From 16a9a6ec97c21b1abe0f6e754888aa6090099464 Mon Sep 17 00:00:00 2001
From: omaus <omaus@bio.uni-kl.de>
Date: Thu, 27 Jul 2023 19:24:11 +0200
Subject: [PATCH] Add OboEntry functionality into OboOntology

---
 playground.fsx                 | 13 ++++++++
 src/FsOboParser/OboOntology.fs | 54 +++++++++++++++++++++++++---------
 src/FsOboParser/OboTypeDef.fs  |  2 +-
 3 files changed, 54 insertions(+), 15 deletions(-)

diff --git a/playground.fsx b/playground.fsx
index 935ef80..b9c29d3 100644
--- a/playground.fsx
+++ b/playground.fsx
@@ -12,6 +12,19 @@ let testPath = Path.Combine(__SOURCE_DIRECTORY__,  "./../../nfdi4plants/arc-vali
 
 let testOntology = OboOntology.fromFile true testPath
 
+let testTerms = [
+    OboTerm.Create("test:000", Name = "test0")
+    OboTerm.Create("test:001", Name = "test1a", IsA = ["test:000"])
+    OboTerm.Create("test:002", Name = "test2", IsA = ["test:001"])
+    OboTerm.Create("test:003", Name = "test1b", IsA = ["test:000"])
+]
+
+let testOntology = OboOntology.create testTerms []
+
+testOntology.GetChildOntologyAnnotations(testTerms.Head.Id)
+testOntology.GetChildOntologyAnnotations(testTerms.Head.Id, Depth = 1)
+testOntology.GetChildOntologyAnnotations(testTerms.Head.Id, Depth = 2)
+
 //let fileLines = File.ReadAllLines testPath
 
 //OboTerm.fromLines true ((fileLines |> Seq.ofArray).GetEnumerator()) 0
diff --git a/src/FsOboParser/OboOntology.fs b/src/FsOboParser/OboOntology.fs
index 43b0b49..895282f 100644
--- a/src/FsOboParser/OboOntology.fs
+++ b/src/FsOboParser/OboOntology.fs
@@ -9,6 +9,35 @@ open ISADotNet
 open System
 
 
+/// Functions for working with OboEntries.
+module OboEntries =
+
+    /// Reads a collection of strings and parses them into a list of OboEntries.
+    let fromLines verbose (input : seq<string>) =
+
+        let en = input.GetEnumerator()
+        let rec loop (en:System.Collections.Generic.IEnumerator<string>) entries lineNumber =
+
+            match en.MoveNext() with
+            | true ->
+                match (en.Current |> trimComment) with
+                | "[Term]" -> 
+                    let lineNumber, parsedTerm = (OboTerm.fromLines verbose en lineNumber "" "" false [] "" "" [] [] [] [] [] [] [] [] false [] [] [] false "" "")
+                    loop en (Term parsedTerm :: entries) lineNumber
+                | "[Typedef]" -> 
+                    let lineNumber, parsedTypeDef = (OboTypeDef.fromLines verbose en lineNumber "" "" "" "" [] [] false false false false false false false)
+                    loop en (TypeDef parsedTypeDef :: entries) lineNumber
+                | _ -> loop en entries (lineNumber + 1)
+            | false -> entries
+
+        loop en [] 1
+
+    /// Reads an OBO file and returns a list of OboEntries.
+    let fromFile verbose filepath =
+        IO.File.ReadAllLines filepath
+        |> fromLines verbose
+
+
 /// Ontology containing OBO Terms and OBO Type Defs (OBO 1.2).
 type OboOntology =
 
@@ -26,22 +55,19 @@ type OboOntology =
     /// Reads an OBO Ontology containing term and type def stanzas from lines.
     static member fromLines verbose (input : seq<string>) =
 
-        let en = input.GetEnumerator()
-        let rec loop (en:System.Collections.Generic.IEnumerator<string>) terms typedefs lineNumber =
+        let rec loop terms typedefs entries =
+            match entries with
+            | h :: t ->
+                match h with
+                | Term term         -> loop (term :: terms) typedefs t
+                | TypeDef typedef   -> loop terms (typedef :: typedefs) t
+            | [] -> terms, typedefs
 
-            match en.MoveNext() with
-            | true ->             
-                match (en.Current |> trimComment) with
-                | "[Term]"    -> 
-                    let lineNumber,parsedTerm = (OboTerm.fromLines verbose en lineNumber "" "" false [] "" "" [] [] [] [] [] [] [] [] false [] [] [] false "" "")
-                    loop en (parsedTerm :: terms) typedefs lineNumber
-                | "[Typedef]" -> 
-                    let lineNumber,parsedTypeDef = (OboTypeDef.fromLines verbose en lineNumber "" "" "" "" [] [] false false false false false false false)
-                    loop en terms (parsedTypeDef :: typedefs) lineNumber
-                | _ -> loop en terms typedefs (lineNumber + 1)
-            | false -> OboOntology.create (List.rev terms) (List.rev typedefs)
+        let terms,typedefs =
+            OboEntries.fromLines verbose input
+            |> loop [] []
 
-        loop en [] [] 1
+        OboOntology.create (List.rev terms) (List.rev typedefs)
 
     /// Reads an OBO Ontology containing term and type def stanzas from a file with the given path.
     static member fromFile verbose (path : string) =
diff --git a/src/FsOboParser/OboTypeDef.fs b/src/FsOboParser/OboTypeDef.fs
index e709524..a1eb21b 100644
--- a/src/FsOboParser/OboTypeDef.fs
+++ b/src/FsOboParser/OboTypeDef.fs
@@ -5,7 +5,7 @@ open DBXref
 open System
 
 
-/// Models the relationship between OBO Terms 
+/// Models the relationship between OBO Terms.
 type OboTypeDef = 
     {
         ///The unique id of the current term.