A public-health data microservice deployed to GKE Autopilot using FastAPI, Docker, and Kubernetes.

About the data:

• MIN_DATE_COLLECTED=2015-01-07
• MAX_DATE_COLLECTED=2018-08-28
• Fetched 11925 traps
• See Phase 4 DATA for a list of species

For professional Python, Git, and VS Code setup and workflow, see pro-analytics-01.

We need to install some additional tools to support containerization and Kubernetes deployments.

We recommend keeping key tools like PowerShell updated to lastest versions. For example:

winget search Microsoft.PowerShell
winget upgrade --id Microsoft.PowerShell --silent --accept-package-agreements --accept-source-agreements

Use Windows Subsystem for Linux. Update (if needed) and launch WSL.

wsl --update
wsl

lsb_release -a

1. Update package lists.
2. Install Python 3.11 and Development Tools.
3. Install helpful tools: curl, unzip
4. Install GitHub CLI (Command Line Interface)
5. Install Kubernetes
6. Uninstall all prior WSL Docker versions

sudo apt-get update -y
sudo apt-get install -y python3.11 python3.11-venv python3.11-dev build-essential
sudo apt-get install -y git curl unzip
sudo apt-get install -y gh
sudo apt-get install -y kubectl
for pkg in docker.io docker-doc docker-compose docker-compose-v2 podman-docker containerd runc; do sudo apt-get remove $pkg; done

Add Docker's official GPG key:

sudo apt-get update
sudo apt-get install ca-certificates curl
sudo install -m 0755 -d /etc/apt/keyrings
curl -fsSL https://packages.cloud.google.com/apt/doc/apt-key.gpg | sudo tee /usr/share/keyrings/cloud.google.gpg > /dev/null
sudo chmod a+r /usr/share/keyrings/cloud.google.gpg

Add the repository to Apt sources:

echo \
  "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/ubuntu \
  $(lsb_release -cs) stable" | sudo tee /etc/apt/sources.list.d/docker.list > /dev/null

Install Docker for WSL

sudo apt-get update
sudo apt-get install -y docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin

Add your user to the docker group so we don't need sudo every time:

sudo usermod -aG docker $USER

Exit and restart WSL

exit
wsl

Verify that the installation is successful and run the hello-world image.

docker version
docker info
docker run hello-world

1. Change directory into ~/Repos.
2. Git clone into ~/Repos folder.
3. Change directory into new repo folder.
4. Start VS Code in the repo folder.

cd ~/Repos
git clone https://github.com/denisecase/k8s-api-mosquito
cd k8s-api-mosquito
code .

Use VS Code menu Terminal / New Terminal to run the following commands. Click yes to use the new .venv after creating it.

1. Create a new virtual environment using Python 3.11.
2. Activate the new virtual environment.
3. Install and upgrade key packages.
4. Install packages from requirements.txt.
5. Run pip check.
6. Save installed versions to req-installed.txt.

python3.11 -m venv .venv
source .venv/bin/activate
python3 -m pip install --upgrade pip setuptools wheel
python3 -m pip install -r requirements.txt --timeout 300 --progress-bar on --no-cache-dir
python3 -m pip check
python3 -m pip list > req-installed.txt

git pull

git add .
git commit -m "did this"
git push -u origin main

This project is organized into development phases:

• Phase 1: Machine & Cloud Setup
• Phase 2: Project Initialization
• Phase 3: Vertical Slice Deployment

• CivicData
• San Diego Mosquito Traps Data

Cite: Routine Mosquito Surveillance Traps

URL: https://www.civicdata.com/api/3/action/datastore_search?resource_id=2c88678b-39b0-48a5-b071-d526d994fc42

This dataset provides information from approximately 130 active routine surveillance traps set on a weekly or bi-weekly basis for adult mosquitos across San Diego County for the years 2015-current. After collection, an ecologist counts and classifies the mosquitos. Mosquitos of the appropriate species are then tested in a laboratory for viruses that can be transmitted to people. This data is managed by the San Diego County Vector Control Program and is extracted from the land use and environment database, Accela. This dataset is intended for public access, use, and education. For a description of this data, see Routine Mosquito Surveillance Trap metadata. If additional information is needed please see our [Public Records Request webpage] (https://www.sandiegocounty.gov/content/sdc/deh/doing_business/records.html).

Note: San Diego County’s Vector Control Program strives to provide complete and accurate data, however, it does not guarantee, either expressed or implied, the accuracy, completeness, or timeliness of the information. The Department of Environmental Health will not be responsible for any error or omission, or for the use of, or the results obtained from the use of this information.

Metadata Created Data: July 2, 2018