diff --git a/src/core-plugins/jupyter-api/1/as/initialize-master-data.py b/src/core-plugins/jupyter-api/1/as/initialize-master-data.py
deleted file mode 100644
index ff8b7629d7cbbf8bad029b2c79c9b6e1483d1c9f..0000000000000000000000000000000000000000
--- a/src/core-plugins/jupyter-api/1/as/initialize-master-data.py
+++ /dev/null
@@ -1,94 +0,0 @@
-#
-# Copyright 2016 ETH Zuerich, Scientific IT Services
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-
-##
-## Configuration
-##
-import sys
-
-# MasterDataRegistrationTransaction Class
-import os
-import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.DataType as DataType
-
-##
-## Globals
-##
-propertiesCache = {};
-samplesCache = {};
-tr = service.transaction();
-
-##
-## API Facade
-##
-
-
-def createDataSetTypeWithProperties(dataSetCode, description, properties):
- newDataSet = tr.getOrCreateNewDataSetType(dataSetCode);
- newDataSet.setDescription(description);
- addProperties(newDataSet, properties);
-
-def addProperties(entity, properties):
- for property in properties:
- addProperty(entity, property[0], property[1], property[2], property[3], property[4], property[5], property[6], property[7]);
-
-def addProperty(entity, propertyCode, section, propertyLabel, dataType, vocabularyCode, propertyDescription, managedScript, dynamicScript):
- property = None;
-
- if propertyCode in propertiesCache:
- property = propertiesCache[propertyCode];
- else:
- property = createProperty(propertyCode, dataType, propertyLabel, propertyDescription, vocabularyCode);
-
- propertyAssignment = tr.assignPropertyType(entity, property);
- if section is not None:
- propertyAssignment.setSection(section);
- propertyAssignment.setShownEdit(True);
-
- if managedScript != None:
- propertyAssignment.setManaged(True);
- propertyAssignment.setScriptName(managedScript);
- if dynamicScript != None:
- propertyAssignment.setDynamic(True);
- propertyAssignment.setShownEdit(False);
- propertyAssignment.setScriptName(dynamicScript);
-
-def createProperty(propertyCode, dataType, propertyLabel, propertyDescription, vocabularyCode):
- property = tr.getOrCreateNewPropertyType(propertyCode, dataType);
- property.setDescription(propertyDescription);
- property.setLabel(propertyLabel);
- propertiesCache[propertyCode] = property;
- if dataType == DataType.CONTROLLEDVOCABULARY:
- property.setVocabulary(vocabulariesCache[vocabularyCode]);
- return property;
-
-def initJupyterMasterData():
- ##
- ## Property Types for annotations
- ##
-
- ##
- ## DataSet Types
- ##
- createDataSetTypeWithProperties("JUPYTER_CONTAINER", "Jupyter Analysis Results", [
- ["NAME", None, "Name", DataType.VARCHAR, None, "Name", None, None],
- ["DESCRIPTION", None, "Description", DataType.MULTILINE_VARCHAR, None, "A Description", None, None],
- ]);
-
- createDataSetTypeWithProperties("JUPYTER_RESULT", "Analysis Results Files", []);
- createDataSetTypeWithProperties("JUPYTER_NOTEBOOK", "Analysis Notebook Files", []);
-
-
-initJupyterMasterData();
\ No newline at end of file
diff --git a/src/core-plugins/jupyter-api/1/dss/reporting-plugins/jupyter-uploader-api/dataset-uploader-api.py b/src/core-plugins/jupyter-api/1/dss/reporting-plugins/jupyter-uploader-api/dataset-uploader-api.py
deleted file mode 100644
index f34791fcf099a27701b1b000a500e7037c76b5e6..0000000000000000000000000000000000000000
--- a/src/core-plugins/jupyter-api/1/dss/reporting-plugins/jupyter-uploader-api/dataset-uploader-api.py
+++ /dev/null
@@ -1,317 +0,0 @@
-#
-# Copyright 2016 ETH Zuerich, Scientific IT Services
-#
-# Licensed under the Apache License, Version 2.0 (the "License")
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-
-# IDataSetRegistrationTransactionV2 Class
-from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
-from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria import MatchClause, SearchOperator, MatchClauseAttribute
-from ch.systemsx.cisd.openbis.dss.generic.shared import ServiceProvider
-
