Merge tag '0.1.1' into develop

first version that works with pip install only

.gitignore

 *.pyc
 .*.swp
 *~
+__pycache__
+ubuntu-bionic-18.04-cloudimg-console.log
+.vagrant
+jupyter_openbis_extension.egg-info
+venv
+.ipynb_checkpoints
+.DS_Store
+*.ipynb

CHANGELOG.md

+## new in jupyter-openbis-extension 0.1.1
+
+- first version that cleanly works with pip install only
+- bugfixes in setup.py
+- typos in .json files in jupyter-config
+- CHANGELOG added
+
+## new in jupyter-openbis-extension 0.1.0
+
+- separation of connection, down- and upload
+- upload let you specify dataset type
+- dataset type specific input fields (properties)
+- input control for all properties
+- checks for missing properties
+- downloaded datasets are new parent datasets by default
+- simplified way to upload files as part of the new dataset
+
+## new in jupyter-openbis-extension 0.0.1
+
+- first published version

LICENSE

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README.md

@@ -4,6 +4,28 @@
 
 The jupyter-openbis-extension needs at least **Python 3.3** in order to run. The Jupyter notebook server starts this extension during startup and must therefore run under the same Python version. The kernel can be anything (Python 2.7, Julia, R, Perl...)
 
+This extension has been successfully tested with Safari 12.0.3, Chrome 72.0 and Firefox 66.0. There is a known incompatibility before Firefox 61.0b13.
+
+## Development with Vagrant
+
+If you want to use a predefined development environment, follow these steps:
+
+1. Install latest version of VirtualBox (<https://www.virtualbox.org>)
+
+2. Install latest version of Vagrant (<https://www.vagrantup.com/downloads.html>)
+
+3. vagrant plugin install vagrant-vbguest vagrant-notify-forwarder vagrant-disksize
+ 
+4. cd vagrant
+
+5. vagrant up
+
+After the setup is complete, you'll have
+
+* Jupyter with openBIS extension running at <http://localhost:8888>.
+* openBIS running at <http://localhost:8122>, with credentials admin/password.
+* Experiment /DEFAULT/DEFAULT with a lot of datasets for testing.
+
 ## Install the extension
 
 If you haven't done yet: download the latest jupyter-openbis-extension from pip. It will automatically install the various dependencies, e.g. Pandas and NumPy.
@@ -12,6 +34,19 @@ If you haven't done yet: download the latest jupyter-openbis-extension from pip.
 pip install --upgrade jupyter-openbis-extension
 ```
 
+or, if you would like to develop:
+
+```
+$ git clone git@sissource.ethz.ch:sispub/jupyter-openbis-extension.git
+$ cd jupyter-openbis-extension
+$ virtualenv venv
+$ source venv/bin/activate
+(venv) $ pip install -e .
+(venv) $ jupyter serverextension enable --py jupyter-openbis-extension
+(venv) $ jupyter nbextension install --py jupyter-openbis-extension --user --symlink
+(venv) $ jupyter nbextension enable jupyter-openbis-extension --user --py
+```
+
 **Register the Jupyter server extension** which will communicate both with openBIS and the notebook:
 
 ```
@@ -50,20 +85,37 @@ connections:
       username            : username
       password            : password
 ```
+**Note  1**: You do not need the usernames or passwords anymore. With the current version, you are able to enter username and password directly from within a Jupyter notebook.
+
+**Note 2**: You can place this file in any of these directories (on Mac OS X):
+
+```
+/Users/your_username/jupyter-openbis-extension/notebooks
+/Users/your_username/.jupyter
+/Users/your_username/.pyenv/versions/3.6.0/etc/jupyter  # or wherever your jupyter installation is located
+/usr/local/etc/jupyter
+/etc/jupyter
+```
+These directories are produced by Jupyters' `nb_server_app.config_file_paths` method.
+
+## Launching Jupyter notebook
 
-Now you are **ready to launch!**
+Now you are **ready to launch jupyter notebook!**
 
 ```
 $ jupyter notebook
 ```
-Observe the terminal. It should tell you that the server(s) have been successfully connected: 
+Observe the terminal. It should tell you which server(s) have been successfully connected (and which not):
 
 ```
 $ jupyter notebook
-connected to TEST local openBIS instance
-connected to PRODUCTION openBIS instance
+Registered: https://localhost:8443
+Cannot establish connection to: https://localhost:8443
+Registered: https://openbis.example.com
+Successfully connected to: https://openbis.example.com
 ```
-**Congratulations!** 
+**Congratulations!** You can retry non-successful connections later, directly from the GUI.
+
 
 ## Uninstall Jupyter extension
 
@@ -142,4 +194,4 @@ Known nbextensions:
     notebook section
       jupyter-openbis-extension/dialog  enabled 
       - Validating: OK
-```
+```
\ No newline at end of file

jupyter-config/jupyter_notebook_config.d/jupyter_openbis_extension.json

+{
+  "NotebookApp": {
+    "nbserver_extensions": {
+      "jupyter-openbis-extension.server": true
+    }
+  }
+}

jupyter-config/nbconfig/notebook.d/jupyter_openbis_extension.json

+{
+  "load_extensions": {
+    "jupyter-openbis-extension/main": true
+  }
+}

jupyter-openbis-extension/__init__.py

 name = 'jupyter-openbis-extension.server'
 __author__ = 'Swen Vermeul'
 __email__ = 'swen@ethz.ch'
-__version__ = '0.0.2'
+__version__ = '0.1.1'
 
 def _jupyter_server_extension_paths():
     return [{
@@ -19,7 +19,7 @@ def _jupyter_nbextension_paths():
     #    # directory in the `nbextension/` namespace
         'dest': "openbis",
         # _also_ in the `nbextension/` namespace
-        'require' : "openbis/dialog"
+        'require' : "openbis/main"
     }]
 
 def load_jupyter_server_extension(nbapp):

jupyter-openbis-extension/connection.py

+import os
+from pybis import Openbis
+from notebook.base.handlers import IPythonHandler
+
+openbis_connections = {}
+
+def register_connection(connection_info):
+
+    conn = OpenBISConnection(
+        name                = connection_info.get('name'),
+        url                 = connection_info.get('url'),
+        verify_certificates = connection_info.get('verify_certificates', False),
+        username            = connection_info.get('username'),
+        password            = connection_info.get('password'),
+        status              = 'not connected',
+    )
+    openbis_connections[conn.name] = conn
+    return conn
+
+
+class OpenBISConnection:
+    """register an openBIS connection
+    """
+
+    def __init__(self, **kwargs):
+        for needed_key in ['name', 'url']:
+            if needed_key not in kwargs:
+                raise KeyError("{} is missing".format(needed_key))
+
+        for key in kwargs:
+            setattr(self, key, kwargs[key])
+
+        openbis = Openbis(
+            url = self.url,
+            verify_certificates = self.verify_certificates
+        )
+        self.openbis = openbis
+        self.status = "not connected"
+
+    def is_session_active(self):
+        return self.openbis.is_session_active()
+
+    def check_status(self):
+        if self.openbis.is_session_active():
+            self.status = "connected"
+        else:
+            self.status = "not connected"
+
+    def login(self, username=None, password=None):
+        if username is None:
+            username=self.username
+        if password is None:
+            password=self.password
+        self.openbis.login(
+            username = username,
+            password = password
+        )
+        # store username and password in memory
+        self.username = username
+        self.password = password
+        self.status  = 'connected'
+
+    def get_info(self):
+        return {
+            'name'    : self.name,
+            'url'     : self.url,
+            'status'  : self.status,
+            'username': self.username,
+            'password': self.password,
+        }
+
+class OpenBISConnections(IPythonHandler):
+
+    def post(self):
+        """create a new connection
+
+        :return: a new connection object
+        """
+        data = self.get_json_body()
+        conn = register_connection(data)
+        if conn.username and conn.password:
+            try:
+                conn.login()
+            except Exception:
+                pass
+        self.get()
+        return
+
+    def get(self):
+        """returns all available openBIS connections
+        """
+
+        connections= []
+        for conn in openbis_connections.values():
+            conn.check_status()
+            connections.append(conn.get_info())
+
+        self.write({
+            'status'     : 200,
+            'connections': connections,
+            'cwd'        : os.getcwd()
+        })
+        return
+
+
+class OpenBISConnectionHandler(IPythonHandler):
+    """Handle the requests to /openbis/conn
+    """
+
+    def put(self, connection_name):
