From 552c9ff93c6e6016b3706bb95e5bdef44c348ac3 Mon Sep 17 00:00:00 2001
From: vermeul <swen@ethz.ch>
Date: Wed, 6 Feb 2019 16:18:56 +0100
Subject: [PATCH] server now sends information about dataset types
---
jupyter-openbis-extension/server.py | 31 ++++++++++++++++++++++++-----
1 file changed, 26 insertions(+), 5 deletions(-)
diff --git a/jupyter-openbis-extension/server.py b/jupyter-openbis-extension/server.py
index c1d72c5..086bffa 100644
--- a/jupyter-openbis-extension/server.py
+++ b/jupyter-openbis-extension/server.py
@@ -37,6 +37,8 @@ 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']:
@@ -51,6 +53,7 @@ def load_jupyter_server_extension(nb_server_app):
base_url = web_app.settings['base_url']
+ # DataSet download
web_app.add_handlers(
host_pattern,
[(url_path_join(
@@ -106,19 +109,33 @@ def register_connection(connection_info):
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
@@ -157,10 +174,12 @@ class OpenBISHandler(IPythonHandler):
"""
connections= []
for conn in openbis_connections.values():
+
connections.append({
- 'name' : conn.name,
- 'url' : conn.url,
- 'status' : conn.status,
+ 'name' : conn.name,
+ 'url' : conn.url,
+ 'status' : conn.status,
+ 'ds_types': conn.ds_types,
})
self.write({
@@ -188,7 +207,9 @@ class SampleHandler(IPythonHandler):
sample = conn.openbis.get_sample(permId)
except Exception as exc:
print(exc)
- self.send_error( reason = 'No such sample found: {}'.format(permId) )
+ self.send_error( 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
--
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