add component and protocoltype parsers to assay xlsx table reader

src/ISADotNet.QueryModel/Row.fs

@@ -124,7 +124,7 @@ type QRow =
         |> List.map (fun ((inputName,outputName),ios) ->
 
             let characteristics = 
-                ios |> List.collect (fst >> API.ProcessInput.tryGetCharacteristics >> (Option.defaultValue []))
+                ios |> List.collect (fst >> API.ProcessInput.tryGetCharacteristicValues >> (Option.defaultValue []))
                 |> List.distinct
             let factors = 
                 ios |> List.collect (snd >> API.ProcessOutput.tryGetFactorValues >> (Option.defaultValue []))

src/ISADotNet.XLSX/AssayFile/AnnotationNode.fs

@@ -211,6 +211,15 @@ module AnnotationNode =
                 OntologyAnnotation.fromStringWithComments value termAccession termSource [order]
         )
 
+    /// If the headers of a node depict a protocolType, returns a function for parsing the values of the matrix to the values of this type
+    let tryGetProtocolREFGetter (columnOrder : int) (headers:string seq) =
+        Seq.tryPick tryParseProtocolREFHeader headers
+        |> Option.map (fun h -> 
+
+            fun matrix i ->
+                Dictionary.tryGetString (i,h.HeaderString) matrix |> Option.defaultValue ""
+        )
+
     /// If the headers of a node depict a parameter, returns the parameter and a function for parsing the values of the matrix to the values of this parameter
     let tryGetParameterGetter (columnOrder : int) (headers:string seq) =
         Seq.tryPick tryParseParameterHeader headers

src/ISADotnet/OptionExtensions.fs

@@ -14,3 +14,9 @@ module Option =
         | Some v -> f v
         | None   -> f d
         |> fromValueWithDefault d
+
+    /// Applies the function f on the value of the option if it exists, else returns the default value. 
+    let mapOrDefault (d : 'T Option) (f: 'U -> 'T) (o : 'U option) =
+        match o with
+        | Some v -> Some (f v)
+        | None   -> d