Rename ARCtrl.Path to ARCtrl.ArcPathHelper #398

src/ARCtrl/ARC.fs

@@ -1,4 +1,4 @@
-namespace ARCtrl
+namespace ARCtrl
 
 open ARCtrl.FileSystem
 open ARCtrl.Contract
@@ -7,6 +7,7 @@ open ARCtrl.Helper
 open ARCtrl.Spreadsheet
 open FsSpreadsheet
 open Fable.Core
+open ARCtrl.ArcPathHelper
 
 module ARCAux =
 
@@ -95,7 +96,7 @@ type ARC(?isa : ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSystem) =
         let studies = assay.StudiesRegisteredIn
         isa.RemoveAssay(assayIdentifier)
         let paths = this.FileSystem.Tree.ToFilePaths()
-        let assayFolderPath = Path.getAssayFolderPath(assayIdentifier)
+        let assayFolderPath = getAssayFolderPath(assayIdentifier)
         let filteredPaths = paths |> Array.filter (fun p -> p.StartsWith(assayFolderPath) |> not)
         this.SetFilePaths(filteredPaths)      
         [
@@ -115,8 +116,8 @@ type ARC(?isa : ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSystem) =
 
         isa.RenameAssay(oldAssayIdentifier,newAssayIdentifier)
         let paths = this.FileSystem.Tree.ToFilePaths()
-        let oldAssayFolderPath = Path.getAssayFolderPath(oldAssayIdentifier)
-        let newAssayFolderPath = Path.getAssayFolderPath(newAssayIdentifier)
+        let oldAssayFolderPath = getAssayFolderPath(oldAssayIdentifier)
+        let newAssayFolderPath = getAssayFolderPath(newAssayIdentifier)
         let renamedPaths = paths |> Array.map (fun p -> p.Replace(oldAssayFolderPath,newAssayFolderPath))
         this.SetFilePaths(renamedPaths)
         [
@@ -132,7 +133,7 @@ type ARC(?isa : ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSystem) =
             | None -> failwith "Cannot remove study from null ISA value."
         isa.RemoveStudy(studyIdentifier)
         let paths = this.FileSystem.Tree.ToFilePaths()
-        let studyFolderPath = Path.getStudyFolderPath(studyIdentifier)
+        let studyFolderPath = getStudyFolderPath(studyIdentifier)
         let filteredPaths = paths |> Array.filter (fun p -> p.StartsWith(studyFolderPath) |> not)
         this.SetFilePaths(filteredPaths)
         [
@@ -150,8 +151,8 @@ type ARC(?isa : ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSystem) =
 
         isa.RenameStudy(oldStudyIdentifier,newStudyIdentifier)
         let paths = this.FileSystem.Tree.ToFilePaths()
-        let oldStudyFolderPath = Path.getStudyFolderPath(oldStudyIdentifier)
-        let newStudyFolderPath = Path.getStudyFolderPath(newStudyIdentifier)
+        let oldStudyFolderPath = getStudyFolderPath(oldStudyIdentifier)
+        let newStudyFolderPath = getStudyFolderPath(newStudyIdentifier)
         let renamedPaths = paths |> Array.map (fun p -> p.Replace(oldStudyFolderPath,newStudyFolderPath))
         this.SetFilePaths(renamedPaths)
         [
@@ -321,7 +322,7 @@ type ARC(?isa : ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSystem) =
         match this.ISA with
         | Some inv -> 
             let investigationConverter = Spreadsheet.ArcInvestigation.toFsWorkbook
-            workbooks.Add (Path.InvestigationFileName, (DTOType.ISA_Investigation, investigationConverter inv))
+            workbooks.Add (InvestigationFileName, (DTOType.ISA_Investigation, investigationConverter inv))
             inv.StaticHash <- inv.GetLightHashCode()
             inv.Studies
             |> Seq.iter (fun s ->
@@ -356,7 +357,7 @@ type ARC(?isa : ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSystem) =
 
         | None -> 
             //printfn "ARC contains no ISA part."
-            workbooks.Add (Path.InvestigationFileName, (DTOType.ISA_Investigation, Spreadsheet.ArcInvestigation.toFsWorkbook (ArcInvestigation.create(Identifier.MISSING_IDENTIFIER))))
+            workbooks.Add (InvestigationFileName, (DTOType.ISA_Investigation, Spreadsheet.ArcInvestigation.toFsWorkbook (ArcInvestigation.create(Identifier.MISSING_IDENTIFIER))))
 
         // Iterates over filesystem and creates a write contract for every file. If possible, include DTO.       
         _fs.Tree.ToFilePaths(true)
@@ -466,46 +467,46 @@ type ARC(?isa : ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSystem) =
 
         let includeRootFiles : Set<string> = 
             set [
-                Path.InvestigationFileName
-                Path.READMEFileName
+                InvestigationFileName
+                READMEFileName
             ]
 
         let includeStudyFiles = 
             registeredStudies
             |> Array.map (fun s -> 
-                let studyFoldername = $"{Path.StudiesFolderName}/{s.Identifier}"
+                let studyFoldername = $"{StudiesFolderName}/{s.Identifier}"
 
                 set [
-                    yield $"{studyFoldername}/{Path.StudyFileName}"
-                    yield $"{studyFoldername}/{Path.READMEFileName}"
+                    yield $"{studyFoldername}/{StudyFileName}"
+                    yield $"{studyFoldername}/{READMEFileName}"
 
                     //just allow any constructed path from cell values. there may be occasions where this includes wrong files, but its good enough for now.
                     for table in s.Tables do
                         for kv in table.Values do
                             let textValue = kv.Value.ToFreeTextCell().AsFreeText
                             yield textValue // from arc root
-                            yield $"{studyFoldername}/{Path.StudiesResourcesFolderName}/{textValue}" // from study root > resources
-                            yield $"{studyFoldername}/{Path.StudiesProtocolsFolderName}/{textValue}" // from study root > protocols
+                            yield $"{studyFoldername}/{StudiesResourcesFolderName}/{textValue}" // from study root > resources
+                            yield $"{studyFoldername}/{StudiesProtocolsFolderName}/{textValue}" // from study root > protocols
                 ]
             )
             |> Set.unionMany
 
         let includeAssayFiles = 
             registeredAssays
             |> Array.map (fun a -> 
-                let assayFoldername = $"{Path.AssaysFolderName}/{a.Identifier}"
+                let assayFoldername = $"{AssaysFolderName}/{a.Identifier}"
 
                 set [
-                    yield $"{assayFoldername}/{Path.AssayFileName}"
-                    yield $"{assayFoldername}/{Path.READMEFileName}"
+                    yield $"{assayFoldername}/{AssayFileName}"
+                    yield $"{assayFoldername}/{READMEFileName}"
 
                     //just allow any constructed path from cell values. there may be occasions where this includes wrong files, but its good enough for now.
                     for table in a.Tables do
                         for kv in table.Values do
                             let textValue = kv.Value.ToFreeTextCell().AsFreeText
                             yield textValue // from arc root
-                            yield $"{assayFoldername}/{Path.AssayDatasetFolderName}/{textValue}" // from assay root > dataset
-                            yield $"{assayFoldername}/{Path.AssayProtocolsFolderName}/{textValue}" // from assay root > protocols
+                            yield $"{assayFoldername}/{AssayDatasetFolderName}/{textValue}" // from assay root > dataset
+                            yield $"{assayFoldername}/{AssayProtocolsFolderName}/{textValue}" // from assay root > protocols
                 ]
             )
             |> Set.unionMany
@@ -519,8 +520,8 @@ type ARC(?isa : ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSystem) =
         fsCopy.Tree
         |> FileSystemTree.toFilePaths()
         |> Array.filter (fun p -> 
-            p.StartsWith(Path.WorkflowsFolderName) 
-            || p.StartsWith(Path.RunsFolderName) 
+            p.StartsWith(WorkflowsFolderName) 
+            || p.StartsWith(RunsFolderName) 
             || includeFiles.Contains(p)
         )
         |> FileSystemTree.fromFilePaths

src/Contract/ARC.fs

@@ -1,6 +1,6 @@
-module ARCtrl.Contract.ARC
+module ARCtrl.Contract.ARC
 
-open ARCtrl.Path
+open ARCtrl.ArcPathHelper
 
 open ARCtrl.Contract
 
@@ -13,7 +13,7 @@ open ARCtrl.Contract
 // 3. We ignore all other .xlsx files.
 /// Tries to create READ contract with DTOType = ISA_Assay, ISA_Study or ISA_Investigation from given path relative to ARC root.
 let tryISAReadContractFromPath (path: string) = 
-    let split = ARCtrl.Path.split path
+    let split = split path
     match split with
     | InvestigationPath p -> 
         Some <| Contract.createRead(p, DTOType.ISA_Investigation) 

src/Contract/ArcAssay.fs

@@ -1,9 +1,9 @@
-namespace ARCtrl.Contract
+namespace ARCtrl.Contract
 
+open ARCtrl
 open ARCtrl.FileSystem
-open ARCtrl.Path
 open ARCtrl.Spreadsheet
-open ARCtrl
+open ARCtrl.ArcPathHelper
 open ARCtrl.Helper
 open FsSpreadsheet
 
@@ -14,7 +14,7 @@ module AssayContractExtensions =
     let (|AssayPath|_|) (input) =
         match input with
         | [|AssaysFolderName; anyAssayName; AssayFileName|] -> 
-            let path = ARCtrl.Path.combineMany input
+            let path = combineMany input
             Some path
         | _ -> None
 

src/Contract/ArcInvestigation.fs

@@ -1,7 +1,7 @@
-namespace ARCtrl.Contract
+namespace ARCtrl.Contract
 
 open ARCtrl.FileSystem
-open ARCtrl.Path
+open ARCtrl.ArcPathHelper
 open ARCtrl.Spreadsheet
 open ARCtrl
 open ARCtrl.Helper
@@ -14,7 +14,7 @@ module InvestigationContractExtensions =
     let (|InvestigationPath|_|) (input) =
         match input with
         | [|InvestigationFileName|] -> 
-            let path = ARCtrl.Path.combineMany input
+            let path = ARCtrl.ArcPathHelper.combineMany input
             Some path
         | _ -> None
 

src/Contract/ArcStudy.fs

@@ -1,7 +1,7 @@
-namespace ARCtrl.Contract
+namespace ARCtrl.Contract
 
 open ARCtrl.FileSystem
-open ARCtrl.Path
+open ARCtrl.ArcPathHelper
 open ARCtrl.Spreadsheet
 open ARCtrl
 open ARCtrl.Helper
@@ -14,7 +14,7 @@ module StudyContractExtensions =
     let (|StudyPath|_|) (input) =
         match input with
         | [|StudiesFolderName; anyStudyName; StudyFileName|] -> 
-            let path = ARCtrl.Path.combineMany input
+            let path = ARCtrl.ArcPathHelper.combineMany input
             Some path
         | _ -> None     
 

src/Contract/Datamap.fs

@@ -1,7 +1,7 @@
-namespace ARCtrl.Contract
+namespace ARCtrl.Contract
 
 open ARCtrl.FileSystem
-open ARCtrl.Path
+open ARCtrl.ArcPathHelper
 open ARCtrl.Spreadsheet
 open ARCtrl
 open ARCtrl.Helper
@@ -13,10 +13,10 @@ module DatamapContractExtensions =
     let (|DatamapPath|_|) (input) =
         match input with
         | [|AssaysFolderName; anyAssayName; DataMapFileName|] -> 
-            let path = ARCtrl.Path.combineMany input
+            let path = ARCtrl.ArcPathHelper.combineMany input
             Some path
         | [|StudiesFolderName; anyStudyName; DataMapFileName|] -> 
-            let path = ARCtrl.Path.combineMany input
+            let path = ARCtrl.ArcPathHelper.combineMany input
             Some path
         | _ -> None
 

src/Contract/ValidationPackagesConfig.fs

@@ -1,7 +1,7 @@
-namespace ARCtrl.Contract
+namespace ARCtrl.Contract
 
 open ARCtrl.FileSystem
-open ARCtrl.Path
+open ARCtrl.ArcPathHelper
 open ARCtrl
 open ARCtrl.Yaml
 open ARCtrl.Helper
@@ -13,11 +13,11 @@ module ValidationPackagesConfigExtensions =
     let (|ValidationPackagesYamlPath|_|) (input) =
         match input with
         | [|ARCConfigFolderName; ValidationPackagesYamlFileName|] -> 
-            let path = ARCtrl.Path.combineMany input
+            let path = ARCtrl.ArcPathHelper.combineMany input
             Some path
         | _ -> None
 
