Merge pull request #426 from nfdi4plants/ro-crate-data-model

Ro crate data model

ARCtrl.sln

@@ -82,6 +82,10 @@ Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.Yaml.Tests", "tests\
 EndProject
 Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.Contract.Tests", "tests\Contract\ARCtrl.Contract.Tests.fsproj", "{D10D12C7-B877-423B-867D-161D99E673C9}"
 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
@@ -168,6 +172,14 @@ Global
 		{D10D12C7-B877-423B-867D-161D99E673C9}.Debug|Any CPU.Build.0 = Debug|Any CPU
 		{D10D12C7-B877-423B-867D-161D99E673C9}.Release|Any CPU.ActiveCfg = Release|Any CPU
 		{D10D12C7-B877-423B-867D-161D99E673C9}.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
@@ -194,6 +206,8 @@ Global
 		{1CA11165-4B70-41D2-A846-50374E85385E} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}
 		{5810EF87-4F85-4B4C-98E3-833AE914C628} = {64B34A6E-318D-4E6E-9262-CE52C9B85A38}
 		{D10D12C7-B877-423B-867D-161D99E673C9} = {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}

build.cmd

@@ -2,5 +2,4 @@
 
 set PYTHONIOENCODING=utf-8
 dotnet tool restore
-cls 
 dotnet run --project ./build/build.fsproj %*

build/ProjectInfo.fs

@@ -16,6 +16,7 @@ let testProjects =
         "tests/Yaml"
         "tests/ValidationPackages"
         "tests/Contract"
+        "tests/ROCrate"
     ]
 
 /// Native JS test paths

build/TestTasks.fs

@@ -1,4 +1,4 @@
-module TestTasks
+module TestTasks
 
 open BlackFox.Fake
 open Fake.DotNet
@@ -59,6 +59,33 @@ module RunTests =
         |> Seq.iter dotnetRun
     }
 
+    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] { 
     ()
 }

src/ROCrate/ARCtrl.ROCrate.fsproj

@@ -0,0 +1,36 @@
+<Project Sdk="Microsoft.NET.Sdk">
+
+  <PropertyGroup>
+    <TargetFramework>netstandard2.0</TargetFramework>
+    <GenerateDocumentationFile>true</GenerateDocumentationFile>
+  </PropertyGroup>
+  <ItemGroup>
+    <Compile Include="ROCrateObject.fs" />
+    <Compile Include="ISAProfile\Dataset.fs" />
+    <Compile Include="ISAProfile\Investigation.fs" />
+    <Compile Include="ISAProfile\Study.fs" />
+    <Compile Include="ISAProfile\Assay.fs" />
+    <Compile Include="ISAProfile\LabProcess.fs" />
+    <Compile Include="ISAProfile\LabProtocol.fs" />
+    <Compile Include="ISAProfile\Sample.fs" />
+    <Compile Include="ISAProfile\Data.fs" />
+    <Compile Include="ISAProfile\PropertyValue.fs" />
+    <Compile Include="ISAProfile\Person.fs" />
+    <Compile Include="ISAProfile\ScholarlyArticle.fs" />
+    <None Include="playground.fsx" />
+    <None Include="../../build/logo.png" Pack="true" PackagePath="\" />
+  </ItemGroup>
+  <ItemGroup>
+    <PackageReference Include="DynamicObj" Version="3.1.0" />
+  </ItemGroup>
+  <PropertyGroup>
+    <Authors>Kevin Schneider, nfdi4plants, DataPLANT OSS contributors</Authors>
+    <Description>A data model of the ARC concept via it's RO Crate profile</Description>
+    <PackageLicenseExpression>MIT</PackageLicenseExpression>
+    <PackageIcon>logo.png</PackageIcon>
+    <PackageTags>ARC F# FSharp dotnet .Net bioinformatics biology fable-library datascience dataplant nfdi metadata</PackageTags>
+    <PackageProjectUrl>https://github.com/nfdi4plants/ARCtrl/tree/main/src/CWL</PackageProjectUrl>
+    <RepositoryUrl>https://github.com/nfdi4plants/ARCtrl</RepositoryUrl>
+    <RepositoryType>git</RepositoryType>
+  </PropertyGroup>
+</Project>

