refactor

chemkg · Dec 9, 2023 · e3b3bfc · e3b3bfc
1 parent 1d53117
commit e3b3bfc
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Showing 14 changed files with 8,221 additions and 5,489 deletions.
diff --git a/Makefile b/Makefile
@@ -71,6 +71,20 @@ project: $(SOURCE_FILES)
 #	$(RUN) gen-owl --no-metaclasses --no-type-objects $< > $@.tmp && mv $@.tmp $@
 
 
+test-examples: examples/output
+
+examples/output: $(SCHEMA_SRC)
+	mkdir -p $@
+	$(RUN) linkml-run-examples \
+		--output-formats json \
+		--output-formats yaml \
+		--counter-example-input-directory src/data/examples/invalid \
+		--input-directory src/data/examples/valid \
+		--output-directory $@ \
+		--schema $< > $@/README.md
+.PHONY: examples/output
+
+
 schema/sssom/chemrof.sssom.tsv: src/schema/chemrof.yaml
 	$(RUN) gen-sssom $< -o $@
 

diff --git a/schema/excel/chemrof.xlsx b/schema/excel/chemrof.xlsx
diff --git a/schema/graphql/chemrof.graphql b/schema/graphql/chemrof.graphql
@@ -201,6 +201,20 @@ type AtomGroupingClass
     classifies: Atom
   }
 
+type AtomicBond implements OwlClass
+  {
+    owlSubclassOf: OwlClass
+    subject: AtomOccurrence
+    object: AtomOccurrence
+    bondType: BondTypeEnum
+    bondOrder: Integer
+    bondLength: Float
+    bondEnergy: Float
+    bondLengthInAngstroms: Float
+    bondAngle: Float
+    torsionalAngle: Float
+  }
+
 interface AtomIonicForm
   {
     id: String!
@@ -232,20 +246,6 @@ type AtomOccurrence implements OwlClass
     coordinationNumber: Integer
   }
 
-type AtomicBond implements OwlClass
-  {
-    owlSubclassOf: OwlClass
-    subject: AtomOccurrence
-    object: AtomOccurrence
-    bondType: BondTypeEnum
-    bondOrder: Integer
-    bondLength: Float
-    bondEnergy: Float
-    bondLengthInAngstroms: Float
-    bondAngle: Float
-    torsionalAngle: Float
-  }
-
 type BronstedAcid
   {
     id: String!
@@ -276,12 +276,12 @@ interface CationState
     elementalCharge: Integer
   }
 
-interface ChargeState
+interface Charged
   {
     elementalCharge: Integer
   }
 
-interface Charged
+interface ChargeState
   {
     elementalCharge: Integer
   }
@@ -452,10 +452,20 @@ type ChemicalSaltGroupingClass
     classifies: ChemicalSalt
   }
 
+type ChemicalSimilarity
+  {
+    owlSubclassOf: OwlClass
+  }
+
 type ChiralityCenter
   {
   }
 
+type Collection
+  {
+    entities: [DomainEntity]
+  }
+
 interface Connectivity
   {
   }
@@ -1560,11 +1570,6 @@ interface SequenceInterval
     hasSequenceRepresentation: SequenceString
   }
 
-type Similarity
-  {
-    owlSubclassOf: OwlClass
-  }
-
 type SmallMolecule
   {
     id: String!

diff --git a/schema/jsonld/chemrof.context.jsonld b/schema/jsonld/chemrof.context.jsonld
@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2023-12-04T19:57:16",
+      "generation_date": "2023-12-05T15:10:40",
       "source": "chemrof.yaml"
    },
    "@context": {
@@ -194,6 +194,9 @@
       "classified_by": {
          "@type": "@id"
       },
+      "entities": {
+         "@type": "@id"
+      },
       "composed_of": {
          "@type": "@id"
       },
@@ -514,7 +517,7 @@
             "meaning": "@id"
          }
       },
-      "count": {
+      "Count": {
          "@type": "xsd:integer"
       },
       "subject_atom_occurrence": {