I have PostGIS database with a table that was exported from a shapefile using 
shp2pgsql. I have verified that the SRID is correct by querying the 
geometry_columns table.

If I use this database table as a data source in Geoserver and create a layer 
from it everything works as expected and the correct SRS is set on the layer.

However, when I try to create an app-schema mapping using this table (I'm 
creating the mapping in Hale and exporting it using the direct upload method) 
the correct CRS is not picked up by Geoserver. Instead the Native SRS is emtpy 
and the Declared SRS is EPSG:404000. I also don't get any position elements if 
I preview the GML. I'm assuming this is because the SRS is incorrect, but I get 
the same problem even if I declare the correct SRS and use the "Force declared" 
option.

I think the problem is related to app-schema because if I import the data in 
Hale the correct SRS gets used and if I do a transformation in Hale the 
resulting GML contains position elements for each feature.

Does anyone know what the problem could be?

I'm running Geoserver 2.17.0 on RHEL 8 using Java 1.8.0_252.

Regards,
Karl Lindström
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