Merge pull request #5 from GenomicsStandardsConsortium/4-is-this-a-re…

…asonable-place-for-determining-who-wins-when-there-is-a-conflict-in-a-slot-definitionusage-between-a-is_a-parent-and-a-mixin

is_a vs mixins

src/mixs_missing_value_sandbox/schema/mixs_missing_value_sandbox.yaml

@@ -80,6 +80,7 @@ classes:
     is_a: Checklist
     mixin: true
     slots:
+      - conflicting
       - adapters
       - alt
       - annot
@@ -127,6 +128,8 @@ classes:
       - tax_class
       - temp
     slot_usage:
+      conflicting:
+        pattern: ^[a-zA-Z]+$
       adapters:
         recommended: true
       alt:
@@ -193,6 +196,7 @@ classes:
     title: soil
     is_a: Extension
     slots:
+      - conflicting
       - agrochem_addition
       - al_sat
       - al_sat_meth
@@ -251,6 +255,8 @@ classes:
       - water_cont_soil_meth
       - water_content
     slot_usage:
+      conflicting:
+        pattern: ^[0-9]+$
       crop_rotation:
         string_serialization: '{boolean};{Rn/start_time/end_time/duration}'
       depth:
@@ -306,6 +312,9 @@ slots:
     inlined: true
     inlined_as_list: true
 
+  conflicting:
+    description: intentionally set to incompatible states between a Checklist and an Extension
+
   adapters:
     annotations:
       Expected_value: adapter A and B sequence

src/scripts/__init__.py

@@ -0,0 +1,8 @@
+from pathlib import Path
+
+# from ..mixs_missing_value_sandbox import *
+
+THIS_PATH = Path(__file__).parent
+
+SCHEMA_DIRECTORY = THIS_PATH.parent / "mixs_missing_value_sandbox" / "schema"
+MAIN_SCHEMA_PATH = SCHEMA_DIRECTORY / "mixs_missing_value_sandbox.yaml"

src/scripts/mims_and_soil_slots.py

@@ -0,0 +1,50 @@
+import pprint
+from pathlib import Path
+
+from linkml_runtime import SchemaView
+from linkml_runtime.dumpers import yaml_dumper
+
+# from ..mixs_missing_value_sandbox import *
+
+THIS_PATH = Path(__file__).parent
+
+SCHEMA_DIRECTORY = THIS_PATH.parent / "mixs_missing_value_sandbox" / "schema"
+MAIN_SCHEMA_PATH = SCHEMA_DIRECTORY / "mixs_missing_value_sandbox.yaml"
+
+schema_view = SchemaView(MAIN_SCHEMA_PATH)
+
+current_checklist = "Mims"
+current_extension = "Soil"
+
+checklist_slots = schema_view.get_class(current_checklist).slots
+
+extension_slots = schema_view.get_class(current_extension).slots
+
+checklist_extension_slots = set(checklist_slots).intersection(set(extension_slots))
+checklist_extension_slots = list(checklist_extension_slots)
+checklist_extension_slots.sort()
+
+checklist_usages = schema_view.get_class(current_checklist).slot_usage
+extension_usages = schema_view.get_class(current_extension).slot_usage
+for slot in checklist_extension_slots:
+    global_definition = schema_view.get_slot(slot)
+    checklist_modifies = slot in checklist_usages
+    extension_modifies = slot in extension_usages
+    if checklist_modifies or extension_modifies:
+        if checklist_modifies:
+            print(f"{slot} slot's usage in {current_checklist}:")
+            print(yaml_dumper.dumps(checklist_usages[slot]))
+        else:
+            print(f"{current_checklist} uses the global definition for {slot}")
+            # print(yaml_dumper.dumps(global_definition))
+        if extension_modifies:
+            print(f"{slot} slot's usage in {current_extension}:")
+            print(yaml_dumper.dumps(extension_usages[slot]))
+        else:
+            print(f"{current_extension} uses the global definition for {slot}")
+            # print(yaml_dumper.dumps(global_definition))
+        print(f"Induced slot {slot} in {current_checklist}{current_extension}\n")
+        print(yaml_dumper.dumps(schema_view.induced_slot(slot, f"{current_checklist}{current_extension}")))
+    else:
+        print(f"{slot} not modified by {current_checklist} or {current_extension}\n")
+        print("----")