From b92b45fa5b72f7c6adf9adae8802d1b6b4f9e992 Mon Sep 17 00:00:00 2001
From: George Thomas <george42@uchicago.edu>
Date: Thu, 26 Oct 2023 10:41:58 -0700
Subject: [PATCH 01/10] (fix PPS-655): upgrade flask, update description of
 tests

---
 docs/local_dev_environment.md |   7 +-
 poetry.lock                   | 950 ++++++++++++++++------------------
 pyproject.toml                |   4 +-
 3 files changed, 449 insertions(+), 512 deletions(-)

diff --git a/docs/local_dev_environment.md b/docs/local_dev_environment.md
index a83239f8..fd01e617 100644
--- a/docs/local_dev_environment.md
+++ b/docs/local_dev_environment.md
@@ -150,7 +150,8 @@ To install the implementation, assure you have poetry installed and simply run:
 poetry install
 ```
 
-To see how the automated tests (run in Travis CI) install Indexd, check out the `.travis.yml` file in the root directory of this repository.
+The automated tests are configured in `.github/workflows/ci.yaml`. The Indexd repo has a
+`tests/ci_commands_script.sh` script that the workflow calls.
 
 ## Installation with Docker
 
@@ -185,7 +186,7 @@ Follow [installation](#installation) guidance and make sure your virtual environ
 You can then update the python dependencies and test from the repository root directory:
 
 ```console
-python3 -m pytest -vv --cov=indexd --cov-report xml --junitxml="test-results.xml" tests
+poetry run pytest -vv --cov=indexd --cov-report xml tests
 ```
 
 > If you're in `wsl1`, you may encounter an error such as `ImportMismatchError` when running pytest.  If this is the case, you can rename the `./tests/__pycache__` folder to `./tests/__pycache__Backup` and re-run the tests.
@@ -235,4 +236,4 @@ With the appropriate settings, you can run the following command to migrate a da
 python3 bin/index_admin.py migrate_database
 ```
 
-If the `bin/local_settings.py` are not reachable, the script will fallback according to these [configuration notes](#configuration).
\ No newline at end of file
+If the `bin/local_settings.py` are not reachable, the script will fallback according to these [configuration notes](#configuration).
diff --git a/poetry.lock b/poetry.lock
index b70402ba..f43db4b5 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,50 +1,49 @@
-# This file is automatically @generated by Poetry and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
 
 [[package]]
 name = "alembic"
-version = "1.9.4"
+version = "1.12.1"
 description = "A database migration tool for SQLAlchemy."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "alembic-1.9.4-py3-none-any.whl", hash = "sha256:6f1c2207369bf4f49f952057a33bb017fbe5c148c2a773b46906b806ea6e825f"},
-    {file = "alembic-1.9.4.tar.gz", hash = "sha256:4d3bd32ecdbb7bbfb48a9fe9e6d6fd6a831a1b59d03e26e292210237373e7db5"},
+    {file = "alembic-1.12.1-py3-none-any.whl", hash = "sha256:47d52e3dfb03666ed945becb723d6482e52190917fdb47071440cfdba05d92cb"},
+    {file = "alembic-1.12.1.tar.gz", hash = "sha256:bca5877e9678b454706347bc10b97cb7d67f300320fa5c3a94423e8266e2823f"},
 ]
 
 [package.dependencies]
 Mako = "*"
 SQLAlchemy = ">=1.3.0"
+typing-extensions = ">=4"
 
 [package.extras]
 tz = ["python-dateutil"]
 
 [[package]]
 name = "anyio"
-version = "3.6.2"
+version = "4.0.0"
 description = "High level compatibility layer for multiple asynchronous event loop implementations"
-category = "main"
 optional = false
-python-versions = ">=3.6.2"
+python-versions = ">=3.8"
 files = [
-    {file = "anyio-3.6.2-py3-none-any.whl", hash = "sha256:fbbe32bd270d2a2ef3ed1c5d45041250284e31fc0a4df4a5a6071842051a51e3"},
-    {file = "anyio-3.6.2.tar.gz", hash = "sha256:25ea0d673ae30af41a0c442f81cf3b38c7e79fdc7b60335a4c14e05eb0947421"},
+    {file = "anyio-4.0.0-py3-none-any.whl", hash = "sha256:cfdb2b588b9fc25ede96d8db56ed50848b0b649dca3dd1df0b11f683bb9e0b5f"},
+    {file = "anyio-4.0.0.tar.gz", hash = "sha256:f7ed51751b2c2add651e5747c891b47e26d2a21be5d32d9311dfe9692f3e5d7a"},
 ]
 
 [package.dependencies]
+exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""}
 idna = ">=2.8"
 sniffio = ">=1.1"
 
 [package.extras]
-doc = ["packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"]
-test = ["contextlib2", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "mock (>=4)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (<0.15)", "uvloop (>=0.15)"]
-trio = ["trio (>=0.16,<0.22)"]
+doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)"]
+test = ["anyio[trio]", "coverage[toml] (>=7)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"]
+trio = ["trio (>=0.22)"]
 
 [[package]]
 name = "atomicwrites"
 version = "1.4.1"
 description = "Atomic file writes."
-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -53,28 +52,26 @@ files = [
 
 [[package]]
 name = "attrs"
-version = "22.2.0"
+version = "23.1.0"
 description = "Classes Without Boilerplate"
-category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "attrs-22.2.0-py3-none-any.whl", hash = "sha256:29e95c7f6778868dbd49170f98f8818f78f3dc5e0e37c0b1f474e3561b240836"},
-    {file = "attrs-22.2.0.tar.gz", hash = "sha256:c9227bfc2f01993c03f68db37d1d15c9690188323c067c641f1a35ca58185f99"},
+    {file = "attrs-23.1.0-py3-none-any.whl", hash = "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04"},
+    {file = "attrs-23.1.0.tar.gz", hash = "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"},
 ]
 
 [package.extras]
-cov = ["attrs[tests]", "coverage-enable-subprocess", "coverage[toml] (>=5.3)"]
-dev = ["attrs[docs,tests]"]
-docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope.interface"]
-tests = ["attrs[tests-no-zope]", "zope.interface"]
-tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy (>=0.971,<0.990)", "mypy (>=0.971,<0.990)", "pympler", "pympler", "pytest (>=4.3.0)", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-mypy-plugins", "pytest-xdist[psutil]", "pytest-xdist[psutil]"]
+cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
+dev = ["attrs[docs,tests]", "pre-commit"]
+docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
+tests = ["attrs[tests-no-zope]", "zope-interface"]
+tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
 
 [[package]]
 name = "authlib"
 version = "0.11"
 description = "The ultimate Python library in building OAuth and OpenID Connect servers."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -88,33 +85,31 @@ requests = "*"
 
 [[package]]
 name = "authutils"
-version = "6.2.2"
+version = "6.1.2"
 description = "Gen3 auth utility functions"
-category = "main"
 optional = false
-python-versions = ">=3.9,<4.0"
+python-versions = ">=3.6,<4.0"
 files = [
-    {file = "authutils-6.2.2-py3-none-any.whl", hash = "sha256:df9b551b4ab561452f0f4b50edaddccc443905b4d77ee69ea7eea78938e7caed"},
-    {file = "authutils-6.2.2.tar.gz", hash = "sha256:ded3e5c0e35160eab83bfb217976920396441e19ed977acacbb769e988323850"},
+    {file = "authutils-6.1.2-py3-none-any.whl", hash = "sha256:5e45b7098a40ee9650326d3f9488f867a538d53d1e03304b59634d5e77a3a258"},
+    {file = "authutils-6.1.2.tar.gz", hash = "sha256:b029daffcc8d1bca481e7ba0528c8982d05c8b8dc7eee72831d37ddc08a36842"},
 ]
 
 [package.dependencies]
 authlib = "0.11.0"
 cached-property = ">=1.4,<2.0"
 cdiserrors = "<2.0.0"
-httpx = ">=0.23.0,<1.0.0"
-pyjwt = {version = ">=2.4.0,<3.0", extras = ["crypto"]}
+httpx = ">=0.12.1,<1.0.0"
+pyjwt = {version = ">=1.5,<2.0", extras = ["crypto"]}
 xmltodict = ">=0.9,<1.0"
 
