rename CvTern Value field -> Name

src/ARCTokenization/Address.fs

@@ -4,11 +4,11 @@ open ControlledVocabulary
 
 module Address = 
 
-    let column = CvTerm.create(accession = "http://purl.obolibrary.org/obo/NCIT_C43379", value = "Column", ref = "NCIT")
+    let column = CvTerm.create(accession = "http://purl.obolibrary.org/obo/NCIT_C43379", name = "Column", ref = "NCIT")
 
-    let row = CvTerm.create(accession = "http://purl.obolibrary.org/obo/NCIT_C43378", value = "Row", ref = "NCIT")
+    let row = CvTerm.create(accession = "http://purl.obolibrary.org/obo/NCIT_C43378", name = "Row", ref = "NCIT")
 
-    let worksheet = CvTerm.create(accession = "http://purl.obolibrary.org/obo/NCIT_C73541", value = "Worksheet", ref = "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.create(accession = tan.Value, value = vl.Value, ref = 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.create(accession = tan.Value, value = vl.Value, ref = 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.create (accession = "(n/a)", value = vl.Value, ref = 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.create(accession = tan.Value, value = "n/a", ref = 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
@@ -291,7 +291,7 @@ module AnnotationTable =
     let getNodeType (cvPar : #IParamBase) =
         //let castedCvPar = cvPar :?> CvParam<string>     // debatable approach
         //let v = Param.getCvName castedCvPar
-        let v = CvBase.getCvValue cvPar
+        let v = CvBase.getCvName cvPar
         match v with
         | "Source Name" -> Source
         | "Sample Name"

src/ARCTokenization/MetadataSheet.fs

@@ -9,7 +9,7 @@ module MetadataSheet =
 
     let (|Term|_|) (terms : CvTerm list) (key : string) : CvTerm Option =
         terms 
-        |> List.tryFind (fun (term) -> term.Value = 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.create(accession = t.Id, value = t.Name, ref = "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.create(accession = t.Id, value = t.Name, ref ="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.create(accession = t.Id, value = t.Name, ref ="ASSMSO"))
+        |> List.map (fun t -> CvTerm.create(accession = t.Id, name = t.Name, ref ="ASSMSO"))
 
 module StructuralTerms =
 
-    let metadataSectionKey = CvTerm.create(accession = "AGMO:00000001", value = "Metadata Section Key", ref = "AGMO")
+    let metadataSectionKey = CvTerm.create(accession = "AGMO:00000001", name = "Metadata Section Key", ref = "AGMO")

src/ControlledVocabulary/CvAttributeCollection.fs

@@ -12,7 +12,7 @@ type CvAttributeCollection(attributes : IDictionary<string,IParam>) =
     new(attributes) =
         let dict = 
             attributes
-            |> Seq.map (fun cvp -> (cvp :> ICvBase).Value, cvp)
+            |> Seq.map (fun cvp -> (cvp :> ICvBase).Name, cvp)
             |> Dictionary.ofSeq
         CvAttributeCollection(dict)
 
@@ -22,12 +22,12 @@ type CvAttributeCollection(attributes : IDictionary<string,IParam>) =
 
     /// Add an IParam as an attribute. Fails, if an attribute with the same key already exists
     member this.AddAttribute (param : IParam) =
-        Dictionary.addInPlace (param |> CvBase.getCvValue) param this
+        Dictionary.addInPlace (param |> CvBase.getCvName) param this
         |> ignore
 
     /// Add an IParam as an attribute. Does not fail, if an attribute with the same key already exists
     member this.TryAddAttribute (param : IParam) =
-        let key = param |> CvBase.getCvValue 
+        let key = param |> CvBase.getCvName 
         if this.ContainsAttribute key then false
         else 
             this.AddAttribute param
@@ -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 term.Value 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 term.Value 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 term.Value this with
+        match Dictionary.tryFind term.Name this with
         | Some param when CvBase.equalsTerm term param -> true
         | _ -> false
 

src/ControlledVocabulary/CvContainer.fs

@@ -13,7 +13,7 @@ module internal Dictionary =
 /// Represents a collection of structured properties, annotated with a controlled vocabulary term.
 type CvContainer (
     cvAccession : string, 
-    cvValue     : string, 
+    cvName     : string, 
     cvRef       : string, 
     attributes  : IDictionary<string,IParam>,
     properties  : IDictionary<string,seq<ICvBase>>
@@ -23,8 +23,8 @@ type CvContainer (
 
     interface ICvBase with 
         member this.Accession   = cvAccession
-        member this.Value       = cvValue
-        member this.RefUri         = cvRef
+        member this.Name        = cvName
+        member this.RefUri      = cvRef
         member this.HasAttributes 
             with get() = this.Attributes |> Seq.isEmpty |> not
 
