Merge branch 'main' into CWL

nfdi4plants · Sep 10, 2024 · 4bfe7ab · 4bfe7ab
2 parents ddb838f + 8b4368a
commit 4bfe7ab
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Showing 61 changed files with 2,201 additions and 246 deletions.
diff --git a/ARCtrl.sln b/ARCtrl.sln
@@ -84,6 +84,10 @@ Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.Contract.Tests", "te
 EndProject
 Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.CWL.Tests", "tests\CWL\ARCtrl.CWL.Tests.fsproj", "{0F2188D3-144C-41BF-89F6-AA85883AE0D3}"
 EndProject
+Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.ROCrate", "src\ROCrate\ARCtrl.ROCrate.fsproj", "{658BF141-B4B5-4B90-891D-AC36A3FD7574}"
+EndProject
+Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.ROCrate.Tests", "tests\ROCrate\ARCtrl.ROCrate.Tests.fsproj", "{212A1C64-02FC-465A-B0FA-F69735F37ACC}"
+EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution
 		Debug|Any CPU = Debug|Any CPU
@@ -174,6 +178,14 @@ Global
 		{0F2188D3-144C-41BF-89F6-AA85883AE0D3}.Debug|Any CPU.Build.0 = Debug|Any CPU
 		{0F2188D3-144C-41BF-89F6-AA85883AE0D3}.Release|Any CPU.ActiveCfg = Release|Any CPU
 		{0F2188D3-144C-41BF-89F6-AA85883AE0D3}.Release|Any CPU.Build.0 = Release|Any CPU
+		{658BF141-B4B5-4B90-891D-AC36A3FD7574}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{658BF141-B4B5-4B90-891D-AC36A3FD7574}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{658BF141-B4B5-4B90-891D-AC36A3FD7574}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{658BF141-B4B5-4B90-891D-AC36A3FD7574}.Release|Any CPU.Build.0 = Release|Any CPU
+		{212A1C64-02FC-465A-B0FA-F69735F37ACC}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{212A1C64-02FC-465A-B0FA-F69735F37ACC}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{212A1C64-02FC-465A-B0FA-F69735F37ACC}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{212A1C64-02FC-465A-B0FA-F69735F37ACC}.Release|Any CPU.Build.0 = Release|Any CPU
 	EndGlobalSection
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE
@@ -201,6 +213,8 @@ Global
 		{5810EF87-4F85-4B4C-98E3-833AE914C628} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}
 		{D10D12C7-B877-423B-867D-161D99E673C9} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}
 		{0F2188D3-144C-41BF-89F6-AA85883AE0D3} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}
+		{658BF141-B4B5-4B90-891D-AC36A3FD7574} = {6DA2330B-D407-4FB1-AF05-B0184034EC44}
+		{212A1C64-02FC-465A-B0FA-F69735F37ACC} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}
 	EndGlobalSection
 	GlobalSection(ExtensibilityGlobals) = postSolution
 		SolutionGuid = {1E354DE6-99BA-421E-9EF8-E808B855A85F}

diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
@@ -1,5 +1,43 @@
-### 2.0.0+06ab9f5 (Released 2024-6-27)
-* Additions:
+### 2.0.1+5e6cc32 (Released 2024-8-29)
+* Bugfixes:
+    * [[#bfaaaf6](https://github.com/nfdi4plants/ARCtrl/commit/bfaaaf614a1a2dc788a1b7de17761b5867aa9fee)] fix single dot in paths being interpreted as folder
+
+### 2.0.0+6c267dd (Released 2024-8-27)
+* Additions:
+    * [[#c250f52](https://github.com/nfdi4plants/ARCtrl/commit/c250f52322e6c22714b02dccb37b93ca2a9cb5d8)] add RO-Crate contexts to docs
+    * [[#55ad878](https://github.com/nfdi4plants/ARCtrl/commit/55ad87892d23a77517cdbe380f5bc4e75cea2744)] Update fsspreadsheet
+    * [[#263db68](https://github.com/nfdi4plants/ARCtrl/commit/263db68d22addaa26552a85a4dd86eac29c2153f)] include fable files
+    * [[#c59b883](https://github.com/nfdi4plants/ARCtrl/commit/c59b8834d09fcdae7e47b575c4d2dff316c44a18)] Add ARCtrl.ValidationPackages project: - base type model for ValidationPackages and the config file
+    * [[#cc879fd](https://github.com/nfdi4plants/ARCtrl/commit/cc879fd276e25d4ead4c9b5051f839567e1a745e)] Add ARCtrl.Yaml: - Uses YAMLicious - tries to mirror ARCtrl.Json - Encoder/Decoder logic for ValidatioNpackages type model
+    * [[#c5a9e7c](https://github.com/nfdi4plants/ARCtrl/commit/c5a9e7c8f25352437c757147203f6df327957da4)] Add contracts for ValidationPackagesConfig
+    * [[#532d310](https://github.com/nfdi4plants/ARCtrl/commit/532d310e4f149a4a7ff48e62d98e836db85982a1)] Update to .NET 8, requested PR changes
+    * [[#137d885](https://github.com/nfdi4plants/ARCtrl/commit/137d885f1a8a76c43fca0e1d631ad70c9eae8667)] add fable files
+    * [[#87ed783](https://github.com/nfdi4plants/ARCtrl/commit/87ed783823ebfa9e56486cd2d5edcb2e406216cd)] add the fable files for real. fable be fablin'
+    * [[#8b55020](https://github.com/nfdi4plants/ARCtrl/commit/8b55020d557e39b78a7f512ff29370bfd53e98aa)] Add classes for index files :sparkles: #386
+    * [[#27d259a](https://github.com/nfdi4plants/ARCtrl/commit/27d259a22b3d357798ac190b867b33972814033d)] Rename ARCtrl.Path to ARCtrl.ArcPathHelper #398
+    * [[#3e427f1](https://github.com/nfdi4plants/ARCtrl/commit/3e427f188ecc5244fffa63e534314e30699efb29)] Add CompositeCell.ToDataCell #404
+    * [[#bf79874](https://github.com/nfdi4plants/ARCtrl/commit/bf798749e0de183502ca52df000943a06ccccee2)] Unifiy expected functionality of CompositeCell conversion utility #402
+    * [[#8432507](https://github.com/nfdi4plants/ARCtrl/commit/8432507efc446ca93f7c0d333a0bbd8d79a96395)] Add api to include datamap in assay/study #406
+    * [[#b00b17e](https://github.com/nfdi4plants/ARCtrl/commit/b00b17eaf6c397e3d3ff30795199767697ab0572)] add swate prerelease target
+    * [[#486d6a7](https://github.com/nfdi4plants/ARCtrl/commit/486d6a7e611c739452aab1d11003478c9940cf62)] rmv comment
+    * [[#d036c31](https://github.com/nfdi4plants/ARCtrl/commit/d036c3161ddc53118bed5aeb5be2b32102ec6b76)] add first json logic for datamap :construction:
+    * [[#22b48f5](https://github.com/nfdi4plants/ARCtrl/commit/22b48f54ae2992269a4ab891035653c5712cf0ec)] Add YAML tests for Validation packages, use custom equality
+    * [[#b510ab2](https://github.com/nfdi4plants/ARCtrl/commit/b510ab2b793c87a6ce0a70fd92ae99791624f307)] add a test placeholder -.-
+    * [[#9c70c5d](https://github.com/nfdi4plants/ARCtrl/commit/9c70c5dffea4a28f262f972651b712bf0e5ffefa)] Add contract handling for `validation_packages.yml` to top-level ARC API
+    * [[#263db27](https://github.com/nfdi4plants/ARCtrl/commit/263db27e067fb1c6af81211be15d6eb80390783a)] wip
+    * [[#6273594](https://github.com/nfdi4plants/ARCtrl/commit/6273594c1a4b7b4813ddffd4a0b0f9beea095892)] Add instance method tests for ARCtrl.ValidationPackages
+    * [[#4101dcb](https://github.com/nfdi4plants/ARCtrl/commit/4101dcb2b0f38e80f77501c5e2dadd1fe422b7a4)] Add Contract tests for ValidationPackagesConfig
+    * [[#995e2f8](https://github.com/nfdi4plants/ARCtrl/commit/995e2f8bef5c5f9510aa3cf9f77b7968d16eb271)] Add topm level api tests for ValidationPackagesConfig
+    * [[#8de0653](https://github.com/nfdi4plants/ARCtrl/commit/8de0653bfd3d361b8571f2c59eb65823e1832022)] Use literal for yaml keys (also in tests)
+    * [[#d64f841](https://github.com/nfdi4plants/ARCtrl/commit/d64f841685b5314627ef6d6829cceeb9d1dc88a3)] Use more Record-like ToString() for ValidationPackages and ValidationpackagesConfig
+    * [[#88c9b9d](https://github.com/nfdi4plants/ARCtrl/commit/88c9b9d831f8918e7eadb511cdaf0e7baf9bfbdf)] add addColumnFill member function with tests
+    * [[#e68ca44](https://github.com/nfdi4plants/ARCtrl/commit/e68ca449ba9aa741e96f4bb9195ac3f354625ac7)] Additional tests for AddColumnFill
+    * [[#df0bda9](https://github.com/nfdi4plants/ARCtrl/commit/df0bda98b004caf1896c91a5d9d69c50885b01d3)] Reviewed AddColumnFill member function and tests
+    * [[#94fba28](https://github.com/nfdi4plants/ARCtrl/commit/94fba285c10678314a9ae7fd47c146862109b77a)] add ARC.ToROCrateJsonString member #344
+    * [[#064b3e0](https://github.com/nfdi4plants/ARCtrl/commit/064b3e0beb10b34cb28d32db7f55342bf5479d22)] added functions for checking assay and study metadata sheet names #414
+    * [[#c5a929d](https://github.com/nfdi4plants/ARCtrl/commit/c5a929df8b140e9bb749fe2f01db386ccadd818c)] check identifiers when creating assay and study objects #415
+    * [[#d40fea9](https://github.com/nfdi4plants/ARCtrl/commit/d40fea9442d34a3b7fa6bff76682423fdcff5992)] add CompositeHeader.IsUnique #416
+    * [[#de4246f](https://github.com/nfdi4plants/ARCtrl/commit/de4246f16d09b81cd94f18784772618bb095a6c8)] add  ArcTable cell accession and manipulation functions
     * [[#485d778](https://github.com/nfdi4plants/ARCtrl/commit/485d778ed49f99b1ae7994d1a1e764ea08091e95)] make process conversion more robust against different outputs
     * [[#0b85fcd](https://github.com/nfdi4plants/ARCtrl/commit/0b85fcd8fc825866c10792465a33c1cf81b92e08)] base spreadsheet parsers on string columns
     * [[#142b6a2](https://github.com/nfdi4plants/ARCtrl/commit/142b6a20c3df620822bfe602136040d3b62fd944)] change main types of spreadsheet parsing collections from list to array
@@ -118,9 +156,20 @@
     * [[#abd3d89](https://github.com/nfdi4plants/ARCtrl/commit/abd3d890fb58a0962d4e7d841df7440d9a4bed90)] Merge pull request #317 from nfdi4plants/python_integration
     * [[#b6e2eca](https://github.com/nfdi4plants/ARCtrl/commit/b6e2ecab5a0a3630e1dd24ae36d34be79ad21d6d)] small change to semver in npm
 * Deletions:
+    * [[#cd1620c](https://github.com/nfdi4plants/ARCtrl/commit/cd1620c615ec500713ba12da7b685eca7305a12f)] remove entry when delete contract is created for validation packages config file, add related tests
+    * [[#e50083c](https://github.com/nfdi4plants/ARCtrl/commit/e50083ce6638fc6e7ac607bd1a090948046d1d84)] remove UI helper functions #329
     * [[#1ce8001](https://github.com/nfdi4plants/ARCtrl/commit/1ce80017ddd48bbe217ee99ac70923cb5dca8bc1)] Remove ALL tabs from fsproj files
     * [[#f055617](https://github.com/nfdi4plants/ARCtrl/commit/f05561709a0a8d1da752d54d5a997db225a3384e)] remove erroneous exe output type from testingutils
 * Bugfixes:
+    * [[#ad6f37f](https://github.com/nfdi4plants/ARCtrl/commit/ad6f37f02cc24c22b9b6744fc59039bf3644eb4b)] Fix spreadsheet writer for data with freetext :bug::white_check_mark: #405
+    * [[#e358522](https://github.com/nfdi4plants/ARCtrl/commit/e358522720ac8343d470c33e13e8cdd1363e18e2)] fix data column spreadsheet export for mixed columns :bug::white_check_mark:
+    * [[#f60e663](https://github.com/nfdi4plants/ARCtrl/commit/f60e663aa68f6fbae2eb0da65f20950b9ee67545)] fix module references :bug:
+    * [[#36ab086](https://github.com/nfdi4plants/ARCtrl/commit/36ab0864dfda70ed078cef089dcc9f3e0847341a)] Added missing datamap to compressed study json :bug:
+    * [[#5cfffe9](https://github.com/nfdi4plants/ARCtrl/commit/5cfffe92e47ffd342a44debcf50ea0d08ef27359)] fix study datamap json key name :bug:
+    * [[#dc3822f](https://github.com/nfdi4plants/ARCtrl/commit/dc3822fd1fec14c6009425e618531adf8828119a)] Fixed json key naming issue, added tests :bug::white_check_mark:
+    * [[#a88344a](https://github.com/nfdi4plants/ARCtrl/commit/a88344a7f5f6d96b82e31af85b582b7425db8d7c)] fix test transpilation for YAML
+    * [[#ba8d69e](https://github.com/nfdi4plants/ARCtrl/commit/ba8d69ef5e3668d986ee2e948699cce8dd1e977b)] Fix path helper usage after rebase
+    * [[#d1b9f9b](https://github.com/nfdi4plants/ARCtrl/commit/d1b9f9b3e640ccf688af7cbd2d34d07589a6f1ac)] fix multi annotationTable writing and unify API #423
     * [[#621f769](https://github.com/nfdi4plants/ARCtrl/commit/621f769ead6a0616a78f5db0ff23c5bfd6d53a5b)] small fix for changes to spreadsheet parsing
     * [[#19b6a4c](https://github.com/nfdi4plants/ARCtrl/commit/19b6a4cb2d9ff89a68428f226ed49ffa34641c93)] fix and test rename leading to update contracts when the renamed entity is registered and remove isalight
     * [[#4ae6bd0](https://github.com/nfdi4plants/ARCtrl/commit/4ae6bd029c7ecd14cb16e6fea221983d29e43fea)] fixes and tests for updateContracts when assays or studies are added

