From b92ce636c485fd937e9a1fb4cfa38efd95efdc2b Mon Sep 17 00:00:00 2001
From: Swen Vermeul <swen@ethz.ch>
Date: Thu, 14 Jul 2016 16:47:19 +0200
Subject: [PATCH] get_spaces and get_datastores are now cached
---
src/python/PyBis/pybis/pybis.py | 82 ++++++++++++++++++++++++---------
1 file changed, 61 insertions(+), 21 deletions(-)
diff --git a/src/python/PyBis/pybis/pybis.py b/src/python/PyBis/pybis/pybis.py
index 84568e59eec..45d70ab0f10 100644
--- a/src/python/PyBis/pybis/pybis.py
+++ b/src/python/PyBis/pybis/pybis.py
@@ -49,6 +49,8 @@ class Openbis:
self.reg_v1 = '/openbis/openbis/rmi-query-v1.json'
self.verify_certificates = verify_certificates
self.token = token
+ self.datastores = []
+ self.spaces = []
self.token_path = None
# use an existing token, if available
@@ -170,15 +172,39 @@ class Openbis:
def get_datastores(self):
- datastores = []
- request = {
- "method": "listDataStores",
- "params": [ self.token ],
- "id": "1",
- "jsonrpc": "2.0"
- }
- resp = self.post_request(self.as_v1, request)
- return resp
+ if len(self.datastores) == 0:
+ request = {
+ "method": "listDataStores",
+ "params": [ self.token ],
+ "id": "1",
+ "jsonrpc": "2.0"
+ }
+ resp = self.post_request(self.as_v1, request)
+ if resp is not None:
+ self.datastores = DataFrame(resp)[['code','downloadUrl', 'hostUrl']]
+ return self.datastores
+ else:
+ raise ValueError("No datastore found!")
+ else:
+ return self.datastores
+
+
+ def get_spaces(self):
+ if len(self.spaces) == 0:
+ request = {
+ "method": "searchSpaces",
+ "params": [ self.token, {}, {} ],
+ "id": "1",
+ "jsonrpc": "2.0"
+ }
+ resp = self.post_request(self.as_v3, request)
+ if resp is not None:
+ self.spaces = DataFrame(resp['objects'])[['code','description']]
+ return self.spaces
+ else:
+ raise ValueError("No spaces found!")
+ else:
+ return self.spaces
def get_sample_types(self):
@@ -548,18 +574,20 @@ class Openbis:
def upload_files(self, dss_code=None, files=None, folder='', wait_until_finished=False):
- for dss in self.get_datastores():
- if dss_code is None:
- # just take first DSS of all available DSSes if none was given
- self.datastore_url = dss['downloadUrl']
- break
- elif dss['code'] == dss_code:
- self.datastore_url = dss['downloadUrl']
- break
-
- if self.datastore_url is None:
- raise ValueError("No such DSS code found: " + dss_code)
-
+ dss = self.datastores
+
+ # create a dictionary of the entry
+ datastore = {}
+ if dss_code is None:
+ # return first datastore if none given
+ datastore = dss.iloc[0].to_dict()
+ else:
+ ds = dss[dss['code'] == 'DSS1']
+ if len(ds) == 1:
+ datastore = ds.T[0].to_dict()
+ else:
+ raise ValueError("No such DSS code found: " + dss_code)
+
if files is None:
raise ValueError("Please provide a filename.")
@@ -824,3 +852,15 @@ class Sample(dict):
if child is not None:
children.append(child)
return children
+
+
+class Space(dict):
+ """ managing openBIS spaces
+ """
+
+ def __init__(self, openbis_obj, *args, **kwargs):
+ super(Space, self).__init__(*args, **kwargs)
+ self.__dict__ = self
+ self.openbis = openbis_obj
+ self.permid = self.permId['permId']
+ self.code = self.code
--
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