diff --git a/src/ARCtrl/ARC.fs b/src/ARCtrl/ARC.fs index 9723bd84..b2d80f02 100644 --- a/src/ARCtrl/ARC.fs +++ b/src/ARCtrl/ARC.fs @@ -15,28 +15,41 @@ module ARCAux = contracts |> Array.choose ArcAssay.tryFromReadContract + let getAssayDataMapFromContracts (assayIdentifier) (contracts: Contract []) = + contracts + |> Array.tryPick (DataMap.tryFromReadContractForAssay assayIdentifier) // No idea where to move this let getArcStudiesFromContracts (contracts: Contract []) = contracts |> Array.choose ArcStudy.tryFromReadContract + let getStudyDataMapFromContracts (studyIdentifier) (contracts: Contract []) = + contracts + |> Array.tryPick (DataMap.tryFromReadContractForStudy studyIdentifier) + let getArcInvestigationFromContracts (contracts: Contract []) = contracts |> Array.choose ArcInvestigation.tryFromReadContract |> Array.exactlyOne let updateFSByISA (isa : ArcInvestigation option) (fs : FileSystem) = - let (studyNames,assayNames) = + let (studies,assays) = match isa with | Some inv -> - inv.StudyIdentifiers |> Seq.toArray, inv.AssayIdentifiers |> Seq.toArray + inv.Studies |> Seq.toArray, inv.Assays |> Seq.toArray | None -> ([||],[||]) - let assays = FileSystemTree.createAssaysFolder (assayNames |> Array.map FileSystemTree.createAssayFolder) - let studies = FileSystemTree.createStudiesFolder (studyNames |> Array.map FileSystemTree.createStudyFolder) + let assaysFolder = + assays + |> Array.map (fun a -> FileSystemTree.createAssayFolder(a.Identifier,a.DataMap.IsSome)) + |> FileSystemTree.createAssaysFolder + let studiesFolder = + studies + |> Array.map (fun s -> FileSystemTree.createStudyFolder(s.Identifier,s.DataMap.IsSome)) + |> FileSystemTree.createStudiesFolder let investigation = FileSystemTree.createInvestigationFile() let tree = - FileSystemTree.createRootFolder [|investigation;assays;studies|] + FileSystemTree.createRootFolder [|investigation;assaysFolder;studiesFolder|] |> FileSystem.create fs.Union(tree) @@ -219,7 +232,7 @@ type ARC(?isa : ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSystem) = investigation.DeleteStudy(si) ) - studies |> Array.iter (fun study -> + studies |> Array.iter (fun study -> /// Try find registered study in parsed READ contracts let registeredStudyOpt = investigation.Studies |> Seq.tryFind (fun s -> s.Identifier = study.Identifier) match registeredStudyOpt with @@ -227,6 +240,8 @@ type ARC(?isa : ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSystem) = registeredStudy.UpdateReferenceByStudyFile(study,true) | None -> investigation.AddStudy(study) + let datamap = ARCAux.getAssayDataMapFromContracts study.Identifier contracts + study.DataMap <- datamap study.StaticHash <- study.GetLightHashCode() ) assays |> Array.iter (fun assay -> @@ -243,9 +258,11 @@ type ARC(?isa : ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSystem) = |> Array.fold (fun tables study -> ArcTables.updateReferenceTablesBySheets(ArcTables(study.Tables),tables,false) ) (ArcTables(assay.Tables)) + let datamap = ARCAux.getAssayDataMapFromContracts assay.Identifier contracts + assay.DataMap <- datamap assay.Tables <- updatedTables.Tables ) - investigation.Assays |> Seq.iter (fun a -> a.StaticHash <- a.GetHashCode()) + investigation.Assays |> Seq.iter (fun a -> a.StaticHash <- a.GetLightHashCode()) investigation.Studies |> Seq.iter (fun s -> s.StaticHash <- s.GetLightHashCode()) investigation.StaticHash <- investigation.GetLightHashCode() this.ISA <- Some investigation @@ -275,13 +292,28 @@ type ARC(?isa : ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSystem) = Identifier.Study.fileNameFromIdentifier s.Identifier, (DTOType.ISA_Study, ArcStudy.toFsWorkbook s) ) + if s.DataMap.IsSome then + let dm = s.DataMap.Value + dm.StaticHash <- dm.GetHashCode() + workbooks.Add ( + Identifier.Study.datamapFileNameFromIdentifier s.Identifier, + (DTOType.ISA_Datamap, Spreadsheet.DataMap.toFsWorkbook dm) + ) + ) inv.Assays |> Seq.iter (fun a -> - a.StaticHash <- a.GetHashCode() + a.StaticHash <- a.GetLightHashCode() workbooks.Add ( Identifier.Assay.fileNameFromIdentifier a.Identifier, - (DTOType.ISA_Assay, Spreadsheet.ArcAssay.toFsWorkbook a)) + (DTOType.ISA_Assay, Spreadsheet.ArcAssay.toFsWorkbook a)) + if a.DataMap.IsSome then + let dm = a.DataMap.Value + dm.StaticHash <- dm.GetHashCode() + workbooks.Add ( + Identifier.Assay.datamapFileNameFromIdentifier a.Identifier, + (DTOType.ISA_Datamap, Spreadsheet.DataMap.toFsWorkbook dm) + ) ) | None -> @@ -329,15 +361,33 @@ type ARC(?isa : ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSystem) = elif s.StaticHash <> hash then yield s.ToUpdateContract() s.StaticHash <- hash + + match s.DataMap with + | Some dm when dm.StaticHash = 0 -> + yield dm.ToCreateContractForStudy(s.Identifier) + dm.StaticHash <- dm.GetHashCode() + | Some dm when dm.StaticHash <> dm.GetHashCode() -> + yield dm.ToUpdateContractForStudy(s.Identifier) + dm.StaticHash <- dm.GetHashCode() + | _ -> () // Get Assay contracts for a in inv.Assays do - let hash = a.GetHashCode() + let hash = a.GetLightHashCode() if a.StaticHash = 0 then yield! a.ToCreateContract(WithFolder = true) elif a.StaticHash <> hash then yield a.ToUpdateContract() a.StaticHash <- hash + + match a.DataMap with + | Some dm when dm.StaticHash = 0 -> + yield dm.ToCreateContractForAssay(a.Identifier) + dm.StaticHash <- dm.GetHashCode() + | Some dm when dm.StaticHash <> dm.GetHashCode() -> + yield dm.ToUpdateContractForAssay(a.Identifier) + dm.StaticHash <- dm.GetHashCode() + | _ -> () |] diff --git a/src/ARCtrl/ARCtrl.fsproj b/src/ARCtrl/ARCtrl.fsproj index 911cff74..90c2db6a 100644 --- a/src/ARCtrl/ARCtrl.fsproj +++ b/src/ARCtrl/ARCtrl.fsproj @@ -47,5 +47,7 @@ - + + + \ No newline at end of file diff --git a/src/ARCtrl/Xlsx.fs b/src/ARCtrl/Xlsx.fs index 2b54c7ea..488681f6 100644 --- a/src/ARCtrl/Xlsx.fs +++ b/src/ARCtrl/Xlsx.fs @@ -7,6 +7,11 @@ open FsSpreadsheet module XlsxHelper = + [] + type DatamapXlsx() = + member _.fromFsWorkbook (fswb: FsWorkbook) = DataMap.fromFsWorkbook fswb + member _.toFsWorkbook (datamap: DataMap) = DataMap.toFsWorkbook datamap + [] type AssayXlsx() = member _.fromFsWorkbook (fswb: FsWorkbook) = ArcAssay.fromFsWorkbook fswb @@ -28,6 +33,7 @@ open XlsxHelper [] type XlsxController = + static member Datamap = DatamapXlsx() static member Assay = AssayXlsx() static member Study = StudyXlsx() static member Investigation = InvestigationXlsx() \ No newline at end of file diff --git a/src/Contract/ARC.fs b/src/Contract/ARC.fs index a8e972ba..726872eb 100644 --- a/src/Contract/ARC.fs +++ b/src/Contract/ARC.fs @@ -21,6 +21,8 @@ let tryISAReadContractFromPath (path: string) = Some <| Contract.createRead(p, DTOType.ISA_Assay) | StudyPath p -> Some <| Contract.createRead(p, DTOType.ISA_Study) + | DatamapPath p -> + Some <| Contract.createRead(p, DTOType.ISA_Datamap) | anyElse -> None diff --git a/src/Contract/ARCtrl.Contract.fsproj b/src/Contract/ARCtrl.Contract.fsproj index c5d5d73a..801ae242 100644 --- a/src/Contract/ARCtrl.Contract.fsproj +++ b/src/Contract/ARCtrl.Contract.fsproj @@ -7,6 +7,7 @@ + @@ -19,9 +20,11 @@ - + + + nfdi4plants, Kevin Frey, Lukas Weil, Kevin Schneider, Oliver Maus ARC helper functions for contracts management. diff --git a/src/Contract/Contract.fs b/src/Contract/Contract.fs index 45628e83..4a9b5f66 100644 --- a/src/Contract/Contract.fs +++ b/src/Contract/Contract.fs @@ -9,8 +9,9 @@ open Fable.Core.JsInterop [] type DTOType = | [] ISA_Assay // isa.assay.xlsx - | [] ISA_Study - | [] ISA_Investigation + | [] ISA_Study // isa.study.xlsx + | [] ISA_Investigation // isa.investigation.xlsx + | [] ISA_Datamap // isa.datamap.xlsx | [] JSON // arc.json | [] Markdown // README.md | [] CWL // workflow.cwl, might be a new DTO once we diff --git a/src/Contract/Datamap.fs b/src/Contract/Datamap.fs new file mode 100644 index 00000000..29e56bbd --- /dev/null +++ b/src/Contract/Datamap.fs @@ -0,0 +1,92 @@ +namespace ARCtrl.Contract + +open ARCtrl.FileSystem +open ARCtrl.Path +open ARCtrl.Spreadsheet +open ARCtrl +open ARCtrl.Helper +open FsSpreadsheet + +[] +module DatamapContractExtensions = + + let (|DatamapPath|_|) (input) = + match input with + | [|AssaysFolderName; anyAssayName; DataMapFileName|] -> + let path = ARCtrl.Path.combineMany input + Some path + | [|StudiesFolderName; anyStudyName; DataMapFileName|] -> + let path = ARCtrl.Path.combineMany input + Some path + | _ -> None + + type DataMap with + + member this.ToCreateContractForAssay (assayIdentifier : string) = + let path = Identifier.Assay.datamapFileNameFromIdentifier assayIdentifier + Contract.createCreate(path, DTOType.ISA_Datamap, DTO.Spreadsheet (this |> DataMap.toFsWorkbook)) + + member this.ToUpdateContractForAssay (assayIdentifier : string) = + let path = Identifier.Assay.datamapFileNameFromIdentifier assayIdentifier + let c = Contract.createUpdate(path, DTOType.ISA_Datamap, DTO.Spreadsheet (this |> DataMap.toFsWorkbook)) + c + + member this.ToDeleteContractForAssay (assayIdentifier : string) = + let path = Identifier.Assay.datamapFileNameFromIdentifier assayIdentifier + let c = Contract.createDelete(path) + c + + static member toDeleteContractForAssay (assayIdentifier : string) = + fun (dataMap : DataMap) -> + dataMap.ToDeleteContractForAssay(assayIdentifier) + + static member toUpdateContractForAssay (assayIdentifier : string) = + fun (dataMap : DataMap) -> + dataMap.ToUpdateContractForAssay(assayIdentifier) + + static member tryFromReadContractForAssay (assayIdentifier : string) (c:Contract) = + let path = Identifier.Assay.datamapFileNameFromIdentifier assayIdentifier + match c with + | {Path = p; Operation = READ; DTOType = Some DTOType.ISA_Datamap; DTO = Some (DTO.Spreadsheet fsworkbook)} when p = path -> + let dm = + fsworkbook :?> FsWorkbook + |> DataMap.fromFsWorkbook + dm.StaticHash <- dm.GetHashCode() + dm + |> Some + | _ -> None + + + member this.ToCreateContractForStudy (studyIdentifier : string) = + let path = Identifier.Study.datamapFileNameFromIdentifier studyIdentifier + Contract.createCreate(path, DTOType.ISA_Datamap, DTO.Spreadsheet (this |> DataMap.toFsWorkbook)) + + member this.ToUpdateContractForStudy (studyIdentifier : string) = + let path = Identifier.Study.datamapFileNameFromIdentifier studyIdentifier + let c = Contract.createUpdate(path, DTOType.ISA_Datamap, DTO.Spreadsheet (this |> DataMap.toFsWorkbook)) + c + + member this.ToDeleteContractForStudy (studyIdentifier : string) = + let path = Identifier.Study.datamapFileNameFromIdentifier studyIdentifier + let c = Contract.createDelete(path) + c + + static member toDeleteContractForStudy (studyIdentifier : string) = + fun (dataMap : DataMap) -> + dataMap.ToDeleteContractForStudy(studyIdentifier) + + static member toUpdateContractForStudy (studyIdentifier : string) = + fun (dataMap : DataMap) -> + dataMap.ToUpdateContractForStudy(studyIdentifier) + + + static member tryFromReadContractForStudy (studyIdentifier : string) (c:Contract) = + let path = Identifier.Study.datamapFileNameFromIdentifier studyIdentifier + match c with + | {Path = p; Operation = READ; DTOType = Some DTOType.ISA_Datamap; DTO = Some (DTO.Spreadsheet fsworkbook)} when p = path-> + let dm = + fsworkbook :?> FsWorkbook + |> DataMap.fromFsWorkbook + dm.StaticHash <- dm.GetHashCode() + Some (dm) + | _ -> None diff --git a/src/Core/ARCtrl.Core.fsproj b/src/Core/ARCtrl.Core.fsproj index 2bccaabf..d6ac0db3 100644 --- a/src/Core/ARCtrl.Core.fsproj +++ b/src/Core/ARCtrl.Core.fsproj @@ -16,6 +16,8 @@ + + @@ -29,8 +31,6 @@ - - @@ -46,6 +46,7 @@ + @@ -57,9 +58,11 @@ - + + + nfdi4plants, Lukas Weil, Kevin Frey, Kevin Schneider, Oliver Maus ARC and ISA compliant experimental metadata toolkit in F#. This project is meant as an easy means to open, manipulate and save ISA (Investigation,Study,Assay) metadata files in the dotnet environment. diff --git a/src/Core/ArcTypes.fs b/src/Core/ArcTypes.fs index bbc35b26..2ca42abc 100644 --- a/src/Core/ArcTypes.fs +++ b/src/Core/ArcTypes.fs @@ -101,7 +101,7 @@ module ArcTypesAux = [] -type ArcAssay(identifier: string, ?measurementType : OntologyAnnotation, ?technologyType : OntologyAnnotation, ?technologyPlatform : OntologyAnnotation, ?tables: ResizeArray, ?performers : ResizeArray, ?comments : ResizeArray) = +type ArcAssay(identifier: string, ?measurementType : OntologyAnnotation, ?technologyType : OntologyAnnotation, ?technologyPlatform : OntologyAnnotation, ?tables: ResizeArray, ?datamap : DataMap, ?performers : ResizeArray, ?comments : ResizeArray) = inherit ArcTables(defaultArg tables <| ResizeArray()) let performers = defaultArg performers <| ResizeArray() @@ -111,6 +111,7 @@ type ArcAssay(identifier: string, ?measurementType : OntologyAnnotation, ?techno let mutable measurementType : OntologyAnnotation option = measurementType let mutable technologyType : OntologyAnnotation option = technologyType let mutable technologyPlatform : OntologyAnnotation option = technologyPlatform + let mutable dataMap : DataMap option = datamap let mutable performers = performers let mutable comments = comments let mutable staticHash : int = 0 @@ -122,13 +123,14 @@ type ArcAssay(identifier: string, ?measurementType : OntologyAnnotation, ?techno member this.MeasurementType with get() = measurementType and set(n) = measurementType <- n member this.TechnologyType with get() = technologyType and set(n) = technologyType <- n member this.TechnologyPlatform with get() = technologyPlatform and set(n) = technologyPlatform <- n + member this.DataMap with get() = dataMap and set(n) = dataMap <- n member this.Performers with get() = performers and set(n) = performers <- n member this.Comments with get() = comments and set(n) = comments <- n member this.StaticHash with get() = staticHash and set(h) = staticHash <- h static member init (identifier : string) = ArcAssay(identifier) - static member create (identifier: string, ?measurementType : OntologyAnnotation, ?technologyType : OntologyAnnotation, ?technologyPlatform : OntologyAnnotation, ?tables: ResizeArray, ?performers : ResizeArray, ?comments : ResizeArray) = - ArcAssay(identifier = identifier, ?measurementType = measurementType, ?technologyType = technologyType, ?technologyPlatform = technologyPlatform, ?tables =tables, ?performers = performers, ?comments = comments) + static member create (identifier: string, ?measurementType : OntologyAnnotation, ?technologyType : OntologyAnnotation, ?technologyPlatform : OntologyAnnotation, ?tables: ResizeArray, ?datamap : DataMap, ?performers : ResizeArray, ?comments : ResizeArray) = + ArcAssay(identifier = identifier, ?measurementType = measurementType, ?technologyType = technologyType, ?technologyPlatform = technologyPlatform, ?tables =tables, ?datamap = datamap, ?performers = performers, ?comments = comments) static member make (identifier : string) @@ -136,9 +138,10 @@ type ArcAssay(identifier: string, ?measurementType : OntologyAnnotation, ?techno (technologyType : OntologyAnnotation option) (technologyPlatform : OntologyAnnotation option) (tables : ResizeArray) + (datamap : DataMap option) (performers : ResizeArray) (comments : ResizeArray) = - ArcAssay(identifier = identifier, ?measurementType = measurementType, ?technologyType = technologyType, ?technologyPlatform = technologyPlatform, tables =tables, performers = performers, comments = comments) + ArcAssay(identifier = identifier, ?measurementType = measurementType, ?technologyType = technologyType, ?technologyPlatform = technologyPlatform, tables =tables, ?datamap = datamap, performers = performers, comments = comments) static member FileName = ARCtrl.Path.AssayFileName member this.StudiesRegisteredIn @@ -380,6 +383,7 @@ type ArcAssay(identifier: string, ?measurementType : OntologyAnnotation, ?techno let copy = table.Copy() nextTables.Add(copy) let nextComments = this.Comments |> ResizeArray.map (fun c -> c.Copy()) + let nextDataMap = this.DataMap |> Option.map (fun d -> d.Copy()) let nextPerformers = this.Performers |> ResizeArray.map (fun c -> c.Copy()) ArcAssay.make this.Identifier @@ -387,6 +391,7 @@ type ArcAssay(identifier: string, ?measurementType : OntologyAnnotation, ?techno this.TechnologyType this.TechnologyPlatform nextTables + nextDataMap nextPerformers nextComments @@ -455,7 +460,8 @@ type ArcAssay(identifier: string, ?measurementType : OntologyAnnotation, ?techno if assay.Tables.Count <> 0 || updateAlways then this.Tables <- assay.Tables if assay.Comments.Count <> 0 || updateAlways then - this.Comments <- assay.Comments + this.Comments <- assay.Comments + this.DataMap <- assay.DataMap if assay.Performers.Count <> 0 || updateAlways then this.Performers <- assay.Performers @@ -464,11 +470,12 @@ type ArcAssay(identifier: string, ?measurementType : OntologyAnnotation, ?techno let mst = this.MeasurementType = other.MeasurementType let tt = this.TechnologyType = other.TechnologyType let tp = this.TechnologyPlatform = other.TechnologyPlatform + let dm = this.DataMap = other.DataMap let tables = Seq.compare this.Tables other.Tables let perf = Seq.compare this.Performers other.Performers let comments = Seq.compare this.Comments other.Comments // Todo maybe add reflection check to prove that all members are compared? - [|i; mst; tt; tp; tables; perf; comments|] |> Seq.forall (fun x -> x = true) + [|i; mst; tt; tp; dm; tables; perf; comments|] |> Seq.forall (fun x -> x = true) /// /// Use this function to check if this ArcAssay and the input ArcAssay refer to the same object. @@ -485,12 +492,27 @@ type ArcAssay(identifier: string, ?measurementType : OntologyAnnotation, ?techno this.StructurallyEquals(assay) | _ -> false + // Hashcode without Datamap + member this.GetLightHashCode() = + [| + box this.Identifier + HashCodes.boxHashOption this.MeasurementType + HashCodes.boxHashOption this.TechnologyType + HashCodes.boxHashOption this.TechnologyPlatform + HashCodes.boxHashSeq this.Tables + HashCodes.boxHashSeq this.Performers + HashCodes.boxHashSeq this.Comments + |] + |> HashCodes.boxHashArray + |> fun x -> x :?