dialog.js

define([
        "base/js/namespace",
        "base/js/dialog",
        "base/js/utils",
        "jquery"
    ],
    function(IPython, dialog, utils, $, mc) {
        var currentConnection = ''
        var selectedPermId = null
        var currentSampleIdentifier = null
        var currentDownloadPath = null
        var ds_type = document.createElement("SELECT")
        ds_type.className = "select-xs"
        ds_type.id = "dataset_type"

        function show_available_connections (data, conn_table) {
            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']
            titles.forEach( function(item, index) {
                thead_row.insertCell().textContent = item
            })

            tbody = table.createTBody()
            data.connections.forEach( function(item, index, arr) {
                //console.log(item)
                var conn = document.createElement("INPUT")
                conn.type = "radio"
                conn.name = "connection_name"
                conn.value = item.name
                conn.setAttribute("url", item.url)

                // Change the list of available dataset types
                conn.onchange = function() {
                    currentConnection = item.name
                    //ds_type.children().remove()
                    while (ds_type.firstChild) {
                        ds_type.removeChild(ds_type.firstChild);
                    }
                    if (item.ds_types != null) {
                        for (ds_type in item.ds_types) {
                            option = document.createElement("OPTION")
                            option.textContent = ds_type.code
                        }
                    }
                }

                if (item.name === currentConnection) {
                    conn.checked = true
                }
                else {
                    conn.checked = false
                }

                var row = tbody.insertRow()
                row.insertCell().appendChild(conn)
                row.insertCell().textContent = item.name
                row.insertCell().textContent = item.url
                row.insertCell().textContent = item.status
            })

            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")
            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 table = $('<table>').addClass('table-bordered table-striped table-condensed text-nowrap')
            //var thead = $('<thead>')
            //var title_row = $('<tr>')
            //    .append($('<th>')
            //        .text('permId')
            //    )
            //    .append($('<th>')
            //        .text('Type')
            //    )
            //    .append($('<th>')
            //        .text('Experiment')
            //    )
            //    .append($('<th>')
            //        .text('Registration Date')
            //    )
            //    .append($('<th>')
            //        .text('Status')
            //    )
            //    .append($('<th>')
            //        .text('Size')
            //    )
            //title_row.appendTo(thead)
            //thead.appendTo(table)

            data.dataSets.forEach( function(item, index, arr) {
                var permId = document.createElement("INPUT")
                permId.type = "radio"
                permId.name = "permId"
                permId.value = item.permId

                //var permId = $('<input type="radio" name="permId">').attr("value", item.permId)
                permId.onchange = function() {
                    if (this.checked) {
                        selectedPermId = this.value
                    }
                }
                //permId.change(function() {
                //    if ($(this).is(':checked')) {
                //        selectedPermId = this.value
                //    }
                //})

                var tbody = table.createTBody()
                var row = tbody.insertRow()
                row.insertCell().appendChild(permId)
                row.insertCell().textContent = item.type
                row.insertCell().textContent = item.experiment
                row.insertCell().textContent = item.registrationDate
                row.insertCell().textContent = item.status
                row.insertCell().textContent = item.size

                //var row = $('<tr>')
                //    .append(
                //        $('<td>').append(permId).append(' ' + item.permId)
                //    )
                //    .append($('<td>')
                //        .text(item.type)
                //    )
                //    .append($('<td>')
                //        .text(item.experiment)
                //    )
                //    .append($('<td>')
                //        .text(item.registrationDate)
                //    )
                //    .append($('<td>')
                //        .text(item.status)
                //    )
                //    .append($('<td>')
                //        .text(item.size)
                //    )
                //table.append(row)
            })

            while (datasets_table.firstChild) {
                datasets_table.removeChild(datasets_table.firstChild);
            }
            datasets_table.appendChild(table)

            //datasets_table.innerHTML = ''
            //datasets_table.innerHTML = table
            //datasets_table.empty().append(table)

        }

        function getOpenBisConnections(env, conn_table) {
             var connectionsUrl = env.notebook.base_url + 'openbis/conn'
             var settings = {
                 url: connectionsUrl,
                 processData: false,
                 type: 'GET',
                 dataType: 'json',
                 contentType: 'application/json'
             }
             return utils.ajax(settings)
        }

        var fetchDatasetFromOpenBis = {
            help: 'Download a openBIS dataset to your local harddrive',
            icon: 'fa-download',
            help_index: '',
            handler: function (env) {
                //var conn_table = $('<div id="openbis_connections"/>')
                var conn_table = document.createElement("DIV")
                conn_table.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()
                    })

