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caroottcaroott
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add workflowgraph core
1 parent 96f47ee commit 23ffa64

10 files changed

Lines changed: 1255 additions & 1 deletion

‎Directory.Packages.props‎

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<PackageVersion Include="Fable.Node" Version="1.2.0" />
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<PackageVersion Include="Fable.Promise" Version="3.2.0" />
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<PackageVersion Include="Fable.Pyxpecto" Version="1.3.0" />
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<PackageVersion Include="Siren" Version="0.3.2" />
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<PackageVersion Include="NJsonSchema" Version="10.8.0" />
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</ItemGroup>
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</Project>
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</Project>

‎src/WorkflowGraph/ARCtrl.WorkflowGraph.fsproj‎

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<?xml version="1.0" encoding="utf-8"?>
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<Project Sdk="Microsoft.NET.Sdk">
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<PropertyGroup>
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<Description>Graph extraction and visualization helpers for CWL processing units used in ARCtrl.</Description>
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<PackageProjectUrl>https://github.com/nfdi4plants/ARCtrl/tree/main/src/WorkflowGraph</PackageProjectUrl>
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<PackageTags>ARC;F#;FSharp;dotnet;fable-library;workflow;graph;cwl;mermaid</PackageTags>
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</PropertyGroup>
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<Import Project="../Package.Metadata.props" />
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<ItemGroup>
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<Compile Include="GraphTypes.fs" />
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<Compile Include="ReferenceParsing.fs" />
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<Compile Include="BuildOptions.fs" />
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<Compile Include="QueryHelpers.fs" />
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<Compile Include="Builder.fs" />
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<Compile Include="Adapters.fs" />
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<Compile Include="Visualization.Siren.fs" />
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<Compile Include="WorkflowGraph.fs" />
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</ItemGroup>
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<ItemGroup>
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<PackageReference Include="Siren" />
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</ItemGroup>
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<ItemGroup>
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<ProjectReference Include="..\CWL\ARCtrl.CWL.fsproj" />
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<ProjectReference Include="..\Core\ARCtrl.Core.fsproj" />
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<ProjectReference Include="..\FileSystem\ARCtrl.FileSystem.fsproj" />
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</ItemGroup>
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</Project>

‎src/WorkflowGraph/Adapters.fs‎

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namespace ARCtrl.WorkflowGraph
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open ARCtrl
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open ARCtrl.Helper
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open ARCtrl.CWL
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[<RequireQualifiedAccess>]
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module Adapters =
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let private createCwlLookupFromInvestigation (investigation: ArcInvestigation option) =
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match investigation with
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| None ->
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Map.empty
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| Some inv ->
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seq {
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for workflow in inv.Workflows do
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match workflow.CWLDescription with
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| Some cwl ->
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yield Identifier.Workflow.cwlFileNameFromIdentifier workflow.Identifier, cwl
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| None ->
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()
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for run in inv.Runs do
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match run.CWLDescription with
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| Some cwl ->
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yield Identifier.Run.cwlFileNameFromIdentifier run.Identifier, cwl
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| None ->
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()
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}
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|> Seq.map (fun (path, cwl) -> ArcPathHelper.normalizePathKey path, cwl)
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|> Map.ofSeq
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let private createResolver (lookup: Map<string, CWLProcessingUnit>) =
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if Map.isEmpty lookup then
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None
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else
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Some (fun (path: string) -> lookup |> Map.tryFind (ArcPathHelper.normalizePathKey path))
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let private createMissingDescriptionError identifier scopeType =
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{
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Kind = GraphIssueKind.MissingCwlDescription
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Message = $"No CWLDescription available for {scopeType} '{identifier}'."
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Scope = Some identifier
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Reference = None
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}
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let ofWorkflow (workflow: ArcWorkflow) : Result<WorkflowGraph, GraphBuildIssue> =
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match workflow.CWLDescription with
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| None ->
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Error (createMissingDescriptionError workflow.Identifier "workflow")
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| Some processingUnit ->
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let cwlLookup = createCwlLookupFromInvestigation workflow.Investigation
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let options =
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WorkflowGraphBuildOptions.defaultOptions
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|> WorkflowGraphBuildOptions.withRootScope workflow.Identifier
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|> WorkflowGraphBuildOptions.withRootWorkflowFilePath (Some (Identifier.Workflow.cwlFileNameFromIdentifier workflow.Identifier))
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|> WorkflowGraphBuildOptions.withTryResolveRunPath (createResolver cwlLookup)
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Builder.buildWith options processingUnit
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|> Ok
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let ofRun (run: ArcRun) : Result<WorkflowGraph, GraphBuildIssue> =
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match run.CWLDescription with
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| None ->
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Error (createMissingDescriptionError run.Identifier "run")
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| Some processingUnit ->
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let cwlLookup = createCwlLookupFromInvestigation run.Investigation
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let options =
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WorkflowGraphBuildOptions.defaultOptions
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|> WorkflowGraphBuildOptions.withRootScope run.Identifier
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|> WorkflowGraphBuildOptions.withRootWorkflowFilePath (Some (Identifier.Run.cwlFileNameFromIdentifier run.Identifier))
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|> WorkflowGraphBuildOptions.withTryResolveRunPath (createResolver cwlLookup)
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Builder.buildWith options processingUnit
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|> Ok
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let ofInvestigation (investigation: ArcInvestigation) : WorkflowGraphIndex =
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let workflowGraphs = ResizeArray()
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let runGraphs = ResizeArray()
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for workflow in investigation.Workflows do
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workflowGraphs.Add(workflow.Identifier, ofWorkflow workflow)
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for run in investigation.Runs do
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runGraphs.Add(run.Identifier, ofRun run)
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{
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WorkflowGraphs = workflowGraphs
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RunGraphs = runGraphs
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}

‎src/WorkflowGraph/BuildOptions.fs‎

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namespace ARCtrl.WorkflowGraph
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open ARCtrl.CWL
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type WorkflowGraphBuildOptions = {
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RootScope: string
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RootWorkflowFilePath: string option
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TryResolveRunPath: (string -> CWLProcessingUnit option) option
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StrictUnresolvedRunReferences: bool
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ExpandNestedWorkflows: bool
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}
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[<RequireQualifiedAccess>]
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module WorkflowGraphBuildOptions =
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let defaultOptions =
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{
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RootScope = "root"
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RootWorkflowFilePath = None
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TryResolveRunPath = None
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StrictUnresolvedRunReferences = false
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ExpandNestedWorkflows = true
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}
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let withRootScope (rootScope: string) (options: WorkflowGraphBuildOptions) =
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{ options with RootScope = rootScope }
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let withRootWorkflowFilePath (rootWorkflowFilePath: string option) (options: WorkflowGraphBuildOptions) =
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{ options with RootWorkflowFilePath = rootWorkflowFilePath }
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let withTryResolveRunPath (tryResolveRunPath: (string -> CWLProcessingUnit option) option) (options: WorkflowGraphBuildOptions) =
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{ options with TryResolveRunPath = tryResolveRunPath }
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let withStrictUnresolvedRunReferences (strict: bool) (options: WorkflowGraphBuildOptions) =
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{ options with StrictUnresolvedRunReferences = strict }
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let withExpandNestedWorkflows (expandNestedWorkflows: bool) (options: WorkflowGraphBuildOptions) =
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{ options with ExpandNestedWorkflows = expandNestedWorkflows }

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