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Template spreadsheet parsers #201
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,303 @@ | ||
| module ARCtrl.Templates.Spreadsheet | ||
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| open FsSpreadsheet | ||
| open ARCtrl.ISA.Aux | ||
| open ARCtrl.ISA.Spreadsheet | ||
| open ARCtrl.ISA | ||
| open System.Collections.Generic | ||
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| module Metadata = | ||
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| module ER = | ||
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| let [<Literal>] erLabel = "ER" | ||
| let [<Literal>] erTermAccessionNumberLabel = "ER Term Accession Number" | ||
| let [<Literal>] erTermSourceREFLabel = "ER Term Source REF" | ||
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| let labels = [erLabel;erTermAccessionNumberLabel;erTermSourceREFLabel] | ||
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| let fromSparseTable (matrix : SparseTable) = | ||
| OntologyAnnotationSection.fromSparseTable erLabel erTermSourceREFLabel erTermAccessionNumberLabel matrix | ||
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| let toSparseTable (designs: OntologyAnnotation list) = | ||
| OntologyAnnotationSection.toSparseTable erLabel erTermSourceREFLabel erTermAccessionNumberLabel designs | ||
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| let fromRows (prefix : string option) (rows : IEnumerator<SparseRow>) = | ||
| let nextHeader, _, _, ers = OntologyAnnotationSection.fromRows prefix erLabel erTermSourceREFLabel erTermAccessionNumberLabel 0 rows | ||
| nextHeader,ers | ||
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| let toRows (prefix : string option) (designs : OntologyAnnotation list) = | ||
| OntologyAnnotationSection.toRows prefix erLabel erTermSourceREFLabel erTermAccessionNumberLabel designs | ||
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| module Tags = | ||
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| let [<Literal>] tagsLabel = "Tags" | ||
| let [<Literal>] tagsTermAccessionNumberLabel = "Tags Term Accession Number" | ||
| let [<Literal>] tagsTermSourceREFLabel = "Tags Term Source REF" | ||
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| let labels = [tagsLabel;tagsTermAccessionNumberLabel;tagsTermSourceREFLabel] | ||
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| let fromSparseTable (matrix : SparseTable) = | ||
| OntologyAnnotationSection.fromSparseTable tagsLabel tagsTermSourceREFLabel tagsTermAccessionNumberLabel matrix | ||
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| let toSparseTable (designs: OntologyAnnotation list) = | ||
| OntologyAnnotationSection.toSparseTable tagsLabel tagsTermSourceREFLabel tagsTermAccessionNumberLabel designs | ||
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| let fromRows (prefix : string option) (rows : IEnumerator<SparseRow>) = | ||
| let nextHeader, _, _, tags = OntologyAnnotationSection.fromRows prefix tagsLabel tagsTermSourceREFLabel tagsTermAccessionNumberLabel 0 rows | ||
| nextHeader, tags | ||
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| let toRows (prefix : string option) (designs : OntologyAnnotation list) = | ||
| OntologyAnnotationSection.toRows prefix tagsLabel tagsTermSourceREFLabel tagsTermAccessionNumberLabel designs | ||
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| module Authors = | ||
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| let [<Literal>] obsoleteORCIDLabel = "Authors ORCID" | ||
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| module Template = | ||
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| let [<Literal>] identifierLabel = "Id" | ||
| let [<Literal>] nameLabel = "Name" | ||
| let [<Literal>] versionLabel = "Version" | ||
| let [<Literal>] descriptionLabel = "Description" | ||
| let [<Literal>] organisationLabel = "Organisation" | ||
| let [<Literal>] tableLabel = "Table" | ||
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| let [<Literal>] authorsLabelPrefix = "Author" | ||
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| let [<Literal>] templateLabel = "TEMPLATE" | ||
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| let [<Literal>] authorsLabel = "AUTHORS" | ||
| let [<Literal>] erLabel = "ERS" | ||
| let [<Literal>] tagsLabel = "TAGS" | ||
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| let [<Literal>] obsoleteAuthorsLabel = "#AUTHORS list" | ||
| let [<Literal>] obsoleteErLabel = "#ER list" | ||
| let [<Literal>] obsoleteTagsLabel = "#TAGS list" | ||
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| type TemplateInfo = | ||
| { | ||
| Id : string | ||
| Name : string | ||
| Version : string | ||
| Description : string | ||
| Organisation : string | ||
| Table : string | ||
| Comments : Comment list | ||
| } | ||
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| static member create id name version description organisation table comments = | ||
