restructure testing environment

ARCtrl.sln

@@ -67,6 +67,8 @@ Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.Contract", "src\Cont
 EndProject
 Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "FileSystem.Tests", "tests\FileSystem\FileSystem.Tests.fsproj", "{D9FE196B-AC21-4C3E-B9AE-DDDEC2158BC3}"
 EndProject
+Project("{F2A71F9B-5D33-465A-A702-920D77279786}") = "TestingUtils", "tests\TestingUtils\TestingUtils.fsproj", "{AA011593-6603-4E16-A7B0-0ED3862511DE}"
+EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution
 		Debug|Any CPU = Debug|Any CPU
@@ -125,6 +127,10 @@ Global
 		{D9FE196B-AC21-4C3E-B9AE-DDDEC2158BC3}.Debug|Any CPU.Build.0 = Debug|Any CPU
 		{D9FE196B-AC21-4C3E-B9AE-DDDEC2158BC3}.Release|Any CPU.ActiveCfg = Release|Any CPU
 		{D9FE196B-AC21-4C3E-B9AE-DDDEC2158BC3}.Release|Any CPU.Build.0 = Release|Any CPU
+		{AA011593-6603-4E16-A7B0-0ED3862511DE}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{AA011593-6603-4E16-A7B0-0ED3862511DE}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{AA011593-6603-4E16-A7B0-0ED3862511DE}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{AA011593-6603-4E16-A7B0-0ED3862511DE}.Release|Any CPU.Build.0 = Release|Any CPU
 	EndGlobalSection
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE
@@ -145,6 +151,7 @@ Global
 		{801247D5-7EE5-49C8-AB26-F822A415BA49} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}
 		{1945EE8A-F105-43A9-91C9-8C4422B9873E} = {6DA2330B-D407-4FB1-AF05-B0184034EC44}
 		{D9FE196B-AC21-4C3E-B9AE-DDDEC2158BC3} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}
+		{AA011593-6603-4E16-A7B0-0ED3862511DE} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}
 	EndGlobalSection
 	GlobalSection(ExtensibilityGlobals) = postSolution
 		SolutionGuid = {1E354DE6-99BA-421E-9EF8-E808B855A85F}

tests/ARCtrl/ARCtrl.Tests.fs

@@ -8,8 +8,9 @@ open Expecto
 
 open ARCtrl
 open ARCtrl.ISA
-open TestObjects.ISAContracts
-
+open TestObjects.Contract.ISA
+open TestObjects.Spreadsheet
+open TestingUtils
 
 let private test_model = testList "model" [
     testCase "create" <| fun _ ->
@@ -53,27 +54,27 @@ let private test_model = testList "model" [
 
 let private test_isaFromContracts = testList "read_contracts" [
     testCase "simpleISA" (fun () ->
-        let iContract = TestObjects.ISAContracts.SimpleISA.investigationReadContract
-        let sContract = TestObjects.ISAContracts.SimpleISA.studyReadContract
-        let aContract = TestObjects.ISAContracts.SimpleISA.assayReadContract
+        let iContract = SimpleISA.investigationReadContract
+        let sContract = SimpleISA.studyReadContract
+        let aContract = SimpleISA.assayReadContract
         let arc = ARC()
         arc.SetISAFromContracts([|iContract; sContract; aContract|])
         Expect.isSome arc.ISA "isa should be filled out"
         let inv = arc.ISA.Value
-        Expect.equal inv.Identifier TestObjects.Investigation.investigationIdentifier "investigation identifier should have been read from investigation contract"
+        Expect.equal inv.Identifier Investigation.investigationIdentifier "investigation identifier should have been read from investigation contract"
 
         Expect.equal inv.Studies.Count 2 "should have read two studies"
         let study1 = inv.Studies.[0]
         let study2 = inv.Studies.[1]
-        Expect.equal study1.Identifier TestObjects.Study.studyIdentifier "study 1 identifier should have been read from study contract"
+        Expect.equal study1.Identifier Study.studyIdentifier "study 1 identifier should have been read from study contract"
         Expect.equal study1.TableCount 8 "study 1 should have the 7 tables from investigation plus one extra. One table should be overwritten."
         Expect.equal study2.TableCount 4 "study 2 should have exactly as many tables as stated in investigation file"
 
