Merge pull request #111 from loinc/logging-updates

Logging updates

comploinc_config.yaml

@@ -61,6 +61,10 @@ logging:
       level: INFO
       handlers: [ console ]
       propagate: False
+    'Module':
+      level: INFO
+      handlers: [ console ]
+      propagate: False
 #    cli_runtime:
 #      handlers: [console]
 #      level: INFO

src/comp_loinc/loinc_builder_steps.py

@@ -786,13 +786,12 @@ def save_to_owl(
         ] = None,
     ):
         """Save the current module to an OWL file."""
-        logger.info(f"Starting save-owl")
+        logger.info(f"save-owl: Starting")
         owl_dumper = OWLDumper()
         document = owl_dumper.to_ontology_document(
             schema=self.runtime.current_schema_view.schema,
             element=list(self.runtime.current_module.get_all_entities()),
         )
-        logger.info(f"save-owl document created.")
         document.ontology.iri = funowl.identifiers.IRI(
             f"https://comploinc/{self.runtime.current_module.name}"
         )
@@ -808,6 +807,5 @@ def save_to_owl(
         owl_file_path.parent.mkdir(parents=True, exist_ok=True)
         typer.echo(f"Writing file: {owl_file_path}")
         with open(owl_file_path, "w") as f:
-            logger.info(f"save-owl writing document.")
             f.write(str(document))
-            logger.info(f"save-owl writing document finished.")
+        logger.info(f"save-owl: Done")

src/comp_loinc/module.py

@@ -1,9 +1,14 @@
+"""Module: Provided a given builder configuration, set up a module where that build will be encapsulated. """
+import logging
 import typing as t
 
 import comp_loinc.datamodel.comp_loinc as v2
 from comp_loinc.datamodel.comp_loinc import Entity
 
 
+logger = logging.getLogger("Module")
+
+
 # class Modules:
 #   def __init__(self, *,
 #       graph: nx.MultiDiGraph = nx.MultiDiGraph(),
@@ -20,41 +25,44 @@
 
 
 class Module:
+    """Module"""
     from comp_loinc import Runtime
 
     def __init__(self, *, name: str, runtime: Runtime):
         from comp_loinc import Runtime
-
+        logger.info(f"Starting: {name}")
         self.name = name
         self.runtime: Runtime = runtime
-
         self.entities_by_type: t.Dict[t.Type[Entity], t.Dict[str, v2.Entity]] = dict()
-
-        # flags for what to include
-        self._include_loinc_long_common_name = None
+        self._include_loinc_long_common_name = None  # flags for what to include
 
     def get_entity(
         self, entity_id: str, entity_class: t.Type[Entity]
     ) -> t.Optional[Entity]:
+        """Get entity"""
         return self.entities_by_type.setdefault(entity_class, {}).get(entity_id, None)
 
     def getsert_entity(self, entity_id: str, entity_class: t.Type[Entity]) -> Entity:
+        """Get entity, or insert if it doesn't exist"""
         entity = self.entities_by_type.setdefault(entity_class, {}).get(entity_id, None)
         if entity is None:
             entity = entity_class(id=entity_id)
             self.add_entity(entity)
         return entity
 
     def add_entity(self, entity: Entity, replace: bool = False):
+        """Add entity"""
         if self.get_entity(entity.id, type(entity)) is not None and not replace:
             raise ValueError(f"Replacing entity {entity} not allowed.")
         self.entities_by_type.setdefault(type(entity), {})[entity.id] = entity
 
     def get_entities_of_type(self, entity_class: t.Type[Entity]) -> t.Iterator[Entity]:
+        """Get entities of type"""
         for entity in self.entities_by_type.get(entity_class, {}).values():
             yield entity
 
     def get_all_entities(self) -> t.Iterator[Entity]:
+        """Get all entities"""
         for entity_map in self.entities_by_type.values():
             for entity in entity_map.values():
                 yield entity