Skip to content

Commit

Permalink
Adapt styling
Browse files Browse the repository at this point in the history
  • Loading branch information
@Etschbeijer
Etschbeijer committed Oct 14, 2024
1 parent 12e5d75 commit 38b9ce8
Show file tree
Hide file tree
Showing 5 changed files with 138 additions and 139 deletions.
22 changes: 11 additions & 11 deletions src/Spreadsheet/ArcAssay.fs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ module ArcAssay =
let [<Literal>] obsoleteMetadataSheetName = "Assay"
let [<Literal>] metadataSheetName = "isa_assay"

let toMetadataSheet (assay : ArcAssay) : FsWorksheet =
let toMetadataSheet (assay: ArcAssay) : FsWorksheet =
let toRows (assay:ArcAssay) =
seq {
yield SparseRow.fromValues [assaysLabel]
Expand All @@ -31,10 +31,10 @@ module ArcAssay =
|> Seq.iteri (fun rowI r -> SparseRow.writeToSheet (rowI + 1) r sheet)
sheet

let fromMetadataSheet (sheet : FsWorksheet) : ArcAssay =
let fromMetadataSheet (sheet: FsWorksheet) : ArcAssay =
try
let fromRows (usePrefixes : bool) (rows: seq<SparseRow>) =
let aPrefix,cPrefix =
let fromRows (usePrefixes: bool) (rows: seq<SparseRow>) =
let aPrefix, cPrefix =
if usePrefixes then
Some assaysPrefix,Some contactsPrefix
else None,None
Expand All @@ -44,11 +44,11 @@ module ArcAssay =
match lastLine with

| Some k when k = assaysLabel || k = obsoleteAssaysLabel ->
let currentLine,lineNumber,_,assays = Assays.fromRows aPrefix (lineNumber + 1) en
let currentLine, lineNumber, _, assays = Assays.fromRows aPrefix (lineNumber + 1) en
loop currentLine assays contacts lineNumber

| Some k when k = contactsLabel ->
let currentLine,lineNumber,_,contacts = Contacts.fromRows cPrefix (lineNumber + 1) en
let currentLine, lineNumber, _, contacts = Contacts.fromRows cPrefix (lineNumber + 1) en
loop currentLine assays contacts lineNumber
| k ->
match assays, contacts with
Expand Down Expand Up @@ -133,13 +133,13 @@ module ArcAssay =
with
| err -> failwithf "Failed while parsing metadatasheet: %s" err.Message

let isMetadataSheetName (name:string) =
let isMetadataSheetName (name: string) =
name = metadataSheetName || name = obsoleteMetadataSheetName

let isMetadataSheet (sheet : FsWorksheet) =
let isMetadataSheet (sheet: FsWorksheet) =
isMetadataSheetName sheet.Name

let tryGetMetadataSheet (doc:FsWorkbook) =
let tryGetMetadataSheet (doc: FsWorkbook) =
doc.GetWorksheets()
|> Seq.tryFind isMetadataSheet

Expand All @@ -149,7 +149,7 @@ module ArcAssayExtensions =
type ArcAssay with

/// Reads an assay from a spreadsheet
static member fromFsWorkbook (doc:FsWorkbook) : ArcAssay =
static member fromFsWorkbook (doc: FsWorkbook) : ArcAssay =
try
// Reading the "Assay" metadata sheet. Here metadata
let assayMetadata =
Expand Down Expand Up @@ -179,7 +179,7 @@ module ArcAssayExtensions =
/// </summary>
/// <param name="assay"></param>
/// <param name="datamapSheet">Default: true</param>
static member toFsWorkbook (assay : ArcAssay, ?datamapSheet: bool) =
static member toFsWorkbook (assay: ArcAssay, ?datamapSheet: bool) =
let datamapSheet = defaultArg datamapSheet true
let doc = new FsWorkbook()
let metadataSheet = ArcAssay.toMetadataSheet (assay)
Expand Down
72 changes: 36 additions & 36 deletions src/Spreadsheet/ArcInvestigation.fs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -30,12 +30,12 @@ module ArcInvestigation =

type InvestigationInfo =
{
Identifier : string
Title : string
Description : string
SubmissionDate : string
PublicReleaseDate : string
Comments : Comment list
Identifier : string
Title : string
Description : string
SubmissionDate : string
PublicReleaseDate : string
Comments : Comment list
}

static member create identifier title description submissionDate publicReleaseDate comments =
Expand All @@ -50,21 +50,21 @@ module ArcInvestigation =

static member Labels = [identifierLabel;titleLabel;descriptionLabel;submissionDateLabel;publicReleaseDateLabel]

static member FromSparseTable (matrix : SparseTable) =
static member FromSparseTable (matrix: SparseTable) =

let i = 0

let comments =
matrix.CommentKeys
|> List.map (fun k ->
Comment.fromString k (matrix.TryGetValueDefault("",(k,i))))
Comment.fromString k (matrix.TryGetValueDefault("", (k, i))))

