diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3e27991ebf8822ddb357c4dbc44c51e54e237a3d..4467ece33e62e9f29dac413c1828847ed9b766c3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,17 @@
+## new in jupyter-openbis-extension 0.4.0
+
+- made it compatible to pybis-1.9.x
+- minor bugfixes and improvements
+
+## new in jupyter-openbis-extension 0.3.0
+
+- removed search-as-you-type feature, as it is not mature yet
+- fixed notebook path problem in special environments
+- improved download path
+- connection dialog: show that connection is being established
+- upload dialog: improved file chooser
+- upload dialog: save notebook automatically before upload
+
## new in jupyter-openbis-extension 0.2.4
- improved entity selection
diff --git a/jupyter-openbis-extension/__init__.py b/jupyter-openbis-extension/__init__.py
index d3d298723cee99d050e7464c5bac6a4660c7483d..c4c2f3ea1bd3b4b9375e676f33f3c6fd73ebcab2 100644
--- a/jupyter-openbis-extension/__init__.py
+++ b/jupyter-openbis-extension/__init__.py
@@ -1,7 +1,7 @@
name = 'jupyter-openbis-extension.server'
__author__ = 'Swen Vermeul'
__email__ = 'swen@ethz.ch'
-__version__ = '0.2.4'
+__version__ = '0.4.0'
def _jupyter_server_extension_paths():
return [{
diff --git a/jupyter-openbis-extension/connection.py b/jupyter-openbis-extension/connection.py
index be36cbb321ce71e2b164d9d06762937d18912706..557bc4966487975ee684799b4d2e2473fe4264ac 100644
--- a/jupyter-openbis-extension/connection.py
+++ b/jupyter-openbis-extension/connection.py
@@ -12,6 +12,7 @@ def register_connection(connection_info):
verify_certificates = connection_info.get('verify_certificates', False),
username = connection_info.get('username'),
password = connection_info.get('password'),
+ http_only = connection_info.get('http_only', False),
status = 'not connected',
)
openbis_connections[conn.name] = conn
@@ -32,7 +33,8 @@ class OpenBISConnection:
openbis = Openbis(
url = self.url,
- verify_certificates = self.verify_certificates
+ verify_certificates = self.verify_certificates,
+ allow_http_but_do_not_use_this_in_production_and_only_within_safe_networks = self.http_only
)
self.openbis = openbis
self.status = "not connected"
@@ -71,6 +73,14 @@ class OpenBISConnection:
class OpenBISConnections(IPythonHandler):
+ def _notebook_dir(self):
+ notebook_dir = os.getcwd()
+ if 'SingleUserNotebookApp' in self.config and 'notebook_dir' in self.config.SingleUserNotebookApp:
+ notebook_dir = self.config.SingleUserNotebookApp.notebook_dir
+ elif 'notebook_dir' in self.config.NotebookApp:
+ notebook_dir = self.config.NotebookApp.notebook_dir
+ return notebook_dir
+
def post(self):
"""create a new connection
@@ -96,9 +106,9 @@ class OpenBISConnections(IPythonHandler):
connections.append(conn.get_info())
self.write({
- 'status' : 200,
- 'connections': connections,
- 'cwd' : os.getcwd()
+ 'status' : 200,
+ 'connections' : connections,
+ 'notebook_dir' : self._notebook_dir()
})
return
@@ -107,6 +117,14 @@ class OpenBISConnectionHandler(IPythonHandler):
"""Handle the requests to /openbis/conn
"""
+ def _notebook_dir(self):
+ notebook_dir = os.getcwd()
+ if 'SingleUserNotebookApp' in self.config and 'notebook_dir' in self.config.SingleUserNotebookApp:
+ notebook_dir = self.config.SingleUserNotebookApp.notebook_dir
+ elif 'notebook_dir' in self.config.NotebookApp:
+ notebook_dir = self.config.NotebookApp.notebook_dir
+ return notebook_dir
+
def put(self, connection_name):
"""reconnect to a current connection
:return: an updated connection object
@@ -136,11 +154,16 @@ class OpenBISConnectionHandler(IPythonHandler):
"reason": "Incorrect username or password for {}".format(connection_name)
})
return
+ except Exception:
+ self.set_status(500)
+ self.write({
+ "reason": "General Network Error"
+ })
self.write({
'status' : 200,
- 'connection': conn.get_info(),
- 'cwd' : os.getcwd()
+ 'connection' : conn.get_info(),
+ '' : self._notebook_dir()
})
def get(self, connection_name):
@@ -159,9 +182,10 @@ class OpenBISConnectionHandler(IPythonHandler):
conn.check_status()
self.write({
- 'status' : 200,
- 'connection': conn.get_info(),
- 'cwd' : os.getcwd()
+ 'status' : 200,
+ 'connection' : conn.get_info(),
+ 'noteboook_dir' : self._notebook_dir()
})
return
+
diff --git a/jupyter-openbis-extension/dataset.py b/jupyter-openbis-extension/dataset.py
index 91c6a89488dead78c42bef4fba4292b6122bfdf3..884c519c1a5159ab260f73208b55dae2dc3e0069 100644
--- a/jupyter-openbis-extension/dataset.py
+++ b/jupyter-openbis-extension/dataset.py
@@ -6,7 +6,6 @@ from .connection import openbis_connections
class DataSetDownloadHandler(IPythonHandler):
"""Handle the requests for /openbis/dataset/connection/permId"""
-
def download_data(self, conn, permId, downloadPath=None):
if not conn.is_session_active():
try:
@@ -46,6 +45,7 @@ class DataSetDownloadHandler(IPythonHandler):
'dataStore' : dataset.dataStore,
'location' : dataset.physicalData.location,
'size' : dataset.physicalData.size,
+ 'files' : dataset.file_list,