 [package.extras]
-fastapi = ["fastapi (>=0.65.2,<0.66.0)"]
+fastapi = ["fastapi (>=0.54.1,<0.55.0)"]
 flask = ["Flask (>=0.10.1)"]
 
 [[package]]
 name = "backoff"
 version = "1.11.1"
 description = "Function decoration for backoff and retry"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -122,11 +117,21 @@ files = [
     {file = "backoff-1.11.1.tar.gz", hash = "sha256:ccb962a2378418c667b3c979b504fdeb7d9e0d29c0579e3b13b86467177728cb"},
 ]
 
+[[package]]
+name = "blinker"
+version = "1.6.3"
+description = "Fast, simple object-to-object and broadcast signaling"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "blinker-1.6.3-py3-none-any.whl", hash = "sha256:296320d6c28b006eb5e32d4712202dbcdcbf5dc482da298c2f44881c43884aaa"},
+    {file = "blinker-1.6.3.tar.gz", hash = "sha256:152090d27c1c5c722ee7e48504b02d76502811ce02e1523553b4cf8c8b3d3a8d"},
+]
+
 [[package]]
 name = "cached-property"
 version = "1.5.2"
 description = "A decorator for caching properties in classes."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -138,7 +143,6 @@ files = [
 name = "cdiserrors"
 version = "1.0.0"
 description = "Gen3 shared exceptions and utilities."
-category = "main"
 optional = false
 python-versions = ">=3.6,<4.0"
 files = [
@@ -156,7 +160,6 @@ flask = ["Flask (>=1.1.2,<2.0.0)"]
 name = "cdislogging"
 version = "1.1.1"
 description = "Standardized logging tool and format for cdis applications"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -167,7 +170,6 @@ files = [
 name = "cdisutilstest"
 version = "0.2.4"
 description = "Collection of test data and tools"
-category = "dev"
 optional = false
 python-versions = "*"
 files = []
@@ -181,88 +183,74 @@ resolved_reference = "bdfdeb05e45407e839fd954ce6d195d847cd8024"
 
 [[package]]
 name = "certifi"
-version = "2022.12.7"
+version = "2023.7.22"
 description = "Python package for providing Mozilla's CA Bundle."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2022.12.7-py3-none-any.whl", hash = "sha256:4ad3232f5e926d6718ec31cfc1fcadfde020920e278684144551c91769c7bc18"},
-    {file = "certifi-2022.12.7.tar.gz", hash = "sha256:35824b4c3a97115964b408844d64aa14db1cc518f6562e8d7261699d1350a9e3"},
+    {file = "certifi-2023.7.22-py3-none-any.whl", hash = "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9"},
+    {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"},
 ]
 
 [[package]]
 name = "cffi"
-version = "1.15.1"
+version = "1.16.0"
 description = "Foreign Function Interface for Python calling C code."
-category = "main"
 optional = false
-python-versions = "*"
+python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -270,112 +258,112 @@ pycparser = "*"
 
 [[package]]
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 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
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 optional = false
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 ]
 
 [[package]]
 name = "click"
-version = "8.1.3"
+version = "8.1.7"
 description = "Composable command line interface toolkit"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "click-8.1.3-py3-none-any.whl", hash = "sha256:bb4d8133cb15a609f44e8213d9b391b0809795062913b383c62be0ee95b1db48"},
-    {file = "click-8.1.3.tar.gz", hash = "sha256:7682dc8afb30297001674575ea00d1814d808d6a36af415a82bd481d37ba7b8e"},
+    {file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"},
+    {file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"},
 ]
 
 [package.dependencies]
@@ -385,7 +373,6 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""}
 name = "colorama"
 version = "0.4.6"
 description = "Cross-platform colored terminal text."
-category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 files = [
@@ -397,7 +384,6 @@ files = [
 name = "coverage"
 version = "6.5.0"
 description = "Code coverage measurement for Python"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -460,7 +446,6 @@ toml = ["tomli"]
 name = "coveralls"
 version = "3.3.1"
 description = "Show coverage stats online via coveralls.io"
-category = "dev"
 optional = false
 python-versions = ">= 3.5"
 files = [
@@ -469,7 +454,7 @@ files = [
 ]
 
 [package.dependencies]
-coverage = ">=4.1,<6.0.0 || >6.1,<6.1.1 || >6.1.1,<7.0"
+coverage = ">=4.1,<6.0.dev0 || >6.1,<6.1.1 || >6.1.1,<7.0"
 docopt = ">=0.6.1"
 requests = ">=1.0.0"
 
@@ -478,35 +463,34 @@ yaml = ["PyYAML (>=3.10)"]
 
 [[package]]
 name = "cryptography"
-version = "39.0.1"
+version = "41.0.5"
 description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
-category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
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 ]
 
 [package.dependencies]
@@ -515,18 +499,17 @@ cffi = ">=1.12"
 [package.extras]
 docs = ["sphinx (>=5.3.0)", "sphinx-rtd-theme (>=1.1.1)"]
 docstest = ["pyenchant (>=1.6.11)", "sphinxcontrib-spelling (>=4.0.1)", "twine (>=1.12.0)"]
-pep8test = ["black", "check-manifest", "mypy", "ruff", "types-pytz", "types-requests"]
-sdist = ["setuptools-rust (>=0.11.4)"]
+nox = ["nox"]
+pep8test = ["black", "check-sdist", "mypy", "ruff"]
+sdist = ["build"]
 ssh = ["bcrypt (>=3.1.5)"]
-test = ["hypothesis (>=1.11.4,!=3.79.2)", "iso8601", "pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-shard (>=0.1.2)", "pytest-subtests", "pytest-xdist", "pytz"]
+test = ["pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-xdist"]
 test-randomorder = ["pytest-randomly"]
-tox = ["tox"]
 
 [[package]]
 name = "docopt"
 version = "0.6.2"
 description = "Pythonic argument parser, that will make you smile"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -537,7 +520,6 @@ files = [
 name = "doiclient"
 version = "0.1"
 description = ""
-category = "main"
 optional = false
 python-versions = "*"
 files = []
@@ -556,7 +538,6 @@ resolved_reference = "1a5f4b2a0b04577f31f3dcec511ade117d9f4ba1"
 name = "dosclient"
 version = "0.1"
 description = ""
-category = "main"
 optional = false
 python-versions = "*"
 files = []
@@ -571,24 +552,38 @@ url = "https://github.com/uc-cdis/dosclient"
 reference = "1.1.0"
 resolved_reference = "38c0f1ab42edf3efb1ad6348d7dbdff81b131360"
 
+[[package]]
+name = "exceptiongroup"
+version = "1.1.3"
+description = "Backport of PEP 654 (exception groups)"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "exceptiongroup-1.1.3-py3-none-any.whl", hash = "sha256:343280667a4585d195ca1cf9cef84a4e178c4b6cf2274caef9859782b567d5e3"},
+    {file = "exceptiongroup-1.1.3.tar.gz", hash = "sha256:097acd85d473d75af5bb98e41b61ff7fe35efe6675e4f9370ec6ec5126d160e9"},
+]
+
+[package.extras]
+test = ["pytest (>=6)"]
+
 [[package]]
 name = "flask"
-version = "2.2.3"
+version = "2.3.3"
 description = "A simple framework for building complex web applications."
-category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "Flask-2.2.3-py3-none-any.whl", hash = "sha256:c0bec9477df1cb867e5a67c9e1ab758de9cb4a3e52dd70681f59fa40a62b3f2d"},
-    {file = "Flask-2.2.3.tar.gz", hash = "sha256:7eb373984bf1c770023fce9db164ed0c3353cd0b53f130f4693da0ca756a2e6d"},
+    {file = "flask-2.3.3-py3-none-any.whl", hash = "sha256:f69fcd559dc907ed196ab9df0e48471709175e696d6e698dd4dbe940f96ce66b"},
+    {file = "flask-2.3.3.tar.gz", hash = "sha256:09c347a92aa7ff4a8e7f3206795f30d826654baf38b873d0744cd571ca609efc"},
 ]
 
 [package.dependencies]
-click = ">=8.0"
+blinker = ">=1.6.2"
+click = ">=8.1.3"
 importlib-metadata = {version = ">=3.6.0", markers = "python_version < \"3.10\""}
-itsdangerous = ">=2.0"
-Jinja2 = ">=3.0"
-Werkzeug = ">=2.2.2"
+itsdangerous = ">=2.1.2"
+Jinja2 = ">=3.1.2"
+Werkzeug = ">=2.3.7"
 
