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Merge pull request #184 from nfdi4plants/developer_TopLevelAssays
ArcInvestigation level assays
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,69 +1,81 @@ | ||
| module ARCtrl.ISA.Spreadsheet.ArcStudy | ||
| namespace ARCtrl.ISA.Spreadsheet | ||
|
|
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| open ARCtrl.ISA | ||
| open FsSpreadsheet | ||
|
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| let [<Literal>] obsoleteStudiesLabel = "STUDY METADATA" | ||
| let [<Literal>] studiesLabel = "STUDY" | ||
|
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| let [<Literal>] obsoleteMetaDataSheetName = "Study" | ||
| let [<Literal>] metaDataSheetName = "isa_study" | ||
| module ArcStudy = | ||
|
|
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| let [<Literal>] obsoleteStudiesLabel = "STUDY METADATA" | ||
| let [<Literal>] studiesLabel = "STUDY" | ||
|
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| let toMetadataSheet (study : ArcStudy) : FsWorksheet = | ||
| let toRows (study:ArcStudy) = | ||
| seq { | ||
| yield SparseRow.fromValues [studiesLabel] | ||
| yield! Studies.StudyInfo.toRows study | ||
| } | ||
| let sheet = FsWorksheet(metaDataSheetName) | ||
| study | ||
| |> toRows | ||
| |> Seq.iteri (fun rowI r -> SparseRow.writeToSheet (rowI + 1) r sheet) | ||
| sheet | ||
| let [<Literal>] obsoleteMetaDataSheetName = "Study" | ||
| let [<Literal>] metaDataSheetName = "isa_study" | ||
|
|
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| let fromMetadataSheet (sheet : FsWorksheet) : ArcStudy = | ||
| let fromRows (rows: seq<SparseRow>) = | ||
| let en = rows.GetEnumerator() | ||
| en.MoveNext() |> ignore | ||
| let _,_,_,study = Studies.fromRows 2 en | ||
| study | ||
| sheet.Rows | ||
| |> Seq.map SparseRow.fromFsRow | ||
| |> fromRows | ||
| |> Option.defaultValue (ArcStudy.create(Identifier.createMissingIdentifier())) | ||
| let toMetadataSheet (study : ArcStudy) (assays : ArcAssay list option) : FsWorksheet = | ||
| //let toRows (study:ArcStudy) assays = | ||
| // seq { | ||
| // yield SparseRow.fromValues [studiesLabel] | ||
| // yield! Studies.StudyInfo.toRows study | ||
| // } | ||
| let sheet = FsWorksheet(metaDataSheetName) | ||
| Studies.toRows study assays | ||
| |> Seq.append [SparseRow.fromValues [studiesLabel]] | ||
| |> Seq.iteri (fun rowI r -> SparseRow.writeToSheet (rowI + 1) r sheet) | ||
| sheet | ||
|
|
||
| /// Reads an assay from a spreadsheet | ||
| let fromFsWorkbook (doc:FsWorkbook) = | ||
| // Reading the "Assay" metadata sheet. Here metadata | ||
| let studyMetadata = | ||
| let fromMetadataSheet (sheet : FsWorksheet) : ArcStudy*ArcAssay list = | ||
| let fromRows (rows: seq<SparseRow>) = | ||
| let en = rows.GetEnumerator() | ||
| en.MoveNext() |> ignore | ||
| let _,_,_,study = Studies.fromRows 2 en | ||
| study | ||
| sheet.Rows | ||
| |> Seq.map SparseRow.fromFsRow | ||
| |> fromRows | ||
| |> Option.defaultValue (ArcStudy.create(Identifier.createMissingIdentifier()),[]) | ||
|
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||
| [<AutoOpen>] | ||
| module Extensions = | ||
|
|
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| type ArcStudy with | ||
|
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| /// Reads an assay from a spreadsheet | ||
| static member fromFsWorkbook (doc:FsWorkbook) = | ||
| // Reading the "Assay" metadata sheet. Here metadata | ||
| let studyMetadata,assays = | ||
|
|
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| match doc.TryGetWorksheetByName metaDataSheetName with | ||
| | Option.Some sheet -> | ||
| fromMetadataSheet sheet | ||
| | None -> | ||
| match doc.TryGetWorksheetByName obsoleteMetaDataSheetName with | ||
| | Option.Some sheet -> | ||
| fromMetadataSheet sheet | ||
| | None -> | ||
| printfn "Cannot retrieve metadata: Study file does not contain \"%s\" or \"%s\" sheet." metaDataSheetName obsoleteMetaDataSheetName | ||
| ArcStudy.create(Identifier.createMissingIdentifier()) | ||
| match doc.TryGetWorksheetByName ArcStudy.metaDataSheetName with | ||
| | Option.Some sheet -> | ||
| ArcStudy.fromMetadataSheet sheet | ||
| | None -> | ||
| match doc.TryGetWorksheetByName ArcStudy.obsoleteMetaDataSheetName with | ||
| | Option.Some sheet -> | ||
| ArcStudy.fromMetadataSheet sheet | ||
| | None -> | ||
| printfn "Cannot retrieve metadata: Study file does not contain \"%s\" or \"%s\" sheet." ArcStudy.metaDataSheetName ArcStudy.obsoleteMetaDataSheetName | ||
| ArcStudy.create(Identifier.createMissingIdentifier()),[] | ||
|
|
||
| let sheets = | ||
| doc.GetWorksheets() | ||
| |> Seq.choose ArcTable.tryFromFsWorksheet | ||
| if sheets |> Seq.isEmpty then | ||
| studyMetadata | ||
| else | ||
| studyMetadata.Tables <- ResizeArray(sheets) | ||
| studyMetadata | ||
| let sheets = | ||
| doc.GetWorksheets() | ||
| |> Seq.choose ArcTable.tryFromFsWorksheet | ||
| if sheets |> Seq.isEmpty |> not then | ||
| let updatedTables = | ||
| ArcTables.updateReferenceTablesBySheets( | ||
| (ArcTables studyMetadata.Tables), | ||
| (ArcTables (ResizeArray sheets)), | ||
| keepUnusedRefTables = true | ||
| ) | ||
| studyMetadata.Tables <- updatedTables.Tables | ||
| studyMetadata | ||
| ,assays | ||
|
|
||
| let toFsWorkbook (study : ArcStudy) = | ||
| let doc = new FsWorkbook() | ||
| let metaDataSheet = toMetadataSheet study | ||
| doc.AddWorksheet metaDataSheet | ||
| static member toFsWorkbook (study : ArcStudy,?assays : ArcAssay list) = | ||
| let doc = new FsWorkbook() | ||
| let metaDataSheet = ArcStudy.toMetadataSheet study assays | ||
| doc.AddWorksheet metaDataSheet | ||
|
|
||
| study.Tables | ||
| |> Seq.iter (ArcTable.toFsWorksheet >> doc.AddWorksheet) | ||
| study.Tables | ||
| |> Seq.iter (ArcTable.toFsWorksheet >> doc.AddWorksheet) | ||
|
|
||
| doc | ||
| doc |
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