some fixes against study idmap test case

Author: HLWeil

src/Json/IDTable.fs

@@ -12,10 +12,15 @@ module IDTable =
 
     type IDTableRead = Dictionary<URI,obj>
 
+    let encodeID id =
+        ["@id",Encode.string id]
+        |> Encode.object
+
     let encode (genID: 'Value -> URI) (encoder : 'Value -> Json) (value : 'Value) (table:IDTableWrite) =
-        match table.TryGetValue(genID value) with
-        | true, v -> v
-        | false, _ -> 
+        let id = genID value
+        if table.ContainsKey id then 
+           encodeID id
+        else
             let v = encoder value
             table.Add(genID value, v)
-            v
+            v            

src/Json/OntologyAnnotation.fs

@@ -22,7 +22,7 @@ module AnnotationValue =
 
 module OntologyAnnotation =  
 
-    let encoder (oa : OntologyAnnotation) = 
+    let encoder (oa : OntologyAnnotation) =         
         [
             Encode.tryInclude "annotationValue" Encode.string (oa.Name)
             Encode.tryInclude "termSource" Encode.string (oa.TermSourceREF)
@@ -127,12 +127,18 @@ module OntologyAnnotation =
 
         let encoder (idMap : IDTable.IDTableWrite option) (oa : OntologyAnnotation) = 
             let f = fun (oa : OntologyAnnotation) ->
+                let comments = 
+                    oa.Comments
+                    |> Seq.filter (fun c -> 
+                        match c.Name with
+                        | Some n when n = Process.ColumnIndex.orderName -> false
+                        | _ -> true)
                 [
                     Encode.tryInclude "@id" Encode.string (ROCrate.genID oa |> Some)
                     Encode.tryInclude "annotationValue" Encode.string (oa.Name)
                     Encode.tryInclude "termSource" Encode.string (oa.TermSourceREF)
                     Encode.tryInclude "termAccession" Encode.string (oa.TermAccessionNumber)
-                    Encode.tryIncludeSeq "comments" Comment.encoder (oa.Comments)
+                    Encode.tryIncludeSeq "comments" Comment.encoder comments
                 ]
                 |> Encode.choose
                 |> Encode.object

src/Json/Process/PropertyValue.fs

@@ -12,9 +12,10 @@ module PropertyValue =
     module ROCrate =
 
         let genID (p : IPropertyValue<'T>) = 
-            match p.GetCategory() with
-            | Some t -> $"{p.GetAdditionalType()}/{OntologyAnnotation.ROCrate.genID t}{p.GetValue()}{p.GetUnit()}"
-            | None -> $"#Empty{p.GetAdditionalType()}"
+            match p.GetCategory(),p.GetValue(),p.GetUnit() with
+            | Some t, Some v, Some u -> $"#{p.GetAdditionalType()}/{t.NameText}={v.Text}{u.NameText}"
+            | Some t, Some v, None-> $"#{p.GetAdditionalType()}/{t.NameText}={v.Text}"
+            | _ -> $"#Empty{p.GetAdditionalType()}"
 
         let encoder<'T> (pv : IPropertyValue<'T>) = 
             let categoryName, categoryURL = 

src/Json/Study.fs

@@ -186,10 +186,20 @@ module Study =
                         n.Add(assay)
                     n
                 let processes = study.GetProcesses()
-                let protocols = ProcessSequence.getProtocols processes
-                let factors = ProcessSequence.getFactors processes
-                let characteristics = ProcessSequence.getCharacteristics processes
-                let units = ProcessSequence.getUnits processes
+                let encodedUnits = 
+                    ProcessSequence.getUnits processes
+                    |> Encode.tryIncludeList "unitCategories" (OntologyAnnotation.ISAJson.encoder idMap) 
+                let encodedFactors = 
+                    ProcessSequence.getFactors processes
+                    |> Encode.tryIncludeList "factors" (Factor.ISAJson.encoder idMap)
+                let encodedCharacteristics =
+                    ProcessSequence.getCharacteristics processes
+                    |> Encode.tryIncludeList "characteristicCategories" (MaterialAttribute.ISAJson.encoder idMap)
+                let encodedMaterials = 
+                    Encode.tryInclude "materials" (StudyMaterials.ISAJson.encoder idMap) (Option.fromValueWithDefault [] processes)
+                let encodedProtocols = 
+                    ProcessSequence.getProtocols processes
+                    |> Encode.tryIncludeList "protocols" (Protocol.ISAJson.encoder (Some s.Identifier) None None idMap)
                 [
                     "@id", Encode.string (study |> ROCrate.genID)
                     "filename", Encode.string fileName
@@ -201,13 +211,13 @@ module Study =
                     Encode.tryIncludeSeq "publications" (Publication.ISAJson.encoder idMap) study.Publications
                     Encode.tryIncludeSeq "people" (Person.ISAJson.encoder idMap) study.Contacts
                     Encode.tryIncludeSeq "studyDesignDescriptors" (OntologyAnnotation.ISAJson.encoder idMap) study.StudyDesignDescriptors
-                    Encode.tryIncludeList "protocols" (Protocol.ISAJson.encoder (Some s.Identifier) None None idMap) protocols
-                    Encode.tryInclude "materials" (StudyMaterials.ISAJson.encoder idMap) (Option.fromValueWithDefault [] processes)
-                    Encode.tryIncludeList "factors" (Factor.ISAJson.encoder idMap) factors
-                    Encode.tryIncludeList "characteristicCategories" (MaterialAttribute.ISAJson.encoder idMap) characteristics     
-                    Encode.tryIncludeList "unitCategories" (OntologyAnnotation.ISAJson.encoder idMap) units
+                    encodedProtocols
+                    encodedMaterials
                     Encode.tryIncludeList "processSequence" (Process.ISAJson.encoder (Some s.Identifier) None idMap) processes
                     Encode.tryIncludeSeq "assays" (Assay.ISAJson.encoder (Some s.Identifier) idMap) assays
+                    encodedFactors
+                    encodedCharacteristics
+                    encodedUnits
                     Encode.tryIncludeSeq "comments" (Comment.ISAJson.encoder idMap) study.Comments
                 ]
                 |> Encode.choose