@@ -38,7 +38,7 @@ type CvContainer (
 
 
     new (term : CvTerm, attributes : IDictionary<string,IParam>) = 
-        CvContainer(term.Accession, term.Value, term.RefUri, attributes, Dictionary<string, ICvBase seq>())
+        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)
@@ -307,7 +307,7 @@ type CvContainer (
     ///
     /// If a value with the same key already exist in the container, appends the new child
     static member addSingle (value : ICvBase) (cvContainer : CvContainer) =
-        Dictionary.addOrAppendInPlace value.Value value cvContainer.Properties
+        Dictionary.addOrAppendInPlace value.Name value cvContainer.Properties
 
 
     /// Sets children as a property of the CvContainer.
@@ -319,15 +319,15 @@ type CvContainer (
     static member setMany (values : seq<ICvBase>) (cvContainer : CvContainer) =
         let propertyName = 
             values
-            |> Seq.countBy (fun v -> v.Value)
+            |> Seq.countBy (fun v -> v.Name)
             |> Seq.exactlyOne
             |> fst
         Dictionary.addOrUpdateInPlace propertyName values cvContainer.Properties
         |> ignore
 
     /// Sets a single child as a property of the CvContainer, accessible by its name.
     static member setSingle (value : ICvBase) (cvContainer : CvContainer) =
-        Dictionary.addOrUpdateInPlace value.Value (Seq.singleton value) cvContainer.Properties
+        Dictionary.addOrUpdateInPlace value.Name (Seq.singleton value) cvContainer.Properties
 
     override this.ToString() = 
-        $"CvContainer: {(this :> ICvBase).Value}\n\tID: {(this :> ICvBase).Accession}\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, cvValue : string, cvRef : 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.Accession   = cvAccession
-        member this.Value       = cvValue
+        member this.Name        = cvName
         member this.RefUri         = cvRef
         member this.HasAttributes 
             with get() = this.Attributes |> Seq.isEmpty |> not
 
-    new (term: CvTerm, object : 'T, attributes) = CvObject (term.Accession, term.Value, term.RefUri, 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).Value}\n\tID: {(this :> ICvBase).Accession}\n\tRefUri: {(this :> ICvBase).RefUri}"
+        $"Name: {(this :> ICvBase).Name}\n\tID: {(this :> ICvBase).Accession}\n\tRefUri: {(this :> ICvBase).RefUri}"

src/ControlledVocabulary/CvParam.fs

@@ -10,16 +10,16 @@ open FSharpAux
 ///
 /// Attributes can be used to further describe the CvParam
 [<StructuredFormatDisplay("{DisplayText}")>]
-type CvParam(cvAccession : string, cvValue : string, cvRef : string, paramValue : ParamValue, attributes : IDictionary<string,IParam>) =
+type CvParam(cvAccession : string, cvName : string, cvRef : string, paramValue : ParamValue, attributes : IDictionary<string,IParam>) =
 
     inherit CvAttributeCollection(attributes)
 
     interface IParam with 
         member this.Accession   = cvAccession
-        member this.Value       = cvValue
-        member this.RefUri         = cvRef
+        member this.Name        = cvName
+        member this.RefUri      = cvRef
         member this.Value       = paramValue
-        member this.WithValue(v : ParamValue) = CvParam(cvAccession,cvValue,cvRef,v,attributes)
+        member this.WithValue(v : ParamValue) = CvParam(cvAccession,cvName,cvRef,v,attributes)
         member this.HasAttributes 
             with get() = this.Attributes |> Seq.isEmpty |> not
 
@@ -32,7 +32,7 @@ type CvParam(cvAccession : string, cvValue : string, cvRef : string, paramValue
         CvParam (id,name,ref,ParamValue.Value v)
 
     new (term : CvTerm, pv, attributes : seq<IParam>) = 
-        CvParam (term.Accession, term.Value, term.RefUri, pv, attributes)
+        CvParam (term.Accession, term.Name, term.RefUri, pv, attributes)
     new (cvTerm,pv : ParamValue) = 
         CvParam (cvTerm,pv,Seq.empty)
     new (cvTerm,v : IConvertible) = 
@@ -87,8 +87,8 @@ type CvParam(cvAccession : string, cvValue : string, cvRef : string, paramValue
     static member tryMapValue (f : ParamValue -> ParamValue option) (param : CvParam) = 
         Param.tryMapValue f param
 
