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Add first release of growth validation package #63

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196 changes: 196 additions & 0 deletions StagingArea/plant-growth/[email protected]
Original file line number Diff line number Diff line change
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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
)