add datamap contract handling tests

tests/ARCtrl/ARCtrl.Contracts.Tests.fs

@@ -20,6 +20,58 @@ let tests_tryFromContract = testList "tryFromContract" [
         |]
         let investigation = contracts |> Array.choose ArcInvestigation.tryFromReadContract
         Expect.hasLength investigation 1 ""
+    testCase "DataMap" <| fun _ ->
+        let fswb = TestObjects.Contract.ISA.SimpleISA.Assay.proteomeDatamapWB
+        let assayName = "myAssay"
+        let contracts = [|
+            Contract.create(
+                READ, 
+                $"assays/{assayName}/isa.datamap.xlsx", 
+                DTOType.ISA_Datamap, 
+                DTO.Spreadsheet fswb
+            )
+        |]
+        let datamap = ARCAux.getAssayDataMapFromContracts assayName contracts
+        Expect.isSome datamap "Datamap should have been parsed"
+    testCase "DataMap_WrongIdentifier" <| fun _ ->
+        let fswb = TestObjects.Contract.ISA.SimpleISA.Assay.proteomeDatamapWB
+        let assayName = "myAssay"
+        let contracts = [|
+            Contract.create(
+                READ, 
+                $"assays/{assayName}/isa.datamap.xlsx", 
+                DTOType.ISA_Datamap, 
+                DTO.Spreadsheet fswb
+            )
+        |]
+        let datamap = ARCAux.getAssayDataMapFromContracts "wrongAssay" contracts
+        Expect.isNone datamap "Datamap should not have been parsed"
+    testCase "DataMap_WrongType" <| fun _ ->
+        let fswb = TestObjects.Contract.ISA.SimpleISA.Assay.proteomeDatamapWB
+        let assayName = "myAssay"
+        let contracts = [|
+            Contract.create(
+                READ, 
+                $"assays/{assayName}/isa.datamap.xlsx", 
+                DTOType.ISA_Assay, 
+                DTO.Spreadsheet fswb
+            )
+        |]
+        let datamap = ARCAux.getAssayDataMapFromContracts assayName contracts
+        Expect.isNone datamap "Datamap should not have been parsed"
+    testCase "DataMap_WrongPath" <| fun _ ->
+        let fswb = TestObjects.Contract.ISA.SimpleISA.Assay.proteomeDatamapWB
+        let assayName = "myAssay"
+        let contracts = [|
+            Contract.create(
+                READ, 
+                $"studies/{assayName}/isa.datamap.xlsx", 
+                DTOType.ISA_Datamap, 
+                DTO.Spreadsheet fswb
+            )
+        |]
+        let datamap = ARCAux.getAssayDataMapFromContracts assayName contracts
+        Expect.isNone datamap "Datamap should not have been parsed"
 ]
 
 let tests_gitContracts = testList "gitContracts" [

tests/ARCtrl/ARCtrl.Tests.fs

@@ -60,7 +60,7 @@ let private simpleISAContracts =
     |]
 
 let private tests_read_contracts = testList "read_contracts" [
-    ptestCase "simpleISA" (fun () -> // set to pending, until performance issues in Study.fromFsWorkbook is resolved.
+    testCase "simpleISA" (fun () -> 
         let arc = ARC()
         arc.SetISAFromContracts simpleISAContracts
         Expect.isSome arc.ISA "isa should be filled out"
@@ -70,15 +70,17 @@ let private tests_read_contracts = testList "read_contracts" [
         Expect.equal inv.Studies.Count 2 "should have read two studies"
         let study1 = inv.Studies.[0]
         Expect.equal study1.Identifier Study.BII_S_1.studyIdentifier "study 1 identifier should have been read from study contract"
-        Expect.equal study1.TableCount 8 "study 1 should have the 7 tables from investigation plus one extra. One table should be overwritten."
+
+        Expect.equal study1.TableCount 2 "study 1 should have the 2 tables. Top level Metadata tables are ignored."
+        //Expect.equal study1.TableCount 8 "study 1 should have the 7 tables from investigation plus one extra. One table should be overwritten."
 
         Expect.equal study1.RegisteredAssays.Count 3 "study 1 should have read three assays"
         let assay1 = study1.RegisteredAssays.[0]
         Expect.equal assay1.Identifier Assay.Proteome.assayIdentifier "assay 1 identifier should have been read from assay contract"
         Expect.equal assay1.TableCount 1 "assay 1 should have read one table"
 
     )
-    ptestCase "StudyAssayOnlyRegistered" (fun () -> // set to pending, until performance issues in Study.fromFsWorkbook is resolved.
+    testCase "StudyAssayOnlyRegistered" (fun () -> // set to pending, until performance issues in Study.fromFsWorkbook is resolved.
         let arc = ARC()
         arc.SetISAFromContracts([|
             SimpleISA.Investigation.investigationReadContract
@@ -94,7 +96,8 @@ let private tests_read_contracts = testList "read_contracts" [
         Expect.equal inv.VacantStudyIdentifiers.Count 1 "should have one vacant study identifier"
         let study1 = inv.Studies.[0]
         Expect.equal study1.Identifier Study.BII_S_1.studyIdentifier "study 1 identifier should have been read from study contract"
-        Expect.equal study1.TableCount 8 "study 1 should have the 7 tables from investigation plus one extra. One table should be overwritten."
+        Expect.equal study1.TableCount 2 "study 1 should have the 2 tables. Top level Metadata tables are ignored."
+        //Expect.equal study1.TableCount 8 "study 1 should have the 7 tables from investigation plus one extra. One table should be overwritten."
 
         Expect.equal study1.RegisteredAssays.Count 1 "study 1 should have read one assay"
         Expect.equal study1.RegisteredAssayIdentifierCount 3 "study 1 should have read three registered assay identifiers"
@@ -148,6 +151,23 @@ let private tests_read_contracts = testList "read_contracts" [
             (Array.create 2 (CompositeCell.createFreeText UpdateAssayWithStudyProtocol.description))
             "Description value was not taken correctly"
     )
+    testCase "SimpleISA_WithDataset" (fun _ ->
+        let contracts = Array.append simpleISAContracts [|SimpleISA.Assay.proteomeDatamapContract|]
+
+        let arc = ARC()
+        arc.SetISAFromContracts contracts
+
+        let inv = Expect.wantSome arc.ISA "Arc should have investigation"
+        let a1 = inv.GetAssay(SimpleISA.Assay.proteomeIdentifer)
+        let datamap = Expect.wantSome a1.DataMap "Proteome Assay was supposed to have datamap"
+
+        Expect.equal 2 datamap.Table.RowCount "Datamap was not read correctly"
+
+        let a2 = inv.GetAssay(SimpleISA.Assay.metabolomeIdentifer)
+        Expect.isNone a2.DataMap "Metabolome Assay was not supposed to have datamap"
+
+    )
+
 ]
 
 let private tests_writeContracts = testList "write_contracts" [
@@ -194,6 +214,33 @@ let private tests_writeContracts = testList "write_contracts" [
         Expect.exists contracts (fun c -> c.Path = "assays/MyAssay/isa.assay.xlsx" && c.DTOType.IsSome && c.DTOType.Value = Contract.DTOType.ISA_Assay) "assay file exisiting but has wrong DTO type"
 
     )
+    testCase "assayWithDatamap" (fun _ ->
+        let inv = ArcInvestigation("MyInvestigation", "BestTitle")
+        let a = inv.InitAssay("MyAssay")
+        let dm = DataMap.init()
+        a.DataMap <- Some dm
+        let arc = ARC(isa = inv)
+        let contracts = arc.GetWriteContracts()
+        let contractPathsString = contracts |> Array.map (fun c -> c.Path) |> String.concat ", "
+        Expect.equal contracts.Length 10 $"Should contain more contracts as base folders but contained: {contractPathsString}"
+
+        // Base 
+        Expect.exists contracts (fun c -> c.Path = "workflows/.gitkeep") "Contract for workflows folder missing"
+        Expect.exists contracts (fun c -> c.Path = "runs/.gitkeep") "Contract for runs folder missing"
+        Expect.exists contracts (fun c -> c.Path = "assays/.gitkeep") "Contract for assays folder missing"
+        Expect.exists contracts (fun c -> c.Path = "studies/.gitkeep") "Contract for studies folder missing"
+        Expect.exists contracts (fun c -> c.Path = "isa.investigation.xlsx") "Contract for investigation folder missing"
+        Expect.exists contracts (fun c -> c.Path = "isa.investigation.xlsx" && c.DTOType.IsSome && c.DTOType.Value = Contract.DTOType.ISA_Investigation) "Contract for investigation existing but has wrong DTO type"
+
+        // Assay folder
+        Expect.exists contracts (fun c -> c.Path = "assays/MyAssay/README.md") "assay readme missing"
+        Expect.exists contracts (fun c -> c.Path = "assays/MyAssay/protocols/.gitkeep") "assay protocols folder missing"
+        Expect.exists contracts (fun c -> c.Path = "assays/MyAssay/dataset/.gitkeep") "assay dataset folder missing"
+        Expect.exists contracts (fun c -> c.Path = "assays/MyAssay/isa.assay.xlsx") "assay file missing"
+        Expect.exists contracts (fun c -> c.Path = "assays/MyAssay/isa.assay.xlsx" && c.DTOType.IsSome && c.DTOType.Value = Contract.DTOType.ISA_Assay) "assay file existing but has wrong DTO type"
+        Expect.exists contracts (fun c -> c.Path = "assays/MyAssay/isa.datamap.xlsx") "assay datamap file missing"
+        Expect.exists contracts (fun c -> c.Path = "assays/MyAssay/isa.datamap.xlsx" && c.DTOType.IsSome && c.DTOType.Value = Contract.DTOType.ISA_Datamap) "assay datamap file existing but has wrong DTO type"
+    )
     testCase "sameAssayAndStudyName" (fun _ ->
         let inv = ArcInvestigation("MyInvestigation", "BestTitle")
         inv.InitStudy("MyAssay").InitRegisteredAssay("MyAssay") |> ignore
@@ -315,6 +362,29 @@ let private tests_updateContracts = testList "update_contracts" [
         let nextContracts = arc.GetUpdateContracts()
         Expect.equal nextContracts.Length 0 "Should contain no contracts as there are no changes"
     )
+    testCase "simpleISA_Datamap_NoChanges" (fun _ ->
+        let arc = ARC()
+        let readContracts = Array.append simpleISAContracts [|SimpleISA.Assay.proteomeDatamapContract|]
+        arc.SetISAFromContracts readContracts
+        let contracts = arc.GetUpdateContracts()
+        Expect.equal contracts.Length 0 "Should contain no contracts as there are no changes"
+    )
+    testCase "simpleISA_Datamap_Changed" (fun _ ->
+        let arc = ARC()
+        let readContracts = Array.append simpleISAContracts [|SimpleISA.Assay.proteomeDatamapContract|]
+        arc.SetISAFromContracts readContracts
+        let isa = arc.ISA.Value
+
+        let dm = Expect.wantSome (isa.GetAssay(SimpleISA.Assay.proteomeIdentifer).DataMap) "Assay should have datamap"       
+        dm.Values.[(0,1)] <- CompositeCell.createDataFromString("Hello")
+
+        let contracts = arc.GetUpdateContracts()
+        Expect.equal contracts.Length 1 $"Should contain only assay datamap change contract"
+        let expectedPath = Identifier.Assay.datamapFileNameFromIdentifier SimpleISA.Assay.proteomeIdentifer
+        Expect.equal contracts.[0].Path expectedPath "Should be the assay datamap file"
+        let nextContracts = arc.GetUpdateContracts()
+        Expect.equal nextContracts.Length 0 "Should contain no contracts as there are no changes"
+    )
     testCase "simpleISA_StudyChange" (fun _ ->
         let arc = ARC()
         arc.SetISAFromContracts simpleISAContracts

