diff --git a/.gitignore b/.gitignore
index c11bd69955f1624a10ca36bdea9898d7e29e24b4..0235d7090c43b8f7b00253c49ba51aa3a9564fb5 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,11 @@
*.pyc
.*.swp
*~
+__pycache__
+ubuntu-bionic-18.04-cloudimg-console.log
+.vagrant
+jupyter_openbis_extension.egg-info
+venv
+.ipynb_checkpoints
+.DS_Store
+*.ipynb
diff --git a/jupyter-openbis-extension/__init__.py b/jupyter-openbis-extension/__init__.py
index 22b2aabac22028215549cb4634d33428f05c7124..032652cf4581de8167edaad981442e54fdc49552 100644
--- a/jupyter-openbis-extension/__init__.py
+++ b/jupyter-openbis-extension/__init__.py
@@ -19,7 +19,7 @@ def _jupyter_nbextension_paths():
# # directory in the `nbextension/` namespace
'dest': "openbis",
# _also_ in the `nbextension/` namespace
- 'require' : "openbis/dialog"
+ 'require' : "openbis/main"
}]
def load_jupyter_server_extension(nbapp):
diff --git a/jupyter-openbis-extension/__pycache__/extension.cpython-36.pyc b/jupyter-openbis-extension/__pycache__/extension.cpython-36.pyc
deleted file mode 100644
index d5f03417cffd6d3922495cb9dca6bf4efab96353..0000000000000000000000000000000000000000
Binary files a/jupyter-openbis-extension/__pycache__/extension.cpython-36.pyc and /dev/null differ
diff --git a/jupyter-openbis-extension/static/common.js b/jupyter-openbis-extension/static/common.js
new file mode 100644
index 0000000000000000000000000000000000000000..41f42fdba90ec6f3205e0f169f00a893e65ca722
--- /dev/null
+++ b/jupyter-openbis-extension/static/common.js
@@ -0,0 +1,30 @@
+define([
+ "base/js/namespace"
+ ],
+ function (IPython) {
+
+ 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)
+ }
+
+ return {
+ createFeedback: createFeedback
+ }
+ }
+)
\ No newline at end of file
diff --git a/jupyter-openbis-extension/static/connectionDialog.js b/jupyter-openbis-extension/static/connectionDialog.js
new file mode 100644
index 0000000000000000000000000000000000000000..4028d6b00862201dd9be12e22d774ccde2c3d901
--- /dev/null
+++ b/jupyter-openbis-extension/static/connectionDialog.js
@@ -0,0 +1,245 @@
+define(
+ [
+ "base/js/dialog",
+ "./state",
+ "./connections"
+ ],
+ function (dialog, state, connections) {
+
+ var currentDownloadPath = null
+
+ function show_available_connections(env, data, conn_table, onclick_cbf) {
+ if (!currentDownloadPath) {
+ currentDownloadPath = data.cwd
+ }
+
+ var table = document.createElement("TABLE")
+ table.className = 'table-bordered table-striped table-condensed'
+ var thead = table.createTHead()
+ var thead_row = thead.insertRow(0)
+ var titles = ['', 'Name', 'URL', 'Status', 'Username / Password']
+ for (title of titles) {
+ thead_row.insertCell().textContent = title
+ }
+
+ tbody = table.createTBody()
+ for (connection of data.connections) {
+ var conn = document.createElement("INPUT")
+ conn.type = "radio"
+ conn.name = "connection_name"
+ conn.value = connection.name
+ conn.setAttribute("url", connection.url)
+
+ conn.checked = connection.name === state.connection.candidateName;
+ if (onclick_cbf === undefined) {
+ conn.onclick = function () {
+ state.connection.candidateName = this.value
+ }
+ } else {
+ conn.onclick = onclick_cbf
+ }
+
+ var row = tbody.insertRow()
+ row.insertCell().appendChild(conn)
+ 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")
+ connections.connect(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 = "username/password incorrect"
+ } else if (response.status === 500) {
+ message.textContent = "Connection error"
+ } 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
+ }
+ }
+ connections.create(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")
+ table_title.textContent = "Please choose a connection"
+ conn_table.appendChild(table_title)
+ conn_table.appendChild(table)
+ }
+
+ return {
+ help: 'configure openBIS connections',
+ icon: 'fa-sliders',
+ help_index: '',
+ handler: function (env) {
+ 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 () {
+ state.connection.candidateName = this.value
+ }
+
+ connections.list(env)
+ .done(function (data) {
+ show_available_connections(env, data, conn_table, onclick_cbf)
+ })
+ .fail(function (data) {
+ alert(data.status)
+ })
+
+ var uploadDialogBox = $('<div/>').append(conn_table)
+
+ // get the canvas for user feedback
+ var container = $('#notebook-container')
+
+ function onOk() {
+ state.connection.name = state.connection.candidateName
+ }
+
+ dialog.modal({
+ body: uploadDialogBox,
+ title: 'Choose openBIS connection',
+ buttons: {
+ 'Cancel': {},
+ 'Choose connection': {
+ class: 'btn-primary btn-large',
+ click: onOk
+ }
+ },
+ notebook: env.notebook,
+ keyboard_manager: env.notebook.keyboard_manager
+ })
+ }
+ }
+ }
+)
\ No newline at end of file
diff --git a/jupyter-openbis-extension/static/connections.js b/jupyter-openbis-extension/static/connections.js
new file mode 100644
index 0000000000000000000000000000000000000000..1f5972cf8f4f83b06d944796970186bba9982853
--- /dev/null
+++ b/jupyter-openbis-extension/static/connections.js
@@ -0,0 +1,67 @@
+define([
+ "base/js/utils"
+ ],
+ function (utils) {
+
+ function list(env) {
+
+ var connectionsUrl = env.notebook.base_url + 'openbis/conns'
+ var settings = {
+ url: connectionsUrl,
+ processData: false,
+ type: 'GET',
+ dataType: 'json',
+ contentType: 'application/json'
+ }
+ return utils.ajax(settings)
+ }
+
+ function connect(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 create(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)
+ })
+ }
+
+ return {
+ list: list,
+ create: create,
+ connect: connect
+ }
+ }
+)
\ No newline at end of file
diff --git a/jupyter-openbis-extension/static/dialog.js b/jupyter-openbis-extension/static/dialog.js
deleted file mode 100644
index 8c999c89682dff741940e0bba896a84448ff209f..0000000000000000000000000000000000000000
--- a/jupyter-openbis-extension/static/dialog.js
+++ /dev/null
@@ -1,826 +0,0 @@
-define([
- "base/js/namespace",
- "base/js/dialog",
- "base/js/utils",
- "jquery"
- ],
- function(IPython, dialog, utils, $) {
- var currentConnection = ''
- 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(env, data, conn_table, onclick_cbf) {
- if (!currentDownloadPath) {
- currentDownloadPath = data.cwd
- }
-
- var table = document.createElement("TABLE")
- table.className = 'table-bordered table-striped table-condensed'
- var thead = table.createTHead()
- var thead_row = thead.insertRow(0)
- var titles = ['', 'Name', 'URL', 'Status', 'Username / Password']
- for (title of titles) {
- thead_row.insertCell().textContent = title
- }
-
- tbody = table.createTBody()
- for (connection of data.connections) {
- var conn = document.createElement("INPUT")
- conn.type = "radio"
- conn.name = "connection_name"
- conn.value = connection.name
- conn.setAttribute("url", connection.url)
-
- conn.checked = connection.name === currentConnection;
- if (onclick_cbf === undefined) {
- conn.onclick = function() {
- currentConnection = this.value
- }
- }
- else {
- conn.onclick = onclick_cbf
- }
-
- var row = tbody.insertRow()
- row.insertCell().appendChild(conn)
- 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 = "username/password incorrect"
- }
- else if (response.status === 500) {
- message.textContent = "Connection error"
- }
- 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")
- table_title.textContent = "Please choose a connection"
- conn_table.appendChild(table_title)
- conn_table.appendChild(table)
- }
-
- 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']
- titles.forEach( function(title) {
- t_row.insertCell().textContent = title
- })
- var tbody = table.createTBody()
-
- for (dataSet of data.dataSets) {
-
- var permId = document.createElement("INPUT")
- permId.type = "checkbox"
- permId.name = "permId"
- permId.value = dataSet.permId
-
- var row = tbody.insertRow()
- row.insertCell().appendChild(permId)
- 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)
- }
-
- // gets the status of the avialable openBIS connections
- function getOpenBisConnections(env) {
-
- var connectionsUrl = env.notebook.base_url + 'openbis/conns'
- var settings = {
- url: connectionsUrl,
- processData: false,
- type: 'GET',
- dataType: 'json',
- contentType: 'application/json'
- }
- 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)
-
- var change_input_fields = 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"))
- }
- }
- dataset_types.onchange = change_input_fields
-
- // remove the old and add the new dataset-types
- 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)
- }