InvestigationInfo.create
(matrix.TryGetValueDefault("",(identifierLabel,i)))
(matrix.TryGetValueDefault("",(titleLabel,i)))
(matrix.TryGetValueDefault("",(descriptionLabel,i)))
(matrix.TryGetValueDefault("",(submissionDateLabel,i)))
(matrix.TryGetValueDefault("",(publicReleaseDateLabel,i)))
(matrix.TryGetValueDefault("", (identifierLabel, i)))
(matrix.TryGetValueDefault("", (titleLabel, i)))
(matrix.TryGetValueDefault("", (descriptionLabel, i)))
(matrix.TryGetValueDefault("", (submissionDateLabel, i)))
(matrix.TryGetValueDefault("", (publicReleaseDateLabel, i)))
comments


Expand All @@ -73,32 +73,32 @@ module ArcInvestigation =
let matrix = SparseTable.Create (keys = InvestigationInfo.Labels,length=2)
let mutable commentKeys = []

do matrix.Matrix.Add ((identifierLabel,i), (investigation.Identifier))
do matrix.Matrix.Add ((titleLabel,i), (Option.defaultValue "" investigation.Title))
do matrix.Matrix.Add ((descriptionLabel,i), (Option.defaultValue "" investigation.Description))
do matrix.Matrix.Add ((submissionDateLabel,i), (Option.defaultValue "" investigation.SubmissionDate))
do matrix.Matrix.Add ((publicReleaseDateLabel,i), (Option.defaultValue "" investigation.PublicReleaseDate))
do matrix.Matrix.Add ((identifierLabel, i), (investigation.Identifier))
do matrix.Matrix.Add ((titleLabel, i), (Option.defaultValue "" investigation.Title))
do matrix.Matrix.Add ((descriptionLabel, i), (Option.defaultValue "" investigation.Description))
do matrix.Matrix.Add ((submissionDateLabel, i), (Option.defaultValue "" investigation.SubmissionDate))
do matrix.Matrix.Add ((publicReleaseDateLabel, i), (Option.defaultValue "" investigation.PublicReleaseDate))

investigation.Comments
|> ResizeArray.iter (fun comment ->
let n,v = comment |> Comment.toString
let n, v = comment |> Comment.toString
commentKeys <- n :: commentKeys
matrix.Matrix.Add((n,i),v)
matrix.Matrix.Add((n, i), v)
)

{matrix with CommentKeys = commentKeys |> List.distinct |> List.rev}


static member fromRows lineNumber (rows : IEnumerator<SparseRow>) =
SparseTable.FromRows(rows,InvestigationInfo.Labels,lineNumber)
|> fun (s,ln,rs,sm) -> (s,ln,rs, InvestigationInfo.FromSparseTable sm)
static member fromRows lineNumber (rows: IEnumerator<SparseRow>) =
SparseTable.FromRows(rows, InvestigationInfo.Labels, lineNumber)
|> fun (s, ln, rs, sm) -> (s, ln, rs, InvestigationInfo.FromSparseTable sm)

static member toRows (investigation : ArcInvestigation) =
static member toRows (investigation: ArcInvestigation) =
investigation
|> InvestigationInfo.ToSparseTable
|> SparseTable.ToRows

let fromParts (investigationInfo:InvestigationInfo) (ontologySourceReference:OntologySourceReference list) (publications: Publication list) (contacts: Person list) (studies: ArcStudy list) (assays: ArcAssay list) (remarks: Remark list) =
let fromParts (investigationInfo: InvestigationInfo) (ontologySourceReference: OntologySourceReference list) (publications: Publication list) (contacts: Person list) (studies: ArcStudy list) (assays: ArcAssay list) (remarks: Remark list) =
let studyIdentifiers = studies |> List.map (fun s -> s.Identifier)
ArcInvestigation.make
(investigationInfo.Identifier)
Expand All @@ -116,7 +116,7 @@ module ArcInvestigation =
(ResizeArray remarks)


