From d85e88ba9cd52ac5279b753c42b9be39e4717496 Mon Sep 17 00:00:00 2001 From: Heinrich Lukas Weil Date: Wed, 22 Nov 2023 14:07:21 +0100 Subject: [PATCH] replace isadotnet by arctrl.isa dependency --- src/OBO.NET/OBO.NET.fsproj | 6 +++++- src/OBO.NET/OboOntology.fs | 38 +++++++++++++++++++------------------- src/OBO.NET/OboTerm.fs | 8 ++++---- 3 files changed, 28 insertions(+), 24 deletions(-) diff --git a/src/OBO.NET/OBO.NET.fsproj b/src/OBO.NET/OBO.NET.fsproj index a194a01..e525b27 100644 --- a/src/OBO.NET/OBO.NET.fsproj +++ b/src/OBO.NET/OBO.NET.fsproj @@ -37,9 +37,13 @@ + - + + + + diff --git a/src/OBO.NET/OboOntology.fs b/src/OBO.NET/OboOntology.fs index 7fe2422..d9b20bc 100644 --- a/src/OBO.NET/OboOntology.fs +++ b/src/OBO.NET/OboOntology.fs @@ -5,7 +5,7 @@ open DBXref //open OboTypeDef open FSharpAux -open ISADotNet +open ARCtrl.ISA open System @@ -149,9 +149,9 @@ type OboOntology = /// For a given ontology term, finsd all equivalent terms that are connected via XRefs. /// /// Depth can be used to restrict the number of iterations by which neighbours of neighbours are checked. - member this.GetEquivalentOntologyAnnotations(term : ISADotNet.OntologyAnnotation, ?Depth : int) = + member this.GetEquivalentOntologyAnnotations(term : OntologyAnnotation, ?Depth : int) = - let rec loop depth (equivalents : ISADotNet.OntologyAnnotation list) (lastLoop : ISADotNet.OntologyAnnotation list) = + let rec loop depth (equivalents : OntologyAnnotation list) (lastLoop : OntologyAnnotation list) = if equivalents.Length = lastLoop.Length then equivalents elif Depth.IsSome && Depth.Value < depth then equivalents else @@ -159,16 +159,16 @@ type OboOntology = equivalents |> List.collect (fun t -> let forward = - match this.TryGetTerm t.ShortAnnotationString with + match this.TryGetTerm t.TermAccessionShort with | Some term -> term.Xrefs |> List.map (fun xref -> - let id = OntologyAnnotation.createShortAnnotation "" xref.Name + let id = OntologyAnnotation.fromTermAnnotation(xref.Name).TermAccessionShort match this.TryGetOntologyAnnotation id with | Some oa -> oa | None -> - OntologyAnnotation.fromString "" "" xref.Name + OntologyAnnotation.fromString(tan = xref.Name) ) | None -> [] @@ -193,24 +193,24 @@ type OboOntology = member this.GetEquivalentOntologyAnnotations(termId : string, ?Depth) = match Depth with | Some d -> - OntologyAnnotation.fromAnnotationId termId + OntologyAnnotation.fromTermAnnotation termId |> fun oa -> this.GetEquivalentOntologyAnnotations(oa, d) | None -> - OntologyAnnotation.fromAnnotationId termId + OntologyAnnotation.fromTermAnnotation termId |> this.GetEquivalentOntologyAnnotations /// For a given ontology term, finds all terms to which this term points in a "isA" relationship. /// /// Depth can be used to restrict the number of iterations by which neighbours of neighbours are checked. - member this.GetParentOntologyAnnotations(term : ISADotNet.OntologyAnnotation, ?Depth) = - let rec loop depth (equivalents : ISADotNet.OntologyAnnotation list) (lastLoop : ISADotNet.OntologyAnnotation list) = + member this.GetParentOntologyAnnotations(term : OntologyAnnotation, ?Depth) = + let rec loop depth (equivalents : OntologyAnnotation list) (lastLoop : OntologyAnnotation list) = if equivalents.Length = lastLoop.Length then equivalents elif Depth.IsSome && Depth.Value < depth then equivalents else let newEquivalents = equivalents |> List.collect (fun t -> - match this.TryGetTerm t.ShortAnnotationString with + match this.TryGetTerm t.TermAccessionShort with | Some term -> term.IsA |> List.map (fun isA -> @@ -218,7 +218,7 @@ type OboOntology = | Some oa -> oa | None -> - OntologyAnnotation.fromString "" "" isA + OntologyAnnotation.fromString(tan = isA) ) | None -> [] @@ -233,17 +233,17 @@ type OboOntology = member this.GetParentOntologyAnnotations(termId : string, ?Depth) = match Depth with | Some d -> - OntologyAnnotation.fromAnnotationId termId + OntologyAnnotation.fromTermAnnotation termId |> fun oa -> this.GetParentOntologyAnnotations(oa, d) | None -> - OntologyAnnotation.fromAnnotationId termId + OntologyAnnotation.fromTermAnnotation termId |> this.GetParentOntologyAnnotations /// For a given ontology term, finds all terms which point to this term "isA" relationship. /// /// Depth can be used to restrict the number of iterations by which neighbours of neighbours are checked. - member this.GetChildOntologyAnnotations(term : ISADotNet.OntologyAnnotation, ?Depth) = - let rec loop depth (equivalents : ISADotNet.OntologyAnnotation list) (lastLoop : ISADotNet.OntologyAnnotation list) = + member this.GetChildOntologyAnnotations(term : OntologyAnnotation, ?Depth) = + let rec loop depth (equivalents : OntologyAnnotation list) (lastLoop : OntologyAnnotation list) = if equivalents.Length = lastLoop.Length then equivalents elif Depth.IsSome && Depth.Value < depth then equivalents else @@ -254,7 +254,7 @@ type OboOntology = |> List.choose (fun pt -> let isChild = pt.IsA - |> List.exists (fun isA -> t.ShortAnnotationString = isA) + |> List.exists (fun isA -> t.TermAccessionShort = isA) if isChild then Some (OboTerm.toOntologyAnnotation(pt)) else @@ -272,10 +272,10 @@ type OboOntology = member this.GetChildOntologyAnnotations(termId : string, ?Depth) = match Depth with | Some d -> - OntologyAnnotation.fromAnnotationId termId + OntologyAnnotation.fromTermAnnotation termId |> fun oa -> this.GetChildOntologyAnnotations(oa, d) | None -> - OntologyAnnotation.fromAnnotationId termId + OntologyAnnotation.fromTermAnnotation termId |> this.GetChildOntologyAnnotations /// Takes an OboTerm and returns all related terms in this ontology as a triple of input term, relationship, and related term. diff --git a/src/OBO.NET/OboTerm.fs b/src/OBO.NET/OboTerm.fs index df22d6a..a3d6f74 100644 --- a/src/OBO.NET/OboTerm.fs +++ b/src/OBO.NET/OboTerm.fs @@ -3,7 +3,7 @@ open DBXref open TermSynonym -open ISADotNet +open ARCtrl.ISA open System @@ -515,12 +515,12 @@ type OboTerm = /// Translates an OBO `term` into an ISADotNet `OntologyAnnotation`. static member toOntologyAnnotation (term : OboTerm) = - let ref,num = OntologyAnnotation.splitAnnotation term.Id - OntologyAnnotation.fromString term.Name ref term.Id + OntologyAnnotation.fromString(term.Name,tan = term.Id) + |> fun o -> {o with TermSourceREF = o.TANInfo |> Option.map (fun t -> t.IDSpace)} /// Translates an ISADotNet `OntologyAnnotation` into an OBO `term`. static member ofOntologyAnnotation (term : OntologyAnnotation) = - OboTerm.Create(term.ShortAnnotationString,term.NameText) + OboTerm.Create(term.TermAccessionShort,term.NameText) /// Takes a relationship and returns a tuple consisting of the name of the relationship and the ID of the OboTerm it matches. static member deconstructRelationship relationship =