-    let internal config_file_path = [|ARCConfigFolderName; ValidationPackagesYamlFileName|] |> ARCtrl.Path.combineMany
+    let internal config_file_path = [|ARCConfigFolderName; ValidationPackagesYamlFileName|] |> ARCtrl.ArcPathHelper.combineMany
 
     type ValidationPackagesConfig with
 

src/Core/ArcTypes.fs

@@ -1,4 +1,4 @@
-namespace rec ARCtrl
+namespace rec ARCtrl
 
 open Fable.Core
 open ARCtrl.Helper
@@ -143,7 +143,7 @@ type ArcAssay(identifier: string, ?measurementType : OntologyAnnotation, ?techno
         (comments : ResizeArray<Comment>) = 
         ArcAssay(identifier = identifier, ?measurementType = measurementType, ?technologyType = technologyType, ?technologyPlatform = technologyPlatform, tables =tables, ?datamap = datamap, performers = performers, comments = comments)
 
-    static member FileName = ARCtrl.Path.AssayFileName
+    static member FileName = ARCtrl.ArcPathHelper.AssayFileName
     member this.StudiesRegisteredIn
         with get () = 
             match this.Investigation with
@@ -585,7 +585,7 @@ type ArcStudy(identifier : string, ?title, ?description, ?submissionDate, ?publi
             (this.Comments.Count = 0)
 
     // Not sure how to handle this best case.
-    static member FileName = ARCtrl.Path.StudyFileName
+    static member FileName = ARCtrl.ArcPathHelper.StudyFileName
     //member this.FileName = ArcStudy.FileName
 
     /// Returns the count of registered assay *identifiers*. This is not necessarily the same as the count of registered assays, as not all identifiers correspond to an existing assay.
@@ -1147,7 +1147,7 @@ type ArcInvestigation(identifier : string, ?title : string, ?description : strin
     member this.Remarks with get() = remarks and set(n) = remarks <- n
     member this.StaticHash with get() = staticHash and set(h) = staticHash <- h
 
-    static member FileName = ARCtrl.Path.InvestigationFileName
+    static member FileName = ARCtrl.ArcPathHelper.InvestigationFileName
 
     static member init(identifier: string) = ArcInvestigation identifier
     static member create(identifier : string, ?title : string, ?description : string, ?submissionDate : string, ?publicReleaseDate : string, ?ontologySourceReferences, ?publications, ?contacts, ?assays : ResizeArray<ArcAssay>, ?studies : ResizeArray<ArcStudy>,?registeredStudyIdentifiers : ResizeArray<string>, ?comments : ResizeArray<Comment>, ?remarks) = 

src/Core/Helper/Identifier.fs

@@ -1,4 +1,4 @@
-/// This module contains helper functions to handle study/assay/investigation identifiers in an unsafe, forced way.
+/// This module contains helper functions to handle study/assay/investigation identifiers in an unsafe, forced way.
 module ARCtrl.Helper.Identifier
 
 open Regex.ActivePatterns
@@ -75,15 +75,15 @@ module Assay =
     /// <param name="identifier">Any correct assay identifier</param>
     let fileNameFromIdentifier (identifier: string) : string =        
         checkValidCharacters (identifier)
-        ARCtrl.Path.combineMany [|ARCtrl.Path.AssaysFolderName; identifier; ARCtrl.Path.AssayFileName|]
+        ARCtrl.ArcPathHelper.combineMany [|ARCtrl.ArcPathHelper.AssaysFolderName; identifier; ARCtrl.ArcPathHelper.AssayFileName|]
 
     /// <summary>
     /// On writing a xlsx file we unify our output to a relative path to ARC root. So: `assays/assayIdentifier/isa.assay.xlsx`.
     /// </summary>
     /// <param name="identifier">Any correct assay identifier</param>
     let tryFileNameFromIdentifier (identifier: string) : string option =        
         if tryCheckValidCharacters (identifier) then
-            ARCtrl.Path.combineMany [|ARCtrl.Path.AssaysFolderName; identifier; ARCtrl.Path.AssayFileName|]
+            ARCtrl.ArcPathHelper.combineMany [|ARCtrl.ArcPathHelper.AssaysFolderName; identifier; ARCtrl.ArcPathHelper.AssayFileName|]
             |> Some
         else None
 
