Merge pull request #35 from CSBiology/feature-DocumentHeaderTags-#33

Add document header tags

src/OBO.NET/OboEntries.fs

@@ -1,14 +1,18 @@
 namespace OBO.NET
 
 
+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 =
+
+        let rec loop (en : Collections.Generic.IEnumerator<string>) entries lineNumber =
 
             match en.MoveNext() with
             | true ->
@@ -26,5 +30,5 @@ module OboEntries =
 
     /// Reads an OBO file and returns a list of OboEntries.
     let fromFile verbose filepath =
-        System.IO.File.ReadAllLines filepath
+        IO.File.ReadAllLines filepath
         |> fromLines verbose

tests/OBO.NET.Tests/OBO.NET.Tests.fsproj

@@ -9,6 +9,9 @@
   </PropertyGroup>
 
   <ItemGroup>
+    <None Include="References\IncorrectHeaderTags.obo" />
+    <None Include="References\DuplicateHeaderTags.obo" />
+    <None Include="references\CorrectHeaderTags.obo" />
     <Compile Include="TermSynonym.Tests.fs" />
     <Compile Include="OboTerm.Tests.fs" />
     <Compile Include="OboOntology.Tests.fs" />
@@ -29,4 +32,6 @@
     <PackageReference Update="FSharp.Core" Version="7.0.401" />
   </ItemGroup>
 
