Merge pull request #17 from nfdi4plants/querymodel

Querymodel fixes

.gitignore

@@ -349,4 +349,5 @@ MigrationBackup/
 # Ionide (cross platform F# VS Code tools) working folder
 .ionide/
 
-**/TestResults/**
+**/TestResults/**
+tests/ARCtrl.Querymodel.Tests/playground_2.fsx

README.md

@@ -1,22 +1,43 @@
 # ARCtrl.NET
 
-> **ARCtrl.NET** is the .NET IO implementation of [ARCtrl](https://github.com/nfdi4plants/ARCtrl)
- 
-| Version | Downloads |
-| :--------|-----------:|
-|<a href="https://www.nuget.org/packages/ARCtrl.NET/"><img alt="Nuget" src="https://img.shields.io/nuget/vpre/ARCtrl.NET?logo=nuget&color=%234fb3d9"></a>|<a href="https://www.nuget.org/packages/ARCtrl/"><img alt="Nuget" src="https://img.shields.io/nuget/dt/ARCtrl?color=%234FB3D9"></a>|
+This library functions as an IO wrapper for the [ARCtrl](https://github.com/nfdi4plants/ARCtrl) library in .NET. 
+
+The documentation for the actual functions for manipulating the ARC datamodel can be found [here](https://github.com/nfdi4plants/ARCtrl/tree/main/docs/scripts_fsharp).
+
+## Usage
 
 ```fsharp
 #r "nuget: ARCtrl.NET, 1.0.0-beta.2"
 
 open ARCtrl.NET
 open ARCtrl
 
-let arc = ARC.load(myArcPath)
 
-// work work work
+let arcPath = ""
+
+let arc = ARC.load(arcPath)
+
+let isa = arc.ISA.Value
 
-arc.Write(myArcPath)
+isa.InitStudy("MyStudy")
+
+arc.Write(arcPath)
 ```
 
-For documentation on manipulationh of the datamodel, see https://github.com/nfdi4plants/ARCtrl/tree/main/docs
+## Development
+
+`./build.cmd runtests`
+
+## ARCtrl.Querymodel
+
+```fsharp
+open ARCtrl
+open ARCtrl.QueryModel
+open ARCtrl.ISA
+
+let i = ArcInvestigation("Dummy Investigation")
+
+i.ArcTables.Values().WithName("Dummy Header").First.ValueText
+
+i.GetAssay("Dummy Assay").LastSamples
+```

src/ARCtrl.QueryModel/Investigation.fs

@@ -11,60 +11,18 @@ open System.Collections
 [<AutoOpen>]
 module ArcInvestigationExtensions = 
 
