diff --git a/nbextension/openbis/main.js b/nbextension/openbis/main.js
index 796eea6df4dfcb725956505dfab0c65a28153726..c6bf7738ac775ec85f9c41361a7cf9505f0af90b 100644
--- a/nbextension/openbis/main.js
+++ b/nbextension/openbis/main.js
@@ -6,33 +6,16 @@ define([
],
function(IPython, dialog, utils, $, mc) {
var currentConnection = ''
- var checkOpenBisConnection = function(env, url, verify_certificates, username, password){
- var payload = {
- 'url' : url,
- 'verify_certificates' : verify_certificates,
- 'username': username,
- 'password': password
- }
- var downloadUrl = env.notebook.base_url + 'openbis/conn'
- var settings = {
- url: downloadUrl,
- processData: false,
- type: 'POST',
- dataType: 'json',
- data: JSON.stringify(payload),
- contentType: 'application/json',
- success: function (data) {
- alert(data.statusText)
- },
- error: function (data) {
- alert(data.statusText)
- }
- }
- utils.ajax(settings)
- }
+ var selectedPermId = null
+ var currentSampleIdentifier = null
+ var currentDownloadPath = null
+
+ function show_available_connections (data, conn_table) {
+ if (!currentDownloadPath) {
+ currentDownloadPath = data.cwd
+ }
- var show_available_connections = function(data, conn_table){
- var table = $('<table>').addClass('table-bordered').addClass('table-condensed');
+ var table = $('<table>').addClass('table-bordered table-striped table-condensed')
var thead = $('<thead>')
var title_row = $('<tr>')
.append($('<th>')
@@ -44,11 +27,16 @@ define([
.append($('<th>')
.text('URL')
)
+ .append($('<th>')
+ .text('Status')
+ )
title_row.appendTo(thead)
thead.appendTo(table)
data.connections.forEach( function(item, index, arr) {
- var conn = $('<input type="radio" name="connection_name">').attr("value", item.name)
+ var conn = $('<input type="radio" name="connection_name">')
+ .attr("value", item.name)
+ .attr("url", item.url)
conn.change( function() {
currentConnection = item.name
})
@@ -69,28 +57,85 @@ define([
.append($('<td>')
.text(item.url)
)
+ .append($('<td>')
+ .text(item.status)
+ )
+
+ table.append(row)
+ })
+
+ conn_table.empty().append($('<strong>').text('Please choose a connection')).append(table)
+ }
+
+ function show_datasets_table( data, datasets_table) {
+ var table = $('<table>').addClass('table-bordered table-striped table-condensed text-nowrap')
+ var thead = $('<thead>')
+ var title_row = $('<tr>')
+ .append($('<th>')
+ .text('permId')
+ )
+ .append($('<th>')
+ .text('Type')
+ )
+ .append($('<th>')
+ .text('Experiment')
+ )
+ .append($('<th>')
+ .text('Registration Date')
+ )
+ .append($('<th>')
+ .text('Status')
+ )
+ .append($('<th>')
+ .text('Size')
+ )
+ title_row.appendTo(thead)
+ thead.appendTo(table)
+
+ data.dataSets.forEach( function(item, index, arr) {
+ var permId = $('<input type="radio" name="permId">').attr("value", item.permId)
+ permId.change(function() {
+ if ($(this).is(':checked')) {
+ selectedPermId = this.value
+ }
+ })
+
+ var row = $('<tr>')
+ .append(
+ $('<td>').append(permId).append(' ' + item.permId)
+ )
+ .append($('<td>')
+ .text(item.type)
+ )
+ .append($('<td>')
+ .text(item.experiment)
+ )
+ .append($('<td>')
+ .text(item.registrationDate)
+ )
+ .append($('<td>')
+ .text(item.status)
+ )
+ .append($('<td>')
+ .text(item.size)
+ )
table.append(row)
})
- conn_table.empty().append('<p><b>Please choose a connection</b></p>').append(table)
+ datasets_table.empty().append(table)
+
}
- var getOpenBisConnections = function(env, conn_table) {
+ function getOpenBisConnections(env, conn_table) {
var connectionsUrl = env.notebook.base_url + 'openbis/conn'
