How to connect SPECIFY with a Geodatabase

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1

We are in the process of installing and use Specify 7 to migrate all collections databases.

Part of the information is about location information from Eurostat and local geospatial data. These will be stored in a geodatabase, either ESRI-based of as GeoPackage.

The idea behind that is to allow the users, when they will manually enter the information of the sample, including the coordinates, automatically to run a spatial query to retrieve information on the NUTS levels and elevation.

Has anybody make such links and functions?

2

Hi @dpoursanidis!

I don’t believe that this functionality currently exists in Specify. I am not familiar with NUTS levels, however it was fun learning about them this morning!

It seems like you would want to send a coordinate pair to a service, and have it return the NUTS level(s) that those coordinates belong to, along with metadata about those NUTS levels? You could then save the NUTS level into one of the user definable fields within the locality table. Note that this would probably have to be done outside of Specify and integrated through the API, I don’t think that there is infrastructure in place to make and receive external API calls beyond the current Geolocate implementation (not to say that a plugin couldn’t be made down the line!).

I was able to find a commercial service called Opencage that provides an API to covert coordinates to NUTS levels, an example of a javascript implementation from their website. Something similar could be done in almost any programming language, it’s just making a call to an endpoint. Note that you need a key, it isn’t a free service.

<script>
  var api_key = 'YOUR-API-KEY';
  var coords = '52.5432379, 13.4142133';  // lat, lng

  var api_url = 'https://api.opencagedata.com/geocode/v1/json'

  var request_url = api_url
    + '?'
    + 'key=' + api_key
    + '&q=' + encodeURIComponent(coords)
    + '&pretty=1';

  // see full list of required and optional parameters:
  // https://opencagedata.com/api#forward

  var request = new XMLHttpRequest();
  request.open('GET', request_url, true);

  request.onload = function() {
      // see full list of possible response codes:
      // https://opencagedata.com/api#codes
      var data = JSON.parse(request.responseText);
      if (request.status === 200){  // Success!
          var nuts = 'no NUTS codes returned';
          if (data.results[0].annotations.NUTS != null){
              nuts = data.results[0].annotations.NUTS;
          }
          console.log('NUTS: ' + nuts);
      } else {
          console.log("unable to geocode! Response code: " + request.status);
          console.log('error msg: ' + data.status.message);
      }
  };

  request.onerror = function() {
      // There was a connection error of some sort
      console.log("unable to connect to server");
  };
  request.send();  // make the request
</script>

A cron job could be set up to run nightly that does the following:

  1. Query for all localities edited or created that day (GET /api/specify/locality with query parameters)
  2. Takes coordinate pairs and sends to NUTS api
  3. Take response and issue PUT request to user definable field(s) with NUTS information.

Alternatively, you could have the script reference something local (a map, reference etc of the boundaries) and then convert the coordinates that way, without having to pay.

It checks some of the boxes, but not all. Wouldn’t be real-time, is more technically complex, and probably wouldn’t do elevation. However, it would allow NUTS levels to be included in the database at whichever interval the script is set to run.