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make ArcAssay TechnologyPlatform an ontology annotation and add helpe…
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…r functions

#162
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@HLWeil
HLWeil committed Aug 14, 2023
1 parent 1887806 commit c33f2dd
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Showing 5 changed files with 80 additions and 19 deletions.
42 changes: 36 additions & 6 deletions src/ISA/ISA/ArcTypes/ArcAssay.fs
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ open ARCtrl.ISA.Aux
// "MyAssay"; "assays/MyAssay/isa.assay.xlsx"

[<AttachMembers>]
type ArcAssay(identifier: string, ?measurementType : OntologyAnnotation, ?technologyType : OntologyAnnotation, ?technologyPlatform : string, ?tables: ResizeArray<ArcTable>, ?performers : Person [], ?comments : Comment []) =
type ArcAssay(identifier: string, ?measurementType : OntologyAnnotation, ?technologyType : OntologyAnnotation, ?technologyPlatform : OntologyAnnotation, ?tables: ResizeArray<ArcTable>, ?performers : Person [], ?comments : Comment []) =
let tables = defaultArg tables <| ResizeArray()
let performers = defaultArg performers [||]
let comments = defaultArg comments [||]
Expand All @@ -21,20 +21,20 @@ type ArcAssay(identifier: string, ?measurementType : OntologyAnnotation, ?techno

member val MeasurementType : OntologyAnnotation option = measurementType with get, set
member val TechnologyType : OntologyAnnotation option = technologyType with get, set
member val TechnologyPlatform : string option = technologyPlatform with get, set
member val TechnologyPlatform : OntologyAnnotation option = technologyPlatform with get, set
member val Tables : ResizeArray<ArcTable> = tables with get, set
member val Performers : Person [] = performers with get, set
member val Comments : Comment [] = comments with get, set

static member init (identifier : string) = ArcAssay(identifier)
static member create (identifier: string, ?measurementType : OntologyAnnotation, ?technologyType : OntologyAnnotation, ?technologyPlatform : string, ?tables: ResizeArray<ArcTable>, ?performers : Person [], ?comments : Comment []) =
static member create (identifier: string, ?measurementType : OntologyAnnotation, ?technologyType : OntologyAnnotation, ?technologyPlatform : OntologyAnnotation, ?tables: ResizeArray<ArcTable>, ?performers : Person [], ?comments : Comment []) =
ArcAssay(identifier = identifier, ?measurementType = measurementType, ?technologyType = technologyType, ?technologyPlatform = technologyPlatform, ?tables =tables, ?performers = performers, ?comments = comments)

static member make
(identifier : string)
(measurementType : OntologyAnnotation option)
(technologyType : OntologyAnnotation option)
(technologyPlatform : string option)
(technologyPlatform : OntologyAnnotation option)
(tables : ResizeArray<ArcTable>)
(performers : Person [])
(comments : Comment []) =
Expand Down Expand Up @@ -370,6 +370,36 @@ type ArcAssay(identifier: string, ?measurementType : OntologyAnnotation, ?techno
comments=nextComments
)

/// This function creates a string containing the name and the ontology short-string of the given ontology annotation term
///
/// TechnologyPlatforms are plain strings in ISA-JSON.
///
/// This function allows us, to parse them as an ontology term.
static member composeTechnologyPlatform (tp : OntologyAnnotation) =
match tp.TANInfo with
| Some _ ->
$"{tp.NameText} ({tp.TermAccessionShort})"
| None ->
$"{tp.NameText}"

/// This function parses the given string containing the name and the ontology short-string of the given ontology annotation term
///
/// TechnologyPlatforms are plain strings in ISA-JSON.
///
/// This function allows us, to parse them as an ontology term.
static member decomposeTechnologyPlatform (name : string) =
let pattern = """(?<value>[^\(]+) \((?<ontology>[^(]*:[^)]*)\)"""

let r = System.Text.RegularExpressions.Regex.Match(name,pattern)


if r.Success then
let oa = (r.Groups.Item "ontology").Value |> OntologyAnnotation.fromTermAnnotation
let v = (r.Groups.Item "value").Value |> Value.fromString
{oa with Name = (Some (AnnotationValue.Text v.Text))}
else
OntologyAnnotation.fromString(termName = name)

