diff --git a/jupyter-openbis-extension/static/dialog.js b/jupyter-openbis-extension/static/dialog.js
index 5ec77c3a2bd9f4863ad757c676f8e390b0174450..7baf6980de33a47e6552bb4d46d94f23a0791424 100644
--- a/jupyter-openbis-extension/static/dialog.js
+++ b/jupyter-openbis-extension/static/dialog.js
@@ -9,10 +9,12 @@ define([
var currentSampleIdentifier = null
var currentDownloadPath = null
var ds_type = document.createElement("SELECT")
+ ds_type.size = '40'
ds_type.className = "select-xs"
ds_type.id = "dataset_type"
+ var conn_table = null
- function show_available_connections (data, conn_table) {
+ function show_available_connections(env, data, conn_table, onclick_cbf) {
if (!currentDownloadPath) {
currentDownloadPath = data.cwd
}
@@ -21,47 +23,178 @@ define([
table.className = 'table-bordered table-striped table-condensed'
var thead = table.createTHead()
var thead_row = thead.insertRow(0)
- var titles = ['', 'Name', 'URL', 'Status']
+ var titles = ['', 'Name', 'URL', 'Status', 'Username / Password']
for (title of titles) {
thead_row.insertCell().textContent = title
}
- //titles.forEach( function(item, index) {
- // thead_row.insertCell().textContent = item
- //})
tbody = table.createTBody()
- for (item of data.connections) {
- //data.connections.forEach( function(item) {
- //console.log(item)
+ for (connection of data.connections) {
var conn = document.createElement("INPUT")
conn.type = "radio"
conn.name = "connection_name"
- conn.value = item.name
- conn.setAttribute("url", item.url)
-
- // Change the list of available dataset types
- conn.onchange = function() {
- currentConnection = item.name
- //ds_type.children().remove()
- while (ds_type.firstChild) {
- ds_type.removeChild(ds_type.firstChild);
- }
- if (item.ds_types != null) {
- for (ds_type of item.ds_types) {
- option = document.createElement("OPTION")
- option.textContent = ds_type.code
- }
+ conn.value = connection.name
+ conn.setAttribute("url", connection.url)
+
+ conn.checked = connection.name === currentConnection;
+ if (onclick_cbf === undefined) {
+ conn.onclick = function() {
+ currentConnection = this.value
}
}
-
- conn.checked = item.name === currentConnection;
+ else {
+ conn.onclick = onclick_cbf
+ }
var row = tbody.insertRow()
row.insertCell().appendChild(conn)
- row.insertCell().textContent = item.name
- row.insertCell().textContent = item.url
- row.insertCell().textContent = item.status
+ row.insertCell().textContent = connection.name
+ row.insertCell().textContent = connection.url
+
+ var status_cell = row.insertCell()
+
+ var status_badge = document.createElement("SPAN")
+ status_badge.id = connection.name + "-badge"
+ status_badge.textContent = connection.status
+ if (connection.status === "connected") {
+ status_badge.className = "label label-success"
+ }
+ else {
+ status_badge.className = "label label-danger"
+ }
+ status_cell.appendChild(status_badge)
+
+ var username = document.createElement("INPUT")
+ username.type = "text"
+ username.name = "username"
+ username.autocomplete = "on"
+ username.value = connection.username
+ username.setAttribute("form", connection.name)
+
+ var password = document.createElement("INPUT")
+ password.type = "password"
+ password.name = "password"
+ password.autocomplete = "current-password"
+ password.value = connection.password
+ password.setAttribute("form", connection.name)
+
+ // Username / Password form
+ var pwform = document.createElement("FORM")
+ pwform.id = connection.name
+ pwform.onsubmit = function(event) {
+ var form_data = new FormData(this)
+ var status_badge = document.getElementById(this.id + "-badge")
+ reconnect_connection(env, this.id,
+ form_data.get("username"), form_data.get("password")
+ )
+ .then( function(response) {
+ //console.log(response)
+ if (status_badge.nextElementSibling !== null) {
+ status_badge.parentNode.removeChild(status_badge.nextElementSibling)
+ }
+ if (response.ok) {
+ status_badge.textContent = "connected"
+ status_badge.className = "label label-success"
+ }
+ else {
+ status_badge.textContent = "not connected"
+ status_badge.className = "label label-danger"
+ message = document.createElement("p")
+ if (response.status === 401) {
+ message.textContent = "Wrong username/password"
+ }
+ else if (response.status === 500) {
+ message.textContent = "Cannot connect server"
+ }
+ else {
+ message.textContent = "General error"
+ }
+ status_badge.parentNode.insertBefore(message, status_badge.nextSibling)
+ }
+ })
+ .catch( error => console.error("Error while attempting to reconnect: ",error) )
+
+ return false
+ }
+
+
+ var connect_button = document.createElement("BUTTON")
+ connect_button.className = "btn btn-primary btn-xs"
