add assay file io tests

src/ISADotNet.XLSX/AssayFile/AnnotationNode.fs

@@ -105,7 +105,7 @@ module AnnotationNode =
                         (termAccessionGetter matrix i)
                         (termSourceGetter matrix i)
 
-            let category = mergeOntology category1 category2 |> Option.map (Some >> ProtocolParameter.create None)
+            let category = mergeOntology h.Term category1 |> mergeOntology category2 |> Option.map (Some >> ProtocolParameter.create None)
 
             category,
             fun (matrix : System.Collections.Generic.Dictionary<(string * int),string>) i ->
@@ -157,7 +157,7 @@ module AnnotationNode =
                         (termSourceGetter matrix i)
 
             let factor = 
-                mergeOntology category1 category2 
+                mergeOntology h.Term category1 |> mergeOntology category2
                 |> Option.map (fun oa ->  Factor.create None (oa.Name |> Option.map AnnotationValue.toString) (Some oa) None)
 
             factor,
@@ -186,6 +186,7 @@ module AnnotationNode =
                         | Some v -> Some v
                         | _ -> None 
                 | None -> None, fun _ _ -> None
+
             let category2, termSourceGetter =
                 match Seq.tryPick (tryParseTermSourceReferenceHeader h) headers with
                 | Some h ->
@@ -210,7 +211,7 @@ module AnnotationNode =
                         (termAccessionGetter matrix i)
                         (termSourceGetter matrix i)
 
-            let characteristic = mergeOntology category1 category2 |> Option.map (Some >> MaterialAttribute.create None)            
+            let characteristic = mergeOntology h.Term category1 |> mergeOntology category2 |> Option.map (Some >> MaterialAttribute.create None)            
 
             characteristic,
             fun (matrix : System.Collections.Generic.Dictionary<(string * int),string>) i ->

src/ISADotNet.XLSX/Conversions.fs

@@ -153,6 +153,17 @@ module ProtocolParameter =
                 sprintf "%s%c%s" sources    separator source
             ) 
 
+module MaterialAttribute =
+
+    /// Create a ISAJson MaterialAttribute from ISATab string entries
+    let fromString (term:string) (accession:string) (source:string) =
+        OntologyAnnotation.fromString term accession source
+        |> Option.fromValueWithDefault OntologyAnnotation.empty
+        |> MaterialAttribute.create None
+
+    /// Get ISATab string entries from an ISAJson MaterialAttribute object
+    let toString (ma : MaterialAttribute) =
+        ma.CharacteristicType |> Option.map OntologyAnnotation.toString |> Option.defaultValue ("","","")    
 
 module Value =
 

src/ISADotNet.XLSX/ISADotNet.XLSX.fsproj

@@ -29,12 +29,16 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="FSharpSpreadsheetML" Version="0.0.3" />
+    <PackageReference Include="FSharpSpreadsheetML" Version="0.0.4" />
   </ItemGroup>
 
   <ItemGroup>
     <ProjectReference Include="..\ISADotnet\ISADotNet.fsproj" />
   </ItemGroup>
+
+  <ItemGroup>
+    <PackageReference Update="FSharp.Core" Version="5.0.1" />
+  </ItemGroup>
 
   <PropertyGroup>
     <Authors>nfdi4plants, Lukas Weil, Kevin Frey</Authors>

src/ISADotnet/ISADotNet.fsproj

@@ -50,6 +50,10 @@
 
   <ItemGroup Condition=" '$(PackageId)' == 'ISADotNet.Fable' ">
     <Content Include="*.fsproj; **\*.fs; **\*.fsi" PackagePath="fable\" />
+  </ItemGroup>
+
+  <ItemGroup>
+    <PackageReference Update="FSharp.Core" Version="5.0.1" />
   </ItemGroup> 
 