-    static member tryAddValue (value : string) (param : CvParam) = 
-        Param.tryAddValue value param
+    static member tryAddName (value : string) (param : CvParam) = 
+        Param.tryAddName value param
 
     static member tryAddAccession (id : string) (param : CvParam) = 
         Param.tryAddAccession id param
@@ -104,7 +104,7 @@ type CvParam(cvAccession : string, cvValue : string, cvRef : string, paramValue
 
 
     override this.ToString() = 
-        $"CvParam: {(this :> ICvBase).Value}\n\tID: {(this :> ICvBase).Accession}\n\tRefUri: {(this :> ICvBase).RefUri}\n\tValue: {(this :> IParamBase).Value}\n\tAttributes: {this.Keys |> Seq.toList}"
+        $"CvParam: {(this :> ICvBase).Name}\n\tID: {(this :> ICvBase).Accession}\n\tRefUri: {(this :> ICvBase).RefUri}\n\tValue: {(this :> IParamBase).Value}\n\tAttributes: {this.Keys |> Seq.toList}"
 
     member this.DisplayText = 
         this.ToString()

src/ControlledVocabulary/CvTerm.fs

@@ -6,21 +6,21 @@
 //[<Struct>]
 type CvTerm = {
     Accession: string
-    Value: string
+    Name: string
     RefUri: string
 } with
     static member create(
         accession: string,
-        value: string,
+        name: string,
         ref : string
     ) = 
-        {Accession = accession; Value = value; RefUri = ref}
+        {Accession = accession; Name = name; RefUri = ref}
 
     static member create(
-        value: string
+        name: string
     ) = 
         CvTerm.create(
-            value = value,
+            name = name,
             accession = "",
             ref = ""
         )

src/ControlledVocabulary/ICvBase.fs

@@ -9,8 +9,8 @@ type IAttributeCollection =
 /// Interface ensures the propterties necessary for CvTerm 
 and ICvBase =
     abstract member Accession   : string
-    abstract member Value       : string
-    abstract member RefUri         : string
+    abstract member Name        : string
+    abstract member RefUri      : string
 
     inherit IAttributeCollection
 
@@ -24,16 +24,16 @@ module CvBase =
         cv.Accession
 
     /// Returns the name of the cv item
-    let getCvValue (cv : #ICvBase) =
-        cv.Value
+    let getCvName (cv : #ICvBase) =
+        cv.Name
 
     /// Returns the reference of the cv item
     let getCvRef (cv : #ICvBase) =
         cv.RefUri
 
     /// Returns the full term of the cv item
     let getTerm (cv : #ICvBase) : CvTerm =
-        CvTerm.create(accession = cv.Accession, value = cv.Value, ref = cv.RefUri)
+        CvTerm.create(accession = cv.Accession, name = cv.Name, ref = cv.RefUri)
 
     /// Returns true, if the given term matches the term of the cv item
     let equalsTerm (term : CvTerm) (cv : #ICvBase) =
@@ -44,8 +44,8 @@ module CvBase =
         getTerm cv1 = getTerm cv2
 
     /// Returns true, if the names of the given cv items match
-    let equalsValue (cv1 : #ICvBase) (cv2 : #ICvBase) =
-        getCvValue cv1 = getCvValue cv2
+    let equalsName (cv1 : #ICvBase) (cv2 : #ICvBase) =
+        getCvName cv1 = getCvName cv2
 
     /// Returns Some Value of type 'T, if the given cv item can be downcast, else returns None
     let inline tryAs<'T when 'T :> ICvBase> (cv : ICvBase) =

src/ControlledVocabulary/IParam.fs

@@ -21,8 +21,8 @@ type Param =
         CvBase.equals param1 param2
 
     /// Returns true, if the value of the given params match
-    static member equalsValue (param1 : IParam) (param2 : IParam) =
-        CvBase.equalsValue param1 param2
+    static member equalsName (param1 : IParam) (param2 : IParam) =
+        CvBase.equalsName param1 param2
 
     /// Returns Some Param, if the given cv item can be downcast, else returns None
     static member tryParam (cv : ICvBase) =
@@ -78,8 +78,8 @@ type Param =
     static member tryMapValue (f : ParamValue -> ParamValue option) (param : IParam) = 
         ParamBase.tryMapValue f param |> Option.map (fun v -> v :?> IParam)
 
-    static member tryAddValue (value : string) (param : IParam) = 
-        ParamBase.tryAddValue value param |> Option.map (fun v -> v :?> IParam)
+    static member tryAddName (value : string) (param : IParam) = 
+        ParamBase.tryAddName value param |> Option.map (fun v -> v :?> IParam)
 
     static member tryAddAccession (id : string) (param : IParam) = 
         ParamBase.tryAddAccession id param |> Option.map (fun v -> v :?> IParam)