1. Merge branch 'dev' into leonlu2/error_on_geo_values.

Author: LeonLu2

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.4.5
+current_version = 0.4.6
 commit = False
 tag = False
 

.github/workflows/performance-tests.yml

@@ -0,0 +1,80 @@
+name: Performance testing
+
+# Run when a PR comment is created (issues and PRs are considered the same entity in the GitHub API)
+on:
+  issue_comment:
+    types: [created]
+
+# Add some extra perms to comment on a PR
+permissions:
+  pull-requests: write
+  contents: read
+
+jobs:
+  run-perftests:
+    # Make sure 1. this is a PR, not an issue 2. it contains "/run performance test" anywhere in the body
+    if: github.event.issue.pull_request && contains(github.event.comment.body, '/run performance test')
+    runs-on: ubuntu-latest
+    steps:
+      - name: Set up WireGuard
+        uses: egor-tensin/[email protected]
+        with:
+          endpoint: '${{ secrets.WG_PERF_ENDPOINT }}'
+          endpoint_public_key: '${{ secrets.WG_PERF_ENDPOINT_PUBLIC_KEY }}'
+          ips: '${{ secrets.WG_PERF_IPS }}'
+          allowed_ips: '${{ secrets.WG_PERF_ALLOWED_IPS }}'
+          private_key: '${{ secrets.WG_PERF_PRIVATE_KEY }}'
+      - name: Check out repository
+        uses: actions/checkout@v3
+      # Previous step checks out default branch, so we check out the pull request's branch
+      - name: Switch to PR branch
+        run: |
+          hub pr checkout ${{ github.event.issue.number }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: Set up repository # mimics install.sh in the README except that delphi is cloned from the PR rather than main
+        run: |
+          cd ..
+          mkdir -p driver/repos/delphi
+          cd driver/repos/delphi
+          git clone https://github.com/cmu-delphi/operations
+          git clone https://github.com/cmu-delphi/utils
+          git clone https://github.com/cmu-delphi/flu-contest
+          git clone https://github.com/cmu-delphi/nowcast
+          cd ../../
+
+          cd ..
+          cp -R delphi-epidata driver/repos/delphi/delphi-epidata
+          cd -
+
+          ln -s repos/delphi/delphi-epidata/dev/local/Makefile
+      - name: Build & run epidata
+        run: |
+          cd ../driver
+          sudo make web sql="${{ secrets.DB_CONN_STRING }}"
+      - name: Build & run Locust
+        run: |
+          cd ../driver/repos/delphi/delphi-epidata/tests/performance
+          docker build -t locust .
+          docker run --net=host -v $PWD:/mnt/locust -e CSV=/mnt/locust/v4-requests-smaller.csv locust -f /mnt/locust/v4.py --host http://127.0.0.1:10080/ --users 10 --spawn-rate 1 --headless -t 15m
+
+  comment-output:
+    runs-on: ubuntu-latest
+    if: success() || failure() # but not if skipped
+    needs: run-perftests
+    steps:
+      - name: Comment run results
+        # URL that links to run results
+        env:
+          GITHUB_WORKFLOW_URL: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}
+        uses: actions/github-script@v5
+        with:
+          github-token: ${{secrets.GITHUB_TOKEN}}
+          script: |
+            github.rest.issues.createComment({
+              issue_number: context.issue.number,
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              body: '✅ Performance tests complete! Click here to view results: ${{ env.GITHUB_WORKFLOW_URL }}'
+            })
+  

dev/local/Makefile

@@ -36,6 +36,7 @@
 #   pdb=1         Drops you into debug mode upon test failure, if running tests.
 #   test=         Only runs tests in the directories provided here, e.g.
 #                 repos/delphi/delphi-epidata/tests/acquisition/covidcast
+#   sql=          Overrides the default SQL connection string.
 
 
 # Set optional argument defaults
@@ -49,6 +50,12 @@ ifndef test
 	test=repos/delphi/delphi-epidata/tests repos/delphi/delphi-epidata/integrations
 endif
 
+ifdef sql
+	sqlalchemy_uri:=$(sql)
+else
+	sqlalchemy_uri:=mysql+mysqldb://user:pass@delphi_database_epidata:3306/epidata
+endif
+
 SHELL:=/bin/sh
 
 # Get the Makefile's absolute path: https://stackoverflow.com/a/324782/4784655
@@ -60,6 +67,11 @@ LOG_DB:=delphi_database_epidata_$(NOW).log
 WEB_CONTAINER_ID:=$(shell docker ps -q --filter 'name=delphi_web_epidata')
 DATABASE_CONTAINER_ID:=$(shell docker ps -q --filter 'name=delphi_database_epidata')
 
+M1=
+ifeq ($(shell uname -smp), Darwin arm64 arm)
+$(info M1 system detected, changing docker platform to linux/amd64.)
+	override M1 =--platform linux/amd64
+endif
 
 .PHONY=web
 web:
@@ -73,12 +85,15 @@ web:
 
 	@# Build the web_epidata image
 	@cd repos/delphi/delphi-epidata;\
-		docker build -t delphi_web_epidata -f ./devops/Dockerfile .;\
+		docker build -t delphi_web_epidata\
+			$(M1) \
+			-f ./devops/Dockerfile .;\
 		cd -
 
 	@# Run the web server
 	@docker run --rm -p 127.0.0.1:10080:80 \
-		--env "SQLALCHEMY_DATABASE_URI=mysql+mysqldb://user:pass@delphi_database_epidata:3306/epidata" \
+		$(M1) \
+		--env "SQLALCHEMY_DATABASE_URI=$(sqlalchemy_uri)" \
 		--env "FLASK_SECRET=abc" --env "FLASK_PREFIX=/epidata" --env "LOG_DEBUG" \
 		--network delphi-net --name delphi_web_epidata \
 		delphi_web_epidata >$(LOG_WEB) 2>&1 &
@@ -95,10 +110,12 @@ db:
 
 	@# Build the database_epidata image
 	@docker build -t delphi_database_epidata \
+		$(M1) \
 		-f repos/delphi/delphi-epidata/dev/docker/database/epidata/Dockerfile .
 
 	@# Run the database
 	@docker run --rm -p 127.0.0.1:13306:3306 \
+		$(M1) \
 		--network delphi-net --name delphi_database_epidata \
                 --cap-add=sys_nice \
 		delphi_database_epidata >$(LOG_DB) 2>&1 &
@@ -113,6 +130,7 @@ db:
 .PHONY=py
 py:
 	@docker build -t delphi_web_python \
+		$(M1) \
 		-f repos/delphi/delphi-epidata/dev/docker/python/Dockerfile .
 
 .PHONY=all
@@ -121,18 +139,20 @@ all: db web py
 .PHONY=test
 test:
 	@docker run -i --rm --network delphi-net \
+		$(M1) \
 		--mount type=bind,source=$(CWD)repos/delphi/delphi-epidata,target=/usr/src/app/repos/delphi/delphi-epidata,readonly \
 		--mount type=bind,source=$(CWD)repos/delphi/delphi-epidata/src,target=/usr/src/app/delphi/epidata,readonly \
-		--env "SQLALCHEMY_DATABASE_URI=mysql+mysqldb://user:pass@delphi_database_epidata:3306/epidata" \
+		--env "SQLALCHEMY_DATABASE_URI=$(sqlalchemy_uri)" \
 		--env "FLASK_SECRET=abc" \
 		delphi_web_python python -m pytest --import-mode importlib $(pdb) $(test) | tee test_output_$(NOW).log
 
 .PHONY=bash
 bash:
 	@docker run -it --rm --network delphi-net \
+		$(M1) \
 		--mount type=bind,source=$(CWD)repos/delphi/delphi-epidata,target=/usr/src/app/repos/delphi/delphi-epidata,readonly \
 		--mount type=bind,source=$(CWD)repos/delphi/delphi-epidata/src,target=/usr/src/app/delphi/epidata,readonly \
-		--env "SQLALCHEMY_DATABASE_URI=mysql+mysqldb://user:pass@delphi_database_epidata:3306/epidata" \
+		--env "SQLALCHEMY_DATABASE_URI=$(sqlalchemy_uri)" \
 		--env "FLASK_SECRET=abc" \
 		delphi_web_python bash
 

dev/local/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = Delphi Development
-version = 0.4.5
+version = 0.4.6
 
 [options]
 packages =

docs/api/covidcast-signals/_source-template.md

@@ -62,6 +62,16 @@ geographic coverage, limits in its interpretation (symptoms in a survey aren't
 always caused by COVID, our healthcare partner only is part of the market, there
 may be a demographic bias in respondents, etc.), known inaccuracies, etc.
 
+## Missingness
+
+Describe *all* situations under which a value may not be reported, and what that
+means. If the signal ever reports NA, describe what that means and how it is
+different from missingness. For example:
+
+When fewer than 100 survey responses are received in a geographic area on a
+specific day, no data is reported for that area on that day; an API query for
+all reported geographic areas on that day will not include it.
+
 ## Lag and Backfill
 
 If this signal is reported with a consistent lag, describe it here.

docs/symptom-survey/end-of-survey.md

@@ -1,7 +1,7 @@
 ---
 title: End of CTIS Data Collection
 parent: COVID-19 Trends and Impact Survey
-nav_order: 10
+nav_order: 11
 ---
 
 # End of CTIS Data Collection

docs/symptom-survey/index.md

@@ -16,12 +16,6 @@ international version is [conducted by the University of
 Maryland](https://covidmap.umd.edu/). Data collection [ceased on June 25,
 2022](end-of-survey.md).
 
-The [survey results dashboard](https://delphi.cmu.edu/covidcast/survey-results/)
-provides a high-level summary of survey results. Geographically aggregated data
-from this survey is publicly available through the [COVIDcast API](../api/covidcast.md)
-as the [`fb-survey` data source](../api/covidcast-signals/fb-survey.md). Demographic breakdowns of survey
-data are publicly available as [downloadable contingency tables](contingency-tables.md).
-
 The [CTIS Methodology
 Report](https://dataforgood.facebook.com/dfg/resources/CTIS-methodology-report)
 describes the survey design, data collection process, weighting, and aggregation
@@ -34,6 +28,16 @@ access to the data, see our page on getting [data access](data-access.md).
 If you have questions about the survey or getting access to data, contact us at
 <[email protected]>.
 
+## Results
+
+The [survey results dashboard](https://delphi.cmu.edu/covidcast/survey-results/)
+provides a high-level summary of survey results. Geographically aggregated data
+from this survey is publicly available through the [COVIDcast API](../api/covidcast.md)
+as the [`fb-survey` data source](../api/covidcast-signals/fb-survey.md). Demographic breakdowns of survey
+data are publicly available as [downloadable contingency tables](contingency-tables.md).
+
+CTIS data has been used in [numerous peer-reviewed publications](publications.md).
+
 ## Credits
 
 The US COVID-19 Trends and Impact Survey (CTIS) is a project of the [Delphi