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Update parser Functions
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- Rework MetadataSheet parsers by using the new Tokens
- Add parseProcessGraphColumnsFromToken  and parseProcessGraphColumnsFromTokens
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@LibraChris
LibraChris committed Feb 28, 2024
1 parent 6519f26 commit 9c643e1
Showing 1 changed file with 127 additions and 66 deletions.
193 changes: 127 additions & 66 deletions src/ARCTokenization/TopLevelParsers.fs
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Original file line number Diff line number Diff line change
Expand Up @@ -9,54 +9,68 @@ module internal ISA =

open System.IO

let tryParseMetadataSheetFromToken (isaFileName: string) (isaMdsParsingF: string -> IParam list) (absFileToken: IParam) =
let tryParseMetadataSheetFromToken (rootPath:string) (isaCvTerm: CvTerm) (isaMdsParsingF: string -> IParam list) (absFileToken: IParam) =

let cvpStr = Param.getValueAsString absFileToken
//printfn $"cvpStr: {cvpStr}"
//if String.contains isaFileName cvpStr then
if Path.GetFileName cvpStr = isaFileName then
let path = Path.Combine(rootPath, cvpStr)
let containsToken = absFileToken|> (fun x -> x.Name = isaCvTerm.Name)

if containsToken then
try
Some (isaMdsParsingF cvpStr)
Some (isaMdsParsingF path)
with _ ->
None
else None

let parseMetadataSheetsFromTokens (isaFileName: string) (isaMdsParsingF: string -> IParam list) (absFileTokens: #IParam seq) =
let parseMetadataSheetsFromTokens (rootPath:string) (isaCvTerm: CvTerm) (isaMdsParsingF: string -> IParam list) (absFileTokens: #IParam seq) =
absFileTokens
|> Seq.choose (fun token -> tryParseMetadataSheetFromToken isaFileName isaMdsParsingF token)

//type löl =


// static member parseStudyMetadataSheetFromCvp absFileTokens =
// parseMetadataSheetsFromCvps "isa.study.xlsx" ARCTokenization.Study.parseMetadataSheetfromFile absFileTokens

// static member parseAssayMetadataSheetFromCvp absFileTokens =
// parseMetadataSheetsFromCvps "isa.assay.xlsx" ARCTokenization.Assay.parseMetadataSheetFromFile absFileTokens

// static member tryParseIsaMetadataSheetFromCvp (isaFileName : string) isaMdsParsingF absFileTokens =
// absFileTokens
// |> Seq.choose (
// fun cvp ->
// let cvpStr = Param.getValueAsString cvp
// //printfn $"cvpStr: {cvpStr}"
// //if String.contains isaFileName cvpStr then
// if isaFileName = Path.GetFileName cvpStr then
// try Some (isaMdsParsingF cvpStr)
// with _ -> None
// else None
// )

// static member tryParseInvestigationMetadataSheetFromCvp (absFileTokens : #IParam seq) =
// try ParamBasedParsers.tryParseIsaMetadataSheetFromCvp "isa.investigation.xlsx" ARCTokenization.Investigation.parseMetadataSheetFromFile absFileTokens
// |> Seq.concat
// with _ -> Seq.empty
|> Seq.choose (fun token -> tryParseMetadataSheetFromToken rootPath isaCvTerm isaMdsParsingF token)

/// <summary>
/// Parses all annotation tables from an ISA XLSX file as a
/// Map of string * `IParam` 2D List representing the individual parts parts of the Process graph,
/// where the string is the name of the worksheet that contained the table,
/// and the 2D lists represent a single table in which the inner 1D lists represent a single column.
/// </summary>
/// <param name="rootPath">ARC root path</param>
/// <param name="absFileToken">he path to the study xlsx file</param>
let parseProcessGraphColumnsFromToken (rootPath:string) (absFileToken: IParam) =
let cvpStr = Param.getValueAsString absFileToken
let path = System.IO.Path.Combine(rootPath, cvpStr)
(FsWorkbook.fromXlsxFile path)
.GetWorksheets()
|> Seq.choose (fun ws ->
ws
|> ARCtrl.ISA.Spreadsheet.ArcTable.tryFromFsWorksheet
|> Option.map (fun t ->
ws.Name,
t
|> Tokenization.ARCtrl.ARCTable.tokenizeColumns
)
)
|> Map.ofSeq