 [package.extras]
 async = ["asgiref (>=3.2)"]
@@ -598,7 +593,6 @@ dotenv = ["python-dotenv"]
 name = "gen3authz"
 version = "1.5.1"
 description = "Gen3 authz client"
-category = "main"
 optional = false
 python-versions = ">=3.6,<4.0"
 files = [
@@ -616,7 +610,6 @@ six = ">=1.16.0,<2.0.0"
 name = "h11"
 version = "0.14.0"
 description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -628,7 +621,6 @@ files = [
 name = "hsclient"
 version = "0.1"
 description = ""
-category = "main"
 optional = false
 python-versions = "*"
 files = []
@@ -645,55 +637,52 @@ resolved_reference = "f122072ee245216da5e4260f718d6f886db81773"
 
 [[package]]
 name = "httpcore"
-version = "0.16.3"
+version = "0.18.0"
 description = "A minimal low-level HTTP client."
-category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "httpcore-0.16.3-py3-none-any.whl", hash = "sha256:da1fb708784a938aa084bde4feb8317056c55037247c787bd7e19eb2c2949dc0"},
-    {file = "httpcore-0.16.3.tar.gz", hash = "sha256:c5d6f04e2fc530f39e0c077e6a30caa53f1451096120f1f38b954afd0b17c0cb"},
+    {file = "httpcore-0.18.0-py3-none-any.whl", hash = "sha256:adc5398ee0a476567bf87467063ee63584a8bce86078bf748e48754f60202ced"},
+    {file = "httpcore-0.18.0.tar.gz", hash = "sha256:13b5e5cd1dca1a6636a6aaea212b19f4f85cd88c366a2b82304181b769aab3c9"},
 ]
 
 [package.dependencies]
 anyio = ">=3.0,<5.0"
 certifi = "*"
 h11 = ">=0.13,<0.15"
-sniffio = ">=1.0.0,<2.0.0"
+sniffio = "==1.*"
 
 [package.extras]
 http2 = ["h2 (>=3,<5)"]
-socks = ["socksio (>=1.0.0,<2.0.0)"]
+socks = ["socksio (==1.*)"]
 
 [[package]]
 name = "httpx"
-version = "0.23.3"
+version = "0.25.0"
 description = "The next generation HTTP client."
-category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "httpx-0.23.3-py3-none-any.whl", hash = "sha256:a211fcce9b1254ea24f0cd6af9869b3d29aba40154e947d2a07bb499b3e310d6"},
-    {file = "httpx-0.23.3.tar.gz", hash = "sha256:9818458eb565bb54898ccb9b8b251a28785dd4a55afbc23d0eb410754fe7d0f9"},
+    {file = "httpx-0.25.0-py3-none-any.whl", hash = "sha256:181ea7f8ba3a82578be86ef4171554dd45fec26a02556a744db029a0a27b7100"},
+    {file = "httpx-0.25.0.tar.gz", hash = "sha256:47ecda285389cb32bb2691cc6e069e3ab0205956f681c5b2ad2325719751d875"},
 ]
 
 [package.dependencies]
 certifi = "*"
-httpcore = ">=0.15.0,<0.17.0"
-rfc3986 = {version = ">=1.3,<2", extras = ["idna2008"]}
+httpcore = ">=0.18.0,<0.19.0"
+idna = "*"
 sniffio = "*"
 
 [package.extras]
 brotli = ["brotli", "brotlicffi"]
-cli = ["click (>=8.0.0,<9.0.0)", "pygments (>=2.0.0,<3.0.0)", "rich (>=10,<13)"]
+cli = ["click (==8.*)", "pygments (==2.*)", "rich (>=10,<14)"]
 http2 = ["h2 (>=3,<5)"]
-socks = ["socksio (>=1.0.0,<2.0.0)"]
+socks = ["socksio (==1.*)"]
 
 [[package]]
 name = "idna"
 version = "3.4"
 description = "Internationalized Domain Names in Applications (IDNA)"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -703,14 +692,13 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "6.0.0"
+version = "6.8.0"
 description = "Read metadata from Python packages"
-category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "importlib_metadata-6.0.0-py3-none-any.whl", hash = "sha256:7efb448ec9a5e313a57655d35aa54cd3e01b7e1fbcf72dce1bf06119420f5bad"},
-    {file = "importlib_metadata-6.0.0.tar.gz", hash = "sha256:e354bedeb60efa6affdcc8ae121b73544a7aa74156d047311948f6d711cd378d"},
+    {file = "importlib_metadata-6.8.0-py3-none-any.whl", hash = "sha256:3ebb78df84a805d7698245025b975d9d67053cd94c79245ba4b3eb694abe68bb"},
+    {file = "importlib_metadata-6.8.0.tar.gz", hash = "sha256:dbace7892d8c0c4ac1ad096662232f831d4e64f4c4545bd53016a3e9d4654743"},
 ]
 
 [package.dependencies]
@@ -719,17 +707,16 @@ zipp = ">=0.5"
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 perf = ["ipython"]
-testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)"]
+testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)", "pytest-ruff"]
 
 [[package]]
 name = "indexclient"
-version = "2.1.1"
+version = "2.2.1"
 description = ""
-category = "main"
 optional = false
 python-versions = "*"
 files = [
-    {file = "indexclient-2.1.1.tar.gz", hash = "sha256:03f0ef104d14e0e4117063892da0747d5db3c0e952143d3408f611797d909b2e"},
+    {file = "indexclient-2.2.1.tar.gz", hash = "sha256:d0374128a340b42042fc2d7c2484a8b1f36b90e05199e6f8357ad764dd6673fd"},
 ]
 
 [package.dependencies]
@@ -739,7 +726,6 @@ requests = ">=2.5.2,<3.0.0"
 name = "iniconfig"
 version = "2.0.0"
 description = "brain-dead simple config-ini parsing"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -751,7 +737,6 @@ files = [
 name = "itsdangerous"
 version = "2.1.2"
 description = "Safely pass data to untrusted environments and back."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -763,7 +748,6 @@ files = [
 name = "jinja2"
 version = "3.1.2"
 description = "A very fast and expressive template engine."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -781,7 +765,6 @@ i18n = ["Babel (>=2.7)"]
 name = "jsonschema"
 version = "3.2.0"
 description = "An implementation of JSON Schema validation for Python"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -803,7 +786,6 @@ format-nongpl = ["idna", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-va
 name = "mako"
 version = "1.2.4"
 description = "A super-fast templating language that borrows the best ideas from the existing templating languages."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -821,69 +803,67 @@ testing = ["pytest"]
 
 [[package]]
 name = "markupsafe"
-version = "2.1.2"
+version = "2.1.3"
 description = "Safely add untrusted strings to HTML/XML markup."
-category = "main"
 optional = false
 python-versions = ">=3.7"
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 version = "4.0.3"
 description = "Rolling backport of unittest.mock for all Pythons"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -898,26 +878,24 @@ test = ["pytest (<5.4)", "pytest-cov"]
 
 [[package]]
 name = "packaging"
-version = "23.0"
+version = "23.2"
 description = "Core utilities for Python packages"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [[package]]
 name = "pluggy"
-version = "1.0.0"
+version = "1.3.0"
 description = "plugin and hook calling mechanisms for python"
-category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -926,32 +904,28 @@ testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
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-version = "2.9.5"
+version = "2.9.9"
 description = "psycopg2 - Python-PostgreSQL Database Adapter"
-category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
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 ]
 
 [[package]]
 name = "py"
 version = "1.11.0"
 description = "library with cross-python path, ini-parsing, io, code, log facilities"
-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -963,7 +937,6 @@ files = [
 name = "pycparser"
 version = "2.21"
 description = "C parser in Python"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -973,67 +946,68 @@ files = [
 
 [[package]]
 name = "pyjwt"
-version = "2.6.0"
+version = "1.7.1"
 description = "JSON Web Token implementation in Python"
-category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = "*"
 files = [
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 ]
 
 [package.dependencies]
-cryptography = {version = ">=3.4.0", optional = true, markers = "extra == \"crypto\""}
+cryptography = {version = ">=1.4", optional = true, markers = "extra == \"crypto\""}
 