-    ///// Queryable representation of an ISA Investigation. Implements the QProcessSequence interface
-    //type ArcInvestigation with
-
-    //    /// Returns the QStudy with the given name
-    //    member this.Study(studyName : string) = 
-    //        this.Studies
-    //        |> List.find (fun s -> s.Identifier.Value = studyName)
-
-    //    /// Returns the nth QStudy
-    //    member this.Study(i : int) = 
-    //        this.Studies
-    //        |> List.item i 
-
-    //    /// Returns the QAssay with the given name (registered in the study with the given study name)
-    //    member this.Assay(assayName : string, ?StudyName : string) = 
-    //        match StudyName with
-    //        | Some sn ->
-    //            this.Study(sn).Assay(assayName)
-    //        | None ->
-    //            this.Studies
-    //            |> List.collect (fun s -> s.Assays)
-    //            |> List.find (fun a -> a.FileName.Value.Contains assayName)
-
-    //    /// get the protocol or sheet (in ISATab logic) with the given name
-    //    member this.Protocol (sheetName : string) =
-    //        base.Protocol(sheetName, $"Assay \"{this.FileName}\"")
-
-    //    /// get the nth protocol or sheet (in ISATab logic) 
-    //    member this.Protocol (index : int) =
-    //        base.Protocol(index, $"Assay \"{this.FileName}\"")
-
-    //    /// Returns the initial inputs final outputs of the assay, to which no processPoints
-    //    static member getRootInputs (investigation : QInvestigation) = QProcessSequence.getRootInputs investigation
-
-    //    /// Returns the final outputs of the investigation, which point to no further nodes
-    //    static member getFinalOutputs (investigation : QInvestigation) = QProcessSequence.getFinalOutputs investigation
-
-    //    /// Returns the initial inputs final outputs of the investigation, to which no processPoints
-    //    static member getRootInputOf (investigation : QInvestigation) (sample : string) = QProcessSequence.getRootInputsOfBy (fun _ -> true) sample investigation 
-
-    //    /// Returns the final outputs of the investigation, which point to no further nodes
-    //    static member getFinalOutputsOf (investigation : QInvestigation) (sample : string) = QProcessSequence.getFinalOutputsOfBy (fun _ -> true) sample investigation
-
-    //    static member toString (rwa : QInvestigation) =  JsonSerializer.Serialize<QInvestigation>(rwa,JsonExtensions.options)
-
-    //    static member toFile (path : string) (rwa:QInvestigation) = 
-    //        File.WriteAllText(path,QInvestigation.toString rwa)
-
-    //    static member fromString (s:string) = 
-    //        JsonSerializer.Deserialize<QInvestigation>(s,JsonExtensions.options)
-
-    //    static member fromFile (path : string) = 
-    //        File.ReadAllText path 
-    //        |> QInvestigation.fromString
+    /// Queryable representation of an ISA Investigation. Implements the QProcessSequence interface
+    type ArcInvestigation with
+
+        /// Returns the QStudy with the given name
+        member this.ArcTables
+            with get() : ArcTables = 
+                seq {
+                    for s in this.Studies do yield! s.Tables
+                    for a in this.Assays do yield! a.Tables
+                }
+                |> ResizeArray
+                |> ArcTables
 
     module Investigation =
 

src/ARCtrl.QueryModel/ResizeArray.fs

@@ -63,4 +63,14 @@ module ResizeArray =
         for i in a do
             if not (b.Contains(i)) then
                 b.Add(i)
+        b
+
+    let distinctBy f (a : ResizeArray<_>) =
+        let b = ResizeArray<_>()
+        let c = ResizeArray<_>()
+        for i in a do
+            let k = f i
+            if not (c.Contains(k)) then
+                c.Add(k)
+                b.Add(i)
         b

src/ARCtrl.QueryModel/Value.fs

@@ -172,11 +172,11 @@ module ISAValueExtensions =
             this.TryUnit |> Option.map (fun u -> u.NameText)
 
         /// Returns the value of the Value as string
-        member this.ValueText = this.Value.AsName()
+        member this.ValueText = this.Value.Text
 
         /// Returns the value of the Value as string if it exists, else returns None
         member this.TryValueText = 
-            this.TryValue |> Option.map (fun v -> v.AsName())
+            this.TryValue |> Option.map (fun v -> v.Text)
 
         /// Returns the value and unit of the Value as string
         member this.ValueWithUnitText =

tests/ARCtrl.Querymodel.Tests/ARCtrl.Querymodel.Tests.fsproj

@@ -7,7 +7,7 @@
   </PropertyGroup>
 
   <ItemGroup>
-    <Compile Include="ArcTable.fs" />
+    <Compile Include="TestARC.fs" />
     <Compile Include="Main.fs" />
     <Folder Include="TestObjects" />
   </ItemGroup>

tests/ARCtrl.Querymodel.Tests/Main.fs

@@ -4,7 +4,7 @@ open Expecto
 
 
 let all = testSequenced <| testList "All" [
-        ArcTable.Tests.testStuff     
+        TestARC.Tests.main     
     ]
 
 [<EntryPoint>]

