@nfdi4plants/arctrl 3.0.0-beta.12 → 3.0.0-beta.13

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

@@ -1,20 +1,20 @@
 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';
@@ -41,7 +41,7 @@ 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,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

@@ -19,21 +19,21 @@ 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 +42,7 @@ const ROCrate = {
   LDRef,
   LDContext,
   initV1_1,
-  initV1_2DRAFT,
+  initV1_2,
   initBioschemasContext,
   LDComment,
   LDDefinedTerm,
@@ -58,7 +58,7 @@ const ROCrate = {
   LDDataset,
   LDGraphIO: LDGraphExtensions_PyJsInterop,
   LDNodeIO: LDNodeExtensions_PyJsInterop,
-  Conversion: TypeExtensions_Conversion
+  Conversion
 };
 
 export { ROCrate };

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

@@ -8,6 +8,8 @@ import { int32 } from '@fable-org/fable-library-js/Int32.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$[], remarks?: Remark[], fs?: FileSystem, license?: License);
     get FileSystem(): FileSystem;
     set FileSystem(fs: FileSystem);
@@ -91,6 +93,9 @@ export declare function ARCAux_getAssayDataMapFromContracts(assayIdentifier: str
 export declare function ARCAux_getStudyDataMapFromContracts(studyIdentifier: string, contracts: Contract[]): Option<DataMap>;
 export declare function ARCAux_getWorkflowDataMapFromContracts(workflowIdentifier: string, contracts: Contract[]): Option<DataMap>;
 export declare function ARCAux_getRunDataMapFromContracts(runIdentifier: string, contracts: Contract[]): Option<DataMap>;
+export declare function ARCAux_getWorkflowCWLFromContracts(workflowIdentifier: string, contracts: Contract[]): Option<CWLProcessingUnit_$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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+{"version":3,"file":"ARC.d.ts","sourceRoot":"","sources":["../../../src/ARCtrl/ts/ARC.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,4BAA4B,CAAC;AACxD,OAAO,EAAoE,MAAM,EAAU,MAAM,uCAAuC,CAAC;AACzI,OAAO,EAAsB,OAAO,EAAE,MAAM,cAAc,CAAC;AAC3D,OAAO,EAAgC,WAAW,EAAE,MAAM,EAAE,QAAQ,EAAE,QAAQ,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AAE7H,OAAO,EAA2C,qBAAqB,EAAE,MAAM,uCAAuC,CAAC;AACvH,OAAO,EAAgB,QAAQ,EAAE,MAAM,wBAAwB,CAAC;AAMhE,OAAO,EAAE,KAAK,EAAE,MAAM,sCAAsC,CAAC;AAgB7D,OAAO,EAAE,OAAO,EAAE,MAAM,mBAAmB,CAAC;AAC5C,OAAO,EAA8C,qBAAqB,EAAkB,MAAM,gCAAgC,CAAC;AAGnI,OAAO,EAAE,UAAU,EAAE,MAAM,qCAAqC,CAAC;AAEjE,OAAO,EAAE,wBAAwB,EAAE,MAAM,4BAA4B,CAAC;AACtE,OAAO,EAAE,qBAAqB,EAAE,MAAM,6BAA6B,CAAC;AAYpE,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,mBAAmB,CAAC;AACrD,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAC;AAC1C,OAAO,EAAE,WAAW,EAAE,MAAM,uBAAuB,CAAC;AACpD,OAAO,EAAE,uBAAuB,EAAE,MAAM,mCAAmC,CAAC;AAC5E,OAAO,EAAE,SAAS,EAAoB,MAAM,oCAAoC,CAAC;AAOjF,OAAO,EAAE,wBAAwB,EAAE,MAAM,kDAAkD,CAAC;AAE5F,OAAO,EAAc,QAAQ,EAAE,MAAM,2CAA2C,CAAC;AAEjF,qBAAa,GAAI,SAAQ,gBAAgB;IACrC,QAAQ,EAAE,MAAM,CAAC,OAAO,CAAC,CAAC;IAC1B,GAAG,EAAE,UAAU,CAAC;IAChB,UAAU,EAAE,KAAK,CAAC;gBACN,UAAU,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,MAAM,EAAE,WAAW,CAAC,EAAE,MAAM,EAAE,cAAc,CAAC,EAAE,MAAM,EAAE,iBAAiB,CAAC,EAAE,MAAM,EAAE,wBAAwB,CAAC,EAAE,uBAAuB,EAAE,EAAE,YAAY,CAAC,EAAE,WAAW,EAAE,EAAE,QAAQ,CAAC,EAAE,MAAM,EAAE,EAAE,MAAM,CAAC,EAAE,QAAQ,EAAE,EAAE,OAAO,CAAC,EAAE,QAAQ,EAAE,EAAE,SAAS,CAAC,EAAE,WAAW,EAAE,EAAE,IAAI,CAAC,EAAE,MAAM,EAAE,EAAE,0BAA0B,CAAC,EAAE,MAAM,EAAE,EAAE,QAAQ,CAAC,EAAE,QAAQ,EAAE,EAAE,OAAO,CAAC,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,EAAE,UAAU,EAAE,OAAO,CAAC,EAAE,OAAO;IAW/a,IAAI,UAAU,IAAI,UAAU,CAG3B;IACD,IAAI,UAAU,CAAC,EAAE,EAAE,UAAU,EAG5B;IACD,IAAI,OAAO,IAAI,OAAO,GAAG,SAAS,CAGjC;IACD,IAAI,OAAO,CAAC,OAAO,EAAE,MAAM,CAAC,OAAO,CAAC,EAGnC;IACD,MAAM,CAAC,oBAAoB,CAAC,GAAG,EAAE,gBAAgB,EAAE,EAAE,CAAC,EAAE,UAAU,EAAE,OAAO,CAAC,EAAE,OAAO,GAAG,GAAG;IAG3F,aAAa,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,qBAAqB,CAAC,QAAQ,EAAE,EAAE,MAAM,EAAE,CAAC,CAAC;IAIpF,cAAc,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,qBAAqB,CAAC,QAAQ,EAAE,EAAE,MAAM,EAAE,CAAC,CAAC;IAIrF,kBAAkB,CAAC,QAAQ,EAAE,MAAM,EAAE,IAAI,CAAC,EAAE,MAAM,GAAG,IAAI;IAmBzD,MAAM,CAAC,YAAY,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,qBAAqB,CAAC,GAAG,EAAE,MAAM,EAAE,CAAC,CAAC;IAkBnF,uBAAuB,CAAC,eAAe,EAAE,MAAM,GAAG,QAAQ,EAAE;IAiB5D,qBAAqB,CAAC,aAAa,EAAE,MAAM,GAAG,QAAQ,EAAE;IAgBxD,0BAA0B,CAAC,kBAAkB,EAAE,MAAM,GAAG,QAAQ,EAAE;IAgBlE,mBAAmB,CAAC,OAAO,EAAE,MAAM,EAAE,eAAe,EAAE,MAAM,GAAG,OAAO,CAAC,qBAAqB,CAAC,QAAQ,EAAE,EAAE,MAAM,EAAE,CAAC,CAAC;IAInH,iBAAiB,CAAC,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,MAAM,GAAG,OAAO,CAAC,qBAAqB,CAAC,QAAQ,EAAE,EAAE,MAAM,EAAE,CAAC,CAAC;IAI/G,sBAAsB,CAAC,OAAO,EAAE,MAAM,EAAE,kBAAkB,EAAE,MAAM,GAAG,OAAO,CAAC,qBAAqB,CAAC,QAAQ,EAAE,EAAE,MAAM,EAAE,CAAC,CAAC;IAIzH,cAAc,CAAC,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAcrE,mBAAmB,CAAC,OAAO,EAAE,MAAM,EAAE,kBAAkB,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAc/E,iBAAiB,CAAC,OAAO,EAAE,MAAM,EAAE,gBAAgB,EAAE,MAAM,EAAE,gBAAgB,EAAE,MAAM,GAAG,OAAO,CAAC,qBAAqB,CAAC,QAAQ,EAAE,EAAE,MAAM,EAAE,CAAC,CAAC;IAI5I,sBAAsB,CAAC,OAAO,EAAE,MAAM,EAAE,qBAAqB,EAAE,MAAM,EAAE,qBAAqB,EAAE,MAAM,GAAG,OAAO,CAAC,qBAAqB,CAAC,QAAQ,EAAE,EAAE,MAAM,EAAE,CAAC,CAAC;IAI3J,cAAc,CAAC,OAAO,EAAE,MAAM,EAAE,gBAAgB,EAAE,MAAM,EAAE,gBAAgB,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAclG,mBAAmB,CAAC,OAAO,EAAE,MAAM,EAAE,qBAAqB,EAAE,MAAM,EAAE,qBAAqB,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAcjH,uBAAuB,CAAC,kBAAkB,EAAE,MAAM,EAAE,kBAAkB,EAAE,MAAM,GAAG,QAAQ,EAAE;IAgB3F,qBAAqB,CAAC,gBAAgB,EAAE,MAAM,EAAE,gBAAgB,EAAE,MAAM,GAAG,QAAQ,EAAE;IAgBrF,0BAA0B,CAAC,qBAAqB,EAAE,MAAM,EAAE,qBAAqB,EAAE,MAAM,GAAG,QAAQ,EAAE;IAgBpG,mBAAmB,CAAC,OAAO,EAAE,MAAM,EAAE,kBAAkB,EAAE,MAAM,EAAE,kBAAkB,EAAE,MAAM,GAAG,OAAO,CAAC,qBAAqB,CAAC,QAAQ,EAAE,EAAE,MAAM,EAAE,CAAC,CAAC;IAIlJ,uBAAuB,CAAC,eAAe,EAAE,MAAM,GAAG,QAAQ,EAAE;IAS5D,mBAAmB,CAAC,OAAO,EAAE,MAAM,EAAE,eAAe,EAAE,MAAM,GAAG,OAAO,CAAC,qBAAqB,CAAC,QAAQ,EAAE,EAAE,MAAM,EAAE,CAAC,CAAC;IAInH,uBAAuB,CAAC,kBAAkB,EAAE,MAAM,EAAE,kBAAkB,EAAE,MAAM,GAAG,QAAQ,EAAE;IAgB3F,mBAAmB,CAAC,OAAO,EAAE,MAAM,EAAE,kBAAkB,EAAE,MAAM,EAAE,kBAAkB,EAAE,MAAM,GAAG,OAAO,CAAC,qBAAqB,CAAC,QAAQ,EAAE,EAAE,MAAM,EAAE,CAAC,CAAC;IAIlJ,UAAU,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAc1C,WAAW,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAc3C,gBAAgB,CAAC,OAAO,EAAE,MAAM,EAAE,eAAe,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAczE,gBAAgB,CAAC,OAAO,EAAE,MAAM,EAAE,kBAAkB,EAAE,MAAM,EAAE,kBAAkB,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAcxG,gBAAgB,CAAC,OAAO,EAAE,MAAM,EAAE,eAAe,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAczE,gBAAgB,CAAC,OAAO,EAAE,MAAM,EAAE,kBAAkB,EAAE,MAAM,EAAE,kBAAkB,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAcxG,MAAM,CAAC,SAAS,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,GAAG,CAAC;IAc/C,qBAAqB,IAAI,IAAI;IAiE7B,MAAM,CAAC,aAAa,CAAC,SAAS,EAAE,MAAM,EAAE,GAAG,GAAG;IAI9C,YAAY,CAAC,SAAS,EAAE,MAAM,EAAE,GAAG,IAAI;IAKvC,gBAAgB,IAAI,QAAQ,EAAE;IAI9B,mBAAmB,CAAC,SAAS,EAAE,QAAQ,EAAE,GAAG,IAAI;IAgGhD,gBAAgB,IAAI,IAAI;IAKxB,iBAAiB,CAAC,YAAY,CAAC,EAAE,OAAO,GAAG,QAAQ,EAAE;IA0ErD,kBAAkB,CAAC,YAAY,CAAC,EAAE,OAAO,GAAG,QAAQ,EAAE;IAyLtD,mBAAmB,CAAC,MAAM,CAAC,EAAE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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$1, tryPick, equalsWith, item } from '../node_modules/@fable-org/fable-library-js/Array.js';
 import { ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract, ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F } from './Contract/ArcInvestigation.js';
@@ -54,7 +54,7 @@ class ARC extends ArcInvestigation {
     this._fs = (fs_1 = defaultArg(fs, FileSystem.create({
       tree: FileSystemTree_Folder("", [])
     })), ARCAux_updateFSByARC(this$.contents, license, fs_1));
-    this["init@96"] = 1;
+    this["init@114"] = 1;
   }
   get FileSystem() {
     const this$ = this;
@@ -568,17 +568,23 @@ class ARC extends ArcInvestigation {
     });
     workflows.forEach((workflow) => {
       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$.AddWorkflow(workflow);
       workflow.StaticHash = workflow.GetLightHashCode() | 0;
     });
     runs.forEach((run) => {
