add first release of growth validation package (#63)

StagingArea/plant-growth/plant-growth@1.0.0.fsx

@@ -0,0 +1,196 @@
+let [<Literal>]PACKAGE_METADATA = """(*
+---
+Name: plant-growth
+Summary: Validates if the ARC contains the necessary metadata to describe conditions for plant growth.
+Description: |
+    Validates if the ARC contains an annotation table with protocol type "Plant Growth Protocol" and if it exists, whether it contains the following fields:
+
+        Critical fields:
+        - organism (OBI:0100026)
+        - growth day length (DPBO:0000041)
+        - light intensity exposure (PECO:0007224)
+        - humidity day (DPBO:0000005)
+        - temperature day (DPBO:0000007)
+        - temperature night (DPBO:0000008)
+        - watering exposure (PECO:0007383)
+
+        Non critical fields:
+        - genotype (EFO:0000513)
+        - study type (PECO:0007231)
+        - Reference Time Point (NCIT:C82576)
+        - growth plot design (DPBO:0000001)
+        - plant growth medium exposure (PECO:0007147)
+        - humidity night (DPBO:0000006)
+        - plant nutrient exposure (PECO:0007241)
+        - abiotic plant exposure (PECO:0007191)
+        - biotic plant exposure (PECO:0007357)
+
+MajorVersion: 1
+MinorVersion: 0
+PatchVersion: 0
+Publish: false
+Authors:
+  - FullName: Heinrich Lukas Weil
+    Email: [email protected]
+    Affiliation: RPTU Kaiserslautern
+    AffiliationLink: http://rptu.de/startseite
+Tags:
+  - Name: validation
+  - Name: growth
+  - Name: plant
+ReleaseNotes: |
+  - initial release
+---
+*)"""
+
+#r "nuget: ARCExpect, 2.0.0"
+
+open ControlledVocabulary
+open Expecto
+open ARCExpect
+open ARCTokenization
+open ARCTokenization.StructuralOntology
+open System.IO
+open System.Text
+open FSharpAux
+
+// Input:
+let arcDir = Directory.GetCurrentDirectory()
+
+// Values:
+let absoluteDirectoryPaths = FileSystem.parseARCFileSystem arcDir
+
+let studyFiles = 
+    try 
+        absoluteDirectoryPaths
+        |> Study.parseProcessGraphColumnsFromTokens arcDir
+    with
+        | _ -> seq{Map.empty}
+
+
+let plantGrowthSheets = 
+    studyFiles
+    |> Seq.collect (fun s ->
+        s
+        |> Seq.filter (fun kv ->
+            kv.Value 
+            |> Seq.concat
+            |> Seq.exists (fun token -> 
+                token.Name = "ProtocolType" 
+                && 
+                //Param.getValueAsTerm token = (CvTerm.create("DPBO:1000164","plant growth protocol","DPBO"))
+                (Param.getValueAsTerm token).Name = "plant growth protocol"
+            )
+        )   
+    )
+
+let containsFilledOutColumn (term : CvTerm) (tokenColumns : IParam list list) =
+    let column = 
+        tokenColumns 
+        |> Seq.tryFind (fun column ->
+            Param.getValueAsTerm column.Head = term
+        )
+    match column with
+    | Some (h :: []) -> Expecto.Tests.failtestNoStackf $"{term.Name} column only contains header"            
+    | Some (h :: vals) -> 
+        vals
+        |> List.iteri (fun i token ->
+            if (Param.getValueAsTerm token).Name = "" then
+                Expecto.Tests.failtestNoStackf $"column {term.Name} contains empty value at index {i}"                  
+        )
+    | _ -> Expecto.Tests.failtestNoStackf $"table contains no {term.Name} header"            
+
+// Validation Cases:
+let cases = 
+    testList "cases" [  // naming is difficult here
+
+        ARCExpect.validationCase (TestID.Name "plant growth table") {
+            if plantGrowthSheets |> Seq.isEmpty then
+                Expecto.Tests.failtestNoStackf "No plant growth table found"            
+        }
+
+        if plantGrowthSheets |> Seq.isEmpty |> not then
+            for table in plantGrowthSheets do
+                ARCExpect.validationCase (TestID.Name $"{table.Key}: organism") {
+                    table.Value
+                    |> containsFilledOutColumn (CvTerm.create("OBI:0100026","organism","OBI"))
+                }
+                ARCExpect.validationCase (TestID.Name $"{table.Key}: growth day length") {
+                    table.Value
