diff --git a/poetry.lock b/poetry.lock
index 56c3cd35..097893a4 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -159,6 +159,17 @@ 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 = "boto"
 version = "2.49.0"
@@ -172,17 +183,17 @@ files = [
 
 [[package]]
 name = "boto3"
-version = "1.28.79"
+version = "1.28.85"
 description = "The AWS SDK for Python"
 optional = false
 python-versions = ">= 3.7"
 files = [
-    {file = "boto3-1.28.79-py3-none-any.whl", hash = "sha256:02ce7dcad2d3b054cd99e7ca6df7a708e016a31b1c98b46d8df3b3891070c121"},
-    {file = "boto3-1.28.79.tar.gz", hash = "sha256:b8acb57a124434284d6ab69c61d32d70e84e13e2c27c33b4ad3c32f15ad407d3"},
+    {file = "boto3-1.28.85-py3-none-any.whl", hash = "sha256:1fb7e7ba32a6701990168eb7a08e1fb624ae48130784dfab25904ed47deabb31"},
+    {file = "boto3-1.28.85.tar.gz", hash = "sha256:96b4cb2708933cef7dbe1177df37ef0593839942978784147aade0e49511eb2b"},
 ]
 
 [package.dependencies]
-botocore = ">=1.31.79,<1.32.0"
+botocore = ">=1.31.85,<1.32.0"
 jmespath = ">=0.7.1,<2.0.0"
 s3transfer = ">=0.7.0,<0.8.0"
 
@@ -191,13 +202,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"]
 
 [[package]]
 name = "botocore"
-version = "1.31.79"
+version = "1.31.85"
 description = "Low-level, data-driven core of boto 3."
 optional = false
 python-versions = ">= 3.7"
 files = [
-    {file = "botocore-1.31.79-py3-none-any.whl", hash = "sha256:6f1fc49e9e12f9772b4fef577837670bc84d772a7c946b4d08fe2890e34a4305"},
-    {file = "botocore-1.31.79.tar.gz", hash = "sha256:07ecb93833475dde68e5c0e02a7ccf8ca22caf68cdc892651c300529894133e1"},
+    {file = "botocore-1.31.85-py3-none-any.whl", hash = "sha256:b8f35d65f2b45af50c36fc25cc1844d6bd61d38d2148b2ef133b8f10e198555d"},
+    {file = "botocore-1.31.85.tar.gz", hash = "sha256:ce58e688222df73ec5691f934be1a2122a52c9d11d3037b586b3fff16ed6d25f"},
 ]
 
 [package.dependencies]
@@ -206,7 +217,7 @@ python-dateutil = ">=2.1,<3.0.0"
 urllib3 = {version = ">=1.25.4,<1.27", markers = "python_version < \"3.10\""}
 
 [package.extras]
-crt = ["awscrt (==0.16.26)"]
+crt = ["awscrt (==0.19.12)"]
 
 [[package]]
 name = "cached-property"
@@ -631,12 +642,12 @@ psqlgraph = ">=3.0.0"
 
 [[package]]
 name = "dictionaryutils"
-version = "3.4.8"
+version = "3.4.9"
 description = "Python wrapper and metaschema for datadictionary."
 optional = false
-python-versions = ">=3.6,<3.10"
+python-versions = ">=3.9,<4"
 files = [
-    {file = "dictionaryutils-3.4.8.tar.gz", hash = "sha256:e543937306585a78f9f646457dcb0983cc26f5f0e8a8151d9354faf539caff83"},
+    {file = "dictionaryutils-3.4.9.tar.gz", hash = "sha256:18bf677a123ec8fd1e6ce5f2887bc7555dd1faca245a31e3cb6b858bfade87c1"},
 ]
 
 [package.dependencies]
@@ -748,21 +759,22 @@ six = ">=1.10.0"
 
 [[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)"]
@@ -943,13 +955,13 @@ resolved_reference = "f122072ee245216da5e4260f718d6f886db81773"
 
 [[package]]
 name = "httpcore"
-version = "1.0.1"
+version = "1.0.2"
 description = "A minimal low-level HTTP client."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "httpcore-1.0.1-py3-none-any.whl", hash = "sha256:c5e97ef177dca2023d0b9aad98e49507ef5423e9f1d94ffe2cfe250aa28e63b0"},
-    {file = "httpcore-1.0.1.tar.gz", hash = "sha256:fce1ddf9b606cfb98132ab58865c3728c52c8e4c3c46e2aabb3674464a186e92"},
+    {file = "httpcore-1.0.2-py3-none-any.whl", hash = "sha256:096cc05bca73b8e459a1fc3dcf585148f63e534eae4339559c9b8a8d6399acc7"},
+    {file = "httpcore-1.0.2.tar.gz", hash = "sha256:9fc092e4799b26174648e54b74ed5f683132a464e95643b226e00c2ed2fa6535"},
 ]
 
 [package.dependencies]
@@ -1056,7 +1068,7 @@ cdiserrors = "^1.0.0"
 cdislogging = "^1.0.0"
 doiclient = {git = "https://github.com/uc-cdis/doiclient", rev = "1.0.0"}
 dosclient = {git = "https://github.com/uc-cdis/dosclient", rev = "1.1.0"}
-flask = "~2.2.5"
+flask = "^2.2.5"
 gen3authz = "^1.0.4"
 hsclient = {git = "https://github.com/uc-cdis/hsclient", rev = "1.0.0"}
 indexclient = "^2.1.0"
@@ -1069,8 +1081,8 @@ sqlalchemy-utils = "^0.37.3"
 [package.source]
 type = "git"
 url = "https://github.com/uc-cdis/indexd"
-reference = "fix/upgrade-flask"
-resolved_reference = "72045a6151ae5b193d5572e42a62ea6bac677c70"
+reference = "5.0.3"
+resolved_reference = "575d497a275e1d285bebc2eec62476ef99db5cd5"
 
 [[package]]
 name = "iniconfig"
@@ -1252,13 +1264,13 @@ source = ["Cython (>=0.29.35)"]
 
 [[package]]
 name = "mako"
-version = "1.2.4"
+version = "1.3.0"
 description = "A super-fast templating language that borrows the best ideas from the existing templating languages."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "Mako-1.2.4-py3-none-any.whl", hash = "sha256:c97c79c018b9165ac9922ae4f32da095ffd3c4e6872b45eded42926deea46818"},
-    {file = "Mako-1.2.4.tar.gz", hash = "sha256:d60a3903dc3bb01a18ad6a89cdbe2e4eadc69c0bc8ef1e3773ba53d44c3f7a34"},
+    {file = "Mako-1.3.0-py3-none-any.whl", hash = "sha256:57d4e997349f1a92035aa25c17ace371a4213f2ca42f99bee9a602500cfd54d9"},
+    {file = "Mako-1.3.0.tar.gz", hash = "sha256:e3a9d388fd00e87043edbe8792f45880ac0114e9c4adc69f6e9bfb2c55e3b11b"},
 ]
 
 [package.dependencies]
@@ -1357,13 +1369,13 @@ test = ["pytest", "pytest-cov"]
 
 [[package]]
 name = "moto"
-version = "4.2.7"
+version = "4.2.8"
 description = ""
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "moto-4.2.7-py2.py3-none-any.whl", hash = "sha256:3e0ef388900448485cd6eff18e9f7fcaa6cf4560b6fb536ba2e2e1278a5ecc59"},
-    {file = "moto-4.2.7.tar.gz", hash = "sha256:1298006aaa6996b886658eb194cac0e3a5679c9fcce6cb13e741ccc5a7247abb"},
+    {file = "moto-4.2.8-py2.py3-none-any.whl", hash = "sha256:e78b49ae8acee06a865e4963174bdf974dd66398fb3bb831a7428498506c0c56"},
+    {file = "moto-4.2.8.tar.gz", hash = "sha256:9b5a363f36f8c3fb36388764e7b8c01c615da2f2cba7da3e681680de14bfc769"},
 ]
 
 [package.dependencies]
@@ -1378,29 +1390,29 @@ werkzeug = ">=0.5,<2.2.0 || >2.2.0,<2.2.1 || >2.2.1"
 xmltodict = "*"
 