+  <ItemGroup />
+
 </Project>

tests/OBO.NET.Tests/OboOntology.Tests.fs

@@ -1,14 +1,19 @@
 namespace OBO.NET.Tests
 
-open Expecto
 open OBO.NET
 
+open Expecto
+
+open System
+open System.IO
+
 
 module OboOntologyTests =
 
     [<Tests>]
     let oboOntologyTest =
         testList "OboOntology" [
+
             let testTerm1 = 
                 OboTerm.Create(
                     "id:1", 
@@ -39,19 +44,103 @@ module OboOntologyTests =
                     Name = "testTerm5",
                     Synonyms = [TermSynonym.parseSynonym None 0 "\"testTerm1\" EXACT []"; TermSynonym.parseSynonym None 1 "\"testTerm2\" BROAD []"; TermSynonym.parseSynonym None 2 "\"testTerm0\" NARROW []"]
                 )
-            let testOntology = OboOntology.create [testTerm1; testTerm2; testTerm3; testTerm4; testTerm5] []
+
+            let testFile1Path = Path.Combine(__SOURCE_DIRECTORY__, "References", "CorrectHeaderTags.obo")
+            let testFile2Path = Path.Combine(__SOURCE_DIRECTORY__, "References", "IncorrectHeaderTags.obo")
+            let testFile3Path = Path.Combine(__SOURCE_DIRECTORY__, "References", "DuplicateHeaderTags.obo")
+            let testFile1 = try OboOntology.fromFile false testFile1Path |> Some with _ -> None
+            let testFile2 = try OboOntology.fromFile false testFile2Path |> Some with _ -> None
+            let testFile3 = try OboOntology.fromFile false testFile3Path |> Some with _ -> None
+
+            testList "fromFile" [
+                testCase "can read files" <| fun _ ->
+                    Expect.isSome testFile1 $"Could not read testFile1: {testFile1Path}"
+                    Expect.isSome testFile2 $"Could not read testFile2: {testFile2Path}"
+                    Expect.isSome testFile3 $"Could not read testFile3: {testFile3Path}"
+                testCase "reads correct headers correctly" <| fun _ ->
+                    let formatVersionActual                                 = Option.map (fun o -> o.FormatVersion)                                 testFile1
+                    let dataVersionActual                                   = Option.map (fun o -> o.DataVersion)                                   testFile1 |> Option.flatten
+                    let ontologyActual                                      = Option.map (fun o -> o.Ontology)                                      testFile1 |> Option.flatten
+                    let dateActual                                          = Option.map (fun o -> o.Date)                                          testFile1 |> Option.flatten
+                    let savedByActual                                       = Option.map (fun o -> o.SavedBy)                                       testFile1 |> Option.flatten
+                    let autoGeneratedByActual                               = Option.map (fun o -> o.AutoGeneratedBy)                               testFile1 |> Option.flatten
+                    let subsetdefsActual                                    = Option.map (fun o -> o.Subsetdefs)                                    testFile1
+                    let importsActual                                       = Option.map (fun o -> o.Imports)                                       testFile1
+                    let synonymtypedefsActual                               = Option.map (fun o -> o.Synonymtypedefs)                               testFile1
+                    let idSpacesActual                                      = Option.map (fun o -> o.Idspaces)                                      testFile1
+                    let defaultRelationshipIdPrefixActual                   = Option.map (fun o -> o.DefaultRelationshipIdPrefix)                   testFile1 |> Option.flatten
+                    let idMappingsActual                                    = Option.map (fun o -> o.IdMappings)                                    testFile1
+                    let remarksActual                                       = Option.map (fun o -> o.Remarks)                                       testFile1
+                    let treatXrefsAsEquivalentsActual                       = Option.map (fun o -> o.TreatXrefsAsEquivalents)                       testFile1
+                    let treatXrefsAsGenusDifferentiasActual                 = Option.map (fun o -> o.TreatXrefsAsGenusDifferentias)                 testFile1
+                    let treatXrefsAsRelationshipsActual                     = Option.map (fun o -> o.TreatXrefsAsRelationships)                     testFile1
+                    let treatXrefsAsIsAsActual                              = Option.map (fun o -> o.TreatXrefsAsIsAs)                              testFile1
+                    let relaxUniqueIdentifierAssumptionForNamespacesActual  = Option.map (fun o -> o.RelaxUniqueIdentifierAssumptionForNamespaces)  testFile1
+                    let relaxUniqueLabelAssumptionForNamespacesActual       = Option.map (fun o -> o.RelaxUniqueLabelAssumptionForNamespaces)       testFile1
+                    let formatVersionExpected                               = "0.0.1" |> Some
+                    let dataVersionExpected                                 = "0.0.1" |> Some
+                    let ontologyExpected                                    = "CL" |> Some
+                    let dateExpected                                        = DateTime(1970, 1, 1, 0, 0, 0) |> Some
+                    let savedByExpected                                     = "Oliver Maus" |> Some
+                    let autoGeneratedByExpected                             = "TalkGPT" |> Some
+                    let subsetdefsExpected                                  = ["GO_SLIM \"GO Slim\""; "GO_BASIC \"GO Basic\""] |> Some
+                    let importsExpected                                     = ["http://purl.obolibrary.org/obo/go.owl"; "http://purl.obolibrary.org/obo/cl.owl"] |> Some
+                    let synonymtypedefsExpected                             = ["UK_SPELLING \"British spelling\" EXACT"; "US_SPELLING \"American spelling\" EXACT"] |> Some