-from org.apache.commons.io import IOUtils
-from java.io import File
-from java.io import FileOutputStream
-from java.lang import System
-#from net.lingala.zip4j.core import ZipFile
-from ch.systemsx.cisd.common.exceptions import UserFailureException
-
-import time
-import subprocess
-import os
-import re
-import sys
-import shutil
-import errno
-
-
-def getSampleByIdentifier(transaction, identifier):
- sample = transaction.getSampleForUpdate(identifier)
- if sample is None:
- raise UserFailureException("no sample found with this identifier: {}".format(identifier))
- return sample
-
-def getExperimentByIdentifier(transaction, identifier):
- experiment = transaction.getExperimentForUpdate(identifier)
- if experiment is None:
- raise UserFailureException("no experiment found with this identifier: {}".format(identifier))
-
- return experiment
-
-def get_dataset_for_name(transaction, dataset_name):
-
- search_service = transaction.getSearchService()
- criteria = SearchCriteria()
- criteria.addMatchClause(MatchClause.createPropertyMatch('NAME', dataset_name))
- found = list(search_service.searchForDataSets(criteria))
- if len(found) == 1:
- #print("DataSetCode of found dataset = " + found[0].getDataSetCode())
- return transaction.getDataSetForUpdate(found[0].getDataSetCode())
- else:
- return None
-
-
-def get_dataset_for_permid(transaction, permid):
-
- search_service = transaction.getSearchService()
- criteria = SearchCriteria()
- criteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, permid));
-
- found = list(search_service.searchForDataSets(criteria))
- if len(found) == 1:
- return found[0]
- else:
- return None
-
-
-def process(transaction, parameters, tableBuilder):
- '''
- This method is called from openBIS DSS.
- The transaction object has a number of methods described in ...
- The parameters are passed with the createReportFromAggregationService method
- and need to be accessed like this:
- parameters.get('my_param')
- tableBuilder is needed to create an appropiate return message.
- A number of magic variables are present, described in PluginScriptRunnerFactory:
- - userSessionToken : the Session Token used by every call
- - userId : the username
- - searchService :
- - searchServiceUnfiltered :
- - queryService :
- - mailService :
- - authorizationService :
- - contentProvider :
- - contentProviderUnfiltered
-
- '''
- transaction.setUserId(userId)
- #print(dir())
- ## any print statements is written to openbis/servers/datastore_server/log/startup_log.txt
- #print('userSessionToken: ' + userSessionToken)
-
-
- # get sample to connect the container to
- sample = None
- sampleId = parameters.get("sampleId")
- if sampleId is not None:
- #print('looking for sample with identifier: ' + sampleId['identifier'])
- sample = getSampleByIdentifier(transaction, sampleId)
-
- experiment = None
- experimentId = parameters.get("experimentId")
- if experimentId is not None:
- #print('looking for experiment with identifier: ' + sampleId['identifier'])
- experiment = getExperimentByIdentifier(transaction, experimentId)
-
- if sample is None and experiment is None:
- raise UserFailureException("to create a DataSet, either a sampleId or an experimentId must be present")
-
- parent_datasets = []
- if parameters.get('parentIds') is not None:
- for parentId in parameters.get('parentIds'):
- parent_datasets.append(parentId)
- #print("parent_datasets = " + str(parent_datasets))
-
- everything_ok = True
-
- permId = None
- dataset_codes= []
-
- if parameters.get("dataSets") is not None:
- for ds in parameters.get("dataSets"):
- dataset_code = register_dataset(
- transaction,
- ds.get("dataSetType"),
- sample,
- experiment,
- ds.get("parentIds"),
- ds.get("properties"),
- ds.get("sessionWorkspaceFolder"),
- ds.get("fileNames"),
- ds.get("folder")
- )
- dataset_codes.append(dataset_code)
-
-
- # put the newly created dataset into a container
- if parameters.get("containers") is not None:
- #print("...creating container...")
