Merge pull request #551 from nfdi4plants/Feature_Excel_UpdateValidate…

…Button

Feature, Excel. Restore full finctionality of the button: "Rectify Ontology Terms"

src/Client/OfficeInterop/OfficeInterop.fs

@@ -1619,6 +1619,59 @@ let getSelectedBuildingBlock (table: Table) (context: RequestContext) =
         )
     }
 
+/// <summary>
+/// Returns a ResizeArray of indices and header names for the selected building block
+/// The indices are rebased to the excel annotation table.
+/// </summary>
+/// <param name="columns"></param>
+/// <param name="selectedIndex"></param>
+let getBuildingBlockByColumnIndex (table: Table) (excelColumnIndex: float) (context: RequestContext) =
+    promise {
+        let headerRange = table.getHeaderRowRange()
+        let _ = headerRange.load(U2.Case2 (ResizeArray [|"columnIndex"; "values"; "columnCount"|])) |> ignore
+
+        return! context.sync().``then``(fun _ ->
+            let rebasedIndex = excelColumnIndex - headerRange.columnIndex |> int
+            if rebasedIndex < 0 || rebasedIndex >= (int headerRange.columnCount) then
+                failwith "Cannot select building block outside of annotation table!"
+            let headers: string [] = [|for v in headerRange.values.[0] do v.Value :?> string|]
+            let selectedHeader = rebasedIndex, headers.[rebasedIndex]
+            let buildingBlockGroups = groupToBuildingBlocks headers
+            let selectedBuildingBlock =
+                buildingBlockGroups.Find(fun bb -> bb.Contains selectedHeader)
+            selectedBuildingBlock
+        )
+    }
+
+/// <summary>
+/// Get the main column of the arc table of the selected building block of the active annotation table
+/// </summary>
+let getArcIndex (excelTable: Table) (excelColumnIndex: float) (context: RequestContext) =
+    promise {
+        let! selectedBlock = getBuildingBlockByColumnIndex excelTable excelColumnIndex context
+
+        let protoHeaders = excelTable.getHeaderRowRange()
+        let _ = protoHeaders.load(U2.Case2 (ResizeArray(["values"])))
+
+        do! context.sync().``then``(fun _ -> ())
+
+        let headers = protoHeaders.values.Item 0 |> Array.ofSeq |> Array.map (fun c -> c.ToString())
+
+        let arcTableIndices = (groupToBuildingBlocks headers) |> Array.ofSeq |> Array.map (fun i -> i |> Array.ofSeq)
+
+        let arcTableIndex =
+            let potResult = arcTableIndices |> Array.mapi (fun i c -> i, c |> Array.tryFind (fun (_, s) -> s = snd selectedBlock.[0]))
+            let result = potResult |> Array.filter (fun (_, c) -> c.IsSome) |> Array.map (fun (i, c) -> i, c.Value)
+            Array.tryHead result
+
+        let arcTableIndex =
+            if arcTableIndex.IsSome then
+                fst arcTableIndex.Value
+            else failwith "Could not find a fitting arc table index"
+
+        return arcTableIndex
+    }
+
 /// <summary>
 /// Returns a ResizeArray of indices and header names for the selected building block
 /// The indices are rebased to the excel annotation table.
@@ -2141,6 +2194,50 @@ let validateSelectedAndNeighbouringBuildingBlocks () =
         }
     )
 
