finish up first version of updated arc read in

src/ARCtrl/ARCtrl.fs

@@ -31,12 +31,7 @@ module ARCAux =
         let (studyNames,assayNames) = 
             match isa with
             | Some inv ->         
-                inv.Studies
-                |> Seq.fold (fun (studyNames,assayNames) s ->
-                    Array.append studyNames [|s.Identifier|],
-                    Array.append assayNames (s.Assays |> Seq.map (fun a -> a.Identifier) |> Array.ofSeq)
-
-                ) ([||],[||])
+                inv.StudyIdentifiers |> Seq.toArray, inv.AssayIdentifiers |> Seq.toArray
             | None -> ([||],[||])
         let assays = FileSystemTree.createAssaysFolder (assayNames |> Array.map FileSystemTree.createAssayFolder)
         let studies = FileSystemTree.createStudiesFolder (studyNames |> Array.map FileSystemTree.createStudyFolder)
@@ -166,32 +161,29 @@ type ARC(?isa : ISA.ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSyste
         /// get investigation from xlsx
         let investigation = ARCAux.getArcInvestigationFromContracts contracts
         /// get studies from xlsx
-        let studies = ARCAux.getArcStudiesFromContracts contracts
+        let studies = ARCAux.getArcStudiesFromContracts contracts |> Array.map fst
         /// get assays from xlsx
         let assays = ARCAux.getArcAssaysFromContracts contracts
 
-        investigation.Studies |> Seq.iter (fun registeredStudy ->
+        studies |> Seq.iter (fun study ->
             /// Try find registered study in parsed READ contracts
-            let studyOpt = studies |> Array.tryFind (fun s -> s.Identifier = registeredStudy.Identifier)
-            match studyOpt with
-            | Some study -> // This study element is parsed from FsWorkbook and has no regsitered assays, yet
-
-                if enableLogging then printfn "Found study: %s" registeredStudy.Identifier
-                registeredStudy.Assays |> Seq.iter (fun registeredAssay ->
-                    /// Try find registered assay in parsed READ contracts
-                    let assayOpt = assays |> Array.tryFind (fun a -> a.Identifier = registeredAssay.Identifier)
-                    match assayOpt with
-                    | Some assay -> 
-                        if enableLogging then printfn "Found assay: %s - %s" registeredStudy.Identifier registeredAssay.Identifier
-                        registeredAssay.AddTables(assay.Tables)
-                    | None -> 
-                        if enableLogging then printfn "Unable to find registered assay '%s' in fullfilled READ contracts!" registeredAssay.Identifier
-                )
-                study.Tables
-                |> Seq.iter (fun table -> registeredStudy.SetTable(table.Name , table))
+            let registeredStudyOpt = investigation.Studies |> Seq.tryFind (fun s -> s.Identifier = study.Identifier)
+            match registeredStudyOpt with
+            | Some registeredStudy -> // This study element is parsed from FsWorkbook and has no regsitered assays, yet
+                registeredStudy.UpdateReferenceByStudyFile(study,true)
+            | None -> 
+                investigation.AddRegisteredStudy(study)
+        )
+        assays |> Seq.iter (fun assay ->
+            /// Try find registered study in parsed READ contracts
+            let registeredAssayOpt = investigation.Assays |> Seq.tryFind (fun a -> a.Identifier = assay.Identifier)
+            match registeredAssayOpt with
+            | Some registeredAssay -> // This study element is parsed from FsWorkbook and has no regsitered assays, yet
+                registeredAssay.UpdateReferenceByAssayFile(assay,true)
             | None -> 
-                if enableLogging then printfn "Unable to find registered study '%s' in fullfilled READ contracts!" registeredStudy.Identifier
+                investigation.AddAssay(assay)
         )
+
         this.ISA <- Some investigation
 
     member this.UpdateFileSystem() =   
@@ -213,18 +205,19 @@ type ARC(?isa : ISA.ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSyste
             workbooks.Add (Path.InvestigationFileName, (DTOType.ISA_Investigation, ISA.Spreadsheet.ArcInvestigation.toFsWorkbook inv))
             inv.Studies
             |> Seq.iter (fun s ->
+
                 workbooks.Add (
                     Identifier.Study.fileNameFromIdentifier s.Identifier,
-                    (DTOType.ISA_Study, ISA.Spreadsheet.ArcStudy.toFsWorkbook s))
-                s.Assays
-                |> Seq.iter (fun a ->
-                    let key = Identifier.Assay.fileNameFromIdentifier a.Identifier
-                    if workbooks.ContainsKey key |> not then
-                        workbooks.Add (
-                            key,
-                            (DTOType.ISA_Assay, ISA.Spreadsheet.ArcAssay.toFsWorkbook a))                
+                    (DTOType.ISA_Study, ArcStudy.toFsWorkbook s)
                 )
             )
+            inv.Assays
+            |> Seq.iter (fun a ->
+                workbooks.Add (
+                    Identifier.Assay.fileNameFromIdentifier a.Identifier,
+                    (DTOType.ISA_Assay, ISA.Spreadsheet.ArcAssay.toFsWorkbook a))                
+            )
+
         | None -> 
             workbooks.Add (Path.InvestigationFileName, (DTOType.ISA_Investigation, ISA.Spreadsheet.ArcInvestigation.toFsWorkbook (ArcInvestigation.create(Identifier.MISSING_IDENTIFIER))))
             printfn "ARC contains no ISA part."

src/ISA/ISA/ArcTypes/ArcTable.fs

@@ -535,6 +535,12 @@ type ArcTable =
         |> fun rows -> ProcessParsing.alignByHeaders rows
         |> fun (headers, rows) -> ArcTable.create(name,headers,rows)
 
+    /// This method is meant to update an ArcTable stored as a protocol in a study or investigation file with the information from an ArcTable actually stored as an annotation table
+    member this.UpdateReferenceByAnnotationTable(table:ArcTable) =
+        ArcTableAux.Unchecked.extendToRowCount table.RowCount this.Headers this.Values
+        for c in table.Columns do
+            this.AddColumn(c.Header, cells = c.Cells,forceReplace = true)
+
     /// Pretty printer 
     override this.ToString() =
         [

src/ISA/ISA/ArcTypes/ArcTableAux.fs

@@ -275,6 +275,16 @@ module Unchecked =
                 for missingColumn,missingRow in missingKeys do
                     setCellAt (missingColumn,missingRow,empty) values
 
+    /// Increases the table size to the given new row count and fills the new rows with the last value of the column
+    let extendToRowCount rowCount (headers: ResizeArray<CompositeHeader>) (values:Dictionary<int*int,CompositeCell>) =
+        let columnCount = getColumnCount headers
+        let previousRowCount = getRowCount values
+        // iterate over columns
+        for columnIndex = 0 to columnCount - 1 do
+            let lastValue = values[columnIndex,previousRowCount-1]
+            for rowIndex = previousRowCount - 1 to rowCount - 1 do
+                setCellAt (columnIndex,rowIndex,lastValue) values
+
     let addRow (index:int) (newCells:CompositeCell []) (headers: ResizeArray<CompositeHeader>) (values:Dictionary<int*int,CompositeCell>) =
         /// Store start rowCount here, so it does not get changed midway through
         let rowCount = getRowCount values

src/ISA/ISA/ArcTypes/ArcTypes.fs

@@ -530,6 +530,23 @@ type ArcAssay(identifier: string, ?measurementType : OntologyAnnotation, ?techno
     member internal this.RemoveFromInvestigation () =
         this.Investigation <- None
 
+    /// Updates given assay stored in an study or investigation file with values from an assay file.
+    member this.UpdateReferenceByAssayFile(assay:ArcAssay,?onlyReplaceExisting : bool) =
+        let onlyReplaceExisting = defaultArg onlyReplaceExisting false
+        let updateAlways = onlyReplaceExisting |> not
+        if assay.MeasurementType.IsSome || updateAlways then 
+            this.MeasurementType <- assay.MeasurementType
+        if assay.TechnologyPlatform.IsSome || updateAlways then 
+            this.TechnologyPlatform <- assay.TechnologyPlatform
+        if assay.TechnologyType.IsSome || updateAlways then 
+            this.TechnologyType <- assay.TechnologyType
+        if assay.Tables.Count <> 0 || updateAlways then          
+            this.Tables <- assay.Tables
+        if assay.Comments.Length <> 0 || updateAlways then          
+            this.Comments <- assay.Comments  
+        if assay.Performers.Length <> 0 || updateAlways then          
+            this.Performers <- assay.Performers  
+
     /// Copies ArcAssay object without the pointer to the parent ArcInvestigation
     ///
     /// In order to copy the pointer to the parent ArcInvestigation as well, use the Copy() method of the ArcInvestigation instead.
@@ -1055,7 +1072,7 @@ type ArcStudy(identifier : string, ?title, ?description, ?submissionDate, ?publi
         this.Investigation <- None
 
 
-    /// Copies ArcStudy objec without the pointer to the parent ArcInvestigation
+    /// Copies ArcStudy object without the pointer to the parent ArcInvestigation
     ///
     /// This copy does only contain the identifiers of the registered ArcAssays and not the actual objects.
     ///
@@ -1087,14 +1104,12 @@ type ArcStudy(identifier : string, ?title, ?description, ?submissionDate, ?publi
         )
 
     /// <summary>
-    /// Updates given study with another study, Identifier will never be updated. By default update is full replace. Optional Parameters can be used to specify update logic.
+    /// Updates given study from an investigation file against a study from a study file. Identifier will never be updated. 
     /// </summary>
     /// <param name="study">The study used for updating this study.</param>
     /// <param name="onlyReplaceExisting">If true, this will only update fields which are `Some` or non-empty lists. Default: **false**</param>
-    /// <param name="appendSequences">If true, this will append lists instead of replacing. Will return only distinct elements. Default: **false**</param>
-    member this.UpdateBy(study:ArcStudy,?onlyReplaceExisting : bool,?appendSequences : bool) =
+    member this.UpdateReferenceByStudyFile(study:ArcStudy,?onlyReplaceExisting : bool) =
         let onlyReplaceExisting = defaultArg onlyReplaceExisting false
-        let appendSequences = defaultArg appendSequences false
         let updateAlways = onlyReplaceExisting |> not
         if study.Title.IsSome || updateAlways then 
             this.Title <- study.Title
@@ -1105,26 +1120,31 @@ type ArcStudy(identifier : string, ?title, ?description, ?submissionDate, ?publi
         if study.PublicReleaseDate.IsSome || updateAlways then 
             this.PublicReleaseDate <- study.PublicReleaseDate
         if study.Publications.Length <> 0 || updateAlways then
-            let s = ArcTypesAux.updateAppendArray appendSequences this.Publications study.Publications
-            this.Publications <- s
+            this.Publications <- study.Publications
         if study.Contacts.Length <> 0 || updateAlways then
-            let s = ArcTypesAux.updateAppendArray appendSequences this.Contacts study.Contacts
-            this.Contacts <- s
+            this.Contacts <- study.Contacts
         if study.StudyDesignDescriptors.Length <> 0 || updateAlways then
-            let s = ArcTypesAux.updateAppendArray appendSequences this.StudyDesignDescriptors study.StudyDesignDescriptors
-            this.StudyDesignDescriptors <- s
+            this.StudyDesignDescriptors <- study.StudyDesignDescriptors
         if study.Tables.Count <> 0 || updateAlways then
-            let s = ArcTypesAux.updateAppendResizeArray appendSequences this.Tables study.Tables
+            let s = 
+                study.Tables
+                |> Seq.append this.Tables
+                |> Seq.groupBy (fun t -> t.Name)
+                |> Seq.map (fun (_,ts) -> 
+                    if Seq.length ts = 2 then
+                        (Seq.item 0 ts).UpdateReferenceByAnnotationTable (Seq.item 1 ts)
+                        Seq.head ts 
+                    else 
+                        Seq.head ts 
+                )
+                |> ResizeArray           
             this.Tables <- s
         if study.RegisteredAssayIdentifiers.Count <> 0 || updateAlways then
-            let s = ArcTypesAux.updateAppendResizeArray appendSequences this.RegisteredAssayIdentifiers study.RegisteredAssayIdentifiers
-            this.RegisteredAssayIdentifiers <- s
-        if study.Factors.Length <> 0 || updateAlways then
-            let s = ArcTypesAux.updateAppendArray appendSequences this.Factors study.Factors
-            this.Factors <- s
+            this.RegisteredAssayIdentifiers <- study.RegisteredAssayIdentifiers
+        if study.Factors.Length <> 0 || updateAlways then            
+            this.Factors <- study.Factors
         if study.Comments.Length <> 0 || updateAlways then
-            let s = ArcTypesAux.updateAppendArray appendSequences this.Comments study.Comments
-            this.Comments <- s
+            this.Comments <- study.Comments
 
     /// <summary>
     /// Creates an ISA-Json compatible Study from ArcStudy.
@@ -1399,6 +1419,18 @@ type ArcInvestigation(identifier : string, ?title : string, ?description : strin
             copy.RegisterStudy(studyIdentifier)
             copy
 
