fix study xlsx reader creating empty lists

#71
nfdi4plants · Dec 2, 2022 · 8f63206 · 8f63206
1 parent 372e07f
commit 8f63206
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Showing 2 changed files with 28 additions and 3 deletions.
diff --git a/src/ISADotNet.XLSX/AssayFile/Assay.fs b/src/ISADotNet.XLSX/AssayFile/Assay.fs
@@ -63,8 +63,14 @@ module Assay =
 
         let processes = Process.fromSparseMatrix processNameRoot matrixHeaders sparseMatrix
         let characteristics = API.ProcessSequence.getCharacteristics processes
-        Assay.create(CharacteristicCategories = characteristics,ProcessSequence = Seq.toList processes)
+        let assay = 
+            match characteristics,processes with
+            | [],[] -> Assay.create()
+            | [],ps -> Assay.create(ProcessSequence = ps)
+            | cs,[] -> Assay.create(CharacteristicCategories = cs)
+            | cs,ps -> Assay.create(CharacteristicCategories = cs,ProcessSequence = ps)
 
+        assay
 
     /// Returns an assay from a sequence of sparseMatrix representations of assay.xlsx sheets
     ///
@@ -192,4 +198,19 @@ module Assay =
         wb.Value.Parse().ToFile(p)
         with
         | err -> failwithf "Could not write Assay to Xlsx file in path \"%s\": \n\t%s" p err.Message
+
+    let updateFile (p : string) (contacts : Person list) (assay : Assay) =
+        try
+        let a = QueryModel.QAssay.fromAssay assay
+        let wb = 
+            workbook {
+                for (i,s) in List.indexed a.Sheets do QSheet.toSheet i s
+                sheet "Assay" {
+                    for r in MetaData.toDSLSheet assay contacts do r
+                }
+            }
+
+        wb.Value.Parse().ToFile(p)
+        with
+        | err -> failwithf "Could not write Assay to Xlsx file in path \"%s\": \n\t%s" p err.Message
     /// ---->  Bis hier
diff --git a/src/ISADotNet.XLSX/StudyFile/Study.fs b/src/ISADotNet.XLSX/StudyFile/Study.fs
@@ -29,7 +29,10 @@ module Study =
         let characteristics = API.ProcessSequence.getCharacteristics processes
         let factors = API.ProcessSequence.getFactors processes
         let protocols = API.ProcessSequence.getProtocols processes
-        Study.create(CharacteristicCategories = characteristics,Factors = factors, Protocols = protocols, ProcessSequence = processes)
+        let units = API.ProcessSequence.getUnits processes |> List.distinct
+        Study.make None None None None None None None None None None (Option.fromValueWithDefault [] protocols) None  (Option.fromValueWithDefault [] processes) None (Option.fromValueWithDefault [] factors) (Option.fromValueWithDefault [] characteristics) (Option.fromValueWithDefault [] units) None
+
+        //Study.create(CharacteristicCategories = characteristics,Factors = factors, Protocols = protocols, ProcessSequence = processes)
 
     /// Returns a study from a sequence of sparseMatrix representations of study.xlsx sheets
     ///
@@ -43,7 +46,8 @@ module Study =
         let characteristics = API.ProcessSequence.getCharacteristics processes
         let factors = API.ProcessSequence.getFactors processes
         let protocols = API.ProcessSequence.getProtocols processes
-        Study.create(CharacteristicCategories = characteristics,Factors = factors, Protocols = protocols, ProcessSequence = processes)
+        let units = API.ProcessSequence.getUnits processes |> List.distinct
+        Study.make None None None None None None None None None None (Option.fromValueWithDefault [] protocols) None  (Option.fromValueWithDefault [] processes) None (Option.fromValueWithDefault [] factors) (Option.fromValueWithDefault [] characteristics) (Option.fromValueWithDefault [] units) None
 
 // Diesen Block durch JS ersetzen ---->