new ro-crate export and context files

nfdi4plants · Mar 21, 2024 · 9b0d7b7 · 9b0d7b7
1 parent 0fb24ee
commit 9b0d7b7
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Showing 36 changed files with 349 additions and 331 deletions.
diff --git a/src/ISA/ISA.Json/ArcTypes/ArcAssay.fs b/src/ISA/ISA.Json/ArcTypes/ArcAssay.fs
@@ -103,11 +103,11 @@ module ArcAssay =
 
     /// exports in json-ld format
     let toJsonldString (a:ArcAssay) = 
-        Assay.encoder (ConverterOptions(SetID=true,IncludeType=true)) None (a.ToAssay())
+        Assay.encoder (ConverterOptions(SetID=true,IsJsonLD=true)) None (a.ToAssay())
         |> GEncode.toJsonString 2
 
     let toJsonldStringWithContext (a:ArcAssay) = 
-        Assay.encoder (ConverterOptions(SetID=true,IncludeType=true,IncludeContext=true)) None (a.ToAssay())
+        Assay.encoder (ConverterOptions(SetID=true,IsJsonLD=true)) None (a.ToAssay())
         |> GEncode.toJsonString 2
 
     let fromJsonString (s:string) = 

diff --git a/src/ISA/ISA.Json/ArcTypes/ArcInvestigation.fs b/src/ISA/ISA.Json/ArcTypes/ArcInvestigation.fs
@@ -59,11 +59,11 @@ module ArcInvestigation =
 
     /// exports in json-ld format
     let toJsonldString (a:ArcInvestigation) = 
-        Investigation.encoder (ConverterOptions(SetID=true,IncludeType=true)) (a.ToInvestigation())
+        Investigation.encoder (ConverterOptions(SetID=true,IsJsonLD=true)) (a.ToInvestigation())
         |> GEncode.toJsonString 2
 
     let toJsonldStringWithContext (a:ArcInvestigation) = 
-        Investigation.encoder (ConverterOptions(SetID=true,IncludeType=true,IncludeContext=true)) (a.ToInvestigation())
+        Investigation.encoder (ConverterOptions(SetID=true,IsJsonLD=true)) (a.ToInvestigation())
         |> GEncode.toJsonString 2
 
     let fromJsonString (s:string) = 

diff --git a/src/ISA/ISA.Json/ArcTypes/ArcStudy.fs b/src/ISA/ISA.Json/ArcTypes/ArcStudy.fs
@@ -102,11 +102,11 @@ module ArcStudy =
 
     /// exports in json-ld format
     let toJsonldString (a:ArcStudy) (assays: ResizeArray<ArcAssay>) = 
-        Study.encoder (ConverterOptions(SetID=true,IncludeType=true)) (a.ToStudy(assays))
+        Study.encoder (ConverterOptions(SetID=true,IsJsonLD=true)) (a.ToStudy(assays))
         |> GEncode.toJsonString 2
 
     let toJsonldStringWithContext (a:ArcStudy) (assays: ResizeArray<ArcAssay>) = 
-        Study.encoder (ConverterOptions(SetID=true,IncludeType=true,IncludeContext=true)) (a.ToStudy(assays))
+        Study.encoder (ConverterOptions(SetID=true,IsJsonLD=true)) (a.ToStudy(assays))
         |> GEncode.toJsonString 2
 
     let fromJsonString (s:string) = 

diff --git a/src/ISA/ISA.Json/Assay.fs b/src/ISA/ISA.Json/Assay.fs
@@ -31,7 +31,7 @@ module Assay =
         match a.ID with
         | Some id -> URI.toString id
         | None -> match a.FileName with
-                  | Some n -> n.Replace(" ","_").Remove(0,1 + (max (n.LastIndexOf('/')) (n.LastIndexOf('\\'))))
+                  | Some n -> n.Replace(" ","_")//.Remove(0,1 + (max (n.LastIndexOf('/')) (n.LastIndexOf('\\'))))
                   | None -> "#EmptyAssay"
 
