microbiomedata · turbomam · Sep 27, 2024 · Sep 27, 2024 · Sep 27, 2024 · Sep 27, 2024
diff --git a/Activity.png b/Activity.png
diff --git a/AttributeValue10.png b/AttributeValue10.png
diff --git a/AttributeValue11.png b/AttributeValue11.png
diff --git a/Configuration.png b/Configuration.png
diff --git a/InformationObject.png b/InformationObject.png
diff --git a/MaterialProcessing.png b/MaterialProcessing.png
diff --git a/MobilePhaseSegment.png b/MobilePhaseSegment.png
diff --git a/PortionOfSubstance.png b/PortionOfSubstance.png
diff --git a/ProtocolExecution.png b/ProtocolExecution.png
diff --git a/pre_vs_berkeley.Makefile b/pre_vs_berkeley.Makefile
@@ -0,0 +1,78 @@
+pre_schema.yaml:
+	poetry run python -c 'from linkml_runtime.utils.schemaview import SchemaView; \
+	from linkml_runtime.dumpers import yaml_dumper; \
+	schema_url = "https://raw.githubusercontent.com/microbiomedata/nmdc-schema/refs/tags/v10.9.1/src/schema/nmdc.yaml"; \
+	sv = SchemaView(schema_url, merge_imports=True); \
+	yaml_dumper.dump(sv.schema, "pre_schema.yaml")'
+
+berkeley_schema.yaml:
+	poetry run python -c 'from linkml_runtime.utils.schemaview import SchemaView; \
+	from linkml_runtime.dumpers import yaml_dumper; \
+	schema_url = "https://raw.githubusercontent.com/microbiomedata/nmdc-schema/refs/tags/v11.0.1/src/schema/nmdc.yaml"; \
+	sv = SchemaView(schema_url, merge_imports=True); \
+	yaml_dumper.dump(sv.schema, "berkeley_schema.yaml")'
+
+pre_study.yaml: pre_schema.yaml
+	yq '.classes.Study' $< | cat > $@
+
+pre_biosample.yaml: pre_schema.yaml
+	yq '.classes.Biosample' $< | cat > $@
+
+pre_types.yaml: pre_schema.yaml
+	yq '.types' $< | cat > $@
+
+pre_settings.yaml: pre_schema.yaml
+	yq '.settings' $< | cat > $@
+
+pre_prefixes.yaml: pre_schema.yaml
+	yq '.prefixes' $< | cat > $@
+
+pre_enums.yaml: pre_schema.yaml
+	yq '.enums' $< | cat > $@
+
+pre_subsets.yaml: pre_schema.yaml
+	yq '.subsets' $< | cat > $@
+
+berkeley_study.yaml: berkeley_schema.yaml
+	yq '.classes.Study' $< | cat > $@
+
+berkeley_biosample.yaml: berkeley_schema.yaml
+	yq '.classes.Biosample' $< | cat > $@
+
+berkeley_types.yaml: berkeley_schema.yaml
+	yq '.types' $< | cat > $@
+
+berkeley_settings.yaml: berkeley_schema.yaml
+	yq '.settings' $< | cat > $@
+
+berkeley_prefixes.yaml: berkeley_schema.yaml
+	yq '.prefixes' $< | cat > $@
+
+berkeley_enums.yaml: berkeley_schema.yaml
+	yq '.enums' $< | cat > $@
+
+berkeley_subsets.yaml: berkeley_schema.yaml
+	yq '.subsets' $< | cat > $@
+
+pre_vs_berkeley_study.yaml: pre_study.yaml berkeley_study.yaml
+	poetry run deep diff --ignore-order $^ | yq -P | cat > $@
+
+pre_vs_berkeley_biosample.yaml: pre_biosample.yaml berkeley_biosample.yaml
+	poetry run deep diff --ignore-order $^ | yq -P | cat > $@
+
+pre_vs_berkeley_types.yaml: pre_types.yaml berkeley_types.yaml
+	poetry run deep diff --ignore-order $^ | yq -P | cat > $@
+
+pre_vs_berkeley_settings.yaml: pre_settings.yaml berkeley_settings.yaml
+	poetry run deep diff --ignore-order $^ | yq -P | cat > $@
+
+pre_vs_berkeley_prefixes.yaml: pre_prefixes.yaml berkeley_prefixes.yaml
+	poetry run deep diff --ignore-order $^ | yq -P | cat > $@
+
+pre_vs_berkeley_enums.yaml: pre_enums.yaml berkeley_enums.yaml
+	poetry run deep diff --ignore-order $^ | yq -P | cat > $@
+
+pre_vs_berkeley_subsets.yaml: pre_subsets.yaml berkeley_subsets.yaml
+	poetry run deep diff --ignore-order $^ | yq -P | cat > $@
+
+
diff --git a/pre_vs_berkeley.md b/pre_vs_berkeley.md
diff --git a/pre_vs_berkeley.py b/pre_vs_berkeley.py
@@ -0,0 +1,121 @@
+import pprint
+
+from linkml_runtime import SchemaView
+from linkml_runtime.dumpers import yaml_dumper
+
+from linkml_runtime.linkml_model.meta import ClassDefinition, SlotDefinition
+
+# from terminado.management import preexec_fn
+
+pre_path = "https://raw.githubusercontent.com/microbiomedata/nmdc-schema/refs/tags/v10.9.1/src/schema/nmdc.yaml"
+
+berkeley_path = "https://raw.githubusercontent.com/microbiomedata/nmdc-schema/refs/tags/v11.0.1/src/schema/nmdc.yaml"
+
+pre_view = SchemaView(pre_path)
+
+berkeley_view = SchemaView(berkeley_path)
+
+pre_classes = pre_view.all_classes()
+pre_class_names = list(pre_classes.keys())
+print(len(pre_class_names))
+
+berkeley_classes = berkeley_view.all_classes()
+berkeley_class_names = list(berkeley_classes.keys())
+print(len(berkeley_class_names))
+
+pre_only = [c for c in pre_class_names if c not in berkeley_class_names]
+
+berkeley_only = [c for c in berkeley_class_names if c not in pre_class_names]
+
+pprint.pprint(pre_only)
+
+pprint.pprint(berkeley_only)
+
+pre_roots = pre_view.class_roots()
+pre_roots.sort()
+pprint.pprint(pre_roots)
+print(len(pre_roots))
+
+berkeley_roots = berkeley_view.class_roots()
+berkeley_roots.sort()
+pprint.pprint(berkeley_roots)
+print(len(berkeley_roots))
+
+pre_only = [c for c in pre_roots if c not in berkeley_roots]
+pprint.pprint(pre_only)
+print(len(pre_only))
+
+berkeley_only = [c for c in berkeley_roots if c not in pre_roots]
+pprint.pprint(berkeley_only)
+print(len(berkeley_only))
+
+####
+
+pre_slots = pre_view.all_slots()
+pre_slot_names = list(pre_slots.keys())
+print(f"{len(pre_slot_names)}")
+
+berkeley_slots = berkeley_view.all_slots()
+berkeley_slot_names = list(berkeley_slots.keys())
+print(f"{len(berkeley_slot_names)}")
+
+pre_only = [s for s in pre_slot_names if s not in berkeley_slot_names]
+pre_only.sort()
+
+berkeley_only = [s for s in berkeley_slot_names if s not in pre_slot_names]
+berkeley_only.sort()
+
+pprint.pprint(pre_only)
+print(f"{len(pre_only)}")
+
+pprint.pprint(berkeley_only)
+print(f"{len(berkeley_only)}")
+
+####
+
+# ChromatographicSeparationProcess, type: <class 'linkml_runtime.linkml_model.meta.ClassDefinition'>
+# OmicsProcessing, type: <class 'linkml_runtime.linkml_model.meta.ClassDefinition'>
+# CreditAssociation, type: <class 'linkml_runtime.linkml_model.meta.ClassDefinition'>
+# total_bases, type: <class 'linkml_runtime.linkml_model.meta.SlotDefinition'>
+# members_id, type: <class 'linkml_runtime.linkml_model.meta.SlotDefinition'>
+# bin_name, type: <class 'linkml_runtime.linkml_model.meta.SlotDefinition'>
+
+pre_abstract = []
+pre_abstract_classes = []
+pre_abstract_slots = []
+pre_elements = pre_view.all_elements()
+for ek, ev in pre_elements.items():
+    if isinstance(ev, ClassDefinition) and ev.abstract:
+        pre_abstract_classes.append(ek)
+    if isinstance(ev, SlotDefinition) and ev.abstract:
+        pre_abstract_slots.append(ek)
+
+print(f"pre_abstract_classes: {len(pre_abstract_classes)}")
+print(f"pre_abstract_slots: {len(pre_abstract_slots)}")
+
+berkeley_abstract = []
+berkeley_abstract_classes = []
+berkeley_abstract_slots = []
+
+berkeley_elements = berkeley_view.all_elements()
+
+for ek, ev in berkeley_elements.items():
+    if isinstance(ev, ClassDefinition) and ev.abstract:
+        berkeley_abstract_classes.append(ek)
+    if isinstance(ev, SlotDefinition) and ev.abstract:
+        berkeley_abstract_slots.append(ek)
+
+print(f"berkeley_abstract_classes: {len(berkeley_abstract_classes)}")
+print(f"berkeley_abstract_slots: {len(berkeley_abstract_slots)}")
+
+print(berkeley_abstract_classes)
+print(pre_abstract_classes)
+
+####
+
+
+pre_study = pre_view.get_class("Study")
+yaml_dumper.dump(pre_study, "pre_study.yaml")
+
+berkeley_study = berkeley_view.get_class("Study")
