From a5143cec1275fffcb3c4f6b83644113f3e94d3ae Mon Sep 17 00:00:00 2001
From: vermeul <swen@ethz.ch>
Date: Fri, 5 Aug 2022 16:55:38 +0200
Subject: [PATCH] feat: implement personal access token methods
---
pybis/src/python/pybis/attribute.py | 2 +-
pybis/src/python/pybis/definitions.py | 11 ++
pybis/src/python/pybis/pybis.py | 215 +++++++++++++++++++-------
3 files changed, 167 insertions(+), 61 deletions(-)
diff --git a/pybis/src/python/pybis/attribute.py b/pybis/src/python/pybis/attribute.py
index 405b21a3c36..880886870c0 100644
--- a/pybis/src/python/pybis/attribute.py
+++ b/pybis/src/python/pybis/attribute.py
@@ -115,7 +115,7 @@ class AttrHolder:
elif attr.endswith("Date"):
self.__dict__["_" + attr] = format_timestamp(data.get(attr))
- elif attr in ["registrator", "modifier", "dataProducer"]:
+ elif attr in ["registrator", "modifier", "dataProducer", "owner"]:
self.__dict__["_" + attr] = extract_person(data.get(attr))
else:
diff --git a/pybis/src/python/pybis/definitions.py b/pybis/src/python/pybis/definitions.py
index 3136f86e3af..3fa68259bbd 100644
--- a/pybis/src/python/pybis/definitions.py
+++ b/pybis/src/python/pybis/definitions.py
@@ -106,6 +106,14 @@ def openbis_definitions(entity):
"delete": {"@type": "as.dto.dataset.delete.DataSetTypeDeletionOptions"},
"identifier": "typeId",
},
+ "personalAccessToken": {
+ "attrs_new": "sessionName validFromDate validToDate accessDate".split(),
+ "attrs_up": "".split(),
+ "attrs": "permId sessionName validFromDate validToDate accessDate owner registrator registrationDate modifier modificationDate".split(),
+ "search": {"@type": "as.dto.pat.search.PersonalAccessTokenSearchCriteria"},
+ "delete": {"@type": "as.dto.pat.delete.PersonalAccessTokenDeletionOptions"},
+ "identifier": "permId",
+ },
"experimentType": {
"attrs_new": "code description validationPlugin".split(),
"attrs_up": "description modificationDate validationPlugin".split(),
@@ -296,6 +304,9 @@ get_definition_for_entity = openbis_definitions # Alias
fetch_option = {
+ "personalAccessToken": {
+ "@type": "as.dto.pat.fetchoptions.PersonalAccessTokenFetchOptions"
+ },
"space": {"@type": "as.dto.space.fetchoptions.SpaceFetchOptions"},
"project": {
"@type": "as.dto.project.fetchoptions.ProjectFetchOptions",
diff --git a/pybis/src/python/pybis/pybis.py b/pybis/src/python/pybis/pybis.py
index b9279007302..6f0c6a1314d 100644
--- a/pybis/src/python/pybis/pybis.py
+++ b/pybis/src/python/pybis/pybis.py
@@ -11,18 +11,17 @@ Work with openBIS using Python.
from __future__ import print_function
import copy
-import errno
import json
-import logging
import os
-import random
import re
import subprocess
import sys
import time
+from xml.dom import NotSupportedErr
import zlib
from collections import defaultdict, namedtuple
from datetime import datetime
+from dateutil.relativedelta import relativedelta
from urllib.parse import quote, urljoin, urlparse
import pandas as pd
@@ -31,6 +30,7 @@ import urllib3
from pandas import DataFrame, Series
from tabulate import tabulate
from texttable import Texttable
+from typing import Optional
from . import data_set as pbds
from .dataset import DataSet
@@ -116,6 +116,7 @@ def get_search_type_for_entity(entity, operator=None):
{'@type': 'as.dto.space.search.SpaceSearchCriteria'}
"""
search_criteria = {
+ "personalAccessToken": "as.dto.pat.search.PersonalAccessTokenSearchCriteria",
"space": "as.dto.space.search.SpaceSearchCriteria",
"userId": "as.dto.person.search.UserIdSearchCriteria",
"email": "as.dto.person.search.EmailSearchCriteria",
@@ -169,6 +170,8 @@ def _type_for_id(ident, entity):
return {"permId": ident, "@type": "as.dto.tag.id.TagPermId"}
else:
return {"code": ident, "@type": "as.dto.tag.id.TagCode"}
+ if entity == "personalAccessToken":
+ return {"permId": ident, "@type": "as.dto.pat.id.PersonalAccessTokenPermId"}
entities = {
"sample": "Sample",
@@ -938,6 +941,7 @@ class Openbis:
self.use_cache = use_cache
self.cache = {}
