Merge pull request #377 from nfdi4plants/datamap

Rework datamap type

.github/workflows/manage-issues.yml

@@ -5,7 +5,6 @@ on:
     types:
       - opened
       - reopened
-      - transferred
 
 jobs:
   label_issues:

src/Core/ARCtrl.Core.fsproj

@@ -18,6 +18,7 @@
     <Compile Include="OntologyAnnotation.fs" />
     <Compile Include="DataFile.fs" />
     <Compile Include="Data.fs" />
+    <Compile Include="DataContext.fs" />
     <Compile Include="Person.fs" />
     <Compile Include="Publication.fs" />
     <Compile Include="OntologySourceReference.fs" />

src/Core/Data.fs

@@ -4,11 +4,28 @@ open ARCtrl
 open ARCtrl.Helper 
 open Fable.Core
 
+module DataAux = 
+
+    let nameFromPathAndSelector (path : string) (selector : string) =
+        sprintf "%s#%s" path selector
+
+    let pathAndSelectorFromName (name : string) =
+        let parts = name.Split('#')
+        if parts.Length = 2 then
+            parts.[0], Some parts.[1]
+        else
+            name, None
+
 [<AttachMembers>]
-type Data(?id,?name,?dataType,?format,?selectorFormat,?comments) =
+type Data(?id,?name : string,?dataType,?format,?selectorFormat,?comments) =
 
     let mutable _id : URI option = id
-    let mutable _name : string option = name
+    let mutable _filePath,_selector  = 
+        match name with
+        | Some n -> 
+            let p,s = DataAux.pathAndSelectorFromName n
+            Some p, s
+        | None -> None, None
     let mutable _dataType : DataFile option = dataType
     let mutable _format : string option = format
     let mutable _selectorFormat : URI option = selectorFormat
@@ -19,8 +36,28 @@ type Data(?id,?name,?dataType,?format,?selectorFormat,?comments) =
         and set(id) = _id <- id
 
     member this.Name
-        with get() = _name
-        and set(name) = _name <- name
+        with get() = 
+            match _filePath,_selector with
+            | Some p, Some s -> DataAux.nameFromPathAndSelector p s |> Some
+            | Some p, None -> p |> Some
+            | None, _ -> None 
+        and set(name) = 
+            match name with
+            | Some n -> 
+                let p,s = DataAux.pathAndSelectorFromName n
+                _filePath <- Some p
+                _selector <- s
+            | None -> 
+                _filePath <- None
+                _selector <- None
+
+    member this.FilePath 
+        with get() = _filePath
+        and set(filePath) = _filePath <- filePath
+
+    member this.Selector
+        with get() = _selector
+        and set(selector) = _selector <- selector
 
     member this.DataType
         with get() = _dataType
@@ -36,8 +73,7 @@ type Data(?id,?name,?dataType,?format,?selectorFormat,?comments) =
 
     member this.Comments
         with get() = _comments
-        and set(comments) = _comments <- comments
-
+        and set(comments) = _comments <- comments    
 
     static member make id name dataType format selectorFormat comments =
         Data(?id=id,?name=name,?dataType=dataType,?format=format,?selectorFormat=selectorFormat,?comments=comments)

src/Core/DataContext.fs

@@ -0,0 +1,74 @@
+namespace ARCtrl
+
+open ARCtrl
+open ARCtrl.Helper 
+open Fable.Core
+
+type DataContext(?id,?name : string,?dataType,?format,?selectorFormat, ?explication, ?unit, ?objectType, ?description, ?generatedBy, ?comments) =
+
+    inherit Data(?id = id,?name = name, ?dataType = dataType, ?format = format, ?selectorFormat = selectorFormat, ?comments = comments)
+
+    let mutable _explication : OntologyAnnotation option = explication
+    let mutable _unit : OntologyAnnotation option = unit
+    let mutable _objectType : OntologyAnnotation option = objectType
+    let mutable _description : string option = description
+    let mutable _generatedBy : string option = generatedBy
+
+    member this.Explication
+        with get() = _explication
+        and set(explication) = _explication <- explication
+
+    member this.Unit
+        with get() = _unit
+        and set(unit) = _unit <- unit
+
+    member this.ObjectType
+        with get() = _objectType
+        and set(objectType) = _objectType <- objectType
+
+    member this.Description
+        with get() = _description
+        and set(description) = _description <- description
+
+    member this.GeneratedBy
+        with get() = _generatedBy
+        and set(generatedBy) = _generatedBy <- generatedBy
+
+
+    member this.AsData() =
+        Data(?id = this.ID,?name = this.Name, ?dataType = this.DataType, ?format = this.Format, ?selectorFormat = this.SelectorFormat, comments = this.Comments)
+
+    member this.Copy() = 
+        let copy = new DataContext()
+        copy.ID <- this.ID
+        copy.Name <- this.Name
+        copy.DataType <- this.DataType
+        copy.Format <- this.Format
+        copy.SelectorFormat <- this.SelectorFormat
+        copy.Explication <- this.Explication
+        copy.Unit <- this.Unit
+        copy.ObjectType <- this.ObjectType
+        copy.Description <- this.Description
+        copy.GeneratedBy <- this.GeneratedBy
+        copy.Comments <- this.Comments
+        copy
+
+    override this.GetHashCode() = 
+        [|
+            HashCodes.boxHashOption this.ID
+            HashCodes.boxHashOption this.Name
+            HashCodes.boxHashOption this.DataType
+            HashCodes.boxHashOption this.Format
+            HashCodes.boxHashOption this.SelectorFormat
+            HashCodes.boxHashSeq this.Comments
+            HashCodes.boxHashOption this.Explication
+            HashCodes.boxHashOption this.Unit
+            HashCodes.boxHashOption this.ObjectType
+            HashCodes.boxHashOption this.Description
+            HashCodes.boxHashOption this.GeneratedBy
+        |]
+        |> HashCodes.boxHashArray
+        |> fun x -> x :?> int
+
+    override this.Equals(obj) =
+        HashCodes.hash this = HashCodes.hash obj