- // change the input fields, since we just received new datasetTypes
- change_input_fields()
-
- })
- .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"
- 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)
- }
-
- function writeMetaData(data) {
- var notebook = IPython.notebook
- if (typeof notebook.metadata.openbis_connections === 'undefined') {
- notebook.metadata.openbis_connections = {}
- }
- if (typeof notebook.metadata.openbis_connections[data.url] === 'undefined') {
- notebook.metadata.openbis_connections[data.url] = {}
- }
- // store metadata about the downloaded files into the notebook-metadata
- if (data.permId) {
- notebook.metadata.openbis_connections[data.url][data.permId] = {
- "permId": data.permId,
- "path": data.path,
- "dataStore": data.dataStore,
- "location": data.location,
- "size": data.size,
- "status": data.statusText
- }
- }
-
- }
-
- var fetchDatasetFromOpenBis = {
- help: 'Download openBIS datasets to your local harddrive',
- icon: 'fa-download',
- help_index: '',
- handler: function (env) {
- conn_table = document.createElement("DIV")
- conn_table.id = "openbis_connections"
- getOpenBisConnections(env)
- .done(function (data) {
- show_available_connections(env, data, conn_table)
- })
- .fail(function (data) {
- alert(data.status)
- })
- .always(function () {
- showDownloadDialog()
- })
-
- 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 showDataSets = document.createElement("DIV")
- var title = document.createElement("STRONG")
- title.textContent = "Sample identfier/permId: "
- showDataSets.appendChild(title)
- showDataSets.style.marginTop = '10px'
-
- var sampleIdentifier = document.createElement("INPUT")
- sampleIdentifier.type = "text"
- sampleIdentifier.name = "sampleIdentifier"
- sampleIdentifier.size = 40
- sampleIdentifier.placeholder = "sample identifier or permId"
- sampleIdentifier.value = currentSampleIdentifier
-
- var datasets_table = document.createElement("DIV")
- datasets_table.id = "dataset_table"
- datasets_table.className = "output output_scroll"
- datasets_table.style.maxHeight = "10em"
-
- var show_datasets_btn = document.createElement("BUTTON")
- show_datasets_btn.className = "btn-info btn-xs"
- show_datasets_btn.textContent = "show datasets"
-
- show_datasets_btn.onclick = function() {
- var selected_conn = document.querySelector('input[name=connection_name]:checked')
- if (!selected_conn) {
- alert('Please choose a connection')
- return false
- }
- connection_name = selected_conn.value
-
- currentConnection = connection_name
- currentSampleIdentifier = sampleIdentifier.value
- if (!currentSampleIdentifier) {
- alert('Please specify a sample identifier/permId')
- return false
- }
- var url = env.notebook.base_url + 'openbis/sample/' + connection_name + '/' + encodeURIComponent(currentSampleIdentifier)
-
- 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)
- })
-
- }
- showDataSets.appendChild(sampleIdentifier)
- showDataSets.appendChild(show_datasets_btn)
- showDataSets.appendChild(datasets_table)
-
- // dataSetPermId only
- var dataset_direct = document.createElement("P")
- dataset_direct.style.marginTop='10px'
- dataset_direct.innerHTML = '<strong>enter DataSet permId directly: </strong>'
-
- //var dataset = $('<p>')
- // .css('margin-top', '10px')
- // .append($('<b>').text('... or enter DataSet permId directly: '))
- var datasetPermId = document.createElement("INPUT")
- datasetPermId.type = "text"
- datasetPermId.name = "datasetPermId"
- datasetPermId.size = "40"
- datasetPermId.placeholder = "dataSet permId"
-
- dataset_direct.appendChild(datasetPermId)
-
- var downloadPath = document.createElement("INPUT")
- downloadPath.type = "text"
- downloadPath.name = "downloadPath"
- downloadPath.size = "90"
- downloadPath.value = currentDownloadPath
-
- var path = document.createElement("DIV")
- path.innerHTML = "<strong>download data to path: </strong>"
- path.appendChild(downloadPath)
-
- 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, selectedPermIds, downloadPath) {
- var connection_name = selected_conn.value
-
- for (permId of selectedPermIds) {
- var downloadUrl = env.notebook.base_url + 'openbis/dataset/'
- + connection_name + '/' + permId + '/' + encodeURIComponent(downloadPath)
-
- fetch(downloadUrl)
- .then( function(response) {
- if (response.ok) {
- response.json()
- .then( function(data) {
- createFeedback('success', data.statusText)
-
- // successful download:
- // write statusText from returned data to notebooks metadata
- writeMetaData(data)
-
- // keep current download path for later use
- currentDownloadPath = downloadPath
- })
- }
- 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)
- })
- }
- }
-
- function onDownloadClick() {
- var selected_conn = document.querySelector('input[name=connection_name]:checked')
- if (! selected_conn) {
- alert('please choose a connection')
- return false
- }
-
- var selectedPermIds = []
- for (row of document.querySelectorAll('input[name=permId]:checked') ) {
- selectedPermIds.push(row.value)
- }
- if (datasetPermId.value) {
- selectedPermIds.push(datasetPermId.value)
- }
- if (!selectedPermIds) {
- alert('please select a dataset or provide a permId')
- return false
- }
-
- if (!downloadPath.value) {
- alert('Please specify where you would like to download your files!')
- return false
- }
- downloadDataset(selected_conn, selectedPermIds, downloadPath.value)
- }
-
- dialog.modal({
- body: download_dialog_box,
- title: 'Download openBIS DataSets',
- 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-upload',
- help_index: '',
- handler: function (env) {
- 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(env, data, conn_table, onclick_cbf)
- })
- .fail(function (data) {
- alert(data.status)
- })
-
- 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')
-
- function onOk () {
- //var connection_name = $('input[name="connection_name"]:checked').val()
- var selected_connection = document.querySelector('input[name=connection_name]:checked')
- if (!selected_connection) {
- alert("No connection selected")
- return false
- }
- var connection_name = selected_connection.value
-
- var uploadUrl = env.notebook.base_url + 'openbis/dataset/' + connection_name
-
- var notebook = IPython.notebook
- var re = /\/notebooks\/(.*?)$/
- var files = []
- var filepath = window.location.pathname.match(re)[1]
- files.push(filepath)
- // FIXME
- //if (ds_files.val()) {
- // files.push(ds_files.value)
- //}
-
- var dataSetInfo = {
- "type" : dataset_types.value,
- "files" : files,
- "sampleIdentifier": sampleIdentifier.value
- }
-
- var settings = {
- url: uploadUrl,
- processData: false,
- type: 'POST',
- dataType: 'json',
- data: JSON.stringify(dataSetInfo),
- contentType: 'application/json',
- success: function (data) {
- // display feedback to user
- createFeedback('success', data.statusText)
-
- // 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 = "<strong>Error: </strong>Dataset was not uploaded.<div>"
- + data.statusText
- + "</div>"
- createFeedback('danger', 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">'
-
- // 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({
- body: uploadDialogBox,
- title: 'Upload openBIS DataSet',
- buttons: {
- 'Cancel': {},
- 'Upload': {
- class: 'btn-primary btn-large',
- click: onOk
- }
- },
- notebook: env.notebook,
- keyboard_manager: env.notebook.keyboard_manager
- })
- }
- }
- }
-
- var configureOpenBisConnections = {
- help: 'configure openBIS connections',
- icon: 'fa-sliders',
- help_index: '',
- handler: function (env) {
- 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(env, data, conn_table, onclick_cbf)
- })
- .fail(function (data) {
- alert(data.status)
- })
-
- var uploadDialogBox = $('<div/>').append(conn_table)
-
- // get the canvas for user feedback
- var container = $('#notebook-container')
-
- function onOk () {
-
- }
-
- dialog.modal({
- body: uploadDialogBox,
- title: 'Choose openBIS connection',
- buttons: {
- 'Cancel': {},
- 'Choose connection': {
- class: 'btn-primary btn-large',
- click: onOk
- }
- },
- notebook: env.notebook,
- keyboard_manager: env.notebook.keyboard_manager
- })
- }
- }
-
- function _onLoad () {
- // show connections
- var configure_openbis_connections = IPython.keyboard_manager.actions.register(
- configureOpenBisConnections, 'openbis-connections', 'jupyter-openBIS')
-
- // dnownload
- var download_datasets = IPython.keyboard_manager.actions.register(
- fetchDatasetFromOpenBis, 'openbis-dataset-download', 'jupyter-openBIS')
-
- // upload
