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HLWeilHLWeil
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add json parser and tests for updated data objects
1 parent 08fcb3b commit 8c67c36

9 files changed

Lines changed: 147 additions & 1 deletion

‎tests/Core/ARCtrl.Core.Tests.fsproj‎

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@@ -9,6 +9,7 @@
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<Compile Include="Regex.Tests.fs" />
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<Compile Include="Person.Tests.fs" />
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<Compile Include="OntologyAnnotation.Tests.fs" />
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<Compile Include="Data.Tests.fs" />
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<Compile Include="CompositeCell.Tests.fs" />
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<Compile Include="CompositeHeader.Tests.fs" />
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<Compile Include="CompositeColumn.Tests.fs" />

‎tests/Core/CompositeCell.Tests.fs‎

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@@ -107,7 +107,18 @@ let private tests_create =
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let expected = CompositeCell.Unitized("42", oa)
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Expect.equal newCell expected ""
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)
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]
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testCase "createData" (fun () ->
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let d = Data(name = "MyData#row=1", format = "text/csv", selectorFormat = "MySelector")
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let newCell : CompositeCell = CompositeCell.createData(d)
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let expected = CompositeCell.Data d
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Expect.equal newCell expected ""
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)
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testCase "createDataFromString" (fun () ->
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let newCell : CompositeCell = CompositeCell.createDataFromString("MyData#row=1", "text/csv", "MySelector")
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let expected = CompositeCell.Data <| Data(name = "MyData#row=1", format = "text/csv", selectorFormat = "MySelector")
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Expect.equal newCell expected ""
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)
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]
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let private tests_ToString = testList "ToString" [
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testCase "FreeText" <| fun _ ->
@@ -125,6 +136,12 @@ let private tests_ToString = testList "ToString" [
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let actual = cc.ToString()
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let expected = "20 degree celcius"
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Expect.equal actual expected ""
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testCase "Data" <| fun _ ->
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let d = Data(name = "MyData#row=1", format = "text/csv", selectorFormat = "MySelector")
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let cc = CompositeCell.createData d
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let actual = cc.ToString()
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let expected = "MyData#row=1"
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Expect.equal actual expected ""
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]
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let private tests_GetContent = testList "GetContent" [
@@ -140,6 +157,11 @@ let private tests_GetContent = testList "GetContent" [
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let cell = CompositeCell.createUnitized ("12", OntologyAnnotation("My Unit Name"))
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let actual = cell.GetContent()
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Expect.equal actual [|"12"; "My Unit Name"; ""; ""|] ""
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testCase "Data" <| fun _ ->
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let d = Data(name = "MyData#row=1", format = "text/csv", selectorFormat = "MySelector")
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let cell = CompositeCell.createData d
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let actual = cell.GetContent()
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Expect.equal actual [|"MyData#row=1"; "text/csv"; "MySelector"|] ""
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testCase "Matching" <| fun _ ->
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let matchContent (content: string []) =
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match content with
@@ -189,6 +211,11 @@ let private tests_GetHashCode = testList "GetHashCode" [
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let cc = CompositeCell.createFreeText("TestTerm")
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cc.GetHashCode() |> ignore
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Expect.isTrue true " "
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testCase "Data" <| fun _ ->
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let d = Data(name = "MyData#row=1", format = "text/csv", selectorFormat = "MySelector")
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let cc = CompositeCell.createData d
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cc.GetHashCode() |> ignore
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Expect.isTrue true " "
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]
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]
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‎tests/Core/Data.Tests.fs‎

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module Data.Tests
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open ARCtrl
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open TestingUtils
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let private tests_GetHashCode = testList "GetHashCode" [
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testCase "equal" <| fun _ ->
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let d1 = Data("MyID","MyName",Process.DataFile.RawDataFile,"text/csv","MySelector",ResizeArray [Comment.create("MyKey","MyValue")])
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let d2 = Data("MyID","MyName",Process.DataFile.RawDataFile,"text/csv","MySelector",ResizeArray [Comment.create("MyKey","MyValue")])
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let hash1 = d1.GetHashCode()
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let hash2 = d2.GetHashCode()
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Expect.equal d1 d2 "Should be equal"
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Expect.equal hash1 hash2 "HashCode should be equal"
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testCase "unequal, different name" <| fun _ ->
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let d1 = Data("MyID","MyName",Process.DataFile.RawDataFile,"text/csv","MySelector",ResizeArray [Comment.create("MyKey","MyValue")])
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let d2 = Data("MyID","MyName2",Process.DataFile.RawDataFile,"text/csv","MySelector",ResizeArray [Comment.create("MyKey","MyValue")])
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let hash1 = d1.GetHashCode()
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let hash2 = d2.GetHashCode()
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Expect.notEqual d1 d2 "Should not be equal"
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Expect.notEqual hash1 hash2 "HashCode should not be equal"
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]
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let main =
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testList "Data" [
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tests_GetHashCode
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]

