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+++ b/jupyter-openbis-extension/server.py
@@ -0,0 +1,238 @@
+from notebook.utils import url_path_join
+from notebook.base.handlers import IPythonHandler
+from pybis import Openbis
+
+import json
+import os
+import urllib
+from subprocess import check_output
+from urllib.parse import urlsplit, urlunsplit
+import yaml
+
+openbis_connections = {}
+
+
+def _jupyter_server_extension_paths():
+ return [{'module': 'jupyter-openbis-extension.server'}]
+
+def _load_configuration(filename='openbis-connections.yaml'):
+
+ home = os.path.expanduser("~")
+ abs_filename = os.path.join(home, '.jupyter', filename)
+
+ with open(abs_filename, 'r') as stream:
+ try:
+ config = yaml.safe_load(stream)
+ return config
+ except yaml.YAMLexception as exc:
+ print(exc)
+ return None
+
+
+def load_jupyter_server_extension(nb_server_app):
+ """Call when the extension is loaded.
+ :param nb_server_app: Handle to the Notebook webserver instance.
+ """
+
+ # load the configuration file
+ config = _load_configuration()
+ if config is not None:
+ for conn in config['connections']:
+ try:
+ register_connection(conn)
+ except Exception as exc:
+ print(exc)
+
+
+ web_app = nb_server_app.web_app
+ host_pattern = '.*$'
+
+ base_url = web_app.settings['base_url']
+
+ web_app.add_handlers(
+ host_pattern,
+ [(url_path_join(
+ base_url,
+ '/openbis/dataset/(?P<connection_name>.*)?/(?P<permId>.*)'),
+ DataSetHandler
+ )]
+ )
+ web_app.add_handlers(
+ host_pattern,
+ [(url_path_join(
+ base_url,
+ '/openbis/sample/(?P<connection_name>.*)?/(?P<permId>.*)'),
+ SampleHandler
+ )]
+ )
+ web_app.add_handlers(
+ host_pattern,
+ [(url_path_join(base_url, '/openbis/conn'), OpenBISHandler)]
+ )
+
+
+ print("pybis loaded: {}".format(Openbis))
+
+
+def register_connection(connection_info):
+
+ conn = OpenBISConnection(
+ name = connection_info['name'],
+ url = connection_info['url'],
+ verify_certificates = connection_info['verify_certificates'],
+ username = connection_info['username'],
+ password = connection_info['password'],
+ status = 'not connected',
+ )
+ openbis_connections[conn.name] = conn
+
+ openbis = Openbis(
+ url = conn.url,
+ verify_certificates = conn.verify_certificates
+ )
+ conn.openbis = openbis
+
+ try:
+ openbis.login(
+ username = conn.username,
+ password = conn.password
+ )
+ conn.status = 'connected'
+ except Exception as exc:
+ conn.status = 'FAILED: {}'.format(exc)
+ raise exc
+
+
+def check_connection(connection_name):
+ """Checks whether connection is valid and session is still active
+ and tries to reconnect, if possible. Returns the active session
+ """
+
+ if connection_name not in openbis_connections:
+ return None
+
+ conn = openbis_connections[connection_name]
+ if not conn.openbis.isSessionActive():
+ conn.openbis.login(conn.username, conn.password)
+
+
+class OpenBISConnection:
+ """register an openBIS connection
+ """
+
+ def __init__(self, **kwargs):
+ for key in kwargs:
+ setattr(self, key, kwargs[key])
+
+ def is_session_active(self):
+ return self.openbis.is_session_active()
+
+ def reconnect(self):
+ openbis.login(self.username, self.password)
+
+
+class OpenBISHandler(IPythonHandler):
+ """Handle the requests to /openbis/conn
+ """
+
+ def get(self):
+ """returns all available openBIS connections
+ """
+ connections= []
+ for conn in openbis_connections.values():
+ connections.append({
+ 'name': conn.name,
+ 'url' : conn.url
+ })
+
+ self.write({
+ 'connections': connections
+ })
+ return
+
+class SampleHandler(IPythonHandler):
+ """Handle the requests for /openbis/sample/connection/permId"""
+
+ def get_datasets(self, conn, permId):
+ sample = None
+ try:
+ sample = conn.openbis.get_sample(permId)
+ except Exception:
+ self.send_error(
+ reason = 'No such sample found: {}'.format(permId)
+ )
+ return
+
+ datasets = sample.get_datasets().df
+ dataset_records = datasets.to_dict(orient='records')
+ self.write({'dataSets': dataset_records })
+ return
+
+ 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.send_error(
+ reason = 'connection {} was not found'.format(params['connection_name'])
+ )
+ return
+
+ results = self.get_datasets(conn, params['permId'])
+
+
+class DataSetHandler(IPythonHandler):
+ """Handle the requests for /openbis/dataset/connection/permId"""
+
+
+ def download_data(self, conn, permId):
+ if not conn.is_session_active():
+ try:
+ conn.reconnect()
+ except Exception as exc:
+ self.send_error(
+ reason = 'connection to {} could not be established: {}'.format(conn.name, exc)
+ )
+ return
+
+ try:
+ dataset = conn.openbis.get_dataset(permId)
+ except Exception as exc:
+ self.send_error(
+ reason = 'No such dataSet found: {}'.format(permId)
+ )
+ return
+
+ # dataset was found, download the data to the disk
+ try:
+ destination = dataset.download()
+ except Exception as exc:
+ print(exc)
+ self.send_error(
+ reason = 'Data for DataSet {} could not be downloaded: {}'.format(permId, exc)
+ )
+ return
+
+ # return success message
+ path = os.path.join(destination, dataset.permId)
+ self.write({
+ 'permId' : dataset.permId,
+ '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.send_error(
+ reason = 'connection {} was not found'.format(params['connection_name'])
+ )
+ return
+
+ results = self.download_data(conn, params['permId'])
+