From b8f61adb93153508e7407f98b19a0d8d3e0d1cfa Mon Sep 17 00:00:00 2001
From: Pauline <ribeyre@uchicago.edu>
Date: Wed, 21 Oct 2020 15:16:17 -0500
Subject: [PATCH] fix for git dependencies

---
 Dockerfile                         |   30 +-
 deployment/uwsgi/uwsgi.ini         |    2 +
 fence/blueprints/data/blueprint.py |    2 +-
 fence/utils.py                     |    2 +-
 notes.txt                          |   10 -
 poetry.lock                        | 1551 +++++++++++-----------------
 pyproject.toml                     |    2 +-
 7 files changed, 633 insertions(+), 966 deletions(-)
 delete mode 100644 notes.txt

diff --git a/Dockerfile b/Dockerfile
index 3c8094d16..fd2b09ca3 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -8,12 +8,8 @@ ENV appname=fence
 RUN apk update \
     && apk add postgresql-libs postgresql-dev libffi-dev libressl-dev \
     && apk add linux-headers musl-dev gcc \
-    && apk add curl bash git vim make lftp
-
-COPY . /$appname
-COPY ./deployment/uwsgi/uwsgi.ini /etc/uwsgi/uwsgi.ini
-COPY ./deployment/uwsgi/wsgi.py /$appname/wsgi.py
-WORKDIR /$appname
+    && apk add curl bash git vim make lftp \
+    && apk update && apk add openssh && apk add libmcrypt-dev
 
 RUN mkdir -p /var/www/$appname \
     && mkdir -p /var/www/.cache/Python-Eggs/ \
@@ -23,8 +19,6 @@ RUN mkdir -p /var/www/$appname \
     && chown nginx -R /var/www/.cache/Python-Eggs/ \
     && chown nginx /var/www/$appname
 
-RUN apk update && apk add openssh && apk add libmcrypt-dev
-
 #
 # libmhash is required by mcrypt - below - no apk package available
 #
@@ -53,26 +47,24 @@ RUN curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2
     && /bin/rm -rf awscliv2.zip ./aws
 
 # install poetry
-ENV POETRY_HOME="$HOME/.poetry/bin"
 RUN curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python
-# ENV PATH="$POETRY_HOME/bin$PATH"
-# ENV PATH="usr/local/src$PATH" <-- pythonpath
-ENV PYTHONPATH="${PYTHONPATH}:/usr/local/src/"
-RUN echo $PYTHONPATH
 
-RUN COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" >$appname/version_data.py \
-    && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >>$appname/version_data.py
+COPY . /$appname
+COPY ./deployment/uwsgi/uwsgi.ini /etc/uwsgi/uwsgi.ini
+COPY ./deployment/uwsgi/wsgi.py /$appname/wsgi.py
+WORKDIR /$appname
 
 # cache so that poetry install will run if these files change
-COPY poetry.lock pyproject.toml /$appname
+COPY poetry.lock pyproject.toml /$appname/
 
 # install Fence and dependencies via poetry
 RUN source $HOME/.poetry/env \
     && poetry config virtualenvs.create false \
     && poetry install -vv --no-dev --no-interaction \
-    && pip list
-RUN pip show flask
-RUN pip show gen3config
+    && poetry show -v
+
+RUN COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" >$appname/version_data.py \
+    && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >>$appname/version_data.py
 
 WORKDIR /var/www/$appname
 
diff --git a/deployment/uwsgi/uwsgi.ini b/deployment/uwsgi/uwsgi.ini
index 72a00fdaa..3c9ba6088 100644
--- a/deployment/uwsgi/uwsgi.ini
+++ b/deployment/uwsgi/uwsgi.ini
@@ -23,6 +23,8 @@ vacuum = true
 pythonpath = /var/www/fence/
 pythonpath = /fence/
 pythonpath = /usr/local/lib/python3.6/site-packages/
+# poetry installs git dependencies at /usr/local/src
+pythonpath = /usr/local/src/*
 
 # Initialize application in worker processes, not master. This prevents the
 # workers from all trying to open the same database connections at startup.
diff --git a/fence/blueprints/data/blueprint.py b/fence/blueprints/data/blueprint.py
index 3ee288032..d6aa736d8 100644
--- a/fence/blueprints/data/blueprint.py
+++ b/fence/blueprints/data/blueprint.py
@@ -100,7 +100,7 @@ def upload_data_file():
     if not authorized:
         raise Forbidden(
             "You do not have access to upload data. You either need "
-            "general file uploader permissions or create & write-storage permissions "
+            "general file uploader permissions or create and write-storage permissions "
             "on the authz resources you specified (if you specified any)."
         )
 
diff --git a/fence/utils.py b/fence/utils.py
index ecc595d99..a23ad5379 100644
--- a/fence/utils.py
+++ b/fence/utils.py
@@ -14,7 +14,7 @@
 from userdatamodel.driver import SQLAlchemyDriver
 from werkzeug.datastructures import ImmutableMultiDict
 
-from fence.models import Client, GrantType, User, query_for_user
+from fence.models import Client, User, query_for_user
 from fence.errors import NotFound, UserError
 from fence.config import config
 
diff --git a/notes.txt b/notes.txt
deleted file mode 100644
index 2286efb81..000000000
--- a/notes.txt
+++ /dev/null
@@ -1,10 +0,0 @@
-not included: boto, datamodelutils, Flask_OAuthlib, httplib2, oauthlib, requests_oauthlib, pysftp, setuptools, six, temps
-not included from setup.py: oauth2client, google_api_python_client
-
-awscli (see https://github.com/uc-cdis/fence/pull/745#discussion_r423441492) 1.18.0 conflicts with botocore<1.13.0 and s3transfer, dependency of storageclient
--> add it in dockerfile instead of poetry
-
-cdiserrors <1: gen3config, cdis-python-utils, authutils
-cdiserrors >=1: gen3authz
-fence works on 4.0.0 but not on 5.0.0 (NIH login through GDC issues?)
--> to discuss
diff --git a/poetry.lock b/poetry.lock
index 7d53cf2f0..60e4254fc 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,121 +1,88 @@
 [[package]]
-category = "dev"
-description = "Addict is a dictionary whose items can be set using both attribute and item syntax."
 name = "addict"
+version = "2.3.0"
+description = "Addict is a dictionary whose items can be set using both attribute and item syntax."
+category = "dev"
 optional = false
 python-versions = "*"
-version = "2.2.1"
 
 [[package]]
-category = "main"
-description = "A library for parsing ISO 8601 strings."
 name = "aniso8601"
+version = "8.0.0"
+description = "A library for parsing ISO 8601 strings."
+category = "main"
 optional = false
 python-versions = "*"
-version = "8.0.0"
 
 [[package]]
-category = "dev"
-description = "Atomic file writes."
 name = "atomicwrites"
+version = "1.4.0"
+description = "Atomic file writes."
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "1.4.0"
 
 [[package]]
-category = "dev"
-description = "Classes Without Boilerplate"
 name = "attrs"
+version = "20.2.0"
+description = "Classes Without Boilerplate"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "19.3.0"
 
 [package.extras]
-azure-pipelines = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "pytest-azurepipelines"]
-dev = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "sphinx", "pre-commit"]
-docs = ["sphinx", "zope.interface"]
-tests = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface"]
+dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "sphinx", "sphinx-rtd-theme", "pre-commit"]
+docs = ["sphinx", "sphinx-rtd-theme", "zope.interface"]
+tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface"]
+tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six"]
 
 [[package]]
-category = "main"
-description = "The ultimate Python library in building OAuth and OpenID Connect servers."
 name = "authlib"
+version = "0.11"
+description = "The ultimate Python library in building OAuth and OpenID Connect servers."
+category = "main"
 optional = false
 python-versions = "*"
-version = "0.11"
 
 [package.dependencies]
 cryptography = "*"
 requests = "*"
 