- var upload_datasets = IPython.keyboard_manager.actions.register(
- uploadDatasetsToOpenBis, 'openbis-dataset-upload', 'jupyter-openBIS')
-
- // add button for new action
- IPython.toolbar.add_buttons_group([configure_openbis_connections, download_datasets, upload_datasets])
- }
-
- return {load_ipython_extension: _onLoad}
- })
diff --git a/jupyter-openbis-extension/static/downloadDialog.js b/jupyter-openbis-extension/static/downloadDialog.js
new file mode 100644
index 0000000000000000000000000000000000000000..973ff5e3066bedc3a272f487cc0329f68119e48f
--- /dev/null
+++ b/jupyter-openbis-extension/static/downloadDialog.js
@@ -0,0 +1,242 @@
+define([
+ "base/js/dialog",
+ "./common",
+ "./state"
+ ],
+ function (dialog, common, state) {
+
+ function writeMetaData(data) {
+ var notebook = IPython.notebook
+ if (typeof notebook.metadata.openbis_connections === 'undefined') {
+ notebook.metadata.openbis_connections = {}
+ }
+ if (typeof notebook.metadata.openbis_connections[data.url] === 'undefined') {
+ notebook.metadata.openbis_connections[data.url] = {}
+ }
+ // store metadata about the downloaded files into the notebook-metadata
+ if (data.permId) {
+ notebook.metadata.openbis_connections[data.url][data.permId] = {
+ "permId": data.permId,
+ "path": data.path,
+ "dataStore": data.dataStore,
+ "location": data.location,
+ "size": data.size,
+ "status": data.statusText
+ }
+ }
+ }
+
+ 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']
+ titles.forEach(function (title) {
+ t_row.insertCell().textContent = title
+ })
+ var tbody = table.createTBody()
+
+ for (dataSet of data.dataSets) {
+
+ var permId = document.createElement("INPUT")
+ permId.type = "checkbox"
+ permId.name = "permId"
+ permId.value = dataSet.permId
+
+ var row = tbody.insertRow()
+ row.insertCell().appendChild(permId)
+ 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)
+ }
+
+
+ return {
+ help: 'Download openBIS datasets to your local harddrive',
+ icon: 'fa-download',
+ help_index: '',
+ handler: function (env) {
+ conn_table = document.createElement("DIV")
+ conn_table.id = "openbis_connections"
+
+ var showDataSets = document.createElement("DIV")
+ var title = document.createElement("STRONG")
+ title.textContent = "Sample identifier / permId: "
+ showDataSets.appendChild(title)
+ showDataSets.style.marginTop = '10px'
+
+ var sampleIdentifier = document.createElement("INPUT")
+ sampleIdentifier.type = "text"
+ sampleIdentifier.name = "sampleIdentifier"
+ sampleIdentifier.size = 40
+ sampleIdentifier.placeholder = "sample identifier or permId"
+ sampleIdentifier.value = ''
+
+ var datasets_table = document.createElement("DIV")
+ datasets_table.id = "dataset_table"
+ datasets_table.className = "output output_scroll"
+ datasets_table.style.maxHeight = "10em"
+
+ var show_datasets_btn = document.createElement("BUTTON")
+ show_datasets_btn.className = "btn-info btn-xs"
+ show_datasets_btn.textContent = "show datasets"
+
+ show_datasets_btn.onclick = function () {
+ var selected_conn = state.connection.name
+ if (!selected_conn) {
+ alert('Please choose a connection')
+ return false
+ }
+ connection_name = state.connection.name
+
+ currentConnection = connection_name
+ currentSampleIdentifier = sampleIdentifier.value
+ if (!currentSampleIdentifier) {
+ alert('Please specify a sample identifier/permId')
+ return false
+ }
+ var url = env.notebook.base_url + 'openbis/sample/' + connection_name + '/' + encodeURIComponent(currentSampleIdentifier)
+
+ 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)
+ })
+
+ }
+ showDataSets.appendChild(sampleIdentifier)
+ showDataSets.appendChild(show_datasets_btn)
+ showDataSets.appendChild(datasets_table)
+
+ // dataSetPermId only
+ var dataset_direct = document.createElement("P")
+ dataset_direct.style.marginTop = '10px'
+ dataset_direct.innerHTML = '<strong>enter DataSet permId directly: </strong>'
+
+ //var dataset = $('<p>')
+ // .css('margin-top', '10px')
+ // .append($('<b>').text('... or enter DataSet permId directly: '))
+ var datasetPermId = document.createElement("INPUT")
+ datasetPermId.type = "text"
+ datasetPermId.name = "datasetPermId"
+ datasetPermId.size = "40"
+ datasetPermId.placeholder = "dataSet permId"
+
+ dataset_direct.appendChild(datasetPermId)
+
+ var downloadPath = document.createElement("INPUT")
+ downloadPath.type = "text"
+ downloadPath.name = "downloadPath"
+ downloadPath.size = "90"
+ downloadPath.value = ''
+
+ var path = document.createElement("DIV")
+ path.innerHTML = "<strong>download data to path: </strong>"
+ path.appendChild(downloadPath)
+
+ 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(connection_name, selectedPermIds, downloadPath) {
+
+ for (permId of selectedPermIds) {
+ var downloadUrl = env.notebook.base_url + 'openbis/dataset/' +
+ connection_name + '/' + permId + '/' + encodeURIComponent(downloadPath)
+
+ fetch(downloadUrl)
+ .then(function (response) {
+ if (response.ok) {
+ response.json()
+ .then(function (data) {
+ common.createFeedback('success', data.statusText)
+
+ // successful download:
+ // write statusText from returned data to notebooks metadata
+ writeMetaData(data)
+
+ // keep current download path for later use
+ currentDownloadPath = downloadPath
+ })
+ } 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)
+ })
+ }
+ }
+
+ function onDownloadClick() {
+ var selected_conn = state.connection.name
+ if (!selected_conn) {
+ alert('please choose a connection')
+ return false
+ }
+
+ var selectedPermIds = []
+ for (row of document.querySelectorAll('input[name=permId]:checked')) {
+ selectedPermIds.push(row.value)
+ }
+ if (datasetPermId.value) {
+ selectedPermIds.push(datasetPermId.value)
+ }
+ if (!selectedPermIds) {
+ alert('please select a dataset or provide a permId')
+ return false
+ }
+
+ if (!downloadPath.value) {
+ alert('Please specify where you would like to download your files!')
+ return false
+ }
+ downloadDataset(selected_conn, selectedPermIds, downloadPath.value)
+ }
+
+ dialog.modal({
+ body: download_dialog_box,
+ title: 'Download openBIS DataSets',
+ buttons: {
+ 'Cancel': {},
+ 'Download': {
+ class: 'btn-primary btn-large',
+ click: onDownloadClick,
+ }
+ },
+ notebook: env.notebook,
+ keyboard_manager: env.notebook.keyboard_manager
+ })
+ }
+ }
+ }
+)
\ No newline at end of file
diff --git a/jupyter-openbis-extension/static/main.js b/jupyter-openbis-extension/static/main.js
new file mode 100644
index 0000000000000000000000000000000000000000..777e69d8ab57d2c25566d5425d904d546db115ef
--- /dev/null
+++ b/jupyter-openbis-extension/static/main.js
@@ -0,0 +1,33 @@
+define([
+ "base/js/namespace",
+ "./connectionDialog",
+ "./uploadDialog",
+ "./downloadDialog"
+ ],
+ function (IPython, connectionDialog, uploadDialog, downloadDialog) {
+ var ds_type = document.createElement("SELECT")
+ ds_type.size = '40'
+ ds_type.className = "select-xs"
+ ds_type.id = "dataset_type"
+
+ function _onLoad() {
+ // show connections
+ var configure_openbis_connections = IPython.keyboard_manager.actions.register(
+ connectionDialog, 'openbis-connections', 'jupyter-openBIS')
+
+ // dnownload
+ var download_datasets = IPython.keyboard_manager.actions.register(
+ downloadDialog, 'openbis-dataset-download', 'jupyter-openBIS')
+
+ // upload
+ var upload_datasets = IPython.keyboard_manager.actions.register(
+ uploadDialog, 'openbis-dataset-upload', 'jupyter-openBIS')
+
+ // add button for new action
+ IPython.toolbar.add_buttons_group([configure_openbis_connections, download_datasets, upload_datasets])
+ }
+
+ return {
+ load_ipython_extension: _onLoad
+ }
+ })
\ No newline at end of file
diff --git a/jupyter-openbis-extension/static/state.js b/jupyter-openbis-extension/static/state.js
new file mode 100644
index 0000000000000000000000000000000000000000..e72d76e13f2952f91369b45130869e27d5c567ec
--- /dev/null
+++ b/jupyter-openbis-extension/static/state.js
@@ -0,0 +1,10 @@
+define([],
+ function () {
+ return {
+ connection: {
+ name: null,
+ candidateName: null
+ }
+ }
+ }
+)
\ No newline at end of file
diff --git a/jupyter-openbis-extension/static/uploadDIalog.js b/jupyter-openbis-extension/static/uploadDIalog.js
new file mode 100644
index 0000000000000000000000000000000000000000..ff3a51d8a54a15f64513bc5df2eebe2055c86792
--- /dev/null
+++ b/jupyter-openbis-extension/static/uploadDIalog.js
@@ -0,0 +1,213 @@
+define([
+ "base/js/dialog",
+ "base/js/utils",
+ "jquery",
+ "./state",
+ "./common",
+ ],
+ function (dialog, utils, $, state, common) {
+
+ 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)