 [package.extras]
-crypto = ["cryptography (>=3.4.0)"]
-dev = ["coverage[toml] (==5.0.4)", "cryptography (>=3.4.0)", "pre-commit", "pytest (>=6.0.0,<7.0.0)", "sphinx (>=4.5.0,<5.0.0)", "sphinx-rtd-theme", "zope.interface"]
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-tests = ["coverage[toml] (==5.0.4)", "pytest (>=6.0.0,<7.0.0)"]
+crypto = ["cryptography (>=1.4)"]
+flake8 = ["flake8", "flake8-import-order", "pep8-naming"]
+test = ["pytest (>=4.0.1,<5.0.0)", "pytest-cov (>=2.6.0,<3.0.0)", "pytest-runner (>=4.2,<5.0.0)"]
 
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+version = "0.20.0"
 description = "Persistent/Functional/Immutable data structures"
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 optional = false
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 [[package]]
 name = "pytest"
 version = "6.2.5"
 description = "pytest: simple powerful testing with Python"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1058,7 +1032,6 @@ testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xm
 name = "pytest-cov"
 version = "2.12.1"
 description = "Pytest plugin for measuring coverage."
-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -1076,80 +1049,61 @@ testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtuale
 
 [[package]]
 name = "pytest-flask"
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+version = "1.3.0"
 description = "A set of py.test fixtures to test Flask applications."
-category = "dev"
 optional = false
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 [package.dependencies]
 Flask = "*"
 pytest = ">=5.2"
-Werkzeug = ">=0.7"
+Werkzeug = "*"
 
 [package.extras]
 docs = ["Sphinx", "sphinx-rtd-theme"]
 
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 ]
 
 [[package]]
 name = "requests"
-version = "2.28.2"
+version = "2.31.0"
 description = "Python HTTP for Humans."
-category = "main"
 optional = false
-python-versions = ">=3.7, <4"
+python-versions = ">=3.7"
 files = [
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+    {file = "requests-2.31.0.tar.gz", hash = "sha256:942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1"},
 ]
 
 [package.dependencies]
 certifi = ">=2017.4.17"
 charset-normalizer = ">=2,<4"
 idna = ">=2.5,<4"
-urllib3 = ">=1.21.1,<1.27"
+urllib3 = ">=1.21.1,<3"
 
 [package.extras]
 socks = ["PySocks (>=1.5.6,!=1.5.7)"]
@@ -1159,7 +1113,6 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 name = "responses"
 version = "0.13.4"
 description = "A utility library for mocking out the `requests` Python library."
-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -1175,46 +1128,26 @@ urllib3 = ">=1.25.10"
 [package.extras]
 tests = ["coverage (>=3.7.1,<6.0.0)", "flake8", "mypy", "pytest (>=4.6)", "pytest (>=4.6,<5.0)", "pytest-cov", "pytest-localserver", "types-mock", "types-requests", "types-six"]
 
-[[package]]
-name = "rfc3986"
-version = "1.5.0"
-description = "Validating URI References per RFC 3986"
-category = "main"
-optional = false
-python-versions = "*"
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-]
-
-[package.dependencies]
-idna = {version = "*", optional = true, markers = "extra == \"idna2008\""}
-
-[package.extras]
-idna2008 = ["idna"]
-
 [[package]]
 name = "setuptools"
-version = "67.4.0"
+version = "68.2.2"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
-category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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+    {file = "setuptools-68.2.2.tar.gz", hash = "sha256:4ac1475276d2f1c48684874089fefcd83bd7162ddaafb81fac866ba0db282a87"},
 ]
 
 [package.extras]
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-testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8 (<5)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
-testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
+testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
+testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.1)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
 
 [[package]]
 name = "six"
 version = "1.16.0"
 description = "Python 2 and 3 compatibility utilities"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 files = [
@@ -1226,7 +1159,6 @@ files = [
 name = "sniffio"
 version = "1.3.0"
 description = "Sniff out which async library your code is running under"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1238,7 +1170,6 @@ files = [
 name = "sqlalchemy"
 version = "1.3.24"
 description = "Database Abstraction Library"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -1294,7 +1225,6 @@ pymysql = ["pymysql", "pymysql (<1)"]
 name = "sqlalchemy-utils"
 version = "0.37.9"
 description = "Various utility functions for SQLAlchemy."
-category = "main"
 optional = false
 python-versions = "~=3.4"
 files = [
@@ -1324,7 +1254,6 @@ url = ["furl (>=0.4.1)"]
 name = "swagger-spec-validator"
 version = "2.7.6"
 description = "Validation of Swagger specifications"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -1341,7 +1270,6 @@ six = "*"
 name = "toml"
 version = "0.10.2"
 description = "Python Library for Tom's Obvious, Minimal Language"
-category = "dev"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
 files = [
@@ -1349,46 +1277,55 @@ files = [
     {file = "toml-0.10.2.tar.gz", hash = "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f"},
 ]
 
+[[package]]
+name = "typing-extensions"
+version = "4.8.0"
+description = "Backported and Experimental Type Hints for Python 3.8+"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "typing_extensions-4.8.0-py3-none-any.whl", hash = "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0"},
+    {file = "typing_extensions-4.8.0.tar.gz", hash = "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef"},
+]
+
 [[package]]
 name = "urllib3"
-version = "1.26.14"
+version = "2.0.7"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
-category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
+python-versions = ">=3.7"
 files = [
-    {file = "urllib3-1.26.14-py2.py3-none-any.whl", hash = "sha256:75edcdc2f7d85b137124a6c3c9fc3933cdeaa12ecb9a6a959f22797a0feca7e1"},
-    {file = "urllib3-1.26.14.tar.gz", hash = "sha256:076907bf8fd355cde77728471316625a4d2f7e713c125f51953bb5b3eecf4f72"},
+    {file = "urllib3-2.0.7-py3-none-any.whl", hash = "sha256:fdb6d215c776278489906c2f8916e6e7d4f5a9b602ccbcfdf7f016fc8da0596e"},
+    {file = "urllib3-2.0.7.tar.gz", hash = "sha256:c97dfde1f7bd43a71c8d2a58e369e9b2bf692d1334ea9f9cae55add7d0dd0f84"},
 ]
 
 [package.extras]
-brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"]
-secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"]
-socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
+brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+secure = ["certifi", "cryptography (>=1.9)", "idna (>=2.0.0)", "pyopenssl (>=17.1.0)", "urllib3-secure-extra"]
+socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
+zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "werkzeug"
-version = "2.2.3"
+version = "3.0.1"
 description = "The comprehensive WSGI web application library."
-category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "Werkzeug-2.2.3-py3-none-any.whl", hash = "sha256:56433961bc1f12533306c624f3be5e744389ac61d722175d543e1751285da612"},
-    {file = "Werkzeug-2.2.3.tar.gz", hash = "sha256:2e1ccc9417d4da358b9de6f174e3ac094391ea1d4fbef2d667865d819dfd0afe"},
+    {file = "werkzeug-3.0.1-py3-none-any.whl", hash = "sha256:90a285dc0e42ad56b34e696398b8122ee4c681833fb35b8334a095d82c56da10"},
+    {file = "werkzeug-3.0.1.tar.gz", hash = "sha256:507e811ecea72b18a404947aded4b3390e1db8f826b494d76550ef45bb3b1dcc"},
 ]
 
 [package.dependencies]
 MarkupSafe = ">=2.1.1"
 
 [package.extras]
-watchdog = ["watchdog"]
+watchdog = ["watchdog (>=2.3)"]
 
 [[package]]
 name = "xmltodict"
 version = "0.13.0"
 description = "Makes working with XML feel like you are working with JSON"
-category = "main"
 optional = false
 python-versions = ">=3.4"
 files = [
@@ -1398,21 +1335,20 @@ files = [
 
 [[package]]
 name = "zipp"
-version = "3.15.0"
+version = "3.17.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
-category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.15.0-py3-none-any.whl", hash = "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"},
-    {file = "zipp-3.15.0.tar.gz", hash = "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b"},
+    {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"},
+    {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
 
