hotfix parsing of old json-ld samples and sources

Author: HLWeil

src/Json/Process/Sample.fs

@@ -54,6 +54,12 @@ module Sample =
         let decoder : Decoder<Sample> =         
 
             Decode.object (fun get ->
+                match get.Optional.Field "additionalType" Decode.uri with
+                | Some "Sample" | None -> ()
+                | Some _ -> get.Required.Field "FailBecauseNotSample" Decode.unit
+                match get.Optional.Field "@type" (Decode.list Decode.string) with
+                | Some ["Sample"] | None -> ()
+                | Some _ -> get.Required.Field "FailBecauseNotSample" Decode.unit
                 let additionalProperties = get.Optional.Field "additionalProperties" (Decode.list additionalPropertyDecoder)
                 let characteristics,factors = 
                     match additionalProperties with
@@ -65,9 +71,6 @@ 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

@@ -33,6 +33,10 @@ module Source =
                 match get.Optional.Field "additionalType" Decode.uri with
                 | Some "Source" | None -> ()
                 | Some _ -> get.Required.Field "FailBecauseNotSample" Decode.unit
+                match get.Optional.Field "@type" (Decode.list Decode.string) 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

tests/Json/Process/ProcessInput.Tests.fs

@@ -6,6 +6,70 @@ open ARCtrl.Json
 open TestingUtils
 open TestObjects.Json
 
+let deprecated_ROCrate_SourceObject = """{
+    "@id": "#Source_HOR_3369",
+    "@type": [
+        "Source"
+    ],
+    "name": "HOR 3369",
+    "characteristics": [
+        {
+            "@id": "#MaterialAttributeValue/Organism=Hordeum vulgare",
+            "@type": "PropertyValue",
+            "additionalType": "MaterialAttributeValue",
+            "category": "Organism",
+            "categoryCode": "MIAPPE:0041",
+            "value": "Hordeum vulgare",
+            "valueCode": "http://purl.obolibrary.org/obo/NCBITaxon_4513",
+            "@context": {
+                "sdo": "http://schema.org/",
+                "additionalType": "sdo:additionalType",
+                "alternateName": "sdo:alternateName",
+                "measurementMethod": "sdo:measurementMethod",
+                "description": "sdo:description",
+                "category": "sdo:name",
+                "categoryCode": "sdo:propertyID",
+                "value": "sdo:value",
+                "valueCode": "sdo:valueReference",
+                "unit": "sdo:unitText",
+                "unitCode": "sdo:unitCode",
+                "comments": "sdo:disambiguatingDescription"
+            }
+}]}"""
+
+let deprecated_ROCrate_SampleObject = """{
+    "@id": "#Sample_HOR_3369",
+    "@type": [
+        "Sample"
+    ],
+    "name": "HOR 3369",
+    "additionalProperties": [
+        {
+            "@id": "#MaterialAttributeValue/Organism=Hordeum vulgare",
+            "@type": "PropertyValue",
+            "additionalType": "MaterialAttributeValue",
+            "category": "Organism",
+            "categoryCode": "MIAPPE:0041",
+            "value": "Hordeum vulgare",
+            "valueCode": "http://purl.obolibrary.org/obo/NCBITaxon_4513",
+            "@context": {
+                "sdo": "http://schema.org/",
+                "additionalType": "sdo:additionalType",
+                "alternateName": "sdo:alternateName",
+                "measurementMethod": "sdo:measurementMethod",
+                "description": "sdo:description",
+                "category": "sdo:name",
+                "categoryCode": "sdo:propertyID",
+                "value": "sdo:value",
+                "valueCode": "sdo:valueReference",
+                "unit": "sdo:unitText",
+                "unitCode": "sdo:unitCode",
+                "comments": "sdo:disambiguatingDescription"
+            }
+}]}"""
+
+
+
 let private tests_source =
     testList "Source" [
         testCase "ReaderSuccess" (fun () -> 
@@ -37,6 +101,19 @@ let private tests_source =
             let inputChara = characteristics.[0]
             Expect.equal inputChara chara "Sample characteristic did not match"
         )
+        testCase "LD_ReadDeprecatedWithCharacteristics" (fun () ->
+            let inputPI = Decode.fromJsonString ProcessInput.ROCrate.decoder deprecated_ROCrate_SourceObject
+            let inputSourceOpt = ProcessInput.trySource inputPI
+            let inputSource = Expect.wantSome inputSourceOpt "Input is not a sample"
+            Expect.equal inputSource.Name.Value "HOR 3369" "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.NameText "Organism" "Sample characteristic name did not match"
+            Expect.equal inputChara.ValueText "Hordeum vulgare" "Sample characteristic value did not match"
+        )
+
+        
     ]
 
 let private tests_material =
@@ -106,6 +183,18 @@ let private tests_sample =
             let inputChara = characteristics.[0]
             Expect.equal inputChara chara "Sample characteristic did not match"
         )
+        testCase "LD_ReadDeprecatedWithCharacteristics" (fun () ->
+            let inputPI = Decode.fromJsonString ProcessInput.ROCrate.decoder deprecated_ROCrate_SampleObject
+            let inputSampleOpt = ProcessInput.trySample inputPI
+            let inputSample = Expect.wantSome inputSampleOpt "Input is not a sample"
+            Expect.equal inputSample.Name.Value "HOR 3369" "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.NameText "Organism" "Sample characteristic name did not match"
+            Expect.equal inputChara.ValueText "Hordeum vulgare" "Sample characteristic value did not match"
+        
+        )
     ]