Merge pull request #297 from nfdi4plants/table_join_296

Extend ArcTable.Join logic

README.md

@@ -6,7 +6,7 @@ and __JavaScript__! ❤️
 | Version | Downloads |
 | :--------|-----------:|
 |<a href="https://www.nuget.org/packages/ARCtrl/"><img alt="Nuget" src="https://img.shields.io/nuget/vpre/ARCtrl?logo=nuget&color=%234fb3d9"></a>|<a href="https://www.nuget.org/packages/ARCtrl/"><img alt="Nuget" src="https://img.shields.io/nuget/dt/ARCtrl?color=%234FB3D9"></a>|
-|<a href="https://www.npmjs.com/package/@nfdi4plants/arctrl"><img alt="NPM" src="https://img.shields.io/npm/v/%40nfdi4plants/arctrl/next?logo=npm&color=%234fb3d9"></a>|<a href="https://www.npmjs.com/package/@nfdi4plants/arctrl"><img alt="NPM" src="https://img.shields.io/npm/dt/%40nfdi4plants%2Farctrl?color=%234fb3d9"></a>|
+|<a href="https://www.npmjs.com/package/@nfdi4plants/arctrl"><img alt="NPM" src="https://img.shields.io/npm/v/%40nfdi4plants/arctrl?logo=npm&color=%234fb3d9"></a>|<a href="https://www.npmjs.com/package/@nfdi4plants/arctrl"><img alt="NPM" src="https://img.shields.io/npm/dt/%40nfdi4plants%2Farctrl?color=%234fb3d9"></a>|
 
 
 ## Install

RELEASE_NOTES.md

@@ -1,3 +1,13 @@
+### 1.0.5+b21e3bc (Released 2024-1-17)
+* Additions:
+    * [[#b21e3bc](https://github.com/nfdi4plants/ARCtrl/commit/b21e3bcb0a5679b5ec5494555d9e9d23822bdc9a)] Extend ArcTable.Join :sparkles::white_check_mark:
+    * [[#a112468](https://github.com/nfdi4plants/ARCtrl/commit/a1124684ea02d23301b67743ff761112fe9389ab)] Update readme badge
+    * [[#a0144e1](https://github.com/nfdi4plants/ARCtrl/commit/a0144e1282bb1e8206378eb6bb8b23619eb666e6)] Merge pull request #295 from nfdi4plants/Freymaurer-patch-1
+    * [[#9e5c1f6](https://github.com/nfdi4plants/ARCtrl/commit/9e5c1f67b676d63dcb69b586089e1e74ca1c2814)] Update README.md
+    * [[#6e0755b](https://github.com/nfdi4plants/ARCtrl/commit/6e0755b5e1c28bb72814247dad1e4ab457e25e40)] update and release version 1.0.4
+* Bugfixes:
+    * [[#8dd99e8](https://github.com/nfdi4plants/ARCtrl/commit/8dd99e82fc93add2950860d6eb185686be21f9ba)] Merge pull request #294 from nfdi4plants/fix_annotationValue_read
+
 ### 1.0.4+167fae8 (Released 2024-1-15)
 * Additions:
     * [[#167fae8](https://github.com/nfdi4plants/ARCtrl/commit/167fae8bcaa14d8e24055f60ac031b13d8b47199)] add json functions for better function names in js :sparkles:

build/release_package.json

@@ -1,6 +1,6 @@
 {
   "name": "@nfdi4plants/arctrl",
-  "version": "1.0.4+167fae8",
+  "version": "1.0.5+b21e3bc",
   "description": "Top level ARC DataModel and API function descriptions.",
   "type": "module",
   "main": "index.js",