     let encoder (options : ConverterOptions) (studyName:string Option) (oa : Assay) = 
@@ -42,32 +42,25 @@ module Assay =
                     | None -> None
                 with 
                     | Failure(msg) -> None
-        let a = ["Assay";"ArcAssay"]
         [
             if options.SetID then 
                 "@id", Encode.string (oa |> genID)
             else 
                 GEncode.tryInclude "@id" Encode.string (oa.ID)
-            if options.IncludeType then 
-                "@type", (Encode.list [ Encode.string "Assay"; Encode.string "ArcAssay"])
+            if options.IsJsonLD then 
+                "@type", (Encode.list [ Encode.string "Assay"])
             GEncode.tryInclude "filename" Encode.string (oa.FileName)
             GEncode.tryInclude "measurementType" (OntologyAnnotation.encoder options) (oa.MeasurementType)
             GEncode.tryInclude "technologyType" (OntologyAnnotation.encoder options) (oa.TechnologyType)
             GEncode.tryInclude "technologyPlatform" Encode.string (oa.TechnologyPlatform)
             GEncode.tryIncludeList "dataFiles" (Data.encoder options) (oa.DataFiles)
-            if options.IsRoCrate then
-                match oa.Materials with
-                | Some m -> 
-                    GEncode.tryIncludeList "samples" (Sample.encoder options) m.Samples
-                    GEncode.tryIncludeList "materials" (Material.encoder options) m.OtherMaterials
-                | None -> ()
-            if not options.IsRoCrate then
+            if not options.IsJsonLD then
                 GEncode.tryInclude "materials" (AssayMaterials.encoder options) oa.Materials
-            GEncode.tryIncludeList "characteristicCategories" (MaterialAttribute.encoder options) (oa.CharacteristicCategories)
-            GEncode.tryIncludeList "unitCategories" (OntologyAnnotation.encoder options) (oa.UnitCategories)
+                GEncode.tryIncludeList "characteristicCategories" (MaterialAttribute.encoder options) (oa.CharacteristicCategories)
+                GEncode.tryIncludeList "unitCategories" (OntologyAnnotation.encoder options) (oa.UnitCategories)
             GEncode.tryIncludeList "processSequence" (Process.encoder options studyName assayName) (oa.ProcessSequence)
             GEncode.tryIncludeList "comments" (Comment.encoder options) (oa.Comments)
-            if options.IncludeContext then
+            if options.IsJsonLD then
                 "@context", ROCrateContext.Assay.context_jsonvalue
         ]
         |> GEncode.choose
@@ -101,11 +94,11 @@ module Assay =
 
     /// exports in json-ld format
     let toJsonldString (a:Assay) = 
-        encoder (ConverterOptions(SetID=true,IncludeType=true)) None a
+        encoder (ConverterOptions(SetID=true,IsJsonLD=true)) None a
         |> GEncode.toJsonString 2
 
     let toJsonldStringWithContext (a:Assay) = 
-        encoder (ConverterOptions(SetID=true,IncludeType=true,IncludeContext=true)) None a
+        encoder (ConverterOptions(SetID=true,IsJsonLD=true)) None a
         |> GEncode.toJsonString 2
 
     //let fromFile (path : string) = 

diff --git a/src/ISA/ISA.Json/Comment.fs b/src/ISA/ISA.Json/Comment.fs
@@ -25,11 +25,11 @@ module Comment =
                 "@id", Encode.string (comment |> genID)
             else 
                 GEncode.tryInclude "@id" Encode.string (comment.ID)
-            if options.IncludeType then 
+            if options.IsJsonLD then 
                 "@type", Encode.string "Comment"
             GEncode.tryInclude "name" Encode.string (comment.Name)
             GEncode.tryInclude "value" Encode.string (comment.Value)
-            if options.IncludeContext then
+            if options.IsJsonLD then
                 "@context", ROCrateContext.Comment.context_jsonvalue
         ]
         |> GEncode.choose
@@ -53,11 +53,11 @@ module Comment =
 
     /// exports in json-ld format
     let toJsonldString (c:Comment) = 
-        encoder (ConverterOptions(SetID=true,IncludeType=true)) c
+        encoder (ConverterOptions(SetID=true,IsJsonLD=true)) c
         |> GEncode.toJsonString 2
 
     let toJsonldStringWithContext (a:Comment) = 
-        encoder (ConverterOptions(SetID=true,IncludeType=true,IncludeContext=true)) a
+        encoder (ConverterOptions(SetID=true,IsJsonLD=true)) a
         |> GEncode.toJsonString 2
 