src/Core/Table/DataMap.fs

@@ -8,7 +8,7 @@ open Fable.Core
 
 [<AttachMembers>]
 module DataMapAux = 
-    
+
     [<Literal>]
     let dataMapName = "DataMap"
 
@@ -51,88 +51,106 @@ module DataMapAux =
     let allowedHeaders = 
         [dataHeader; explicationHeader; unitHeader; objectTypeHeader; descriptionHeader; generatedByHeader]
 
-    let validate (headers : ResizeArray<CompositeHeader>) (values : System.Collections.Generic.Dictionary<int*int,CompositeCell>) (raiseException : bool) =  
-        let headersAreValid = 
-            headers
-            |> Seq.exists (fun h -> 
-                let hasForeignHeader =
-                    not (allowedHeaders |> List.exists (fun ah -> ah = h))
-                if raiseException && hasForeignHeader then
-                    failwithf "Header %O is not allowed in DataMap" h
-                hasForeignHeader
-            )
-        let tableIsValid = ArcTableAux.SanityChecks.validate headers values raiseException
-        headersAreValid && tableIsValid
-
-type DataMap(headers: ResizeArray<CompositeHeader>, values: System.Collections.Generic.Dictionary<int*int,CompositeCell>) = 
-
-    let _ = DataMapAux.validate headers values true
+    let getOntologyColumn (f : DataContext -> OntologyAnnotation option) (dataContexts : ResizeArray<DataContext>) = 
+        dataContexts
+        |> Seq.map (fun dc -> 
+            match f dc with
+            | Some s -> CompositeCell.Term(s)
+            | None -> CompositeCell.emptyTerm
+        )
+        |> ResizeArray
+
+    let getStringColumn (f : DataContext -> string option) (dataContexts : ResizeArray<DataContext>) = 
+        dataContexts
+        |> Seq.map (fun dc -> 
+            match f dc with
+            | Some s -> CompositeCell.FreeText(s)
+            | None -> CompositeCell.emptyFreeText
+        )
+        |> ResizeArray
+
+    let setOntologyColumn (f : DataContext -> OntologyAnnotation option -> unit) (column : CompositeCell []) (dataContexts : ResizeArray<DataContext>) = 
+        column
+        |> Seq.iteri (fun i cell -> 
+            match cell with
+            | CompositeCell.Term s -> f (dataContexts.[i]) (Some s)
+            | _ -> ()
+        )
 
-    let table = ArcTable(DataMapAux.dataMapName, headers, values)
-    let mutable staticHash = 0
+    let setStringColumn (f : DataContext -> string option -> unit) (column : CompositeCell []) (dataContexts : ResizeArray<DataContext>) =
+        column
+        |> Seq.iteri (fun i cell -> 
+            match cell with
+            | CompositeCell.FreeText s -> f (dataContexts.[i]) (Some s)
+            | _ -> ()
+        )
 
-    member this.Headers = table.Headers
-    member this.Values = table.Values
-    member this.StaticHash with get() = staticHash and set(value) = staticHash <- value
+    module SanityChecks =
+
+        let rowIndexInBoundaries (row : int) (dataContexts : ResizeArray<DataContext>) = 
+            if row < 0 then 
+                failwith "Row index must be greater or equal to 0."
+            if row >= dataContexts.Count then 
+                failwith "Row index must be less than the number of rows."
 
-    static member init() = DataMap(ResizeArray(),Dictionary())
+        let lengthOfNewColumn (newColumn : CompositeCell []) (dataContexts : ResizeArray<DataContext>) = 
+            if newColumn.Length <> dataContexts.Count then
+                failwith "Length of new column does not match length of data contexts."
 
