Merge pull request #294 from nfdi4plants/fix_annotationValue_read

Fix annotation value read 🐛

RELEASE_NOTES.md

@@ -1,3 +1,22 @@
+### 1.0.4+167fae8 (Released 2024-1-15)
+* Additions:
+    * [[#167fae8](https://github.com/nfdi4plants/ARCtrl/commit/167fae8bcaa14d8e24055f60ac031b13d8b47199)] add json functions for better function names in js :sparkles:
+
+### 1.0.3+533dab0 (Released 2024-1-15)
+* Additions:
+    * [[#208839a](https://github.com/nfdi4plants/ARCtrl/commit/208839a2d50e3c7ffd2722a5e65262bea1e185cd)] change annotationValue of Ontology Annotation to string
+    * [[#533dab0](https://github.com/nfdi4plants/ARCtrl/commit/533dab0039404d3dc0ba8e9612e1a083198ee056)] Add tests for edgecase :white_check_mark:
+* Bugfixes:
+    * [[#d42faaf](https://github.com/nfdi4plants/ARCtrl/commit/d42faaf5e41712b06991b111894bb6a7b3b09d58)] Fix template read issue. annotationvalue not correctly read :bug:
+
+### 1.0.2+533dab0 (Released 2024-1-15)
+* Additions:
+    * [[#cc7f35f](https://github.com/nfdi4plants/ARCtrl/commit/cc7f35f911b3960c9996276f808d8ee4bc7204d3)] add speedtest and make some small experimental changes
+    * [[#e85dba4](https://github.com/nfdi4plants/ARCtrl/commit/e85dba44d675a0896cf185c4ee39e5047896eb9c)] make some validation and checks optional for speed improvements
+    * [[#208839a](https://github.com/nfdi4plants/ARCtrl/commit/208839a2d50e3c7ffd2722a5e65262bea1e185cd)] change annotationValue of Ontology Annotation to string
+    * [[#a1921ef](https://github.com/nfdi4plants/ARCtrl/commit/a1921ef104e4f168cb6846b2b9de886e4ae774da)] make fillmissingcells optional for addcolumns
+    * [[#2aca309](https://github.com/nfdi4plants/ARCtrl/commit/2aca309623061171dc1c3ec3897d2c5cd388bf11)] Make ArcStudy IO performance test more strict
+
 ### 1.0.1+5576d43 (Released 2023-12-21)
 * Additions:
     * [[#66ff8f4](https://github.com/nfdi4plants/ARCtrl/commit/66ff8f4bb902e1234e84dfaec5411fd7ea5237b3)] improve github ci

build/release_package.json

@@ -1,6 +1,6 @@
 {
   "name": "@nfdi4plants/arctrl",
-  "version": "1.0.1+5576d43",
+  "version": "1.0.4+167fae8",
   "description": "Top level ARC DataModel and API function descriptions.",
   "type": "module",
   "main": "index.js",

src/ISA/ISA.Json/ArcTypes/ArcAssay.fs

@@ -82,6 +82,15 @@ module ArcAssay =
         Assay.encoder (ConverterOptions()) (a.ToAssay())
         |> Encode.toString 2
 
+    let toArcJsonString (a:ArcAssay) : string =
+        let spaces = 0
+        Encode.toString spaces (encoder a)
+
+    let fromArcJsonString (jsonString: string) =
+        match Decode.fromString decoder jsonString with
+        | Ok a -> a
+        | Error e -> failwithf "Error. Unable to parse json string to ArcAssay: %s" e
+
 [<AutoOpen>]
 module ArcAssayExtensions =
 

src/ISA/ISA.Json/ArcTypes/ArcInvestigation.fs

@@ -73,6 +73,15 @@ module ArcInvestigation =
         Investigation.encoder (ConverterOptions()) (a.ToInvestigation())
         |> Encode.toString 2
 
