added doi and pubmed helper functions to LDPropertyValue and LDSchola…

…rlyArticle converters

src/ARCtrl/Conversion.fs

@@ -1000,41 +1000,6 @@ type PersonConversion =
 
 type ScholarlyArticleConversion =
 
-
-    static member doiKey = "DOI"
-
-    static member doiURL = "http://purl.obolibrary.org/obo/OBI_0002110"
-
-    static member pubmedIDKey = "PubMedID"
-
-    static member pubmedIDURL = "http://purl.obolibrary.org/obo/OBI_0001617"
-
-    static member composeDOI (doi : string) : LDNode =
-        LDPropertyValue.create(name = ScholarlyArticleConversion.doiKey, value = doi, propertyID = ScholarlyArticleConversion.doiURL)
-
-    static member tryDecomposeDOI (doi : LDNode, ?context : LDContext) : string option =
-        match
-            LDPropertyValue.tryGetNameAsString(doi, ?context = context),
-            LDPropertyValue.tryGetValueAsString(doi, ?context = context),
-            LDPropertyValue.tryGetPropertyIDAsString(doi, ?context = context)
-        with
-        | Some name, Some value, Some id when name = ScholarlyArticleConversion.doiKey && id = ScholarlyArticleConversion.doiURL ->
-            Some value
-        | _ -> None
-
-    static member composePubMedID (pubMedID : string) : LDNode =
-        LDPropertyValue.create(name = ScholarlyArticleConversion.pubmedIDKey, value = pubMedID, propertyID = ScholarlyArticleConversion.pubmedIDURL)
-
-    static member tryDecomposePubMedID (pubMedID : LDNode, ?context : LDContext) : string option =
-        match
-            LDPropertyValue.tryGetNameAsString(pubMedID, ?context = context),
-            LDPropertyValue.tryGetValueAsString(pubMedID, ?context = context),
-            LDPropertyValue.tryGetPropertyIDAsString(pubMedID, ?context = context)
-        with
-        | Some name, Some value, Some id when name = ScholarlyArticleConversion.pubmedIDKey && id = ScholarlyArticleConversion.pubmedIDURL ->
-            Some value
-        | _ -> None
-
     static member composeAuthor (author : string) : LDNode =
         try 
             ARCtrl.Json.Decode.fromJsonString Json.LDNode.decoder author
@@ -1092,9 +1057,9 @@ type ScholarlyArticleConversion =
             |> Option.fromSeq
         let identifiers = ResizeArray [
             if publication.DOI.IsSome && publication.DOI.Value <> "" then
-                ScholarlyArticleConversion.composeDOI publication.DOI.Value
+                LDPropertyValue.createDOI publication.DOI.Value
             if publication.PubMedID.IsSome && publication.PubMedID.Value <> "" then
-                ScholarlyArticleConversion.composePubMedID publication.PubMedID.Value
+                LDPropertyValue.createPubMedID publication.PubMedID.Value
         ]
         let status = publication.Status |> Option.map BaseTypes.composeDefinedTerm
         let scholarlyArticle = 
@@ -1121,8 +1086,18 @@ type ScholarlyArticleConversion =
             LDScholarlyArticle.tryGetCreativeWorkStatus(sa, ?graph = graph, ?context = context)
             |> Option.map (fun s -> BaseTypes.decomposeDefinedTerm(s, ?context = context))
         let identifiers = LDScholarlyArticle.getIdentifiersAsPropertyValue(sa, ?graph = graph, ?context = context)
-        let pubMedID = identifiers |> ResizeArray.tryPick (fun i -> ScholarlyArticleConversion.tryDecomposePubMedID(i, ?context = context))
-        let doi = identifiers |> ResizeArray.tryPick (fun i -> ScholarlyArticleConversion.tryDecomposeDOI(i, ?context = context))
+        let doi =
+            identifiers
+            |> ResizeArray.tryPick (fun i -> LDPropertyValue.tryGetAsDOI(i, ?context = context))
+            |> function
+               | Some p -> Some p
+               | None -> LDScholarlyArticle.tryGetSameAsAsString(sa, ?context = context)
+        let pubMedID =
+            identifiers
+            |> ResizeArray.tryPick (fun i -> LDPropertyValue.tryGetAsPubMedID(i, ?context = context))
+            |> function
+               | Some p -> Some p
+               | None -> LDScholarlyArticle.tryGetUrlAsString(sa, ?context = context)
         ARCtrl.Publication.create(
             title = title,
             ?authors = authors,

src/ROCrate/Generic/PropertyValue.fs

@@ -22,6 +22,14 @@ type LDPropertyValue =
 
     static member valueReference = "http://schema.org/valueReference"
 
+    static member doiKey = "DOI"
+
+    static member doiURL = "http://purl.obolibrary.org/obo/OBI_0002110"
+
+    static member pubmedIDKey = "PubMedID"
+
+    static member pubmedIDURL = "http://purl.obolibrary.org/obo/OBI_0001617"
+
     static member tryGetNameAsString(pv : LDNode, ?context : LDContext) =
         match pv.TryGetPropertyAsSingleton(LDPropertyValue.name, ?context = context) with
         | Some (:? string as n) -> Some n
@@ -103,6 +111,28 @@ type LDPropertyValue =
         LDPropertyValue.validate(pv, ?context = context)
         && pv.AdditionalType.Contains("FactorValue")
 