var settings = {
url: connectionsUrl,
processData: false,
type: 'GET',
dataType: 'json',
- contentType: 'application/json',
- success: function (data) {
- show_available_connections(data, conn_table)
- },
- error: function (data) {
- alert(data.status)
- }
+ contentType: 'application/json'
}
- utils.ajax(settings)
+ return utils.ajax(settings)
}
var fetchDatasetFromOpenBis = {
@@ -100,130 +145,178 @@ define([
handler: function (env) {
var conn_table = $('<div id="openbis_connections"/>')
getOpenBisConnections(env, conn_table)
+ .done(function (data) {
+ show_available_connections(data, conn_table)
+ })
+ .fail(function (data) {
+ alert(data.status)
+ })
+ .always(function () {
+ showDownloadDialog()
+ })
- var sample = $('<p>').append($('<b>').text('Sample identifier/permId: '))
- var sampleIdentifier = $('<input type="text" name="sampleIdentifier" size=40>')
- var show_datasets_btn = $('<button type="button" class="btn-info btn-xs">show datasets</button>')
- var datasets_table = $('<div id="dataset_table">')
- show_datasets_btn.click( function() {
- var connection = $('input[name="connection_name"]:checked').val()
- var settings = {
- url: env.notebook.base_url + 'openbis/sample/' + connection + '/' + encodeURIComponent(sampleIdentifier.val()),
- processData: false,
- type: 'GET',
- dataType: 'json',
- contentType: 'application/json',
- }
- utils.ajax(settings)
- .done(function(data) {
- alert('success')
- console.log(data);
- })
- .fail(function(data) {
- alert('failed')
- console.log(data);
- })
- })
- sample.append(sampleIdentifier).append(show_datasets_btn).append(datasets_table)
-
- var dataset = $('<p>').append($('<b>').text('DataSet permId: '))
- var datasetPermId = $('<input type="text" name="datasetPermId" size=40>')
- dataset.append(datasetPermId)
-
- var div = $('<div/>')
- div.append(conn_table).append(sample).append(dataset)
-
- // get the canvas for user feedback
- var container = $('#notebook-container')
+ function showDownloadDialog() {
+ // This function gets called after loading the openBIS connections
+ // to make sure we can display the download path provided by the server.
+
+ // show DataSets for Sample identifier/permid
+ var sample = $("<div>")
+ sample.append($('<strong>').text('Sample identfier/permId: '))
+ sample.css('margin-top', '10px')
+ var sampleIdentifier = $('<input type="text" name="sampleIdentifier" size=40 placeholder="sample identifier">')
+ .val(currentSampleIdentifier)
+ var show_datasets_btn = $('<button type="button" class="btn-info btn-xs">show datasets</button>')
+ var datasets_table = $('<div id="dataset_table">')
+ .addClass("output output_scroll")
+ .css('max-height', '10em')
+ show_datasets_btn.click(function () {
+ var connection_name = $('input[name="connection_name"]:checked').val()
+ currentConnection = connection_name
+ currentSampleIdentifier = sampleIdentifier.val()
+ if (!connection_name) {
+ alert('Please choose a connection')
+ return false
+ }
+ if (!currentSampleIdentifier) {
+ alert('Please specify a sample identifier/permId')
+ return false
+ }
+ var settings = {
+ url: env.notebook.base_url + 'openbis/sample/' + connection_name + '/' + encodeURIComponent(currentSampleIdentifier),
+ processData: false,
+ type: 'GET',
+ dataType: 'json',
+ contentType: 'application/json',
+ success: function(data) {
+ show_datasets_table(data, datasets_table)
+ },
+ error: function(data) {
+ console.log(data);
+
+ console.log(data.statusText);
+ alert('Error: ' + data.statusText)
+ }
+ }
+ utils.ajax(settings)
- function downloadDataset () {
- var notebook = IPython.notebook
- var re = /\/notebooks(.*?)$/
- var connection = $('input[name="connection_name"]:checked').val()
- var downloadUrl = env.notebook.base_url + 'openbis/dataset/' + connection + '/' + datasetPermId.val()
+ })
+ sample.append(sampleIdentifier).append(show_datasets_btn).append(datasets_table)
+
+ // dataSetPermId only
+ var dataset = $('<p>')
+ .css('margin-top', '10px')
+ .append($('<b>').text('... or enter DataSet permId directly: '))
+ var datasetPermId = $('<input type="text" name="datasetPermId" size=40 placeholder="dataset permId">')
+ dataset.append(datasetPermId)
+
+ // download path
+ var downloadPath =$('<input type="text" name="downloadPath" size=100>')
+ .val(currentDownloadPath)
+ var path = $('<div>')
+ .append($('<strong>').text('download data to path: '))
+ .append(downloadPath)
+
+ var download_dialog_box = $('<div/>')
+ download_dialog_box.append(conn_table).append(sample).append(dataset).append(path)
+
+ function downloadDataset(permId, path) {
+ var notebook = IPython.notebook
+ var connection_name = $('input[name="connection_name"]:checked').val()
+ var connection_url = $('input[name="connection_name"]:checked').attr('url')
+ var downloadUrl = env.notebook.base_url + 'openbis/dataset/'
+ + connection_name + '/' + permId + '/' + encodeURIComponent(path)
+
+ // get the canvas for user feedback
+ var container = $('#notebook-container')
+
+ var settings = {
+ url: downloadUrl,
+ processData: false,
+ type: 'GET',
+ dataType: 'json',
+ contentType: 'application/json'
+ }
- var settings = {
- url: downloadUrl,
- processData: false,
- type: 'GET',
- dataType: 'json',
- contentType: 'application/json'
+ // download the dataset files
+ utils.ajax(settings)
+ .done(function (data) {
+ // display feedback to user
+ var feedback = '<div class="openbis-feedback alert alert-success alert-dismissible" role="alert">' +
+ '<button type="button" class="close" data-dismiss="alert" aria-label="Close">' +
+ '<span aria-hidden="true">×</span></button>' +
+ data.statusText +
+ '</div>'
+
+ // display feedback
+ $('.openbis-feedback').remove()
+ container.prepend(feedback)
+
+ // write statusText from returned data to notebooks metadata
+ if (typeof notebook.metadata.openbis_connections === 'undefined') {
+ notebook.metadata.openbis_connections = {}
+ }
+ if (typeof notebook.metadata.openbis_connections[connection_url] === 'undefined') {
+ notebook.metadata.openbis_connections[connection_url] = {}
+ }
+ // store metadata about the downloaded files into the notebook-metadata
+ if (data.permId) {
+ notebook.metadata.openbis_connections[connection_url][data.permId] = {
+ "permId": data.permId,
+ "path": data.path,
+ "dataStore": data.dataStore,
+ "location": data.location,
+ "size": data.size,
+ "status": data.statusText
+ }
+ }
+ currentDownloadPath = path
+ })
+ .fail(function (data) {
+ // display feedback to user
+ var feedback =
+ '<div class="openbis-feedback alert alert-danger alert-dismissible" role="alert">' +
+ '<button type="button" class="close" data-dismiss="alert" aria-label="Close"><span aria-hidden="true">×</span></button>' +
+ '<strong>Error: </strong>Dataset was not downloaded.<div>' + data.statusText + '</div></div>'
+
+ // display feedback
+ $('.openbis-feedback').remove()
+ container.prepend(feedback)
+ })
}
- //console.log(IPython.notebook)
- // display preloader during commit and push
- var preloader = '<img class="openbis-feedback" src="https://cdnjs.cloudflare.com/ajax/libs/slick-carousel/1.5.8/ajax-loader.gif">'