> int + override this.GetHashCode() = [| box this.Identifier HashCodes.boxHashOption this.MeasurementType HashCodes.boxHashOption this.TechnologyType HashCodes.boxHashOption this.TechnologyPlatform + HashCodes.boxHashOption this.DataMap HashCodes.boxHashSeq this.Tables HashCodes.boxHashSeq this.Performers HashCodes.boxHashSeq this.Comments @@ -499,7 +521,7 @@ type ArcAssay(identifier: string, ?measurementType : OntologyAnnotation, ?techno |> fun x -> x :?> int [] -type ArcStudy(identifier : string, ?title, ?description, ?submissionDate, ?publicReleaseDate, ?publications, ?contacts, ?studyDesignDescriptors, ?tables, ?registeredAssayIdentifiers: ResizeArray, ?comments) = +type ArcStudy(identifier : string, ?title, ?description, ?submissionDate, ?publicReleaseDate, ?publications, ?contacts, ?studyDesignDescriptors, ?tables, ?datamap, ?registeredAssayIdentifiers: ResizeArray, ?comments) = inherit ArcTables(defaultArg tables <| ResizeArray()) let publications = defaultArg publications <| ResizeArray() @@ -517,6 +539,7 @@ type ArcStudy(identifier : string, ?title, ?description, ?submissionDate, ?publi let mutable publications : ResizeArray = publications let mutable contacts : ResizeArray = contacts let mutable studyDesignDescriptors : ResizeArray = studyDesignDescriptors + let mutable datamap : DataMap option = datamap let mutable registeredAssayIdentifiers : ResizeArray = registeredAssayIdentifiers let mutable comments : ResizeArray = comments let mutable staticHash : int = 0 @@ -532,17 +555,18 @@ type ArcStudy(identifier : string, ?title, ?description, ?submissionDate, ?publi member this.Publications with get() = publications and set(n) = publications <- n member this.Contacts with get() = contacts and set(n) = contacts <- n member this.StudyDesignDescriptors with get() = studyDesignDescriptors and set(n) = studyDesignDescriptors <- n + member this.DataMap with get() = datamap and set(n) = datamap <- n member this.RegisteredAssayIdentifiers with get() = registeredAssayIdentifiers and set(n) = registeredAssayIdentifiers <- n member this.Comments with get() = comments and set(n) = comments <- n member this.StaticHash with get() = staticHash and set(h) = staticHash <- h static member init(identifier : string) = ArcStudy identifier - static member create(identifier : string, ?title, ?description, ?submissionDate, ?publicReleaseDate, ?publications, ?contacts, ?studyDesignDescriptors, ?tables, ?registeredAssayIdentifiers, ?comments) = - ArcStudy(identifier, ?title = title, ?description = description, ?submissionDate = submissionDate, ?publicReleaseDate = publicReleaseDate, ?publications = publications, ?contacts = contacts, ?studyDesignDescriptors = studyDesignDescriptors, ?tables = tables, ?registeredAssayIdentifiers = registeredAssayIdentifiers, ?comments = comments) + static member create(identifier : string, ?title, ?description, ?submissionDate, ?publicReleaseDate, ?publications, ?contacts, ?studyDesignDescriptors, ?tables, ?datamap, ?registeredAssayIdentifiers, ?comments) = + ArcStudy(identifier, ?title = title, ?description = description, ?submissionDate = submissionDate, ?publicReleaseDate = publicReleaseDate, ?publications = publications, ?contacts = contacts, ?studyDesignDescriptors = studyDesignDescriptors, ?tables = tables, ?datamap = datamap, ?registeredAssayIdentifiers = registeredAssayIdentifiers, ?comments = comments) - static member make identifier title description submissionDate publicReleaseDate publications contacts studyDesignDescriptors tables registeredAssayIdentifiers comments = - ArcStudy(identifier, ?title = title, ?description = description, ?submissionDate = submissionDate, ?publicReleaseDate = publicReleaseDate, publications = publications, contacts = contacts, studyDesignDescriptors = studyDesignDescriptors, tables = tables, registeredAssayIdentifiers = registeredAssayIdentifiers, comments = comments) + static member make identifier title description submissionDate publicReleaseDate publications contacts studyDesignDescriptors tables datamap registeredAssayIdentifiers comments = + ArcStudy(identifier, ?title = title, ?description = description, ?submissionDate = submissionDate, ?publicReleaseDate = publicReleaseDate, publications = publications, contacts = contacts, studyDesignDescriptors = studyDesignDescriptors, tables = tables, ?datamap = datamap, registeredAssayIdentifiers = registeredAssayIdentifiers, comments = comments) /// /// Returns true if all fields are None/ empty sequences **except** Identifier. @@ -929,6 +953,7 @@ type ArcStudy(identifier : string, ?title, ?description, ?submissionDate, ?publi let nextContacts = this.Contacts |> ResizeArray.map (fun c -> c.Copy()) let nextPublications = this.Publications |> ResizeArray.map (fun c -> c.Copy()) let nextStudyDesignDescriptors = this.StudyDesignDescriptors |> ResizeArray.map (fun c -> c.Copy()) + let nextDataMap = this.DataMap |> Option.map (fun d -> d.Copy()) let study = ArcStudy.make this.Identifier @@ -940,6 +965,7 @@ type ArcStudy(identifier : string, ?title, ?description, ?submissionDate, ?publi nextContacts nextStudyDesignDescriptors nextTables + nextDataMap nextAssayIdentifiers nextComments if copyInvestigationRef then study.Investigation <- this.Investigation @@ -970,6 +996,7 @@ type ArcStudy(identifier : string, ?title, ?description, ?submissionDate, ?publi if study.Tables.Count <> 0 || updateAlways then let tables = ArcTables.updateReferenceTablesBySheets(ArcTables(this.Tables),ArcTables(study.Tables),?keepUnusedRefTables = keepUnusedRefTables) this.Tables <- tables.Tables + this.DataMap <- study.DataMap if study.RegisteredAssayIdentifiers.Count <> 0 || updateAlways then this.RegisteredAssayIdentifiers <- study.RegisteredAssayIdentifiers if study.Comments.Count <> 0 || updateAlways then @@ -981,6 +1008,7 @@ type ArcStudy(identifier : string, ?title, ?description, ?submissionDate, ?publi let d = this.Description = other.Description let sd = this.SubmissionDate = other.SubmissionDate let prd = this.PublicReleaseDate = other.PublicReleaseDate + let dm = this.DataMap = other.DataMap let pub = Seq.compare this.Publications other.Publications let con = Seq.compare this.Contacts other.Contacts let sdd = Seq.compare this.StudyDesignDescriptors other.StudyDesignDescriptors @@ -988,7 +1016,7 @@ type ArcStudy(identifier : string, ?title, ?description, ?submissionDate, ?publi let reg_tables = Seq.compare this.RegisteredAssayIdentifiers other.RegisteredAssayIdentifiers let comments = Seq.compare this.Comments other.Comments // Todo maybe add reflection check to prove that all members are compared? - [|i; t; d; sd; prd; pub; con; sdd; tables; reg_tables; comments|] |> Seq.forall (fun x -> x = true) + [|i; t; d; sd; prd; dm; pub; con; sdd; tables; reg_tables; comments|] |> Seq.forall (fun x -> x = true) /// /// Use this function to check if this ArcStudy and the input ArcStudy refer to the same object. @@ -1040,6 +1068,7 @@ type ArcStudy(identifier : string, ?title, ?description, ?submissionDate, ?publi HashCodes.boxHashOption this.Description HashCodes.boxHashOption this.SubmissionDate HashCodes.boxHashOption this.PublicReleaseDate + HashCodes.boxHashOption this.DataMap HashCodes.boxHashSeq this.Publications HashCodes.boxHashSeq this.Contacts HashCodes.boxHashSeq this.StudyDesignDescriptors diff --git a/src/Core/Conversion.fs b/src/Core/Conversion.fs index 9fd97ffa..929ebb23 100644 --- a/src/Core/Conversion.fs +++ b/src/Core/Conversion.fs @@ -75,6 +75,7 @@ module JsonTypes = | CompositeCell.Unitized (text,unit) -> (if text = "" then None else Value.fromString text |> Some), if unit.isEmpty() then None else unit |> Some + | CompositeCell.Data (data) -> failwith "Data cell should not be parsed to isa value" /// Convert a CompositeHeader and Cell tuple to a ISA Component let composeComponent (header : CompositeHeader) (value : CompositeCell) : Component = @@ -105,9 +106,7 @@ module JsonTypes = | CompositeHeader.Input IOType.Source -> ProcessInput.createSource(value.ToString()) | CompositeHeader.Input IOType.Sample -> ProcessInput.createSample(value.ToString()) | CompositeHeader.Input IOType.Material -> ProcessInput.createMaterial(value.ToString()) - | CompositeHeader.Input IOType.ImageFile -> ProcessInput.createImageFile(value.ToString()) - | CompositeHeader.Input IOType.RawDataFile -> ProcessInput.createRawData(value.ToString()) - | CompositeHeader.Input IOType.DerivedDataFile -> ProcessInput.createDerivedData(value.ToString()) + | CompositeHeader.Input IOType.Data -> ProcessInput.createRawData(value.ToString()) | _ -> failwithf "Could not parse input header %O" header @@ -117,9 +116,7 @@ module JsonTypes = match header with | CompositeHeader.Output IOType.Sample -> ProcessOutput.createSample(value.ToString()) | CompositeHeader.Output IOType.Material -> ProcessOutput.createMaterial(value.ToString()) - | CompositeHeader.Output IOType.ImageFile -> ProcessOutput.createImageFile(value.ToString()) - | CompositeHeader.Output IOType.RawDataFile -> ProcessOutput.createRawData(value.ToString()) - | CompositeHeader.Output IOType.DerivedDataFile -> ProcessOutput.createDerivedData(value.ToString()) + | CompositeHeader.Output IOType.Data -> ProcessOutput.createRawData(value.ToString()) | _ -> failwithf "Could not parse output header %O" header @@ -167,9 +164,9 @@ module JsonTypes = | ProcessInput.Data d -> let dataType = d.DataType.Value match dataType with - | DataFile.ImageFile -> CompositeHeader.Input IOType.ImageFile, CompositeCell.FreeText (d.Name |> Option.defaultValue "") - | DataFile.RawDataFile -> CompositeHeader.Input IOType.RawDataFile, CompositeCell.FreeText (d.Name |> Option.defaultValue "") - | DataFile.DerivedDataFile -> CompositeHeader.Input IOType.DerivedDataFile, CompositeCell.FreeText (d.Name |> Option.defaultValue "") + | DataFile.ImageFile -> CompositeHeader.Input IOType.Data, CompositeCell.FreeText (d.Name |> Option.defaultValue "") + | DataFile.RawDataFile -> CompositeHeader.Input IOType.Data, CompositeCell.FreeText (d.Name |> Option.defaultValue "") + | DataFile.DerivedDataFile -> CompositeHeader.Input IOType.Data, CompositeCell.FreeText (d.Name |> Option.defaultValue "") /// Convert an ISA ProcessOutput to a CompositeHeader and Cell tuple let decomposeProcessOutput (po : ProcessOutput) : CompositeHeader*CompositeCell = @@ -179,9 +176,9 @@ module JsonTypes = | ProcessOutput.Data d -> let dataType = d.DataType.Value match dataType with - | DataFile.ImageFile -> CompositeHeader.Output IOType.ImageFile, CompositeCell.FreeText (d.Name |> Option.defaultValue "") - | DataFile.RawDataFile -> CompositeHeader.Output IOType.RawDataFile, CompositeCell.FreeText (d.Name |> Option.defaultValue "") - | DataFile.DerivedDataFile -> CompositeHeader.Output IOType.DerivedDataFile, CompositeCell.FreeText (d.Name |> Option.defaultValue "") + | DataFile.ImageFile -> CompositeHeader.Output IOType.Data, CompositeCell.FreeText (d.Name |> Option.defaultValue "") + | DataFile.RawDataFile -> CompositeHeader.Output IOType.Data, CompositeCell.FreeText (d.Name |> Option.defaultValue "") + | DataFile.DerivedDataFile -> CompositeHeader.Output IOType.Data, CompositeCell.FreeText (d.Name |> Option.defaultValue "") /// This function creates a string containing the name and the ontology short-string of the given ontology annotation term diff --git a/src/Core/Data.fs b/src/Core/Data.fs new file mode 100644 index 00000000..18649f6d --- /dev/null +++ b/src/Core/Data.fs @@ -0,0 +1,81 @@ +namespace ARCtrl + +open ARCtrl +open ARCtrl.Helper +open Fable.Core + +[] +type Data(?id,?name,?dataType,?format,?selectorFormat,?comments) = + + let mutable _id : URI option = id + let mutable _name : string option = name + let mutable _dataType : DataFile option = dataType + let mutable _format : string option = format + let mutable _selectorFormat : URI option = selectorFormat + let mutable _comments : Comment ResizeArray = Option.defaultValue (ResizeArray()) comments + + member this.ID + with get() = _id + and set(id) = _id <- id + + member this.Name + with get() = _name + and set(name) = _name <- name + + member this.DataType + with get() = _dataType + and set(dataType) = _dataType <- dataType + + member this.Format + with get() = _format + and set(format) = _format <- format + + member this.SelectorFormat + with get() = _selectorFormat + and set(selectorFormat) = _selectorFormat <- selectorFormat + + member this.Comments + with get() = _comments + and set(comments) = _comments <- comments + + + static member make id name dataType format selectorFormat comments = + Data(?id=id,?name=name,?dataType=dataType,?format=format,?selectorFormat=selectorFormat,?comments=comments) + + static member create (?Id,?Name,?DataType,?Format,?SelectorFormat,?Comments) = + Data.make Id Name DataType Format SelectorFormat Comments + + static member empty = + Data.create() + + member this.NameText = + this.Name + |> Option.defaultValue "" + + member this.Copy() = + let nextComments = this.Comments |> ResizeArray.map (fun c -> c.Copy()) + Data(?id=this.ID,?name=this.Name,?dataType=this.DataType,?format=this.Format,?selectorFormat=this.SelectorFormat,comments=nextComments) + + override this.GetHashCode() = + [| + HashCodes.boxHashOption this.ID + HashCodes.boxHashOption this.Name + HashCodes.boxHashOption this.DataType + HashCodes.boxHashOption this.Format + HashCodes.boxHashOption this.SelectorFormat + HashCodes.boxHashSeq this.Comments + |] + |> HashCodes.boxHashArray + |> fun x -> x :?> int + + override this.Equals(obj) = + HashCodes.hash this = HashCodes.hash obj + + interface IISAPrintable with + member this.Print() = + this.ToString() + member this.PrintCompact() = + match this.DataType with + | Some t -> + sprintf "%s [%s]" this.NameText t.AsString + | None -> sprintf "%s" this.NameText diff --git a/src/Core/Process/DataFile.fs b/src/Core/DataFile.fs similarity index 96% rename from src/Core/Process/DataFile.fs rename to src/Core/DataFile.fs index 79118b1a..b8c3ecef 100644 --- a/src/Core/Process/DataFile.fs +++ b/src/Core/DataFile.fs @@ -1,4 +1,4 @@ -namespace ARCtrl.Process +namespace ARCtrl open ARCtrl diff --git a/src/Core/Helper/Identifier.fs b/src/Core/Helper/Identifier.fs index 411c4baa..ff9ed736 100644 --- a/src/Core/Helper/Identifier.fs +++ b/src/Core/Helper/Identifier.fs @@ -88,6 +88,24 @@ module Assay = else None + /// + /// On writing a xlsx file we unify our output to a relative path to ARC root. So: `assays/assayIdentifier/isa.datamap.xlsx`. + /// + /// Any correct assay identifier + let datamapFileNameFromIdentifier (identifier: string) : string = + checkValidCharacters (identifier) + ARCtrl.Path.combineMany [|ARCtrl.Path.AssaysFolderName; identifier; ARCtrl.Path.DataMapFileName|] + + /// + /// On writing a xlsx file we unify our output to a relative path to ARC root. So: `assays/assayIdentifier/isa.datamap.xlsx`. + /// + /// Any correct assay identifier + let tryDatamapFileNameFromIdentifier (identifier: string) : string option = + if tryCheckValidCharacters (identifier) then + ARCtrl.Path.combineMany [|ARCtrl.Path.AssaysFolderName; identifier; ARCtrl.Path.DataMapFileName|] + |> Some + else None + /// Assay only contains "FileName" in isa.assay.xlsx. To unify naming in our model, on read-in we transform fileName to identifier and reverse for writing. [] module Study = @@ -135,4 +153,22 @@ module Study = if tryCheckValidCharacters (identifier) then ARCtrl.Path.combineMany [|ARCtrl.Path.StudiesFolderName; identifier; ARCtrl.Path.StudyFileName|] |> Some + else None + + /// + /// On writing a xlsx file we unify our output to a relative path to ARC root. So: `studies/studyIdentifier/isa.investigation.xlsx`. + /// + /// Any correct study identifier + let datamapFileNameFromIdentifier (identifier: string) : string = + checkValidCharacters (identifier) + ARCtrl.Path.combineMany [|ARCtrl.Path.StudiesFolderName; identifier; ARCtrl.Path.DataMapFileName|] + + /// + /// On writing a xlsx file we unify our output to a relative path to ARC root. So: `studies/studyIdentifier/isa.investigation.xlsx`. + /// + /// Any correct study identifier + let tryDatamapFileNameFromIdentifier (identifier: string) : string option = + if tryCheckValidCharacters (identifier) then + ARCtrl.Path.combineMany [|ARCtrl.Path.StudiesFolderName; identifier; ARCtrl.Path.DataMapFileName|] + |> Some else None \ No newline at end of file diff --git a/src/Core/Process/Data.fs b/src/Core/Process/Data.fs deleted file mode 100644 index ae2b87a0..00000000 --- a/src/Core/Process/Data.fs +++ /dev/null @@ -1,39 +0,0 @@ -namespace ARCtrl.Process - -open ARCtrl -open ARCtrl.Helper - -type Data = - { - ID : URI option - Name : string option - DataType : DataFile option - Comments : Comment list option - } - - static member make id name dataType comments = - { - ID = id - Name = name - DataType = dataType - Comments = comments - } - - static member create (?Id,?Name,?DataType,?Comments) = - Data.make Id Name DataType Comments - - static member empty = - Data.create() - - member this.NameAsString = - this.Name - |> Option.defaultValue "" - - interface IISAPrintable with - member this.Print() = - this.ToString() - member this.PrintCompact() = - match this.DataType with - | Some t -> - sprintf "%s [%s]" this.NameAsString t.AsString - | None -> sprintf "%s" this.NameAsString diff --git a/src/Core/Table/ArcTableAux.fs b/src/Core/Table/ArcTableAux.fs index 82895f8d..106e1bc4 100644 --- a/src/Core/Table/ArcTableAux.fs +++ b/src/Core/Table/ArcTableAux.fs @@ -113,10 +113,15 @@ module SanityChecks = while isValid && en.MoveNext() do let (ci,_),cell = en.Current.Key,en.Current.Value let header = headers.[ci] - let headerIsFreetext = not header.IsTermColumn + let headerIsData = header.IsDataColumn + let headerIsFreetext = (not header.IsTermColumn) && (not header.IsDataColumn) let cellIsNotFreetext = not cell.isFreeText + let cellIsNotData = not cell.isData + if headerIsData && (cellIsNotData && cellIsNotFreetext) then + (if raiseException then failwith else printfn "%s") $"Invalid combination of header `{header}` and cell `{cell}`. Data header should contain either Data or Freetext cells." + isValid <- false if headerIsFreetext && cellIsNotFreetext then - (if raiseException then failwith else printfn "%s") $"Invalid combination of header `{header}` and cell `{cell}`." + (if raiseException then failwith else printfn "%s") $"Invalid combination of header `{header}` and cell `{cell}`. Freetext header should not contain non-freetext cells." isValid <- false isValid diff --git a/src/Core/Table/CompositeCell.fs b/src/Core/Table/CompositeCell.fs index af4a7d3d..2a5dd8fa 100644 --- a/src/Core/Table/CompositeCell.fs +++ b/src/Core/Table/CompositeCell.fs @@ -15,10 +15,12 @@ type CompositeCell = /// /// https://isa-specs.readthedocs.io/en/latest/isatab.html#unit | Unitized of string*OntologyAnnotation + | Data of Data member this.isUnitized = match this with | Unitized _ -> true | _ -> false member this.isTerm = match this with | Term _ -> true | _ -> false member this.isFreeText = match this with | FreeText _ -> true | _ -> false + member this.isData = match this with | Data _ -> true | _ -> false /// /// This returns the default empty cell from an existing CompositeCell. @@ -28,6 +30,7 @@ type CompositeCell = | CompositeCell.Term _ -> CompositeCell.emptyTerm | CompositeCell.Unitized _ -> CompositeCell.emptyUnitized | CompositeCell.FreeText _ -> CompositeCell.emptyFreeText + | CompositeCell.Data _ -> CompositeCell.emptyData /// /// This function returns an array of all values as string @@ -44,6 +47,7 @@ type CompositeCell = | FreeText s -> [|s|] | Term oa -> [| oa.NameText; defaultArg oa.TermSourceREF ""; defaultArg oa.TermAccessionNumber ""|] | Unitized (v,oa) -> [| v; oa.NameText; defaultArg oa.TermSourceREF ""; defaultArg oa.TermAccessionNumber ""|] + | Data d -> [| defaultArg d.Name ""; defaultArg d.Format ""; defaultArg d.SelectorFormat ""|] /// FreeText string will be converted to unit term name. /// @@ -53,6 +57,7 @@ type CompositeCell = | Unitized _ -> this | FreeText text -> CompositeCell.Unitized ("", OntologyAnnotation.create(text)) | Term term -> CompositeCell.Unitized ("", term) + | Data d -> failwith "Data cell cannot be converted to Unitized cell." /// FreeText string will be converted to term name. /// @@ -62,6 +67,7 @@ type CompositeCell = | Term _ -> this | Unitized (_,unit) -> CompositeCell.Term unit | FreeText text -> CompositeCell.Term(OntologyAnnotation.create(text)) + | Data d -> failwith "Data cell cannot be converted to Term cell." /// Will always keep `OntologyAnnotation.NameText` from Term or Unit. member this.ToFreeTextCell() = @@ -69,6 +75,7 @@ type CompositeCell = | FreeText _ -> this | Term term -> FreeText(term.NameText) | Unitized (v,unit) -> FreeText(unit.NameText) + | Data d -> FreeText (Option.defaultValue "" d.Name) // Suggest this syntax for easy "of-something" access member this.AsUnitized = @@ -79,12 +86,17 @@ type CompositeCell = member this.AsTerm = match this with | Term c -> c - | _ -> failwith "Not a Swate TermCell." + | _ -> failwith "Not a Term Cell." member this.AsFreeText = match this with | FreeText c -> c - | _ -> failwith "Not a Swate TermCell." + | _ -> failwith "Not a FreeText Cell." + + member this.AsData = + match this with + | Data d -> d + | _ -> failwith "Not a Data Cell." // TODO: i would really love to have an overload here accepting string input static member createTerm (oa:OntologyAnnotation) = Term oa @@ -99,9 +111,15 @@ type CompositeCell = static member createFreeText (value: string) = FreeText value + static member createData (d:Data) = Data d + + static member createDataFromString (value : string, ?format : string, ?selectorFormat : string) = + Data(Data.create(Name = value, ?Format = format, ?SelectorFormat = selectorFormat)) + static member emptyTerm = Term (OntologyAnnotation()) static member emptyFreeText = FreeText "" static member emptyUnitized = Unitized ("", OntologyAnnotation()) + static member emptyData = Data(Data.create()) /// /// Updates current CompositeCell with information from OntologyAnnotation. @@ -115,6 +133,7 @@ type CompositeCell = | CompositeCell.Term _ -> CompositeCell.createTerm oa | CompositeCell.Unitized (v,_) -> CompositeCell.createUnitized (v,oa) | CompositeCell.FreeText _ -> CompositeCell.createFreeText oa.NameText + | CompositeCell.Data d -> failwith "Data cell cannot be updated with OntologyAnnotation." /// /// Updates current CompositeCell with information from OntologyAnnotation. @@ -132,6 +151,7 @@ type CompositeCell = | Term oa -> $"{oa.NameText}" | FreeText s -> s | Unitized (v,oa) -> $"{v} {oa.NameText}" + | Data d -> $"{d.NameText}" #if FABLE_COMPILER //[] @@ -143,5 +163,7 @@ type CompositeCell = //[] static member unitized (v:string, oa:OntologyAnnotation) = CompositeCell.Unitized(v, oa) + //[] + static member data (d:Data) = CompositeCell.Data(d) #else #endif \ No newline at end of file diff --git a/src/Core/Table/CompositeColumn.fs b/src/Core/Table/CompositeColumn.fs index 29567b96..0b79e8a2 100644 --- a/src/Core/Table/CompositeColumn.fs +++ b/src/Core/Table/CompositeColumn.fs @@ -26,9 +26,17 @@ type CompositeColumn = { // no cell values will be handled later and is no error case | _, emptyCell when cells.Length = 0 -> true + | isData when header.IsDataColumn && (cells.[0].isData || cells.[0].isFreeText) -> + true + | isData when header.IsDataColumn -> + if raiseExeption then + let exampleCells = cells.[0] + let msg = $"Invalid combination of header `{header}` and cells `{exampleCells}`, Data header should have either Data or Freetext cells" + failwith msg + false | isTerm when header.IsTermColumn && (cells.[0].isTerm || cells.[0].isUnitized) -> true - | isNotTerm when not header.IsTermColumn && cells.[0].isFreeText -> + | isNotTerm when (not header.IsTermColumn) && cells.[0].isFreeText -> true | h, c -> if raiseExeption then diff --git a/src/Core/Table/CompositeHeader.fs b/src/Core/Table/CompositeHeader.fs index b6e0f308..97bea594 100644 --- a/src/Core/Table/CompositeHeader.fs +++ b/src/Core/Table/CompositeHeader.fs @@ -9,9 +9,7 @@ open ARCtrl.Helper type IOType = | Source | Sample - | RawDataFile - | DerivedDataFile - | ImageFile + | Data | Material | FreeText of string @@ -21,9 +19,7 @@ type IOType = static member All = [| Source Sample - RawDataFile - DerivedDataFile - ImageFile + Data Material |] @@ -52,21 +48,8 @@ type IOType = | FreeText s1, FreeText s2 when s1 = s2 -> FreeText (s1) | FreeText s1, FreeText s2 -> failwith $"FreeText IO column names {s1} and {s2} do differ" | FreeText s, _ -> failwith $"FreeText IO column and {other} can not be merged" - | ImageFile, Source -> ImageFile - | ImageFile, RawDataFile -> ImageFile - | ImageFile, DerivedDataFile -> ImageFile - | ImageFile, ImageFile -> ImageFile - | ImageFile, _ -> failwith $"ImageFile IO column and {other} can not be merged" - | DerivedDataFile, Source -> DerivedDataFile - | DerivedDataFile, RawDataFile -> DerivedDataFile - | DerivedDataFile, DerivedDataFile -> DerivedDataFile - | DerivedDataFile, ImageFile -> ImageFile - | DerivedDataFile, _ -> failwith $"DerivedDataFile IO column and {other} can not be merged" - | RawDataFile, Source -> RawDataFile - | RawDataFile, RawDataFile -> RawDataFile - | RawDataFile, DerivedDataFile -> DerivedDataFile - | RawDataFile, ImageFile -> ImageFile - | RawDataFile, _ -> failwith $"RawDataFile IO column and {other} can not be merged" + | Data, Source -> Data + | Data, _ -> failwith $"Data IO column and {other} can not be merged" | Sample, Source -> Sample | Sample, Sample -> Sample | Sample, _ -> failwith $"Sample IO column and {other} can not be merged" @@ -79,13 +62,11 @@ type IOType = override this.ToString() = match this with - | Source -> "Source Name" - | Sample -> "Sample Name" - | RawDataFile -> "Raw Data File" - | DerivedDataFile -> "Derived Data File" - | ImageFile -> "Image File" - | Material -> "Material" - | FreeText s -> s + | Source -> "Source Name" + | Sample -> "Sample Name" + | Data -> "Data" + | Material -> "Material" + | FreeText s -> s /// Used to match only(!) IOType string to IOType (without Input/Output). This matching is case sensitive. /// @@ -96,9 +77,10 @@ type IOType = match str with | "Source" | "Source Name" -> Source | "Sample" | "Sample Name" -> Sample - | "RawDataFile" | "Raw Data File" -> RawDataFile - | "DerivedDataFile" | "Derived Data File" -> DerivedDataFile - | "ImageFile" | "Image File" -> ImageFile + | "RawDataFile" | "Raw Data File" + | "DerivedDataFile" | "Derived Data File" + | "ImageFile" | "Image File" + | "Data" -> Data | "Material" -> Material | _ -> FreeText str // use str to not store `str.ToLower()` @@ -118,29 +100,24 @@ type IOType = "The source value must be a unique identifier for an organism or a sample." | U2.Case1 Sample | U2.Case2 "Sample" -> "The Sample Name column describes specifc laboratory samples with a unique identifier." - | U2.Case1 RawDataFile | U2.Case2 "RawDataFile" -> + | U2.Case1 Data | U2.Case2 "RawDataFile" -> "The Raw Data File column defines untransformed and unprocessed data files." - | U2.Case1 DerivedDataFile | U2.Case2 "DerivedDataFile" -> + | U2.Case1 Data | U2.Case2 "DerivedDataFile" -> "The Derived Data File column defines transformed and/or processed data files." - | U2.Case1 ImageFile | U2.Case2 "ImageFile" -> + | U2.Case1 Data | U2.Case2 "ImageFile" -> "Placeholder" | U2.Case1 Material | U2.Case2 "Material" -> "Placeholder" | U2.Case1 (FreeText _) | U2.Case2 "FreeText" -> "Placeholder" | _ -> failwith $"Unable to parse combination to existing IOType: `{iotype}`" - #if FABLE_COMPILER static member source() = IOType.Source static member sample() = IOType.Sample - static member rawDataFile() = IOType.RawDataFile - - static member derivedDataFile() = IOType.DerivedDataFile - - static member imageFile() = IOType.ImageFile + static member data() = IOType.Data static member material() = IOType.Material @@ -310,6 +287,11 @@ type CompositeHeader = | ProtocolType -> true | anythingElse -> false + member this.IsDataColumn = + match this with + | Input IOType.Data | Output IOType.Data -> true + | anythingElse -> false + /// /// Is true if the Building Block type is a FeaturedColumn. /// diff --git a/src/Core/Table/DataMap.fs b/src/Core/Table/DataMap.fs new file mode 100644 index 00000000..3b7fedb3 --- /dev/null +++ b/src/Core/Table/DataMap.fs @@ -0,0 +1,138 @@ +namespace ARCtrl + +open System.Collections.Generic +open ARCtrl.Helper +open ARCtrl +open Fable.Core + + +[] +module DataMapAux = + + [] + let dataMapName = "DataMap" + + let dataHeader = CompositeHeader.Input IOType.Data + + [] + let dataShortHand = "Data" + + let explication = OntologyAnnotation("Clarification","NCIT","http://purl.obolibrary.org/obo/NCIT_C94778") + + [] + let explicationShortHand = "Explication" + + let explicationHeader = CompositeHeader.Parameter explication + + let unit = OntologyAnnotation("Unit","UO","http://purl.obolibrary.org/obo/UO_0000000") + + [] + let unitShortHand = "Unit" + + let unitHeader = CompositeHeader.Parameter unit + + let objectType = OntologyAnnotation("Data Type","NCIT","http://purl.obolibrary.org/obo/NCIT_C42645") + + let objectTypeHeader = CompositeHeader.Parameter objectType + + [] + let objectTypeShortHand = "Object Type" + + let descriptionHeader = CompositeHeader.FreeText "Description" + + [] + let descriptionShortHand = "Description" + + let generatedByHeader = CompositeHeader.FreeText "Generated By" + + [] + let generatedByShortHand = "Generated By" + + let allowedHeaders = + [dataHeader; explicationHeader; unitHeader; objectTypeHeader; descriptionHeader; generatedByHeader] + + let validate (headers : ResizeArray) (values : System.Collections.Generic.Dictionary) (raiseException : bool) = + let headersAreValid = + headers + |> Seq.exists (fun h -> + let hasForeignHeader = + not (allowedHeaders |> List.exists (fun ah -> ah = h)) + if raiseException && hasForeignHeader then + failwithf "Header %O is not allowed in DataMap" h + hasForeignHeader + ) + let tableIsValid = ArcTableAux.SanityChecks.validate headers values raiseException + headersAreValid && tableIsValid + +type DataMap(headers: ResizeArray, values: System.Collections.Generic.Dictionary) = + + let _ = DataMapAux.validate headers values true + + let table = ArcTable(DataMapAux.dataMapName, headers, values) + let mutable staticHash = 0 + + member this.Headers = table.Headers + member this.Values = table.Values + member this.StaticHash with get() = staticHash and set(value) = staticHash <- value + + static member init() = DataMap(ResizeArray(),Dictionary()) + + member this.AddColumns(columns : CompositeColumn [], ?skipFillMissing : bool) = + columns |> Array.iter (fun c -> c.Validate(true) |> ignore) + table.AddColumns(columns, ?skipFillMissing = skipFillMissing) + DataMapAux.validate table.Headers table.Values true |> ignore + + static member addColumns (columns : CompositeColumn [], ?skipFillMissing : bool) = + fun (dm : DataMap) -> + let dm : DataMap = dm.Copy() + dm.AddColumns(columns, ?skipFillMissing = skipFillMissing) + dm + + member this.Table = table + + member this.TryGetCellAt (row: int, column: int) = table.TryGetCellAt(row, column) + + member this.GetExplicationColumn() = + table.GetColumnByHeader(DataMapAux.explicationHeader) + + member this.AddExplicationColumn(cells : CompositeCell []) = + table.AddColumn(DataMapAux.explicationHeader, cells) + + member this.GetUnitColumn() = + table.GetColumnByHeader(DataMapAux.unitHeader) + + member this.AddUnitColumn(cells : CompositeCell []) = + table.AddColumn(DataMapAux.unitHeader, cells) + + member this.GetDataTypeColumn() = + table.GetColumnByHeader(DataMapAux.objectTypeHeader) + + member this.AddDataTypeColumn(cells : CompositeCell []) = + table.AddColumn(DataMapAux.objectTypeHeader, cells) + + member this.GetDescriptionColumn() = + table.GetColumnByHeader(DataMapAux.descriptionHeader) + + member this.AddDescriptionColumn(cells : CompositeCell []) = + table.AddColumn(DataMapAux.descriptionHeader, cells) + + + member this.GetRow(row: int, ?SkipValidation) = table.GetRow(row,?SkipValidation = SkipValidation) + + static member getRow(row: int, ?SkipValidation) = + fun (dm : DataMap) -> dm.GetRow(row,?SkipValidation = SkipValidation) + + member this.Copy() = + DataMap( + ResizeArray(this.Headers), + Dictionary(this.Values) + ) + + override this.Equals(obj) = + match obj with + | :? DataMap as dm -> + this.Table.Equals(dm.Table) + | _ -> false + + override this.GetHashCode() = + this.Table.GetHashCode() \ No newline at end of file diff --git a/src/FileSystem/FileSystemTree.fs b/src/FileSystem/FileSystemTree.fs index 01ba3c33..daac3433 100644 --- a/src/FileSystem/FileSystemTree.fs +++ b/src/FileSystem/FileSystemTree.fs @@ -195,19 +195,29 @@ type FileSystemTree = static member createEmptyFolder (name : string) = FileSystemTree.createFolder(name, [|FileSystemTree.createGitKeepFile()|]) - static member createAssayFolder(assayName : string) = + static member createAssayFolder(assayName : string, ?hasDataMap) = + let hasDataMap = defaultArg hasDataMap false let dataset = FileSystemTree.createEmptyFolder ARCtrl.Path.AssayDatasetFolderName let protocols = FileSystemTree.createEmptyFolder ARCtrl.Path.AssayProtocolsFolderName let readme = FileSystemTree.createReadmeFile() let assayFile = FileSystemTree.createFile ARCtrl.Path.AssayFileName - FileSystemTree.createFolder(assayName, [|dataset; protocols; assayFile; readme|]) + if hasDataMap then + let dataMapFile = FileSystemTree.createFile ARCtrl.Path.DataMapFileName + FileSystemTree.createFolder(assayName, [|dataset; protocols; assayFile; readme; dataMapFile|]) + else + FileSystemTree.createFolder(assayName, [|dataset; protocols; assayFile; readme|]) - static member createStudyFolder(studyName : string) = + static member createStudyFolder(studyName : string, ?hasDataMap) = + let hasDataMap = defaultArg hasDataMap false let resources = FileSystemTree.createEmptyFolder ARCtrl.Path.StudiesResourcesFolderName let protocols = FileSystemTree.createEmptyFolder ARCtrl.Path.StudiesProtocolsFolderName let readme = FileSystemTree.createReadmeFile() let studyFile = FileSystemTree.createFile ARCtrl.Path.StudyFileName - FileSystemTree.createFolder(studyName, [|resources; protocols; studyFile; readme|]) + if hasDataMap then + let dataMapFile = FileSystemTree.createFile ARCtrl.Path.DataMapFileName + FileSystemTree.createFolder(studyName, [|resources; protocols; studyFile; readme; dataMapFile|]) + else + FileSystemTree.createFolder(studyName, [|resources; protocols; studyFile; readme|]) static member createInvestigationFile() = FileSystemTree.createFile ARCtrl.Path.InvestigationFileName diff --git a/src/FileSystem/Path.fs b/src/FileSystem/Path.fs index 3b2aad05..36953def 100644 --- a/src/FileSystem/Path.fs +++ b/src/FileSystem/Path.fs @@ -9,6 +9,7 @@ let seperators = [|PathSeperator; PathSeperatorWindows|] // Files +let [] DataMapFileName = "isa.datamap.xlsx" let [] AssayFileName = "isa.assay.xlsx" let [] StudyFileName = "isa.study.xlsx" let [] InvestigationFileName = "isa.investigation.xlsx" diff --git a/src/Json/ARCtrl.Json.fsproj b/src/Json/ARCtrl.Json.fsproj index 392c447f..fc08786d 100644 --- a/src/Json/ARCtrl.Json.fsproj +++ b/src/Json/ARCtrl.Json.fsproj @@ -87,6 +87,9 @@ + + + nfdi4plants, Lukas Weil, Florian Wetzels, Kevin Frey ARC and ISA json compliant parser for experimental metadata toolkit in F#. This project is meant as an easy means to open, manipulate and save ISA (Investigation,Study,Assay) metadata files in isa-json format. diff --git a/src/Json/Assay.fs b/src/Json/Assay.fs index 8014406a..93c1d81b 100644 --- a/src/Json/Assay.fs +++ b/src/Json/Assay.fs @@ -189,7 +189,7 @@ module AssayExtensions = Decode.fromJsonString Assay.ROCrate.decoder s /// exports in json-ld format - static member toROCrateJsonString(studyName, ?spaces) = + static member toROCrateJsonString(?studyName, ?spaces) = fun (obj: ArcAssay) -> Assay.ROCrate.encoder studyName obj |> Encode.toJsonString (Encode.defaultSpaces spaces) diff --git a/src/Json/Process/Data.fs b/src/Json/Process/Data.fs index 5c3088a5..7e372445 100644 --- a/src/Json/Process/Data.fs +++ b/src/Json/Process/Data.fs @@ -2,11 +2,69 @@ namespace ARCtrl.Json open Thoth.Json.Core +open StringTable + open ARCtrl open ARCtrl.Process module Data = + // let mutable _id : URI option = id + // let mutable _name : string option = name + // let mutable _dataType : DataFile option = dataType + // let mutable _format : string option = format + // let mutable _selectorFormat : URI option = selectorFormat + // let mutable _comments : Comment list option = comments + let encoder (d : Data) = + [ + Encode.tryInclude "@id" Encode.string d.ID + Encode.tryInclude "name" Encode.string d.Name + Encode.tryInclude "dataType" DataFile.ISAJson.encoder d.DataType + Encode.tryInclude "format" Encode.string d.Format + Encode.tryInclude "selectorFormat" Encode.string d.SelectorFormat + Encode.tryIncludeSeq "comments" Comment.encoder d.Comments + ] + |> Encode.choose + |> Encode.object + + + let decoder : Decoder = + Decode.object (fun get -> + Data( + ?id = get.Optional.Field "@id" Decode.uri, + ?name = get.Optional.Field "name" Decode.string, + ?dataType = get.Optional.Field "dataType" DataFile.ISAJson.decoder, + ?format = get.Optional.Field "format" Decode.string, + ?selectorFormat = get.Optional.Field "selectorFormat" Decode.uri, + ?comments = get.Optional.Field "comments" (Decode.resizeArray Comment.decoder) + ) + ) + + let compressedEncoder (stringTable : StringTableMap) (d : Data) = + [ + Encode.tryInclude "i" (StringTable.encodeString stringTable) d.ID + Encode.tryInclude "n" (StringTable.encodeString stringTable) d.Name + Encode.tryInclude "d" DataFile.ISAJson.encoder d.DataType + Encode.tryInclude "f" (StringTable.encodeString stringTable) d.Format + Encode.tryInclude "s" (StringTable.encodeString stringTable) d.SelectorFormat + Encode.tryIncludeSeq "c" Comment.encoder d.Comments + ] + |> Encode.choose + |> Encode.object + + + let compressedDecoder (stringTable : StringTableArray) : Decoder = + Decode.object (fun get -> + Data( + ?id = get.Optional.Field "i" (StringTable.decodeString stringTable), + ?name = get.Optional.Field "n" (StringTable.decodeString stringTable), + ?dataType = get.Optional.Field "d" DataFile.ISAJson.decoder, + ?format = get.Optional.Field "f" (StringTable.decodeString stringTable), + ?selectorFormat = get.Optional.Field "s" (StringTable.decodeString stringTable), + ?comments = get.Optional.Field "c" (Decode.resizeArray Comment.decoder) + ) + ) + module ROCrate = let genID (d:Data) : string = @@ -22,7 +80,9 @@ module Data = "@type", (Encode.list [Encode.string "Data"]) Encode.tryInclude "name" Encode.string (oa.Name) Encode.tryInclude "type" DataFile.ROCrate.encoder oa.DataType - Encode.tryIncludeListOpt "comments" Comment.ROCrate.encoder oa.Comments + Encode.tryInclude "encodingFormat" Encode.string oa.Format + Encode.tryInclude "usageInfo" Encode.string oa.SelectorFormat + Encode.tryIncludeSeq "comments" Comment.ROCrate.encoder oa.Comments "@context", ROCrateContext.Data.context_jsonvalue ] |> Encode.choose @@ -30,12 +90,14 @@ module Data = let decoder : Decoder = Decode.object (fun get -> - { - ID = get.Optional.Field "@id" Decode.uri - Name = get.Optional.Field "name" Decode.string - DataType = get.Optional.Field "type" DataFile.ROCrate.decoder - Comments = get.Optional.Field "comments" (Decode.list Comment.ROCrate.decoder) - } + Data( + ?id = get.Optional.Field "@id" Decode.uri, + ?name = get.Optional.Field "name" Decode.string, + ?dataType = get.Optional.Field "type" DataFile.ROCrate.decoder, + ?format = get.Optional.Field "encodingFormat" Decode.string, + ?selectorFormat = get.Optional.Field "usageInfo" Decode.uri, + ?comments = get.Optional.Field "comments" (Decode.resizeArray Comment.ROCrate.decoder) + ) ) @@ -47,7 +109,7 @@ module Data = Encode.tryInclude "@id" Encode.string oa.ID Encode.tryInclude "name" Encode.string oa.Name Encode.tryInclude "type" DataFile.ISAJson.encoder oa.DataType - Encode.tryIncludeListOpt "comments" Comment.ISAJson.encoder oa.Comments + Encode.tryIncludeSeq "comments" Comment.ISAJson.encoder oa.Comments ] |> Encode.choose |> Encode.object @@ -56,12 +118,12 @@ module Data = let decoder: Decoder = Decode.objectNoAdditionalProperties allowedFields (fun get -> - { - ID = get.Optional.Field "@id" Decode.uri - Name = get.Optional.Field "name" Decode.string - DataType = get.Optional.Field "type" DataFile.ISAJson.decoder - Comments = get.Optional.Field "comments" (Decode.list Comment.ISAJson.decoder) - } + Data( + ?id = get.Optional.Field "@id" Decode.uri, + ?name = get.Optional.Field "name" Decode.string, + ?dataType = get.Optional.Field "type" DataFile.ISAJson.decoder, + ?comments = get.Optional.Field "comments" (Decode.resizeArray Comment.ISAJson.decoder) + ) ) [] diff --git a/src/Json/Table/CompositeCell.fs b/src/Json/Table/CompositeCell.fs index e989b8f0..2f076dde 100644 --- a/src/Json/Table/CompositeCell.fs +++ b/src/Json/Table/CompositeCell.fs @@ -15,11 +15,13 @@ module CompositeCell = let encoder (cc: CompositeCell) = let oaToJsonString (oa:OntologyAnnotation) = OntologyAnnotation.encoder oa + let t, v = match cc with | CompositeCell.FreeText s-> "FreeText", [Encode.string s] | CompositeCell.Term t -> "Term", [oaToJsonString t] | CompositeCell.Unitized (v, unit) -> "Unitized", [Encode.string v; oaToJsonString unit] + | CompositeCell.Data d -> "Data", [Data.encoder d] Encode.object [ CellType, Encode.string t CellValues, v |> Encode.list @@ -38,6 +40,9 @@ module CompositeCell = let v = get.Required.Field (CellValues) (Decode.index 0 Decode.string) let oa = get.Required.Field (CellValues) (Decode.index 1 OntologyAnnotation.decoder) CompositeCell.Unitized (v, oa) + | "Data" -> + let d = get.Required.Field (CellValues) (Decode.index 0 Data.decoder) + CompositeCell.Data d | anyelse -> failwithf "Error reading CompositeCell from json string: %A" anyelse ) @@ -50,6 +55,7 @@ module CompositeCell = | CompositeCell.FreeText s -> "FreeText", [StringTable.encodeString stringTable s] | CompositeCell.Term t -> "Term", [OATable.encodeOA oaTable t] | CompositeCell.Unitized (v, unit) -> "Unitized", [StringTable.encodeString stringTable v; OATable.encodeOA oaTable unit] + | CompositeCell.Data d -> "Data", [Data.compressedEncoder stringTable d] Encode.object [ CompressedCellType, StringTable.encodeString stringTable t CompressedCellValues, v |> Encode.list @@ -69,6 +75,9 @@ module CompositeCell = let v = get.Required.Field (CompressedCellValues) (Decode.index 0 <| (StringTable.decodeString stringTable) ) let oa = get.Required.Field (CompressedCellValues) (Decode.index 1 <| OATable.decodeOA oaTable ) CompositeCell.Unitized (v, oa) + | "Data" -> + let d = get.Required.Field (CompressedCellValues) (Decode.index 0 <| Data.compressedDecoder stringTable) + CompositeCell.Data d | anyelse -> failwithf "Error reading CompositeCell from json string: %A" anyelse ) diff --git a/src/Spreadsheet/ARCtrl.Spreadsheet.fsproj b/src/Spreadsheet/ARCtrl.Spreadsheet.fsproj index 826c3ec6..0ed1fe7d 100644 --- a/src/Spreadsheet/ARCtrl.Spreadsheet.fsproj +++ b/src/Spreadsheet/ARCtrl.Spreadsheet.fsproj @@ -19,20 +19,23 @@ - + + + + + - + - @@ -42,6 +45,9 @@ + + + nfdi4plants, Lukas Weil ARC and ISA xlsx compliant parser for experimental metadata toolkit in F#. This project is meant as an easy means to open, manipulate and save ISA (Investigation,Study,Assay) metadata files in isa-xlsx format. diff --git a/src/Spreadsheet/AnnotationTable/ArcTable.fs b/src/Spreadsheet/AnnotationTable/ArcTable.fs index e7573d0a..3a7e5212 100644 --- a/src/Spreadsheet/AnnotationTable/ArcTable.fs +++ b/src/Spreadsheet/AnnotationTable/ArcTable.fs @@ -61,14 +61,22 @@ let classifyColumnOrder (column : CompositeColumn) = [] let annotationTablePrefix = "annotationTable" +let helperColumnStrings = + [ + "Term Source REF" + "Term Accession Number" + "Unit" + "Data Format" + "Data Selector Format" + ] + let groupColumnsByHeader (columns : list) = columns |> Aux.List.groupWhen (fun c -> let v = c.[1].ValueAsString() - Regex.tryParseReferenceColumnHeader v - |> Option.isNone - && - (v.StartsWith "Unit" |> not) + helperColumnStrings + |> List.exists (fun s -> v.StartsWith s) + |> not ) /// Returns the annotation table of the worksheet if it exists, else returns None diff --git a/src/Spreadsheet/AnnotationTable/CompositeCell.fs b/src/Spreadsheet/AnnotationTable/CompositeCell.fs index da43f5b3..74d0e294 100644 --- a/src/Spreadsheet/AnnotationTable/CompositeCell.fs +++ b/src/Spreadsheet/AnnotationTable/CompositeCell.fs @@ -4,14 +4,38 @@ open ARCtrl open ARCtrl.Helper open FsSpreadsheet -let fromFsCells (cells : list) : CompositeCell = +//let fromFsCells (cells : list) : CompositeCell = +// let cellValues = cells |> List.map (fun c -> c.ValueAsString()) +// match cellValues with +// | [v] -> CompositeCell.createFreeText v +// | [v1;v2;v3] -> CompositeCell.createTermFromString(v1,v2,v3) +// | [v1;v2;v3;v4] -> CompositeCell.createUnitizedFromString(v1,v2,v3,v4) +// | _ -> +// failwithf "Dafuq" + +let termFromFsCells (tsrCol : int option) (tanCol : int option ) (cells : list) : CompositeCell= + let cellValues = cells |> List.map (fun c -> c.ValueAsString()) + let tan = Option.map (fun i -> cellValues.[i]) tanCol + let tsr = Option.map (fun i -> cellValues.[i]) tsrCol + CompositeCell.createTermFromString(cellValues.[0],?tsr = tsr, ?tan = tan) + +let unitizedFromFsCells (unitCol : int) (tsrCol : int option ) (tanCol : int option) (cells : list) : CompositeCell = + let cellValues = cells |> List.map (fun c -> c.ValueAsString()) + let unit = cellValues.[unitCol] + let tan = Option.map (fun i -> cellValues.[i]) tanCol + let tsr = Option.map (fun i -> cellValues.[i]) tsrCol + CompositeCell.createUnitizedFromString(cellValues.[0],unit,?tsr = tsr, ?tan = tan) + +let freeTextFromFsCells (cells : list) : CompositeCell = + let cellValues = cells |> List.map (fun c -> c.ValueAsString()) + CompositeCell.createFreeText cellValues.[0] + +let dataFromFsCells (format : int option) (selectorFormat : int option) (cells : list) : CompositeCell = let cellValues = cells |> List.map (fun c -> c.ValueAsString()) - match cellValues with - | [v] -> CompositeCell.createFreeText v - | [v1;v2;v3] -> CompositeCell.createTermFromString(v1,v2,v3) - | [v1;v2;v3;v4] -> CompositeCell.createUnitizedFromString(v1,v2,v3,v4) - | _ -> - failwithf "Dafuq" + let format = Option.map (fun i -> cellValues.[i]) format + let selectorFormat = Option.map (fun i -> cellValues.[i]) selectorFormat + CompositeCell.createDataFromString(cellValues.[0],?format = format, ?selectorFormat = selectorFormat) + let toFsCells isTerm hasUnit (cell : CompositeCell) : list = match cell with @@ -22,4 +46,8 @@ let toFsCells isTerm hasUnit (cell : CompositeCell) : list = | CompositeCell.Term v when hasUnit -> [FsCell(v.NameText); FsCell(""); FsCell(Option.defaultValue "" v.TermSourceREF); FsCell(v.TermAccessionOntobeeUrl)] | CompositeCell.Term v -> [FsCell(v.NameText); FsCell(Option.defaultValue "" v.TermSourceREF); FsCell(v.TermAccessionOntobeeUrl)] - | CompositeCell.Unitized (v,unit) -> [FsCell(v); FsCell(unit.NameText); FsCell(Option.defaultValue "" unit.TermSourceREF); FsCell(unit.TermAccessionOntobeeUrl)] \ No newline at end of file + | CompositeCell.Unitized (v,unit) -> [FsCell(v); FsCell(unit.NameText); FsCell(Option.defaultValue "" unit.TermSourceREF); FsCell(unit.TermAccessionOntobeeUrl)] + | CompositeCell.Data d -> + let format = d.Format |> Option.defaultValue "" |> FsCell + let selectorFormat = d.SelectorFormat |> Option.defaultValue "" |> FsCell + [FsCell(d.Name |> Option.defaultValue ""); format; selectorFormat] \ No newline at end of file diff --git a/src/Spreadsheet/AnnotationTable/CompositeColumn.fs b/src/Spreadsheet/AnnotationTable/CompositeColumn.fs index 4cc5e7d9..5126de73 100644 --- a/src/Spreadsheet/AnnotationTable/CompositeColumn.fs +++ b/src/Spreadsheet/AnnotationTable/CompositeColumn.fs @@ -22,7 +22,7 @@ let fixDeprecatedIOHeader (col : FsColumn) = col let fromFsColumns (columns : list) : CompositeColumn = - let header = + let header, cellParser = columns |> List.map (fun c -> c.[1]) |> CompositeHeader.fromFsCells @@ -32,7 +32,7 @@ let fromFsColumns (columns : list) : CompositeColumn = for i = 2 to l do columns |> List.map (fun c -> c.[i]) - |> CompositeCell.fromFsCells + |> cellParser |] CompositeColumn.create(header,cells) @@ -40,6 +40,7 @@ let fromFsColumns (columns : list) : CompositeColumn = let toFsColumns (column : CompositeColumn) : FsCell list list = let hasUnit = column.Cells |> Seq.exists (fun c -> c.isUnitized) let isTerm = column.Header.IsTermColumn + let isData = column.Header.IsDataColumn let header = CompositeHeader.toFsCells hasUnit column.Header let cells = column.Cells |> Array.map (CompositeCell.toFsCells isTerm hasUnit) if hasUnit then @@ -55,6 +56,17 @@ let toFsColumns (column : CompositeColumn) : FsCell list list = [header.[1]; for i = 0 to column.Cells.Length - 1 do cells.[i].[1]] [header.[2]; for i = 0 to column.Cells.Length - 1 do cells.[i].[2]] ] + elif isData then + let hasFormat = column.Cells |> Seq.exists (fun c -> c.AsData.Format.IsSome) + let hasSelectorFormat = column.Cells |> Seq.exists (fun c -> c.AsData.SelectorFormat.IsSome) + + [ + [header.[0]; for i = 0 to column.Cells.Length - 1 do cells.[i].[0]] + if hasFormat then + [header.[1]; for i = 0 to column.Cells.Length - 1 do cells.[i].[1]] + if hasSelectorFormat then + [header.[2]; for i = 0 to column.Cells.Length - 1 do cells.[i].[2]] + ] else [ [header.[0]; for i = 0 to column.Cells.Length - 1 do cells.[i].