+let getTermData names =
+    promise {
+        let terms =
+            names
+            |> List.map (fun name ->
+                TermQuery.create(name, searchMode=Database.FullTextSearch.Exact)
+            )
+            |> Array.ofSeq
+        let! result = Async.StartAsPromise (Api.ontology.searchTerms terms)
+
+        return
+            result
+            |> Array.map (fun item -> Array.tryHead item.results)
+    }
+
+let updateSelectedBuildingBlocks (excelTable: Table) (arcTable: ArcTable) (propertyColumns: array<int*string []>) (indexedTerms: list<int*Term option>) =
+    promise {
+        let headers = ARCtrl.Spreadsheet.ArcTable.helperColumnStrings |> Array.ofSeq
+
+        for pi in 0..propertyColumns.Length-1 do
+            let pIndex, pcv = propertyColumns.[pi]
+            let values = Array.create (arcTable.RowCount + 1) ""
+            indexedTerms
+            |> List.iter (fun (mainIndex, potTerm) ->
+                match potTerm with
+                | Some term ->
+                    match pcv.[0] with
+                    | header when header = headers.[2] -> //Unit
+                        values.[mainIndex] <- term.Name
+                    | header when header.Contains(headers.[0]) -> //Term Source REF
+                        values.[mainIndex] <- term.FK_Ontology
+                    | header when header.Contains(headers.[1]) -> //Term Accession Number
+                        values.[mainIndex] <- term.Accession
+                    | _ -> ()
+                | None -> values.[mainIndex] <- pcv.[mainIndex]
+
+                let bodyValues =
+                    values
+                    |> Array.map (box >> Some)
+                    |> Array.map (fun c -> ResizeArray[c])
+                    |> ResizeArray
+                excelTable.columns.items.[pIndex].values <- bodyValues
+            )
+        }
 /// <summary>
 /// Validates the arc table of the currently selected work sheet
 /// When the validations returns an error, an error is returned to the user
@@ -2164,14 +2261,13 @@ let rectifyTermColumns () =
 
                 let arcTable = arcTable.Value
                 let columns = arcTable.Columns
-                let _ = excelTable.columns.load(propertyNames = U2.Case2 (ResizeArray[|"items"; "values"; "rowCount"|]))
+                let _ = excelTable.columns.load(propertyNames = U2.Case2 (ResizeArray[|"items"; "rowCount"; "values";|]))
 
                 do! context.sync().``then``(fun _ -> ())
                 let items = excelTable.columns.items
                 do! context.sync().``then``(fun _ -> ())
 
                 let termAndUnitHeaders = columns |> Array.choose (fun item -> if item.Header.IsTermColumn then Some (item.Header.ToString()) else None)
-
                 let columns =
                     items
                     |> Array.ofSeq
@@ -2231,25 +2327,35 @@ let rectifyTermColumns () =
                                 |> Array.map (fun cv -> cv, String.IsNullOrEmpty(cv))
                             )
 
+                        let mutable names = []
+                        let mutable indices = []
+
                         //Check whether value of property colum is fitting for value of main column and adapt if not
                         //Delete values of property columns when main column is empty
-                        propertyColumns
-                        |> Array.iter (fun (pIndex, pcv) ->
+                        for pi in 0..propertyColumns.Length-1 do
+                            let pIndex, pcv = propertyColumns.[pi]
                             let values = Array.create (arcTable.RowCount + 1) ""
-                            mainColumnHasValues
-                            |> Array.iteri (fun mainIndex (mc, isNull) ->
-                                //if isNull for main column, then use empty string as value for properties
+                            for mainIndex in 0..mainColumnHasValues.Length-1 do
+                                let mc, isNull = mainColumnHasValues.[mainIndex]
                                 if not isNull then
+                                    names <- mc::names
+                                    indices <- mainIndex::indices
                                     values.[mainIndex] <- pcv.[mainIndex]
-                            )
-
                             let bodyValues =
                                 values
                                 |> Array.map (box >> Some)
                                 |> Array.map (fun c -> ResizeArray[c])
                                 |> ResizeArray
                             excelTable.columns.items.[pIndex].values <- bodyValues
-                        )
+
+                        let! terms = getTermData names
+
+                        let indexedTerms =
+                            indices
+                            |> List.mapi (fun ii index ->
+                                index, terms.[ii])
+
+                        do! updateSelectedBuildingBlocks excelTable arcTable propertyColumns indexedTerms
 
                 do! ExcelHelper.adoptTableFormats(excelTable, context, true)
 

src/Client/SidebarComponents/Navbar.fs

@@ -289,7 +289,7 @@ let private ShortCutIconList navState setNavState model (dispatch: Messages.Msg
         | _ ->
             ()
         QuickAccessButton.create(
-            "Validate / Update Ontology Terms",
+            "Rectify Ontology Terms",
             [
                 Html.i [prop.className "fa-solid fa-spell-check"]
                 Html.span model.ExcelState.FillHiddenColsStateStore.toReadableString