Merge pull request #29 from ber-data/28-omit-none-valued-fields-from-json-objects-dumped-by-ingester-nmdc

Refine behavior of NMDC ingest script

Author: eecavanna

contrib/nmdc/.gitignore

@@ -4,3 +4,7 @@
 # Ignore tool cache directories.
 /.mypy_cache
 /.ruff_cache
+
+# Ignore `cache.json` file (commonly-used filename for caching
+# the fetched NMDC data between runs of the script).
+/cache.json

contrib/nmdc/README.md

@@ -10,7 +10,7 @@ graph LR
 ## Usage
 
 ```sh
-python ingest.py --help
+uv run python ingest.py --help
 ```
 
 <!-- 

contrib/nmdc/ingest.py

@@ -264,7 +264,7 @@ def _append_property(slot_definition: SlotDefinition, slot_value: Any) -> None:
             self.class_name
         ):
             slot_value = getattr(self, slot_definition.name, None)
-            if not slot_value:
+            if slot_value in (None, [], {}):
                 continue
             _append_property(slot_definition, slot_value)
 
@@ -334,7 +334,7 @@ class Token(str, Enum):
                     buffer.write(Token.OPEN.value)
 
                 # Write this entity to the buffer.
-                buffer.write(entity.model_dump_json(indent=2))
+                buffer.write(entity.model_dump_json(exclude_none=True, indent=2))
                 num_entities_in_buffer += 1
 
                 # If either (a) this was the final entity in our list or (b) the buffer size is