 [[package]]
-category = "main"
-description = "Gen3 auth utility functions"
 name = "authutils"
+version = "5.0.4"
+description = "Gen3 auth utility functions"
+category = "main"
 optional = false
 python-versions = ">=3.6,<4.0"
-version = "5.0.4"
 
 [package.dependencies]
 authlib = ">=0.11,<1.0"
 cached-property = ">=1.4,<2.0"
 cdiserrors = ">=1.0,<2.0"
 httpx = ">=0.12.1,<0.13.0"
+pyjwt = {version = ">=1.5,<2.0", extras = ["crypto"]}
 xmltodict = ">=0.9,<1.0"
 
-[package.dependencies.pyjwt]
-extras = ["crypto"]
-version = ">=1.5,<2.0"
-
 [package.extras]
-fastapi = ["fastapi (>=0.54.1,<0.55.0)"]
 flask = ["Flask (>=0.10.1)"]
+fastapi = ["fastapi (>=0.54.1,<0.55.0)"]
 
 [[package]]
-category = "dev"
-description = "AWS SAM Translator is a library that transform SAM templates into AWS CloudFormation templates"
-name = "aws-sam-translator"
-optional = false
-python-versions = "*"
-version = "1.25.0"
-
-[package.dependencies]
-boto3 = ">=1.5,<2.0"
-jsonschema = ">=3.0,<4.0"
-six = ">=1.11,<2.0"
-
-[package.extras]
-dev = ["coverage (>=4.4.0)", "flake8 (>=3.3.0)", "tox (>=2.2.1)", "pytest-cov (>=2.4.0)", "pylint (>=1.7.2,<2.0)", "pyyaml (>=5.1)", "pytest (>=3.0.7)", "mock (>=2.0.0)", "parameterized (>=0.6.1)", "requests (>=2.20.0)", "docopt (>=0.6.2)"]
-
-[[package]]
-category = "dev"
-description = "The AWS X-Ray SDK for Python (the SDK) enables Python developers to record and emit information from within their applications to the AWS X-Ray service."
-name = "aws-xray-sdk"
-optional = false
-python-versions = "*"
-version = "2.6.0"
-
-[package.dependencies]
-botocore = ">=1.11.3"
-future = "*"
-jsonpickle = "*"
-wrapt = "*"
-
-[[package]]
-category = "main"
-description = "Function decoration for backoff and retry"
 name = "backoff"
+version = "1.10.0"
+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.*"
-version = "1.10.0"
 
 [[package]]
-category = "main"
-description = "Modern password hashing for your software and your servers"
 name = "bcrypt"
+version = "3.2.0"
+description = "Modern password hashing for your software and your servers"
+category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "3.1.7"
+python-versions = ">=3.6"
 
 [package.dependencies]
 cffi = ">=1.1"
@@ -123,22 +90,23 @@ six = ">=1.4.1"
 
 [package.extras]
 tests = ["pytest (>=3.2.1,<3.3.0 || >3.3.0)"]
+typecheck = ["mypy"]
 
 [[package]]
-category = "main"
-description = "Amazon Web Services Library"
 name = "boto"
+version = "2.49.0"
+description = "Amazon Web Services Library"
+category = "main"
 optional = false
 python-versions = "*"
-version = "2.49.0"
 
 [[package]]
-category = "main"
-description = "The AWS SDK for Python"
 name = "boto3"
+version = "1.9.253"
+description = "The AWS SDK for Python"
+category = "main"
 optional = false
 python-versions = "*"
-version = "1.9.253"
 
 [package.dependencies]
 botocore = ">=1.12.253,<1.13.0"
@@ -146,48 +114,42 @@ jmespath = ">=0.7.1,<1.0.0"
 s3transfer = ">=0.2.0,<0.3.0"
 
 [[package]]
-category = "main"
-description = "Low-level, data-driven core of boto 3."
 name = "botocore"
+version = "1.12.253"
+description = "Low-level, data-driven core of boto 3."
+category = "main"
 optional = false
 python-versions = "*"
-version = "1.12.253"
 
 [package.dependencies]
 docutils = ">=0.10,<0.16"
 jmespath = ">=0.7.1,<1.0.0"
-
-[package.dependencies.python-dateutil]
-python = ">=2.7"
-version = ">=2.1,<3.0.0"
-
-[package.dependencies.urllib3]
-python = ">=3.4"
-version = ">=1.20,<1.26"
+python-dateutil = {version = ">=2.1,<3.0.0", markers = "python_version >= \"2.7\""}
+urllib3 = {version = ">=1.20,<1.26", markers = "python_version >= \"3.4\""}
 
 [[package]]
-category = "main"
-description = "A decorator for caching properties in classes."
 name = "cached-property"
+version = "1.5.2"
+description = "A decorator for caching properties in classes."
+category = "main"
 optional = false
 python-versions = "*"
-version = "1.5.1"
 
 [[package]]
-category = "main"
-description = "Extensible memoizing collections and decorators"
 name = "cachetools"
+version = "4.1.1"
+description = "Extensible memoizing collections and decorators"
+category = "main"
 optional = false
 python-versions = "~=3.5"
-version = "4.1.1"
 
 [[package]]
-category = "main"
-description = "Gen3 shared exceptions and utilities."
 name = "cdiserrors"
+version = "1.0.0"
+description = "Gen3 shared exceptions and utilities."
+category = "main"
 optional = false
 python-versions = ">=3.6,<4.0"
-version = "1.0.0"
 
 [package.dependencies]
 cdislogging = ">=1.0.0,<2.0.0"
@@ -196,119 +158,93 @@ cdislogging = ">=1.0.0,<2.0.0"
 flask = ["Flask (>=1.1.2,<2.0.0)"]
 
 [[package]]
-category = "main"
-description = "Standardized logging tool and format for cdis applications"
 name = "cdislogging"
+version = "1.0.0"
+description = "Standardized logging tool and format for cdis applications"
+category = "main"
 optional = false
 python-versions = "*"
-version = "1.0.0"
 
 [[package]]
-category = "main"
-description = "General utilities for Gen3 development"
 name = "cdispyutils"
+version = "1.0.4"
+description = "General utilities for Gen3 development"
+category = "main"
 optional = false
 python-versions = "*"
-version = "1.0.4"
 
 [package.dependencies]
-Flask = "*"
-PyJWT = ">=1.5,<2.0"
 cdiserrors = ">=1.0,<2.0"
 cryptography = "2.8"
+Flask = "*"
+PyJWT = ">=1.5,<2.0"
 requests = ">=2.5,<3.0"
 
 [package.extras]
 profiling = ["Werkzeug (>=0.9,<1.0)", "matplotlib (>=2.2,<3.0)", "numpy (>=1.15,<2.0)"]
 
 [package.source]
-reference = "555bfae90ee1ca390377b9ae5f9c95ce60960256"
 type = "git"
 url = "https://github.com/uc-cdis/cdis-python-utils"
+reference = "paulineribeyre-patch-1"
+resolved_reference = "555bfae90ee1ca390377b9ae5f9c95ce60960256"
+
 [[package]]
-category = "dev"
-description = "Collection of test data and tools"
 name = "cdisutilstest"
+version = "0.2.4"
+description = "Collection of test data and tools"
+category = "dev"
 optional = false
 python-versions = "*"
-version = "0.2.4"
 
 [package.source]
-reference = "bdfdeb05e45407e839fd954ce6d195d847cd8024"
 type = "git"
 url = "https://github.com/uc-cdis/cdisutils-test"
+reference = "1.0.0"
+resolved_reference = "bdfdeb05e45407e839fd954ce6d195d847cd8024"
+
 [[package]]
-category = "main"
-description = "Python package for providing Mozilla's CA Bundle."
 name = "certifi"
+version = "2020.6.20"
+description = "Python package for providing Mozilla's CA Bundle."
+category = "main"
 optional = false
 python-versions = "*"
-version = "2020.6.20"
 
