adapt isaSampleToRawDataSeq to start from Source (not Sample)

workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.fsx

@@ -2,17 +2,25 @@
 
 // Dependencies
 
-#r "nuget: ARCtrl.NET"
+#r "nuget: ARCtrl"
 #r "nuget: ARCtrl.QueryModel"
 #r "nuget: FsSpreadsheet.CsvIO"
 
-open ARCtrl.NET
 open ARCtrl
 open ARCtrl.QueryModel
 open ARCtrl.Helper
 open FsSpreadsheet.Net
 open FsSpreadsheet.CsvIO
 
+
+// test parameters
+// let source = __SOURCE_DIRECTORY__
+// let arcPath = System.IO.Path.Combine(source, "../../")
+// let assayName = "Talinum_RNASeq_minimal"
+// let startingNodeNum = 0
+// let outName = "rnaseq-samples"
+
+
 // input parameters
 
 let args : string array = fsi.CommandLineArgs |> Array.tail
@@ -31,13 +39,6 @@ type ArcTables with
         )
         |> ArcTables
 
-// // test parameters
-// let source = __SOURCE_DIRECTORY__
-// let arcPath = Path.Combine(source, "../../")
-// let assayName = "Talinum_RNASeq_minimal"
-// let startingNodeNum = 0
-// let outName = "rnaseq-samples"
-
 // Load ARC
 
 // Remove all tables with either an input or output column missing
@@ -97,8 +98,6 @@ let shittify (a : ARC) =
 let arc = ARC.load(arcPath) |> clean |> shittify
 
 
-
-
 let inv = arc.ISA.Value 
 
 // Load first data node
@@ -108,7 +107,11 @@ let firstData = inv.GetAssay(assayName).FirstData
 
 // Create headers for output table
 let headers = [
-    CompositeHeader.Input IOType.Sample
+    
+    CompositeHeader.Input IOType.Source
+    
+    // CompositeHeader.Input IOType.Sample
+
     for v in inv.ArcTables.IgnoreShitty().ValuesOf firstData.[0].Name do
         if v.IsCharacteristicValue then
             CompositeHeader.Characteristic v.Category
@@ -128,7 +131,7 @@ let headers = [
 
 let getRow (d: QNode) = 
     [|
-    CompositeCell.createFreeText (inv.ArcTables.SamplesOf d).[startingNodeNum].Name
+    CompositeCell.createFreeText (inv.ArcTables.SourcesOf d).[startingNodeNum].Name
 
     for v in inv.ArcTables.ValuesOf d do
         if v.HasUnit then
@@ -165,4 +168,4 @@ wb.AddWorksheet ws
 wb.ToXlsxFile ($"{outName}.xlsx")
 
 // Write to csv
-wb.ToCsvFile ($"{outName}.csv")
\ No newline at end of file
+wb.ToCsvFile ($"{outName}.csv")