       const datamap_3 = ARCAux_getRunDataMapFromContracts(run.Identifier, contracts);
+      const cwl_1 = ARCAux_getRunCWLFromContracts(run.Identifier, contracts);
+      const yml = ARCAux_getRunYMLFromContracts(run.Identifier, contracts);
       if (run.DataMap == null) {
         run.DataMap = datamap_3;
       }
+      run.CWLInput = defaultArg(yml, []);
+      run.CWLDescription = cwl_1;
       this$.AddRun(run);
       run.StaticHash = run.GetLightHashCode() | 0;
     });
@@ -625,6 +631,9 @@ 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.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;
@@ -634,6 +643,12 @@ 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.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;
@@ -1081,6 +1096,15 @@ function ARCAux_getWorkflowDataMapFromContracts(workflowIdentifier, contracts) {
 function ARCAux_getRunDataMapFromContracts(runIdentifier, contracts) {
   return tryPick((c) => ARCtrl_DataMap__DataMap_tryFromReadContractForRun_Static(runIdentifier, c), contracts);
 }
+function ARCAux_getWorkflowCWLFromContracts(workflowIdentifier, contracts) {
+  return tryPick((c) => ARCtrl_ArcWorkflow__ArcWorkflow_tryCWLFromReadContract_Static(workflowIdentifier, c), contracts);
+}
+function ARCAux_getRunCWLFromContracts(runIdentifier, contracts) {
+  return tryPick((c) => ARCtrl_ArcRun__ArcRun_tryCWLFromReadContract_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);
   if (!equalsWith(equals, matchValue, defaultOf()) && matchValue.length === 1) {
@@ -1101,10 +1125,10 @@ function ARCAux_updateFSByARC(isa, license, fs) {
   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 @@
+{"version":3,"file":"CWLProcessingUnit.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/CWL/CWLProcessingUnit.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,sCAAsC,CAAC;AAC7D,OAAO,EAAkC,kBAAkB,EAAE,MAAM,sBAAsB,CAAC;AAC1F,OAAO,EAAsC,sBAAsB,EAAE,MAAM,0BAA0B,CAAC;AACtG,OAAO,EAAc,QAAQ,EAAE,MAAM,2CAA2C,CAAC;AAEjF,MAAM,MAAM,wBAAwB,GAC9B,iBAAiB,CAAC,CAAC,CAAC,GACpB,iBAAiB,CAAC,CAAC,CAAC,CAAA;AAE1B,MAAM,MAAM,wBAAwB,GAAG;IACnC,CAAC,EAAE,CAAC,iBAAiB,EAAE,CAAC,kBAAkB,CAAC,CAAC,CAAC;IAC7C,CAAC,EAAE,CAAC,UAAU,EAAE,CAAC,sBAAsB,CAAC,CAAC,CAAA;CAC5C,CAAA;AAED,wBAAgB,iCAAiC,CAAC,IAAI,EAAE,kBAAkB,wBAEzE;AAED,wBAAgB,0BAA0B,CAAC,IAAI,EAAE,sBAAsB,wBAEtE;AAED,qBAAa,iBAAiB,CAAC,GAAG,SAAS,MAAM,wBAAwB,CAAE,SAAQ,KAAK,CAAC,GAAG,EAAE,wBAAwB,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;IAC/G,QAAQ,CAAC,GAAG,EAAE,GAAG;IAAE,QAAQ,CAAC,MAAM,EAAE,wBAAwB,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;gBAA3D,GAAG,EAAE,GAAG,EAAW,MAAM,EAAE,wBAAwB,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;IAGhF,KAAK;CAGR;AAED,wBAAgB,6BAA6B,IAAI,QAAQ,CAExD"}

package/dist/ts/ts/CWL/CWLProcessingUnit.js

@@ -0,0 +1,26 @@
+import { Union } from '../../node_modules/@fable-org/fable-library-js/Types.js';
+import { CWLToolDescription_$reflection } from './ToolDescription.js';
+import { CWLWorkflowDescription_$reflection } from './WorkflowDescription.js';
+import { union_type } from '../../node_modules/@fable-org/fable-library-js/Reflection.js';
+
+function CWLProcessingUnit_CommandLineTool(Item) {
+  return new CWLProcessingUnit(0, [Item]);
+}
+function CWLProcessingUnit_Workflow(Item) {
+  return new CWLProcessingUnit(1, [Item]);
+}
+class CWLProcessingUnit extends Union {
+  constructor(tag, fields) {
+    super();
+    this.tag = tag;
+    this.fields = fields;
+  }
+  cases() {
+    return ["CommandLineTool", "Workflow"];
+  }
+}
+function CWLProcessingUnit_$reflection() {
+  return union_type("ARCtrl.CWL.CWLProcessingUnit", [], CWLProcessingUnit, () => [[["Item", CWLToolDescription_$reflection()]], [["Item", CWLWorkflowDescription_$reflection()]]]);
+}
+
+export { CWLProcessingUnit, CWLProcessingUnit_$reflection, CWLProcessingUnit_CommandLineTool, CWLProcessingUnit_Workflow };

package/dist/ts/ts/CWL/CWLTypes.d.ts

@@ -0,0 +1,92 @@
+import { IComparable, IEquatable } from '@fable-org/fable-library-js/Util.js';
+import { int32 } from '@fable-org/fable-library-js/Int32.js';
+import { DynamicObj } from '../fable_modules/DynamicObj.7.1.0/DynamicObj.fs.js';
+import { TypeInfo } from '@fable-org/fable-library-js/Reflection.js';
+import { Union, Record } from '@fable-org/fable-library-js/Types.js';
+import { Option } from '@fable-org/fable-library-js/Option.js';
+export declare class FileInstance extends DynamicObj {
+    constructor();
+    GetHashCode(): int32;
+    Equals(o: any): boolean;
+}
+export declare function FileInstance_$reflection(): TypeInfo;
+export declare function FileInstance_$ctor(): FileInstance;
+export declare class DirectoryInstance extends DynamicObj {
+    constructor();
+    Equals(o: any): boolean;
+    GetHashCode(): int32;
+}
+export declare function DirectoryInstance_$reflection(): TypeInfo;
+export declare function DirectoryInstance_$ctor(): DirectoryInstance;
+export declare class DirentInstance extends Record implements IEquatable<DirentInstance>, IComparable<DirentInstance> {
+    readonly Entry: string;
+    readonly Entryname: Option<string>;
+    readonly Writable: Option<boolean>;
+    constructor(Entry: string, Entryname: Option<string>, Writable: Option<boolean>);
+}
+export declare function DirentInstance_$reflection(): TypeInfo;
+export type CWLType_$union = CWLType<0> | CWLType<1> | CWLType<2> | CWLType<3> | CWLType<4> | CWLType<5> | CWLType<6> | CWLType<7> | CWLType<8> | CWLType<9> | CWLType<10> | CWLType<11>;
+export type CWLType_$cases = {
+    0: ["File", [FileInstance]];
+    1: ["Directory", [DirectoryInstance]];
+    2: ["Dirent", [DirentInstance]];
+    3: ["String", []];
+    4: ["Int", []];
+    5: ["Long", []];
+    6: ["Float", []];
+    7: ["Double", []];
+    8: ["Boolean", []];
+    9: ["Stdout", []];
+    10: ["Null", []];
+    11: ["Array", [CWLType_$union]];
+};
+export declare function CWLType_File(Item: FileInstance): CWLType<0>;
+export declare function CWLType_Directory(Item: DirectoryInstance): CWLType<1>;
+export declare function CWLType_Dirent(Item: DirentInstance): CWLType<2>;
+export declare function CWLType_String(): CWLType<3>;
+export declare function CWLType_Int(): CWLType<4>;
+export declare function CWLType_Long(): CWLType<5>;
+export declare function CWLType_Float(): CWLType<6>;
+export declare function CWLType_Double(): CWLType<7>;
+export declare function CWLType_Boolean(): CWLType<8>;
+export declare function CWLType_Stdout(): CWLType<9>;
+export declare function CWLType_Null(): CWLType<10>;
+export declare function CWLType_Array(Item: CWLType_$union): CWLType<11>;
+export declare class CWLType<Tag extends keyof CWLType_$cases> extends Union<Tag, CWLType_$cases[Tag][0]> {
+    readonly tag: Tag;
+    readonly fields: CWLType_$cases[Tag][1];
+    constructor(tag: Tag, fields: CWLType_$cases[Tag][1]);
+    cases(): string[];
+}
+export declare function CWLType_$reflection(): TypeInfo;
+export declare function CWLType_file(): CWLType_$union;
+export declare function CWLType_directory(): CWLType_$union;
+export declare class InputRecordSchema extends DynamicObj {
+    constructor();
+}
+export declare function InputRecordSchema_$reflection(): TypeInfo;
+export declare function InputRecordSchema_$ctor(): InputRecordSchema;
+export declare class InputEnumSchema extends DynamicObj {
+    constructor();
+}
+export declare function InputEnumSchema_$reflection(): TypeInfo;
+export declare function InputEnumSchema_$ctor(): InputEnumSchema;
+export declare class InputArraySchema extends DynamicObj {
+    constructor();
+}
+export declare function InputArraySchema_$reflection(): TypeInfo;
+export declare function InputArraySchema_$ctor(): InputArraySchema;
+export declare class SchemaDefRequirementType extends DynamicObj {
+    "init@69": int32;
+    constructor(types: any, definitions: any);
+}
+export declare function SchemaDefRequirementType_$reflection(): TypeInfo;
+export declare function SchemaDefRequirementType_$ctor_541DA560(types: any, definitions: any): SchemaDefRequirementType;
+export declare class SoftwarePackage extends Record implements IEquatable<SoftwarePackage> {
+    readonly Package: string;
+    readonly Version: Option<string[]>;
+    readonly Specs: Option<string[]>;
+    constructor(Package: string, Version: Option<string[]>, Specs: Option<string[]>);
+}
+export declare function SoftwarePackage_$reflection(): TypeInfo;
+//# sourceMappingURL=CWLTypes.d.ts.map

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

@@ -0,0 +1 @@
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