+
+ var change_input_fields = 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_types.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"))
+ }
+ }
+ dataset_types.onchange = change_input_fields
+
+ // remove the old and add the new dataset-types
+ 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)
+ }
+ // change the input fields, since we just received new datasetTypes
+ change_input_fields()
+
+ })
+ .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)
+ })
+ }
+
+ return {
+ help: 'upload Notebook and Data to openBIS',
+ icon: 'fa-upload',
+ help_index: '',
+ handler: function (env) {
+
+ 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"
+
+ getDatasetTypes(env, state.connection.name, dataset_types, input_fields)
+
+ 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 = ''
+ 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 = $('<div/>').append(conn_table).append(inputs)
+
+ function onOk() {
+ var connection_name = state.connection.name
+
+ if (!connection_name) {
+ alert("No connection selected")
+ return false
+ }
+
+ var uploadUrl = env.notebook.base_url + 'openbis/dataset/' + connection_name
+
+ var notebook = IPython.notebook
+ var re = /\/notebooks\/(.*?)$/
+ var files = []
+ var filepath = window.location.pathname.match(re)[1]
+ files.push(filepath)
+ // FIXME
+ //if (ds_files.val()) {
+ // files.push(ds_files.value)
+ //}
+
+ var dataSetInfo = {
+ "type": dataset_types.value,
+ "files": files,
+ "sampleIdentifier": sampleIdentifier.value
+ }
+
+ var settings = {
+ url: uploadUrl,
+ processData: false,
+ type: 'POST',
+ dataType: 'json',
+ data: JSON.stringify(dataSetInfo),
+ contentType: 'application/json',
+ success: function (data) {
+ // display feedback to user
+ common.createFeedback('success', data.statusText)
+
+ // 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 = "<strong>Error: </strong>Dataset was not uploaded.<div>" +
+ data.statusText +
+ "</div>"
+ common.createFeedback('danger', 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">'
+
+ // 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({
+ body: uploadDialogBox,
+ title: 'Upload openBIS DataSet',
+ buttons: {
+ 'Cancel': {},
+ 'Upload': {
+ class: 'btn-primary btn-large',
+ click: onOk
+ }
+ },
+ notebook: env.notebook,
+ keyboard_manager: env.notebook.keyboard_manager
+ })
+ }
+ }
+ }
+ }
+)
\ No newline at end of file
diff --git a/openbis-connections.yaml b/openbis-connections.yaml
index 4e02d7ff96ecd04da4ee3b7195f6a75e416c719d..754cd1c4c91dfe88e34e94d6368a2e36304705da 100644
--- a/openbis-connections.yaml
+++ b/openbis-connections.yaml
@@ -1,11 +1,16 @@
connections:
- - name : local test openBIS instance
- url : https://localhost:8443
- verify_certificates : false
- username : username
- password : password
- - name : productive openBIS instance
- url : https://openbis.example.com
- verify_certificates : true
- username : username
- password : password
+ - name: local test openBIS instance
+ url: https://localhost:8443
+ verify_certificates: false
+ username: username
+ password: password
+ - name: vagrant openBIS instance
+ url: https://localhost:8122
+ verify_certificates: false
+ username: admin
+ password: password
+ - name: productive openBIS instance
+ url: https://openbis.example.com
+ verify_certificates: true
+ username: username
+ password: password
diff --git a/setup.py b/setup.py
index 15616447e27ea2606253377bd93f459a8a43d147..5eb05d0e8fa2ed017d3c0c8b07134ecc7377537e 100644
--- a/setup.py
+++ b/setup.py
@@ -36,7 +36,7 @@ setup(
data_files=[
# like `jupyter nbextension install --sys-prefix`
("share/jupyter/nbextensions/jupyter-openbis-extension", [
- "jupyter-openbis-extension/static/dialog.js",
+ "jupyter-openbis-extension/static/main.js",
]),
# like `jupyter nbextension enable --sys-prefix`
("etc/jupyter/nbconfig/notebook.d", [
diff --git a/vagrant/Vagrantfile b/vagrant/Vagrantfile
new file mode 100644
index 0000000000000000000000000000000000000000..b21d6f4e6bf9ebc4cf8ecda3d33c32897b9aedf2
--- /dev/null
+++ b/vagrant/Vagrantfile
@@ -0,0 +1,28 @@
+# -*- mode: ruby -*-
+# vi: set ft=ruby :
+
+Vagrant.configure("2") do |config|
+ config.vm.box = "ubuntu/bionic64"
+ config.vm.box_version = "20180531.0.0"
+
+ config.vm.provider "virtualbox" do |v|
+ v.memory = 4096
+ v.cpus = 4
+ v.name = "jupyter-openbis-extension"
+ end
+
+ # Needs to be unique among VMs
+ config.notify_forwarder.port = 27282
+
+ config.vm.synced_folder "..", "/home/vagrant/jupyter-openbis-extension"
+ config.vm.synced_folder '.', '/vagrant', disabled: true
+ config.vm.synced_folder "files", "/files", :mount_options => ["ro"]
+ config.vm.synced_folder "shared", "/shared"
+
+ config.vm.network "forwarded_port", guest: 8122, host: 8122, host_ip: "0.0.0.0"
+ config.vm.network "forwarded_port", guest: 8123, host: 8123, host_ip: "0.0.0.0"
+ config.vm.network "forwarded_port", guest: 8888, host: 8888, host_ip: "0.0.0.0"
+
+ config.vm.provision :shell, path: "bootstrap.sh"
+ config.vm.provision :shell, path: "files/start-services.sh", run: "always", privileged: true
+end
diff --git a/vagrant/bootstrap.sh b/vagrant/bootstrap.sh
new file mode 100644
index 0000000000000000000000000000000000000000..64620765b3dc52e51c25bb8de94bc42f0df97988
--- /dev/null
+++ b/vagrant/bootstrap.sh
@@ -0,0 +1,18 @@
+#!/usr/bin/env bash
+
+sudo locale-gen en_US.UTF-8
+
+echo "
+LC_ALL=en_US.UTF-8
+LANG=en_US.UTF-8
+" >> /etc/environment
+
+apt update
+apt install -y python3 python3-pip openjdk-8-jdk postgresql unzip
+
+cp /files/pg_hba.conf /etc/postgresql/10/main/pg_hba.conf
+service postgresql restart
+sleep 10 # let the db engine start
+
+sudo -E -u postgres -H -i /files/setup-postgres.sh
+sudo -E -u vagrant -H -i /files/setup-vagrant.sh
diff --git a/vagrant/files/console.properties b/vagrant/files/console.properties
new file mode 100644
index 0000000000000000000000000000000000000000..faa327b56b38bcb8352771ef160acba48fddf193
--- /dev/null
+++ b/vagrant/files/console.properties
@@ -0,0 +1,62 @@
+#
+# The path where openBIS will be installed.
+#
+# Example :
+# INSTALL_PATH=/home/openbis/
+#
+# will result in the following directory structure
+#
+# + /home/openbis
+# + bin/
+# + servers/
+# + core-plugins/
+# + openBIS-server/
+# + datastore_server/
+#
+INSTALL_PATH=/home/vagrant/openbis
+
+#
+# The path where openBIS will keep the imported data (e.g. images, analysis files)
+# and its incoming folders.
+#
+DSS_ROOT_DIR=/home/vagrant/dss_root
+
+# Possible configuration options
+# 'local' - if the openBIS servers will only be accessed from this machine
+# 'server' - if the installation is meant to be accessible for remote users
+INSTALLATION_TYPE=local
+
+# Path to the file which should replace the current Java key store file
+#KEY_STORE_FILE = <path to key store>
+
+# Password of the key store
+KEY_STORE_PASSWORD = changeit
+
+# Password of the key
+KEY_PASSWORD = changeit
+
+# Standard technology PROTEOMICS is disabled by default
+#PROTEOMICS = true
+
+# Standard technology SCREENING is disabled by default
+#SCREENING = true
+
+# Standard technology ILLUMINA-NGS (ETH BSSE Setup) is disabled by default
+#ILLUMINA-NGS = true
+
+# Standard technology ELN-LIMS is disabled by default
+#ELN-LIMS = true
+
+# Standard technology MICROSCOPY is disabled by default
+#MICROSCOPY = true
+
+# Standard technology FLOW CYTOMETRY is disabled by default
+#FLOW = true
+
+# Full ELN/LIMS master data is enabled by default. This setting is meaningful only if ELN-LIMS is enabled
+ELN-LIMS-MASTER-DATA = false
+
+#
+# Comma-separated list of databases to backup. If the list is empty or undefined all databases
+# will be backauped.
+#DATABASES_TO_BACKUP =
\ No newline at end of file
diff --git a/vagrant/files/jupyter_notebook_config.py b/vagrant/files/jupyter_notebook_config.py
new file mode 100644
index 0000000000000000000000000000000000000000..e137e1661539d2436a296e0332a2219a90ec8fd1
--- /dev/null
+++ b/vagrant/files/jupyter_notebook_config.py
@@ -0,0 +1,765 @@
+# Configuration file for jupyter-notebook.
+
+# ------------------------------------------------------------------------------
+# Application(SingletonConfigurable) configuration
+# ------------------------------------------------------------------------------
+
+# This is an application.
+
+# The date format used by logging formatters for %(asctime)s
+#c.Application.log_datefmt = '%Y-%m-%d %H:%M:%S'
+
+# The Logging format template
+#c.Application.log_format = '[%(name)s]%(highlevel)s %(message)s'
+
+# Set the log level by value or name.
