From fda61973e8f981085bd9482868ee8d94b121d5a3 Mon Sep 17 00:00:00 2001
From: William Ronchetti <wrr33@cornell.edu>
Date: Tue, 7 Jun 2022 14:55:35 -0400
Subject: [PATCH 1/3] auth0 changes + supd, py38

---
 Dockerfile                                    | 37 +++++++------
 base.ini                                      |  3 +-
 deploy/docker/production/entrypoint_portal.sh | 14 ++---
 deploy/docker/production/nginx.conf           |  6 ++-
 deploy/docker/production/supervisord.conf     | 54 +++++++++++++++++++
 pyproject.toml                                |  9 ++--
 src/encoded/__init__.py                       | 18 ++++++-
 7 files changed, 106 insertions(+), 35 deletions(-)
 create mode 100644 deploy/docker/production/supervisord.conf

diff --git a/Dockerfile b/Dockerfile
index 80c782b88a..868f82af51 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,8 +1,6 @@
 # CGAP-Portal (Production) Dockerfile
-# Take latest 3.7.12 Debian variant
-FROM python:3.7.12-slim-buster
-# bullseye seems to perform worse
-#FROM python:3.7.12-slim-bullseye
+# Take latest 3.8.13 Debian variant
+FROM python:3.8.13-slim-buster
 
 MAINTAINER William Ronchetti "william_ronchetti@hms.harvard.edu"
 
@@ -35,7 +33,7 @@ WORKDIR /home/nginx/.nvm
 ENV NVM_DIR=/home/nginx/.nvm
 COPY deploy/docker/production/install_nginx.sh /install_nginx.sh
 RUN apt-get update && apt-get upgrade -y && \
-    apt-get install -y --no-install-recommends vim emacs net-tools ca-certificates \
+    apt-get install -y --no-install-recommends vim emacs net-tools ca-certificates build-essential \
     gcc zlib1g-dev postgresql-client libpq-dev git make curl libmagic-dev && \
     pip install --upgrade pip && \
     curl -sSL https://install.python-poetry.org | POETRY_HOME=/opt/venv python - && \
@@ -114,24 +112,31 @@ RUN chown nginx:nginx development.ini
 RUN chmod +x entrypoint_local.sh
 
 # Production setup
-RUN touch production.ini
-RUN touch session-secret.b64
-RUN chown nginx:nginx session-secret.b64
-RUN chown nginx:nginx production.ini
-RUN chown nginx:nginx poetry.toml
+RUN chown nginx:nginx poetry.toml && \
+    touch production.ini && \
+    chown nginx:nginx production.ini && \
+    touch session-secret.b64 && \
+    chown nginx:nginx session-secret.b64 &&  \
+    touch supervisord.log && \
+    chown nginx:nginx supervisord.log && \
+    touch supervisord.sock && \
+    chown nginx:nginx supervisord.sock && \
+    touch supervisord.pid && \
+    chown nginx:nginx supervisord.pid
 COPY deploy/docker/production/$INI_BASE deploy/ini_files/.
 COPY deploy/docker/production/entrypoint.sh .
 COPY deploy/docker/production/entrypoint_portal.sh .
 COPY deploy/docker/production/entrypoint_deployment.sh .
 COPY deploy/docker/production/entrypoint_indexer.sh .
 COPY deploy/docker/production/entrypoint_ingester.sh .
+COPY deploy/docker/production/supervisord.conf .
 COPY deploy/docker/production/assume_identity.py .
-RUN chmod +x entrypoint.sh
-RUN chmod +x entrypoint_deployment.sh
-RUN chmod +x entrypoint_deployment.sh
-RUN chmod +x entrypoint_indexer.sh
-RUN chmod +x entrypoint_ingester.sh
-RUN chmod +x assume_identity.py
+RUN chmod +x entrypoint.sh && \
+    chmod +x entrypoint_deployment.sh && \
+    chmod +x entrypoint_deployment.sh && \
+    chmod +x entrypoint_indexer.sh && \
+    chmod +x entrypoint_ingester.sh && \
+    chmod +x assume_identity.py
 EXPOSE 8000
 
 # Container does not run as root
diff --git a/base.ini b/base.ini
index 019fd4aee1..c77079ecb6 100644
--- a/base.ini
+++ b/base.ini
@@ -61,5 +61,4 @@ timeout = 60
 
 [filter:memlimit]
 use = egg:encoded#memlimit
-rss_limit = 500MB
-rss_percent_limit = 20
+rss_limit = 450MB
diff --git a/deploy/docker/production/entrypoint_portal.sh b/deploy/docker/production/entrypoint_portal.sh
index 44d1dfc0fb..a5c45c0737 100644
--- a/deploy/docker/production/entrypoint_portal.sh
+++ b/deploy/docker/production/entrypoint_portal.sh
@@ -9,14 +9,6 @@ poetry run python -m assume_identity
 # Start nginx proxy
 service nginx start
 