+        """reconnect to a current connection
+        :return: an updated connection object
+        """
+        data = self.get_json_body()
+
+        try:
+            conn = openbis_connections[connection_name]
+        except KeyError:
+            self.set_status(404)
+            self.write({
+                "reason" : 'No such connection: {}'.format(data)
+            })
+            return
+
+        try:
+            conn.login(data.get('username'), data.get('password'))
+        except ConnectionError:
+            self.set_status(500)
+            self.write({
+                "reason": "Could not establish connection to {}".format(connection_name)
+            })
+            return
+        except ValueError:
+            self.set_status(401)
+            self.write({
+                "reason": "Incorrect username or password for {}".format(connection_name)
+            })
+            return
+
+        self.write({
+            'status'     : 200,
+            'connection': conn.get_info(),
+            'cwd'        : os.getcwd()
+        })
+
+    def get(self, connection_name):
+        """returns  information about a connection name
+        """
+
+        try:
+            conn = openbis_connections[connection_name]
+        except KeyError:
+            self.set_status(404)
+            self.write({
+                "reason" : 'No such connection: {}'.format(connection_name)
+            })
+            return
+
+        conn.check_status()
+
+        self.write({
+            'status'     : 200,
+            'connection': conn.get_info(),
+            'cwd'        : os.getcwd()
+        })
+        return
+

jupyter-openbis-extension/dataset.py

+import os
+from urllib.parse import unquote
+from notebook.base.handlers import IPythonHandler
+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:
+                conn.login()
+            except Exception as exc:
+                self.set_status(500)
+                self.write({
+                    "reason" : 'connection to {} could not be established: {}'.format(conn.name, exc)
+                })
+                return
+
+        try:
+            dataset = conn.openbis.get_dataset(permId)
+        except Exception as exc:
+            self.set_status(404)
+            self.write({
+                "reason" : 'No such dataSet found: {}'.format(permId)
+            })
+            return
+
+        # dataset was found, download the data to the disk
+        try:
+            destination = dataset.download(destination=downloadPath)
+        except Exception as exc:
+            self.set_status(500)
+            self.write({
+                "reason": 'Data for DataSet {} could not be downloaded: {}'.format(permId, exc)
+            })
+            return
+
+        # return success message
+        path = os.path.join(downloadPath, dataset.permId)
+        self.write({
+            'url'       : conn.url,
+            'permId'    : dataset.permId,
+            'path'      : path,
+            'dataStore' : dataset.dataStore,
+            'location'  : dataset.physicalData.location,
+            'size'      : dataset.physicalData.size,
+            'statusText': 'Data for DataSet {} was successfully downloaded to: {}.'.format(dataset.permId, path)
+        })
+
+    def get(self, **params):
+        """Handle a request to /openbis/dataset/connection_name/permId
+        download the data and return a message
+        """
+
+        try:
+            conn = openbis_connections[params['connection_name']]
+        except KeyError:
+            self.set_status(404)
+            self.write({
+                "reason":'connection {} was not found'.format(params['connection_name'])
+            })
+            return
+
+        results = self.download_data(conn=conn, permId=params['permId'], downloadPath=params['downloadPath'])
+
+
+class DataSetTypesHandler(IPythonHandler):
+    def get(self, **params):
+        """Handle a request to /openbis/datasetTypes/connection_name
+        """
+
+        try:
+            conn = openbis_connections[params['connection_name']]
+        except KeyError:
+            self.set_status(404)
+            self.write({
+                "reason":'connection {} was not found'.format(params['connection_name'])
+            })
+            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
+
+            self.write({
+                "dataSetTypes": dts
+            })
+            return
+
+        except Exception as e:
+            print(e)
+            self.set_status(500)
+            self.write({
+                "reason":'Could not fetch dataset-types: {}'.format(e)
+            })
+            return
+
+
+class DataSetUploadHandler(IPythonHandler):
+    """Handle the POST requests for /openbis/dataset/connection_name"""
+
+    def upload_data(self, conn, data):
+        if not conn.is_session_active():
+            try:
+                conn.login()
+            except Exception as e:
+                print(e)
+                self.set_status(500)
+                self.write({
+                    "reason": 'connection to {} could not be established: {}'.format(conn.name, e)
+                })
+                return
+
+        errors = []
+        print("--------------_HERE_-----------1")
+
+        sample = None
+        experiment = None
+
+        if (data.get('entityIdentifier')):
+            try:
+                sample = conn.openbis.get_sample(data.get('entityIdentifier'))
+            except Exception as e:
+                pass
+            if sample is None:
+                try:
+                    experiment = conn.openbis.get_experiment(data.get('entityIdentifier'))
+                except Exception as e:
+                    pass
+
+            if sample is None and experiment is None:
+                errors.append(
+                    {"entityIdentifier" : 'No such sample or experiment: {}'.format(data.get('entityIdentifier')) }
+                )
+        else:
+            errors.append(
+                {"entityIdentifier": "please provide a sample or experiment identifier"}
+            )
+
+        print("--------------_HERE_-----------2")
+
+        parents = []
+        if data.get('parents'):
+            parents = data.get('parents')
+            for parent in parents:
+                try:
+                    conn.openbis.get_dataset(parent)
+                except Exception as e:
+                    errors.append({
+                        "parent": "Parent DataSet not found: {}".format(parent)
+                    })
+
+        print("--------------_HERE_-----------2a")
+
+        filenames = []
+        for filename in data.get('files'):
+            filename = unquote(filename)
+            if os.path.isfile(filename):
+                filenames.append(filename)
+            else:
+                errors.append({
+                    "file": "File not found: {}".format(filename)
+                })
+        print("--------------_HERE_-----------3")
+
+        try:
+            dataset = conn.openbis.new_dataset(
+                type   = data.get('type'),
+                sample = sample,
+                parents = parents,
+                experiment = experiment,
+                files  = filenames,
+            )
+        except Exception as e:
+            print(e)
+            errors.append({
+                "create": 'Error while creating the dataset: {}'.format(e)
+            })
+        print("--------------_HERE_-----------4")
+
+        # try to set the properties
+        if data.get('props'):
+            props = data.get('props')
+            for prop, value in props.items():
+                try:
+                    setattr(dataset.props, prop.lower(), value)
+                except Exception as e:
+                    errors.append({
+                        "prop."+prop : str(e)
+                    })
+
+        # check if any mandatory property is missing
+        for prop_name, prop in dataset.props._property_names.items():
+            if prop['mandatory']:
+                if getattr(dataset.props, prop_name) is None or getattr(dataset.props, prop_name) == "":
+                    errors.append({
+                        "prop."+prop_name : "is mandatory"
+                    })
+        print("--------------_HERE_-----------5")
+
+        # write errors back if already occured
+        if errors:
+            self.set_status(500)
+            self.write({ "errors": errors })
+            return
+        print("--------------_HERE_-----------6")
+
+        try:
+            dataset.save()
+        except Exception as e:
+            errors.append({