// static member tryParseStudyMetadataSheetFromCvp (absFileTokens : #IParam seq) =
// ParamBasedParsers.tryParseIsaMetadataSheetFromCvp "isa.study.xlsx" ARCTokenization.Study.parseMetadataSheetfromFile absFileTokens
/// <summary>
/// Parses all annotation tables from an ISA XLSX file as a
/// Map of string * `IParam` 2D List representing the individual parts parts of the Process graph,
/// where the string is the name of the worksheet that contained the table,
/// and the 2D lists represent a single table in which the inner 1D lists represent a single column.
/// </summary>
/// <param name="rootPath">ARC root path</param>
/// <param name="isaCvTerm">The term to which the token should be found</param>
/// <param name="absFileToken">he path to the study xlsx file</param>
let parseProcessGraphColumnsFromTokens (rootPath:string) (isaCvTerm: CvTerm) (absFileTokens: #IParam seq) =
absFileTokens
|> Seq.choose (fun token ->
match token.Name = isaCvTerm.Name with
| true -> Some (parseProcessGraphColumnsFromToken rootPath token)
| false -> None
)
|> fun x ->
match Seq.length x with
| 0 -> failwith "No token found"
| _ -> x

// static member tryParseAssayMetadataSheetFromCvp (absFileTokens : #IParam seq) =
// ParamBasedParsers.tryParseIsaMetadataSheetFromCvp "isa.assay.xlsx" ARCTokenization.Assay.parseMetadataSheetFromFile absFileTokens

type FileSystem =

Expand Down Expand Up @@ -152,14 +166,14 @@ type Investigation =
/// <param name="UseLastSheetOnIncorrectName">Wether or not to try parse the last sheet as metadata sheet when there is no sheet with the correct name ("isa_investigation") in the workbook</param>
/// <param name="FileName">The name of the investigation file, note that this should not be set if the file follows spec (as "isa.investigation.xlsx" is the default)</param>
static member tryParseMetadataSheetFromToken(
?UseLastSheetOnIncorrectName: bool,
?FileName: string
?UseLastSheetOnIncorrectName: bool
) =
let fileName = defaultArg FileName Globals.INVESTIGATION_FILE_NAME
let fileToken = StructuralOntology.AFSO.``Investigation File``

fun (token: #IParam) ->
fun (rootPath:string) (token: #IParam) ->
ISA.tryParseMetadataSheetFromToken
fileName
rootPath
fileToken
(Investigation.parseMetadataSheetFromFile(?UseLastSheetOnIncorrectName = UseLastSheetOnIncorrectName))
token

Expand All @@ -173,14 +187,14 @@ type Investigation =
/// <param name="UseLastSheetOnIncorrectName">Wether or not to try parse the last sheet as metadata sheet when there is no sheet with the correct name ("isa_investigation") in the workbook</param>
/// <param name="FileName">The name of the investigation file, note that this should not be set if the file follows spec (as "isa.investigation.xlsx" is the default)</param>
static member parseMetadataSheetsFromTokens(
?UseLastSheetOnIncorrectName: bool,
?FileName: string
?UseLastSheetOnIncorrectName: bool
) =
let fileName = defaultArg FileName Globals.INVESTIGATION_FILE_NAME
let fileToken = StructuralOntology.AFSO.``Investigation File``

fun (tokens: #seq<#IParam>) ->
fun (rootPath:string) (tokens: #seq<#IParam>) ->
ISA.parseMetadataSheetsFromTokens
fileName
rootPath
fileToken
(Investigation.parseMetadataSheetFromFile(?UseLastSheetOnIncorrectName = UseLastSheetOnIncorrectName))
tokens
|> List.ofSeq
Expand Down Expand Up @@ -222,14 +236,15 @@ type Study =
/// <param name="UseLastSheetOnIncorrectName">Wether or not to try parse the last sheet as metadata sheet when there is no sheet with the correct name ("isa_study") in the workbook</param>
/// <param name="FileName">The name of the study file, note that this should not be set if the file follows spec (as "isa.study.xlsx" is the default)</param>
static member tryParseMetadataSheetFromToken(
?UseLastSheetOnIncorrectName: bool,
?FileName: string
?UseLastSheetOnIncorrectName: bool
) =
let fileName = defaultArg FileName Globals.STUDY_FILE_NAME

fun (token: #IParam) ->
let fileToken = StructuralOntology.AFSO.``Study File``

fun (rootPath:string) (token: #IParam) ->
ISA.tryParseMetadataSheetFromToken
fileName
rootPath
fileToken
(Study.parseMetadataSheetFromFile(?UseLastSheetOnIncorrectName = UseLastSheetOnIncorrectName))
token

Expand All @@ -243,19 +258,18 @@ type Study =
/// <param name="UseLastSheetOnIncorrectName">Wether or not to try parse the last sheet as metadata sheet when there is no sheet with the correct name ("isa_study") in the workbook</param>
/// <param name="FileName">The name of the study file, note that this should not be set if the file follows spec (as "isa.study.xlsx" is the default)</param>
static member parseMetadataSheetsFromTokens(
?UseLastSheetOnIncorrectName: bool,
?FileName: string
?UseLastSheetOnIncorrectName: bool
) =
let fileName = defaultArg FileName Globals.STUDY_FILE_NAME
let fileToken = StructuralOntology.AFSO.``Study File``

fun (tokens: #seq<#IParam>) ->
fun (rootPath:string) (tokens: #seq<#IParam>) ->
ISA.parseMetadataSheetsFromTokens
fileName
rootPath
fileToken
(Study.parseMetadataSheetFromFile(?UseLastSheetOnIncorrectName = UseLastSheetOnIncorrectName))
tokens
|> List.ofSeq