-# Start application
-echo "Starting server 1"
-pserve production.ini http_port=6543 &
-echo "Starting server 2"
-pserve production.ini http_port=6544 &
-echo "Starting server 3"
-pserve production.ini http_port=6545 &
-echo "Starting server 4"
-pserve production.ini http_port=6546 &
-echo "Starting server 5"
-pserve production.ini http_port=6547
+# Start application workers
+echo "Starting supervisor"
+supervisord -c supervisord.conf
diff --git a/deploy/docker/production/nginx.conf b/deploy/docker/production/nginx.conf
index 985f23bb5c..b0ab9ce935 100644
--- a/deploy/docker/production/nginx.conf
+++ b/deploy/docker/production/nginx.conf
@@ -36,6 +36,10 @@ http {
     types_hash_max_size 2048;
     types_hash_bucket_size 64;
 
+    # If 502 is encountered, we may have been killed for memory
+    # fall back to the next server, until one is back
+    proxy_next_upstream error timeout http_502;
+
     # Allow large POST requests
     client_body_buffer_size 128K;
     client_header_buffer_size 1k;
@@ -66,7 +70,7 @@ http {
         server 0.0.0.0:6544 fail_timeout=45;
         server 0.0.0.0:6545 fail_timeout=45;
         server 0.0.0.0:6546 fail_timeout=45;
-        server 0.0.0.0:6547 fail_timeout=45;
+        server 0.0.0.0:6547 fail_timeout=45 backup;
         keepalive 64;
     }
 
diff --git a/deploy/docker/production/supervisord.conf b/deploy/docker/production/supervisord.conf
new file mode 100644
index 0000000000..9f2840a2a8
--- /dev/null
+++ b/deploy/docker/production/supervisord.conf
@@ -0,0 +1,54 @@
+[supervisord]
+pidfile=%(here)s/supervisord.pid
+logfile_maxbytes=50MB
+logfile_backups=10
+loglevel=info
+nodaemon=true
+minfds=1024
+minprocs=200
+user=nginx
+
+[program:cgap1]
+autorestart=true
+startsecs=6
+command=pserve production.ini http_port=6543
+stdout_logfile=/dev/stdout
+stdout_logfile_maxbytes=0
+stderr_logfile_maxbytes=0
+redirect_stderr=true
+
+[program:cgap2]
+autorestart=true
+startsecs=6
+command=pserve production.ini http_port=6544
+stdout_logfile=/dev/stdout
+stdout_logfile_maxbytes=0
+stderr_logfile_maxbytes=0
+redirect_stderr=true
+
+[program:cgap3]
+autorestart=true
+startsecs=6
+command=pserve production.ini http_port=6545
+stdout_logfile=/dev/stdout
+stdout_logfile_maxbytes=0
+stderr_logfile_maxbytes=0
+redirect_stderr=true
+
+[program:cgap4]
+autorestart=true
+startsecs=6
+command=pserve production.ini http_port=6546
+stdout_logfile=/dev/stdout
+stdout_logfile_maxbytes=0
+stderr_logfile_maxbytes=0
+redirect_stderr=true
+
+[program:cgap5]
+autorestart=true
+startsecs=6
+command=pserve production.ini http_port=6547
+stdout_logfile=/dev/stdout
+stdout_logfile_maxbytes=0
+stderr_logfile_maxbytes=0
+redirect_stderr=true
diff --git a/pyproject.toml b/pyproject.toml
index e5f9ff3318..c3ae268d52 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,7 +1,7 @@
 [tool.poetry]
 # Note: Various modules refer to this system as "encoded", not "cgap-portal".
 name = "encoded"
-version = "8.9.2"
+version = "9.0.0"
 description = "Clinical Genomics Analysis Platform"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"
@@ -36,14 +36,15 @@ classifiers = [
 ]
 
 [tool.poetry.dependencies]
-python = ">=3.7.1,<3.8"
+python = ">=3.7.1,<3.9"
 boto3 = "^1.21.5"
 botocore = "^1.24.5"
 certifi = ">=2021.5.30"
 chardet = "3.0.4"
+codeguru-profiler-agent = "^1.2.4"
 colorama = "0.3.3"
 dcicpyvcf = "1.0.0"
-dcicsnovault = "^5.4.0"
+dcicsnovault = "^5.6.0"
 dcicutils = "^3.9.0"
 elasticsearch = "6.8.1"
 execnet = "1.4.1"
@@ -104,6 +105,7 @@ SQLAlchemy = "1.3.16"  # Pinned because >=1.3.17 is broken for us (circular cons
 structlog = ">=19.2.0,<20"
 #submit4dn = "0.9.7"
 subprocess-middleware = "^0.3.0"
+supervisor = "^4.2.4"
 # Useful for picking apart pyproject.toml
 toml = ">=0.10.1,<1"
 tqdm = "^4.59.0"
@@ -120,7 +122,6 @@ WSGIProxy2 = "0.4.2"
 "zope.deprecation" = "^4.4.0"
 "zope.interface" = "^4.7.2"
 "zope.sqlalchemy" = "1.3"
-codeguru-profiler-agent = "^1.2.4"
 