 [package.extras]
-all = ["PyYAML (>=5.1)", "aws-xray-sdk (>=0.93,!=0.96)", "cfn-lint (>=0.40.0)", "docker (>=3.0.0)", "ecdsa (!=0.15)", "graphql-core", "jsondiff (>=1.1.2)", "multipart", "openapi-spec-validator (>=0.5.0)", "py-partiql-parser (==0.4.1)", "pyparsing (>=3.0.7)", "python-jose[cryptography] (>=3.1.0,<4.0.0)", "setuptools", "sshpubkeys (>=3.1.0)"]
+all = ["PyYAML (>=5.1)", "aws-xray-sdk (>=0.93,!=0.96)", "cfn-lint (>=0.40.0)", "docker (>=3.0.0)", "ecdsa (!=0.15)", "graphql-core", "jsondiff (>=1.1.2)", "multipart", "openapi-spec-validator (>=0.5.0)", "py-partiql-parser (==0.4.2)", "pyparsing (>=3.0.7)", "python-jose[cryptography] (>=3.1.0,<4.0.0)", "setuptools", "sshpubkeys (>=3.1.0)"]
 apigateway = ["PyYAML (>=5.1)", "ecdsa (!=0.15)", "openapi-spec-validator (>=0.5.0)", "python-jose[cryptography] (>=3.1.0,<4.0.0)"]
 apigatewayv2 = ["PyYAML (>=5.1)"]
 appsync = ["graphql-core"]
 awslambda = ["docker (>=3.0.0)"]
 batch = ["docker (>=3.0.0)"]
-cloudformation = ["PyYAML (>=5.1)", "aws-xray-sdk (>=0.93,!=0.96)", "cfn-lint (>=0.40.0)", "docker (>=3.0.0)", "ecdsa (!=0.15)", "graphql-core", "jsondiff (>=1.1.2)", "openapi-spec-validator (>=0.5.0)", "py-partiql-parser (==0.4.1)", "pyparsing (>=3.0.7)", "python-jose[cryptography] (>=3.1.0,<4.0.0)", "setuptools", "sshpubkeys (>=3.1.0)"]
+cloudformation = ["PyYAML (>=5.1)", "aws-xray-sdk (>=0.93,!=0.96)", "cfn-lint (>=0.40.0)", "docker (>=3.0.0)", "ecdsa (!=0.15)", "graphql-core", "jsondiff (>=1.1.2)", "openapi-spec-validator (>=0.5.0)", "py-partiql-parser (==0.4.2)", "pyparsing (>=3.0.7)", "python-jose[cryptography] (>=3.1.0,<4.0.0)", "setuptools", "sshpubkeys (>=3.1.0)"]
 cognitoidp = ["ecdsa (!=0.15)", "python-jose[cryptography] (>=3.1.0,<4.0.0)"]
 ds = ["sshpubkeys (>=3.1.0)"]
-dynamodb = ["docker (>=3.0.0)", "py-partiql-parser (==0.4.1)"]
-dynamodbstreams = ["docker (>=3.0.0)", "py-partiql-parser (==0.4.1)"]
+dynamodb = ["docker (>=3.0.0)", "py-partiql-parser (==0.4.2)"]
+dynamodbstreams = ["docker (>=3.0.0)", "py-partiql-parser (==0.4.2)"]
 ebs = ["sshpubkeys (>=3.1.0)"]
 ec2 = ["sshpubkeys (>=3.1.0)"]
 efs = ["sshpubkeys (>=3.1.0)"]
 eks = ["sshpubkeys (>=3.1.0)"]
 glue = ["pyparsing (>=3.0.7)"]
 iotdata = ["jsondiff (>=1.1.2)"]
-proxy = ["PyYAML (>=5.1)", "aws-xray-sdk (>=0.93,!=0.96)", "cfn-lint (>=0.40.0)", "docker (>=2.5.1)", "ecdsa (!=0.15)", "graphql-core", "jsondiff (>=1.1.2)", "multipart", "openapi-spec-validator (>=0.5.0)", "py-partiql-parser (==0.4.1)", "pyparsing (>=3.0.7)", "python-jose[cryptography] (>=3.1.0,<4.0.0)", "setuptools", "sshpubkeys (>=3.1.0)"]
