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EtschbeijerEtschbeijer
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Implement run and workflow json methods
1 parent 70cdacf commit e8a74ff

15 files changed

Lines changed: 347 additions & 9 deletions

‎src/ARCtrl/ARCtrl.Javascript.fsproj‎

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@@ -16,6 +16,8 @@
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<Compile Include="JsonIO\Comment.fs" />
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<Compile Include="JsonIO\OntologyAnnotation.fs" />
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<Compile Include="JsonIO\OntologySourceReference.fs" />
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<Compile Include="JsonIO\Run.fs" />
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<Compile Include="JsonIO\Workflow.fs" />
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<Compile Include="JsonIO\DataFile.fs" />
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<Compile Include="JsonIO\Data.fs" />
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<Compile Include="JsonIO\Datamap.fs" />

‎src/ARCtrl/ARCtrl.Python.fsproj‎

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<Compile Include="JsonIO\Comment.fs" />
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<Compile Include="JsonIO\OntologyAnnotation.fs" />
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<Compile Include="JsonIO\OntologySourceReference.fs" />
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<Compile Include="JsonIO\Run.fs" />
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<Compile Include="JsonIO\Workflow.fs" />
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<Compile Include="JsonIO\DataFile.fs" />
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<Compile Include="JsonIO\Data.fs" />
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<Compile Include="JsonIO\Datamap.fs" />

‎src/ARCtrl/ARCtrl.fsproj‎

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<Compile Include="JsonIO\Assay.fs" />
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<Compile Include="JsonIO\Study.fs" />
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<Compile Include="JsonIO\Investigation.fs" />
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<Compile Include="JsonIO\Run.fs" />
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<Compile Include="JsonIO\Workflow.fs" />
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<Compile Include="JsonIO\Datamap.fs" />
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<Compile Include="JsonIO\LDObject.fs" />
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<Compile Include="Conversion.fs" />

‎src/ARCtrl/JsonIO/Assay.fs‎

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@@ -6,8 +6,6 @@ open ARCtrl.Helper
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[<AutoOpen>]
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module AssayExtensions =
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9-
open System.Collections.Generic
10-
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type ArcAssay with
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static member fromJsonString (s:string) =

‎src/ARCtrl/JsonIO/Run.fs‎

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namespace ARCtrl.Json
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open ARCtrl
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open ARCtrl.Helper
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[<AutoOpen>]
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module RunExtensions =
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type ArcRun with
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static member fromJsonString (s:string) =
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Decode.fromJsonString Run.decoder s
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static member toJsonString(?spaces) =
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fun (obj:ArcRun) ->
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Run.encoder obj
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|> Encode.toJsonString (Encode.defaultSpaces spaces)
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member this.ToJsonString(?spaces) =
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ArcRun.toJsonString(?spaces=spaces) this

‎src/ARCtrl/JsonIO/Workflow.fs‎

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namespace ARCtrl.Json
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open ARCtrl
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open ARCtrl.Helper
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[<AutoOpen>]
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module WorkflowExtensions =
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type ArcWorkflow with
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static member fromJsonString (s:string) =
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Decode.fromJsonString Workflow.decoder s
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static member toJsonString(?spaces) =
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fun (obj:ArcWorkflow) ->
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Workflow.encoder obj
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|> Encode.toJsonString (Encode.defaultSpaces spaces)
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member this.ToJsonString(?spaces) =
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ArcWorkflow.toJsonString(?spaces=spaces) this

‎src/Core/IdentifierSetters.fs‎

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@@ -1,4 +1,4 @@
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module ARCtrl.IdentifierSetters
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module ARCtrl.IdentifierSetters
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open ARCtrl.Helper
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open Identifier
@@ -23,3 +23,13 @@ let setInvestigationIdentifier (newIdentifier: string) (investigation: ArcInvest
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checkValidCharacters newIdentifier
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investigation.Identifier <- newIdentifier
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investigation
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let setRunIdentifier (newIdentifier: string) (run: ArcRun) =
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checkValidCharacters newIdentifier
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run.Identifier <- newIdentifier
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run
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let setWorkflowIdentifier (newIdentifier: string) (workflow: ArcWorkflow) =
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checkValidCharacters newIdentifier
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workflow.Identifier <- newIdentifier
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workflow