/// Transform an ArcAssay to an ISA Json Assay.
member this.ToAssay() : Assay =
let processSeq = ArcTables(this.Tables).GetProcesses()
Expand All @@ -388,7 +418,7 @@ type ArcAssay(identifier: string, ?measurementType : OntologyAnnotation, ?techno
?FileName = fileName,
?MeasurementType = this.MeasurementType,
?TechnologyType = this.TechnologyType,
?TechnologyPlatform = this.TechnologyPlatform,
?TechnologyPlatform = (this.TechnologyPlatform |> Option.map ArcAssay.composeTechnologyPlatform),
?DataFiles = (ProcessSequence.getData processSeq |> Option.fromValueWithDefault []),
?Materials = assayMaterials,
?CharacteristicCategories = (ProcessSequence.getCharacteristics processSeq |> Option.fromValueWithDefault []),
Expand All @@ -408,7 +438,7 @@ type ArcAssay(identifier: string, ?measurementType : OntologyAnnotation, ?techno
identifer,
?measurementType = (a.MeasurementType |> Option.map (fun x -> x.Copy())),
?technologyType = (a.TechnologyType |> Option.map (fun x -> x.Copy())),
?technologyPlatform = a.TechnologyPlatform,
?technologyPlatform = (a.TechnologyPlatform |> Option.map ArcAssay.decomposeTechnologyPlatform),
?tables = tables,
?comments = (a.Comments |> Option.map Array.ofList)
)
36 changes: 33 additions & 3 deletions tests/ISA/ISA.Tests/ArcAssay.Tests.fs
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Original file line number Diff line number Diff line change
Expand Up @@ -76,7 +76,7 @@ let private test_create =
let identifier = "MyIdentifier"
let oa_mt = OntologyAnnotation.fromString("measurement type")
let oa_tt = OntologyAnnotation.fromString("technology type")
let technologyPlatform = "tp"
let technologyPlatform = OntologyAnnotation.fromString("tp")
let tables = ResizeArray([ArcTable.init("MyTable1")])
let performers = Person.create(FirstName = "Kevin", LastName = "Frey") |> Array.singleton
let comments = Comment.create("Comment Name") |> Array.singleton
Expand All @@ -92,7 +92,7 @@ let private test_create =
let identifier = "MyIdentifier"
let oa_mt = OntologyAnnotation.fromString("measurement type")
let oa_tt = OntologyAnnotation.fromString("technology type")
let technologyPlatform = "tp"
let technologyPlatform = OntologyAnnotation.fromString("tp")
let tables = ResizeArray([ArcTable.init("MyTable1")])
let performers = Person.create(FirstName = "Kevin", LastName = "Frey") |> Array.singleton
let comments = Comment.create("Comment Name") |> Array.singleton
Expand All @@ -118,7 +118,7 @@ let private test_create =
let identifier = "MyIdentifier"
let measurementType = Some (OntologyAnnotation.fromString("Measurement Type"))
let technologyType = Some (OntologyAnnotation.fromString("Technology Type"))
let technologyPlatform = Some "Technology Platform"
let technologyPlatform = Some (OntologyAnnotation.fromString("Technology Platform"))
let tables = ResizeArray([ArcTable.init("Table 1")])
let performers = Person.create(FirstName = "John", LastName = "Doe") |> Array.singleton
let comments = Comment.create("Comment 1") |> Array.singleton
Expand Down Expand Up @@ -457,6 +457,35 @@ let private tests_updateTable =
)
]