tests/ARCtrl.Querymodel.Tests/TestARC.fs

@@ -0,0 +1,165 @@
+module TestARC.Tests
+
+open Expecto
+open System.Text.Json
+open ARCtrl
+open ARCtrl.NET
+open ARCtrl.QueryModel
+open ARCtrl.ISA
+let testArcPath = __SOURCE_DIRECTORY__ + @"\TestObjects\TestArc"
+let testArc = ARC.load(testArcPath)
+
+
+let ArcTables_getNodes =
+    let isa = testArc.ISA.Value
+    testList "ARCTables_GetNodes" [
+        testCase "LastData" (fun () -> 
+            let nodes = isa.ArcTables.LastData
+            let nodeNames = nodes |> List.map (fun n -> n.Name)
+            let expected = ["sampleOutCold.txt"; "sampleOutHeat.txt"]
+            Expect.sequenceEqual nodeNames expected "LastData of full sequence"            
+        )
+        testCase "LastSamples" (fun () ->
+            let nodes = isa.ArcTables.LastSamples
+            let nodeNames = nodes |> List.map (fun n -> n.Name)
+            let expected = ["CC1_prep"; "CC2_prep"; "CC3_prep"; "Co1_prep"; "Co2_prep"; "Co3_prep"; "C1_prep"; "C2_prep"; "C3_prep"; "H1_prep"; "H2_prep"; "H3_prep"]
+            Expect.sequenceEqual expected nodeNames "LastSamples of full sequence"                 
+        )
+        testCase "LastNodes" (fun () ->
+            let nodes = isa.ArcTables.LastNodes
+            let nodeNames = nodes |> Seq.map (fun n -> n.Name)
+            let expected = ["sampleOutCold.txt"; "sampleOutHeat.txt"]
+            Expect.sequenceEqual nodeNames expected "LastData of full sequence"    
+        )
+        testCase "RawData" (fun () ->
+            let nodes = isa.ArcTables.RawData
+            let nodeNames = nodes |> Seq.map (fun n -> n.Name)        
+            let expected = ["CC1_measured";"CC2_measured";"CC3_measured";"Co1_measured";"Co2_measured";"Co3_measured";"C1_measured";"C2_measured";"C3_measured";"H1_measured";"H2_measured";"H3_measured"]
+            Expect.sequenceEqual nodeNames expected "RawData of full sequence"    
+        )
+        testCase "LastRawData" (fun () ->
+            let nodes = isa.ArcTables.LastRawData
+            let nodeNames = nodes |> Seq.map (fun n -> n.Name)        
+            let expected = ["CC1_measured";"CC2_measured";"CC3_measured";"Co1_measured";"Co2_measured";"Co3_measured";"C1_measured";"C2_measured";"C3_measured";"H1_measured";"H2_measured";"H3_measured"]
+            Expect.sequenceEqual nodeNames expected "RawData of full sequence"    
+        )
+        testCase "FirstRawData" (fun () ->
+            let nodes = isa.ArcTables.FirstRawData
+            let nodeNames = nodes |> Seq.map (fun n -> n.Name)        
+            let expected = ["CC1_measured";"CC2_measured";"CC3_measured";"Co1_measured";"Co2_measured";"Co3_measured";"C1_measured";"C2_measured";"C3_measured";"H1_measured";"H2_measured";"H3_measured"]
+            Expect.sequenceEqual nodeNames expected "RawData of full sequence"    
+        )
+    ]
+
+let Assay_getNodes =
+    let isa = testArc.ISA.Value
+    testList "Assay_GetNodes" [
+
+        testCase "LastNodes" (fun () ->
+            let nodes = isa.GetAssay("MSEval_Heat").LastNodes
+            let nodeNames = nodes |> Seq.map (fun n -> n.Name)
+            let expected = ["sampleOutHeat.txt"]
+            Expect.sequenceEqual nodeNames expected "LastData of full sequence"    
+        )
+    ]
+let Assay_ValuesOf =
+    let isa = testArc.ISA.Value
+    testList "Assay_ValuesOf" [
+
+        testCase "ValuesOfOutput_PooledOutput" (fun () ->
+            let values = isa.GetAssay("MSEval_Heat").ValuesOf("sampleOutHeat.txt").WithName("Column")
+            let valueValues = values |> Seq.map (fun n -> n.ValueText)
+            let expected = ["C1 Intensity";"C2 Intensity";"C3 Intensity";"H1 Intensity";"H2 Intensity";"H3 Intensity"]
+            Expect.sequenceEqual valueValues expected "Did not return all values correctly"    
+        )
+        testCase "SucceedingValuesOfInput_PooledOutput" (fun () ->
+            let values = isa.GetAssay("MSEval_Heat").SucceedingValuesOf("C2_measured").WithName("Column")
+            let valueValues = values |> Seq.map (fun n -> n.ValueText)
+            let expected = ["C2 Intensity"]
+            Expect.sequenceEqual valueValues expected "Did not return the single value correctly"    