+                    let idspacesExpected                                    = ["GO urn:lsid:bioontology.org:GO: \"gene ontology terms\""; "GO urn:lsid:bioontology.org:GO: \"gene ontology types\""] |> Some
+                    let defaultRelationshipIdPrefixExpected                 = "OBO_REL" |> Some
+                    let idMappingsExpected                                  = ["part_of OBO_REL:part_of"; "has_a OBO_REL:has_a"] |> Some
+                    let remarksExpected                                     = ["test1"; "test2"] |> Some
+                    let treatXrefsAsEquivalentExpected                      = ["CL"; "GO"] |> Some
+                    let treatXrefsAsGenusDifferentiaExpected                = ["CL part_of NCBITaxon:7955"; "CL part_of NCBITaxon:7956"] |> Some
+                    let treatXrefsAsRelationshipExpected                    = ["MA homologous_to"; "MA analogous_to"] |> Some
+                    let treatXrefsAsIsAExpected                             = ["CL"; "GO"] |> Some
+                    let relaxUniqueIdentifierAssumptionForNamespaceExpected = ["my_combined_ontology"; "my_combined_ontology2"] |> Some
+                    let relaxUniqueLabelAssumptionForNamespaceExpected      = ["my_combined_ontology"; "my_combined_ontology2"] |> Some
+                    Expect.equal formatVersionActual formatVersionExpected "format-version is not identical"
+                    Expect.equal dataVersionActual dataVersionExpected "data-version is not identical"
+                    Expect.equal ontologyActual ontologyExpected "ontology is not identical"
+                    Expect.equal dateActual dateExpected "date is not identical"
+                    Expect.equal savedByActual savedByExpected "saved-by is not identical"
+                    Expect.equal autoGeneratedByActual autoGeneratedByExpected "auto-generated-by is not identical"
+                    Expect.equal subsetdefsActual subsetdefsExpected "subsetdefs is not identical"
+                    Expect.equal importsActual importsExpected "imports are not identical"
+                    Expect.equal synonymtypedefsActual synonymtypedefsExpected "synonymtypedefs are not identical"
+                    Expect.equal idSpacesActual idspacesExpected "idspaces are not identical"
+                    Expect.equal defaultRelationshipIdPrefixActual defaultRelationshipIdPrefixExpected "default-relationship-id-prefix is not identical"
+                    Expect.equal idMappingsActual idMappingsExpected "id-mappings are not identical"
+                    Expect.equal remarksActual remarksExpected "remarks are not identical"
+                    Expect.equal treatXrefsAsEquivalentsActual treatXrefsAsEquivalentExpected "treat-xrefs-as-equivalents are not identical"
+                    Expect.equal treatXrefsAsGenusDifferentiasActual treatXrefsAsGenusDifferentiaExpected "treat-xrefs-as-genus-differentia are not identical"
+                    Expect.equal treatXrefsAsRelationshipsActual treatXrefsAsRelationshipExpected "treat-xrefs-as-relationships are not identical"
+                    Expect.equal treatXrefsAsIsAsActual treatXrefsAsIsAExpected "treat-xrefs-as-is-a are not identical"
+                    Expect.equal relaxUniqueIdentifierAssumptionForNamespacesActual relaxUniqueIdentifierAssumptionForNamespaceExpected "relax-unique-identifier-assumption-for-namespaces are not identical"
+                    Expect.equal relaxUniqueLabelAssumptionForNamespacesActual relaxUniqueLabelAssumptionForNamespaceExpected "relax-unique-label-assumption-for-namespaces are not identical"
+                testCase "reads incorrect headers correctly" <| fun _ ->
+                    Expect.isNone (Option.map (fun o -> o.Date) testFile2 |> Option.flatten) "Date should be missing but was still parsed"
+                testCase "reads Terms correctly" <| fun _ ->
+                    let termsExpected = List.init 2 (fun i -> OboTerm.Create $"Test:000{i + 1}") |> Some
+                    Expect.equal (Option.map (fun o -> o.Terms) testFile1) termsExpected "Terms did not match"
+                testCase "reads Typedefs correctly" <| fun _ ->
+                    let typedefsExpected = List.init 2 (fun i -> OboTypeDef.Create($"Test:000{i + 3}", "", "")) |> Some
+                    Expect.equal (Option.map (fun o -> o.TypeDefs) testFile1) typedefsExpected "Terms did not match"
+            ]
+
+            let testOntology = OboOntology.Create([testTerm1; testTerm2; testTerm3; testTerm4; testTerm5], [], "")
+
             testList "GetRelatedTerms" [
                 testCase "returns correct related terms" <| fun _ ->
                     let actual = testOntology.GetRelatedTerms(testTerm1)
                     let expected = [testTerm1, "related_to", Some testTerm2; testTerm1, "unrelated_to", Some testTerm3; testTerm1, "antirelated_to", None]
                     Expect.sequenceEqual actual expected "is not equal"
             ]
+
             testList "GetIsAs" [
                 testCase "returns correct related terms" <| fun _ ->
                     let actual = testOntology.GetIsAs testTerm3
                     let expected = [testTerm3, Some testTerm1; testTerm3, Some testTerm2]
                     Expect.sequenceEqual actual expected "is not equal"
             ]
+
             testList "GetRelations" [
                 testCase "returns correct TermRelations" <| fun _ ->
                     let actual = testOntology.GetRelations()
@@ -68,12 +157,14 @@ module OboOntologyTests =
                     ]
                     Expect.sequenceEqual actual expected "is not equal"
             ]
+
             testList "GetSynonyms" [
                 testCase "returns correct synonymous terms" <| fun _ ->
                     let actual = testOntology.GetSynonyms testTerm5
                     let expected = seq {Exact, testTerm5, testTerm1; Broad, testTerm5, testTerm2}
                     Expect.sequenceEqual actual expected "is not equal"
             ]
+
             testList "TryGetSynonyms" [
                 testCase "returns correct synonymous terms" <| fun _ ->
                     let actual = testOntology.TryGetSynonyms testTerm5