 [tool.poetry.dev-dependencies]
 # PyCharm says boto3-stubs contains useful type hints
diff --git a/src/encoded/__init__.py b/src/encoded/__init__.py
index 7a9d702761..65b91bbcf7 100644
--- a/src/encoded/__init__.py
+++ b/src/encoded/__init__.py
@@ -1,5 +1,4 @@
 import hashlib
-# import json
 import logging  # not used in Fourfront, but used in CGAP? -kmp 8-Apr-2020
 import mimetypes
 import netaddr
@@ -38,6 +37,7 @@
 # default trace_rate for sentry
 # tune this to get more data points when analyzing performance
 SENTRY_TRACE_RATE = .1
+DEFAULT_AUTH0_DOMAIN = 'hms-dbmi.auth0.com'
 
 
 def static_resources(config):
@@ -138,9 +138,25 @@ def main(global_config, **local_config):
     # settings['snovault.jsonld.terms_namespace'] = 'https://www.encodeproject.org/terms/'
     settings['snovault.jsonld.terms_prefix'] = 'encode'
     # set auth0 keys
+    settings['auth0.domain'] = settings.get('auth0.domain', os.environ.get('Auth0Domain', DEFAULT_AUTH0_DOMAIN))
     settings['auth0.client'] = settings.get('auth0.client', os.environ.get('Auth0Client'))
     settings['auth0.secret'] = settings.get('auth0.secret', os.environ.get('Auth0Secret'))
+    settings['auth0.options'] = {
+        'auth': {
+            'sso': False,
+            'redirect': False,
+            'responseType': 'token',
+            'params': {
+                'scope': 'openid email',
+                'prompt': 'select_account'
+            }
+        },
+        'allowedConnections': [  # TODO: make at least this part configurable
+            'github', 'google-oauth2', 'partners'
+        ]
+    }
     # set google reCAPTCHA keys
+    # TODO propagate from GAC
     settings['g.recaptcha.key'] = os.environ.get('reCaptchaKey')
     settings['g.recaptcha.secret'] = os.environ.get('reCaptchaSecret')
     # enable invalidation scope

From 68c9b6f498e48ff74200b65ef3018fcaf14687ce Mon Sep 17 00:00:00 2001
From: William Ronchetti <wrr33@cornell.edu>
Date: Tue, 7 Jun 2022 14:58:01 -0400
Subject: [PATCH 2/3] lock changes

---
 poetry.lock | 1434 ++++++++++++++++++++++++++-------------------------
 1 file changed, 732 insertions(+), 702 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index af772d5138..5ca9b13ff1 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,10 +1,10 @@
 [[package]]
 name = "apipkg"
-version = "2.1.0"
+version = "3.0.0"
 description = "apipkg: namespace control and lazy-import mechanism"
 category = "main"
 optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7"
+python-versions = ">=3.7"
 
 [[package]]
 name = "atomicwrites"
@@ -62,11 +62,11 @@ python-versions = "*"
 
 [[package]]
 name = "beautifulsoup4"
-version = "4.10.0"
+version = "4.11.1"
 description = "Screen-scraping library"
 category = "main"
 optional = false
-python-versions = ">3.0.0"
+python-versions = ">=3.6.0"
 
 [package.dependencies]
 soupsieve = ">1.2"
@@ -77,7 +77,7 @@ lxml = ["lxml"]
 
 [[package]]
 name = "bitarray"
-version = "2.4.1"
+version = "2.5.1"
 description = "efficient arrays of booleans -- C extension"
 category = "main"
 optional = false
@@ -93,24 +93,24 @@ python-versions = "*"
 
 [[package]]
 name = "boto3"
-version = "1.21.29"
+version = "1.24.3"
 description = "The AWS SDK for Python"
 category = "main"
 optional = false
-python-versions = ">= 3.6"
+python-versions = ">= 3.7"
 
 [package.dependencies]
-botocore = ">=1.24.29,<1.25.0"
+botocore = ">=1.27.3,<1.28.0"
 jmespath = ">=0.7.1,<2.0.0"
-s3transfer = ">=0.5.0,<0.6.0"
+s3transfer = ">=0.6.0,<0.7.0"
 
 [package.extras]
 crt = ["botocore[crt] (>=1.21.0,<2.0a0)"]
 
 [[package]]
 name = "boto3-stubs"
-version = "1.21.29"
-description = "Type annotations for boto3 1.21.29 generated with mypy-boto3-builder 7.5.4"
+version = "1.24.3"
+description = "Type annotations for boto3 1.24.3 generated with mypy-boto3-builder 7.6.1"
 category = "dev"
 optional = false
 python-versions = ">=3.6"
@@ -120,318 +120,322 @@ botocore-stubs = "*"
 typing-extensions = ">=4.1.0"
 
 [package.extras]
-accessanalyzer = ["mypy-boto3-accessanalyzer (>=1.21.0)"]
-account = ["mypy-boto3-account (>=1.21.0)"]
-acm = ["mypy-boto3-acm (>=1.21.0)"]
-acm-pca = ["mypy-boto3-acm-pca (>=1.21.0)"]
-alexaforbusiness = ["mypy-boto3-alexaforbusiness (>=1.21.0)"]
-all = ["mypy-boto3-accessanalyzer (>=1.21.0)", "mypy-boto3-account (>=1.21.0)", "mypy-boto3-acm (>=1.21.0)", "mypy-boto3-acm-pca (>=1.21.0)", "mypy-boto3-alexaforbusiness (>=1.21.0)", "mypy-boto3-amp (>=1.21.0)", "mypy-boto3-amplify (>=1.21.0)", "mypy-boto3-amplifybackend (>=1.21.0)", "mypy-boto3-amplifyuibuilder (>=1.21.0)", "mypy-boto3-apigateway (>=1.21.0)", "mypy-boto3-apigatewaymanagementapi (>=1.21.0)", "mypy-boto3-apigatewayv2 (>=1.21.0)", "mypy-boto3-appconfig (>=1.21.0)", "mypy-boto3-appconfigdata (>=1.21.0)", "mypy-boto3-appflow (>=1.21.0)", "mypy-boto3-appintegrations (>=1.21.0)", "mypy-boto3-application-autoscaling (>=1.21.0)", "mypy-boto3-application-insights (>=1.21.0)", "mypy-boto3-applicationcostprofiler (>=1.21.0)", "mypy-boto3-appmesh (>=1.21.0)", "mypy-boto3-apprunner (>=1.21.0)", "mypy-boto3-appstream (>=1.21.0)", "mypy-boto3-appsync (>=1.21.0)", "mypy-boto3-athena (>=1.21.0)", "mypy-boto3-auditmanager (>=1.21.0)", "mypy-boto3-autoscaling (>=1.21.0)", "mypy-boto3-autoscaling-plans (>=1.21.0)", "mypy-boto3-backup (>=1.21.0)", "mypy-boto3-backup-gateway (>=1.21.0)", "mypy-boto3-batch (>=1.21.0)", "mypy-boto3-billingconductor (>=1.21.0)", "mypy-boto3-braket (>=1.21.0)", "mypy-boto3-budgets (>=1.21.0)", "mypy-boto3-ce (>=1.21.0)", "mypy-boto3-chime (>=1.21.0)", "mypy-boto3-chime-sdk-identity (>=1.21.0)", "mypy-boto3-chime-sdk-meetings (>=1.21.0)", "mypy-boto3-chime-sdk-messaging (>=1.21.0)", "mypy-boto3-cloud9 (>=1.21.0)", "mypy-boto3-cloudcontrol (>=1.21.0)", "mypy-boto3-clouddirectory (>=1.21.0)", "mypy-boto3-cloudformation (>=1.21.0)", "mypy-boto3-cloudfront (>=1.21.0)", "mypy-boto3-cloudhsm (>=1.21.0)", "mypy-boto3-cloudhsmv2 (>=1.21.0)", "mypy-boto3-cloudsearch (>=1.21.0)", "mypy-boto3-cloudsearchdomain (>=1.21.0)", "mypy-boto3-cloudtrail (>=1.21.0)", "mypy-boto3-cloudwatch (>=1.21.0)", "mypy-boto3-codeartifact (>=1.21.0)", "mypy-boto3-codebuild (>=1.21.0)", "mypy-boto3-codecommit (>=1.21.0)", "mypy-boto3-codedeploy (>=1.21.0)", "mypy-boto3-codeguru-reviewer (>=1.21.0)", "mypy-boto3-codeguruprofiler (>=1.21.0)", "mypy-boto3-codepipeline (>=1.21.0)", "mypy-boto3-codestar (>=1.21.0)", "mypy-boto3-codestar-connections (>=1.21.0)", "mypy-boto3-codestar-notifications (>=1.21.0)", "mypy-boto3-cognito-identity (>=1.21.0)", "mypy-boto3-cognito-idp (>=1.21.0)", "mypy-boto3-cognito-sync (>=1.21.0)", "mypy-boto3-comprehend (>=1.21.0)", "mypy-boto3-comprehendmedical (>=1.21.0)", "mypy-boto3-compute-optimizer (>=1.21.0)", "mypy-boto3-config (>=1.21.0)", "mypy-boto3-connect (>=1.21.0)", "mypy-boto3-connect-contact-lens (>=1.21.0)", "mypy-boto3-connectparticipant (>=1.21.0)", "mypy-boto3-cur (>=1.21.0)", "mypy-boto3-customer-profiles (>=1.21.0)", "mypy-boto3-databrew (>=1.21.0)", "mypy-boto3-dataexchange (>=1.21.0)", "mypy-boto3-datapipeline (>=1.21.0)", "mypy-boto3-datasync (>=1.21.0)", "mypy-boto3-dax (>=1.21.0)", "mypy-boto3-detective (>=1.21.0)", "mypy-boto3-devicefarm (>=1.21.0)", "mypy-boto3-devops-guru (>=1.21.0)", "mypy-boto3-directconnect (>=1.21.0)", "mypy-boto3-discovery (>=1.21.0)", "mypy-boto3-dlm (>=1.21.0)", "mypy-boto3-dms (>=1.21.0)", "mypy-boto3-docdb (>=1.21.0)", "mypy-boto3-drs (>=1.21.0)", "mypy-boto3-ds (>=1.21.0)", "mypy-boto3-dynamodb (>=1.21.0)", "mypy-boto3-dynamodbstreams (>=1.21.0)", "mypy-boto3-ebs (>=1.21.0)", "mypy-boto3-ec2 (>=1.21.0)", "mypy-boto3-ec2-instance-connect (>=1.21.0)", "mypy-boto3-ecr (>=1.21.0)", "mypy-boto3-ecr-public (>=1.21.0)", "mypy-boto3-ecs (>=1.21.0)", "mypy-boto3-efs (>=1.21.0)", "mypy-boto3-eks (>=1.21.0)", "mypy-boto3-elastic-inference (>=1.21.0)", "mypy-boto3-elasticache (>=1.21.0)", "mypy-boto3-elasticbeanstalk (>=1.21.0)", "mypy-boto3-elastictranscoder (>=1.21.0)", "mypy-boto3-elb (>=1.21.0)", "mypy-boto3-elbv2 (>=1.21.0)", "mypy-boto3-emr (>=1.21.0)", "mypy-boto3-emr-containers (>=1.21.0)", "mypy-boto3-es (>=1.21.0)", "mypy-boto3-events (>=1.21.0)", "mypy-boto3-evidently (>=1.21.0)", "mypy-boto3-finspace (>=1.21.0)", "mypy-boto3-finspace-data (>=1.21.0)", "mypy-boto3-firehose (>=1.21.0)", "mypy-boto3-fis (>=1.21.0)", "mypy-boto3-fms (>=1.21.0)", "mypy-boto3-forecast (>=1.21.0)", "mypy-boto3-forecastquery (>=1.21.0)", "mypy-boto3-frauddetector (>=1.21.0)", "mypy-boto3-fsx (>=1.21.0)", "mypy-boto3-gamelift (>=1.21.0)", "mypy-boto3-gamesparks (>=1.21.0)", "mypy-boto3-glacier (>=1.21.0)", "mypy-boto3-globalaccelerator (>=1.21.0)", "mypy-boto3-glue (>=1.21.0)", "mypy-boto3-grafana (>=1.21.0)", "mypy-boto3-greengrass (>=1.21.0)", "mypy-boto3-greengrassv2 (>=1.21.0)", "mypy-boto3-groundstation (>=1.21.0)", "mypy-boto3-guardduty (>=1.21.0)", "mypy-boto3-health (>=1.21.0)", "mypy-boto3-healthlake (>=1.21.0)", "mypy-boto3-honeycode (>=1.21.0)", "mypy-boto3-iam (>=1.21.0)", "mypy-boto3-identitystore (>=1.21.0)", "mypy-boto3-imagebuilder (>=1.21.0)", "mypy-boto3-importexport (>=1.21.0)", "mypy-boto3-inspector (>=1.21.0)", "mypy-boto3-inspector2 (>=1.21.0)", "mypy-boto3-iot (>=1.21.0)", "mypy-boto3-iot-data (>=1.21.0)", "mypy-boto3-iot-jobs-data (>=1.21.0)", "mypy-boto3-iot1click-devices (>=1.21.0)", "mypy-boto3-iot1click-projects (>=1.21.0)", "mypy-boto3-iotanalytics (>=1.21.0)", "mypy-boto3-iotdeviceadvisor (>=1.21.0)", "mypy-boto3-iotevents (>=1.21.0)", "mypy-boto3-iotevents-data (>=1.21.0)", "mypy-boto3-iotfleethub (>=1.21.0)", "mypy-boto3-iotsecuretunneling (>=1.21.0)", "mypy-boto3-iotsitewise (>=1.21.0)", "mypy-boto3-iotthingsgraph (>=1.21.0)", "mypy-boto3-iottwinmaker (>=1.21.0)", "mypy-boto3-iotwireless (>=1.21.0)", "mypy-boto3-ivs (>=1.21.0)", "mypy-boto3-kafka (>=1.21.0)", "mypy-boto3-kafkaconnect (>=1.21.0)", "mypy-boto3-kendra (>=1.21.0)", "mypy-boto3-keyspaces (>=1.21.0)", "mypy-boto3-kinesis (>=1.21.0)", "mypy-boto3-kinesis-video-archived-media (>=1.21.0)", "mypy-boto3-kinesis-video-media (>=1.21.0)", "mypy-boto3-kinesis-video-signaling (>=1.21.0)", "mypy-boto3-kinesisanalytics (>=1.21.0)", "mypy-boto3-kinesisanalyticsv2 (>=1.21.0)", "mypy-boto3-kinesisvideo (>=1.21.0)", "mypy-boto3-kms 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+voice-id = ["mypy-boto3-voice-id (>=1.24.0,<1.25.0)"]
+waf = ["mypy-boto3-waf (>=1.24.0,<1.25.0)"]
+waf-regional = ["mypy-boto3-waf-regional (>=1.24.0,<1.25.0)"]
+wafv2 = ["mypy-boto3-wafv2 (>=1.24.0,<1.25.0)"]
+wellarchitected = ["mypy-boto3-wellarchitected (>=1.24.0,<1.25.0)"]
+wisdom = ["mypy-boto3-wisdom (>=1.24.0,<1.25.0)"]
+workdocs = ["mypy-boto3-workdocs (>=1.24.0,<1.25.0)"]
+worklink = ["mypy-boto3-worklink (>=1.24.0,<1.25.0)"]
+workmail = ["mypy-boto3-workmail (>=1.24.0,<1.25.0)"]
+workmailmessageflow = ["mypy-boto3-workmailmessageflow (>=1.24.0,<1.25.0)"]
+workspaces = ["mypy-boto3-workspaces (>=1.24.0,<1.25.0)"]
+workspaces-web = ["mypy-boto3-workspaces-web (>=1.24.0,<1.25.0)"]
+xray = ["mypy-boto3-xray (>=1.24.0,<1.25.0)"]
 