diff --git a/build.cmd b/build.cmd
@@ -2,5 +2,4 @@
 
 set PYTHONIOENCODING=utf-8
 dotnet tool restore
-cls 
 dotnet run --project ./build/build.fsproj %*
diff --git a/build/PackageTasks.fs b/build/PackageTasks.fs
@@ -48,6 +48,12 @@ let packDotNetPrerelease = BuildTask.create "PackDotNetPrerelease" [setPrereleas
     BundleDotNet.bundle prereleaseTag (Some prereleaseTag)
 }
 
+let packDotNetSwate = BuildTask.create "packDotNetSwate" [clean; build; RunTests.runTestsDotnet; RunTests.runTestsJs; RunTests.runTestsJsNative] {
+    let semVer = release.SemVer
+    let releaseTag = sprintf "%i.%i.%i-swate" semVer.Major semVer.Minor semVer.Patch
+    BundleDotNet.bundle releaseTag (Some releaseTag)
+}
+
 module BundleJs =
     let bundle (versionTag: string) =
         Fake.JavaScript.Npm.run "bundlejs" (fun o -> o)

diff --git a/build/ProjectInfo.fs b/build/ProjectInfo.fs
@@ -16,6 +16,7 @@ let testProjects =
         "tests/Yaml"
         "tests/ValidationPackages"
         "tests/Contract"
+        "tests/ROCrate"
     ]
 