+                "save": 'Error while saving the dataset: {}'.format(e)
+            })
+        print("--------------_HERE_-----------7")
+
+        # write errors back if they occured
+        if errors:
+            self.set_status(500)
+            self.write({ "errors": errors })
+        else:
+            # ...or return a success message
+            self.write({
+                'status': 200,
+                'statusText': 'Jupyter Notebook was successfully uploaded to: {} with permId: {}'.format(conn.name, dataset.permId)
+            })
+
+        print('Jupyter Notebook was successfully uploaded to: {} with permId: {}'.format(conn.name, dataset.permId))
+        print("--------------_HERE_-----------8")
+
+    def post(self, **params):
+        """Handle a request to /openbis/dataset/connection_name/permId
+        download the data and return a message
+        """
+
+        try:
+            conn = openbis_connections[params['connection_name']]
+        except KeyError:
+            self.write({
+                "reason": 'connection {} was not found'.format(params['connection_name'])
+            })
+            return
+
+        data = self.get_json_body()
+        print("Received DATA")
+        print(data)
+        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
+        })
+

jupyter-openbis-extension/sample.py

+from notebook.base.handlers import IPythonHandler
+import numpy as np
+import os
+from .connection import openbis_connections
+from urllib.parse import parse_qs
+
+
+
+def get_entity_for_identifier(conn, identifier):
+    try:
+        entity = conn.openbis.get_sample(identifier)
+    except Exception as exc:
+        pass
+
+    if entity is None:
+        try:
+            entity = conn.openbis.get_experiment(identifier)
+        except Exception as exc:
+            pass
+
+    return entity
+
+def get_datasets(entity, start_with=None, count=None):
+
+    datasets = entity.get_datasets(start_with=start_with, count=count)
+    totalCount = datasets.totalCount
+    df = datasets.df
+    df.replace({np.nan:None}, inplace=True)  # replace NaN with None, otherwise we cannot convert it correctly
+    datasets_dict = df.to_dict(orient='records')   # is too stupid to handle NaN
+
+    return {
+        "datasets_dict": datasets_dict,
+        "totalCount": totalCount
+    }
+
+
+class SampleHandler(IPythonHandler):
+    """Handle the requests for /openbis/sample/connection/permId"""
+
+    def get(self, **params):
+        """Handle a request to /openbis/sample/connection_name/permId
+        download the dataset list and return a message
+        """
+        try:
+            conn = openbis_connections[params['connection_name']]
+        except KeyError:
+            self.set_status(500)
+            self.write({
+                "reason" : 'connection {} was not found'.format(
+                    params['connection_name']
+                )
+            })
+            return
+
+        if not conn.is_session_active():
+            try:
+                conn.login()
+            except Exception as exc:
+                self.set_status(500)
+                self.write({
+                    "reason" : 'connection to {} could not be established: {}'.format(conn.name, exc)
+                })
+                return
+
+        entity = get_entity_for_identifier(conn, params['identifier'])
+        if entity is None:
+            self.set_status(404)
+            self.write({
+                "reason" : 'No such Sample or Experiment: {}'.format(params['identifier'])
+            })
+            return None
+
+        querystring = parse_qs(self.request.query)
+        start_with = querystring.get('start_with', ['0'])[0]
+        count      = querystring.get('count', ['10'])[0]
+
+        datasets = get_datasets(entity, start_with=start_with, count=count)
+        if datasets is not None:
+            self.set_status(200)
+            self.write({
+                "dataSets"    : datasets.get('datasets_dict'),
+                "entity_attrs": entity.attrs.all(),
+                "entity_props": entity.props.all(),
+                "start_with"  : start_with,
+                "count"       : count,
+                "totalCount"  : datasets.get('totalCount'),
+                "cwd"         : os.getcwd()
+            })
+

jupyter-openbis-extension/server.py

 from notebook.utils import url_path_join
-from notebook.base.handlers import IPythonHandler
-from pybis import Openbis
-import numpy as np
-
 import os
-from urllib.parse import unquote
 import yaml
 
-openbis_connections = {}
+from .connection import OpenBISConnections, OpenBISConnectionHandler, register_connection
+from .dataset import DataSetTypesHandler, DataSetDownloadHandler, DataSetUploadHandler, FileListHandler
+from .sample import SampleHandler
 
 
 def _jupyter_server_extension_paths():
@@ -31,8 +28,8 @@ def _load_configuration(paths, filename='openbis-connections.yaml'):
                     config = yaml.safe_load(stream)
                     for connection in config['connections']:
                         connections.append(connection)
-                except yaml.YAMLexception as exc:
-                    print(exc)
+                except yaml.YAMLexception as e:
+                    print(e)
                     return None
 
     return connections
@@ -69,6 +66,15 @@ 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(
         host_pattern, 
@@ -81,10 +87,7 @@ def load_jupyter_server_extension(nb_server_app):
 
     # DataSet upload
     web_app.add_handlers( host_pattern, [(
-            url_path_join(
-                base_url,
-                '/openbis/dataset/(?P<connection_name>.*)'
-            ),
+            url_path_join( base_url, '/openbis/dataset/(?P<connection_name>.*)' ),
             DataSetUploadHandler
         )]
     )
@@ -93,9 +96,7 @@ def load_jupyter_server_extension(nb_server_app):
     web_app.add_handlers(
         host_pattern,
         [(
-            url_path_join(
-                base_url,
-                '/openbis/datasetTypes/(?P<connection_name>.*)'
+            url_path_join( base_url, '/openbis/datasetTypes/(?P<connection_name>.*)'
             ),
             DataSetTypesHandler
         )]
@@ -107,7 +108,7 @@ def load_jupyter_server_extension(nb_server_app):
         [(  
             url_path_join(
                 base_url,
-                '/openbis/sample/(?P<connection_name>.*)?/(?P<permId>.*)'
+                '/openbis/sample/(?P<connection_name>.*)?/(?P<identifier>.*)'
             ), 
             SampleHandler
         )]
@@ -137,392 +138,4 @@ def load_jupyter_server_extension(nb_server_app):
         )]
     )
 
-    print("pybis loaded: {}".format(Openbis))
-
-
-def register_connection(connection_info):
-
-    conn = OpenBISConnection(
-        name                = connection_info.get('name'),
-        url                 = connection_info.get('url'),
-        verify_certificates = connection_info.get('verify_certificates', False),
-        username            = connection_info.get('username'),
-        password            = connection_info.get('password'),
-        status              = 'not connected',
-    )
-    openbis_connections[conn.name] = conn
-    return conn
-
-
-class OpenBISConnection:
-    """register an openBIS connection
-    """
-
-    def __init__(self, **kwargs):
-        for needed_key in ['name', 'url']:
-            if needed_key not in kwargs:
-                raise KeyError("{} is missing".format(needed_key))
-
-        for key in kwargs:
-            setattr(self, key, kwargs[key])
-
-        openbis = Openbis(
-            url = self.url,
-            verify_certificates = self.verify_certificates
-        )
-        self.openbis = openbis
-        self.status = "not connected"
-
-    def is_session_active(self):
-        return self.openbis.is_session_active()
-
-    def check_status(self):
-        if self.openbis.is_session_active():
-            self.status = "connected"
-        else:
-            self.status = "not connected"
-
-    def login(self, username=None, password=None):
-        if username is None:
-            username=self.username
-        if password is None:
-            password=self.password
-        self.openbis.login(
-            username = username,
-            password = password
-        )
-        # store username and password in memory
-        self.username = username
-        self.password = password
-        self.status  = 'connected'
-
-    def get_info(self):
-        return {
-            'name'    : self.name,
-            'url'     : self.url,
-            'status'  : self.status,
-            'username': self.username,
-            'password': self.password,
