define([
"base/js/dialog",
"base/js/utils",
"jquery",
"./state",
"./common",
],
function (dialog, utils, $, state, common) {
var errorElements = { }
function createErrorElement(name) {
var element = document.createElement("STRONG")
element.textContent = ""
element.style.marginLeft = "8px"
element.style.color = "red"
errorElements[name] = element
return element
}
function cleanErrors() {
Object.keys(errorElements).forEach(key => errorElements[key].textContent="")
}
var spinner = document.createElement("IMG")
spinner.className="openbis-feedback"
spinner.src=""
function showSpinner() {
spinner.src="https://cdnjs.cloudflare.com/ajax/libs/slick-carousel/1.5.8/ajax-loader.gif"
}
function hideSpinner() {
spinner.src=""
}
function get_file_list(env, container) {
var url = env.notebook.base_url + 'general/filelist'
fetch(url)
.then( function(response) {
if (response.ok) {
response.json()
.then(function(data){
var values = Object.keys(data.files)
values.sort()
state.fileCheckboxes = createSelectTable(values, container, false, state.selectedFiles)
})
}
else {
console.error(response.status)
}
})
}
function get_dataset_list(env, container) {
console.log(env.notebook.metadata.datasets)
var datasets = env.notebook.metadata.datasets
if (datasets != null) {
var values = Object.keys(datasets)
values.sort()
state.datasetCheckboxes = createSelectTable(values, container, true, state.unselectedDatasets)
}
}
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) {
var change_input_fields = function () {
hideSpinner()
cleanErrors()
var oldType = state.uploadDataSetType
if (oldType != null && !(oldType in state.uploadDataSetTypes)) {
state.uploadDataSetTypes[oldType] = {}
}
state.uploadDataSetType = dataset_types.options[dataset_types.selectedIndex].value
// remove existing input fields
while (input_fields.firstChild) {
var element = input_fields.firstChild
if (element.nodeName === "INPUT" && state.uploadDataSetType != null) {
state.uploadDataSetTypes[oldType][element.name] = element.value
}
input_fields.removeChild(element)
}
// for every property assignment, create an input field.
for (pa of dts[dataset_types.selectedIndex].propertyAssignments) {
var input_title = document.createElement("STRONG")
input_title.textContent = pa.mandatory ? pa.label + " (mandatory)" : pa.label
var input_error = createErrorElement('prop.'+pa.code)
var input_field = document.createElement("INPUT")
input_field.type = "text"
input_field.name = pa.code
input_field.placeholder = pa.description ? pa.description : pa.label
input_field.size = 90
input_field.style.width="100%"
var mem = state.uploadDataSetTypes[dts[dataset_types.selectedIndex].code]
if (mem == null) {
mem = {}
}
input_field.value = pa.code in mem ? mem[pa.code] : ""
input_fields.appendChild(input_title)
input_fields.appendChild(input_error)
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);
}
var index = 0
var selectedIndex = -1
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)
if (dt.code === state.uploadDataSetType) {
selectedIndex = index
}
index++
}
dataset_types.selectedIndex = selectedIndex === -1 ? 0 : selectedIndex
// 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 createSelectTable(values, container, checked, overrides) {
var table = document.createElement("TABLE")
table.className = 'table-bordered table-striped table-condensed'
table.style.width = "100%"
var body = table.createTBody()
var checkboxes = []
values.forEach( value => {
var row = body.insertRow()
var checkbox = document.createElement("INPUT")
checkbox.type = "checkbox"
checkbox.value = value
checkbox.checked = overrides.includes(value) ? !checked : checked
checkboxes.push(checkbox)
row.insertCell().appendChild(checkbox)
var valueCell = row.insertCell()
valueCell.textContent = value
valueCell.style.width = "100%"
})
container.appendChild(table)
return checkboxes
}
return {
help: 'upload Notebook and Data to openBIS',
icon: 'fa-upload',
help_index: '',
handler: function (env) {
var main_error = createErrorElement('main')
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"