 [[package]]
-category = "main"
-description = "Foreign Function Interface for Python calling C code."
 name = "cffi"
+version = "1.14.3"
+description = "Foreign Function Interface for Python calling C code."
+category = "main"
 optional = false
 python-versions = "*"
-version = "1.14.0"
 
 [package.dependencies]
 pycparser = "*"
 
 [[package]]
-category = "dev"
-description = "Checks CloudFormation templates for practices and behaviour that could potentially be improved"
-name = "cfn-lint"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "0.34.0"
-
-[package.dependencies]
-aws-sam-translator = ">=1.25.0"
-jsonschema = ">=3.0,<4.0"
-junit-xml = ">=1.9,<2.0"
-six = ">=1.11,<2.0"
-
-[package.dependencies.importlib-resources]
-python = "<3.4.0 || >=3.5.0,<3.7"
-version = ">=1.4,<2.0"
-
-[package.dependencies.jsonpatch]
-python = "<3.4.0 || >=3.5.0"
-version = "*"
-
-[package.dependencies.networkx]
-python = ">=3.5"
-version = ">=2.4,<3.0"
-
-[package.dependencies.pyyaml]
-python = "<3.4.0 || >=3.5.0"
-version = "*"
-
-[[package]]
-category = "main"
-description = "Universal encoding detector for Python 2 and 3"
 name = "chardet"
+version = "3.0.4"
+description = "Universal encoding detector for Python 2 and 3"
+category = "main"
 optional = false
 python-versions = "*"
-version = "3.0.4"
 
 [[package]]
-category = "main"
-description = "Composable command line interface toolkit"
 name = "click"
+version = "7.1.2"
+description = "Composable command line interface toolkit"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-version = "7.1.2"
 
 [[package]]
-category = "dev"
-description = "Codacy coverage reporter for Python"
 name = "codacy-coverage"
+version = "1.3.11"
+description = "Codacy coverage reporter for Python"
+category = "dev"
 optional = false
 python-versions = "*"
-version = "1.3.11"
 
 [package.dependencies]
 requests = ">=2.9.1"
@@ -318,44 +254,42 @@ dev = ["check-manifest"]
 test = ["coverage", "nosetests"]
 
 [[package]]
-category = "dev"
-description = "Cross-platform colored terminal text."
-marker = "sys_platform == \"win32\""
 name = "colorama"
+version = "0.4.4"
+description = "Cross-platform colored terminal text."
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-version = "0.4.3"
 
 [[package]]
-category = "main"
-description = "PEP 567 Backport"
-marker = "python_version < \"3.7\""
 name = "contextvars"
+version = "2.4"
+description = "PEP 567 Backport"
+category = "main"
 optional = false
 python-versions = "*"
-version = "2.4"
 
 [package.dependencies]
 immutables = ">=0.9"
 
 [[package]]
-category = "dev"
-description = "Code coverage measurement for Python"
 name = "coverage"
+version = "5.3"
+description = "Code coverage measurement for Python"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4"
-version = "5.2"
 
 [package.extras]
 toml = ["toml"]
 
 [[package]]
-category = "dev"
-description = "Show coverage stats online via coveralls.io"
 name = "coveralls"
+version = "2.1.2"
+description = "Show coverage stats online via coveralls.io"
+category = "dev"
 optional = false
 python-versions = ">= 3.5"
-version = "2.1.1"
 
 [package.dependencies]
 coverage = ">=4.1,<6.0"
@@ -366,12 +300,12 @@ requests = ">=1.0.0"
 yaml = ["PyYAML (>=3.10)"]
 
 [[package]]
-category = "main"
-description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
 name = "cryptography"
+version = "2.8"
+description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
+category = "main"
 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*"
-version = "2.8"
 
 [package.dependencies]
 cffi = ">=1.8,<1.11.3 || >1.11.3"
@@ -385,72 +319,51 @@ pep8test = ["flake8", "flake8-import-order", "pep8-naming"]
 test = ["pytest (>=3.6.0,<3.9.0 || >3.9.0,<3.9.1 || >3.9.1,<3.9.2 || >3.9.2)", "pretend", "iso8601", "pytz", "hypothesis (>=1.11.4,<3.79.2 || >3.79.2)"]
 
 [[package]]
-category = "main"
-description = "Decorators for Humans"
 name = "decorator"
+version = "4.4.2"
+description = "Decorators for Humans"
+category = "main"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*"
-version = "4.4.2"
 
 [[package]]
-category = "main"
-description = "DNS toolkit"
 name = "dnspython"
+version = "2.0.0"
+description = "DNS toolkit"
+category = "main"
 optional = false
 python-versions = ">=3.6"
-version = "2.0.0"
 
 [package.extras]
-curio = ["curio (>=1.2)", "sniffio (>=1.1)"]
 dnssec = ["cryptography (>=2.6)"]
 doh = ["requests", "requests-toolbelt"]
 idna = ["idna (>=2.1)"]
+curio = ["curio (>=1.2)", "sniffio (>=1.1)"]
 trio = ["trio (>=0.14.0)", "sniffio (>=1.1)"]
 
 [[package]]
-category = "dev"
-description = "A Python library for the Docker Engine API."
-name = "docker"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-version = "4.2.2"
-
-[package.dependencies]
-requests = ">=2.14.2,<2.18.0 || >2.18.0"
-six = ">=1.4.0"
-websocket-client = ">=0.32.0"
-
-[package.dependencies.pypiwin32]
-python = ">=3.6"
-version = "223"
-
-[package.extras]
-ssh = ["paramiko (>=2.4.2)"]
-tls = ["pyOpenSSL (>=17.5.0)", "cryptography (>=1.3.4)", "idna (>=2.0.0)"]
-
-[[package]]
-category = "dev"
-description = "Pythonic argument parser, that will make you smile"
 name = "docopt"
+version = "0.6.2"
+description = "Pythonic argument parser, that will make you smile"
+category = "dev"
 optional = false
 python-versions = "*"
-version = "0.6.2"
 
 [[package]]
-category = "main"
-description = "Docutils -- Python Documentation Utilities"
 name = "docutils"
+version = "0.15.2"
+description = "Docutils -- Python Documentation Utilities"
+category = "main"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
-version = "0.15.2"
 
 [[package]]
-category = "main"
-description = "ECDSA cryptographic signature library (pure python)"
 name = "ecdsa"
+version = "0.16.0"
+description = "ECDSA cryptographic signature library (pure python)"
+category = "main"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
-version = "0.15"
 
 [package.dependencies]
 six = ">=1.9.0"
@@ -460,30 +373,30 @@ gmpy = ["gmpy"]
 gmpy2 = ["gmpy2"]
 
 [[package]]
-category = "main"
-description = "A robust email syntax and deliverability validation library for Python 2.x/3.x."
 name = "email-validator"
+version = "1.1.1"
+description = "A robust email syntax and deliverability validation library for Python 2.x/3.x."
+category = "main"
 optional = false
 python-versions = "*"
-version = "1.1.1"
 
 [package.dependencies]
 dnspython = ">=1.15.0"
 idna = ">=2.0.0"
 
 [[package]]
-category = "main"
-description = "A simple framework for building complex web applications."
 name = "flask"
+version = "1.1.2"
+description = "A simple framework for building complex web applications."
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-version = "1.1.2"
 
 [package.dependencies]
-Jinja2 = ">=2.10.1"
-Werkzeug = ">=0.15"
 click = ">=5.1"
 itsdangerous = ">=0.24"
+Jinja2 = ">=2.10.1"
+Werkzeug = ">=0.15"
 
 [package.extras]
 dev = ["pytest", "coverage", "tox", "sphinx", "pallets-sphinx-themes", "sphinxcontrib-log-cabinet", "sphinx-issues"]
@@ -491,28 +404,28 @@ docs = ["sphinx", "pallets-sphinx-themes", "sphinxcontrib-log-cabinet", "sphinx-
 dotenv = ["python-dotenv"]
 
 [[package]]
-category = "main"
-description = "A Flask extension adding a decorator for CORS support"
 name = "flask-cors"
+version = "3.0.9"
+description = "A Flask extension adding a decorator for CORS support"
+category = "main"
 optional = false
 python-versions = "*"
-version = "3.0.8"
 