 [metadata]
 lock-version = "2.0"
-python-versions = "^3.9"
-content-hash = "dbb013e70567b96835a357dfe393b4ca95e5fb973b73d81e228aef0dc884c1b9"
+python-versions = "3.9.*"
+content-hash = "0291aad12a33bb82825922b9d36e013551cb0493e7ef5a1b5c79669d62ffaa72"
diff --git a/pyproject.toml b/pyproject.toml
index 1ee236a9..94fba800 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,11 +21,11 @@ gen3authz = "^1.0.4"
 hsclient = {git = "https://github.com/uc-cdis/hsclient", rev = "1.0.0"}
 indexclient = "^2.1.0"
 jsonschema = "^3.2"
-flask = "^2.0.1"
+flask = "^2.2.5"
 psycopg2 = "^2.7"
 sqlalchemy = "~1.3.3"
 sqlalchemy-utils = "^0.37.3"
-PyYAML = "^5.4"
+PyYAML = "5.3.1"
 
 
 [tool.poetry.dev-dependencies]

From 0a4f2167637feef60bbb75ca74450681f3e3869e Mon Sep 17 00:00:00 2001
From: George Thomas <george42@uchicago.edu>
Date: Fri, 27 Oct 2023 08:01:31 -0700
Subject: [PATCH 02/10] (fix PPS-629): allow upgrade of PyYAML

---
 poetry.lock    | 59 ++++++++++++++++++++++++++++++++++++--------------
 pyproject.toml |  2 +-
 2 files changed, 44 insertions(+), 17 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index f43db4b5..98dfdfb5 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1068,24 +1068,51 @@ docs = ["Sphinx", "sphinx-rtd-theme"]
 
 [[package]]
 name = "pyyaml"
-version = "5.3.1"
+version = "6.0.1"
 description = "YAML parser and emitter for Python"
 optional = false
-python-versions = "*"
+python-versions = ">=3.6"
 files = [
-    {file = "PyYAML-5.3.1-cp27-cp27m-win32.whl", hash = "sha256:74809a57b329d6cc0fdccee6318f44b9b8649961fa73144a98735b0aaf029f1f"},
-    {file = "PyYAML-5.3.1-cp27-cp27m-win_amd64.whl", hash = "sha256:240097ff019d7c70a4922b6869d8a86407758333f02203e0fc6ff79c5dcede76"},
-    {file = "PyYAML-5.3.1-cp35-cp35m-win32.whl", hash = "sha256:4f4b913ca1a7319b33cfb1369e91e50354d6f07a135f3b901aca02aa95940bd2"},
-    {file = "PyYAML-5.3.1-cp35-cp35m-win_amd64.whl", hash = "sha256:cc8955cfbfc7a115fa81d85284ee61147059a753344bc51098f3ccd69b0d7e0c"},
-    {file = "PyYAML-5.3.1-cp36-cp36m-win32.whl", hash = "sha256:7739fc0fa8205b3ee8808aea45e968bc90082c10aef6ea95e855e10abf4a37b2"},
-    {file = "PyYAML-5.3.1-cp36-cp36m-win_amd64.whl", hash = "sha256:69f00dca373f240f842b2931fb2c7e14ddbacd1397d57157a9b005a6a9942648"},
-    {file = "PyYAML-5.3.1-cp37-cp37m-win32.whl", hash = "sha256:d13155f591e6fcc1ec3b30685d50bf0711574e2c0dfffd7644babf8b5102ca1a"},
-    {file = "PyYAML-5.3.1-cp37-cp37m-win_amd64.whl", hash = "sha256:73f099454b799e05e5ab51423c7bcf361c58d3206fa7b0d555426b1f4d9a3eaf"},
-    {file = "PyYAML-5.3.1-cp38-cp38-win32.whl", hash = "sha256:06a0d7ba600ce0b2d2fe2e78453a470b5a6e000a985dd4a4e54e436cc36b0e97"},
-    {file = "PyYAML-5.3.1-cp38-cp38-win_amd64.whl", hash = "sha256:95f71d2af0ff4227885f7a6605c37fd53d3a106fcab511b8860ecca9fcf400ee"},
-    {file = "PyYAML-5.3.1-cp39-cp39-win32.whl", hash = "sha256:ad9c67312c84def58f3c04504727ca879cb0013b2517c85a9a253f0cb6380c0a"},
-    {file = "PyYAML-5.3.1-cp39-cp39-win_amd64.whl", hash = "sha256:6034f55dab5fea9e53f436aa68fa3ace2634918e8b5994d82f3621c04ff5ed2e"},
-    {file = "PyYAML-5.3.1.tar.gz", hash = "sha256:b8eac752c5e14d3eca0e6dd9199cd627518cb5ec06add0de9d32baeee6fe645d"},
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+    {file = "PyYAML-6.0.1-cp38-cp38-win_amd64.whl", hash = "sha256:1e2722cc9fbb45d9b87631ac70924c11d3a401b2d7f410cc0e3bbf249f2dca62"},
+    {file = "PyYAML-6.0.1-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:9eb6caa9a297fc2c2fb8862bc5370d0303ddba53ba97e71f08023b6cd73d16a8"},
+    {file = "PyYAML-6.0.1-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:c8098ddcc2a85b61647b2590f825f3db38891662cfc2fc776415143f599bb859"},
+    {file = "PyYAML-6.0.1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:5773183b6446b2c99bb77e77595dd486303b4faab2b086e7b17bc6bef28865f6"},
+    {file = "PyYAML-6.0.1-cp39-cp39-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:b786eecbdf8499b9ca1d697215862083bd6d2a99965554781d0d8d1ad31e13a0"},
+    {file = "PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:bc1bf2925a1ecd43da378f4db9e4f799775d6367bdb94671027b73b393a7c42c"},
+    {file = "PyYAML-6.0.1-cp39-cp39-win32.whl", hash = "sha256:faca3bdcf85b2fc05d06ff3fbc1f83e1391b3e724afa3feba7d13eeab355484c"},
+    {file = "PyYAML-6.0.1-cp39-cp39-win_amd64.whl", hash = "sha256:510c9deebc5c0225e8c96813043e62b680ba2f9c50a08d3724c7f28a747d1486"},
+    {file = "PyYAML-6.0.1.tar.gz", hash = "sha256:bfdf460b1736c775f2ba9f6a92bca30bc2095067b8a9d77876d1fad6cc3b4a43"},
 ]
 
 [[package]]
@@ -1351,4 +1378,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = "3.9.*"
-content-hash = "0291aad12a33bb82825922b9d36e013551cb0493e7ef5a1b5c79669d62ffaa72"
+content-hash = "034498a9c4e35e1151a5b2d4604476ed46ac7b8183e7a4b3d23f3fc451d66aaa"
diff --git a/pyproject.toml b/pyproject.toml
index 94fba800..27860c79 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,7 +25,7 @@ flask = "^2.2.5"
 psycopg2 = "^2.7"
 sqlalchemy = "~1.3.3"
 sqlalchemy-utils = "^0.37.3"
-PyYAML = "5.3.1"
+PyYAML = ">=5.3,<7"
 
 
 [tool.poetry.dev-dependencies]

From 10b042370d073a8ba626f31b35e064b89d41915b Mon Sep 17 00:00:00 2001
From: George Thomas <george42@uchicago.edu>
Date: Fri, 27 Oct 2023 12:29:41 -0700
Subject: [PATCH 03/10] use consistent python version spec across repos

---
 poetry.lock    | 50 +++++++++++++++++++++++++-------------------------
 pyproject.toml |  2 +-
 2 files changed, 26 insertions(+), 26 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 98dfdfb5..029254c3 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -70,41 +70,40 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte
 
 [[package]]
 name = "authlib"
-version = "0.11"
-description = "The ultimate Python library in building OAuth and OpenID Connect servers."
+version = "1.2.1"
+description = "The ultimate Python library in building OAuth and OpenID Connect servers and clients."
 optional = false
 python-versions = "*"
 files = [
-    {file = "Authlib-0.11-py2.py3-none-any.whl", hash = "sha256:3a226f231e962a16dd5f6fcf0c113235805ba206e294717a64fa8e04ae3ad9c4"},
-    {file = "Authlib-0.11.tar.gz", hash = "sha256:9741db6de2950a0a5cefbdb72ec7ab12f7e9fd530ff47219f1530e79183cbaaf"},
+    {file = "Authlib-1.2.1-py2.py3-none-any.whl", hash = "sha256:c88984ea00149a90e3537c964327da930779afa4564e354edfd98410bea01911"},
+    {file = "Authlib-1.2.1.tar.gz", hash = "sha256:421f7c6b468d907ca2d9afede256f068f87e34d23dd221c07d13d4c234726afb"},
 ]
 