- container.prepend(preloader)
- $('.openbis-feedback').remove()
+ function onDownloadClick() {
+ connection_name = $('input[name="connection_name"]:checked').val()
+ if (typeof connection_name === "undefined") {
+ alert('please choose a connection')
+ return false
+ }
- // download the dataset files
- utils.ajax(settings)
- .done( function (data) {
- console.log(data);
- // display feedback to user
- var container = $('#notebook-container')
- var feedback = '<div class="openbis-feedback alert alert-success alert-dismissible" role="alert">' +
- '<button type="button" class="close" data-dismiss="alert" aria-label="Close">' +
- '<span aria-hidden="true">×</span></button>' +
- data.statusText +
- '</div>'
+ if (!selectedPermId) {
+ selectedPermId = datasetPermId.val()
+ }
- // display feedback
- $('.openbis-feedback').remove()
- container.prepend(feedback)
+ if (!selectedPermId) {
+ alert('please select a dataset or provide a permId')
+ return false
+ }
+ downloadDataset(selectedPermId, downloadPath.val())
+ }
- // 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
+ dialog.modal({
+ body: download_dialog_box,
+ title: 'Download openBIS DataSet',
+ buttons: {
+ 'Cancel': {},
+ 'Download': {
+ class: 'btn-primary btn-large',
+ click: onDownloadClick,
}
- })
- .fail( function (data) {
- // display feedback to user
- var feedback =
- '<div class="openbis-feedback alert alert-danger alert-dismissible" role="alert">' +
- '<button type="button" class="close" data-dismiss="alert" aria-label="Close"><span aria-hidden="true">×</span></button>' +
- '<strong>Error: </strong>Dataset was not downloaded.<div>' + data.statusText + '</div></div>'
- console.log(data);
-
- // display feedback
- $('.openbis-feedback').remove()
- container.prepend(feedback)
- })
- }
-
- function onDownloadClick () {
- connection_name = $('input[name="connection_name"]:checked').val()
- if (typeof connection_name === "undefined") {
- alert('please choose a connection')
- return false
- }
- if (!datasetPermId.val()) {
- alert('please provide a permId')
- return false
- }
- downloadDataset()
+ },
+ notebook: env.notebook,
+ keyboard_manager: env.notebook.keyboard_manager
+ })
}
-
- dialog.modal({
- body: div,
- title: 'Download openBIS DataSet',
- buttons: {
- 'Cancel': {},
- 'Download': {
- class: 'btn-primary btn-large',
- click: onDownloadClick,
- }
- },
- notebook: env.notebook,
- keyboard_manager: env.notebook.keyboard_manager
- })
}
}
@@ -232,33 +325,66 @@ define([
icon: 'fa-cloud-upload',
help_index: '',
handler: function (env) {
- var p = $('<p/>').text('Please enter a Sample or DataSet identifier/permId')
- var input = $('<textarea rows="4" cols="72"></textarea>')
- var div = $('<div/>')
- var uploadUrl = env.notebook.base_url + 'openbis/dataset'
+ var conn_table = $('<div id="openbis_connections"/>')
+ getOpenBisConnections(env, conn_table)
+ .done(function (data) {
+ show_available_connections(data, conn_table)
+ })
+ .fail(function (data) {
+ alert(data.status)
+ })
+ var ds_name = $('<input type="text" name="ds_name" size=40 placeholder="name">')
+ var ds_description = $('<input type="text" name="ds_description" size=40 placeholder="description">')
+ var ds_type = $('<input type="text" name="ds_type" size=40 placeholder="type">')
+ var sampleIdentifier = $('<input type="text" name="sampleIdentifier" size=40 placeholder="sample identifier">')
+ .val(currentSampleIdentifier)
+ var ds_files = $('<input type="text" name="files" size=40 placeholder="filenames">')
+
- div.append(p).append(input)
