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a/pyproject.toml b/pyproject.toml index 4bcf91d5..cd81e890 100644 --- 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 index 5ee5ebaf..1fa578ae 100644 --- 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) : CompositeCell = CompositeCell.createFreeText cellValues.[0] let dataFromStringCells (format : int option) (selectorFormat : int option) (cellValues : array) : 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 index 7db346bd..b412939b 100644 --- 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 index acc70263..7b304197 100644 --- a/src/Spreadsheet/Template.fs +++ b/src/Spreadsheet/Template.fs @@ -223,9 +223,16 @@ module Template = open Metadata open Template + [] let [] metaDataSheetName = "isa_template" + + [] let [] 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 index 2a0e99e6..78781b62 100644 --- 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 index 58e99be7..4bffbfd9 100644 --- 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 index 56b92fa6..e680b5cf 100644 --- 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()