tests/OBO.NET.Tests/References/CorrectHeaderTags.obo

@@ -0,0 +1,47 @@
+format-version: 0.0.1
+data-version: 0.0.1
+ontology: CL
+date: 01:01:1970 00:00
+saved-by: Oliver Maus
+auto-generated-by: TalkGPT
+subsetdef: GO_SLIM "GO Slim"
+subsetdef: GO_BASIC "GO Basic"
+import: http://purl.obolibrary.org/obo/go.owl
+import: http://purl.obolibrary.org/obo/cl.owl
+synonymtypedef: UK_SPELLING "British spelling" EXACT
+synonymtypedef: US_SPELLING "American spelling" EXACT
+idspace: GO urn:lsid:bioontology.org:GO: "gene ontology terms"
+idspace: GO urn:lsid:bioontology.org:GO: "gene ontology types"
+default-relationship-id-prefix: OBO_REL
+id-mapping: part_of OBO_REL:part_of
+id-mapping: has_a OBO_REL:has_a
+remark: test1
+remark: test2
+treat-xrefs-as-equivalent: CL 
+treat-xrefs-as-equivalent: GO 
+treat-xrefs-as-genus-differentia: CL part_of NCBITaxon:7955 
+treat-xrefs-as-genus-differentia: CL part_of NCBITaxon:7956 
+treat-xrefs-as-relationship: MA homologous_to
+treat-xrefs-as-relationship: MA analogous_to
+treat-xrefs-as-is_a: CL 
+treat-xrefs-as-is_a: GO 
+relax-unique-identifier-assumption-for-namespace: my_combined_ontology 
+relax-unique-identifier-assumption-for-namespace: my_combined_ontology2
+relax-unique-label-assumption-for-namespace: my_combined_ontology 
+relax-unique-label-assumption-for-namespace: my_combined_ontology2
+
+[Term]
+id: Test:0001
+
+[Term]
+id: Test:0002
+
+[Typedef]
+id: Test:0003
+name: 
+range: 
+
+[Typedef]
+id: Test:0004
+name: 
+range: 

tests/OBO.NET.Tests/References/DuplicateHeaderTags.obo

@@ -0,0 +1,28 @@
+format-version: 0.0.1
+format-version: 0.0.2
+data-version: 0.0.1
+data-version: 0.0.2
+date: 01:01:1970 00:00
+date: 01:01:1970 00:01
+saved-by: Oliver Maus
+saved-by: Loliver Laus
+auto-generated-by: TalkGPT
+auto-generated-by: SpeakGPT
+default-relationship-id-prefix: OBO_REL
+default-relationship-id-prefix: BABO_REL
+
+[Term]
+id: Test:0001
+
+[Term]
+id: Test:0002
+
+[Typedef]
+id: Test:0003
+name: 
+range: 
+
+[Typedef]
+id: Test:0004
+name: 
+range: 

tests/OBO.NET.Tests/References/IncorrectHeaderTags.obo

@@ -0,0 +1,17 @@
+date: 32:14:1970 25:61
+
+[Term]
+id: Test:0001
+
+[Term]
+id: Test:0002
+
+[Typedef]
+id: Test:0003
+name: 
+range: 
+
+[Typedef]
+id: Test:0004
+name: 
+range: