Merge pull request #1119 from cmu-delphi/release/delphi-epidata-0.4.8

Release Delphi Epidata 0.4.8

Author: krivard

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.4.7
+current_version = 0.4.8
 commit = False
 tag = False
 

.github/workflows/ci.yaml

@@ -57,11 +57,13 @@ jobs:
           docker build -t delphi_web_epidata -f ./devops/Dockerfile .
           cd ../../../
 
+      # 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
       - name: Start services
         run: |
           docker network create --driver bridge delphi-net
           docker run --rm -d -p 13306:3306 --network delphi-net --name delphi_database_epidata --cap-add=sys_nice delphi_database_epidata
-          docker run --rm -d -p 10080:80 --env "SQLALCHEMY_DATABASE_URI=mysql+mysqldb://user:pass@delphi_database_epidata:3306/epidata" --env "FLASK_SECRET=abc" --env "FLASK_PREFIX=/epidata" --network delphi-net --name delphi_web_epidata delphi_web_epidata
+          docker run --rm -d -p 10080:80 --env "MODULE_NAME=delphi.epidata.server.main" --env "SQLALCHEMY_DATABASE_URI=mysql+mysqldb://user:pass@delphi_database_epidata:3306/epidata" --env "FLASK_SECRET=abc" --env "FLASK_PREFIX=/epidata" --network delphi-net --name delphi_web_epidata delphi_web_epidata
           docker ps
 
       - run: |

.github/workflows/performance-tests.yml

@@ -71,7 +71,7 @@ jobs:
         run: |
           cd delphi-admin/load-testing/locust
           docker build -t locust .
-          export CSV=v4-requests-small.csv
+          export CSV=v4-requests-as_of.csv
           touch output_stats.csv && chmod 666 output_stats.csv
           touch output_stats_history.csv && chmod 666 output_stats_history.csv
           touch output_failures.csv && chmod 666 output_failures.csv

deploy.json

@@ -17,6 +17,15 @@
       "add-header-comment": true
     },
 
+    "// common",
+    {
+      "type": "move",
+      "src": "src/common/",
+      "dst": "[[package]]/common/",
+      "match": "^.*\\.(py)$",
+      "add-header-comment": true
+    },
+
     "// server",
     {
       "type": "move",
@@ -47,15 +56,6 @@
       "add-header-comment": true
     },
 
-    "// acquisition - common",
-    {
-      "type": "move",
-      "src": "src/acquisition/common/",
-      "dst": "[[package]]/acquisition/common/",
-      "match": "^.*\\.(py)$",
-      "add-header-comment": true
-    },
-
     "// acquisition - fluview",
     {
       "type": "move",

dev/local/Makefile

@@ -91,8 +91,11 @@ web:
 		cd -
 
 	@# 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
 	@docker run --rm -p 127.0.0.1:10080:80 \
 		$(M1) \
+		--env "MODULE_NAME=delphi.epidata.server.main" \
 		--env "SQLALCHEMY_DATABASE_URI=$(sqlalchemy_uri)" \
 		--env "FLASK_SECRET=abc" --env "FLASK_PREFIX=/epidata" --env "LOG_DEBUG" \
 		--network delphi-net --name delphi_web_epidata \

dev/local/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = Delphi Development
-version = 0.4.7
+version = 0.4.8
 
 [options]
 packages =

devops/Dockerfile

@@ -8,14 +8,16 @@ LABEL org.opencontainers.image.source=https://github.com/cmu-delphi/delphi-epida
 
 COPY ./devops/gunicorn_conf.py /app
 COPY ./devops/start_wrapper.sh /
-COPY ./src/server/ /app/app/
-COPY --from=builder ./src/build/lib/ /app/app/lib/
+RUN mkdir -p /app/delphi/epidata
+COPY ./src/server /app/delphi/epidata/server
+COPY ./src/common /app/delphi/epidata/common
+COPY --from=builder ./src/build/lib/ /app/delphi/epidata/lib/
 
