Merge pull request #28 from nfdi4plants/rework-cv

Type model and API rework

src/ARCTokenization/Address.fs

@@ -4,11 +4,11 @@ open ControlledVocabulary
 
 module Address = 
 
-    let column : CvTerm = "http://purl.obolibrary.org/obo/NCIT_C43379","Column","NCIT"
+    let column = CvTerm.create(accession = "http://purl.obolibrary.org/obo/NCIT_C43379", name = "Column", ref = "NCIT")
 
-    let row : CvTerm = "http://purl.obolibrary.org/obo/NCIT_C43378","Row","NCIT"
+    let row = CvTerm.create(accession = "http://purl.obolibrary.org/obo/NCIT_C43378", name = "Row", ref = "NCIT")
 
-    let worksheet : CvTerm = "http://purl.obolibrary.org/obo/NCIT_C73541","Worksheet","NCIT"
+    let worksheet = CvTerm.create(accession = "http://purl.obolibrary.org/obo/NCIT_C73541", name = "Worksheet", ref = "NCIT")
 
     //"isa_investigation!A1"
 

src/ARCTokenization/AnnotationTable.fs

@@ -151,7 +151,7 @@ module AnnotationTable =
                     let cvPars =
                         List.map4 (
                             fun (vl : FsCell) unt tan tsr -> 
-                                let valTerm = CvUnit(tan.Value, vl.Value, tsr.Value)
+                                let valTerm = CvUnit.create(accession = tan.Value, name = vl.Value, ref = tsr.Value)
                                 CvParam(d.Value, a.Value, c.Value, WithCvUnitAccession (unt.Value, valTerm))
                         ) dataCellsVal dataCellsUnt dataCellsTan dataCellsTsr 
                     yield! cvPars
@@ -166,7 +166,7 @@ module AnnotationTable =
                         (dataCellsVal, dataCellsTsr, dataCellsTan)
                         |||> List.map3 (
                             fun vl tsr tan ->
-                                let valTerm = CvTerm(tan.Value, vl.Value, tsr.Value)
+                                let valTerm = CvTerm.create(accession = tan.Value, name = vl.Value, ref = tsr.Value)
                                 CvParam(c.Value, a.Value, b.Value, CvValue valTerm)
                         )
                     yield! cvPars
@@ -182,7 +182,7 @@ module AnnotationTable =
                             (dataCellsVal, dataCellsTsr)
                             ||> List.map2 (
                                 fun vl tsr ->
-                                    let valTerm = CvTerm("(n/a)", vl.Value, tsr.Value)
+                                    let valTerm = CvTerm.create (accession = "(n/a)", name = vl.Value, ref = tsr.Value)
                                     CvParam("n/a", a.Value, b.Value, CvValue valTerm)
                             )
                         yield! cvPars
@@ -195,7 +195,7 @@ module AnnotationTable =
                             (dataCellsTsr, dataCellsTan)
                             ||> List.map2 (
                                 fun tsr tan ->
-                                    let valTerm = CvTerm(tan.Value, "n/a", tsr.Value)
+                                    let valTerm = CvTerm.create(accession = tan.Value, name = "n/a", ref = tsr.Value)
                                     CvParam(b.Value, "(n/a)", a.Value, CvValue valTerm)
                             )
                         yield! cvPars

src/ARCTokenization/MetadataSheet.fs

@@ -9,7 +9,7 @@ module MetadataSheet =
 
     let (|Term|_|) (terms : CvTerm list) (key : string) : CvTerm Option =
         terms 
-        |> List.tryFind (fun (term) -> CvTerm.getName term = key)
+        |> List.tryFind (fun (term) -> term.Name = key)
 
     let (|UnMatchable|) (key : string) : string =
         key

src/ARCTokenization/Terms.fs

@@ -24,7 +24,7 @@ module InvestigationMetadata =
 
     let cvTerms = 
         ontology.Terms
-        |> List.map (fun t -> CvTerm(t.Id,t.Name,"INVMSO"))
+        |> List.map (fun t -> CvTerm.create(accession = t.Id, name = t.Name, ref = "INVMSO"))
 