'statusText': 'Data for DataSet {} was successfully downloaded to: {}.'.format(dataset.permId, path)
})
@@ -69,6 +69,15 @@ class DataSetDownloadHandler(IPythonHandler):
class DataSetTypesHandler(IPythonHandler):
def get(self, **params):
"""Handle a request to /openbis/datasetTypes/connection_name
+ This meta-metadata is used in the dataset upload dialog (uploadDialog.js)
+ to check data directly in the UI
+
+ Returns all datasetTypes of a given connection
+ - with all assigned properties
+ - with some details about the property types
+ - with the vocabulary, if exists
+
+ The result will be cached, as it is a costly operation with many fetches
"""
try:
@@ -80,26 +89,44 @@ class DataSetTypesHandler(IPythonHandler):
})
return
+ if getattr(conn, 'dataset_types', False):
+ self.write({
+ "dataSetTypes": conn.dataset_types
+ })
+ return
+
try:
dataset_types = conn.openbis.get_dataset_types()
- dts = dataset_types.df.to_dict(orient='records')
-
- # get property assignments for every dataset-type
- # and add it to the dataset collection
- for dt in dts:
- dataset_type = conn.openbis.get_dataset_type(dt['code'])
- pa = dataset_type.get_propertyAssignments(including_vocabulary=True)
- pa_dicts = pa.to_dict(orient='records')
- for pa_dict in pa_dicts:
- if pa_dict['dataType'] == 'CONTROLLEDVOCABULARY':
- terms = conn.openbis.get_terms(pa_dict['vocabulary']['code'])
- pa_dict['terms'] = terms.df[['code','label','description','official','ordinal']].to_dict(orient='records')
- dt['propertyAssignments'] = pa_dicts
+ # get all dataset types
+ ds_type_dicts = []
+ for dt in conn.openbis.get_dataset_types():
+ dt_dict = dt.attrs.all()
+ # get property assignments for every dataset-type
+ # and add them in the key «propertyAssignments»
+ pas = dt.get_property_assignments()
+ pa_dicts = pas.df[['propertyType','mandatory','ordinal','section']].to_dict(orient='records')
+ dt_dict['propertyAssignments'] = pa_dicts
+
+ for pa_dict in pa_dicts:
+ # add a few more attributes to the property assignments
+ pt = conn.openbis.get_property_type(pa_dict['propertyType'])
+ pa_dict['code'] = pt.code
+ pa_dict['label'] = pt.label
+ pa_dict['description'] = pt.description
+ pa_dict['dataType'] = pt.dataType
+ # add vocabulary, if exists, as key «terms»
+ if pt.dataType == 'CONTROLLEDVOCABULARY':
+ terms = conn.openbis.get_terms(pt.vocabulary)
+ terms_dict = terms.df[['code','label','description','official','ordinal']].to_dict(orient='records')
+ pa_dict['terms'] = terms_dict
+
+ ds_type_dicts.append(dt_dict)
self.write({
- "dataSetTypes": dts
+ "dataSetTypes": ds_type_dicts
})
+ conn.dataset_types = ds_type_dicts
return
except Exception as e:
@@ -114,6 +141,14 @@ class DataSetTypesHandler(IPythonHandler):
class DataSetUploadHandler(IPythonHandler):
"""Handle the POST requests for /openbis/dataset/connection_name"""
+ def _notebook_dir(self):
+ notebook_dir = os.getcwd()
+ if 'SingleUserNotebookApp' in self.config and 'notebook_dir' in self.config.SingleUserNotebookApp:
+ notebook_dir = self.config.SingleUserNotebookApp.notebook_dir
+ elif 'notebook_dir' in self.config.NotebookApp:
+ notebook_dir = self.config.NotebookApp.notebook_dir
+ return notebook_dir
+
def upload_data(self, conn, data):
if not conn.is_session_active():
try:
@@ -165,13 +200,15 @@ class DataSetUploadHandler(IPythonHandler):
})
filenames = []
+ notebook_dir = self._notebook_dir()
for filename in data.get('files'):
filename = unquote(filename)
- if os.path.isfile(filename):
- filenames.append(filename)
+ full_filename_path = os.path.join(notebook_dir, filename)
+ if os.path.isfile(full_filename_path):
+ filenames.append(full_filename_path)
else:
errors.append({
- "file": "File not found: {}".format(filename)
+ "file": "File not found: {}".format(full_filename_path)
})
try:
@@ -183,9 +220,9 @@ class DataSetUploadHandler(IPythonHandler):
files = filenames,
)
except Exception as e:
- print(e)
- errors.append({
- "create": 'Error while creating the dataset: {}'.format(e)
+ self.set_status(500)
+ self.write({
+ "reason": 'Error while creating the dataset: {}'.format(e)
})
# try to set the properties
@@ -249,34 +286,3 @@ class DataSetUploadHandler(IPythonHandler):
self.upload_data(conn=conn,data=data)
-class FileListHandler(IPythonHandler):
-
- def get(self, **params):
- """
- Returns the file list of the current working directory
-
- :param params:
- :return: dictionary of files, key is the fully qualified name,
- value is the relative name (for display)
- """
-
- cwd = os.getcwd()
- files = {}
- for (dirpath, dirnames, filenames) in os.walk(cwd):
- if filenames:
- for filename in filenames:
- # ignore hidden files
- if filename.startswith('.'):
- continue
- # ignore hidden folders
- if os.path.relpath(dirpath) != '.' \
- and os.path.relpath(dirpath).startswith('.'):
- continue
- fqn = os.path.join(dirpath, filename)
- files[fqn] = os.path.relpath(fqn, cwd)
-
- self.set_status(200)
- self.write({
- "files": files
- })
-
diff --git a/jupyter-openbis-extension/server.py b/jupyter-openbis-extension/server.py
