Fix json tests ✔️

src/Core/OntologyAnnotation.fs

@@ -134,11 +134,18 @@ type OntologyAnnotation(?name,?tsr,?tan, ?comments) =
     override this.GetHashCode() = 
         [|
             HashCodes.boxHashOption this.Name
-            HashCodes.boxHashOption this.TermSourceREF
-            if this.TANInfo.IsSome then
-                HashCodes.hash this.TANInfo
-            else
-                HashCodes.boxHashOption this.TermAccessionNumber
+            match this.TermSourceREF, this.TANInfo with
+            | None, Some taninfo -> // if we get taninfo we assume tsr to be inferrable by taninfo
+                HashCodes.hash {|tsr = taninfo.IDSpace; tan = taninfo.IDSpace + ":" + taninfo.LocalID|}
+            | Some tsr, Some taninfo -> // if we get taninfo + tsr we do NOT override tsr
+                HashCodes.hash {|tsr = tsr; tan = taninfo.IDSpace + ":" + taninfo.LocalID|}
+            | Some tsr, None ->
+                let tan = this.TermAccessionNumber |> Option.defaultValue ""
+                HashCodes.hash {|tsr = tsr; tan = tan|}
+            | None, None ->
+                let tan = this.TermAccessionNumber |> Option.defaultValue ""
+                let tsr = this.TermAccessionNumber |> Option.defaultValue ""
+                HashCodes.hash {|tsr = tsr; tan = tan|}
             //HashCodes.boxHashSeq this.Comments
         |]
         |> HashCodes.boxHashArray

tests/Core/OntologyAnnotation.Tests.fs

@@ -60,14 +60,19 @@ let private tests_equals = testList "Equals" [
         let oa1 = OntologyAnnotation("instrument model", "MS", "MS:00000001", ResizeArray [Comment("KeyName", "Value1")])
         let oa2 = OntologyAnnotation("instrument model", "MS", "MS:00000001")
         Expect.equal oa1 oa2 ""
-    testCase "TANInfo1" <| fun _ ->   
+    testCase "TANInfo" <| fun _ ->   
         let oa1 = OntologyAnnotation("instrument model", "MS", "http://purl.obolibrary.org/obo/MS_00000001", ResizeArray [Comment("KeyName", "Value1")])
         let oa2 = OntologyAnnotation("instrument model", "MS", "MS:00000001", ResizeArray [Comment("KeyName", "Value1")])
         Expect.equal oa1 oa2 ""
-    testCase "TANInfo, different tsr" <| fun _ ->   
+    testCase "TANInfo, missing tsr" <| fun _ ->   
         let oa1 = OntologyAnnotation("instrument model", "MS", "http://purl.obolibrary.org/obo/MS_00000001", ResizeArray [Comment("KeyName", "Value1")])
         let oa2 = OntologyAnnotation("instrument model", tan= "MS:00000001", comments=ResizeArray [Comment("KeyName", "Value1")])
+        Expect.equal oa1 oa2 "This should not fail"
+    testCase "TANInfo, different tsr" <| fun _ ->   
+        let oa1 = OntologyAnnotation("instrument model", "MS", "http://purl.obolibrary.org/obo/MS_00000001", ResizeArray [Comment("KeyName", "Value1")])
+        let oa2 = OntologyAnnotation("instrument model", "MSS", tan= "MS:00000001", comments=ResizeArray [Comment("KeyName", "Value1")])
         Expect.notEqual oa1 oa2 ""
+        Expect.isFalse (oa1 = oa2) ""
     testCase "not equal" <| fun _ ->   
         let oa1 = OntologyAnnotation("instrument model", "MS", "http://purl.obolibrary.org/obo/MS_00000001", ResizeArray [Comment("KeyName", "Value1")])
         let oa2 = OntologyAnnotation(tan= "MS:00000001", comments=ResizeArray [Comment("KeyName", "Value1")])

tests/Json/ARCtrl.Json.Tests.fsproj

@@ -23,7 +23,7 @@
     <Compile Include="ArcTable.Tests.fs" />
     <Compile Include="Person.Tests.fs" />
     <Compile Include="Publication.Tests.fs" />
-    <Compile Include="Assay.Tests..fs" />
+    <Compile Include="Assay.Tests.fs" />
     <Compile Include="Study.Tests.fs" />
     <Compile Include="Investigation.Tests.fs" />
     <Compile Include="Process\ProcessInput.Tests.fs" />