+    let toArcJsonString (a:ArcInvestigation) : string =
+        let spaces = 0
+        Encode.toString spaces (encoder a)
+
+    let fromArcJsonString (jsonString: string) =
+        match Decode.fromString decoder jsonString with
+        | Ok a -> a
+        | Error e -> failwithf "Error. Unable to parse json string to ArcInvestigation: %s" e
+
 [<AutoOpen>]
 module ArcInvestigationExtensions =
 

src/ISA/ISA.Json/ArcTypes/ArcStudy.fs

@@ -67,6 +67,15 @@ module ArcStudy =
         Study.encoder (ConverterOptions()) (a.ToStudy(assays))
         |> Encode.toString 2
 
+    let toArcJsonString (a:ArcStudy) : string =
+        let spaces = 0
+        Encode.toString spaces (encoder a)
+
+    let fromArcJsonString (jsonString: string) =
+        match Decode.fromString decoder jsonString with
+        | Ok a -> a
+        | Error e -> failwithf "Error. Unable to parse json string to ArcStudy: %s" e
+
 [<AutoOpen>]
 module ArcStudyExtensions =
 

src/ISA/ISA.Json/Ontology.fs

@@ -10,26 +10,23 @@ open System.IO
 
 module AnnotationValue =
 
-    let encoder (options : ConverterOptions) (value : obj) = 
-        match value with
-        | :? AnnotationValue as AnnotationValue.Float f -> 
-            Encode.float f
-        | :? AnnotationValue as AnnotationValue.Int i -> 
-            Encode.int i
-        | :? AnnotationValue as AnnotationValue.Text s -> 
-            Encode.string s
-        | _ -> Encode.nil
-
-    let decoder (options : ConverterOptions) : Decoder<AnnotationValue> =
+    /// <summary>
+    /// This decodes from integer, float or string to string only!
+    /// </summary>
+    /// <param name="options"></param>
+    /// <param name="s"></param>
+    /// <param name="json"></param>
+    let decoder (options : ConverterOptions) : Decoder<string> =
         fun s json ->
+            // is there a option to decode force to string?
             match Decode.int s json with
-            | Ok i -> Ok (AnnotationValue.Int i)
+            | Ok i -> Ok <| string i
             | Error _ -> 
                 match Decode.float s json with
-                | Ok f -> Ok (AnnotationValue.Float f)
+                | Ok f -> Ok <| string f
                 | Error _ -> 
                     match Decode.string s json with
-                    | Ok s -> Ok (AnnotationValue.Text s)
+                    | Ok s -> Ok <| s
                     | Error e -> Error e
 
 
@@ -38,9 +35,10 @@ module OntologySourceReference =
     let genID (o:OntologySourceReference) = 
         match o.File with
         | Some f -> f
-        | None -> match o.Name with
-                  | Some n -> "#OntologySourceRef_" + n.Replace(" ","_")
-                  | None -> "#DummyOntologySourceRef"
+        | None -> 
+            match o.Name with
+            | Some n -> "#OntologySourceRef_" + n.Replace(" ","_")
+            | None -> "#DummyOntologySourceRef"
 
     let encoder (options : ConverterOptions) (osr : obj) = 
         [
@@ -114,7 +112,7 @@ module OntologyAnnotation =
         Decode.object (fun get ->
             OntologyAnnotation.create(
                 ?Id = get.Optional.Field "@id" GDecode.uri,
-                ?Name = get.Optional.Field "annotationValue" Decode.string,
+                ?Name = get.Optional.Field "annotationValue" (AnnotationValue.decoder options),
                 ?TermSourceREF = get.Optional.Field "termSource" Decode.string,
                 ?TermAccessionNumber = get.Optional.Field "termAccession" Decode.string,
                 ?Comments = get.Optional.Field "comments" (Decode.array (Comment.decoder options))               