 [[package]]
 name = "botocore"
-version = "1.24.29"
+version = "1.27.3"
 description = "Low-level, data-driven core of boto 3."
 category = "main"
 optional = false
-python-versions = ">= 3.6"
+python-versions = ">= 3.7"
 
 [package.dependencies]
 jmespath = ">=0.7.1,<2.0.0"
@@ -439,12 +443,12 @@ python-dateutil = ">=2.1,<3.0.0"
 urllib3 = ">=1.25.4,<1.27"
 
 [package.extras]
-crt = ["awscrt (==0.13.5)"]
+crt = ["awscrt (==0.13.8)"]
 
 [[package]]
 name = "botocore-stubs"
-version = "1.24.29"
-description = "Type annotations for botocore 1.24.29 generated with mypy-boto3-builder 7.5.4"
+version = "1.27.3"
+description = "Type annotations for botocore 1.27.3 generated with mypy-boto3-builder 7.6.1"
 category = "dev"
 optional = false
 python-versions = ">=3.6"
@@ -454,11 +458,11 @@ typing-extensions = ">=4.1.0"
 
 [[package]]
 name = "certifi"
-version = "2021.10.8"
+version = "2022.5.18.1"
 description = "Python package for providing Mozilla's CA Bundle."
 category = "main"
 optional = false
-python-versions = "*"
+python-versions = ">=3.6"
 
 [[package]]
 name = "cffi"
@@ -492,7 +496,7 @@ unicode_backport = ["unicodedata2"]
 
 [[package]]
 name = "click"
-version = "8.1.0"
+version = "8.1.3"
 description = "Composable command line interface toolkit"
 category = "dev"
 optional = false
@@ -538,7 +542,7 @@ python-versions = "*"
 
 [[package]]
 name = "coverage"
-version = "6.3.2"
+version = "6.4.1"
 description = "Code coverage measurement for Python"
 category = "dev"
 optional = false
@@ -565,7 +569,7 @@ yaml = ["PyYAML (>=3.10)"]
 
 [[package]]
 name = "cryptography"
-version = "36.0.2"
+version = "37.0.2"
 description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
 category = "dev"
 optional = false
@@ -580,7 +584,7 @@ docstest = ["pyenchant (>=1.6.11)", "twine (>=1.12.0)", "sphinxcontrib-spelling
 pep8test = ["black", "flake8", "flake8-import-order", "pep8-naming"]
 sdist = ["setuptools_rust (>=0.11.4)"]
 ssh = ["bcrypt (>=3.1.5)"]
-test = ["pytest (>=6.2.0)", "pytest-cov", "pytest-subtests", "pytest-xdist", "pretend", "iso8601", "pytz", "hypothesis (>=1.11.4,!=3.79.2)"]
+test = ["pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-subtests", "pytest-xdist", "pretend", "iso8601", "pytz", "hypothesis (>=1.11.4,!=3.79.2)"]
 
 [[package]]
 name = "cycler"
@@ -600,11 +604,11 @@ python-versions = "*"
 
 [[package]]
 name = "dcicsnovault"
-version = "5.4.0"
+version = "5.6.0"
 description = "Storage support for 4DN Data Portals."
 category = "main"
 optional = false
-python-versions = ">=3.6.1,<3.8"
+python-versions = ">=3.7.1,<3.9"
 
 [package.dependencies]
 aws_requests_auth = ">=0.4.1,<0.5.0"
@@ -652,7 +656,7 @@ xlrd = ">=1.0.0,<2.0.0"
 
 [[package]]
 name = "dcicutils"
-version = "3.11.0"
+version = "3.13.1"
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 category = "main"
 optional = false
@@ -789,7 +793,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "flask"
-version = "2.1.0"
+version = "2.1.2"
 description = "A simple framework for building complex web applications."
 category = "dev"
 optional = false
@@ -797,7 +801,7 @@ python-versions = ">=3.7"
 
 [package.dependencies]
 click = ">=8.0"
-importlib-metadata = {version = "*", markers = "python_version < \"3.10\""}
+importlib-metadata = {version = ">=3.6.0", markers = "python_version < \"3.10\""}
 itsdangerous = ">=2.0"
 Jinja2 = ">=3.0"
 Werkzeug = ">=2.0"
@@ -953,7 +957,7 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "jinja2"
-version = "3.1.1"
+version = "3.1.2"
 description = "A very fast and expressive template engine."
 category = "dev"
 optional = false
@@ -983,7 +987,7 @@ python-versions = "*"
 
 [[package]]
 name = "jsonpickle"
-version = "2.1.0"
+version = "2.2.0"
 description = "Python library for serializing any arbitrary object graph into JSON"
 category = "dev"
 optional = false
@@ -994,8 +998,8 @@ importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
 
 [package.extras]
 docs = ["sphinx", "jaraco.packaging (>=3.2)", "rst.linker (>=1.9)"]
-testing = ["pytest (>=3.5,!=3.7.3)", "pytest-checkdocs (>=1.2.3)", "pytest-flake8", "pytest-black-multipy", "pytest-cov", "ecdsa", "feedparser", "numpy", "pandas", "pymongo", "scikit-learn", "sqlalchemy", "enum34", "jsonlib"]
-"testing.libs" = ["demjson", "simplejson", "ujson", "yajl"]
+testing = ["pytest (>=3.5,!=3.7.3)", "pytest-checkdocs (>=1.2.3)", "pytest-black-multipy", "pytest-cov", "ecdsa", "feedparser", "numpy", "pandas", "pymongo", "scikit-learn", "sqlalchemy", "pytest-flake8 (<1.1.0)", "enum34", "jsonlib", "pytest-flake8 (>=1.1.1)"]
+"testing.libs" = ["simplejson", "ujson", "yajl"]
 