index 97d4909c5b85e9b1b1b5358257a6e933b0599a0b..6d95bd59f0cf163c1bc92f74ede90df13e633634 100644
--- a/jupyter-openbis-extension/server.py
+++ b/jupyter-openbis-extension/server.py
@@ -3,7 +3,7 @@ import os
import yaml
from .connection import OpenBISConnections, OpenBISConnectionHandler, register_connection
-from .dataset import DataSetTypesHandler, DataSetDownloadHandler, DataSetUploadHandler, FileListHandler
+from .dataset import DataSetTypesHandler, DataSetDownloadHandler, DataSetUploadHandler
from .sample import SampleHandler
@@ -48,6 +48,7 @@ def load_jupyter_server_extension(nb_server_app):
filename = 'openbis-connections.yaml'
)
+
for connection_info in connections:
conn = register_connection(connection_info)
print("Registered: {}".format(conn.url))
@@ -66,14 +67,6 @@ def load_jupyter_server_extension(nb_server_app):
host_pattern = '.*$'
base_url = web_app.settings['base_url']
- # get the file list
- web_app.add_handlers(
- host_pattern,
- [(url_path_join( base_url, '/general/filelist'),
- FileListHandler
- )]
- )
-
# DataSet download
web_app.add_handlers(
@@ -139,3 +132,4 @@ def load_jupyter_server_extension(nb_server_app):
)
+
diff --git a/jupyter-openbis-extension/static/common.js b/jupyter-openbis-extension/static/common.js
index 15280a1e178c749e5e17292270e226bd061452ca..edcb4af10533d72158d37de5d428a2d27025c3a5 100644
--- a/jupyter-openbis-extension/static/common.js
+++ b/jupyter-openbis-extension/static/common.js
@@ -39,9 +39,18 @@ define([
return "";
}
+ function createErrorElement() {
+ var element = document.createElement("STRONG")
+ element.textContent = ""
+ element.style.marginLeft = "8px"
+ element.style.color = "red"
+ return element
+ }
+
return {
createFeedback: createFeedback,
- getCookie: getCookie
+ getCookie: getCookie,
+ createErrorElement: createErrorElement
}
}
)
\ No newline at end of file
diff --git a/jupyter-openbis-extension/static/connectionDialog.js b/jupyter-openbis-extension/static/connectionDialog.js
index 40c88225a504b0971efb6bb05afcbed4a8c652da..c8d01ab61e699f759c8569df0dea540df3242bf2 100644
--- a/jupyter-openbis-extension/static/connectionDialog.js
+++ b/jupyter-openbis-extension/static/connectionDialog.js
@@ -7,34 +7,35 @@ define(
],
function (dialog, $, state, connections) {
- var currentDownloadPath = null
+ let currentDownloadPath = null;
function show_available_connections(env, data, conn_table) {
+
if (!currentDownloadPath) {
currentDownloadPath = data.cwd
}
- var table = document.createElement("TABLE")
+ let 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']
+ let thead = table.createTHead();
+ let thead_row = thead.insertRow(0)
+ let titles = ['', 'Name', 'URL', 'Status', 'Username / Password']
for (title of titles) {
thead_row.insertCell().textContent = title
}
tbody = table.createTBody()
- var getConnectionByName = function(name) {
- for (connection of data.connections) {
- if(connection.name === name) {
- return connection;
- }
- }
- }
-
+ let getConnectionByName = function (name) {
+ for (connection of data.connections) {
+ if (connection.name === name) {
+ return connection;
+ }
+ }
+ };
+
for (connection of data.connections) {
- var conn = document.createElement("INPUT")
+ let conn = document.createElement("INPUT")
conn.type = "radio"
conn.name = "connection_name"
conn.value = connection.name
@@ -46,14 +47,28 @@ define(
state.connection.candidateDTO = getConnectionByName(state.connection.candidateName);
}
- var row = tbody.insertRow()
+ let row = tbody.insertRow()
row.insertCell().appendChild(conn)
- row.insertCell().textContent = connection.name
- row.insertCell().textContent = connection.url
+ let nameCell = row.insertCell()
+ nameCell.textContent = connection.name
+ nameCell.onclick = function () {
+ let radio = this.parentElement.firstElementChild.firstElementChild
+ radio.checked = 1
+ state.connection.candidateName = radio.value
+ state.connection.candidateDTO = getConnectionByName(state.connection.candidateName);
+ }
+ let urlCell = row.insertCell()
+ urlCell.textContent = connection.url
+ urlCell.onclick = function () {
+ let radio = this.parentElement.firstElementChild.firstElementChild
+ radio.checked = 1
+ state.connection.candidateName = radio.value
+ state.connection.candidateDTO = getConnectionByName(state.connection.candidateName);
+ }
- var status_cell = row.insertCell()
+ let status_cell = row.insertCell()
- var status_badge = document.createElement("SPAN")
+ let status_badge = document.createElement("SPAN")
status_badge.id = connection.name + "-badge"
status_badge.textContent = connection.status
if (connection.status === "connected") {
@@ -63,31 +78,33 @@ define(
}
status_cell.appendChild(status_badge)
- var username = document.createElement("INPUT")
+ let 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")
+ let 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")
+ let 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")
+ let form_data = new FormData(this)
+ let status_badge = document.getElementById(this.id + "-badge")
+ status_badge.textContent = "connecting..."