[0]] diff --git a/src/Spreadsheet/AnnotationTable/CompositeHeader.fs b/src/Spreadsheet/AnnotationTable/CompositeHeader.fs index 74e83ffa..31921c68 100644 --- a/src/Spreadsheet/AnnotationTable/CompositeHeader.fs +++ b/src/Spreadsheet/AnnotationTable/CompositeHeader.fs @@ -13,22 +13,34 @@ module ActivePattern = if localID1 <> localID2 then failwithf "LocalID %s and %s do not match" localID1 localID2 {|TermSourceRef = idSpace1; TermAccessionNumber = $"{idSpace1}:{localID1}"|} - let (|Term|_|) (categoryParser : string -> string option) (f : OntologyAnnotation -> CompositeHeader) (cells : FsCell list) = + let (|Term|_|) (categoryParser : string -> string option) (f : OntologyAnnotation -> CompositeHeader) (cells : FsCell list) : (CompositeHeader*(FsCell list -> CompositeCell)) option = let (|AC|_|) s = categoryParser s let cellValues = cells |> List.map (fun c -> c.ValueAsString()) match cellValues with | [AC name] -> let ont = OntologyAnnotation.create(name) - f ont + (f ont, CompositeCell.termFromFsCells None None) + |> Some + | [AC name; TSRColumnHeader term1; TANColumnHeader term2] -> + let term = mergeIDInfo term1.IDSpace term1.LocalID term2.IDSpace term2.LocalID + let ont = OntologyAnnotation.create(name, term.TermSourceRef, term.TermAccessionNumber) + (f ont, CompositeCell.termFromFsCells (Some 1) (Some 2)) + |> Some + | [AC name; TANColumnHeader term2; TSRColumnHeader term1] -> + let term = mergeIDInfo term1.IDSpace term1.LocalID term2.IDSpace term2.LocalID + let ont = OntologyAnnotation.create(name, term.TermSourceRef, term.TermAccessionNumber) + (f ont, CompositeCell.termFromFsCells (Some 2) (Some 1)) |> Some - | [AC name; TSRColumnHeader term1; TANColumnHeader term2] - //| [AC name; TermAccessionNumber term1; TermSourceREF term2] - //| [AC name; Unit; TermAccessionNumber term1; TermSourceREF term2] | [AC name; UnitColumnHeader _; TSRColumnHeader term1; TANColumnHeader term2] -> let term = mergeIDInfo term1.IDSpace term1.LocalID term2.IDSpace term2.LocalID let ont = OntologyAnnotation.create(name, term.TermSourceRef, term.TermAccessionNumber) - f ont + (f ont, CompositeCell.unitizedFromFsCells 1 (Some 2) (Some 3)) + |> Some + | [AC name; UnitColumnHeader _; TANColumnHeader term2; TSRColumnHeader term1] -> + let term = mergeIDInfo term1.IDSpace term1.LocalID term2.IDSpace term2.LocalID + let ont = OntologyAnnotation.create(name, term.TermSourceRef, term.TermAccessionNumber) + (f ont, CompositeCell.unitizedFromFsCells 1 (Some 3) (Some 2)) |> Some | _ -> None @@ -59,45 +71,62 @@ module ActivePattern = let (|Input|_|) (cells : FsCell list) = let cellValues = cells |> List.map (fun c -> c.ValueAsString()) match cellValues with - | [InputColumnHeader ioType] -> - IOType.ofString ioType - |> CompositeHeader.Input - |> Some + | InputColumnHeader ioType :: cols -> + match IOType.ofString ioType with + | IOType.Data -> + let format = cols |> List.tryFindIndex (fun s -> s.StartsWith("Data Format")) |> Option.map ((+) 1) + let selectorFormat = cols |> List.tryFindIndex (fun s -> s.StartsWith("Data Selector Format")) |> Option.map ((+) 1) + (CompositeHeader.Input (IOType.Data), CompositeCell.dataFromFsCells format selectorFormat) + |> Some + | ioType -> + (CompositeHeader.Input ioType, CompositeCell.freeTextFromFsCells) + |> Some | _ -> None let (|Output|_|) (cells : FsCell list) = let cellValues = cells |> List.map (fun c -> c.ValueAsString()) match cellValues with - | [OutputColumnHeader ioType] -> - IOType.ofString ioType - |> CompositeHeader.Output - |> Some + | OutputColumnHeader ioType :: cols -> + match IOType.ofString ioType with + | IOType.Data -> + let format = cols |> List.tryFindIndex (fun s -> s.StartsWith("Data Format")) |> Option.map ((+) 1) + let selectorFormat = cols |> List.tryFindIndex (fun s -> s.StartsWith("Data Selector Format")) |> Option.map ((+) 1) + (CompositeHeader.Output (IOType.Data), CompositeCell.dataFromFsCells format selectorFormat) + |> Some + | ioType -> + (CompositeHeader.Output ioType, CompositeCell.freeTextFromFsCells) + |> Some + | _ -> None + + let (|ProtocolType|_|) (cells : FsCell list) = + let parser s = if s = "Protocol Type" then Some s else None + let header _ = CompositeHeader.ProtocolType + match cells with + | Term parser header r -> Some r | _ -> None let (|ProtocolHeader|_|) (cells : FsCell list) = let cellValues = cells |> List.map (fun c -> c.ValueAsString()) match cellValues with - | "Protocol Type" :: _ -> - Some CompositeHeader.ProtocolType - | ["Protocol REF"] -> Some CompositeHeader.ProtocolREF - | ["Protocol Description"] -> Some CompositeHeader.ProtocolDescription - | ["Protocol Uri"] -> Some CompositeHeader.ProtocolUri - | ["Protocol Version"] -> Some CompositeHeader.ProtocolVersion - | ["Performer"] -> Some CompositeHeader.Performer - | ["Date"] -> Some CompositeHeader.Date + | ["Protocol REF"] -> Some (CompositeHeader.ProtocolREF, CompositeCell.freeTextFromFsCells) + | ["Protocol Description"] -> Some (CompositeHeader.ProtocolDescription, CompositeCell.freeTextFromFsCells) + | ["Protocol Uri"] -> Some (CompositeHeader.ProtocolUri, CompositeCell.freeTextFromFsCells) + | ["Protocol Version"] -> Some (CompositeHeader.ProtocolVersion, CompositeCell.freeTextFromFsCells) + | ["Performer"] -> Some (CompositeHeader.Performer, CompositeCell.freeTextFromFsCells) + | ["Date"] -> Some (CompositeHeader.Date, CompositeCell.freeTextFromFsCells) | _ -> None let (|FreeText|_|) (cells : FsCell list) = let cellValues = cells |> List.map (fun c -> c.ValueAsString()) match cellValues with | [text] -> - CompositeHeader.FreeText text + (CompositeHeader.FreeText text, CompositeCell.freeTextFromFsCells) |> Some | _ -> None open ActivePattern -let fromFsCells (cells : list) : CompositeHeader = +let fromFsCells (cells : list) : CompositeHeader*(FsCell list -> CompositeCell) = match cells with | Parameter p -> p | Factor f -> f @@ -105,13 +134,16 @@ let fromFsCells (cells : list) : CompositeHeader = | Component c -> c | Input i -> i | Output o -> o + | ProtocolType pt -> pt | ProtocolHeader ph -> ph | FreeText ft -> ft | _ -> failwithf "Could not parse header group %O" cells let toFsCells (hasUnit : bool) (header : CompositeHeader) : list = - if header.IsSingleColumn then + if header.IsDataColumn then + [FsCell(header.ToString()); FsCell "Data Format"; FsCell "Data Selector Format"] + elif header.IsSingleColumn then [FsCell(header.ToString())] elif header.IsTermColumn then [ diff --git a/src/Spreadsheet/DataMap.fs b/src/Spreadsheet/DataMap.fs new file mode 100644 index 00000000..b1c21e67 --- /dev/null +++ b/src/Spreadsheet/DataMap.fs @@ -0,0 +1,25 @@ +module ARCtrl.Spreadsheet.DataMap + +open ARCtrl +open ArcTable +open FsSpreadsheet + + +/// Reads an assay from a spreadsheet +let fromFsWorkbook (doc:FsWorkbook) = + try + let dataMapTable = + doc.GetWorksheets() + |> Seq.tryPick DataMapTable.tryFromFsWorksheet + match dataMapTable with + | Some table -> table + | None -> failwith "No DataMapTable found in workbook" + with + | err -> failwithf "Could not parse datamap: \n%s" err.Message + +let toFsWorkbook (dataMap : DataMap) = + let doc = new FsWorkbook() + + DataMapTable.toFsWorksheet dataMap + |> doc.AddWorksheet + doc \ No newline at end of file diff --git a/src/Spreadsheet/DataMapTable/DataMapColumn.fs b/src/Spreadsheet/DataMapTable/DataMapColumn.fs new file mode 100644 index 00000000..84b97854 --- /dev/null +++ b/src/Spreadsheet/DataMapTable/DataMapColumn.fs @@ -0,0 +1,48 @@ +module ARCtrl.Spreadsheet.DataMapColumn + +open ARCtrl +open ArcTable +open FsSpreadsheet + +let fromFsColumns (columns : list) : CompositeColumn = + let header, cellParser = + columns + |> List.map (fun c -> c.[1]) + |> DataMapHeader.fromFsCells + let l = columns.[0].RangeAddress.LastAddress.RowNumber + let cells = + [| + for i = 2 to l do + columns + |> List.map (fun c -> c.[i]) + |> cellParser + |] + CompositeColumn.create(header,cells) + + +let toFsColumns (column : CompositeColumn) : FsCell list list = + let isTerm = column.Header.IsTermColumn + let isData = column.Header.IsDataColumn + let header = DataMapHeader.toFsCells column.Header + let cells = column.Cells |> Array.map (CompositeCell.toFsCells isTerm false) + if isTerm then + [ + [header.[0]; for i = 0 to column.Cells.Length - 1 do cells.[i].[0]] + [header.[1]; for i = 0 to column.Cells.Length - 1 do cells.[i].[1]] + [header.[2]; for i = 0 to column.Cells.Length - 1 do cells.[i].[2]] + ] + elif isData then + let hasFormat = column.Cells |> Seq.exists (fun c -> c.AsData.Format.IsSome) + let hasSelectorFormat = column.Cells |> Seq.exists (fun c -> c.AsData.SelectorFormat.IsSome) + + [ + [header.[0]; for i = 0 to column.Cells.Length - 1 do cells.[i].[0]] + if hasFormat then + [header.[1]; for i = 0 to column.Cells.Length - 1 do cells.[i].[1]] + if hasSelectorFormat then + [header.[2]; for i = 0 to column.Cells.Length - 1 do cells.[i].[2]] + ] + else + [ + [header.[0]; for i = 0 to column.Cells.Length - 1 do cells.[i].[0]] + ] \ No newline at end of file diff --git a/src/Spreadsheet/DataMapTable/DataMapHeader.fs b/src/Spreadsheet/DataMapTable/DataMapHeader.fs new file mode 100644 index 00000000..013f60f2 --- /dev/null +++ b/src/Spreadsheet/DataMapTable/DataMapHeader.fs @@ -0,0 +1,122 @@ +module ARCtrl.Spreadsheet.DataMapHeader + +open ARCtrl +open ARCtrl.Helper +open FsSpreadsheet + +module ActivePattern = + + open Regex.ActivePatterns + + let (|Term|_|) (categoryString : string) (categoryHeader : CompositeHeader) (cells : FsCell list) : (CompositeHeader*(FsCell list -> CompositeCell)) option = + let (|AC|_|) s = + if s = categoryString then Some categoryHeader else None + let (|TSRColumnHeaderRaw|_|) (s : string) = + if s.StartsWith("Term Source REF") then Some s else None + let (|TANColumnHeaderRaw|_|) (s : string) = + if s.StartsWith("Term Accession Number") then Some s else None + let cellValues = cells |> List.map (fun c -> c.ValueAsString()) + match cellValues with + | [AC header] -> + (header, CompositeCell.termFromFsCells None None) + |> Some + | [AC header; TSRColumnHeaderRaw _; TANColumnHeaderRaw _] -> + (header, CompositeCell.termFromFsCells (Some 1) (Some 2)) + |> Some + | [AC header; TANColumnHeaderRaw _; TSRColumnHeaderRaw _] -> + (header, CompositeCell.termFromFsCells (Some 2) (Some 1)) + |> Some + | _ -> None + + let (|Explication|_|) (cells : FsCell list) = + match cells with + | Term DataMapAux.explicationShortHand DataMapAux.explicationHeader r -> + Some r + | _ -> None + + let (|Unit|_|) (cells : FsCell list) = + match cells with + | Term DataMapAux.unitShortHand DataMapAux.unitHeader r -> + Some r + | _ -> None + + let (|ObjectType|_|) (cells : FsCell list) = + match cells with + | Term DataMapAux.objectTypeShortHand DataMapAux.objectTypeHeader r -> + Some r + | _ -> None + + let (|Description|_|) (cells : FsCell list) = + let cellValues = cells |> List.map (fun c -> c.ValueAsString()) + match cellValues with + | [DataMapAux.descriptionShortHand] -> Some(DataMapAux.descriptionHeader, CompositeCell.freeTextFromFsCells) + | _ -> None + + let (|GeneratedBy|_|) (cells : FsCell list) = + let cellValues = cells |> List.map (fun c -> c.ValueAsString()) + match cellValues with + | [DataMapAux.generatedByShortHand] -> Some(DataMapAux.generatedByHeader, CompositeCell.freeTextFromFsCells) + | _ -> None + + let (|Data|_|) (cells : FsCell list) = + let cellValues = cells |> List.map (fun c -> c.ValueAsString()) + match cellValues with + | DataMapAux.dataShortHand :: cols -> + + let format = cols |> List.tryFindIndex (fun s -> s.StartsWith("Data Format")) |> Option.map ((+) 1) + let selectorFormat = cols |> List.tryFindIndex (fun s -> s.StartsWith("Data Selector Format")) |> Option.map ((+) 1) + (CompositeHeader.Input (IOType.Data), CompositeCell.dataFromFsCells format selectorFormat) + |> Some + + | _ -> None + + let (|FreeText|_|) (cells : FsCell list) = + let cellValues = cells |> List.map (fun c -> c.ValueAsString()) + match cellValues with + | [text] -> + (CompositeHeader.FreeText text, CompositeCell.freeTextFromFsCells) + |> Some + | _ -> None + +open ActivePattern + +let fromFsCells (cells : list) : CompositeHeader*(FsCell list -> CompositeCell) = + match cells with + | Data d -> d + | Explication e -> e + | Unit u -> u + | ObjectType ot -> ot + | Description d -> d + | GeneratedBy gb -> gb + | FreeText ft -> ft + | _ -> failwithf "Could not parse header group %O" cells + +let toFsCells (header : CompositeHeader) : list = + match header with + | CompositeHeader.Input IOType.Data -> + [ + FsCell("Data") + FsCell("Data Format") + FsCell("Data Selector Format") + ] + | h when h = DataMapAux.explicationHeader -> + [ + FsCell(DataMapAux.explicationShortHand) + FsCell("Term Source REF") + FsCell("Term Accession Number") + ] + | h when h = DataMapAux.unitHeader -> + [ + FsCell(DataMapAux.unitShortHand) + FsCell("Term Source REF") + FsCell("Term Accession Number") + ] + | h when h = DataMapAux.objectTypeHeader -> + [ + FsCell(DataMapAux.objectTypeShortHand) + FsCell("Term Source REF") + FsCell("Term Accession Number") + ] + | CompositeHeader.FreeText text -> + [FsCell(text)] + | _ -> failwithf "Could not parse DataMap header %O." header diff --git a/src/Spreadsheet/DataMapTable/DataMapTable.fs b/src/Spreadsheet/DataMapTable/DataMapTable.fs new file mode 100644 index 00000000..b188e514 --- /dev/null +++ b/src/Spreadsheet/DataMapTable/DataMapTable.fs @@ -0,0 +1,94 @@ +module ARCtrl.Spreadsheet.DataMapTable + +open ARCtrl +open ArcTable +open FsSpreadsheet + +[] +let datamapTablePrefix = "datamapTable" + +let helperColumnStrings = + [ + "Term Source REF" + "Term Accession Number" + "Data Format" + "Data Selector Format" + ] + +let groupColumnsByHeader (columns : list) = + columns + |> Aux.List.groupWhen (fun c -> + let v = c.[1].ValueAsString() + helperColumnStrings + |> List.exists (fun s -> v.StartsWith s) + |> not + ) + +/// Returns the annotation table of the worksheet if it exists, else returns None +let tryDataMapTable (sheet : FsWorksheet) = + sheet.Tables + |> Seq.tryFind (fun t -> t.Name.StartsWith datamapTablePrefix) + +/// Groups and parses a collection of single columns into the according ISA composite columns +let composeColumns (columns : seq) : CompositeColumn [] = + columns + |> Seq.toList + |> groupColumnsByHeader + |> List.map DataMapColumn.fromFsColumns + |> List.toArray + + +/// Returns the protocol described by the headers and a function for parsing the values of the matrix to the processes of this protocol +let tryFromFsWorksheet (sheet : FsWorksheet) = + try + match tryDataMapTable sheet with + | Some (t: FsTable) -> + let compositeColumns = + t.GetColumns(sheet.CellCollection) + |> composeColumns + DataMap.init() + |> DataMap.addColumns(compositeColumns,skipFillMissing = true) + |> Some + | None -> + None + with + | err -> failwithf "Could not parse datamap table with name \"%s\":\n%s" sheet.Name err.Message + +let toFsWorksheet (table : DataMap) = + /// This dictionary is used to add spaces at the end of duplicate headers. + let stringCount = System.Collections.Generic.Dictionary() + let ws = FsWorksheet("isa_datamap") + + // Cancel if there are no columns + if table.Table.Columns.Length = 0 then ws + else + + let columns = + table.Table.Columns + |> List.ofArray + |> List.sortBy classifyColumnOrder + |> List.collect DataMapColumn.toFsColumns + let maxRow = columns.Head.Length + let maxCol = columns.Length + let fsTable = ws.Table("datamapTable",FsRangeAddress(FsAddress(1,1),FsAddress(maxRow,maxCol))) + columns + |> List.iteri (fun colI col -> + col + |> List.iteri (fun rowI cell -> + let value = + let v = cell.ValueAsString() + if rowI = 0 then + + match Dictionary.tryGet v stringCount with + | Some spaces -> + stringCount.[v] <- spaces + " " + v + " " + spaces + | None -> + stringCount.Add(cell.ValueAsString(),"") + v + else v + let address = FsAddress(rowI+1,colI+1) + fsTable.Cell(address, ws.CellCollection).SetValueAs value + ) + ) + ws \ No newline at end of file diff --git a/src/Spreadsheet/Metadata/Assays.fs b/src/Spreadsheet/Metadata/Assays.fs index f3c2efe3..5f0cf1bb 100644 --- a/src/Spreadsheet/Metadata/Assays.fs +++ b/src/Spreadsheet/Metadata/Assays.fs @@ -35,6 +35,7 @@ module Assays = (Option.fromValueWithDefault (OntologyAnnotation()) technologyType) (technologyPlatform |> Option.map JsonTypes.decomposeTechnologyPlatform) (ResizeArray()) + None (ResizeArray()) (comments) diff --git a/src/Spreadsheet/Metadata/Study.fs b/src/Spreadsheet/Metadata/Study.fs index 23c51e1e..19e546f5 100644 --- a/src/Spreadsheet/Metadata/Study.fs +++ b/src/Spreadsheet/Metadata/Study.fs @@ -121,6 +121,7 @@ module Studies = (ResizeArray contacts) (ResizeArray designDescriptors) (ResizeArray()) + None (ResizeArray(assayIdentifiers)) (ResizeArray studyInfo.Comments) |> fun arcstudy -> diff --git a/tests/ARCtrl/ARCtrl.Contracts.Tests.fs b/tests/ARCtrl/ARCtrl.Contracts.Tests.fs index 36f96f6d..71b63cbe 100644 --- a/tests/ARCtrl/ARCtrl.Contracts.Tests.fs +++ b/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" [ diff --git a/tests/ARCtrl/ARCtrl.Tests.fs b/tests/ARCtrl/ARCtrl.Tests.fs index 95237d31..9c4afe55 100644 --- a/tests/ARCtrl/ARCtrl.Tests.fs +++ b/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" @@ -70,7 +70,9 @@ 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] @@ -78,7 +80,7 @@ let private tests_read_contracts = testList "read_contracts" [ 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 @@ -427,9 +497,9 @@ let private ``payload_file_filters`` = let assay = ArcAssay("registered_assay") let assayTable = assay.InitTable("MyAssayTable") - assayTable.AppendColumn(CompositeHeader.Input (IOType.RawDataFile), [|CompositeCell.createFreeText "registered_assay_input.txt"|]) + assayTable.AppendColumn(CompositeHeader.Input (IOType.Data), [|CompositeCell.createFreeText "registered_assay_input.txt"|]) assayTable.AppendColumn(CompositeHeader.ProtocolREF, [|CompositeCell.createFreeText "assay_protocol.rtf"|]) - assayTable.AppendColumn(CompositeHeader.Output (IOType.DerivedDataFile), [|CompositeCell.createFreeText "registered_assay_output.txt"|]) + assayTable.AppendColumn(CompositeHeader.Output (IOType.Data), [|CompositeCell.createFreeText "registered_assay_output.txt"|]) let study = ArcStudy("registered_study") inv.AddRegisteredStudy(study) @@ -437,7 +507,7 @@ let private ``payload_file_filters`` = studyTable.AppendColumn(CompositeHeader.Input (IOType.Sample), [|CompositeCell.createFreeText "some_study_input_material"|]) studyTable.AppendColumn(CompositeHeader.FreeText "Some File", [|CompositeCell.createFreeText "xd/some_file_that_lies_in_slashxd.txt"|]) studyTable.AppendColumn(CompositeHeader.ProtocolREF, [|CompositeCell.createFreeText "study_protocol.pdf"|]) - studyTable.AppendColumn(CompositeHeader.Output (IOType.RawDataFile), [|CompositeCell.createFreeText "registered_study_output.txt"|]) + studyTable.AppendColumn(CompositeHeader.Output (IOType.Data), [|CompositeCell.createFreeText "registered_study_output.txt"|]) study.AddRegisteredAssay(assay) diff --git a/tests/ARCtrl/ARCtrl.Tests.fsproj b/tests/ARCtrl/ARCtrl.Tests.fsproj index d3737d30..f03693c4 100644 --- a/tests/ARCtrl/ARCtrl.Tests.fsproj +++ b/tests/ARCtrl/ARCtrl.Tests.fsproj @@ -18,6 +18,6 @@ - + \ No newline at end of file diff --git a/tests/Core/ARCtrl.Core.Tests.fsproj b/tests/Core/ARCtrl.Core.Tests.fsproj index 5eab9fe3..9a9eca43 100644 --- a/tests/Core/ARCtrl.Core.Tests.fsproj +++ b/tests/Core/ARCtrl.Core.Tests.fsproj @@ -9,6 +9,7 @@ + @@ -25,10 +26,6 @@ - - - - diff --git