Feat/dpop

.pre-commit-config.yaml

@@ -1,16 +1,16 @@
 repos:
 -   repo: git@github.com:Yelp/detect-secrets
-    rev: v1.2.0
+    rev: v1.5.0
     hooks:
     -   id: detect-secrets
         args: ['--baseline', '.secrets.baseline']
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.4.0
+    rev: v6.0.0
     hooks:
     -   id: end-of-file-fixer
     -   id: no-commit-to-branch
         args: [--branch, develop, --branch, master, --pattern, release/.*]
 -   repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 26.5.1
     hooks:
     -   id: black

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "authutils"
-version = "8.0.0"
+version = "9.0.0"
 description = "Gen3 auth utility functions"
 authors = ["CTDS UChicago <cdis@uchicago.edu>"]
 license = "Apache-2.0"
@@ -15,13 +15,14 @@ werkzeug = ">=3.1.5"
 xmltodict = "~=0.9"
 
 authlib = ">=1.6.6"
-httpx = ">=0.23.0,<1.0.0"
-pyjwt = {version = ">=2.4.0,<3.0", extras = ["crypto"]}
+httpx2 = ">=2.9.1"
+pyjwt = {version = ">=2.11.0,<3.0", extras = ["crypto"]}
 cryptography = ">=48.0.1"
 
 Flask = {version = "*", optional = true}
 fastapi = {version = "*", optional = true}
 datamodelutils = { version = "*", optional = true }
+joserfc = ">=1.7.3"
 
 [tool.poetry.extras]
 flask = ["Flask"]

src/authutils/dbgap.py

@@ -3,7 +3,7 @@
 Defines functionality to check case existence in dbGaP.
 """
 
-import httpx
+import httpx2
 import re
 
 import xmltodict
@@ -32,14 +32,14 @@ class dbGaPXReferencer(object):
         "GetSampleStatus.cgi?study_id={phsid}&rettype=xml"
     )
 
-    def __init__(self, db, logger=None, proxies={}):
+    def __init__(self, db, logger=None, proxy=None):
         """Instantiate a class to crossvalidate entity existence in dbGaP."""
         self._cached_telemetry_xmls = {
             # "phsid": "telemetry xml"
         }
 
         self.db = db
-        self.proxies = proxies
+        self.proxy = proxy
         self.logger = logger or get_logger("dbGapXReferencer", log_level="info")
         self.logger.info("Creating new dbGaP Cross Referencer")
 
@@ -96,7 +96,7 @@ def get_xml(self, phsid):
             self.logger.info("Pulling telemetry report from {0}".format(url))
 
             # Request the XML
-            with httpx.Client(proxies=self.proxies) as client:
+            with httpx2.Client(proxy=self.proxy) as client:
                 r = client.get(url)
             if r.status_code != 200:
                 msg = (
@@ -217,7 +217,7 @@ def assert_project_exists(self, project_code, phsid):
         self.logger.info("Pulling telemetry report from {0}".format(url))
 
         # Request the XML
-        with httpx.Client(proxies=self.proxies) as client:
+        with httpx2.Client(proxy=self.proxy) as client:
             r = client.get(url)
         if r.status_code == 400:
             msg = "Project appears not to exist in dbGaP."