+    static member validateDOI (pv : LDNode, ?context : LDContext) =
+        LDPropertyValue.validate(pv, ?context = context)
+        && 
+        match
+            LDPropertyValue.tryGetNameAsString(pv, ?context = context),
+            LDPropertyValue.tryGetValueAsString(pv, ?context = context),
+            LDPropertyValue.tryGetPropertyIDAsString(pv, ?context = context)
+        with
+        | Some name, Some value, Some id when name = LDPropertyValue.doiKey && id = LDPropertyValue.doiURL -> true
+        | _ -> false
+
+    static member validatePubMedID (pv : LDNode, ?context : LDContext) =
+        LDPropertyValue.validate(pv, ?context = context)
+        && 
+        match
+            LDPropertyValue.tryGetNameAsString(pv, ?context = context),
+            LDPropertyValue.tryGetValueAsString(pv, ?context = context),
+            LDPropertyValue.tryGetPropertyIDAsString(pv, ?context = context)
+        with
+        | Some name, Some value, Some id when name = LDPropertyValue.pubmedIDKey && id = LDPropertyValue.pubmedIDURL -> true
+        | _ -> false
+
     static member genId(name : string, ?value : string, ?propertyID : string, ?prefix) =
         let prefix = Option.defaultValue "PV" prefix
         match value,propertyID with
@@ -168,4 +198,22 @@ type LDPropertyValue =
                  | None -> LDPropertyValue.genIdFactorValue(name, ?value = value, ?propertyID = propertyID)
         let fv = LDPropertyValue.create(name, id = id, ?value = value, ?propertyID = propertyID, ?unitCode = unitCode, ?unitText = unitText, ?valueReference = valueReference, ?context = context)
         fv.AdditionalType <- ResizeArray ["FactorValue"]
-        fv
+        fv
+
+    static member createDOI(value, ?context : LDContext) =
+        let id = value
+        LDPropertyValue.create(name = LDPropertyValue.doiKey, value = value, id = id, propertyID = LDPropertyValue.doiURL, ?context = context)
+
+    static member createPubMedID(value, ?context : LDContext) =
+        let id = value
+        LDPropertyValue.create(name = LDPropertyValue.pubmedIDKey, value = value, id = id, propertyID = LDPropertyValue.pubmedIDURL, ?context = context)
+
+    static member tryGetAsDOI(pv : LDNode, ?context : LDContext) =
+        if LDPropertyValue.validateDOI(pv, ?context = context) then
+            Some (LDPropertyValue.getValueAsString(pv, ?context = context))
+        else None
+
+    static member tryGetAsPubMedID(pv : LDNode, ?context : LDContext) =
+        if LDPropertyValue.validatePubMedID(pv, ?context = context) then
+            Some (LDPropertyValue.getValueAsString(pv, ?context = context))
+        else None

src/ROCrate/Generic/ScholarlyArticle.fs

@@ -18,6 +18,8 @@ type LDScholarlyArticle =
 
     static member url = "http://schema.org/url"
 
+    static member sameAs = "http://schema.org/sameAs"
+
     static member creativeWorkStatus = "http://schema.org/creativeWorkStatus"
 
     static member comment = "http://schema.org/comment"
@@ -53,13 +55,15 @@ type LDScholarlyArticle =
     static member setAuthors(s : LDNode, authors : ResizeArray<LDNode>, ?context : LDContext) =
         s.SetProperty(LDScholarlyArticle.author, authors, ?context = context)
 
-    static member tryGetUrl(s : LDNode, ?context : LDContext) =
+    static member tryGetUrlAsString(s : LDNode, ?context : LDContext) =
         match s.TryGetPropertyAsSingleton(LDScholarlyArticle.url, ?context = context) with
         | Some (:? string as u) -> Some u
         | _ -> None
 
-    static member setUrl(s : LDNode, u : string, ?context : LDContext) =
-        s.SetProperty(LDScholarlyArticle.url, u, ?context = context)
+    static member tryGetSameAsAsString(s : LDNode, ?context : LDContext) =
+        match s.TryGetPropertyAsSingleton(LDScholarlyArticle.sameAs, ?context = context) with
+        | Some (:? string as sa) -> Some sa
+        | _ -> None
 
     static member tryGetCreativeWorkStatus(s : LDNode, ?graph : LDGraph, ?context : LDContext) =
         match s.TryGetPropertyAsSingleNode(LDScholarlyArticle.creativeWorkStatus, ?graph  = graph, ?context = context) with

tests/ARCtrl/ROCrateConversion.Tests.fs

@@ -1071,6 +1071,17 @@ let tests_Publication =
             let p' = ScholarlyArticleConversion.decomposeScholarlyArticle ro_Publication
             Expect.equal p' p "Publication should match"
         )
+        testCase "DOI_PubMedID_FromScaffold_ToDeprecatedROCrate" (fun () ->
+            let doi = "10.1234/5678"
+            let pubMedID = "12345678"
+            let p = ARCtrl.Publication.create(title = "My Paper", doi = doi, pubMedID = pubMedID)
+            let json =
+                Json.Publication.ROCrate.encoder p
+                |> Json.Encode.toJsonString 0
+            let ldNode = Json.Decode.fromJsonString Json.LDNode.decoder json
+            let p' = ScholarlyArticleConversion.decomposeScholarlyArticle ldNode
+            Expect.equal p' p "Publication should match"
+        )
         testCase "Full_FromScaffold_Flattened" (fun () ->
             let authors = "Lukas Weil, John Doe"
             let comment = Comment("MyCommentKey","MyCommentValue")