@@ -94,15 +94,15 @@ module Assay =
     /// <param name="identifier">Any correct assay identifier</param>
     let datamapFileNameFromIdentifier (identifier: string) : string =        
         checkValidCharacters (identifier)
-        ARCtrl.Path.combineMany [|ARCtrl.Path.AssaysFolderName; identifier; ARCtrl.Path.DataMapFileName|]
+        ARCtrl.ArcPathHelper.combineMany [|ARCtrl.ArcPathHelper.AssaysFolderName; identifier; ARCtrl.ArcPathHelper.DataMapFileName|]
 
     /// <summary>
     /// On writing a xlsx file we unify our output to a relative path to ARC root. So: `assays/assayIdentifier/isa.datamap.xlsx`.
     /// </summary>
     /// <param name="identifier">Any correct assay identifier</param>
     let tryDatamapFileNameFromIdentifier (identifier: string) : string option =        
         if tryCheckValidCharacters (identifier) then
-            ARCtrl.Path.combineMany [|ARCtrl.Path.AssaysFolderName; identifier; ARCtrl.Path.DataMapFileName|]
+            ARCtrl.ArcPathHelper.combineMany [|ARCtrl.ArcPathHelper.AssaysFolderName; identifier; ARCtrl.ArcPathHelper.DataMapFileName|]
             |> Some
         else None
 
@@ -143,15 +143,15 @@ module Study =
     /// <param name="identifier">Any correct study identifier</param>
     let fileNameFromIdentifier (identifier: string) : string =
         checkValidCharacters (identifier)
-        ARCtrl.Path.combineMany [|ARCtrl.Path.StudiesFolderName; identifier; ARCtrl.Path.StudyFileName|]
+        ARCtrl.ArcPathHelper.combineMany [|ARCtrl.ArcPathHelper.StudiesFolderName; identifier; ARCtrl.ArcPathHelper.StudyFileName|]
 
     /// <summary>
     /// On writing a xlsx file we unify our output to a relative path to ARC root. So: `studies/studyIdentifier/isa.study.xlsx`.
     /// </summary>
     /// <param name="identifier">Any correct study identifier</param>
     let tryFileNameFromIdentifier (identifier: string) : string option =
         if tryCheckValidCharacters (identifier) then
-            ARCtrl.Path.combineMany [|ARCtrl.Path.StudiesFolderName; identifier; ARCtrl.Path.StudyFileName|]
+            ARCtrl.ArcPathHelper.combineMany [|ARCtrl.ArcPathHelper.StudiesFolderName; identifier; ARCtrl.ArcPathHelper.StudyFileName|]
             |> Some
         else None
 
@@ -161,14 +161,14 @@ module Study =
     /// <param name="identifier">Any correct study identifier</param>
     let datamapFileNameFromIdentifier (identifier: string) : string =
         checkValidCharacters (identifier)
-        ARCtrl.Path.combineMany [|ARCtrl.Path.StudiesFolderName; identifier; ARCtrl.Path.DataMapFileName|]
+        ARCtrl.ArcPathHelper.combineMany [|ARCtrl.ArcPathHelper.StudiesFolderName; identifier; ARCtrl.ArcPathHelper.DataMapFileName|]
 
     /// <summary>
     /// On writing a xlsx file we unify our output to a relative path to ARC root. So: `studies/studyIdentifier/isa.investigation.xlsx`.
     /// </summary>
     /// <param name="identifier">Any correct study identifier</param>
     let tryDatamapFileNameFromIdentifier (identifier: string) : string option =
         if tryCheckValidCharacters (identifier) then
-            ARCtrl.Path.combineMany [|ARCtrl.Path.StudiesFolderName; identifier; ARCtrl.Path.DataMapFileName|]
+            ARCtrl.ArcPathHelper.combineMany [|ARCtrl.ArcPathHelper.StudiesFolderName; identifier; ARCtrl.ArcPathHelper.DataMapFileName|]
             |> Some
         else None