 [package.dependencies]
 Flask = ">=0.9"
 Six = "*"
 
 [[package]]
-category = "main"
-description = "Simple framework for creating REST APIs"
 name = "flask-restful"
+version = "0.3.8"
+description = "Simple framework for creating REST APIs"
+category = "main"
 optional = false
 python-versions = "*"
-version = "0.3.8"
 
 [package.dependencies]
-Flask = ">=0.8"
 aniso8601 = ">=0.82"
+Flask = ">=0.8"
 pytz = "*"
 six = ">=1.3.0"
 
@@ -520,110 +433,103 @@ six = ">=1.3.0"
 docs = ["sphinx"]
 
 [[package]]
-category = "main"
-description = "SQL Alchemy session scoped on Flask requests."
 name = "flask-sqlalchemy-session"
+version = "1.1"
+description = "SQL Alchemy session scoped on Flask requests."
+category = "main"
 optional = false
 python-versions = "*"
-version = "1.1"
 
 [package.dependencies]
 Flask = ">=0.9"
-Werkzeug = ">=0.6.1"
 sqlalchemy = ">=0.9"
+Werkzeug = ">=0.6.1"
 
 [package.extras]
 docs = ["Sphinx (>=1.2.3)", "alabaster (>=0.6.3)"]
 
 [[package]]
-category = "main"
-description = "Clean single-source support for Python 3 and 2"
 name = "future"
+version = "0.18.2"
+description = "Clean single-source support for Python 3 and 2"
+category = "main"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
-version = "0.18.2"
 
 [[package]]
-category = "main"
+name = "gen3authz"
+version = "1.0.0"
 description = "Gen3 authz client"
-name = "gen3authz"
+category = "main"
 optional = false
 python-versions = ">=3.6,<4.0"
-version = "1.0.0"
 
 [package.dependencies]
 backoff = ">=1.6,<2.0"
 cdiserrors = ">=1.0.0,<2.0.0"
+contextvars = {version = ">=2.4,<3.0", markers = "python_version < \"3.7\""}
 httpx = ">=0.12.1,<0.13.0"
 
-[package.dependencies.contextvars]
-python = "<3.7"
-version = ">=2.4,<3.0"
-
 [[package]]
-category = "main"
-description = ""
 name = "gen3cirrus"
+version = "1.3.0"
+description = ""
+category = "main"
 optional = false
 python-versions = "*"
-version = "1.1.2"
 
 [package.dependencies]
 backoff = ">=1.6,<2.0"
 cdislogging = "*"
-google-api-python-client = ">=1.6,<2.0"
+google-api-python-client = "1.11.0"
 google-auth = ">=1.4,<2.0"
 google-auth-httplib2 = ">=0.0.3"
 google-cloud-storage = ">=1.10,<2.0"
 oauth2client = ">=2.0.0,<4.0dev"
 
 [[package]]
-category = "main"
-description = "Gen3 Configuration Library"
 name = "gen3config"
+version = "0.1.8"
+description = "Gen3 Configuration Library"
+category = "main"
 optional = false
 python-versions = "*"
-version = "0.1.7"
 
 [package.dependencies]
-PyYAML = ">=5.1,<6.0"
 cdiserrors = ">=1.0,<2.0"
 cdislogging = ">=1.0,<2.0"
+jinja2 = ">=2.10.1,<2.11.0"
+PyYAML = ">=5.1,<6.0"
 six = ">=1.0,<2.0"
 
-[package.source]
-reference = "69b8b862b37248590a31cf9f68e3834e8ec722f7"
-type = "git"
-url = "https://github.com/uc-cdis/gen3config"
 [[package]]
-category = "main"
-description = "Utils for Gen3 commons user management"
 name = "gen3users"
+version = "0.6.0"
+description = "Utils for Gen3 commons user management"
+category = "main"
 optional = false
 python-versions = "*"
-version = "0.6.0"
 
 [package.dependencies]
-PyYAML = ">=5.1,<6.0"
 cdislogging = ">=1.0.0,<1.1.0"
 click = "*"
+PyYAML = ">=5.1,<6.0"
 
 [[package]]
-category = "main"
-description = "Google API client core library"
 name = "google-api-core"
+version = "1.23.0"
+description = "Google API client core library"
+category = "main"
 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*"
-version = "1.21.0"
 
 [package.dependencies]
-google-auth = ">=1.18.0,<2.0dev"
+google-auth = ">=1.21.1,<2.0dev"
 googleapis-common-protos = ">=1.6.0,<2.0dev"
 protobuf = ">=3.12.0"
 pytz = "*"
 requests = ">=2.18.0,<3.0.0dev"
-setuptools = ">=34.0.0"
-six = ">=1.10.0"
+six = ">=1.13.0"
 
 [package.extras]
 grpc = ["grpcio (>=1.29.0,<2.0dev)"]
@@ -631,12 +537,12 @@ grpcgcp = ["grpcio-gcp (>=0.2.2)"]
 grpcio-gcp = ["grpcio-gcp (>=0.2.2)"]
 
 [[package]]
-category = "main"
-description = "Google API Client Library for Python"
 name = "google-api-python-client"
+version = "1.11.0"
+description = "Google API Client Library for Python"
+category = "main"
 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*"
-version = "1.10.0"
 
 [package.dependencies]
 google-api-core = ">=1.18.0,<2dev"
@@ -647,30 +553,29 @@ six = ">=1.6.1,<2dev"
 uritemplate = ">=3.0.0,<4dev"
 
 [[package]]
-category = "main"
-description = "Google Authentication Library"
 name = "google-auth"
+version = "1.22.1"
+description = "Google Authentication Library"
+category = "main"
 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*"
-version = "1.19.2"
 
 [package.dependencies]
 cachetools = ">=2.0.0,<5.0"
 pyasn1-modules = ">=0.2.1"
-setuptools = ">=40.3.0"
+rsa = {version = ">=3.1.4,<5", markers = "python_version >= \"3.5\""}
 six = ">=1.9.0"
 
-[package.dependencies.rsa]
-python = ">=3"
-version = ">=3.1.4,<5"
+[package.extras]
+aiohttp = ["aiohttp (>=3.6.2,<4.0.0dev)"]
 
 [[package]]
-category = "main"
-description = "Google Authentication Library: httplib2 transport"
 name = "google-auth-httplib2"
+version = "0.0.4"
+description = "Google Authentication Library: httplib2 transport"
+category = "main"
 optional = false
 python-versions = "*"
-version = "0.0.4"
 
 [package.dependencies]
 google-auth = "*"
@@ -678,53 +583,70 @@ httplib2 = ">=0.9.1"
 six = "*"
 
 [[package]]
-category = "main"
-description = "Google Cloud API client core library"
 name = "google-cloud-core"
+version = "1.4.3"
+description = "Google Cloud API client core library"
+category = "main"
 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*"
-version = "1.3.0"
 
 [package.dependencies]
-google-api-core = ">=1.16.0,<2.0.0dev"
+google-api-core = ">=1.19.0,<2.0.0dev"
 
 [package.extras]
 grpc = ["grpcio (>=1.8.2,<2.0dev)"]
 
 [[package]]
-category = "main"
-description = "Google Cloud Storage API client library"
 name = "google-cloud-storage"
+version = "1.32.0"
+description = "Google Cloud Storage API client library"
+category = "main"
 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*"
-version = "1.29.0"
 
 [package.dependencies]
 google-auth = ">=1.11.0,<2.0dev"
-google-cloud-core = ">=1.2.0,<2.0dev"
-google-resumable-media = ">=0.5.0,<0.6dev"
+google-cloud-core = ">=1.4.1,<2.0dev"
+google-resumable-media = ">=1.0.0,<2.0dev"
+requests = ">=2.18.0,<3.0.0dev"
 
