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caroottcaroott
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refine workflowgraph core
1 parent 0920492 commit 0892600

11 files changed

Lines changed: 196 additions & 92 deletions

‎src/WorkflowGraph/ARCtrl.WorkflowGraph.fsproj‎

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@@ -19,6 +19,7 @@
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</ItemGroup>
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<ItemGroup>
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<PackageReference Include="DynamicObj" />
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<PackageReference Include="Siren" />
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</ItemGroup>
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‎src/WorkflowGraph/Builder.fs‎

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@@ -571,8 +571,7 @@ module Builder =
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addStepPorts state stepNodeId step
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let runScope = GraphId.childScope scope $"{step.Id}/run"
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let resolvedRun, runNodeId = buildRunNode state runScope stepNodeId workflowFilePath step.Run
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step.Run <- resolvedRun
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let _, runNodeId = buildRunNode state runScope stepNodeId workflowFilePath step.Run
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addEdgeByType state EdgeKind.Calls stepNodeId runNodeId (Some "calls")
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workflow.Steps

‎src/WorkflowGraph/README.md‎

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@@ -37,22 +37,8 @@ let index = Adapters.ofInvestigation investigation
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## Output formats
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```fsharp
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// Native outputs
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let mermaidText = WorkflowGraphSiren.toMermaid graph
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let markdown = WorkflowGraphSiren.toMarkdown graph
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// Optional image conversion via external renderer callbacks
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// (for example Mermaid CLI or a rendering web service)
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let svgOpt = WorkflowGraphSiren.toSvgWith renderMermaidToSvg graph
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let pngBytesOpt = WorkflowGraphSiren.toPngBytesWith renderMermaidToPng graph
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```
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50-
Only Mermaid text and Markdown are produced directly by this library.
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SVG/PNG are callback-based extension points and require you to provide the renderer.
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For .NET targets, save helpers are available:
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- `WorkflowGraphSiren.saveMermaid`
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- `WorkflowGraphSiren.saveMarkdown`
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- `WorkflowGraphSiren.saveSvgWith`
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- `WorkflowGraphSiren.savePngWith`
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This library directly produces Mermaid text and Markdown-wrapped Mermaid output.

‎src/WorkflowGraph/WorkflowGraph.fs‎

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@@ -27,13 +27,6 @@ module WorkflowGraphApi =
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let fromProcessingUnitToSiren = WorkflowGraphSiren.fromProcessingUnit
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let fromProcessingUnitToSirenResolved = WorkflowGraphSiren.fromProcessingUnitResolved
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#if !FABLE_COMPILER
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let saveMermaid = WorkflowGraphSiren.saveMermaid
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let saveMarkdown = WorkflowGraphSiren.saveMarkdown
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let saveSvgWith = WorkflowGraphSiren.saveSvgWith
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let savePngWith = WorkflowGraphSiren.savePngWith
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#endif
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let fromArcWorkflow = ofWorkflow
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let fromArcRun = ofRun
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let fromArcInvestigation = ofInvestigation

‎tests/WorkflowGraph/ARCtrl.WorkflowGraph.Tests.fsproj‎

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@@ -6,12 +6,14 @@
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<GenerateProgramFile>false</GenerateProgramFile>
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</PropertyGroup>
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<ItemGroup>
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<Compile Include="TestHelpers.fs" />
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<Compile Include="ReferenceParsing.Tests.fs" />
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<Compile Include="Builder.Tests.fs" />
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<Compile Include="Integration.Tests.fs" />
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<Compile Include="Adapters.Tests.fs" />
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<Compile Include="EdgeCases.Tests.fs" />
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<Compile Include="Visualization.Siren.Tests.fs" />
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<Compile Include="WorkflowGraph.Extensions.Tests.fs" />
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<Compile Include="Main.fs" />
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</ItemGroup>
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<ItemGroup>

‎tests/WorkflowGraph/Adapters.Tests.fs‎

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@@ -2,32 +2,10 @@ module Tests.Adapters
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33
open ARCtrl
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open ARCtrl.CWL
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open ARCtrl.FileSystem
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open ARCtrl.WorkflowGraph
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open TestingUtils
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open CrossAsync
9-
10-
let private workflowFixturePath =
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ArcPathHelper.combineMany [|
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TestObjects.IO.testSimpleARCWithCWL
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"workflows"
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"ProteomIQon"
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"workflow.cwl"
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|]
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18-
let private runFixturePath =
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ArcPathHelper.combineMany [|
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TestObjects.IO.testSimpleARCWithCWL
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"runs"
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"tests"
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"run.cwl"
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|]
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26-
let private loadProcessingUnitFromPath (path: string) =
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crossAsync {
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let! content = FileSystemHelper.readFileTextAsync path
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return Decode.decodeCWLProcessingUnit content
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}
8+
open Tests.WorkflowGraphTestHelpers
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3210
let tests_adapters =
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testList "Adapters" [