tests/Json/ArcTable.Tests.fs

@@ -34,6 +34,7 @@ let private tests_core =
         ArcTable.toJsonString
         ArcTable.fromJsonString
         None
+        None
 
 let private tests_coreEmpty = 
     let json = """{"name":"New Table"}""" 
@@ -43,6 +44,7 @@ let private tests_coreEmpty =
         ArcTable.toJsonString
         ArcTable.fromJsonString
         None
+        None
 
 let private tests_compressedEmpty = 
     let json = """{"cellTable":[],"oaTable":[],"stringTable":["New Table"],"table":{"n":0}}""" 
@@ -52,6 +54,7 @@ let private tests_compressedEmpty =
         ArcTable.toCompressedJsonString
         ArcTable.fromCompressedJsonString
         None
+        None
 
 let private tests_compressedFilled = 
     let json = """{"cellTable":[{"t":2,"v":[1]},{"t":2,"v":[3]},{"t":4,"v":[0]},{"t":2,"v":[5]},{"t":2,"v":[6]}],"oaTable":[{"a":7}],"stringTable":["New Table","Input 1","FreeText","Input 2","Term","Output 1","Output 2","SCIEX instrument model"],"table":{"n":0,"h":[{"headertype":"Input","values":["Source Name"]},{"headertype":"Component","values":[{"annotationValue":"instrument model","termSource":"MS","termAccession":"MS:424242"}]},{"headertype":"Output","values":["Sample Name"]}],"c":[[0,1],[2,2],[3,4]]}}"""
@@ -61,6 +64,7 @@ let private tests_compressedFilled =
         ArcTable.toCompressedJsonString
         ArcTable.fromCompressedJsonString
         None
+        None
 
 let private tests = testList "extended" [
     testList "compressed" [

tests/Json/Assay.Tests..fs → tests/Json/Assay.Tests.fs

@@ -17,6 +17,17 @@ module Helper =
             ResizeArray [|Comment.create("Hello", "World")|]
         )
 
+    let compare =
+        fun (a1: ArcAssay) (a2: ArcAssay) ->
+            Expect.equal a1.Identifier a2.Identifier "Identifier"
+            Expect.equal a1.MeasurementType a2.MeasurementType "MeasurementType"
+            Expect.equal a1.TechnologyType a2.TechnologyType "TechnologyType"
+            Expect.equal a1.TechnologyPlatform a2.TechnologyPlatform "TechnologyPlatform"
+            Expect.sequenceEqual a1.Tables a2.Tables "Tables"
+            Expect.sequenceEqual a1.Performers a2.Performers "Performers"
+            Expect.sequenceEqual a1.Comments a2.Comments "Comments"
+        |> Some
+
 open Helper
 
 let private test_coreEmpty =
@@ -26,6 +37,7 @@ let private test_coreEmpty =
         ArcAssay.toJsonString
         ArcAssay.fromJsonString
         None
+        compare
 
 let private test_compressedEmpty =
     createBaseJsonTests
@@ -34,6 +46,7 @@ let private test_compressedEmpty =
         ArcAssay.toCompressedJsonString
         ArcAssay.fromCompressedJsonString
         None
+        compare
 
 let private test_isaEmpty =
     createBaseJsonTests
@@ -46,6 +59,7 @@ let private test_isaEmpty =
         #else
         None
         #endif
+        compare
 
 let private test_roCrateEmpty =
     createBaseJsonTests
@@ -54,6 +68,7 @@ let private test_roCrateEmpty =
         (fun () -> ArcAssay.toROCrateJsonString None)
         ArcAssay.fromROCrateJsonString
         None
+        compare
 
 let private test_core =
     createBaseJsonTests
@@ -62,6 +77,7 @@ let private test_core =
         ArcAssay.toJsonString
         ArcAssay.fromJsonString
         None
+        compare
 
 let private test_compressed =
     createBaseJsonTests
@@ -70,6 +86,7 @@ let private test_compressed =
         ArcAssay.toCompressedJsonString
         ArcAssay.fromCompressedJsonString
         None
+        compare
 
 open TestObjects.Json
 
@@ -87,6 +104,7 @@ let private test_isa =
         #else
         None
         #endif
+        compare
 
 let private test_roCrate = testList "ROCrate" [
     // Wait for some issues to be resolved: https://github.com/nfdi4plants/isa-ro-crate-profile/issues
@@ -101,6 +119,7 @@ let private test_roCrate = testList "ROCrate" [
         (fun () -> ArcAssay.toROCrateJsonString None)
         ArcAssay.fromROCrateJsonString
         None
+        compare
 ]
 
 let main = testList "Assay" [

tests/Json/BaseJsonTests.fs

@@ -6,22 +6,31 @@ open ARCtrl.Json
 
 
 
