add components to querymodel and assay xlsx writing

nfdi4plants · Aug 2, 2022 · f8f94c6 · f8f94c6
1 parent 9b85296
commit f8f94c6
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Showing 4 changed files with 19 additions and 15 deletions.
diff --git a/src/ISADotNet.QueryModel/Row.fs b/src/ISADotNet.QueryModel/Row.fs
@@ -102,19 +102,20 @@ type QRow =
             Vals = Values |> Option.defaultValue []
         }
 
-    static member create(?Input,?Output,?InputType,?OutputType,?CharValues,?ParamValues,?FactorValues) : QRow =
-        let combineValues (characteristics : MaterialAttributeValue list) (parameters : ProcessParameterValue list) (factors : FactorValue list) : ISAValue list =           
+    static member create(?Input,?Output,?InputType,?OutputType,?CharValues,?ParamValues,?FactorValues,?Components) : QRow =
+        let combineValues (characteristics : MaterialAttributeValue list) (parameters : ProcessParameterValue list) (factors : FactorValue list) (components : Component list) : ISAValue list =           
             (characteristics |> List.map Characteristic)
             @ (parameters |> List.map Parameter)
             @ (factors |> List.map Factor)
+            @ (components |> List.map Component)
             |> List.sortBy (fun v -> v.TryValueIndex() |> Option.defaultValue System.Int32.MaxValue)
 
         {
             Input = Input |> Option.defaultValue ""
             Output = Output |> Option.defaultValue ""
             InputType = InputType
             OutputType = OutputType
-            Vals = combineValues (CharValues |> Option.defaultValue []) (ParamValues |> Option.defaultValue []) (FactorValues |> Option.defaultValue [])
+            Vals = combineValues (CharValues |> Option.defaultValue []) (ParamValues |> Option.defaultValue []) (FactorValues |> Option.defaultValue []) (Components |> Option.defaultValue []) 
         }
 
     static member fromProcess (proc : Process) : QRow list =
@@ -129,11 +130,12 @@ type QRow =
             let factors = 
                 ios |> List.collect (snd >> API.ProcessOutput.tryGetFactorValues >> (Option.defaultValue []))
                 |> List.distinct
+            let components = proc.ExecutesProtocol |> Option.bind (fun p -> p.Components) |> Option.defaultValue []
 
             let inputType = ios |> List.map (fst >> IOType.fromInput) |> IOType.reduce
             let outputType = ios |> List.map (snd >> IOType.fromOutput) |> IOType.reduce
 
-            QRow.create(inputName, outputName, inputType, outputType, characteristics, parameterValues, factors)
+            QRow.create(inputName, outputName, inputType, outputType, characteristics, parameterValues, factors, components)
 
         )
 

diff --git a/src/ISADotNet.QueryModel/Sheet.fs b/src/ISADotNet.QueryModel/Sheet.fs
@@ -88,6 +88,17 @@ module ProtocolExtensions =
                 OntologyAnnotation.isChildTerm(parentProtocolType,pt,obo)
             | _ -> false
 
+
+    type ProtocolDescriptor<'T> =
+        | ForAll of 'T
+        | ForSpecific of Map<int,'T>
+
+        with member this.TryGet(i) =
+                match this with
+                | ForAll x -> Some x
+                | ForSpecific m -> Map.tryFind i m
+
+
 /// Queryable type representing a collection of processes implementing the same protocol. Or in ISAtab / ISAXLSX logic a sheet in an assay or study file.
 ///
 /// Values are represented rowwise with input and output entities.

diff --git a/src/ISADotNet.QueryModel/Value.fs b/src/ISADotNet.QueryModel/Value.fs
@@ -79,7 +79,7 @@ module ISAValueExtensions =
         member this.HeaderText = 
             match this with
             | Parameter p       -> $"Parameter [{this.NameText}]"       
-            | Characteristic c  -> $"Characteristics [{this.NameText}]" 
+            | Characteristic c  -> $"Characteristic [{this.NameText}]" 
             | Factor f          -> $"Factor [{this.NameText}]"          
             | Component c       -> $"Component [{this.NameText}]" 
 

diff --git a/src/ISADotNet.XLSX/AssayFile/AnnotationTable.fs b/src/ISADotNet.XLSX/AssayFile/AnnotationTable.fs
@@ -163,7 +163,7 @@ module AnnotationTable =
     /// Merges processes with the same parameter values, grouping the input and output files
     let mergeIdenticalProcesses processNameRoot (processes : seq<Process>) =
         processes
-        |> Seq.groupBy (fun p -> p.ExecutesProtocol.Value.ProtocolType, p.ExecutesProtocol.Value.Name, p.ParameterValues)
+        |> Seq.groupBy (fun p -> p.ExecutesProtocol.Value.ProtocolType, p.ExecutesProtocol.Value.Name, p.ParameterValues, p.ExecutesProtocol.Value.Components)
         |> Seq.mapi (fun i (_,processGroup) ->
             let p = processGroup |> Seq.choose (fun pr -> pr.ExecutesProtocol) |> Seq.toList |> Protocol.mergeIndicesToRange
             processGroup
@@ -364,15 +364,6 @@ module QSheet =
     open FsSpreadsheet.DSL
     open ISADotNet.QueryModel
 
-    type ProtocolDescriptor<'T> =
-        | ForAll of 'T
-        | ForSpecific of Map<int,'T>
-
-        with member this.TryGet(i) =
-                match this with
-                | ForAll x -> Some x
-                | ForSpecific m -> Map.tryFind i m
-
     let toSheet i (s : QueryModel.QSheet) =
         let hasRef,refs = 
             if s.Protocols |> List.exists (fun p -> p.Name.IsSome && p.Name.Value <> s.SheetName) then