                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 = document.createElement("DIV")
                    var title = document.createElement("STRONG")
                    title.textContent = "Sample identfier/permId: "
                    sample.appendChild(title)
                    sample.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 settings = {
                        //    url: env.notebook.base_url + 'openbis/sample/' + connection_name + '/' + encodeURIComponent(currentSampleIdentifier),
                        //    processData: false,
                        //    type: 'GET',
                        //    dataType: 'json',
                        //    contentType: 'application/json'
                        //}
                        var url = env.notebook.base_url + 'openbis/sample/' + connection_name + '/' + encodeURIComponent(currentSampleIdentifier)

                        var xhttp = new XMLHttpRequest()
                        xhttp.onreadystatechange = function() {
                            var data = JSON.parse(this.responseText)
                            //if (this.readyState == 4 && this.status == 200) {
                            if (this.status == 200) {
                                show_datasets_table(data, datasets_table)
                            }
                            else {
                                alert("Error:" + data.statusText)
                            }
                        };
                        xhttp.open("GET", url, true);
                        xhttp.send();

                        //utils.ajax(settings)
                        //    .done(function(data) {
                        //        show_datasets_table(data, datasets_table)
                        //    })
                        //    .fail(function(data) {
                        //        alert('Error:' + data.statusText)
                        //    })
                    }
                    sample.appendChild(sampleIdentifier)
                    sample.appendChild(show_datasets_btn)
                    //sample.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(dataset_direct)
                    download_dialog_box.appendChild(path)

                    function downloadDataset(selected_conn, permId, path) {
                        var notebook = IPython.notebook
                        var connection_name = selected_conn.value()
                        var connection_url  = selected_conn.getAttribute("url")
                        //var connection_name = $('input[name="connection_name"]:checked').val()
                        //var connection_url = $('input[name="connection_name"]:checked').attr('url')
                        var downloadUrl = env.notebook.base_url + 'openbis/dataset/'
                            + connection_name + '/' + permId + '/' + encodeURIComponent(path)

                        // get the canvas for user feedback
                        //var container = $('#notebook-container')
                        var container = document.getElementById('notebook-container')

                        var settings = {
                            url: downloadUrl,
                            processData: false,
                            type: 'GET',
                            dataType: 'json',
                            contentType: 'application/json'
                        }

                        var close = document.createElement("BUTTON")
                        close.className = "close"
                        close.setAttribute("data-dismiss", "alert")
                        close.setAttribute("aria-label", "Close")

                        var x = document.createElement("SPAN")
                        x.setAttribute("aria-hidden", true)
                        x.textContent = "&times;"

                        // remove existing feedbacks
                        for (element in document.getElementsByClassName("openbis-feedback")) {
                            element.remove()
                        }

                        // download the dataset files
                        utils.ajax(settings)
                            .done(function (data) {
                                // display feedback to user
                                var feedback = document.createElement( "DIV" )
                                feedback.className = "openbis-feedback alert alert-success alert-dismissible"
                                feedback.setAttribute("role","alert")
                                feedback.append(data.statusText)

                                close.appendChild(x)
                                feedback.appendChild(close)


                                //var feedback = '<div class="openbis-feedback alert alert-success alert-dismissible" role="alert">' +
                                //    '<button type="button" class="close" data-dismiss="alert" aria-label="Close">' +
                                //    '<span aria-hidden="true">&times;</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 = document.createElement( "DIV" )
                                feedback.className = "openbis-feedback alert alert-danger alert-dismissible"
                                feedback.setAttribute("role","alert")
                                feedback.innerHTML = "<strong>Error: </strong>Dataset was not downloaded.<div>"
                                                   + data.statusText
                                                   + "</div>"

                                //var feedback =
                                //    '<div class="openbis-feedback alert alert-danger alert-dismissible" role="alert">' +
                                //    '<button type="button" class="close" data-dismiss="alert" aria-label="Close"><span aria-hidden="true">&times;</span></button>' +
                                //    '<strong>Error: </strong>Dataset was not downloaded.<div>' + data.statusText + '</div></div>'

                                close.appendChild(x)
                                feedback.appendChild(close)
                                container.prepend(feedback)
                            })
                    }

                    function onDownloadClick() {
                        var selected_conn = document.querySelector('input[name=connection_name]:checked')
                        //connection_name = $('input[name="connection_name"]:checked').val()
                        if (! selected_conn) {
                            alert('Please choose a connection')
                            return false
                        }

                        if (!selectedPermId) {
                            selectedPermId = datasetPermId.val()
                        }

                        if (!selectedPermId) {
                            alert('please select a dataset or provide a permId')
                            return false
                        }

