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Merge pull request #982 from cmu-delphi/release/delphi-epidata-0.4.0
Release Delphi Epidata 0.4.0
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‎.bumpversion.cfg

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[bumpversion]
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current_version = 0.3.21
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current_version = 0.4.0
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commit = False
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tag = False
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‎.github/workflows/ci.yaml

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- name: Start services
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run: |
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docker network create --driver bridge delphi-net
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docker run --rm -d -p 13306:3306 --network delphi-net --name delphi_database_epidata delphi_database_epidata
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docker run --rm -d -p 13306:3306 --network delphi-net --name delphi_database_epidata --cap-add=sys_nice delphi_database_epidata
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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
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docker ps
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needs: build
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# only on main and dev branch
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if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/dev'
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runs-on: ubuntu-latest
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steps:
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- name: Check out code

‎.gitignore

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__pycache__/
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*.pyc
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*~
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\#*#
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.DS_Store
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/.vscode
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/delphi-epidata

‎dev/docker/database/epidata/Dockerfile

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# start with the `delphi_database` image
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FROM delphi_database
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# start with a standard percona mysql image
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FROM percona:ps-8
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# percona exits with the mysql user but we need root for additional setup
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USER root
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# use delphi's timezome
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RUN ln -s -f /usr/share/zoneinfo/America/New_York /etc/localtime
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# specify a development-only password for the database user "root"
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ENV MYSQL_ROOT_PASSWORD pass
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# create the `epidata` database
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ENV MYSQL_DATABASE epidata
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ENV MYSQL_USER user
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ENV MYSQL_PASSWORD pass
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# provide DDL which will configure dev environment at container startup
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COPY repos/delphi/delphi-epidata/dev/docker/database/epidata/_init.sql /docker-entrypoint-initdb.d/
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# provide DDL which will create empty tables at container startup
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COPY repos/delphi/delphi-epidata/src/ddl/*.sql /docker-entrypoint-initdb.d/
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# provide additional configuration needed for percona
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COPY repos/delphi/delphi-epidata/dev/docker/database/mysql.d/*.cnf /etc/my.cnf.d/
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# grant access to SQL scripts
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RUN chmod o+r /docker-entrypoint-initdb.d/*.sql
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# restore mysql user for percona
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USER mysql

‎dev/docker/database/epidata/_init.sql

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CREATE DATABASE covid;
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GRANT ALL ON covid.* TO 'user';

‎dev/docker/database/mysql.d/my.cnf

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[mysqld]
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default_authentication_plugin=mysql_native_password

‎dev/local/Makefile

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# Creates all prereq images (delphi_database, delphi_python) only if they don't
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# exist. If you need to rebuild a prereq, you're probably doing something
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# complicated, and can figure out the rebuild command on your own.
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#
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#
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#
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#
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# Commands:
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#
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#
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# web: Stops currently-running delphi_web_epidata instances, if any.
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# Rebuilds delphi_web_epidata image.
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# Runs image in the background and pipes stdout to a log file.
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#
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#
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# db: Stops currently-running delphi_database_epidata instances, if any.
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# Rebuilds delphi_database_epidata image.
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# Runs image in the background and pipes stdout to a log file.
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# Blocks until database is ready to receive connections.
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#
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#
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# python: Rebuilds delphi_web_python image. You shouldn't need to do this
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# often; only if you are installing a new environment, or have
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# made changes to delphi-epidata/dev/docker/python/Dockerfile.
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#
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# clean: Cleans up dangling Docker images.
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#
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#
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#
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# Optional arguments:
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# pdb=1 Drops you into debug mode upon test failure, if running tests.
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# test= Only runs tests in the directories provided here, e.g.
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docker stop $(DATABASE_CONTAINER_ID);\
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fi
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@# Setup virtual network if it doesn't exist
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@docker network ls | grep delphi-net || docker network create --driver bridge delphi-net
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@# Only build prereqs if we need them
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@docker images delphi_database | grep delphi || \
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docker build -t delphi_database -f repos/delphi/operations/dev/docker/database/Dockerfile .
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@# Run the database
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@docker run --rm -p 127.0.0.1:13306:3306 \
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--network delphi-net --name delphi_database_epidata \
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--cap-add=sys_nice \
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delphi_database_epidata >$(LOG_DB) 2>&1 &
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@# Block until DB is ready
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@while true; do \
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sed -n '/Temporary server stopped/,/mysqld: ready for connections/p' $(LOG_DB) | grep "ready for connections" && break; \
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sed -n '/mysqld: ready for connections/p' $(LOG_DB) | grep "ready for connections" && break; \
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tail -1 $(LOG_DB); \
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sleep 1; \
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done
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-f repos/delphi/delphi-epidata/dev/docker/python/Dockerfile .
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.PHONY=all
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all: web db py
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all: db web py
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.PHONY=test
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test:
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test:
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@docker run -i --rm --network delphi-net \
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--mount type=bind,source=$(CWD)repos/delphi/delphi-epidata,target=/usr/src/app/repos/delphi/delphi-epidata,readonly \
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--mount type=bind,source=$(CWD)repos/delphi/delphi-epidata/src,target=/usr/src/app/delphi/epidata,readonly \