let fromRows (rows:seq<SparseRow>) =
let fromRows (rows: seq<SparseRow>) =
let en = rows.GetEnumerator()

let emptyInvestigationInfo = InvestigationInfo.create "" "" "" "" "" []
Expand All @@ -125,7 +125,7 @@ module ArcInvestigation =
match lastLine with

| Some k when k = ontologySourceReferenceLabel ->
let currentLine,lineNumber,newRemarks,ontologySourceReferences = OntologySourceReference.fromRows (lineNumber + 1) en
let currentLine, lineNumber, newRemarks, ontologySourceReferences = OntologySourceReference.fromRows (lineNumber + 1) en
loop currentLine ontologySourceReferences investigationInfo publications contacts studies (List.append remarks newRemarks) lineNumber

| Some k when k = investigationLabel ->
Expand All @@ -148,10 +148,10 @@ module ArcInvestigation =
loop currentLine ontologySourceReferences investigationInfo publications contacts studies (List.append remarks newRemarks) lineNumber

| k ->
let studies,assays =
let studies, assays =
studies
|> List.unzip
|> fun (s,a) ->
|> fun (s, a) ->
s |> List.rev,
a |> List.concat |> List.distinctBy (fun a -> a.Identifier)
fromParts investigationInfo ontologySourceReferences publications contacts studies assays remarks
Expand All @@ -164,8 +164,8 @@ module ArcInvestigation =
failwith "emptyInvestigationFile"


let toRows (investigation:ArcInvestigation) : seq<SparseRow> =
let insertRemarks (remarks:Remark list) (rows:seq<SparseRow>) =
let toRows (investigation: ArcInvestigation) : seq<SparseRow> =
let insertRemarks (remarks: Remark list) (rows: seq<SparseRow>) =
try
let rm = remarks |> List.map Remark.toTuple |> Map.ofList
let rec loop i l nl =
Expand Down Expand Up @@ -202,13 +202,13 @@ module ArcInvestigation =
|> insertRemarks (List.ofSeq investigation.Remarks)
|> seq

let isMetadataSheetName (name : string) =
let isMetadataSheetName (name: string) =
name = metadataSheetName || name = obsoleteMetadataSheetName

let isMetadataSheet (sheet : FsWorksheet) =
let isMetadataSheet (sheet: FsWorksheet) =
isMetadataSheetName sheet.Name

let tryGetMetadataSheet (doc:FsWorkbook) =
let tryGetMetadataSheet (doc: FsWorkbook) =
doc.GetWorksheets()
|> Seq.tryFind isMetadataSheet

Expand All @@ -220,7 +220,7 @@ module ArcInvestigationExtensions =

type ArcInvestigation with

static member fromFsWorkbook (doc:FsWorkbook) =
static member fromFsWorkbook (doc: FsWorkbook) =
try
match ArcInvestigation.tryGetMetadataSheet doc with
| Some sheet -> sheet
Expand All @@ -231,7 +231,7 @@ module ArcInvestigationExtensions =
with
| err -> failwithf "Could not read investigation from spreadsheet: %s" err.Message

static member toFsWorkbook (investigation:ArcInvestigation) : FsWorkbook =
static member toFsWorkbook (investigation: ArcInvestigation) : FsWorkbook =
try
let wb = new FsWorkbook()
let sheet = FsWorksheet(metadataSheetName)
Expand Down
22 changes: 11 additions & 11 deletions src/Spreadsheet/ArcStudy.fs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ module ArcStudy =
let [<Literal>] obsoleteMetadataSheetName = "Study"
let [<Literal>] metadataSheetName = "isa_study"

let toMetadataSheet (study : ArcStudy) (assays : ArcAssay list option) : FsWorksheet =
let toMetadataSheet (study: ArcStudy) (assays: ArcAssay list option) : FsWorksheet =
//let toRows (study:ArcStudy) assays =
// seq {
// yield SparseRow.fromValues [studiesLabel]
Expand All @@ -25,12 +25,12 @@ module ArcStudy =
|> Seq.iteri (fun rowI r -> SparseRow.writeToSheet (rowI + 1) r sheet)
sheet

