start working on assay query model

src/ISADotNet.XLSX/StudyFile/Study.fs

@@ -44,7 +44,7 @@ module Study =
 
         Study.create(CharacteristicCategories = characteristics,Factors = factors, Protocols = protocols, ProcessSequence = processes)
 
-/// Diesen Block durch JS ersetzen ----> 
+// Diesen Block durch JS ersetzen ----> 
 
     /// Create a new ISADotNet.XLSX study file constisting of two sheets. The first has the name of the studyIdentifier and is meant to store parameters used in the study. The second stores additional study metadata
     let init study studyIdentifier path =

src/ISADotnet/DataModel/Material.fs

@@ -67,6 +67,12 @@ type MaterialAttribute =
         |> Option.map (fun oa -> oa.GetName)
         |> Option.defaultValue ""
 
+    /// Returns number of Material attribute
+    member this.Number =       
+        this.CharacteristicType
+        |> Option.bind (fun oa -> oa.Number)
+        |> Option.defaultValue ""
+
     /// Returns the name of the characteristic with the number as string (e.g. "temperature #2")
     member this.GetNameWithNumber =       
         this.CharacteristicType

src/ISADotnet/DataModel/Ontology.fs

@@ -86,11 +86,14 @@ type OntologyAnnotation =
         )
         |> Option.defaultValue ""
 
+    /// Returns number of Ontology annotation
+    member this.Number =       
+        this.Comments |> Option.bind (List.tryPick (fun c -> if c.Name = Some "Number" then c.Value else None))       
+
     /// Returns the name of the ontology with the number as string (e.g. "temperature #2")
     member this.GetNameWithNumber =       
-        let number = this.Comments |> Option.bind (List.tryPick (fun c -> if c.Name = Some "Number" then c.Value else None))
         let name = this.GetName
-        match number with
+        match this.Number with
         | Some n -> name + " #" + n
         | None -> name
 

src/ISADotnet/JsonIO/AssayCommonAPI.fs

@@ -5,13 +5,69 @@ open System.Text.Json.Serialization
 open System.Text.Json
 open System.IO
 
+open System.Collections.Generic
+open System.Collections
+
+
+
 module AssayCommonAPI = 
 
-    //[<AnyOf>]
-    //type NamedValue =
-    //    | [<SerializationOrder(0)>] Parameter of ProcessParameterValue
-    //    | [<SerializationOrder(1)>] Characteristic of MaterialAttributeValue
-    //    | [<SerializationOrder(2)>] Factor of FactorValue
+    [<AnyOf>]
+    type ISAValue =
+        | [<SerializationOrder(0)>] Parameter of ProcessParameterValue
+        | [<SerializationOrder(1)>] Characteristic of MaterialAttributeValue
+        | [<SerializationOrder(2)>] Factor of FactorValue
+
+        /// Returns the ontology of the category of the Value as string
+        member this.Category =
+            match this with
+            | Parameter p       -> p.Category.Value.ParameterName.Value
+            | Characteristic c  -> c.Category.Value.CharacteristicType.Value
+            | Factor f          -> f.Category.Value.FactorType.Value
+
+        ///// Returns the name of the Value as string
+        //member this.GetTableHeader =
+        //    match this with
+        //    | Parameter p       -> p.GetName
+        //    | Characteristic c  -> c.GetName
+        //    | Factor f          -> f.GetName
+
+        /// Returns the name of the Value as string
+        member this.Name = this.Category.GetName
+
+        /// Returns the name of the Value with the number as string (e.g. "temperature #2")
+        member this.NameWithNumber = this.Category.GetNameWithNumber
+
+        /// Returns the name of the Value with the number as string (e.g. "temperature #2")
+        member this.Number = this.Category.Number
+
+        //member this.Value =
+        //    match this with
+        //    | Parameter p       -> p.GetValue
+        //    | Characteristic c  -> c.GetValue
+        //    | Factor f          -> f.GetValue
+
+        member this.ValueString =
+            match this with
+            | Parameter p       -> p.GetValue
+            | Characteristic c  -> c.GetValue
+            | Factor f          -> f.GetValue
+
+        member this.ValueWithUnit =
+            match this with
+            | Parameter p       -> p.GetValueWithUnit
+            | Characteristic c  -> c.GetValueWithUnit
+            | Factor f          -> f.GetValueWithUnit
+
+    let combineValues (characteristics : MaterialAttributeValue list) (parameters : ProcessParameterValue list) (factors : FactorValue list) : ISAValue list =
+        let l = 
+            (characteristics |> List.map Characteristic)
+            @ (parameters |> List.map Parameter)
+            @ (factors |> List.map Factor)
+        l
+
+    type IPrintable =
+       abstract member Print : unit -> unit
 
