Exercise 1 - Your first dataset¶

In this section you are going to publish a vector dataset.

For this exercise, we will use a CSV dataset of Bathing waters in Estonia, kindly provided by Estonian Health Board.

You can find this dataset in workshop/exercises/data/tartu/bathingwater-estonia.csv.

This exercise consists of adjusting workshop/exercises/pygeoapi.config.yml to define this dataset as an OGC API - Features collection

Verify the existing Docker Compose config¶

Before making any changes, we will make sure that the initial Docker Compose setup provided to you is actually working.

To test:

Test the workshop configuration

In a terminal shell navigate to the workshop folder and type:

Linux/MacWindows (PowerShell)

cd workshop/exercises
docker compose up

cd workshop/exercises
docker compose up

Open http://localhost:5000 in your browser, verify some collections
Close by typing CTRL-C

Note

You may also run the Docker container in the background (detached) as follows:

Linux/MacWindows (PowerShell)

docker compose up -d
docker ps  # verify that the pygeoapi container is running
# visit http://localhost:5000 in your browser, verify some collections
docker logs --follow pygeoapi  # view logs
docker compose down --remove-orphans

docker compose up -d
docker ps  # verify that the pygeoapi container is running
# visit http://localhost:5000 in your browser, verify some collections
docker logs --follow pygeoapi  # view logs
docker compose down --remove-orphans

Publish first dataset¶

You are now ready to publish your first dataset.

Setting up the pygeoapi config file

Open the file workshop/exercises/pygeoapi/pygeoapi.config.yml in your text editor
Look for the commented config section starting with # START - EXERCISE 1 - Your First Collection
Uncomment all lines until # END - EXERCISE 1 - Your First Collection

Make sure that the indentation aligns (hint: directly under # START ...)

The config section reads:

    Bathing_Water_Estonia:
        type: collection
        title: Bathing Water Estonia
        description: Locations where the Estonian Health Board monitors the bathing water quality
        keywords:
            - bathing water
            - estonia
        links:
            - type: text/csv
              rel: canonical
              title: data
              href: https://avaandmed.eesti.ee/datasets/supluskohad
              hreflang: EE
        extents:
            spatial:
                bbox: [20,57,29,60]
                crs: http://www.opengis.net/def/crs/EPSG/0/4326
        providers:
            - type: feature
              name: CSV
              data: /data/tartu/bathingwater-estonia.csv
              id_field: id
              title_field: Name
              geometry:
                x_field: x
                y_field: y
              storage_crs: http://www.opengis.net/def/crs/EPSG/0/3300

The most relevant part is the providers section. Here, we define a CSV Provider, pointing the file path to the /data directory we will mount (see next) from the local directory into the Docker container above. Because a CSV is not a spatial file, we explicitly configure pygeoapi so that the longitude and latitude (x and y) is mapped from the columns lon and lat in the CSV file. Notice the storage_crs parameter, which indicates the coordinate system which is used in the source data.

Tip

To learn more about the pygeoapi configuration syntax and conventions see the relevant section in the documentation.

Tip

pygeoapi includes numerous data providers which enable access to a variety of data formats. Via the OGR/GDAL plugin the number of supported formats is almost limitless. Consult the data provider page how you can set up a connection to your dataset of choice. You can always copy a relevant example configuration and place it in the datasets section of the pygeoapi configuration file for your future project.

Test¶

Start with updated configuration

Start by typing docker compose up
Observe logging output
If no errors: open http://localhost:5000
Look for the Point of interest collection
Browse through the items of the collection
Check the json representation by adding ?f=json to url (or click 'json' in top right)

Debugging configuration errors¶

Incidentally you may run into errors, briefly discussed here:

A file cannot be found, a typo in the configuration
The format or structure of the spatial file is not fully supported
The port (5000) is already taken. Is a previous pygeoapi still running? If you change the port, consider that you also have to update the pygeoapi config file

There are two parameters in the configuration file which help to address these issues. Set the logging level to DEBUG and indicate a path to a log file.

Tip

On Docker, set the path of the logfile to the mounted folder, so you can easily access it from your host system. You can also view the console logs from your Docker container as follows:

Linux/MacWindows (PowerShell)

docker logs --follow pygeoapi

docker logs --follow pygeoapi

Tip

Errors related to file paths typically happen on initial setup. However, they may also happen at unexpected moments, resulting in a broken service. Products such as GeoHealthCheck aim to monitor, detect and notify service health and availability. The OGC API - Features tests in GeoHealthCheck poll the availability of the service at intervals. Consult the GeoHealthCheck documentation for more information.