+#c.Application.log_level = 30
+
+# ------------------------------------------------------------------------------
+# JupyterApp(Application) configuration
+# ------------------------------------------------------------------------------
+
+# Base class for Jupyter applications
+
+# Answer yes to any prompts.
+#c.JupyterApp.answer_yes = False
+
+# Full path of a config file.
+#c.JupyterApp.config_file = ''
+
+# Specify a config file to load.
+#c.JupyterApp.config_file_name = ''
+
+# Generate default config file.
+#c.JupyterApp.generate_config = False
+
+# ------------------------------------------------------------------------------
+# NotebookApp(JupyterApp) configuration
+# ------------------------------------------------------------------------------
+
+# Set the Access-Control-Allow-Credentials: true header
+#c.NotebookApp.allow_credentials = False
+
+# Set the Access-Control-Allow-Origin header
+#
+# Use '*' to allow any origin to access your server.
+#
+# Takes precedence over allow_origin_pat.
+c.NotebookApp.allow_origin = '*'
+
+# Use a regular expression for the Access-Control-Allow-Origin header
+#
+# Requests from an origin matching the expression will get replies with:
+#
+# Access-Control-Allow-Origin: origin
+#
+# where `origin` is the origin of the request.
+#
+# Ignored if allow_origin is set.
+#c.NotebookApp.allow_origin_pat = ''
+
+# Allow password to be changed at login for the notebook server.
+#
+# While loggin in with a token, the notebook server UI will give the opportunity
+# to the user to enter a new password at the same time that will replace the
+# token login mechanism.
+#
+# This can be set to false to prevent changing password from the UI/API.
+#c.NotebookApp.allow_password_change = True
+
+# Allow requests where the Host header doesn't point to a local server
+#
+# By default, requests get a 403 forbidden response if the 'Host' header shows
+# that the browser thinks it's on a non-local domain. Setting this option to
+# True disables this check.
+#
+# This protects against 'DNS rebinding' attacks, where a remote web server
+# serves you a page and then changes its DNS to send later requests to a local
+# IP, bypassing same-origin checks.
+#
+# Local IP addresses (such as 127.0.0.1 and ::1) are allowed as local, along
+# with hostnames configured in local_hostnames.
+c.NotebookApp.allow_remote_access = True
+
+# Whether to allow the user to run the notebook as root.
+#c.NotebookApp.allow_root = False
+
+# DEPRECATED use base_url
+#c.NotebookApp.base_project_url = '/'
+
+# The base URL for the notebook server.
+#
+# Leading and trailing slashes can be omitted, and will automatically be added.
+#c.NotebookApp.base_url = '/'
+
+# Specify what command to use to invoke a web browser when opening the notebook.
+# If not specified, the default browser will be determined by the `webbrowser`
+# standard library module, which allows setting of the BROWSER environment
+# variable to override it.
+#c.NotebookApp.browser = ''
+
+# The full path to an SSL/TLS certificate file.
+#c.NotebookApp.certfile = ''
+
+# The full path to a certificate authority certificate for SSL/TLS client
+# authentication.
+#c.NotebookApp.client_ca = ''
+
+# The config manager class to use
+#c.NotebookApp.config_manager_class = 'notebook.services.config.manager.ConfigManager'
+
+# The notebook manager class to use.
+#c.NotebookApp.contents_manager_class = 'notebook.services.contents.largefilemanager.LargeFileManager'
+
+# Extra keyword arguments to pass to `set_secure_cookie`. See tornado's
+# set_secure_cookie docs for details.
+#c.NotebookApp.cookie_options = {}
+
+# The random bytes used to secure cookies. By default this is a new random
+# number every time you start the Notebook. Set it to a value in a config file
+# to enable logins to persist across server sessions.
+#
+# Note: Cookie secrets should be kept private, do not share config files with
+# cookie_secret stored in plaintext (you can read the value from a file).
+#c.NotebookApp.cookie_secret = b''
+
+# The file where the cookie secret is stored.
+#c.NotebookApp.cookie_secret_file = ''
+
+# Override URL shown to users.
+#
+# Replace actual URL, including protocol, address, port and base URL, with the
+# given value when displaying URL to the users. Do not change the actual
+# connection URL. If authentication token is enabled, the token is added to the
+# custom URL automatically.
+#
+# This option is intended to be used when the URL to display to the user cannot
+# be determined reliably by the Jupyter notebook server (proxified or
+# containerized setups for example).
+#c.NotebookApp.custom_display_url = ''
+
+# The default URL to redirect to from `/`
+#c.NotebookApp.default_url = '/tree'
+
+# Disable cross-site-request-forgery protection
+#
+# Jupyter notebook 4.3.1 introduces protection from cross-site request
+# forgeries, requiring API requests to either:
+#
+# - originate from pages served by this server (validated with XSRF cookie and
+# token), or - authenticate with a token
+#
+# Some anonymous compute resources still desire the ability to run code,
+# completely without authentication. These services can disable all
+# authentication and security checks, with the full knowledge of what that
+# implies.
+c.NotebookApp.disable_check_xsrf = True
+
+# Whether to enable MathJax for typesetting math/TeX
+#
+# MathJax is the javascript library Jupyter uses to render math/LaTeX. It is
+# very large, so you may want to disable it if you have a slow internet
+# connection, or for offline use of the notebook.
+#
+# When disabled, equations etc. will appear as their untransformed TeX source.
+#c.NotebookApp.enable_mathjax = True
+
+# extra paths to look for Javascript notebook extensions
+#c.NotebookApp.extra_nbextensions_path = []
+
+# handlers that should be loaded at higher priority than the default services
+#c.NotebookApp.extra_services = []
+
+# Extra paths to search for serving static files.
+#
+# This allows adding javascript/css to be available from the notebook server
+# machine, or overriding individual files in the IPython
+#c.NotebookApp.extra_static_paths = []
+
+# Extra paths to search for serving jinja templates.
+#
+# Can be used to override templates from notebook.templates.
+#c.NotebookApp.extra_template_paths = []
+
+##
+#c.NotebookApp.file_to_run = ''
+
+# Extra keyword arguments to pass to `get_secure_cookie`. See tornado's
+# get_secure_cookie docs for details.
+#c.NotebookApp.get_secure_cookie_kwargs = {}
+
+# Deprecated: Use minified JS file or not, mainly use during dev to avoid JS
+# recompilation
+#c.NotebookApp.ignore_minified_js = False
+
+# (bytes/sec) Maximum rate at which stream output can be sent on iopub before
+# they are limited.
+#c.NotebookApp.iopub_data_rate_limit = 1000000
+
+# (msgs/sec) Maximum rate at which messages can be sent on iopub before they are
+# limited.
+#c.NotebookApp.iopub_msg_rate_limit = 1000
+
+# The IP address the notebook server will listen on.
+c.NotebookApp.ip = '0.0.0.0'
+
+# Supply extra arguments that will be passed to Jinja environment.
+#c.NotebookApp.jinja_environment_options = {}
+
+# Extra variables to supply to jinja templates when rendering.
+#c.NotebookApp.jinja_template_vars = {}
+
+# The kernel manager class to use.
+#c.NotebookApp.kernel_manager_class = 'notebook.services.kernels.kernelmanager.MappingKernelManager'
+
+# The kernel spec manager class to use. Should be a subclass of
+# `jupyter_client.kernelspec.KernelSpecManager`.
+#
+# The Api of KernelSpecManager is provisional and might change without warning
+# between this version of Jupyter and the next stable one.
+#c.NotebookApp.kernel_spec_manager_class = 'jupyter_client.kernelspec.KernelSpecManager'
+
+# The full path to a private key file for usage with SSL/TLS.
+#c.NotebookApp.keyfile = ''
+
+# Hostnames to allow as local when allow_remote_access is False.
+#
+# Local IP addresses (such as 127.0.0.1 and ::1) are automatically accepted as
+# local as well.
+#c.NotebookApp.local_hostnames = ['localhost']
+
+# The login handler class to use.
+#c.NotebookApp.login_handler_class = 'notebook.auth.login.LoginHandler'
+
+# The logout handler class to use.
+#c.NotebookApp.logout_handler_class = 'notebook.auth.logout.LogoutHandler'
+
+# The MathJax.js configuration file that is to be used.
+#c.NotebookApp.mathjax_config = 'TeX-AMS-MML_HTMLorMML-full,Safe'
+
+# A custom url for MathJax.js. Should be in the form of a case-sensitive url to
+# MathJax, for example: /static/components/MathJax/MathJax.js
+#c.NotebookApp.mathjax_url = ''
+
+# Sets the maximum allowed size of the client request body, specified in the
+# Content-Length request header field. If the size in a request exceeds the
+# configured value, a malformed HTTP message is returned to the client.
+#
+# Note: max_body_size is applied even in streaming mode.
+#c.NotebookApp.max_body_size = 536870912
+
+# Gets or sets the maximum amount of memory, in bytes, that is allocated for
+# use by the buffer manager.
+#c.NotebookApp.max_buffer_size = 536870912
+
+# Dict of Python modules to load as notebook server extensions.Entry values can
+# be used to enable and disable the loading ofthe extensions. The extensions
+# will be loaded in alphabetical order.
