diff --git a/ARCtrl.sln b/ARCtrl.sln index 5f87c45f..8c608dcc 100644 --- a/ARCtrl.sln +++ b/ARCtrl.sln @@ -16,9 +16,9 @@ Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Solution Items", "Solution RELEASE_NOTES.md = RELEASE_NOTES.md EndProjectSection EndProject -Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "CWL", "src\CWL\CWL.fsproj", "{1CD34A01-D19A-441F-8F3D-6EF69D9DDA8D}" +Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.CWL", "src\CWL\ARCtrl.CWL.fsproj", "{1CD34A01-D19A-441F-8F3D-6EF69D9DDA8D}" EndProject -Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "FileSystem", "src\FileSystem\FileSystem.fsproj", "{F47E23C3-8415-4725-9E85-57271694DEB3}" +Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.FileSystem", "src\FileSystem\ARCtrl.FileSystem.fsproj", "{F47E23C3-8415-4725-9E85-57271694DEB3}" EndProject Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "js", "js", "{A3669129-8963-4F6E-A1D6-C691555EF125}" ProjectSection(SolutionItems) = preProject @@ -76,13 +76,14 @@ Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "Build", "build\Build.fsproj EndProject Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "ISA", "ISA", "{C61B3F43-2255-4585-9110-F8AB74F02654}" ProjectSection(SolutionItems) = preProject + src\ISA\ISA\ArcTypes\ArcInvestigation.fs = src\ISA\ISA\ArcTypes\ArcInvestigation.fs src\ISA\package.json = src\ISA\package.json src\ISA\README.md = src\ISA\README.md EndProjectSection EndProject -Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ISA", "src\ISA\ISA\ISA.fsproj", "{67CF6725-6AC0-47FB-A725-6DC2192713B5}" +Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.ISA", "src\ISA\ISA\ARCtrl.ISA.fsproj", "{67CF6725-6AC0-47FB-A725-6DC2192713B5}" EndProject -Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ISA.Json", "src\ISA\ISA.Json\ISA.Json.fsproj", "{2CA397B2-0220-49A3-AD79-2F9F53633EC1}" +Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.ISA.Json", "src\ISA\ISA.Json\ARCtrl.ISA.Json.fsproj", "{2CA397B2-0220-49A3-AD79-2F9F53633EC1}" EndProject Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "tests", "tests", "{64B34A6E-318D-4E6E-9262-CE52C9B85A38}" EndProject @@ -92,7 +93,7 @@ Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ISA.Tests", "tests\ISA\ISA. EndProject Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ISA.Json.Tests", "tests\ISA\ISA.Json.Tests\ISA.Json.Tests.fsproj", "{04789F17-3DC2-4A09-848D-376E5D269740}" EndProject -Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ISA.Spreadsheet", "src\ISA\ISA.Spreadsheet\ISA.Spreadsheet.fsproj", "{07C7942E-FC34-4C27-82C1-6B2972654BA7}" +Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.ISA.Spreadsheet", "src\ISA\ISA.Spreadsheet\ARCtrl.ISA.Spreadsheet.fsproj", "{07C7942E-FC34-4C27-82C1-6B2972654BA7}" EndProject Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ISA.Spreadsheet.Tests", "tests\ISA\ISA.Spreadsheet.Tests\ISA.Spreadsheet.Tests.fsproj", "{656E8DAF-EFCF-472E-91D0-987D09B74523}" EndProject @@ -115,7 +116,7 @@ Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl", "src\ARCtrl\ARCtrl EndProject Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.Tests", "tests\ARCtrl\ARCtrl.Tests.fsproj", "{801247D5-7EE5-49C8-AB26-F822A415BA49}" EndProject -Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "Contract", "src\Contract\Contract.fsproj", "{1945EE8A-F105-43A9-91C9-8C4422B9873E}" +Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.Contract", "src\Contract\ARCtrl.Contract.fsproj", "{1945EE8A-F105-43A9-91C9-8C4422B9873E}" EndProject Global GlobalSection(SolutionConfigurationPlatforms) = preSolution diff --git a/playground/KevinF.fsx b/playground/KevinF.fsx index 83ad1a13..58e3dfa1 100644 --- a/playground/KevinF.fsx +++ b/playground/KevinF.fsx @@ -15,7 +15,7 @@ let [] rootPath = @"C:\Users\Kevin\Desktop\TestARC" open Contract open ARCtrl -open FileSystem +open ARCtrl.FileSystem module ARC_IO = open FsSpreadsheet @@ -45,10 +45,10 @@ let myarc = ARC_IO.initExistingARC(rootPath) let newArcPath = System.IO.Path.Combine(__SOURCE_DIRECTORY__, "TestArc") -open ISA +open ARCtrl.ISA open FsSpreadsheet open FsSpreadsheet.ExcelIO -open ISA.Spreadsheet +open ARCtrl.ISA.Spreadsheet module WriteContracts = diff --git a/playground/testScript.fsx b/playground/testScript.fsx index b10c6bda..f2e0fea6 100644 --- a/playground/testScript.fsx +++ b/playground/testScript.fsx @@ -10,8 +10,8 @@ #r "ISA.dll" open ARC -open FileSystem -open ISA +open ARCtrl.FileSystem +open ARCtrl.ISA open System.IO let arcPath = Path.Combine(__SOURCE_DIRECTORY__, "testArc") diff --git a/src/ARCtrl/ARCtrl.fs b/src/ARCtrl/ARCtrl.fs index b780a897..08fa314a 100644 --- a/src/ARCtrl/ARCtrl.fs +++ b/src/ARCtrl/ARCtrl.fs @@ -1,8 +1,8 @@ namespace ARCtrl -open FileSystem -open Contract -open ISA +open ARCtrl.FileSystem +open ARCtrl.Contract +open ARCtrl.ISA open FsSpreadsheet open Fable.Core @@ -11,18 +11,18 @@ module ARCAux = // No idea where to move this let getArcAssaysFromContracts (contracts: Contract []) = contracts - |> Array.choose Contracts.ArcAssay.tryFromContract + |> Array.choose ARCtrl.Contract.ArcAssay.tryFromContract |> Array.map (fun x -> x :?> FsWorkbook |> ISA.Spreadsheet.ArcAssay.fromFsWorkbook) // No idea where to move this let getArcStudiesFromContracts (contracts: Contract []) = contracts - |> Array.choose Contracts.ArcStudy.tryFromContract + |> Array.choose Contract.ArcStudy.tryFromContract |> Array.map (fun x -> x :?> FsWorkbook |> ISA.Spreadsheet.ArcStudy.fromFsWorkbook) let getArcInvestigationFromContracts (contracts: Contract []) = contracts - |> Array.choose Contracts.ArcInvestigation.tryFromContract + |> Array.choose Contract.ArcInvestigation.tryFromContract |> Array.exactlyOne |> fun x -> x :?> FsWorkbook |> ISA.Spreadsheet.ArcInvestigation.fromFsWorkbook @@ -151,7 +151,7 @@ type ARC(?isa : ISA.ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSyste // to-do: function that returns read contracts based on a list of paths. member this.GetReadContracts () = - fs.Tree.ToFilePaths() |> Array.choose Contracts.ARCtrl.tryISAReadContractFromPath + fs.Tree.ToFilePaths() |> Array.choose Contract.ARC.tryISAReadContractFromPath /// /// This function creates the ARC-model from fullfilled READ contracts. The necessary READ contracts can be created with `ARC.getReadContracts`. diff --git a/src/ARCtrl/ARCtrl.fsproj b/src/ARCtrl/ARCtrl.fsproj index 7b760de6..6ca25014 100644 --- a/src/ARCtrl/ARCtrl.fsproj +++ b/src/ARCtrl/ARCtrl.fsproj @@ -21,12 +21,12 @@ - - - - - - + + + + + + diff --git a/src/ARCtrl/Contracts/Contracts.ARCtrl.fs b/src/ARCtrl/Contracts/Contracts.ARCtrl.fs index e349efbc..78c5477d 100644 --- a/src/ARCtrl/Contracts/Contracts.ARCtrl.fs +++ b/src/ARCtrl/Contracts/Contracts.ARCtrl.fs @@ -1,11 +1,10 @@ -module Contracts.ARCtrl +module ARCtrl.Contract.ARC open ARCtrl.Path -open Contract -open Contracts.ArcInvestigation -open Contracts.ArcAssay -open Contracts.ArcStudy +open ARCtrl.Contract.ArcInvestigation +open ARCtrl.Contract.ArcAssay +open ARCtrl.Contract.ArcStudy // Assumptions: // 1. All ISA .xlsx files MUST have the same names, either "isa.investigation.xlsx", "isa.assay.xlsx" or "isa.study.xlsx" diff --git a/src/ARCtrl/Contracts/Contracts.ArcAssay.fs b/src/ARCtrl/Contracts/Contracts.ArcAssay.fs index 4450a19c..de790e65 100644 --- a/src/ARCtrl/Contracts/Contracts.ArcAssay.fs +++ b/src/ARCtrl/Contracts/Contracts.ArcAssay.fs @@ -1,6 +1,4 @@ -module Contracts.ArcAssay - -open Contract +module ARCtrl.Contract.ArcAssay let tryFromContract (c:Contract) = match c with diff --git a/src/ARCtrl/Contracts/Contracts.ArcInvestigation.fs b/src/ARCtrl/Contracts/Contracts.ArcInvestigation.fs index e8e5c794..7aabd4aa 100644 --- a/src/ARCtrl/Contracts/Contracts.ArcInvestigation.fs +++ b/src/ARCtrl/Contracts/Contracts.ArcInvestigation.fs @@ -1,6 +1,4 @@ -module Contracts.ArcInvestigation - -open Contract +module ARCtrl.Contract.ArcInvestigation let tryFromContract (c:Contract) = match c with diff --git a/src/ARCtrl/Contracts/Contracts.ArcStudy.fs b/src/ARCtrl/Contracts/Contracts.ArcStudy.fs index d008915d..b7706bf0 100644 --- a/src/ARCtrl/Contracts/Contracts.ArcStudy.fs +++ b/src/ARCtrl/Contracts/Contracts.ArcStudy.fs @@ -1,6 +1,4 @@ -module Contracts.ArcStudy - -open Contract +module ARCtrl.Contract.ArcStudy let tryFromContract (c:Contract) = match c with diff --git a/src/ARCtrl/FileSystemTree.fs b/src/ARCtrl/FileSystemTree.fs index 613efdcb..66d742d3 100644 --- a/src/ARCtrl/FileSystemTree.fs +++ b/src/ARCtrl/FileSystemTree.fs @@ -1,6 +1,6 @@ module ARCtrl.FileSystemTree -open FileSystem +open ARCtrl.FileSystem let createGitKeepFile() = FileSystemTree.createFile ARCtrl.Path.GitKeepFileName diff --git a/src/ARCtrl/Path.fs b/src/ARCtrl/Path.fs index 925cca93..626ef940 100644 --- a/src/ARCtrl/Path.fs +++ b/src/ARCtrl/Path.fs @@ -1,7 +1,7 @@ module ARCtrl.Path -open ISA -open FileSystem +open ARCtrl.ISA +open ARCtrl.FileSystem // Files let [] GitKeepFileName = ".gitkeep" diff --git a/src/CWL/CWL.fsproj b/src/CWL/ARCtrl.CWL.fsproj similarity index 100% rename from src/CWL/CWL.fsproj rename to src/CWL/ARCtrl.CWL.fsproj diff --git a/src/CWL/Library.fs b/src/CWL/Library.fs index 7056c318..13b78b55 100644 --- a/src/CWL/Library.fs +++ b/src/CWL/Library.fs @@ -1,3 +1,3 @@ -namespace CWL +namespace ARCtrl.CWL type CWL = unit \ No newline at end of file diff --git a/src/Contract/Contract.fsproj b/src/Contract/ARCtrl.Contract.fsproj similarity index 100% rename from src/Contract/Contract.fsproj rename to src/Contract/ARCtrl.Contract.fsproj diff --git a/src/Contract/Contract.fs b/src/Contract/Contract.fs index b5c310fc..aa85ec76 100644 --- a/src/Contract/Contract.fs +++ b/src/Contract/Contract.fs @@ -1,4 +1,4 @@ -namespace Contract +namespace ARCtrl.Contract open Fable.Core open FsSpreadsheet diff --git a/src/FileSystem/FileSystem.fsproj b/src/FileSystem/ARCtrl.FileSystem.fsproj similarity index 100% rename from src/FileSystem/FileSystem.fsproj rename to src/FileSystem/ARCtrl.FileSystem.fsproj diff --git a/src/FileSystem/Commit.fs b/src/FileSystem/Commit.fs index 5414d6b4..7449d0dd 100644 --- a/src/FileSystem/Commit.fs +++ b/src/FileSystem/Commit.fs @@ -1,4 +1,4 @@ -namespace FileSystem +namespace ARCtrl.FileSystem open Fable.Core diff --git a/src/FileSystem/FileSystem.fs b/src/FileSystem/FileSystem.fs index 9594ee54..33b18d8a 100644 --- a/src/FileSystem/FileSystem.fs +++ b/src/FileSystem/FileSystem.fs @@ -1,4 +1,4 @@ -namespace FileSystem +namespace ARCtrl.FileSystem open Fable.Core diff --git a/src/FileSystem/FileSystemTree.fs b/src/FileSystem/FileSystemTree.fs index 794aa33e..31d07856 100644 --- a/src/FileSystem/FileSystemTree.fs +++ b/src/FileSystem/FileSystemTree.fs @@ -1,4 +1,4 @@ -namespace FileSystem +namespace ARCtrl.FileSystem open Fable.Core diff --git a/src/ISA/ISA.Json/ISA.Json.fsproj b/src/ISA/ISA.Json/ARCtrl.ISA.Json.fsproj similarity index 96% rename from src/ISA/ISA.Json/ISA.Json.fsproj rename to src/ISA/ISA.Json/ARCtrl.ISA.Json.fsproj index 6b8babe4..3d4b8903 100644 --- a/src/ISA/ISA.Json/ISA.Json.fsproj +++ b/src/ISA/ISA.Json/ARCtrl.ISA.Json.fsproj @@ -31,14 +31,14 @@ - - - + + + diff --git a/src/ISA/ISA.Json/Assay.fs b/src/ISA/ISA.Json/Assay.fs index cd82763c..724ddaa7 100644 --- a/src/ISA/ISA.Json/Assay.fs +++ b/src/ISA/ISA.Json/Assay.fs @@ -1,11 +1,11 @@ -namespace ISA.Json +namespace ARCtrl.ISA.Json #if FABLE_COMPILER open Thoth.Json #else open Thoth.Json.Net #endif -open ISA +open ARCtrl.ISA open System.IO module AssayMaterials = diff --git a/src/ISA/ISA.Json/Comment.fs b/src/ISA/ISA.Json/Comment.fs index aca64f96..9d5cc98a 100644 --- a/src/ISA/ISA.Json/Comment.fs +++ b/src/ISA/ISA.Json/Comment.fs @@ -1,4 +1,4 @@ -namespace ISA.Json +namespace ARCtrl.ISA.Json #if FABLE_COMPILER @@ -6,7 +6,7 @@ open Thoth.Json #else open Thoth.Json.Net #endif -open ISA +open ARCtrl.ISA open System.IO module Comment = diff --git a/src/ISA/ISA.Json/ConverterOptions.fs b/src/ISA/ISA.Json/ConverterOptions.fs index 2e3a8575..9c0a08db 100644 --- a/src/ISA/ISA.Json/ConverterOptions.fs +++ b/src/ISA/ISA.Json/ConverterOptions.fs @@ -1,4 +1,4 @@ -namespace ISA.Json +namespace ARCtrl.ISA.Json type ConverterOptions() = diff --git a/src/ISA/ISA.Json/Data.fs b/src/ISA/ISA.Json/Data.fs index f27b0f2d..12bdf82c 100644 --- a/src/ISA/ISA.Json/Data.fs +++ b/src/ISA/ISA.Json/Data.fs @@ -1,11 +1,11 @@ -namespace ISA.Json +namespace ARCtrl.ISA.Json #if FABLE_COMPILER open Thoth.Json #else open Thoth.Json.Net #endif -open ISA +open ARCtrl.ISA open System.IO module DataFile = diff --git a/src/ISA/ISA.Json/Decode.fs b/src/ISA/ISA.Json/Decode.fs index 05529d12..0da7bcd0 100644 --- a/src/ISA/ISA.Json/Decode.fs +++ b/src/ISA/ISA.Json/Decode.fs @@ -1,4 +1,4 @@ -namespace ISA.Json +namespace ARCtrl.ISA.Json #if FABLE_COMPILER open Thoth.Json @@ -7,7 +7,7 @@ open Thoth.Json.Net open Newtonsoft.Json.Linq #endif -open ISA +open ARCtrl.ISA open Fable.Core module GDecode = diff --git a/src/ISA/ISA.Json/Factor.fs b/src/ISA/ISA.Json/Factor.fs index b7636f78..57e995cd 100644 --- a/src/ISA/ISA.Json/Factor.fs +++ b/src/ISA/ISA.Json/Factor.fs @@ -1,11 +1,11 @@ -namespace ISA.Json +namespace ARCtrl.ISA.Json #if FABLE_COMPILER open Thoth.Json #else open Thoth.Json.Net #endif -open ISA +open ARCtrl.ISA open System.IO module Value = diff --git a/src/ISA/ISA.Json/GEncode.fs b/src/ISA/ISA.Json/GEncode.fs index a6a096a6..5287cb6a 100644 --- a/src/ISA/ISA.Json/GEncode.fs +++ b/src/ISA/ISA.Json/GEncode.fs @@ -1,4 +1,4 @@ -namespace ISA.Json +namespace ARCtrl.ISA.Json #if FABLE_COMPILER open Thoth.Json @@ -26,7 +26,7 @@ module GEncode = property |> Option.bind (fun property -> match FSharp.Reflection.FSharpValue.GetRecordField (object,property) with - | ISA.Aux.Update.SomeObj o -> + | ARCtrl.ISA.Aux.Update.SomeObj o -> Some o | o when isNull o -> None diff --git a/src/ISA/ISA.Json/Investigation.fs b/src/ISA/ISA.Json/Investigation.fs index c637524a..c3920986 100644 --- a/src/ISA/ISA.Json/Investigation.fs +++ b/src/ISA/ISA.Json/Investigation.fs @@ -1,11 +1,11 @@ -namespace ISA.Json +namespace ARCtrl.ISA.Json #if FABLE_COMPILER open Thoth.Json #else open Thoth.Json.Net #endif -open ISA +open ARCtrl.ISA open System.IO module Investigation = diff --git a/src/ISA/ISA.Json/JsonSchemaValidation.fs b/src/ISA/ISA.Json/JsonSchemaValidation.fs index 9b0cc000..a6a7a6e5 100644 --- a/src/ISA/ISA.Json/JsonSchemaValidation.fs +++ b/src/ISA/ISA.Json/JsonSchemaValidation.fs @@ -1,4 +1,4 @@ -namespace ISA.Validation +namespace ARCtrl.ISA.Validation module JSchema = diff --git a/src/ISA/ISA.Json/Material.fs b/src/ISA/ISA.Json/Material.fs index ec07f431..4646a22c 100644 --- a/src/ISA/ISA.Json/Material.fs +++ b/src/ISA/ISA.Json/Material.fs @@ -1,11 +1,11 @@ -namespace ISA.Json +namespace ARCtrl.ISA.Json #if FABLE_COMPILER open Thoth.Json #else open Thoth.Json.Net #endif -open ISA +open ARCtrl.ISA open System.IO diff --git a/src/ISA/ISA.Json/Ontology.fs b/src/ISA/ISA.Json/Ontology.fs index 03d37f88..74b677fc 100644 --- a/src/ISA/ISA.Json/Ontology.fs +++ b/src/ISA/ISA.Json/Ontology.fs @@ -1,11 +1,11 @@ -namespace ISA.Json +namespace ARCtrl.ISA.Json #if FABLE_COMPILER open Thoth.Json #else open Thoth.Json.Net #endif -open ISA +open ARCtrl.ISA open System.IO module AnnotationValue = diff --git a/src/ISA/ISA.Json/Person.fs b/src/ISA/ISA.Json/Person.fs index df2da880..fb32bf96 100644 --- a/src/ISA/ISA.Json/Person.fs +++ b/src/ISA/ISA.Json/Person.fs @@ -1,11 +1,11 @@ -namespace ISA.Json +namespace ARCtrl.ISA.Json #if FABLE_COMPILER open Thoth.Json #else open Thoth.Json.Net #endif -open ISA +open ARCtrl.ISA open System.IO module Person = diff --git a/src/ISA/ISA.Json/Process.fs b/src/ISA/ISA.Json/Process.fs index 3f010a92..410eeec7 100644 --- a/src/ISA/ISA.Json/Process.fs +++ b/src/ISA/ISA.Json/Process.fs @@ -1,11 +1,11 @@ -namespace ISA.Json +namespace ARCtrl.ISA.Json #if FABLE_COMPILER open Thoth.Json #else open Thoth.Json.Net #endif -open ISA +open ARCtrl.ISA open System.IO module ProcessParameterValue = diff --git a/src/ISA/ISA.Json/Protocol.fs b/src/ISA/ISA.Json/Protocol.fs index 5de74657..38531549 100644 --- a/src/ISA/ISA.Json/Protocol.fs +++ b/src/ISA/ISA.Json/Protocol.fs @@ -1,11 +1,11 @@ -namespace ISA.Json +namespace ARCtrl.ISA.Json #if FABLE_COMPILER open Thoth.Json #else open Thoth.Json.Net #endif -open ISA +open ARCtrl.ISA module ProtocolParameter = diff --git a/src/ISA/ISA.Json/Publication.fs b/src/ISA/ISA.Json/Publication.fs index a7695bbc..c710f875 100644 --- a/src/ISA/ISA.Json/Publication.fs +++ b/src/ISA/ISA.Json/Publication.fs @@ -1,11 +1,11 @@ -namespace ISA.Json +namespace ARCtrl.ISA.Json #if FABLE_COMPILER open Thoth.Json #else open Thoth.Json.Net #endif -open ISA +open ARCtrl.ISA open System.IO module Publication = diff --git a/src/ISA/ISA.Json/Study.fs b/src/ISA/ISA.Json/Study.fs index 7a25f8de..a9a79bbc 100644 --- a/src/ISA/ISA.Json/Study.fs +++ b/src/ISA/ISA.Json/Study.fs @@ -1,11 +1,11 @@ -namespace ISA.Json +namespace ARCtrl.ISA.Json #if FABLE_COMPILER open Thoth.Json #else open Thoth.Json.Net #endif -open ISA +open ARCtrl.ISA open System.IO module StudyMaterials = diff --git a/src/ISA/ISA.Json/Validation/Fable.fs b/src/ISA/ISA.Json/Validation/Fable.fs index 13276767..6add8b2e 100644 --- a/src/ISA/ISA.Json/Validation/Fable.fs +++ b/src/ISA/ISA.Json/Validation/Fable.fs @@ -1,4 +1,4 @@ -namespace ISA.Json +namespace ARCtrl.ISA.Json module Fable = diff --git a/src/ISA/ISA.Json/Validation/JsonSchemaValidation.fs b/src/ISA/ISA.Json/Validation/JsonSchemaValidation.fs index 3a8f0648..cb714abb 100644 --- a/src/ISA/ISA.Json/Validation/JsonSchemaValidation.fs +++ b/src/ISA/ISA.Json/Validation/JsonSchemaValidation.fs @@ -1,4 +1,4 @@ -namespace ISA.Json +namespace ARCtrl.ISA.Json open ValidationTypes diff --git a/src/ISA/ISA.Json/Validation/ValidationResult.fs b/src/ISA/ISA.Json/Validation/ValidationResult.fs index e62c410a..3debc28a 100644 --- a/src/ISA/ISA.Json/Validation/ValidationResult.fs +++ b/src/ISA/ISA.Json/Validation/ValidationResult.fs @@ -1,4 +1,4 @@ -module ISA.Json.ValidationTypes +module ARCtrl.ISA.Json.ValidationTypes type ValidationResult = | Ok diff --git a/src/ISA/ISA.Json/ValidationResult.fs b/src/ISA/ISA.Json/ValidationResult.fs index 0a68fd43..2e806579 100644 --- a/src/ISA/ISA.Json/ValidationResult.fs +++ b/src/ISA/ISA.Json/ValidationResult.fs @@ -1,4 +1,4 @@ -namespace ISA.Validation +namespace ARCtrl.ISA.Validation type ValidationResult = | Ok diff --git a/src/ISA/ISA.Spreadsheet/ISA.Spreadsheet.fsproj b/src/ISA/ISA.Spreadsheet/ARCtrl.ISA.Spreadsheet.fsproj similarity index 92% rename from src/ISA/ISA.Spreadsheet/ISA.Spreadsheet.fsproj rename to src/ISA/ISA.Spreadsheet/ARCtrl.ISA.Spreadsheet.fsproj index 303af82e..99730437 100644 --- a/src/ISA/ISA.Spreadsheet/ISA.Spreadsheet.fsproj +++ b/src/ISA/ISA.Spreadsheet/ARCtrl.ISA.Spreadsheet.fsproj @@ -33,7 +33,7 @@ - + @@ -41,8 +41,8 @@ - - + + diff --git a/src/ISA/ISA.Spreadsheet/ArcAssay.fs b/src/ISA/ISA.Spreadsheet/ArcAssay.fs index 43f522fd..5dfbc93f 100644 --- a/src/ISA/ISA.Spreadsheet/ArcAssay.fs +++ b/src/ISA/ISA.Spreadsheet/ArcAssay.fs @@ -1,6 +1,6 @@ -module ISA.Spreadsheet.ArcAssay +module ARCtrl.ISA.Spreadsheet.ArcAssay -open ISA +open ARCtrl.ISA open FsSpreadsheet let [] obsoleteAssaysLabel = "ASSAY METADATA" diff --git a/src/ISA/ISA.Spreadsheet/ArcStudy.fs b/src/ISA/ISA.Spreadsheet/ArcStudy.fs index 811c5d0c..e6f385fe 100644 --- a/src/ISA/ISA.Spreadsheet/ArcStudy.fs +++ b/src/ISA/ISA.Spreadsheet/ArcStudy.fs @@ -1,6 +1,6 @@ -module ISA.Spreadsheet.ArcStudy +module ARCtrl.ISA.Spreadsheet.ArcStudy -open ISA +open ARCtrl.ISA open FsSpreadsheet let [] obsoleteStudiesLabel = "STUDY METADATA" diff --git a/src/ISA/ISA.Spreadsheet/ArcTable.fs b/src/ISA/ISA.Spreadsheet/ArcTable.fs index df1213f6..28091de7 100644 --- a/src/ISA/ISA.Spreadsheet/ArcTable.fs +++ b/src/ISA/ISA.Spreadsheet/ArcTable.fs @@ -1,6 +1,6 @@ -module ISA.Spreadsheet.ArcTable +module ARCtrl.ISA.Spreadsheet.ArcTable -open ISA +open ARCtrl.ISA open FsSpreadsheet // I think we really should not add FSharpAux for exactly one function. @@ -63,7 +63,7 @@ let annotationTablePrefix = "annotationTable" let groupColumnsByHeader (columns : list) = columns |> Aux.List.groupWhen (fun c -> - ISA.Regex.tryParseReferenceColumnHeader c.[1].Value + Regex.tryParseReferenceColumnHeader c.[1].Value |> Option.isNone && (c.[1].Value.StartsWith "Unit" |> not) diff --git a/src/ISA/ISA.Spreadsheet/CollectionAux.fs b/src/ISA/ISA.Spreadsheet/CollectionAux.fs index 2708aec1..642c081f 100644 --- a/src/ISA/ISA.Spreadsheet/CollectionAux.fs +++ b/src/ISA/ISA.Spreadsheet/CollectionAux.fs @@ -1,4 +1,4 @@ -namespace ISA.Spreadsheet +namespace ARCtrl.ISA.Spreadsheet module Seq = diff --git a/src/ISA/ISA.Spreadsheet/Comment.fs b/src/ISA/ISA.Spreadsheet/Comment.fs index 90d3e9c5..453edecf 100644 --- a/src/ISA/ISA.Spreadsheet/Comment.fs +++ b/src/ISA/ISA.Spreadsheet/Comment.fs @@ -1,6 +1,6 @@ -namespace ISA.Spreadsheet +namespace ARCtrl.ISA.Spreadsheet -open ISA +open ARCtrl.ISA open System.Text.RegularExpressions module Comment = diff --git a/src/ISA/ISA.Spreadsheet/CompositeCell.fs b/src/ISA/ISA.Spreadsheet/CompositeCell.fs index 4e102c3d..e8a7c110 100644 --- a/src/ISA/ISA.Spreadsheet/CompositeCell.fs +++ b/src/ISA/ISA.Spreadsheet/CompositeCell.fs @@ -1,6 +1,6 @@ -module ISA.Spreadsheet.CompositeCell +module ARCtrl.ISA.Spreadsheet.CompositeCell -open ISA +open ARCtrl.ISA open FsSpreadsheet let fromFsCells (cells : list) : CompositeCell = diff --git a/src/ISA/ISA.Spreadsheet/CompositeColumn.fs b/src/ISA/ISA.Spreadsheet/CompositeColumn.fs index eaed6126..225a3c6c 100644 --- a/src/ISA/ISA.Spreadsheet/CompositeColumn.fs +++ b/src/ISA/ISA.Spreadsheet/CompositeColumn.fs @@ -1,6 +1,6 @@ -module ISA.Spreadsheet.CompositeColumn +module ARCtrl.ISA.Spreadsheet.CompositeColumn -open ISA +open ARCtrl.ISA open FsSpreadsheet /// Checks if the column header is a deprecated IO Header. If so, fixes it. diff --git a/src/ISA/ISA.Spreadsheet/CompositeHeader.fs b/src/ISA/ISA.Spreadsheet/CompositeHeader.fs index 41045d9b..8787555f 100644 --- a/src/ISA/ISA.Spreadsheet/CompositeHeader.fs +++ b/src/ISA/ISA.Spreadsheet/CompositeHeader.fs @@ -1,11 +1,11 @@ -module ISA.Spreadsheet.CompositeHeader +module ARCtrl.ISA.Spreadsheet.CompositeHeader -open ISA +open ARCtrl.ISA open FsSpreadsheet module ActivePattern = - open ISA.Regex.ActivePatterns + open ARCtrl.ISA.Regex.ActivePatterns let mergeTerms tsr1 tan1 tsr2 tan2 = if tsr1 <> tsr2 then failwithf "TermSourceRef %s and %s do not match" tsr1 tsr2 diff --git a/src/ISA/ISA.Spreadsheet/Conversions.fs b/src/ISA/ISA.Spreadsheet/Conversions.fs index f5c9d043..0a912dd8 100644 --- a/src/ISA/ISA.Spreadsheet/Conversions.fs +++ b/src/ISA/ISA.Spreadsheet/Conversions.fs @@ -1,6 +1,6 @@ -namespace ISA.Spreadsheet +namespace ARCtrl.ISA.Spreadsheet -open ISA +open ARCtrl.ISA module internal Option = diff --git a/src/ISA/ISA.Spreadsheet/InvestigationFile/Assays.fs b/src/ISA/ISA.Spreadsheet/InvestigationFile/Assays.fs index 17815b38..ac1d521a 100644 --- a/src/ISA/ISA.Spreadsheet/InvestigationFile/Assays.fs +++ b/src/ISA/ISA.Spreadsheet/InvestigationFile/Assays.fs @@ -1,6 +1,6 @@ -namespace ISA.Spreadsheet +namespace ARCtrl.ISA.Spreadsheet -open ISA +open ARCtrl.ISA open Comment open Remark open System.Collections.Generic diff --git a/src/ISA/ISA.Spreadsheet/InvestigationFile/Contacts.fs b/src/ISA/ISA.Spreadsheet/InvestigationFile/Contacts.fs index 0f9621fd..8e0b257f 100644 --- a/src/ISA/ISA.Spreadsheet/InvestigationFile/Contacts.fs +++ b/src/ISA/ISA.Spreadsheet/InvestigationFile/Contacts.fs @@ -1,6 +1,6 @@ -namespace ISA.Spreadsheet +namespace ARCtrl.ISA.Spreadsheet -open ISA +open ARCtrl.ISA open Comment open Remark open System.Collections.Generic diff --git a/src/ISA/ISA.Spreadsheet/InvestigationFile/DesignDescriptors.fs b/src/ISA/ISA.Spreadsheet/InvestigationFile/DesignDescriptors.fs index 125e592c..7a6a7b4d 100644 --- a/src/ISA/ISA.Spreadsheet/InvestigationFile/DesignDescriptors.fs +++ b/src/ISA/ISA.Spreadsheet/InvestigationFile/DesignDescriptors.fs @@ -1,6 +1,6 @@ -namespace ISA.Spreadsheet +namespace ARCtrl.ISA.Spreadsheet -open ISA +open ARCtrl.ISA open Comment open Remark open System.Collections.Generic diff --git a/src/ISA/ISA.Spreadsheet/InvestigationFile/Factors.fs b/src/ISA/ISA.Spreadsheet/InvestigationFile/Factors.fs index 8850fc66..373b2843 100644 --- a/src/ISA/ISA.Spreadsheet/InvestigationFile/Factors.fs +++ b/src/ISA/ISA.Spreadsheet/InvestigationFile/Factors.fs @@ -1,6 +1,6 @@ -namespace ISA.Spreadsheet +namespace ARCtrl.ISA.Spreadsheet -open ISA +open ARCtrl.ISA open Comment open Remark open System.Collections.Generic diff --git a/src/ISA/ISA.Spreadsheet/InvestigationFile/Investigation.fs b/src/ISA/ISA.Spreadsheet/InvestigationFile/Investigation.fs index ee0e401e..d6c8d397 100644 --- a/src/ISA/ISA.Spreadsheet/InvestigationFile/Investigation.fs +++ b/src/ISA/ISA.Spreadsheet/InvestigationFile/Investigation.fs @@ -1,6 +1,6 @@ -namespace ISA.Spreadsheet +namespace ARCtrl.ISA.Spreadsheet -open ISA +open ARCtrl.ISA open FsSpreadsheet open Comment open Remark diff --git a/src/ISA/ISA.Spreadsheet/InvestigationFile/OntologySourceReference.fs b/src/ISA/ISA.Spreadsheet/InvestigationFile/OntologySourceReference.fs index 9210296a..1ab4cf3b 100644 --- a/src/ISA/ISA.Spreadsheet/InvestigationFile/OntologySourceReference.fs +++ b/src/ISA/ISA.Spreadsheet/InvestigationFile/OntologySourceReference.fs @@ -1,7 +1,7 @@ -namespace ISA.Spreadsheet +namespace ARCtrl.ISA.Spreadsheet open FsSpreadsheet -open ISA +open ARCtrl.ISA open System.Collections.Generic diff --git a/src/ISA/ISA.Spreadsheet/InvestigationFile/Protocols.fs b/src/ISA/ISA.Spreadsheet/InvestigationFile/Protocols.fs index 2c13536e..aaf3cebb 100644 --- a/src/ISA/ISA.Spreadsheet/InvestigationFile/Protocols.fs +++ b/src/ISA/ISA.Spreadsheet/InvestigationFile/Protocols.fs @@ -1,6 +1,6 @@ -namespace ISA.Spreadsheet +namespace ARCtrl.ISA.Spreadsheet -open ISA +open ARCtrl.ISA open Comment open Remark open System.Collections.Generic diff --git a/src/ISA/ISA.Spreadsheet/InvestigationFile/Publication.fs b/src/ISA/ISA.Spreadsheet/InvestigationFile/Publication.fs index e9df9619..183d73b0 100644 --- a/src/ISA/ISA.Spreadsheet/InvestigationFile/Publication.fs +++ b/src/ISA/ISA.Spreadsheet/InvestigationFile/Publication.fs @@ -1,6 +1,6 @@ -namespace ISA.Spreadsheet +namespace ARCtrl.ISA.Spreadsheet -open ISA +open ARCtrl.ISA open Comment open Remark open System.Collections.Generic diff --git a/src/ISA/ISA.Spreadsheet/InvestigationFile/Study.fs b/src/ISA/ISA.Spreadsheet/InvestigationFile/Study.fs index 28e9806c..d7c4748f 100644 --- a/src/ISA/ISA.Spreadsheet/InvestigationFile/Study.fs +++ b/src/ISA/ISA.Spreadsheet/InvestigationFile/Study.fs @@ -1,6 +1,6 @@ -namespace ISA.Spreadsheet +namespace ARCtrl.ISA.Spreadsheet -open ISA +open ARCtrl.ISA open Comment open Remark open System.Collections.Generic diff --git a/src/ISA/ISA.Spreadsheet/SparseTable.fs b/src/ISA/ISA.Spreadsheet/SparseTable.fs index 67c10c70..338793b3 100644 --- a/src/ISA/ISA.Spreadsheet/SparseTable.fs +++ b/src/ISA/ISA.Spreadsheet/SparseTable.fs @@ -1,7 +1,7 @@ -namespace ISA.Spreadsheet +namespace ARCtrl.ISA.Spreadsheet -open ISA -open ISA.Aux +open ARCtrl.ISA +open ARCtrl.ISA.Aux open System.Collections.Generic open FsSpreadsheet.DSL open FsSpreadsheet diff --git a/src/ISA/ISA.Viz/ISA.Viz.fsproj b/src/ISA/ISA.Viz/ISA.Viz.fsproj_ similarity index 100% rename from src/ISA/ISA.Viz/ISA.Viz.fsproj rename to src/ISA/ISA.Viz/ISA.Viz.fsproj_ diff --git a/src/ISA/ISA/ISA.fsproj b/src/ISA/ISA/ARCtrl.ISA.fsproj similarity index 98% rename from src/ISA/ISA/ISA.fsproj rename to src/ISA/ISA/ARCtrl.ISA.fsproj index 5573630f..7a140b40 100644 --- a/src/ISA/ISA/ISA.fsproj +++ b/src/ISA/ISA/ARCtrl.ISA.fsproj @@ -69,7 +69,7 @@ - + diff --git a/src/ISA/ISA/ArcTypes/ArcAssay.fs b/src/ISA/ISA/ArcTypes/ArcAssay.fs index 016b14c1..ae5ab9e5 100644 --- a/src/ISA/ISA/ArcTypes/ArcAssay.fs +++ b/src/ISA/ISA/ArcTypes/ArcAssay.fs @@ -1,7 +1,7 @@ -namespace ISA +namespace ARCtrl.ISA open Fable.Core -open ISA.Aux +open ARCtrl.ISA.Aux // "MyAssay"; "assays/MyAssay/isa.assay.xlsx" @@ -360,10 +360,10 @@ type ArcAssay(identifier: string, ?measurementType : OntologyAnnotation, ?techno ) |> Option.fromValueWithDefault AssayMaterials.empty let fileName = - if ISA.Identifier.isMissingIdentifier this.Identifier then + if ARCtrl.ISA.Identifier.isMissingIdentifier this.Identifier then None else - Some (ISA.Identifier.Assay.fileNameFromIdentifier this.Identifier) + Some (ARCtrl.ISA.Identifier.Assay.fileNameFromIdentifier this.Identifier) Assay.create( ?FileName = fileName, ?MeasurementType = this.MeasurementType, diff --git a/src/ISA/ISA/ArcTypes/ArcInvestigation.fs b/src/ISA/ISA/ArcTypes/ArcInvestigation.fs index b95cdd52..48f08876 100644 --- a/src/ISA/ISA/ArcTypes/ArcInvestigation.fs +++ b/src/ISA/ISA/ArcTypes/ArcInvestigation.fs @@ -1,7 +1,7 @@ -namespace ISA +namespace ARCtrl.ISA open Fable.Core -open ISA.Aux +open ARCtrl.ISA.Aux module ArcInvestigationAux = module SanityChecks = @@ -270,7 +270,7 @@ type ArcInvestigation(identifier : string, ?title : string, ?description : strin member this.ToInvestigation() : Investigation = let studies = this.Studies |> Seq.toList |> List.map (fun a -> a.ToStudy()) |> Option.fromValueWithDefault [] let identifier = - if ISA.Identifier.isMissingIdentifier this.Identifier then None + if ARCtrl.ISA.Identifier.isMissingIdentifier this.Identifier then None else Some this.Identifier Investigation.create( FileName = ARCtrl.Path.InvestigationFileName, diff --git a/src/ISA/ISA/ArcTypes/ArcStudy.fs b/src/ISA/ISA/ArcTypes/ArcStudy.fs index a38e2746..cafe313d 100644 --- a/src/ISA/ISA/ArcTypes/ArcStudy.fs +++ b/src/ISA/ISA/ArcTypes/ArcStudy.fs @@ -1,7 +1,7 @@ -namespace ISA +namespace ARCtrl.ISA open Fable.Core -open ISA.Aux +open ARCtrl.ISA.Aux module ArcStudyAux = module SanityChecks = @@ -488,7 +488,7 @@ type ArcStudy(identifier : string, ?title, ?description, ?submissionDate, ?publi ) |> Option.fromValueWithDefault StudyMaterials.empty let identifier,fileName = - if ISA.Identifier.isMissingIdentifier this.Identifier then + if ARCtrl.ISA.Identifier.isMissingIdentifier this.Identifier then None, None else Some this.Identifier, Some (Identifier.Study.fileNameFromIdentifier this.Identifier) diff --git a/src/ISA/ISA/ArcTypes/ArcTable.fs b/src/ISA/ISA/ArcTypes/ArcTable.fs index 5499efb9..4c88e3ac 100644 --- a/src/ISA/ISA/ArcTypes/ArcTable.fs +++ b/src/ISA/ISA/ArcTypes/ArcTable.fs @@ -1,4 +1,4 @@ -namespace ISA +namespace ARCtrl.ISA open Fable.Core open System.Collections.Generic diff --git a/src/ISA/ISA/ArcTypes/ArcTableAux.fs b/src/ISA/ISA/ArcTypes/ArcTableAux.fs index 62c0efeb..30f1e607 100644 --- a/src/ISA/ISA/ArcTypes/ArcTableAux.fs +++ b/src/ISA/ISA/ArcTypes/ArcTableAux.fs @@ -1,6 +1,6 @@ -module ISA.ArcTableAux +module ARCtrl.ISA.ArcTableAux -open ISA +open ARCtrl.ISA open System.Collections.Generic // Taken from FSharpAux.Core @@ -414,7 +414,7 @@ module JsonTypes = /// Functions for parsing ArcTables to ISA json Processes and vice versa module ProcessParsing = - open ISA.ColumnIndex + open ARCtrl.ISA.ColumnIndex /// If the headers of a node depict a component, returns a function for parsing the values of the matrix to the values of this component let tryComponentGetter (generalI : int) (valueI : int) (valueHeader : CompositeHeader) = @@ -667,7 +667,7 @@ module ProcessParsing = elif x.ExecutesProtocol.IsSome && x.ExecutesProtocol.Value.ID.IsSome then x.ExecutesProtocol.Value.ID.Value else - ISA.Identifier.createMissingIdentifier() + ARCtrl.ISA.Identifier.createMissingIdentifier() ) // Transform a isa json process into a isa tab row, where each row is a header+value list diff --git a/src/ISA/ISA/ArcTypes/ArcTables.fs b/src/ISA/ISA/ArcTypes/ArcTables.fs index f3da550f..6b2b2ca6 100644 --- a/src/ISA/ISA/ArcTypes/ArcTables.fs +++ b/src/ISA/ISA/ArcTypes/ArcTables.fs @@ -1,4 +1,4 @@ -namespace ISA +namespace ARCtrl.ISA module ArcTablesAux = diff --git a/src/ISA/ISA/ArcTypes/CompositeCell.fs b/src/ISA/ISA/ArcTypes/CompositeCell.fs index 8fa1f507..61d99aa8 100644 --- a/src/ISA/ISA/ArcTypes/CompositeCell.fs +++ b/src/ISA/ISA/ArcTypes/CompositeCell.fs @@ -1,4 +1,4 @@ -namespace ISA +namespace ARCtrl.ISA open Fable.Core diff --git a/src/ISA/ISA/ArcTypes/CompositeColumn.fs b/src/ISA/ISA/ArcTypes/CompositeColumn.fs index 90f00bbb..03b23ed1 100644 --- a/src/ISA/ISA/ArcTypes/CompositeColumn.fs +++ b/src/ISA/ISA/ArcTypes/CompositeColumn.fs @@ -1,4 +1,4 @@ -namespace ISA +namespace ARCtrl.ISA open Fable.Core diff --git a/src/ISA/ISA/ArcTypes/CompositeHeader.fs b/src/ISA/ISA/ArcTypes/CompositeHeader.fs index d4839654..04c439f2 100644 --- a/src/ISA/ISA/ArcTypes/CompositeHeader.fs +++ b/src/ISA/ISA/ArcTypes/CompositeHeader.fs @@ -1,4 +1,4 @@ -namespace ISA +namespace ARCtrl.ISA open Fable.Core diff --git a/src/ISA/ISA/ArcTypes/CompositeRow.fs b/src/ISA/ISA/ArcTypes/CompositeRow.fs index 8384d5e7..d3db4612 100644 --- a/src/ISA/ISA/ArcTypes/CompositeRow.fs +++ b/src/ISA/ISA/ArcTypes/CompositeRow.fs @@ -1,4 +1,4 @@ -module ISA.CompositeRow +module ARCtrl.ISA.CompositeRow let toProtocol (row : (CompositeHeader*CompositeCell) seq) = row diff --git a/src/ISA/ISA/ArcTypes/Identifier.fs b/src/ISA/ISA/ArcTypes/Identifier.fs index c16aadb8..fdc89bd4 100644 --- a/src/ISA/ISA/ArcTypes/Identifier.fs +++ b/src/ISA/ISA/ArcTypes/Identifier.fs @@ -1,5 +1,5 @@ /// This module contains helper functions to handle study/assay/investigation identifiers in an unsafe, forced way. -module ISA.Identifier +module ARCtrl.ISA.Identifier open System.Text.RegularExpressions diff --git a/src/ISA/ISA/ArcTypes/IdentifierSetters.fs b/src/ISA/ISA/ArcTypes/IdentifierSetters.fs index 45b88a26..b01519ea 100644 --- a/src/ISA/ISA/ArcTypes/IdentifierSetters.fs +++ b/src/ISA/ISA/ArcTypes/IdentifierSetters.fs @@ -1,6 +1,6 @@ -module ISA.IdentifierSetters +module ARCtrl.ISA.IdentifierSetters -open ISA.Identifier +open ARCtrl.ISA.Identifier let setAssayIdentifier (newIdentifier: string) (assay: ArcAssay) = checkValidCharacters newIdentifier diff --git a/src/ISA/ISA/Builder/Transform.fs b/src/ISA/ISA/Builder/Transform.fs index c6ffb899..e8deb9ae 100644 --- a/src/ISA/ISA/Builder/Transform.fs +++ b/src/ISA/ISA/Builder/Transform.fs @@ -1,6 +1,6 @@ -namespace ISA.Builder +namespace ARCtrl.ISA.Builder -open ISA +open ARCtrl.ISA //module Transform = diff --git a/src/ISA/ISA/Builder/Types.fs b/src/ISA/ISA/Builder/Types.fs index 1a338d29..d3a9eac3 100644 --- a/src/ISA/ISA/Builder/Types.fs +++ b/src/ISA/ISA/Builder/Types.fs @@ -1,6 +1,6 @@ -namespace ISA.Builder +namespace ARCtrl.ISA.Builder -open ISA +open ARCtrl.ISA type ProtocolTransformation = diff --git a/src/ISA/ISA/Fable.fs b/src/ISA/ISA/Fable.fs index 0e6f0056..b96bf4c1 100644 --- a/src/ISA/ISA/Fable.fs +++ b/src/ISA/ISA/Fable.fs @@ -1,5 +1,5 @@ [] -module ISA.Fable +module ARCtrl.ISA.Fable open Fable.Core open Fable.Core.JsInterop diff --git a/src/ISA/ISA/JsonTypes/AnnotationValue.fs b/src/ISA/ISA/JsonTypes/AnnotationValue.fs index fbfae8de..d8a7c5dc 100644 --- a/src/ISA/ISA/JsonTypes/AnnotationValue.fs +++ b/src/ISA/ISA/JsonTypes/AnnotationValue.fs @@ -1,4 +1,4 @@ -namespace ISA +namespace ARCtrl.ISA type AnnotationValue = | Text of string diff --git a/src/ISA/ISA/JsonTypes/Assay.fs b/src/ISA/ISA/JsonTypes/Assay.fs index e9113724..f9661417 100644 --- a/src/ISA/ISA/JsonTypes/Assay.fs +++ b/src/ISA/ISA/JsonTypes/Assay.fs @@ -1,6 +1,6 @@ -namespace ISA +namespace ARCtrl.ISA -open ISA.Aux +open ARCtrl.ISA.Aux open Update type Assay = diff --git a/src/ISA/ISA/JsonTypes/AssayMaterials.fs b/src/ISA/ISA/JsonTypes/AssayMaterials.fs index 76c9c7cf..ce35a08c 100644 --- a/src/ISA/ISA/JsonTypes/AssayMaterials.fs +++ b/src/ISA/ISA/JsonTypes/AssayMaterials.fs @@ -1,4 +1,4 @@ -namespace ISA +namespace ARCtrl.ISA type AssayMaterials = { diff --git a/src/ISA/ISA/JsonTypes/ColumnIndex.fs b/src/ISA/ISA/JsonTypes/ColumnIndex.fs index 91672df1..f96e036a 100644 --- a/src/ISA/ISA/JsonTypes/ColumnIndex.fs +++ b/src/ISA/ISA/JsonTypes/ColumnIndex.fs @@ -1,4 +1,4 @@ -module ISA.ColumnIndex +module ARCtrl.ISA.ColumnIndex let private tryInt (str:string) = diff --git a/src/ISA/ISA/JsonTypes/Comment.fs b/src/ISA/ISA/JsonTypes/Comment.fs index 2ada0dd6..29916e07 100644 --- a/src/ISA/ISA/JsonTypes/Comment.fs +++ b/src/ISA/ISA/JsonTypes/Comment.fs @@ -1,4 +1,4 @@ -namespace ISA +namespace ARCtrl.ISA type EMail = string diff --git a/src/ISA/ISA/JsonTypes/CommentList.fs b/src/ISA/ISA/JsonTypes/CommentList.fs index f4d3a0cc..82e5f51e 100644 --- a/src/ISA/ISA/JsonTypes/CommentList.fs +++ b/src/ISA/ISA/JsonTypes/CommentList.fs @@ -1,4 +1,4 @@ -module ISA.CommentArray +module ARCtrl.ISA.CommentArray /// If a comment with the given key exists in the [], return its value, else return None let tryItem (key: string) (comments : Comment []) = diff --git a/src/ISA/ISA/JsonTypes/Component.fs b/src/ISA/ISA/JsonTypes/Component.fs index 92336090..3962e69d 100644 --- a/src/ISA/ISA/JsonTypes/Component.fs +++ b/src/ISA/ISA/JsonTypes/Component.fs @@ -1,6 +1,6 @@ -namespace ISA +namespace ARCtrl.ISA -open ISA.Aux +open ARCtrl.ISA.Aux type Component = { diff --git a/src/ISA/ISA/JsonTypes/Data.fs b/src/ISA/ISA/JsonTypes/Data.fs index f1e6cfce..30944a83 100644 --- a/src/ISA/ISA/JsonTypes/Data.fs +++ b/src/ISA/ISA/JsonTypes/Data.fs @@ -1,4 +1,4 @@ -namespace ISA +namespace ARCtrl.ISA type Data = { diff --git a/src/ISA/ISA/JsonTypes/DataFile.fs b/src/ISA/ISA/JsonTypes/DataFile.fs index f0edd43e..effa7bad 100644 --- a/src/ISA/ISA/JsonTypes/DataFile.fs +++ b/src/ISA/ISA/JsonTypes/DataFile.fs @@ -1,4 +1,4 @@ -namespace ISA +namespace ARCtrl.ISA [] type DataFile = diff --git a/src/ISA/ISA/JsonTypes/Factor.fs b/src/ISA/ISA/JsonTypes/Factor.fs index 05d17212..e7b96383 100644 --- a/src/ISA/ISA/JsonTypes/Factor.fs +++ b/src/ISA/ISA/JsonTypes/Factor.fs @@ -1,6 +1,6 @@ -namespace ISA +namespace ARCtrl.ISA -open ISA.Aux +open ARCtrl.ISA.Aux open Update type Factor = diff --git a/src/ISA/ISA/JsonTypes/FactorValue.fs b/src/ISA/ISA/JsonTypes/FactorValue.fs index f50af012..053a09c6 100644 --- a/src/ISA/ISA/JsonTypes/FactorValue.fs +++ b/src/ISA/ISA/JsonTypes/FactorValue.fs @@ -1,4 +1,4 @@ -namespace ISA +namespace ARCtrl.ISA type FactorValue = { diff --git a/src/ISA/ISA/JsonTypes/Investigation.fs b/src/ISA/ISA/JsonTypes/Investigation.fs index 04875a20..34da5445 100644 --- a/src/ISA/ISA/JsonTypes/Investigation.fs +++ b/src/ISA/ISA/JsonTypes/Investigation.fs @@ -1,6 +1,6 @@ -namespace ISA +namespace ARCtrl.ISA -open ISA.Aux +open ARCtrl.ISA.Aux type Investigation = { diff --git a/src/ISA/ISA/JsonTypes/Material.fs b/src/ISA/ISA/JsonTypes/Material.fs index 4851c926..46e03407 100644 --- a/src/ISA/ISA/JsonTypes/Material.fs +++ b/src/ISA/ISA/JsonTypes/Material.fs @@ -1,4 +1,4 @@ -namespace ISA +namespace ARCtrl.ISA type Material = { diff --git a/src/ISA/ISA/JsonTypes/MaterialAttribute.fs b/src/ISA/ISA/JsonTypes/MaterialAttribute.fs index da25d58f..272a8330 100644 --- a/src/ISA/ISA/JsonTypes/MaterialAttribute.fs +++ b/src/ISA/ISA/JsonTypes/MaterialAttribute.fs @@ -1,6 +1,6 @@ -namespace ISA +namespace ARCtrl.ISA -open ISA.Aux +open ARCtrl.ISA.Aux open Update type MaterialAttribute = diff --git a/src/ISA/ISA/JsonTypes/MaterialAttributeValue.fs b/src/ISA/ISA/JsonTypes/MaterialAttributeValue.fs index 2bcb7dec..6c3d0450 100644 --- a/src/ISA/ISA/JsonTypes/MaterialAttributeValue.fs +++ b/src/ISA/ISA/JsonTypes/MaterialAttributeValue.fs @@ -1,4 +1,4 @@ -namespace ISA +namespace ARCtrl.ISA type MaterialAttributeValue = { diff --git a/src/ISA/ISA/JsonTypes/MaterialType.fs b/src/ISA/ISA/JsonTypes/MaterialType.fs index fedbceb2..eabab783 100644 --- a/src/ISA/ISA/JsonTypes/MaterialType.fs +++ b/src/ISA/ISA/JsonTypes/MaterialType.fs @@ -1,4 +1,4 @@ -namespace ISA +namespace ARCtrl.ISA type MaterialType = | ExtractName // "Extract Name" diff --git a/src/ISA/ISA/JsonTypes/OntologyAnnotation.fs b/src/ISA/ISA/JsonTypes/OntologyAnnotation.fs index 9d62230b..e34e6876 100644 --- a/src/ISA/ISA/JsonTypes/OntologyAnnotation.fs +++ b/src/ISA/ISA/JsonTypes/OntologyAnnotation.fs @@ -1,6 +1,6 @@ -namespace ISA +namespace ARCtrl.ISA -open ISA.Aux +open ARCtrl.ISA.Aux open Update [] diff --git a/src/ISA/ISA/JsonTypes/OntologySourceReference.fs b/src/ISA/ISA/JsonTypes/OntologySourceReference.fs index d948ec7f..3718d098 100644 --- a/src/ISA/ISA/JsonTypes/OntologySourceReference.fs +++ b/src/ISA/ISA/JsonTypes/OntologySourceReference.fs @@ -1,6 +1,6 @@ -namespace ISA +namespace ARCtrl.ISA -open ISA.Aux +open ARCtrl.ISA.Aux open Update type OntologySourceReference = diff --git a/src/ISA/ISA/JsonTypes/Person.fs b/src/ISA/ISA/JsonTypes/Person.fs index 5ea1f34b..f04019e2 100644 --- a/src/ISA/ISA/JsonTypes/Person.fs +++ b/src/ISA/ISA/JsonTypes/Person.fs @@ -1,6 +1,6 @@ -namespace ISA +namespace ARCtrl.ISA -open ISA.Aux +open ARCtrl.ISA.Aux open Update type Person = diff --git a/src/ISA/ISA/JsonTypes/Process.fs b/src/ISA/ISA/JsonTypes/Process.fs index 3cb8476f..12fe09c9 100644 --- a/src/ISA/ISA/JsonTypes/Process.fs +++ b/src/ISA/ISA/JsonTypes/Process.fs @@ -1,6 +1,6 @@ -namespace ISA +namespace ARCtrl.ISA -open ISA.Aux +open ARCtrl.ISA.Aux open Update type Process = diff --git a/src/ISA/ISA/JsonTypes/ProcessInput.fs b/src/ISA/ISA/JsonTypes/ProcessInput.fs index a4d2a7a5..a8f65311 100644 --- a/src/ISA/ISA/JsonTypes/ProcessInput.fs +++ b/src/ISA/ISA/JsonTypes/ProcessInput.fs @@ -1,6 +1,6 @@ -namespace ISA +namespace ARCtrl.ISA -open ISA.Aux +open ARCtrl.ISA.Aux open Update [] diff --git a/src/ISA/ISA/JsonTypes/ProcessOutput.fs b/src/ISA/ISA/JsonTypes/ProcessOutput.fs index 6cf5b05e..e53f6ac3 100644 --- a/src/ISA/ISA/JsonTypes/ProcessOutput.fs +++ b/src/ISA/ISA/JsonTypes/ProcessOutput.fs @@ -1,6 +1,6 @@ -namespace ISA +namespace ARCtrl.ISA -open ISA.Aux +open ARCtrl.ISA.Aux open Update [] diff --git a/src/ISA/ISA/JsonTypes/ProcessParameterValue.fs b/src/ISA/ISA/JsonTypes/ProcessParameterValue.fs index 251cd58c..babfa8e4 100644 --- a/src/ISA/ISA/JsonTypes/ProcessParameterValue.fs +++ b/src/ISA/ISA/JsonTypes/ProcessParameterValue.fs @@ -1,4 +1,4 @@ -namespace ISA +namespace ARCtrl.ISA type ProcessParameterValue = diff --git a/src/ISA/ISA/JsonTypes/ProcessSequence.fs