diff --git a/jupyter-openbis-extension/server.py b/jupyter-openbis-extension/server.py
index ec0ef7f2cf48f957ce696e2a25e42362a3be61eb..996a942b3b379a113ffc035a5599f81a1ee6853f 100644
--- a/jupyter-openbis-extension/server.py
+++ b/jupyter-openbis-extension/server.py
@@ -3,12 +3,8 @@ from notebook.base.handlers import IPythonHandler
from pybis import Openbis
import numpy as np
-import json
import os
-import urllib
-from urllib.parse import unquote, unquote_plus
-from subprocess import check_output
-from urllib.parse import urlsplit, urlunsplit
+from urllib.parse import unquote
import yaml
openbis_connections = {}
@@ -17,18 +13,29 @@ 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_configuration(paths, filename='openbis-connections.yaml'):
+
+ if paths is None:
+ paths = []
+ home = os.path.expanduser("~")
+ paths.append(os.path.join(home, '.jupyter'))
+
+ # look in all config file paths of jupyter
+ # for openbis connection files and load them
+ connections = []
+ for path in paths:
+ abs_filename = os.path.join(path, filename)
+ if os.path.isfile(abs_filename):
+ with open(abs_filename, 'r') as stream:
+ try:
+ config = yaml.safe_load(stream)
+ for connection in config['connections']:
+ connections.append(connection)
+ except yaml.YAMLexception as exc:
+ print(exc)
+ return None
+
+ return connections
def load_jupyter_server_extension(nb_server_app):
@@ -37,20 +44,29 @@ def load_jupyter_server_extension(nb_server_app):
"""
# load the configuration file
- #print(dir(nb_server_app))
- print(nb_server_app.config_file_paths)
- config = _load_configuration()
- if config is not None:
- for conn in config['connections']:
- try:
- register_connection(conn)
- except Exception as exc:
- print(exc)
-
+ # and register the openBIS connections.
+ # If username and password is available, try to connect to the server
+ connections = _load_configuration(
+ paths = nb_server_app.config_file_paths,
+ filename = 'openbis-connections.yaml'
+ )
+ for connection_info in connections:
+ conn = register_connection(connection_info)
+ print("Registered: {}".format(conn.url))
+ if conn.username and conn.password:
+ try:
+ conn.login()
+ print("Successfully connected to: {}".format(conn.url))
+ except ValueError:
+ print("Incorrect username or password for: {}".format(conn.url))
+ except Exception:
+ print("Cannot establish connection to: {}".format(conn.url))
+
+ # Add URL handlers to our web_app
+ # see Tornado documentation: https://www.tornadoweb.org
web_app = nb_server_app.web_app
host_pattern = '.*$'
-
base_url = web_app.settings['base_url']
# DataSet download
@@ -61,7 +77,9 @@ def load_jupyter_server_extension(nb_server_app):
'/openbis/dataset/(?P<connection_name>.*)?/(?P<permId>.*)?/(?P<downloadPath>.*)'),
DataSetDownloadHandler
)]
- )
+ )
+
+ # DataSet upload
web_app.add_handlers( host_pattern, [(
url_path_join(
base_url,
@@ -69,7 +87,21 @@ def load_jupyter_server_extension(nb_server_app):
),
DataSetUploadHandler
)]
- )
+ )
+
+ # DataSet-Types
+ web_app.add_handlers(
+ host_pattern,
+ [(
+ url_path_join(
+ base_url,
+ '/openbis/datasetTypes/(?P<connection_name>.*)'
+ ),
+ DataSetTypesHandler
+ )]
+ )
+
+ # DataSets for Sample identifier/permId
web_app.add_handlers(
host_pattern,
[(
@@ -79,12 +111,29 @@ def load_jupyter_server_extension(nb_server_app):
),
SampleHandler
)]
- )
+ )
+
+ # OpenBIS connections
+ web_app.add_handlers(
+ host_pattern,
+ [(
+ url_path_join(
+ base_url,
+ '/openbis/conns'
+ ),
+ OpenBISConnections
+ )]
+ )
+
+ # Modify / reconnect to a connection
web_app.add_handlers(
host_pattern,
[(
- url_path_join(base_url, '/openbis/conn'),
- OpenBISHandler
+ url_path_join(
+ base_url,
+ '/openbis/conn/(?P<connection_name>.*)'
+ ),
+ OpenBISConnectionHandler
)]
)
@@ -92,110 +141,174 @@ def load_jupyter_server_extension(nb_server_app):
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',
+ 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
- try:
- openbis = Openbis(
- url = conn.url,
- verify_certificates = conn.verify_certificates
- )
- conn.openbis = openbis
- conn.ds_types = {}
-
- openbis.login(
- username = conn.username,
- password = conn.password
- )
- conn.status = 'connected'
-
- print('connected to {}'.format(conn.name))
- except Exception as exc:
- conn.status = 'FAILED: {}'.format(exc)
- print('ERROR: could not connected to {}. Reason: {}'.format(conn.name, exc))
- raise exc
-
- try:
- # add dataset types to the connection
- dataset_types = conn.openbis.get_dataset_types()
- dts = dataset_types.df.to_dict(orient='records')
- 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
- conn.ds_types = dts
- except Exception as e:
- print('ERROR: {}'.format(e))
-
-
-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 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 reconnect(self):
- self.openbis.login(self.username, self.password)
-
-
-class OpenBISHandler(IPythonHandler):
- """Handle the requests to /openbis/conn
- """
+ 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()
- connections.append({
- 'name' : conn.name,
- 'url' : conn.url,
- 'status' : conn.status,
- 'ds_types': conn.ds_types,
+ 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,
- 'connections': connections,
+ '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.reconnect()
+ conn.login()
except Exception as exc:
self.write({
"reason" : 'connection to {} could not be established: {}'.format(conn.name, exc)
@@ -229,6 +342,7 @@ class SampleHandler(IPythonHandler):
params['connection_name']
)
})
+ return
datasets = self.get_datasets(conn, params['permId'])
if datasets is not None:
@@ -246,8 +360,9 @@ class DataSetDownloadHandler(IPythonHandler):
def download_data(self, conn, permId, downloadPath=None):
if not conn.is_session_active():
try:
- conn.reconnect()
+ conn.login()
except Exception as exc:
+ self.set_status(500)
self.write({
"reason" : 'connection to {} could not be established: {}'.format(conn.name, exc)
})
@@ -266,6 +381,7 @@ class DataSetDownloadHandler(IPythonHandler):
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)
})
@@ -274,6 +390,7 @@ class DataSetDownloadHandler(IPythonHandler):
# return success message
path = os.path.join(downloadPath, dataset.permId)
self.write({
+ 'url' : conn.url,
'permId' : dataset.permId,
'path' : path,
'dataStore' : dataset.dataStore,
@@ -290,6 +407,7 @@ class DataSetDownloadHandler(IPythonHandler):
try:
conn = openbis_connections[params['connection_name']]
except KeyError:
+ self.set_status(404)
self.write({
"reason":'connection {} was not found'.format(params['connection_name'])
})
@@ -298,14 +416,52 @@ class DataSetDownloadHandler(IPythonHandler):
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.reconnect()
+ conn.login()
except Exception as exc:
self.write({
"reason": 'connection to {} could not be established: {}'.format(conn.name, exc)