‎devops/Dockerfile

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COPY . /src
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RUN npm ci && npm run build
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FROM tiangolo/meinheld-gunicorn:python3.7
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FROM tiangolo/meinheld-gunicorn:python3.8
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LABEL org.opencontainers.image.source=https://github.com/cmu-delphi/delphi-epidata
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# use delphi's timezome
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RUN ln -s -f /usr/share/zoneinfo/America/New_York /etc/localtime
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COPY requirements.txt /app
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RUN pip install --no-cache-dir -r requirements.txt
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COPY requirements.txt /app/requirements_also.txt
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RUN pip install --no-cache-dir -r /tmp/requirements.txt -r requirements_also.txt
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# the file /tmp/requirements.txt is created in the parent docker definition. (see:
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# https://github.com/tiangolo/meinheld-gunicorn-docker/blob/master/docker-images/python3.8.dockerfile#L5 )
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# this combined requirements installation ensures all version constrants are accounted for.
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# disable python stdout buffering
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ENV PYTHONUNBUFFERED 1

‎docs/api/README.md

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---
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title: Epidata API (Other Diseases)
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nav_order: 3
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title: Other Endpoints (COVID-19 and Other Diseases)
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nav_order: 2
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has_children: true
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---
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‎docs/api/afhsb.md

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---
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title: AFHSB
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parent: Epidata API (Other Diseases)
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parent: Other Endpoints (COVID-19 and Other Diseases)
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---
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# AFHSB
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## Response
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| Field | Description | Type |
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| --- | --- | --- |
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| `result` | result code: 1 = success, 2 = too many results, -2 = no results | integer |
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| `epidata` | list of results | array of objects |
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| ... | ... | ... | <!-- TODO -->
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| `message` | `success` or error message | string |
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| Field | Description | Type |
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|-----------|-----------------------------------------------------------------|------------------|
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| `result` | result code: 1 = success, 2 = too many results, -2 = no results | integer |
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| `epidata` | list of results | array of objects |
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| ... | ... | ... | <!-- TODO -->
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| `message` | `success` or error message | string |
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# Example URLs
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‎docs/api/cdc.md

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---
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title: CDC
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parent: Epidata API (Other Diseases)
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parent: Other Endpoints (COVID-19 and Other Diseases)
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---
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# CDC
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## Response
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| Field | Description | Type |
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| --- | --- | --- |
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| `result` | result code: 1 = success, 2 = too many results, -2 = no results | integer |
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| `epidata` | list of results | array of objects |
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| ... | ... | ... | <!-- TODO -->
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| `message` | `success` or error message | string |
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| Field | Description | Type |
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|-----------|-----------------------------------------------------------------|------------------|
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| `result` | result code: 1 = success, 2 = too many results, -2 = no results | integer |
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| `epidata` | list of results | array of objects |
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| ... | ... | ... | <!-- TODO -->
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| `message` | `success` or error message | string |
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# Example URLs
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‎docs/api/client_libraries.md

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---
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title: Epidata API Client Libraries
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parent: Epidata API (Other Diseases)
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parent: Other Endpoints (COVID-19 and Other Diseases)
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nav_order: 1
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---
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‎docs/api/covid_hosp.md

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---
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title: COVID-19 Reported Patient Impact and Hospital Capacity by State Timeseries
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parent: Epidata API (Other Diseases)
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parent: Other Endpoints (COVID-19 and Other Diseases)
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---
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# COVID-19 Hospitalization by State
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### Required
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| Parameter | Description | Type |
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| --- | --- | --- |
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| `states` | two-letter state abbreviations | `list` of states |
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| `dates` | dates | `list` of dates or date ranges |
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| Parameter | Description | Type |
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|-----------|--------------------------------|--------------------------------|
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| `states` | two-letter state abbreviations | `list` of states |
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| `dates` | dates | `list` of dates or date ranges |
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### Optional
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| Parameter | Description | Type |
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| --- | --- | --- |
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| `issues` | issues | `list` of "issue" dates or date ranges |
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| Parameter | Description | Type |
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|-----------|-------------|----------------------------------------|
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| `issues` | issues | `list` of "issue" dates or date ranges |
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If `issues` is not specified, then the most recent issue is used by default.
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‎docs/api/covid_hosp_facility.md

