Merge pull request #1349 from cmu-delphi/release/delphi-epidata-4.1.14

Release Delphi Epidata 4.1.14

Author: melange396

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.1.13
+current_version = 4.1.14
 commit = False
 tag = False
 

.env.example

@@ -4,3 +4,6 @@ FLASK_SECRET=abc
 #API_KEY_REQUIRED_STARTING_AT=2021-07-30
 API_KEY_ADMIN_PASSWORD=abc
 API_KEY_REGISTER_WEBHOOK_TOKEN=abc
+
+# Sentry
+# If setting a Sentry DSN, note that the URL should NOT be quoted!

.github/workflows/performance-tests-one-time.yml

@@ -1,9 +1,9 @@
-name: One-time performance testing - 26th October 2023
+name: One-time performance testing - 8th November 2023
 
-# Run "At every 30th minute on day-of-month 26 in October"
+# Run "At every 30th minute on day-of-month 8 in November"
 on:
   schedule:
-    - cron: '*/30 * 26 10 *'
+    - cron: '*/30 * 8 11 *'
 
 # Add some extra perms to comment on a PR
 permissions:
@@ -65,6 +65,8 @@ jobs:
           path: delphi-admin
       - name: Build & run Locust
         continue-on-error: true # sometimes ~2-5 queries fail, we shouldn't end the run if that's the case
+        env:
+          PERFTEST_API_KEY: ${{secrets.PERFTEST_API_KEY}}
         run: |
           cd delphi-admin/load-testing/locust
           docker build -t locust .

.github/workflows/performance-tests.yml

@@ -73,6 +73,8 @@ jobs:
           path: delphi-admin
       - name: Build & run Locust
         continue-on-error: true # sometimes ~2-5 queries fail, we shouldn't end the run if that's the case
+        env:
+          PERFTEST_API_KEY: ${{secrets.PERFTEST_API_KEY}}
         run: |
           cd delphi-admin/load-testing/locust
           docker build -t locust .

dev/local/Makefile

@@ -77,6 +77,7 @@ LOG_REDIS:=delphi_redis_instance_$(NOW).log
 WEB_CONTAINER_ID:=$(shell docker ps -q --filter 'name=delphi_web_epidata')
 DATABASE_CONTAINER_ID:=$(shell docker ps -q --filter 'name=delphi_database_epidata')
 REDIS_CONTAINER_ID:=$(shell docker ps -q --filter 'name=delphi_redis')
+ENV_FILE:=repos/delphi/delphi-epidata/.env
 
 M1=
 ifeq ($(shell uname -smp), Darwin arm64 arm)
@@ -104,8 +105,10 @@ web:
 	@# Run the web server
 	@# MODULE_NAME specifies the location of the `app` variable, the actual WSGI application object to run.
 	@# see https://github.com/tiangolo/meinheld-gunicorn-docker#module_name
+	@touch $(ENV_FILE)
 	@docker run --rm -p 127.0.0.1:10080:80 \
 		$(M1) \
+		--env-file $(ENV_FILE) \
 		--env "MODULE_NAME=delphi.epidata.server.main" \
 		--env "SQLALCHEMY_DATABASE_URI=$(sqlalchemy_uri)" \
 		--env "FLASK_SECRET=abc" --env "FLASK_PREFIX=/epidata" --env "LOG_DEBUG" \

dev/local/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = Delphi Development
-version = 4.1.13
+version = 4.1.14
 
 [options]
 packages =

devops/Dockerfile

@@ -7,7 +7,6 @@ FROM tiangolo/meinheld-gunicorn:python3.8
 LABEL org.opencontainers.image.source=https://github.com/cmu-delphi/delphi-epidata
 
 COPY ./devops/gunicorn_conf.py /app
-COPY ./devops/start_wrapper.sh /
 RUN mkdir -p /app/delphi/epidata
 COPY ./src/server /app/delphi/epidata/server
 COPY ./src/common /app/delphi/epidata/common
@@ -18,7 +17,6 @@ COPY requirements.api.txt /app/requirements_also.txt
 RUN ln -s -f /usr/share/zoneinfo/America/New_York /etc/localtime \
       && rm -rf /app/delphi/epidata/__pycache__ \
       && chmod -R o+r /app/delphi/epidata \
-      && chmod 755 /start_wrapper.sh \
       && pip install --no-cache-dir -r /tmp/requirements.txt -r requirements_also.txt
 # the file /tmp/requirements.txt is created in the parent docker definition.  (see:
 #   https://github.com/tiangolo/meinheld-gunicorn-docker/blob/master/docker-images/python3.8.dockerfile#L5 )
@@ -28,4 +26,4 @@ RUN ln -s -f /usr/share/zoneinfo/America/New_York /etc/localtime \
 ENV PYTHONUNBUFFERED 1
 
 ENTRYPOINT [ "/entrypoint.sh" ]
-CMD [ "/start_wrapper.sh" ]
+CMD [ "/start.sh" ]

devops/start_wrapper.sh

@@ -388,3 +388,13 @@ The command above maps two local directories into the container:
 - `/repos/delphi/delphi-epidata/src`: Just the source code, which forms the
   container's `delphi.epidata` python package.
 
+## instrumentation with Sentry
+
+Delphi uses [Sentry](https://sentry.io/welcome/) in production for debugging, APM, and other observability purposes. You can instrument your local environment if you want to take advantage of Sentry's features during the development process. In most cases this option is available to internal Delphi team members only.
+
+The bare minimum to set up instrumentation is to supply the DSN for the [epidata-api](https://cmu-delphi.sentry.io/projects/epidata-api/?project=4506123377442816) Sentry project to the application environment.
+
+- You can get the DSN from the Sentry [project's keys config](https://cmu-delphi.sentry.io/settings/projects/epidata-api/keys/), or by asking someone in the prodsys, DevOps, or sysadmin space.
+- Once you have the DSN, add it to your local `.env` file and rebuild your containers to start sending telemetry to Sentry.
+
+Additional internal documentation for Sentry can be found [here](https://bookstack.delphi.cmu.edu/books/systems-handbook/page/sentry).

docs/epidata_development.md

@@ -26,14 +26,17 @@ Pandemic"](https://www.pnas.org/topic/548) in *PNAS*:
 
 Research publications using the survey data include:
 
+- W. Dempsey (2023). [Addressing selection bias and measurement error in
+  COVID-19 case count data using auxiliary information](https://doi.org/10.1214/23-AOAS1744).
+  *Annals of Applied Statistics* 17 (4), 2903-2923.
 - Ma, M.Z., Chen, S.X. (2023). [Beyond the surface: accounting for confounders
   in understanding the link between collectivism and COVID-19 pandemic in the
   United States](https://doi.org/10.1186/s12889-023-16384-2). *BMC Public
   Health* 23, 1513.
 - C.K. Ettman, E. Badillo Goicoechea, and E.A. Stuart (2023). [Evolution of
   depression and anxiety over the COVID-19 pandemic and across demographic
   groups in a large sample of U.S. adults](https://doi.org/10.1016/j.focus.2023.100140).
-  *AJPM Focus*.
+  *AJPM Focus* 2 (4), 100140.
 - M. Rubinstein, Z. Branson, and E.H. Kennedy (2023). [Heterogeneous
   interventional effects with multiple mediators: Semiparametric and
   nonparametric approaches](https://doi.org/10.1515/jci-2022-0070). *Journal of