Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add first release of growth validation package #63

Merged
merged 1 commit into from
Nov 15, 2024
Merged
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
add first release of growth validation package
HLWeil committed Nov 15, 2024
commit 0cfde3af0216e00d6a987d979c2b205bffcdbc12
196 changes: 196 additions & 0 deletions StagingArea/plant-growth/plant-growth@1.0.0.fsx
Original file line number Diff line number Diff line change
@@ -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: weil@nfdi4plants.org
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
)