let fromMetadataSheet (sheet : FsWorksheet) : ArcStudy*ArcAssay list =
let fromMetadataSheet (sheet: FsWorksheet) : ArcStudy*ArcAssay list =
try
let fromRows (rows: seq<SparseRow>) =
let en = rows.GetEnumerator()
en.MoveNext() |> ignore
let _,_,_,study = Studies.fromRows 2 en
let _, _, _,study = Studies.fromRows 2 en
study
sheet.Rows
|> Seq.map SparseRow.fromFsRow
Expand All @@ -39,7 +39,7 @@ module ArcStudy =
with
| err -> failwithf "Failed while parsing metadatasheet: %s" err.Message

let toMetadataCollection (study : ArcStudy) (assays : ArcAssay list option) =
let toMetadataCollection (study: ArcStudy) (assays: ArcAssay list option) =
Studies.toRows study assays
|> Seq.append [SparseRow.fromValues [studiesLabel]]
|> Seq.map (fun row -> SparseRow.getAllValues row)
Expand All @@ -49,7 +49,7 @@ module ArcStudy =
let fromRows (rows: seq<SparseRow>) =
let en = rows.GetEnumerator()
en.MoveNext() |> ignore
let _,_,_,study = Studies.fromRows 2 en
let _, _, _,study = Studies.fromRows 2 en
study
collection
|> Seq.map SparseRow.fromAllValues
Expand All @@ -58,13 +58,13 @@ module ArcStudy =
with
| err -> failwithf "Failed while parsing metadatasheet: %s" err.Message

let isMetadataSheetName (name : string) =
let isMetadataSheetName (name: string) =
name = metadataSheetName || name = obsoleteMetadataSheetName

let isMetadataSheet (sheet : FsWorksheet) =
let isMetadataSheet (sheet: FsWorksheet) =
isMetadataSheetName sheet.Name

let tryGetMetadataSheet (doc:FsWorkbook) =
let tryGetMetadataSheet (doc: FsWorkbook) =
doc.GetWorksheets()
|> Seq.tryFind isMetadataSheet

Expand All @@ -74,7 +74,7 @@ module ArcStudyExtensions =
type ArcStudy with

/// Reads an assay from a spreadsheet
static member fromFsWorkbook (doc:FsWorkbook) =
static member fromFsWorkbook (doc: FsWorkbook) =
try
// Reading the "Assay" metadata sheet. Here metadata
let studyMetadata,assays =
Expand Down Expand Up @@ -116,7 +116,7 @@ module ArcStudyExtensions =
/// <param name="study"></param>
/// <param name="assays"></param>
/// <param name="datamapSheet"></param>
static member toFsWorkbook (study : ArcStudy, ?assays : ArcAssay list, ?datamapSheet: bool) =
static member toFsWorkbook (study: ArcStudy, ?assays: ArcAssay list, ?datamapSheet: bool) =
let datamapSheet = defaultArg datamapSheet true
let doc = new FsWorkbook()
let metadataSheet = ArcStudy.toMetadataSheet study assays
Expand All @@ -131,5 +131,5 @@ module ArcStudyExtensions =

doc

member this.ToFsWorkbook (?assays : ArcAssay list, ?datamapSheet: bool) =
member this.ToFsWorkbook (?assays: ArcAssay list, ?datamapSheet: bool) =
ArcStudy.toFsWorkbook (this, ?assays = assays, ?datamapSheet = datamapSheet)
5 changes: 2 additions & 3 deletions src/Spreadsheet/DataMap.fs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,8 @@ open ARCtrl
open ArcTable
open FsSpreadsheet


/// Reads an datamap from a spreadsheet
let fromFsWorkbook (doc:FsWorkbook) =
let fromFsWorkbook (doc: FsWorkbook) =
try
let dataMapTable =
doc.GetWorksheets()
Expand All @@ -17,7 +16,7 @@ let fromFsWorkbook (doc:FsWorkbook) =
with
| err -> failwithf "Could not parse datamap: \n%s" err.Message

let toFsWorkbook (dataMap : DataMap) =
let toFsWorkbook (dataMap: DataMap) =
let doc = new FsWorkbook()

DataMapTable.toFsWorksheet dataMap
Expand Down
Loading

0 comments on commit 38b9ce8

Please sign in to comment.