     //let fromFile (path : string) = 

diff --git a/src/ISA/ISA.Json/ConverterOptions.fs b/src/ISA/ISA.Json/ConverterOptions.fs
@@ -3,15 +3,9 @@
 type ConverterOptions() = 
 
     let mutable setID = false
-    let mutable includeType = false
-    let mutable includeContext = false
-    let mutable isRoCrate = false
+    let mutable isJsonLD = false
 
     member this.SetID with get() = setID
                       and set(setId) = setID <- setId
-    member this.IncludeType with get() = includeType
-                            and set(iT) = includeType <- iT
-    member this.IncludeContext with get() = includeContext
-                               and set(iC) = includeContext <- iC
-    member this.IsRoCrate with get() = isRoCrate
-                          and set(iR) = isRoCrate <- iR
+    member this.IsJsonLD with get() = isJsonLD
+                            and set(iJ) = isJsonLD <- iJ
diff --git a/src/ISA/ISA.Json/Data.fs b/src/ISA/ISA.Json/Data.fs
@@ -45,12 +45,12 @@ module Data =
                 "@id", Encode.string (oa |> genID)
             else 
                 GEncode.tryInclude "@id" Encode.string (oa.ID)
-            if options.IncludeType then 
-                "@type", (Encode.list [Encode.string "Data"; Encode.string "ArcData"])
+            if options.IsJsonLD then 
+                "@type", (Encode.list [Encode.string "Data"])
             GEncode.tryInclude "name" Encode.string (oa.Name)
             GEncode.tryInclude "type" (DataFile.encoder options) (oa.DataType)
             GEncode.tryIncludeList "comments" (Comment.encoder options) (oa.Comments)
-            if options.IncludeContext then
+            if options.IsJsonLD then
                 "@context", ROCrateContext.Data.context_jsonvalue
         ]
         |> GEncode.choose
@@ -78,10 +78,10 @@ module Data =
 
     /// exports in json-ld format
     let toJsonldString (d:Data) = 
-        encoder (ConverterOptions(SetID=true,IncludeType=true)) d
+        encoder (ConverterOptions(SetID=true,IsJsonLD=true)) d
         |> GEncode.toJsonString 2
     let toJsonldStringWithContext (a:Data) = 
-        encoder (ConverterOptions(SetID=true,IncludeType=true,IncludeContext=true)) a
+        encoder (ConverterOptions(SetID=true,IsJsonLD=true)) a
         |> GEncode.toJsonString 2
 
     //let fromFile (path : string) = 
@@ -107,11 +107,11 @@ module Source =
                 "@id", Encode.string (oa |> genID)
             else 
                 GEncode.tryInclude "@id" Encode.string (oa.ID)
-            if options.IncludeType then 
-                "@type", (Encode.list [ Encode.string "Source"; Encode.string "ArcSource"])
+            if options.IsJsonLD then 
+                "@type", (Encode.list [ Encode.string "Source"])
             GEncode.tryInclude "name" Encode.string (oa.Name)
             GEncode.tryIncludeList "characteristics" (MaterialAttributeValue.encoder options) (oa.Characteristics)      
-            if options.IncludeContext then
+            if options.IsJsonLD then
                 "@context", ROCrateContext.Source.context_jsonvalue
             ]
         |> GEncode.choose
@@ -139,11 +139,11 @@ module Source =
 
     /// exports in json-ld format
     let toJsonldString (s:Source) = 
-        encoder (ConverterOptions(SetID=true,IncludeType=true)) s
+        encoder (ConverterOptions(SetID=true,IsJsonLD=true)) s
         |> GEncode.toJsonString 2
 
     let toJsonldStringWithContext (a:Source) = 
-        encoder (ConverterOptions(SetID=true,IncludeType=true,IncludeContext=true)) a
+        encoder (ConverterOptions(SetID=true,IsJsonLD=true)) a
         |> GEncode.toJsonString 2
 
     //let fromFile (path : string) = 
@@ -168,13 +168,14 @@ module Sample =
                 "@id", Encode.string (oa |> genID)
             else 
                 GEncode.tryInclude "@id" Encode.string (oa.ID)
-            if options.IncludeType then 
-                "@type", (Encode.list [ Encode.string "Sample";  Encode.string "ArcSample"])
+            if options.IsJsonLD then 
+                "@type", (Encode.list [ Encode.string "Sample"])
             GEncode.tryInclude "name" Encode.string (oa.Name)
             GEncode.tryIncludeList "characteristics" (MaterialAttributeValue.encoder options) (oa.Characteristics)
             GEncode.tryIncludeList "factorValues" (FactorValue.encoder options) (oa.FactorValues)
-            GEncode.tryIncludeList "derivesFrom" (Source.encoder options) (oa.DerivesFrom)
-            if options.IncludeContext then
+            if not options.IsJsonLD then 
+                GEncode.tryIncludeList "derivesFrom" (Source.encoder options) (oa.DerivesFrom)
+            if options.IsJsonLD then
                 "@context", ROCrateContext.Sample.context_jsonvalue
         ]
         |> GEncode.choose
@@ -203,11 +204,11 @@ module Sample =
 
     /// exports in json-ld format
     let toJsonldString (s:Sample) = 
-        encoder (ConverterOptions(SetID=true,IncludeType=true)) s
+        encoder (ConverterOptions(SetID=true,IsJsonLD=true)) s
         |> GEncode.toJsonString 2
 
     let toJsonldStringWithContext (a:Sample) = 
-        encoder (ConverterOptions(SetID=true,IncludeType=true,IncludeContext=true)) a
+        encoder (ConverterOptions(SetID=true,IsJsonLD=true)) a
         |> GEncode.toJsonString 2
 
     //let fromFile (path : string) = 

diff --git a/src/ISA/ISA.Json/Factor.fs b/src/ISA/ISA.Json/Factor.fs
@@ -68,12 +68,18 @@ module Factor =
                 "@id", Encode.string (oa |> genID)
             else 
                 GEncode.tryInclude "@id" Encode.string (oa.ID)
-            if options.IncludeType then 
-                "@type", (Encode.list [Encode.string "Factor"; Encode.string "ArcFactor"])
+            if options.IsJsonLD then 
+                "@type", (Encode.list [Encode.string "Factor"])
             GEncode.tryInclude "factorName" Encode.string (oa.Name)
-            GEncode.tryInclude "factorType" (OntologyAnnotation.encoder options) (oa.FactorType)
+            if options.IsJsonLD then
+                if oa.FactorType.IsSome then
+                    GEncode.tryInclude "annotationValue" Encode.string (oa.Name)
+                    GEncode.tryInclude "termSource" Encode.string (oa.FactorType.Value.TermSourceREF)
+                    GEncode.tryInclude "termAccession" Encode.string (oa.FactorType.Value.TermAccessionNumber)
+            else
+                GEncode.tryInclude "factorType" (OntologyAnnotation.encoder options) (oa.FactorType)
             GEncode.tryIncludeArray "comments" (Comment.encoder options) (oa.Comments)
-            if options.IncludeContext then
+            if options.IsJsonLD then
                 "@context", ROCrateContext.Factor.context_jsonvalue
         ]
         |> GEncode.choose
@@ -98,11 +104,11 @@ module Factor =
 
     /// exports in json-ld format
     let toJsonldString (f:Factor) = 
-        encoder (ConverterOptions(SetID=true,IncludeType=true)) f
+        encoder (ConverterOptions(SetID=true,IsJsonLD=true)) f
         |> GEncode.toJsonString 2
 
     let toJsonldStringWithContext (a:Factor) = 
-        encoder (ConverterOptions(SetID=true,IncludeType=true,IncludeContext=true)) a
+        encoder (ConverterOptions(SetID=true,IsJsonLD=true)) a
         |> GEncode.toJsonString 2
 
     //let fromFile (path : string) = 
@@ -126,12 +132,25 @@ module FactorValue =
                 "@id", Encode.string (oa |> genID)
             else 
                 GEncode.tryInclude "@id" Encode.string (oa.ID)
-            if options.IncludeType then 
-                "@type", (Encode.list [Encode.string "FactorValue"; Encode.string "ArcFactorValue"])
-            GEncode.tryInclude "category" (Factor.encoder options) (oa.Category)
-            GEncode.tryInclude "value" (Value.encoder options) (oa.Value)
-            GEncode.tryInclude "unit" (OntologyAnnotation.encoder options) (oa.Unit)
-            if options.IncludeContext then
+            if options.IsJsonLD then 
+                "@type", (Encode.list [Encode.string "FactorValue"])
+            if options.IsJsonLD then
+                if oa.Category.IsSome then
+                    GEncode.tryInclude "categoryName" Encode.string (oa.Category.Value.Name)
+                if oa.Category.IsSome && oa.Category.Value.FactorType.IsSome then
+                    GEncode.tryInclude "category" Encode.string (oa.Category.Value.FactorType.Value.Name)
+                if oa.Category.IsSome && oa.Category.Value.FactorType.IsSome then
+                    GEncode.tryInclude "categoryCode" Encode.string (oa.Category.Value.FactorType.Value.TermAccessionNumber)
+                if oa.Value.IsSome then "value", Encode.string (oa.ValueText)
+                if oa.Value.IsSome && oa.Value.Value.IsAnOntology then
+                    GEncode.tryInclude "valueCode" Encode.string (oa.Value.Value.AsOntology()).TermAccessionNumber
+                if oa.Unit.IsSome then GEncode.tryInclude "unit" Encode.string (oa.Unit.Value.Name)
+                if oa.Unit.IsSome then GEncode.tryInclude "unitCode" Encode.string (oa.Unit.Value.TermAccessionNumber)
+            else
+                GEncode.tryInclude "category" (Factor.encoder options) (oa.Category)
+                GEncode.tryInclude "value" (Value.encoder options) (oa.Value)
+                GEncode.tryInclude "unit" (OntologyAnnotation.encoder options) (oa.Unit)
+            if options.IsJsonLD then
                 "@context", ROCrateContext.FactorValue.context_jsonvalue
         ]
         |> GEncode.choose
@@ -156,11 +175,11 @@ module FactorValue =
 
