+ //xhttp.send();
+
}
- sample.appendChild(sampleIdentifier)
- sample.appendChild(show_datasets_btn)
- //sample.appendChild(datasets_table)
+ showDataSets.appendChild(sampleIdentifier)
+ showDataSets.appendChild(show_datasets_btn)
+ showDataSets.appendChild(datasets_table)
// dataSetPermId only
var dataset_direct = document.createElement("P")
@@ -300,127 +286,105 @@ define([
var download_dialog_box = document.createElement("DIV")
download_dialog_box.appendChild(conn_table)
+ download_dialog_box.appendChild(showDataSets)
download_dialog_box.appendChild(dataset_direct)
download_dialog_box.appendChild(path)
- function downloadDataset(selected_conn, permId, path) {
+ function downloadDataset(selected_conn, selectedPermIds, downloadPath) {
var notebook = IPython.notebook
- var connection_name = selected_conn.value()
+ var connection_name = selected_conn.value
var connection_url = selected_conn.getAttribute("url")
- //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 container = document.getElementById('notebook-container')
-
- var settings = {
- url: downloadUrl,
- processData: false,
- type: 'GET',
- dataType: 'json',
- contentType: 'application/json'
- }
+ var nb_container = document.getElementById('notebook-container')
- var close = document.createElement("BUTTON")
- close.className = "close"
- close.setAttribute("data-dismiss", "alert")
- close.setAttribute("aria-label", "Close")
- var x = document.createElement("SPAN")
- x.setAttribute("aria-hidden", true)
- x.textContent = "×"
+ for (permId of selectedPermIds) {
- // remove existing feedbacks
- for (element in document.getElementsByClassName("openbis-feedback")) {
- element.remove()
- }
+ var downloadUrl = env.notebook.base_url + 'openbis/dataset/'
+ + connection_name + '/' + permId + '/' + encodeURIComponent(downloadPath)
- // download the dataset files
- utils.ajax(settings)
- .done(function (data) {
- // display feedback to user
- var feedback = document.createElement( "DIV" )
- feedback.className = "openbis-feedback alert alert-success alert-dismissible"
- feedback.setAttribute("role","alert")
- feedback.append(data.statusText)
+ var xhttp = new XMLHttpRequest()
+ xhttp.onreadystatechange = function() {
+ // feedback elements
+ var close = document.createElement("BUTTON")
+ close.className = "close"
+ close.setAttribute("data-dismiss", "alert")
+ close.setAttribute("aria-label", "Close")
+ var x = document.createElement("SPAN")
+ x.setAttribute("aria-hidden", true)
+ x.innerHTML = "×"
close.appendChild(x)
- feedback.appendChild(close)
-
- //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>'
+ if (this.readyState === 4 && this.status >= 200 && this.status < 300) {
+ var data = JSON.parse(this.response)
- // display feedback
- //$('.openbis-feedback').remove()
+ createFeedback('success', data.statusText)
- 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
+ // successful download:
+ // 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 = downloadPath
}
- currentDownloadPath = path
- })
- .fail(function (data) {
- // display feedback to user
- var feedback = document.createElement( "DIV" )
- feedback.className = "openbis-feedback alert alert-danger alert-dismissible"
- feedback.setAttribute("role","alert")
- feedback.innerHTML = "<strong>Error: </strong>Dataset was not downloaded.<div>"
- + data.statusText
- + "</div>"
-
- //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>'
+ else if (this.readyState === 4 && this.status >= 400) {
+ // download failed:
+ // display feedback to user
+ var feedback = "<strong>Error: </strong>Dataset was not downloaded.<div>"
+ + this.statusText
+ + "</div>"
+ createFeedback("danger", feedback)
+ //var feedbackBox = document.createElement( "DIV" )
+ //feedbackBox.className = "openbis-feedback alert alert-danger alert-dismissible"
+ //feedbackBox.setAttribute("role","alert")
+ //feedbackBox.prepend(close)
+ //nb_container.prepend(feedbackBox)
+ }
+ };
+ xhttp.open("GET", downloadUrl, true);
+ xhttp.send();
- close.appendChild(x)
- feedback.appendChild(close)
- container.prepend(feedback)
- })
+ }
}
function onDownloadClick() {
var selected_conn = document.querySelector('input[name=connection_name]:checked')
- //connection_name = $('input[name="connection_name"]:checked').val()
if (! selected_conn) {
- alert('Please choose a connection')
+ alert('please choose a connection')
return false
}
- if (!selectedPermId) {
- selectedPermId = datasetPermId.val()
+ selectedPermIds = []
+ for (row of document.querySelectorAll('input[name=permId]:checked') ) {
+ selectedPermIds.push(row.value)
}
-
- if (!selectedPermId) {
+ if (datasetPermId.value) {
+ selectedPermIds.push(datasetPermId.value)
+ }
+ if (!selectedPermIds) {
alert('please select a dataset or provide a permId')
return false
}
- if (!downloadPath.value)
- downloadDataset(selected_conn, selectedPermId, downloadPath.val())
+ if (!downloadPath.value) {
+ alert('Please specify where you would like to download your files!')
+ return false
+ }
+ downloadDataset(selected_conn, selectedPermIds, downloadPath.value)
}
dialog.modal({
@@ -476,7 +440,14 @@ define([
var container = $('#notebook-container')
function onOk () {
- var connection_name = $('input[name="connection_name"]:checked').val()
+ //var connection_name = $('input[name="connection_name"]:checked').val()
+ var selected_connection = document.querySelector('input[name=connection_name]:checked')
+ if (!selected_connection) {
+ alert("No connection selected")
+ return false
+ }
+ var connection_name = selected_connection.value
+
var uploadUrl = env.notebook.base_url + 'openbis/dataset/' + connection_name
var notebook = IPython.notebook
@@ -506,15 +477,7 @@ define([
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)
+ createFeedback('success', data.statusText)
// write statusText from returned data to notebooks metadata
if ( typeof notebook.metadata.openbis === 'undefined') {
@@ -530,14 +493,10 @@ define([
},
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)
+ var feedback = "<strong>Error: </strong>Dataset was not uploaded.<div>"
+ + data.statusText
+ + "</div>"
+ createFeedback('danger', feedback)
}
}