Update to FsSpreadsheet 3.4 (soon 4.0), fix nbackwards incompatible s…

…tuff, use dense rows
nfdi4plants · Aug 11, 2023 · c6e2072 · c6e2072
1 parent 28599f7
commit c6e2072
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Showing 7 changed files with 25 additions and 28 deletions.
diff --git a/src/ARCTokenization/ARCTokenization.fsproj b/src/ARCTokenization/ARCTokenization.fsproj
@@ -45,8 +45,8 @@
     <ProjectReference Include="..\ControlledVocabulary\ControlledVocabulary.fsproj" PackageVersion="[0.0.0, 1.0.0)" />
     <PackageReference Include="FSharpAux.Core" Version="[2.0.0]" />
     <PackageReference Include="FsOboParser" Version="[0.1.0]" />
-    <PackageReference Include="FsSpreadsheet" Version="[3.1.1]" />
-    <PackageReference Include="FsSpreadsheet.ExcelIO" Version="[3.1.1]" />
+    <PackageReference Include="FsSpreadsheet" Version="[3.4.0]" />
+    <PackageReference Include="FsSpreadsheet.ExcelIO" Version="[3.4.0]" />
     <PackageReference Include="Microsoft.SourceLink.GitHub" Version="1.1.1" PrivateAssets="All"/>
   </ItemGroup>
 

diff --git a/src/ARCTokenization/AnnotationTable.fs b/src/ARCTokenization/AnnotationTable.fs
@@ -84,7 +84,7 @@ module AnnotationTable =
     /// Takes an FsWorkbook and returns all Annotation Tables it contains.
     /// </summary>
     let getAnnotationTables workbook =
-        let tables = FsWorkbook.getTables workbook
+        let tables = FsWorkbook.getTables workbook |> List.ofArray
         tables |> List.filter (fun t -> String.contains "annotationTable" t.Name)
 
     /// <summary>
@@ -254,19 +254,19 @@ module AnnotationTable =
         // get worksheet and its AnnotationTable as tuple
         let worksheetsAndTables =
             tables
-            |> List.map (
+            |> Seq.map (
                 fun t ->
                     let associatedWs = 
                         worksheets
-                        |> List.find (
+                        |> Seq.find (
                             fun ws -> 
                                 ws.Tables
-                                |> List.exists (fun t2 -> t2.Name = t.Name)
+                                |> Seq.exists (fun t2 -> t2.Name = t.Name)
                         )
                     associatedWs, t
             )
         worksheetsAndTables
-        |> List.map (
+        |> Seq.map (
             fun (ws,t) ->
                 let ioHeaderCells, termRelatedBuildingBlockHeaderCells = 
                     getHeaderCellsOf ws.CellCollection t 
@@ -282,6 +282,7 @@ module AnnotationTable =
                 ws.Name,
                 TokenizedAnnotationTable.create ioColumns termRelatedBuildingBlocks
         )
+        |> List.ofSeq
 
     /// <summary>
     /// Takes a CvParam and returns the type of Node it contains.

diff --git a/src/ARCTokenization/Workbook.fs b/src/ARCTokenization/Workbook.fs
@@ -13,7 +13,7 @@ module Workbook =
         with _ ->
             if useLastSheetOnIncorrectName then
                 FsWorkbook.getWorksheets investigation
-                |> List.last
+                |> Seq.last
             else
                 failwith "No worksheet named 'isa_investigation' found in the workbook"
 
@@ -24,7 +24,7 @@ module Workbook =
         with _ ->
             if useLastSheetOnIncorrectName then
                 FsWorkbook.getWorksheets study
-                |> List.last
+                |> Seq.last
             else
                 failwith "No worksheet named 'Study' or 'isa_study' found in the workbook"
 
@@ -35,6 +35,6 @@ module Workbook =
         with _ ->
             if useLastSheetOnIncorrectName then
                 FsWorkbook.getWorksheets assay
-                |> List.last
+                |> Seq.last
             else
                 failwith "No worksheet named 'Assay' or 'isa_assay' found in the workbook"
diff --git a/src/ARCTokenization/Worksheet.fs b/src/ARCTokenization/Worksheet.fs
@@ -37,12 +37,12 @@ module Worksheet =
 
     /// Parses rows of a given FsWorksheet via a given tokenization function and returns the resulting IParam list.
     let parseRowsWith tokenizationFunction (worksheet : FsWorksheet) = 
-        parseCellsWith (worksheet.Rows) tokenizationFunction worksheet
+        parseCellsWith (worksheet.Rows |> Seq.map FsRow.toDenseRow |> Seq.toList) tokenizationFunction worksheet
 
     /// Parses rows of a given FsWorksheet via a given tokenization function and returns the resulting IParam list.
     /// Concatenates the resulting lists of IParams into a single list.
     let parseRowsFlatWith tokenizationFunction (worksheet : FsWorksheet) = 
-        parseCellsFlatWith (worksheet.Rows) tokenizationFunction worksheet
+        parseCellsFlatWith (worksheet.Rows |> Seq.map FsRow.toDenseRow |> Seq.toList) tokenizationFunction worksheet
 
     /// Parses columns of a given FsWorksheet via a given tokenization function and returns the resulting IParam list.
     let parseColumnsWith tokenizationFunction (worksheet : FsWorksheet) = 

diff --git a/src/ARCTokenization/packages.lock.json b/src/ARCTokenization/packages.lock.json
@@ -29,22 +29,22 @@
       },
       "FsSpreadsheet": {
         "type": "Direct",
-        "requested": "[3.1.1, 3.1.1]",
-        "resolved": "3.1.1",
-        "contentHash": "dD9Je8u6XO8J2ZMrfRTljmlD992pW+8tvxsbCtvnvmDnzzuos/cxP1jYRjsEneSG4FSpRRQhzwtqkyvhCqxS1Q==",
+        "requested": "[3.4.0, 3.4.0]",
+        "resolved": "3.4.0",
+        "contentHash": "Uza3yL6hh/kiFhj+SYq91oeR08FVH95ce1b5gr64nPx3MXTo7bHJ2j5YJB63WaRwMwBKonsASD1fws58FC/ARA==",
         "dependencies": {
-          "FSharp.Core": "6.0.6",
+          "FSharp.Core": "6.0.7",
           "Fable.Core": "4.0.0"
         }
       },
       "FsSpreadsheet.ExcelIO": {
         "type": "Direct",
-        "requested": "[3.1.1, 3.1.1]",
-        "resolved": "3.1.1",
-        "contentHash": "HVxKVw2lF+/1EWr6571thtHbEVcCP7MjFS1+OMEpQLTMZH3M8dJbNA0xFKaP2mMVzK2HESobbn7hrMzc6hi6zQ==",
+        "requested": "[3.4.0, 3.4.0]",
+        "resolved": "3.4.0",
+        "contentHash": "UVPbuoQQDsfrjVdpN88396HUgX0OwtYBaDb2N4u29FxNRzcKaK6VVMlIVRatMURnHy4ofqLW9PkPqYBzNvgz4w==",
         "dependencies": {
           "DocumentFormat.OpenXml": "[2.12.3]",
-          "FSharp.Core": "6.0.6",
+          "FSharp.Core": "6.0.7",
           "FsSpreadsheet": "[3.0.0, 4.0.0)"
         }
       },

diff --git a/tests/ARCTokenization.Tests/ARCTokenization.Tests.fsproj b/tests/ARCTokenization.Tests/ARCTokenization.Tests.fsproj
@@ -34,10 +34,6 @@
 
   <ItemGroup>
     <ProjectReference Include="..\..\src\ARCTokenization\ARCTokenization.fsproj" />
-    <PackageReference Include="FSharp.FGL.ArrayAdjacencyGraph" Version="[0.0.2]" />
-    <PackageReference Include="FSharpAux.Core" Version="[2.0.0]" />
-    <PackageReference Include="FsSpreadsheet" Version="[3.1.1]" />
-    <PackageReference Include="FsSpreadsheet.ExcelIO" Version="[3.1.1]" />
   </ItemGroup>
 
 </Project>
diff --git a/tests/ARCTokenization.Tests/IntegrationTests/InvestigationMetadata.fs b/tests/ARCTokenization.Tests/IntegrationTests/InvestigationMetadata.fs
@@ -145,14 +145,14 @@ let expectedTermValuesSimple =
         [""]
         [""]
         [""]
-        [""; "Maus"; "Keider"; "müller"; "oih"]
-        [""; "Oliver"; "andreas"]
+        [""; "Maus"; "Keider"; "müller"; ""; "oih"]
+        [""; "Oliver"; ""; "andreas";]
         [""; "L. I."; "C."]
         [""; "maus@nfdi4plants.org"]
         [""]
         [""]
         [""]
-        [""; "Affe"]
+        [""; ""; "Affe"]
         [""]
         [""]
         [""]
@@ -206,7 +206,7 @@ let expectedTermValuesSimple =
         [""]
         [""]
         [""; "weil"]
-        [""; "lukas"]
+        [""; ""; "lukas"]
         [""]
         [""]
         [""]