+ status_badge.className = "label label-warning"
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)
}
@@ -114,7 +131,7 @@ define(
}
- var connect_button = document.createElement("BUTTON")
+ let connect_button = document.createElement("BUTTON")
connect_button.className = "btn btn-primary btn-xs"
connect_button.textContent = "connect"
@@ -122,17 +139,24 @@ define(
pwform.appendChild(password)
pwform.appendChild(connect_button)
- var cell = row.insertCell()
- cell.appendChild(pwform)
+ let pwCell = row.insertCell()
+ pwCell.appendChild(pwform)
+
+ pwCell.onclick = function () {
+ let radio = this.parentElement.firstElementChild.firstElementChild
+ radio.checked = 1
+ state.connection.candidateName = radio.value
+ state.connection.candidateDTO = getConnectionByName(state.connection.candidateName);
+ }
}
// add row for new connection
- var row = tbody.insertRow()
+ let row = tbody.insertRow()
- var conn_form = document.createElement("FORM")
+ let conn_form = document.createElement("FORM")
conn_form.id = "new_connection"
conn_form.onsubmit = function (event) {
- var inputs = document.querySelectorAll("input[form=new_connection]")
+ let inputs = document.querySelectorAll("input[form=new_connection]")
data = {}
for (input of inputs) {
@@ -155,7 +179,7 @@ define(
})
return false
}
- var conn_name = document.createElement("INPUT")
+ let conn_name = document.createElement("INPUT")
conn_name.type = "input"
conn_name.name = "connection_name"
conn_name.setAttribute("form", conn_form.id)
@@ -163,7 +187,7 @@ define(
row.insertCell().appendChild(conn_form)
row.insertCell().appendChild(conn_name)
- var conn_url = document.createElement("INPUT")
+ let conn_url = document.createElement("INPUT")
conn_url.type = "input"
conn_url.name = "url"
conn_url.setAttribute("form", conn_form.id)
@@ -171,30 +195,68 @@ define(
row.insertCell().appendChild(conn_url)
row.insertCell()
- var username = document.createElement("INPUT")
+ let 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")
+ let 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")
+ let create_btn = document.createElement("BUTTON")
create_btn.setAttribute("form", conn_form.id)
create_btn.textContent = "create"
- var uname_pw_cell = row.insertCell()
+ let 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")
+ let table_title = document.createElement("STRONG")
table_title.textContent = "Please choose a connection"
+
+ let working_dir_title = document.createElement("STRONG")
+ working_dir_title.textContent = "Your working directory "
+ let working_dir_in = document.createElement("INPUT")
+ working_dir_in.type = "text"
+ working_dir_in.name = "working_dir"
+ working_dir_in.autocomplete = "on"
+ working_dir_in.style.width = "100%"
+
+
+ // calculate the default working directory
+ // by combining the notebook_dir (from the jupyter configuration) and the relative notebook_path
+ let re = new RegExp(env.notebook.notebook_name+"$")
+ rel_path = env.notebook.notebook_path.replace(re, "")
+ let default_working_dir = ""
+ if (data.notebook_dir.endsWith('/')) {
+ default_working_dir = data.notebook_dir + rel_path
+ }
+ else {
+ default_working_dir = data.notebook_dir + "/" + rel_path
+ }
+
+ working_dir_in.value = state.working_dir ? state.working_dir : default_working_dir
+ state.working_dir_element = working_dir_in
+
+ let working_dir_reset = document.createElement("A")
+ working_dir_reset.className = "btn"
+ working_dir_reset.innerText = "reset to default"
+ working_dir_reset.onclick = function() {
+ working_dir_in.value = default_working_dir
+ }
+
conn_table.appendChild(table_title)
conn_table.appendChild(table)
+
+ conn_table.appendChild(working_dir_title)
+ conn_table.appendChild(working_dir_reset)
+ conn_table.appendChild(document.createElement("BR"))
+ conn_table.append(working_dir_in)
+
}
return {
@@ -203,13 +265,12 @@ define(
help_index: '',
handler: function (env) {
conn_table = document.createElement("DIV")
- var dst_title = document.createElement("STRONG")
+ let dst_title = document.createElement("STRONG")
dst_title.textContent = "DataSet type"
- var dataset_types = document.createElement("SELECT")
+ let 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"
connections.list(env)
@@ -220,11 +281,12 @@ define(
alert(data.status)
})
- var uploadDialogBox = $('<div/>').append(conn_table)
+ let uploadDialogBox = $('<div/>').append(conn_table)
function onOk() {
state.connection.name = state.connection.candidateName
state.connection.dto = state.connection.candidateDTO
+ state.working_dir = state.working_dir_element.value
}
function onCancel() {
@@ -250,4 +312,4 @@ define(
}
}
}
-)
\ No newline at end of file
+)
diff --git a/jupyter-openbis-extension/static/downloadDialog.js b/jupyter-openbis-extension/static/downloadDialog.js
index b948043a7f2c414249b059b0513df21177ad0239..bd251b818e18358f47e3837ded8fe8848461ffe4 100644
--- a/jupyter-openbis-extension/static/downloadDialog.js
+++ b/jupyter-openbis-extension/static/downloadDialog.js
@@ -3,15 +3,16 @@ define([
"jquery",
"./common",
"./state",
- "./entitySearcher"
+ //"./entitySearcher"
],
- function (dialog, $, common, state, entitySearcher) {
+ function (dialog, $, common, state) {
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"
+ var userName = window.location.pathname.split("/")[2];
+ spinner.src = '/user/' + userName+ '/nbextensions/jupyter-openbis-extension/spinner.gif'
}
function hideSpinner() {
spinner.src=""
@@ -30,16 +31,13 @@ define([
"dataStore": data.dataStore,
"location": data.location,
"size": data.size,
+ "files": data.files,
"status": data.statusText
}
}
}
function show_datasets_table(env, data, datasets_table, pagingContainer, downloadPath, entityIdentifier) {
- if (downloadPath.value === '') {
- downloadPath.value = data.cwd
- }
-
var table = document.createElement("TABLE")
table.className = "table-bordered table-striped table-condensed text-nowrap"
table.style.width = "100%"
@@ -87,25 +85,45 @@ define([
const previousCmd = () => getDatasets(env, startWith-5, 5, entityIdentifier, datasets_table, pagingContainer, downloadPath)
var previous = document.createElement("A")
- var linkText = document.createTextNode("<<< Previous")
- previous.appendChild(linkText)
- previous.href = "#"
- previous.onclick = previousCmd
+ previous.className = "fas fa fa-caret-left fa-2x"
+ previous.style.verticalAlign="middle"
+ if (hasPrevious) {
+ previous.href = "#"
+ previous.onclick = previousCmd
+ }
var next = document.createElement("A")
