Add excel get and create template meta data from sequence of strings

nfdi4plants · Oct 10, 2024 · 12e5d75 · 12e5d75
1 parent 3c383de
commit 12e5d75
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Showing 4 changed files with 35 additions and 6 deletions.
diff --git a/src/Spreadsheet/ArcStudy.fs b/src/Spreadsheet/ArcStudy.fs
@@ -42,7 +42,7 @@ module ArcStudy =
     let toMetadataCollection (study : ArcStudy) (assays : ArcAssay list option) =
         Studies.toRows study assays
         |> Seq.append [SparseRow.fromValues [studiesLabel]]
-        |> Seq.map (fun r -> SparseRow.getAllValues r)
+        |> Seq.map (fun row -> SparseRow.getAllValues row)
 
     let fromMetadataCollection (collection: seq<seq<string option>>) : ArcStudy*ArcAssay list =
         try

diff --git a/src/Spreadsheet/Template.fs b/src/Spreadsheet/Template.fs
@@ -226,7 +226,6 @@ module Template =
     let [<Literal>] metaDataSheetName = "isa_template"
     let [<Literal>] obsoletemetaDataSheetName = "SwateTemplateMetadata"
 
-
     let fromParts (templateInfo:TemplateInfo) (ers:OntologyAnnotation list) (tags: OntologyAnnotation list) (authors : Person list) (table : ArcTable) (lastUpdated : System.DateTime)=
             Template.make 
                 (System.Guid templateInfo.Id)
@@ -240,8 +239,7 @@ module Template =
                 (ResizeArray tags)  
                 (lastUpdated)
 
-    let toMetadataSheet (template : Template) : FsWorksheet =
-
+    let toMetadataSheet (template : Template) : FsWorksheet =        
         let sheet = FsWorksheet(metaDataSheetName)
         Template.toRows template
         |> Seq.iteri (fun rowI r -> SparseRow.writeToSheet (rowI + 1) r sheet)    
@@ -252,6 +250,15 @@ module Template =
         |> Seq.map SparseRow.fromFsRow
         |> Template.fromRows
 
+    let toMetadataCollection (template : Template) =
+        Template.toRows template
+        |> Seq.map (fun row -> SparseRow.getAllValues row)
+
+    let fromMetadataCollection (collection: seq<seq<string option>>) =
+        collection
+        |> Seq.map SparseRow.fromAllValues
+        |> Template.fromRows
+
     /// Reads an assay from a spreadsheet
     let fromFsWorkbook (doc:FsWorkbook) = 
         // Reading the "Assay" metadata sheet. Here metadata 

diff --git a/tests/Spreadsheet/TemplateTests.fs b/tests/Spreadsheet/TemplateTests.fs
@@ -1,4 +1,4 @@
-module TemplateTests
+module TemplateTests
 
 
 open ARCtrl
@@ -51,6 +51,23 @@ let tests_Spreadsheet =  testList "Template_Spreadsheet" [
             let sheet = Spreadsheet.Template.toMetadataSheet template
 
             Expect.workSheetEqual sheet TestObjects.Spreadsheet.Template.templateMetadata "Metadata sheet should be equal"
+        testCase "TestMetadataFromCollection" (fun _ ->
+
+            let table = ArcTable.init(TestObjects.Spreadsheet.Template.templateTableName)
+            let templateInfo, ers,tags,authors = Spreadsheet.Template.fromMetadataCollection (TestObjects.Spreadsheet.Template.templateetadataCollection table)
+
+            let template = ARCtrl.Spreadsheet.Template.fromParts templateInfo ers tags authors table System.DateTime.Now
+
+            Expect.stringEqual template.Name "Plant growth" "Name should be equal"
+            Expect.stringEqual template.Version "1.2.0" "Version should be equal"
+
+            Expect.isSome (template.EndpointRepositories.Item 0).TermAccessionNumber (ARCtrl.Helper.Url.createOAUri "DPBO" "1000096")
+            Expect.isSome (template.EndpointRepositories.Item 0).TermAccessionNumber (ARCtrl.Helper.Url.createOAUri "NFDI4PSO" "1000097")
+            Expect.isSome (template.EndpointRepositories.Item 0).TermAccessionNumber (ARCtrl.Helper.Url.createOAUri "NFDI4PSO" "1000098")
+            Expect.isSome (template.EndpointRepositories.Item 0).TermAccessionNumber (ARCtrl.Helper.Url.createOAUri "NFDI4PSO" "0010002")
+            Expect.isSome (template.EndpointRepositories.Item 0).TermAccessionNumber (ARCtrl.Helper.Url.createOAUri "DPBO" "0010000")
+
+        )
     ]
     testList "fullFile" [
         testCase "simple" <| fun _ ->

diff --git a/tests/TestingUtils/TestObjects.Spreadsheet/Spreadsheet.Template.fs b/tests/TestingUtils/TestObjects.Spreadsheet/Spreadsheet.Template.fs
@@ -1,4 +1,4 @@
-module TestObjects.Spreadsheet.Template
+module TestObjects.Spreadsheet.Template
 
 open FsSpreadsheet
 
@@ -163,6 +163,11 @@ let templateMetadata =
     row28.[6].Value <- ""
     ws
 
+let templateetadataCollection table =
+    let template, ers, tags, authors = ARCtrl.Spreadsheet.Template.fromMetadataSheet templateMetadata
+    ARCtrl.Spreadsheet.Template.fromParts template ers tags authors table System.DateTime.Now
+    |> ARCtrl.Spreadsheet.Template.toMetadataCollection
+
 let templateMetadata_deprecatedKeys = 
     let ws = FsWorksheet("SwateTemplateMetadata")
     let row1 = ws.Row(1)