         Expect.equal study1.RegisteredAssayCount 3 "study 1 should have read three assays"
         let assay1 = study1.RegisteredAssays.[0]
         let assay2 = study1.RegisteredAssays.[1]
         let assay3 = study1.RegisteredAssays.[2]
-        Expect.equal assay1.Identifier TestObjects.Assay.assayIdentifier "assay 1 identifier should have been read from assay contract"
+        Expect.equal assay1.Identifier Assay.assayIdentifier "assay 1 identifier should have been read from assay contract"
         Expect.equal assay1.TableCount 1 "assay 1 should have read one table"
         Expect.equal assay2.TableCount 0 "assay 2 should have read no tables"
         Expect.equal assay3.TableCount 0 "assay 3 should have read no tables"  
@@ -95,11 +96,11 @@ let private test_isaFromContracts = testList "read_contracts" [
         Expect.equal study.TableCount 1 "study should have read one table"
         let studyTable = study.Tables.[0]
         Expect.equal studyTable.ColumnCount 2 "study column number should be unchanged"
-        TestingUtils.mySequenceEqual
+        Expect.mySequenceEqual
             (studyTable.GetProtocolDescriptionColumn()).Cells
             [CompositeCell.createFreeText UpdateAssayWithStudyProtocol.description]
             "Description value was not kept correctly"
-        TestingUtils.mySequenceEqual
+        Expect.mySequenceEqual
             (studyTable.GetProtocolNameColumn()).Cells
             [CompositeCell.createFreeText UpdateAssayWithStudyProtocol.protocolName]
             "Protocol ref value was not kept correctly"
@@ -109,15 +110,15 @@ let private test_isaFromContracts = testList "read_contracts" [
         Expect.equal assay.TableCount 1 "assay should have read one table"
         let assayTable = assay.Tables.[0]
         Expect.equal assayTable.ColumnCount 3 "assay column number should be updated"
-        TestingUtils.mySequenceEqual
+        Expect.mySequenceEqual
             (assayTable.GetProtocolNameColumn()).Cells
             (Array.create 2 (CompositeCell.createFreeText UpdateAssayWithStudyProtocol.protocolName))
             "Protocol ref value was not kept correctly"
-        TestingUtils.mySequenceEqual
+        Expect.mySequenceEqual
             (assayTable.GetColumnByHeader(UpdateAssayWithStudyProtocol.inputHeader)).Cells
             (Array.create 2 UpdateAssayWithStudyProtocol.inputCell)
             "Protocol ref value was not kept correctly"
-        TestingUtils.mySequenceEqual
+        Expect.mySequenceEqual
             (assayTable.GetProtocolDescriptionColumn()).Cells
             (Array.create 2 (CompositeCell.createFreeText UpdateAssayWithStudyProtocol.description))
             "Description value was not taken correctly"

tests/ARCtrl/ARCtrl.Tests.fsproj

@@ -6,21 +6,16 @@
     <GenerateProgramFile>false</GenerateProgramFile>
   </PropertyGroup>
   <ItemGroup>
-    <Compile Include="Utils.fs" />
-    <Compile Include="ArcTable.fs" />
-    <Compile Include="Assay.fs" />
-    <Compile Include="Study.fs" />
-    <Compile Include="InvestigationFile.fs" />
     <Compile Include="Templates.Tests.fs" />
     <Compile Include="SemVer.Tests.fs" />
-    <Compile Include="TestObjects/ISAContracts.fs" />
     <None Include="paket.references" />
     <Compile Include="ARCtrl.Contracts.Tests.fs" />
     <Compile Include="ARCtrl.Tests.fs" />
     <Compile Include="Main.fs" />
   </ItemGroup>
   <ItemGroup>
     <ProjectReference Include="..\..\src\ARCtrl\ARCtrl.fsproj" />
+    <ProjectReference Include="..\TestingUtils\TestingUtils.fsproj" />
   </ItemGroup>
   <Import Project="..\..\.paket\Paket.Restore.targets" />
 </Project>

tests/ARCtrl/Templates.Tests.fs

@@ -13,6 +13,7 @@ open ARCtrl.ISA
 
 open System
 open System.Text
+open TestingUtils
 
 let private fableReplaceLineEndings(str: string) =
     str.Replace("\r\n","\n").Replace("\n\r","\n")
@@ -143,8 +144,8 @@ let tests_Template = testList "Template" [
                 //printfn "EXPECTED: %A" expected.Table
 
                 Expect.equal actualValue.Table.Name expected.Table.Name "Name should be equal"
-                TestingUtils.mySequenceEqual actualValue.Table.Headers expected.Table.Headers "Headers should be equal"
-                TestingUtils.mySequenceEqual actualValue.Table.Values expected.Table.Values "Headers should be equal"
+                Expect.mySequenceEqual actualValue.Table.Headers expected.Table.Headers "Headers should be equal"
+                Expect.mySequenceEqual actualValue.Table.Values expected.Table.Values "Headers should be equal"
 