self.server_information = None
+ self.token = None
if (
token is not None
): # We try to set the token, during initialisation instead of errors, a message is printed
@@ -1016,6 +1020,8 @@ class Openbis:
"get_object_types()",
"get_property_types()",
"get_property_type()",
+ "get_personal_access_tokens()",
+ "get_personal_access_token()",
"new_property_type()",
"get_semantic_annotations()",
"get_semantic_annotation()",
@@ -1054,6 +1060,7 @@ class Openbis:
"new_material_type()",
"new_semantic_annotation()",
"new_transaction()",
+ "create_personal_access_token()",
"set_token()",
]
@@ -1886,6 +1893,143 @@ class Openbis:
df_initializer=create_data_frame,
)
+ def create_personal_access_token(
+ self, sessionName: str, validFrom: datetime = None, validTo: datetime = None
+ ) -> 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)
+
+ entity = "personalAccessToken"
+ request = {
+ "method": get_method_for_entity(entity, "create"),
+ "params": [
+ self.token,
+ {
+ "@type": "as.dto.pat.create.PersonalAccessTokenCreation",
+ "sessionName": sessionName,
+ "validFromDate": int(validFrom.timestamp() * 1000),
+ "validToDate": int(validTo.timestamp() * 1000),
+ },
+ ],
+ }
+ try:
+ resp = self._post_request(self.as_v3, request)
+ except ValueError as exc:
+ raise NotSupportedErr(
+ "Your openBIS instance does not support personal access tokens. Please upgrade your server and activate them."
+ )
+ try:
+ token = resp[0]["permId"]
+ return token
+ except KeyError:
+ pass
+ # if "error" in resp and resp["error"]["message"] == "method not found":
+
+ def get_personal_access_tokens(
+ self, permId=None, start_with=None, count=None, **search_args
+ ):
+ """Get Personal Access Tokens"""
+ entity = "personalAccessToken"
+
+ search_criteria = get_search_criteria(entity, **search_args)
+ if permId:
+ sub_crit = _subcriteria_for_permid(permids=permId, entity=entity)
+ search_criteria["criteria"].append(sub_crit)
+ fetchopts = get_fetchoption_for_entity(entity)
+ fetchopts["from"] = start_with
+ fetchopts["count"] = count
+
+ for person in ["owner", "registrator", "modifier"]:
+ fetchopts[person] = get_fetchoption_for_entity(person)
+ request = {
+ "method": get_method_for_entity(entity, "search"),
+ "params": [self.token, search_criteria, fetchopts],
+ }
+ try:
+ resp = self._post_request(self.as_v3, request)
+ except ValueError:
+ raise NotSupportedErr(
+ "This method is not supported by your openBIS instance."
+ )
+
+ defs = get_definition_for_entity(entity)
+
+ def create_data_frame(attrs, props, response):
+ attrs = defs["attrs"]
+ objects = response["objects"]
+ if len(objects) == 0:
+ persons = DataFrame(columns=attrs)
+ else:
+ parse_jackson(objects)
+
+ pats = DataFrame(objects)
+ pats["permId"] = pats["permId"].map(extract_permid)
+ for date in [
+ "validFromDate",
+ "validToDate",
+ "accessDate",
+ "registrationDate",
+ "modificationDate",
+ ]:
+ pats[date] = pats[date].map(format_timestamp)
+ for person in ["owner", "registrator", "modifier"]:
+ pats[person] = pats[person].map(extract_person)
+ return pats[attrs]
+
+ return Things(
+ openbis_obj=self,
+ entity=entity,
+ identifier_name="permId",
+ single_item_method=self.get_personal_access_token,
+ start_with=start_with,
+ count=count,
+ totalCount=resp.get("totalCount"),
+ response=resp,
+ df_initializer=create_data_frame,
+ )
+
+ def get_personal_access_token(self, permId, only_data=False):
+ entity = "personalAccessToken"
+ identifiers = []
+ only_one = True
+ if isinstance(permId, list):
+ only_one = False
+ for ident in permId:
+ identifiers.append(_type_for_id(ident, entity))
+ else:
+ identifiers.append(_type_for_id(permId, entity))
+
+ defs = get_definition_for_entity(entity)
+ fetchopts = get_fetchoption_for_entity(entity)
+ for person in ["owner", "registrator", "modifier"]:
+ fetchopts[person] = get_fetchoption_for_entity(person)
+ request = {
+ "method": get_method_for_entity(entity, "get"),