                        if (!downloadPath.value)
                        downloadDataset(selected_conn, selectedPermId, downloadPath.val())
                    }

                    dialog.modal({
                        body: download_dialog_box,
                        title: 'Download openBIS DataSet',
                        buttons: {
                            'Cancel': {},
                            'Download': {
                                class: 'btn-primary btn-large',
                                click: onDownloadClick,
                            }
                        },
                        notebook: env.notebook,
                        keyboard_manager: env.notebook.keyboard_manager
                    })
                }
            }
        }

        var uploadDatasetsToOpenBis = {
            help: 'upload Notebook and Data to openBIS',
            icon: 'fa-cloud-upload',
            help_index: '',
            handler: function (env) {
                var conn_table = document.createElement("DIV")
                conn_table.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 ds_type = $('<select class="form-control select-xs" id="dataset_type">')
                var sampleIdentifier = $('<input type="text" name="sampleIdentifier" size=40 placeholder="sample identifier">')
                    .val(currentSampleIdentifier)
                var ds_files = $('<input type="text" name="files" size=40 placeholder="filenames">')

                var inputs = $('<div>')
                    .css('margin-top', '10px')
                    .append($('<p>').text('Name: ').append(ds_name))
                    .append($('<p>').text('Description: ').append(ds_description))
                    .append($('<p>').text('DatasetType: ').append(ds_type))
                    .append($('<p>').text('Sample: ').append(sampleIdentifier))
                    .append($('<p>').text('Files: ').append(ds_files))

                var 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 files = []
                    var filepath = window.location.pathname.match(re)[1]
                    files.push(filepath)
                    if (ds_files.val()) {
                        files.push(ds_files.val())
                    }

                    var dataSetInfo = {
                        "name"            : ds_name.val(),
                        "description"     : ds_description.val(),
                        "type"            : ds_type.val(),
                        "files"           : files,
                        "sampleIdentifier": sampleIdentifier.val()
                    }
                    //console.log(dataSetInfo);

                    var settings = {
                        url: uploadUrl,
                        processData: false,
                        type: 'POST',
                        dataType: 'json',
                        data: JSON.stringify(dataSetInfo),
                        contentType: 'application/json',
                        success: function (data) {
                            // display feedback to user
                            var feedback = '<div class="openbis-feedback alert alert-success alert-dismissible" role="alert">' +
                                '<button type="button" class="close" data-dismiss="alert" aria-label="Close">' +
                                '<span aria-hidden="true">&times;</span></button>' +
                                data.statusText +
                                '</div>'

                            // display feedback
                            $('.openbis-feedback').remove()
                            container.prepend(feedback)

                            // write statusText from returned data to notebooks metadata
                            if ( typeof notebook.metadata.openbis === 'undefined') {
                                notebook.metadata.openbis = {}
                            }
                            if ( typeof notebook.metadata.openbis.permIds === 'undefined' ) {
                                notebook.metadata.openbis.permIds = {}
                            }
                            if ( data.permId ) {
                                notebook.metadata.openbis.permIds[data.permId] = data.statusText
                            }

                        },
                        error: function (data) {
                            // display feedback to user
                            var feedback =
                                '<div class="openbis-feedback alert alert-danger alert-dismissible" role="alert">' +
                                '<button type="button" class="close" data-dismiss="alert" aria-label="Close"><span aria-hidden="true">&times;</span></button>' +
                                '<strong>Warning!</strong> Something went wrong.<div>' + data.statusText + '</div></div>'

                            // display feedback
                            $('.openbis-feedback').remove()
                            container.prepend(feedback)
                        }
                    }

                    // display preloader during commit and push
                    var preloader = '<img class="openbis-feedback" src="https://cdnjs.cloudflare.com/ajax/libs/slick-carousel/1.5.8/ajax-loader.gif">'
                    container.prepend(preloader)
                    $('.openbis-feedback').remove()

                    // commit and push
                    utils.ajax(settings)
                }

                if (IPython.notebook.dirty === true) {
                    dialog.modal({
                        body: 'Please save the notebook before uploading it to openBIS.',
                        title: 'Save notebook first',
                        buttons: {
                            'Back': {}
                        },
                        notebook: env.notebook,
                        keyboard_manager: env.notebook.keyboard_manager
                    })
                }
                else {
                    dialog.modal({
                        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
                    })
                }
            }
        }

        function _onLoad () {
            // register new action
            var download_datasets = IPython.keyboard_manager.actions.register(
                fetchDatasetFromOpenBis, 'openbis-dataset-download', 'jupyter-openBIS')

            var upload_datasets = IPython.keyboard_manager.actions.register(
                uploadDatasetsToOpenBis, 'openbis-dataset-upload', 'jupyter-openBIS')

            // add button for new action
            IPython.toolbar.add_buttons_group([download_datasets, upload_datasets])
        }

        return {load_ipython_extension: _onLoad}
    })