+ var inputs = $('<div>')
+ .css('margin-top', '10px')
+ .append($('<p>').text('Name: ').append(ds_name))
+ .append($('<p>').text('Description: ').append(ds_description))
+ .append($('<p>').text('Type: ').append(ds_type))
+ .append($('<p>').text('Sample: ').append(sampleIdentifier))
+ .append($('<p>').text('Files: ').append(ds_files))
+
+ var uploadDialogBox = $('<div/>').append(conn_table).append(inputs)
// get the canvas for user feedback
var container = $('#notebook-container')
function onOk () {
+ var connection_name = $('input[name="connection_name"]:checked').val()
+ var uploadUrl = env.notebook.base_url + 'openbis/dataset/' + connection_name
+
var notebook = IPython.notebook
- var re = /\/notebooks(.*?)$/
+ var re = /\/notebooks\/(.*?)$/
+ var files = []
var filepath = window.location.pathname.match(re)[1]
- //var payload = {'filename': filepath, 'msg': input.val()}
+ files.push(filepath)
+ if (ds_files.val()) {
+ files.push(ds_files.val())
+ }
+
+ var dataSetInfo = {
+ "name" : ds_name.val(),
+ "description" : ds_description.val(),
+ "type" : ds_type.val(),
+ "files" : files,
+ "sampleIdentifier": sampleIdentifier.val()
+ }
+ console.log(dataSetInfo);
- payload = JSON.stringify(input.val())
var settings = {
- url: commitUrl,
+ url: uploadUrl,
processData: false,
- type: 'PUT',
+ type: 'POST',
dataType: 'json',
- data: payload,
+ data: JSON.stringify(dataSetInfo),
contentType: 'application/json',
success: function (data) {
// display feedback to user
- var container = $('#notebook-container')
var feedback = '<div class="openbis-feedback alert alert-success alert-dismissible" role="alert">' +
'<button type="button" class="close" data-dismiss="alert" aria-label="Close">' +
'<span aria-hidden="true">×</span></button>' +
@@ -293,7 +419,6 @@ define([
container.prepend(feedback)
}
}
- //console.log(IPython.notebook)
// 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">'
@@ -306,8 +431,8 @@ define([
if (IPython.notebook.dirty === true) {
dialog.modal({
- body: 'Please, save the notebook before registering in openBIS.',
- title: 'Action required',
+ body: 'Please save the notebook before uploading it to openBIS.',
+ title: 'Save notebook first',
buttons: {
'Back': {}
},
@@ -317,7 +442,7 @@ define([
}
else {
dialog.modal({
- body: div,
+ body: uploadDialogBox,
title: 'Upload openBIS DataSet',
buttons: {
'Cancel': {},
@@ -334,8 +459,6 @@ define([
}
function _onLoad () {
- // log to console
- //console.info('Loaded Jupyter extension: openbis-jupyter-extension')
// register new action
var download_datasets = IPython.keyboard_manager.actions.register(
fetchDatasetFromOpenBis, 'openbis-dataset-download', 'jupyter-openBIS')
@@ -343,8 +466,6 @@ define([
var upload_datasets = IPython.keyboard_manager.actions.register(
uploadDatasetsToOpenBis, 'openbis-dataset-upload', 'jupyter-openBIS')
- console.info(download_datasets)
- console.info(upload_datasets)
// add button for new action
IPython.toolbar.add_buttons_group([download_datasets, upload_datasets])
}
diff --git a/openbis-connections.yaml-example b/openbis-connections.yaml-example
new file mode 100644
index 0000000000000000000000000000000000000000..d8dfe123d941fe08f38a9d924b335ab678a30832
--- /dev/null
+++ b/openbis-connections.yaml-example
@@ -0,0 +1,11 @@
+connections:
+ - name : local test openBIS instance
+ url : localhost:8443
+ verify_certificates : false
+ username : username
+ password : password
+ - name : productive openBIS instance
+ url : openbis.example.com
+ verify_certificates : true
+ username : username
+ password : password