b/src/ISA/ISA/JsonTypes/ProcessSequence.fs index c2fe6299..cf6f8a50 100644 --- a/src/ISA/ISA/JsonTypes/ProcessSequence.fs +++ b/src/ISA/ISA/JsonTypes/ProcessSequence.fs @@ -1,6 +1,6 @@ -module ISA.ProcessSequence +module ARCtrl.ISA.ProcessSequence -open ISA.Aux +open ARCtrl.ISA.Aux open Update /// Returns the names of the protocols the given processes impelement diff --git a/src/ISA/ISA/JsonTypes/Protocol.fs b/src/ISA/ISA/JsonTypes/Protocol.fs index 0a25c0e0..b02320f9 100644 --- a/src/ISA/ISA/JsonTypes/Protocol.fs +++ b/src/ISA/ISA/JsonTypes/Protocol.fs @@ -1,6 +1,6 @@ -namespace ISA +namespace ARCtrl.ISA -open ISA.Aux +open ARCtrl.ISA.Aux open Update type Protocol = diff --git a/src/ISA/ISA/JsonTypes/ProtocolParameter.fs b/src/ISA/ISA/JsonTypes/ProtocolParameter.fs index 4e932556..55558e67 100644 --- a/src/ISA/ISA/JsonTypes/ProtocolParameter.fs +++ b/src/ISA/ISA/JsonTypes/ProtocolParameter.fs @@ -1,6 +1,6 @@ -namespace ISA +namespace ARCtrl.ISA -open ISA.Aux +open ARCtrl.ISA.Aux open Update type ProtocolParameter = diff --git a/src/ISA/ISA/JsonTypes/Publication.fs b/src/ISA/ISA/JsonTypes/Publication.fs index bd3ab284..0745a5ab 100644 --- a/src/ISA/ISA/JsonTypes/Publication.fs +++ b/src/ISA/ISA/JsonTypes/Publication.fs @@ -1,6 +1,6 @@ -namespace ISA +namespace ARCtrl.ISA -open ISA.Aux +open ARCtrl.ISA.Aux open Update type Publication = diff --git a/src/ISA/ISA/JsonTypes/Sample.fs b/src/ISA/ISA/JsonTypes/Sample.fs index eddb76a3..dcebb978 100644 --- a/src/ISA/ISA/JsonTypes/Sample.fs +++ b/src/ISA/ISA/JsonTypes/Sample.fs @@ -1,4 +1,4 @@ -namespace ISA +namespace ARCtrl.ISA type Sample = { diff --git a/src/ISA/ISA/JsonTypes/Source.fs b/src/ISA/ISA/JsonTypes/Source.fs index bd55e2a0..bfd05b57 100644 --- a/src/ISA/ISA/JsonTypes/Source.fs +++ b/src/ISA/ISA/JsonTypes/Source.fs @@ -1,4 +1,4 @@ -namespace ISA +namespace ARCtrl.ISA type Source = diff --git a/src/ISA/ISA/JsonTypes/Study.fs b/src/ISA/ISA/JsonTypes/Study.fs index 533fd659..1d90868b 100644 --- a/src/ISA/ISA/JsonTypes/Study.fs +++ b/src/ISA/ISA/JsonTypes/Study.fs @@ -1,6 +1,6 @@ -namespace ISA +namespace ARCtrl.ISA -open ISA.Aux +open ARCtrl.ISA.Aux open Update diff --git a/src/ISA/ISA/JsonTypes/StudyMaterials.fs b/src/ISA/ISA/JsonTypes/StudyMaterials.fs index 55a9406b..01be6370 100644 --- a/src/ISA/ISA/JsonTypes/StudyMaterials.fs +++ b/src/ISA/ISA/JsonTypes/StudyMaterials.fs @@ -1,4 +1,4 @@ -namespace ISA +namespace ARCtrl.ISA type StudyMaterials = { diff --git a/src/ISA/ISA/JsonTypes/URI.fs b/src/ISA/ISA/JsonTypes/URI.fs index ee93161b..a324a6ef 100644 --- a/src/ISA/ISA/JsonTypes/URI.fs +++ b/src/ISA/ISA/JsonTypes/URI.fs @@ -1,4 +1,4 @@ -namespace ISA +namespace ARCtrl.ISA type URI = string diff --git a/src/ISA/ISA/JsonTypes/Value.fs b/src/ISA/ISA/JsonTypes/Value.fs index 8dcbc6a0..9372a7e2 100644 --- a/src/ISA/ISA/JsonTypes/Value.fs +++ b/src/ISA/ISA/JsonTypes/Value.fs @@ -1,4 +1,4 @@ -namespace ISA +namespace ARCtrl.ISA type Value = diff --git a/src/ISA/ISA/OptionExtensions.fs b/src/ISA/ISA/OptionExtensions.fs index 8aa1b2d6..a98e6c90 100644 --- a/src/ISA/ISA/OptionExtensions.fs +++ b/src/ISA/ISA/OptionExtensions.fs @@ -1,4 +1,4 @@ -namespace ISA.Aux +namespace ARCtrl.ISA.Aux [] module Option = diff --git a/src/ISA/ISA/Printer.fs b/src/ISA/ISA/Printer.fs index 162e593e..b3bfce32 100644 --- a/src/ISA/ISA/Printer.fs +++ b/src/ISA/ISA/Printer.fs @@ -1,4 +1,4 @@ -namespace ISA +namespace ARCtrl.ISA type IISAPrintable = abstract member Print : unit -> string diff --git a/src/ISA/ISA/Regex.fs b/src/ISA/ISA/Regex.fs index 109e4ea4..e06a5f61 100644 --- a/src/ISA/ISA/Regex.fs +++ b/src/ISA/ISA/Regex.fs @@ -1,7 +1,7 @@ /// /// This module contains unified regex patterns and matching functions to parse isa tab column headers to BuildingBlock information. /// -module ISA.Regex +module ARCtrl.ISA.Regex open System diff --git a/src/ISA/ISA/Update.fs b/src/ISA/ISA/Update.fs index 0e17af89..ff685e13 100644 --- a/src/ISA/ISA/Update.fs +++ b/src/ISA/ISA/Update.fs @@ -1,4 +1,4 @@ -namespace ISA.Aux +namespace ARCtrl.ISA.Aux module Dict = @@ -64,7 +64,7 @@ module Update = /// Get the type of the IEnumerable elements. E.g. for Array<'T> it would be 'T let isMapType (v:obj) = #if FABLE_COMPILER - ISA.Fable.isMap_generic v + ARCtrl.ISA.Fable.isMap_generic v #else let t = v.GetType() // Maps are IEnumerables but are not easily to append. TODO(?) @@ -74,7 +74,7 @@ module Update = let isListType (v:obj) = #if FABLE_COMPILER - ISA.Fable.isList_generic v + ARCtrl.ISA.Fable.isList_generic v #else v.GetType().Name.StartsWith "FSharpList`1" #endif @@ -105,7 +105,7 @@ module Update = /// This function accesses the append method of the list/array module and applies it accordingly to the element type. let inline appendGenericListsByType l1 l2 (t:Type) = #if FABLE_COMPILER - ISA.Fable.append_generic l1 l2 + ARCtrl.ISA.Fable.append_generic l1 l2 #else let fieldT = l1.GetType() // https://stackoverflow.com/questions/41253131/how-to-create-an-empty-list-of-a-specific-runtime-type @@ -120,7 +120,7 @@ module Update = /// This function accesses the distinct method of the list/array module and applies it accordingly to the element type. let inline distinctGenericList l1 (t:Type) = #if FABLE_COMPILER - ISA.Fable.distinct_generic l1 + ARCtrl.ISA.Fable.distinct_generic l1 #else let fieldT = l1.GetType() // https://stackoverflow.com/questions/41253131/how-to-create-an-empty-list-of-a-specific-runtime-type diff --git a/src/ISA/ISA/Url.fs b/src/ISA/ISA/Url.fs index d0d0e7d2..7a908064 100644 --- a/src/ISA/ISA/Url.fs +++ b/src/ISA/ISA/Url.fs @@ -1,4 +1,4 @@ -module ISA.Url +module ARCtrl.ISA.Url [] let OntobeeOboPurl = @"http://purl.obolibrary.org/obo/" \ No newline at end of file diff --git a/tests/ARCtrl/ARCtrl.Contracts.Tests.fs b/tests/ARCtrl/ARCtrl.Contracts.Tests.fs index f700114c..4a0f8d0f 100644 --- a/tests/ARCtrl/ARCtrl.Contracts.Tests.fs +++ b/tests/ARCtrl/ARCtrl.Contracts.Tests.fs @@ -7,7 +7,7 @@ open Expecto #endif open ARCtrl -open Contract +open ARCtrl.Contract open FsSpreadsheet let tests_tryFromContract = testList "tryFromContract" [ @@ -21,7 +21,7 @@ let tests_tryFromContract = testList "tryFromContract" [ DTO.Spreadsheet fswb ) |] - let investigation = contracts |> Array.choose Contracts.ArcInvestigation.tryFromContract + let investigation = contracts |> Array.choose ArcInvestigation.tryFromContract Expect.hasLength investigation 1 "" ] diff --git a/tests/ARCtrl/ARCtrl.Tests.fs b/tests/ARCtrl/ARCtrl.Tests.fs index bed9e4f4..3e62eb95 100644 --- a/tests/ARCtrl/ARCtrl.Tests.fs +++ b/tests/ARCtrl/ARCtrl.Tests.fs @@ -7,7 +7,7 @@ open Expecto #endif open ARCtrl -open ISA +open ARCtrl.ISA let private test_model = testList "model" [ testCase "create" <| fun _ -> diff --git a/tests/FileSystem/FileSystem.Tests/FileSystem.Tests.fsproj b/tests/FileSystem/FileSystem.Tests/FileSystem.Tests.fsproj index 1bee690a..2685a07e 100644 --- a/tests/FileSystem/FileSystem.Tests/FileSystem.Tests.fsproj +++ b/tests/FileSystem/FileSystem.Tests/FileSystem.Tests.fsproj @@ -21,6 +21,6 @@ - + diff --git a/tests/FileSystem/FileSystem.Tests/FileSystemTree.Tests.fs b/tests/FileSystem/FileSystem.Tests/FileSystemTree.Tests.fs index ae2b6ec5..001d3d9d 100644 --- a/tests/FileSystem/FileSystem.Tests/FileSystemTree.Tests.fs +++ b/tests/FileSystem/FileSystem.Tests/FileSystemTree.Tests.fs @@ -1,4 +1,4 @@ -module FileSystemTree.Tests +module ARCtrl.FileSystemTree.Tests #if FABLE_COMPILER open Fable.Mocha @@ -6,7 +6,7 @@ open Fable.Mocha open Expecto #endif -open FileSystem +open ARCtrl.FileSystem let private newArcRelativePaths = [| @"isa.investigation.xlsx"; @".arc\.gitkeep"; @".git\config"; diff --git a/tests/FileSystem/FileSystem.Tests/Main.fs b/tests/FileSystem/FileSystem.Tests/Main.fs index 499d94df..c2e06182 100644 --- a/tests/FileSystem/FileSystem.Tests/Main.fs +++ b/tests/FileSystem/FileSystem.Tests/Main.fs @@ -1,4 +1,4 @@ -module FileSystem.Tests +module ARCtrl.FileSystem.Tests #if FABLE_COMPILER open Fable.Mocha @@ -8,7 +8,7 @@ open Expecto [] #endif let all = testSequenced <| testList "All" [ - FileSystemTree.Tests.main + ARCtrl.FileSystemTree.Tests.main ] let [] main argv = diff --git a/tests/FileSystem/FileSystem.Tests/Utils.fs b/tests/FileSystem/FileSystem.Tests/Utils.fs index bcea0186..a345837e 100644 --- a/tests/FileSystem/FileSystem.Tests/Utils.fs +++ b/tests/FileSystem/FileSystem.Tests/Utils.fs @@ -24,7 +24,7 @@ let mySequenceEqual actual expected