In order to view data in the GIS module, you must import your geographical data into your DHIS installation. Once you have produced GeoJSON files according to the procedure above, and imported them into the system, you will need to establish a correspondence between the information in the DHIS database, and the GeoJSON file.

The level of the organization units displayed in the GeoJSON file.
The GeoJSON file name. These files must be placed in the mapping/geojson folder. Use e.g. Geoserver 2.0 (currently RC1) to easily produce GeoJSON from your shapefiles.
Represents your map in the Map combo box in the Thematic map panel.
The shapefile data column (case sensitive!) that will be matched against DHIS organisation unit names. If you have an instance of Geoserver installed, you can view the layer through the built-in OpenLayers client. Click on a particular area, and the possible fields will be displayed.
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The longitude and latitude refer to the approximate point where the map will be centered after rendering. If you have Geoserver running, you can view the layer through the integrated OpenLayers client and determine a good center point for your map. You can also use the background map of the DHIS GIS module, and determine an approximate location. You may need to experiment a bit with the center point and zoom level in order to get it correct.
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The zoom level controls the extent of the map. Some experimentation will be required to get the correct zoom level. Start with a value of "7" and increase or decrease the zoom level depending on the extent of the map that should be displayed.