 [[package]]
 name = "jsonschema-serialize-fork"
@@ -1079,7 +1083,7 @@ test = ["pytest (<5.4)", "pytest-cov"]
 
 [[package]]
 name = "more-itertools"
-version = "8.12.0"
+version = "8.13.0"
 description = "More routines for operating on iterables, beyond itertools"
 category = "dev"
 optional = false
@@ -1142,7 +1146,7 @@ python-versions = ">=3.6"
 
 [[package]]
 name = "openpyxl"
-version = "3.0.9"
+version = "3.0.10"
 description = "A Python library to read/write Excel 2010 xlsx/xlsm files"
 category = "main"
 optional = false
@@ -1186,15 +1190,19 @@ python-versions = "*"
 
 [[package]]
 name = "pillow"
-version = "9.0.1"
+version = "9.1.1"
 description = "Python Imaging Library (Fork)"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 
+[package.extras]
+docs = ["olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-issues (>=3.0.1)", "sphinx-removed-in", "sphinx-rtd-theme (>=1.0)", "sphinxext-opengraph"]
+tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
+
 [[package]]
 name = "pip-licenses"
-version = "3.5.3"
+version = "3.5.4"
 description = "Dump the software license list of Python packages installed with pip."
 category = "dev"
 optional = false
@@ -1261,14 +1269,14 @@ testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
 name = "psutil"
-version = "5.9.0"
+version = "5.9.1"
 description = "Cross-platform lib for process and system monitoring in Python."
 category = "main"
 optional = false
-python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [package.extras]
-test = ["ipaddress", "mock", "unittest2", "enum34", "pywin32", "wmi"]
+test = ["ipaddress", "mock", "enum34", "pywin32", "wmi"]
 
 [[package]]
 name = "psycopg2-binary"
@@ -1463,7 +1471,7 @@ python-versions = "*"
 
 [[package]]
 name = "pysam"
-version = "0.19.0"
+version = "0.19.1"
 description = "pysam"
 category = "main"
 optional = false
@@ -1613,7 +1621,7 @@ pycrypto = ["pycrypto (>=2.6.0,<2.7.0)"]
 
 [[package]]
 name = "python-magic"
-version = "0.4.25"
+version = "0.4.26"
 description = "File type identification using libmagic"
 category = "main"
 optional = false
@@ -1705,7 +1713,7 @@ use_chardet_on_py3 = ["chardet (>=3.0.2,<5)"]
 
 [[package]]
 name = "responses"
-version = "0.20.0"
+version = "0.21.0"
 description = "A utility library for mocking out the `requests` Python library."
 category = "dev"
 optional = false
@@ -1713,6 +1721,7 @@ python-versions = ">=3.7"
 
 [package.dependencies]
 requests = ">=2.0,<3.0"
+typing-extensions = {version = "*", markers = "python_version < \"3.8\""}
 urllib3 = ">=1.25.10"
 
 [package.extras]
@@ -1756,11 +1765,11 @@ testing = ["pytest", "pytest-cov", "coverage", "webtest"]
 
 [[package]]
 name = "s3transfer"
-version = "0.5.2"
+version = "0.6.0"
 description = "An Amazon S3 Transfer Manager"
 category = "main"
 optional = false
-python-versions = ">= 3.6"
+python-versions = ">= 3.7"
 
 [package.dependencies]
 botocore = ">=1.12.36,<2.0a.0"
@@ -1770,7 +1779,7 @@ crt = ["botocore[crt] (>=1.20.29,<2.0a.0)"]
 
 [[package]]
 name = "sentry-sdk"
-version = "1.5.8"
+version = "1.5.12"
 description = "Python client for Sentry (https://sentry.io)"
 category = "main"
 optional = false
@@ -1824,7 +1833,7 @@ python-versions = ">=3.6"
 
 [[package]]
 name = "soupsieve"
-version = "2.3.1"
+version = "2.3.2.post1"
 description = "A modern CSS selector implementation for Beautiful Soup."
 category = "main"
 optional = false
@@ -1895,6 +1904,17 @@ WebOb = "*"
 [package.extras]
 test = ["webtest", "pyramid", "pytest"]
 
+[[package]]
+name = "supervisor"
+version = "4.2.4"
+description = "A system for controlling process state under UNIX"
+category = "main"
+optional = false
+python-versions = "*"
+
+[package.extras]
+testing = ["pytest", "pytest-cov"]
+
 [[package]]
 name = "toml"
 version = "0.10.2"
@@ -1905,7 +1925,7 @@ python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
 
 [[package]]
 name = "tqdm"
-version = "4.63.1"
+version = "4.64.0"
 description = "Fast, Extensible Progress Meter"
 category = "main"
 optional = false
@@ -1917,6 +1937,7 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""}
 [package.extras]
 dev = ["py-make (>=0.1.0)", "twine", "wheel"]
 notebook = ["ipywidgets (>=6)"]
+slack = ["slack-sdk"]
 telegram = ["requests"]
 
