From 05d4f68c382c4891eac40b00cba1cd9677f99e91 Mon Sep 17 00:00:00 2001
From: vermeul <swen@ethz.ch>
Date: Wed, 20 Mar 2019 10:10:20 +0100
Subject: [PATCH] divided server into several pieces
---
jupyter-openbis-extension/connection.py | 168 ++++++++
jupyter-openbis-extension/dataset.py | 280 ++++++++++++++
jupyter-openbis-extension/sample.py | 54 +++
jupyter-openbis-extension/server.py | 487 +-----------------------
setup.py | 2 +-
5 files changed, 506 insertions(+), 485 deletions(-)
create mode 100644 jupyter-openbis-extension/connection.py
create mode 100644 jupyter-openbis-extension/dataset.py
create mode 100644 jupyter-openbis-extension/sample.py
diff --git a/jupyter-openbis-extension/connection.py b/jupyter-openbis-extension/connection.py
new file mode 100644
index 0000000..4999b5c
--- /dev/null
+++ b/jupyter-openbis-extension/connection.py
@@ -0,0 +1,168 @@
+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
+
diff --git a/jupyter-openbis-extension/dataset.py b/jupyter-openbis-extension/dataset.py
new file mode 100644
index 0000000..d105181
--- /dev/null
+++ b/jupyter-openbis-extension/dataset.py
@@ -0,0 +1,280 @@
+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 = []
+
+ sample = None
+ experiment = None
+
+ if (data.get('sampleIdentifier')):
+ try:
+ sample = conn.openbis.get_sample(data.get('sampleIdentifier'))
+ except Exception as e:
+ print(e)
+ errors.append(
+ {"sampleIdentifier" : 'No such sample: {}'.format(data.get('sampleIdentifier')) }
+ )
+ else:
+ errors.append(
+ {"sampleIdentifier": "please provide a sample identifier"}
+ )
+ print("--------------_HERE_-----------1")
+
+ if (data.get('experimentIdentifier')):
+ try:
+ experiment = conn.openbis.get_experiment(data.get('experimentIdentifier'))
+ except Exception as e:
+ print(e)
+ errors.append(
+ {"experimentIdentifier" : 'No such experiment: {}'.format(data.get('experimentIdentifier')) }
+ )
+ print("--------------_HERE_-----------2")
+
+
+ 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,
+ 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("--------------_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
+ })
+
diff --git a/jupyter-openbis-extension/sample.py b/jupyter-openbis-extension/sample.py
new file mode 100644
index 0000000..e892c8f
--- /dev/null
+++ b/jupyter-openbis-extension/sample.py
@@ -0,0 +1,54 @@
+from notebook.base.handlers import IPythonHandler
+import numpy as np
+from .connection import openbis_connections
+
+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
+ })
+
+
diff --git a/jupyter-openbis-extension/server.py b/jupyter-openbis-extension/server.py
index f44078d..df56bbc 100644
--- a/jupyter-openbis-extension/server.py
+++ b/jupyter-openbis-extension/server.py
@@ -1,12 +1,10 @@
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():
@@ -140,483 +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 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
- })
-
-
-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 = []
-
- sample = None
- experiment = None
-
- if (data.get('sampleIdentifier')):
- try:
- sample = conn.openbis.get_sample(data.get('sampleIdentifier'))
- except Exception as e:
- print(e)
- errors.append(
- {"sampleIdentifier" : 'No such sample: {}'.format(data.get('sampleIdentifier')) }
- )
- else:
- errors.append(
- {"sampleIdentifier": "please provide a sample identifier"}
- )
- print("--------------_HERE_-----------1")
-
- if (data.get('experimentIdentifier')):
- try:
- experiment = conn.openbis.get_experiment(data.get('experimentIdentifier'))
- except Exception as e:
- print(e)
- errors.append(
- {"experimentIdentifier" : 'No such experiment: {}'.format(data.get('experimentIdentifier')) }
- )
- print("--------------_HERE_-----------2")
-
- 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,
- 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)
- })
- 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("--------------_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)
diff --git a/setup.py b/setup.py
index affc104..63ce3a6 100644
--- a/setup.py
+++ b/setup.py
@@ -1,4 +1,3 @@
-import os
import sys
if sys.version_info < (3,3):
@@ -25,6 +24,7 @@ setup(
'jupyter-nbextensions-configurator',
'jupyter',
'pybis>=1.8.1',
+ 'numpy',
],
python_requires=">=3.3",
classifiers=[
--
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