- for container in parameters.get("containers"):
- new_cont = register_container(
- transaction,
- container.get("dataSetType"),
- sample,
- experiment,
- parent_datasets,
- container.get("properties"),
- dataset_codes
- )
- # just return the permId of the container, not of all created dataSets
- dataset_codes = [new_cont.getDataSetCode()]
-
- permId = dataset_codes[0]
-
- # create the dataset
- if everything_ok:
- # Success message
- tableBuilder.addHeader("STATUS")
- tableBuilder.addHeader("MESSAGE")
- tableBuilder.addHeader("RESULT")
- row = tableBuilder.addRow()
- row.setCell("STATUS","OK")
- row.setCell("MESSAGE", "Dataset registration successful")
- row.setCell("RESULT", permId)
-
- else:
- # Error message
- tableBuilder.addHeader("STATUS")
- tableBuilder.addHeader("MESSAGE")
- row = tableBuilder.addRow()
- row.setCell("STATUS","FAIL")
- row.setCell("MESSAGE", "Dataset registration failed")
-
-
-def register_container(transaction, dataset_type, sample, experiment, parent_datasets, properties, contained_dataset_codes ):
-
- container_name = properties.get("NAME")
- #print("check if the JUPYTER_CONTAINER already exists with name: "+ container_name)
- # make sure container dataset doesn't exist yet
- container = get_dataset_for_name(transaction, container_name)
-
- if container is None:
- #print("creating new JUPYTER_CONTAINER dataset... with name: " + container_name)
- # Create new container (a dataset of type "JUPYTER_CONTAINER")
- container = transaction.createNewDataSet(dataset_type)
- container.setSample(sample)
- container.setExperiment(experiment)
- container.setParentDatasets(parent_datasets)
- #container.setRegistrator(userId)
- else:
- print("JUPYTER_CONTAINER already exists: " + container_name)
-
- #print("setting properties...")
- for key in properties.keySet():
- propertyValue = unicode(properties[key])
- #print("container: setting "+key+"="+propertyValue)
-
- if propertyValue == "":
- propertyValue = None
- container.setPropertyValue(key,propertyValue)
-
- container.setContainedDataSetCodes(contained_dataset_codes)
- print("JUPYTER_CONTAINER permId: " + container.getDataSetCode())
-
- return container
-
-
-def register_dataset(transaction, dataset_type, sample, experiment, parentIds, properties, ws_folder, file_names, folder):
- """ creates a new dataset of a given type.
- - the result files are copied from the session workspace
- to a temp dir close to the DSS: prepareFilesForRegistration()
- - from there, the files are moved to the DSS: transaction.moveFile()
- - finally, the remaining files are deleted from the session workspace
- """
-
- print("creating dataset of type: " + dataset_type)
- dataset = transaction.createNewDataSet(dataset_type)
- dataset.setSample(sample)
- dataset.setExperiment(experiment)
-
- parents = []
- if parentIds is not None:
- for parentId in parentIds:
- parents.append(parentId)
- dataset.setParentDatasets(parents)
-
- # setting any given properties
- for key in properties.keySet():
- propertyValue = unicode(properties[key]);
- print("setting propertyValue: "+key + " = " + propertyValue)
- if propertyValue == "":
- propertyValue = None;
- dataset.setPropertyValue(key,propertyValue);
-
- print("dataset created with permId: " + dataset.getDataSetCode())
- print("workspace folder is: " + ws_folder)
-
- # create temporary folder in incoming-dir ( openbis/servers/datastore_server/data/incoming )
- threadProperties = getThreadProperties(transaction)
- #incoming_dir = os.path.join( threadProperties[u'incoming-dir'], str(time.time()) )
- if folder is None:
- folder = dataset_type
- incoming_dir = os.path.join( threadProperties[u'incoming-dir'], folder )
- print("incoming folder is: " + incoming_dir)
-
- dss_service = ServiceProvider.getDssServiceRpcGeneric().getService()
-
- # copy all files from session workspace to (temporary) incoming directory.
- for file_name in file_names:
- ws_file_path = os.path.join(ws_folder, file_name)
- print("copying file from session workspace: " + ws_file_path)
- # JUPYTER_RESULT/file_name
- incoming_file_path = os.path.join(incoming_dir, file_name)
- print("to incoming: "+incoming_file_path)
-
- # ensure that all necessary folders exist
- try:
- os.makedirs(os.path.dirname(incoming_file_path))
- print("subdir created: " + os.path.dirname(incoming_file_path))
- except:
- pass
-
-
- # copy files from session user workspace
- # to incoming path, because they might
- # not be on the same drive.
- inputStream = dss_service.getFileFromSessionWorkspace(userSessionToken, ws_file_path)
- outputStream = FileOutputStream(File(incoming_file_path))
- IOUtils.copyLarge(inputStream, outputStream)
- IOUtils.closeQuietly(inputStream)
- IOUtils.closeQuietly(outputStream)
-
-
- # there is only one transation move per dataset.