tests/Core/ArcAssay.Tests.fs

@@ -76,7 +76,7 @@ let private test_create =
             let tables = ResizeArray([ArcTable.init("MyTable1")])
             let performers = ResizeArray [|Person(firstName = "Kevin", lastName = "Frey")|]
             let comments = ResizeArray [|Comment.create("Comment Name")|]
-            let actual = ArcAssay(identifier, oa_mt, oa_tt, technologyPlatform, tables, performers, comments)
+            let actual = ArcAssay(identifier, oa_mt, oa_tt, technologyPlatform, tables, performers = performers, comments = comments)
             Expect.equal actual.Identifier identifier "identifier"
             Expect.equal actual.MeasurementType (Some oa_mt) "MeasurementType"
             Expect.equal actual.TechnologyType (Some oa_tt) "TechnologyType"
@@ -92,7 +92,7 @@ let private test_create =
             let tables = ResizeArray([ArcTable.init("MyTable1")])
             let performers = ResizeArray [|Person.create(firstName = "Kevin", lastName = "Frey")|]
             let comments = ResizeArray [|Comment.create("Comment Name")|]
-            let actual = ArcAssay(identifier, oa_mt, oa_tt, technologyPlatform, tables, performers, comments)
+            let actual = ArcAssay(identifier, oa_mt, oa_tt, technologyPlatform, tables, performers = performers, comments = comments)
             Expect.equal actual.Identifier identifier "identifier"
             Expect.equal actual.MeasurementType (Some oa_mt) "MeasurementType"
             Expect.equal actual.TechnologyType (Some oa_tt) "TechnologyType"
@@ -108,7 +108,7 @@ let private test_create =
             let tables = ResizeArray([ArcTable.init("MyTable1")])
             let performers = ResizeArray[|Person.create(firstName = "Kevin", lastName = "Frey")|]
             let comments = ResizeArray[|Comment.create("Comment Name")|]
-            let actual = ArcAssay.create(identifier, oa_mt, oa_tt, technologyPlatform, tables, performers, comments)
+            let actual = ArcAssay.create(identifier, oa_mt, oa_tt, technologyPlatform, tables, performers = performers, comments = comments)
             Expect.equal actual.Identifier identifier "identifier"
             Expect.equal actual.MeasurementType (Some oa_mt) "MeasurementType"
             Expect.equal actual.TechnologyType (Some oa_tt) "TechnologyType"
@@ -142,6 +142,7 @@ let private test_create =
                     technologyType
                     technologyPlatform
                     tables
+                    None
                     performers
                     comments
 
@@ -507,8 +508,8 @@ let private tests_UpdateBy = testList "UpdateBy" [
             OntologyAnnotation("MyTechnologyType"),
             OntologyAnnotation("MyTechnologyPlatform"),
             ResizeArray([ArcTable.init("MyTable")]),
-            ResizeArray [|Person(firstName="Kevin", lastName="Frey")|],
-            ResizeArray [|Comment(name="CommentName", value="CommentValue")|]
+            performers = ResizeArray [|Person(firstName="Kevin", lastName="Frey")|],
+            comments = ResizeArray [|Comment(name="CommentName", value="CommentValue")|]
         )
     testCase "UpdateBy, full replace" <| fun _ ->
         let actual = create_testAssay()
@@ -611,6 +612,7 @@ let private tests_GetHashCode = testList "GetHashCode" [
             (OntologyAnnotation "tt" |> Some)
             (OntologyAnnotation "tp" |> Some)
             (ResizeArray([ArcTable.init("My Table"); ArcTable.Tests.create_testTable()]))
+            None
             (ResizeArray [|Person(firstName="John",lastName="Doe"); Person(firstName="Jane",lastName="Doe")|])
             (ResizeArray [|Comment("Hello", "World"); Comment("ByeBye", "World") |])
     testCase "passing" <| fun _ ->

tests/Core/ArcStudy.Tests.fs

@@ -130,6 +130,7 @@ let private test_create =
                     contacts
                     studyDesignDescriptors
                     tables
+                    None
                     assay_identifiers
                     comments
 