 [package.dependencies]
-cryptography = "*"
-requests = "*"
+cryptography = ">=3.2"
 
 [[package]]
 name = "authutils"
-version = "6.1.2"
+version = "6.2.3"
 description = "Gen3 auth utility functions"
 optional = false
-python-versions = ">=3.6,<4.0"
+python-versions = ">=3.9,<4.0"
 files = [
-    {file = "authutils-6.1.2-py3-none-any.whl", hash = "sha256:5e45b7098a40ee9650326d3f9488f867a538d53d1e03304b59634d5e77a3a258"},
-    {file = "authutils-6.1.2.tar.gz", hash = "sha256:b029daffcc8d1bca481e7ba0528c8982d05c8b8dc7eee72831d37ddc08a36842"},
+    {file = "authutils-6.2.3-py3-none-any.whl", hash = "sha256:8c4e7e24183cbc1055ab91eaf9d2966f0da5b739be0fabfe380749674ba3057e"},
+    {file = "authutils-6.2.3.tar.gz", hash = "sha256:c44e1f309b2b5b6db1276f69e1e18ec5c6be1ae33bfe52608a30049b8669ff7b"},
 ]
 
 [package.dependencies]
-authlib = "0.11.0"
+authlib = ">=1.1.0"
 cached-property = ">=1.4,<2.0"
 cdiserrors = "<2.0.0"
-httpx = ">=0.12.1,<1.0.0"
-pyjwt = {version = ">=1.5,<2.0", extras = ["crypto"]}
+httpx = ">=0.23.0,<1.0.0"
+pyjwt = {version = ">=2.4.0,<3.0", extras = ["crypto"]}
 xmltodict = ">=0.9,<1.0"
 
 [package.extras]
-fastapi = ["fastapi (>=0.54.1,<0.55.0)"]
-flask = ["Flask (>=0.10.1)"]
+fastapi = ["fastapi (>=0.65.2,<0.66.0)"]
+flask = ["Flask (<=2.3.3)"]
 
 [[package]]
 name = "backoff"
@@ -946,22 +945,23 @@ files = [
 
 [[package]]
 name = "pyjwt"
-version = "1.7.1"
+version = "2.8.0"
 description = "JSON Web Token implementation in Python"
 optional = false
-python-versions = "*"
+python-versions = ">=3.7"
 files = [
-    {file = "PyJWT-1.7.1-py2.py3-none-any.whl", hash = "sha256:5c6eca3c2940464d106b99ba83b00c6add741c9becaec087fb7ccdefea71350e"},
-    {file = "PyJWT-1.7.1.tar.gz", hash = "sha256:8d59a976fb773f3e6a39c85636357c4f0e242707394cadadd9814f5cbaa20e96"},
+    {file = "PyJWT-2.8.0-py3-none-any.whl", hash = "sha256:59127c392cc44c2da5bb3192169a91f429924e17aff6534d70fdc02ab3e04320"},
+    {file = "PyJWT-2.8.0.tar.gz", hash = "sha256:57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de"},
 ]
 
 [package.dependencies]
-cryptography = {version = ">=1.4", optional = true, markers = "extra == \"crypto\""}
+cryptography = {version = ">=3.4.0", optional = true, markers = "extra == \"crypto\""}
 
 [package.extras]
-crypto = ["cryptography (>=1.4)"]
-flake8 = ["flake8", "flake8-import-order", "pep8-naming"]
-test = ["pytest (>=4.0.1,<5.0.0)", "pytest-cov (>=2.6.0,<3.0.0)", "pytest-runner (>=4.2,<5.0.0)"]
+crypto = ["cryptography (>=3.4.0)"]
+dev = ["coverage[toml] (==5.0.4)", "cryptography (>=3.4.0)", "pre-commit", "pytest (>=6.0.0,<7.0.0)", "sphinx (>=4.5.0,<5.0.0)", "sphinx-rtd-theme", "zope.interface"]
+docs = ["sphinx (>=4.5.0,<5.0.0)", "sphinx-rtd-theme", "zope.interface"]
+tests = ["coverage[toml] (==5.0.4)", "pytest (>=6.0.0,<7.0.0)"]
 
 [[package]]
 name = "pyrsistent"
@@ -1377,5 +1377,5 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 
 [metadata]
 lock-version = "2.0"
-python-versions = "3.9.*"
-content-hash = "034498a9c4e35e1151a5b2d4604476ed46ac7b8183e7a4b3d23f3fc451d66aaa"
+python-versions = ">=3.9,<4.0"
+content-hash = "79da5985265b226bc0022b58a032a8c85a2695a1b023f093743fa169af96bdaa"
diff --git a/pyproject.toml b/pyproject.toml
index 27860c79..7a7f7167 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,7 +10,7 @@ include = [
 ]
 
 [tool.poetry.dependencies]
-python = "3.9.*"
+python = ">=3.9,<4.0"
 alembic = "^1.9.4"
 authutils = "^6.0.0"
 cdislogging = "^1.0.0"

From b4c3e7e78cf7d18feccd0519317b8ad23dceec74 Mon Sep 17 00:00:00 2001
From: George Thomas <george42@uchicago.edu>
Date: Tue, 31 Oct 2023 07:48:56 -0700
Subject: [PATCH 04/10] bump version

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 7a7f7167..7e29d885 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "indexd"
-version = "5.0.2"
+version = "5.0.3"
 description = "Gen3 Indexing Service"
 authors = ["CTDS UChicago <cdis@uchicago.edu>"]
 license = "Apache-2.0"

From 151a5128f08384b6109e7d73c985d59b26ab42aa Mon Sep 17 00:00:00 2001
From: George Thomas <george42@uchicago.edu>
Date: Thu, 2 Nov 2023 16:13:05 -0700
Subject: [PATCH 05/10] (fix): add debug statements

---
 indexd/auth/drivers/alchemy.py | 1 +
 indexd/index/blueprint.py      | 1 +
 2 files changed, 2 insertions(+)

diff --git a/indexd/auth/drivers/alchemy.py b/indexd/auth/drivers/alchemy.py
index 6268cb3a..d6c5fd8b 100644
--- a/indexd/auth/drivers/alchemy.py
+++ b/indexd/auth/drivers/alchemy.py
@@ -102,6 +102,7 @@ def auth(self, username, password):
         Returns a dict of user information.
         Raises AutheError otherwise.
         """
+        logger.debug(f"Checking username/password={username}/{password}")
         password = self.digest(password)
         with self.session as session:
             query = session.query(AuthRecord)
diff --git a/indexd/index/blueprint.py b/indexd/index/blueprint.py
index c7fb3c32..d75f1c04 100644
--- a/indexd/index/blueprint.py
+++ b/indexd/index/blueprint.py
@@ -392,6 +392,7 @@ def post_index_record():
         raise UserError(err)
 
     authz = flask.request.json.get("authz", [])
+    logger.debug("Checking authorization")
     auth.authorize("create", authz)
 
     did = flask.request.json.get("did")

From 9ff8ccb10bdd83da3daf020d5c9635272ef6fe1a Mon Sep 17 00:00:00 2001
From: George Thomas <george42@uchicago.edu>
Date: Thu, 2 Nov 2023 16:39:20 -0700
Subject: [PATCH 06/10] (fix): change log level

---
 indexd/auth/drivers/alchemy.py | 2 +-
 indexd/index/blueprint.py      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/indexd/auth/drivers/alchemy.py b/indexd/auth/drivers/alchemy.py
index d6c5fd8b..dc7bae00 100644
--- a/indexd/auth/drivers/alchemy.py
+++ b/indexd/auth/drivers/alchemy.py
@@ -102,7 +102,7 @@ def auth(self, username, password):
         Returns a dict of user information.
         Raises AutheError otherwise.
         """
-        logger.debug(f"Checking username/password={username}/{password}")
+        logger.info(f"Checking username/password={username}/{password}")
         password = self.digest(password)
         with self.session as session:
             query = session.query(AuthRecord)
diff --git a/indexd/index/blueprint.py b/indexd/index/blueprint.py
index d75f1c04..75f26807 100644
--- a/indexd/index/blueprint.py
+++ b/indexd/index/blueprint.py
@@ -392,7 +392,7 @@ def post_index_record():
         raise UserError(err)
 
     authz = flask.request.json.get("authz", [])
-    logger.debug("Checking authorization")
+    logger.info("Checking authorization")
     auth.authorize("create", authz)
 
     did = flask.request.json.get("did")