   <PropertyGroup>

src/ISADotnet/JsonIO/IO.fs

@@ -5,6 +5,21 @@ open System.Text.Json
 open System.IO
 open FSharp.SystemTextJson
 
+module OntologyAnnotation = 
+
+    let fromString (s:string) = 
+        JsonSerializer.Deserialize<OntologyAnnotation>(s,JsonExtensions.options)
+
+    let toString (oa:OntologyAnnotation) = 
+        JsonSerializer.Serialize<OntologyAnnotation>(oa,JsonExtensions.options)
+
+    let fromFile (path : string) = 
+        File.ReadAllText path 
+        |> fromString
+
+    let toFile (path : string) (oa:OntologyAnnotation) = 
+        File.WriteAllText(path,toString oa)
+
 module Protocol = 
 
     let fromString (s:string) = 

tests/ISADotNet.Tests/ISADotNet.XLSX/AssayFileTests.fs

@@ -7,6 +7,7 @@ open ISADotNet
 open Expecto
 open TestingUtils
 
+open ISADotNet
 open ISADotNet.XLSX
 open ISADotNet.XLSX.AssayFile
 
@@ -142,6 +143,88 @@ let testHeaderSplittingFunctions =
         )
     ]
 
+[<Tests>]
+let testNodeGetterFunctions =
+
+    let sourceDirectory = __SOURCE_DIRECTORY__ + @"/TestFiles/"
+
+    let assayFilePath = System.IO.Path.Combine(sourceDirectory,"AssayTableTestFile.xlsx")
+
+    let doc = Spreadsheet.fromFile assayFilePath false
+    let sst = Spreadsheet.tryGetSharedStringTable doc
+    let wsp = Spreadsheet.tryGetWorksheetPartBySheetIndex 0u doc |> Option.get
+    let table = Table.tryGetByNameBy (fun s -> s.Contains "annotationTable") wsp |> Option.get
+
+    let m = Table.toSparseValueMatrix sst (Worksheet.getSheetData wsp.Worksheet) table
+
+    testList "NodGetterTests" [
+        testCase "RetreiveValueFromMatrix" (fun () ->
+            let tryGetValue k (dict:System.Collections.Generic.Dictionary<'K,'V>) = 
+                let b,v = dict.TryGetValue(k)
+                if b then Some v
+                else None
+
+            let v = tryGetValue ("Unit [square centimeter] (#h; #tUO:0000081; #u)",0) m
+
+            Expect.isSome v "Value could not be retrieved from matrix"
+
+            let expectedValue = "square centimeter"
+
+            Expect.equal v.Value expectedValue "Value retrieved from matrix is not correct"
+
+        )
+
+        testCase "GetUnitGetter" (fun () ->
+
+            let headers = ["Unit [square centimeter] (#h; #tUO:0000081; #u)";"Term Source REF [square centimeter] (#h; #tUO:0000081; #u)";"Term Accession Number [square centimeter] (#h; #tUO:0000081; #u)"]
+
+            let unitGetterOption = AnnotationNode.tryGetUnitGetterFunction headers
+
+            Expect.isSome unitGetterOption "Unit Getter was not returned even though headers should have matched"
+
+            let unitGetter = unitGetterOption.Value
+
+            let unit = unitGetter m 0
+
+            let expectedUnit = OntologyAnnotation.fromString "square centimeter" "http://purl.obolibrary.org/obo/UO_0000081" "UO" 
+
+            Expect.equal unit expectedUnit "Retrieved Unit is wrong"
+        )
+        testCase "GetUnitGetterWrongHeaders" (fun () ->
+
+            let headers = ["Parameter [square centimeter] (#h; #tUO:0000081; #u)";"Term Source REF [square centimeter] (#h; #tUO:0000081; #u)";"Term Accession Number [square centimeter] (#h; #tUO:0000081; #u)"]
+
+            let unitGetterOption = AnnotationNode.tryGetUnitGetterFunction headers
+
+            Expect.isNone unitGetterOption "Unit Getter was returned even though headers should not have matched"
+        )
+        testCase "GetCharacteristicsGetter" (fun () ->
+
+            let headers = ["Characteristics [leaf size]";"Term Source REF [leaf size] (#h; #tTO:0002637)";"Term Accession Number [leaf size] (#h; #tTO:0002637)";"Unit [square centimeter] (#h; #tUO:0000081; #u)";"Term Source REF [square centimeter] (#h; #tUO:0000081; #u)";"Term Accession Number [square centimeter] (#h; #tUO:0000081; #u)"]
+
+            let characteristicGetterOption = AnnotationNode.tryGetCharacteristicGetterFunction headers
+
+            Expect.isSome characteristicGetterOption "Characteristic Getter was not returned even though headers should have matched"
+
+            let characteristic,characteristicValue = characteristicGetterOption.Value
+
+            //let unit = unitGetter m 0
+
+            let expectedCharacteristic = MaterialAttribute.fromString "leaf size" "0002637" "TO" 
+
+            Expect.equal characteristic.Value expectedCharacteristic "Retrieved Characteristic is wrong"
+        )
+        testCase "GetCharacteristicsGetterWrongHeaders" (fun () ->
+
+            let headers = ["Parameter [square centimeter] (#h; #tUO:0000081; #u)";"Term Source REF [square centimeter] (#h; #tUO:0000081; #u)";"Term Accession Number [square centimeter] (#h; #tUO:0000081; #u)"]
+
+            let unitGetterOption = AnnotationNode.tryGetCharacteristicGetterFunction headers
+
+            Expect.isNone unitGetterOption "Characteristic Getter was returned even though headers should not have matched"
+        )
+    ]
+
+
 [<Tests>]
 let testProcessComparisonFunctions = 
 
@@ -250,15 +333,29 @@ let testProcessComparisonFunctions =
             Expect.sequenceEqual mergedProcess2.Outputs.Value [ProcessOutput.Sample sample2;ProcessOutput.Sample sample4] "Inputs were not merged correctly for mergedProcess2"
 
         )
+        testCase "IndexIdenticalProcessesByProtocolName" (fun () ->
+
+            let process1 = Process.create None None (Some protocol1) (Some parameterValues1) None None None None (Some [Source source1]) (Some [Sample sample1]) None
+            let process2 = Process.create None None (Some protocol1) (Some parameterValues2) None None None None (Some [Source source2]) (Some [Sample sample2]) None
+            let process3 = Process.create None None (Some protocol2) (Some parameterValues1) None None None None (Some [Source source3]) (Some [Sample sample3]) None
+            let process4 = Process.create None None (Some protocol2) (Some parameterValues2) None None None None (Some [Source source4]) (Some [Sample sample4]) None
+
+            let indexedProcesses = AnnotationTable.indexRelatedProcessesByProtocolName [process1;process2;process3;process4]
+
+            let names = indexedProcesses |> Seq.map (fun p -> Option.defaultValue "" p.Name)
+
+            let expectedNames = ["Protocol1_0";"Protocol1_1";"Protocol2_0";"Protocol2_1"]
+
+            Expect.sequenceEqual names expectedNames "Processes were not indexed correctly"
+        )
     ]
 
 
 [<Tests>]
 let testMetaDataFunctions = 
 
     let sourceDirectory = __SOURCE_DIRECTORY__ + @"/TestFiles/"
-    let sinkDirectory = System.IO.Directory.CreateDirectory(__SOURCE_DIRECTORY__ + @"/TestResult/").FullName
-    let referenceAssayFilePath = System.IO.Path.Combine(sourceDirectory,"AssayTestFile.xlsx")
+    let referenceAssayFilePath = System.IO.Path.Combine(sourceDirectory,"AssayMetadataTestFile.xlsx")
 
     testList "MetaDataTests" [
         testCase "CanReadMetaData" (fun () ->