+#c.NotebookApp.nbserver_extensions = {}
+
+# The directory to use for notebooks and kernels.
+#c.NotebookApp.notebook_dir = ''
+
+# Whether to open in a browser after starting. The specific browser used is
+# platform dependent and determined by the python standard library `webbrowser`
+# module, unless it is overridden using the --browser (NotebookApp.browser)
+# configuration option.
+c.NotebookApp.open_browser = False
+
+# Hashed password to use for web authentication.
+#
+# To generate, type in a python/IPython shell:
+#
+# from notebook.auth import passwd; passwd()
+#
+# The string should be of the form type:salt:hashed-password.
+#c.NotebookApp.password = ''
+
+# Forces users to use a password for the Notebook server. This is useful in a
+# multi user environment, for instance when everybody in the LAN can access each
+# other's machine through ssh.
+#
+# In such a case, server the notebook server on localhost is not secure since
+# any user can connect to the notebook server via ssh.
+c.NotebookApp.password_required = False
+
+# The port the notebook server will listen on.
+#c.NotebookApp.port = 8888
+
+# The number of additional ports to try if the specified port is not available.
+#c.NotebookApp.port_retries = 50
+
+# DISABLED: use %pylab or %matplotlib in the notebook to enable matplotlib.
+#c.NotebookApp.pylab = 'disabled'
+
+# If True, display a button in the dashboard to quit (shutdown the notebook
+# server).
+#c.NotebookApp.quit_button = True
+
+# (sec) Time window used to check the message and data rate limits.
+#c.NotebookApp.rate_limit_window = 3
+
+# Reraise exceptions encountered loading server extensions?
+#c.NotebookApp.reraise_server_extension_failures = False
+
+# DEPRECATED use the nbserver_extensions dict instead
+#c.NotebookApp.server_extensions = []
+
+# The session manager class to use.
+#c.NotebookApp.session_manager_class = 'notebook.services.sessions.sessionmanager.SessionManager'
+
+# Shut down the server after N seconds with no kernels or terminals running and
+# no activity. This can be used together with culling idle kernels
+# (MappingKernelManager.cull_idle_timeout) to shutdown the notebook server when
+# it's not in use. This is not precisely timed: it may shut down up to a minute
+# later. 0 (the default) disables this automatic shutdown.
+#c.NotebookApp.shutdown_no_activity_timeout = 0
+
+# Supply SSL options for the tornado HTTPServer. See the tornado docs for
+# details.
+#c.NotebookApp.ssl_options = {}
+
+# Supply overrides for terminado. Currently only supports "shell_command".
+#c.NotebookApp.terminado_settings = {}
+
+# Set to False to disable terminals.
+#
+# This does *not* make the notebook server more secure by itself. Anything the
+# user can in a terminal, they can also do in a notebook.
+#
+# Terminals may also be automatically disabled if the terminado package is not
+# available.
+#c.NotebookApp.terminals_enabled = True
+
+# Token used for authenticating first-time connections to the server.
+#
+# When no password is enabled, the default is to generate a new, random token.
+#
+# Setting to an empty string disables authentication altogether, which is NOT
+# RECOMMENDED.
+c.NotebookApp.token = ''
+
+# Supply overrides for the tornado.web.Application that the Jupyter notebook
+# uses.
+#c.NotebookApp.tornado_settings = {}
+
+# Whether to trust or not X-Scheme/X-Forwarded-Proto and X-Real-Ip/X-Forwarded-
+# For headerssent by the upstream reverse proxy. Necessary if the proxy handles
+# SSL
+#c.NotebookApp.trust_xheaders = False
+
+# DEPRECATED, use tornado_settings
+#c.NotebookApp.webapp_settings = {}
+
+# Specify Where to open the notebook on startup. This is the `new` argument
+# passed to the standard library method `webbrowser.open`. The behaviour is not
+# guaranteed, but depends on browser support. Valid values are:
+#
+# - 2 opens a new tab,
+# - 1 opens a new window,
+# - 0 opens in an existing window.
+#
+# See the `webbrowser.open` documentation for details.
+#c.NotebookApp.webbrowser_open_new = 2
+
+# Set the tornado compression options for websocket connections.
+#
+# This value will be returned from
+# :meth:`WebSocketHandler.get_compression_options`. None (default) will disable
+# compression. A dict (even an empty one) will enable compression.
+#
+# See the tornado docs for WebSocketHandler.get_compression_options for details.
+#c.NotebookApp.websocket_compression_options = None
+
+# The base URL for websockets, if it differs from the HTTP server (hint: it
+# almost certainly doesn't).
+#
+# Should be in the form of an HTTP origin: ws[s]://hostname[:port]
+#c.NotebookApp.websocket_url = ''
+
+# ------------------------------------------------------------------------------
+# ConnectionFileMixin(LoggingConfigurable) configuration
+# ------------------------------------------------------------------------------
+
+# Mixin for configurable classes that work with connection files
+
+# JSON file in which to store connection info [default: kernel-<pid>.json]
+#
+# This file will contain the IP, ports, and authentication key needed to connect
+# clients to this kernel. By default, this file will be created in the security
+# dir of the current profile, but can be specified by absolute path.
+#c.ConnectionFileMixin.connection_file = ''
+
+# set the control (ROUTER) port [default: random]
+#c.ConnectionFileMixin.control_port = 0
+
+# set the heartbeat port [default: random]
+#c.ConnectionFileMixin.hb_port = 0
+
+# set the iopub (PUB) port [default: random]
+#c.ConnectionFileMixin.iopub_port = 0
+
+# Set the kernel's IP address [default localhost]. If the IP address is
+# something other than localhost, then Consoles on other machines will be able
+# to connect to the Kernel, so be careful!
+#c.ConnectionFileMixin.ip = ''
+
+# set the shell (ROUTER) port [default: random]
+#c.ConnectionFileMixin.shell_port = 0
+
+# set the stdin (ROUTER) port [default: random]
+#c.ConnectionFileMixin.stdin_port = 0
+
+##
+#c.ConnectionFileMixin.transport = 'tcp'
+
+# ------------------------------------------------------------------------------
+# KernelManager(ConnectionFileMixin) configuration
+# ------------------------------------------------------------------------------
+
+# Manages a single kernel in a subprocess on this host.
+#
+# This version starts kernels with Popen.
+
+# Should we autorestart the kernel if it dies.
+#c.KernelManager.autorestart = True
+
+# DEPRECATED: Use kernel_name instead.
+#
+# The Popen Command to launch the kernel. Override this if you have a custom
+# kernel. If kernel_cmd is specified in a configuration file, Jupyter does not
+# pass any arguments to the kernel, because it cannot make any assumptions about
+# the arguments that the kernel understands. In particular, this means that the
+# kernel does not receive the option --debug if it given on the Jupyter command
+# line.
+#c.KernelManager.kernel_cmd = []
+
+# Time to wait for a kernel to terminate before killing it, in seconds.
+#c.KernelManager.shutdown_wait_time = 5.0
+
+# ------------------------------------------------------------------------------
+# Session(Configurable) configuration
+# ------------------------------------------------------------------------------
+
+# Object for handling serialization and sending of messages.
+#
+# The Session object handles building messages and sending them with ZMQ sockets
+# or ZMQStream objects. Objects can communicate with each other over the
+# network via Session objects, and only need to work with the dict-based IPython
+# message spec. The Session will handle serialization/deserialization, security,
+# and metadata.
+#
+# Sessions support configurable serialization via packer/unpacker traits, and
+# signing with HMAC digests via the key/keyfile traits.
+#
+# Parameters ----------
+#
+# debug : bool
+# whether to trigger extra debugging statements
+# packer/unpacker : str : 'json', 'pickle' or import_string
+# importstrings for methods to serialize message parts. If just
+# 'json' or 'pickle', predefined JSON and pickle packers will be used.
+# Otherwise, the entire importstring must be used.
+#
+# The functions must accept at least valid JSON input, and output *bytes*.
+#
+# For example, to use msgpack:
+# packer = 'msgpack.packb', unpacker='msgpack.unpackb'
+# pack/unpack : callables
+# You can also set the pack/unpack callables for serialization directly.
+# session : bytes
+# the ID of this Session object. The default is to generate a new UUID.
+# username : unicode
+# username added to message headers. The default is to ask the OS.
+# key : bytes
+# The key used to initialize an HMAC signature. If unset, messages
+# will not be signed or checked.
+# keyfile : filepath
+# The file containing a key. If this is set, `key` will be initialized
+# to the contents of the file.
+
+# Threshold (in bytes) beyond which an object's buffer should be extracted to
+# avoid pickling.
+#c.Session.buffer_threshold = 1024
+
+# Whether to check PID to protect against calls after fork.
+#
+# This check can be disabled if fork-safety is handled elsewhere.
+#c.Session.check_pid = True
+
+# Threshold (in bytes) beyond which a buffer should be sent without copying.
+#c.Session.copy_threshold = 65536
+
+# Debug output in the Session
+#c.Session.debug = False
+
+# The maximum number of digests to remember.
+#
+# The digest history will be culled when it exceeds this value.