 module StudyMetadata =
 
@@ -34,7 +34,7 @@ module StudyMetadata =
 
     let cvTerms = 
         ontology.Terms
-        |> List.map (fun t -> CvTerm(t.Id,t.Name,"STDMSO"))    
+        |> List.map (fun t -> CvTerm.create(accession = t.Id, name = t.Name, ref ="STDMSO"))    
 
 module AssayMetadata = 
 
@@ -44,8 +44,8 @@ module AssayMetadata =
 
     let cvTerms = 
         ontology.Terms
-        |> List.map (fun t -> CvTerm(t.Id,t.Name,"ASSMSO"))
+        |> List.map (fun t -> CvTerm.create(accession = t.Id, name = t.Name, ref ="ASSMSO"))
 
 module StructuralTerms =
 
-    let metadataSectionKey = CvTerm("AGMO:00000001","Metadata Section Key","AGMO")
+    let metadataSectionKey = CvTerm.create(accession = "AGMO:00000001", name = "Metadata Section Key", ref = "AGMO")

src/ControlledVocabulary/CvAttributeCollection.fs

@@ -39,7 +39,7 @@ type CvAttributeCollection(attributes : IDictionary<string,IParam>) =
 
     /// Retrieves an IParam attribute by its term, if it exists, else returns None
     member this.TryGetAttribute (term : CvTerm) =
-        Dictionary.tryFind (CvTerm.getName term) this
+        Dictionary.tryFind term.Name this
         |> Option.bind (fun param -> 
             if CvBase.equalsTerm term param then 
                 Some param 
@@ -51,15 +51,15 @@ type CvAttributeCollection(attributes : IDictionary<string,IParam>) =
 
     /// Retrieves an IParam attribute by its term, if it exists, else fails
     member this.GetAttribute (term : CvTerm) =
-        Dictionary.item (CvTerm.getName term) this
+        Dictionary.item term.Name this
 
     /// Returns true, if an attribute with the given name exists in the collection
     member this.ContainsAttribute (name : string) =
         Dictionary.containsKey name this
 
     /// Returns true, if an attribute with the given term exists in the collection
     member this.ContainsAttribute (term : CvTerm) =
-        match Dictionary.tryFind (CvTerm.getName term) this with
+        match Dictionary.tryFind term.Name this with
         | Some param when CvBase.equalsTerm term param -> true
         | _ -> false
 

src/ControlledVocabulary/CvContainer.fs

@@ -13,18 +13,18 @@ module internal Dictionary =
 /// Represents a collection of structured properties, annotated with a controlled vocabulary term.
 type CvContainer (
     cvAccession : string, 
-    cvName : string, 
-    cvRefUri : string, 
-    attributes : IDictionary<string,IParam>,
-    properties : IDictionary<string,seq<ICvBase>>
+    cvName     : string, 
+    cvRef       : string, 
+    attributes  : IDictionary<string,IParam>,
+    properties  : IDictionary<string,seq<ICvBase>>
     ) =
 
     inherit CvAttributeCollection(attributes)
 
     interface ICvBase with 
-        member this.ID     = cvAccession
-        member this.Name   = cvName
-        member this.RefUri = cvRefUri    
+        member this.Accession   = cvAccession
+        member this.Name        = cvName
+        member this.RefUri      = cvRef
         member this.HasAttributes 
             with get() = this.Attributes |> Seq.isEmpty |> not
 
@@ -37,8 +37,8 @@ type CvContainer (
         CvContainer(cvAccession, cvName, cvRefUri, Seq.empty)
 