-        }
-
-class OpenBISConnections(IPythonHandler):
-
-    def post(self):
-        """create a new connection
-
-        :return: a new connection object
-        """
-        data = self.get_json_body()
-        conn = register_connection(data)
-        if conn.username and conn.password:
-            try:
-                conn.login()
-            except Exception:
-                pass
-        self.get()
-        return
-
-    def get(self):
-        """returns all available openBIS connections
-        """
-
-        connections= []
-        for conn in openbis_connections.values():
-            conn.check_status()
-            connections.append(conn.get_info())
-
-        self.write({
-            'status'     : 200,
-            'connections': connections,
-            'cwd'        : os.getcwd()
-        })
-        return
-
-
-class OpenBISConnectionHandler(IPythonHandler):
-    """Handle the requests to /openbis/conn
-    """
-
-    def put(self, connection_name):
-        """reconnect to a current connection
-        :return: an updated connection object
-        """
-        data = self.get_json_body()
-
-        try:
-            conn = openbis_connections[connection_name]
-        except KeyError:
-            self.set_status(404)
-            self.write({
-                "reason" : 'No such connection: {}'.format(data)
-            })
-            return
-
-        try:
-            conn.login(data.get('username'), data.get('password'))
-        except ConnectionError:
-            self.set_status(500)
-            self.write({
-                "reason": "Could not establish connection to {}".format(connection_name)
-            })
-            return
-        except ValueError:
-            self.set_status(401)
-            self.write({
-                "reason": "Incorrect username or password for {}".format(connection_name)
-            })
-            return
-
-        self.write({
-            'status'     : 200,
-            'connection': conn.get_info(),
-            'cwd'        : os.getcwd()
-        })
-
-    def get(self, connection_name):
-        """returns  information about a connection name
-        """
-
-        try:
-            conn = openbis_connections[connection_name]
-        except KeyError:
-            self.set_status(404)
-            self.write({
-                "reason" : 'No such connection: {}'.format(data)
-            })
-            return
-
-        conn.check_status()
-
-        self.write({
-            'status'     : 200,
-            'connection': conn.get_info(),
-            'cwd'        : os.getcwd()
-        })
-        return
-
-
-class SampleHandler(IPythonHandler):
-    """Handle the requests for /openbis/sample/connection/permId"""
-
-    def get_datasets(self, conn, permId):
-        if not conn.is_session_active():
-            try:
-                conn.login()
-            except Exception as exc:
-                self.write({
-                    "reason" : 'connection to {} could not be established: {}'.format(conn.name, exc)
-                })
-
-        sample = None
-        try:
-            sample = conn.openbis.get_sample(permId)
-        except Exception as exc:
-            self.set_status(404)
-            self.write({
-                "reason" : 'No such sample: {}'.format(permId)
-            })
-        if sample is None:
-            return
-
-        datasets = sample.get_datasets().df
-        datasets.replace({np.nan:None}, inplace=True)  # replace NaN with None, otherwise we cannot convert it correctly
-        return datasets.to_dict(orient='records')   # is too stupid to handle NaN
-
-
-    def get(self, **params):
-        """Handle a request to /openbis/sample/connection_name/permId
-        download the data and return a message
-        """
-        try:
-            conn = openbis_connections[params['connection_name']]
-        except KeyError:
-            self.write({
-                "reason" : 'connection {} was not found'.format(
-                    params['connection_name']
-                )
-            })
-            return
-        
-        datasets = self.get_datasets(conn, params['permId'])
-        if datasets is not None:
-            self.set_status(200)
-            self.write({
-                "dataSets": datasets
-            })
-
-
-
-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:
-                conn.login()
-            except Exception as exc:
-                self.set_status(500)
-                self.write({
-                    "reason" : 'connection to {} could not be established: {}'.format(conn.name, exc)
-                })
-                return
-
-        try:
-            dataset = conn.openbis.get_dataset(permId)
-        except Exception as exc:
-            self.set_status(404)
-            self.write({
-                "reason" : 'No such dataSet found: {}'.format(permId)
-            })
-            return
-
-        # dataset was found, download the data to the disk
-        try: 
-            destination = dataset.download(destination=downloadPath)
-        except Exception as exc:
-            self.set_status(500)
-            self.write({
-                "reason": 'Data for DataSet {} could not be downloaded: {}'.format(permId, exc)
-            })
-            return
-            
-        # return success message
-        path = os.path.join(downloadPath, dataset.permId)
-        self.write({
-            'url'       : conn.url,
-            'permId'    : dataset.permId,
-            'path'      : path,
-            'dataStore' : dataset.dataStore,
-            'location'  : dataset.physicalData.location,
-            'size'      : dataset.physicalData.size,
-            'statusText': 'Data for DataSet {} was successfully downloaded to: {}.'.format(dataset.permId, path)
-        })
-
-    def get(self, **params):
-        """Handle a request to /openbis/dataset/connection_name/permId
-        download the data and return a message
-        """
-
-        try:
-            conn = openbis_connections[params['connection_name']]
-        except KeyError:
-            self.set_status(404)
-            self.write({
-                "reason":'connection {} was not found'.format(params['connection_name'])
-            })
-            return
-        
-        results = self.download_data(conn=conn, permId=params['permId'], downloadPath=params['downloadPath'])
-
-
-class DataSetTypesHandler(IPythonHandler):
-    def get(self, **params):
-        """Handle a request to /openbis/datasetTypes/connection_name
-        """
-
-        try:
-            conn = openbis_connections[params['connection_name']]
-        except KeyError:
-            self.set_status(404)
-            self.write({
-                "reason":'connection {} was not found'.format(params['connection_name'])
-            })
-            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()
-                pa_dict = pa.to_dict(orient='records')
-                dt['propertyAssignments'] = pa_dict
-
-            self.write({
-                "dataSetTypes": dts
-            })
-            return
-
-        except Exception as e:
-            self.set_status(500)
-            self.write({
-                "reason":'Could not fetch dataset-types: {}'.format(e)
-            })
-            return
-
-
-class DataSetUploadHandler(IPythonHandler):
-    """Handle the requests for /openbis/dataset/connection"""
-
-    def upload_data(self, conn, data):
-        if not conn.is_session_active():
-            try:
-                conn.login()
-            except Exception as exc:
-                self.write({
-                    "reason": 'connection to {} could not be established: {}'.format(conn.name, exc)
-                })
-                return
-
-        try:
-            sample = conn.openbis.get_sample(data.get('sampleIdentifier'))
-        except Exception as exc:
-            self.set_status(404)
-            self.write({
-                "reason" : 'No such sample: {}'.format(data.get('sampleIdentifier'))
-            })
-            return
-
-        filenames = []
-        for filename in data.get('files'):
-            filename = unquote(filename)
-            filenames.append(filename)
-
-        try: 
-            ds = conn.openbis.new_dataset(
-                name        = data.get('name'),
-                description = data.get('description'),
-                type        = data.get('type'),
-                sample      = sample,
-                files       = filenames
-            ) 
-        except Exception as exc:
-            self.write({
-                "reason": 'Error while creating the dataset: {}'.format(exc)