                 Expect.equal actualValue.Table.RowCount expected.Table.RowCount "RowCount should be equal"
                 Expect.equal actualValue.Table.ColumnCount expected.Table.ColumnCount "ColumnCount should be equal"

tests/FileSystem/FileSystem.Tests.fsproj

@@ -7,12 +7,12 @@
   </PropertyGroup>
   <ItemGroup>
     <None Include="paket.references" />
-    <Compile Include="Utils.fs" />
     <Compile Include="FileSystemTree.Tests.fs" />
     <Compile Include="Main.fs" />
   </ItemGroup>
   <ItemGroup>
     <ProjectReference Include="..\..\src\FileSystem\ARCtrl.FileSystem.fsproj" />
+    <ProjectReference Include="..\TestingUtils\TestingUtils.fsproj" />
   </ItemGroup>
   <Import Project="..\..\.paket\Paket.Restore.targets" />
 </Project>

tests/FileSystem/FileSystemTree.Tests.fs

@@ -7,6 +7,7 @@ open Expecto
 #endif
 
 open ARCtrl.FileSystem
+open TestingUtils
 
 let private newArcRelativePaths = [|
     @"isa.investigation.xlsx"; @".arc\.gitkeep"; @".git\config";
@@ -97,7 +98,7 @@ let private tests_fromFilePaths =
             let filest = FileSystemTree.fromFilePaths newArcRelativePaths
             // damn... i made this, because i thought equal would somehow not work. But i missed adding "@" in front of paths.
             // i'll leave it for improved error message.
-            TestingUtils.testFileSystemTree filest newArcFST 
+            Expect.testFileSystemTree filest newArcFST 
             Expect.equal filest newArcFST "isEqual"
     ]
 
@@ -373,7 +374,7 @@ let private tests_AddFile =
             |])
             let newPath = @"studies\TestAssay1\resources\MyAwesomeRessource.pdf"
             let actual = newArcFST.AddFile newPath
-            TestingUtils.testFileSystemTree actual expected // use this instead of equal to ensure order of Folder children does not matter
+            Expect.testFileSystemTree actual expected // use this instead of equal to ensure order of Folder children does not matter
         testCase "new arc, add root file" <| fun _ ->
             let expected = Folder("root",[|
                 File "isa.investigation.xlsx"; File "Test.md";
@@ -428,7 +429,7 @@ let private tests_AddFile =
             |])
             let newPath = @"Test.md"
             let actual = newArcFST.AddFile newPath
-            TestingUtils.testFileSystemTree actual expected // use this instead of equal to ensure order of Folder children does not matter
+            Expect.testFileSystemTree actual expected // use this instead of equal to ensure order of Folder children does not matter
         testCase "new arc, add new folder" <| fun _ ->
             let expected = Folder("root",[|
                 File "isa.investigation.xlsx"; 
@@ -484,7 +485,7 @@ let private tests_AddFile =
             |])
             let newPath = @"MyNewFolder/README.md"
             let actual = newArcFST.AddFile newPath
-            TestingUtils.testFileSystemTree actual expected // use this instead of equal to ensure order of Folder children does not matter
+            Expect.testFileSystemTree actual expected // use this instead of equal to ensure order of Folder children does not matter
     ]
 
 let main = testList "FileSystemTree" [

tests/ISA/ISA.Json.Tests/ISA.Json.Tests.fsproj

@@ -7,22 +7,13 @@
   </PropertyGroup>
   <ItemGroup>
     <None Include="paket.references" />
-    <Compile Include="TestObjects\OntologyAnnotation.fs" />
-    <Compile Include="TestObjects\ProcessInput.fs" />
-    <Compile Include="TestObjects\Validation.fs" />
-    <Compile Include="TestObjects\Protocol.fs" />
-    <Compile Include="TestObjects\Investigation.fs" />
-    <Compile Include="TestObjects\Assay.fs" />
-    <Compile Include="TestObjects\Person.fs" />
-    <Compile Include="TestObjects\Process.fs" />
-    <Compile Include="TestObjects\Publication.fs" />
-    <Compile Include="Utils.fs" />
     <Compile Include="JsonSchema.Tests.fs" />
     <Compile Include="Json.Tests.fs" />
     <Compile Include="Main.fs" />
   </ItemGroup>
   <ItemGroup>
     <ProjectReference Include="..\..\..\src\ISA\ISA.Json\ARCtrl.ISA.Json.fsproj" />
+    <ProjectReference Include="..\..\TestingUtils\TestingUtils.fsproj" />
   </ItemGroup>
   <Import Project="..\..\..\.paket\Paket.Restore.targets" />
 </Project>