Add first simple integration test for annotation table parsing

playground.fsx

@@ -40,19 +40,7 @@ open ArcGraphModel
 
 // Assay annotation table parsing
 
-let assay = FsWorkbook.fromXlsxFile (__SOURCE_DIRECTORY__ + "/tests/ArcGraphModel.Tests/Fixtures/isa.assay.xlsx")
-
-let sheet1 = FsWorkbook.getWorksheets assay |> Seq.item 0
-let sheet2 = FsWorkbook.getWorksheets assay |> Seq.item 1
-
-sheet1.Rows[0] |> Seq.toList
-sheet2.Rows[0] |> Seq.toList
-
-let assayTables = AnnotationTable.parseWorkbook assay
-
-assayTables[1] 
-|> snd
-|> fun x -> x.TermRelatedBuildingBlocks
+let assayTokens = Assay.parseAnnotationTablesFromFile (__SOURCE_DIRECTORY__ + "/tests/ArcGraphModel.Tests/Fixtures/correct/assay_with_only_source_and_sample_column.xlsx")
 
 // Investigation metadata parsing
 

tests/ArcGraphModel.Tests/ArcGraphModel.Tests.fsproj

@@ -9,6 +9,8 @@
   <ItemGroup>
     <None Include="Fixtures\**" CopyToOutputDirectory="Always" />
     <Compile Include="TestUtils.fs" />
+    <Compile Include="TestObjects.fs" />
+    <Compile Include="IntegrationTests\Assay.fs" />
     <Compile Include="IntegrationTests\ParseInvestigationTests.fs" />
     <Compile Include="Program.fs" />
   </ItemGroup>

tests/ArcGraphModel.Tests/IntegrationTests/Assay.fs

@@ -0,0 +1,75 @@
+module IntegrationTests.Assay
+
+open ControlledVocabulary
+open FsSpreadsheet
+open FsSpreadsheet.ExcelIO
+open ArcGraphModel
+open Xunit
+
+open TestUtils
+open TestObjects
+
+module Correct  =
+
+    module ``Assay with only source and sample column`` = 
+
+        let assay = Assays.Correct.``assay with only source and sample column``
+
+        [<Fact>]
+        let ``AnnotationTable count`` () =
+            Assert.Equal(assay.Length, 1) 
+
+        let table = assay.[0] |> snd
+
+        [<Fact>]
+        let ``TokenizedAnnotationTable IOColumn count`` () =
+            TokenizedAnnotationTable.hasIOColumnAmount 2 table
+
+        [<Fact>]
+        let ``TokenizedAnnotationTable TermRelatedBuildingBlocksAmount`` () =
+            TokenizedAnnotationTable.hasTermRelatedBuildingBlockAmount 0 table
+
+        let expectedIOColumns = 
+            [
+                [
+                    CvParam(
+                        id = "(n/a)",
+                        name = "Source Name",
+                        ref = "(n/a)",
+                        pv = (ParamValue.Value "Source A"),
+                        attributes = []
+                    )
+                ]
+                [
+                    CvParam(
+                        id = "(n/a)",
+                        name = "Sample Name",
+                        ref = "(n/a)",
+                        pv = (ParamValue.Value "Sample A"),
+                        attributes = []
+                    )
+                ]
+            ]
+
+        let expectedTermRelatedBuildingBlocks: CvParam list list = []
+
+        [<Fact>]
+        let ``TokenizedAnnotationTable IOColumns`` () =
+            (expectedIOColumns, table.IOColumns)
+            ||> List.iter2 (fun expectedGroup actualGroup ->
+                (expectedGroup, actualGroup)
+                ||> List.iter2 (fun expectedParam actualParam ->
+                    CvParam.structuralEquality expectedParam actualParam
+                )
+            )
+
+        [<Fact>]
+        let ``TokenizedAnnotationTable TermRelatedBuildingBlocks`` () =
+            (expectedTermRelatedBuildingBlocks, table.TermRelatedBuildingBlocks)
+            ||> List.iter2 (fun expectedGroup actualGroup ->
+                (expectedGroup, actualGroup)
+                ||> List.iter2 (fun expectedParam actualParam ->
+                    CvParam.structuralEquality expectedParam actualParam
+                )
+            )
+

tests/ArcGraphModel.Tests/IntegrationTests/ParseInvestigationTests.fs

@@ -8,7 +8,6 @@ open Xunit
 
 open TestUtils
 
-
 let inves = FsWorkbook.fromXlsxFile "Fixtures/isa.investigation.xlsx"
 let invesWs = FsWorkbook.getWorksheets inves |> Seq.head
 let invesWsParsed = Worksheet.parseRowsFlat invesWs

tests/ArcGraphModel.Tests/TestObjects.fs

@@ -0,0 +1,13 @@
+module TestObjects
+
+open ArcGraphModel
+
+module Assays =
+
+    module Correct =
+
+        let ``assay with only source and sample column`` =
+            Assay.parseAnnotationTablesFromFile "Fixtures/correct/assay_with_only_source_and_sample_column.xlsx"
+
+        let ``assay with characteristics`` = 
+            Assay.parseAnnotationTablesFromFile "Fixtures/correct/assay_with_single_characteristics.xlsx"

tests/ArcGraphModel.Tests/TestUtils.fs

@@ -7,14 +7,61 @@ open ArcGraphModel.AnnotationTable
 
 module CvParam =
 
-    open ArcGraphModel
+    let termNamesEqual (cvpExpectec : CvParam) (cvpActual : CvParam) =
+        Assert.Equal(
+            (CvBase.getCvName cvpExpectec),
+            (CvBase.getCvName cvpActual)
+        )
+
+    let hasTermName (expectedName : string) (cvpActual : CvParam) =
+        Assert.Equal(
+            expectedName,
+            (CvBase.getCvName cvpActual)
+        )
+
+    let accessionsEqual (cvpExpectec : CvParam) (cvpActual : CvParam) =
+        Assert.Equal(
+            (CvBase.getCvAccession cvpExpectec),
+            (CvBase.getCvAccession cvpActual)
+        )
+
+    let hasAccession (expectedID : string) (cvpActual : CvParam) =
+        Assert.Equal(
+            expectedID,
+            (CvBase.getCvAccession cvpActual)
+        )
 
-    let termNamesEqual (cvpActual : CvParam) (cvpExpectec : CvParam) =
+    let refUrisEqual (cvpExpectec : CvParam) (cvpActual : CvParam) =
         Assert.Equal(
-            (CvBase.getCvName cvpActual),
-            (CvBase.getCvName cvpExpectec)
+            (CvBase.getCvRef cvpExpectec),
+            (CvBase.getCvRef cvpActual)
         )
 
+    let hasRefUri (expectedRefUri : string) (cvpActual : CvParam) =
+        Assert.Equal(
+            expectedRefUri,
+            (CvBase.getCvRef cvpActual)
+        )
+
+    let valuesEqual (cvpExpectec : CvParam) (cvpActual : CvParam) =
+        Assert.Equal(
+            (Param.getParamValue cvpExpectec),
+            (Param.getParamValue cvpActual)
+        )
+
+    let hasValue (expectedValue : ParamValue) (cvpActual : CvParam) =
+        Assert.Equal(
+            expectedValue,
+            (Param.getParamValue cvpActual)
+        )
+
+    let structuralEquality (cvpExpectec : CvParam) (cvpActual : CvParam) =
+        termNamesEqual cvpExpectec cvpActual
+        accessionsEqual cvpExpectec cvpActual
+        refUrisEqual cvpExpectec cvpActual
+        valuesEqual cvpExpectec cvpActual
+
+
 module UserParam =
 
     open ArcGraphModel
@@ -27,4 +74,8 @@ module UserParam =
 
 module TokenizedAnnotationTable =
 
-    ()
+    let hasIOColumnAmount (expectedIOColumnAmount : int) (table : TokenizedAnnotationTable) =
+        Assert.Equal(expectedIOColumnAmount, table.IOColumns.Length)
+
+    let hasTermRelatedBuildingBlockAmount (expectedTermRelatedBuildingBlockAmount : int) (table : TokenizedAnnotationTable) =
+        Assert.Equal(expectedTermRelatedBuildingBlockAmount, table.TermRelatedBuildingBlocks.Length)