-            })
-            return
-
-        try:
-            ds.save()
-        except Exception as exc:
-            self.write({
-                "reason": 'Error while saving the dataset: {}'.format(exc)
-            })
-            return
-        
-            
-        # return success message
-        self.write({
-            'status': 200,
-            'statusText': 'Jupyter Notebook was successfully uploaded to: {} with permId: {}'.format(conn.name, ds.permId)
-        })
-
-    def post(self, **params):
-        """Handle a request to /openbis/dataset/connection_name/permId
-        download the data and return a message
-        """
-
-        try:
-            conn = openbis_connections[params['connection_name']]
-        except KeyError:
-            self.write({
-                "reason": 'connection {} was not found'.format(params['connection_name'])
-            })
-            return
 
-        data = self.get_json_body()
-        results = self.upload_data(conn=conn,data=data)

jupyter-openbis-extension/static/common.js

+define([
+        "base/js/namespace"
+    ],
+    function (IPython) {
+
+        function createFeedback(type, content) {
+            var close = document.createElement("BUTTON")
+            close.className = "close"
+            close.setAttribute("data-dismiss", "alert")
+            close.setAttribute("aria-label", "Close")
+            var x = document.createElement("SPAN")
+            x.setAttribute("aria-hidden", true)
+            x.innerHTML = "×"
+            close.appendChild(x)
+
+            var feedbackBox = document.createElement("DIV")
+            feedbackBox.className = "openbis-feedback alert alert-dismissible alert-" + type
+            feedbackBox.setAttribute("role", "alert")
+            feedbackBox.innerHTML = content
+            feedbackBox.prepend(close)
+
+            var nb_container = document.getElementById('notebook-container')
+            nb_container.prepend(feedbackBox)
+        }
+
+        function getCookie(cname) {
+            var name = cname + "=";
+            var decodedCookie = decodeURIComponent(document.cookie);
+            var ca = decodedCookie.split(';');
+            for(var i = 0; i <ca.length; i++) {
+                var c = ca[i];
+                while (c.charAt(0) === ' ') {
+                    c = c.substring(1);
+                }
+                if (c.indexOf(name) === 0) {
+                    return c.substring(name.length, c.length);
+                }
+            }
+            return "";
+        }
+
+        return {
+            createFeedback: createFeedback,
+            getCookie: getCookie
+        }
+    }
+)
\ No newline at end of file

jupyter-openbis-extension/static/connectionDialog.js

+define(
+    [
+        "base/js/dialog",
+        "jquery",
+        "./state",
+        "./connections"
+    ],
+    function (dialog, $, state, connections) {
+
+        var currentDownloadPath = null
+
+        function show_available_connections(env, data, conn_table, onclick_cbf) {
+            if (!currentDownloadPath) {
+                currentDownloadPath = data.cwd
+            }
+
+            var table = document.createElement("TABLE")
+            table.className = 'table-bordered table-striped table-condensed'
+            var thead = table.createTHead()
+            var thead_row = thead.insertRow(0)
+            var titles = ['', 'Name', 'URL', 'Status', 'Username / Password']
+            for (title of titles) {
+                thead_row.insertCell().textContent = title
+            }
+
+            tbody = table.createTBody()
+            for (connection of data.connections) {
+                var conn = document.createElement("INPUT")
+                conn.type = "radio"
+                conn.name = "connection_name"
+                conn.value = connection.name
+                conn.setAttribute("url", connection.url)
+
+                conn.checked = connection.name === state.connection.candidateName;
+                if (onclick_cbf === undefined) {
+                    conn.onclick = function () {
+                        state.connection.candidateName = this.value
+                    }
+                } else {
+                    conn.onclick = onclick_cbf
+                }
+
+                var row = tbody.insertRow()
+                row.insertCell().appendChild(conn)
+                row.insertCell().textContent = connection.name
+                row.insertCell().textContent = connection.url
+
+                var status_cell = row.insertCell()
+
+                var status_badge = document.createElement("SPAN")
+                status_badge.id = connection.name + "-badge"
+                status_badge.textContent = connection.status
+                if (connection.status === "connected") {
+                    status_badge.className = "label label-success"
+                } else {
+                    status_badge.className = "label label-danger"
+                }
+                status_cell.appendChild(status_badge)
+
+                var username = document.createElement("INPUT")
+                username.type = "text"
+                username.name = "username"
+                username.autocomplete = "on"
+                username.value = connection.username
+                username.setAttribute("form", connection.name)
+
+                var password = document.createElement("INPUT")
+                password.type = "password"
+                password.name = "password"
+                password.autocomplete = "current-password"
+                password.value = connection.password
+                password.setAttribute("form", connection.name)
+
+                // Username / Password form
+                var pwform = document.createElement("FORM")
+                pwform.id = connection.name
+                pwform.onsubmit = function (event) {
+                    var form_data = new FormData(this)
+                    var status_badge = document.getElementById(this.id + "-badge")
+                    connections.connect(env, this.id,
+                            form_data.get("username"), form_data.get("password")
+                        )
+                        .then(function (response) {
+                            //console.log(response)
+                            if (status_badge.nextElementSibling !== null) {
+                                status_badge.parentNode.removeChild(status_badge.nextElementSibling)
+                            }
+                            if (response.ok) {
+                                status_badge.textContent = "connected"
+                                status_badge.className = "label label-success"
+                            } else {
+                                status_badge.textContent = "not connected"
+                                status_badge.className = "label label-danger"
+                                message = document.createElement("p")
+                                if (response.status === 401) {
+                                    message.textContent = "username/password incorrect"
+                                } else if (response.status === 500) {
+                                    message.textContent = "Connection error"
+                                } else {
+                                    message.textContent = "General error"
+                                }
+                                status_badge.parentNode.insertBefore(message, status_badge.nextSibling)
+                            }
+                        })
+                        .catch(error => console.error("Error while attempting to reconnect: ", error))
+
+                    return false
+                }
+
+
+                var connect_button = document.createElement("BUTTON")
+                connect_button.className = "btn btn-primary btn-xs"
+                connect_button.textContent = "connect"
+
+                pwform.appendChild(username)
+                pwform.appendChild(password)
+                pwform.appendChild(connect_button)
+
+                var cell = row.insertCell()
+                cell.appendChild(pwform)
+            }
+
+            // add row for new connection
+            var row = tbody.insertRow()
+
+            var conn_form = document.createElement("FORM")
+            conn_form.id = "new_connection"
+            conn_form.onsubmit = function (event) {
+                var inputs = document.querySelectorAll("input[form=new_connection]")
+
+                data = {}
+                for (input of inputs) {
+                    data[input.name] = input.value
+                }