‎tests/WorkflowGraph/EdgeCases.Tests.fs‎

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@@ -82,6 +82,68 @@ steps:
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Expect.sequenceEqual nodeIds1 nodeIds2 ""
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Expect.sequenceEqual edgeIds1 edgeIds2 ""
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85+
testCase "building same processing unit instance twice is deterministic" <| fun () ->
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let yaml = """cwlVersion: v1.2
87+
class: Workflow
88+
inputs: {}
89+
outputs: {}
90+
steps:
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step1:
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run: ./tool.cwl
93+
in: {}
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out: [out]"""
95+
let processingUnit = Decode.decodeCWLProcessingUnit yaml
96+
let resolvedTool = Decode.decodeCommandLineTool TestObjects.CWL.CommandLineTool.cwlFile
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let options =
98+
WorkflowGraphBuildOptions.defaultOptions
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|> WorkflowGraphBuildOptions.withRootWorkflowFilePath (Some "workflow.cwl")
100+
|> WorkflowGraphBuildOptions.withTryResolveRunPath (Some (fun path ->
101+
if path.EndsWith("tool.cwl") then Some (CommandLineTool resolvedTool) else None
102+
))
103+
104+
let graph1 = Builder.buildWith options processingUnit
105+
let graph2 = Builder.buildWith options processingUnit
106+
107+
let nodeIds1 = graph1.Nodes |> Seq.map (fun n -> n.Id) |> Seq.sort |> Seq.toArray
108+
let nodeIds2 = graph2.Nodes |> Seq.map (fun n -> n.Id) |> Seq.sort |> Seq.toArray
109+
let edgeIds1 = graph1.Edges |> Seq.map (fun e -> e.Id) |> Seq.sort |> Seq.toArray
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let edgeIds2 = graph2.Edges |> Seq.map (fun e -> e.Id) |> Seq.sort |> Seq.toArray
111+
112+
Expect.sequenceEqual nodeIds1 nodeIds2 ""
113+
Expect.sequenceEqual edgeIds1 edgeIds2 ""
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115+
testCase "buildWith does not mutate workflow step run payloads" <| fun () ->
116+
let yaml = """cwlVersion: v1.2
117+
class: Workflow
118+
inputs: {}
119+
outputs: {}
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steps:
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step1:
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run: ./tool.cwl
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in: {}
124+
out: [out]"""
125+
let processingUnit = Decode.decodeCWLProcessingUnit yaml
126+
let resolvedTool = Decode.decodeCommandLineTool TestObjects.CWL.CommandLineTool.cwlFile
127+
let options =
128+
WorkflowGraphBuildOptions.defaultOptions
129+
|> WorkflowGraphBuildOptions.withRootWorkflowFilePath (Some "workflow.cwl")
130+
|> WorkflowGraphBuildOptions.withTryResolveRunPath (Some (fun path ->
131+
if path.EndsWith("tool.cwl") then Some (CommandLineTool resolvedTool) else None
132+
))
133+
134+
let assertRunString () =
135+
match processingUnit with
136+
| Workflow wf ->
137+
match wf.Steps.[0].Run with
138+
| RunString runPath -> Expect.equal runPath "./tool.cwl" ""
139+
| other -> Expect.isTrue false $"Expected RunString but got %A{other}"
140+
| _ ->
141+
Expect.isTrue false "Expected workflow processing unit"
142+
143+
assertRunString ()
144+
let _graph = Builder.buildWith options processingUnit
145+
assertRunString ()
146+
85147
testCase "scatter fields do not break graph build and are preserved as metadata" <| fun () ->
86148
let graph = buildGraphFromYaml TestObjects.CWL.Workflow.workflowWithScatterAndScatterMethodFile
87149
let stepNodeOpt =

‎tests/WorkflowGraph/Integration.Tests.fs‎

Lines changed: 2 additions & 45 deletions
Original file line numberDiff line numberDiff line change
@@ -2,26 +2,10 @@ module Tests.Integration
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33
open ARCtrl
44
open ARCtrl.CWL
5-
open ARCtrl.FileSystem
65
open ARCtrl.WorkflowGraph
7-
open TestingUtils
86
open CrossAsync
9-
10-
let private workflowFixturePath =
11-
ArcPathHelper.combineMany [|
12-
TestObjects.IO.testSimpleARCWithCWL
13-
"workflows"
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"ProteomIQon"
15-
"workflow.cwl"
16-
|]
17-
18-
let private runFixturePath =
19-
ArcPathHelper.combineMany [|
20-
TestObjects.IO.testSimpleARCWithCWL
21-
"runs"
22-
"tests"
23-
"run.cwl"
24-
|]
7+
open TestingUtils
8+
open Tests.WorkflowGraphTestHelpers
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2610
let private countEdges kind (graph: WorkflowGraph) =
2711
graph.Edges
@@ -33,33 +17,6 @@ let private countNodes predicate (graph: WorkflowGraph) =
3317
|> Seq.filter predicate
3418
|> Seq.length
3519