let private tests_technologyPlatform =
testList "technologyPlatformTests" [
let name = "MyOntology"
let tsr = "ABC"
let tan = "ABC:123"
let tp_Term = OntologyAnnotation.fromString(name,tsr,tan)
let tp_String = OntologyAnnotation.fromString(name)
testCase "compose Term" (fun () ->
let s = ArcAssay.composeTechnologyPlatform tp_Term
Expect.equal s $"{name} ({tan})" "Term was not correctly composed as string."
)
testCase "decompose Term" (fun () ->
let s = ArcAssay.composeTechnologyPlatform tp_Term
let pt_new = ArcAssay.decomposeTechnologyPlatform s
Expect.equal pt_new.NameText name "NameText should match"
Expect.equal pt_new.TermAccessionShort tan "ShortTan should match"
)
testCase "compose String" (fun () ->
let s = ArcAssay.composeTechnologyPlatform tp_String
Expect.equal s $"{name}" "String was not correctly composed as string."
)
testCase "decompose String" (fun () ->
let s = ArcAssay.composeTechnologyPlatform tp_String
let pt_new = ArcAssay.decomposeTechnologyPlatform s
Expect.equal pt_new.NameText name "NameText should match"
Expect.isNone pt_new.TermAccessionNumber "TermAccessionNumber should be None"
Expect.equal pt_new.TermAccessionShort "" "ShortTan should match"
)
]
let main =
testList "ArcAssay" [
test_create
Expand All @@ -467,4 +496,5 @@ let main =
tests_UpdateTableAt
tests_UpdateTable
tests_updateTable
tests_technologyPlatform
]
12 changes: 6 additions & 6 deletions tests/ISA/ISA.Tests/ArcInvestigation.Tests.fs
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Original file line number Diff line number Diff line change
Expand Up @@ -318,7 +318,7 @@ let tests_Assay = testList "CRUD Assay" [
testCase "by index" <| fun _ ->
let i = createExampleInvestigation()
let assay_ident = "New Assay"
let assay_techPlatform = "Assay Tech"
let assay_techPlatform = OntologyAnnotation.fromString("Assay Tech")
let expected = ArcAssay(assay_ident, technologyPlatform = assay_techPlatform)
i.AddAssayAt(0, expected)
Expect.equal i.StudyCount 2 "StudyCount"
Expand All @@ -329,7 +329,7 @@ let tests_Assay = testList "CRUD Assay" [
testCase "by identifier" <| fun _ ->
let i = createExampleInvestigation()
let assay_ident = "New Assay"
let assay_techPlatform = "Assay Tech"
let assay_techPlatform = OntologyAnnotation.fromString("Assay Tech")
let expected = ArcAssay(assay_ident, technologyPlatform = assay_techPlatform)
i.AddAssay("Study 1", expected)
Expect.equal i.StudyCount 2 "StudyCount"
Expand All @@ -342,7 +342,7 @@ let tests_Assay = testList "CRUD Assay" [
testCase "by index" <| fun _ ->
let i = createExampleInvestigation()
let assay_ident = "New Assay"
let assay_techPlatform = "Assay Tech"
let assay_techPlatform = OntologyAnnotation.fromString("Assay Tech")
let expected = ArcAssay(assay_ident, technologyPlatform = assay_techPlatform)
i.SetAssayAt("Study 1", 0, expected)
Expect.equal i.StudyCount 2 "StudyCount"
Expand All @@ -353,7 +353,7 @@ let tests_Assay = testList "CRUD Assay" [
testCase "by identifier" <| fun _ ->
let i = createExampleInvestigation()
let assay_ident = "New Assay"
let assay_techPlatform = "Assay Tech"
let assay_techPlatform = OntologyAnnotation.fromString("Assay Tech")
let expected = ArcAssay(assay_ident, technologyPlatform = assay_techPlatform)
i.SetAssay("Study 1", "Assay 2", expected)
Expect.equal i.StudyCount 2 "StudyCount"
Expand All @@ -373,7 +373,7 @@ let tests_Assay = testList "CRUD Assay" [
Expect.equal a.Identifier "Assay 2" "FileName"
testCase "mutable propagation" <| fun _ ->
let i = createExampleInvestigation()
let tech = Some "New Tech Stuff"
let tech = Some (OntologyAnnotation.fromString("New Tech Stuff"))
let a = i.GetAssayAt("Study 1", 0)
Expect.equal a.Identifier "Assay 1" "FileName"
Expect.equal a.TechnologyPlatform None "TechnologyPlatform"
Expand All @@ -383,7 +383,7 @@ let tests_Assay = testList "CRUD Assay" [
testCase "mutable propagation, copy" <| fun _ ->
let i = createExampleInvestigation()
let copy = createExampleInvestigation()
let tech = Some "New Tech Stuff"
let tech = Some (OntologyAnnotation.fromString("New Tech Stuff"))
let a = i.GetAssayAt("Study 1", 0)
Expect.equal a.Identifier "Assay 1" "FileName"
Expect.equal a.TechnologyPlatform None "TechnologyPlatform"
Expand Down
5 changes: 3 additions & 2 deletions tests/ISA/ISA.Tests/ArcJsonConversionTests.fs
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Original file line number Diff line number Diff line change
Expand Up @@ -377,7 +377,8 @@ let private tests_arcAssay =
let identifier = "MyIdentifier"
let measurementType = OntologyAnnotation.fromString("Measurement Type")
let technologyType = OntologyAnnotation.fromString("Technology Type")
let technologyPlatform = "Technology Platform"
let technologyPlatformString = "Technology Platform"
let technologyPlatform = OntologyAnnotation.fromString(technologyPlatformString)
let t1 = singleRowSingleParam.Copy()
let t2 =
singleRowDataInputWithCharacteristic.Copy() |> fun t -> ArcTable.create(tableName2, t.Headers, t.Values)
Expand Down Expand Up @@ -418,7 +419,7 @@ let private tests_arcAssay =
Expect.equal assay.TechnologyType.Value technologyType "Assay technologyType should match"