- var linkText = document.createTextNode("Next >>>")
- next.appendChild(linkText)
- next.href = "#"
- next.onclick = nextCmd
- next.style.float="right"
+ next.className = "fas fa fa-caret-right fa-2x"
+ next.style.verticalAlign = "middle"
+ if (hasNext) {
+ next.href = "#"
+ next.onclick = nextCmd
+ }
+
+ var countStr = document.createElement("STRONG")
+ var until = startWith + count > totalCount ? totalCount : startWith + count
+ var startWithStr = startWith + 1
+ countStr.innerHTML = startWithStr + "–" + until + "/" + totalCount
+ countStr.style.paddingLeft = "10px"
+ countStr.style.paddingRight = "10px"
+ countStr.style.verticalAlign="middle"
var paging = document.createElement("DIV")
paging.style.width = "100%"
+ paging.appendChild(previous)
if (hasPrevious) {
- paging.appendChild(previous)
+ previous.style.color = "inherit"
+ }
+ else {
+ previous.style.color="transparent"
}
+ paging.appendChild(countStr)
+ paging.appendChild(next)
if (hasNext) {
- paging.appendChild(next)
+ next.style.color="inherit"
+ }
+ else {
+ next.style.color="transparent"
}
while (pagingContainer.firstChild) {
@@ -121,7 +139,7 @@ define([
return false
}
- currentEntityIdentifier = entityIdentifier.firstChild.value
+ currentEntityIdentifier = entityIdentifier.value
if (!currentEntityIdentifier) {
alert('Please specify an Entity identifier/permId')
return false
@@ -158,10 +176,11 @@ define([
return {
- help: 'Download openBIS datasets to your local harddrive',
+ help: 'Download openBIS datasets',
icon: 'fa-download',
help_index: '',
handler: function (env) {
+ console.log(env);
state.selectedDatasets = new Set([])
conn_table = document.createElement("DIV")
@@ -173,7 +192,13 @@ define([
showDataSets.appendChild(title)
showDataSets.style.marginTop = '10px'
- var entityIdentifier = entitySearcher.getEntitySearcherForDownload(state)
+ var entityIdentifier = document.createElement("INPUT")
+ entityIdentifier.type = "text"
+ entityIdentifier.name = "entityIdentifier"
+ entityIdentifier.size = 40
+ entityIdentifier.placeholder = "Sample or Experiment identifier/permId"
+ entityIdentifier.value = state.entityIdentifier ? state.entityIdentifier : ""
+
var datasets_table = document.createElement("DIV")
var pagingContainer = document.createElement("DIV")
@@ -185,8 +210,9 @@ define([
showDataSets.appendChild(entityIdentifier)
showDataSets.appendChild(show_datasets_btn)
- showDataSets.appendChild(datasets_table)
showDataSets.appendChild(pagingContainer)
+ showDataSets.appendChild(document.createElement('BR'))
+ showDataSets.appendChild(datasets_table)
var dataset_direct = document.createElement("P")
dataset_direct.style.marginTop = '10px'
@@ -204,25 +230,39 @@ define([
downloadPath.type = "text"
downloadPath.name = "downloadPath"
downloadPath.size = "90"
- downloadPath.value = state.workingDirectory
+ downloadPath.value = state.download_dir ? state.download_dir : state.working_dir
- show_datasets_btn.onclick =
+ show_datasets_btn.onclick =
() => getDatasets(env, 0, 5, entityIdentifier, datasets_table, pagingContainer, downloadPath)
-
+
+
var path = document.createElement("DIV")
path.innerHTML = "<strong>download data to path: </strong>"
path.appendChild(downloadPath)
var download_dialog_box = document.createElement("DIV")
+
+ let mainError = common.createErrorElement()
+ if (!state.connection.name) {
+ mainError.textContent = "Please choose a connection first."
+ //mainError.textContent = "Network problem: please check your connection first."
+ }
+ download_dialog_box.appendChild(mainError)
download_dialog_box.appendChild(spinner)
download_dialog_box.appendChild(conn_table)
download_dialog_box.appendChild(showDataSets)
download_dialog_box.appendChild(dataset_direct)
download_dialog_box.appendChild(path)
- function saveState() {
+ function onOk() {
+ state.entityIdentifier = entityIdentifier.value
+ state.directPermId = datasetPermId.value
+ state.download_dir = downloadPath.value
+ }
+
+ function onCancel() {
+ state.entityIdentifier = entityIdentifier.value
state.directPermId = datasetPermId.value
- state.workingDirectory = downloadPath.value
}
function downloadDataset(connection_name, selectedPermIds, downloadPath) {
@@ -252,7 +292,8 @@ define([
// keep current download path for later use
currentDownloadPath = downloadPath
})
- } else {
+ }
+ else {
response.json()
.then(function (error) {
console.log(error.reason)
@@ -292,7 +333,7 @@ define([
downloadDataset(selected_conn, selectedPermIds, downloadPath.value)
showSpinner()
- saveState()
+ onOk()
return false
}
@@ -301,7 +342,7 @@ define([
title: 'Download openBIS DataSets',
buttons: {
'Cancel': {
- click: () => saveState()
+ click: () => onCancel()
},
'Download': {
class: 'btn-primary btn-large',
diff --git a/jupyter-openbis-extension/static/entitySearcher.js b/jupyter-openbis-extension/static/entitySearcher.js
index 889db406d2be343c36739cf6107c6ed26a4c455a..70cf4c29922d9f1d07cc8f47e1b5dadd7bcc0124 100644
--- a/jupyter-openbis-extension/static/entitySearcher.js
+++ b/jupyter-openbis-extension/static/entitySearcher.js
@@ -64,24 +64,34 @@ define(["jquery", "./jquery-select2/js/select2.min"],
element.innerHTML = "<span style='color:orange;margin:5px'>loading...</span>"
if (!state.openbisService) {
require.config(this.getRequireJSV3Config(state.connection.dto.url))
- require(["openbis", "as/dto/experiment/search/ExperimentSearchCriteria",
- "as/dto/experiment/fetchoptions/ExperimentFetchOptions",
- "as/dto/sample/search/SampleSearchCriteria",
- "as/dto/sample/fetchoptions/SampleFetchOptions"], function(openbis) {
+ require(["openbis", "as/dto/experiment/search/ExperimentSearchCriteria",
+ "as/dto/experiment/fetchoptions/ExperimentFetchOptions",
+ "as/dto/sample/search/SampleSearchCriteria",
+ "as/dto/sample/fetchoptions/SampleFetchOptions"],
+
+ function (openbis) {
var apiUrl = state.connection.dto.url + "/openbis/openbis/rmi-application-server-v3.json"
var v3 = new openbis(apiUrl)
v3.login(state.connection.dto.username, state.connection.dto.password)
- .done(function(sessionToken) {
+ .done(function (sessionToken) {
+ console.log("sessionToken heisst:");
+ console.log(sessionToken);
state.openbisService = v3
- _this.loadResource("/nbextensions/openbis/jquery-select2/css/select2.min.css", 'css', function() {
- _this.createDropdown(element, state, upload)
- })
- }).fail(function(result) {
- alert('openbis v3 service login failed for ' + apiUrl
- + " : property 'trusted-cross-origin-domains' is probably not set in service.properties.")