- print("transaction.moveFile from incoming folder: " + incoming_dir)
- transaction.moveFile(File(incoming_dir).getAbsolutePath(), dataset, folder);
-
- # ...and delete all files from the session workspace
- # TODO: delete it later
- #dss_service = ServiceProvider.getDssServiceRpcGeneric().getService()
- #for file_name in file_names:
- # file_path = os.path.join(temp_dir, file_name)
- # dss_service.deleteSessionWorkspaceFile(userSessionToken, file_name)
-
- return dataset.getDataSetCode()
-
-
-def getThreadProperties(transaction):
- threadPropertyDict = {}
- threadProperties = transaction.getGlobalState().getThreadParameters().getThreadProperties()
- for key in threadProperties:
- try:
- threadPropertyDict[key] = threadProperties.getProperty(key)
- except:
- pass
- return threadPropertyDict
-
-
-def getThreadProperties(transaction):
- threadPropertyDict = {}
- threadProperties = transaction.getGlobalState().getThreadParameters().getThreadProperties()
- for key in threadProperties:
- try:
- threadPropertyDict[key] = threadProperties.getProperty(key)
- except:
- pass
- return threadPropertyDict
-
diff --git a/src/core-plugins/jupyter-api/1/dss/reporting-plugins/jupyter-uploader-api/lib/zip4j_1.3.2.jar b/src/core-plugins/jupyter-api/1/dss/reporting-plugins/jupyter-uploader-api/lib/zip4j_1.3.2.jar
deleted file mode 100644
index 66a19e49a2a29b39b76ade1b619de9db0a8fdcaa..0000000000000000000000000000000000000000
Binary files a/src/core-plugins/jupyter-api/1/dss/reporting-plugins/jupyter-uploader-api/lib/zip4j_1.3.2.jar and /dev/null differ
diff --git a/src/core-plugins/jupyter-api/1/dss/reporting-plugins/jupyter-uploader-api/plugin.properties b/src/core-plugins/jupyter-api/1/dss/reporting-plugins/jupyter-uploader-api/plugin.properties
deleted file mode 100644
index 7793216f064386376370bc47ddc02d3c6acf0593..0000000000000000000000000000000000000000
--- a/src/core-plugins/jupyter-api/1/dss/reporting-plugins/jupyter-uploader-api/plugin.properties
+++ /dev/null
@@ -1,3 +0,0 @@
-label = Dataset Uploader API
-class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.JythonIngestionService
-script-path = dataset-uploader-api.py
diff --git a/src/python/ELNJupyter/README.md b/src/python/ELNJupyter/README.md
deleted file mode 100644
index 9868b86ea7a17cc6e1cd0135fade5d7fbca383e7..0000000000000000000000000000000000000000
--- a/src/python/ELNJupyter/README.md
+++ /dev/null
@@ -1,80 +0,0 @@
-# ELN-Jupyter webservice
-
-This is a small webservice which is running on a server and allows to write Jupyter notebook files directly into the users' home folder.
-
-- always use utf-8
-- always use https
-- the body should contain the content of the Jupyter notebook.
-- respones are always in JSON
-- if the POST request fails, a response with HTTP status code ≠200 is sent back, including an error message
-- the openBIS token is always tested for validity against the openBIS server
-- the user is extracted from the token
-- the user must exist on the server (no automatic user creation)
-- if folder or file exists on the system, a new folder is added with a sequence number, to prevent previous work from being overwritten
-
-## Usage
-
-```
-POST
-https://servername:8123?token=[openBIS token]&folder=my_folder&filename=20160929145446460-369.ipynb
-
-{
- "cells": [
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {
- "collapsed": false
- },
- "outputs": [],
- "source": [
- "from pybis import Openbis\n",
- "o = Openbis(url='https://localhost:8443', verify_certificates=False)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {
- "collapsed": true
- },
- "outputs": [],
- "source": [
- "ds = o.get_dataset('20160929145446460-367')"
- ]
- }
- ],
- "metadata": {
- "kernelspec": {
- "display_name": "Python 3",
- "language": "python",
- "name": "python3"
- },
- "language_info": {
- "codemirror_mode": {
- "name": "ipython",
- "version": 3
- },
- "file_extension": ".py",
- "mimetype": "text/x-python",
- "name": "python",
- "nbconvert_exporter": "python",
- "pygments_lexer": "ipython3",
- "version": "3.5.2"
- }
- },
- "nbformat": 4,
- "nbformat_minor": 2
-}
-
-```
-
-## Response from server (not yet implemented)
-```
-{
- "link": "http://servername:8000/home/testuser/notebooks/my_folder/20160929145446460-369.ipynb"
-}
-```
-
-Using this link, the user should be directly routed to the notebook we just created.
