diff --git a/pybis/src/python/pybis/pybis.py b/pybis/src/python/pybis/pybis.py
index f913fcf186ad484296b1c059b76d1e83bf7bbf1c..82aad44abd64a4396cee42c2e7472e091bb2aca0 100644
--- a/pybis/src/python/pybis/pybis.py
+++ b/pybis/src/python/pybis/pybis.py
@@ -59,7 +59,6 @@ from .tag import Tag
from .things import Things
from .utils import (
VERBOSE,
- check_datatype,
extract_attr,
extract_code,
extract_deletion,
@@ -71,15 +70,12 @@ from .utils import (
extract_nested_permids,
extract_permid,
extract_person,
- extract_person_details,
- extract_property_assignments,
- extract_role_assignments,
extract_userId,
+ extract_username_from_token,
format_timestamp,
is_identifier,
is_number,
is_permid,
- nvl,
parse_jackson,
split_identifier,
)
@@ -232,7 +228,7 @@ def get_token_for_hostname(hostname, session_token_needed=True):
return
-def save_pats_to_disk(hostname: str, resp: dict) -> None:
+def save_pats_to_disk(hostname: str, url: str, resp: dict) -> None:
pats = resp["objects"]
parse_jackson(pats)
path = PYBIS_FOLDER / hostname
@@ -242,6 +238,7 @@ def save_pats_to_disk(hostname: str, resp: dict) -> None:
for token in pats:
data = {
+ "url": url,
"hostname": hostname,
"owner": token["owner"]["userId"],
"registrationDate": format_timestamp(token["owner"]["registrationDate"]),
@@ -1079,21 +1076,22 @@ class Openbis:
else:
while True:
try:
- self.token = self._get_saved_token()
+ self.token = config_local.get("token")
break
except ValueError:
- self._delete_saved_token()
pass
try:
- self.token = config_local.get("token")
+ self.token = config_global.get("token")
break
except ValueError:
pass
try:
- self.token = config_global.get("token")
+ self.token = self._get_saved_token()
break
except ValueError:
+ self._delete_saved_token()
pass
+ break
def _get_username(self):
if self.token:
@@ -1397,6 +1395,7 @@ class Openbis:
if save_token:
self._save_token_to_disk()
self._password(password)
+ self.username = username
return self.token
def _password(self, password=None, pstore={}):
@@ -1641,17 +1640,6 @@ class Openbis:
}
resp = self._post_request(self.as_v3, request)
if resp is not None:
- # result is a dict of strings - use more useful types
- keys_boolean = ["archiving-configured", "project-samples-enabled"]
- keys_csv = ["enabled-technologies"]
- for key in keys_boolean:
- if key in resp:
- resp[key] = resp[key] == "true"
- for key in keys_csv:
- if key in resp:
- resp[key] = list(
- map(lambda item: item.strip(), resp[key].split(","))
- )
self.server_information = ServerInformation(resp)
return self.server_information
else:
@@ -2045,15 +2033,22 @@ class Openbis:
) -> str:
"""Creates a new personal access token (PAT)"""
- if validFrom is None:
- validFrom = datetime.now()
- if validTo is None:
- validTo = datetime.now() + relativedelta(years=1)
+ session_token = self.token
+ if not is_session_token(session_token):
+ session_token = self.session_token
+ if not session_token:
+ session_token = get_token_for_hostname(
+ self.hostname, session_token_needed=True
+ )
- if is_personal_access_token(self.token):
+ if not self.is_token_valid(session_token):
raise ValueError(
"You you need a session token to create a new personal access token."
)
+ if validFrom is None:
+ validFrom = datetime.now()
+ if validTo is None:
+ validTo = datetime.now() + relativedelta(years=1)
entity = "personalAccessToken"
request = {
@@ -2182,7 +2177,7 @@ class Openbis:
return pats[attrs]
if save_to_disk:
- save_pats_to_disk(hostname=self.hostname, resp=resp)
+ save_pats_to_disk(hostname=self.hostname, url=self.url, resp=resp)
return Things(
openbis_obj=self,
@@ -4441,6 +4436,7 @@ class Openbis:
# just in case we need it later
self.session_token = self.token
self.__dict__["token"] = token
+ self.username = extract_username_from_token(token)
if save_token:
self._save_token_to_disk()
@@ -5385,15 +5381,44 @@ class ExternalDMS:
class ServerInformation:
def __init__(self, info):
- self._info = info
+ self._info = self._reformat_info(info)
self.attrs = [
"api_version",
"archiving_configured",
"authentication_service",
+ "authentication-service.switch-aai.label",
+ "authentication-service.switch-aai.link",
+ "create-continuous-sample-codes",
"enabled_technologies",
- "project_samples_enabled",
+ "openbis-version",
+ "openbis.support.email",
+ "personal-access-tokens-enabled",
+ "personal-access-tokens-max-validity-period",
+ "personal-access-tokens-validity-warning-period",
+ "project-samples-enabled",
]
+ def _reformat_info(self, info):
+ for bool_field in [
+ "archiving-configured",
+ "project-samples-enabled",
+ "personal-access-tokens-enabled",
+ ]:
+ if bool_field in info:
+ info[bool_field] = info[bool_field] == "true"
+ for csv_field in ["enabled-technologies"]:
+ if csv_field in info:
+ info[csv_field] = list(
+ map(lambda item: item.strip(), info[csv_field].split(","))
+ )
+ for int_field in [
+ "personal-access-tokens-max-validity-period",
+ "personal-access-tokens-validity-warning-period",
+ ]:
+ if int_field in info:
+ info[int_field] = int(info[int_field])
+ return info
+
def __dir__(self):
return self.attrs
@@ -5449,7 +5474,22 @@ class PersonalAccessToken(
entity="personalAccessToken",
single_item_method_name="get_personal_access_token",
):
- pass
+ def renew(self, validFrom: datetime = None, validTo: datetime = None):
+ if not validFrom:
+ validFrom = datetime.now()
+
+ if not validTo:
+ validFrom_orig = datetime.strptime(self.validFromDate, "%Y-%m-%d %H:%M:%S")
+ validTo_orig = datetime.strptime(self.validToDate, "%Y-%m-%d %H:%M:%S")
+ days_delta = abs(validFrom_orig - validTo_orig).days
+ validTo = validFrom + relativedelta(days=days_delta)
+
+ new_pat = self.openbis.new_personal_access_token(
+ sessionName=self.sessionName, validFrom=validFrom, validTo=validTo
+ )
+ self.openbis.set_token(new_pat)
+ if VERBOSE:
+ print(self.openbis.token)
class SessionInformation(