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title: COVID-19 Reported Patient Impact and Hospital Capacity by Facility
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parent: Epidata API (Other Diseases)
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parent: Other Endpoints (COVID-19 and Other Diseases)
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# COVID-19 Hospitalization by Facility
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### Required
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| Parameter | Description | Type |
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| --- | --- | --- |
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| `hospital_pks` | facility unique identifiers | `list` of identifiers |
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| `collection_weeks` | dates | `list` of dates or date ranges |
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| Parameter | Description | Type |
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|--------------------|-----------------------------|--------------------------------|
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| `hospital_pks` | facility unique identifiers | `list` of identifiers |
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| `collection_weeks` | dates | `list` of dates or date ranges |
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NOTE: The companion
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[`covid_hosp_facility_lookup` endpoint](covid_hosp_facility_lookup.md) can be
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### Optional
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| Parameter | Description | Type |
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| --- | --- | --- |
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| Parameter | Description | Type |
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|---------------------|---------------------|----------------------------------------|
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| `publication_dates` | date of publication | `list` of "issue" dates or date ranges |
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If `publication_dates` is not specified, then the most recent issue is used by

‎docs/api/covid_hosp_facility_lookup.md

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title: COVID-19 Reported Patient Impact and Hospital Capacity - Facility lookup
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parent: Epidata API (Other Diseases)
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parent: Other Endpoints (COVID-19 and Other Diseases)
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---
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# COVID-19 Hospitalization: Facility Lookup
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## Parameters
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| Parameter | Description | Type |
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| --- | --- | --- |
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| `state` | two-letter state abbreviation | string |
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| `ccn` | facility CMS Certification Number | string |
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| `city` | city name | string |
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| `zip` | 5-digit ZIP code | string |
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| `fips_code` | 5-digit FIPS county code | string |
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| Parameter | Description | Type |
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|-------------|-----------------------------------|--------|
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| `state` | two-letter state abbreviation | string |
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| `ccn` | facility CMS Certification Number | string |
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| `city` | city name | string |
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| `zip` | 5-digit ZIP code | string |
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| `fips_code` | 5-digit FIPS county code | string |
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NOTE: Exactly one of the above parameters must be present in requests.
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Combinations of parameters (e.g. specifying both `city` and `state`) are not

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

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---
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title: SOURCE NAME
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parent: Data Sources and Signals
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grand_parent: COVIDcast Epidata API
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grand_parent: COVIDcast Main Endpoint
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---
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# SOURCE NAME
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A brief description of what this source measures.
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| Signal | Description |
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| --- | --- |
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| Signal | Description |
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|---------------|----------------------------------------------------------------------------------------------------------|
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| `signal_name` | Brief description of the signal, including the units it is measured in and any smoothing that is applied |
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## Table of contents

‎docs/api/covidcast-signals/chng.md

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title: Change Healthcare
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parent: Data Sources and Signals
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grand_parent: COVIDcast Epidata API
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grand_parent: COVIDcast Main Endpoint
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---
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# Change Healthcare

‎docs/api/covidcast-signals/covid-act-now.md

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title: COVID Act Now
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parent: Data Sources and Signals
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grand_parent: COVIDcast Epidata API
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grand_parent: COVIDcast Main Endpoint
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---
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# COVID Act Now (CAN)
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[CDC's COVID-19 Integrated County View](https://covid.cdc.gov/covid-data-tracker/#county-view).
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| Signal | Description |
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| --- | --- |
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| Signal | Description |
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|--------------------------------|----------------------------------------------------------------|
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| `pcr_specimen_positivity_rate` | Proportion of PCR specimens tested that have a positive result |
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| `pcr_specimen_total_tests` | Total number of PCR specimens tested |
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| `pcr_specimen_total_tests` | Total number of PCR specimens tested |
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## Table of contents
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{: .no_toc .text-delta}

‎docs/api/covidcast-signals/doctor-visits.md

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title: Doctor Visits
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parent: Data Sources and Signals
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grand_parent: COVIDcast Epidata API
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grand_parent: COVIDcast Main Endpoint
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---
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# Doctor Visits

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