@nfdi4plants/arctrl 3.2.2 → 3.3.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +0 -64
- package/dist/ts/index.d.ts +44 -7
- package/dist/ts/index.d.ts.map +1 -1
- package/dist/ts/index.js +45 -8
- package/dist/ts/node_modules/@fable-org/fable-library-ts/Array.js +195 -92
- package/dist/ts/node_modules/@fable-org/fable-library-ts/Async.js +251 -30
- package/dist/ts/node_modules/@fable-org/fable-library-ts/AsyncBuilder.js +61 -11
- package/dist/ts/node_modules/@fable-org/fable-library-ts/BigInt.js +15 -5
- package/dist/ts/node_modules/@fable-org/fable-library-ts/BitConverter.js +139 -0
- package/dist/ts/node_modules/@fable-org/fable-library-ts/Date.js +1 -1
- package/dist/ts/node_modules/@fable-org/fable-library-ts/Decimal.js +68 -12
- package/dist/ts/node_modules/@fable-org/fable-library-ts/Double.js +24 -10
- package/dist/ts/node_modules/@fable-org/fable-library-ts/FSharp.Core.js +8 -2
- package/dist/ts/node_modules/@fable-org/fable-library-ts/Global.js +1 -1
- package/dist/ts/node_modules/@fable-org/fable-library-ts/Int32.js +11 -2
- package/dist/ts/node_modules/@fable-org/fable-library-ts/List.js +220 -155
- package/dist/ts/node_modules/@fable-org/fable-library-ts/Long.js +7 -2
- package/dist/ts/node_modules/@fable-org/fable-library-ts/Map.js +46 -39
- package/dist/ts/node_modules/@fable-org/fable-library-ts/MutableMap.js +75 -92
- package/dist/ts/node_modules/@fable-org/fable-library-ts/MutableSet.js +56 -76
- package/dist/ts/node_modules/@fable-org/fable-library-ts/NumberStyles.js +54 -0
- package/dist/ts/node_modules/@fable-org/fable-library-ts/Numeric.js +10 -5
- package/dist/ts/node_modules/@fable-org/fable-library-ts/Random.js +3 -4
- package/dist/ts/node_modules/@fable-org/fable-library-ts/Range.js +4 -3
- package/dist/ts/node_modules/@fable-org/fable-library-ts/RegExp.js +2 -2
- package/dist/ts/node_modules/@fable-org/fable-library-ts/Seq.js +128 -64
- package/dist/ts/node_modules/@fable-org/fable-library-ts/Seq2.js +4 -8
- package/dist/ts/node_modules/@fable-org/fable-library-ts/Set.js +64 -57
- package/dist/ts/node_modules/@fable-org/fable-library-ts/String.js +68 -21
- package/dist/ts/node_modules/@fable-org/fable-library-ts/System.Collections.Generic.js +3 -2
- package/dist/ts/node_modules/@fable-org/fable-library-ts/System.Text.js +2 -2
- package/dist/ts/node_modules/@fable-org/fable-library-ts/System.js +5 -5
- package/dist/ts/node_modules/@fable-org/fable-library-ts/Types.js +23 -12
- package/dist/ts/node_modules/@fable-org/fable-library-ts/Util.js +88 -49
- package/dist/ts/node_modules/@fable-org/fable-library-ts/lib/big.js +121 -74
- package/dist/ts/ts/ARC.d.ts +22 -5
- package/dist/ts/ts/ARC.d.ts.map +1 -1
- package/dist/ts/ts/ARC.js +282 -185
- package/dist/ts/ts/CWL/CWLKnownFieldNames.d.ts +0 -2
- package/dist/ts/ts/CWL/CWLKnownFieldNames.d.ts.map +1 -1
- package/dist/ts/ts/CWL/CWLKnownFieldNames.js +1 -7
- package/dist/ts/ts/CWL/CWLProcessingUnit.d.ts +46 -27
- package/dist/ts/ts/CWL/CWLProcessingUnit.d.ts.map +1 -1
- package/dist/ts/ts/CWL/CWLProcessingUnit.js +312 -123
- package/dist/ts/ts/CWL/CWLTypes.d.ts +481 -148
- package/dist/ts/ts/CWL/CWLTypes.d.ts.map +1 -1
- package/dist/ts/ts/CWL/CWLTypes.js +887 -201
- package/dist/ts/ts/CWL/Decode.d.ts +480 -211
- package/dist/ts/ts/CWL/Decode.d.ts.map +1 -1
- package/dist/ts/ts/CWL/Decode.js +3614 -2462
- package/dist/ts/ts/CWL/DynamicObjHelpers.d.ts +9 -0
- package/dist/ts/ts/CWL/DynamicObjHelpers.d.ts.map +1 -1
- package/dist/ts/ts/CWL/DynamicObjHelpers.js +55 -5
- package/dist/ts/ts/CWL/Encode.d.ts +225 -85
- package/dist/ts/ts/CWL/Encode.d.ts.map +1 -1
- package/dist/ts/ts/CWL/Encode.js +1858 -970
- package/dist/ts/ts/CWL/ExpressionToolDescription.d.ts +42 -28
- package/dist/ts/ts/CWL/ExpressionToolDescription.d.ts.map +1 -1
- package/dist/ts/ts/CWL/ExpressionToolDescription.js +34 -13
- package/dist/ts/ts/CWL/HashHelpers.d.ts +38 -0
- package/dist/ts/ts/CWL/HashHelpers.d.ts.map +1 -1
- package/dist/ts/ts/CWL/HashHelpers.js +255 -6
- package/dist/ts/ts/CWL/Inputs.d.ts +127 -56
- package/dist/ts/ts/CWL/Inputs.d.ts.map +1 -1
- package/dist/ts/ts/CWL/Inputs.js +107 -16
- package/dist/ts/ts/CWL/OperationDescription.d.ts +41 -21
- package/dist/ts/ts/CWL/OperationDescription.d.ts.map +1 -1
- package/dist/ts/ts/CWL/OperationDescription.js +35 -9
- package/dist/ts/ts/CWL/Outputs.d.ts +93 -42
- package/dist/ts/ts/CWL/Outputs.d.ts.map +1 -1
- package/dist/ts/ts/CWL/Outputs.js +101 -19
- package/dist/ts/ts/CWL/ParameterReference.d.ts +11 -8
- package/dist/ts/ts/CWL/ParameterReference.d.ts.map +1 -1
- package/dist/ts/ts/CWL/ParameterReference.js +18 -25
- package/dist/ts/ts/CWL/ParameterValue.d.ts +15 -1
- package/dist/ts/ts/CWL/ParameterValue.d.ts.map +1 -1
- package/dist/ts/ts/CWL/ParameterValue.js +59 -35
- package/dist/ts/ts/CWL/Requirements.d.ts +240 -98
- package/dist/ts/ts/CWL/Requirements.d.ts.map +1 -1
- package/dist/ts/ts/CWL/Requirements.js +462 -89
- package/dist/ts/ts/CWL/ScalarQuoting.d.ts +51 -0
- package/dist/ts/ts/CWL/ScalarQuoting.d.ts.map +1 -0
- package/dist/ts/ts/CWL/ScalarQuoting.js +250 -0
- package/dist/ts/ts/CWL/ToolDescription.d.ts +63 -50
- package/dist/ts/ts/CWL/ToolDescription.d.ts.map +1 -1
- package/dist/ts/ts/CWL/ToolDescription.js +34 -13
- package/dist/ts/ts/CWL/WorkflowDescription.d.ts +45 -26
- package/dist/ts/ts/CWL/WorkflowDescription.d.ts.map +1 -1
- package/dist/ts/ts/CWL/WorkflowDescription.js +38 -11
- package/dist/ts/ts/CWL/WorkflowSteps.d.ts +248 -65
- package/dist/ts/ts/CWL/WorkflowSteps.d.ts.map +1 -1
- package/dist/ts/ts/CWL/WorkflowSteps.js +413 -43
- package/dist/ts/ts/CWLRunResolver.d.ts +30 -12
- package/dist/ts/ts/CWLRunResolver.d.ts.map +1 -1
- package/dist/ts/ts/CWLRunResolver.js +221 -86
- package/dist/ts/ts/Contract/ARC.d.ts.map +1 -1
- package/dist/ts/ts/Contract/ARC.js +13 -14
- package/dist/ts/ts/Contract/ArcAssay.d.ts.map +1 -1
- package/dist/ts/ts/Contract/ArcAssay.js +4 -4
- package/dist/ts/ts/Contract/ArcInvestigation.d.ts.map +1 -1
- package/dist/ts/ts/Contract/ArcInvestigation.js +3 -4
- package/dist/ts/ts/Contract/ArcRun.d.ts +12 -2
- package/dist/ts/ts/Contract/ArcRun.d.ts.map +1 -1
- package/dist/ts/ts/Contract/ArcRun.js +47 -20
- package/dist/ts/ts/Contract/ArcStudy.d.ts.map +1 -1
- package/dist/ts/ts/Contract/ArcStudy.js +4 -4
- package/dist/ts/ts/Contract/ArcWorkflow.d.ts +18 -4
- package/dist/ts/ts/Contract/ArcWorkflow.d.ts.map +1 -1
- package/dist/ts/ts/Contract/ArcWorkflow.js +55 -17
- package/dist/ts/ts/Contract/Datamap.d.ts.map +1 -1
- package/dist/ts/ts/Contract/Datamap.js +16 -17
- package/dist/ts/ts/Contract/Git.js +1 -1
- package/dist/ts/ts/Contract/ValidationPackagesConfig.d.ts.map +1 -1
- package/dist/ts/ts/Contract/ValidationPackagesConfig.js +4 -5
- package/dist/ts/ts/ContractIO/ContractIO.d.ts +7 -0
- package/dist/ts/ts/ContractIO/ContractIO.d.ts.map +1 -1
- package/dist/ts/ts/ContractIO/ContractIO.js +95 -18
- package/dist/ts/ts/ContractIO/FileSystemHelper.d.ts +1 -0
- package/dist/ts/ts/ContractIO/FileSystemHelper.d.ts.map +1 -1
- package/dist/ts/ts/ContractIO/FileSystemHelper.js +12 -5
- package/dist/ts/ts/Conversion/Assay.d.ts.map +1 -1
- package/dist/ts/ts/Conversion/Assay.js +26 -18
- package/dist/ts/ts/Conversion/Basic.d.ts +4 -0
- package/dist/ts/ts/Conversion/Basic.d.ts.map +1 -1
- package/dist/ts/ts/Conversion/Basic.js +55 -31
- package/dist/ts/ts/Conversion/ColumnIndex.d.ts.map +1 -1
- package/dist/ts/ts/Conversion/ColumnIndex.js +2 -4
- package/dist/ts/ts/Conversion/DateTime.d.ts.map +1 -1
- package/dist/ts/ts/Conversion/DateTime.js +1 -2
- package/dist/ts/ts/Conversion/Investigation.d.ts.map +1 -1
- package/dist/ts/ts/Conversion/Investigation.js +15 -14
- package/dist/ts/ts/Conversion/Person.js +11 -11
- package/dist/ts/ts/Conversion/Process.d.ts +4 -2
- package/dist/ts/ts/Conversion/Process.d.ts.map +1 -1
- package/dist/ts/ts/Conversion/Process.js +134 -97
- package/dist/ts/ts/Conversion/Run.d.ts +36 -6
- package/dist/ts/ts/Conversion/Run.d.ts.map +1 -1
- package/dist/ts/ts/Conversion/Run.js +320 -136
- package/dist/ts/ts/Conversion/ScholarlyArticle.d.ts.map +1 -1
- package/dist/ts/ts/Conversion/ScholarlyArticle.js +75 -9
- package/dist/ts/ts/Conversion/Study.d.ts.map +1 -1
- package/dist/ts/ts/Conversion/Study.js +23 -12
- package/dist/ts/ts/Conversion/Table.d.ts +3 -2
- package/dist/ts/ts/Conversion/Table.d.ts.map +1 -1
- package/dist/ts/ts/Conversion/Table.js +8 -8
- package/dist/ts/ts/Conversion/Workflow.d.ts +48 -9
- package/dist/ts/ts/Conversion/Workflow.d.ts.map +1 -1
- package/dist/ts/ts/Conversion/Workflow.js +655 -163
- package/dist/ts/ts/Conversion.js +6 -6
- package/dist/ts/ts/Core/ArcTypes.d.ts +73 -28
- package/dist/ts/ts/Core/ArcTypes.d.ts.map +1 -1
- package/dist/ts/ts/Core/ArcTypes.js +219 -129
- package/dist/ts/ts/Core/Comment.d.ts.map +1 -1
- package/dist/ts/ts/Core/Comment.js +2 -2
- package/dist/ts/ts/Core/CommentList.js +7 -7
- package/dist/ts/ts/Core/Conversion.d.ts.map +1 -1
- package/dist/ts/ts/Core/Conversion.js +68 -59
- package/dist/ts/ts/Core/Data.d.ts +6 -0
- package/dist/ts/ts/Core/Data.d.ts.map +1 -1
- package/dist/ts/ts/Core/Data.js +32 -12
- package/dist/ts/ts/Core/DataContext.d.ts +1 -1
- package/dist/ts/ts/Core/DataContext.d.ts.map +1 -1
- package/dist/ts/ts/Core/DataContext.js +4 -4
- package/dist/ts/ts/Core/DataFile.d.ts +11 -8
- package/dist/ts/ts/Core/DataFile.d.ts.map +1 -1
- package/dist/ts/ts/Core/DataFile.js +55 -61
- package/dist/ts/ts/Core/Datamap.d.ts.map +1 -1
- package/dist/ts/ts/Core/Datamap.js +2 -3
- package/dist/ts/ts/Core/Helper/Collections.d.ts.map +1 -1
- package/dist/ts/ts/Core/Helper/Collections.js +2 -4
- package/dist/ts/ts/Core/Helper/Identifier.d.ts.map +1 -1
- package/dist/ts/ts/Core/Helper/Identifier.js +12 -15
- package/dist/ts/ts/Core/Helper/ORCID.d.ts.map +1 -1
- package/dist/ts/ts/Core/Helper/ORCID.js +2 -3
- package/dist/ts/ts/Core/Helper/Regex.d.ts.map +1 -1
- package/dist/ts/ts/Core/Helper/Regex.js +52 -53
- package/dist/ts/ts/Core/Helper/SemVer.d.ts +13 -3
- package/dist/ts/ts/Core/Helper/SemVer.d.ts.map +1 -1
- package/dist/ts/ts/Core/Helper/SemVer.js +96 -6
- package/dist/ts/ts/Core/Helper/Url.d.ts.map +1 -1
- package/dist/ts/ts/Core/Helper/Url.js +1 -1
- package/dist/ts/ts/Core/OntologyAnnotation.js +22 -22
- package/dist/ts/ts/Core/Person.d.ts.map +1 -1
- package/dist/ts/ts/Core/Person.js +2 -2
- package/dist/ts/ts/Core/Process/ColumnIndex.d.ts.map +1 -1
- package/dist/ts/ts/Core/Process/ColumnIndex.js +10 -12
- package/dist/ts/ts/Core/Process/Component.d.ts.map +1 -1
- package/dist/ts/ts/Core/Process/Component.js +22 -22
- package/dist/ts/ts/Core/Process/Factor.d.ts.map +1 -1
- package/dist/ts/ts/Core/Process/Factor.js +7 -7
- package/dist/ts/ts/Core/Process/FactorValue.d.ts.map +1 -1
- package/dist/ts/ts/Core/Process/FactorValue.js +15 -15
- package/dist/ts/ts/Core/Process/Material.d.ts.map +1 -1
- package/dist/ts/ts/Core/Process/Material.js +2 -2
- package/dist/ts/ts/Core/Process/MaterialAttribute.d.ts.map +1 -1
- package/dist/ts/ts/Core/Process/MaterialAttribute.js +6 -6
- package/dist/ts/ts/Core/Process/MaterialAttributeValue.d.ts.map +1 -1
- package/dist/ts/ts/Core/Process/MaterialAttributeValue.js +16 -16
- package/dist/ts/ts/Core/Process/Process.js +21 -21
- package/dist/ts/ts/Core/Process/ProcessInput.d.ts.map +1 -1
- package/dist/ts/ts/Core/Process/ProcessInput.js +2 -2
- package/dist/ts/ts/Core/Process/ProcessOutput.d.ts.map +1 -1
- package/dist/ts/ts/Core/Process/ProcessOutput.js +2 -2
- package/dist/ts/ts/Core/Process/ProcessParameterValue.d.ts.map +1 -1
- package/dist/ts/ts/Core/Process/ProcessParameterValue.js +17 -17
- package/dist/ts/ts/Core/Process/ProcessSequence.js +4 -4
- package/dist/ts/ts/Core/Process/Protocol.d.ts.map +1 -1
- package/dist/ts/ts/Core/Process/Protocol.js +9 -9
- package/dist/ts/ts/Core/Process/ProtocolParameter.d.ts.map +1 -1
- package/dist/ts/ts/Core/Process/ProtocolParameter.js +6 -6
- package/dist/ts/ts/Core/Publication.d.ts.map +1 -1
- package/dist/ts/ts/Core/Publication.js +3 -3
- package/dist/ts/ts/Core/ScalarValue.d.ts.map +1 -1
- package/dist/ts/ts/Core/ScalarValue.js +9 -13
- package/dist/ts/ts/Core/Table/ArcTable.d.ts.map +1 -1
- package/dist/ts/ts/Core/Table/ArcTable.js +18 -18
- package/dist/ts/ts/Core/Table/ArcTableAux.d.ts +1 -1
- package/dist/ts/ts/Core/Table/ArcTableAux.d.ts.map +1 -1
- package/dist/ts/ts/Core/Table/ArcTableAux.js +59 -70
- package/dist/ts/ts/Core/Table/ArcTables.js +16 -16
- package/dist/ts/ts/Core/Table/CompositeCell.d.ts +4 -0
- package/dist/ts/ts/Core/Table/CompositeCell.d.ts.map +1 -1
- package/dist/ts/ts/Core/Table/CompositeCell.js +39 -2
- package/dist/ts/ts/Core/Table/CompositeHeader.d.ts.map +1 -1
- package/dist/ts/ts/Core/Table/CompositeHeader.js +5 -6
- package/dist/ts/ts/Core/Templates.d.ts.map +1 -1
- package/dist/ts/ts/Core/Templates.js +2 -2
- package/dist/ts/ts/FileSystem/Path.d.ts +13 -2
- package/dist/ts/ts/FileSystem/Path.d.ts.map +1 -1
- package/dist/ts/ts/FileSystem/Path.js +37 -19
- package/dist/ts/ts/Json/Assay.js +22 -22
- package/dist/ts/ts/Json/Comment.js +9 -9
- package/dist/ts/ts/Json/Data.d.ts.map +1 -1
- package/dist/ts/ts/Json/Data.js +11 -11
- package/dist/ts/ts/Json/Datamap/DataContext.js +2 -2
- package/dist/ts/ts/Json/Decode.d.ts.map +1 -1
- package/dist/ts/ts/Json/Decode.js +3 -5
- package/dist/ts/ts/Json/Encode.js +2 -2
- package/dist/ts/ts/Json/Investigation.d.ts.map +1 -1
- package/dist/ts/ts/Json/Investigation.js +20 -20
- package/dist/ts/ts/Json/OntologyAnnotation.d.ts.map +1 -1
- package/dist/ts/ts/Json/OntologyAnnotation.js +18 -18
- package/dist/ts/ts/Json/OntologySourceReference.d.ts.map +1 -1
- package/dist/ts/ts/Json/OntologySourceReference.js +9 -9
- package/dist/ts/ts/Json/Person.d.ts.map +1 -1
- package/dist/ts/ts/Json/Person.js +20 -20
- package/dist/ts/ts/Json/Process/AssayMaterials.d.ts.map +1 -1
- package/dist/ts/ts/Json/Process/AssayMaterials.js +1 -2
- package/dist/ts/ts/Json/Process/Component.d.ts.map +1 -1
- package/dist/ts/ts/Json/Process/Component.js +5 -6
- package/dist/ts/ts/Json/Process/Factor.d.ts.map +1 -1
- package/dist/ts/ts/Json/Process/Factor.js +7 -7
- package/dist/ts/ts/Json/Process/FactorValue.d.ts.map +1 -1
- package/dist/ts/ts/Json/Process/FactorValue.js +2 -3
- package/dist/ts/ts/Json/Process/Material.d.ts.map +1 -1
- package/dist/ts/ts/Json/Process/Material.js +9 -10
- package/dist/ts/ts/Json/Process/MaterialAttribute.d.ts.map +1 -1
- package/dist/ts/ts/Json/Process/MaterialAttribute.js +5 -6
- package/dist/ts/ts/Json/Process/MaterialAttributeValue.d.ts.map +1 -1
- package/dist/ts/ts/Json/Process/MaterialAttributeValue.js +2 -3
- package/dist/ts/ts/Json/Process/Process.d.ts.map +1 -1
- package/dist/ts/ts/Json/Process/Process.js +8 -9
- package/dist/ts/ts/Json/Process/ProcessParameterValue.d.ts.map +1 -1
- package/dist/ts/ts/Json/Process/ProcessParameterValue.js +1 -2
- package/dist/ts/ts/Json/Process/Protocol.d.ts.map +1 -1
- package/dist/ts/ts/Json/Process/Protocol.js +17 -17
- package/dist/ts/ts/Json/Process/ProtocolParameter.d.ts.map +1 -1
- package/dist/ts/ts/Json/Process/ProtocolParameter.js +6 -6
- package/dist/ts/ts/Json/Process/Sample.d.ts.map +1 -1
- package/dist/ts/ts/Json/Process/Sample.js +9 -9
- package/dist/ts/ts/Json/Process/Source.d.ts.map +1 -1
- package/dist/ts/ts/Json/Process/Source.js +10 -11
- package/dist/ts/ts/Json/Process/StudyMaterials.d.ts.map +1 -1
- package/dist/ts/ts/Json/Process/StudyMaterials.js +1 -2
- package/dist/ts/ts/Json/PropertyValue.d.ts.map +1 -1
- package/dist/ts/ts/Json/PropertyValue.js +24 -24
- package/dist/ts/ts/Json/Publication.d.ts.map +1 -1
- package/dist/ts/ts/Json/Publication.js +10 -10
- package/dist/ts/ts/Json/ROCrate/LDContext.js +1 -2
- package/dist/ts/ts/Json/ROCrate/LDGraph.js +2 -2
- package/dist/ts/ts/Json/ROCrate/LDNode.js +5 -5
- package/dist/ts/ts/Json/Run.js +9 -9
- package/dist/ts/ts/Json/StringTable.d.ts.map +1 -1
- package/dist/ts/ts/Json/StringTable.js +4 -7
- package/dist/ts/ts/Json/Study.js +20 -20
- package/dist/ts/ts/Json/Table/CellTable.js +1 -2
- package/dist/ts/ts/Json/Table/OATable.js +1 -2
- package/dist/ts/ts/Json/Workflow.js +9 -9
- package/dist/ts/ts/Json.d.ts +121 -1
- package/dist/ts/ts/Json.d.ts.map +1 -1
- package/dist/ts/ts/Json.js +310 -2
- package/dist/ts/ts/JsonIO/Comment.d.ts +15 -0
- package/dist/ts/ts/JsonIO/Comment.d.ts.map +1 -0
- package/dist/ts/ts/JsonIO/Comment.js +67 -0
- package/dist/ts/ts/JsonIO/Data.d.ts +9 -0
- package/dist/ts/ts/JsonIO/Data.d.ts.map +1 -0
- package/dist/ts/ts/JsonIO/Data.js +49 -0
- package/dist/ts/ts/JsonIO/DataFile.d.ts +9 -0
- package/dist/ts/ts/JsonIO/DataFile.d.ts.map +1 -0
- package/dist/ts/ts/JsonIO/DataFile.js +48 -0
- package/dist/ts/ts/JsonIO/LDObject.d.ts +6 -0
- package/dist/ts/ts/JsonIO/LDObject.d.ts.map +1 -1
- package/dist/ts/ts/JsonIO/LDObject.js +173 -17
- package/dist/ts/ts/JsonIO/OntologySourceReference.d.ts +15 -0
- package/dist/ts/ts/JsonIO/OntologySourceReference.d.ts.map +1 -0
- package/dist/ts/ts/JsonIO/OntologySourceReference.js +67 -0
- package/dist/ts/ts/JsonIO/Publication.d.ts +15 -0
- package/dist/ts/ts/JsonIO/Publication.d.ts.map +1 -0
- package/dist/ts/ts/JsonIO/Publication.js +68 -0
- package/dist/ts/ts/JsonIO/Table/ArcTable.d.ts +9 -0
- package/dist/ts/ts/JsonIO/Table/ArcTable.d.ts.map +1 -0
- package/dist/ts/ts/JsonIO/Table/ArcTable.js +74 -0
- package/dist/ts/ts/JsonIO/Table/CompositeCell.d.ts +6 -0
- package/dist/ts/ts/JsonIO/Table/CompositeCell.d.ts.map +1 -0
- package/dist/ts/ts/JsonIO/Table/CompositeCell.js +29 -0
- package/dist/ts/ts/JsonIO/Table/CompositeHeader.d.ts +6 -0
- package/dist/ts/ts/JsonIO/Table/CompositeHeader.d.ts.map +1 -0
- package/dist/ts/ts/JsonIO/Table/CompositeHeader.js +29 -0
- package/dist/ts/ts/JsonIO/Table/IOType.d.ts +6 -0
- package/dist/ts/ts/JsonIO/Table/IOType.d.ts.map +1 -0
- package/dist/ts/ts/JsonIO/Table/IOType.js +29 -0
- package/dist/ts/ts/License.d.ts.map +1 -1
- package/dist/ts/ts/License.js +6 -6
- package/dist/ts/ts/ROCrate/LDContext.d.ts.map +1 -1
- package/dist/ts/ts/ROCrate/LDContext.js +31 -39
- package/dist/ts/ts/ROCrate/LDObject.d.ts.map +1 -1
- package/dist/ts/ts/ROCrate/LDObject.js +56 -49
- package/dist/ts/ts/ROCrate/LDTypes/Comment.js +2 -2
- package/dist/ts/ts/ROCrate/LDTypes/ComputationalWorkflow.js +3 -3
- package/dist/ts/ts/ROCrate/LDTypes/ComputerLanguage.js +2 -2
- package/dist/ts/ts/ROCrate/LDTypes/CreateAction.js +5 -5
- package/dist/ts/ts/ROCrate/LDTypes/CreativeWork.d.ts +1 -0
- package/dist/ts/ts/ROCrate/LDTypes/CreativeWork.d.ts.map +1 -1
- package/dist/ts/ts/ROCrate/LDTypes/CreativeWork.js +3 -0
- package/dist/ts/ts/ROCrate/LDTypes/Dataset.d.ts.map +1 -1
- package/dist/ts/ts/ROCrate/LDTypes/Dataset.js +22 -17
- package/dist/ts/ts/ROCrate/LDTypes/DefinedTerm.js +2 -2
- package/dist/ts/ts/ROCrate/LDTypes/File.js +5 -5
- package/dist/ts/ts/ROCrate/LDTypes/FormalParameter.js +2 -2
- package/dist/ts/ts/ROCrate/LDTypes/LabProcess.js +9 -9
- package/dist/ts/ts/ROCrate/LDTypes/LabProtocol.js +4 -4
- package/dist/ts/ts/ROCrate/LDTypes/Organization.js +1 -1
- package/dist/ts/ts/ROCrate/LDTypes/Person.js +7 -7
- package/dist/ts/ts/ROCrate/LDTypes/PostalAddress.js +1 -1
- package/dist/ts/ts/ROCrate/LDTypes/PropertyValue.d.ts.map +1 -1
- package/dist/ts/ts/ROCrate/LDTypes/PropertyValue.js +45 -48
- package/dist/ts/ts/ROCrate/LDTypes/Sample.js +3 -3
- package/dist/ts/ts/ROCrate/LDTypes/ScholarlyArticle.js +4 -4
- package/dist/ts/ts/ROCrate/LDTypes/SoftwareSourceCode.js +3 -3
- package/dist/ts/ts/ROCrate/LDTypes/WorkflowInvocation.js +3 -3
- package/dist/ts/ts/ROCrate/LDTypes/WorkflowProtocol.js +2 -2
- package/dist/ts/ts/ROCrateIO.d.ts +18 -4
- package/dist/ts/ts/ROCrateIO.d.ts.map +1 -1
- package/dist/ts/ts/ROCrateIO.js +49 -38
- package/dist/ts/ts/Spreadsheet/AnnotationTable/ArcTable.d.ts.map +1 -1
- package/dist/ts/ts/Spreadsheet/AnnotationTable/ArcTable.js +9 -10
- package/dist/ts/ts/Spreadsheet/AnnotationTable/CompositeCell.d.ts.map +1 -1
- package/dist/ts/ts/Spreadsheet/AnnotationTable/CompositeCell.js +7 -7
- package/dist/ts/ts/Spreadsheet/AnnotationTable/CompositeColumn.d.ts.map +1 -1
- package/dist/ts/ts/Spreadsheet/AnnotationTable/CompositeColumn.js +6 -8
- package/dist/ts/ts/Spreadsheet/AnnotationTable/CompositeHeader.js +20 -20
- package/dist/ts/ts/Spreadsheet/ArcAssay.d.ts.map +1 -1
- package/dist/ts/ts/Spreadsheet/ArcAssay.js +7 -7
- package/dist/ts/ts/Spreadsheet/ArcInvestigation.d.ts.map +1 -1
- package/dist/ts/ts/Spreadsheet/ArcInvestigation.js +10 -12
- package/dist/ts/ts/Spreadsheet/ArcRun.d.ts.map +1 -1
- package/dist/ts/ts/Spreadsheet/ArcRun.js +5 -6
- package/dist/ts/ts/Spreadsheet/ArcStudy.d.ts.map +1 -1
- package/dist/ts/ts/Spreadsheet/ArcStudy.js +3 -3
- package/dist/ts/ts/Spreadsheet/ArcWorkflow.d.ts.map +1 -1
- package/dist/ts/ts/Spreadsheet/ArcWorkflow.js +5 -6
- package/dist/ts/ts/Spreadsheet/CollectionAux.d.ts.map +1 -1
- package/dist/ts/ts/Spreadsheet/CollectionAux.js +10 -14
- package/dist/ts/ts/Spreadsheet/Datamap.js +1 -2
- package/dist/ts/ts/Spreadsheet/DatamapTable/DatamapColumn.js +3 -3
- package/dist/ts/ts/Spreadsheet/DatamapTable/DatamapHeader.js +10 -10
- package/dist/ts/ts/Spreadsheet/DatamapTable/DatamapTable.d.ts.map +1 -1
- package/dist/ts/ts/Spreadsheet/DatamapTable/DatamapTable.js +9 -10
- package/dist/ts/ts/Spreadsheet/Metadata/Assays.d.ts.map +1 -1
- package/dist/ts/ts/Spreadsheet/Metadata/Assays.js +8 -10
- package/dist/ts/ts/Spreadsheet/Metadata/Comment.d.ts +8 -0
- package/dist/ts/ts/Spreadsheet/Metadata/Comment.d.ts.map +1 -1
- package/dist/ts/ts/Spreadsheet/Metadata/Comment.js +18 -7
- package/dist/ts/ts/Spreadsheet/Metadata/Contacts.d.ts.map +1 -1
- package/dist/ts/ts/Spreadsheet/Metadata/Contacts.js +4 -6
- package/dist/ts/ts/Spreadsheet/Metadata/Factors.d.ts.map +1 -1
- package/dist/ts/ts/Spreadsheet/Metadata/Factors.js +6 -8
- package/dist/ts/ts/Spreadsheet/Metadata/OntologyAnnotation.d.ts.map +1 -1
- package/dist/ts/ts/Spreadsheet/Metadata/OntologyAnnotation.js +5 -7
- package/dist/ts/ts/Spreadsheet/Metadata/OntologySourceReference.d.ts.map +1 -1
- package/dist/ts/ts/Spreadsheet/Metadata/OntologySourceReference.js +2 -4
- package/dist/ts/ts/Spreadsheet/Metadata/Protocols.d.ts.map +1 -1
- package/dist/ts/ts/Spreadsheet/Metadata/Protocols.js +7 -9
- package/dist/ts/ts/Spreadsheet/Metadata/Publication.d.ts.map +1 -1
- package/dist/ts/ts/Spreadsheet/Metadata/Publication.js +6 -8
- package/dist/ts/ts/Spreadsheet/Metadata/Run.d.ts +1 -1
- package/dist/ts/ts/Spreadsheet/Metadata/Run.d.ts.map +1 -1
- package/dist/ts/ts/Spreadsheet/Metadata/Run.js +9 -11
- package/dist/ts/ts/Spreadsheet/Metadata/SparseTable.d.ts.map +1 -1
- package/dist/ts/ts/Spreadsheet/Metadata/SparseTable.js +17 -17
- package/dist/ts/ts/Spreadsheet/Metadata/Study.d.ts.map +1 -1
- package/dist/ts/ts/Spreadsheet/Metadata/Study.js +10 -12
- package/dist/ts/ts/Spreadsheet/Metadata/Workflow.d.ts.map +1 -1
- package/dist/ts/ts/Spreadsheet/Metadata/Workflow.js +7 -9
- package/dist/ts/ts/WorkflowGraph/Adapters.d.ts +1 -1
- package/dist/ts/ts/WorkflowGraph/Adapters.d.ts.map +1 -1
- package/dist/ts/ts/WorkflowGraph/Adapters.js +5 -6
- package/dist/ts/ts/WorkflowGraph/Builder.d.ts +25 -6
- package/dist/ts/ts/WorkflowGraph/Builder.d.ts.map +1 -1
- package/dist/ts/ts/WorkflowGraph/Builder.js +264 -138
- package/dist/ts/ts/WorkflowGraph/GraphTypes.d.ts +6 -0
- package/dist/ts/ts/WorkflowGraph/GraphTypes.d.ts.map +1 -1
- package/dist/ts/ts/WorkflowGraph/GraphTypes.js +4 -1
- package/dist/ts/ts/WorkflowGraph/ReferenceParsing.d.ts +8 -5
- package/dist/ts/ts/WorkflowGraph/ReferenceParsing.d.ts.map +1 -1
- package/dist/ts/ts/WorkflowGraph/ReferenceParsing.js +27 -10
- package/dist/ts/ts/Xlsx.js +3 -3
- package/dist/ts/ts/Yaml/ValidationPackage.d.ts +3 -3
- package/dist/ts/ts/Yaml/ValidationPackage.d.ts.map +1 -1
- package/dist/ts/ts/Yaml/ValidationPackage.js +11 -23
- package/dist/ts/ts/Yaml/ValidationPackagesConfig.d.ts +3 -3
- package/dist/ts/ts/Yaml/ValidationPackagesConfig.d.ts.map +1 -1
- package/dist/ts/ts/Yaml/ValidationPackagesConfig.js +11 -23
- package/dist/ts/ts/fable_modules/DynamicObj.8.0.0/DynamicObj.fs.js +16 -20
- package/dist/ts/ts/fable_modules/DynamicObj.8.0.0/FableJS.fs.js +1 -1
- package/dist/ts/ts/fable_modules/DynamicObj.8.0.0/ReflectionUtils.fs.js +8 -8
- package/dist/ts/ts/fable_modules/Fable.Promise.3.2.0/Promise.fs.js +1 -2
- package/dist/ts/ts/fable_modules/Fable.SimpleHttp.3.6.0/Http.fs.js +4 -4
- package/dist/ts/ts/fable_modules/FsSpreadsheet.7.0.1/Cells/FsCell.fs.js +8 -8
- package/dist/ts/ts/fable_modules/FsSpreadsheet.7.0.1/Cells/FsCellsCollection.fs.js +18 -18
- package/dist/ts/ts/fable_modules/FsSpreadsheet.7.0.1/FsAddress.fs.js +3 -3
- package/dist/ts/ts/fable_modules/FsSpreadsheet.7.0.1/FsWorkbook.fs.js +1 -1
- package/dist/ts/ts/fable_modules/FsSpreadsheet.7.0.1/FsWorksheet.fs.js +7 -7
- package/dist/ts/ts/fable_modules/FsSpreadsheet.7.0.1/Json/Value.fs.js +3 -5
- package/dist/ts/ts/fable_modules/FsSpreadsheet.7.0.1/Json/Worksheet.fs.js +7 -7
- package/dist/ts/ts/fable_modules/FsSpreadsheet.7.0.1/Ranges/FsRangeBase.fs.js +1 -2
- package/dist/ts/ts/fable_modules/FsSpreadsheet.7.0.1/Tables/FsTable.fs.js +7 -7
- package/dist/ts/ts/fable_modules/FsSpreadsheet.Js.7.0.1/Cell.fs.js +2 -2
- package/dist/ts/ts/fable_modules/FsSpreadsheet.Js.7.0.1/Table.fs.js +1 -2
- package/dist/ts/ts/fable_modules/Thoth.Json.Core.0.9.1/Decode.fs.js +49 -71
- package/dist/ts/ts/fable_modules/Thoth.Json.Core.0.9.1/Encode.fs.js +1 -1
- package/dist/ts/ts/fable_modules/Thoth.Json.JavaScript.0.5.0/Decode.fs.js +1 -2
- package/dist/ts/ts/fable_modules/YAMLicious.2.0.0/Compare.fs.js +857 -0
- package/dist/ts/ts/fable_modules/YAMLicious.2.0.0/CoreSchema.fs.js +725 -0
- package/dist/ts/ts/fable_modules/YAMLicious.2.0.0/Decode.fs.js +1175 -0
- package/dist/ts/ts/fable_modules/YAMLicious.2.0.0/Encode.fs.js +123 -0
- package/dist/ts/ts/fable_modules/YAMLicious.2.0.0/Layout.fs.js +282 -0
- package/dist/ts/ts/fable_modules/YAMLicious.2.0.0/Lexeme.fs.js +203 -0
- package/dist/ts/ts/fable_modules/YAMLicious.2.0.0/Lexer.fs.js +1502 -0
- package/dist/ts/ts/fable_modules/YAMLicious.2.0.0/Model.fs.js +564 -0
- package/dist/ts/ts/fable_modules/YAMLicious.2.0.0/Node.fs.js +453 -0
- package/dist/ts/ts/fable_modules/YAMLicious.2.0.0/Parser.fs.js +2622 -0
- package/dist/ts/ts/fable_modules/YAMLicious.2.0.0/Reader.fs.js +108 -0
- package/dist/ts/ts/fable_modules/YAMLicious.2.0.0/Source.fs.js +649 -0
- package/dist/ts/ts/fable_modules/YAMLicious.2.0.0/Tag.fs.js +32 -0
- package/dist/ts/ts/fable_modules/YAMLicious.2.0.0/Validate.fs.js +1084 -0
- package/dist/ts/ts/fable_modules/YAMLicious.2.0.0/Writer.fs.js +2927 -0
- package/package.json +5 -4
- package/dist/ts/ts/fable_modules/YAMLicious.1.0.0/Decode.fs.js +0 -1669
- package/dist/ts/ts/fable_modules/YAMLicious.1.0.0/Encode.fs.js +0 -57
- package/dist/ts/ts/fable_modules/YAMLicious.1.0.0/Escapes.fs.js +0 -320
- package/dist/ts/ts/fable_modules/YAMLicious.1.0.0/Interop/JsInterop.fs.js +0 -10
- package/dist/ts/ts/fable_modules/YAMLicious.1.0.0/Persil.fs.js +0 -414
- package/dist/ts/ts/fable_modules/YAMLicious.1.0.0/Preprocessing.fs.js +0 -319
- package/dist/ts/ts/fable_modules/YAMLicious.1.0.0/Reader.fs.js +0 -1884
- package/dist/ts/ts/fable_modules/YAMLicious.1.0.0/Regex.fs.js +0 -23
- package/dist/ts/ts/fable_modules/YAMLicious.1.0.0/RegexActivePatterns.fs.js +0 -313
- package/dist/ts/ts/fable_modules/YAMLicious.1.0.0/Syntax.fs.js +0 -840
- package/dist/ts/ts/fable_modules/YAMLicious.1.0.0/Writer.fs.js +0 -689
- package/dist/ts/ts/fable_modules/YAMLicious.1.0.0/YAMLiciousTypes.fs.js +0 -359
|
@@ -1,37 +1,43 @@
|
|
|
1
1
|
import { Record } from '../../node_modules/@fable-org/fable-library-ts/Types.js';
|
|
2
|
-
import { WorkflowGraph_$reflection, WorkflowGraph_create_4D231A1, GraphBuildIssue_create_Z2F3B511A, WorkflowGraphEdge_create_5E4B5E48, GraphId_edgeId, GraphId_unitNodeId, WorkflowGraphNode_create_62C775C0, NodeKind_ProcessingUnitNode, GraphId_portNodeId, NodeKind_PortNode, GraphId_stepNodeId, NodeKind, EdgeKind, PortDirection, GraphIssueKind, ProcessingUnitKind, GraphId_childScope, GraphId_normalizeSegment } from './GraphTypes.js';
|
|
2
|
+
import { WorkflowGraph_$reflection, WorkflowGraph_create_4D231A1, GraphBuildIssue_create_Z2F3B511A, WorkflowGraphEdge_create_5E4B5E48, GraphId_edgeId, GraphId_unitNodeId, WorkflowGraphNode_create_62C775C0, NodeKind_ProcessingUnitNode, GraphId_portNodeId, NodeKind_PortNode, GraphId_anonymousStepNodeId, GraphId_stepNodeId, NodeKind, EdgeKind, PortDirection, GraphIssueKind, ProcessingUnitKind, GraphId_childScope, GraphId_normalizeSegment } from './GraphTypes.js';
|
|
3
3
|
import { empty, FSharpSet__Contains, FSharpSet__Add } from '../../node_modules/@fable-org/fable-library-ts/Set.js';
|
|
4
|
-
import { empty as empty$1,
|
|
5
|
-
import {
|
|
4
|
+
import { empty as empty$1, ofArray, tryPick, singleton, exists, cons, iterate as iterate$1 } from '../../node_modules/@fable-org/fable-library-ts/List.js';
|
|
5
|
+
import { CWLProcessingUnit_$reflection, WorkflowStepRunOps_fromOperation, WorkflowStepRunOps_fromExpressionTool, WorkflowStepRunOps_fromWorkflow, WorkflowStepRunOps_fromTool, CWLProcessingUnit, WorkflowStepRunOps_tryGetOperation, CWLProcessingUnit_Operation, WorkflowStepRunOps_tryGetExpressionTool, CWLProcessingUnit_ExpressionTool, WorkflowStepRunOps_tryGetWorkflow, CWLProcessingUnit_Workflow, WorkflowStepRunOps_tryGetTool, CWLProcessingUnit_CommandLineTool } from '../CWL/CWLProcessingUnit.js';
|
|
6
|
+
import { empty as empty$2, FSharpMap__ContainsKey, FSharpMap__get_Item, FSharpMap__Add, tryFind } from '../../node_modules/@fable-org/fable-library-ts/Map.js';
|
|
7
|
+
import { WorkflowStepRun_$reflection, WorkflowStep, StepOutput, WorkflowStepRun_RunString } from '../CWL/WorkflowSteps.js';
|
|
6
8
|
import { WorkflowGraphBuildOptions_$reflection, WorkflowGraphBuildOptionsModule_defaultOptions } from './BuildOptions.js';
|
|
7
|
-
import { record_type, class_type, string_type, option_type, bool_type, array_type } from '../../node_modules/@fable-org/fable-library-ts/Reflection.js';
|
|
9
|
+
import { record_type, class_type, list_type, string_type, option_type, bool_type, array_type } from '../../node_modules/@fable-org/fable-library-ts/Reflection.js';
|
|
8
10
|
import { unwrap, value, some, defaultArg } from '../../node_modules/@fable-org/fable-library-ts/Option.js';
|
|
9
11
|
import { comparePrimitives, getEnumerator, disposeSafe, stringHash } from '../../node_modules/@fable-org/fable-library-ts/Util.js';
|
|
10
12
|
import { DynamicObj } from '../fable_modules/DynamicObj.8.0.0/DynamicObj.fs.js';
|
|
11
13
|
import { setProperty } from '../fable_modules/DynamicObj.8.0.0/DynObj.fs.js';
|
|
12
|
-
import {
|
|
13
|
-
import {
|
|
14
|
-
import {
|
|
15
|
-
import {
|
|
14
|
+
import { ReferenceParsing_relativeId, ReferenceParsing_parseSourceReference } from './ReferenceParsing.js';
|
|
15
|
+
import { concat, isNullOrWhiteSpace, substring, endsWith } from '../../node_modules/@fable-org/fable-library-ts/String.js';
|
|
16
|
+
import { SchemaSaladStringModule_tryLiteral, RawYaml__TryScalarField_Z721C83C5, ListEntry$1 } from '../CWL/CWLTypes.js';
|
|
17
|
+
import { toArray, map, iterate, choose, tryHead, toList, delay, singleton as singleton$1, indexed } from '../../node_modules/@fable-org/fable-library-ts/Seq.js';
|
|
18
|
+
import { CWLWorkflowDescription } from '../CWL/WorkflowDescription.js';
|
|
19
|
+
import { CWLToolDescription } from '../CWL/ToolDescription.js';
|
|
20
|
+
import { CWLExpressionToolDescription } from '../CWL/ExpressionToolDescription.js';
|
|
21
|
+
import { CWLOperationDescription } from '../CWL/OperationDescription.js';
|
|
16
22
|
import { getFileName, normalize, resolvePathFromFile, normalizePathKey } from '../FileSystem/Path.js';
|
|
17
23
|
import { Array_distinct } from '../../node_modules/@fable-org/fable-library-ts/Seq2.js';
|
|
18
|
-
import {
|
|
19
|
-
import { map, item, tryPick as tryPick$1 } from '../../node_modules/@fable-org/fable-library-ts/Array.js';
|
|
24
|
+
import { map as map$1, item, tryPick as tryPick$1 } from '../../node_modules/@fable-org/fable-library-ts/Array.js';
|
|
20
25
|
|
|
21
26
|
class BuildState extends Record {
|
|
22
|
-
constructor(Graph, NodeIds, EdgeIds, RunResolutionStack, RunResolutionCache, RunNodeCache, Options) {
|
|
27
|
+
constructor(Graph, NodeIds, EdgeIds, RunResolutionStack, ActiveWorkflows, RunResolutionCache, RunNodeCache, Options) {
|
|
23
28
|
super();
|
|
24
29
|
this.Graph = Graph;
|
|
25
30
|
this.NodeIds = NodeIds;
|
|
26
31
|
this.EdgeIds = EdgeIds;
|
|
27
32
|
this.RunResolutionStack = RunResolutionStack;
|
|
33
|
+
this.ActiveWorkflows = ActiveWorkflows;
|
|
28
34
|
this.RunResolutionCache = RunResolutionCache;
|
|
29
35
|
this.RunNodeCache = RunNodeCache;
|
|
30
36
|
this.Options = Options;
|
|
31
37
|
}
|
|
32
38
|
}
|
|
33
39
|
function BuildState_$reflection() {
|
|
34
|
-
return record_type("ARCtrl.WorkflowGraph.Builder.BuildState", [], BuildState, () => [["Graph", WorkflowGraph_$reflection()], ["NodeIds", class_type("Microsoft.FSharp.Collections.FSharpSet`1", [string_type])], ["EdgeIds", class_type("Microsoft.FSharp.Collections.FSharpSet`1", [string_type])], ["RunResolutionStack", class_type("Microsoft.FSharp.Collections.FSharpSet`1", [string_type])], ["RunResolutionCache", class_type("Microsoft.FSharp.Collections.FSharpMap`2", [string_type, WorkflowStepRun_$reflection()])], ["RunNodeCache", class_type("Microsoft.FSharp.Collections.FSharpMap`2", [string_type, string_type])], ["Options", WorkflowGraphBuildOptions_$reflection()]]);
|
|
40
|
+
return record_type("ARCtrl.WorkflowGraph.Builder.BuildState", [], BuildState, () => [["Graph", WorkflowGraph_$reflection()], ["NodeIds", class_type("Microsoft.FSharp.Collections.FSharpSet`1", [string_type])], ["EdgeIds", class_type("Microsoft.FSharp.Collections.FSharpSet`1", [string_type])], ["RunResolutionStack", class_type("Microsoft.FSharp.Collections.FSharpSet`1", [string_type])], ["ActiveWorkflows", list_type(CWLProcessingUnit_$reflection())], ["RunResolutionCache", class_type("Microsoft.FSharp.Collections.FSharpMap`2", [string_type, WorkflowStepRun_$reflection()])], ["RunNodeCache", class_type("Microsoft.FSharp.Collections.FSharpMap`2", [string_type, string_type])], ["Options", WorkflowGraphBuildOptions_$reflection()]]);
|
|
35
41
|
}
|
|
36
42
|
class RunResolutionResult extends Record {
|
|
37
43
|
constructor(ResolvedRun, ResolvedFromPath, AttemptedLookup, ResolutionPathKeys) {
|
|
@@ -55,9 +61,9 @@ function createState(options, rootNodeId) {
|
|
|
55
61
|
Compare: (x_1, y_1) => comparePrimitives(x_1, y_1) | 0
|
|
56
62
|
}), empty({
|
|
57
63
|
Compare: (x_2, y_2) => comparePrimitives(x_2, y_2) | 0
|
|
58
|
-
}), empty$1({
|
|
64
|
+
}), empty$1(), empty$2({
|
|
59
65
|
Compare: (x_3, y_3) => comparePrimitives(x_3, y_3) | 0
|
|
60
|
-
}), empty$
|
|
66
|
+
}), empty$2({
|
|
61
67
|
Compare: (x_4, y_4) => comparePrimitives(x_4, y_4) | 0
|
|
62
68
|
}), options);
|
|
63
69
|
}
|
|
@@ -116,54 +122,80 @@ function addPortNode(state, ownerNodeId, direction, portId, label) {
|
|
|
116
122
|
addNode(state, WorkflowGraphNode_create_62C775C0(nodeId, NodeKind_PortNode(direction), label, ownerNodeId));
|
|
117
123
|
return nodeId;
|
|
118
124
|
}
|
|
119
|
-
|
|
120
|
-
|
|
121
|
-
|
|
122
|
-
|
|
123
|
-
|
|
125
|
+
class StepIdentity extends Record {
|
|
126
|
+
constructor(NodeId, Name, RunSegment) {
|
|
127
|
+
super();
|
|
128
|
+
this.NodeId = NodeId;
|
|
129
|
+
this.Name = Name;
|
|
130
|
+
this.RunSegment = RunSegment;
|
|
131
|
+
}
|
|
132
|
+
}
|
|
133
|
+
function StepIdentity_$reflection() {
|
|
134
|
+
return record_type("ARCtrl.WorkflowGraph.Builder.StepIdentity", [], StepIdentity, () => [["NodeId", string_type], ["Name", string_type], ["RunSegment", string_type]]);
|
|
135
|
+
}
|
|
136
|
+
function stepIdentity(scope, workflowId, position, step) {
|
|
137
|
+
const matchValue = step.Id;
|
|
138
|
+
if (matchValue == null) {
|
|
139
|
+
return new StepIdentity(GraphId_anonymousStepNodeId(scope, position), `steps[${position}]`, `anonymous:${position}/run`);
|
|
140
|
+
} else {
|
|
141
|
+
const name = ReferenceParsing_relativeId(workflowId, matchValue);
|
|
142
|
+
return new StepIdentity(GraphId_stepNodeId(scope, name), name, concat(name, "/run"));
|
|
143
|
+
}
|
|
144
|
+
}
|
|
145
|
+
function addStepNode(state, workflowNodeId, identity, step) {
|
|
146
|
+
let option_1 = void 0, expression = void 0, option_3 = void 0, sm = void 0, option_5 = void 0, option_7 = void 0;
|
|
147
|
+
const stepNodeId = identity.NodeId;
|
|
148
|
+
const metadata = createMetadata(ofArray([["when", (option_1 = step.When_, option_1 != null ? some((expression = option_1, expression.AsDirectiveString)) : void 0)], ["scatterMethod", (option_3 = step.ScatterMethod, option_3 != null ? some((sm = option_3, sm.AsCwlString)) : void 0)], ["scatter", (option_5 = step.Scatter, option_5 != null ? some(toArray(map((value_1) => value_1.AsDirectiveString, option_5))) : void 0)]]));
|
|
149
|
+
addNode(state, WorkflowGraphNode_create_62C775C0(stepNodeId, NodeKind.StepNode, defaultArg((option_7 = step.Label, option_7 != null ? SchemaSaladStringModule_tryLiteral(option_7) : void 0), identity.Name), workflowNodeId, void 0, unwrap(metadata)));
|
|
124
150
|
addEdgeByType(state, EdgeKind.Contains, workflowNodeId, stepNodeId, void 0);
|
|
125
151
|
return stepNodeId;
|
|
126
152
|
}
|
|
127
153
|
function addWorkflowPorts(state, workflowNodeId, workflow) {
|
|
154
|
+
let relative;
|
|
155
|
+
const holderId = workflow.Id;
|
|
156
|
+
relative = (id) => ReferenceParsing_relativeId(holderId, id);
|
|
128
157
|
iterate((input) => {
|
|
129
|
-
addPortNode(state, workflowNodeId, PortDirection.Input, input.Name, input.Name);
|
|
130
|
-
}, workflow
|
|
158
|
+
addPortNode(state, workflowNodeId, PortDirection.Input, relative(input.Name), relative(input.Name));
|
|
159
|
+
}, CWLWorkflowDescription.getInputValues(workflow));
|
|
131
160
|
iterate((output) => {
|
|
132
|
-
addPortNode(state, workflowNodeId, PortDirection.Output, output.Name, output.Name);
|
|
133
|
-
}, workflow
|
|
161
|
+
addPortNode(state, workflowNodeId, PortDirection.Output, relative(output.Name), relative(output.Name));
|
|
162
|
+
}, CWLWorkflowDescription.getOutputValues(workflow));
|
|
134
163
|
}
|
|
135
164
|
function addToolPorts(state, toolNodeId, tool) {
|
|
136
165
|
iterate((input) => {
|
|
137
166
|
addPortNode(state, toolNodeId, PortDirection.Input, input.Name, input.Name);
|
|
138
|
-
},
|
|
167
|
+
}, CWLToolDescription.getInputValuesOrEmpty(tool));
|
|
139
168
|
iterate((output) => {
|
|
140
169
|
addPortNode(state, toolNodeId, PortDirection.Output, output.Name, output.Name);
|
|
141
|
-
}, tool
|
|
170
|
+
}, CWLToolDescription.getOutputValues(tool));
|
|
142
171
|
}
|
|
143
172
|
function addExpressionToolPorts(state, toolNodeId, tool) {
|
|
144
173
|
iterate((input) => {
|
|
145
174
|
addPortNode(state, toolNodeId, PortDirection.Input, input.Name, input.Name);
|
|
146
|
-
},
|
|
175
|
+
}, CWLExpressionToolDescription.getInputValuesOrEmpty(tool));
|
|
147
176
|
iterate((output) => {
|
|
148
177
|
addPortNode(state, toolNodeId, PortDirection.Output, output.Name, output.Name);
|
|
149
|
-
}, tool
|
|
178
|
+
}, CWLExpressionToolDescription.getOutputValues(tool));
|
|
150
179
|
}
|
|
151
180
|
function addOperationPorts(state, operationNodeId, operation) {
|
|
152
181
|
iterate((input) => {
|
|
153
182
|
addPortNode(state, operationNodeId, PortDirection.Input, input.Name, input.Name);
|
|
154
|
-
}, operation
|
|
183
|
+
}, CWLOperationDescription.getInputValues(operation));
|
|
155
184
|
iterate((output) => {
|
|
156
185
|
addPortNode(state, operationNodeId, PortDirection.Output, output.Name, output.Name);
|
|
157
|
-
}, operation
|
|
186
|
+
}, CWLOperationDescription.getOutputValues(operation));
|
|
158
187
|
}
|
|
159
188
|
function addStepPorts(state, stepNodeId, step) {
|
|
189
|
+
let relative;
|
|
190
|
+
const holderId = step.Id;
|
|
191
|
+
relative = (id) => ReferenceParsing_relativeId(holderId, id);
|
|
160
192
|
iterate((input) => {
|
|
161
|
-
addPortNode(state, stepNodeId, PortDirection.Input, input.Id, input.Id);
|
|
162
|
-
}, step
|
|
163
|
-
iterate((
|
|
164
|
-
const outputId =
|
|
193
|
+
addPortNode(state, stepNodeId, PortDirection.Input, relative(input.Id), relative(input.Id));
|
|
194
|
+
}, WorkflowStep.getInputValues(step));
|
|
195
|
+
iterate((id_1) => {
|
|
196
|
+
const outputId = relative(id_1);
|
|
165
197
|
addPortNode(state, stepNodeId, PortDirection.Output, outputId, outputId);
|
|
166
|
-
}, step.Out);
|
|
198
|
+
}, choose((output) => StepOutput.tryId(output), step.Out));
|
|
167
199
|
}
|
|
168
200
|
function trimToNameCandidate(value) {
|
|
169
201
|
if (isNullOrWhiteSpace(value)) {
|
|
@@ -218,7 +250,7 @@ function tryGetProcessingUnitName(processingUnit) {
|
|
|
218
250
|
option_1 = void 0;
|
|
219
251
|
}
|
|
220
252
|
if (option_1 != null) {
|
|
221
|
-
return tryBasenameNoCwlExtension(
|
|
253
|
+
return tryBasenameNoCwlExtension(option_1);
|
|
222
254
|
} else {
|
|
223
255
|
return void 0;
|
|
224
256
|
}
|
|
@@ -236,9 +268,9 @@ function getRunPathCandidates(workflowFilePath, runPath) {
|
|
|
236
268
|
const normalizedRunPath = normalize(trimmedRunPath);
|
|
237
269
|
let matchResult = void 0, workflowPath_1 = void 0;
|
|
238
270
|
if (workflowFilePath != null) {
|
|
239
|
-
if (!isNullOrWhiteSpace(
|
|
271
|
+
if (!isNullOrWhiteSpace(workflowFilePath)) {
|
|
240
272
|
matchResult = 0;
|
|
241
|
-
workflowPath_1 =
|
|
273
|
+
workflowPath_1 = workflowFilePath;
|
|
242
274
|
} else {
|
|
243
275
|
matchResult = 1;
|
|
244
276
|
}
|
|
@@ -269,7 +301,7 @@ function resolveRunString(state, workflowFilePath, runPath) {
|
|
|
269
301
|
if (matchValue != null) {
|
|
270
302
|
const tryResolveRunPath = value(matchValue);
|
|
271
303
|
const candidates = getRunPathCandidates(workflowFilePath, runPath);
|
|
272
|
-
const candidateKeys = Array_distinct(map(normalizePathKey, candidates), {
|
|
304
|
+
const candidateKeys = Array_distinct(map$1(normalizePathKey, candidates), {
|
|
273
305
|
Equals: (x, y) => x === y,
|
|
274
306
|
GetHashCode: (x) => stringHash(x) | 0
|
|
275
307
|
});
|
|
@@ -284,51 +316,76 @@ function resolveRunString(state, workflowFilePath, runPath) {
|
|
|
284
316
|
resolvedRun = [FSharpMap__get_Item(state.RunResolutionCache, pathKey), candidate];
|
|
285
317
|
} else {
|
|
286
318
|
const matchValue_1 = tryResolveRunPath(candidate);
|
|
319
|
+
let matchResult = void 0, tool = void 0, workflow = void 0, expressionTool = void 0, operation = void 0;
|
|
287
320
|
if (matchValue_1 == null) {
|
|
321
|
+
matchResult = 4;
|
|
288
322
|
} else {
|
|
289
|
-
switch (
|
|
323
|
+
switch (matchValue_1.tag) {
|
|
290
324
|
case /* Workflow */
|
|
291
325
|
1: {
|
|
292
|
-
|
|
293
|
-
|
|
294
|
-
for (let idx_2 = 0; idx_2 <= candidateKeys.length - 1; idx_2++) {
|
|
295
|
-
const key_1 = item(idx_2, candidateKeys);
|
|
296
|
-
state.RunResolutionCache = FSharpMap__Add(state.RunResolutionCache, key_1, run_1);
|
|
297
|
-
}
|
|
298
|
-
resolvedRun = [run_1, candidate];
|
|
326
|
+
matchResult = 1;
|
|
327
|
+
workflow = matchValue_1.fields[0];
|
|
299
328
|
break;
|
|
300
329
|
}
|
|
301
330
|
case /* ExpressionTool */
|
|
302
331
|
2: {
|
|
303
|
-
|
|
304
|
-
|
|
305
|
-
for (let idx_3 = 0; idx_3 <= candidateKeys.length - 1; idx_3++) {
|
|
306
|
-
const key_2 = item(idx_3, candidateKeys);
|
|
307
|
-
state.RunResolutionCache = FSharpMap__Add(state.RunResolutionCache, key_2, run_2);
|
|
308
|
-
}
|
|
309
|
-
resolvedRun = [run_2, candidate];
|
|
332
|
+
matchResult = 2;
|
|
333
|
+
expressionTool = matchValue_1.fields[0];
|
|
310
334
|
break;
|
|
311
335
|
}
|
|
312
336
|
case /* Operation */
|
|
313
337
|
3: {
|
|
314
|
-
|
|
315
|
-
|
|
316
|
-
|
|
317
|
-
|
|
318
|
-
|
|
319
|
-
|
|
320
|
-
|
|
338
|
+
matchResult = 3;
|
|
339
|
+
operation = matchValue_1.fields[0];
|
|
340
|
+
break;
|
|
341
|
+
}
|
|
342
|
+
case /* RawProcess */
|
|
343
|
+
4: {
|
|
344
|
+
matchResult = 4;
|
|
321
345
|
break;
|
|
322
346
|
}
|
|
323
347
|
default: {
|
|
324
|
-
|
|
325
|
-
|
|
326
|
-
|
|
327
|
-
|
|
328
|
-
|
|
329
|
-
|
|
330
|
-
|
|
348
|
+
matchResult = 0;
|
|
349
|
+
tool = matchValue_1.fields[0];
|
|
350
|
+
}
|
|
351
|
+
}
|
|
352
|
+
}
|
|
353
|
+
switch (matchResult) {
|
|
354
|
+
case 0: {
|
|
355
|
+
const run = WorkflowStepRunOps_fromTool(tool);
|
|
356
|
+
for (let idx_1 = 0; idx_1 <= candidateKeys.length - 1; idx_1++) {
|
|
357
|
+
const key = item(idx_1, candidateKeys);
|
|
358
|
+
state.RunResolutionCache = FSharpMap__Add(state.RunResolutionCache, key, run);
|
|
331
359
|
}
|
|
360
|
+
resolvedRun = [run, candidate];
|
|
361
|
+
break;
|
|
362
|
+
}
|
|
363
|
+
case 1: {
|
|
364
|
+
const run_1 = WorkflowStepRunOps_fromWorkflow(workflow);
|
|
365
|
+
for (let idx_2 = 0; idx_2 <= candidateKeys.length - 1; idx_2++) {
|
|
366
|
+
const key_1 = item(idx_2, candidateKeys);
|
|
367
|
+
state.RunResolutionCache = FSharpMap__Add(state.RunResolutionCache, key_1, run_1);
|
|
368
|
+
}
|
|
369
|
+
resolvedRun = [run_1, candidate];
|
|
370
|
+
break;
|
|
371
|
+
}
|
|
372
|
+
case 2: {
|
|
373
|
+
const run_2 = WorkflowStepRunOps_fromExpressionTool(expressionTool);
|
|
374
|
+
for (let idx_3 = 0; idx_3 <= candidateKeys.length - 1; idx_3++) {
|
|
375
|
+
const key_2 = item(idx_3, candidateKeys);
|
|
376
|
+
state.RunResolutionCache = FSharpMap__Add(state.RunResolutionCache, key_2, run_2);
|
|
377
|
+
}
|
|
378
|
+
resolvedRun = [run_2, candidate];
|
|
379
|
+
break;
|
|
380
|
+
}
|
|
381
|
+
case 3: {
|
|
382
|
+
const run_3 = WorkflowStepRunOps_fromOperation(operation);
|
|
383
|
+
for (let idx_4 = 0; idx_4 <= candidateKeys.length - 1; idx_4++) {
|
|
384
|
+
const key_3 = item(idx_4, candidateKeys);
|
|
385
|
+
state.RunResolutionCache = FSharpMap__Add(state.RunResolutionCache, key_3, run_3);
|
|
386
|
+
}
|
|
387
|
+
resolvedRun = [run_3, candidate];
|
|
388
|
+
break;
|
|
332
389
|
}
|
|
333
390
|
}
|
|
334
391
|
}
|
|
@@ -338,7 +395,7 @@ function resolveRunString(state, workflowFilePath, runPath) {
|
|
|
338
395
|
addDiagnostic(state, GraphIssueKind.ResolutionFailed, concat("Unable to resolve CWL run reference '", runPath, "'."), workflowFilePath, runPath);
|
|
339
396
|
return new RunResolutionResult(WorkflowStepRun_RunString(runPath), void 0, true, candidateKeys);
|
|
340
397
|
} else {
|
|
341
|
-
return new RunResolutionResult(
|
|
398
|
+
return new RunResolutionResult(resolvedRun[0], resolvedRun[1], true, candidateKeys);
|
|
342
399
|
}
|
|
343
400
|
} else {
|
|
344
401
|
if (state.Options.StrictUnresolvedRunReferences) {
|
|
@@ -349,90 +406,102 @@ function resolveRunString(state, workflowFilePath, runPath) {
|
|
|
349
406
|
}
|
|
350
407
|
}
|
|
351
408
|
function buildProcessingUnit(state, scope, workflowFilePath, ownerNodeId, isRoot, processingUnit) {
|
|
352
|
-
let
|
|
409
|
+
let option_15 = void 0, option_13 = void 0, option_17 = void 0, option_21 = void 0, option_19 = void 0, option_23 = void 0, option_27 = void 0, option_25 = void 0, option_29 = void 0, option_31 = void 0, option_33 = void 0, option_3 = void 0, option_1 = void 0, option_9 = void 0, option_7 = void 0, option_5 = void 0, option_11 = void 0;
|
|
353
410
|
switch (processingUnit.tag) {
|
|
354
411
|
case /* ExpressionTool */
|
|
355
412
|
2: {
|
|
356
413
|
const expressionTool = processingUnit.fields[0];
|
|
357
|
-
const nodeId_1 = addProcessingUnitNode(state, scope, ProcessingUnitKind.ExpressionTool, chooseLabel("ExpressionTool", ofArray([tryGetProcessingUnitName(expressionTool), (
|
|
414
|
+
const nodeId_1 = addProcessingUnitNode(state, scope, ProcessingUnitKind.ExpressionTool, chooseLabel("ExpressionTool", ofArray([tryGetProcessingUnitName(expressionTool), (option_15 = (option_13 = expressionTool.Label, option_13 != null ? SchemaSaladStringModule_tryLiteral(option_13) : void 0), option_15 != null ? tryBasenameNoCwlExtension(option_15) : void 0), (option_17 = workflowFilePath, option_17 != null ? tryBasenameNoCwlExtension(option_17) : void 0)])), ownerNodeId, void 0, createMetadata(ofArray([["cwlVersion", some(expressionTool.CWLVersion)], ["expression", some(expressionTool.Expression.AsDirectiveString)]])));
|
|
358
415
|
addExpressionToolPorts(state, nodeId_1, expressionTool);
|
|
359
416
|
return nodeId_1;
|
|
360
417
|
}
|
|
361
418
|
case /* Operation */
|
|
362
419
|
3: {
|
|
363
420
|
const operation = processingUnit.fields[0];
|
|
364
|
-
const nodeId_2 = addProcessingUnitNode(state, scope, ProcessingUnitKind.Operation, chooseLabel("Operation", ofArray([tryGetProcessingUnitName(operation), (
|
|
421
|
+
const nodeId_2 = addProcessingUnitNode(state, scope, ProcessingUnitKind.Operation, chooseLabel("Operation", ofArray([tryGetProcessingUnitName(operation), (option_21 = (option_19 = operation.Label, option_19 != null ? SchemaSaladStringModule_tryLiteral(option_19) : void 0), option_21 != null ? tryBasenameNoCwlExtension(option_21) : void 0), (option_23 = workflowFilePath, option_23 != null ? tryBasenameNoCwlExtension(option_23) : void 0)])), ownerNodeId, void 0, createMetadata(singleton(["cwlVersion", some(operation.CWLVersion)])));
|
|
365
422
|
addOperationPorts(state, nodeId_2, operation);
|
|
366
423
|
return nodeId_2;
|
|
367
424
|
}
|
|
368
425
|
case /* Workflow */
|
|
369
426
|
1: {
|
|
370
427
|
const workflow = processingUnit.fields[0];
|
|
371
|
-
const
|
|
428
|
+
const label_3 = chooseLabel("Workflow", ofArray([tryGetProcessingUnitName(workflow), (option_27 = (option_25 = workflow.Label, option_25 != null ? SchemaSaladStringModule_tryLiteral(option_25) : void 0), option_27 != null ? tryBasenameNoCwlExtension(option_27) : void 0), (option_29 = workflowFilePath, option_29 != null ? tryBasenameNoCwlExtension(option_29) : void 0)]));
|
|
429
|
+
const nodeId_3 = addProcessingUnitNode(state, scope, ProcessingUnitKind.Workflow, label_3, ownerNodeId, void 0, createMetadata(singleton(["cwlVersion", some(workflow.CWLVersion)])));
|
|
372
430
|
addWorkflowPorts(state, nodeId_3, workflow);
|
|
373
431
|
if (isRoot ? true : state.Options.ExpandNestedWorkflows) {
|
|
374
|
-
|
|
432
|
+
if (exists((right) => CWLProcessingUnit.isSameObject(processingUnit, right), state.ActiveWorkflows)) {
|
|
433
|
+
addDiagnostic(state, GraphIssueKind.CycleDetected, concat("Cycle detected: the workflow '", label_3, "' runs itself through its steps."), workflowFilePath, void 0);
|
|
434
|
+
} else {
|
|
435
|
+
const previousWorkflows = state.ActiveWorkflows;
|
|
436
|
+
state.ActiveWorkflows = cons(processingUnit, previousWorkflows);
|
|
437
|
+
try {
|
|
438
|
+
buildWorkflowSteps(state, scope, workflowFilePath, nodeId_3, workflow);
|
|
439
|
+
} finally {
|
|
440
|
+
state.ActiveWorkflows = previousWorkflows;
|
|
441
|
+
}
|
|
442
|
+
}
|
|
375
443
|
}
|
|
376
444
|
return nodeId_3;
|
|
377
445
|
}
|
|
446
|
+
case /* RawProcess */
|
|
447
|
+
4:
|
|
448
|
+
return addProcessingUnitNode(state, scope, ProcessingUnitKind.ExternalReference, chooseLabel("Process with a directive as its class", ofArray([(option_31 = RawYaml__TryScalarField_Z721C83C5(processingUnit.fields[0], "id"), option_31 != null ? tryBasenameNoCwlExtension(option_31) : void 0), (option_33 = workflowFilePath, option_33 != null ? tryBasenameNoCwlExtension(option_33) : void 0)])), ownerNodeId, void 0, void 0);
|
|
378
449
|
default: {
|
|
379
450
|
const tool = processingUnit.fields[0];
|
|
380
|
-
const nodeId = addProcessingUnitNode(state, scope, ProcessingUnitKind.CommandLineTool, chooseLabel("CommandLineTool", ofArray([tryGetProcessingUnitName(tool), (option_1 = tool.Label, option_1 != null ?
|
|
451
|
+
const nodeId = addProcessingUnitNode(state, scope, ProcessingUnitKind.CommandLineTool, chooseLabel("CommandLineTool", ofArray([tryGetProcessingUnitName(tool), (option_3 = (option_1 = tool.Label, option_1 != null ? SchemaSaladStringModule_tryLiteral(option_1) : void 0), option_3 != null ? tryBasenameNoCwlExtension(option_3) : void 0), (option_9 = (option_7 = (option_5 = tool.BaseCommand, option_5 != null ? tryHead(option_5) : void 0), option_7 != null ? SchemaSaladStringModule_tryLiteral(option_7) : void 0), option_9 != null ? tryBasenameNoCwlExtension(option_9) : void 0), (option_11 = workflowFilePath, option_11 != null ? tryBasenameNoCwlExtension(option_11) : void 0)])), ownerNodeId, void 0, createMetadata(singleton(["cwlVersion", some(tool.CWLVersion)])));
|
|
381
452
|
addToolPorts(state, nodeId, tool);
|
|
382
453
|
return nodeId;
|
|
383
454
|
}
|
|
384
455
|
}
|
|
385
456
|
}
|
|
386
457
|
function buildRunNode(state, runScope, stepNodeId, workflowFilePath, run) {
|
|
387
|
-
let currentPath = void 0;
|
|
458
|
+
let option_1 = void 0, currentPath = void 0;
|
|
459
|
+
let matchResult = void 0, runPath = void 0;
|
|
388
460
|
switch (run.tag) {
|
|
389
|
-
case /*
|
|
461
|
+
case /* RunImport */
|
|
390
462
|
1: {
|
|
391
|
-
|
|
392
|
-
|
|
393
|
-
|
|
394
|
-
addDiagnostic(state, GraphIssueKind.UnexpectedRuntimeType, "WorkflowStepRun.RunCommandLineTool had an unexpected payload type.", workflowFilePath, void 0);
|
|
395
|
-
return [run, badNodeId];
|
|
396
|
-
} else {
|
|
397
|
-
return [run, buildProcessingUnit(state, runScope, workflowFilePath, stepNodeId, false, CWLProcessingUnit_CommandLineTool(value(matchValue_2)))];
|
|
398
|
-
}
|
|
463
|
+
matchResult = 0;
|
|
464
|
+
runPath = run.fields[0];
|
|
465
|
+
break;
|
|
399
466
|
}
|
|
400
|
-
case /*
|
|
467
|
+
case /* RunMixed */
|
|
401
468
|
2: {
|
|
402
|
-
|
|
403
|
-
|
|
404
|
-
const badNodeId_1 = addProcessingUnitNode(state, runScope, ProcessingUnitKind.UnresolvedReference, "Invalid Workflow payload", stepNodeId, void 0, void 0);
|
|
405
|
-
addDiagnostic(state, GraphIssueKind.UnexpectedRuntimeType, "WorkflowStepRun.RunWorkflow had an unexpected payload type.", workflowFilePath, void 0);
|
|
406
|
-
return [run, badNodeId_1];
|
|
407
|
-
} else {
|
|
408
|
-
const workflow = value(matchValue_3);
|
|
409
|
-
return [run, buildProcessingUnit(state, runScope, (currentPath = defaultArg(workflowFilePath, ""), isNullOrWhiteSpace(currentPath) ? void 0 : currentPath), stepNodeId, false, CWLProcessingUnit_Workflow(workflow))];
|
|
410
|
-
}
|
|
469
|
+
matchResult = 1;
|
|
470
|
+
break;
|
|
411
471
|
}
|
|
412
|
-
case /*
|
|
472
|
+
case /* RunRaw */
|
|
413
473
|
3: {
|
|
414
|
-
|
|
415
|
-
|
|
416
|
-
const badNodeId_2 = addProcessingUnitNode(state, runScope, ProcessingUnitKind.UnresolvedReference, "Invalid ExpressionTool payload", stepNodeId, void 0, void 0);
|
|
417
|
-
addDiagnostic(state, GraphIssueKind.UnexpectedRuntimeType, "WorkflowStepRun.RunExpressionTool had an unexpected payload type.", workflowFilePath, void 0);
|
|
418
|
-
return [run, badNodeId_2];
|
|
419
|
-
} else {
|
|
420
|
-
return [run, buildProcessingUnit(state, runScope, workflowFilePath, stepNodeId, false, CWLProcessingUnit_ExpressionTool(value(matchValue_4)))];
|
|
421
|
-
}
|
|
474
|
+
matchResult = 2;
|
|
475
|
+
break;
|
|
422
476
|
}
|
|
423
|
-
case /*
|
|
477
|
+
case /* RunCommandLineTool */
|
|
424
478
|
4: {
|
|
425
|
-
|
|
426
|
-
|
|
427
|
-
|
|
428
|
-
|
|
429
|
-
|
|
430
|
-
|
|
431
|
-
|
|
432
|
-
|
|
479
|
+
matchResult = 3;
|
|
480
|
+
break;
|
|
481
|
+
}
|
|
482
|
+
case /* RunWorkflow */
|
|
483
|
+
5: {
|
|
484
|
+
matchResult = 4;
|
|
485
|
+
break;
|
|
486
|
+
}
|
|
487
|
+
case /* RunExpressionTool */
|
|
488
|
+
6: {
|
|
489
|
+
matchResult = 5;
|
|
490
|
+
break;
|
|
491
|
+
}
|
|
492
|
+
case /* RunOperation */
|
|
493
|
+
7: {
|
|
494
|
+
matchResult = 6;
|
|
495
|
+
break;
|
|
433
496
|
}
|
|
434
497
|
default: {
|
|
435
|
-
|
|
498
|
+
matchResult = 0;
|
|
499
|
+
runPath = run.fields[0];
|
|
500
|
+
}
|
|
501
|
+
}
|
|
502
|
+
switch (matchResult) {
|
|
503
|
+
case 0: {
|
|
504
|
+
const resolution = resolveRunString(state, workflowFilePath, runPath);
|
|
436
505
|
const matchValue = resolution.ResolvedRun;
|
|
437
506
|
if (matchValue.tag === /* RunString */
|
|
438
507
|
0) {
|
|
@@ -448,7 +517,7 @@ function buildRunNode(state, runScope, stepNodeId, workflowFilePath, run) {
|
|
|
448
517
|
if (matchValue_1 == null) {
|
|
449
518
|
patternInput = buildRunNode(state, runScope, stepNodeId, resolution.ResolvedFromPath, resolvedRun);
|
|
450
519
|
} else {
|
|
451
|
-
const resolvedPathKey = normalizePathKey(
|
|
520
|
+
const resolvedPathKey = normalizePathKey(matchValue_1);
|
|
452
521
|
const previousStack = state.RunResolutionStack;
|
|
453
522
|
state.RunResolutionStack = FSharpSet__Add(previousStack, resolvedPathKey);
|
|
454
523
|
try {
|
|
@@ -465,36 +534,81 @@ function buildRunNode(state, runScope, stepNodeId, workflowFilePath, run) {
|
|
|
465
534
|
}
|
|
466
535
|
return [patternInput[0], builtNodeId];
|
|
467
536
|
} else {
|
|
468
|
-
return [resolvedRun,
|
|
537
|
+
return [resolvedRun, cachedRunNodeId];
|
|
469
538
|
}
|
|
470
539
|
}
|
|
471
540
|
}
|
|
541
|
+
case 1:
|
|
542
|
+
return [run, addProcessingUnitNode(state, runScope, ProcessingUnitKind.ExternalReference, "Process with a mixin", stepNodeId, void 0, void 0)];
|
|
543
|
+
case 2:
|
|
544
|
+
return [run, addProcessingUnitNode(state, runScope, ProcessingUnitKind.ExternalReference, chooseLabel("Process with a directive as its class", singleton((option_1 = RawYaml__TryScalarField_Z721C83C5(run.fields[0], "id"), option_1 != null ? tryBasenameNoCwlExtension(option_1) : void 0))), stepNodeId, void 0, void 0)];
|
|
545
|
+
case 3: {
|
|
546
|
+
const matchValue_2 = WorkflowStepRunOps_tryGetTool(run);
|
|
547
|
+
if (matchValue_2 == null) {
|
|
548
|
+
const badNodeId = addProcessingUnitNode(state, runScope, ProcessingUnitKind.UnresolvedReference, "Invalid CommandLineTool payload", stepNodeId, void 0, void 0);
|
|
549
|
+
addDiagnostic(state, GraphIssueKind.UnexpectedRuntimeType, "WorkflowStepRun.RunCommandLineTool had an unexpected payload type.", workflowFilePath, void 0);
|
|
550
|
+
return [run, badNodeId];
|
|
551
|
+
} else {
|
|
552
|
+
return [run, buildProcessingUnit(state, runScope, workflowFilePath, stepNodeId, false, CWLProcessingUnit_CommandLineTool(matchValue_2))];
|
|
553
|
+
}
|
|
554
|
+
}
|
|
555
|
+
case 4: {
|
|
556
|
+
const matchValue_3 = WorkflowStepRunOps_tryGetWorkflow(run);
|
|
557
|
+
if (matchValue_3 == null) {
|
|
558
|
+
const badNodeId_1 = addProcessingUnitNode(state, runScope, ProcessingUnitKind.UnresolvedReference, "Invalid Workflow payload", stepNodeId, void 0, void 0);
|
|
559
|
+
addDiagnostic(state, GraphIssueKind.UnexpectedRuntimeType, "WorkflowStepRun.RunWorkflow had an unexpected payload type.", workflowFilePath, void 0);
|
|
560
|
+
return [run, badNodeId_1];
|
|
561
|
+
} else {
|
|
562
|
+
const workflow = matchValue_3;
|
|
563
|
+
return [run, buildProcessingUnit(state, runScope, (currentPath = defaultArg(workflowFilePath, ""), isNullOrWhiteSpace(currentPath) ? void 0 : currentPath), stepNodeId, false, CWLProcessingUnit_Workflow(workflow))];
|
|
564
|
+
}
|
|
565
|
+
}
|
|
566
|
+
case 5: {
|
|
567
|
+
const matchValue_4 = WorkflowStepRunOps_tryGetExpressionTool(run);
|
|
568
|
+
if (matchValue_4 == null) {
|
|
569
|
+
const badNodeId_2 = addProcessingUnitNode(state, runScope, ProcessingUnitKind.UnresolvedReference, "Invalid ExpressionTool payload", stepNodeId, void 0, void 0);
|
|
570
|
+
addDiagnostic(state, GraphIssueKind.UnexpectedRuntimeType, "WorkflowStepRun.RunExpressionTool had an unexpected payload type.", workflowFilePath, void 0);
|
|
571
|
+
return [run, badNodeId_2];
|
|
572
|
+
} else {
|
|
573
|
+
return [run, buildProcessingUnit(state, runScope, workflowFilePath, stepNodeId, false, CWLProcessingUnit_ExpressionTool(matchValue_4))];
|
|
574
|
+
}
|
|
575
|
+
}
|
|
576
|
+
default: {
|
|
577
|
+
const matchValue_5 = WorkflowStepRunOps_tryGetOperation(run);
|
|
578
|
+
if (matchValue_5 == null) {
|
|
579
|
+
const badNodeId_3 = addProcessingUnitNode(state, runScope, ProcessingUnitKind.UnresolvedReference, "Invalid Operation payload", stepNodeId, void 0, void 0);
|
|
580
|
+
addDiagnostic(state, GraphIssueKind.UnexpectedRuntimeType, "WorkflowStepRun.RunOperation had an unexpected payload type.", workflowFilePath, void 0);
|
|
581
|
+
return [run, badNodeId_3];
|
|
582
|
+
} else {
|
|
583
|
+
return [run, buildProcessingUnit(state, runScope, workflowFilePath, stepNodeId, false, CWLProcessingUnit_Operation(matchValue_5))];
|
|
584
|
+
}
|
|
585
|
+
}
|
|
472
586
|
}
|
|
473
587
|
}
|
|
474
|
-
function wireStepInputs(state, scope, workflowNodeId, step) {
|
|
475
|
-
|
|
476
|
-
let enumerator = getEnumerator(step.In);
|
|
588
|
+
function wireStepInputs(state, scope, workflowNodeId, workflowId, identity, step) {
|
|
589
|
+
let enumerator = getEnumerator(WorkflowStep.getInputValues(step));
|
|
477
590
|
try {
|
|
478
591
|
while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
|
|
479
592
|
const stepInput = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
|
|
480
|
-
const targetInputPortId = GraphId_portNodeId(
|
|
593
|
+
const targetInputPortId = GraphId_portNodeId(identity.NodeId, PortDirection.Input, ReferenceParsing_relativeId(step.Id, stepInput.Id));
|
|
481
594
|
const matchValue = stepInput.Source;
|
|
482
595
|
if (matchValue != null) {
|
|
483
|
-
|
|
596
|
+
const sources = matchValue;
|
|
597
|
+
const enumerator_1 = getEnumerator(choose(SchemaSaladStringModule_tryLiteral, sources.AsValues()));
|
|
484
598
|
try {
|
|
485
599
|
while (enumerator_1["System.Collections.IEnumerator.MoveNext"]()) {
|
|
486
|
-
const
|
|
487
|
-
const sourceRef = ReferenceParsing_parseSourceReference(
|
|
600
|
+
const source_1 = enumerator_1["System.Collections.Generic.IEnumerator`1.get_Current"]();
|
|
601
|
+
const sourceRef = ReferenceParsing_parseSourceReference(ReferenceParsing_relativeId(workflowId, source_1));
|
|
488
602
|
if (isNullOrWhiteSpace(sourceRef.PortId)) {
|
|
489
|
-
addDiagnostic(state, GraphIssueKind.InvalidReference, `Step '${
|
|
603
|
+
addDiagnostic(state, GraphIssueKind.InvalidReference, `Step '${identity.Name}' input '${stepInput.Id}' has invalid source '${source_1}'.`, scope, source_1);
|
|
490
604
|
} else {
|
|
491
605
|
let sourcePortId;
|
|
492
606
|
const matchValue_1 = sourceRef.StepId;
|
|
493
|
-
sourcePortId = matchValue_1 == null ? GraphId_portNodeId(workflowNodeId, PortDirection.Input, sourceRef.PortId) : GraphId_portNodeId(GraphId_stepNodeId(scope,
|
|
607
|
+
sourcePortId = matchValue_1 == null ? GraphId_portNodeId(workflowNodeId, PortDirection.Input, sourceRef.PortId) : GraphId_portNodeId(GraphId_stepNodeId(scope, matchValue_1), PortDirection.Output, sourceRef.PortId);
|
|
494
608
|
if (hasNode(state, sourcePortId) && hasNode(state, targetInputPortId)) {
|
|
495
609
|
addEdgeByType(state, sourceRef.StepId == null ? EdgeKind.BindsWorkflowInput : EdgeKind.DataFlow, sourcePortId, targetInputPortId, void 0);
|
|
496
610
|
} else {
|
|
497
|
-
addDiagnostic(state, GraphIssueKind.MissingReference, `Unable to wire source '${
|
|
611
|
+
addDiagnostic(state, GraphIssueKind.MissingReference, `Unable to wire source '${source_1}' to step input '${identity.Name}/${stepInput.Id}'.`, scope, source_1);
|
|
498
612
|
}
|
|
499
613
|
}
|
|
500
614
|
}
|
|
@@ -508,22 +622,23 @@ function wireStepInputs(state, scope, workflowNodeId, step) {
|
|
|
508
622
|
}
|
|
509
623
|
}
|
|
510
624
|
function wireWorkflowOutputs(state, scope, workflowNodeId, workflow) {
|
|
511
|
-
let enumerator = getEnumerator(workflow
|
|
625
|
+
let enumerator = getEnumerator(CWLWorkflowDescription.getOutputValues(workflow));
|
|
512
626
|
try {
|
|
513
627
|
while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
|
|
514
628
|
const output = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
|
|
629
|
+
const outputName = ReferenceParsing_relativeId(workflow.Id, output.Name);
|
|
515
630
|
let enumerator_1 = getEnumerator(output.GetOutputSources());
|
|
516
631
|
try {
|
|
517
632
|
while (enumerator_1["System.Collections.IEnumerator.MoveNext"]()) {
|
|
518
633
|
const outputSource = enumerator_1["System.Collections.Generic.IEnumerator`1.get_Current"]();
|
|
519
|
-
const parsedSource = ReferenceParsing_parseSourceReference(outputSource);
|
|
634
|
+
const parsedSource = ReferenceParsing_parseSourceReference(ReferenceParsing_relativeId(workflow.Id, outputSource));
|
|
520
635
|
if (isNullOrWhiteSpace(parsedSource.PortId)) {
|
|
521
636
|
addDiagnostic(state, GraphIssueKind.InvalidReference, `Workflow output '${output.Name}' has invalid outputSource '${outputSource}'.`, scope, outputSource);
|
|
522
637
|
} else {
|
|
523
638
|
let sourcePortId;
|
|
524
639
|
const matchValue = parsedSource.StepId;
|
|
525
|
-
sourcePortId = matchValue == null ? GraphId_portNodeId(workflowNodeId, PortDirection.Input, parsedSource.PortId) : GraphId_portNodeId(GraphId_stepNodeId(scope,
|
|
526
|
-
const targetPortId = GraphId_portNodeId(workflowNodeId, PortDirection.Output,
|
|
640
|
+
sourcePortId = matchValue == null ? GraphId_portNodeId(workflowNodeId, PortDirection.Input, parsedSource.PortId) : GraphId_portNodeId(GraphId_stepNodeId(scope, matchValue), PortDirection.Output, parsedSource.PortId);
|
|
641
|
+
const targetPortId = GraphId_portNodeId(workflowNodeId, PortDirection.Output, outputName);
|
|
527
642
|
if (hasNode(state, sourcePortId) && hasNode(state, targetPortId)) {
|
|
528
643
|
addEdgeByType(state, EdgeKind.BindsWorkflowOutput, sourcePortId, targetPortId, void 0);
|
|
529
644
|
} else {
|
|
@@ -540,20 +655,31 @@ function wireWorkflowOutputs(state, scope, workflowNodeId, workflow) {
|
|
|
540
655
|
}
|
|
541
656
|
}
|
|
542
657
|
function buildWorkflowSteps(state, scope, workflowFilePath, workflowNodeId, workflow) {
|
|
543
|
-
|
|
658
|
+
const steps = toList(choose((tupledArg) => {
|
|
659
|
+
let step = void 0;
|
|
660
|
+
const option_1 = ListEntry$1.tryValue(tupledArg[1]);
|
|
661
|
+
if (option_1 != null) {
|
|
662
|
+
return step = option_1, [step, stepIdentity(scope, workflow.Id, tupledArg[0], step)];
|
|
663
|
+
} else {
|
|
664
|
+
return void 0;
|
|
665
|
+
}
|
|
666
|
+
}, indexed(workflow.Steps)));
|
|
667
|
+
const enumerator = getEnumerator(steps);
|
|
544
668
|
try {
|
|
545
669
|
while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
|
|
546
|
-
const
|
|
547
|
-
const
|
|
548
|
-
|
|
549
|
-
|
|
670
|
+
const forLoopVar = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
|
|
671
|
+
const step_1 = forLoopVar[0];
|
|
672
|
+
const identity = forLoopVar[1];
|
|
673
|
+
const stepNodeId = addStepNode(state, workflowNodeId, identity, step_1);
|
|
674
|
+
addStepPorts(state, stepNodeId, step_1);
|
|
675
|
+
addEdgeByType(state, EdgeKind.Calls, stepNodeId, buildRunNode(state, GraphId_childScope(scope, identity.RunSegment), stepNodeId, workflowFilePath, WorkflowStep.getResolvedRun(step_1))[1], "calls");
|
|
550
676
|
}
|
|
551
677
|
} finally {
|
|
552
678
|
disposeSafe(enumerator);
|
|
553
679
|
}
|
|
554
|
-
iterate((
|
|
555
|
-
wireStepInputs(state, scope, workflowNodeId,
|
|
556
|
-
},
|
|
680
|
+
iterate$1((tupledArg_1) => {
|
|
681
|
+
wireStepInputs(state, scope, workflowNodeId, workflow.Id, tupledArg_1[1], tupledArg_1[0]);
|
|
682
|
+
}, steps);
|
|
557
683
|
wireWorkflowOutputs(state, scope, workflowNodeId, workflow);
|
|
558
684
|
}
|
|
559
685
|
function buildWith(options, processingUnit) {
|
|
@@ -567,4 +693,4 @@ function build(processingUnit) {
|
|
|
567
693
|
return buildWith(WorkflowGraphBuildOptionsModule_defaultOptions, processingUnit);
|
|
568
694
|
}
|
|
569
695
|
|
|
570
|
-
export { BuildState, BuildState_$reflection, RunResolutionResult, RunResolutionResult_$reflection, addDiagnostic, addEdge, addEdgeByType, addExpressionToolPorts, addNode, addOperationPorts, addPortNode, addProcessingUnitNode, addStepNode, addStepPorts, addToolPorts, addWorkflowPorts, build, buildProcessingUnit, buildRunNode, buildWith, buildWorkflowSteps, chooseLabel, createGraph, createMetadata, createState, getRunPathCandidates, hasNode, isCwlReference, resolveRunString, trimToNameCandidate, tryBasenameNoCwlExtension, tryGetProcessingUnitName, wireStepInputs, wireWorkflowOutputs };
|
|
696
|
+
export { BuildState, BuildState_$reflection, RunResolutionResult, RunResolutionResult_$reflection, StepIdentity, StepIdentity_$reflection, addDiagnostic, addEdge, addEdgeByType, addExpressionToolPorts, addNode, addOperationPorts, addPortNode, addProcessingUnitNode, addStepNode, addStepPorts, addToolPorts, addWorkflowPorts, build, buildProcessingUnit, buildRunNode, buildWith, buildWorkflowSteps, chooseLabel, createGraph, createMetadata, createState, getRunPathCandidates, hasNode, isCwlReference, resolveRunString, stepIdentity, trimToNameCandidate, tryBasenameNoCwlExtension, tryGetProcessingUnitName, wireStepInputs, wireWorkflowOutputs };
|