From f0642eddbc63ddce456c2e1e45759529319c2904 Mon Sep 17 00:00:00 2001
From: Swen Vermeul <swen@ethz.ch>
Date: Tue, 7 Feb 2017 15:01:45 +0100
Subject: [PATCH] added a __iter__ function to iterate through Samples,
Experiments, DataSets etc.
---
src/python/PyBis/pybis/pybis.py | 14 +++++++++++---
1 file changed, 11 insertions(+), 3 deletions(-)
diff --git a/src/python/PyBis/pybis/pybis.py b/src/python/PyBis/pybis/pybis.py
index de27079c3e2..2101c4bc97a 100644
--- a/src/python/PyBis/pybis/pybis.py
+++ b/src/python/PyBis/pybis/pybis.py
@@ -8,6 +8,7 @@ Work with openBIS from Python.
"""
+from __future__ import print_function
import os
import requests
from requests.packages.urllib3.exceptions import InsecureRequestWarning
@@ -501,15 +502,16 @@ class Openbis:
(minimum version 16.05).
"""
- def __init__(self, url='https://localhost:8443', verify_certificates=True, token=None):
+ def __init__(self, url, verify_certificates=True, token=None):
"""Initialize a new connection to an openBIS server.
-
:param host:
"""
url_obj = urlparse(url)
if url_obj.netloc is None:
raise ValueError("please provide the url in this format: https://openbis.host.ch:8443")
+ if url_obj.hostname is None:
+ raise ValueError("hostname is missing")
self.url_obj = url_obj
self.url = url_obj.geturl()
@@ -1406,7 +1408,7 @@ class Openbis:
if additional_attributes is None:
additional_attributes = []
- attributes = ['code', 'description', *additional_attributes, 'modificationDate']
+ attributes = ['code', 'description'] + additional_attributes + ['modificationDate']
search_request = {}
fetch_options = {}
@@ -2725,6 +2727,12 @@ class Things():
# invoke the openbis.get_entity() method
return getattr(self.openbis, 'get_'+self.entity)(row[self.identifier_name].values[0])
+ def __iter__(self):
+ for item in self.df[[self.identifier_name]][self.identifier_name].iteritems():
+ yield getattr(self.openbis, 'get_'+self.entity)(item[1])
+
+ #return self.df[[self.identifier_name]].to_dict()[self.identifier_name]
+
class Experiment(OpenBisObject):
"""
--
GitLab