Expect.isSome assay.TechnologyPlatform "Assay should have technologyPlatform"
Expect.equal assay.TechnologyPlatform.Value technologyPlatform "Assay technologyPlatform should match"
Expect.equal assay.TechnologyPlatform.Value technologyPlatformString "Assay technologyPlatform should match"

Expect.isSome assay.ProcessSequence "Assay should have processes"
Expect.equal assay.ProcessSequence.Value.Length 2 "Should have 2 processes"
Expand Down
4 changes: 2 additions & 2 deletions tests/ISA/ISA.Tests/ArcStudy.Tests.fs
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Original file line number Diff line number Diff line change
Expand Up @@ -158,7 +158,7 @@ let tests_copy =
let _study_identifier = "My Study"
let _study_description = Some "Lorem Ipsum"
let _assay_identifier = "My Assay"
let _assay_technologyPlatform = "Awesome Technology"
let _assay_technologyPlatform = OntologyAnnotation.fromString("Awesome Technology")
let createTestStudy() =
let s = ArcStudy(_study_identifier)
s.Description <- _study_description
Expand Down Expand Up @@ -198,7 +198,7 @@ let tests_copy =
Expect.equal assay.TechnologyPlatform (Some _assay_technologyPlatform) "copy _assay_technologyPlatform"
()
testCase "test mutable fields on assay children" <| fun _ ->
let newTechnologyPlatform = Some "New TechnologyPlatform"
let newTechnologyPlatform = Some (OntologyAnnotation.fromString("New TechnologyPlatform"))
let newTechnologyType = Some <| OntologyAnnotation.fromString("nice technology type")
let study = createTestStudy()
let copy = study.Copy()
Expand Down

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