     type Row = 
         {
@@ -23,23 +79,27 @@ module AssayCommonAPI =
             InputType : string option
             [<JsonPropertyName(@"outputType")>]
             OutputType : string option
-            [<JsonPropertyName(@"parameterValues")>]
-            ParameterValues : ProcessParameterValue list
-            [<JsonPropertyName(@"characteristicValues")>]
-            CharacteristicValues : MaterialAttributeValue list
-            [<JsonPropertyName(@"factorValues")>]
-            FactorValues : FactorValue list
+            [<JsonPropertyName(@"values")>]
+            Values : ISAValue list
         }
 
-        static member create(?Input,?Output,?InputType,?OutputType,?ParamValues,?CharValues,?FactorValues) : Row=
+        static member create (?Input,?Output,?InputType,?OutputType,?Values) : Row =
+
+            {
+                Input = Input |> Option.defaultValue ""
+                Output = Output |> Option.defaultValue ""
+                InputType = InputType
+                OutputType = OutputType
+                Values = Values |> Option.defaultValue []
+            }
+
+        static member create(?Input,?Output,?InputType,?OutputType,?CharValues,?ParamValues,?FactorValues) : Row =
             {
                 Input = Input |> Option.defaultValue ""
                 Output = Output |> Option.defaultValue ""
                 InputType = InputType
                 OutputType = OutputType
-                ParameterValues = ParamValues |> Option.defaultValue []
-                CharacteristicValues = CharValues |> Option.defaultValue []
-                FactorValues = FactorValues |> Option.defaultValue []
+                Values = combineValues (CharValues |> Option.defaultValue []) (ParamValues |> Option.defaultValue []) (FactorValues |> Option.defaultValue [])
             }
 
         static member fromProcess (proc : Process) : Row list =
@@ -55,6 +115,28 @@ module AssayCommonAPI =
                 Row.create(inputName,outputName,ParamValues = parameterValues, CharValues = characteristics,FactorValues = factors)
             )
 
+        member this.Item (i : int) =
+            this.Values 
+            |> Seq.item i
+
+        member this.Item (s : string) =
+            this.Values 
+            |> List.find (fun v -> 
+                s = v.NameWithNumber || v.Name = s
+            )
+
+        member this.Item (oa : OntologyAnnotation) =
+            this.Values 
+            |> List.pick (fun v -> 
+                if v.Category = oa then Some v
+                else None
+            )
+
+        interface IEnumerable<ISAValue> with
+            member this.GetEnumerator() : System.Collections.Generic.IEnumerator<ISAValue> = (seq this.Values).GetEnumerator()
+
+        interface IEnumerable with
+            member this.GetEnumerator() = (this :> IEnumerable<ISAValue>).GetEnumerator() :> IEnumerator
 
     type RowWiseSheet = 
         {
@@ -75,6 +157,19 @@ module AssayCommonAPI =
             |> List.collect (Row.fromProcess)
             |> RowWiseSheet.create name 
 