-If the user never used JupyterHub before or is logged out, he is asked for his password before being redirected to the notebook.
\ No newline at end of file
diff --git a/src/python/ELNJupyter/elnjupyter/__init__.py b/src/python/ELNJupyter/elnjupyter/__init__.py
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/src/python/ELNJupyter/elnjupyter/server.py b/src/python/ELNJupyter/elnjupyter/server.py
deleted file mode 100755
index c201df2f7c827615ad5100ea0e069f92378908b5..0000000000000000000000000000000000000000
--- a/src/python/ELNJupyter/elnjupyter/server.py
+++ /dev/null
@@ -1,139 +0,0 @@
-#!/usr/bin/env python
-import tornado.web
-import tornado.ioloop
-import json
-import os
-import pwd
-import ssl
-import sys
-import click
-from pybis import Openbis
-
-
-class CreateNotebook(tornado.web.RequestHandler):
-
- def set_default_headers(self):
- self.set_header("Access-Control-Allow-Origin", "*")
- self.set_header("Access-Control-Allow-Headers", "x-requested-with")
- self.set_header('Access-Control-Allow-Methods', 'POST, GET, OPTIONS')
-
- def get(self, whatever):
- self.send_error(401, message='this webservice does not allow any GET requests.')
-
- def options(self):
- # no body
- self.set_status(204)
- self.finish()
-
- def post(self, whatever):
- test = self.get_argument(name='test')
- token = self.get_argument(name='token')
- folder = self.get_argument(name='folder')
- filename = self.get_argument(name='filename')
- content = self.request.body
-
-
- # check if token is still valid
- if not self.openbis.is_token_valid(token):
- self.send_error(401, message="token is invalid")
- return
-
- # extract username
- username, code = token.split('-')
-
- try:
- user = pwd.getpwnam(username)
- except KeyError:
- self.create_user(username)
- user = pwd.getpwnam(username)
- #self.send_error(401, message="User {} does not exist on host system".format(username))
-
- path_to_notebook = os.path.join(
- user.pw_dir,
- folder,
- filename
- )
-
- # create necessary directories
- os.makedirs(os.path.dirname(path_to_notebook), exist_ok=True)
-
- # add sequence to the filename if file already exists
- filename_name_end = filename.rfind('.')
- filename_name = filename[:filename_name_end]
- filename_extension = filename[filename_name_end:]
- filename_new = filename_name + filename_extension
-
- path_to_notebook_new = os.path.join(
- user.pw_dir,
- folder,
- filename_new
- )
-
- i = 1
- while os.path.isfile(path_to_notebook_new):
- i += 1
- filename_new = filename_name + " " + str(i) + filename_extension
- path_to_notebook_new = os.path.join(
- user.pw_dir,
- folder,
- filename_new
- )
- path_to_notebook = path_to_notebook_new
-
- if (test == None) or (test == 'False'):
- with open(path_to_notebook, 'wb') as f:
- f.write(content)
- os.chown(path_to_notebook, user.pw_uid, user.pw_gid)
- os.chmod(path_to_notebook, 0o777)
- path_to_notebook_folder = os.path.join(
- user.pw_dir,
- folder
- )
- os.chmod(path_to_notebook_folder, 0o777)
- print(path_to_notebook)
-
- link_to_notebook = {
- "fileName": filename_new
- }
- self.write(json.dumps(link_to_notebook))
-
- def create_user(self, username):
- os.system("useradd " + username)
-
- def send_error(self, status_code=500, message=""):
- self.set_status(status_code)
- self.write(message)
-
- def initialize(self, openbis):
- self.openbis = openbis
- self.set_header('Content-Type', 'application/json')
-
-def make_app(openbis):
- """All the routing goes here...
