Merge pull request #469 from nfdi4plants/fixes2

fix additionalProperties being lost in RO-Crate write read

src/Json/Process/Material.fs

@@ -20,6 +20,7 @@ module Material =
             [
                 "@id", Encode.string (oa |> genID) |> Some
                 "@type", (Encode.list [Encode.string "Material"]) |> Some
+                "additionalType", Encode.string "Material" |> Some
                 Encode.tryInclude "name" Encode.string oa.Name
                 Encode.tryInclude "type" MaterialType.ROCrate.encoder oa.MaterialType
                 Encode.tryIncludeListOpt "characteristics" MaterialAttributeValue.ROCrate.encoder oa.Characteristics
@@ -31,7 +32,10 @@ module Material =
 
         let decoder : Decoder<Material> =       
             let rec decode() =
-                Decode.object (fun get -> 
+                Decode.object (fun get ->
+                    match get.Optional.Field "additionalType" Decode.uri with
+                    | Some "Material" | None -> ()
+                    | Some _ -> get.Required.Field "FailBecauseNotSample" Decode.unit
                     {                       
                         ID = get.Optional.Field "@id" Decode.uri
                         Name = get.Optional.Field "name" Decode.string

src/Json/Process/ProcessInput.fs

@@ -22,8 +22,8 @@ module ProcessInput =
 
         let decoder : Decoder<ProcessInput> =
             Decode.oneOf [
-                Decode.map ProcessInput.Source Source.ROCrate.decoder
                 Decode.map ProcessInput.Sample Sample.ROCrate.decoder
+                Decode.map ProcessInput.Source Source.ROCrate.decoder
                 Decode.map ProcessInput.Data Data.ROCrate.decoder
                 Decode.map ProcessInput.Material Material.ROCrate.decoder
             ]

src/Json/Process/Sample.fs

@@ -24,6 +24,7 @@ module Sample =
             [
                 "@id", Encode.string (oa |> genID) |> Some
                 "@type", (Encode.list [ Encode.string "Sample"]) |> Some
+                "additionalType", Encode.string "Sample" |> Some
                 Encode.tryInclude "name" Encode.string (oa.Name)
                 Encode.tryIncludeList "additionalProperties" id additionalProperties
                 "@context", ROCrateContext.Sample.context_jsonvalue |> Some
@@ -64,6 +65,9 @@ module Sample =
                         additionalProperties 
                         |> List.choose snd
                         |> Helper.Option.fromValueWithDefault []
+                match get.Optional.Field "additionalType" Decode.uri with
+                | Some "Sample" | None -> ()
+                | Some _ -> get.Required.Field "FailBecauseNotSample" Decode.unit
                 {
                     ID = get.Optional.Field "@id" Decode.uri
                     Name = get.Optional.Field "name" Decode.string

src/Json/Process/Source.fs

@@ -20,6 +20,7 @@ module Source =
             [
                 "@id", Encode.string (oa |> genID) |> Some
                 "@type", (Encode.list [ Encode.string "Source"]) |> Some
+                "additionalType", Encode.string "Source" |> Some
                 Encode.tryInclude "name" Encode.string (oa.Name)
                 Encode.tryIncludeListOpt "characteristics" MaterialAttributeValue.ROCrate.encoder (oa.Characteristics)      
                 "@context", ROCrateContext.Source.context_jsonvalue |> Some
@@ -29,7 +30,9 @@ module Source =
 
         let rec decoder : Decoder<Source> =     
             Decode.object (fun get ->
-
+                match get.Optional.Field "additionalType" Decode.uri with
+                | Some "Source" | None -> ()
+                | Some _ -> get.Required.Field "FailBecauseNotSample" Decode.unit
                 {
                     ID = get.Optional.Field "@id" Decode.uri
                     Name = get.Optional.Field "name" Decode.string

src/Json/context/rocrate/isa_assay_context.fs

@@ -19,7 +19,7 @@ module Assay =
     otherMaterials: string
     samples: string
     characteristicCategories: string
-    processSequences: string
+    processSequence: string
     unitCategories: string
 
     comments: string
@@ -38,7 +38,7 @@ module Assay =
       "technologyPlatform", Encode.string "sdo:measurementMethod"
       "dataFiles", Encode.string "sdo:hasPart"
       "performers", Encode.string "sdo:creator"
-      "processSequences", Encode.string "sdo:about"
+      "processSequence", Encode.string "sdo:about"
 