src/ISA/ISA/ARCtrl.ISA.fsproj

@@ -16,7 +16,6 @@
     <Compile Include="JsonTypes\URI.fs" />
     <Compile Include="JsonTypes\Comment.fs" />
     <Compile Include="JsonTypes\CommentList.fs" />
-    <Compile Include="JsonTypes\AnnotationValue.fs" />
     <Compile Include="JsonTypes\OntologyAnnotation.fs" />
     <Compile Include="JsonTypes\OntologySourceReference.fs" />
     <Compile Include="JsonTypes\Value.fs" />

tests/ARCtrl/Template.Tests.fs

@@ -262,7 +262,7 @@ let private tests_equality = testList "equality" [
 ]
 
 let private tests_Web = testList "Web" [
-    ptestCaseAsync "getTemplates" <| async {
+    testCaseAsync "getTemplates" <| async {
         let! templatesMap = ARCtrl.Template.Web.getTemplates(None)
         Expect.isTrue (templatesMap.Length > 0) "Count > 0"
     }

tests/ISA/ISA.Json.Tests/Json.Tests.fs

@@ -135,33 +135,55 @@ let testDecode =
 
 let testOntoloyAnnotation =
     testList "OntologyAnnotation" [
-        
-            testCase "ReaderSuccess" (fun () -> 
+
+        testCase "ReaderSuccess" (fun () -> 
 
-                let result = OntologyAnnotation.fromJsonString OntologyAnnotation.peptidase
+            let result = OntologyAnnotation.fromJsonString OntologyAnnotation.peptidase
 
 
-                let comment = Comment.create(Name = "comment",Value = "This is a comment")
-                let expected = 
-                    OntologyAnnotation.create("protease","Peptidase", "MS", "http://purl.obolibrary.org/obo/NCIT_C16965",Comments = [|comment|])
+            let comment = Comment.create(Name = "comment",Value = "This is a comment")
+            let expected = 
+                OntologyAnnotation.create("protease","Peptidase", "MS", "http://purl.obolibrary.org/obo/NCIT_C16965",Comments = [|comment|])
 
-                Expect.equal result expected "Source did not match"
-            )
-            testCase "WriterOutputMatchesInput" (fun () -> 
+            Expect.equal result expected "Source did not match"
+        )
+        testCase "WriterOutputMatchesInput" (fun () -> 
 
-                let o_read_in = OntologyAnnotation.fromJsonString OntologyAnnotation.peptidase
-                let o_out = OntologyAnnotation.toJsonString o_read_in
+            let o_read_in = OntologyAnnotation.fromJsonString OntologyAnnotation.peptidase
+            let o_out = OntologyAnnotation.toJsonString o_read_in
 
-                let expected = 
-                    OntologyAnnotation.peptidase
-                    |> Utils.wordFrequency
+            let expected = 
+                OntologyAnnotation.peptidase
+                |> Utils.wordFrequency
 
-                let actual = 
-                    o_out
-                    |> Utils.wordFrequency
+            let actual = 
+                o_out
+                |> Utils.wordFrequency
 
-                Expect.sequenceEqual actual expected "Written processInput does not match read process input"
-            )
+            Expect.sequenceEqual actual expected "Written processInput does not match read process input"
+        )
+
+        testCase "Read AnnotationValue - integer" <| fun _ ->
+            let json = """{
+  "annotationValue": 4242424
+}"""
+            let oa = OntologyAnnotation.fromJsonString json
+            let name = Expect.wantSome oa.Name ""
+            Expect.equal name "4242424" ""
+        testCase "Read AnnotationValue - float" <| fun _ ->
+            let json = """{
+  "annotationValue": 42.42
+}"""
+            let oa = OntologyAnnotation.fromJsonString json
+            let name = Expect.wantSome oa.Name ""
+            Expect.equal name "42.42" ""
+        testCase "Read AnnotationValue - string" <| fun _ ->
+            let json = """{
+  "annotationValue": "Example"
+}"""
+            let oa = OntologyAnnotation.fromJsonString json
+            let name = Expect.wantSome oa.Name ""
+            Expect.equal name "Example" ""
     ]
 
 let testOntoloyAnnotationLD =