From 24ba3c7c53da51d40276425dde4cfcbf6db55790 Mon Sep 17 00:00:00 2001
From: George Thomas <george42@uchicago.edu>
Date: Thu, 2 Nov 2023 19:02:01 -0700
Subject: [PATCH 07/10] (fix): limit flask upgrade

---
 poetry.lock    | 212 +++++++++++++++++++++++--------------------------
 pyproject.toml |   2 +-
 2 files changed, 101 insertions(+), 113 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 029254c3..0b9f5df5 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -116,17 +116,6 @@ files = [
     {file = "backoff-1.11.1.tar.gz", hash = "sha256:ccb962a2378418c667b3c979b504fdeb7d9e0d29c0579e3b13b86467177728cb"},
 ]
 
-[[package]]
-name = "blinker"
-version = "1.6.3"
-description = "Fast, simple object-to-object and broadcast signaling"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "blinker-1.6.3-py3-none-any.whl", hash = "sha256:296320d6c28b006eb5e32d4712202dbcdcbf5dc482da298c2f44881c43884aaa"},
-    {file = "blinker-1.6.3.tar.gz", hash = "sha256:152090d27c1c5c722ee7e48504b02d76502811ce02e1523553b4cf8c8b3d3a8d"},
-]
-
 [[package]]
 name = "cached-property"
 version = "1.5.2"
@@ -257,101 +246,101 @@ pycparser = "*"
 
 [[package]]
 name = "charset-normalizer"
-version = "3.3.1"
+version = "3.3.2"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 optional = false
 python-versions = ">=3.7.0"
 files = [
-    {file = "charset-normalizer-3.3.1.tar.gz", hash = "sha256:d9137a876020661972ca6eec0766d81aef8a5627df628b664b234b73396e727e"},
-    {file = "charset_normalizer-3.3.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:8aee051c89e13565c6bd366813c386939f8e928af93c29fda4af86d25b73d8f8"},
-    {file = "charset_normalizer-3.3.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:352a88c3df0d1fa886562384b86f9a9e27563d4704ee0e9d56ec6fcd270ea690"},
-    {file = "charset_normalizer-3.3.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:223b4d54561c01048f657fa6ce41461d5ad8ff128b9678cfe8b2ecd951e3f8a2"},
-    {file = "charset_normalizer-3.3.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:4f861d94c2a450b974b86093c6c027888627b8082f1299dfd5a4bae8e2292821"},
-    {file = "charset_normalizer-3.3.1-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:1171ef1fc5ab4693c5d151ae0fdad7f7349920eabbaca6271f95969fa0756c2d"},
-    {file = "charset_normalizer-3.3.1-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:28f512b9a33235545fbbdac6a330a510b63be278a50071a336afc1b78781b147"},
-    {file = "charset_normalizer-3.3.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c0e842112fe3f1a4ffcf64b06dc4c61a88441c2f02f373367f7b4c1aa9be2ad5"},
-    {file = "charset_normalizer-3.3.1-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:3f9bc2ce123637a60ebe819f9fccc614da1bcc05798bbbaf2dd4ec91f3e08846"},
-    {file = "charset_normalizer-3.3.1-cp310-cp310-musllinux_1_1_aarch64.whl", hash = "sha256:f194cce575e59ffe442c10a360182a986535fd90b57f7debfaa5c845c409ecc3"},
-    {file = "charset_normalizer-3.3.1-cp310-cp310-musllinux_1_1_i686.whl", hash = "sha256:9a74041ba0bfa9bc9b9bb2cd3238a6ab3b7618e759b41bd15b5f6ad958d17605"},
-    {file = "charset_normalizer-3.3.1-cp310-cp310-musllinux_1_1_ppc64le.whl", hash = "sha256:b578cbe580e3b41ad17b1c428f382c814b32a6ce90f2d8e39e2e635d49e498d1"},
-    {file = "charset_normalizer-3.3.1-cp310-cp310-musllinux_1_1_s390x.whl", hash = "sha256:6db3cfb9b4fcecb4390db154e75b49578c87a3b9979b40cdf90d7e4b945656e1"},
-    {file = "charset_normalizer-3.3.1-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:debb633f3f7856f95ad957d9b9c781f8e2c6303ef21724ec94bea2ce2fcbd056"},
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-    {file = "charset_normalizer-3.3.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:58e875eb7016fd014c0eea46c6fa92b87b62c0cb31b9feae25cbbe62c919f54d"},
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-    {file = "charset_normalizer-3.3.1-cp311-cp311-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:985c7965f62f6f32bf432e2681173db41336a9c2611693247069288bcb0c7f8b"},
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-    {file = "charset_normalizer-3.3.1-cp311-cp311-musllinux_1_1_ppc64le.whl", hash = "sha256:871d045d6ccc181fd863a3cd66ee8e395523ebfbc57f85f91f035f50cee8e3d4"},
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+    {file = "charset_normalizer-3.3.2-py3-none-any.whl", hash = "sha256:3e4d1f6587322d2788836a99c69062fbb091331ec940e02d12d179c1d53e25fc"},
 ]
 
 [[package]]
@@ -567,22 +556,21 @@ test = ["pytest (>=6)"]
 
 [[package]]
 name = "flask"
-version = "2.3.3"
+version = "2.2.5"
 description = "A simple framework for building complex web applications."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.7"
 files = [
-    {file = "flask-2.3.3-py3-none-any.whl", hash = "sha256:f69fcd559dc907ed196ab9df0e48471709175e696d6e698dd4dbe940f96ce66b"},
-    {file = "flask-2.3.3.tar.gz", hash = "sha256:09c347a92aa7ff4a8e7f3206795f30d826654baf38b873d0744cd571ca609efc"},
+    {file = "Flask-2.2.5-py3-none-any.whl", hash = "sha256:58107ed83443e86067e41eff4631b058178191a355886f8e479e347fa1285fdf"},
+    {file = "Flask-2.2.5.tar.gz", hash = "sha256:edee9b0a7ff26621bd5a8c10ff484ae28737a2410d99b0bb9a6850c7fb977aa0"},
 ]
 
 [package.dependencies]
-blinker = ">=1.6.2"
-click = ">=8.1.3"
+click = ">=8.0"
 importlib-metadata = {version = ">=3.6.0", markers = "python_version < \"3.10\""}
-itsdangerous = ">=2.1.2"
-Jinja2 = ">=3.1.2"
-Werkzeug = ">=2.3.7"
+itsdangerous = ">=2.0"
+Jinja2 = ">=3.0"
+Werkzeug = ">=2.2.2"
 
 [package.extras]
 async = ["asgiref (>=3.2)"]
@@ -1378,4 +1366,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<4.0"
-content-hash = "79da5985265b226bc0022b58a032a8c85a2695a1b023f093743fa169af96bdaa"
+content-hash = "869a5e179c6feb4fe5a32ec0ae0b55d2c8e087c3b632e8316ef3f8b7d7ee176d"
diff --git a/pyproject.toml b/pyproject.toml
index 7e29d885..b8a8ec1f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,7 +21,7 @@ gen3authz = "^1.0.4"
 hsclient = {git = "https://github.com/uc-cdis/hsclient", rev = "1.0.0"}
 indexclient = "^2.1.0"
 jsonschema = "^3.2"
-flask = "^2.2.5"
+flask = "~2.2.5"
 psycopg2 = "^2.7"
 sqlalchemy = "~1.3.3"
 sqlalchemy-utils = "^0.37.3"

From 0859c639f99a7cbce0a0cd15564ed9847814a5ff Mon Sep 17 00:00:00 2001
From: George Thomas <george42@uchicago.edu>
Date: Fri, 3 Nov 2023 12:52:29 -0700
Subject: [PATCH 08/10] (fix PPS-655): access user/pass via parameters