+ connect_button.textContent = "connect"
+
+ pwform.appendChild(username)
+ pwform.appendChild(password)
+ pwform.appendChild(connect_button)
+
+ var cell = row.insertCell()
+ cell.appendChild(pwform)
+ }
+
+ // add row for new connection
+ var row = tbody.insertRow()
+
+ var conn_form = document.createElement("FORM")
+ conn_form.id = "new_connection"
+ conn_form.onsubmit = function(event) {
+ var inputs = document.querySelectorAll("input[form=new_connection]")
+
+ data = {}
+ for (input of inputs) {
+ data[input.name] = input.value
+ }
+ for (missing of ['connection_name','url', 'username', 'password']) {
+ if (data[missing] === ""){
+ alert("Please provide: " + missing)
+ return false
+ }
+ }
+ new_connection(
+ env, data.connection_name, data.url, data.username, data.password
+ )
+ .then( function(response){
+ if (response.ok) {
+ response.json()
+ .then( function(data){
+ show_available_connections(env, data, conn_table)
+ })
+ }
+ })
+ return false
}
+ var conn_name = document.createElement("INPUT")
+ conn_name.type = "input"
+ conn_name.name = "connection_name"
+ conn_name.setAttribute("form", conn_form.id)
+ conn_name.placeholder = "openBIS instance name"
+ row.insertCell().appendChild(conn_form)
+ row.insertCell().appendChild(conn_name)
+
+ var conn_url = document.createElement("INPUT")
+ conn_url.type = "input"
+ conn_url.name = "url"
+ conn_url.setAttribute("form", conn_form.id)
+ conn_url.placeholder = "https://openbis.domain:port"
+ row.insertCell().appendChild(conn_url)
+ row.insertCell()
+
+ var username = document.createElement("INPUT")
+ username.autocomplete = "off"
+ username.type = "text"
+ username.name = "username"
+ username.setAttribute("form", conn_form.id)
+ username.placeholder = "username"
+ var password = document.createElement("INPUT")
+ password.type = "password"
+ password.name = "password"
+ password.autocomplete = "new-password"
+ password.setAttribute("form", conn_form.id)
+ var create_btn = document.createElement("BUTTON")
+ create_btn.setAttribute("form", conn_form.id)
+ create_btn.textContent = "create"
+ var uname_pw_cell = row.insertCell()
+ uname_pw_cell.appendChild(username)
+ uname_pw_cell.appendChild(password)
+ uname_pw_cell.appendChild(create_btn)
conn_table.innerHTML = ""
table_title = document.createElement("STRONG")
@@ -104,8 +237,10 @@ define([
datasets_table.appendChild(table)
}
+ // gets the status of the avialable openBIS connections
function getOpenBisConnections(env) {
- var connectionsUrl = env.notebook.base_url + 'openbis/conn'
+
+ var connectionsUrl = env.notebook.base_url + 'openbis/conns'
var settings = {
url: connectionsUrl,
processData: false,
@@ -116,6 +251,106 @@ define([
return utils.ajax(settings)
}
+ function reconnect_connection(env, connection, username, password){
+ var url = env.notebook.base_url + 'openbis/conn/' + connection
+ body = {
+ "username": username,
+ "password": password
+ }
+
+ var cookie = decodeURIComponent(document.cookie)
+ var xsrf_token = cookie.split("_xsrf=")[1]
+
+ return fetch(url, {
+ method: "PUT",
+ headers: {
+ "Content-Type": "application/json",
+ "X-XSRFToken": xsrf_token,
+ },
+ body: JSON.stringify(body)
+ })
+ }
+
+ function new_connection(env, connection_name, connection_url, username, password){
+ var endpoint = env.notebook.base_url + 'openbis/conns'
+ body = {
+ "name" : connection_name,
+ "url" : connection_url,
+ "username": username,
+ "password": password
+ }
+
+ var cookie = decodeURIComponent(document.cookie)
+ var xsrf_token = cookie.split("_xsrf=")[1]
+
+ return fetch(endpoint, {
+ method: "POST",
+ headers: {
+ "Content-Type": "application/json",
+ "X-XSRFToken": xsrf_token,
+ },
+ body: JSON.stringify(body)
+ })
+ }
+
+ function getDatasetTypes(env, connection_name, dataset_types, input_fields) {
+ // get all DatasetTypes of a given connection
+
+ var url = env.notebook.base_url + 'openbis/datasetTypes/'+ connection_name
+ fetch(url)
+ .then( function(response) {
+ if (response.ok) {
+ response.json()
+ .then( function(data) {
+ //console.log(data.dataSetTypes)
+ dts = data.dataSetTypes
+ while (dataset_types.firstChild) {
+ dataset_types.removeChild(dataset_types.firstChild);
+ }
+
+ for (dt of dts) {
+ var option = document.createElement("OPTION")
+ option.value = dt.code
+ option.textContent = dt.description ? dt.code + ": " + dt.description : dt.code
+ dataset_types.appendChild(option)
+ }
+ dataset_types.onchange = function() {
+ // remove existing input fields
+ while (input_fields.firstChild) {
+ input_fields.removeChild(input_fields.firstChild)
+ }
+
+ // for every property assignment, create an input field.