src/ROCrate/ISAProfile/Assay.fs

@@ -0,0 +1,31 @@
+namespace ARCtrl.ROCrate
+
+open DynamicObj
+open Fable.Core
+
+///
+[<AttachMembers>]
+type Assay(
+    id,
+    identifier,
+    ?about,
+    ?comment,
+    ?creator,
+    ?hasPart,
+    ?measurementMethod,
+    ?measurementTechnique,
+    ?url,
+    ?variableMeasured
+) as this =
+    inherit Dataset(id, "Assay")
+    do
+        DynObj.setValue this (nameof identifier) identifier
+
+        DynObj.setValueOpt this (nameof measurementMethod) measurementMethod
+        DynObj.setValueOpt this (nameof measurementTechnique) measurementTechnique
+        DynObj.setValueOpt this (nameof variableMeasured) variableMeasured
+        DynObj.setValueOpt this (nameof about) about
+        DynObj.setValueOpt this (nameof comment) comment
+        DynObj.setValueOpt this (nameof creator) creator
+        DynObj.setValueOpt this (nameof hasPart) hasPart
+        DynObj.setValueOpt this (nameof url) url

src/ROCrate/ISAProfile/Data.fs

@@ -0,0 +1,23 @@
+namespace ARCtrl.ROCrate
+
+open DynamicObj
+open Fable.Core
+
+///
+[<AttachMembers>]
+type Data(
+    id,
+    name,
+    ?additionalType,
+    ?comment,
+    ?encodingFormat,
+    ?disambiguatingDescription
+) as this =
+    inherit ROCrateObject(id = id, schemaType = "schema.org/MediaObject", ?additionalType = additionalType)
+    do
+        DynObj.setValue this (nameof name) name
+
+        DynObj.setValueOpt this (nameof comment) comment
+        DynObj.setValueOpt this (nameof encodingFormat) encodingFormat
+        DynObj.setValueOpt this (nameof disambiguatingDescription) disambiguatingDescription
+

src/ROCrate/ISAProfile/Dataset.fs

@@ -0,0 +1,9 @@
+namespace ARCtrl.ROCrate
+
+open DynamicObj
+open Fable.Core
+
+///
+[<AttachMembers>]
+type Dataset (id: string, ?additionalType: string) =
+    inherit ROCrateObject(id = id, schemaType = "schema.org/Dataset", ?additionalType = additionalType)

src/ROCrate/ISAProfile/Investigation.fs

@@ -0,0 +1,37 @@
+namespace ARCtrl.ROCrate
+
+open DynamicObj
+open Fable.Core
+
+///
+[<AttachMembers>]
+type Investigation(
+    id,
+    identifier,
+    ?citation,
+    ?comment,
+    ?creator,
+    ?dateCreated,
+    ?dateModified,
+    ?datePublished,
+    ?hasPart,
+    ?headline,
+    ?mentions,
+    ?url,
+    ?description
+) as this =
+    inherit Dataset(id, "Investigation")
+    do 
+        DynObj.setValue this (nameof identifier) identifier
+
+        DynObj.setValueOpt this (nameof citation) citation
+        DynObj.setValueOpt this (nameof comment) comment
+        DynObj.setValueOpt this (nameof creator) creator
+        DynObj.setValueOpt this (nameof dateCreated) dateCreated
+        DynObj.setValueOpt this (nameof dateModified) dateModified
+        DynObj.setValueOpt this (nameof datePublished) datePublished
+        DynObj.setValueOpt this (nameof hasPart) hasPart
+        DynObj.setValueOpt this (nameof headline) headline
+        DynObj.setValueOpt this (nameof mentions) mentions
+        DynObj.setValueOpt this (nameof url) url
+        DynObj.setValueOpt this (nameof description) description

src/ROCrate/ISAProfile/LabProcess.fs

@@ -0,0 +1,30 @@
+namespace ARCtrl.ROCrate
+
+open DynamicObj
+open Fable.Core
+
+///
+[<AttachMembers>]
+type LabProcess(
+    id,
+    name,
+    agent,
+    object,
+    result,
+    ?additionalType,
+    ?executesLabProtocol,
+    ?parameterValue,
+    ?endTime,
+    ?disambiguatingDescription
+) as this =
+    inherit ROCrateObject(id = id, schemaType = "bioschemas.org/LabProcess", ?additionalType = additionalType)
+    do
+        DynObj.setValue this (nameof name) name
+        DynObj.setValue this (nameof agent) agent
+        DynObj.setValue this (nameof object) object
+        DynObj.setValue this (nameof result) result
+
+        DynObj.setValueOpt this (nameof executesLabProtocol) executesLabProtocol
+        DynObj.setValueOpt this (nameof parameterValue) parameterValue
+        DynObj.setValueOpt this (nameof endTime) endTime
+        DynObj.setValueOpt this (nameof disambiguatingDescription) disambiguatingDescription

