wbtools 3.2.0__tar.gz → 3.3.0__tar.gz

{wbtools-3.2.0/wbtools.egg-info → wbtools-3.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: wbtools
-Version: 3.2.0
+Version: 3.3.0
 Summary: Interface to WormBase (www.wormbase.org) curation data, including literature management and NLP functions
 Author-email: Valerio Arnaboldi <valearna@caltech.edu>
 Project-URL: Homepage, https://github.com/WormBase/wbtools
@@ -24,6 +24,7 @@ Requires-Dist: requests~=2.31.0
 Requires-Dist: python-dateutil~=2.8.2
 Requires-Dist: python-dotenv~=1.0.0
 Requires-Dist: grobid-client
+Requires-Dist: agr-cognito-py
 
 # WBtools
 > Interface to WormBase curation database and Text Mining functions

{wbtools-3.2.0 → wbtools-3.3.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "wbtools"
-version = "3.2.0"
+version = "3.3.0"
 authors = [
     {name = "Valerio Arnaboldi", email = "valearna@caltech.edu"},
 ]
@@ -30,6 +30,7 @@ dependencies = [
     "python-dateutil~=2.8.2",
     "python-dotenv~=1.0.0",
     "grobid-client",
+    "agr-cognito-py",
 ]
 
 [project.urls]

{wbtools-3.2.0 → wbtools-3.3.0}/wbtools/literature/paper.py

@@ -26,7 +26,7 @@ from wbtools.lib.nlp.entity_extraction.email_addresses import get_email_addresse
 from wbtools.lib.nlp.text_preprocessing import preprocess, get_documents_from_text, PaperSections
 from wbtools.lib.timeout import timeout
 from wbtools.literature.person import WBAuthor
-from wbtools.utils.okta_utils import get_authentication_token, generate_headers
+from wbtools.utils.auth_utils import get_authentication_token, generate_headers
 
 logger = logging.getLogger(__name__)
 
@@ -193,6 +193,7 @@ class WBPaper(object):
             blue_api_base_url = os.environ.get('API_SERVER', "literature-rest.alliancegenome.org")
             all_reffiles_for_pap_api = f'https://{blue_api_base_url}/reference/referencefile/show_all/{self.agr_curie}'
             request = urllib.request.Request(url=all_reffiles_for_pap_api)
+            request.add_header("Authorization", f"Bearer {get_authentication_token()}")
             request.add_header("Content-type", "application/json")
             request.add_header("Accept", "application/json")
             added_ref_files = 0
@@ -227,7 +228,9 @@ class WBPaper(object):
             raise Exception("PaperDBManager not set")
         # Get Alliance reference info from WBPaperID
         ref_info_from_xref_api = f"https://{ABC_API}/reference/by_cross_reference/WB:WBPaper{self.paper_id}"
-        ref_info: dict = get_data_from_url(ref_info_from_xref_api)
+        token = get_authentication_token()
+        headers = generate_headers(token)
+        ref_info: dict = get_data_from_url(ref_info_from_xref_api, headers)
         if ref_info:
             self.abstract = ref_info["abstract"]
             self.title = ref_info["title"]

{wbtools-3.2.0 → wbtools-3.3.0}/wbtools/utils/alliance.py

@@ -3,7 +3,7 @@ import logging
 import urllib.request
 
 from wbtools.lib.nlp.common import EntityType
-from wbtools.utils.okta_utils import get_authentication_token
+from wbtools.utils.auth_utils import get_authentication_token
 
 
 logger = logging.getLogger(__name__)

wbtools-3.3.0/wbtools/utils/auth_utils.py

@@ -0,0 +1,21 @@
+"""
+Authentication utilities for AGR API access.
+
+This module provides authentication token generation using AWS Cognito
+via the agr_cognito_py library. The functions are re-exported for
+backward compatibility with code that was using the old Okta-based
+authentication.
+
+Required environment variables for Cognito authentication:
+- COGNITO_ADMIN_CLIENT_ID
+- COGNITO_ADMIN_CLIENT_SECRET
+- COGNITO_TOKEN_URL
+- COGNITO_ADMIN_SCOPE
+"""
+
+from agr_cognito_py import (
+    get_admin_token as get_authentication_token,
+    generate_headers
+)
+
+__all__ = ['get_authentication_token', 'generate_headers']

{wbtools-3.2.0 → wbtools-3.3.0/wbtools.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: wbtools
-Version: 3.2.0
+Version: 3.3.0
 Summary: Interface to WormBase (www.wormbase.org) curation data, including literature management and NLP functions
 Author-email: Valerio Arnaboldi <valearna@caltech.edu>
 Project-URL: Homepage, https://github.com/WormBase/wbtools
@@ -24,6 +24,7 @@ Requires-Dist: requests~=2.31.0
 Requires-Dist: python-dateutil~=2.8.2
 Requires-Dist: python-dotenv~=1.0.0
 Requires-Dist: grobid-client
+Requires-Dist: agr-cognito-py
 
 # WBtools
 > Interface to WormBase curation database and Text Mining functions

{wbtools-3.2.0 → wbtools-3.3.0}/wbtools.egg-info/SOURCES.txt

@@ -39,4 +39,4 @@ wbtools/literature/paper.py
 wbtools/literature/person.py
 wbtools/utils/__init__.py
 wbtools/utils/alliance.py
-wbtools/utils/okta_utils.py
+wbtools/utils/auth_utils.py

{wbtools-3.2.0 → wbtools-3.3.0}/wbtools.egg-info/requires.txt

@@ -11,3 +11,4 @@ requests~=2.31.0
 python-dateutil~=2.8.2
 python-dotenv~=1.0.0
 grobid-client
+agr-cognito-py

wbtools-3.2.0/wbtools/utils/okta_utils.py

@@ -1,67 +0,0 @@
-import os
-from json import loads
-from os import environ, path
-import logging
-import logging.config
-from datetime import datetime
-from dateutil.relativedelta import relativedelta
-import requests
-
-
-def generate_headers(token):
-    """
-
-    :param token:
-    :return:
-    """
-
-    authorization = 'Bearer ' + token
-    headers = {
-        'Authorization': authorization,
-        'Content-Type': 'application/json',
-        'Accept': 'application/json'
-    }
-    return headers
-
-
-def update_okta_token():  # pragma: no cover
-    """
-
-    :return:
-    """
-
-    url = f"https://{os.environ.get('OKTA_DOMAIN')}/v1/token"
-    headers = {
-        'Content-Type': 'application/x-www-form-urlencoded',
-        'Accept': 'application/json'
-    }
-    data_dict = dict()
-    data_dict['grant_type'] = 'client_credentials'
-    data_dict['client_id'] = environ.get('OKTA_CLIENT_ID')
-    data_dict['client_secret'] = environ.get('OKTA_CLIENT_SECRET')
-    data_dict['scope'] = 'admin'
-    post_return = requests.post(url, headers=headers, data=data_dict)
-    logging.warning(post_return.text)
-    response_dict = loads(post_return.text)
-    token = response_dict['access_token']
-    okta_file = environ.get('TMP_PATH') + 'okta_token'
-    os.makedirs(environ.get('TMP_PATH'), exist_ok=True)
-    with open(okta_file, 'w') as okta_fh:
-        okta_fh.write("%s" % token)
-    return token
-
-
-def get_authentication_token():  # pragma: no cover
-    okta_file = environ.get('TMP_PATH') + 'okta_token'
-    token = ''
-    if path.isfile(okta_file):
-        one_day_ago = datetime.now() - relativedelta(days=1)
-        file_time = datetime.fromtimestamp(path.getmtime(okta_file))
-        if file_time > one_day_ago:
-            with open(okta_file, 'r') as okta_fh:
-                token = okta_fh.read().replace("\n", "")
-        else:
-            token = update_okta_token()
-    else:
-        token = update_okta_token()
-    return token