message = | i,Some a,None -> failwithf "%s. Sequence actual longer than expected, at pos %i found item %A." message i a -open FileSystem +open ARCtrl.FileSystem #if FABLE_COMPILER open Fable.Mocha diff --git a/tests/ISA/ISA.Json.Tests/ISA.Json.Tests.fsproj b/tests/ISA/ISA.Json.Tests/ISA.Json.Tests.fsproj index ecb06327..504210c1 100644 --- a/tests/ISA/ISA.Json.Tests/ISA.Json.Tests.fsproj +++ b/tests/ISA/ISA.Json.Tests/ISA.Json.Tests.fsproj @@ -33,6 +33,6 @@ - + diff --git a/tests/ISA/ISA.Json.Tests/Json.Tests.fs b/tests/ISA/ISA.Json.Tests/Json.Tests.fs index a5f7261c..a910da96 100644 --- a/tests/ISA/ISA.Json.Tests/Json.Tests.fs +++ b/tests/ISA/ISA.Json.Tests/Json.Tests.fs @@ -1,8 +1,8 @@ module Json.Tests -open ISA -open ISA.Json -open ISA +open ARCtrl.ISA +open ARCtrl.ISA.Json +open ARCtrl.ISA #if FABLE_COMPILER open Fable.Core @@ -55,7 +55,7 @@ let testEncode = testList "Encode" [ testCase "tryGetPropertyValueExists" (fun () -> - let oa = ISA.OntologyAnnotation.fromString ("MyAnnotation", "ABC:123", "ABC") + let oa = ARCtrl.ISA.OntologyAnnotation.fromString ("MyAnnotation", "ABC:123", "ABC") let field = "Name" @@ -72,7 +72,7 @@ let testEncode = testCase "tryGetPropertyValueMissing" (fun () -> - let oa = ISA.OntologyAnnotation.fromString("MyAnnotation", "ABC:123", "ABC") + let oa = ARCtrl.ISA.OntologyAnnotation.fromString("MyAnnotation", "ABC:123", "ABC") let field = "FantasyValue" @@ -83,12 +83,12 @@ let testEncode = testCase "tryGetPropertyValueSequence" (fun () -> - let comments = [|ISA.Comment.fromString "k1" "v1"; ISA.Comment.fromString "k2" "vv"|] - let oa = ISA.OntologyAnnotation.fromString ("MyAnnotation", "ABC:123", "ABC", comments) + let comments = [|ARCtrl.ISA.Comment.fromString "k1" "v1"; ARCtrl.ISA.Comment.fromString "k2" "vv"|] + let oa = ARCtrl.ISA.OntologyAnnotation.fromString ("MyAnnotation", "ABC:123", "ABC", comments) let field = "Comments" - let result = GEncode.tryGetPropertyValue field oa + let result : obj option = GEncode.tryGetPropertyValue field oa Expect.isSome result "Could not find the field, even though it exists" diff --git a/tests/ISA/ISA.Json.Tests/JsonSchema.Tests.fs b/tests/ISA/ISA.Json.Tests/JsonSchema.Tests.fs index 36915658..353bceaf 100644 --- a/tests/ISA/ISA.Json.Tests/JsonSchema.Tests.fs +++ b/tests/ISA/ISA.Json.Tests/JsonSchema.Tests.fs @@ -6,7 +6,7 @@ open Fable.Mocha open Expecto #endif -open ISA.Json +open ARCtrl.ISA.Json /// ⚠️ This testlist is only used to test correct execution of Fable bindings on `JsonValidation.js` functions. /// ⚠️ Never execute in dotnet environment @@ -38,7 +38,7 @@ let tests_FableBindings = testList "FableBindings" [ } ] -open ISA +open ARCtrl.ISA let tests_Process = diff --git a/tests/ISA/ISA.Json.Tests/Main.fs b/tests/ISA/ISA.Json.Tests/Main.fs index 41bde52e..cf3b6b7e 100644 --- a/tests/ISA/ISA.Json.Tests/Main.fs +++ b/tests/ISA/ISA.Json.Tests/Main.fs @@ -1,4 +1,4 @@ -module ISA.Json.Tests +module ARCtrl.ISA.Json.Tests #if FABLE_COMPILER open Fable.Mocha diff --git a/tests/ISA/ISA.Json.Tests/Utils.fs b/tests/ISA/ISA.Json.Tests/Utils.fs index 3cca06c2..3911092c 100644 --- a/tests/ISA/ISA.Json.Tests/Utils.fs +++ b/tests/ISA/ISA.Json.Tests/Utils.fs @@ -1,7 +1,7 @@ module TestingUtils open Expecto -open ISA.Json +open ARCtrl.ISA.Json module Async = diff --git a/tests/ISA/ISA.Spreadsheet.Tests/ArcTableTests.fs b/tests/ISA/ISA.Spreadsheet.Tests/ArcTableTests.fs index 3afed99d..eb3bbf53 100644 --- a/tests/ISA/ISA.Spreadsheet.Tests/ArcTableTests.fs +++ b/tests/ISA/ISA.Spreadsheet.Tests/ArcTableTests.fs @@ -7,8 +7,8 @@ open Expecto #endif -open ISA -open ISA.Spreadsheet +open ARCtrl.ISA +open ARCtrl.ISA.Spreadsheet open TestingUtils open TestObjects.ArcTable diff --git a/tests/ISA/ISA.Spreadsheet.Tests/AssayFileTests.fs b/tests/ISA/ISA.Spreadsheet.Tests/AssayFileTests.fs index 5587e5a2..bc9c8393 100644 --- a/tests/ISA/ISA.Spreadsheet.Tests/AssayFileTests.fs +++ b/tests/ISA/ISA.Spreadsheet.Tests/AssayFileTests.fs @@ -7,9 +7,9 @@ open Fable.Mocha open Expecto #endif -open ISA +open ARCtrl.ISA open TestingUtils -open ISA.Spreadsheet +open ARCtrl.ISA.Spreadsheet let testMetaDataFunctions = diff --git a/tests/ISA/ISA.Spreadsheet.Tests/CompositeColumnTests.fs b/tests/ISA/ISA.Spreadsheet.Tests/CompositeColumnTests.fs index e824f9dd..10f32876 100644 --- a/tests/ISA/ISA.Spreadsheet.Tests/CompositeColumnTests.fs +++ b/tests/ISA/ISA.Spreadsheet.Tests/CompositeColumnTests.fs @@ -6,9 +6,9 @@ open Fable.Mocha open Expecto #endif -open ISA +open ARCtrl.ISA open TestingUtils -open ISA.Spreadsheet +open ARCtrl.ISA.Spreadsheet open TestObjects.ArcTable diff --git a/tests/ISA/ISA.Spreadsheet.Tests/FableTests.fs b/tests/ISA/ISA.Spreadsheet.Tests/FableTests.fs index dc96b403..0c251a30 100644 --- a/tests/ISA/ISA.Spreadsheet.Tests/FableTests.fs +++ b/tests/ISA/ISA.Spreadsheet.Tests/FableTests.fs @@ -1,6 +1,6 @@ module FableTests -open ISA.Spreadsheet +open ARCtrl.ISA.Spreadsheet open FsSpreadsheet #if FABLE_COMPILER diff --git a/tests/ISA/ISA.Spreadsheet.Tests/ISA.Spreadsheet.Tests.fsproj b/tests/ISA/ISA.Spreadsheet.Tests/ISA.Spreadsheet.Tests.fsproj index ae668219..f25b614a 100644 --- a/tests/ISA/ISA.Spreadsheet.Tests/ISA.Spreadsheet.Tests.fsproj +++ b/tests/ISA/ISA.Spreadsheet.Tests/ISA.Spreadsheet.Tests.fsproj @@ -33,6 +33,6 @@ - + diff --git a/tests/ISA/ISA.Spreadsheet.Tests/Identifier.Tests.fs b/tests/ISA/ISA.Spreadsheet.Tests/Identifier.Tests.fs index 67bfa174..9d51a129 100644 --- a/tests/ISA/ISA.Spreadsheet.Tests/Identifier.Tests.fs +++ b/tests/ISA/ISA.Spreadsheet.Tests/Identifier.Tests.fs @@ -6,7 +6,7 @@ open Fable.Mocha open Expecto #endif -open ISA.Identifier +open ARCtrl.ISA.Identifier // Function to test identifierFromFileName let private testIdentifierFromFileName () = diff --git a/tests/ISA/ISA.Spreadsheet.Tests/InvestigationFileTests.fs b/tests/ISA/ISA.Spreadsheet.Tests/InvestigationFileTests.fs index 5fc22537..d522c556 100644 --- a/tests/ISA/ISA.Spreadsheet.Tests/InvestigationFileTests.fs +++ b/tests/ISA/ISA.Spreadsheet.Tests/InvestigationFileTests.fs @@ -6,10 +6,10 @@ open Fable.Mocha open Expecto #endif -open ISA +open ARCtrl.ISA open FsSpreadsheet open TestingUtils -open ISA.Spreadsheet +open ARCtrl.ISA.Spreadsheet let private testInvestigationWriterComponents = /// Test the single components of invesigation file writing diff --git a/tests/ISA/ISA.Spreadsheet.Tests/Main.fs b/tests/ISA/ISA.Spreadsheet.Tests/Main.fs index 76f5a5b1..23a21087 100644 --- a/tests/ISA/ISA.Spreadsheet.Tests/Main.fs +++ b/tests/ISA/ISA.Spreadsheet.Tests/Main.fs @@ -1,4 +1,4 @@ -module ISA.XLSX.Tests +module ARCtrl.ISA.XLSX.Tests #if FABLE_COMPILER open Fable.Mocha diff --git a/tests/ISA/ISA.Spreadsheet.Tests/SparseTableTests.fs b/tests/ISA/ISA.Spreadsheet.Tests/SparseTableTests.fs index 9e33efe3..3dbe0dc0 100644 --- a/tests/ISA/ISA.Spreadsheet.Tests/SparseTableTests.fs +++ b/tests/ISA/ISA.Spreadsheet.Tests/SparseTableTests.fs @@ -1,6 +1,6 @@ module SparseTableTests -open ISA.Spreadsheet +open ARCtrl.ISA.Spreadsheet #if FABLE_COMPILER open Fable.Mocha diff --git a/tests/ISA/ISA.Spreadsheet.Tests/StringConversionTests.fs b/tests/ISA/ISA.Spreadsheet.Tests/StringConversionTests.fs index 788acebc..c00e432b 100644 --- a/tests/ISA/ISA.Spreadsheet.Tests/StringConversionTests.fs +++ b/tests/ISA/ISA.Spreadsheet.Tests/StringConversionTests.fs @@ -1,6 +1,6 @@ module StringConversionTests -open ISA +open ARCtrl.ISA #if FABLE_COMPILER open Fable.Mocha diff --git a/tests/ISA/ISA.Spreadsheet.Tests/StudyFileTests.fs b/tests/ISA/ISA.Spreadsheet.Tests/StudyFileTests.fs index 795cfdfb..b6b805fb 100644 --- a/tests/ISA/ISA.Spreadsheet.Tests/StudyFileTests.fs +++ b/tests/ISA/ISA.Spreadsheet.Tests/StudyFileTests.fs @@ -6,9 +6,9 @@ open Fable.Mocha open Expecto #endif -open ISA +open ARCtrl.ISA open TestingUtils -open ISA.Spreadsheet +open ARCtrl.ISA.Spreadsheet let testMetaDataFunctions = diff --git a/tests/ISA/ISA.Spreadsheet.Tests/TestObjects/ArcTable.fs b/tests/ISA/ISA.Spreadsheet.Tests/TestObjects/ArcTable.fs index 5417cc64..7040af62 100644 --- a/tests/ISA/ISA.Spreadsheet.Tests/TestObjects/ArcTable.fs +++ b/tests/ISA/ISA.Spreadsheet.Tests/TestObjects/ArcTable.fs @@ -1,8 +1,8 @@ module TestObjects.ArcTable open FsSpreadsheet -open ISA -open ISA.Spreadsheet +open ARCtrl.ISA +open ARCtrl.ISA.Spreadsheet type FsTable with member this.IsEmpty(c : FsCellsCollection) = diff --git a/tests/ISA/ISA.Tests/ArcAssay.Tests.fs b/tests/ISA/ISA.Tests/ArcAssay.Tests.fs