+ var userName = window.location.pathname.split("/")[2];
+ //_this.loadResource('/user/' + userName+ '/nbextensions/jupyter-openbis-extension/jquery-select2/css/select2.min.css', 'css', function() {
+ _this.createDropdown(element, state, upload)
+ //})
})
+ .fail(function (result) {
+ alert('openbis v3 service login failed for ' + apiUrl
+ + " : property 'trusted-cross-origin-domains' is probably not set in service.properties.")
+ })
+ },
+ function (err){
+ alert('failed to load required libraries')
})
- } else {
+ }
+ else {
_this.createDropdown(element, state, upload)
}
diff --git a/jupyter-openbis-extension/static/state.js b/jupyter-openbis-extension/static/state.js
index 71ea8e23d5a13982ed94c120171ef2e9674048d1..bcbe83fe121570577138ac2a503ac24d91bd5951 100644
--- a/jupyter-openbis-extension/static/state.js
+++ b/jupyter-openbis-extension/static/state.js
@@ -8,6 +8,9 @@ define([],
candidateName: null,
candidateDTO: null
},
+ working_dir: null,
+ working_dir_element: null,
+ download_dir: null,
// upload dialog
uploadDataSetType: null,
@@ -21,7 +24,6 @@ define([],
// download dialog
selectedDatasets: new Set([]),
entity: null,
- workingDirectory: '',
// openBIS v3 connection
openbisService : null
diff --git a/jupyter-openbis-extension/static/uploadDialog.js b/jupyter-openbis-extension/static/uploadDialog.js
index 11cc7f651666265f1820a8f6b01bb53e82c09373..16e86669d0fbbee5cee2bafd112a66ea0b135591 100644
--- a/jupyter-openbis-extension/static/uploadDialog.js
+++ b/jupyter-openbis-extension/static/uploadDialog.js
@@ -24,23 +24,27 @@ define([
spinner.className="openbis-feedback"
spinner.src=""
function showSpinner(env) {
- spinner.src = env.notebook.base_url + "nbextensions/openbis/spinner.gif"
+ var userName = window.location.pathname.split("/")[2];
+ spinner.src = '/user/' + userName+ '/nbextensions/jupyter-openbis-extension/spinner.gif'
}
function hideSpinner(env) {
spinner.src=""
}
- function get_file_list(env, container) {
- var url = env.notebook.base_url + 'general/filelist'
-
+ function get_file_list(env, container, path) {
+ // get the file list (relative to the notebook) using the existing jupyter api
+ var url = env.notebook.base_url + 'api/contents'
+ if (path !== "") {
+ url = url + '/' + path
+ }
+
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)
+ createFileTable(env, data, container, state)
+ //state.fileCheckboxes = createFileTable(env, data, container, state.selectedFiles)
})
}
else {
@@ -173,7 +177,10 @@ define([
console.error("Error while parsing dataset types", error)
})
- } else {
+ }
+ else {
+ // ! response.ok
+ errorElements.main.textContent = "Network problem: please check your connection first."
while (dataset_types.firstChild) {
dataset_types.removeChild(dataset_types.firstChild);
}
@@ -182,6 +189,7 @@ define([
.catch(function (error) {
console.error("Error while fetching dataset types:", error)
})
+
}
function createSelectTable(values, container, checked, overrides) {
@@ -210,6 +218,96 @@ define([
return checkboxes
}
+ function createFileTable(env, data, container, state) {
+ // list of files that will be uploaded as a dataSet.
+
+ var table = document.createElement("TABLE")
+ table.className = 'table-bordered table-striped table-condensed'
+ table.style.width = "100%"
+
+ var body = table.createTBody()
+ if (data.path !== "") {
+ var row = body.insertRow()
+ row.insertCell()
+ var iconCell = row.insertCell()
+ iconCell.className = "item_icon folder_icon icon-fixed-width"
+ var filenameCell = row.insertCell()
+ filenameCell.textContent = ".."