+                for (missing of ['connection_name', 'url', 'username', 'password']) {
+                    if (data[missing] === "") {
+                        alert("Please provide: " + missing)
+                        return false
+                    }
+                }
+                connections.create(env, data.connection_name, data.url, data.username, data.password)
+                    .then(function (response) {
+                        if (response.ok) {
+                            response.json()
+                                .then(function (data) {
+                                    show_available_connections(env, data, conn_table)
+                                })
+                        }
+                    })
+                return false
+            }
+            var conn_name = document.createElement("INPUT")
+            conn_name.type = "input"
+            conn_name.name = "connection_name"
+            conn_name.setAttribute("form", conn_form.id)
+            conn_name.placeholder = "openBIS instance name"
+            row.insertCell().appendChild(conn_form)
+            row.insertCell().appendChild(conn_name)
+
+            var conn_url = document.createElement("INPUT")
+            conn_url.type = "input"
+            conn_url.name = "url"
+            conn_url.setAttribute("form", conn_form.id)
+            conn_url.placeholder = "https://openbis.domain:port"
+            row.insertCell().appendChild(conn_url)
+            row.insertCell()
+
+            var username = document.createElement("INPUT")
+            username.autocomplete = "off"
+            username.type = "text"
+            username.name = "username"
+            username.setAttribute("form", conn_form.id)
+            username.placeholder = "username"
+            var password = document.createElement("INPUT")
+            password.type = "password"
+            password.name = "password"
+            password.autocomplete = "new-password"
+            password.setAttribute("form", conn_form.id)
+            var create_btn = document.createElement("BUTTON")
+            create_btn.setAttribute("form", conn_form.id)
+            create_btn.textContent = "create"
+            var uname_pw_cell = row.insertCell()
+            uname_pw_cell.appendChild(username)
+            uname_pw_cell.appendChild(password)
+            uname_pw_cell.appendChild(create_btn)
+
+            conn_table.innerHTML = ""
+            table_title = document.createElement("STRONG")
+            table_title.textContent = "Please choose a connection"
+            conn_table.appendChild(table_title)
+            conn_table.appendChild(table)
+        }
+
+        return {
+            help: 'configure openBIS connections',
+            icon: 'fa-sliders',
+            help_index: '',
+            handler: function (env) {
+                conn_table = document.createElement("DIV")
+                var dst_title = document.createElement("STRONG")
+                dst_title.textContent = "DataSet type"
+                var dataset_types = document.createElement("SELECT")
+                dataset_types.id = "dataset_type"
+                dataset_types.className = "form-control select-xs"
+
+                var input_fields = document.createElement("DIV")
+                conn_table.id = "openbis_connections"
+
+                var onclick_cbf = function () {
+                    state.connection.candidateName = this.value
+                }
+
+                connections.list(env)
+                    .done(function (data) {
+                        show_available_connections(env, data, conn_table, onclick_cbf)
+                    })
+                    .fail(function (data) {
+                        alert(data.status)
+                    })
+
+                var uploadDialogBox = $('<div/>').append(conn_table)
+
+                function onOk() {
+                    state.connection.name = state.connection.candidateName
+                }
+
+                function onCancel() {
+                    state.connection.candidateName = state.connection.name
+                }
+
+                dialog.modal({
+                    body: uploadDialogBox,
+                    title: 'Choose openBIS connection',
+                    buttons: {
+                        'Cancel': {
+                            click: onCancel
+                        },
+                        'Choose connection': {
+                            class: 'btn-primary btn-large',
+                            click: onOk
+                        }
+                    },
+                    notebook: env.notebook,
+                    keyboard_manager: env.notebook.keyboard_manager
+                })
+            }
+        }
+    }
+)
\ No newline at end of file

jupyter-openbis-extension/static/connections.js

+define([
+        "base/js/utils",
+        "./common"
+    ],
+    function (utils, common) {
+
+        function list(env) {
+
+            var connectionsUrl = env.notebook.base_url + 'openbis/conns'
+            var settings = {
+                url: connectionsUrl,
+                processData: false,
+                type: 'GET',
+                dataType: 'json',
+                contentType: 'application/json'
+            }
+            return utils.ajax(settings)
+        }
+
+
+        function connect(env, connection, username, password) {
+            var url = env.notebook.base_url + 'openbis/conn/' + connection
+            body = {
+                "username": username,
+                "password": password
+            }
+
+            var xsrf_token = common.getCookie('_xsrf')
+            return fetch(url, {
+                method: "PUT",
+                headers: {
+                    "Content-Type": "application/json",
+                    "X-XSRFToken": xsrf_token,
+                    "credentials": "same-origin",
+                },
+                body: JSON.stringify(body)
+            })
+        }
+
+        function create(env, connection_name, connection_url, username, password) {
+            var endpoint = env.notebook.base_url + 'openbis/conns'
+            body = {
+                "name": connection_name,
+                "url": connection_url,
+                "username": username,
+                "password": password
+            }
+
+            var xsrf_token = common.getCookie('_xsrf')
+            return fetch(endpoint, {
+                method: "POST",
+                headers: {
+                    "Content-Type": "application/json",
+                    "X-XSRFToken": xsrf_token,
+                    "credentials": "same-origin",
+                },
+                body: JSON.stringify(body)
+            })
+        }
+
+        return {
+            list: list,
+            create: create,
+            connect: connect
+        }
+    }
+)
\ No newline at end of file

jupyter-openbis-extension/static/downloadDialog.js

+define([
+        "base/js/dialog",
+        "./common",
+        "./state"
+    ],
+    function (dialog, common, state) {
+
+        function writeMetaData(data) {
+            var notebook = IPython.notebook
+            if (typeof notebook.metadata.datasets === 'undefined') {
+                notebook.metadata.datasets = {}
+            }
+            // store metadata about the downloaded files into the notebook-metadata
+            if (data.permId) {
+                notebook.metadata.datasets[data.permId] = {
+                    "permId": data.permId,
+                    "path": data.path,
+                    "dataStore": data.dataStore,
+                    "location": data.location,
+                    "size": data.size,
+                    "status": data.statusText
+                }
+            }
+        }
+
+        function show_datasets_table(env, data, datasets_table, 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%"
+
+            var thead = table.createTHead()
+            var t_row = thead.insertRow()
+            var titles = ['', 'permId', 'Type', 'Experiment', 'Registration Date', 'Status', 'Size']
+            titles.forEach(function (title) {
+                t_row.insertCell().textContent = title
+            })
+            var tbody = table.createTBody()
+
+            for (dataSet of data.dataSets) {
+
+                const permId = document.createElement("INPUT")
+                permId.type = "checkbox"
+                permId.name = "permId"
+                permId.value = dataSet.permId
+                permId.checked = state.selectedDatasets.has(permId.value)
+                permId.onclick = () => permId.checked ? state.selectedDatasets.add(permId.value) : state.selectedDatasets.delete(permId.value)
