fix issue with data nodes now being objects (not free text)

workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.fsx

@@ -31,16 +31,16 @@ type ArcTables with
         )
         |> ArcTables
 
-
 // test parameters
 let source = __SOURCE_DIRECTORY__
 let arcPath = Path.Combine(source, "../../")
 let assayName = "Talinum_RNASeq_minimal"
-let startingNodeNum = 1
+let startingNodeNum = 0
 let outName = "rnaseq-samples"
 
 // Load ARC
 
+// Remove all tables with either an input or output column missing 🤣😀
 let clean (a : ARC)  = 
     a.ISA.Value.Assays |> Seq.iter (fun a -> 
         a.Tables
@@ -64,7 +64,39 @@ let clean (a : ARC)  =
     )
     a
 
-let arc = ARC.load(arcPath) |> clean
+// transform all data cells to freetext cells 😀🤣😀😀🤣😀😀🤣😀😀🤣😀😀🤣😀😀🤣😀😀🤣😀
+let shittify (a : ARC) = 
+    a.ISA.Value.Assays |> Seq.iter (fun a -> 
+        a.Tables
+        |> Seq.toArray
+        |> Seq.iter (fun t -> 
+            t.Values
+            |> Seq.toArray
+            |> Seq.iter (fun kv ->
+                if kv.Value.isData then 
+                    t.Values.[kv.Key] <- CompositeCell.createFreeText(kv.Value.AsData.NameText)         
+            )
+        )
+    
+    )
+    a.ISA.Value.Studies |> Seq.iter (fun s -> 
+        s.Tables
+        |> Seq.toArray
+        |> Seq.iter (fun t -> 
+            t.Values
+            |> Seq.toArray
+            |> Seq.iter (fun kv ->
+                if kv.Value.isData then 
+                    t.Values.[kv.Key] <- CompositeCell.createFreeText(kv.Value.AsData.NameText)         
+            )
+        )
+    )
+    a
+
+
+let arc = ARC.load(arcPath) |> clean |> shittify
+
+
 
 
 let inv = arc.ISA.Value 
@@ -73,6 +105,7 @@ let inv = arc.ISA.Value
 
 let firstData = inv.GetAssay(assayName).FirstData
 
+
 // Create headers for output table
 let headers = [
     CompositeHeader.Input IOType.Sample
@@ -95,7 +128,6 @@ let headers = [
 
 let getRow (d: QNode) = 
     [|
-
     CompositeCell.createFreeText (inv.ArcTables.SamplesOf d).[startingNodeNum].Name
 
     for v in inv.ArcTables.ValuesOf d do
@@ -104,7 +136,7 @@ let getRow (d: QNode) =
         else
             CompositeCell.Term(v.Value.AsOntology())
 
-    CompositeCell.FreeText d.Name
+    CompositeCell.Data (Data(name = d.Name))
     
     |]
 
@@ -113,6 +145,12 @@ let getRow (d: QNode) =
 let t = ArcTable.init "FullTable"
 t.Headers <- ResizeArray headers
 
+
+let d = firstData.Head
+
+inv.ArcTables.SamplesOf d
+
+
 for d in firstData do
     t.AddRow (getRow d)
 
@@ -125,5 +163,4 @@ wb.AddWorksheet ws
 
 // Write to csv
 
-// wb.To (outName + ".tsv", Separator = '\t')
-wb.ToXlsxFile (outName + ".xlsx")
+wb.ToXlsxFile (outName + ".xlsx")
\ No newline at end of file