src/ISA/ISA/ArcTypes/ArcTable.fs

@@ -503,12 +503,17 @@ type ArcTable(name: string, headers: ResizeArray<CompositeHeader>, values: Syste
     /// <summary>
     /// This function can be used to join two arc tables.
     /// </summary>
+    /// <param name="index">If not set default to append. -1 will also append.</param>
     /// <param name="table">The table to join to this table.</param>
     /// <param name="joinOptions">Can add only headers, header with unitized cell information, headers with values.</param>
     /// <param name="forceReplace">if set to true will replace unique columns.</param>
-    member this.Join(table:ArcTable, ?joinOptions: TableJoinOptions, ?forceReplace: bool, ?SkipFillMissing) : unit =
+    member this.Join(table:ArcTable, ?index: int, ?joinOptions: TableJoinOptions, ?forceReplace: bool, ?skipFillMissing) : unit =
         let joinOptions = defaultArg joinOptions TableJoinOptions.Headers
         let forceReplace = defaultArg forceReplace false
+        let skipFillMissing = defaultArg skipFillMissing false
+        let mutable index = defaultArg index this.ColumnCount
+        index <- if index = -1 then this.ColumnCount else index //make -1 default to append to make function usage more fluent.
+        SanityChecks.validateColumnIndex index this.ColumnCount true
         let onlyHeaders = joinOptions = TableJoinOptions.Headers
         let columns = 
             let pre = table.Columns
@@ -528,20 +533,19 @@ type ArcTable(name: string, headers: ResizeArray<CompositeHeader>, values: Syste
             | WithValues -> pre
         SanityChecks.validateNoDuplicateUniqueColumns columns
         columns |> Array.iter (fun x -> SanityChecks.validateColumn x)
-        let mutable index = this.ColumnCount
         columns
         |> Array.iter (fun col -> 
             let prevHeadersCount = this.Headers.Count
             Unchecked.addColumn col.Header col.Cells index forceReplace onlyHeaders this.Headers this.Values
             // Check if more headers, otherwise `ArcTableAux.insertColumn` replaced a column and we do not need to increase index.
             if this.Headers.Count > prevHeadersCount then index <- index + 1
         )
-        if not(SkipFillMissing = Some true) then Unchecked.fillMissingCells this.Headers this.Values
+        if not(skipFillMissing) then Unchecked.fillMissingCells this.Headers this.Values
 
-    static member join(table:ArcTable, ?joinOptions: TableJoinOptions, ?forceReplace: bool) =
+    static member join(table:ArcTable, ?index: int, ?joinOptions: TableJoinOptions, ?forceReplace: bool) =
         fun (this: ArcTable) ->
             let copy = this.Copy()
-            copy.Join(table,?joinOptions=joinOptions,?forceReplace=forceReplace)
+            copy.Join(table,?index=index,?joinOptions=joinOptions,?forceReplace=forceReplace)
             copy
 
     static member insertParameterValue (t : ArcTable) (p : ProcessParameterValue) : ArcTable = 

tests/ISA/ISA.Tests/ArcTable.Tests.fs

@@ -2081,11 +2081,43 @@ let private tests_UpdateRefWithSheet =
     ]
 