‎tests/Core/Main.fs‎

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@@ -8,6 +8,7 @@ let all = testSequenced <| testList "Core" [
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Regex.Tests.main
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Person.Tests.main
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CompositeHeader.Tests.main
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Data.Tests.main
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CompositeCell.Tests.main
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CompositeColumn.Tests.main
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ArcTables.Tests.main

‎tests/Json/ARCtrl.Json.Tests.fsproj‎

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@@ -17,6 +17,7 @@
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<Compile Include="BaseJsonTests.fs" />
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<Compile Include="Comment.Tests.fs" />
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<Compile Include="OntologyAnnotation.Tests.fs" />
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<Compile Include="Data.Tests.fs" />
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<Compile Include="CompositeCell.Tests.fs" />
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<Compile Include="IOType.Tests.fs" />
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<Compile Include="CompositeHeader.Tests.fs" />

‎tests/Json/ArcTable.Tests.fs‎

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@@ -91,10 +91,24 @@ let private tests = testList "extended" [
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]
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]
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let private tests_dataColumns =
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testList "dataColumns" [
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testCase "dataColumns" <| fun _ ->
97+
let testTable = ArcTable.init("Test")
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testTable.AddColumn (CompositeHeader.Input IOType.Data, [|CompositeCell.Data (Data(name="MyInputDataFile.csv"))|])
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testTable.AddColumn (CompositeHeader.Output IOType.Data, [|CompositeCell.Data (Data(name="MyData.csv#row=1",format="text/csv",selectorFormat = "MySelector"))|])
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let encoded = testTable.ToJsonString()
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let decoded = ArcTable.fromJsonString encoded
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Expect.arcTableEqual decoded testTable "decompressed table should be equal to original table"
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]
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let main = testList "ArcTable" [
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tests
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tests_core
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tests_coreEmpty
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tests_compressedEmpty
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tests_compressedFilled
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tests_dataColumns
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]

‎tests/Json/CompositeCell.Tests.fs‎

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@@ -15,6 +15,9 @@ let tests_extended = testList "extended" [
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let cell_term_empty_jsonString = sprintf """{"%s":"Term","values":[{}]}""" CompositeCell.CellType
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let cell_unitized_jsonString = sprintf """{"%s":"Unitized","values":["42",{"annotationValue":"My Name","termSource":"MY","termAccession":"MY:1"}]}""" CompositeCell.CellType
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let cell_unitized_empty_jsonString = sprintf """{"%s":"Unitized","values":["",{}]}""" CompositeCell.CellType
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let cell_data_empty_jsonString = sprintf """{"%s":"Data","values":[{}]}""" CompositeCell.CellType
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let cell_data_jsonString = sprintf """{"%s":"Data","values":[{"@id":"MyID","name":"MyName","dataType":"Raw Data File","format":"text/csv","selectorFormat":"MySelector","comments":[{"key":"MyKey","value":"MyValue"}]}]}""" CompositeCell.CellType
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1821
testList "encoder (toJsonString)" [
1922
testCase "FreeText" <| fun _ ->
2023
let actual = CompositeCell.encoder cell_freetext |> Encode.toJsonString 0
@@ -36,6 +39,14 @@ let tests_extended = testList "extended" [
3639
let actual = CompositeCell.encoder cell_unitized_empty |> Encode.toJsonString 0
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let expected = cell_unitized_empty_jsonString
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Expect.equal actual expected ""
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testCase "Data" <| fun _ ->
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let actual = CompositeCell.encoder (CompositeCell.Data(Data("MyID","MyName",Process.DataFile.RawDataFile,"text/csv","MySelector",ResizeArray [Comment.create("MyKey","MyValue")])) ) |> Encode.toJsonString 0
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let expected = cell_data_jsonString
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Expect.equal actual expected ""
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testCase "Data empty" <| fun _ ->
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let actual = CompositeCell.encoder (CompositeCell.Data(Data())) |> Encode.toJsonString 0
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let expected = cell_data_empty_jsonString
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Expect.equal actual expected ""
3950
]
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testList "decoder (fromJsonString)" [
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testCase "FreeText" <| fun _ ->
@@ -58,6 +69,14 @@ let tests_extended = testList "extended" [
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let actual = Decode.fromJsonString CompositeCell.decoder cell_unitized_empty_jsonString
5970
let expected = cell_unitized_empty
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Expect.equal actual expected ""
72+
testCase "Data" <| fun _ ->
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let actual = Decode.fromJsonString CompositeCell.decoder cell_data_jsonString
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let expected = CompositeCell.Data(Data("MyID","MyName",Process.DataFile.RawDataFile,"text/csv","MySelector",ResizeArray [Comment.create("MyKey","MyValue")]))
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Expect.equal actual expected ""
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testCase "Data empty" <| fun _ ->
77+
let actual = Decode.fromJsonString CompositeCell.decoder cell_data_empty_jsonString
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let expected = CompositeCell.Data(Data())
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Expect.equal actual expected ""
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]
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]
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‎tests/Json/Data.Tests.fs‎