+    // - Study API - CRUD //
+    member this.AddRegisteredStudy (study: ArcStudy) = 
+        this.AddStudy study
+        this.RegisterStudy(study.Identifier)
+
+    static member addRegisteredStudy(study: ArcStudy) =
+        fun (inv: ArcInvestigation) ->
+            let copy = inv.Copy()
+            let study = study.Copy()
+            copy.AddRegisteredStudy(study)
+            copy
+
     // - Study API - CRUD //
     member this.RemoveStudyAt(index: int) =
         this.Studies.RemoveAt(index)

tests/ARCtrl/ARCtrl.Tests.fs

@@ -168,7 +168,7 @@ let private test_writeContracts = testList "write_contracts" [
         let inv = ArcInvestigation("MyInvestigation", "BestTitle")
         let assay = ArcAssay("MyAssay")
         inv.InitStudy("Study1").AddRegisteredAssay(assay) |> ignore
-        inv.InitStudy("Study2").AddRegisteredAssay(assay) |> ignore
+        inv.InitStudy("Study2").RegisterAssay(assay.Identifier) |> ignore
         let arc = ARC(isa = inv)
         let contracts = arc.GetWriteContracts()
         let contractPathsString = contracts |> Array.map (fun c -> c.Path) |> String.concat ", "

tests/ISA/ISA.Tests/ArcStudy.Tests.fs

@@ -314,7 +314,7 @@ let tests_copy =
             ()
     ]
 
-let tests_UpdateBy = testList "UpdateBy" [
+let tests_UpdateBy = testList "UpdateReferenceByStudyFile" [
     let createFullStudy() =
         let identifier = "MyIdentifier"
         let title = "Study Title"
@@ -329,7 +329,6 @@ let tests_UpdateBy = testList "UpdateBy" [
         let assay_identifiers = getAssayIdentifiers assays
         let factors = [|Factor.create("Factor 1")|]
         let comments = [|Comment.create("Comment 1")|]
-
         ArcStudy(
             identifier = identifier,
             title = title,
@@ -361,7 +360,7 @@ let tests_UpdateBy = testList "UpdateBy" [
                 factors = [||],
                 comments = [||]
             )
-        actual.UpdateBy(next)
+        actual.UpdateReferenceByStudyFile(next)
         Expect.notEqual actual next "not equal"
         Expect.notEqual actual.Identifier next.Identifier "Identifier"
         Expect.equal actual.Title next.Title "Title"
@@ -381,7 +380,7 @@ let tests_UpdateBy = testList "UpdateBy" [
         let actual = createFullStudy()
         let next = ArcStudy.init("NextIdentifier")
         let expected = createFullStudy()
-        actual.UpdateBy(next, true)
+        actual.UpdateReferenceByStudyFile(next, true)
         Expect.notEqual actual next "not equal"
         Expect.notEqual actual.Identifier next.Identifier "Identifier"
         Expect.equal actual.Title expected.Title "Title"
@@ -412,7 +411,7 @@ let tests_UpdateBy = testList "UpdateBy" [
                 factors = [|Factor.create(Name="NextFactor")|],
                 comments = [|Comment.create(Name="NextCommentName", Value="NextCommentValue")|]
             )
-        actual.UpdateBy(next, true)
+        actual.UpdateReferenceByStudyFile(next, true)
         Expect.notEqual actual next "not equal"
         Expect.notEqual actual.Identifier next.Identifier "Identifier"
         Expect.equal actual.Title next.Title "Title"
@@ -441,7 +440,7 @@ let tests_UpdateBy = testList "UpdateBy" [
                 tables = ResizeArray([ArcTable.init("NextTable")])
             )
         let original = createFullStudy()
-        actual.UpdateBy(next, true, true)
+        actual.UpdateReferenceByStudyFile(next, true)
         Expect.notEqual actual next "not equal"
         Expect.notEqual actual.Identifier next.Identifier "Identifier"
         Expect.equal actual.Title next.Title "Title"
@@ -470,7 +469,7 @@ let tests_UpdateBy = testList "UpdateBy" [
                 tables = ResizeArray([ArcTable.init("NextTable")])
             )
         let original = createFullStudy()
-        actual.UpdateBy(next, false, true)
+        actual.UpdateReferenceByStudyFile(next, false)
         Expect.notEqual actual next "not equal"
         Expect.notEqual actual.Identifier next.Identifier "Identifier"
         Expect.equal actual.Title next.Title "Title"