 let private tests_Join = testList "Join" [
+    testList "index" [
+        testCase "ensure default is append" <| fun _ ->
+            let table1 = create_testTable()
+            let columnCount = table1.ColumnCount
+            let table2 = create_testTable()
+            table2.RemoveColumn 0 // rmv input
+            table2.RemoveColumn 0 // rmv output
+            let expectedJoinCount = columnCount + table2.ColumnCount
+            table1.Join(table2)
+            Expect.equal table1.ColumnCount expectedJoinCount "new column count"
+            Expect.equal (table1.Headers.[columnCount]) (table2.Headers.[0]) "column equal"
+        testCase "ensure -1 defaults to append" <| fun _ ->
+            let table1 = create_testTable()
+            let columnCount = table1.ColumnCount
+            let table2 = create_testTable()
+            table2.RemoveColumn 0 // rmv input
+            table2.RemoveColumn 0 // rmv output
+            let expectedJoinCount = columnCount + table2.ColumnCount
+            table1.Join(table2,-1)
+            Expect.equal table1.ColumnCount expectedJoinCount "new column count"
+            Expect.equal (table1.Headers.[columnCount]) (table2.Headers.[0]) "column equal"
+        testCase "insert at start" <| fun _ ->
+            let table1 = create_testTable()
+            let columnCount = table1.ColumnCount
+            let table2 = create_testTable()
+            table2.RemoveColumn 0 // rmv input
+            table2.RemoveColumn 0 // rmv output
+            let expectedJoinCount = columnCount + table2.ColumnCount
+            table1.Join(table2,0)
+            Expect.equal table1.ColumnCount expectedJoinCount "new column count"
+            Expect.equal (table1.Headers.[0]) (table2.Headers.[0]) "column equal"
+    ]
     testList "TableJoinOption.Headers" [
         testCase "Add to empty" <| fun _ ->
             let table = ArcTable.init("MyTable")
             let joinTable = create_testTable()
-            table.Join(joinTable,TableJoinOptions.Headers)
+            table.Join(joinTable,-1,TableJoinOptions.Headers)
             Expect.equal table.ColumnCount 5 "columnCount"
             // test headers
             Expect.equal table.Headers.[0] (CompositeHeader.Input IOType.Source) "Header input"
@@ -2098,12 +2130,12 @@ let private tests_Join = testList "Join" [
         testCase "Add to duplicate" <| fun _ ->
             let table = create_testTable()
             let joinTable = create_testTable()
-            let func = fun () -> table.Join(joinTable,TableJoinOptions.Headers)
+            let func = fun () -> table.Join(joinTable,-1,TableJoinOptions.Headers)
             Expect.throws func "This should fail as we try to add multiple inputs/outputs to one table"
         testCase "Add to duplicate, forceReplace" <| fun _ ->
             let table = create_testTable()
             let joinTable = create_testTable()
-            table.Join(joinTable,TableJoinOptions.Headers, true)
+            table.Join(joinTable,-1,TableJoinOptions.Headers,true)
             Expect.equal table.ColumnCount 8 "We expect 8 columns as there are 5 per table with 2 unique 5 + (5-2) = 8"
             // headers
             Expect.equal table.Headers.[0] (CompositeHeader.Input IOType.Source) "Header input"
@@ -2123,7 +2155,7 @@ let private tests_Join = testList "Join" [
                 ResizeArray([CompositeHeader.Input IOType.ImageFile]),
                 System.Collections.Generic.Dictionary()
             )
-            table.Join(joinTable,TableJoinOptions.Headers, true)
+            table.Join(joinTable,-1,TableJoinOptions.Headers,true)
             Expect.equal table.ColumnCount 5 "columnCount"
             // test headers
             Expect.equal table.Headers.[0] (CompositeHeader.Input IOType.ImageFile) "Here should be new image input"
@@ -2142,7 +2174,7 @@ let private tests_Join = testList "Join" [
                 column_component 
             |]
             joinTable.AddColumns(columns)
-            table.Join(joinTable,TableJoinOptions.WithUnit)
+            table.Join(joinTable,-1,TableJoinOptions.WithUnit)
             Expect.equal table.ColumnCount 1 "column count"
             Expect.equal table.RowCount 0 "row count"
         testCase "Add to empty, with unit" <| fun _ ->
@@ -2158,11 +2190,11 @@ let private tests_Join = testList "Join" [
                 )
             |]
             joinTable.AddColumns(columns)
-            table.Join(joinTable,TableJoinOptions.WithUnit)
+            table.Join(joinTable,-1,TableJoinOptions.WithUnit, skipFillMissing=false)
             Expect.equal table.ColumnCount 2 "column count"
             Expect.equal table.RowCount 5 "row count"
-            Expect.equal table.Values.[0,0] (CompositeCell.createTerm OntologyAnnotation.empty) "empty term cell"
-            Expect.equal table.Values.[1,0] (CompositeCell.createUnitized("",oa_temperature)) "temperature unit cell"
+            Expect.equal table.Values.[(0,0)] (CompositeCell.createTerm OntologyAnnotation.empty) "empty term cell"
+            Expect.equal table.Values.[(1,0)] (CompositeCell.createUnitized("",oa_temperature)) "temperature unit cell"
     ]
     testList "TableJoinOption.WithValues" [
         testCase "Add to empty" <| fun _ ->
@@ -2178,7 +2210,7 @@ let private tests_Join = testList "Join" [
                 )
             |]
             joinTable.AddColumns(columns)
-            table.Join(joinTable,TableJoinOptions.WithValues)
+            table.Join(joinTable,-1,TableJoinOptions.WithValues)
             Expect.equal table.ColumnCount 2 "column count"
             Expect.equal table.RowCount 5 "row count"
             Expect.equal table.Values.[0,0] (CompositeCell.createTerm oa_SCIEXInstrumentModel) "sciex instrument model"