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module Tests.Data
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3+
open TestingUtils
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open ARCtrl
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open ARCtrl.Json
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let basic_tests = testList "BasicJson" [
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testCase "AllFields" <| fun _ ->
9+
let d = Data("MyID","MyName",Process.DataFile.RawDataFile,"text/csv","MySelector",ResizeArray [Comment.create("MyKey","MyValue")])
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let json = Data.encoder d |> Encode.toJsonString 2
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let d2 = Decode.fromJsonString Data.decoder json
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Expect.equal d2 d "Different after write and read"
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]
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let isa_tests = testList "ISAJson" [
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testCase "NativeISAFieldsIO" <| fun _ ->
17+
let d = Data("MyID","MyName",Process.DataFile.RawDataFile,comments = ResizeArray [Comment.create("MyKey","MyValue")])
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let json = Data.ISAJson.encoder d |> Encode.toJsonString 2
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let d2 = Decode.fromJsonString Data.ISAJson.decoder json
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Expect.equal d2 d "Different after write and read"
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#if !FABLE_COMPILER_PYTHON
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testAsync "WriterSchemaCorrectness" {
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let d = Data("MyID","MyName",Process.DataFile.RawDataFile, "text/csv", "MySelector", ResizeArray [Comment.create("MyKey","MyValue")])
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let json = Data.ISAJson.encoder d |> Encode.toJsonString 2
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let! validation = Validation.validateData json
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Expect.isTrue validation.Success $"Data did not match schema: {validation.GetErrors()}"
27+
}
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#endif
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]
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let rocrate_tests = testList "RO-CrateJson" [
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testCase "AllFields" <| fun _ ->
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let d = Data("MyID","MyName",Process.DataFile.RawDataFile,"text/csv","MySelector",ResizeArray [Comment.create("MyKey","MyValue")])
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let json = Data.ROCrate.encoder d |> Encode.toJsonString 2
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let d2 = Decode.fromJsonString Data.ROCrate.decoder json
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Expect.equal d2 d "Different after write and read"
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]
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let compressed_tests =
40+
testList "CompressedJson" [
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testCase "AllFields" <| fun _ ->
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let d = Data("MyID","MyName",Process.DataFile.RawDataFile,"text/csv","MySelector",ResizeArray [Comment.create("MyKey","MyValue")])
43+
let stringTable = StringTable.StringTableMap()
44+
let json = Data.compressedEncoder stringTable d |> Encode.toJsonString 2
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let d2 = Decode.fromJsonString (Data.compressedDecoder (StringTable.arrayFromMap stringTable)) json
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Expect.equal d2 d "Different after write and read"
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]
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let main = testList "Data" [
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basic_tests
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isa_tests
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rocrate_tests
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compressed_tests
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]

‎tests/Json/Main.fs‎

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@@ -6,6 +6,7 @@ let all = testSequenced <| testList "Json" [
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Tests.Decoder.main
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Tests.Comment.main
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Tests.OntologyAnnotation.main
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Tests.Data.main
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Tests.CompositeCell.main
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Tests.IOType.main
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Tests.CompositeHeader.main

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