a/tests/Core/ArcAssay.Tests.fs b/tests/Core/ArcAssay.Tests.fs index 3a70045e..47ddb06f 100644 --- a/tests/Core/ArcAssay.Tests.fs +++ b/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 _ -> diff --git a/tests/Core/ArcInvestigation.Tests.fs b/tests/Core/ArcInvestigation.Tests.fs index 10bdb096..b8521763 100644 --- a/tests/Core/ArcInvestigation.Tests.fs +++ b/tests/Core/ArcInvestigation.Tests.fs @@ -627,7 +627,7 @@ let tests_UpdateIOTypeByEntityIDTypes = testList "UpdateIOTypeByEntityIDType" [ CompositeColumn.create (CompositeHeader.Output IOType.Sample, Array.init 3 (fun i -> CompositeCell.createFreeText (sprintf "Sample %i" i))) |] t2.AddColumns [| - CompositeColumn.create (CompositeHeader.Input IOType.DerivedDataFile, Array.init 3 (fun i -> CompositeCell.createFreeText (sprintf "Sample %i" i))) + CompositeColumn.create (CompositeHeader.Input IOType.Data, Array.init 3 (fun i -> CompositeCell.createFreeText (sprintf "Sample %i" i))) CompositeColumn.create (CompositeHeader.Output IOType.Sample, Array.init 3 (fun i -> CompositeCell.createFreeText (sprintf "Sample_Alt %i" i))) |] Expect.throws (fun () -> i.UpdateIOTypeByEntityID()) "Update should fail as sample and data can not be updated against each other." @@ -680,7 +680,7 @@ let tests_UpdateIOTypeByEntityIDTypes = testList "UpdateIOTypeByEntityIDType" [ CompositeColumn.create (CompositeHeader.Output IOType.Sample, Array.init 3 (fun i -> CompositeCell.createFreeText (sprintf "Sample %i" i))) |] t2.AddColumns [| - CompositeColumn.create (CompositeHeader.Input IOType.DerivedDataFile, Array.init 3 (fun i -> CompositeCell.createFreeText (sprintf "Sample %i" i))) + CompositeColumn.create (CompositeHeader.Input IOType.Data, Array.init 3 (fun i -> CompositeCell.createFreeText (sprintf "Sample %i" i))) CompositeColumn.create (CompositeHeader.Output IOType.Sample, Array.init 3 (fun i -> CompositeCell.createFreeText (sprintf "Sample_Alt %i" i))) |] Expect.throws (fun () -> i.UpdateIOTypeByEntityID()) "Update should fail as sample and data can not be updated against each other." diff --git a/tests/Core/ArcJsonConversion.Tests.fs b/tests/Core/ArcJsonConversion.Tests.fs index dced8450..4a731a36 100644 --- a/tests/Core/ArcJsonConversion.Tests.fs +++ b/tests/Core/ArcJsonConversion.Tests.fs @@ -60,9 +60,9 @@ module Helper = let singleRowDataInputWithCharacteristic = let columns = [| - CompositeColumn.create(CompositeHeader.Input IOType.RawDataFile, createCells_FreeText "RData" 1) + CompositeColumn.create(CompositeHeader.Input IOType.Data, createCells_FreeText "RData" 1) CompositeColumn.create(CompositeHeader.Characteristic oa_species, createCells_chlamy 1) - CompositeColumn.create(CompositeHeader.Output IOType.DerivedDataFile, createCells_FreeText "DData" 1) + CompositeColumn.create(CompositeHeader.Output IOType.Data, createCells_FreeText "DData" 1) |] let t = ArcTable.init(tableName1) t.AddColumns(columns) @@ -71,9 +71,9 @@ module Helper = let singleRowDataOutputWithFactor = let columns = [| - CompositeColumn.create(CompositeHeader.Input IOType.RawDataFile, createCells_FreeText "RData" 1) + CompositeColumn.create(CompositeHeader.Input IOType.Data, createCells_FreeText "RData" 1) CompositeColumn.create(CompositeHeader.Factor oa_temperature, createCells_DegreeCelsius 1) - CompositeColumn.create(CompositeHeader.Output IOType.DerivedDataFile, createCells_FreeText "DData" 1) + CompositeColumn.create(CompositeHeader.Output IOType.Data, createCells_FreeText "DData" 1) |] let t = ArcTable.init(tableName1) t.AddColumns(columns) diff --git a/tests/Core/ArcStudy.Tests.fs b/tests/Core/ArcStudy.Tests.fs index ebd55a51..cb97399e 100644 --- a/tests/Core/ArcStudy.Tests.fs +++ b/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 _ -> diff --git a/tests/Core/ArcTable.Tests.fs b/tests/Core/ArcTable.Tests.fs index 012ec438..0da8c4a2 100644 --- a/tests/Core/ArcTable.Tests.fs +++ b/tests/Core/ArcTable.Tests.fs @@ -87,7 +87,7 @@ let private tests_GetHashCode = testList "GetHashCode" [ Expect.equal hash1 hash2 "HashCode" testCase "equal, table-order does not matter" <| fun _ -> let column_inputHeader, column_inputValues = CompositeHeader.Input IOType.Source, [|for i in 0 .. 20 do yield (0,i), sprintf "Source_%i" i |> CompositeCell.createFreeText|] - let column_outputHeader, column_outputValues = CompositeHeader.Output IOType.RawDataFile, [|for i in 0 .. 20 do yield (1,i), sprintf "File_%i" i |> CompositeCell.createFreeText|] + let column_outputHeader, column_outputValues = CompositeHeader.Output IOType.Data, [|for i in 0 .. 20 do yield (1,i), sprintf "File_%i" i |> CompositeCell.createFreeText|] let createTable(reverse:bool) = let t = ArcTable.init("MyTable") let shuffled = if reverse then [|yield! column_outputValues; yield! column_inputValues|] else [|yield! column_inputValues; yield! column_outputValues|] @@ -142,7 +142,7 @@ let private tests_SanityChecks = testList "SanityChecks" [ CompositeHeader.Component (OntologyAnnotation()) CompositeHeader.ProtocolREF CompositeHeader.ProtocolType - CompositeHeader.Output IOType.DerivedDataFile + CompositeHeader.Output IOType.Data ] testCase "valid headers" (fun () -> let columns = headers_valid |> Seq.map (fun x -> CompositeColumn.create(x)) @@ -237,7 +237,7 @@ let private tests_ArcTableAux = CompositeHeader.Component (OntologyAnnotation()) CompositeHeader.ProtocolREF CompositeHeader.ProtocolType - CompositeHeader.Output IOType.DerivedDataFile + CompositeHeader.Output IOType.Data ] testCase "No duplicate, component" (fun () -> let header = CompositeHeader.Component (OntologyAnnotation()) @@ -329,12 +329,12 @@ let private tests_UpdateHeader = ) testCase "set unique at different index" (fun () -> let testTable = create_testTable() - let table() = testTable.UpdateHeader(2, CompositeHeader.Input IOType.DerivedDataFile) + let table() = testTable.UpdateHeader(2, CompositeHeader.Input IOType.Data) Expect.throws (table >> ignore) "" ) testCase "set unique at same index" (fun () -> let table = create_testTable() - let newHeader = CompositeHeader.Input IOType.DerivedDataFile + let newHeader = CompositeHeader.Input IOType.Data table.UpdateHeader(0, newHeader) Expect.equal table.RowCount 5 "RowCount" Expect.equal table.ColumnCount 5 "ColumnCount" @@ -518,7 +518,7 @@ let private tests_UpdateColumn = ) testCase "set unique duplicate, different index" (fun () -> let table = create_testTable() - let h = CompositeHeader.Input IOType.RawDataFile + let h = CompositeHeader.Input IOType.Data let cells = createCells_FreeText "NEWSOURCE" 5 let column = CompositeColumn.create(h, cells) let eval() = table.UpdateColumn(1, h, cells) @@ -526,7 +526,7 @@ let private tests_UpdateColumn = ) testCase "set unique duplicate, same index" (fun () -> let table = create_testTable() - let h = CompositeHeader.Input IOType.RawDataFile + let h = CompositeHeader.Input IOType.Data let cells = createCells_FreeText "NEWSOURCE" 5 table.UpdateColumn(0, h, cells) Expect.equal table.RowCount 5 "RowCount" @@ -1429,7 +1429,7 @@ let private tests_AddColumns = ) testCase "multiple columns, same rowCount, duplicate replace" (fun () -> let testTable = create_testTable() - let newInputCol = CompositeColumn.create(CompositeHeader.Input IOType.RawDataFile, createCells_FreeText "NEW" 5) + let newInputCol = CompositeColumn.create(CompositeHeader.Input IOType.Data, createCells_FreeText "NEW" 5) let columns = [| column_param newInputCol @@ -1455,7 +1455,7 @@ let private tests_AddColumns = ) testCase "multiple columns, same rowCount, duplicate replace, insert at" (fun () -> let testTable = create_testTable() - let newInputCol = CompositeColumn.create(CompositeHeader.Input IOType.RawDataFile, createCells_FreeText "NEW" 5) + let newInputCol = CompositeColumn.create(CompositeHeader.Input IOType.Data, createCells_FreeText "NEW" 5) let columns = [| column_param newInputCol @@ -1481,7 +1481,7 @@ let private tests_AddColumns = ) testCase "multiple columns, same rowCount, duplicate replace, insert at2" (fun () -> let testTable = create_testTable() - let newInputCol = CompositeColumn.create(CompositeHeader.Input IOType.RawDataFile, createCells_FreeText "NEW" 5) + let newInputCol = CompositeColumn.create(CompositeHeader.Input IOType.Data, createCells_FreeText "NEW" 5) let columns = [| column_param newInputCol @@ -1563,7 +1563,7 @@ let private tests_AddColumns = ) testCase "multiple columns, more rowCount, duplicate replace" (fun () -> let testTable = create_testTable() - let newInput = CompositeColumn.create(CompositeHeader.Input IOType.RawDataFile, createCells_FreeText "NEW" 8) + let newInput = CompositeColumn.create(CompositeHeader.Input IOType.Data, createCells_FreeText "NEW" 8) let newColumn = CompositeColumn.create(CompositeHeader.Characteristic oa_species, createCells_Term 8) let columns = [| newColumn @@ -1592,7 +1592,7 @@ let private tests_AddColumns = ) testCase "multiple columns, different rowCount, duplicate replace" (fun () -> let testTable = create_testTable() - let newInput = CompositeColumn.create(CompositeHeader.Input IOType.RawDataFile, createCells_FreeText "NEW" 2) + let newInput = CompositeColumn.create(CompositeHeader.Input IOType.Data, createCells_FreeText "NEW" 2) let newColumn = CompositeColumn.create(CompositeHeader.Characteristic oa_species, createCells_Term 8) let columns = [| newColumn @@ -2152,13 +2152,13 @@ let private tests_Join = testList "Join" [ let table = create_testTable() let joinTable = ArcTable.create( "jointable", - ResizeArray([CompositeHeader.Input IOType.ImageFile]), + ResizeArray([CompositeHeader.Input IOType.Data]), System.Collections.Generic.Dictionary() ) table.Join(joinTable,-1,TableJoinOptions.Headers,true) Expect.equal table.ColumnCount 5 "columnCount" // test headers - Expect.equal table.Headers.[0] (CompositeHeader.Input IOType.ImageFile) "Here should be new image input" + Expect.equal table.Headers.[0] (CompositeHeader.Input IOType.Data) "Here should be new image input" Expect.equal table.Headers.[1] (CompositeHeader.Output IOType.Sample) "Header output" Expect.equal table.Headers.[2] (CompositeHeader.Parameter (OntologyAnnotation())) "Header parameter [empty]" Expect.equal table.Headers.[3] (CompositeHeader.Component oa_instrumentModel) "Header component [instrument model]" @@ -2221,7 +2221,7 @@ let private tests_Join = testList "Join" [ let private tests_IterColumns = testList "IterColumns" [ testCase "Replace input column header" <| fun _ -> let table = create_testTable() - let expected = CompositeHeader.Input IOType.RawDataFile + let expected = CompositeHeader.Input IOType.Data table.IteriColumns (fun i c -> if c.Header.isInput then table.UpdateHeader(i,expected) diff --git a/tests/Core/CompositeCell.Tests.fs b/tests/Core/CompositeCell.Tests.fs index 9dd48808..740c26e2 100644 --- a/tests/Core/CompositeCell.Tests.fs +++ b/tests/Core/CompositeCell.Tests.fs @@ -107,7 +107,18 @@ let private tests_create = let expected = CompositeCell.Unitized("42", oa) Expect.equal newCell expected "" ) - ] + testCase "createData" (fun () -> + let d = Data(name = "MyData#row=1", format = "text/csv", selectorFormat = "MySelector") + let newCell : CompositeCell = CompositeCell.createData(d) + let expected = CompositeCell.Data d + Expect.equal newCell expected "" + ) + testCase "createDataFromString" (fun () -> + let newCell : CompositeCell = CompositeCell.createDataFromString("MyData#row=1", "text/csv", "MySelector") + let expected = CompositeCell.Data <| Data(name = "MyData#row=1", format = "text/csv", selectorFormat = "MySelector") + Expect.equal newCell expected "" + ) + ] let private tests_ToString = testList "ToString" [ testCase "FreeText" <| fun _ -> @@ -125,6 +136,12 @@ let private tests_ToString = testList "ToString" [ let actual = cc.ToString() let expected = "20 degree celcius" Expect.equal actual expected "" + testCase "Data" <| fun _ -> + let d = Data(name = "MyData#row=1", format = "text/csv", selectorFormat = "MySelector") + let cc = CompositeCell.createData d + let actual = cc.ToString() + let expected = "MyData#row=1" + Expect.equal actual expected "" ] let private tests_GetContent = testList "GetContent" [ @@ -140,6 +157,11 @@ let private tests_GetContent = testList "GetContent" [ let cell = CompositeCell.createUnitized ("12", OntologyAnnotation("My Unit Name")) let actual = cell.GetContent() Expect.equal actual [|"12"; "My Unit Name"; ""; ""|] "" + testCase "Data" <| fun _ -> + let d = Data(name = "MyData#row=1", format = "text/csv", selectorFormat = "MySelector") + let cell = CompositeCell.createData d + let actual = cell.GetContent() + Expect.equal actual [|"MyData#row=1"; "text/csv"; "MySelector"|] "" testCase "Matching" <| fun _ -> let matchContent (content: string []) = match content with @@ -189,6 +211,11 @@ let private tests_GetHashCode = testList "GetHashCode" [ let cc = CompositeCell.createFreeText("TestTerm") cc.GetHashCode() |> ignore Expect.isTrue true " " + testCase "Data" <| fun _ -> + let d = Data(name = "MyData#row=1", format = "text/csv", selectorFormat = "MySelector") + let cc = CompositeCell.createData d + cc.GetHashCode() |> ignore + Expect.isTrue true " " ] ] diff --git a/tests/Core/CompositeColumn.Tests.fs b/tests/Core/CompositeColumn.Tests.fs index 195ae1aa..3823dd52 100644 --- a/tests/Core/CompositeColumn.Tests.fs +++ b/tests/Core/CompositeColumn.Tests.fs @@ -53,7 +53,7 @@ let private tests_Validate = Expect.throws eval "" ) testCase "Invalid io column with term cells" (fun () -> - let header : CompositeHeader = CompositeHeader.Input IOType.ImageFile + let header : CompositeHeader = CompositeHeader.Input IOType.Data let cells : CompositeCell [] = Array.init 2 (fun _ -> CompositeCell.emptyTerm) let column = CompositeColumn.create(header, cells).Validate() let eval() = CompositeColumn.create(header, cells).Validate(true) |> ignore @@ -61,7 +61,7 @@ let private tests_Validate = Expect.throws eval "" ) testCase "Invalid io column with unit cells" (fun () -> - let header : CompositeHeader = CompositeHeader.Input IOType.ImageFile + let header : CompositeHeader = CompositeHeader.Input IOType.Data let cells : CompositeCell [] = Array.init 2 (fun _ -> CompositeCell.emptyUnitized) let column = CompositeColumn.create(header, cells).Validate() let eval() = CompositeColumn.create(header, cells).Validate(true) |> ignore diff --git a/tests/Core/CompositeHeader.Tests.fs b/tests/Core/CompositeHeader.Tests.fs index 422f184e..25437a5b 100644 --- a/tests/Core/CompositeHeader.Tests.fs +++ b/tests/Core/CompositeHeader.Tests.fs @@ -10,18 +10,14 @@ let private tests_iotype = testCase "asInput" (fun () -> Expect.equal IOType.Source.asInput "Input [Source Name]" "Source" Expect.equal IOType.Sample.asInput "Input [Sample Name]" "Sample" - Expect.equal IOType.RawDataFile.asInput "Input [Raw Data File]" "Raw Data File" - Expect.equal IOType.DerivedDataFile.asInput "Input [Derived Data File]" "Derived Data File" - Expect.equal IOType.ImageFile.asInput "Input [Image File]" "Image File" + Expect.equal IOType.Data.asInput "Input [Data]" "Data" Expect.equal IOType.Material.asInput "Input [Material]" "Material" Expect.equal (IOType.FreeText "Test").asInput "Input [Test]" "FreeText Test" ) testCase "asOutput" (fun () -> Expect.equal IOType.Source.asOutput "Output [Source Name]" "Source" Expect.equal IOType.Sample.asOutput "Output [Sample Name]" "Sample" - Expect.equal IOType.RawDataFile.asOutput "Output [Raw Data File]" "Raw Data File" - Expect.equal IOType.DerivedDataFile.asOutput "Output [Derived Data File]" "Derived Data File" - Expect.equal IOType.ImageFile.asOutput "Output [Image File]" "Image File" + Expect.equal IOType.Data.asOutput "Output [Data]" "Data" Expect.equal IOType.Material.asOutput "Output [Material]" "Material" Expect.equal (IOType.FreeText "Test").asOutput "Output [Test]" "FreeText Test" ) @@ -30,7 +26,7 @@ let private tests_iotype = let caseInfos = IOType.Cases Expect.hasLength IOType.All (caseInfos.Length-1) "Expect one less than all because we do not want to track `FreeText` case." ) - testCase "getUIToolTip" <| fun _ -> + ptestCase "getUIToolTip" <| fun _ -> let cases = IOType.Cases |> Array.map snd for case in cases do let actual = IOType.getUITooltip(U2.Case2 case) @@ -102,10 +98,10 @@ let private tests_compositeHeader = let expected = "Input [Source Name]" Expect.equal actual expected "" ) - testCase "Output ImageFile" (fun () -> - let header = CompositeHeader.Input IOType.ImageFile + testCase "Output Data" (fun () -> + let header = CompositeHeader.Output IOType.Data let actual = header.ToString() - let expected = "Input [Image File]" + let expected = "Output [Data]" Expect.equal actual expected "" ) ] @@ -375,7 +371,7 @@ let tests_GetHashCode = testList "GetHashCode" [ ) testCase "InputDifferentType" (fun () -> let i1 = CompositeHeader.Input(IOType.Sample) - let i2 = CompositeHeader.Input(IOType.RawDataFile) + let i2 = CompositeHeader.Input(IOType.Data) let h1 = i1.GetHashCode() let h2 = i2.GetHashCode() Expect.notEqual h1 h2 "Input Sample Header should be unequal to Input Data" diff --git a/tests/Core/Data.Tests.fs b/tests/Core/Data.Tests.fs new file mode 100644 index 00000000..4da482f6 --- /dev/null +++ b/tests/Core/Data.Tests.fs @@ -0,0 +1,28 @@ +module Data.Tests + +open ARCtrl + +open TestingUtils + +let private tests_GetHashCode = testList "GetHashCode" [ + testCase "equal" <| fun _ -> + let d1 = Data("MyID","MyName",DataFile.RawDataFile,"text/csv","MySelector",ResizeArray [Comment.create("MyKey","MyValue")]) + let d2 = Data("MyID","MyName",DataFile.RawDataFile,"text/csv","MySelector",ResizeArray [Comment.create("MyKey","MyValue")]) + let hash1 = d1.GetHashCode() + let hash2 = d2.GetHashCode() + Expect.equal d1 d2 "Should be equal" + Expect.equal hash1 hash2 "HashCode should be equal" + testCase "unequal, different name" <| fun _ -> + let d1 = Data("MyID","MyName",DataFile.RawDataFile,"text/csv","MySelector",ResizeArray [Comment.create("MyKey","MyValue")]) + let d2 = Data("MyID","MyName2",DataFile.RawDataFile,"text/csv","MySelector",ResizeArray [Comment.create("MyKey","MyValue")]) + let hash1 = d1.GetHashCode() + let hash2 = d2.GetHashCode() + Expect.notEqual d1 d2 "Should not be equal" + Expect.notEqual hash1 hash2 "HashCode should not be equal" + ] + + +let main = + testList "Data" [ + tests_GetHashCode + ] \ No newline at end of file diff --git a/tests/Core/Main.fs b/tests/Core/Main.fs index 56851605..ddc81d2c 100644 --- a/tests/Core/Main.fs +++ b/tests/Core/Main.fs @@ -8,6 +8,7 @@ let all = testSequenced <| testList "Core" [ Regex.Tests.main Person.Tests.main CompositeHeader.Tests.main + Data.Tests.main CompositeCell.Tests.main CompositeColumn.Tests.main ArcTables.Tests.main diff --git a/tests/Core/Template.Tests.fs b/tests/Core/Template.Tests.fs index 4a5102eb..e59f449a 100644 --- a/tests/Core/Template.Tests.fs +++ b/tests/Core/Template.Tests.fs @@ -11,7 +11,7 @@ open TestingUtils let create_TestTemplate() = let table = ArcTable.init("My Table") table.AddColumn(CompositeHeader.Input IOType.Source, [|for i in 0 .. 