- """
- app = tornado.web.Application([
- (r"/(.*)", CreateNotebook, {"openbis": openbis})
- ])
- return app
-
-@click.command()
-@click.option('--port', default=8123, help='Port where this server listens to')
-@click.option('--ssl-cert', '--cert', default='/etc/ssl/certs/cert.pem', help='Path to your cert-file in PEM format')
-@click.option('--ssl-key', '--key', default='/etc/ssl/certs/key.pem', help='Path to your key-file in PEM format')
-@click.option('--openbis', help='URL and port of your openBIS installation')
-def start_server(port, cert, key, openbis):
- o = Openbis(url=openbis, verify_certificates=False)
-
- application = make_app(o)
- application.listen(
- port,
- ssl_options={
- "certfile": cert,
- "keyfile": key
- }
- )
- tornado.ioloop.IOLoop.current().start()
-
-
-if __name__ == "__main__":
- start_server()
diff --git a/src/python/ELNJupyter/setup.py b/src/python/ELNJupyter/setup.py
deleted file mode 100644
index 45144e92679dd9edfc3edbb93a892de2568ef5a2..0000000000000000000000000000000000000000
--- a/src/python/ELNJupyter/setup.py
+++ /dev/null
@@ -1,22 +0,0 @@
-import os
-
-from setuptools import setup
-
-setup(
- name='elnjupyter',
- version='0.1.4',
- description='A webservice to create jupyter notebooks in the users home directory',
- url='https://sissource.ethz.ch/sis/pybis/',
- author='SIS | ID | ETH Zuerich',
- author_email='swen@ethz.ch',
- license='BSD',
- packages=['elnjupyter'],
- install_requires=[
- 'tornado',
- ],
- zip_safe=False,
- entry_points='''
- [console_scripts]
- elnjupyter=elnjupyter.server:start_server
- '''
-)
diff --git a/src/python/JupyterBis/jupyterbis/auth.py b/src/python/JupyterBis/jupyterbis/auth.py
deleted file mode 100644
index a885385c4498dff79a5b97bd14dee78176b6e7a2..0000000000000000000000000000000000000000
--- a/src/python/JupyterBis/jupyterbis/auth.py
+++ /dev/null
@@ -1,114 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-"""
-auth.py
-
-
-Created by Chandrasekhar Ramakrishnan on 2016-05-25.
-Copyright (c) 2016 ETH Zuerich All rights reserved.
-"""
-
-import os
-import re
-
-from jupyterhub.auth import LocalAuthenticator
-from tornado import gen
-from traitlets import Unicode, Bool
-
-from pybis.pybis import Openbis
-
-user_to_openbis_dict = {}
-
-
-class OpenbisAuthenticator(LocalAuthenticator):
- server_url = Unicode(
- config=True,
- help='URL of openBIS server to contact'
- )
-
- verify_certificates = Bool(
- config=True,
- default_value=True,
- help='Should certificates be verified? Normally True, but maybe False for debugging.'
- )
-
- valid_username_regex = Unicode(
- r'^[a-z][.a-z0-9_-]*$',
- config=True,
- help="""Regex to use to validate usernames before sending to openBIS."""
- )
-
-
- @gen.coroutine
- def authenticate(self, handler, data):
- username = data['username']
- password = data['password']
-
- # Protect against invalid usernames as well as LDAP injection attacks
- if not re.match(self.valid_username_regex, username):
- self.log.warn('Invalid username')
- return None
-
- # No empty passwords!