| {Id = id;Name = name;Version = version;Description = description;Organisation = organisation;Table = table;Comments = comments} | ||
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| static member empty = | ||
| TemplateInfo.create "" "" "" "" "" "" [] | ||
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| static member Labels = | ||
| [identifierLabel;nameLabel;versionLabel;descriptionLabel;organisationLabel;tableLabel] | ||
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| static member FromSparseTable (matrix : SparseTable) = | ||
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| let i = 0 | ||
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| let comments = | ||
| matrix.CommentKeys | ||
| |> List.map (fun k -> | ||
| Comment.fromString k (matrix.TryGetValueDefault("",(k,i)))) | ||
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| TemplateInfo.create | ||
| (matrix.TryGetValueDefault(Identifier.createMissingIdentifier(),(identifierLabel,i))) | ||
| (matrix.TryGetValueDefault("",(nameLabel,i))) | ||
| (matrix.TryGetValueDefault("",(versionLabel,i))) | ||
| (matrix.TryGetValueDefault("",(descriptionLabel,i))) | ||
| (matrix.TryGetValueDefault("",(organisationLabel,i))) | ||
| (matrix.TryGetValueDefault("",(tableLabel,i))) | ||
| comments | ||
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| static member ToSparseTable (template: Template) = | ||
| let i = 1 | ||
| let matrix = SparseTable.Create (keys = TemplateInfo.Labels,length = 2) | ||
| let mutable commentKeys = [] | ||
| let processedIdentifier = | ||
| if template.Id.ToString().StartsWith(Identifier.MISSING_IDENTIFIER) then "" else | ||
| template.Id.ToString() | ||
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| do matrix.Matrix.Add ((identifierLabel,i), processedIdentifier) | ||
| do matrix.Matrix.Add ((nameLabel,i), (template.Name)) | ||
| do matrix.Matrix.Add ((versionLabel,i), (template.Version)) | ||
| do matrix.Matrix.Add ((descriptionLabel,i), (template.Description)) | ||
| do matrix.Matrix.Add ((organisationLabel,i), (template.Organisation.ToString())) | ||
| do matrix.Matrix.Add ((tableLabel,i), template.Table.Name) | ||
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| {matrix with CommentKeys = commentKeys |> List.distinct |> List.rev} | ||
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| static member fromRows (rows : IEnumerator<SparseRow>) = | ||
| SparseTable.FromRows(rows,TemplateInfo.Labels,0) | ||
| |> fun (s,ln,rs,sm) -> (s,TemplateInfo.FromSparseTable sm) | ||
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| static member toRows (template : Template) = | ||
| template | ||
| |> TemplateInfo.ToSparseTable | ||
| |> SparseTable.ToRows | ||
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| let mapDeprecatedKeys (rows : seq<SparseRow>) = | ||
| rows | ||
| |> Seq.map (fun r -> | ||
| r | ||
| |> Seq.map (fun (k,v) -> | ||
| if k = 0 then | ||
| match v with | ||
| | v when v = obsoleteAuthorsLabel -> k,authorsLabel | ||
| | v when v = obsoleteErLabel -> k,erLabel | ||
| | v when v = obsoleteTagsLabel -> k,tagsLabel | ||
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| | v when v = Authors.obsoleteORCIDLabel -> k,$"Comment[{Person.orcidKey}]" | ||
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| | v when v = "Authors Last Name" -> k,"Author Last Name" | ||
| | v when v = "Authors First Name" -> k,"Author First Name" | ||
| | v when v = "Authors Mid Initials" -> k,"Author Mid Initials" | ||
| | v when v = "Authors Email" -> k,"Author Email" | ||
| | v when v = "Authors Phone" -> k,"Author Phone" | ||
| | v when v = "Authors Fax" -> k,"Author Fax" | ||
| | v when v = "Authors Address" -> k,"Author Address" | ||
| | v when v = "Authors Affiliation" -> k,"Author Affiliation" | ||
| | v when v = "Authors Role" -> k,"Author Roles" | ||
| | v when v = "Authors Role Term Accession Number" -> k,"Author Roles Term Accession Number" | ||
| | v when v = "Authors Role Term Source REF" -> k,"Author Roles Term Source REF" | ||
| | v -> (k,v) | ||
| else (k,v) | ||
| ) | ||
| ) | ||
| |> fun s -> | ||
| if Seq.head s |> SparseRow.tryGetValueAt 0 |> Option.exists (fun v -> v = templateLabel) then s else | ||
| Seq.append (SparseRow.fromValues [templateLabel] |> Seq.singleton) s | ||
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| let fromRows (rows : seq<SparseRow>) = | ||
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| let rec loop en lastLine (templateInfo : TemplateInfo) ers tags authors = | ||
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| match lastLine with | ||
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| | Some k when k = erLabel -> | ||
| let currentLine,newERs = ER.fromRows None en | ||
| loop en currentLine templateInfo (List.append ers newERs) tags authors | ||
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| | Some k when k = tagsLabel -> | ||
| let currentLine,newTags = Tags.fromRows None en | ||