+ for (pa of dts[dataset_type.selectedIndex].propertyAssignments) {
+ //var input_title = document.createTextNode(pa.label + ": ")
+ var input_field = document.createElement("INPUT")
+ input_field.type = "text"
+ input_field.name = pa.code
+ input_field.placeholder = pa.description ? pa.label + ": " + pa.description : pa.label
+ input_field.size = 90
+
+ //input_fields.appendChild(input_title)
+ input_fields.appendChild(input_field)
+ input_fields.appendChild(document.createElement("BR"))
+ }
+ }
+ })
+ .catch( function(error){
+ console.error("Error while parsing dataset types", error)
+ })
+
+ }
+ else {
+ while (dataset_types.firstChild) {
+ dataset_types.removeChild(dataset_types.firstChild);
+ }
+ }
+ })
+ .catch (function(error) {
+ console.error("Error while fetching dataset types:", error)
+ })
+ }
+
function createFeedback(type, content) {
var close = document.createElement("BUTTON")
close.className = "close"
@@ -159,16 +394,15 @@ define([
}
var fetchDatasetFromOpenBis = {
- help: 'Download a openBIS dataset to your local harddrive',
+ help: 'Download openBIS datasets to your local harddrive',
icon: 'fa-download',
help_index: '',
handler: function (env) {
- //var conn_table = $('<div id="openbis_connections"/>')
- var conn_table = document.createElement("DIV")
+ conn_table = document.createElement("DIV")
conn_table.id = "openbis_connections"
getOpenBisConnections(env)
.done(function (data) {
- show_available_connections(data, conn_table)
+ show_available_connections(env, data, conn_table)
})
.fail(function (data) {
alert(data.status)
@@ -341,7 +575,7 @@ define([
dialog.modal({
body: download_dialog_box,
- title: 'Download openBIS DataSet',
+ title: 'Download openBIS DataSets',
buttons: {
'Cancel': {},
'Download': {
@@ -361,33 +595,59 @@ define([
icon: 'fa-cloud-upload',
help_index: '',
handler: function (env) {
- var conn_table = document.createElement("DIV")
+ conn_table = document.createElement("DIV")
+ var dst_title = document.createElement("STRONG")
+ dst_title.textContent = "DataSet type"
+ var dataset_types = document.createElement("SELECT")
+ dataset_types.id = "dataset_type"
+ dataset_types.className = "form-control select-xs"
+
+ var input_fields = document.createElement("DIV")
conn_table.id = "openbis_connections"
+
+ var onclick_cbf = function() {
+ currentConnection = this.value
+ getDatasetTypes(env, this.value, dataset_types, input_fields)
+ }
+
getOpenBisConnections(env)
.done(function (data) {
- show_available_connections(data, conn_table)
+ show_available_connections(env, data, conn_table, onclick_cbf)
})
.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 ds_type = $('<select class="form-control select-xs" id="dataset_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('DatasetType: ').append(ds_type))
- .append($('<p>').text('Sample: ').append(sampleIdentifier))
- .append($('<p>').text('Files: ').append(ds_files))
+
+ var sample_title = document.createElement("STRONG")
+ sample_title.textContent = "Sample Identifier"
+ var sampleIdentifier = document.createElement("INPUT")
+ sampleIdentifier.type = "text"
+ sampleIdentifier.name = 'sampleIdentifier'
+ sampleIdentifier.placeholder = "Sample Identifier or permId"
+ sampleIdentifier.value = currentSampleIdentifier
+ sampleIdentifier.size = "90"
+
+ var ds_title = document.createElement("STRONG")
+ ds_title.textContent = "DataSet files"
+ var ds_files = document.createElement("INPUT")
+ ds_files.type = "text"
+ ds_files.placeholder = "filenames"
+ ds_files.name = "ds_files"
+ ds_files.size = "90"
+
+ var inputs = document.createElement("DIV")
+ inputs.style.marginTop = '10px'
+ inputs.appendChild(dst_title)
+ inputs.appendChild(dataset_types)
+ inputs.appendChild(input_fields)
+ inputs.appendChild(sample_title)
+ inputs.appendChild(sampleIdentifier)
+ inputs.appendChild(ds_title)
+ inputs.appendChild(ds_files)
var uploadDialogBox = $('<div/>').append(conn_table).append(inputs)
+
// get the canvas for user feedback
var container = $('#notebook-container')
@@ -407,18 +667,16 @@ define([
var files = []
var filepath = window.location.pathname.match(re)[1]
files.push(filepath)
- if (ds_files.val()) {
- files.push(ds_files.val())
- }
+ // FIXME
+ //if (ds_files.val()) {
+ // files.push(ds_files.value)
+ //}
var dataSetInfo = {
- "name" : ds_name.val(),
- "description" : ds_description.val(),
- "type" : ds_type.val(),
+ "type" : dataset_types.value,
"files" : files,
- "sampleIdentifier": sampleIdentifier.val()
+ "sampleIdentifier": sampleIdentifier.value
}
- //console.log(dataSetInfo);
var settings = {
url: uploadUrl,
@@ -454,8 +712,6 @@ define([
// 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)