- if password is None or password.strip() == '':
- self.log.warn('Empty password')
- return None
-
-
- openbis = Openbis(self.server_url, verify_certificates=self.verify_certificates)
- try:
- # authenticate against openBIS and store the token (if possible)
- openbis.login(username, password)
- user_to_openbis_dict[username] = openbis
- self.refresh_token(username)
- return username
- except ValueError as err:
- self.log.warn(str(err))
- return None
-
-
- def refresh_token(self, username):
- if username in user_to_openbis_dict:
- openbis = user_to_openbis_dict[username]
- else:
- return None
-
- # user has no home directory yet:
- # there is no reason to save the token
- homedir = os.path.expanduser("~"+username)
- if not os.path.exists(homedir):
- return None
-
- # remove existing token
- parent_folder = os.path.join(homedir, '.pybis' )
- token_path = openbis.gen_token_path(parent_folder)
- try:
- openbis.delete_token(token_path)
- except:
- pass
-
- # save the new token
- openbis.save_token(
- token=openbis.token,
- parent_folder=parent_folder
- )
-
- # change the ownership of the token to make sure it is not owned by root
- change_ownership = "sudo chown %s:%s %s" % (username, username, parent_folder)
- os.system(change_ownership)
- change_ownership = "sudo chown %s:%s %s" % (username, username, openbis.token_path)
- os.system(change_ownership)
-
-
- def pre_spawn_start(self, user, spawner):
- """After successful login and creating user on the system,
- write the token to a file"""
-
- self.refresh_token(user.name)
-
-
- def logout_url(self, base_url):
- ''' Custon logout
- '''
- pass
diff --git a/src/python/JupyterBis/setup.py b/src/python/JupyterBis/setup.py
deleted file mode 100644
index 9d5021fb582d6b644e7b88090f5e648e2b1ec40a..0000000000000000000000000000000000000000
--- a/src/python/JupyterBis/setup.py
+++ /dev/null
@@ -1,18 +0,0 @@
-import os
-
-from setuptools import setup
-
-setup(name='jupyterbis',
- version='0.1.0',
- description='A package that allows integration between Jupyter and openBIS.',
- url='https://sissource.ethz.ch/sis/pybis/',
- author='SIS | ID |ETH Zuerich',
- author_email='chandrasekhar.ramakrishnan@id.ethz.ch',
- license='BSD',
- packages=['jupyterbis'],
- install_requires=[
- 'pytest',
- 'jupyterhub',
- 'pybis'
- ],
- zip_safe=True)
diff --git a/src/python/PyBis/pybis/pybis.py b/src/python/PyBis/pybis/pybis.py
index a39c1c95079a3027629d28e91bfd37bedc7b7670..514481af8aee0dbd380b4051136328ed4abcbb8d 100644
--- a/src/python/PyBis/pybis/pybis.py
+++ b/src/python/PyBis/pybis/pybis.py
@@ -42,7 +42,7 @@ from queue import Queue
from datetime import datetime
-PYBIS_PLUGIN = "jupyter-uploader-api"
+PYBIS_PLUGIN = "dataset-uploader-api"
def _definitions(entity):
@@ -627,9 +627,13 @@ class Openbis:
"get_project('project')",
"get_projects(space=None, code=None)",
"get_sample('id')",
+ "get_object('id')", # "get_sample('id')" alias
"get_samples()",
+ "get_objects()", # "get_samples()" alias
"get_sample_type(type))",
+ "get_object_type(type))", # "get_sample_type(type))" alias
"get_sample_types()",
+ "get_object_types()", # "get_sample_types()" alias
"get_semantic_annotations()",
"get_semantic_annotation(permId, only_data = False)",
"get_space(code)",
@@ -640,8 +644,11 @@ class Openbis:
'new_project(space, code, description)',
'new_experiment(type, code, project, props={})',
'new_sample(type, space, project, experiment)',
+ 'new_object(type, space, project, experiment)', # 'new_sample(type, space, project, experiment)' alias
'new_dataset(type, parent, experiment, sample, files=[], folder, props={})',
'new_semantic_annotation(entityType, propertyType)',
+ 'update_sample(sampleId, space, project, experiment, parents, children, components, properties, tagIds, attachments)',
+ 'update_object(sampleId, space, project, experiment, parents, children, components, properties, tagIds, attachments)', # 'update_sample(sampleId, space, project, experiment, parents, children, components, properties, tagIds, attachments)' alias
]
@property
@@ -972,6 +979,8 @@ class Openbis:
ss = samples[attrs]
return Things(self, 'sample', ss, 'identifier')
+ get_objects = get_samples # Alias
+
def get_experiments(self, code=None, type=None, space=None, project=None, tags=None, is_finished=None, props=None,
**properties):
""" Get a list of all experiment for a given space or project (or any combination)
@@ -1226,6 +1235,8 @@ class Openbis:
resp = self._post_request(self.as_v3, request)
return self.get_sample(resp[0]['permId'])
+ create_object = create_sample # Alias
+
def create_external_data_management_system(self, code, label, address, address_type='FILE_SYSTEM'):
"""Create an external DMS.
:param code: An openBIS code for the external DMS.