‎src/Json/ARCtrl.Json.fsproj‎

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@@ -80,6 +80,8 @@
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<Compile Include="Assay.fs" />
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<Compile Include="Study.fs" />
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<Compile Include="Investigation.fs" />
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<Compile Include="Run.fs" />
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<Compile Include="Workflow.fs" />
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</ItemGroup>
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<ItemGroup>
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<PackageReference Include="Thoth.Json.Core" />

‎src/Json/Assay.fs‎

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@@ -19,8 +19,8 @@ module Assay =
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Encode.tryInclude "TechnologyPlatform" OntologyAnnotation.encoder assay.TechnologyPlatform
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Encode.tryInclude "DataMap" DataMap.encoder assay.DataMap
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Encode.tryIncludeSeq "Tables" ArcTable.encoder assay.Tables
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Encode.tryIncludeSeq "Performers" Person.encoder assay.Performers
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Encode.tryIncludeSeq "Comments" Comment.encoder assay.Comments
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Encode.tryIncludeSeq "Performers" Person.encoder assay.Performers
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Encode.tryIncludeSeq "Comments" Comment.encoder assay.Comments
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]
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|> Encode.choose
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|> Encode.object
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let identifier = i.Replace(" ","_")
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$"assays/{identifier}/"
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let encoder (studyName:string Option) (a : ArcAssay) =
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let encoder (assayName:string Option) (a : ArcAssay) =
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let fileName = Identifier.Assay.fileNameFromIdentifier a.Identifier
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let processes = a.GetProcesses()
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let dataFiles = ProcessSequence.getData processes
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Encode.tryInclude "technologyPlatform" OntologyAnnotation.ROCrate.encoderDefinedTerm a.TechnologyPlatform
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Encode.tryIncludeSeq "performers" Person.ROCrate.encoder a.Performers
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Encode.tryIncludeList "dataFiles" Data.ROCrate.encoder dataFiles
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Encode.tryIncludeList "processSequence" (Process.ROCrate.encoder studyName (Some a.Identifier)) processes
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Encode.tryIncludeList "processSequence" (Process.ROCrate.encoder assayName (Some a.Identifier)) processes
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Encode.tryIncludeSeq "comments" Comment.ROCrate.encoder a.Comments
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"@context", ROCrateContext.Assay.context_jsonvalue |> Some
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]

‎src/Json/Run.fs‎

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namespace ARCtrl.Json
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open Thoth.Json.Core
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open ARCtrl
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open ARCtrl.Process
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open ARCtrl.Helper
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open Conversion
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module Run =
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let rec encoder (run: ArcRun) =
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[
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"Identifier", Encode.string run.Identifier |> Some
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Encode.tryInclude "Title" Encode.string run.Title
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Encode.tryInclude "Description" Encode.string run.Description
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Encode.tryInclude "MeasurementType" OntologyAnnotation.encoder run.MeasurementType
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Encode.tryInclude "TechnologyType" OntologyAnnotation.encoder run.TechnologyType
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Encode.tryInclude "TechnologyPlatform" OntologyAnnotation.encoder run.TechnologyPlatform
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Encode.tryInclude "DataMap" DataMap.encoder run.DataMap
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Encode.tryIncludeSeq "WorkflowIdentifiers" Encode.string run.WorkflowIdentifiers
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Encode.tryIncludeSeq "Tables" ArcTable.encoder run.Tables
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Encode.tryIncludeSeq "Performers" Person.encoder run.Performers
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Encode.tryIncludeSeq "Comments" Comment.encoder run.Comments
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]
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|> Encode.choose
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|> Encode.object
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let decoder: Decoder<ArcRun> =
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Decode.object (fun get ->
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ArcRun.create(
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get.Required.Field("Identifier") Decode.string,
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?title = get.Optional.Field "Title" Decode.string,
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?description = get.Optional.Field "Description" Decode.string,
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?measurementType = get.Optional.Field "MeasurementType" OntologyAnnotation.decoder,
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?technologyType = get.Optional.Field "TechnologyType" OntologyAnnotation.decoder,
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?technologyPlatform = get.Optional.Field "TechnologyPlatform" OntologyAnnotation.decoder,
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?workflowIdentifiers = get.Optional.Field "WorkflowIdentifiers" (Decode.resizeArray Decode.string),
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?tables = get.Optional.Field "Tables" (Decode.resizeArray ArcTable.decoder),
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?datamap = get.Optional.Field "DataMap" DataMap.decoder,
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?performers = get.Optional.Field "Performers" (Decode.resizeArray Person.decoder),
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?comments = get.Optional.Field "Comments" (Decode.resizeArray Comment.decoder)
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)
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)

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