-let createBaseJsonTests (name:string) (createObj: unit -> 'A) (toJson: unit -> 'A -> string) (fromJson: string -> 'A) (schemaValidation : Validation.ValidateFunction option) =
-    testList $"baseTests - {name}" [
+let createBaseJsonTests (name:string) (createObj: unit -> 'A) (toJson: unit -> 'A -> string) (fromJson: string -> 'A) (schemaValidation : Validation.ValidateFunction option) (detailedCompareFunc: option<'A -> 'A -> unit>) =
+    let name = if name = "" then "baseTests" else $"baseTests - {name}"
+    testList name [
 
-        if schemaValidation.IsSome then
-            testAsync "WriterSchemaCorrectness" {
+        if detailedCompareFunc.IsSome then
+            testCase "detailed" <| fun _ ->
                 let obj = createObj()
                 let json = toJson () obj
-                let! validation = schemaValidation.Value json
-                let errorList = validation.GetErrors() |> Array.fold (fun acc x -> acc + x + "\n") ""
-                Expect.isTrue validation.Success $"Object did not match schema: {errorList}"
-            }
+                let actual = fromJson json
+                let expected = createObj()
+                detailedCompareFunc.Value actual expected
 
         testCase "roundabout" <| fun _ ->
             let obj = createObj()
             let json = toJson () obj
             let actual = fromJson json
             let expected = createObj()
             Expect.equal actual expected ""
+
+        if schemaValidation.IsSome then
+            testAsync "WriterSchemaCorrectness" {
+                let obj = createObj()
+                let json = toJson () obj
+                let! validation = schemaValidation.Value json
+                let errorList = validation.GetErrors() |> Array.fold (fun acc x -> acc + x + "\n") ""
+                Expect.isTrue validation.Success $"Object did not match schema: {errorList}"
+            }
     ]

tests/Json/Investigation.Tests.fs

@@ -37,20 +37,22 @@ module Helper =
         inv.AddAssay(assay2, inv.Studies)
         inv
 
-    let compareFields (expected: ArcInvestigation) (actual: ArcInvestigation) =
-        Expect.equal actual.Identifier expected.Identifier "Identifier"
-        Expect.equal actual.Title expected.Title "Title"
-        Expect.equal actual.Description expected.Description "Description"
-        Expect.equal actual.SubmissionDate expected.SubmissionDate "SubmissionDate"
-        Expect.equal actual.PublicReleaseDate expected.PublicReleaseDate "PublicReleaseDate"
-        Expect.sequenceEqual actual.OntologySourceReferences expected.OntologySourceReferences "OntologySourceReferences"
-        Expect.sequenceEqual actual.Publications expected.Publications "Publications"
-        Expect.sequenceEqual actual.Contacts expected.Contacts "Contacts"
-        Expect.sequenceEqual actual.Assays expected.Assays "Assays"
-        Expect.sequenceEqual actual.Studies expected.Studies "Studies"
-        Expect.sequenceEqual actual.RegisteredStudyIdentifiers expected.RegisteredStudyIdentifiers "RegisteredStudyIdentifiers"
-        Expect.sequenceEqual actual.Comments expected.Comments "Comments"
-        Expect.sequenceEqual actual.Remarks expected.Remarks "Remarks"
+    let compareFields =
+        fun (actual: ArcInvestigation) (expected: ArcInvestigation) ->  
+            Expect.equal actual.Identifier expected.Identifier "Identifier"
+            Expect.equal actual.Title expected.Title "Title"
+            Expect.equal actual.Description expected.Description "Description"
+            Expect.equal actual.SubmissionDate expected.SubmissionDate "SubmissionDate"
+            Expect.equal actual.PublicReleaseDate expected.PublicReleaseDate "PublicReleaseDate"
+            Expect.sequenceEqual actual.OntologySourceReferences expected.OntologySourceReferences "OntologySourceReferences"
+            Expect.sequenceEqual actual.Publications expected.Publications "Publications"
+            Expect.sequenceEqual actual.Contacts expected.Contacts "Contacts"
+            Expect.sequenceEqual actual.Assays expected.Assays "Assays"
+            Expect.sequenceEqual actual.Studies expected.Studies "Studies"
+            Expect.sequenceEqual actual.RegisteredStudyIdentifiers expected.RegisteredStudyIdentifiers "RegisteredStudyIdentifiers"
+            Expect.sequenceEqual actual.Comments expected.Comments "Comments"
+            Expect.sequenceEqual actual.Remarks expected.Remarks "Remarks"
+        |> Some
 
