Merge pull request #476 from nfdi4plants/fixes

Several small fixes
nfdi4plants · Nov 18, 2024 · 440a84e · 440a84e
2 parents 30e5a19 + 852686c
commit 440a84e
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Showing 8 changed files with 245 additions and 62 deletions.
diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -10,7 +10,7 @@ keywords = ["arc", "annotated research context", "isa", "research data", "multi
 
 [tool.poetry.dependencies]
 python = "^3.10"
-requests = "2.28.1"
+requests = ">= 2.28.1, <3.0.0"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^8.1.1"

diff --git a/src/Spreadsheet/AnnotationTable/CompositeCell.fs b/src/Spreadsheet/AnnotationTable/CompositeCell.fs
@@ -1,4 +1,4 @@
-module ARCtrl.Spreadsheet.CompositeCell
+module ARCtrl.Spreadsheet.CompositeCell
 
 open ARCtrl
 open ARCtrl.Helper
@@ -19,8 +19,8 @@ let freeTextFromStringCells (cellValues : array<string>) : CompositeCell =
     CompositeCell.createFreeText cellValues.[0]
 
 let dataFromStringCells (format : int option) (selectorFormat : int option) (cellValues : array<string>) : CompositeCell =
-    let format = Option.map (fun i -> cellValues.[i]) format
-    let selectorFormat = Option.map (fun i -> cellValues.[i]) selectorFormat
+    let format = Option.bind (fun i -> cellValues.[i] |> Option.fromValueWithDefault "") format
+    let selectorFormat = Option.bind (fun i -> cellValues.[i] |> Option.fromValueWithDefault "") selectorFormat
     CompositeCell.createDataFromString(cellValues.[0],?format = format, ?selectorFormat = selectorFormat)
 
 

diff --git a/src/Spreadsheet/AnnotationTable/CompositeColumn.fs b/src/Spreadsheet/AnnotationTable/CompositeColumn.fs
@@ -72,14 +72,10 @@ let toStringCellColumns (column : CompositeColumn) : string list list =
             [header.[2]; for i = 0 to column.Cells.Length - 1 do getCellOrDefault i 2 cells]
         ]
     elif isData then
-        let hasFormat = column.Cells |> Seq.exists (fun c -> c.ToDataCell().AsData.Format.IsSome)
-        let hasSelectorFormat = column.Cells |> Seq.exists (fun c -> c.ToDataCell().AsData.SelectorFormat.IsSome)
         [
             [header.[0]; for i = 0 to column.Cells.Length - 1 do getCellOrDefault i 0 cells]
-            if hasFormat then 
-                [header.[1]; for i = 0 to column.Cells.Length - 1 do getCellOrDefault i 1 cells]
-            if hasSelectorFormat then 
-                [header.[2]; for i = 0 to column.Cells.Length - 1 do getCellOrDefault i 2 cells]
+            [header.[1]; for i = 0 to column.Cells.Length - 1 do getCellOrDefault i 1 cells]
+            [header.[2]; for i = 0 to column.Cells.Length - 1 do getCellOrDefault i 2 cells]
         ]
     else
         [

diff --git a/src/Spreadsheet/Template.fs b/src/Spreadsheet/Template.fs
@@ -223,9 +223,16 @@ module Template =
     open Metadata
     open Template
 
+    [<System.Obsolete>]
     let [<Literal>] metaDataSheetName = "isa_template"
+
+    [<System.Obsolete>]
     let [<Literal>] obsoletemetaDataSheetName = "SwateTemplateMetadata"
 
+    let metadataSheetName = "isa_template"
+    let obsoleteMetadataSheetName = "SwateTemplateMetadata"
+
+
     let fromParts (templateInfo : TemplateInfo) (ers : OntologyAnnotation list) (tags : OntologyAnnotation list) (authors : Person list) (table : ArcTable) (lastUpdated : System.DateTime) =
         Template.make 
             (System.Guid templateInfo.Id)
@@ -240,7 +247,7 @@ module Template =
             lastUpdated
 
     let isMetadataSheetName (name : string) =
-        name = metaDataSheetName || name = obsoletemetaDataSheetName
+        name = metadataSheetName || name = obsoleteMetadataSheetName
 
     let isMetadataSheet (sheet : FsWorksheet) =
         isMetadataSheetName sheet.Name
@@ -250,7 +257,7 @@ module Template =
         |> Seq.tryFind isMetadataSheet
 
     let toMetadataSheet (template : Template) : FsWorksheet =        
-        let sheet = FsWorksheet(metaDataSheetName)
+        let sheet = FsWorksheet(metadataSheetName)
         Template.toRows template
         |> Seq.iteri (fun rowI r -> SparseRow.writeToSheet (rowI + 1) r sheet)    
         sheet

diff --git a/tests/Spreadsheet/ArcTableTests.fs b/tests/Spreadsheet/ArcTableTests.fs
@@ -329,6 +329,71 @@ let private ioTable =
         )
     ]
 
