diff --git a/pybis/src/python/pybis/pybis.py b/pybis/src/python/pybis/pybis.py
index 06083ca4fd7b6cf3730c55a7f10d7346d99d1042..a987a89388b30f0a8165011750b8b9f903a0a787 100644
--- a/pybis/src/python/pybis/pybis.py
+++ b/pybis/src/python/pybis/pybis.py
@@ -417,8 +417,22 @@ def _subcriteria_for_is_finished(is_finished):
def _subcriteria_for_properties(prop, value, entity):
- str_type= "as.dto.common.search.StringPropertySearchCriteria"
- eq_type = "as.dto.common.search.StringEqualToValue"
+ if isinstance(value, tuple):
+ str_type = "as.dto.common.search.NumberPropertySearchCriteria"
+ comparator, value = value
+ if comparator == '>':
+ eq_type = "as.dto.common.search.NumberGreaterThanValue"
+ elif comparator == '>=':
+ eq_type = "as.dto.common.search.NumberGreaterThanOrEqualToValue"
+ elif comparator == '<':
+ eq_type = "as.dto.common.search.NumberLessThanValue"
+ elif comparator == '<=':
+ eq_type = "as.dto.common.search.NumberLessThanOrEqualToValue"
+ else:
+ eq_type = "as.dto.common.search.NumberEqualToValue"
+ else:
+ eq_type = "as.dto.common.search.StringEqualToValue"
+ str_type= "as.dto.common.search.StringPropertySearchCriteria"
fieldType = "PROPERTY"
search_types = {
'sample': {
@@ -717,7 +731,8 @@ class Openbis:
def __init__(self, url=None, verify_certificates=True, token=None,
use_cache=True,
- allow_http_but_do_not_use_this_in_production_and_only_within_safe_networks=False
+ allow_http_but_do_not_use_this_in_production_and_only_within_safe_networks=False,
+ token_path=None
):
"""Initialize a new connection to an openBIS server.
@@ -729,6 +744,7 @@ class Openbis:
url (str): https://openbis.example.com
verify_certificates (bool): set to False when you use self-signed certificates
token (str): a valid openBIS token. If not set, pybis will try to read a valid token from ~/.pybis
+ token_path: a path to a file which contains an openBIS token
use_cache: make openBIS to store spaces, projects, sample types, vocabulary terms and oder more-or-less static objects to optimise speed
allow_http_but_do_not_use_this_in_production_and_only_within_safe_networks (bool): False
"""
@@ -757,19 +773,17 @@ class Openbis:
self.url = url_obj.geturl()
self.port = url_obj.port
self.hostname = url_obj.hostname
- self.token = token or os.environ.get("OPENBIS_TOKEN") or self._get_cached_token()
-
self.download_prefix = os.path.join('data', self.hostname)
-
self.use_cache = use_cache
self.cache = {}
-
self.server_information = None
- self.token_path = None
+ self.token_path = token_path or self.gen_token_path()
+ self.token = token or os.environ.get("OPENBIS_TOKEN") or self._get_saved_token()
if self.is_token_valid(self.token):
pass
else:
+ self._delete_saved_token()
print("Session is no longer valid. Please log in again.")
def _get_username(self):
@@ -900,26 +914,6 @@ class Openbis:
def projects(self):
return self.get_projects()
- def _get_cached_token(self):
- """Read the token from the .pybis
- If the token is not valid anymore, delete it.
- """
- token_path = self.gen_token_path()
- if not os.path.exists(token_path):
- return None
- try:
- with open(token_path) as f:
- token = f.read()
- if token == "":
- return None
- if not self.is_token_valid(token):
- os.remove(token_path)
- return None
- else:
- return token
- except FileNotFoundError:
- return None
-
def gen_token_path(self, parent_folder=None):
"""generates a path to the token file.
The token is usually saved in a file called
@@ -934,7 +928,7 @@ class Openbis:
path = os.path.join(parent_folder, self.hostname + '.token')
return path
- def save_token(self, token=None, parent_folder=None):
+ def _save_token(self, token=None, parent_folder=None):
""" saves the session token to the disk, usually here: ~/.pybis/hostname.token. When a new Openbis instance is created, it tries to read this saved token by default.
"""
if token is None:
@@ -952,12 +946,29 @@ class Openbis:
f.write(token)
self.token_path = token_path
- def delete_token(self, token_path=None):
- """ deletes a stored session token.
+ def _get_saved_token(self):
+ """Read the token from the .pybis
+ If the token is not valid anymore, delete it.
"""
- if token_path is None:
- token_path = self.token_path
- os.remove(token_path)
+ token_path = self.token_path or self.gen_token_path()
+ if not os.path.exists(token_path):
+ return None
+ try:
+ with open(token_path) as f:
+ token = f.read()
+ if token == "":
+ return None
+ else:
+ return token
+ except FileNotFoundError:
+ return None
+
+ def _delete_saved_token(self):
+ if self.token_path:
+ try:
+ os.remove(self.token_path)
+ except FileNotFoundError:
+ return None
def _post_request(self, resource, request):
""" internal method, used to handle all post requests and serializing / deserializing
@@ -977,7 +988,6 @@ class Openbis:
raise ValueError("Your session expired, please log in again")
if DEBUG_LEVEL >=LOG_DEBUG: print(json.dumps(request))
-
resp = requests.post(
full_url,
json.dumps(request),
@@ -1035,7 +1045,7 @@ class Openbis:
self.token = result
if save_token:
- self.save_token()
+ self._save_token()
self._password(password)
# update the OPENBIS_TOKEN environment variable, if OPENBIS_URL is identical to self.url
if os.environ.get('OPENBIS_URL') == self.url:
@@ -2216,7 +2226,6 @@ class Openbis:
search_criteria['operator'] = 'AND'
fetchopts = get_fetchoptions('dataSet', including=['type','parents'])
- print(fetchopts)
fetchopts['from'] = start_with
fetchopts['count'] = count