+ filenameCell.style.width = "80%"
+ filenameCell.style.cursor = "pointer"
+ filenameCell.onclick = function(){
+ var elems = data.path.split('/')
+ elems.pop()
+ get_file_list(env, container, elems.join('/'))
+ }
+
+ var sizeCell = row.insertCell()
+ sizeCell.style.textAlign = "right"
+ sizeCell.style.width = "15%"
+ }
+
+ var registerFile = function () {
+ if (this.checked) {
+ // add file to state
+ state.selectedFiles.push(this.value)
+ }
+ else {
+ // remove file from state
+ state.selectedFiles.splice(state.selectedFiles.indexOf(this.value), 1)
+ }
+ }
+
+ var checkboxes = []
+ data.content.sort( (a, b) => a.name.localeCompare(b.name, undefined, {sensitivity: 'base'}) ).forEach( file => {
+
+ var row = body.insertRow()
+ var checkboxCell = row.insertCell()
+ checkboxCell.style.width="5%"
+ var iconCell = row.insertCell()
+ var filenameCell = row.insertCell()
+
+ filenameCell.textContent = file.name
+ filenameCell.style.width = "100%"
+ filenameCell.style.cursor = "pointer"
+
+ if (file.type === "directory") {
+ iconCell.className = "item_icon folder_icon icon-fixed-width"
+ filenameCell.onclick = function () {
+ get_file_list(env, container, file.path)
+ }
+ }
+ else {
+ var checkbox = document.createElement("INPUT")
+ checkbox.type = "checkbox"
+ checkbox.value = file.path
+ checkbox.checked = state.selectedFiles.includes(file.path) ? true: false
+ checkbox.onclick = registerFile
+ checkboxes.push(checkbox)
+ checkboxCell.appendChild(checkbox)
+
+ if (file.type === "notebook") {
+ iconCell.className = "item_icon notebook_icon icon-fixed-width"
+ }
+ else {
+ iconCell.className = "item_icon file_icon icon-fixed-width"
+ }
+ filenameCell.onclick = function () {
+ checkbox.checked = !checkbox.checked
+ registerFile.call(checkbox)
+ }
+ }
+
+ var sizeCell = row.insertCell()
+ sizeCell.textContent = file.size
+ sizeCell.style.textAlign = "right"
+ sizeCell.style.width = "15%"
+
+ })
+ container.innerHTML = ""
+ container.appendChild(table)
+ return checkboxes
+ }
+
return {
help: 'upload Notebook and Data to openBIS',
icon: 'fa-upload',
@@ -219,7 +317,7 @@ define([
var main_error = createErrorElement('main')
var dst_title = document.createElement("STRONG")
- dst_title.textContent = "DataSet type"
+ dst_title.textContent = "choose a dataSet type"
var dataset_types = document.createElement("SELECT")
dataset_types.id = "dataset_type"
dataset_types.className = "form-control select-xs"
@@ -232,13 +330,20 @@ define([
getDatasetTypes(env, state.connection.name, dataset_types, input_fields)
var sample_title = document.createElement("STRONG")
- sample_title.textContent = "Entity"
+ sample_title.textContent = "enter a sample/experiment identifier to attach this dataSet to:"
var sample_error = createErrorElement('entityIdentifier')
- var entityIdentifier = entitySearcher.getEntitySearcherForUpload(state)
+ //var entityIdentifier = entitySearcher.getEntitySearcherForUpload(state)
+ var entityIdentifier = document.createElement("INPUT")
+ entityIdentifier.type = "text"
+ entityIdentifier.name = "entityIdentifier"
+ entityIdentifier.size = 40
+ entityIdentifier.placeholder = "Sample or Experiment identifier/permId"
+ entityIdentifier.value = state.entityIdentifier ? state.entityIdentifier : ""
var ds_title = document.createElement("STRONG")
+
var dataSetListContainer = document.createElement("DIV")
if (env.notebook.metadata.datasets) {
ds_title.textContent = "Parent DataSets"
@@ -248,11 +353,14 @@ define([
}
var files_title = document.createElement("STRONG")
- files_title.textContent = "Files"
+ files_title.textContent = "Files to upload"
var fileListContainer = document.createElement("DIV")
- fileListContainer.style.maxHeight="150px"
+ fileListContainer.style.height="200px"
fileListContainer.style.overflow="auto"
- get_file_list(env, fileListContainer)
+ // get the relative path
+ let re = new RegExp(env.notebook.notebook_name+"$")
+ rel_path = env.notebook.notebook_path.replace(re, "")
+ get_file_list(env, fileListContainer, rel_path)
var inputs = document.createElement("DIV")
inputs.style.marginTop = '10px'
@@ -263,9 +371,12 @@ define([
inputs.appendChild(dataset_types)
inputs.appendChild(input_fields)
inputs.appendChild(sample_title)
+ inputs.appendChild(document.createElement('BR'))
inputs.appendChild(sample_error)
inputs.appendChild(entityIdentifier)
+ inputs.appendChild(document.createElement('BR'))
inputs.appendChild(ds_title)
+ inputs.appendChild(document.createElement('BR'))
inputs.appendChild(dataSetListContainer)
inputs.appendChild(files_title)
inputs.appendChild(fileListContainer)
@@ -280,7 +391,7 @@ define([
}
}
state.unselectedDatasets = state.datasetCheckboxes.filter(cb => !cb.checked).map(cb => cb.value)
- state.selectedFiles = state.fileCheckboxes.filter(cb => cb.checked).map(cb => cb.value)
+ //state.selectedFiles = state.fileCheckboxes.filter(cb => cb.checked).map(cb => cb.value)
}
function onOk() {
@@ -293,12 +404,13 @@ define([
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)
-
+ // add this notebook to the list of files
+ var files = state.selectedFiles
+ if (! files.includes(env.notebook.notebook_path)) {