+                    |> containsFilledOutColumn (CvTerm.create("DPBO:0000041","growth day length","DPBO"))
+                }
+                ARCExpect.validationCase (TestID.Name $"{table.Key}: light intensity exposure") {
+                    table.Value
+                    |> containsFilledOutColumn (CvTerm.create("PECO:0007224","light intensity exposure","PECO"))
+                }
+                ARCExpect.validationCase (TestID.Name $"{table.Key}: humidity day") {
+                    table.Value
+                    |> containsFilledOutColumn (CvTerm.create("DPBO:0000005","humidity day","DPBO"))
+                }
+                ARCExpect.validationCase (TestID.Name $"{table.Key}: temperature day") {
+                    table.Value
+                    |> containsFilledOutColumn (CvTerm.create("DPBO:0000007","temperature day","DPBO"))
+                }
+                ARCExpect.validationCase (TestID.Name $"{table.Key}: temperature night") {
+                    table.Value
+                    |> containsFilledOutColumn (CvTerm.create("DPBO:0000008","temperature night","DPBO"))
+                }
+                ARCExpect.validationCase (TestID.Name $"{table.Key}: watering exposure") {
+                    table.Value
+                    |> containsFilledOutColumn (CvTerm.create("PECO:0007383","watering exposure","PECO"))
+                }
+    ]
+
+let nonCriticalCases = 
+    testList "cases" [  // naming is difficult here
+
+
+        if plantGrowthSheets |> Seq.isEmpty |> not then
+            for table in plantGrowthSheets do
+                ARCExpect.validationCase (TestID.Name $"{table.Key}: genotype") {
+                    table.Value
+                    |> containsFilledOutColumn (CvTerm.create("EFO:0000513","genotype","EFO"))
+                }
+                ARCExpect.validationCase (TestID.Name $"{table.Key}: study type") {
+                    table.Value
+                    |> containsFilledOutColumn (CvTerm.create("PECO:0007231","study type","PECO"))
+                }
+                ARCExpect.validationCase (TestID.Name $"{table.Key}: Reference Time Point") {
+                    table.Value
+                    |> containsFilledOutColumn (CvTerm.create("NCIT:C82576","Reference Time Point","NCIT"))
+                }
+                ARCExpect.validationCase (TestID.Name $"{table.Key}: growth plot design") {
+                    table.Value
+                    |> containsFilledOutColumn (CvTerm.create("DPBO:0000001","growth plot design","DPBO"))
+                }
+                ARCExpect.validationCase (TestID.Name $"{table.Key}: plant growth medium exposure") {
+                    table.Value
+                    |> containsFilledOutColumn (CvTerm.create("PECO:0007147","plant growth medium exposure","PECO"))
+                }
+                ARCExpect.validationCase (TestID.Name $"{table.Key}: humidity night") {
+                    table.Value
+                    |> containsFilledOutColumn (CvTerm.create("DPBO:0000006","humidity night","DPBO"))
+                }
+                ARCExpect.validationCase (TestID.Name $"{table.Key}: plant nutrient exposure") {
+                    table.Value
+                    |> containsFilledOutColumn (CvTerm.create("PECO:0007241","plant nutrient exposure","PECO"))
+                }
+                ARCExpect.validationCase (TestID.Name $"{table.Key}: abiotic plant exposure") {
+                    table.Value
+                    |> containsFilledOutColumn (CvTerm.create("PECO:0007191","abiotic plant exposure","PECO"))
+                }
+                ARCExpect.validationCase (TestID.Name $"{table.Key}: biotic plant exposure") {
+                    table.Value
+                    |> containsFilledOutColumn (CvTerm.create("PECO:0007357","biotic plant exposure","PECO"))
+                }
+    ]
+
+// Execution:
+Setup.ValidationPackage(
+    metadata = Setup.Metadata(PACKAGE_METADATA),
+    CriticalValidationCases = [cases],
+    NonCriticalValidationCases = [nonCriticalCases]
+)
+|> Execute.ValidationPipeline(
+    basePath = arcDir
+)