+        member this.Item (input : string) =
+            this.Rows 
+            |> List.pick (fun r -> 
+                if r.Input = input then Some r
+                else None
+            )
+
+        interface IEnumerable<Row> with
+            member this.GetEnumerator() = (seq this.Rows).GetEnumerator()
+
+        interface IEnumerable with
+            member this.GetEnumerator() = (this :> IEnumerable<Row>).GetEnumerator() :> IEnumerator
+
     type RowWiseAssay =
         {
             //[<JsonPropertyName(@"assayName")>]
@@ -83,6 +178,12 @@ module AssayCommonAPI =
             Sheets : RowWiseSheet list
         }
 
+        interface IEnumerable<RowWiseSheet> with
+            member this.GetEnumerator() = (Seq.ofList this.Sheets).GetEnumerator()
+
+        interface IEnumerable with
+            member this.GetEnumerator() = (this :> IEnumerable<RowWiseSheet>).GetEnumerator() :> IEnumerator
+
         static member create (*assayName*) sheets : RowWiseAssay =
             {
                 //AssayName = assayName
@@ -102,6 +203,16 @@ module AssayCommonAPI =
             )
             |> List.map (fun (name,processes) -> RowWiseSheet.fromProcesses name processes)
             |> RowWiseAssay.create (*(assay.FileName |> Option.defaultValue "")*)
+
+        member this.Item (sheetName) =
+            this.Sheets 
+            |> List.pick (fun sheet -> 
+                if sheet.SheetName = sheetName then 
+                    Some sheet
+                else None
+            )
+
+
 
         static member toString (rwa : RowWiseAssay) =  JsonSerializer.Serialize<RowWiseAssay>(rwa,JsonExtensions.options)
 
@@ -219,23 +330,23 @@ module AssayCommonAPI =
                 FactorColumns = factorColumns
             }
 
-        static member fromRowWiseSheet (rws : RowWiseSheet) = 
-            let parameters = 
-                rws.Rows
-                |> List.map (fun row -> row.ParameterValues)
-                |> List.transpose 
-                |> List.map ParameterColumn.fromParams
-            let characteristics = 
-                rws.Rows
-                |> List.map (fun row -> row.CharacteristicValues)
-                |> List.transpose 
-                |> List.map CharacteristicColumn.fromCharacteristics
-            let factors = 
-                rws.Rows
-                |> List.map (fun row -> row.FactorValues)
-                |> List.transpose 
-                |> List.map FactorColumn.fromFactors
-            ColumnWiseSheet.create rws.SheetName parameters characteristics factors
+        //static member fromRowWiseSheet (rws : RowWiseSheet) = 
+        //    let parameters = 
+        //        rws.Rows
+        //        |> List.map (fun row -> row.ParameterValues)
+        //        |> List.transpose 
+        //        |> List.map ParameterColumn.fromParams
+        //    let characteristics = 
+        //        rws.Rows
+        //        |> List.map (fun row -> row.CharacteristicValues)
+        //        |> List.transpose 
+        //        |> List.map CharacteristicColumn.fromCharacteristics
+        //    let factors = 
+        //        rws.Rows
+        //        |> List.map (fun row -> row.FactorValues)
+        //        |> List.transpose 
+        //        |> List.map FactorColumn.fromFactors
+        //    ColumnWiseSheet.create rws.SheetName parameters characteristics factors
 
     type ColumnWiseAssay =
         {
@@ -250,7 +361,7 @@ module AssayCommonAPI =
                 Sheets = sheets
             }
 
-        static member fromRowWiseAssay (rwa : RowWiseAssay) = 
-            rwa.Sheets
-            |> List.map ColumnWiseSheet.fromRowWiseSheet
-            |> ColumnWiseAssay.create
+        //static member fromRowWiseAssay (rwa : RowWiseAssay) = 
+        //    rwa.Sheets
+        //    |> List.map ColumnWiseSheet.fromRowWiseSheet
+        //    |> ColumnWiseAssay.create