add additional ontology helper functions to querymodel

nfdi4plants · Jul 20, 2022 · 6eb5c44 · 6eb5c44
1 parent 11ef6b8
commit 6eb5c44
Show file tree

Hide file tree

Showing 3 changed files with 86 additions and 3 deletions.
diff --git a/src/ISADotNet.QueryModel/OntologyAnnotation.fs b/src/ISADotNet.QueryModel/OntologyAnnotation.fs
@@ -74,3 +74,54 @@ module OntologyAnnotation =
 
         member this.GetAs(targetOntology : string, ont : Obo.OboOntology) =
             OntologyAnnotation.getAs(this,targetOntology,ont)
+
+        static member tryGetAs (term : OntologyAnnotation, targetOntology : string, ont : Obo.OboOntology) =
+            ont.GetEquivalentOntologyAnnotations(term)
+            |> List.tryFind (fun t -> t.TermSourceREFString = targetOntology)
+
+        member this.TryGetAs(targetOntology : string, ont : Obo.OboOntology) =
+            OntologyAnnotation.tryGetAs(this,targetOntology,ont)
+
+    type Value with
+
+        member this.GetAs(targetOntology : string, ont : Obo.OboOntology) =
+            match this with
+            | Ontology oa -> Ontology (oa.GetAs(targetOntology, ont))
+            | _ -> this
+
+        member this.TryGetAs(targetOntology : string, ont : Obo.OboOntology) =
+            match this with
+            | Ontology oa -> 
+                oa.TryGetAs(targetOntology, ont)
+                |> Option.map Ontology
+            | _ -> None
+
+    type ProcessParameterValue with
+
+        member this.GetAs(targetOntology : string, ont : Obo.OboOntology) =
+            {this with Value = this.Value |> Option.map (fun v -> v.GetAs(targetOntology,ont))}
+
+        member this.TryGetAs(targetOntology : string, ont : Obo.OboOntology) =
+            this.Value
+            |> Option.bind (fun v -> v.TryGetAs(targetOntology,ont))
+            |> Option.map (fun v -> {this with Value = Some v})
+
+    type MaterialAttributeValue with
+
+        member this.GetAs(targetOntology : string, ont : Obo.OboOntology) =
+            {this with Value = this.Value |> Option.map (fun v -> v.GetAs(targetOntology,ont))}
+
+        member this.TryGetAs(targetOntology : string, ont : Obo.OboOntology) =
+            this.Value
+            |> Option.bind (fun v -> v.TryGetAs(targetOntology,ont))
+            |> Option.map (fun v -> {this with Value = Some v})
+
+    type FactorValue with
+
+        member this.GetAs(targetOntology : string, ont : Obo.OboOntology) =
+            {this with Value = this.Value |> Option.map (fun v -> v.GetAs(targetOntology,ont))}
+
+        member this.TryGetAs(targetOntology : string, ont : Obo.OboOntology) =
+            this.Value
+            |> Option.bind (fun v -> v.TryGetAs(targetOntology,ont))
+            |> Option.map (fun v -> {this with Value = Some v})
diff --git a/src/ISADotNet.QueryModel/Value.fs b/src/ISADotNet.QueryModel/Value.fs
@@ -108,4 +108,16 @@ type ISAValue =
         match this with
         | Parameter p       -> p.TryGetValueIndex()
         | Characteristic c  -> c.TryGetValueIndex()
-        | Factor f          -> f.TryGetValueIndex()
+        | Factor f          -> f.TryGetValueIndex()
+
+    member this.GetAs(targetOntology : string, ont : Obo.OboOntology) = 
+        match this with
+        | Parameter p       -> p.GetAs(targetOntology,ont) |> Parameter
+        | Characteristic c  -> c.GetAs(targetOntology,ont) |> Characteristic
+        | Factor f          -> f.GetAs(targetOntology,ont) |> Factor
+
+    member this.TryGetAs(targetOntology : string, ont : Obo.OboOntology) = 
+        match this with
+        | Parameter p       -> p.TryGetAs(targetOntology,ont) |> Option.map Parameter
+        | Characteristic c  -> c.TryGetAs(targetOntology,ont) |> Option.map Characteristic
+        | Factor f          -> f.TryGetAs(targetOntology,ont) |> Option.map Factor
diff --git a/src/ISADotNet.QueryModel/ValueCollection.fs b/src/ISADotNet.QueryModel/ValueCollection.fs
@@ -86,19 +86,39 @@ type ValueCollection(values : ISAValue list) =
         )
         |> ValueCollection
 
+    member this.WithName(name : string) = 
+        values
+        |> List.filter (fun v -> v.Category.NameText = name)
+        |> ValueCollection
+
     member this.WithCategory(category : OntologyAnnotation) = 
         values
         |> List.filter (fun v -> v.Category = category)
         |> ValueCollection
 
+    member this.WithEquivalentCategory(equivalentCategory : OntologyAnnotation, ont : Obo.OboOntology) = 
+        values
+        |> List.filter (fun v -> v.Category.IsEquivalentTo(equivalentCategory, ont))
+        |> ValueCollection
+
+    member this.WithChildCategory(childCategory : OntologyAnnotation) = 
+        values
+        |> List.filter (fun v -> childCategory.IsChildTermOf(v.Category))
+        |> ValueCollection
+
+    member this.WithChildCategory(childCategory : OntologyAnnotation, ont : Obo.OboOntology) = 
+        values
+        |> List.filter (fun v -> childCategory.IsChildTermOf(v.Category, ont))
+        |> ValueCollection
+
     member this.WithParentCategory(parentCategory : OntologyAnnotation) = 
         values
         |> List.filter (fun v -> v.Category.IsChildTermOf(parentCategory))
         |> ValueCollection
 
-    member this.WithName(name : string) = 
+    member this.WithParentCategory(parentCategory : OntologyAnnotation, ont : Obo.OboOntology) = 
         values
-        |> List.filter (fun v -> v.Category.NameText = name)
+        |> List.filter (fun v -> v.Category.IsChildTermOf(parentCategory,ont))
         |> ValueCollection
 
     member this.Distinct() =