     /// exports in json-ld format
     let toJsonldString (f:FactorValue) = 
-        encoder (ConverterOptions(SetID=true,IncludeType=true)) f
+        encoder (ConverterOptions(SetID=true,IsJsonLD=true)) f
         |> GEncode.toJsonString 2
 
     let toJsonldStringWithContext (a:FactorValue) = 
-        encoder (ConverterOptions(SetID=true,IncludeType=true,IncludeContext=true)) a
+        encoder (ConverterOptions(SetID=true,IsJsonLD=true)) a
         |> GEncode.toJsonString 2
 
     //let fromFile (path : string) = 

diff --git a/src/ISA/ISA.Json/Investigation.fs b/src/ISA/ISA.Json/Investigation.fs
@@ -25,20 +25,21 @@ module Investigation =
                 "@id", Encode.string (oa |> genID)
             else 
                 GEncode.tryInclude "@id" Encode.string (oa.ID)
-            if options.IncludeType then 
+            if options.IsJsonLD then 
                 "@type", Encode.string "Investigation"
             GEncode.tryInclude "filename" Encode.string (oa.FileName)
             GEncode.tryInclude "identifier" Encode.string (oa.Identifier)
             GEncode.tryInclude "title" Encode.string (oa.Title)
             GEncode.tryInclude "description" Encode.string (oa.Description)
             GEncode.tryInclude "submissionDate" Encode.string (oa.SubmissionDate)
             GEncode.tryInclude "publicReleaseDate" Encode.string (oa.PublicReleaseDate)
-            GEncode.tryIncludeList "ontologySourceReferences" (OntologySourceReference.encoder options) (oa.OntologySourceReferences)
+            if not options.IsJsonLD then
+                GEncode.tryIncludeList "ontologySourceReferences" (OntologySourceReference.encoder options) (oa.OntologySourceReferences)
             GEncode.tryIncludeList "publications" (Publication.encoder options) (oa.Publications)
             GEncode.tryIncludeList "people" (Person.encoder options) (oa.Contacts)
             GEncode.tryIncludeList "studies" (Study.encoder options) (oa.Studies)
             GEncode.tryIncludeList "comments" (Comment.encoder options) (oa.Comments)
-            if options.IncludeContext then
+            if options.IsJsonLD then
                 "@context", ROCrateContext.Investigation.context_jsonvalue
         ]
         |> GEncode.choose
@@ -50,7 +51,7 @@ module Investigation =
             GEncode.tryInclude "@id" Encode.string (Some "ro-crate-metadata.json")
             GEncode.tryInclude "about" (encoder options) (Some oa)
             "conformsTo", ROCrateContext.ROCrate.conformsTo_jsonvalue
-            if options.IncludeContext then
+            if options.IsJsonLD then
                 "@context", ROCrateContext.ROCrate.context_jsonvalue
             ]
         |> GEncode.choose
@@ -87,13 +88,13 @@ module Investigation =
 
     /// exports in json-ld format
     let toJsonldString (i:Investigation) = 
-        encoder (ConverterOptions(SetID=true,IncludeType=true)) i
+        encoder (ConverterOptions(SetID=true,IsJsonLD=true)) i
         |> GEncode.toJsonString 2
 
     let toJsonldStringWithContext (i:Investigation) = 
-        encoder (ConverterOptions(SetID=true,IncludeType=true,IncludeContext=true)) i
+        encoder (ConverterOptions(SetID=true,IsJsonLD=true)) i
         |> GEncode.toJsonString 2
 
     let toRoCrateString (i:Investigation) = 
-        encodeRoCrate (ConverterOptions(SetID=true,IncludeType=true,IncludeContext=true,IsRoCrate=true)) i
+        encodeRoCrate (ConverterOptions(SetID=true,IsJsonLD=true)) i
         |> GEncode.toJsonString 2