@nfdi4plants/arctrl 3.0.0-beta.12 → 3.0.0-beta.14

package/README.md

@@ -19,7 +19,7 @@
 
 ```fsharp
 #r "nuget: ARCtrl"
-``` 
+```
 
 ```bash
 <PackageReference Include="ARCtrl" Version="1.1.0" />
@@ -55,6 +55,8 @@ Documentation can be found [here](https://nfdi4plants.github.io/nfdi4plants.know
 
 #### Local Setup
 
+##### Windows
+
 On windows you can use the `setup.cmd` to run the following steps automatically!
 
 1. Setup dotnet tools
@@ -63,11 +65,11 @@ On windows you can use the `setup.cmd` to run the following steps automatically!
 
 
 2. Install NPM dependencies
-   
+
     `npm install`
 
 3. Setup python environment
-    
+
     `py -m venv .venv`
 
 4. Install [uv](https://docs.astral.sh/uv/) and dependencies
@@ -78,6 +80,31 @@ On windows you can use the `setup.cmd` to run the following steps automatically!
 
 Verify correct setup with `./build.cmd runtests` ✨
 
+##### Linux / macOS
+
+On unix you can use the `setup.sh` to run the following steps automatically!
+
+1. Setup dotnet tools
+
+   `dotnet tool restore`
+
+
+2. Install NPM dependencies
+
+    `npm install`
+
+3. Setup python environment
+
+    `python -m venv .venv`
+
+4. Install [uv](https://docs.astral.sh/uv/) and dependencies
+
+   1. `.venv/bin/python -m pip install -U pip setuptools`
+   2. `.venv/bin/python -m pip install uv`
+   3. `.venv/bin/python -m uv pip install -r pyproject.toml --group dev`
+
+Verify correct setup with `bash build.sh runtests` ✨
+
 ## Branding
 
 Feel free to reference `ARCtrl` on slides or elsewhere using our logos:

package/dist/ts/index.d.ts

@@ -1,23 +1,24 @@
 import { LDNode, LDGraph, LDRef, LDValue } from './ts/ROCrate/LDObject.js';
 import { LDContext } from './ts/ROCrate/LDContext.js';
-import { initV1_1, initV1_2DRAFT, initBioschemasContext } from './ts/ROCrate/ROCrateContext.js';
-import { LDComment } from './ts/ROCrate/Generic/Comment.js';
-import { LDDefinedTerm } from './ts/ROCrate/Generic/DefinedTerm.js';
-import { LDFile } from './ts/ROCrate/Generic/File.js';
-import { LDLabProcess } from './ts/ROCrate/Generic/LabProcess.js';
-import { LDLabProtocol } from './ts/ROCrate/Generic/LabProtocol.js';
-import { LDOrganization } from './ts/ROCrate/Generic/Organization.js';
-import { LDPerson } from './ts/ROCrate/Generic/Person.js';
-import { LDPostalAddress } from './ts/ROCrate/Generic/PostalAddress.js';
-import { LDPropertyValue } from './ts/ROCrate/Generic/PropertyValue.js';
-import { LDSample } from './ts/ROCrate/Generic/Sample.js';
-import { LDScholarlyArticle } from './ts/ROCrate/Generic/ScholarlyArticle.js';
-import { LDDataset } from './ts/ROCrate/Generic/Dataset.js';
+import { initV1_1, initV1_2, initBioschemasContext } from './ts/ROCrate/ROCrateContext.js';
+import { LDComment } from './ts/ROCrate/LDTypes/Comment.js';
+import { LDDefinedTerm } from './ts/ROCrate/LDTypes/DefinedTerm.js';
+import { LDFile } from './ts/ROCrate/LDTypes/File.js';
+import { LDLabProcess } from './ts/ROCrate/LDTypes/LabProcess.js';
+import { LDLabProtocol } from './ts/ROCrate/LDTypes/LabProtocol.js';
+import { LDOrganization } from './ts/ROCrate/LDTypes/Organization.js';
+import { LDPerson } from './ts/ROCrate/LDTypes/Person.js';
+import { LDPostalAddress } from './ts/ROCrate/LDTypes/PostalAddress.js';
+import { LDPropertyValue } from './ts/ROCrate/LDTypes/PropertyValue.js';
+import { LDSample } from './ts/ROCrate/LDTypes/Sample.js';
+import { LDScholarlyArticle } from './ts/ROCrate/LDTypes/ScholarlyArticle.js';
+import { LDDataset } from './ts/ROCrate/LDTypes/Dataset.js';
 import { LDGraphExtensions_PyJsInterop as LDGraphIO, LDNodeExtensions_PyJsInterop as LDNodeIO } from './ts/JsonIO/LDObject.js';
-import { TypeExtensions_Conversion as Conversion } from './ts/Conversion.js';
+import { Conversion as Conversion } from './ts/Conversion.js';
 export { ARC } from './ts/ARC.js';
 export { ArcAssay, ArcStudy, ArcRun, ArcWorkflow, ArcInvestigation } from './ts/Core/ArcTypes.js';
-export { DataMap } from './ts/Core/DataMap.js';
+export { Datamap } from './ts/Core/Datamap.js';
+export { DataContext } from './ts/Core/DataContext.js';
 export { CompositeCell } from './ts/Core/Table/CompositeCell.js';
 export { CompositeHeader, IOType } from './ts/Core/Table/CompositeHeader.js';
 export { CompositeColumn } from './ts/Core/Table/CompositeColumn.js';
@@ -41,7 +42,7 @@ export declare const ROCrate: {
     LDRef: typeof LDRef;
     LDContext: typeof LDContext;
     initV1_1: typeof initV1_1;
-    initV1_2DRAFT: typeof initV1_2DRAFT;
+    initV1_2: typeof initV1_2;
     initBioschemasContext: typeof initBioschemasContext;
     LDComment: typeof LDComment;
     LDDefinedTerm: typeof LDDefinedTerm;

package/dist/ts/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/ARCtrl/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,GAAG,EAAE,MAAM,aAAa,CAAA;AACjC,OAAO,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,EAAE,WAAW,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAA;AACjG,OAAO,EAAE,OAAO,EAAE,MAAM,sBAAsB,CAAA;AAC9C,OAAO,EAAE,WAAW,EAAE,MAAM,0BAA0B,CAAA;AACtD,OAAO,EAAE,aAAa,EAAE,MAAM,kCAAkC,CAAA;AAChE,OAAO,EAAE,eAAe,EAAE,MAAM,EAAE,MAAM,oCAAoC,CAAA;AAC5E,OAAO,EAAE,eAAe,EAAE,MAAM,oCAAoC,CAAA;AACpE,OAAO,EAAE,QAAQ,EAAE,MAAM,6BAA6B,CAAA;AACtD,OAAO,EAAE,QAAQ,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AAC9D,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAA;AAClD,OAAO,EAAE,cAAc,EAAE,MAAM,cAAc,CAAA;AAC7C,OAAO,EAAE,cAAc,EAAE,MAAM,cAAc,CAAA;AAC7C,OAAO,EAAE,MAAM,EAAE,MAAM,qBAAqB,CAAA;AAC5C,OAAO,EAAE,WAAW,EAAE,MAAM,0BAA0B,CAAA;AACtD,OAAO,EAAE,kBAAkB,EAAE,MAAM,iCAAiC,CAAA;AACpE,OAAO,EAAE,QAAQ,IAAI,OAAO,EAAE,MAAM,sBAAsB,CAAA;AAC1D,OAAO,EAAE,QAAQ,EAAE,MAAM,2BAA2B,CAAA;AACpD,OAAO,EAAE,aAAa,EAAC,MAAM,sBAAsB,CAAA;AACnD,OAAO,EAAE,UAAU,EAAE,MAAM,+BAA+B,CAAA;AAC1D,OAAO,EAAE,cAAc,EAAE,MAAM,mCAAmC,CAAA;AAGlE,OAAO,EAAE,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,OAAO,EAAC,MAAM,0BAA0B,CAAA;AACzE,OAAO,EAAE,SAAS,EAAE,MAAM,2BAA2B,CAAA;AACrD,OAAO,EAAE,QAAQ,EAAE,QAAQ,EAAE,qBAAqB,EAAE,MAAM,gCAAgC,CAAA;AAC1F,OAAO,EAAE,SAAS,EAAE,MAAM,iCAAiC,CAAA;AAC3D,OAAO,EAAE,aAAa,EAAE,MAAM,qCAAqC,CAAA;AACnE,OAAO,EAAE,MAAM,EAAE,MAAM,8BAA8B,CAAA;AACrD,OAAO,EAAE,YAAY,EAAE,MAAM,oCAAoC,CAAA;AACjE,OAAO,EAAE,aAAa,EAAE,MAAM,qCAAqC,CAAA;AACnE,OAAO,EAAE,cAAc,EAAE,MAAM,sCAAsC,CAAA;AACrE,OAAO,EAAE,QAAQ,EAAE,MAAM,gCAAgC,CAAA;AACzD,OAAO,EAAE,eAAe,EAAE,MAAM,uCAAuC,CAAA;AACvE,OAAO,EAAE,eAAe,EAAE,MAAM,uCAAuC,CAAA;AACvE,OAAO,EAAE,QAAQ,EAAE,MAAM,gCAAgC,CAAA;AACzD,OAAO,EAAE,kBAAkB,EAAE,MAAM,0CAA0C,CAAA;AAC7E,OAAO,EAAE,SAAS,EAAE,MAAM,iCAAiC,CAAA;AAC3D,OAAO,EAAE,6BAA6B,IAAI,SAAS,EAAE,MAAM,yBAAyB,CAAA;AACpF,OAAO,EAAE,4BAA4B,IAAI,QAAQ,EAAE,MAAM,yBAAyB,CAAA;AAClF,OAAO,EAAE,UAAU,IAAI,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAE7D,eAAO,MAAM,OAAO;;;;;;;;;;;;;;;;;;;;;;;;CAwBnB,CAAC"}

package/dist/ts/index.js

@@ -1,6 +1,7 @@
 export { ARC } from './ts/ARC.js';
 export { ArcAssay, ArcInvestigation, ArcRun, ArcStudy, ArcWorkflow } from './ts/Core/ArcTypes.js';
-export { DataMap } from './ts/Core/DataMap.js';
+export { Datamap } from './ts/Core/Datamap.js';
+export { DataContext } from './ts/Core/DataContext.js';
 export { CompositeCell } from './ts/Core/Table/CompositeCell.js';
 export { CompositeHeader, IOType } from './ts/Core/Table/CompositeHeader.js';
 export { CompositeColumn } from './ts/Core/Table/CompositeColumn.js';
@@ -19,21 +20,21 @@ export { FileSystem } from './ts/FileSystem/FileSystem.js';
 export { FileSystemTree } from './ts/FileSystem/FileSystemTree.js';
 import { LDRef, LDValue, LDGraph, LDNode } from './ts/ROCrate/LDObject.js';
 import { LDContext } from './ts/ROCrate/LDContext.js';
-import { initBioschemasContext, initV1_2DRAFT, initV1_1 } from './ts/ROCrate/ROCrateContext.js';
-import { LDComment } from './ts/ROCrate/Generic/Comment.js';
-import { LDDefinedTerm } from './ts/ROCrate/Generic/DefinedTerm.js';
-import { LDFile } from './ts/ROCrate/Generic/File.js';
-import { LDLabProcess } from './ts/ROCrate/Generic/LabProcess.js';
-import { LDLabProtocol } from './ts/ROCrate/Generic/LabProtocol.js';
-import { LDOrganization } from './ts/ROCrate/Generic/Organization.js';
-import { LDPerson } from './ts/ROCrate/Generic/Person.js';
-import { LDPostalAddress } from './ts/ROCrate/Generic/PostalAddress.js';
-import { LDPropertyValue } from './ts/ROCrate/Generic/PropertyValue.js';
-import { LDSample } from './ts/ROCrate/Generic/Sample.js';
-import { LDScholarlyArticle } from './ts/ROCrate/Generic/ScholarlyArticle.js';
-import { LDDataset } from './ts/ROCrate/Generic/Dataset.js';
+import { initBioschemasContext, initV1_2, initV1_1 } from './ts/ROCrate/ROCrateContext.js';
+import { LDComment } from './ts/ROCrate/LDTypes/Comment.js';
+import { LDDefinedTerm } from './ts/ROCrate/LDTypes/DefinedTerm.js';
+import { LDFile } from './ts/ROCrate/LDTypes/File.js';
+import { LDLabProcess } from './ts/ROCrate/LDTypes/LabProcess.js';
+import { LDLabProtocol } from './ts/ROCrate/LDTypes/LabProtocol.js';
+import { LDOrganization } from './ts/ROCrate/LDTypes/Organization.js';
+import { LDPerson } from './ts/ROCrate/LDTypes/Person.js';
+import { LDPostalAddress } from './ts/ROCrate/LDTypes/PostalAddress.js';
+import { LDPropertyValue } from './ts/ROCrate/LDTypes/PropertyValue.js';
+import { LDSample } from './ts/ROCrate/LDTypes/Sample.js';
+import { LDScholarlyArticle } from './ts/ROCrate/LDTypes/ScholarlyArticle.js';
+import { LDDataset } from './ts/ROCrate/LDTypes/Dataset.js';
 import { LDNodeExtensions_PyJsInterop, LDGraphExtensions_PyJsInterop } from './ts/JsonIO/LDObject.js';
-import { TypeExtensions_Conversion } from './ts/Conversion.js';
+import { Conversion } from './ts/Conversion.js';
 
 const ROCrate = {
   LDNode,
@@ -42,7 +43,7 @@ const ROCrate = {
   LDRef,
   LDContext,
   initV1_1,
-  initV1_2DRAFT,
+  initV1_2,
   initBioschemasContext,
   LDComment,
   LDDefinedTerm,
@@ -58,7 +59,7 @@ const ROCrate = {
   LDDataset,
   LDGraphIO: LDGraphExtensions_PyJsInterop,
   LDNodeIO: LDNodeExtensions_PyJsInterop,
-  Conversion: TypeExtensions_Conversion
+  Conversion
 };
 
 export { ROCrate };

package/dist/ts/ts/ARC.d.ts

@@ -5,9 +5,11 @@ import { ArcWorkflow, ArcRun, ArcStudy, ArcAssay, ArcInvestigation } from './Cor
 import { FSharpResult$2_$union } from '@fable-org/fable-library-js/Result.js';
 import { Contract } from './Contract/Contract.js';
 import { int32 } from '@fable-org/fable-library-js/Int32.js';
-import { DataMap } from './Core/DataMap.js';
+import { Datamap } from './Core/Datamap.js';
 import { FileSystemTree_$union } from './FileSystem/FileSystemTree.js';
 import { FSharpList } from '@fable-org/fable-library-js/List.js';
+import { CWLProcessingUnit_$union } from './CWL/CWLProcessingUnit.js';
+import { CWLParameterReference } from './CWL/ParameterReference.js';
 import { Remark, Comment$ } from './Core/Comment.js';
 import { Person } from './Core/Person.js';
 import { Publication } from './Core/Publication.js';
@@ -18,7 +20,7 @@ import { TypeInfo } from '@fable-org/fable-library-js/Reflection.js';
 export declare class ARC extends ArcInvestigation {
     _license: Option<License>;
     _fs: FileSystem;
-    "init@96": int32;
+    "init@114": int32;
     constructor(identifier: string, title?: string, description?: string, submissionDate?: string, publicReleaseDate?: string, ontologySourceReferences?: OntologySourceReference[], publications?: Publication[], contacts?: Person[], assays?: ArcAssay[], studies?: ArcStudy[], workflows?: ArcWorkflow[], runs?: ArcRun[], registeredStudyIdentifiers?: string[], comments?: Comment$[], remarks?: Remark[], fs?: FileSystem, license?: License);
     get FileSystem(): FileSystem;
     set FileSystem(fs: FileSystem);
@@ -87,10 +89,13 @@ export declare function ARCAux_getArcAssaysFromContracts(contracts: Contract[]):
 export declare function ARCAux_getArcStudiesFromContracts(contracts: Contract[]): [ArcStudy, FSharpList<ArcAssay>][];
 export declare function ARCAux_getArcWorkflowsFromContracts(contracts: Contract[]): ArcWorkflow[];
 export declare function ARCAux_getArcRunsFromContracts(contracts: Contract[]): ArcRun[];
-export declare function ARCAux_getAssayDataMapFromContracts(assayIdentifier: string, contracts: Contract[]): Option<DataMap>;
-export declare function ARCAux_getStudyDataMapFromContracts(studyIdentifier: string, contracts: Contract[]): Option<DataMap>;
-export declare function ARCAux_getWorkflowDataMapFromContracts(workflowIdentifier: string, contracts: Contract[]): Option<DataMap>;
-export declare function ARCAux_getRunDataMapFromContracts(runIdentifier: string, contracts: Contract[]): Option<DataMap>;
+export declare function ARCAux_getAssayDatamapFromContracts(assayIdentifier: string, contracts: Contract[]): Option<Datamap>;
+export declare function ARCAux_getStudyDatamapFromContracts(studyIdentifier: string, contracts: Contract[]): Option<Datamap>;
+export declare function ARCAux_getWorkflowDatamapFromContracts(workflowIdentifier: string, contracts: Contract[]): Option<Datamap>;
+export declare function ARCAux_getRunDatamapFromContracts(runIdentifier: string, contracts: Contract[]): Option<Datamap>;
+export declare function ARCAux_getWorkflowCWLFromContracts(workflowIdentifier: string, contracts: Contract[]): Option<CWLProcessingUnit_$union>;
+export declare function ARCAux_getRunCWLFromContracts(runIdentifier: string, contracts: Contract[]): Option<CWLProcessingUnit_$union>;
+export declare function ARCAux_getRunYMLFromContracts(runIdentifier: string, contracts: Contract[]): Option<CWLParameterReference[]>;
 export declare function ARCAux_getArcInvestigationFromContracts(contracts: Contract[]): ArcInvestigation;
 export declare function ARCAux_getLicenseFromContracts(contracts: Contract[]): Option<License>;
 export declare function ARCAux_updateFSByARC(isa: ArcInvestigation, license: Option<License>, fs: FileSystem): FileSystem;

package/dist/ts/ts/ARC.d.ts.map

@@ -1 +1 @@
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package/dist/ts/ts/ARC.js

@@ -12,8 +12,8 @@ import { toArray, contains, delay, append, singleton, iterate, tryFind, find, em
 import { defaultOf, stringHash, comparePrimitives, curry2, safeHash, getEnumerator, disposeSafe, equals } from '../node_modules/@fable-org/fable-library-js/Util.js';
 import { getAssayFolderPath, getRunFolderPath, getWorkflowFolderPath, getStudyFolderPath } from './FileSystem/Path.js';
 import { ARCtrl_ArcAssay__ArcAssay_ToDeleteContract, ARCtrl_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49, ARCtrl_ArcAssay__ArcAssay_ToUpdateContract, ARCtrl_ArcAssay__ArcAssay_tryFromReadContract_Static_7570923F } from './Contract/ArcAssay.js';
-import { ARCtrl_ArcRun__ArcRun_ToDeleteContract, ARCtrl_ArcRun__ArcRun_ToCreateContract_6FCE9E49, ARCtrl_ArcRun__ArcRun_ToUpdateContract, ARCtrl_ArcRun__ArcRun_tryFromReadContract_Static_7570923F } from './Contract/ArcRun.js';
-import { ARCtrl_ArcWorkflow__ArcWorkflow_ToDeleteContract, ARCtrl_ArcWorkflow__ArcWorkflow_ToCreateContract_6FCE9E49, ARCtrl_ArcWorkflow__ArcWorkflow_ToUpdateContract, ARCtrl_ArcWorkflow__ArcWorkflow_tryFromReadContract_Static_7570923F } from './Contract/ArcWorkflow.js';
+import { ARCtrl_ArcRun__ArcRun_ToDeleteContract, ARCtrl_ArcRun__ArcRun_ToCreateContract_6FCE9E49, ARCtrl_ArcRun__ArcRun_ToUpdateContract, ARCtrl_ArcRun__ArcRun_tryFromReadContract_Static_7570923F, ARCtrl_ArcRun__ArcRun_tryCWLFromReadContract_Static, ARCtrl_ArcRun__ArcRun_tryYMLFromReadContract_Static } from './Contract/ArcRun.js';
+import { ARCtrl_ArcWorkflow__ArcWorkflow_ToDeleteContract, ARCtrl_ArcWorkflow__ArcWorkflow_ToCreateContract_6FCE9E49, ARCtrl_ArcWorkflow__ArcWorkflow_ToUpdateContract, ARCtrl_ArcWorkflow__ArcWorkflow_tryFromReadContract_Static_7570923F, ARCtrl_ArcWorkflow__ArcWorkflow_tryCWLFromReadContract_Static } from './Contract/ArcWorkflow.js';
 import { join, toFail, printf, replace, toText } from '../node_modules/@fable-org/fable-library-js/String.js';
 import { map, choose, fold, concat, contains as contains$2, append as append$1, tryPick, equalsWith, item } from '../node_modules/@fable-org/fable-library-js/Array.js';
 import { ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract, ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F } from './Contract/ArcInvestigation.js';
@@ -27,13 +27,13 @@ import { ArcTables } from './Core/Table/ArcTables.js';
 import { addToDict } from '../node_modules/@fable-org/fable-library-js/MapUtil.js';
 import { ARCtrl_ArcInvestigation__ArcInvestigation_toFsWorkbook_Static_Z720BD3FF } from './Spreadsheet/ArcInvestigation.js';
 import { ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_Z4CEFA522 } from './Spreadsheet/ArcStudy.js';
-import { toFsWorkbook } from './Spreadsheet/DataMap.js';
+import { toFsWorkbook } from './Spreadsheet/Datamap.js';
 import { ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F } from './Spreadsheet/ArcAssay.js';
 import { ARCtrl_ArcWorkflow__ArcWorkflow_toFsWorkbook_Static_Z1C75CB0E } from './Spreadsheet/ArcWorkflow.js';
 import { ARCtrl_ArcRun__ArcRun_toFsWorkbook_Static_Z3EFAF6F8 } from './Spreadsheet/ArcRun.js';
 import { Dictionary_tryGet } from './fable_modules/FsSpreadsheet.7.0.0-alpha.1/Cells/FsCellsCollection.fs.js';
 import { ARCtrl_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49, ARCtrl_ArcStudy__ArcStudy_ToUpdateContract, ARCtrl_ArcStudy__ArcStudy_tryFromReadContract_Static_7570923F } from './Contract/ArcStudy.js';
-import { ARCtrl_DataMap__DataMap_ToUpdateContractForStudy_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForStudy_Z721C83C5, ARCtrl_DataMap__DataMap_ToUpdateContractForAssay_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForAssay_Z721C83C5, ARCtrl_DataMap__DataMap_ToUpdateContractForWorkflow_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForWorkflow_Z721C83C5, ARCtrl_DataMap__DataMap_ToUpdateContractForRun_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForRun_Z721C83C5, ARCtrl_DataMap__DataMap_tryFromReadContractForAssay_Static, ARCtrl_DataMap__DataMap_tryFromReadContractForStudy_Static, ARCtrl_DataMap__DataMap_tryFromReadContractForWorkflow_Static, ARCtrl_DataMap__DataMap_tryFromReadContractForRun_Static } from './Contract/Datamap.js';
+import { ARCtrl_Datamap__Datamap_ToUpdateContractForStudy_Z721C83C5, ARCtrl_Datamap__Datamap_ToCreateContractForStudy_Z721C83C5, ARCtrl_Datamap__Datamap_ToUpdateContractForAssay_Z721C83C5, ARCtrl_Datamap__Datamap_ToCreateContractForAssay_Z721C83C5, ARCtrl_Datamap__Datamap_ToUpdateContractForWorkflow_Z721C83C5, ARCtrl_Datamap__Datamap_ToCreateContractForWorkflow_Z721C83C5, ARCtrl_Datamap__Datamap_ToUpdateContractForRun_Z721C83C5, ARCtrl_Datamap__Datamap_ToCreateContractForRun_Z721C83C5, ARCtrl_Datamap__Datamap_tryFromReadContractForAssay_Static, ARCtrl_Datamap__Datamap_tryFromReadContractForStudy_Static, ARCtrl_Datamap__Datamap_tryFromReadContractForWorkflow_Static, ARCtrl_Datamap__Datamap_tryFromReadContractForRun_Static } from './Contract/Datamap.js';
 import { Init_createInitContract_6DFDD678, gitignoreContract, gitattributesContract, Init_createAddRemoteContract_Z721C83C5, Clone_createCloneContract_5000466F } from './Contract/Git.js';
 import { ofSeq as ofSeq$1 } from '../node_modules/@fable-org/fable-library-js/Map.js';
 import { fromString } from './fable_modules/Thoth.Json.JavaScript.0.4.1/Decode.fs.js';
@@ -54,7 +54,7 @@ class ARC extends ArcInvestigation {
     this._fs = (fs_1 = defaultArg(fs, FileSystem.create({
       tree: FileSystemTree_Folder("", [])
     })), ARCAux_updateFSByARC(this$.contents, license, fs_1));
-    this["init@96"] = 1;
+    this["init@114"] = 1;
   }
   get FileSystem() {
     const this$ = this;
@@ -465,7 +465,7 @@ class ARC extends ArcInvestigation {
       updateColumnOption(dataNameFunction_1, t.TryGetInputColumn());
       updateColumnOption(dataNameFunction_1, t.TryGetOutputColumn());
     };
-    const updateDataMap = (dataNameFunction_2, dm) => {
+    const updateDatamap = (dataNameFunction_2, dm) => {
       iterate((c_1) => {
         if (c_1.FilePath != null) {
           const newFilePath_1 = dataNameFunction_2(c_1);
@@ -477,16 +477,16 @@ class ARC extends ArcInvestigation {
       const f_1 = (d) => d.GetAbsolutePathForStudy(s.Identifier, checkExistenceFromRoot);
       const source_1 = s.Tables;
       iterate(curry2(updateTable)(f_1), source_1);
-      if (s.DataMap != null) {
-        updateDataMap(f_1, value(s.DataMap));
+      if (s.Datamap != null) {
+        updateDatamap(f_1, value(s.Datamap));
       }
     }, this$.Studies);
     iterate((a_1) => {
       const f_2 = (d_1) => d_1.GetAbsolutePathForAssay(a_1.Identifier, checkExistenceFromRoot);
       const source_3 = a_1.Tables;
       iterate(curry2(updateTable)(f_2), source_3);
-      if (a_1.DataMap != null) {
-        updateDataMap(f_2, value(a_1.DataMap));
+      if (a_1.Datamap != null) {
+        updateDatamap(f_2, value(a_1.Datamap));
       }
     }, this$.Assays);
   }
@@ -542,9 +542,9 @@ class ARC extends ArcInvestigation {
         const registeredStudy = value(registeredStudyOpt);
         registeredStudy.UpdateReferenceByStudyFile(study, true);
       }
-      const datamap = ARCAux_getStudyDataMapFromContracts(study.Identifier, contracts);
-      if (study.DataMap == null) {
-        study.DataMap = datamap;
+      const datamap = ARCAux_getStudyDatamapFromContracts(study.Identifier, contracts);
+      if (study.Datamap == null) {
+        study.Datamap = datamap;
       }
       study.StaticHash = study.GetLightHashCode() | 0;
     });
@@ -560,25 +560,31 @@ class ARC extends ArcInvestigation {
       let updatedTables;
       const array_6 = assay_1.StudiesRegisteredIn;
       updatedTables = fold((tables, study_1) => ArcTables.updateReferenceTablesBySheets(new ArcTables(study_1.Tables), tables, false), new ArcTables(assay_1.Tables), array_6);
-      const datamap_1 = ARCAux_getAssayDataMapFromContracts(assay_1.Identifier, contracts);
-      if (assay_1.DataMap == null) {
-        assay_1.DataMap = datamap_1;
+      const datamap_1 = ARCAux_getAssayDatamapFromContracts(assay_1.Identifier, contracts);
+      if (assay_1.Datamap == null) {
+        assay_1.Datamap = datamap_1;
       }
       assay_1.Tables = updatedTables.Tables;
     });
     workflows.forEach((workflow) => {
-      const datamap_2 = ARCAux_getWorkflowDataMapFromContracts(workflow.Identifier, contracts);
-      if (workflow.DataMap == null) {
-        workflow.DataMap = datamap_2;
+      const datamap_2 = ARCAux_getWorkflowDatamapFromContracts(workflow.Identifier, contracts);
+      const cwl = ARCAux_getWorkflowCWLFromContracts(workflow.Identifier, contracts);
+      if (workflow.Datamap == null) {
+        workflow.Datamap = datamap_2;
       }
+      workflow.CWLDescription = cwl;
       this$.AddWorkflow(workflow);
       workflow.StaticHash = workflow.GetLightHashCode() | 0;
     });
     runs.forEach((run) => {
-      const datamap_3 = ARCAux_getRunDataMapFromContracts(run.Identifier, contracts);
-      if (run.DataMap == null) {
-        run.DataMap = datamap_3;
+      const datamap_3 = ARCAux_getRunDatamapFromContracts(run.Identifier, contracts);
+      const cwl_1 = ARCAux_getRunCWLFromContracts(run.Identifier, contracts);
+      const yml = ARCAux_getRunYMLFromContracts(run.Identifier, contracts);
+      if (run.Datamap == null) {
+        run.Datamap = datamap_3;
       }
+      run.CWLInput = defaultArg(yml, []);
+      run.CWLDescription = cwl_1;
       this$.AddRun(run);
       run.StaticHash = run.GetLightHashCode() | 0;
     });
@@ -607,8 +613,8 @@ class ARC extends ArcInvestigation {
     iterate((s) => {
       s.StaticHash = s.GetLightHashCode() | 0;
       addToDict(filemap, Study_fileNameFromIdentifier(s.Identifier), ["ISA_Study", ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_Z4CEFA522(s)]);
-      if (s.DataMap != null) {
-        const dm = value(s.DataMap);
+      if (s.Datamap != null) {
+        const dm = value(s.Datamap);
         dm.StaticHash = safeHash(dm) | 0;
         addToDict(filemap, Study_datamapFileNameFromIdentifier(s.Identifier), ["ISA_Datamap", toFsWorkbook(dm)]);
       }
@@ -616,8 +622,8 @@ class ARC extends ArcInvestigation {
     iterate((a) => {
       a.StaticHash = a.GetLightHashCode() | 0;
       addToDict(filemap, Assay_fileNameFromIdentifier(a.Identifier), ["ISA_Assay", ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F(a)]);
-      if (a.DataMap != null) {
-        const dm_1 = value(a.DataMap);
+      if (a.Datamap != null) {
+        const dm_1 = value(a.Datamap);
         dm_1.StaticHash = safeHash(dm_1) | 0;
         addToDict(filemap, Assay_datamapFileNameFromIdentifier(a.Identifier), ["ISA_Datamap", toFsWorkbook(dm_1)]);
       }
@@ -625,8 +631,11 @@ class ARC extends ArcInvestigation {
     iterate((w) => {
       w.StaticHash = w.GetLightHashCode() | 0;
       addToDict(filemap, Workflow_fileNameFromIdentifier(w.Identifier), ["ISA_Workflow", ARCtrl_ArcWorkflow__ArcWorkflow_toFsWorkbook_Static_Z1C75CB0E(w)]);
-      if (w.DataMap != null) {
-        const dm_2 = value(w.DataMap);
+      if (w.CWLDescription != null) {
+        throw new Error("Not implemented yet: CWL description in ARC.GetWriteContracts");
+      }
+      if (w.Datamap != null) {
+        const dm_2 = value(w.Datamap);
         dm_2.StaticHash = safeHash(dm_2) | 0;
         addToDict(filemap, Workflow_datamapFileNameFromIdentifier(w.Identifier), ["ISA_Datamap", toFsWorkbook(dm_2)]);
       }
@@ -634,8 +643,14 @@ class ARC extends ArcInvestigation {
     iterate((r) => {
       r.StaticHash = r.GetLightHashCode() | 0;
       addToDict(filemap, Run_fileNameFromIdentifier(r.Identifier), ["ISA_Run", ARCtrl_ArcRun__ArcRun_toFsWorkbook_Static_Z3EFAF6F8(r)]);
-      if (r.DataMap != null) {
-        const dm_3 = value(r.DataMap);
+      if (r.CWLDescription != null) {
+        throw new Error("Not implemented yet: CWL description in ARC.GetWriteContracts");
+      }
+      if (r.CWLInput.length > 0) {
+        throw new Error("Not implemented yet: CWL YAML input in ARC.GetWriteContracts");
+      }
+      if (r.Datamap != null) {
+        const dm_3 = value(r.Datamap);
         dm_3.StaticHash = safeHash(dm_3) | 0;
         addToDict(filemap, Run_datamapFileNameFromIdentifier(r.Identifier), ["ISA_Datamap", toFsWorkbook(dm_3)]);
       }
@@ -674,7 +689,7 @@ class ARC extends ArcInvestigation {
             return append(s.StaticHash === 0 ? ARCtrl_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49(s, true) : s.StaticHash !== hash_1 ? singleton(ARCtrl_ArcStudy__ArcStudy_ToUpdateContract(s)) : empty(), delay(() => {
               let dm, dm_1;
               s.StaticHash = hash_1 | 0;
-              const matchValue = s.DataMap;
+              const matchValue = s.Datamap;
               let matchResult, dm_2, dm_3;
               if (matchValue != null) {
                 if (dm = value(matchValue), dm.StaticHash === 0) {
@@ -691,12 +706,12 @@ class ARC extends ArcInvestigation {
               }
               switch (matchResult) {
                 case 0:
-                  return append(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForStudy_Z721C83C5(dm_2, s.Identifier)), delay(() => {
+                  return append(singleton(ARCtrl_Datamap__Datamap_ToCreateContractForStudy_Z721C83C5(dm_2, s.Identifier)), delay(() => {
                     dm_2.StaticHash = safeHash(dm_2) | 0;
                     return empty();
                   }));
                 case 1:
-                  return append(singleton(ARCtrl_DataMap__DataMap_ToUpdateContractForStudy_Z721C83C5(dm_3, s.Identifier)), delay(() => {
+                  return append(singleton(ARCtrl_Datamap__Datamap_ToUpdateContractForStudy_Z721C83C5(dm_3, s.Identifier)), delay(() => {
                     dm_3.StaticHash = safeHash(dm_3) | 0;
                     return empty();
                   }));
@@ -710,7 +725,7 @@ class ARC extends ArcInvestigation {
             return append(a.StaticHash === 0 ? ARCtrl_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49(a, true) : a.StaticHash !== hash_2 ? singleton(ARCtrl_ArcAssay__ArcAssay_ToUpdateContract(a)) : empty(), delay(() => {
               let dm_4, dm_5;
               a.StaticHash = hash_2 | 0;
-              const matchValue_1 = a.DataMap;
+              const matchValue_1 = a.Datamap;
               let matchResult_1, dm_6, dm_7;
               if (matchValue_1 != null) {
                 if (dm_4 = value(matchValue_1), dm_4.StaticHash === 0) {
@@ -727,12 +742,12 @@ class ARC extends ArcInvestigation {
               }
               switch (matchResult_1) {
                 case 0:
-                  return append(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForAssay_Z721C83C5(dm_6, a.Identifier)), delay(() => {
+                  return append(singleton(ARCtrl_Datamap__Datamap_ToCreateContractForAssay_Z721C83C5(dm_6, a.Identifier)), delay(() => {
                     dm_6.StaticHash = safeHash(dm_6) | 0;
                     return empty();
                   }));
                 case 1:
-                  return append(singleton(ARCtrl_DataMap__DataMap_ToUpdateContractForAssay_Z721C83C5(dm_7, a.Identifier)), delay(() => {
+                  return append(singleton(ARCtrl_Datamap__Datamap_ToUpdateContractForAssay_Z721C83C5(dm_7, a.Identifier)), delay(() => {
                     dm_7.StaticHash = safeHash(dm_7) | 0;
                     return empty();
                   }));
@@ -746,7 +761,7 @@ class ARC extends ArcInvestigation {
             return append(w.StaticHash === 0 ? ARCtrl_ArcWorkflow__ArcWorkflow_ToCreateContract_6FCE9E49(w, true) : w.StaticHash !== hash_3 ? singleton(ARCtrl_ArcWorkflow__ArcWorkflow_ToUpdateContract(w)) : empty(), delay(() => {
               let dm_8, dm_9;
               w.StaticHash = hash_3 | 0;
-              const matchValue_2 = w.DataMap;
+              const matchValue_2 = w.Datamap;
               let matchResult_2, dm_10, dm_11;
               if (matchValue_2 != null) {
                 if (dm_8 = value(matchValue_2), dm_8.StaticHash === 0) {
@@ -763,12 +778,12 @@ class ARC extends ArcInvestigation {
               }
               switch (matchResult_2) {
                 case 0:
-                  return append(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForWorkflow_Z721C83C5(dm_10, w.Identifier)), delay(() => {
+                  return append(singleton(ARCtrl_Datamap__Datamap_ToCreateContractForWorkflow_Z721C83C5(dm_10, w.Identifier)), delay(() => {
                     dm_10.StaticHash = safeHash(dm_10) | 0;
                     return empty();
                   }));
                 case 1:
-                  return append(singleton(ARCtrl_DataMap__DataMap_ToUpdateContractForWorkflow_Z721C83C5(dm_11, w.Identifier)), delay(() => {
+                  return append(singleton(ARCtrl_Datamap__Datamap_ToUpdateContractForWorkflow_Z721C83C5(dm_11, w.Identifier)), delay(() => {
                     dm_11.StaticHash = safeHash(dm_11) | 0;
                     return empty();
                   }));
@@ -782,7 +797,7 @@ class ARC extends ArcInvestigation {
             return append(r.StaticHash === 0 ? ARCtrl_ArcRun__ArcRun_ToCreateContract_6FCE9E49(r, true) : r.StaticHash !== hash_4 ? singleton(ARCtrl_ArcRun__ArcRun_ToUpdateContract(r)) : empty(), delay(() => {
               let dm_12, dm_13;
               r.StaticHash = hash_4 | 0;
-              const matchValue_3 = r.DataMap;
+              const matchValue_3 = r.Datamap;
               let matchResult_3, dm_14, dm_15;
               if (matchValue_3 != null) {
                 if (dm_12 = value(matchValue_3), dm_12.StaticHash === 0) {
@@ -799,12 +814,12 @@ class ARC extends ArcInvestigation {
               }
               switch (matchResult_3) {
                 case 0:
-                  return append(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForRun_Z721C83C5(dm_14, r.Identifier)), delay(() => {
+                  return append(singleton(ARCtrl_Datamap__Datamap_ToCreateContractForRun_Z721C83C5(dm_14, r.Identifier)), delay(() => {
                     dm_14.StaticHash = safeHash(dm_14) | 0;
                     return empty();
                   }));
                 case 1:
-                  return append(singleton(ARCtrl_DataMap__DataMap_ToUpdateContractForRun_Z721C83C5(dm_15, r.Identifier)), delay(() => {
+                  return append(singleton(ARCtrl_Datamap__Datamap_ToUpdateContractForRun_Z721C83C5(dm_15, r.Identifier)), delay(() => {
                     dm_15.StaticHash = safeHash(dm_15) | 0;
                     return empty();
                   }));
@@ -1069,17 +1084,26 @@ function ARCAux_getArcWorkflowsFromContracts(contracts) {
 function ARCAux_getArcRunsFromContracts(contracts) {
   return choose(ARCtrl_ArcRun__ArcRun_tryFromReadContract_Static_7570923F, contracts);
 }
-function ARCAux_getAssayDataMapFromContracts(assayIdentifier, contracts) {
-  return tryPick((c) => ARCtrl_DataMap__DataMap_tryFromReadContractForAssay_Static(assayIdentifier, c), contracts);
+function ARCAux_getAssayDatamapFromContracts(assayIdentifier, contracts) {
+  return tryPick((c) => ARCtrl_Datamap__Datamap_tryFromReadContractForAssay_Static(assayIdentifier, c), contracts);
+}
+function ARCAux_getStudyDatamapFromContracts(studyIdentifier, contracts) {
+  return tryPick((c) => ARCtrl_Datamap__Datamap_tryFromReadContractForStudy_Static(studyIdentifier, c), contracts);
+}
+function ARCAux_getWorkflowDatamapFromContracts(workflowIdentifier, contracts) {
+  return tryPick((c) => ARCtrl_Datamap__Datamap_tryFromReadContractForWorkflow_Static(workflowIdentifier, c), contracts);
+}
+function ARCAux_getRunDatamapFromContracts(runIdentifier, contracts) {
+  return tryPick((c) => ARCtrl_Datamap__Datamap_tryFromReadContractForRun_Static(runIdentifier, c), contracts);
 }
-function ARCAux_getStudyDataMapFromContracts(studyIdentifier, contracts) {
-  return tryPick((c) => ARCtrl_DataMap__DataMap_tryFromReadContractForStudy_Static(studyIdentifier, c), contracts);
+function ARCAux_getWorkflowCWLFromContracts(workflowIdentifier, contracts) {
+  return tryPick((c) => ARCtrl_ArcWorkflow__ArcWorkflow_tryCWLFromReadContract_Static(workflowIdentifier, c), contracts);
 }
-function ARCAux_getWorkflowDataMapFromContracts(workflowIdentifier, contracts) {
-  return tryPick((c) => ARCtrl_DataMap__DataMap_tryFromReadContractForWorkflow_Static(workflowIdentifier, c), contracts);
+function ARCAux_getRunCWLFromContracts(runIdentifier, contracts) {
+  return tryPick((c) => ARCtrl_ArcRun__ArcRun_tryCWLFromReadContract_Static(runIdentifier, c), contracts);
 }
-function ARCAux_getRunDataMapFromContracts(runIdentifier, contracts) {
-  return tryPick((c) => ARCtrl_DataMap__DataMap_tryFromReadContractForRun_Static(runIdentifier, c), contracts);
+function ARCAux_getRunYMLFromContracts(runIdentifier, contracts) {
+  return tryPick((c) => ARCtrl_ArcRun__ArcRun_tryYMLFromReadContract_Static(runIdentifier, c), contracts);
 }
 function ARCAux_getArcInvestigationFromContracts(contracts) {
   const matchValue = choose(ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F, contracts);
@@ -1095,16 +1119,16 @@ function ARCAux_getLicenseFromContracts(contracts) {
 }
 function ARCAux_updateFSByARC(isa, license, fs) {
   let assaysFolder;
-  const assays = map((a) => FileSystemTree.createAssayFolder(a.Identifier, a.DataMap != null), toArray(isa.Assays));
+  const assays = map((a) => FileSystemTree.createAssayFolder(a.Identifier, a.Datamap != null), toArray(isa.Assays));
   assaysFolder = FileSystemTree.createAssaysFolder(assays);
   let studiesFolder;
-  const studies = map((s) => FileSystemTree.createStudyFolder(s.Identifier, s.DataMap != null), toArray(isa.Studies));
+  const studies = map((s) => FileSystemTree.createStudyFolder(s.Identifier, s.Datamap != null), toArray(isa.Studies));
   studiesFolder = FileSystemTree.createStudiesFolder(studies);
   let workflowsFolder;
-  const workflows = map((w) => FileSystemTree.createWorkflowFolder(w.Identifier, w.DataMap != null), toArray(isa.Workflows));
+  const workflows = map((w) => FileSystemTree.createWorkflowFolder(w.Identifier, w.CWLDescription != null, w.Datamap != null), toArray(isa.Workflows));
   workflowsFolder = FileSystemTree.createWorkflowsFolder(workflows);
   let runsFolder;
-  const runs = map((r) => FileSystemTree.createRunFolder(r.Identifier, r.DataMap != null), toArray(isa.Runs));
+  const runs = map((r) => FileSystemTree.createRunFolder(r.Identifier, r.CWLDescription != null, r.CWLInput.length > 0, r.Datamap != null), toArray(isa.Runs));
   runsFolder = FileSystemTree.createRunsFolder(runs);
   const investigation = FileSystemTree.createInvestigationFile();
   let tree_1;
@@ -1115,4 +1139,4 @@ function ARCAux_updateFSByARC(isa, license, fs) {
   return fs.Union(tree_1);
 }
 
-export { ARC, ARCAux_getArcAssaysFromContracts, ARCAux_getArcInvestigationFromContracts, ARCAux_getArcRunsFromContracts, ARCAux_getArcStudiesFromContracts, ARCAux_getArcWorkflowsFromContracts, ARCAux_getAssayDataMapFromContracts, ARCAux_getLicenseFromContracts, ARCAux_getRunDataMapFromContracts, ARCAux_getStudyDataMapFromContracts, ARCAux_getWorkflowDataMapFromContracts, ARCAux_updateFSByARC, ARC_$ctor_Z443FB9BF, ARC_$reflection };
+export { ARC, ARCAux_getArcAssaysFromContracts, ARCAux_getArcInvestigationFromContracts, ARCAux_getArcRunsFromContracts, ARCAux_getArcStudiesFromContracts, ARCAux_getArcWorkflowsFromContracts, ARCAux_getAssayDatamapFromContracts, ARCAux_getLicenseFromContracts, ARCAux_getRunCWLFromContracts, ARCAux_getRunDatamapFromContracts, ARCAux_getRunYMLFromContracts, ARCAux_getStudyDatamapFromContracts, ARCAux_getWorkflowCWLFromContracts, ARCAux_getWorkflowDatamapFromContracts, ARCAux_updateFSByARC, ARC_$ctor_Z443FB9BF, ARC_$reflection };

package/dist/ts/ts/CWL/CWLProcessingUnit.d.ts

@@ -0,0 +1,19 @@
+import { Union } from '@fable-org/fable-library-js/Types.js';
+import { CWLToolDescription } from './ToolDescription.js';
+import { CWLWorkflowDescription } from './WorkflowDescription.js';
+import { TypeInfo } from '@fable-org/fable-library-js/Reflection.js';
+export type CWLProcessingUnit_$union = CWLProcessingUnit<0> | CWLProcessingUnit<1>;
+export type CWLProcessingUnit_$cases = {
+    0: ["CommandLineTool", [CWLToolDescription]];
+    1: ["Workflow", [CWLWorkflowDescription]];
+};
+export declare function CWLProcessingUnit_CommandLineTool(Item: CWLToolDescription): CWLProcessingUnit<0>;
+export declare function CWLProcessingUnit_Workflow(Item: CWLWorkflowDescription): CWLProcessingUnit<1>;
+export declare class CWLProcessingUnit<Tag extends keyof CWLProcessingUnit_$cases> extends Union<Tag, CWLProcessingUnit_$cases[Tag][0]> {
+    readonly tag: Tag;
+    readonly fields: CWLProcessingUnit_$cases[Tag][1];
+    constructor(tag: Tag, fields: CWLProcessingUnit_$cases[Tag][1]);
+    cases(): string[];
+}
+export declare function CWLProcessingUnit_$reflection(): TypeInfo;
+//# sourceMappingURL=CWLProcessingUnit.d.ts.map

package/dist/ts/ts/CWL/CWLProcessingUnit.d.ts.map

@@ -0,0 +1 @@
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