 [[package]]
+name = "google-crc32c"
+version = "1.0.0"
+description = "A python wrapper of the C library 'Google CRC32C'"
 category = "main"
-description = "Utilities for Google Media Downloads and Resumable Uploads"
+optional = false
+python-versions = ">=3.5"
+
+[package.dependencies]
+cffi = ">=1.0.0"
+
+[package.extras]
+testing = ["pytest"]
+
+[[package]]
 name = "google-resumable-media"
+version = "1.1.0"
+description = "Utilities for Google Media Downloads and Resumable Uploads"
+category = "main"
 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*"
-version = "0.5.1"
 
 [package.dependencies]
+google-crc32c = {version = ">=1.0,<2.0dev", markers = "python_version >= \"3.5\""}
 six = "*"
 
 [package.extras]
+aiohttp = ["aiohttp (>=3.6.2,<4.0.0dev)"]
 requests = ["requests (>=2.18.0,<3.0.0dev)"]
 
 [[package]]
-category = "main"
-description = "Common protobufs used in Google APIs"
 name = "googleapis-common-protos"
+version = "1.52.0"
+description = "Common protobufs used in Google APIs"
+category = "main"
 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*"
-version = "1.52.0"
 
 [package.dependencies]
 protobuf = ">=3.6.0"
@@ -733,56 +655,56 @@ protobuf = ">=3.6.0"
 grpc = ["grpcio (>=1.0.0)"]
 
 [[package]]
-category = "main"
-description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1"
 name = "h11"
+version = "0.9.0"
+description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1"
+category = "main"
 optional = false
 python-versions = "*"
-version = "0.9.0"
 
 [[package]]
-category = "main"
-description = "HTTP/2 State-Machine based protocol implementation"
 name = "h2"
+version = "3.2.0"
+description = "HTTP/2 State-Machine based protocol implementation"
+category = "main"
 optional = false
 python-versions = "*"
-version = "3.2.0"
 
 [package.dependencies]
 hpack = ">=3.0,<4"
 hyperframe = ">=5.2.0,<6"
 
 [[package]]
-category = "main"
-description = "Pure-Python HPACK header compression"
 name = "hpack"
+version = "3.0.0"
+description = "Pure-Python HPACK header compression"
+category = "main"
 optional = false
 python-versions = "*"
-version = "3.0.0"
 
 [[package]]
-category = "main"
-description = "Chromium HSTS Preload list as a Python package and updated daily"
 name = "hstspreload"
+version = "2020.10.20"
+description = "Chromium HSTS Preload list as a Python package and updated daily"
+category = "main"
 optional = false
 python-versions = ">=3.6"
-version = "2020.7.17"
 
 [[package]]
-category = "main"
-description = "A comprehensive HTTP client library."
 name = "httplib2"
+version = "0.18.1"
+description = "A comprehensive HTTP client library."
+category = "main"
 optional = false
 python-versions = "*"
-version = "0.18.1"
 
 [[package]]
-category = "main"
-description = "The next generation HTTP client."
 name = "httpx"
+version = "0.12.1"
+description = "The next generation HTTP client."
+category = "main"
 optional = false
 python-versions = ">=3.6"
-version = "0.12.1"
 
 [package.dependencies]
 certifi = "*"
@@ -796,37 +718,36 @@ sniffio = ">=1.0.0,<2.0.0"
 urllib3 = ">=1.0.0,<2.0.0"
 
 [[package]]
-category = "main"
-description = "HTTP/2 framing layer for Python"
 name = "hyperframe"
+version = "5.2.0"
+description = "HTTP/2 framing layer for Python"
+category = "main"
 optional = false
 python-versions = "*"
-version = "5.2.0"
 
 [[package]]
-category = "main"
-description = "Internationalized Domain Names in Applications (IDNA)"
 name = "idna"
+version = "2.10"
+description = "Internationalized Domain Names in Applications (IDNA)"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "2.8"
 
 [[package]]
-category = "main"
-description = "Immutable Collections"
-marker = "python_version < \"3.7\""
 name = "immutables"
+version = "0.14"
+description = "Immutable Collections"
+category = "main"
 optional = false
 python-versions = ">=3.5"
-version = "0.14"
 
 [[package]]
-category = "main"
-description = "Read metadata from Python packages"
 name = "importlib-metadata"
+version = "2.0.0"
+description = "Read metadata from Python packages"
+category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
-version = "1.7.0"
 
 [package.dependencies]
 zipp = ">=0.5"
@@ -836,41 +757,20 @@ docs = ["sphinx", "rst.linker"]
 testing = ["packaging", "pep517", "importlib-resources (>=1.3)"]
 
 [[package]]
-category = "dev"
-description = "Read resources from Python packages"
-marker = "python_version < \"3.7\" and python_version != \"3.4\""
-name = "importlib-resources"
-optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
-version = "1.5.0"
-
-[package.dependencies]
-[package.dependencies.importlib-metadata]
-python = "<3.8"
-version = "*"
-
-[package.dependencies.zipp]
-python = "<3.8"
-version = ">=0.4"
-
-[package.extras]
-docs = ["sphinx", "rst.linker", "jaraco.packaging"]
-
-[[package]]
-category = "main"
-description = "Various helpers to pass data to untrusted environments and back."
 name = "itsdangerous"
+version = "1.1.0"
+description = "Various helpers to pass data to untrusted environments and back."
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "1.1.0"
 
 [[package]]
-category = "main"
-description = "A very fast and expressive template engine."
 name = "jinja2"
+version = "2.10.3"
+description = "A very fast and expressive template engine."
+category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-version = "2.11.2"
+python-versions = "*"
 
 [package.dependencies]
 MarkupSafe = ">=0.23"
@@ -879,122 +779,42 @@ MarkupSafe = ">=0.23"
 i18n = ["Babel (>=0.8)"]
 
 [[package]]
-category = "main"
-description = "JSON Matching Expressions"
 name = "jmespath"
-optional = false
-python-versions = "*"
 version = "0.9.2"
-
-[[package]]
-category = "dev"
-description = "Diff JSON and JSON-like structures in Python"
-name = "jsondiff"
-optional = false
-python-versions = "*"
-version = "1.1.2"
-
-[[package]]
-category = "dev"
-description = "Apply JSON-Patches (RFC 6902)"
-marker = "python_version != \"3.4\""
-name = "jsonpatch"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-version = "1.26"
-
-[package.dependencies]
-jsonpointer = ">=1.9"
-
-[[package]]
-category = "dev"
-description = "Python library for serializing any arbitrary object graph into JSON"
-name = "jsonpickle"
-optional = false
-python-versions = ">=2.7"
-version = "1.4.1"
-
-[package.dependencies]
-importlib-metadata = "*"
-
-[package.extras]
-docs = ["sphinx", "jaraco.packaging (>=3.2)", "rst.linker (>=1.9)"]
-testing = ["coverage (<5)", "pytest (>=3.5,<3.7.3 || >3.7.3)", "pytest-checkdocs (>=1.2.3)", "pytest-flake8", "pytest-black-multipy", "pytest-cov", "ecdsa", "feedparser", "numpy", "pandas", "pymongo", "sqlalchemy", "enum34", "jsonlib"]
-"testing.libs" = ["demjson", "simplejson", "ujson", "yajl"]
-
-[[package]]
-category = "dev"
-description = "Identify specific nodes in a JSON document (RFC 6901)"
-marker = "python_version != \"3.4\""
-name = "jsonpointer"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "2.0"
-
-[[package]]
-category = "dev"
-description = "An implementation of JSON Schema validation for Python"
-name = "jsonschema"
-optional = false
-python-versions = "*"
-version = "3.2.0"
-
-[package.dependencies]
-attrs = ">=17.4.0"
-pyrsistent = ">=0.14.0"
-setuptools = "*"
-six = ">=1.11.0"
-
-[package.dependencies.importlib-metadata]
-python = "<3.8"
-version = "*"
-
-[package.extras]
-format = ["idna", "jsonpointer (>1.13)", "rfc3987", "strict-rfc3339", "webcolors"]
-format_nongpl = ["idna", "jsonpointer (>1.13)", "webcolors", "rfc3986-validator (>0.1.0)", "rfc3339-validator"]
-
-[[package]]
-category = "dev"
-description = "Creates JUnit XML test result documents that can be read by tools such as Jenkins"
-name = "junit-xml"
+description = "JSON Matching Expressions"
+category = "main"
 optional = false
 python-versions = "*"
-version = "1.9"
-
-[package.dependencies]
-six = "*"
 