9 do yield CompositeCell.createFreeText($"Source {i}")|]) - table.AddColumn(CompositeHeader.Output IOType.RawDataFile, [|for i in 0 .. 9 do yield CompositeCell.createFreeText($"Output {i}")|]) + table.AddColumn(CompositeHeader.Output IOType.Data, [|for i in 0 .. 9 do yield CompositeCell.createFreeText($"Output {i}")|]) let guid = System.Guid(String.init 32 (fun _ -> "d")) Template.make guid diff --git a/tests/JavaScript/CompositeHeader.js b/tests/JavaScript/CompositeHeader.js index 956771ee..ce530680 100644 --- a/tests/JavaScript/CompositeHeader.js +++ b/tests/JavaScript/CompositeHeader.js @@ -8,7 +8,7 @@ function tests_IOType() { it('cases', function () { let cases = IOType.Cases //console.log(cases) - equal(cases.length, 7); + equal(cases.length, 5); }); it('Create non Freetext', function () { for (let mycase of IOType.Cases) { @@ -22,25 +22,19 @@ function tests_IOType() { equal(iotype.asInput, "Input [Sample Name]"); break; case 2: - equal(iotype.asInput, "Input [Raw Data File]"); + equal(iotype.asInput, "Input [Data]"); break; case 3: - equal(iotype.asInput, "Input [Derived Data File]"); - break; - case 4: - equal(iotype.asInput, "Input [Image File]"); - break; - case 5: equal(iotype.asInput, "Input [Material]"); break; - case 6: + case 4: equal(iotype.asInput, "Input [undefined]"); break; } } }); it('Create FreeText', function () { - let freetext = new IOType(6, ["My FreeTextValue"]) + let freetext = new IOType(4, ["My FreeTextValue"]) let asinput = freetext.asInput equal(asinput, "Input [My FreeTextValue]") }); @@ -53,26 +47,17 @@ function tests_IOType() { let sa2 = new IOType(1, []) assertEqual(sa1, sa2); - let ra1 = IOType.rawDataFile() + let ra1 = IOType.data() let ra2 = new IOType(2, []) assertEqual(ra1, ra2); - let da1 = IOType.derivedDataFile() - let da2 = new IOType(3, []) - assertEqual(da1, da2); - - let im1 = IOType.imageFile() - let im2 = new IOType(4, []) - //let imb = equals(im1, im2); - assertEqual(im1, im2); - let ma1 = IOType.material() - let ma2 = new IOType(5, []) + let ma2 = new IOType(3, []) assertEqual(ma1, ma2); let ft = "My FreeTextValue" let ft1 = IOType.freeText(ft) - let ft2 = new IOType(6, [ft]) + let ft2 = new IOType(4, [ft]) assertEqual(ft1, ft2); }); @@ -82,7 +67,7 @@ function tests_IOType() { describe('CompositeHeader', function () { tests_IOType(); it("Input", function () { - let iotype = new IOType(6, ["My FreeTextValue"]) + let iotype = new IOType(4, ["My FreeTextValue"]) let header = new CompositeHeader(11, [iotype]) let actual = header.toString() equal(actual, "Input [My FreeTextValue]") diff --git a/tests/Json/ARCtrl.Json.Tests.fsproj b/tests/Json/ARCtrl.Json.Tests.fsproj index d0ac62b9..9835cf5f 100644 --- a/tests/Json/ARCtrl.Json.Tests.fsproj +++ b/tests/Json/ARCtrl.Json.Tests.fsproj @@ -17,6 +17,7 @@ + diff --git a/tests/Json/ArcTable.Tests.fs b/tests/Json/ArcTable.Tests.fs index e83a4d61..a7486342 100644 --- a/tests/Json/ArcTable.Tests.fs +++ b/tests/Json/ArcTable.Tests.fs @@ -91,10 +91,24 @@ let private tests = testList "extended" [ ] ] +let private tests_dataColumns = + testList "dataColumns" [ + testCase "dataColumns" <| fun _ -> + let testTable = ArcTable.init("Test") + testTable.AddColumn (CompositeHeader.Input IOType.Data, [|CompositeCell.Data (Data(name="MyInputDataFile.csv"))|]) + testTable.AddColumn (CompositeHeader.Output IOType.Data, [|CompositeCell.Data (Data(name="MyData.csv#row=1",format="text/csv",selectorFormat = "MySelector"))|]) + + let encoded = testTable.ToJsonString() + let decoded = ArcTable.fromJsonString encoded + Expect.arcTableEqual decoded testTable "decompressed table should be equal to original table" + ] + + let main = testList "ArcTable" [ tests tests_core tests_coreEmpty tests_compressedEmpty tests_compressedFilled + tests_dataColumns ] \ No newline at end of file diff --git a/tests/Json/Assay.Tests.fs b/tests/Json/Assay.Tests.fs index 47dcc2ce..d4fbff9c 100644 --- a/tests/Json/Assay.Tests.fs +++ b/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 = @@ -65,7 +65,7 @@ let private test_roCrateEmpty = createBaseJsonTests "ROCrate-empty" create_empty - (fun () -> ArcAssay.toROCrateJsonString None) + (fun () -> ArcAssay.toROCrateJsonString()) ArcAssay.fromROCrateJsonString None compare @@ -111,12 +111,12 @@ let private test_roCrate = testList "ROCrate" [ // Mainly: #12, #9, #10, #13 ptestCase "Write" <| fun _ -> let a = create_filled() - let json = ArcAssay.toROCrateJsonString None a + let json = ArcAssay.toROCrateJsonString() a printfn "%s" json createBaseJsonTests "" create_filled - (fun () -> ArcAssay.toROCrateJsonString None) + (fun () -> ArcAssay.toROCrateJsonString()) ArcAssay.fromROCrateJsonString None compare diff --git a/tests/Json/CompositeCell.Tests.fs b/tests/Json/CompositeCell.Tests.fs index 63222dcf..464631bb 100644 --- a/tests/Json/CompositeCell.Tests.fs +++ b/tests/Json/CompositeCell.Tests.fs @@ -15,6 +15,9 @@ let tests_extended = testList "extended" [ let cell_term_empty_jsonString = sprintf """{"%s":"Term","values":[{}]}""" CompositeCell.CellType let cell_unitized_jsonString = sprintf """{"%s":"Unitized","values":["42",{"annotationValue":"My Name","termSource":"MY","termAccession":"MY:1"}]}""" CompositeCell.CellType let cell_unitized_empty_jsonString = sprintf """{"%s":"Unitized","values":["",{}]}""" CompositeCell.CellType + let cell_data_empty_jsonString = sprintf """{"%s":"Data","values":[{}]}""" CompositeCell.CellType + let cell_data_jsonString = sprintf """{"%s":"Data","values":[{"@id":"MyID","name":"MyName","dataType":"Raw Data File","format":"text/csv","selectorFormat":"MySelector","comments":[{"name":"MyKey","value":"MyValue"}]}]}""" CompositeCell.CellType + testList "encoder (toJsonString)" [ testCase "FreeText" <| fun _ -> let actual = CompositeCell.encoder cell_freetext |> Encode.toJsonString 0 @@ -36,6 +39,14 @@ let tests_extended = testList "extended" [ let actual = CompositeCell.encoder cell_unitized_empty |> Encode.toJsonString 0 let expected = cell_unitized_empty_jsonString Expect.equal actual expected "" + testCase "Data" <| fun _ -> + let actual = CompositeCell.encoder (CompositeCell.Data(Data("MyID","MyName",DataFile.RawDataFile,"text/csv","MySelector",ResizeArray [Comment.create("MyKey","MyValue")])) ) |> Encode.toJsonString 0 + let expected = cell_data_jsonString + Expect.equal actual expected "" + testCase "Data empty" <| fun _ -> + let actual = CompositeCell.encoder (CompositeCell.Data(Data())) |> Encode.toJsonString 0 + let expected = cell_data_empty_jsonString + Expect.equal actual expected "" ] testList "decoder (fromJsonString)" [ testCase "FreeText" <| fun _ -> @@ -58,6 +69,14 @@ let tests_extended = testList "extended" [ let actual = Decode.fromJsonString CompositeCell.decoder cell_unitized_empty_jsonString let expected = cell_unitized_empty Expect.equal actual expected "" + testCase "Data" <| fun _ -> + let actual = Decode.fromJsonString CompositeCell.decoder cell_data_jsonString + let expected = CompositeCell.Data(Data("MyID","MyName",DataFile.RawDataFile,"text/csv","MySelector",ResizeArray [Comment.create("MyKey","MyValue")])) + Expect.equal actual expected "" + testCase "Data empty" <| fun _ -> + let actual = Decode.fromJsonString CompositeCell.decoder cell_data_empty_jsonString + let expected = CompositeCell.Data(Data()) + Expect.equal actual expected "" ] ] diff --git a/tests/Json/Data.Tests.fs b/tests/Json/Data.Tests.fs new file mode 100644 index 00000000..78d5ece0 --- /dev/null +++ b/tests/Json/Data.Tests.fs @@ -0,0 +1,59 @@ +module Tests.Data + +open TestingUtils +open ARCtrl +open ARCtrl.Json + +let basic_tests = testList "BasicJson" [ + testCase "AllFields" <| fun _ -> + let d = Data("MyID","MyName",DataFile.RawDataFile,"text/csv","MySelector",ResizeArray [Comment.create("MyKey","MyValue")]) + let json = Data.encoder d |> Encode.toJsonString 2 + let d2 = Decode.fromJsonString Data.decoder json + Expect.equal d2 d "Different after write and read" + ] + +let isa_tests = testList "ISAJson" [ + testCase "NativeISAFieldsIO" <| fun _ -> + let d = Data("MyID","MyName",DataFile.RawDataFile,comments = ResizeArray [Comment.create("MyKey","MyValue")]) + let json = Data.ISAJson.encoder d |> Encode.toJsonString 2 + let d2 = Decode.fromJsonString Data.ISAJson.decoder json + Expect.equal d2 d "Different after write and read" + ptestCase "AllFieldsLossless" <| fun _ -> + let d = Data("MyID","MyName",DataFile.RawDataFile,"text/csv","MySelector",ResizeArray [Comment.create("MyKey","MyValue")]) + let json = Data.ISAJson.encoder d |> Encode.toJsonString 2 + let d2 = Decode.fromJsonString Data.ISAJson.decoder json + Expect.equal d2 d "Different after write and read" + #if !FABLE_COMPILER_PYTHON + testAsync "WriterSchemaCorrectness" { + let d = Data("MyID","MyName",DataFile.RawDataFile, "text/csv", "MySelector", ResizeArray [Comment.create("MyKey","MyValue")]) + let json = Data.ISAJson.encoder d |> Encode.toJsonString 2 + let! validation = Validation.validateData json + Expect.isTrue validation.Success $"Data did not match schema: {validation.GetErrors()}" + } + #endif +] + +let rocrate_tests = testList "RO-CrateJson" [ + testCase "AllFields" <| fun _ -> + let d = Data("MyID","MyName",DataFile.RawDataFile,"text/csv","MySelector",ResizeArray [Comment.create("MyKey","MyValue")]) + let json = Data.ROCrate.encoder d |> Encode.toJsonString 2 + let d2 = Decode.fromJsonString Data.ROCrate.decoder json + Expect.equal d2 d "Different after write and read" + ] + +let compressed_tests = + testList "CompressedJson" [ + testCase "AllFields" <| fun _ -> + let d = Data("MyID","MyName",DataFile.RawDataFile,"text/csv","MySelector",ResizeArray [Comment.create("MyKey","MyValue")]) + let stringTable = StringTable.StringTableMap() + let json = Data.compressedEncoder stringTable d |> Encode.toJsonString 2 + let d2 = Decode.fromJsonString (Data.compressedDecoder (StringTable.arrayFromMap stringTable)) json + Expect.equal d2 d "Different after write and read" + ] + +let main = testList "Data" [ + basic_tests + isa_tests + rocrate_tests + compressed_tests +] \ No newline at end of file diff --git a/tests/Json/Main.fs b/tests/Json/Main.fs index 9b4043a1..ca032176 100644 --- a/tests/Json/Main.fs +++ b/tests/Json/Main.fs @@ -6,6 +6,7 @@ let all = testSequenced <| testList "Json" [ Tests.Decoder.main Tests.Comment.main Tests.OntologyAnnotation.main + Tests.Data.main Tests.CompositeCell.main Tests.IOType.main Tests.CompositeHeader.main diff --git a/tests/Json/Study.Tests.fs b/tests/Json/Study.Tests.fs index 2bbbf52d..e029bc10 100644 --- a/tests/Json/Study.Tests.fs +++ b/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 = diff --git a/tests/Json/Template.Tests.fs b/tests/Json/Template.Tests.fs index baf2bb4a..f5c00dd4 100644 --- a/tests/Json/Template.Tests.fs +++ b/tests/Json/Template.Tests.fs @@ -55,7 +55,7 @@ let tests_Template = testCase "complete" <| fun _ -> let table = ArcTable.init("My Table") table.AddColumn(CompositeHeader.Input IOType.Source, [|for i in 0 .. 9 do yield CompositeCell.createFreeText($"Source {i}")|]) - table.AddColumn(CompositeHeader.Output IOType.RawDataFile, [|for i in 0 .. 9 do yield CompositeCell.createFreeText($"Output {i}")|]) + table.AddColumn(CompositeHeader.Output IOType.Data, [|for i in 0 .. 9 do yield CompositeCell.createFreeText($"Output {i}")|]) let o = Template.init("MyTemplate") o.Table <- table o.Authors <- ResizeArray [|ARCtrl.Person.create(firstName="John", lastName="Doe"); ARCtrl.Person.create(firstName="Jane", lastName="Doe");|] diff --git a/tests/Spreadsheet/ARCtrl.Spreadsheet.Tests.fsproj b/tests/Spreadsheet/ARCtrl.Spreadsheet.Tests.fsproj index 339ff304..7cbc904b 100644 --- a/tests/Spreadsheet/ARCtrl.Spreadsheet.Tests.fsproj +++ b/tests/Spreadsheet/ARCtrl.Spreadsheet.Tests.fsproj @@ -13,6 +13,7 @@ + diff --git a/tests/Spreadsheet/ArcTableTests.fs b/tests/Spreadsheet/ArcTableTests.fs index 84bd2a80..915d3f12 100644 --- a/tests/Spreadsheet/ArcTableTests.fs +++ b/tests/Spreadsheet/ArcTableTests.fs @@ -236,7 +236,7 @@ let private ioTable = Parameter.appendTemperatureColumn 1 Characteristic.appendOrganismColumn 1 Factor.appendTimeColumn 1 - Output.appendRawDataColumn 1 + Output.appendSimpleDataColumn 1 ] testCase "Read" (fun () -> @@ -256,7 +256,7 @@ let private ioTable = Parameter.temperatureHeader Characteristic.organismHeader Factor.timeHeader - Output.rawDataHeader + Output.simpleDataHeader ] Expect.sequenceEqual table.Headers expectedHeaders "Headers did not match" let expectedCells = @@ -266,7 +266,7 @@ let private ioTable = Parameter.temperatureValue Characteristic.organismValue Factor.timeValue - Output.rawDataValue + Output.simpleDataValue ] Expect.sequenceEqual (table.GetRow(0)) expectedCells "Cells did not match" ) @@ -280,7 +280,54 @@ let private ioTable = ) ] +let private fullDataTable = + testList "fullDataTable" [ + let wsName = "MyWorksheet" + let ws = + initWorksheet wsName + [ + Input.appenddataColumn 1 + Protocol.REF.appendLolColumn 1 + Parameter.appendTemperatureColumn 1 + Output.appendFullDataColumn 1 + ] + testCase "Read" (fun () -> + + let table = ArcTable.tryFromFsWorksheet ws + + Expect.isSome table "Table was not created" + let table = table.Value + + Expect.equal table.Name wsName "Name did not match" + Expect.equal table.ColumnCount 4 "Wrong number of columns" + Expect.equal table.RowCount 1 "Wrong number of rows" + let expectedHeaders = + [ + Input.dataHeader + Protocol.REF.lolHeader + Parameter.temperatureHeader + Output.fullDataHeader + ] + Expect.sequenceEqual table.Headers expectedHeaders "Headers did not match" + let expectedCells = + [ + Input.dataValue + Protocol.REF.lolValue + Parameter.temperatureValue + Output.fullDataValue + ] + Expect.sequenceEqual (table.GetRow(0)) expectedCells "Cells did not match" + ) + testCase "Write" (fun () -> + + let table = ArcTable.tryFromFsWorksheet ws + Expect.isSome table "Table was not created" + let out = ArcTable.toFsWorksheet table.Value + Expect.workSheetEqual out ws "Worksheet was not correctly written" + + ) + ] let private deprecatedColumnTable = testList "deprecatedIOColumnTable" [ @@ -317,11 +364,11 @@ let private deprecatedColumnTable = let expectedCells = [ - Input.sampleValue + Input.sourceValue Protocol.REF.lolValue Protocol.Type.collectionValue Parameter.temperatureValue - Output.rawDataValue + Output.sampleValue ] Expect.sequenceEqual (table.GetRow(0)) expectedCells "Cells did not match" ) @@ -338,7 +385,7 @@ let private writeOrder = [ Parameter.appendTemperatureColumn 1 Characteristic.appendOrganismColumn 1 - Output.appendRawDataColumn 1 + Output.appendSimpleDataColumn 1 Protocol.REF.appendLolColumn 1 Input.appendSampleColumn 1 Factor.appendTimeColumn 1 @@ -355,7 +402,7 @@ let private writeOrder = Parameter.appendTemperatureColumn 1 Characteristic.appendOrganismColumn 1 Factor.appendTimeColumn 1 - Output.appendRawDataColumn 1 + Output.appendSimpleDataColumn 1 ] Expect.workSheetEqual mixedOut orderedWs "Columns were not ordered correctly" @@ -386,6 +433,7 @@ let main = mixedTable ioTable valuelessTable + fullDataTable deprecatedColumnTable writeOrder emptyTable diff --git a/tests/Spreadsheet/CompositeHeaderTests.fs b/tests/Spreadsheet/CompositeHeaderTests.fs index 21cc62ad..cb09be00 100644 --- a/tests/Spreadsheet/CompositeHeaderTests.fs +++ b/tests/Spreadsheet/CompositeHeaderTests.fs @@ -2,6 +2,28 @@ open TestingUtils +open ARCtrl +open ARCtrl.Spreadsheet +open FsSpreadsheet + +let deprecatedDataHeaders = + testList "DeprecatedIOHeaders" [ + testCase "Raw Data File" <| fun _ -> + let cells = FsCell.create 1 1 "Input [Raw Data File]" + let header,_ = CompositeHeader.fromFsCells [cells] + Expect.equal header (CompositeHeader.Input IOType.Data) "Should be Input [Data]" + testCase "Derived Data File" <| fun _ -> + let cells = FsCell.create 1 1 "Output [Derived Data File]" + let header,_ = CompositeHeader.fromFsCells [cells] + Expect.equal header (CompositeHeader.Output IOType.Data) "Should be Output [Data]" + testCase "Image File" <| fun _ -> + let cells = FsCell.create 1 1 "Output [Image File]" + let header,_ = CompositeHeader.fromFsCells [cells] + Expect.equal header (CompositeHeader.Output IOType.Data) "Should be Output [Image]" + ] + + let main = testList "CompositeHeader" [ + deprecatedDataHeaders ] \ No newline at end of file diff --git a/tests/Spreadsheet/DataMapTests.fs b/tests/Spreadsheet/DataMapTests.fs new file mode 100644 index 00000000..6d43065f --- /dev/null +++ b/tests/Spreadsheet/DataMapTests.fs @@ -0,0 +1,192 @@ +module DataMapTests + + +open ARCtrl +open ARCtrl.Spreadsheet +open FsSpreadsheet + +open TestingUtils +open TestObjects.Spreadsheet.DataMap + +let private simpleTable = + testList "simpleTable" [ + let wsName = "isa_datamap" + let ws = + initWorksheet wsName + [ + Data.appendDataColumn 1 + Explication.appendMeanColumn 1 + Unit.appendPPMColumn 1 + ObjectType.appendFloatColumn 1 + Description.appendDescriptionColumn 1 + GeneratedBy.appendGeneratedByColumn 1 + + ] + testCase "Read" (fun () -> + + let table = DataMapTable.tryFromFsWorksheet ws + + Expect.isSome table "Table was not created" + let table = table.Value + + Expect.equal table.Table.ColumnCount 6 "Wrong number of columns" + Expect.equal table.Table.RowCount 1 "Wrong number of rows" + + let expectedHeaders = + [ + DataMapAux.dataHeader + DataMapAux.explicationHeader + DataMapAux.unitHeader + DataMapAux.objectTypeHeader + DataMapAux.descriptionHeader + DataMapAux.generatedByHeader + ] + Expect.sequenceEqual table.Headers expectedHeaders "Headers did not match" + + let expectedCells = + [ + Data.dataValue + Explication.meanValue + Unit.ppmValue + ObjectType.floatValue + Description.descriptionValue + GeneratedBy.generatedByValue + ] + Expect.sequenceEqual (table.GetRow(0)) expectedCells "Cells did not match" + ) + testCase "Write" (fun () -> + + let table = DataMapTable.tryFromFsWorksheet ws + Expect.isSome table "Table was not created" + let out = DataMapTable.toFsWorksheet table.Value + Expect.workSheetEqual out ws "Worksheet was not correctly written" + + ) + ] + +let private valuelessTable = + testList "valuelessTable" [ + let wsName = "isa_datamap" + let ws = + initWorksheet wsName + [ + Data.appendDataColumn 0 + Explication.appendMeanColumn 0 + Unit.appendPPMColumn 0 + ObjectType.appendFloatColumn 0 + Description.appendDescriptionColumn 0 + GeneratedBy.appendGeneratedByColumn 0 + ] + testCase "Read" (fun () -> + + let table = DataMapTable.tryFromFsWorksheet ws + + Expect.isSome table "Table was not created" + let table = table.Value + + Expect.equal table.Table.ColumnCount 6 "Wrong number of columns" + Expect.equal table.Table.RowCount 0 "Wrong number of rows" + + let expectedHeaders = + [ + DataMapAux.dataHeader + DataMapAux.explicationHeader + DataMapAux.unitHeader + DataMapAux.objectTypeHeader + DataMapAux.descriptionHeader + DataMapAux.generatedByHeader + ] + Expect.sequenceEqual table.Headers expectedHeaders "Headers did not match" + ) + // TODO: What should we do with units of empty columns? + //testCase "Write" (fun () -> + + // let table = ArcTable.tryFromFsWorksheet ws + // Expect.isSome table "Table was not created" + // let out = ArcTable.toFsWorksheet table.Value + // Expect.workSheetEqual out ws "Worksheet was not correctly written" + + //) + ] + +let private emptyTable = + testList "emptyTable" [ + let t = DataMap.init() + testCase "Write" (fun () -> + let sheet = DataMapTable.toFsWorksheet t + Expect.equal "isa_datamap" sheet.Name "Worksheet name did not match" + Expect.equal 0 sheet.Rows.Count "Row count should be 0" + ) + testCase "Read" (fun () -> + let sheet = DataMapTable.toFsWorksheet t + Expect.isNone (DataMapTable.tryFromFsWorksheet sheet) "Table was not created" + ) + ] + +let private simpleFile = + testList "simpleFile" [ + let wb = new FsWorkbook() + let wsName = "isa_datamap" + let ws = + initWorksheet wsName + [ + Data.appendDataColumn 1 + Explication.appendMeanColumn 1 + Unit.appendPPMColumn 1 + ObjectType.appendFloatColumn 1 + Description.appendDescriptionColumn 1 + GeneratedBy.appendGeneratedByColumn 1 + + ] + wb.AddWorksheet ws + testCase "Read" (fun () -> + + let table = DataMap.fromFsWorkbook wb + + Expect.equal table.Table.ColumnCount 6 "Wrong number of columns" + Expect.equal table.Table.RowCount 1 "Wrong number of rows" + + let expectedHeaders = + [ + DataMapAux.dataHeader + DataMapAux.explicationHeader + DataMapAux.unitHeader + DataMapAux.objectTypeHeader + DataMapAux.descriptionHeader + DataMapAux.generatedByHeader + ] + Expect.sequenceEqual table.Headers expectedHeaders "Headers did not match" + + let expectedCells = + [ + Data.dataValue + Explication.meanValue + Unit.ppmValue + ObjectType.floatValue + Description.descriptionValue + GeneratedBy.generatedByValue + ] + Expect.sequenceEqual (table.GetRow(0)) expectedCells "Cells did not match" + ) + testCase "Write" (fun () -> + + let table = DataMap.fromFsWorkbook wb + + let out = DataMap.toFsWorkbook table + + Expect.equal (out.GetWorksheets().Count) 1 "Wrong number of worksheets" + + let wsOut = out.GetWorksheets().[0] + + Expect.workSheetEqual wsOut ws "Worksheet was not correctly written" + + ) + ] + +let main = + testList "DataMapTableTests" [ + simpleTable + valuelessTable + emptyTable + simpleFile + ] \ No newline at end of file diff --git a/tests/Spreadsheet/Main.fs b/tests/Spreadsheet/Main.fs index 400135c6..076a55d5 100644 --- a/tests/Spreadsheet/Main.fs +++ b/tests/Spreadsheet/Main.fs @@ -7,7 +7,9 @@ let all = testSequenced <| testList "ISA.Spreadsheet" [ RegexTests.main ArcInvestigationTests.main CompositeColumnTests.main + CompositeHeaderTests.main ArcTableTests.main + DataMapTests.main ArcAssayTests.main ArcStudyTests.main SparseTableTests.main diff --git a/tests/TestingUtils/TestObjects.Contract/ISA.fs b/tests/TestingUtils/TestObjects.Contract/ISA.fs index ab87e2c3..d6bc59b6 100644 --- a/tests/TestingUtils/TestObjects.Contract/ISA.fs +++ b/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" diff --git a/tests/TestingUtils/TestObjects.Spreadsheet/Spreadsheet.ArcTable.fs b/tests/TestingUtils/TestObjects.Spreadsheet/Spreadsheet.ArcTable.fs index d3c940be..e399c1d6 100644 --- a/tests/TestingUtils/TestObjects.Spreadsheet/Spreadsheet.ArcTable.fs +++ b/tests/TestingUtils/TestObjects.Spreadsheet/Spreadsheet.ArcTable.fs @@ -158,6 +158,18 @@ module Factor = t.Cell(FsAddress(i, colCount + 4),c).SetValueAs timeValueV4 module Input = + + let sourceValue = + CompositeCell.FreeText "MySource" + + let sourceValueV1 = "MySource" + + let dataHeader = + CompositeHeader.Input IOType.Data + + let dataValue = + CompositeCell.Data (Data.create(Name = "MyInputData", Format = "text/csv", SelectorFormat = "https://datatracker.ietf.org/doc/html/rfc7111")) + let sampleHeader = CompositeHeader.Input IOType.Sample @@ -174,6 +186,28 @@ module Input = for i = 2 to l + 1 do t.Cell(FsAddress(i, colCount + 1),c).SetValueAs sampleValueV1 + let dataHeaderV1 = "Input [Data]" + + let dataValueV1 = "MyInputData" + + let dataHeaderV2 = "Data Format" + + let dataValueV2 = "text/csv" + + let dataHeaderV3 = "Data Selector Format" + + let dataValueV3 = "https://datatracker.ietf.org/doc/html/rfc7111" + + let appenddataColumn l (c : FsCellsCollection) (t : FsTable) = + let colCount = if t.IsEmpty(c) then 0 else t.ColumnCount() + t.Cell(FsAddress(1, colCount + 1),c).SetValueAs dataHeaderV1 + t.Cell(FsAddress(1, colCount + 2),c).SetValueAs dataHeaderV2 + t.Cell(FsAddress(1, colCount + 3),c).SetValueAs dataHeaderV3 + for i = 2 to l + 1 do + t.Cell(FsAddress(i, colCount + 1),c).SetValueAs dataValueV1 + t.Cell(FsAddress(i, colCount + 2),c).SetValueAs dataValueV2 + t.Cell(FsAddress(i, colCount + 3),c).SetValueAs dataValueV3 + let deprecatedSourceHeader = CompositeHeader.Input IOType.Source let deprecatedSourceHeaderV1 = "Source Name" @@ -182,20 +216,61 @@ module Input = let colCount = if t.IsEmpty(c) then 0 else t.ColumnCount() t.Cell(FsAddress(1, colCount + 1),c).SetValueAs deprecatedSourceHeaderV1 for i = 2 to l + 1 do - t.Cell(FsAddress(i, colCount + 1),c).SetValueAs sampleValueV1 + t.Cell(FsAddress(i, colCount + 1),c).SetValueAs sourceValueV1 module Output = - let rawDataHeader = - CompositeHeader.Output IOType.RawDataFile + let simpleDataHeader = + CompositeHeader.Output IOType.Data + + let simpleDataValue = + CompositeCell.Data (Data.create (Name = "MyData")) + + let fullDataHeader = + CompositeHeader.Output IOType.Data + + let fullDataValue = + CompositeCell.Data (Data.create(Name = "MyData", Format = "text/csv", SelectorFormat = "https://datatracker.ietf.org/doc/html/rfc7111")) - let rawDataValue = - CompositeCell.FreeText "MyRawData" let rawDataHeaderV1 = "Output [Raw Data File]" let rawDataValueV1 = "MyRawData" + let dataHeaderV1 = "Output [Data]" + + let dataValueV1 = "MyData" + + let dataHeaderV2 = "Data Format" + + let dataValueV2 = "text/csv" + + let dataHeaderV3 = "Data Selector Format" + + let dataValueV3 = "https://datatracker.ietf.org/doc/html/rfc7111" + + + let sampleValue = + CompositeCell.FreeText "MySample" + + let sampleValueV1 = "MySample" + + let appendSimpleDataColumn l (c : FsCellsCollection) (t : FsTable) = + let colCount = if t.IsEmpty(c) then 0 else t.ColumnCount() + t.Cell(FsAddress(1, colCount + 1),c).SetValueAs dataHeaderV1 + for i = 2 to l + 1 do + t.Cell(FsAddress(i, colCount + 1),c).SetValueAs dataValueV1 + + let appendFullDataColumn l (c : FsCellsCollection) (t : FsTable) = + let colCount = if t.IsEmpty(c) then 0 else t.ColumnCount() + t.Cell(FsAddress(1, colCount + 1),c).SetValueAs dataHeaderV1 + t.Cell(FsAddress(1, colCount + 2),c).SetValueAs dataHeaderV2 + t.Cell(FsAddress(1, colCount + 3),c).SetValueAs dataHeaderV3 + for i = 2 to l + 1 do + t.Cell(FsAddress(i, colCount + 1),c).SetValueAs dataValueV1 + t.Cell(FsAddress(i, colCount + 2),c).SetValueAs dataValueV2 + t.Cell(FsAddress(i, colCount + 3),c).SetValueAs dataValueV3 + let appendRawDataColumn l (c : FsCellsCollection) (t : FsTable) = let colCount = if t.IsEmpty(c) then 0 else t.ColumnCount() t.Cell(FsAddress(1, colCount + 1),c).SetValueAs rawDataHeaderV1 @@ -210,7 +285,7 @@ module Output = let colCount = if t.IsEmpty(c) then 0 else t.ColumnCount() t.Cell(FsAddress(1, colCount + 1),c).SetValueAs deprecatedSampleHeaderV1 for i = 2 to l + 1 do - t.Cell(FsAddress(i, colCount + 1),c).SetValueAs rawDataValueV1 + t.Cell(FsAddress(i, colCount + 1),c).SetValueAs sampleValueV1 module Protocol = module REF = diff --git a/tests/TestingUtils/TestObjects.Spreadsheet/Spreadsheet.DataMap.fs b/tests/TestingUtils/TestObjects.Spreadsheet/Spreadsheet.DataMap.fs new file mode 100644 index 00000000..adc5777c --- /dev/null +++ b/tests/TestingUtils/TestObjects.Spreadsheet/Spreadsheet.DataMap.fs @@ -0,0 +1,165 @@ +module TestObjects.Spreadsheet.DataMap + +open ARCtrl +open FsSpreadsheet +open ARCtrl.Spreadsheet + +type FsTable with + member this.IsEmpty(c : FsCellsCollection) = + this.RangeAddress.Range = "A1:A1" + && + (this.Cell(FsAddress("A1"),c).Value = null) + || + (this.Cell(FsAddress("A1"),c).Value = "") + +module Data = + + let dataValue = + Data.create(Name = "MyDataFile.csv#col=1",Format = "text/csv", SelectorFormat = "https://datatracker.ietf.org/doc/html/rfc7111") + |> CompositeCell.Data + + let dataHeaderV1 = "Data" + let dataHeaderV2 = "Data Format" + let dataHeaderV3 = "Data Selector Format" + + let dataValueV1 = "MyDataFile.csv#col=1" + let dataValueV2 = "text/csv" + let dataValueV3 = "https://datatracker.ietf.org/doc/html/rfc7111" + + let appendDataColumn l (c : FsCellsCollection) (t : FsTable) = + let colCount = if t.IsEmpty(c) then 0 else t.ColumnCount() + t.Cell(FsAddress(1, colCount + 1),c).SetValueAs dataHeaderV1 + t.Cell(FsAddress(1, colCount + 2),c).SetValueAs dataHeaderV2 + t.Cell(FsAddress(1, colCount + 3),c).SetValueAs dataHeaderV3 + for i = 2 to l + 1 do + t.Cell(FsAddress(i, colCount + 1),c).SetValueAs dataValueV1 + t.Cell(FsAddress(i, colCount + 2),c).SetValueAs dataValueV2 + t.Cell(FsAddress(i, colCount + 3),c).SetValueAs dataValueV3 + +module Explication = + + let pValueValue = + OntologyAnnotation("p-value","NCIT","http://purl.obolibrary.org/obo/NCIT_C44185") + |> CompositeCell.Term + + let explicationHeaderV1 = "Explication" + let explicationHeaderV2 = "Term Source REF" + let explicationHeaderV3 = "Term Accession Number" + + let pValueValueV1 = "p-value" + let pValueValueV2 = "NCIT" + let pValueValueV3 = "http://purl.obolibrary.org/obo/NCIT_C44185" + + let appendPValueColumn l (c : FsCellsCollection) (t : FsTable) = + let colCount = if t.IsEmpty(c) then 0 else t.ColumnCount() + t.Cell(FsAddress(1, colCount + 1),c).SetValueAs explicationHeaderV1 + t.Cell(FsAddress(1, colCount + 2),c).SetValueAs explicationHeaderV2 + t.Cell(FsAddress(1, colCount + 3),c).SetValueAs explicationHeaderV3 + for i = 2 to l + 1 do + t.Cell(FsAddress(i, colCount + 1),c).SetValueAs pValueValueV1 + t.Cell(FsAddress(i, colCount + 2),c).SetValueAs pValueValueV2 + t.Cell(FsAddress(i, colCount + 3),c).SetValueAs pValueValueV3 + + // Arithmetic Mean, http://purl.obolibrary.org/obo/NCIT_C53319 + let meanValue = + OntologyAnnotation("Arithmetic Mean","NCIT","http://purl.obolibrary.org/obo/NCIT_C53319") + |> CompositeCell.Term + + let meanValueV1 = "Arithmetic Mean" + let meanValueV2 = "NCIT" + let meanValueV3 = "http://purl.obolibrary.org/obo/NCIT_C53319" + + let appendMeanColumn l (c : FsCellsCollection) (t : FsTable) = + let colCount = if t.IsEmpty(c) then 0 else t.ColumnCount() + t.Cell(FsAddress(1, colCount + 1),c).SetValueAs explicationHeaderV1 + t.Cell(FsAddress(1, colCount + 2),c).SetValueAs explicationHeaderV2 + t.Cell(FsAddress(1, colCount + 3),c).SetValueAs explicationHeaderV3 + for i = 2 to l + 1 do + t.Cell(FsAddress(i, colCount + 1),c).SetValueAs meanValueV1 + t.Cell(FsAddress(i, colCount + 2),c).SetValueAs meanValueV2 + t.Cell(FsAddress(i, colCount + 3),c).SetValueAs meanValueV3 + +module Unit = + + let ppmValue = + OntologyAnnotation("parts per million","UO","http://purl.obolibrary.org/obo/UO_0000169") + |> CompositeCell.Term + + let unitHeaderV1 = "Unit" + let unitHeaderV2 = "Term Source REF" + let unitHeaderV3 = "Term Accession Number" + + let ppmValueV1 = "parts per million" + let ppmValueV2 = "UO" + let ppmValueV3 = "http://purl.obolibrary.org/obo/UO_0000169" + + let appendPPMColumn l (c : FsCellsCollection) (t : FsTable) = + let colCount = if t.IsEmpty(c) then 0 else t.ColumnCount() + t.Cell(FsAddress(1, colCount + 1),c).SetValueAs unitHeaderV1 + t.Cell(FsAddress(1, colCount + 2),c).SetValueAs unitHeaderV2 + t.Cell(FsAddress(1, colCount + 3),c).SetValueAs unitHeaderV3 + for i = 2 to l + 1 do + t.Cell(FsAddress(i, colCount + 1),c).SetValueAs ppmValueV1 + t.Cell(FsAddress(i, colCount + 2),c).SetValueAs ppmValueV2 + t.Cell(FsAddress(i, colCount + 3),c).SetValueAs ppmValueV3 + +module ObjectType = + + let floatValue = + OntologyAnnotation("float","NCIT","http://purl.obolibrary.org/obo/NCIT_C42645") + |> CompositeCell.Term + + let objectTypeHeaderV1 = "Object Type" + let objectTypeHeaderV2 = "Term Source REF" + let objectTypeHeaderV3 = "Term Accession Number" + + let floatValueV1 = "float" + let floatValueV2 = "NCIT" + let floatValueV3 = "http://purl.obolibrary.org/obo/NCIT_C42645" + + let appendFloatColumn l (c : FsCellsCollection) (t : FsTable) = + let colCount = if t.IsEmpty(c) then 0 else t.ColumnCount() + t.Cell(FsAddress(1, colCount + 1),c).SetValueAs objectTypeHeaderV1 + t.Cell(FsAddress(1, colCount + 2),c).SetValueAs objectTypeHeaderV2 + t.Cell(FsAddress(1, colCount + 3),c).SetValueAs objectTypeHeaderV3 + for i = 2 to l + 1 do + t.Cell(FsAddress(i, colCount + 1),c).SetValueAs floatValueV1 + t.Cell(FsAddress(i, colCount + 2),c).SetValueAs floatValueV2 + t.Cell(FsAddress(i, colCount + 3),c).SetValueAs floatValueV3 + +module Description = + + let descriptionValue = CompositeCell.FreeText "This is a description" + + let descriptionHeaderV1 = "Description" + + let descriptionValueV1 = "This is a description" + + let appendDescriptionColumn l (c : FsCellsCollection) (t : FsTable) = + let colCount = if t.IsEmpty(c) then 0 else t.ColumnCount() + t.Cell(FsAddress(1, colCount + 1),c).SetValueAs descriptionHeaderV1 + for i = 2 to l + 1 do + t.Cell(FsAddress(i, colCount + 1),c).SetValueAs descriptionValueV1 + +module GeneratedBy = + + let generatedByValue = CompositeCell.FreeText "MyTool.exe" + + let generatedByHeaderV1 = "Generated By" + + let generatedByValueV1 = "MyTool.exe" + + let appendGeneratedByColumn l (c : FsCellsCollection) (t : FsTable) = + let colCount = if t.IsEmpty(c) then 0 else t.ColumnCount() + t.Cell(FsAddress(1, colCount + 1),c).SetValueAs generatedByHeaderV1 + for i = 2 to l + 1 do + t.Cell(FsAddress(i, colCount + 1),c).SetValueAs generatedByValueV1 + +let initWorksheet (name : string) (appendOperations : (FsCellsCollection -> FsTable -> unit) list) = + let w = FsWorksheet(name) + let t = w.Table(DataMapTable.datamapTablePrefix, FsRangeAddress("A1:A1")) + appendOperations + |> List.iter (fun o -> o w.CellCollection t) + ArcTable.addSpacesToEnd w.CellCollection t + t.RescanFieldNames(w.CellCollection) + w \ No newline at end of file diff --git a/tests/TestingUtils/TestingUtils.fsproj b/tests/TestingUtils/TestingUtils.fsproj index 31589ba3..eb22605e 100644 --- a/tests/TestingUtils/TestingUtils.fsproj +++ b/tests/TestingUtils/TestingUtils.fsproj @@ -17,6 +17,7 @@ + @@ -26,7 +27,7 @@ - +