dataset_types.style.marginLeft = 0
var input_fields = document.createElement("DIV")
input_fields.setAttribute("id", "upload-input-fields");
getDatasetTypes(env, state.connection.name, dataset_types, input_fields)
var sample_title = document.createElement("STRONG")
sample_title.textContent = "Sample Identifier"
var sample_error = createErrorElement('sampleIdentifier')
var sampleIdentifier = document.createElement("INPUT")
sampleIdentifier.type = "text"
sampleIdentifier.name = 'sampleIdentifier'
sampleIdentifier.placeholder = "Sample Identifier or permId"
sampleIdentifier.value = state.uploadEntityIdentifier
sampleIdentifier.size = "90"
sampleIdentifier.style.width="100%"
var ds_title = document.createElement("STRONG")
ds_title.textContent = "DataSets"
var dataSetListContainer = document.createElement("DIV")
dataSetListContainer.style.height="150px"
dataSetListContainer.style.overflow="scroll"
get_dataset_list(env, dataSetListContainer)
var files_title = document.createElement("STRONG")
files_title.textContent = "Files"
var fileListContainer = document.createElement("DIV")
fileListContainer.style.height="150px"
fileListContainer.style.overflow="scroll"
get_file_list(env, fileListContainer)
var inputs = document.createElement("DIV")
inputs.style.marginTop = '10px'
inputs.appendChild(main_error)
inputs.appendChild(spinner)
inputs.appendChild(document.createElement("BR"))
inputs.appendChild(dst_title)
inputs.appendChild(dataset_types)
inputs.appendChild(input_fields)
inputs.appendChild(sample_title)
inputs.appendChild(sample_error)
inputs.appendChild(sampleIdentifier)
inputs.appendChild(ds_title)
inputs.appendChild(dataSetListContainer)
inputs.appendChild(files_title)
inputs.appendChild(fileListContainer)
var uploadDialogBox = $('<div/>').append(inputs)
function saveState() {
state.uploadDataSetTypes[state.uploadDataSetType] = {}
for (element of input_fields.children) {
if (element.nodeName === "INPUT" && state.uploadDataSetType != null) {
state.uploadDataSetTypes[state.uploadDataSetType][element.name] = element.value
}
}
state.uploadEntityIdentifier = sampleIdentifier.value
state.unselectedDatasets = state.datasetCheckboxes.filter(cb => !cb.checked).map(cb => cb.value)
state.selectedFiles = state.fileCheckboxes.filter(cb => cb.checked).map(cb => cb.value)
}
function onOk() {
var connection_name = state.connection.name
if (!connection_name) {
alert("No connection selected")
return false
}
var uploadUrl = env.notebook.base_url + 'openbis/dataset/' + connection_name
var notebook = IPython.notebook
var files = state.fileCheckboxes.filter(cb => cb.checked).map(cb => cb.value)
var re = /\/notebooks\/(.*?)$/
var filepath = window.location.pathname.match(re)[1]
files.push(filepath)
var props = {}
for (input of $('#upload-input-fields').find('input')) {
props[input.name] = input.value
}
var dataSetInfo = {
"type": dataset_types.value,
"files": files,
"parents": state.datasetCheckboxes.filter(cb => cb.checked).map(cb => cb.value),
"sampleIdentifier": sampleIdentifier.value,
"props": props
}
var settings = {
url: uploadUrl,
processData: false,
type: 'POST',
dataType: 'json',
data: JSON.stringify(dataSetInfo),
contentType: 'application/json',
success: function (data) {
saveState()
$('div.modal').remove()
$('div.modal-backdrop').remove()
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) {
hideSpinner()
if ("errors" in data.responseJSON) {
var errors = data.responseJSON.errors
for (error of errors) {
let key, value
Object.keys(error).forEach(k => {
key = k
value = error[k]
})
errorElements[key in errorElements ? key : "main"].textContent = value
}
} else {
errorElements["main"].textContent = "Server error"
}
}
}
showSpinner()
cleanErrors()
utils.ajax(settings)
return false
}
function onCancel() {
saveState()
return true
}
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': {
click: onCancel
},
'Upload': {
class: 'btn-primary btn-large',
click: onOk
}
},
notebook: env.notebook,
keyboard_manager: env.notebook.keyboard_manager
})
}
}
}
}
)