-resourcegroupstaggingapi = ["PyYAML (>=5.1)", "cfn-lint (>=0.40.0)", "docker (>=3.0.0)", "ecdsa (!=0.15)", "graphql-core", "jsondiff (>=1.1.2)", "openapi-spec-validator (>=0.5.0)", "py-partiql-parser (==0.4.1)", "pyparsing (>=3.0.7)", "python-jose[cryptography] (>=3.1.0,<4.0.0)", "sshpubkeys (>=3.1.0)"]
+proxy = ["PyYAML (>=5.1)", "aws-xray-sdk (>=0.93,!=0.96)", "cfn-lint (>=0.40.0)", "docker (>=2.5.1)", "ecdsa (!=0.15)", "graphql-core", "jsondiff (>=1.1.2)", "multipart", "openapi-spec-validator (>=0.5.0)", "py-partiql-parser (==0.4.2)", "pyparsing (>=3.0.7)", "python-jose[cryptography] (>=3.1.0,<4.0.0)", "setuptools", "sshpubkeys (>=3.1.0)"]
+resourcegroupstaggingapi = ["PyYAML (>=5.1)", "cfn-lint (>=0.40.0)", "docker (>=3.0.0)", "ecdsa (!=0.15)", "graphql-core", "jsondiff (>=1.1.2)", "openapi-spec-validator (>=0.5.0)", "py-partiql-parser (==0.4.2)", "pyparsing (>=3.0.7)", "python-jose[cryptography] (>=3.1.0,<4.0.0)", "sshpubkeys (>=3.1.0)"]
 route53resolver = ["sshpubkeys (>=3.1.0)"]
-s3 = ["PyYAML (>=5.1)", "py-partiql-parser (==0.4.1)"]
-s3crc32c = ["PyYAML (>=5.1)", "crc32c", "py-partiql-parser (==0.4.1)"]
-server = ["PyYAML (>=5.1)", "aws-xray-sdk (>=0.93,!=0.96)", "cfn-lint (>=0.40.0)", "docker (>=3.0.0)", "ecdsa (!=0.15)", "flask (!=2.2.0,!=2.2.1)", "flask-cors", "graphql-core", "jsondiff (>=1.1.2)", "openapi-spec-validator (>=0.5.0)", "py-partiql-parser (==0.4.1)", "pyparsing (>=3.0.7)", "python-jose[cryptography] (>=3.1.0,<4.0.0)", "setuptools", "sshpubkeys (>=3.1.0)"]
+s3 = ["PyYAML (>=5.1)", "py-partiql-parser (==0.4.2)"]
+s3crc32c = ["PyYAML (>=5.1)", "crc32c", "py-partiql-parser (==0.4.2)"]
+server = ["PyYAML (>=5.1)", "aws-xray-sdk (>=0.93,!=0.96)", "cfn-lint (>=0.40.0)", "docker (>=3.0.0)", "ecdsa (!=0.15)", "flask (!=2.2.0,!=2.2.1)", "flask-cors", "graphql-core", "jsondiff (>=1.1.2)", "openapi-spec-validator (>=0.5.0)", "py-partiql-parser (==0.4.2)", "pyparsing (>=3.0.7)", "python-jose[cryptography] (>=3.1.0,<4.0.0)", "setuptools", "sshpubkeys (>=3.1.0)"]
 ssm = ["PyYAML (>=5.1)"]
 xray = ["aws-xray-sdk (>=0.93,!=0.96)", "setuptools"]
 
@@ -2427,4 +2439,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.10"
-content-hash = "347a781d17681f6ce025c70b90efdd00dfece40a02e8da3d957856165f241ca5"
+content-hash = "24454f7a21f3494fe774e1b51977cee3914c1274ff99f33a1888cbd9cc2b3348"
diff --git a/pyproject.toml b/pyproject.toml
index 971b3fa2..68d63f55 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -57,7 +57,7 @@ codacy-coverage = ">=1.3.11"
 Sphinx = ">=1.6.5"
 sphinx_rtd_theme = "*"
 flasgger = ">=0.9.1"
-indexd = {git = "https://github.com/uc-cdis/indexd", branch = "fix/upgrade-flask"}
+indexd = {git = "https://github.com/uc-cdis/indexd", rev = "5.0.3"}
 
 [build-system]
 requires = ["poetry>=0.12"]