 [[package]]
-category = "main"
-description = "Python implementation of Markdown."
 name = "markdown"
+version = "3.3.2"
+description = "Python implementation of Markdown."
+category = "main"
 optional = false
-python-versions = ">=3.5"
-version = "3.2.2"
+python-versions = ">=3.6"
 
 [package.dependencies]
-[package.dependencies.importlib-metadata]
-python = "<3.8"
-version = "*"
+importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
 
 [package.extras]
 testing = ["coverage", "pyyaml"]
 
 [[package]]
-category = "main"
-description = "Safely add untrusted strings to HTML/XML markup."
 name = "markupsafe"
+version = "1.1.1"
+description = "Safely add untrusted strings to HTML/XML markup."
+category = "main"
 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*"
-version = "1.1.1"
 
 [[package]]
-category = "dev"
-description = "Rolling backport of unittest.mock for all Pythons"
 name = "mock"
+version = "2.0.0"
+description = "Rolling backport of unittest.mock for all Pythons"
+category = "dev"
 optional = false
 python-versions = "*"
-version = "2.0.0"
 
 [package.dependencies]
 pbr = ">=0.11"
@@ -1005,79 +825,58 @@ docs = ["sphinx", "Pygments (<2)", "jinja2 (<2.7)", "sphinx (<1.3)"]
 test = ["unittest2 (>=1.1.0)"]
 
 [[package]]
-category = "dev"
-description = "More routines for operating on iterables, beyond itertools"
 name = "more-itertools"
+version = "8.5.0"
+description = "More routines for operating on iterables, beyond itertools"
+category = "dev"
 optional = false
 python-versions = ">=3.5"
-version = "8.4.0"
 
 [[package]]
-category = "dev"
-description = "A library that allows your python tests to easily mock out the boto library"
 name = "moto"
+version = "1.3.15"
+description = "A library that allows your python tests to easily mock out the boto library"
+category = "dev"
 optional = false
 python-versions = "*"
-version = "1.3.14"
 
 [package.dependencies]
-Jinja2 = ">=2.10.1"
-PyYAML = ">=5.1"
-aws-xray-sdk = ">=0.93,<0.96 || >0.96"
 boto = ">=2.36.0"
 boto3 = ">=1.9.201"
 botocore = ">=1.12.201"
-cfn-lint = ">=0.4.0"
-cryptography = ">=2.3.0"
-docker = ">=2.5.1"
-idna = ">=2.5,<2.9"
-jsondiff = "1.1.2"
+Jinja2 = ">=2.10.1"
+MarkupSafe = "<2.0"
 mock = "*"
+more-itertools = "*"
 python-dateutil = ">=2.1,<3.0.0"
-python-jose = "<4.0.0"
 pytz = "*"
 requests = ">=2.5"
 responses = ">=0.9.0"
 six = ">1.9"
-sshpubkeys = ">=3.1.0,<4.0"
 werkzeug = "*"
 xmltodict = "*"
+zipp = "*"
 
 [package.extras]
+acm = ["cryptography (>=2.3.0)"]
+all = ["cryptography (>=2.3.0)", "PyYAML (>=5.1)", "python-jose[cryptography] (>=3.1.0,<4.0.0)", "ecdsa (<0.15)", "docker (>=2.5.1)", "jsondiff (>=1.1.2)", "aws-xray-sdk (>=0.93,<0.96 || >0.96)", "idna (>=2.5,<3)", "cfn-lint (>=0.4.0)", "sshpubkeys (>=3.1.0,<4.0)", "sshpubkeys (>=3.1.0)"]
+awslambda = ["docker (>=2.5.1)"]
+batch = ["docker (>=2.5.1)"]
+cloudformation = ["PyYAML (>=5.1)", "cfn-lint (>=0.4.0)"]
+cognitoidp = ["python-jose[cryptography] (>=3.1.0,<4.0.0)", "ecdsa (<0.15)"]
+ec2 = ["cryptography (>=2.3.0)", "sshpubkeys (>=3.1.0,<4.0)", "sshpubkeys (>=3.1.0)"]
+iam = ["cryptography (>=2.3.0)"]
+iotdata = ["jsondiff (>=1.1.2)"]
 server = ["flask"]
+xray = ["aws-xray-sdk (>=0.93,<0.96 || >0.96)"]
 
 [[package]]
-category = "dev"
-description = "Python package for creating and manipulating graphs and networks"
-marker = "python_version >= \"3.5\""
-name = "networkx"
-optional = false
-python-versions = ">=3.5"
-version = "2.4"
-
-[package.dependencies]
-decorator = ">=4.3.0"
-
-[package.extras]
-all = ["numpy", "scipy", "pandas", "matplotlib", "pygraphviz", "pydot", "pyyaml", "gdal", "lxml", "pytest"]
-gdal = ["gdal"]
-lxml = ["lxml"]
-matplotlib = ["matplotlib"]
-numpy = ["numpy"]
-pandas = ["pandas"]
-pydot = ["pydot"]
-pygraphviz = ["pygraphviz"]
-pytest = ["pytest"]
-pyyaml = ["pyyaml"]
-scipy = ["scipy"]
-
-[[package]]
-category = "main"
-description = "OAuth 2.0 client library"
 name = "oauth2client"
+version = "3.0.0"
+description = "OAuth 2.0 client library"
+category = "main"
 optional = false
 python-versions = "*"
-version = "3.0.0"
 
 [package.dependencies]
 httplib2 = ">=0.9.1"
@@ -1087,12 +886,12 @@ rsa = ">=3.1.4"
 six = ">=1.6.1"
 
 [[package]]
-category = "main"
-description = "SSH2 protocol library"
 name = "paramiko"
+version = "2.7.2"
+description = "SSH2 protocol library"
+category = "main"
 optional = false
 python-versions = "*"
-version = "2.7.1"
 
 [package.dependencies]
 bcrypt = ">=3.1.3"
@@ -1105,100 +904,100 @@ ed25519 = ["pynacl (>=1.0.1)", "bcrypt (>=3.1.3)"]
 gssapi = ["pyasn1 (>=0.1.7)", "gssapi (>=1.4.1)", "pywin32 (>=2.1.8)"]
 invoke = ["invoke (>=1.3)"]
 
-[[package]]
-category = "main"
-description = "Python Build Reasonableness"
+[[package]]
 name = "pbr"
+version = "2.0.0"
+description = "Python Build Reasonableness"
+category = "main"
 optional = false
 python-versions = "*"
-version = "2.0.0"
 
 [[package]]
-category = "dev"
-description = "plugin and hook calling mechanisms for python"
 name = "pluggy"
+version = "0.13.1"
+description = "plugin and hook calling mechanisms for python"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "0.13.1"
 
 [package.dependencies]
-[package.dependencies.importlib-metadata]
-python = "<3.8"
-version = ">=0.12"
+importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
 
 [package.extras]
 dev = ["pre-commit", "tox"]
 
 [[package]]
-category = "main"
-description = "Protocol Buffers"
 name = "protobuf"
+version = "3.13.0"
+description = "Protocol Buffers"
+category = "main"
 optional = false
 python-versions = "*"
-version = "3.12.2"
 
 [package.dependencies]
-setuptools = "*"
 six = ">=1.9"
 
 [[package]]
-category = "main"
-description = "psycopg2 - Python-PostgreSQL Database Adapter"
 name = "psycopg2"
+version = "2.8.6"
+description = "psycopg2 - Python-PostgreSQL Database Adapter"
+category = "main"
 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*"
-version = "2.8.5"
 