+#c.Session.digest_history_size = 65536
+
+# The maximum number of items for a container to be introspected for custom
+# serialization. Containers larger than this are pickled outright.
+#c.Session.item_threshold = 64
+
+# execution key, for signing messages.
+#c.Session.key = b''
+
+# path to file containing execution key.
+#c.Session.keyfile = ''
+
+# Metadata dictionary, which serves as the default top-level metadata dict for
+# each message.
+#c.Session.metadata = {}
+
+# The name of the packer for serializing messages. Should be one of 'json',
+# 'pickle', or an import name for a custom callable serializer.
+#c.Session.packer = 'json'
+
+# The UUID identifying this session.
+#c.Session.session = ''
+
+# The digest scheme used to construct the message signatures. Must have the form
+# 'hmac-HASH'.
+#c.Session.signature_scheme = 'hmac-sha256'
+
+# The name of the unpacker for unserializing messages. Only used with custom
+# functions for `packer`.
+#c.Session.unpacker = 'json'
+
+# Username for the Session. Default is your system username.
+#c.Session.username = 'vagrant'
+
+# ------------------------------------------------------------------------------
+# MultiKernelManager(LoggingConfigurable) configuration
+# ------------------------------------------------------------------------------
+
+# A class for managing multiple kernels.
+
+# The name of the default kernel to start
+#c.MultiKernelManager.default_kernel_name = 'python3'
+
+# The kernel manager class. This is configurable to allow subclassing of the
+# KernelManager for customized behavior.
+#c.MultiKernelManager.kernel_manager_class = 'jupyter_client.ioloop.IOLoopKernelManager'
+
+# ------------------------------------------------------------------------------
+# MappingKernelManager(MultiKernelManager) configuration
+# ------------------------------------------------------------------------------
+
+# A KernelManager that handles notebook mapping and HTTP error handling
+
+# Whether messages from kernels whose frontends have disconnected should be
+# buffered in-memory.
+#
+# When True (default), messages are buffered and replayed on reconnect, avoiding
+# lost messages due to interrupted connectivity.
+#
+# Disable if long-running kernels will produce too much output while no
+# frontends are connected.
+#c.MappingKernelManager.buffer_offline_messages = True
+
+# Whether to consider culling kernels which are busy. Only effective if
+# cull_idle_timeout > 0.
+#c.MappingKernelManager.cull_busy = False
+
+# Whether to consider culling kernels which have one or more connections. Only
+# effective if cull_idle_timeout > 0.
+#c.MappingKernelManager.cull_connected = False
+
+# Timeout (in seconds) after which a kernel is considered idle and ready to be
+# culled. Values of 0 or lower disable culling. Very short timeouts may result
+# in kernels being culled for users with poor network connections.
+#c.MappingKernelManager.cull_idle_timeout = 0
+
+# The interval (in seconds) on which to check for idle kernels exceeding the
+# cull timeout value.
+#c.MappingKernelManager.cull_interval = 300
+
+# Timeout for giving up on a kernel (in seconds).
+#
+# On starting and restarting kernels, we check whether the kernel is running and
+# responsive by sending kernel_info_requests. This sets the timeout in seconds
+# for how long the kernel can take before being presumed dead. This affects the
+# MappingKernelManager (which handles kernel restarts) and the
+# ZMQChannelsHandler (which handles the startup).
+#c.MappingKernelManager.kernel_info_timeout = 60
+
+##
+#c.MappingKernelManager.root_dir = ''
+
+# ------------------------------------------------------------------------------
+# ContentsManager(LoggingConfigurable) configuration
+# ------------------------------------------------------------------------------
+
+# Base class for serving files and directories.
+#
+# This serves any text or binary file, as well as directories, with special
+# handling for JSON notebook documents.
+#
+# Most APIs take a path argument, which is always an API-style unicode path, and
+# always refers to a directory.
+#
+# - unicode, not url-escaped
+# - '/'-separated
+# - leading and trailing '/' will be stripped
+# - if unspecified, path defaults to '',
+# indicating the root path.
+
+# Allow access to hidden files
+#c.ContentsManager.allow_hidden = False
+
+##
+#c.ContentsManager.checkpoints = None
+
+##
+#c.ContentsManager.checkpoints_class = 'notebook.services.contents.checkpoints.Checkpoints'
+
+##
+#c.ContentsManager.checkpoints_kwargs = {}
+
+# handler class to use when serving raw file requests.
+#
+# Default is a fallback that talks to the ContentsManager API, which may be
+# inefficient, especially for large files.
+#
+# Local files-based ContentsManagers can use a StaticFileHandler subclass, which
+# will be much more efficient.
+#
+# Access to these files should be Authenticated.
+#c.ContentsManager.files_handler_class = 'notebook.files.handlers.FilesHandler'
+
+# Extra parameters to pass to files_handler_class.
+#
+# For example, StaticFileHandlers generally expect a `path` argument specifying
+# the root directory from which to serve files.
+#c.ContentsManager.files_handler_params = {}
+
+# Glob patterns to hide in file and directory listings.
+#c.ContentsManager.hide_globs = ['__pycache__', '*.pyc', '*.pyo', '.DS_Store', '*.so', '*.dylib', '*~']
+
+# Python callable or importstring thereof
+#
+# To be called on a contents model prior to save.
+#
+# This can be used to process the structure, such as removing notebook outputs
+# or other side effects that should not be saved.
+#
+# It will be called as (all arguments passed by keyword)::
+#
+# hook(path=path, model=model, contents_manager=self)
+#
+# - model: the model to be saved. Includes file contents.
+# Modifying this dict will affect the file that is stored.
+# - path: the API path of the save destination
+# - contents_manager: this ContentsManager instance
+#c.ContentsManager.pre_save_hook = None
+
+##
+#c.ContentsManager.root_dir = '/'
+
+# The base name used when creating untitled directories.
+#c.ContentsManager.untitled_directory = 'Untitled Folder'
+
+# The base name used when creating untitled files.
+#c.ContentsManager.untitled_file = 'untitled'
+
+# The base name used when creating untitled notebooks.
+#c.ContentsManager.untitled_notebook = 'Untitled'
+
+# ------------------------------------------------------------------------------
+# FileManagerMixin(Configurable) configuration
+# ------------------------------------------------------------------------------
+
+# Mixin for ContentsAPI classes that interact with the filesystem.
+#
+# Provides facilities for reading, writing, and copying both notebooks and
+# generic files.
+#
+# Shared by FileContentsManager and FileCheckpoints.
+#
+# Note ---- Classes using this mixin must provide the following attributes:
+#
+# root_dir : unicode
+# A directory against against which API-style paths are to be resolved.
+#
+# log : logging.Logger
+
+# By default notebooks are saved on disk on a temporary file and then if
+# succefully written, it replaces the old ones. This procedure, namely
+# 'atomic_writing', causes some bugs on file system whitout operation order
+# enforcement (like some networked fs). If set to False, the new notebook is
+# written directly on the old one which could fail (eg: full filesystem or quota
+# )
+#c.FileManagerMixin.use_atomic_writing = True
+
+# ------------------------------------------------------------------------------
+# FileContentsManager(FileManagerMixin,ContentsManager) configuration
+# ------------------------------------------------------------------------------
+
+# If True (default), deleting files will send them to the platform's
+# trash/recycle bin, where they can be recovered. If False, deleting files
+# really deletes them.
+#c.FileContentsManager.delete_to_trash = True
+
+# Python callable or importstring thereof
+#
+# to be called on the path of a file just saved.
+#
+# This can be used to process the file on disk, such as converting the notebook
+# to a script or HTML via nbconvert.
+#
+# It will be called as (all arguments passed by keyword)::
+#
+# hook(os_path=os_path, model=model, contents_manager=instance)
+#
+# - path: the filesystem path to the file just written - model: the model
+# representing the file - contents_manager: this ContentsManager instance
+#c.FileContentsManager.post_save_hook = None
+
+##
+#c.FileContentsManager.root_dir = ''
+
+# DEPRECATED, use post_save_hook. Will be removed in Notebook 5.0
+#c.FileContentsManager.save_script = False
+
+# ------------------------------------------------------------------------------
+# NotebookNotary(LoggingConfigurable) configuration
+# ------------------------------------------------------------------------------
+
+# A class for computing and verifying notebook signatures.
+
+# The hashing algorithm used to sign notebooks.
+#c.NotebookNotary.algorithm = 'sha256'
+
+# The sqlite file in which to store notebook signatures. By default, this will
+# be in your Jupyter data directory. You can set it to ':memory:' to disable
+# sqlite writing to the filesystem.
+#c.NotebookNotary.db_file = ''
+
+# The secret key with which notebooks are signed.
+#c.NotebookNotary.secret = b''
+
+# The file where the secret key is stored.
+#c.NotebookNotary.secret_file = ''
+
+# A callable returning the storage backend for notebook signatures. The default
+# uses an SQLite database.
+#c.NotebookNotary.store_factory = traitlets.Undefined
+
+# ------------------------------------------------------------------------------
+# KernelSpecManager(LoggingConfigurable) configuration
+# ------------------------------------------------------------------------------
+
+# If there is no Python kernelspec registered and the IPython kernel is
+# available, ensure it is added to the spec list.