+
+                var row = tbody.insertRow()
+                row.insertCell().appendChild(permId)
+                row.insertCell().textContent = dataSet.permId
+                row.insertCell().textContent = dataSet.type
+                row.insertCell().textContent = dataSet.experiment
+                row.insertCell().textContent = dataSet.registrationDate
+                row.insertCell().textContent = dataSet.status
+                row.insertCell().textContent = dataSet.size
+            }
+
+            while (datasets_table.firstChild) {
+                datasets_table.removeChild(datasets_table.firstChild);
+            }
+            datasets_table.appendChild(table)
+
+            const totalCount = parseInt(data.totalCount)
+            const count = parseInt(data.count)
+            const startWith = parseInt(data.start_with)
+            const hasNext = startWith + count < totalCount
+            const hasPrevious = startWith > 0
+            const nextCmd = () => getDatasets(env, startWith+5, 5, entityIdentifier, datasets_table, downloadPath)
+            const previousCmd = () => getDatasets(env, startWith-5, 5, entityIdentifier, datasets_table, downloadPath)
+
+            var previous = document.createElement("A")
+            var linkText = document.createTextNode("<<< Previous")
+            previous.appendChild(linkText)
+            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"
+
+            var paging = document.createElement("DIV")
+            paging.style.width = "100%"
+            if (hasPrevious) {
+                paging.appendChild(previous)
+            }
+            if (hasNext) {
+                paging.appendChild(next)
+            }
+
+            datasets_table.appendChild(paging)
+        }
+
+        function getDatasets(env, startWith, count, entityIdentifier, datasets_table, downloadPath) {
+            var connection_name = state.connection.name
+            if (!connection_name) {
+                alert('Please choose a connection')
+                return false
+            }
+
+            currentEntityIdentifier = entityIdentifier.value
+            if (!currentEntityIdentifier) {
+                alert('Please specify a Sample or Experiment identifier/permId')
+                return false
+            }
+            var url = env.notebook.base_url 
+                + 'openbis/sample/' 
+                + connection_name 
+                + '/' 
+                + encodeURIComponent(currentEntityIdentifier)
+                + "?start_with="
+                + startWith 
+                + "&count="
+                + count
+
+            fetch(url)
+                .then(function (response) {
+                    if (response.ok) {
+                        response.json()
+                            .then(function (data) {
+                                show_datasets_table(env, data, datasets_table, downloadPath, entityIdentifier)
+                            })
+                    } else {
+                        response.json()
+                            .then(function (error) {
+                                console.log(error.reason)
+                                alert("Error: " + error.reason)
+                            })
+                    }
+                })
+                .catch(function (error) {
+                    console.error('A serious network problem occured:', error)
+                })
+        }
+
+
+        return {
+            help: 'Download openBIS datasets to your local harddrive',
+            icon: 'fa-download',
+            help_index: '',
+            handler: function (env) {
+                state.selectedDatasets = new Set([])
+
+                conn_table = document.createElement("DIV")
+                conn_table.id = "openbis_connections"
+
+                var showDataSets = document.createElement("DIV")
+                var title = document.createElement("STRONG")
+                title.textContent = "Sample or Experiment identifier/permId: "
+                showDataSets.appendChild(title)
+                showDataSets.style.marginTop = '10px'
+
+                var entityIdentifier = document.createElement("INPUT")
+                entityIdentifier.type = "text"
+                entityIdentifier.name = "entityIdentifier"
+                entityIdentifier.size = 40
+                entityIdentifier.placeholder = "Sample or Experiment identifier/permId"
+                entityIdentifier.value = ''
+
+                var datasets_table = document.createElement("DIV")
+
+                var show_datasets_btn = document.createElement("BUTTON")
+                show_datasets_btn.className = "btn-info btn-xs"
+                show_datasets_btn.textContent = "show datasets"
+                show_datasets_btn.style.margin="10px"
+
+                showDataSets.appendChild(entityIdentifier)
+                showDataSets.appendChild(show_datasets_btn)
+                showDataSets.appendChild(datasets_table)
+
+                var dataset_direct = document.createElement("P")
+                dataset_direct.style.marginTop = '10px'
+                dataset_direct.innerHTML = '<strong>Enter DataSet permId directly: </strong>'
+
+                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 = ''
+
+                show_datasets_btn.onclick = 
+                    () => getDatasets(env, 0, 5, entityIdentifier, datasets_table, downloadPath)
+                
+                var path = document.createElement("DIV")
+                path.innerHTML = "<strong>download data to path: </strong>"
+                path.appendChild(downloadPath)
+
+                var download_dialog_box = document.createElement("DIV")
+                download_dialog_box.appendChild(conn_table)
+                download_dialog_box.appendChild(showDataSets)
+                download_dialog_box.appendChild(dataset_direct)
+                download_dialog_box.appendChild(path)
+
+                function downloadDataset(connection_name, selectedPermIds, downloadPath) {
+
+                    for (permId of selectedPermIds) {
+                        var downloadUrl = env.notebook.base_url + 'openbis/dataset/' +
+                            connection_name + '/' + permId + '/' + encodeURIComponent(downloadPath)
+
+                        fetch(downloadUrl)
+                            .then(function (response) {
+                                if (response.ok) {
+                                    response.json()
+                                        .then(function (data) {
+                                            common.createFeedback('success', data.statusText)
+
+                                            // successful download:
+                                            // write statusText from returned data to notebooks metadata
+                                            writeMetaData(data)
+
+                                            // keep current download path for later use
+                                            currentDownloadPath = downloadPath
+                                        })
+                                } else {
+                                    response.json()
+                                        .then(function (error) {
+                                            console.log(error.reason)
+                                            alert("Error: " + error.reason)
+                                        })
+                                }
+                            })
+                            .catch(function (error) {
+                                console.error('A serious network problem occured:', error)
+                            })
+                    }
+                }
+
+                function onDownloadClick() {
+                    var selected_conn = state.connection.name
+                    if (!selected_conn) {
+                        alert('please choose a connection')
+                        return false
+                    }
+
+                    var selectedPermIds = []
+                    for (row of state.selectedDatasets) {
+                        selectedPermIds.push(row)
+                    }
+                    if (datasetPermId.value) {
+                        selectedPermIds.push(datasetPermId.value)
+                    }
+                    if (!selectedPermIds) {
+                        alert('please select a dataset or provide a permId')
+                        return false
+                    }
+
+                    if (!downloadPath.value) {
+                        alert('Please specify where you would like to download your files!')