 [[package]]
-category = "main"
-description = "library with cross-python path, ini-parsing, io, code, log facilities"
 name = "py"
+version = "1.9.0"
+description = "library with cross-python path, ini-parsing, io, code, log facilities"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "1.9.0"
 
 [[package]]
-category = "main"
-description = "ASN.1 types and codecs"
 name = "pyasn1"
+version = "0.4.8"
+description = "ASN.1 types and codecs"
+category = "main"
 optional = false
 python-versions = "*"
-version = "0.4.8"
 
 [[package]]
-category = "main"
-description = "A collection of ASN.1-based protocols modules."
 name = "pyasn1-modules"
+version = "0.2.8"
+description = "A collection of ASN.1-based protocols modules."
+category = "main"
 optional = false
 python-versions = "*"
-version = "0.2.8"
 
 [package.dependencies]
 pyasn1 = ">=0.4.6,<0.5.0"
 
 [[package]]
-category = "main"
-description = "C parser in Python"
 name = "pycparser"
+version = "2.20"
+description = "C parser in Python"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "2.20"
 
 [[package]]
-category = "main"
-description = "Cryptographic library for Python"
 name = "pycryptodome"
+version = "3.9.8"
+description = "Cryptographic library for Python"
+category = "main"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "3.9.8"
 
 [[package]]
-category = "main"
-description = "JSON Web Token implementation in Python"
 name = "pyjwt"
+version = "1.7.1"
+description = "JSON Web Token implementation in Python"
+category = "main"
 optional = false
 python-versions = "*"
-version = "1.7.1"
+
+[package.dependencies]
+cryptography = {version = ">=1.4", optional = true, markers = "extra == \"crypto\""}
 
 [package.extras]
 crypto = ["cryptography (>=1.4)"]
@@ -1206,12 +1005,12 @@ 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)"]
 
 [[package]]
-category = "main"
-description = "Python binding to the Networking and Cryptography (NaCl) library"
 name = "pynacl"
+version = "1.4.0"
+description = "Python binding to the Networking and Cryptography (NaCl) library"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "1.4.0"
 
 [package.dependencies]
 cffi = ">=1.4.1"
@@ -1222,53 +1021,29 @@ docs = ["sphinx (>=1.6.5)", "sphinx-rtd-theme"]
 tests = ["pytest (>=3.2.1,<3.3.0 || >3.3.0)", "hypothesis (>=3.27.0)"]
 
 [[package]]
-category = "dev"
-description = ""
-marker = "sys_platform == \"win32\" and python_version >= \"3.6\""
-name = "pypiwin32"
-optional = false
-python-versions = "*"
-version = "223"
-
-[package.dependencies]
-pywin32 = ">=223"
-
-[[package]]
-category = "dev"
-description = "Persistent/Functional/Immutable data structures"
-name = "pyrsistent"
-optional = false
-python-versions = "*"
-version = "0.16.0"
-
-[package.dependencies]
-six = "*"
-
-[[package]]
-category = "dev"
-description = "pytest: simple powerful testing with Python"
 name = "pytest"
+version = "3.10.1"
+description = "pytest: simple powerful testing with Python"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "3.10.1"
 
 [package.dependencies]
 atomicwrites = ">=1.0"
 attrs = ">=17.4.0"
-colorama = "*"
+colorama = {version = "*", markers = "sys_platform == \"win32\""}
 more-itertools = ">=4.0.0"
 pluggy = ">=0.7"
 py = ">=1.5.0"
-setuptools = "*"
 six = ">=1.10.0"
 
 [[package]]
-category = "dev"
-description = "Pytest plugin for measuring coverage."
 name = "pytest-cov"
+version = "2.9.0"
+description = "Pytest plugin for measuring coverage."
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-version = "2.9.0"
 
 [package.dependencies]
 coverage = ">=4.4"
@@ -1278,39 +1053,39 @@ pytest = ">=3.6"
 testing = ["fields", "hunter", "process-tests (2.0.2)", "six", "pytest-xdist", "virtualenv"]
 
 [[package]]
-category = "dev"
-description = "A set of py.test fixtures to test Flask applications."
 name = "pytest-flask"
+version = "0.11.0"
+description = "A set of py.test fixtures to test Flask applications."
+category = "dev"
 optional = false
 python-versions = "*"
-version = "0.11.0"
 
 [package.dependencies]
 Flask = "*"
-Werkzeug = ">=0.7"
 pytest = "*"
+Werkzeug = ">=0.7"
 
 [package.extras]
 docs = ["sphinx", "sphinx-rtd-theme"]
 
 [[package]]
-category = "main"
-description = "Extensions to the standard Python datetime module"
 name = "python-dateutil"
+version = "2.8.1"
+description = "Extensions to the standard Python datetime module"
+category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
-version = "2.8.1"
 
 [package.dependencies]
 six = ">=1.5"
 
 [[package]]
-category = "main"
-description = "JOSE implementation in Python"
 name = "python-jose"
+version = "2.0.2"
+description = "JOSE implementation in Python"
+category = "main"
 optional = false
 python-versions = "*"
-version = "2.0.2"
 
 [package.dependencies]
 ecdsa = "<1.0"
@@ -1323,37 +1098,28 @@ cryptography = ["cryptography"]
 pycrypto = ["pycrypto (>=2.6.0,<2.7.0)"]
 
 [[package]]
-category = "main"
-description = "World timezone definitions, modern and historical"
 name = "pytz"
-optional = false
-python-versions = "*"
 version = "2020.1"
-
-[[package]]
-category = "dev"
-description = "Python for Window Extensions"
-marker = "sys_platform == \"win32\" and python_version >= \"3.6\""
-name = "pywin32"
+description = "World timezone definitions, modern and historical"
+category = "main"
 optional = false
 python-versions = "*"
-version = "228"
 
 [[package]]
-category = "main"
-description = "YAML parser and emitter for Python"
 name = "pyyaml"
+version = "5.3.1"
+description = "YAML parser and emitter for Python"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-version = "5.3.1"
 
 [[package]]
-category = "main"
-description = "Python HTTP for Humans."
 name = "requests"
+version = "2.24.0"
+description = "Python HTTP for Humans."
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-version = "2.24.0"
 
 [package.dependencies]
 certifi = ">=2017.4.17"
@@ -1366,93 +1132,92 @@ security = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)"]
 socks = ["PySocks (>=1.5.6,<1.5.7 || >1.5.7)", "win-inet-pton"]
 
 [[package]]
-category = "dev"
-description = "A utility library for mocking out the `requests` Python library."
 name = "responses"
+version = "0.12.0"
+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.*"
-version = "0.10.15"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [package.dependencies]
 requests = ">=2.0"
 six = "*"
+urllib3 = ">=1.25.10"
 
 [package.extras]
-tests = ["coverage (>=3.7.1,<5.0.0)", "pytest-cov", "pytest-localserver", "flake8", "pytest (>=4.6,<5.0)", "pytest"]
+tests = ["coverage (>=3.7.1,<6.0.0)", "pytest-cov", "pytest-localserver", "flake8", "pytest (>=4.6,<5.0)", "pytest (>=4.6)"]
 
 [[package]]
-category = "main"
-description = "Easy to use retry decorator."
 name = "retry"
+version = "0.9.2"
+description = "Easy to use retry decorator."
+category = "main"
 optional = false
 python-versions = "*"
-version = "0.9.2"
 
 [package.dependencies]
 decorator = ">=3.4.2"
 py = ">=1.4.26,<2.0.0"
 
 [[package]]
-category = "main"
-description = "Validating URI References per RFC 3986"
 name = "rfc3986"
+version = "1.4.0"
+description = "Validating URI References per RFC 3986"
+category = "main"
 optional = false
 python-versions = "*"
-version = "1.4.0"
 
 [package.extras]
 idna2008 = ["idna"]
 