-    member this.AddColumns(columns : CompositeColumn [], ?skipFillMissing : bool) =
-        columns |> Array.iter (fun c -> c.Validate(true) |> ignore)
-        table.AddColumns(columns, ?skipFillMissing = skipFillMissing)
-        DataMapAux.validate table.Headers table.Values true |> ignore
+type DataMap(dataContexts : ResizeArray<DataContext>) = 
+
+    let mutable staticHash = 0
+    let mutable dataContexts = dataContexts
 
-    static member addColumns (columns : CompositeColumn [], ?skipFillMissing : bool) = 
-        fun (dm : DataMap) -> 
-            let dm : DataMap = dm.Copy()
-            dm.AddColumns(columns, ?skipFillMissing = skipFillMissing)
-            dm
+    member this.StaticHash with get() = staticHash and set(value) = staticHash <- value
+
+    member this.DataContexts with get() = dataContexts
 
-    member this.Table = table
+    static member init() = DataMap(ResizeArray())
 
-    member this.TryGetCellAt (row: int, column: int) = table.TryGetCellAt(row, column)
 
-    member this.GetExplicationColumn() = 
-        table.GetColumnByHeader(DataMapAux.explicationHeader)
+    member this.GetExplicationColumn() =     
+        DataMapAux.getOntologyColumn (fun dc -> dc.Explication) dataContexts
 
-    member this.AddExplicationColumn(cells : CompositeCell []) = 
-        table.AddColumn(DataMapAux.explicationHeader, cells)
+    member this.SetExplicationColumn(cells : CompositeCell []) = 
+        DataMapAux.setOntologyColumn (fun dc oa -> dc.Explication <- oa) cells dataContexts
 
     member this.GetUnitColumn() = 
-        table.GetColumnByHeader(DataMapAux.unitHeader)
+        DataMapAux.getOntologyColumn (fun dc -> dc.Unit) dataContexts
 
-    member this.AddUnitColumn(cells : CompositeCell []) =   
-        table.AddColumn(DataMapAux.unitHeader, cells)
+    member this.SetUnitColumn(cells : CompositeCell []) =   
+        DataMapAux.setOntologyColumn (fun dc oa -> dc.Unit <- oa) cells dataContexts
 
-    member this.GetDataTypeColumn() =
-        table.GetColumnByHeader(DataMapAux.objectTypeHeader)
+    member this.GetObjectTypeColumn() =
+        DataMapAux.getOntologyColumn (fun dc -> dc.ObjectType) dataContexts
 
-    member this.AddDataTypeColumn(cells : CompositeCell []) =
-        table.AddColumn(DataMapAux.objectTypeHeader, cells)
+    member this.SetDataTypeColumn(cells : CompositeCell []) =
+        DataMapAux.setOntologyColumn (fun dc oa -> dc.ObjectType <- oa) cells dataContexts
 
     member this.GetDescriptionColumn() =
-        table.GetColumnByHeader(DataMapAux.descriptionHeader)
-
-    member this.AddDescriptionColumn(cells : CompositeCell []) =
-        table.AddColumn(DataMapAux.descriptionHeader, cells)
+        DataMapAux.getStringColumn (fun dc -> dc.Description) dataContexts
 
+    member this.SetDescriptionColumn(cells : CompositeCell []) =
+        DataMapAux.setStringColumn (fun dc s -> dc.Description <- s) cells dataContexts
 
-    member this.GetRow(row: int, ?SkipValidation) = table.GetRow(row,?SkipValidation = SkipValidation)
+    member this.GetDataContext(row: int, ?SkipValidation) = 
+        DataMapAux.SanityChecks.rowIndexInBoundaries row dataContexts
+        dataContexts.Item(row)
 
-    static member getRow(row: int, ?SkipValidation) = 
-        fun (dm : DataMap) -> dm.GetRow(row,?SkipValidation = SkipValidation)
+    static member getDataContext(row: int, ?SkipValidation) = 
+        fun (dm : DataMap) -> dm.GetDataContext(row,?SkipValidation = SkipValidation)
 
     member this.Copy() =
         DataMap(
-            ResizeArray(this.Headers), 
-            Dictionary(this.Values)
+            dataContexts
+            |> Seq.map (fun dc -> dc.Copy())
+            |> ResizeArray
         )
 
     override this.Equals(obj) = 
-        match obj with
-        | :? DataMap as dm -> 
-            this.Table.Equals(dm.Table)
-        | _ -> false
+        HashCodes.hash this = HashCodes.hash obj
 
     override this.GetHashCode() = 
-        this.Table.GetHashCode()
+        dataContexts
+        |> HashCodes.boxHashSeq
+        |> fun x -> x :?> int

src/Spreadsheet/AnnotationTable/CompositeCell.fs

@@ -4,15 +4,6 @@ open ARCtrl
 open ARCtrl.Helper
 open FsSpreadsheet
 
-//let fromFsCells (cells : list<FsCell>) : CompositeCell =
-//    let cellValues = cells |> List.map (fun c -> c.ValueAsString())
-//    match cellValues with
-//    | [v] -> CompositeCell.createFreeText v
-//    | [v1;v2;v3] -> CompositeCell.createTermFromString(v1,v2,v3)
-//    | [v1;v2;v3;v4] -> CompositeCell.createUnitizedFromString(v1,v2,v3,v4)
-//    | _ -> 
-//        failwithf "Dafuq"
-
 let termFromFsCells (tsrCol : int option) (tanCol : int option ) (cells : list<FsCell>) : CompositeCell= 
     let cellValues = cells |> List.map (fun c -> c.ValueAsString())
     let tan = Option.map (fun i -> cellValues.[i]) tanCol