+ files.push(env.notebook.notebook_path)
+ }
+ console.log(files)
+
var props = {}
for (input of $('#upload-input-fields').find('input')) {
props[input.name] = input.value
@@ -308,9 +420,10 @@ define([
"type": dataset_types.value,
"files": files,
"parents": state.datasetCheckboxes.filter(cb => cb.checked).map(cb => cb.value),
- "entityIdentifier": entityIdentifier.firstChild.value,
+ "entityIdentifier": entityIdentifier.value,
"props": props
}
+ console.log(dataSetInfo);
var settings = {
url: uploadUrl,
@@ -326,14 +439,14 @@ define([
common.createFeedback('success', data.statusText)
// write statusText from returned data to notebooks metadata
- if (typeof notebook.metadata.openbis === 'undefined') {
- notebook.metadata.openbis = {}
+ if (typeof env.notebook.metadata.openbis === 'undefined') {
+ env.notebook.metadata.openbis = {}
}
- if (typeof notebook.metadata.openbis.permIds === 'undefined') {
- notebook.metadata.openbis.permIds = {}
+ if (typeof env.notebook.metadata.openbis.permIds === 'undefined') {
+ env.notebook.metadata.openbis.permIds = {}
}
if (data.permId) {
- notebook.metadata.openbis.permIds[data.permId] = data.statusText
+ env.notebook.metadata.openbis.permIds[data.permId] = data.statusText
}
},
error: function (data) {
@@ -365,35 +478,43 @@ define([
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
- }
+ dialog_params = {
+ body: uploadDialogBox,
+ title: 'Upload openBIS DataSet',
+ buttons: {
+ 'Cancel': {
+ click: onCancel
},
- notebook: env.notebook,
- keyboard_manager: env.notebook.keyboard_manager
- })
+ 'Upload': {
+ class: 'btn-primary btn-large',
+ click: onOk
+ }
+ },
+ notebook: env.notebook,
+ keyboard_manager: env.notebook.keyboard_manager
+ }
+
+ if (env.notebook.dirty === true) {
+ env.notebook.save_notebook()
+ .then(function () {
+ dialog.modal(dialog_params)
+ })
+ .catch(function (error) {
+ dialog.modal({
+ body: error,
+ title: 'Error saving the notebook',
+ buttons: {
+ 'Back': {}
+ },
+ notebook: env.notebook,
+ keyboard_manager: env.notebook.keyboard_manager
+ })
+ })
+ }
+ else {
+ dialog.modal(dialog_params)
}
}
}
}
-)
\ No newline at end of file
+)
diff --git a/setup.py b/setup.py
index fb238db129b39ed313e0757152948972883c359e..dc56ee882d12e85791ccce9874f138aa3b2ee854 100644
--- a/setup.py
+++ b/setup.py
@@ -11,7 +11,7 @@ with open("README.md", "r", encoding="utf-8") as fh:
setup(
name='jupyter-openbis-extension',
- version= '0.2.4',
+ version= '0.4.0',
author='Swen Vermeul | ID SIS | ETH Zürich',
author_email='swen@ethz.ch',
description='Extension for Jupyter notebooks to connect to openBIS and download/upload datasets, inluding the notebook itself',
@@ -23,7 +23,7 @@ setup(
install_requires=[
'jupyter-nbextensions-configurator',
'jupyter',
- 'pybis>=1.8.4',
+ 'pybis>=1.9.5',
'numpy',
'tornado==5.1.1',
],
@@ -43,18 +43,24 @@ setup(
"jupyter-openbis-extension/static/connectionDialog.js",
"jupyter-openbis-extension/static/uploadDialog.js",
"jupyter-openbis-extension/static/spinner.gif",
- "jupyter-openbis-extension/static/jquery-select2",
- "jupyter-openbis-extension/static/jquery-select2/css",
+ "jupyter-openbis-extension/static/entitySearcher.js",
+ "jupyter-openbis-extension/static/main.js",
+ "jupyter-openbis-extension/static/state.js",
+ "jupyter-openbis-extension/static/common.js",
+ ]),
+ ("share/jupyter/nbextensions/jupyter-openbis-extension/jquery-select2/css", [
"jupyter-openbis-extension/static/jquery-select2/css/select2.min.css",
"jupyter-openbis-extension/static/jquery-select2/css/select2-bootstrap.css",
"jupyter-openbis-extension/static/jquery-select2/css/select2-bootstrap.min.css",
"jupyter-openbis-extension/static/jquery-select2/css/select2.css",
- "jupyter-openbis-extension/static/jquery-select2/js",
+ ]),
+ ("share/jupyter/nbextensions/jupyter-openbis-extension/jquery-select2/js", [
"jupyter-openbis-extension/static/jquery-select2/js/select2.min.js",
"jupyter-openbis-extension/static/jquery-select2/js/select2.full.min.js",
"jupyter-openbis-extension/static/jquery-select2/js/select2.js",
"jupyter-openbis-extension/static/jquery-select2/js/select2.full.js",
- "jupyter-openbis-extension/static/jquery-select2/js/i18n",
+ ]),
+ ("share/jupyter/nbextensions/jupyter-openbis-extension/jquery-select2/js/i18n", [
"jupyter-openbis-extension/static/jquery-select2/js/i18n/pt.js",
"jupyter-openbis-extension/static/jquery-select2/js/i18n/vi.js",
"jupyter-openbis-extension/static/jquery-select2/js/i18n/lv.js",
@@ -102,12 +108,6 @@ setup(
"jupyter-openbis-extension/static/jquery-select2/js/i18n/es.js",
"jupyter-openbis-extension/static/jquery-select2/js/i18n/ro.js",
"jupyter-openbis-extension/static/jquery-select2/js/i18n/tr.js",
- "jupyter-openbis-extension/static/jquery-select2/VERSION.txt",
- "jupyter-openbis-extension/static/jquery-select2/LICENSE.txt",
- "jupyter-openbis-extension/static/entitySearcher.js",
- "jupyter-openbis-extension/static/main.js",
- "jupyter-openbis-extension/static/state.js",
- "jupyter-openbis-extension/static/common.js",
]),
# like `jupyter nbextension enable --sys-prefix`
("etc/jupyter/nbconfig/notebook.d", [