fix #47, add full test for structural ontologies

src/ARCTokenization/ARCMock.fs

@@ -366,6 +366,7 @@ type ARCMock =
         ?Assay_Measurement_Type_Term_Accession_Number: seq<string>,
         ?Assay_Measurement_Type_Term_Source_REF: seq<string>,
         ?Assay_Technology_Type: seq<string>,
+        ?Assay_Technology_Type_Term_Accession_Number: seq<string>,
         ?Assay_Technology_Type_Term_Source_REF: seq<string>,
         ?Assay_Technology_Platform: seq<string>,
         ?Assay_File_Name: seq<string>,
@@ -388,6 +389,7 @@ type ARCMock =
             [""; yield! Assay_Measurement_Type_Term_Accession_Number |> Option.defaultValue Seq.empty ]
             [""; yield! Assay_Measurement_Type_Term_Source_REF |> Option.defaultValue Seq.empty ]
             [""; yield! Assay_Technology_Type |> Option.defaultValue Seq.empty ]
+            [""; yield! Assay_Technology_Type_Term_Accession_Number |> Option.defaultValue Seq.empty ]
             [""; yield! Assay_Technology_Type_Term_Source_REF |> Option.defaultValue Seq.empty ]
             [""; yield! Assay_Technology_Platform |> Option.defaultValue Seq.empty ]
             [""; yield! Assay_File_Name |> Option.defaultValue Seq.empty ]

src/ARCTokenization/structural_ontologies/arc_file_structure_ontology.obo

@@ -1,4 +1,4 @@
-!This file was auto generated on 2024-01-05. Do not edit it. All manual changes will be overwritten by the next generator run eventually.
+!This file was auto generated on 1/8/2024. Do not edit it. All manual changes will be overwritten by the next generator run eventually.
 format-version: 1.2
 data-version: init/2023-10-26
 saved-by: Kevin Schneider

src/ARCTokenization/structural_ontologies/assay_metadata_structural_ontology.obo

@@ -1,4 +1,4 @@
-!This file was auto generated on 2024-01-05. Do not edit it. All manual changes will be overwritten by the next generator run eventually.
+!This file was auto generated on 1/8/2024. Do not edit it. All manual changes will be overwritten by the next generator run eventually.
 format-version: 1.2
 data-version: init/2023-07-27
 saved-by: Kevin Schneider
@@ -125,7 +125,6 @@ id: ASSMSO:00000013
 name: Assay Technology Type Term Accession Number
 def: ""
 synonym: "Technology Type Term Accession Number" EXACT []
-is_obsolete: true
 relationship: part_of ASSMSO:00000002 ! ASSAY
 relationship: part_of ASSMSO:00000003 ! ASSAY METADATA
 relationship: follows ASSMSO:00000010 ! Technology Type

src/ARCTokenization/structural_ontologies/assay_metadata_structural_ontology.yml

@@ -124,7 +124,6 @@ def: ""
     name: Assay Technology Type Term Accession Number
     def: ""
     synonym: "Technology Type Term Accession Number" EXACT []
-    is_obsolete: true
     relationship: part_of ASSMSO:00000002 ! ASSAY
     relationship: part_of ASSMSO:00000003 ! ASSAY METADATA
     relationship: follows ASSMSO:00000010 ! Technology Type

src/ARCTokenization/structural_ontologies/investigation_metadata_structural_ontology.obo

@@ -1,4 +1,4 @@
-!This file was auto generated on 2024-01-05. Do not edit it. All manual changes will be overwritten by the next generator run eventually.
+!This file was auto generated on 1/8/2024. Do not edit it. All manual changes will be overwritten by the next generator run eventually.
 format-version: 1.2
 data-version: init/2023-07-20
 saved-by: Kevin Schneider

src/ARCTokenization/structural_ontologies/study_metadata_structural_ontology.obo

@@ -1,4 +1,4 @@
-!This file was auto generated on 2024-01-05. Do not edit it. All manual changes will be overwritten by the next generator run eventually.
+!This file was auto generated on 1/8/2024. Do not edit it. All manual changes will be overwritten by the next generator run eventually.
 format-version: 1.2
 data-version: init/2023-07-27
 saved-by: Kevin Schneider

tests/ARCTokenization.Tests/StructuralOntologyTests.fs

@@ -23,14 +23,38 @@ module InvestigationMetadata =
             (fun (e,a) -> Assert.Equal(e,a))
         )
 