---
 indexd/auth/__init__.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/indexd/auth/__init__.py b/indexd/auth/__init__.py
index 244a26f8..f30945a6 100644
--- a/indexd/auth/__init__.py
+++ b/indexd/auth/__init__.py
@@ -23,7 +23,8 @@ def check_auth(*args, **kwargs):
             if not request.authorization:
                 raise AuthError("Username / password required.")
             current_app.auth.auth(
-                request.authorization.username, request.authorization.password
+                request.authorization.parameters.get("username"),
+                request.authorization.parameters.get("password"),
             )
 
             return f(*args, **kwargs)
@@ -31,9 +32,10 @@ def check_auth(*args, **kwargs):
         return check_auth
     else:
         method, resources = p
-        if request.authorization:
+        if request.authorization and request.authorization.type == "basic":
             current_app.auth.auth(
-                request.authorization.username, request.authorization.password
+                request.authorization.parameters.get("username"),
+                request.authorization.parameters.get("password"),
             )
         else:
             if not isinstance(resources, list):

From 1fac99adce23e5161c8b02a450ed655115e21e43 Mon Sep 17 00:00:00 2001
From: George Thomas <george42@uchicago.edu>
Date: Fri, 3 Nov 2023 14:53:04 -0700
Subject: [PATCH 09/10] (fix PPS-655): remove debugging statements

---
 indexd/auth/drivers/alchemy.py | 1 -
 indexd/index/blueprint.py      | 1 -
 2 files changed, 2 deletions(-)

diff --git a/indexd/auth/drivers/alchemy.py b/indexd/auth/drivers/alchemy.py
index dc7bae00..6268cb3a 100644
--- a/indexd/auth/drivers/alchemy.py
+++ b/indexd/auth/drivers/alchemy.py
@@ -102,7 +102,6 @@ def auth(self, username, password):
         Returns a dict of user information.
         Raises AutheError otherwise.
         """
-        logger.info(f"Checking username/password={username}/{password}")
         password = self.digest(password)
         with self.session as session:
             query = session.query(AuthRecord)
diff --git a/indexd/index/blueprint.py b/indexd/index/blueprint.py
index 75f26807..c7fb3c32 100644
--- a/indexd/index/blueprint.py
+++ b/indexd/index/blueprint.py
@@ -392,7 +392,6 @@ def post_index_record():
         raise UserError(err)
 
     authz = flask.request.json.get("authz", [])
-    logger.info("Checking authorization")
     auth.authorize("create", authz)
 
     did = flask.request.json.get("did")

From d628bec2bce1e291ef1c6239c1e3c2263d005c84 Mon Sep 17 00:00:00 2001
From: George Thomas <george42@uchicago.edu>
Date: Wed, 8 Nov 2023 13:57:11 -0800
Subject: [PATCH 10/10] (fix PPS-655): revert the limit on flask upgrades

---
 poetry.lock    | 49 +++++++++++++++++++++++++++++++------------------
 pyproject.toml |  2 +-
 2 files changed, 32 insertions(+), 19 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 0b9f5df5..dba2a42c 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -116,6 +116,17 @@ files = [
     {file = "backoff-1.11.1.tar.gz", hash = "sha256:ccb962a2378418c667b3c979b504fdeb7d9e0d29c0579e3b13b86467177728cb"},
 ]
 
+[[package]]
+name = "blinker"
+version = "1.7.0"
+description = "Fast, simple object-to-object and broadcast signaling"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "blinker-1.7.0-py3-none-any.whl", hash = "sha256:c3f865d4d54db7abc53758a01601cf343fe55b84c1de4e3fa910e420b438d5b9"},
+    {file = "blinker-1.7.0.tar.gz", hash = "sha256:e6820ff6fa4e4d1d8e2747c2283749c3f547e4fee112b98555cdcdae32996182"},
+]
+
 [[package]]
 name = "cached-property"
 version = "1.5.2"
@@ -556,21 +567,22 @@ test = ["pytest (>=6)"]
 
 [[package]]
 name = "flask"
-version = "2.2.5"
+version = "2.3.3"
 description = "A simple framework for building complex web applications."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "Flask-2.2.5-py3-none-any.whl", hash = "sha256:58107ed83443e86067e41eff4631b058178191a355886f8e479e347fa1285fdf"},
-    {file = "Flask-2.2.5.tar.gz", hash = "sha256:edee9b0a7ff26621bd5a8c10ff484ae28737a2410d99b0bb9a6850c7fb977aa0"},
+    {file = "flask-2.3.3-py3-none-any.whl", hash = "sha256:f69fcd559dc907ed196ab9df0e48471709175e696d6e698dd4dbe940f96ce66b"},
+    {file = "flask-2.3.3.tar.gz", hash = "sha256:09c347a92aa7ff4a8e7f3206795f30d826654baf38b873d0744cd571ca609efc"},
 ]
 
 [package.dependencies]
-click = ">=8.0"
+blinker = ">=1.6.2"
+click = ">=8.1.3"
 importlib-metadata = {version = ">=3.6.0", markers = "python_version < \"3.10\""}
-itsdangerous = ">=2.0"
-Jinja2 = ">=3.0"
-Werkzeug = ">=2.2.2"
+itsdangerous = ">=2.1.2"
+Jinja2 = ">=3.1.2"
+Werkzeug = ">=2.3.7"
 
 [package.extras]
 async = ["asgiref (>=3.2)"]
@@ -624,39 +636,40 @@ resolved_reference = "f122072ee245216da5e4260f718d6f886db81773"
 
 [[package]]
 name = "httpcore"
-version = "0.18.0"
+version = "1.0.1"
 description = "A minimal low-level HTTP client."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "httpcore-0.18.0-py3-none-any.whl", hash = "sha256:adc5398ee0a476567bf87467063ee63584a8bce86078bf748e48754f60202ced"},
-    {file = "httpcore-0.18.0.tar.gz", hash = "sha256:13b5e5cd1dca1a6636a6aaea212b19f4f85cd88c366a2b82304181b769aab3c9"},
+    {file = "httpcore-1.0.1-py3-none-any.whl", hash = "sha256:c5e97ef177dca2023d0b9aad98e49507ef5423e9f1d94ffe2cfe250aa28e63b0"},
+    {file = "httpcore-1.0.1.tar.gz", hash = "sha256:fce1ddf9b606cfb98132ab58865c3728c52c8e4c3c46e2aabb3674464a186e92"},
 ]
 
 [package.dependencies]
-anyio = ">=3.0,<5.0"
 certifi = "*"
 h11 = ">=0.13,<0.15"
-sniffio = "==1.*"
 
 [package.extras]
+asyncio = ["anyio (>=4.0,<5.0)"]
 http2 = ["h2 (>=3,<5)"]
 socks = ["socksio (==1.*)"]
+trio = ["trio (>=0.22.0,<0.23.0)"]
 
 [[package]]
 name = "httpx"
-version = "0.25.0"
+version = "0.25.1"
 description = "The next generation HTTP client."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "httpx-0.25.0-py3-none-any.whl", hash = "sha256:181ea7f8ba3a82578be86ef4171554dd45fec26a02556a744db029a0a27b7100"},
-    {file = "httpx-0.25.0.tar.gz", hash = "sha256:47ecda285389cb32bb2691cc6e069e3ab0205956f681c5b2ad2325719751d875"},
+    {file = "httpx-0.25.1-py3-none-any.whl", hash = "sha256:fec7d6cc5c27c578a391f7e87b9aa7d3d8fbcd034f6399f9f79b45bcc12a866a"},
+    {file = "httpx-0.25.1.tar.gz", hash = "sha256:ffd96d5cf901e63863d9f1b4b6807861dbea4d301613415d9e6e57ead15fc5d0"},
 ]
 
 [package.dependencies]
+anyio = "*"
 certifi = "*"
-httpcore = ">=0.18.0,<0.19.0"
+httpcore = "*"
 idna = "*"
 sniffio = "*"
 
@@ -1366,4 +1379,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<4.0"
-content-hash = "869a5e179c6feb4fe5a32ec0ae0b55d2c8e087c3b632e8316ef3f8b7d7ee176d"
+content-hash = "79da5985265b226bc0022b58a032a8c85a2695a1b023f093743fa169af96bdaa"
diff --git a/pyproject.toml b/pyproject.toml
index b8a8ec1f..7e29d885 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,7 +21,7 @@ gen3authz = "^1.0.4"
 hsclient = {git = "https://github.com/uc-cdis/hsclient", rev = "1.0.0"}
 indexclient = "^2.1.0"
 jsonschema = "^3.2"
-flask = "~2.2.5"
+flask = "^2.2.5"
 psycopg2 = "^2.7"
 sqlalchemy = "~1.3.3"
 sqlalchemy-utils = "^0.37.3"