+yaml_dumper.dump(berkeley_study, "berkeley_study.yaml")
diff --git a/pre_vs_berkeley/Activity.png b/pre_vs_berkeley/Activity.png
diff --git a/pre_vs_berkeley/AttributeValue10.png b/pre_vs_berkeley/AttributeValue10.png
diff --git a/pre_vs_berkeley/AttributeValue11.png b/pre_vs_berkeley/AttributeValue11.png
diff --git a/pre_vs_berkeley/Configuration.png b/pre_vs_berkeley/Configuration.png
diff --git a/pre_vs_berkeley/InformationObject.png b/pre_vs_berkeley/InformationObject.png
diff --git a/pre_vs_berkeley/MaterialProcessing.png b/pre_vs_berkeley/MaterialProcessing.png
diff --git a/pre_vs_berkeley/MobilePhaseSegment.png b/pre_vs_berkeley/MobilePhaseSegment.png
diff --git a/pre_vs_berkeley/PortionOfSubstance.png b/pre_vs_berkeley/PortionOfSubstance.png
diff --git a/pre_vs_berkeley/ProtocolExecution.png b/pre_vs_berkeley/ProtocolExecution.png
diff --git a/pre_vs_berkeley/pre_vs_berkeley.Makefile b/pre_vs_berkeley/pre_vs_berkeley.Makefile
@@ -0,0 +1,78 @@
+pre_schema.yaml:
+	poetry run python -c 'from linkml_runtime.utils.schemaview import SchemaView; \
+	from linkml_runtime.dumpers import yaml_dumper; \
+	schema_url = "https://raw.githubusercontent.com/microbiomedata/nmdc-schema/refs/tags/v10.9.1/src/schema/nmdc.yaml"; \
+	sv = SchemaView(schema_url, merge_imports=True); \
+	yaml_dumper.dump(sv.schema, "pre_schema.yaml")'
+
+berkeley_schema.yaml:
+	poetry run python -c 'from linkml_runtime.utils.schemaview import SchemaView; \
+	from linkml_runtime.dumpers import yaml_dumper; \
+	schema_url = "https://raw.githubusercontent.com/microbiomedata/nmdc-schema/refs/tags/v11.0.1/src/schema/nmdc.yaml"; \
+	sv = SchemaView(schema_url, merge_imports=True); \
+	yaml_dumper.dump(sv.schema, "berkeley_schema.yaml")'
+
+pre_study.yaml: pre_schema.yaml
+	yq '.classes.Study' $< | cat > $@
+
+pre_biosample.yaml: pre_schema.yaml
+	yq '.classes.Biosample' $< | cat > $@
+
+pre_types.yaml: pre_schema.yaml
+	yq '.types' $< | cat > $@
+
+pre_settings.yaml: pre_schema.yaml
+	yq '.settings' $< | cat > $@
+
+pre_prefixes.yaml: pre_schema.yaml
+	yq '.prefixes' $< | cat > $@
+
+pre_enums.yaml: pre_schema.yaml
+	yq '.enums' $< | cat > $@
+
+pre_subsets.yaml: pre_schema.yaml
+	yq '.subsets' $< | cat > $@
+
+berkeley_study.yaml: berkeley_schema.yaml
+	yq '.classes.Study' $< | cat > $@
+
+berkeley_biosample.yaml: berkeley_schema.yaml
+	yq '.classes.Biosample' $< | cat > $@
+
+berkeley_types.yaml: berkeley_schema.yaml
+	yq '.types' $< | cat > $@
+
+berkeley_settings.yaml: berkeley_schema.yaml
+	yq '.settings' $< | cat > $@
+
+berkeley_prefixes.yaml: berkeley_schema.yaml
+	yq '.prefixes' $< | cat > $@
+
+berkeley_enums.yaml: berkeley_schema.yaml
+	yq '.enums' $< | cat > $@
+
+berkeley_subsets.yaml: berkeley_schema.yaml
+	yq '.subsets' $< | cat > $@
+
+pre_vs_berkeley_study.yaml: pre_study.yaml berkeley_study.yaml
+	poetry run deep diff --ignore-order $^ | yq -P | cat > $@
+
+pre_vs_berkeley_biosample.yaml: pre_biosample.yaml berkeley_biosample.yaml
+	poetry run deep diff --ignore-order $^ | yq -P | cat > $@
+
+pre_vs_berkeley_types.yaml: pre_types.yaml berkeley_types.yaml
+	poetry run deep diff --ignore-order $^ | yq -P | cat > $@
+
+pre_vs_berkeley_settings.yaml: pre_settings.yaml berkeley_settings.yaml
+	poetry run deep diff --ignore-order $^ | yq -P | cat > $@
+
+pre_vs_berkeley_prefixes.yaml: pre_prefixes.yaml berkeley_prefixes.yaml
+	poetry run deep diff --ignore-order $^ | yq -P | cat > $@
+
+pre_vs_berkeley_enums.yaml: pre_enums.yaml berkeley_enums.yaml
+	poetry run deep diff --ignore-order $^ | yq -P | cat > $@
+
+pre_vs_berkeley_subsets.yaml: pre_subsets.yaml berkeley_subsets.yaml
+	poetry run deep diff --ignore-order $^ | yq -P | cat > $@
+
+