+        )
+        testCase "PreviousValuesOfInput_PooledOutput" (fun () ->
+            let values = isa.GetAssay("MSEval_Heat").PreviousValuesOf("C2_measured").WithName("Column")
+            let valueValues = values |> Seq.map (fun n -> n.ValueText)
+            let expected = []
+            Expect.sequenceEqual valueValues expected "Should return no values"    
+        )
+        testCase "ValuesOfInput_PooledOutput" (fun () ->
+            let values = isa.GetAssay("MSEval_Heat").ValuesOf("C2_measured").WithName("Column")
+            let valueValues = values |> Seq.map (fun n -> n.ValueText)
+            let expected = ["C2 Intensity"]
+            Expect.sequenceEqual valueValues expected "Did not return the single value correctly"    
+        )
+
+    ]
+
+let ArcTables_ValueOf =
+    let isa = testArc.ISA.Value
+    testList "ArcTable_Values" [
+        testCase "ValuesOf_SpecificTable" (fun () ->
+            let nodeName = "sampleOutHeat.txt"
+            let protocolName =  "MS"            
+            let values = isa.ArcTables.ValuesOf(nodeName,protocolName)
+            let expectedTechRep =
+                ISAValue.Parameter (
+                        ProcessParameterValue.create(
+                            ProtocolParameter.fromString("technical replicate","MS","MS:1001808"), 
+                            Value.Ontology (OntologyAnnotation.fromString("1"))
+                        )
+                    )
+            let expectedInjVol =
+                ISAValue.Parameter (
+                        ProcessParameterValue.create(
+                            ProtocolParameter.fromString("injection volume setting","AFR","AFR:0001577"), 
+                            Value.Int 20,
+                            OntologyAnnotation.fromString("microliter","UO","http://purl.obolibrary.org/obo/UO_0000101")
+                        )
+                    )
+            let expected = 
+                [
+                    expectedTechRep;expectedInjVol
+                    expectedTechRep;expectedInjVol
+                    expectedTechRep;expectedInjVol
+                    expectedTechRep;expectedInjVol
+                    expectedTechRep;expectedInjVol
+                    expectedTechRep;expectedInjVol
+                ]
+            Expect.sequenceEqual values expected "Did not return correct values for specific table"
+        )
+        testCase "ValuesOf" (fun () ->
+            let nodeName = "sampleOutHeat.txt"
+
+            let valueHeaders = 
+                isa.ArcTables.ValuesOf(nodeName).DistinctHeaderCategories()
+                |> Seq.map (fun x -> x.NameText)
+            let expected = 
+                ["biological replicate";"organism";"temperature day";"pH";"technical replicate"; "injection volume setting";"analysis software";"Column"]
+            Expect.sequenceEqual valueHeaders expected "Did not return correct values for all table"
+        )
+        testCase "GetSpecificValue" (fun () ->
+            let rep1 = isa.ArcTables.ValuesOf("C1_measured").WithName("biological replicate").First.ValueText
+            Expect.equal rep1 "1" "Did not return correct value for specific table"
+            let rep2 = isa.ArcTables.ValuesOf("C2_measured").WithName("biological replicate").First.ValueText
+            Expect.equal rep2 "2" "Did not return correct value for specific table"
+        )
+        testCase "ValuesOf_SpecificTable_PooledOutput" (fun () ->
+            let vals = isa.ArcTables.ValuesOf("sampleOutHeat.txt","Growth").WithName("biological replicate").Values |> List.map (fun v -> v.ValueText)         
+            Expect.sequenceEqual vals ["1";"2";"3";"1";"2";"3"] "Did not return correct values"
+        )
+        testCase "SpecificValue_SpecificTable_PooledOutput" (fun () ->
+            let vals = isa.ArcTables.ValuesOf("C2_prep","Growth").WithName("biological replicate").First.ValueText
+            Expect.equal vals "2" "Did not return correct value"
+        )
+    ]
+
+
+
+
+
+[<Tests>]
+let main = testList "TestArcTests" [
+    ArcTables_getNodes
+    Assay_getNodes
+    Assay_ValuesOf
+    ArcTables_ValueOf
+]