+ "params": [self.token, identifiers, fetchopts],
+ }
+ resp = self._post_request(self.as_v3, request)
+ if only_one:
+ if len(resp) == 0:
+ raise ValueError(f"no such {entity} found: {permId}")
+
+ parse_jackson(resp)
+ for permId in resp:
+ if only_data:
+ return resp[permId]
+ else:
+ return PersonalAccessToken(
+ openbis_obj=self,
+ data=resp[permId],
+ # single_item_method_name=self.get_personal_access_token,
+ # count=len(resp),
+ # totalCount=len(resp),
+ # response=resp,
+ )
+
def get_persons(self, start_with=None, count=None, **search_args):
"""Get openBIS users"""
@@ -2107,10 +2251,6 @@ class Openbis:
b) property is not defined for this sampleType
"""
- logger = logging.getLogger("get_samples")
- logger.setLevel(logging.CRITICAL)
- logger.addHandler(logging.StreamHandler(sys.stdout))
-
if collection is not None:
experiment = collection
if attrs is None:
@@ -2200,23 +2340,11 @@ class Openbis:
],
}
- time1 = now()
- logger.debug("get_samples posting request")
resp = self._post_request(self.as_v3, request)
- time2 = now()
-
- logger.debug(f"get_samples got response. Delay: {time2 - time1}")
parse_jackson(resp)
- time3 = now()
-
response = resp["objects"]
- logger.debug(f"get_samples got JSON. Delay: {time3 - time2}")
-
- time4 = now()
-
- logger.debug(f"get_samples after result mapping. Delay: {time4 - time3}")
result = self._sample_list_for_response(
response=response,
@@ -2228,9 +2356,6 @@ class Openbis:
parsed=True,
)
- time5 = now()
-
- logger.debug(f"get_samples computed final result. Delay: {time5 - time4}")
return result
get_objects = get_samples # Alias
@@ -4420,24 +4545,9 @@ class Openbis:
totalCount=0,
parsed=False,
):
- logger = logging.getLogger("_sample_list_for_response")
- logger.setLevel(logging.CRITICAL)
- logger.disabled = True
- logger.addHandler(logging.StreamHandler(sys.stdout))
-
- time1 = now()
-
- logger.debug("_sample_list_for_response before parsing JSON")
if not parsed:
parse_jackson(response)
- time2 = now()
-
- logger.debug(f"_sample_list_for_response got response. Delay: {time2 - time1}")
-
- time6 = now()
- logger.debug("_sample_list_for_response computing result.")
-
def create_data_frame(attrs, props, response):
"""returns a Things object, containing a DataFrame plus additional information"""
@@ -4449,12 +4559,6 @@ class Openbis:
return return_attribute
- logger = logging.getLogger("create_data_frame")
- logger.setLevel(logging.CRITICAL)
- logger.addHandler(logging.StreamHandler(sys.stdout))
-
- time2 = now()
-
if attrs is None:
attrs = []
default_attrs = [
@@ -4479,10 +4583,6 @@ class Openbis:
display_attrs.append(prop)
samples = DataFrame(columns=display_attrs)
else:
- time3 = now()
- logger.debug(
- f"createDataFrame computing attributes. Delay: {time3 - time2}"
- )
samples = DataFrame(response)
for attr in attrs:
@@ -4515,11 +4615,6 @@ class Openbis:
samples["permId"] = samples["permId"].map(extract_permid)
samples["type"] = samples["type"].map(extract_nested_permid)
- time4 = now()
- logger.debug(
- f"_sample_list_for_response computed attributes. Delay: {time4 - time3}"
- )
-
for prop in props:
if prop == "*":
# include all properties in dataFrame.
@@ -4545,10 +4640,6 @@ class Openbis:
samples.loc[i, prop.upper()] = ""
display_attrs.append(prop.upper())
- time5 = now()
- logger.debug(
- f"_sample_list_for_response computed properties. Delay: {time5 - time4}"
- )
return samples[display_attrs]
def create_objects(response):
@@ -4577,10 +4668,6 @@ class Openbis:
props=props,
)
- time7 = now()
- logger.debug(
- f"_sample_list_for_response computed result. Delay: {time7 - time6}"
- )
return result
@staticmethod
@@ -5144,3 +5231,11 @@ class PropertyType(
class Plugin(OpenBisObject, entity="plugin", single_item_method_name="get_plugin"):
pass
+
+
+class PersonalAccessToken(
+ OpenBisObject,
+ entity="personalAccessToken",
+ single_item_method_name="get_personal_access_token",
+):
+ pass
--
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