Fast run updates

- Add: --fast-run logic to more methods.
- Add: config.py: Initialized with constants to use for controlling --fast-run.

src/comp_loinc/config.py

@@ -0,0 +1,4 @@
+"""Additional internal configuration"""
+FAST_RUN_N_TERMS = 5000
+FAST_RUN_N_PARTS = 100
+

src/comp_loinc/loinc_builder_steps.py

@@ -10,6 +10,7 @@
 from linkml_runtime.linkml_model import ClassDefinition, SlotDefinition, Annotation
 
 from comp_loinc import Runtime
+from comp_loinc.config import FAST_RUN_N_PARTS, FAST_RUN_N_TERMS
 from comp_loinc.datamodel import (
     LoincPart,
     LoincPartId,
@@ -121,7 +122,7 @@ def loinc_terms_all(
         count = 0
         for node in self.runtime.graph.get_nodes(LoincNodeType.LoincTerm):
             count += 1
-            if self.configuration.fast_run and count > 5000:
+            if self.configuration.fast_run and count > FAST_RUN_N_TERMS:
                 break
             if count % 1000 == 0:
                 logger.info(f"Finished {count}")
@@ -161,8 +162,8 @@ def loinc_parts_all(
 
         count = 0
         for node in self.runtime.graph.get_nodes(LoincNodeType.LoincPart):
-            count = count + 1
-            if self.configuration.fast_run and count > 100:
+            count += 1
+            if self.configuration.fast_run and count > FAST_RUN_N_PARTS:
                 break
             status = node.get_property(LoincPartProps.status)
             if active_only and status != "ACTIVE":
@@ -197,8 +198,12 @@ def entity_labels(self):
         loinc_tree_loader.load_method_tree()
         loinc_tree_loader.load_document_tree()
 
+        count = 0
         loinc_term: LoincTerm
         for loinc_term in self.runtime.current_module.get_entities_of_type(LoincTerm):
+            count += 1
+            if self.configuration.fast_run and count > FAST_RUN_N_TERMS:
+                break
             node = self.runtime.graph.get_node_by_code(
                 type_=LoincNodeType.LoincTerm, code=loinc_term.id
             )
@@ -253,8 +258,12 @@ def entity_annotations(self):
         loinc_tree_loader.load_method_tree()
         loinc_tree_loader.load_document_tree()
 
+        count = 0
         loinc_term: LoincTerm
         for loinc_term in self.runtime.current_module.get_entities_of_type(LoincTerm):
+            count += 1
+            if self.configuration.fast_run and count > FAST_RUN_N_TERMS:
+                break
             node = self.runtime.graph.get_node_by_code(
                 type_=LoincNodeType.LoincTerm, code=loinc_term.id
             )
@@ -364,7 +373,11 @@ def loinc_part_hierarchy_all(self):
         loinc_tree_loader.load_method_tree()
         loinc_tree_loader.load_document_tree()
 
+        count = 0
         for child_part_node in graph.get_nodes(type_=LoincNodeType.LoincPart):
+            count += 1
+            if self.configuration.fast_run and count > FAST_RUN_N_PARTS:
+                break
             child_part_number = child_part_node.get_property(
                 type_=LoincPartProps.part_number
             )
@@ -406,10 +419,14 @@ def loinc_term_primary_def(self):
         loinc_loader = LoincLoader(graph=graph, configuration=self.configuration)
         loinc_loader.load_accessory_files__part_file__loinc_part_link_primary_csv()
 
+        count = 0
         loinc_term: LoincTerm
         for loinc_term in self.runtime.current_module.get_entities_of_type(
             entity_class=LoincTerm
         ):
+            count += 1
+            if self.configuration.fast_run and count > FAST_RUN_N_TERMS:
+                break
             loinc_term_id = loinc_term.id
             loinc_term_node = self.runtime.graph.get_node_by_code(
                 type_=LoincNodeType.LoincTerm, code=loinc_term_id
@@ -510,10 +527,14 @@ def loinc_term_supplementary_def(self):
         loinc_loader = LoincLoader(graph=graph, configuration=self.configuration)
         loinc_loader.load_accessory_files__part_file__loinc_part_link_supplementary_csv()
 
+        count = 0
         loinc_term: LoincTerm
         for loinc_term in self.runtime.current_module.get_entities_of_type(
             entity_class=LoincTerm
         ):
+            count += 1
+            if self.configuration.fast_run and count > FAST_RUN_N_TERMS:
+                break
             loinc_term_id = loinc_term.id
             loinc_term_node = self.runtime.graph.get_node_by_code(
                 type_=LoincNodeType.LoincTerm, code=loinc_term_id
@@ -618,6 +639,8 @@ def loinc_term_class_roots(self):
             entity_class=LoincTerm
         ):
             count += 1
+            if self.configuration.fast_run and count > FAST_RUN_N_TERMS:
+                break
             if count % 1000 == 0:
                 logger.info(f"Finished {count}")
             loinc_term_node = self.runtime.graph.get_node_by_code(

src/comp_loinc/snomed_builder_steps.py

@@ -3,6 +3,7 @@
 import typing as t
 
 from comp_loinc import Runtime
+from comp_loinc.config import FAST_RUN_N_PARTS
 from comp_loinc.datamodel import SnomedConcept
 from loinclib import (
     Configuration,
@@ -50,7 +51,7 @@ def loinc_part_mapping_instances(self):
         count = 0
         for part in self.runtime.graph.get_nodes(type_=LoincNodeType.LoincPart):
             count = count + 1
-            if self.configuration.fast_run and count > 100:
+            if self.configuration.fast_run and count > FAST_RUN_N_PARTS:
                 break
             for edge in part.get_all_out_edges():
                 if edge.edge_type.type_ is SnomedEdges.maps_to: