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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 |
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@@ -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 | ||
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/// 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()),[] | ||
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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 | ||
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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 | ||
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study.Tables | ||
|> Seq.iter (ArcTable.toFsWorksheet >> doc.AddWorksheet) | ||
study.Tables | ||
|> Seq.iter (ArcTable.toFsWorksheet >> doc.AddWorksheet) | ||
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doc | ||
doc |
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