 [[package]]
-category = "main"
-description = "Pure-Python RSA implementation"
 name = "rsa"
+version = "4.6"
+description = "Pure-Python RSA implementation"
+category = "main"
 optional = false
 python-versions = ">=3.5, <4"
-version = "4.6"
 
 [package.dependencies]
 pyasn1 = ">=0.1.3"
 
 [[package]]
-category = "main"
-description = "An Amazon S3 Transfer Manager"
 name = "s3transfer"
+version = "0.2.1"
+description = "An Amazon S3 Transfer Manager"
+category = "main"
 optional = false
 python-versions = "*"
-version = "0.2.1"
 
 [package.dependencies]
 botocore = ">=1.12.36,<2.0.0"
 
 [[package]]
-category = "main"
-description = "Python 2 and 3 compatibility utilities"
 name = "six"
+version = "1.15.0"
+description = "Python 2 and 3 compatibility utilities"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
-version = "1.15.0"
 
 [[package]]
-category = "main"
-description = "Sniff out which async library your code is running under"
 name = "sniffio"
+version = "1.2.0"
+description = "Sniff out which async library your code is running under"
+category = "main"
 optional = false
 python-versions = ">=3.5"
-version = "1.1.0"
 
 [package.dependencies]
-[package.dependencies.contextvars]
-python = "<3.7"
-version = ">=2.1"
+contextvars = {version = ">=2.1", markers = "python_version < \"3.7\""}
 
 [[package]]
-category = "main"
-description = "Database Abstraction Library"
 name = "sqlalchemy"
+version = "1.3.20"
+description = "Database Abstraction Library"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "1.3.18"
 
 [package.extras]
 mssql = ["pyodbc"]
@@ -1467,27 +1232,12 @@ postgresql_psycopg2cffi = ["psycopg2cffi"]
 pymysql = ["pymysql"]
 
 [[package]]
-category = "dev"
-description = "SSH public key parser"
-name = "sshpubkeys"
-optional = false
-python-versions = "*"
-version = "3.1.0"
-
-[package.dependencies]
-cryptography = ">=2.1.4"
-ecdsa = ">=0.13"
-
-[package.extras]
-dev = ["twine", "wheel"]
-
-[[package]]
-category = "main"
-description = "Python client to interact with ceph/cleversafe backend"
 name = "storageclient"
+version = "0.1.0"
+description = ""
+category = "main"
 optional = false
 python-versions = "*"
-version = "0.1.0"
 
 [package.dependencies]
 boto = ">=2.36.0,<3.0.0"
@@ -1500,60 +1250,51 @@ requests = ">=2.5.2,<3.0.0"
 s3transfer = ">=0.2.0,<0.3.0"
 
 [package.source]
-reference = "885c59d83fc075527af44968c353d1ac93bec37e"
 type = "git"
 url = "https://github.com/uc-cdis/storage-client"
+reference = "1.0.1"
+resolved_reference = "885c59d83fc075527af44968c353d1ac93bec37e"
+
 [[package]]
-category = "main"
-description = "URI templates"
 name = "uritemplate"
+version = "3.0.1"
+description = "URI templates"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "3.0.1"
 
 [[package]]
-category = "main"
-description = "HTTP library with thread-safe connection pooling, file post, and more."
 name = "urllib3"
+version = "1.25.11"
+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.*, <4"
-version = "1.25.9"
 
 [package.extras]
 brotli = ["brotlipy (>=0.6.0)"]
-secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "pyOpenSSL (>=0.14)", "ipaddress"]
+secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "ipaddress"]
 socks = ["PySocks (>=1.5.6,<1.5.7 || >1.5.7,<2.0)"]
 
 [[package]]
-category = "main"
-description = ""
 name = "userdatamodel"
+version = "2.3.3"
+description = ""
+category = "main"
 optional = false
 python-versions = "*"
-version = "2.3.3"
 
 [package.dependencies]
 cdislogging = "*"
 sqlalchemy = ">=1.3.3,<1.4.0"
 
 [[package]]
-category = "dev"
-description = "WebSocket client for Python. hybi13 is supported."
-name = "websocket-client"
-optional = false
-python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "0.57.0"
-
-[package.dependencies]
-six = "*"
-
-[[package]]
-category = "main"
-description = "The comprehensive WSGI web application library."
 name = "werkzeug"
+version = "0.16.1"
+description = "The comprehensive WSGI web application library."
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "0.16.1"
 
 [package.extras]
 dev = ["pytest", "coverage", "tox", "sphinx", "pallets-sphinx-themes", "sphinx-issues"]
@@ -1561,42 +1302,34 @@ termcolor = ["termcolor"]
 watchdog = ["watchdog"]
 
 [[package]]
-category = "dev"
-description = "Module for decorators, wrappers and monkey patching."
-name = "wrapt"
-optional = false
-python-versions = "*"
-version = "1.12.1"
-
-[[package]]
-category = "main"
-description = "Makes working with XML feel like you are working with JSON"
 name = "xmltodict"
+version = "0.12.0"
+description = "Makes working with XML feel like you are working with JSON"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "0.12.0"
 
 [[package]]
-category = "main"
-description = "Backport of pathlib-compatible object wrapper for zip files"
-marker = "python_version < \"3.7\" and python_version != \"3.4\" or python_version < \"3.8\""
 name = "zipp"
+version = "3.3.1"
+description = "Backport of pathlib-compatible object wrapper for zip files"
+category = "main"
 optional = false
 python-versions = ">=3.6"
-version = "3.1.0"
 
 [package.extras]
 docs = ["sphinx", "jaraco.packaging (>=3.2)", "rst.linker (>=1.9)"]
-testing = ["jaraco.itertools", "func-timeout"]
+testing = ["pytest (>=3.5,<3.7.3 || >3.7.3)", "pytest-checkdocs (>=1.2.3)", "pytest-flake8", "pytest-cov", "jaraco.test (>=3.2.0)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"]
 
 [metadata]
-content-hash = "e2397635da693d8814f714a899a0fa89640de1876f57af4e8db7d878f4f16f68"
+lock-version = "1.1"
 python-versions = "^3.6"
+content-hash = "d80abec1f808f23636f26a1030421071f861c34d9281e2a4be7ea2f76eb3d73d"
 
 [metadata.files]
 addict = [
-    {file = "addict-2.2.1-py3-none-any.whl", hash = "sha256:1948c2a5d93ba6026eb91aef2c971234aaf72488a9c07ab8a7950f82ae30eea7"},
-    {file = "addict-2.2.1.tar.gz", hash = "sha256:f22493f056032f50e4931a82444fcba8ef74c8fc994c5d06aa546a1433c2b8b0"},
+    {file = "addict-2.3.0-py3-none-any.whl", hash = "sha256:69904f5650015d93043522b27316649b6dc877ab1eabb9ea9eb7b11386882edc"},
+    {file = "addict-2.3.0.tar.gz", hash = "sha256:e8085624d18a9eecd7ec8a427f378f1e5036dfafba34c33fa29f0be8cd3a80b2"},
 ]
 aniso8601 = [
     {file = "aniso8601-8.0.0-py2.py3-none-any.whl", hash = "sha256:c033f63d028b9a58e3ab0c2c7d0532ab4bfa7452bfc788fbfe3ddabd327b181a"},
@@ -1607,8 +1340,8 @@ atomicwrites = [
     {file = "atomicwrites-1.4.0.tar.gz", hash = "sha256:ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a"},
 ]
 attrs = [
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 storageclient = []
 uritemplate = [
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diff --git a/pyproject.toml b/pyproject.toml
index 5999f57f1..849acd58f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -29,7 +29,7 @@ flask_sqlalchemy_session = "^1.1"
 email_validator = "^1.1.1"
 gen3authz = "^1.0.0"
 gen3cirrus = "^1.1.2"
-gen3config = {git = "https://github.com/uc-cdis/gen3config", rev = "chore/cdiserrors"}
+gen3config = "~0.1.8"
 gen3users = "^0.6.0"
 markdown = "^3.1.1"
 paramiko = "^2.6.0"