+#c.KernelSpecManager.ensure_native_kernel = True
+
+# The kernel spec class. This is configurable to allow subclassing of the
+# KernelSpecManager for customized behavior.
+#c.KernelSpecManager.kernel_spec_class = 'jupyter_client.kernelspec.KernelSpec'
+
+# Whitelist of allowed kernel names.
+#
+# By default, all installed kernels are allowed.
+#c.KernelSpecManager.whitelist = set()
diff --git a/vagrant/files/pg_hba.conf b/vagrant/files/pg_hba.conf
new file mode 100644
index 0000000000000000000000000000000000000000..5383ee2765aad917cb2c909e743f2a9cf8b335e3
--- /dev/null
+++ b/vagrant/files/pg_hba.conf
@@ -0,0 +1,99 @@
+# PostgreSQL Client Authentication Configuration File
+# ===================================================
+#
+# Refer to the "Client Authentication" section in the PostgreSQL
+# documentation for a complete description of this file. A short
+# synopsis follows.
+#
+# This file controls: which hosts are allowed to connect, how clients
+# are authenticated, which PostgreSQL user names they can use, which
+# databases they can access. Records take one of these forms:
+#
+# local DATABASE USER METHOD [OPTIONS]
+# host DATABASE USER ADDRESS METHOD [OPTIONS]
+# hostssl DATABASE USER ADDRESS METHOD [OPTIONS]
+# hostnossl DATABASE USER ADDRESS METHOD [OPTIONS]
+#
+# (The uppercase items must be replaced by actual values.)
+#
+# The first field is the connection type: "local" is a Unix-domain
+# socket, "host" is either a plain or SSL-encrypted TCP/IP socket,
+# "hostssl" is an SSL-encrypted TCP/IP socket, and "hostnossl" is a
+# plain TCP/IP socket.
+#
+# DATABASE can be "all", "sameuser", "samerole", "replication", a
+# database name, or a comma-separated list thereof. The "all"
+# keyword does not match "replication". Access to replication
+# must be enabled in a separate record (see example below).
+#
+# USER can be "all", a user name, a group name prefixed with "+", or a
+# comma-separated list thereof. In both the DATABASE and USER fields
+# you can also write a file name prefixed with "@" to include names
+# from a separate file.
+#
+# ADDRESS specifies the set of hosts the record matches. It can be a
+# host name, or it is made up of an IP address and a CIDR mask that is
+# an integer (between 0 and 32 (IPv4) or 128 (IPv6) inclusive) that
+# specifies the number of significant bits in the mask. A host name
+# that starts with a dot (.) matches a suffix of the actual host name.
+# Alternatively, you can write an IP address and netmask in separate
+# columns to specify the set of hosts. Instead of a CIDR-address, you
+# can write "samehost" to match any of the server's own IP addresses,
+# or "samenet" to match any address in any subnet that the server is
+# directly connected to.
+#
+# METHOD can be "trust", "reject", "md5", "password", "scram-sha-256",
+# "gss", "sspi", "ident", "peer", "pam", "ldap", "radius" or "cert".
+# Note that "password" sends passwords in clear text; "md5" or
+# "scram-sha-256" are preferred since they send encrypted passwords.
+#
+# OPTIONS are a set of options for the authentication in the format
+# NAME=VALUE. The available options depend on the different
+# authentication methods -- refer to the "Client Authentication"
+# section in the documentation for a list of which options are
+# available for which authentication methods.
+#
+# Database and user names containing spaces, commas, quotes and other
+# special characters must be quoted. Quoting one of the keywords
+# "all", "sameuser", "samerole" or "replication" makes the name lose
+# its special character, and just match a database or username with
+# that name.
+#
+# This file is read on server startup and when the server receives a
+# SIGHUP signal. If you edit the file on a running system, you have to
+# SIGHUP the server for the changes to take effect, run "pg_ctl reload",
+# or execute "SELECT pg_reload_conf()".
+#
+# Put your actual configuration here
+# ----------------------------------
+#
+# If you want to allow non-local connections, you need to add more
+# "host" records. In that case you will also need to make PostgreSQL
+# listen on a non-local interface via the listen_addresses
+# configuration parameter, or via the -i or -h command line switches.
+
+
+
+
+# DO NOT DISABLE!
+# If you change this first entry you will need to make sure that the
+# database superuser can access the database using some other method.
+# Noninteractive access to all databases is required during automatic
+# maintenance (custom daily cronjobs, replication, and similar tasks).
+#
+# Database administrative login by Unix domain socket
+#local all postgres peer
+
+# TYPE DATABASE USER ADDRESS METHOD
+
+# "local" is for Unix domain socket connections only
+local all all trust
+# IPv4 local connections:
+host all all 127.0.0.1/32 trust
+# IPv6 local connections:
+host all all ::1/128 md5
+# Allow replication connections from localhost, by a user with the
+# replication privilege.
+#local replication all peer
+#host replication all 127.0.0.1/32 md5
+#host replication all ::1/128 md5
\ No newline at end of file
diff --git a/vagrant/files/setup-postgres.sh b/vagrant/files/setup-postgres.sh
new file mode 100755
index 0000000000000000000000000000000000000000..5e9f9f54c71da14349f5f60cbdca240d55f6b2fa
--- /dev/null
+++ b/vagrant/files/setup-postgres.sh
@@ -0,0 +1,3 @@
+echo " --- setup-postgres.sh ---"
+
+createuser vagrant
diff --git a/vagrant/files/setup-vagrant.sh b/vagrant/files/setup-vagrant.sh
new file mode 100755
index 0000000000000000000000000000000000000000..0d0ff35f4ba280a128d5223bc8d2ac448553ad0b
--- /dev/null
+++ b/vagrant/files/setup-vagrant.sh
@@ -0,0 +1,35 @@
+echo " --- setup-vagrant.sh ---"
+
+rm -rf ~/jupyter-openbis-extension/venv
+rm -rf ~/jupyter-openbis-extension/jupyter_openbis_extension.egg-info
+rm -rf ~/jupyter-openbis-extension/.ipynb_checkpoints
+
+build="http://stage-jenkins.ethz.ch:8090/job/installation-18.06/lastSuccessfulBuild"
+path=$(curl -s "$build/api/xml?xpath=//relativePath"|sed -e "s/<relativePath>//"|sed -e "s/<\/relativePath>//")
+wget -q $build/artifact/$path
+archive=$(basename $path)
+tar xvfz $archive
+directory=$(echo "$archive" | cut -f 1 -d '.')
+cp /files/console.properties $directory
+export ADMIN_PASSWORD='password'
+$directory/run-console.sh
+
+sed -i "/jetty.ssl.port=/ s/=.*/=8122/" /home/vagrant/openbis/servers/openBIS-server/jetty/start.d/ssl.ini
+sed -i "/host-address =/ s/=.*/= https:\/\/localhost/" /home/vagrant/openbis/servers/datastore_server/etc/service.properties
+sed -i "/port =/ s/=.*/= 8123/" /home/vagrant/openbis/servers/datastore_server/etc/service.properties
+sed -i "/server-url =/ s/=.*/= \${host-address}:8122/" /home/vagrant/openbis/servers/datastore_server/etc/service.properties
+
+rm -rf ~/openBIS-installation-*
+
+mkdir ~/.jupyter
+cp /files/jupyter_notebook_config.py ~/.jupyter
+
+cd jupyter-openbis-extension
+pip3 install -e .
+export PATH=$PATH:/home/vagrant/.local/bin
+pip3 install --upgrade pybis
+pip3 install 'tornado==5.1.1' --force-reinstall
+jupyter serverextension enable --py jupyter-openbis-extension
+jupyter nbextension install --py jupyter-openbis-extension --user --symlink
+jupyter nbextension enable jupyter-openbis-extension --user --py
+cd
diff --git a/vagrant/files/start-services-vagrant.sh b/vagrant/files/start-services-vagrant.sh
new file mode 100755
index 0000000000000000000000000000000000000000..9bcd30ff0584281f51a4c098b51a0664a0da9c39
--- /dev/null
+++ b/vagrant/files/start-services-vagrant.sh
@@ -0,0 +1,8 @@
+echo " --- start-services-vagrant.sh ---"
+/home/vagrant/openbis/bin/allup.sh
+
+screen -S dev -t jupyter -Adm bash -c "
+ cd ~/jupyter-openbis-extension;
+ jupyter notebook;
+ bash;
+"
diff --git a/vagrant/files/start-services.sh b/vagrant/files/start-services.sh
new file mode 100755
index 0000000000000000000000000000000000000000..4fd56076ced3de09010ec899d8129d1b1b503621
--- /dev/null
+++ b/vagrant/files/start-services.sh
@@ -0,0 +1,2 @@
+echo " --- start-services.sh ---"
+runuser -l vagrant bash -c /files/start-services-vagrant.sh
diff --git a/vagrant/shared/.gitignore b/vagrant/shared/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..c96a04f008ee21e260b28f7701595ed59e2839e3
--- /dev/null
+++ b/vagrant/shared/.gitignore
@@ -0,0 +1,2 @@
+*
+!.gitignore
\ No newline at end of file