/// <summary>
/// Parses all annotation tables from an ISA Study XLSX file as a
/// Map of string * `IParam` 2D List representing the individual parts parts of the Process graph,
Expand All @@ -277,6 +291,29 @@ type Study =
)
|> Map.ofSeq

/// <summary>
/// Parses all annotation tables from an ISA XLSX file as a
/// Map of string * `IParam` 2D List representing the individual parts parts of the Process graph,
/// where the string is the name of the worksheet that contained the table,
/// and the 2D lists represent a single table in which the inner 1D lists represent a single column.
/// </summary>
/// <param name="rootPath">ARC root path</param>
/// <param name="absFileToken">he path to the study xlsx file</param>
static member parseProcessGraphColumnsFromToken (rootPath:string) (absFileToken: IParam) =
ISA.parseProcessGraphColumnsFromToken rootPath absFileToken


/// <summary>
/// Parses all annotation tables from an ISA XLSX file as a
/// Map of string * `IParam` 2D List representing the individual parts parts of the Process graph,
/// where the string is the name of the worksheet that contained the table,
/// and the 2D lists represent a single table in which the inner 1D lists represent a single column.
/// </summary>
/// <param name="rootPath">ARC root path</param>
/// <param name="absFileToken">he path to the xlsx file</param>
static member parseProcessGraphColumnsFromTokens (rootPath:string) (isaCsvTerm) (absFileTokens: #IParam seq) =
ISA.parseProcessGraphColumnsFromTokens rootPath isaCsvTerm absFileTokens

type Assay =

/// <summary>
Expand Down Expand Up @@ -317,11 +354,12 @@ type Assay =
?UseLastSheetOnIncorrectName: bool,
?FileName: string
) =
let fileName = defaultArg FileName Globals.ASSAY_FILE_NAME
let fileToken = StructuralOntology.AFSO.``Assay File``

fun (token: #IParam) ->
fun (rootPath:string) (token: #IParam) ->
ISA.tryParseMetadataSheetFromToken
fileName
rootPath
fileToken
(Assay.parseMetadataSheetFromFile(?UseLastSheetOnIncorrectName = UseLastSheetOnIncorrectName))
token

Expand All @@ -338,11 +376,12 @@ type Assay =
?UseLastSheetOnIncorrectName: bool,
?FileName: string
) =
let fileName = defaultArg FileName Globals.ASSAY_FILE_NAME
let fileToken = StructuralOntology.AFSO.``Assay File``

fun (tokens: #seq<#IParam>) ->
fun (rootPath:string) (tokens: #seq<#IParam>) ->
ISA.parseMetadataSheetsFromTokens
fileName
rootPath
fileToken
(Assay.parseMetadataSheetFromFile(?UseLastSheetOnIncorrectName = UseLastSheetOnIncorrectName))
tokens
|> List.ofSeq
Expand All @@ -366,4 +405,26 @@ type Assay =
|> Tokenization.ARCtrl.ARCTable.tokenizeColumns
)
)
|> Map.ofSeq
|> Map.ofSeq

/// <summary>
/// Parses all annotation tables from an ISA XLSX file as a
/// Map of string * `IParam` 2D List representing the individual parts parts of the Process graph,
/// where the string is the name of the worksheet that contained the table,
/// and the 2D lists represent a single table in which the inner 1D lists represent a single column.
/// </summary>
/// <param name="rootPath">ARC root path</param>
/// <param name="absFileToken">he path to the study xlsx file</param>
static member parseProcessGraphColumnsFromToken (rootPath:string) (absFileToken: IParam) =
ISA.parseProcessGraphColumnsFromToken rootPath absFileToken

/// <summary>
/// Parses all annotation tables from an ISA XLSX file as a
/// Map of string * `IParam` 2D List representing the individual parts parts of the Process graph,
/// where the string is the name of the worksheet that contained the table,
/// and the 2D lists represent a single table in which the inner 1D lists represent a single column.
/// </summary>
/// <param name="rootPath">ARC root path</param>
/// <param name="absFileToken">he path to the xlsx file</param>
static member parseProcessGraphColumnsFromTokens (rootPath:string) (isaCsvTerm) (absFileTokens: #IParam seq) =
ISA.parseProcessGraphColumnsFromTokens rootPath isaCsvTerm absFileTokens

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