+                        return false
+                    }
+
+                    downloadDataset(selected_conn, selectedPermIds, downloadPath.value)
+                }
+
+                dialog.modal({
+                    body: download_dialog_box,
+                    title: 'Download openBIS DataSets',
+                    buttons: {
+                        'Cancel': {},
+                        'Download': {
+                            class: 'btn-primary btn-large',
+                            click: onDownloadClick,
+                        }
+                    },
+                    notebook: env.notebook,
+                    keyboard_manager: env.notebook.keyboard_manager
+                })
+            }
+        }
+    }
+)
\ No newline at end of file

jupyter-openbis-extension/static/main.js

+define([
+        "base/js/namespace",
+        "./connectionDialog",
+        "./uploadDialog",
+        "./downloadDialog"
+    ],
+    function (IPython, connectionDialog, uploadDialog, downloadDialog) {
+        var ds_type = document.createElement("SELECT")
+        ds_type.size = '40'
+        ds_type.className = "select-xs"
+        ds_type.id = "dataset_type"
+
+        function _onLoad() {
+            // show connections
+            var configure_openbis_connections = IPython.keyboard_manager.actions.register(
+                connectionDialog, 'openbis-connections', 'jupyter-openBIS')
+
+            // dnownload
+            var download_datasets = IPython.keyboard_manager.actions.register(
+                downloadDialog, 'openbis-dataset-download', 'jupyter-openBIS')
+
+            // upload
+            var upload_datasets = IPython.keyboard_manager.actions.register(
+                uploadDialog, 'openbis-dataset-upload', 'jupyter-openBIS')
+
+            // add button for new action
+            IPython.toolbar.add_buttons_group([configure_openbis_connections, download_datasets, upload_datasets])
+        }
+
+        return {
+            load_ipython_extension: _onLoad
+        }
+    })
\ No newline at end of file

jupyter-openbis-extension/static/state.js

+define([],
+    function () {
+        return {
+            // connection dialog
+            connection: {
+                name: null,
+                candidateName: null
+            },
+
+            // upload dialog
+            uploadDataSetType: null,
+            uploadDataSetTypes: {},
+            uploadEntityIdentifier: '',
+            datasetCheckboxes: [],
+            fileCheckboxes: [],
+            selectedFiles: [],
+            unselectedDatasets: [],
+
+            // download dialog
+            selectedDatasets: new Set([])
+        }
+    }
+)
\ No newline at end of file

jupyter-openbis-extension/static/uploadDialog.js

+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.toLowerCase()] = 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) {
+            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
+                dataset_types.style.padding = 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 or Experiment identifier/permId"
+
+                var sample_error = createErrorElement('entityIdentifier')
+
+                var entityIdentifier = document.createElement("INPUT")
+                entityIdentifier.type = "text"
+                entityIdentifier.name = 'entityIdentifier'
+                entityIdentifier.placeholder = "Sample or Experiment identifier/permId"
+                entityIdentifier.value = state.uploadEntityIdentifier
+                entityIdentifier.size = "90"
+                entityIdentifier.style.width="100%"
+
+                var ds_title = document.createElement("STRONG")
+                var dataSetListContainer = document.createElement("DIV")
+                if (env.notebook.metadata.datasets) {
+                    ds_title.textContent = "DataSets"
+                    dataSetListContainer.style.maxHeight="150px"
+                    dataSetListContainer.style.overflow="auto"
+                    get_dataset_list(env, dataSetListContainer)
+                }
+
+                var files_title = document.createElement("STRONG")
+                files_title.textContent = "Files"
+                var fileListContainer = document.createElement("DIV")
+                fileListContainer.style.maxHeight="150px"
+                fileListContainer.style.overflow="auto"
+                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(entityIdentifier)
+                inputs.appendChild(ds_title)
+                inputs.appendChild(dataSetListContainer)
+                inputs.appendChild(files_title)
+                inputs.appendChild(fileListContainer)
+
+                var uploadDialogBox = $('<div/>').append(inputs)
+
+                function saveState() {
+                    state.uploadDataSetTypes[state.uploadDataSetType] = {}
+                    for (element of input_fields.children) {
+                        if (element.nodeName === "INPUT" && state.uploadDataSetType != null) {
+                            state.uploadDataSetTypes[state.uploadDataSetType][element.name] = element.value
+                        }
+                    }
+                    state.uploadEntityIdentifier = entityIdentifier.value
+                    state.unselectedDatasets = state.datasetCheckboxes.filter(cb => !cb.checked).map(cb => cb.value)
+                    state.selectedFiles = state.fileCheckboxes.filter(cb => cb.checked).map(cb => cb.value)
+                }
+
+                function onOk() {
+                    var connection_name = state.connection.name
+
+                    if (!connection_name) {
+                        alert("No connection selected")
+                        return false
+                    }
+
+                    var uploadUrl = env.notebook.base_url + 'openbis/dataset/' + connection_name
+
+                    var notebook = IPython.notebook
+                    var files = state.fileCheckboxes.filter(cb => cb.checked).map(cb => cb.value)
+                    var re = /\/notebooks\/(.*?)$/
+                    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),
+                        "entityIdentifier": entityIdentifier.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.toLowerCase()
+                                        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
+                    })
+                }
+            }
+        }
+    }
+)
\ No newline at end of file