 [[package]]
@@ -1945,11 +1966,11 @@ python-versions = "*"
 
 [[package]]
 name = "typing-extensions"
-version = "4.1.1"
-description = "Backported and Experimental Type Hints for Python 3.6+"
+version = "4.2.0"
+description = "Backported and Experimental Type Hints for Python 3.7+"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [[package]]
 name = "uptime"
@@ -1986,7 +2007,7 @@ testing = ["pytest", "coverage", "pytest-cov"]
 
 [[package]]
 name = "waitress"
-version = "2.1.1"
+version = "2.1.2"
 description = "Waitress WSGI server"
 category = "main"
 optional = false
@@ -2060,7 +2081,7 @@ tests = ["nose (<1.3.0)", "coverage", "mock", "pastedeploy", "wsgiproxy2", "pyqu
 
 [[package]]
 name = "werkzeug"
-version = "2.1.0"
+version = "2.1.2"
 description = "The comprehensive WSGI web application library."
 category = "dev"
 optional = false
@@ -2071,7 +2092,7 @@ watchdog = ["watchdog"]
 
 [[package]]
 name = "wrapt"
-version = "1.14.0"
+version = "1.14.1"
 description = "Module for decorators, wrappers and monkey patching."
 category = "dev"
 optional = false
@@ -2099,23 +2120,23 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "xmltodict"
-version = "0.12.0"
+version = "0.13.0"
 description = "Makes working with XML feel like you are working with JSON"
 category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=3.4"
 
 [[package]]
 name = "zipp"
-version = "3.7.0"
+version = "3.8.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 
 [package.extras]
-docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"]
+docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
 
 [[package]]
 name = "zope.deprecation"
@@ -2160,13 +2181,13 @@ test = ["zope.testing"]
 
 [metadata]
 lock-version = "1.1"
-python-versions = ">=3.7.1,<3.8"
-content-hash = "3368fb721bf314cce927366565091bbff9013c987bbc373014ad1a8d0ada5033"
+python-versions = ">=3.7.1,<3.9"
+content-hash = "fff825e7ec688c1705588f639095442d43c8d2f7a459ffe764847e5c913b07fd"
 
 [metadata.files]
 apipkg = [
-    {file = "apipkg-2.1.0-py2.py3-none-any.whl", hash = "sha256:e5d85ce3a2e622734c5daebb213df044d4cedee1031fbe98add3c73ca5995b94"},
-    {file = "apipkg-2.1.0.tar.gz", hash = "sha256:a4be31cf8081e660d2cdea6edfb8a0f39f385866abdcfcfa45e5a0887345cb70"},
+    {file = "apipkg-3.0.0-py3-none-any.whl", hash = "sha256:e0f98b9b426a0569d8dc0ca318e050319500fc546681d600414f09b8bfecb44c"},
+    {file = "apipkg-3.0.0.tar.gz", hash = "sha256:f8e504547b753fdff33d126f27b5cfbb5f67864db3ecfdd4bf34aeefb6709bf9"},
 ]
 atomicwrites = [
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@@ -2189,106 +2210,106 @@ aws-xray-sdk = [
     {file = "backports.statistics-0.1.0.tar.gz", hash = "sha256:714ab29b9b9937c6ec65d8c6a3dcc39ee4972f929d55977b018bb9f204ba1f98"},
 ]
 beautifulsoup4 = [
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+    {file = "beautifulsoup4-4.11.1-py3-none-any.whl", hash = "sha256:58d5c3d29f5a36ffeb94f02f0d786cd53014cf9b3b3951d42e0080d8a9498d30"},
+    {file = "beautifulsoup4-4.11.1.tar.gz", hash = "sha256:ad9aa55b65ef2808eb405f46cf74df7fcb7044d5cbc26487f96eb2ef2e436693"},
 ]
 bitarray = [
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@@ -3432,12 +3462,12 @@ xlrd = [
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+    {file = "zipp-3.8.0.tar.gz", hash = "sha256:56bf8aadb83c24db6c4b577e13de374ccfb67da2078beba1d037c17980bf43ad"},
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 "zope.deprecation" = [
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From 809863ab0ae5636f96e2787130e64541392e7055 Mon Sep 17 00:00:00 2001
From: William Ronchetti <wrr33@cornell.edu>
Date: Tue, 7 Jun 2022 14:59:54 -0400
Subject: [PATCH 3/3] build in 3.8

---
 .github/workflows/main.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 0dea9ed431..d34580ac52 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -17,7 +17,7 @@ on:
 jobs:
   # This workflow contains a single job called "build"
   build:
-    name: Test Suite for cgap-portal (Python 3.7, Node 16)
+    name: Test Suite for cgap-portal (Python 3.8, Node 16)
 
     # The type of runner that the job will run on
     runs-on: ubuntu-18.04
@@ -27,7 +27,7 @@ jobs:
       matrix:
         test_type: ['UNIT', 'NPM', 'Docker']
         # We are really not set up for these next two to be multiplicative, so be careful adding more.
-        python_version: ['3.7']
+        python_version: ['3.8']
         node_version: ['16']
 
     # Steps represent a sequence of tasks that will be executed as part of the job