@@ -452,6 +453,7 @@ let private tests_GetHashCode = testList "GetHashCode" [
             (ResizeArray [|Person(firstName="John",lastName="Doe"); Person(firstName="Jane",lastName="Doe")|])
             (ResizeArray [|OntologyAnnotation(); OntologyAnnotation(); OntologyAnnotation("Name", "tsr", "Tan")|])
             (ResizeArray([ArcTable.init("My Table"); ArcTable.Tests.create_testTable()]))
+            None
             (ResizeArray(["Registered Assay1"; "Registered Assay2"]))
             (ResizeArray [|Comment("Hello", "World"); Comment("ByeBye", "World") |])
     testCase "passing" <| fun _ ->

tests/Json/Assay.Tests.fs

@@ -13,8 +13,8 @@ module Helper =
             OntologyAnnotation("TT", "MS", "MS:696969"), 
             OntologyAnnotation("TP", "MS", "MS:123456", ResizeArray [Comment.create("Hello","Space")]), 
             ResizeArray([Tests.ArcTable.Helper.create_filled(); ArcTable.init("My Second Table")]),
-            ResizeArray [|Person.create(firstName="Kevin", lastName="Frey")|],
-            ResizeArray [|Comment.create("Hello", "World")|]
+            performers = ResizeArray [|Person.create(firstName="Kevin", lastName="Frey")|],
+            comments = ResizeArray [|Comment.create("Hello", "World")|]
         )
 
     let compare =

tests/Json/Study.Tests.fs

@@ -22,8 +22,8 @@ module Helper =
         ResizeArray [|Person.create(firstName="Kevin", lastName="Frey", phone="023382093810")|], 
         ResizeArray [|OntologyAnnotation(); OntologyAnnotation()|],
         ResizeArray [ArcTable.Helper.create_filled(); ArcTable.init("Table 2")],
-        ResizeArray ["Assay 1"; "Assay 2"],
-        ResizeArray [|Comment.create("Hello", "World")|]
+        registeredAssayIdentifiers = ResizeArray ["Assay 1"; "Assay 2"],
+        comments = ResizeArray [|Comment.create("Hello", "World")|]
     )
 
     let compareFields =

tests/TestingUtils/TestObjects.Contract/ISA.fs

@@ -13,6 +13,7 @@ module SimpleISA =
 
     module Assay = 
 
+        let proteomeIdentifer = Assay.Proteome.assayIdentifier
         let proteomeMetadataWorksheet = Assay.Proteome.assayMetadata
         let proteomeWsName = "Measurement"
         let proteomeTable =
@@ -37,6 +38,31 @@ module SimpleISA =
                 dtoType = DTOType.ISA_Assay,
                 dto = DTO.Spreadsheet proteomeWB)
 
+        let proteomeDatamapTable =
+            DataMap.initWorksheet "Proteome"
+                [
+                    DataMap.Data.appendDataColumn 2
+                    DataMap.Explication.appendMeanColumn 2
+                    DataMap.Unit.appendPPMColumn 2
+                    DataMap.ObjectType.appendFloatColumn 2
+                    DataMap.Description.appendDescriptionColumn 2
+                    DataMap.GeneratedBy.appendGeneratedByColumn 2
+                ]
+
+        let proteomeDatamapWB = 
+            let wb = new FsWorkbook()
+            wb.AddWorksheet(proteomeDatamapTable)
+            wb
+
+        let proteomeDatamapContract = 
+            Contract.create(
+                Operation.READ, 
+                path = Identifier.Assay.datamapFileNameFromIdentifier Assay.Proteome.assayIdentifier,
+                dtoType = DTOType.ISA_Datamap,
+                dto = DTO.Spreadsheet proteomeDatamapWB)
+
+
+        let metabolomeIdentifer = Assay.Metabolome.assayIdentifier
         let metabolomeMetadataWorksheet = Assay.Metabolome.assayMetadata
 
         let metabolomeWB = 
@@ -125,7 +151,6 @@ module SimpleISA =
                 dtoType = DTOType.ISA_Investigation,
                 dto = DTO.Spreadsheet Investigation.BII_I_1.fullInvestigation)
 
-
 module UpdateAssayWithStudyProtocol = 
 
     let assayIdentifier = "MyAssay"