 COPY requirements.api.txt /app/requirements_also.txt
 
 RUN ln -s -f /usr/share/zoneinfo/America/New_York /etc/localtime \
-      && rm -rf /app/app/__pycache__ /app/app/*.php \
-      && chmod -R o+r /app/app \
+      && 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:

docs/Gemfile.lock

@@ -1,11 +1,12 @@
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (5.2.5)
+    activesupport (6.0.6.1)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 0.7, < 2)
       minitest (~> 5.1)
       tzinfo (~> 1.1)
+      zeitwerk (~> 2.2, >= 2.2.2)
     addressable (2.8.0)
       public_suffix (>= 2.0.2, < 5.0)
     coffee-script (2.4.1)
@@ -15,7 +16,7 @@ GEM
     colorator (1.1.0)
     commonmarker (0.17.13)
       ruby-enum (~> 0.5)
-    concurrent-ruby (1.1.8)
+    concurrent-ruby (1.2.0)
     dnsruby (1.61.5)
       simpleidn (~> 0.1)
     em-websocket (0.5.2)
@@ -209,7 +210,7 @@ GEM
       jekyll (>= 3.5, < 5.0)
       jekyll-feed (~> 0.9)
       jekyll-seo-tag (~> 2.1)
-    minitest (5.14.4)
+    minitest (5.17.0)
     multipart-post (2.1.1)
     nokogiri (1.13.10)
       mini_portile2 (~> 2.8.0)
@@ -255,6 +256,7 @@ GEM
     unf_ext (0.0.7.7)
     unicode-display_width (1.7.0)
     wdm (0.1.1)
+    zeitwerk (2.6.6)
 
 PLATFORMS
   ruby

docs/symptom-survey/publications.md

@@ -26,10 +26,14 @@ Pandemic"](https://www.pnas.org/topic/548) in *PNAS*:
 
 Research publications using the survey data include:
 
+- Taube JC, Susswein Z, Bansal S (2023). [Spatiotemporal Trends in Self-Reported
+  Mask-Wearing Behavior in the United States: Analysis of a Large
+  Cross-sectional Survey](https://doi.org/10.2196/42128). *JMIR Public Health
+  and Surveillance* 9:e42128.
 - Rebecca L. Weintraub et al (2023). [Identifying COVID-19 Vaccine Deserts and
   Ways to Reduce Them: A Digital Tool to Support Public Health
   Decision-Making](https://doi.org/10.2105/AJPH.2022.307198). *American Journal
-  of Public Health*.
+  of Public Health* 113 (4), 363-367.
 - Anzalone AJ, Sun J, Vinson AJ, Beasley WH, Hillegass WB, Murray K, et al.
   (2023). [Community risks for SARS-CoV-2 infection among fully vaccinated US
   adults by rurality: A retrospective cohort study from the National COVID
@@ -38,7 +42,7 @@ Research publications using the survey data include:
 - Rufino, J., Baquero, C., Frey, D. et al (2023). [Using survey data to estimate
   the impact of the omicron variant on vaccine efficacy against COVID-19
   infection](https://doi.org/10.1038/s41598-023-27951-3). *Scientific Reports*
-  13, 900 (2023).
+  13, 900.
 - Rader, B., Astley, C.M., Sewalk, K. et al (2022). [Spatial modeling of vaccine
   deserts as barriers to controlling
   SARS-CoV-2](https://doi.org/10.1038/s43856-022-00183-8). *Communications

integrations/acquisition/covidcast/delete_batch.csv

@@ -1,4 +1,4 @@
 geo_id,value,stderr,sample_size,issue,time_value,geo_type,signal,source
-d_nonlatest,0,0,0,1,0,county,sig,src
-d_latest,   0,0,0,3,0,county,sig,src
-d_justone,  0,0,0,1,0,county,sig,src
+d_nonlatest,0,0,0,1,0,msa,sig,src
+d_latest,   0,0,0,3,0,msa,sig,src
+d_justone,  0,0,0,1,0,msa,sig,src