 /// Native JS test paths

diff --git a/build/ReleaseTasks.fs b/build/ReleaseTasks.fs
@@ -60,6 +60,21 @@ let publishNugetPrerelease = BuildTask.create "PublishNugetPrerelease" [clean; b
     else failwith "aborted"
 }
 
+let publishNugetSwate = BuildTask.create "publishNugetSwate" [clean; build; packDotNetSwate] {
+    let targets = (!! (sprintf "%s/*.*pkg" netPkgDir ))
+    for target in targets do printfn "%A" target
+    let semVer = release.SemVer
+    let releaseTag = sprintf "%i.%i.%i-swate" semVer.Major semVer.Minor semVer.Patch
+    let msg = sprintf "[NUGET] release package with version %s?" releaseTag
+    if promptYesNo msg then
+        let source = "https://api.nuget.org/v3/index.json"
+        let apikey =  Environment.environVar "NUGET_KEY"
+        for artifact in targets do
+            let result = DotNet.exec id "nuget" (sprintf "push -s %s -k %s %s --skip-duplicate" source apikey artifact)
+            if not result.OK then failwith "failed to push packages"
+    else failwith "aborted"
+}
+
 let publishNPM = BuildTask.create "PublishNPM" [clean; build; runTests; packJS] {
     let target = 
         (!! (sprintf "%s/*.tgz" npmPkgDir ))

diff --git a/build/TestTasks.fs b/build/TestTasks.fs
@@ -59,6 +59,32 @@ module RunTests =
         |> Seq.iter dotnetRun
     }
 
-let runTests = BuildTask.create "RunTests" [clean; build; (*RunTests.runTestsJs; RunTests.runTestsJsNative; RunTests.runTestsPy; RunTests.runTestsPyNative;*) RunTests.runTestsDotnet] { 
+    let runTestProject = BuildTask.createFn "runTestProject" [clean; build] (fun config ->
+        let dotnetRun = run dotnet "run"
+        match config.Context.Arguments with
+        | projectName::[] ->
+            let dotnetRun = run dotnet "run"
+            match List.tryFind (fun (p:string) -> p.EndsWith(projectName)) testProjects with
+            | Some p ->
+                //
+                printfn $"running tests for test project {p}"
+                dotnetRun p
+                //
+                run dotnet $"fable {p} -o {p}/js" ""
+                //transpile py files from fsharp code
+                run dotnet $"fable {p} -o {p}/py --lang python" ""
+                // run pyxpecto in target path to execute tests in python
+                run python $"{p}/py/main.py" ""
+                // transpile js files from fsharp code
+                run dotnet $"fable {p} -o {p}/js" ""
+                // run mocha in target path to execute tests
+                // "--timeout 20000" is used, because json schema validation takes a bit of time.
+                run node $"{p}/js/Main.js" ""
+            | _ ->
+                failwithf "Project %s not found" projectName
+        | _ -> failwith "Please provide a project name to run tests for as the single argument"
+    )
+
+let runTests = BuildTask.create "RunTests" [clean; build; RunTests.runTestsJs; RunTests.runTestsJsNative; RunTests.runTestsPy; RunTests.runTestsPyNative; RunTests.runTestsDotnet] { 
     ()
 }
diff --git a/build/release_package.json b/build/release_package.json
@@ -1,6 +1,6 @@
 {
   "name": "@nfdi4plants/arctrl",
-  "version": "2.0.0",
+  "version": "2.0.1",
   "description": "Top level ARC DataModel and API function descriptions.",
   "type": "module",
   "main": "index.js",