@@ -1281,6 +1292,8 @@ class Openbis:
}
self._post_request(self.as_v3, request)
+ update_object = update_sample # Alias
+
def delete_entity(self, entity, permid, reason, capitalize=True):
"""Deletes Spaces, Projects, Experiments, Samples and DataSets
"""
@@ -1579,6 +1592,8 @@ class Openbis:
["generatedCodePrefix"]
)
+ get_object_types = get_sample_types # Alias
+
def get_sample_type(self, type):
try:
return self._get_types_of(
@@ -1590,6 +1605,8 @@ class Openbis:
except Exception:
raise ValueError("no such sample type: {}".format(type))
+ get_object_type = get_sample_type # Alias
+
def get_experiment_types(self, type=None):
""" Returns a list of all available experiment types
"""
@@ -1794,6 +1811,8 @@ class Openbis:
else:
return Sample(self, self.get_sample_type(resp[sample_ident]["type"]["code"]), resp[sample_ident])
+ get_object = get_sample # Alias
+
def get_external_data_management_system(self, permId, only_data=False):
"""Retrieve metadata for the external data management system.
:param permId: A permId for an external DMS.
@@ -1999,6 +2018,8 @@ class Openbis:
"""
return Sample(self, self.get_sample_type(type), None, props, **kwargs)
+ new_object = new_sample # Alias
+
def new_dataset(self, type=None, files=None, props=None, folder=None, **kwargs):
""" Creates a new dataset of a given sample type.
"""
@@ -2219,6 +2240,8 @@ class OpenBisObject():
except Exception:
pass
+ object = sample # Alias
+
def __getattr__(self, name):
return getattr(self.__dict__['a'], name)
@@ -2530,7 +2553,7 @@ class DataSet(OpenBisObject):
parentIds = self.parents
dataset_type = self.type.code
- metadata = self.props.all_nonempty()
+ properties = self.props.all_nonempty()
request = {
"method": "createReportFromAggregationService",
@@ -2539,16 +2562,15 @@ class DataSet(OpenBisObject):
dss,
PYBIS_PLUGIN,
{
- "sampleId": sample_identifier,
- "experimentId": experiment_identifier,
- "dataSets": [ {
- "dataSetType": dataset_type,
- "folder": self.folder,
- "sessionWorkspaceFolder": "",
- "fileNames": self.files,
- "properties": metadata,
- "parentIds": parentIds
- } ]
+ "method" : "insertDataSet",
+ "sampleIdentifier" : sample_identifier,
+ "experimentIdentifier" : experiment_identifier,
+ "dataSetType" : dataset_type,
+ "folderName" : self.folder,
+ "fileNames" : self.files,
+ "isZipDirectoryUpload" : False,
+ "properties" : properties,
+ "parentIdentifiers": parentIds
}
],
}
@@ -3358,6 +3380,8 @@ class Space(OpenBisObject):
def get_samples(self, **kwargs):
return self.openbis.get_samples(space=self.code, **kwargs)
+ get_objects = get_samples #Alias
+
def get_projects(self, **kwargs):
return self.openbis.get_projects(space=self.code, **kwargs)
@@ -3489,6 +3513,8 @@ class Things():
else:
return Things(self.openbis, 'sample', DataFrame(), 'identifier')
+ get_objects = get_samples # Alias
+
def get_datasets(self, **kwargs):
if self.entity not in ['sample', 'experiment']:
raise ValueError("{}s do not have datasets".format(self.entity))
@@ -3657,6 +3683,8 @@ class Experiment(OpenBisObject):
return None
return self.openbis.get_samples(experiment=self.permId, **kwargs)
+ get_objects = get_samples # Alias
+
def add_samples(self, *samples):
for sample in samples:
@@ -3682,6 +3710,7 @@ class Experiment(OpenBisObject):
obj.save()
self.a.__dict__['_samples'].append(obj._identifier)
+ add_objects = add_samples # Alias
def del_samples(self, samples):
if not isinstance(samples, list):
@@ -3698,6 +3727,8 @@ class Experiment(OpenBisObject):
self.samples = objects
+ del_objects = del_samples # Alias
+
class Attachment():
def __init__(self, filename, title=None, description=None):
if not os.path.exists(filename):
@@ -3756,6 +3787,8 @@ class Project(OpenBisObject):
def get_samples(self, **kwargs):
return self.openbis.get_samples(project=self.permId, **kwargs)
+ get_objects = get_samples # Alias
+
def get_experiments(self):
return self.openbis.get_experiments(project=self.permId)