src/ROCrate/ISAProfile/LabProtocol.fs

@@ -0,0 +1,31 @@
+namespace ARCtrl.ROCrate
+
+open DynamicObj
+open Fable.Core
+
+///
+[<AttachMembers>]
+type LabProtocol(
+    id,
+    ?additionalType,
+    ?name,
+    ?intendedUse,
+    ?description,
+    ?url,
+    ?comment,
+    ?version,
+    ?labEquipment,
+    ?reagent,
+    ?computationalTool
+) as this =
+    inherit ROCrateObject(id = id, schemaType = "bioschemas.org/LabProtocol", ?additionalType = additionalType)
+    do
+        DynObj.setValueOpt this (nameof name) name
+        DynObj.setValueOpt this (nameof intendedUse) intendedUse
+        DynObj.setValueOpt this (nameof description) description
+        DynObj.setValueOpt this (nameof url) url
+        DynObj.setValueOpt this (nameof comment) comment
+        DynObj.setValueOpt this (nameof version) version
+        DynObj.setValueOpt this (nameof labEquipment) labEquipment
+        DynObj.setValueOpt this (nameof reagent) reagent
+        DynObj.setValueOpt this (nameof computationalTool) computationalTool

src/ROCrate/ISAProfile/Person.fs

@@ -0,0 +1,37 @@
+namespace ARCtrl.ROCrate
+
+open DynamicObj
+open Fable.Core
+
+///
+[<AttachMembers>]
+type Person(
+    id,
+    givenName,
+    ?additionalType,
+    ?familyName,
+    ?email,
+    ?identifier,
+    ?affiliation,
+    ?jobTitle,
+    ?additionalName,
+    ?address,
+    ?telephone,
+    ?faxNumber,
+    ?disambiguatingDescription
+) as this=
+    inherit ROCrateObject(id = id, schemaType = "schema.org/Person", ?additionalType = additionalType)
+    do
+
+        DynObj.setValue this (nameof givenName) givenName
+
+        DynObj.setValueOpt this (nameof familyName) familyName
+        DynObj.setValueOpt this (nameof email) email
+        DynObj.setValueOpt this (nameof identifier) identifier
+        DynObj.setValueOpt this (nameof affiliation) affiliation
+        DynObj.setValueOpt this (nameof jobTitle) jobTitle
+        DynObj.setValueOpt this (nameof additionalName) additionalName
+        DynObj.setValueOpt this (nameof address) address
+        DynObj.setValueOpt this (nameof telephone) telephone
+        DynObj.setValueOpt this (nameof faxNumber) faxNumber
+        DynObj.setValueOpt this (nameof disambiguatingDescription) disambiguatingDescription

src/ROCrate/ISAProfile/PropertyValue.fs

@@ -0,0 +1,27 @@
+namespace ARCtrl.ROCrate
+
+open DynamicObj
+open Fable.Core
+
+///
+[<AttachMembers>]
+type PropertyValue(
+    id,
+    name,
+    value,
+    ?propertyID,
+    ?unitCode,
+    ?unitText,
+    ?valueReference,
+    ?additionalType
+) as this =
+    inherit ROCrateObject(id = id, schemaType = "schema.org/PropertyValue", ?additionalType = additionalType)
+    do
+
+        DynObj.setValue this (nameof name) name
+        DynObj.setValue this (nameof value) value
+
+        DynObj.setValueOpt this (nameof propertyID) propertyID
+        DynObj.setValueOpt this (nameof unitCode) unitCode
+        DynObj.setValueOpt this (nameof unitText) unitText
+        DynObj.setValueOpt this (nameof valueReference) valueReference

src/ROCrate/ISAProfile/Sample.fs

@@ -0,0 +1,20 @@
+namespace ARCtrl.ROCrate
+
+open DynamicObj
+open Fable.Core
+
+///
+[<AttachMembers>]
+type Sample(
+    id,
+    name,
+    ?additionalType,
+    ?additionalProperty,
+    ?derivesFrom
+) as this =
+    inherit ROCrateObject(id = id, schemaType = "bioschemas.org/Sample", ?additionalType = additionalType)
+    do
+        DynObj.setValue this (nameof name) name
+
+        DynObj.setValueOpt this (nameof additionalProperty) additionalProperty
+        DynObj.setValueOpt this (nameof derivesFrom) derivesFrom