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "ARCtrl"
-version = "2.0.0"
+version = "2.0.1"
 description = "Library for management of Annotated Research Contexts (ARCs) using an in-memory representation and runtimer agnostic contract systems."
 authors = ["Heinrich Lukas Weil <[email protected]>", "Kevin Frey <[email protected]>"]
 maintainers = ["Florian Wetzels"]

diff --git a/src/ARCtrl/ARC.fs b/src/ARCtrl/ARC.fs
@@ -329,7 +329,7 @@ type ARC(?isa : ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSystem) =
         let workbooks = System.Collections.Generic.Dictionary<string, DTOType*FsWorkbook>()
         match this.ISA with
         | Some inv -> 
-            let investigationConverter = Spreadsheet.ArcInvestigation.toFsWorkbook
+            let investigationConverter = ArcInvestigation.toFsWorkbook
             workbooks.Add (InvestigationFileName, (DTOType.ISA_Investigation, investigationConverter inv))
             inv.StaticHash <- inv.GetLightHashCode()
             inv.Studies
@@ -365,7 +365,7 @@ type ARC(?isa : ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSystem) =
 
         | None -> 
             //printfn "ARC contains no ISA part."
-            workbooks.Add (InvestigationFileName, (DTOType.ISA_Investigation, Spreadsheet.ArcInvestigation.toFsWorkbook (ArcInvestigation.create(Identifier.MISSING_IDENTIFIER))))
+            workbooks.Add (InvestigationFileName, (DTOType.ISA_Investigation, 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)
@@ -566,11 +566,14 @@ type ARC(?isa : ArcInvestigation, ?cwl : CWL.CWL, ?fs : FileSystem.FileSystem) =
         let isa = ARCtrl.Json.Decode.fromJsonString ARCtrl.Json.ARC.ROCrate.decoder s
         ARC(?isa = isa)
 
+    member this.ToROCrateJsonString(?spaces) =
+        ARCtrl.Json.ARC.ROCrate.encoder (Option.get _isa)
+        |> ARCtrl.Json.Encode.toJsonString (ARCtrl.Json.Encode.defaultSpaces spaces)
+
         /// exports in json-ld format
     static member toROCrateJsonString(?spaces) =
         fun (obj:ARC) ->
-            ARCtrl.Json.ARC.ROCrate.encoder (Option.get obj.ISA)
-            |> ARCtrl.Json.Encode.toJsonString (ARCtrl.Json.Encode.defaultSpaces spaces)
+            obj.ToROCrateJsonString(?spaces = spaces)
 
     /// <summary>
     /// Returns the write contract for the input ValidationPackagesConfig object.

diff --git a/src/Core/ArcTypes.fs b/src/Core/ArcTypes.fs
@@ -103,10 +103,13 @@ module ArcTypesAux =
 [<AttachMembers>]
 type ArcAssay(identifier: string, ?measurementType : OntologyAnnotation, ?technologyType : OntologyAnnotation, ?technologyPlatform : OntologyAnnotation, ?tables: ResizeArray<ArcTable>, ?datamap : DataMap, ?performers : ResizeArray<Person>, ?comments : ResizeArray<Comment>) = 
     inherit ArcTables(defaultArg tables <| ResizeArray())
-    
+
     let performers = defaultArg performers <| ResizeArray()
     let comments = defaultArg comments <| ResizeArray()
-    let mutable identifier : string = identifier
+    let mutable identifier : string =
+        let identifier = identifier.Trim()
+        Helper.Identifier.checkValidCharacters identifier
+        identifier
     let mutable investigation : ArcInvestigation option = None
     let mutable measurementType : OntologyAnnotation option = measurementType
     let mutable technologyType : OntologyAnnotation option = technologyType
@@ -530,7 +533,10 @@ type ArcStudy(identifier : string, ?title, ?description, ?submissionDate, ?publi
     let registeredAssayIdentifiers = defaultArg registeredAssayIdentifiers <| ResizeArray()
     let comments = defaultArg comments <| ResizeArray()
 
-    let mutable identifier = identifier
+    let mutable identifier : string =
+        let identifier = identifier.Trim()
+        Helper.Identifier.checkValidCharacters identifier
+        identifier
     let mutable investigation : ArcInvestigation option = None
     let mutable title : string option = title
     let mutable description : string option = description