diff --git a/README.md b/README.md
index e9bcc25c13962ede2210be00889309c16a16626c..aae03bf42200727fc9cdb044a6c148b01867e4cf 100644
--- a/README.md
+++ b/README.md
@@ -12,6 +12,19 @@ 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:
```
@@ -159,4 +172,4 @@ Known nbextensions:
notebook section
jupyter-openbis-extension/dialog enabled
- Validating: OK
-```
\ No newline at end of file
+```
diff --git a/jupyter-openbis-extension/server.py b/jupyter-openbis-extension/server.py
index beccb3252d0e7b672813a35b9742c51e5d28fa6d..8c5fb7847e5163e223649e16222ea4c5429d91b9 100644
--- a/jupyter-openbis-extension/server.py
+++ b/jupyter-openbis-extension/server.py
@@ -2,7 +2,6 @@ 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
@@ -31,8 +30,8 @@ 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
@@ -473,9 +472,14 @@ class DataSetTypesHandler(IPythonHandler):
# 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
+ 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
@@ -483,6 +487,7 @@ class DataSetTypesHandler(IPythonHandler):
return
except Exception as e:
+ print(e)
self.set_status(500)
self.write({
"reason":'Could not fetch dataset-types: {}'.format(e)
@@ -491,60 +496,112 @@ class DataSetTypesHandler(IPythonHandler):
class DataSetUploadHandler(IPythonHandler):
- """Handle the requests for /openbis/dataset/connection"""
+ """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 exc:
+ except Exception as e:
+ print(e)
+ self.set_status(500)
self.write({
- "reason": 'connection to {} could not be established: {}'.format(conn.name, exc)
+ "reason": 'connection to {} could not be established: {}'.format(conn.name, e)
})
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
+ 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)
- filenames.append(filename)
+ if os.path.isfile(filename):
+ filenames.append(filename)
+ else:
+ errors.append({
+ "file": "File not found: {}".format(filename)
+ })
+ print("--------------_HERE_-----------3")
- 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)
+ 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")
+
+ # write errors back if already occured
+ if errors:
+ self.set_status(500)
+ self.write({ "errors": errors })
return
+ print("--------------_HERE_-----------5")
+
+ # try to set the properties
+ if (data.get('props')):
+ props = data.et('props')
+ for prop, value in props.items():
+ try:
+ setattr(dataset.props, prop, value)
+ except Exception as e:
+ errors.append({
+ "prop."+prop : e
+ })
+ print("--------------_HERE_-----------6")
try:
- ds.save()
- except Exception as exc:
+ 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({
- "reason": 'Error while saving the dataset: {}'.format(exc)
+ 'status': 200,
+ 'statusText': 'Jupyter Notebook was successfully uploaded to: {} with permId: {}'.format(conn.name, dataset.permId)
})
- return
-
-
- # return success message
- self.write({
- 'status': 200,
- 'statusText': 'Jupyter Notebook was successfully uploaded to: {} with permId: {}'.format(conn.name, ds.permId)
- })
+ print("--------------_HERE_-----------8")
def post(self, **params):
"""Handle a request to /openbis/dataset/connection_name/permId
@@ -560,4 +617,6 @@ class DataSetUploadHandler(IPythonHandler):
return
data = self.get_json_body()
- results = self.upload_data(conn=conn,data=data)
+ print("Received DATA")
+ print(data)
+ self.upload_data(conn=conn,data=data)
diff --git a/setup.py b/setup.py
index d3942628b5236082ccf3c9c14312236185e60736..5eb05d0e8fa2ed017d3c0c8b07134ecc7377537e 100644
--- a/setup.py
+++ b/setup.py
@@ -24,7 +24,7 @@ setup(
install_requires=[
'jupyter-nbextensions-configurator',
'jupyter',
- 'pybis',
+ 'pybis=>1.8.1',
],
python_requires=">=3.3",
classifiers=[