 open Helper
 
@@ -61,6 +63,7 @@ let private test_coreEmpty =
         ArcInvestigation.toJsonString
         ArcInvestigation.fromJsonString
         None
+        compareFields
 
 let private test_compressedEmpty =
     createBaseJsonTests
@@ -69,6 +72,7 @@ let private test_compressedEmpty =
         ArcInvestigation.toCompressedJsonString
         ArcInvestigation.fromCompressedJsonString
         None
+        compareFields
 
 let private test_isaEmpty =
     createBaseJsonTests
@@ -81,6 +85,7 @@ let private test_isaEmpty =
         #else
         None
         #endif
+        compareFields
 
 let private test_roCrateEmpty =
     createBaseJsonTests
@@ -89,7 +94,7 @@ let private test_roCrateEmpty =
         ArcInvestigation.toROCrateJsonString
         ArcInvestigation.fromROCrateJsonString
         None
-
+        compareFields
 
 let private test_core =
     createBaseJsonTests
@@ -98,6 +103,7 @@ let private test_core =
         ArcInvestigation.toJsonString
         ArcInvestigation.fromJsonString
         None
+        compareFields
 
 let private test_compressed =
 
@@ -107,6 +113,7 @@ let private test_compressed =
         ArcInvestigation.toCompressedJsonString
         ArcInvestigation.fromCompressedJsonString
         None
+        compareFields
 
 let private test_isa =
 
@@ -120,6 +127,7 @@ let private test_isa =
         #else
         None
         #endif
+        compareFields
 
 let private test_roCrate =
     createBaseJsonTests
@@ -128,6 +136,7 @@ let private test_roCrate =
         ArcInvestigation.toROCrateJsonString
         ArcInvestigation.fromROCrateJsonString
         None
+        compareFields
 
 let main = testList "Investigation" [
     test_coreEmpty

tests/Json/OntologyAnnotation.Tests.fs

@@ -19,19 +19,20 @@ let private tests_core =
         OntologyAnnotation.toJsonString
         OntologyAnnotation.fromJsonString
         None
+        None
 
 let private tests_isa =
     createBaseJsonTests
         "isa"
         create_oa
-
         OntologyAnnotation.toISAJsonString
         OntologyAnnotation.fromISAJsonString
         #if !FABLE_COMPILER_PYTHON
         (Some Validation.validateOntologyAnnotation)
         #else
         None
         #endif
+        None
 
 let private tests_roCrate = testList "ROCrate" [
     testCase "Write-PropertyValue" <| fun _ -> 
@@ -50,6 +51,7 @@ let private tests_roCrate = testList "ROCrate" [
         OntologyAnnotation.toROCrateJsonString
         OntologyAnnotation.fromROCrateJsonString
         None
+        None
 ]
 
 let main = testList "OntologyAnnotation" [

tests/Json/Person.Tests.fs

@@ -29,6 +29,7 @@ let private tests_isa = testList "ISA" [
         Person.toISAJsonString
         Person.fromISAJsonString
         None
+        None
     testCase "ReaderSuccess" (fun () -> 
         let readingSuccess = 
             try 
@@ -106,6 +107,7 @@ let private tests_rocrate = testList "ROCrate" [
         Person.toROCrateJsonString
         Person.fromROCrateJsonString
         None
+        None
 ]
 
 let tests = testList "core" [
@@ -115,6 +117,7 @@ let tests = testList "core" [
         Person.toJsonString
         Person.fromJsonString
         None
+        None
 ]
 
 let main = testList "Person" [