       "comments", Encode.string "sdo:comment"
       "filename", Encode.string "sdo:url"

tests/Json/Process/ProcessInput.Tests.fs

@@ -1,4 +1,4 @@
-module Tests.Process.ProcessInput
+module Tests.Process.ProcessInput
 
 open ARCtrl
 open ARCtrl.Process
@@ -22,7 +22,23 @@ let private tests_source =
             let actual =  o_out
             Expect.stringEqual actual expected "Written processInput does not match read process input"
         )
+        testCase "LD_WriteReadWithCharacteristics" (fun () ->
+            let charaHeader = Process.MaterialAttribute.create(CharacteristicType = OntologyAnnotation.create("MyAnnotation","NCIT","http://purl.obolibrary.org/obo/NCIT_C42781"))
+            let charaValue = OntologyAnnotation.create("MyAnnotationValue","NCIT","http://purl.obolibrary.org/obo/NCIT_C42782")
+            let chara = Process.MaterialAttributeValue.create(Category = charaHeader, Value = Value.Ontology charaValue)
+            let source = Source.create(Name = "#sample/sample-P-0.1-aliquot7", Characteristics = [chara])
+            let o_out = ProcessInput.ROCrate.encoder (ProcessInput.Source source) |> Encode.toJsonString 0
+            let inputPI = Decode.fromJsonString ProcessInput.ROCrate.decoder o_out
+            let inputSourceOpt = ProcessInput.trySource inputPI
+            let inputSource = Expect.wantSome inputSourceOpt "Input is not a sample"
+            Expect.equal inputSource.Name source.Name "Sample name did not match"
+            let characteristics = Expect.wantSome inputSource.Characteristics "No characteristics found"
+            Expect.hasLength characteristics 1 "Sample characteristics length did not match"
+            let inputChara = characteristics.[0]
+            Expect.equal inputChara chara "Sample characteristic did not match"
+        )
     ]
+
 let private tests_material =
     testList "Material" [
         testCase "ReaderSuccess" (fun () ->           
@@ -75,6 +91,21 @@ let private tests_sample =
             let actual = o_out
             Expect.stringEqual actual expected "Written processInput does not match read process input"
         )
+        testCase "LD_WriteReadWithCharacteristics" (fun () ->
+            let charaHeader = Process.MaterialAttribute.create(CharacteristicType = OntologyAnnotation.create("MyAnnotation","NCIT","http://purl.obolibrary.org/obo/NCIT_C42781"))
+            let charaValue = OntologyAnnotation.create("MyAnnotationValue","NCIT","http://purl.obolibrary.org/obo/NCIT_C42782")
+            let chara = Process.MaterialAttributeValue.create(Category = charaHeader, Value = Value.Ontology charaValue)
+            let sample = Sample.create(Name = "#sample/sample-P-0.1-aliquot7", Characteristics = [chara])
+            let o_out = ProcessInput.ROCrate.encoder (ProcessInput.Sample sample) |> Encode.toJsonString 0
+            let inputPI = Decode.fromJsonString ProcessInput.ROCrate.decoder o_out
+            let inputSampleOpt = ProcessInput.trySample inputPI
+            let inputSample = Expect.wantSome inputSampleOpt "Input is not a sample"
+            Expect.equal inputSample.Name sample.Name "Sample name did not match"
+            let characteristics = Expect.wantSome inputSample.Characteristics "No characteristics found"
+            Expect.hasLength characteristics 1 "Sample characteristics length did not match"
+            let inputChara = characteristics.[0]
+            Expect.equal inputChara chara "Sample characteristic did not match"
+        )
     ]