+let private ioTable_obsoleteData = 
+    testList "ioTable_obsoleteData" [
+        let wsName = "MyWorksheet"
+        let ws_obsoleteData = 
+            initWorksheet wsName
+                [
+                    Input.appendSampleColumn                1
+                    Protocol.REF.appendLolColumn            1          
+                    Parameter.appendTemperatureColumn       1
+                    Characteristic.appendOrganismColumn     1
+                    Factor.appendTimeColumn                 1
+                    Output.appendObsoleteDataColumn         1
+                ]
+        let ws = 
+            initWorksheet wsName
+                [
+                    Input.appendSampleColumn                1
+                    Protocol.REF.appendLolColumn            1          
+                    Parameter.appendTemperatureColumn       1
+                    Characteristic.appendOrganismColumn     1
+                    Factor.appendTimeColumn                 1
+                    Output.appendSimpleDataColumn           1
+                ]
+        testCase "Read" (fun () -> 
+
+            let table = ArcTable.tryFromFsWorksheet ws_obsoleteData        
+
+            Expect.isSome table "Table was not created"
+            let table = table.Value
+
+            Expect.equal table.Name wsName "Name did not match"
+            Expect.equal table.ColumnCount 6 "Wrong number of columns"
+            Expect.equal table.RowCount 1 "Wrong number of rows"
+
+            let expectedHeaders = 
+                [
+                    Input.sampleHeader 
+                    Protocol.REF.lolHeader        
+                    Parameter.temperatureHeader 
+                    Characteristic.organismHeader 
+                    Factor.timeHeader 
+                    Output.simpleDataHeader 
+                ]
+            Expect.sequenceEqual table.Headers expectedHeaders "Headers did not match"
+            let expectedCells = 
+                [
+                    Input.sampleValue 
+                    Protocol.REF.lolValue        
+                    Parameter.temperatureValue 
+                    Characteristic.organismValue 
+                    Factor.timeValue 
+                    Output.simpleDataValue 
+                ]
+            Expect.sequenceEqual (table.GetRow(0)) expectedCells "Cells did not match"
+        )
+        testCase "Write" (fun () -> 
+
+            let table = ArcTable.tryFromFsWorksheet ws_obsoleteData        
+            Expect.isSome table "Table was not created"
+            let out = ArcTable.toFsWorksheet None table.Value
+            Expect.workSheetEqual out ws "Worksheet was not correctly written"
+
+        )
+    ]
+
 let private fullDataTable = 
     testList "fullDataTable" [
         let wsName = "MyWorksheet"
@@ -530,6 +595,7 @@ let main =
         simpleTable
         mixedTable
         ioTable
+        ioTable_obsoleteData
         valuelessTable
         fullDataTable
         commentTable

diff --git a/tests/Spreadsheet/Main.fs b/tests/Spreadsheet/Main.fs
@@ -2,7 +2,7 @@ module ARCtrl.Spreadsheet.Tests
 
 open Fable.Pyxpecto
 
-let all = testSequenced <| testList "ISA.Spreadsheet" [
+let all = testSequenced <| testList "Spreadsheet" [
     FableTests.main
     RegexTests.main
     ArcInvestigationTests.main

diff --git a/tests/TestingUtils/TestObjects.Spreadsheet/Spreadsheet.ArcTable.fs b/tests/TestingUtils/TestObjects.Spreadsheet/Spreadsheet.ArcTable.fs
@@ -1,4 +1,4 @@
-module TestObjects.Spreadsheet.ArcTable
+module TestObjects.Spreadsheet.ArcTable
 
 open FsSpreadsheet
 open ARCtrl
@@ -256,11 +256,21 @@ module Output =
 
     let sampleValueV1 = "MySample"
 
+    let appendObsoleteDataColumn l (c : FsCellsCollection) (t : FsTable) = 
+        let colCount = if t.IsEmpty(c) then 0 else t.ColumnCount()
+        t.Cell(FsAddress(1, colCount + 1),c).SetValueAs dataHeaderV1
+        for i = 2 to l + 1 do  
+            t.Cell(FsAddress(i, colCount + 1),c).SetValueAs dataValueV1
+
     let appendSimpleDataColumn l (c : FsCellsCollection) (t : FsTable) = 
         let colCount = if t.IsEmpty(c) then 0 else t.ColumnCount()
         t.Cell(FsAddress(1, colCount + 1),c).SetValueAs dataHeaderV1
+        t.Cell(FsAddress(1, colCount + 2),c).SetValueAs dataHeaderV2
+        t.Cell(FsAddress(1, colCount + 3),c).SetValueAs dataHeaderV3
         for i = 2 to l + 1 do  
             t.Cell(FsAddress(i, colCount + 1),c).SetValueAs dataValueV1
+            t.Cell(FsAddress(i, colCount + 2),c).SetValueAs ""
+            t.Cell(FsAddress(i, colCount + 3),c).SetValueAs ""
 
     let appendFullDataColumn l (c : FsCellsCollection) (t : FsTable) =
         let colCount = if t.IsEmpty(c) then 0 else t.ColumnCount()