+    [<Fact>] 
+    let ``all ontology names correct`` () =
+        Assert.All(
+            InvestigationMetadata.cvTerms,
+            (fun t -> Assert.True(t.RefUri = ReferenceObjects.Terms.InvestigationMetadata.referenceOntologyName))
+        )
+
     [<Fact>] 
     let ``no root term in non root terms`` () =
         Assert.All(
             InvestigationMetadata.nonRootCvTerms,
             (fun t -> 
                 Assert.True(
-                    t.Name <> ReferenceObjects.Terms.referenceInvestigationMetadataOntologyRootTerm.Name
-                    && t.Accession <> ReferenceObjects.Terms.referenceInvestigationMetadataOntologyRootTerm.Accession
+                    t.Name <> ReferenceObjects.Terms.InvestigationMetadata.referenceOntologyRootTerm.Name
+                    && t.Accession <> ReferenceObjects.Terms.InvestigationMetadata.referenceOntologyRootTerm.Accession
+                )
+            )
+        )
+
+    [<Fact>]
+    let ``all non root non obsolete CvTerms are correct`` () =
+        Assert.All(
+            (
+                List.zip
+                    InvestigationMetadata.nonObsoleteNonRootCvTerms
+                    ReferenceObjects.Terms.InvestigationMetadata.epectedNonObsoleteNonRootTerms
+            ),
+            (fun (actual, expected) -> 
+                Assert.True(
+                    (actual.Name = expected.Name)
+                    && (actual.Accession = expected.Accession)
+                    && (actual.RefUri = expected.RefUri)
                 )
             )
         )
@@ -51,14 +75,38 @@ module StudyMetadata =
             (fun (e,a) -> Assert.Equal(e,a))
         )
 
+    [<Fact>] 
+    let ``all ontology names correct`` () =
+        Assert.All(
+            StudyMetadata.cvTerms,
+            (fun t -> Assert.True(t.RefUri = ReferenceObjects.Terms.StudyMetadata.referenceOntologyName))
+        )
+
     [<Fact>] 
     let ``no root term in non root terms`` () =
         Assert.All(
             StudyMetadata.nonRootCvTerms,
             (fun t -> 
                 Assert.True(
-                    t.Name <> ReferenceObjects.Terms.referenceStudyMetadataOntologyRootTerm.Name
-                    && t.Accession <> ReferenceObjects.Terms.referenceStudyMetadataOntologyRootTerm.Accession
+                    t.Name <> ReferenceObjects.Terms.StudyMetadata.referenceOntologyRootTerm.Name
+                    && t.Accession <> ReferenceObjects.Terms.StudyMetadata.referenceOntologyRootTerm.Accession
+                )
+            )
+        )
+
+    [<Fact>]
+    let ``all non root non obsolete CvTerms are correct`` () =
+        Assert.All(
+            (
+                List.zip
+                    StudyMetadata.nonObsoleteNonRootCvTerms
+                    ReferenceObjects.Terms.StudyMetadata.epectedNonObsoleteNonRootTerms
+            ),
+            (fun (actual, expected) -> 
+                Assert.True(
+                    (actual.Name = expected.Name)
+                    && (actual.Accession = expected.Accession)
+                    && (actual.RefUri = expected.RefUri)
                 )
             )
         )
@@ -128,14 +176,38 @@ module AssayMetadata =
             (fun (e,a) -> Assert.Equal(e,a))
         )
 
+    [<Fact>] 
+    let ``all ontology names correct`` () =
+        Assert.All(
+            AssayMetadata.cvTerms,
+            (fun t -> Assert.True(t.RefUri = ReferenceObjects.Terms.AssayMetadata.referenceOntologyName))
+        )
+
     [<Fact>] 
     let ``no root term in non root terms`` () =
         Assert.All(
             AssayMetadata.nonRootCvTerms,
             (fun t -> 
                 Assert.True(
-                    t.Name <> ReferenceObjects.Terms.referenceAssayMetadataOntologyRootTerm.Name
-                    && t.Accession <> ReferenceObjects.Terms.referenceAssayMetadataOntologyRootTerm.Accession
+                    t.Name <> ReferenceObjects.Terms.AssayMetadata.referenceOntologyRootTerm.Name
+                    && t.Accession <> ReferenceObjects.Terms.AssayMetadata.referenceOntologyRootTerm.Accession
+                )
+            )
+        )
+
+    [<Fact>]
+    let ``all non root non obsolete CvTerms are correct`` () =
+        Assert.All(
+            (
+                List.zip
+                    AssayMetadata.nonObsoleteNonRootCvTerms
+                    ReferenceObjects.Terms.AssayMetadata.epectedNonObsoleteNonRootTerms
+            ),
+            (fun (actual, expected) -> 
+                Assert.True(
+                    (actual.Name = expected.Name)
+                    && (actual.Accession = expected.Accession)
+                    && (actual.RefUri = expected.RefUri)
                 )
             )
         )