FUNCZ-352 Translate synapse properties in input to internal naming

Otherwise, columns like `gsyn` will be produced again, and be renamed to
`conductance` when writing to disk. If a `conductance` was already
present in the input, this will result in a crash.

src/spykfunc/io/circuit.py

@@ -17,6 +17,7 @@
 from spykfunc import schema
 from spykfunc.utils import get_logger
 from spykfunc.utils.filesystem import adjust_for_spark
+from spykfunc.schema import OUTPUT_MAPPING
 
 
 BASIC_EDGE_SCHEMA = ["source_node_id long", "target_node_id long", "synapse_id long"]
@@ -541,7 +542,13 @@ def _loader():
             edges = parts.repartition(total_parts).mapInPandas(
                 _create_touch_loader(filename, population), columns
             )
-            return shift_branch_type(edges, -BRANCH_OFFSET).cache()
+            edges = shift_branch_type(edges, -BRANCH_OFFSET)
+
+            for new, (old, _) in OUTPUT_MAPPING.items():
+                if old in edges.columns:
+                    edges = edges.withColumnRenamed(old, new)
+
+            return edges.cache()
 
         return _loader
 

src/spykfunc/schema.py

@@ -78,7 +78,7 @@
 }
 
 
-# Maps from the internal naming scheme to SONATA one. The third component
+# Maps from the internal naming scheme to SONATA one. The second component
 # of the tuple specifies the datatype to convert to. If None, no conversion
 # is performed.
 OUTPUT_MAPPING = {

tests/test_data_input_sonata.py

@@ -61,7 +61,7 @@ def test_sonata_properties(tmp_path_factory):
     )
     fz.process_filters()
 
-    assert "delay" in fz.circuit.df.columns
+    assert "axonal_delay" in fz.circuit.df.columns
     assert "gsyn" in fz.circuit.df.columns
     assert "u" in fz.circuit.df.columns
     assert "d" in fz.circuit.df.columns