36-
let private loadProcessingUnitFromPath (path: string) =
37-
crossAsync {
38-
let! content = FileSystemHelper.readFileTextAsync path
39-
return Decode.decodeCWLProcessingUnit content
40-
}
41-
42-
let private buildRunResolverFromFixtures () =
43-
crossAsync {
44-
let! relativePaths = FileSystemHelper.getAllFilePathsAsync TestObjects.IO.testSimpleARCWithCWL
45-
let cwlRelativePaths =
46-
relativePaths
47-
|> Array.filter (fun p -> p.EndsWith(".cwl", System.StringComparison.OrdinalIgnoreCase))
48-
let! resolvedEntries =
49-
cwlRelativePaths
50-
|> Array.map (fun relativePath ->
51-
crossAsync {
52-
let absolutePath = ArcPathHelper.combine TestObjects.IO.testSimpleARCWithCWL relativePath
53-
let! content = FileSystemHelper.readFileTextAsync absolutePath
54-
let unit = Decode.decodeCWLProcessingUnit content
55-
return ArcPathHelper.normalizePathKey relativePath, unit
56-
}
57-
)
58-
|> CrossAsync.all
59-
let map = resolvedEntries |> Map.ofArray
60-
return fun (path: string) -> map |> Map.tryFind (ArcPathHelper.normalizePathKey path)
61-
}
62-
6320
let tests_workflowFixture =
6421
testList "workflow.cwl fixture" [
6522
testCaseCrossAsync "builds without diagnostics" (crossAsync {

‎tests/WorkflowGraph/Main.fs‎

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@@ -11,6 +11,7 @@ let all =
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Tests.Adapters.main
1212
Tests.EdgeCases.main
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Tests.VisualizationSiren.main
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Tests.WorkflowGraphExtensions.main
1415
]
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1617
#if !TESTS_ALL

‎tests/WorkflowGraph/TestHelpers.fs‎

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@@ -0,0 +1,50 @@
1+
module Tests.WorkflowGraphTestHelpers
2+
3+
open ARCtrl
4+
open ARCtrl.CWL
5+
open ARCtrl.FileSystem
6+
open TestingUtils
7+
open CrossAsync
8+
9+
let workflowFixturePath =
10+
ArcPathHelper.combineMany [|
11+
TestObjects.IO.testSimpleARCWithCWL
12+
"workflows"
13+
"ProteomIQon"
14+
"workflow.cwl"
15+
|]
16+
17+
let runFixturePath =
18+
ArcPathHelper.combineMany [|
19+
TestObjects.IO.testSimpleARCWithCWL
20+
"runs"
21+
"tests"
22+
"run.cwl"
23+
|]
24+
25+
let loadProcessingUnitFromPath (path: string) =
26+
crossAsync {
27+
let! content = FileSystemHelper.readFileTextAsync path
28+
return Decode.decodeCWLProcessingUnit content
29+
}
30+
31+
let buildRunResolverFromFixtures () =
32+
crossAsync {
33+
let! relativePaths = FileSystemHelper.getAllFilePathsAsync TestObjects.IO.testSimpleARCWithCWL
34+
let cwlRelativePaths =
35+
relativePaths
36+
|> Array.filter (fun p -> p.EndsWith(".cwl", System.StringComparison.OrdinalIgnoreCase))
37+
let! resolvedEntries =
38+
cwlRelativePaths
39+
|> Array.map (fun relativePath ->
40+
crossAsync {
41+
let absolutePath = ArcPathHelper.combine TestObjects.IO.testSimpleARCWithCWL relativePath
42+
let! content = FileSystemHelper.readFileTextAsync absolutePath
43+
let processingUnit = Decode.decodeCWLProcessingUnit content
44+
return ArcPathHelper.normalizePathKey relativePath, processingUnit
45+
}
46+
)
47+
|> CrossAsync.all
48+
let map = resolvedEntries |> Map.ofArray
49+
return fun (path: string) -> map |> Map.tryFind (ArcPathHelper.normalizePathKey path)
50+
}

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