CWL Model, Encoding & Decoding #421
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| Original file line number | Diff line number | Diff line change |
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| namespace ARCtrl | ||
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| open ARCtrl.CWL | ||
| open DynamicObj | ||
| open CWLTypes | ||
| open Requirements | ||
| open Inputs | ||
| open Outputs | ||
| open WorkflowSteps | ||
| open Fable.Core | ||
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| module CWLProcessingUnits = | ||
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| [<AttachMembers>] | ||
| type CWLToolDescription ( | ||
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There was a problem hiding this comment. add [AttachMembers] attribute to each class. See ArcAssay as reference. This is important for js and py usability |
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| cwlVersion: string, | ||
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There was a problem hiding this comment. How vastly differing are the cwl versions? Do we have a default version in the specs? If not, we should pick one and set this field here to optional with a default value. There was a problem hiding this comment. We ask for version 1.2 (current one) or higher. The version is a mandatory field in cwl files and always present, so it can always be read. There was a problem hiding this comment. Yes, but this type is not exclusively for parsing but also for being created, edited and such. I don't think we should have this as a mandatory field in the constructor. There was a problem hiding this comment. Even if you want to create or edit cwl, you need this field for it to be valid. So making it optional wouldn't make sense imo. A creator which automatically sets it to 1.2 could be an option. There was a problem hiding this comment. Yes, having it as an optional parameter in the constructor with an internal default value is exactly what I meant. |
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| cls: CWLClass, | ||
| outputs: ResizeArray<Output>, | ||
| ?baseCommand: ResizeArray<string>, | ||
| ?requirements: ResizeArray<Requirement>, | ||
| ?hints: ResizeArray<Requirement>, | ||
| ?inputs: ResizeArray<Input>, | ||
| ?metadata: DynamicObj | ||
| ) = | ||
| inherit DynamicObj () | ||
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| let mutable _cwlVersion: string = cwlVersion | ||
| let mutable _class: CWLClass = cls | ||
| let mutable _outputs: ResizeArray<Output> = outputs | ||
| let mutable _baseCommand: ResizeArray<string> option = baseCommand | ||
| let mutable _requirements: ResizeArray<Requirement> option = requirements | ||
| let mutable _hints: ResizeArray<Requirement> option = hints | ||
| let mutable _inputs: ResizeArray<Input> option = inputs | ||
| let mutable _metadata: DynamicObj option = metadata | ||
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| member this.CWLVersion | ||
| with get() = _cwlVersion | ||
| and set(version) = _cwlVersion <- version | ||
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| member this.Class | ||
| with get() = _class | ||
| and set(cls) = _class <- cls | ||
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| member this.Outputs | ||
| with get() = _outputs | ||
| and set(outputs) = _outputs <- outputs | ||
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| member this.BaseCommand | ||
| with get() = _baseCommand | ||
| and set(baseCommand) = _baseCommand <- baseCommand | ||
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| member this.Requirements | ||
| with get() = _requirements | ||
| and set(requirements) = _requirements <- requirements | ||
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| member this.Hints | ||
| with get() = _hints | ||
| and set(hints) = _hints <- hints | ||
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| member this.Inputs | ||
| with get() = _inputs | ||
| and set(inputs) = _inputs <- inputs | ||
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| member this.Metadata | ||
| with get() = _metadata | ||
| and set(metadata) = _metadata <- metadata | ||
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| [<AttachMembers>] | ||
| type CWLWorkflowDescription( | ||
| cwlVersion: string, | ||
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| cls: CWLClass, | ||
| steps: ResizeArray<WorkflowStep>, | ||
| inputs: ResizeArray<Input>, | ||
| outputs: ResizeArray<Output>, | ||
| ?requirements: ResizeArray<Requirement>, | ||
| ?hints: ResizeArray<Requirement>, | ||
| ?metadata: DynamicObj | ||
| ) = | ||
| inherit DynamicObj() | ||
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| let mutable _cwlVersion: string = cwlVersion | ||
| let mutable _class: CWLClass = cls | ||
| let mutable _steps: ResizeArray<WorkflowStep> = steps | ||
| let mutable _inputs: ResizeArray<Input> = inputs | ||
| let mutable _outputs: ResizeArray<Output> = outputs | ||
| let mutable _requirements: ResizeArray<Requirement> option = requirements | ||
| let mutable _hints: ResizeArray<Requirement> option = hints | ||
| let mutable _metadata: DynamicObj option = metadata | ||
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| member this.CWLVersion | ||
| with get() = _cwlVersion | ||
| and set(version) = _cwlVersion <- version | ||
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| member this.Class | ||
| with get() = _class | ||
| and set(cls) = _class <- cls | ||
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| member this.Steps | ||
| with get() = _steps | ||
| and set(steps) = _steps <- steps | ||
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| member this.Inputs | ||
| with get() = _inputs | ||
| and set(inputs) = _inputs <- inputs | ||
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| member this.Outputs | ||
| with get() = _outputs | ||
| and set(outputs) = _outputs <- outputs | ||
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| member this.Requirements | ||
| with get() = _requirements | ||
| and set(requirements) = _requirements <- requirements | ||
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| member this.Hints | ||
| with get() = _hints | ||
| and set(hints) = _hints <- hints | ||
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| member this.Metadata | ||
| with get() = _metadata | ||
| and set(metadata) = _metadata <- metadata | ||
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Some of these types (the top-level ones) should definitely be directly in the ARCtrl namespace. Maybe take a look at ARCtrl.Core, where ArcAssay and such are directly in the ARCtrl namespace.