 
-    new ((id,name,ref) : CvTerm, attributes : IDictionary<string,IParam>) = 
-        CvContainer(id,name,ref, attributes, Dictionary<string, ICvBase seq>())
+    new (term : CvTerm, attributes : IDictionary<string,IParam>) = 
+        CvContainer(term.Accession, term.Name, term.RefUri, attributes, Dictionary<string, ICvBase seq>())
     new (term : CvTerm,attributes : seq<IParam>) = 
         let dict = CvAttributeCollection(attributes)
         CvContainer(term, dict)
@@ -79,7 +79,7 @@ type CvContainer (
     /// Fails if the propertyName cannot be found.
     member this.GetManyParams propertyName =
         Dictionary.item propertyName this.Properties
-        |> Seq.choose Param.tryParam
+        |> Seq.choose CvBase.tryParam
 
     /// Retrieves child with the given name of the CvContainer.
     ///
@@ -109,7 +109,7 @@ type CvContainer (
     /// Fails if there is not exactly one child with the given name or if the propertyName cannot be found.
     member this.GetSingleParam propertyName =
         Dictionary.item propertyName this.Properties
-        |> Seq.choose Param.tryParam
+        |> Seq.choose CvBase.tryParam
         |> Seq.exactlyOne
 
 
@@ -146,7 +146,7 @@ type CvContainer (
         Dictionary.tryFind propertyName this.Properties
         |> Option.bind (fun many ->
             many
-            |> Seq.choose Param.tryParam
+            |> Seq.choose CvBase.tryParam
             |> fun items -> if Seq.isEmpty items then None else Some items
         )
 
@@ -176,7 +176,7 @@ type CvContainer (
     /// Returns None if there is not exactly one child with the given name or if the propertyName cannot be found.
     member this.TryGetSingleParam propertyName =
         Dictionary.tryFind propertyName this.Properties
-        |> Option.bind (Seq.choose Param.tryParam >> Seq.tryExactlyOne)
+        |> Option.bind (Seq.choose CvBase.tryParam >> Seq.tryExactlyOne)
 
 
 
@@ -330,4 +330,4 @@ type CvContainer (
         Dictionary.addOrUpdateInPlace value.Name (Seq.singleton value) cvContainer.Properties
 
     override this.ToString() = 
-        $"CvContainer: {(this :> ICvBase).Name}\n\tID: {(this :> ICvBase).ID}\n\tRefUri: {(this :> ICvBase).RefUri}\n\tProperties: {this.Properties.Keys |> Seq.toList}"
+        $"CvContainer: {(this :> ICvBase).Name}\n\tID: {(this :> ICvBase).Accession}\n\tRefUri: {(this :> ICvBase).RefUri}\n\tProperties: {this.Properties.Keys |> Seq.toList}"

src/ControlledVocabulary/CvObject.fs

@@ -3,20 +3,20 @@
 open System.Collections.Generic
 
 /// Represents a generic object, annotated with a controlled vocabulary term
-type CvObject<'T>(cvAccession : string, cvName : string, cvRefUri : string, object : 'T, attributes : Dictionary<string,IParam>) =
+type CvObject<'T>(cvAccession : string, cvName : string, cvRef : string, object : 'T, attributes : Dictionary<string,IParam>) =
 
     inherit CvAttributeCollection(attributes)
 
     interface ICvBase with 
-        member this.ID     = cvAccession
-        member this.Name   = cvName
-        member this.RefUri = cvRefUri
+        member this.Accession   = cvAccession
+        member this.Name        = cvName
+        member this.RefUri         = cvRef
         member this.HasAttributes 
             with get() = this.Attributes |> Seq.isEmpty |> not
 
-    new ((id,name,ref) : CvTerm,object : 'T, attributes) = CvObject (id,name,ref,object,attributes)
+    new (term: CvTerm, object : 'T, attributes) = CvObject (term.Accession, term.Name, term.RefUri, object, attributes)
 
     member this.Object = object
 
     override this.ToString() = 
-        $"Name: {(this :> ICvBase).Name}\n\tID: {(this :> ICvBase).ID}\n\tRefUri: {(this :> ICvBase).RefUri}"
+        $"Name: {(this :> ICvBase).Name}\n\tID: {(this :> ICvBase).Accession}\n\tRefUri: {(this :> ICvBase).RefUri}"