index 7a5dccc8..79081729 100644 --- a/tests/ISA/ISA.Tests/ArcAssay.Tests.fs +++ b/tests/ISA/ISA.Tests/ArcAssay.Tests.fs @@ -1,6 +1,6 @@ module ArcAssay.Tests -open ISA +open ARCtrl.ISA #if FABLE_COMPILER open Fable.Mocha diff --git a/tests/ISA/ISA.Tests/ArcInvestigation.Tests.fs b/tests/ISA/ISA.Tests/ArcInvestigation.Tests.fs index 958afcaf..383306b0 100644 --- a/tests/ISA/ISA.Tests/ArcInvestigation.Tests.fs +++ b/tests/ISA/ISA.Tests/ArcInvestigation.Tests.fs @@ -1,6 +1,6 @@ module ArcInvestigation.Tests -open ISA +open ARCtrl.ISA #if FABLE_COMPILER open Fable.Mocha diff --git a/tests/ISA/ISA.Tests/ArcJsonConversionTests.fs b/tests/ISA/ISA.Tests/ArcJsonConversionTests.fs index 11ba5bae..f0f1cb0a 100644 --- a/tests/ISA/ISA.Tests/ArcJsonConversionTests.fs +++ b/tests/ISA/ISA.Tests/ArcJsonConversionTests.fs @@ -1,6 +1,6 @@ module ArcJsonConversion.Tests -open ISA +open ARCtrl.ISA #if FABLE_COMPILER open Fable.Mocha @@ -390,25 +390,25 @@ let private tests_arcAssay = let arcAssay = ArcAssay.create(identifier) let assay = arcAssay.ToAssay() Expect.isSome assay.FileName "Assay should have fileName" - let expectedFileName = ISA.Identifier.Assay.fileNameFromIdentifier identifier + let expectedFileName = Identifier.Assay.fileNameFromIdentifier identifier Expect.equal assay.FileName.Value expectedFileName "Assay fileName should match" let resultArcAssay = ArcAssay.fromAssay assay Expect.equal resultArcAssay.Identifier identifier "ArcAssay identifier should match" ) testCase "No Identifier Set" (fun () -> - let identifier = ISA.Identifier.createMissingIdentifier() + let identifier = Identifier.createMissingIdentifier() let arcAssay = ArcAssay.create(identifier) let assay = arcAssay.ToAssay() Expect.isNone assay.FileName "Assay should not have fileName" let resultArcAssay = ArcAssay.fromAssay assay - Expect.isTrue (ISA.Identifier.isMissingIdentifier resultArcAssay.Identifier) "ArcAssay identifier should be missing" + Expect.isTrue (Identifier.isMissingIdentifier resultArcAssay.Identifier) "ArcAssay identifier should be missing" ) testCase "FullAssay ToAssay" (fun () -> let arcAssay = fullArcAssay.Copy() let assay = arcAssay.ToAssay() Expect.isSome assay.FileName "Assay should have fileName" - let expectedFileName = ISA.Identifier.Assay.fileNameFromIdentifier identifier + let expectedFileName = Identifier.Assay.fileNameFromIdentifier identifier Expect.equal assay.FileName.Value expectedFileName "Assay fileName should match" Expect.isSome assay.MeasurementType "Assay should have measurementType" @@ -475,12 +475,12 @@ let private tests_arcStudy = Expect.equal resultArcStudy.Identifier identifier "ArcStudy identifier should match" ) testCase "No Identifier Set" (fun () -> - let identifier = ISA.Identifier.createMissingIdentifier() + let identifier = Identifier.createMissingIdentifier() let arcStudy = ArcStudy.create(identifier) let study = arcStudy.ToStudy() Expect.isNone study.Identifier "Study should not have identifier" let resultArcStudy = ArcStudy.fromStudy study - Expect.isTrue (ISA.Identifier.isMissingIdentifier resultArcStudy.Identifier) "ArcStudy identifier should be missing" + Expect.isTrue (Identifier.isMissingIdentifier resultArcStudy.Identifier) "ArcStudy identifier should be missing" ) ] @@ -498,12 +498,12 @@ let private tests_arcInvestigation = Expect.equal resultArcInvestigation.Identifier identifier "ArcInvestigation identifier should match" ) testCase "No Identifier Set" (fun () -> - let identifier = ISA.Identifier.createMissingIdentifier() + let identifier = Identifier.createMissingIdentifier() let arcInvestigation = ArcInvestigation.create(identifier) let investigation = arcInvestigation.ToInvestigation() Expect.isNone investigation.Identifier "Investigation should not have identifier" let resultArcInvestigation = ArcInvestigation.fromInvestigation investigation - Expect.isTrue (ISA.Identifier.isMissingIdentifier resultArcInvestigation.Identifier) "ArcInvestigation identifier should be missing" + Expect.isTrue (Identifier.isMissingIdentifier resultArcInvestigation.Identifier) "ArcInvestigation identifier should be missing" ) ] diff --git a/tests/ISA/ISA.Tests/ArcStudy.Tests.fs b/tests/ISA/ISA.Tests/ArcStudy.Tests.fs index 2bf37146..67fd2732 100644 --- a/tests/ISA/ISA.Tests/ArcStudy.Tests.fs +++ b/tests/ISA/ISA.Tests/ArcStudy.Tests.fs @@ -1,6 +1,6 @@ module ArcStudy.Tests -open ISA +open ARCtrl.ISA #if FABLE_COMPILER open Fable.Mocha diff --git a/tests/ISA/ISA.Tests/ArcTable.Tests.fs b/tests/ISA/ISA.Tests/ArcTable.Tests.fs index b953ffaa..f781b976 100644 --- a/tests/ISA/ISA.Tests/ArcTable.Tests.fs +++ b/tests/ISA/ISA.Tests/ArcTable.Tests.fs @@ -1,6 +1,6 @@ module ArcTable.Tests -open ISA +open ARCtrl.ISA #if FABLE_COMPILER open Fable.Mocha diff --git a/tests/ISA/ISA.Tests/CompositeCell.Tests.fs b/tests/ISA/ISA.Tests/CompositeCell.Tests.fs index e04297ab..59527597 100644 --- a/tests/ISA/ISA.Tests/CompositeCell.Tests.fs +++ b/tests/ISA/ISA.Tests/CompositeCell.Tests.fs @@ -1,6 +1,6 @@ module CompositeCell.Tests -open ISA +open ARCtrl.ISA #if FABLE_COMPILER open Fable.Mocha diff --git a/tests/ISA/ISA.Tests/CompositeColumn.Tests.fs b/tests/ISA/ISA.Tests/CompositeColumn.Tests.fs index eb5d263e..5ea1a1e9 100644 --- a/tests/ISA/ISA.Tests/CompositeColumn.Tests.fs +++ b/tests/ISA/ISA.Tests/CompositeColumn.Tests.fs @@ -1,6 +1,6 @@ module CompositeColumn.Tests -open ISA +open ARCtrl.ISA #if FABLE_COMPILER open Fable.Mocha diff --git a/tests/ISA/ISA.Tests/CompositeHeader.Tests.fs b/tests/ISA/ISA.Tests/CompositeHeader.Tests.fs index a03a2f22..6b25f871 100644 --- a/tests/ISA/ISA.Tests/CompositeHeader.Tests.fs +++ b/tests/ISA/ISA.Tests/CompositeHeader.Tests.fs @@ -1,6 +1,6 @@ module CompositeHeader.Tests -open ISA +open ARCtrl.ISA #if FABLE_COMPILER open Fable.Mocha diff --git a/tests/ISA/ISA.Tests/DataModel.Tests.fs b/tests/ISA/ISA.Tests/DataModel.Tests.fs index 79e9143f..a0811a1f 100644 --- a/tests/ISA/ISA.Tests/DataModel.Tests.fs +++ b/tests/ISA/ISA.Tests/DataModel.Tests.fs @@ -5,7 +5,7 @@ open Fable.Mocha #else open Expecto #endif -open ISA +open ARCtrl.ISA let componentCastingTests = diff --git a/tests/ISA/ISA.Tests/Fable.Tests.fs b/tests/ISA/ISA.Tests/Fable.Tests.fs index d91c9fae..db5e0623 100644 --- a/tests/ISA/ISA.Tests/Fable.Tests.fs +++ b/tests/ISA/ISA.Tests/Fable.Tests.fs @@ -1,6 +1,6 @@ module Fable.Tests -open ISA +open ARCtrl.ISA #if FABLE_COMPILER open Fable.Mocha diff --git a/tests/ISA/ISA.Tests/ISA.Tests.fsproj b/tests/ISA/ISA.Tests/ISA.Tests.fsproj index 2d0397fb..ce704485 100644 --- a/tests/ISA/ISA.Tests/ISA.Tests.fsproj +++ b/tests/ISA/ISA.Tests/ISA.Tests.fsproj @@ -34,6 +34,6 @@ - + \ No newline at end of file diff --git a/tests/ISA/ISA.Tests/Identifier.Tests.fs b/tests/ISA/ISA.Tests/Identifier.Tests.fs index 0ad6d956..86a3b774 100644 --- a/tests/ISA/ISA.Tests/Identifier.Tests.fs +++ b/tests/ISA/ISA.Tests/Identifier.Tests.fs @@ -1,6 +1,6 @@ module Identifier.Tests -open ISA +open ARCtrl.ISA #if FABLE_COMPILER open Fable.Mocha @@ -8,7 +8,7 @@ open Fable.Mocha open Expecto #endif -open ISA.Identifier +open ARCtrl.ISA.Identifier let private tests_checkValidCharacters = testList "checkValidCharacters" [ // Function to test the checkValidCharacters function with a given identifier diff --git a/tests/ISA/ISA.Tests/Main.fs b/tests/ISA/ISA.Tests/Main.fs index d4200927..86157087 100644 --- a/tests/ISA/ISA.Tests/Main.fs +++ b/tests/ISA/ISA.Tests/Main.fs @@ -1,4 +1,4 @@ -module ISADotnet.Tests +module ARCtrl.ISADotnet.Tests #if FABLE_COMPILER open Fable.Mocha diff --git a/tests/ISA/ISA.Tests/Regex.Tests.fs b/tests/ISA/ISA.Tests/Regex.Tests.fs index b27c215e..d9383a83 100644 --- a/tests/ISA/ISA.Tests/Regex.Tests.fs +++ b/tests/ISA/ISA.Tests/Regex.Tests.fs @@ -1,6 +1,6 @@ module Regex.Tests -open ISA +open ARCtrl.ISA #if FABLE_COMPILER open Fable.Mocha diff --git a/tests/ISA/ISA.Tests/Update.Tests.fs b/tests/ISA/ISA.Tests/Update.Tests.fs index 6befd170..aeb47e5a 100644 --- a/tests/ISA/ISA.Tests/Update.Tests.fs +++ b/tests/ISA/ISA.Tests/Update.Tests.fs @@ -6,7 +6,7 @@ open Fable.Mocha open Expecto #endif -open ISA.Aux +open ARCtrl.ISA.Aux open Update module TestTypes = diff --git a/tests/ISA/ISA.Tests/Utils.fs b/tests/ISA/ISA.Tests/Utils.fs index 5a2855ed..c05f61ac 100644 --- a/tests/ISA/ISA.Tests/Utils.fs +++ b/tests/ISA/ISA.Tests/Utils.fs @@ -1,6 +1,6 @@ module TestingUtils -open ISA +open ARCtrl.ISA #if FABLE_COMPILER open Fable.Mocha