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I have a shapefile with areas (eg. a simple world map with countries - polygons, epsg:4326). I also have a point (lat, lon coordinates).

What's the simplest/easiest way to figure out in which polygon (country) that point is? Polygons are not overlapping.

I have to do this server-side for many points, so i'm thinking about using mapnik, or any other library for that. (Linux server, opensource/free software only).

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I think you are looking for a "Spatial Join": assigning attributes of the polygon to any point that is overlapping it. (Ex: Chicago city point overlaps Illinois polygon, therefore Illinois attribute is assigned to Chicago point)

ArcGIS has a simple tool to for this. For open-source I would consider this QGIS tutorial: http://www.qgistutorials.com/en/docs/performing_spatial_joins.html

I have used the open-source Geospatial Modeling Environment (GME) to do "Count Points in Polygon" - I can't remember if that tool can also assign the polygon attribute to the point: http://www.spatialecology.com/gme/countpntsinpolys.htm

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