| loop en currentLine templateInfo ers (List.append tags newTags) authors | ||
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| | Some k when k = authorsLabel -> | ||
| let currentLine,_,_,newAuthors = Contacts.fromRows (Some authorsLabelPrefix) 0 en | ||
| loop en currentLine templateInfo ers tags (List.append authors newAuthors) | ||
| | k -> | ||
| templateInfo,ers,tags,authors | ||
| let rows = mapDeprecatedKeys rows | ||
| let en = rows.GetEnumerator() | ||
| en.MoveNext() |> ignore | ||
| let currentLine,item = TemplateInfo.fromRows en | ||
| loop en currentLine item [] [] [] | ||
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| let toRows (template : Template) = | ||
| seq { | ||
| yield SparseRow.fromValues [templateLabel] | ||
| yield! TemplateInfo.toRows template | ||
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| yield SparseRow.fromValues [erLabel] | ||
| yield! ER.toRows (None) (template.EndpointRepositories |> Array.toList) | ||
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| yield SparseRow.fromValues [tagsLabel] | ||
| yield! Tags.toRows (None) (template.Tags |> Array.toList) | ||
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| yield SparseRow.fromValues [authorsLabel] | ||
| yield! Contacts.toRows (Some authorsLabelPrefix) (List.ofArray template.Authors) | ||
| } | ||
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| module Template = | ||
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| open Metadata | ||
| open Template | ||
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| let [<Literal>] metaDataSheetName = "isa_template" | ||
| let [<Literal>] obsoletemetaDataSheetName = "SwateTemplateMetadata" | ||
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| let fromParts (templateInfo:TemplateInfo) (ers:OntologyAnnotation list) (tags: OntologyAnnotation list) (authors : Person list) (table : ArcTable) (lastUpdated : System.DateTime)= | ||
| Template.make | ||
| (System.Guid templateInfo.Id) | ||
| table | ||
| (templateInfo.Name) | ||
| (templateInfo.Description) | ||
| (Organisation.ofString templateInfo.Organisation) | ||
| (templateInfo.Version) | ||
| (Array.ofList authors) | ||
| (Array.ofList ers) | ||
| (Array.ofList tags) | ||
| (lastUpdated) | ||
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| let toMetadataSheet (template : Template) : FsWorksheet = | ||
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| let sheet = FsWorksheet(metaDataSheetName) | ||
| Template.toRows template | ||
| |> Seq.iteri (fun rowI r -> SparseRow.writeToSheet (rowI + 1) r sheet) | ||
| sheet | ||
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| let fromMetadataSheet (sheet : FsWorksheet) = | ||
| sheet.Rows | ||
| |> Seq.map SparseRow.fromFsRow | ||
| |> Template.fromRows | ||
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| /// Reads an assay from a spreadsheet | ||
| let fromFsWorkbook (doc:FsWorkbook) = | ||
| // Reading the "Assay" metadata sheet. Here metadata | ||
| let templateInfo,ers,tags,authors = | ||
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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 -> | ||
| Metadata.Template.TemplateInfo.empty,[],[],[] | ||
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| let tryTableNameMatches (ws : FsWorksheet) = | ||
| if ws.Tables |> Seq.exists (fun t -> t.Name = templateInfo.Table) then Some ws else None | ||
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| let tryWSNameMatches (ws : FsWorksheet) = | ||
| if ws.Name = templateInfo.Table then Some ws else None | ||
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| let sheets = doc.GetWorksheets() | ||
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| let table = | ||
| match sheets |> Seq.tryPick tryTableNameMatches with | ||
| | Some ws -> | ||
| match ArcTable.tryFromFsWorksheet ws with | ||
| | Some t -> t | ||
| | None -> failwithf "Ws with name %s could not be converted to a table" ws.Name | ||
| | None -> | ||
| match sheets |> Seq.tryPick tryWSNameMatches with | ||
| | Some ws -> | ||
| match ArcTable.tryFromFsWorksheet ws with | ||
| | Some t -> t | ||
| | None -> failwithf "Ws with name %s could not be converted to a table" ws.Name | ||
| | None -> failwithf "No worksheet with name %s found" templateInfo.Table | ||
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| fromParts templateInfo ers tags authors table (System.DateTime.Now) | ||
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| let toFsWorkbook (template : Template) = | ||
| let doc = new FsWorkbook() | ||
| let metaDataSheet = toMetadataSheet template | ||
| doc.AddWorksheet metaDataSheet | ||
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| template.Table | ||
| |> ArcTable.toFsWorksheet | ||
| |> doc.AddWorksheet | ||
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| doc | ||
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Good to use make, as this avoids issues with optional parameters.