@nfdi4plants/arctrl 3.0.0-beta.14 → 3.0.0-beta.15

package/dist/ts/ts/Conversion/Run.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"Run.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Conversion/Run.ts"],"names":[],"mappings":"AAAA,OAAO,EAAc,QAAQ,EAAE,MAAM,2CAA2C,CAAC;AAQjF,OAAO,EAAE,QAAQ,EAAgB,MAAM,kBAAkB,CAAC;AAI1D,OAAO,EAAE,qBAAqB,EAAE,MAAM,8BAA8B,CAAC;AACrE,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,wBAAwB,CAAC;AAEzD,OAAO,EAAE,SAAS,EAAE,MAAM,yBAAyB,CAAC;AAEpD,OAAO,EAAE,wBAAwB,EAAE,MAAM,6BAA6B,CAAC;AASvE,OAAO,EAAE,MAAM,EAAE,MAAM,qBAAqB,CAAC;AAC7C,OAAO,EAAE,UAAU,EAAE,MAAM,6BAA6B,CAAC;AAWzD,qBAAa,aAAa;;CAGzB;AAED,wBAAgB,yBAAyB,IAAI,QAAQ,CAEpD;AAED;;;;GAIG;AACH,wBAAgB,+CAA+C,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,GAAG,MAAM,CAOrG;AAED,wBAAgB,iDAAiD,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,GAAG,MAAM,CAQvG;AAED,wBAAgB,2CAA2C,CAAC,UAAU,EAAE,qBAAqB,EAAE,aAAa,EAAE,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,OAAO,EAAE,MAAM,GAAG,MAAM,CAwCnK;AAED,wBAAgB,8CAA8C,CAAC,UAAU,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,SAAS,EAAE,KAAK,CAAC,EAAE,OAAO,GAAG,qBAAqB,CAqB/J;AAED,wBAAgB,0DAA0D,CAAC,GAAG,EAAE,MAAM,EAAE,EAAE,CAAC,EAAE,UAAU,GAAG,MAAM,EAAE,CAkDjH;AAED,wBAAgB,uDAAuD,CAAC,kBAAkB,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,SAAS,EAAE,KAAK,CAAC,EAAE,OAAO,GAAG,CAAC,wBAAwB,EAAE,qBAAqB,EAAE,CAAC,CAK9M;AAED,wBAAgB,iCAAiC,CAAC,GAAG,EAAE,MAAM,EAAE,EAAE,CAAC,EAAE,UAAU,GAAG,MAAM,CAYtF;AAED,wBAAgB,oCAAoC,CAAC,GAAG,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,MAAM,CAa9G"}
+{"version":3,"file":"Run.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Conversion/Run.ts"],"names":[],"mappings":"AAAA,OAAO,EAAc,QAAQ,EAAE,MAAM,2CAA2C,CAAC;AAQjF,OAAO,EAAE,QAAQ,EAAgB,MAAM,kBAAkB,CAAC;AAI1D,OAAO,EAAE,qBAAqB,EAAE,MAAM,8BAA8B,CAAC;AACrE,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,wBAAwB,CAAC;AAEzD,OAAO,EAAE,SAAS,EAAE,MAAM,yBAAyB,CAAC;AAEpD,OAAO,EAAE,wBAAwB,EAAE,MAAM,6BAA6B,CAAC;AASvE,OAAO,EAAE,MAAM,EAAE,MAAM,qBAAqB,CAAC;AAC7C,OAAO,EAAE,UAAU,EAAE,MAAM,6BAA6B,CAAC;AAYzD,qBAAa,aAAa;;CAGzB;AAED,wBAAgB,yBAAyB,IAAI,QAAQ,CAEpD;AAED;;;;GAIG;AACH,wBAAgB,+CAA+C,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,GAAG,MAAM,CAOrG;AAED,wBAAgB,iDAAiD,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,GAAG,MAAM,CAQvG;AAED,wBAAgB,2CAA2C,CAAC,UAAU,EAAE,qBAAqB,EAAE,aAAa,EAAE,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,OAAO,EAAE,MAAM,GAAG,MAAM,CAwCnK;AAED,wBAAgB,8CAA8C,CAAC,UAAU,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,SAAS,EAAE,KAAK,CAAC,EAAE,OAAO,GAAG,qBAAqB,CAqB/J;AAED,wBAAgB,0DAA0D,CAAC,GAAG,EAAE,MAAM,EAAE,EAAE,CAAC,EAAE,UAAU,GAAG,MAAM,EAAE,CAkDjH;AAED,wBAAgB,uDAAuD,CAAC,kBAAkB,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,SAAS,EAAE,KAAK,CAAC,EAAE,OAAO,GAAG,CAAC,wBAAwB,EAAE,qBAAqB,EAAE,CAAC,CAK9M;AAED,wBAAgB,iCAAiC,CAAC,GAAG,EAAE,MAAM,EAAE,EAAE,CAAC,EAAE,UAAU,GAAG,MAAM,CAYtF;AAED,wBAAgB,oCAAoC,CAAC,GAAG,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,MAAM,CAmC9G"}

package/dist/ts/ts/Conversion/Run.js

@@ -12,7 +12,7 @@ import { CWLParameterReference } from '../CWL/ParameterReference.js';
 import { LDFormalParameter } from '../ROCrate/LDTypes/FormalParameter.js';
 import { Run_cwlFileNameFromIdentifier } from '../Core/Helper/Identifier.js';
 import { WorkflowConversion_composeWorkflowProtocolFromProcessingUnit_Z3099C0F7, WorkflowConversion_getInputParametersFromProcessingUnit_30922B92, WorkflowConversion_decomposeWorkflowProtocolToProcessingUnit_2664C4B8 } from './Workflow.js';
-import { tryPick, find, exists } from '../../node_modules/@fable-org/fable-library-js/Seq.js';
+import { tryPick, find } from '../../node_modules/@fable-org/fable-library-js/Seq.js';
 import { LDComputationalWorkflow } from '../ROCrate/LDTypes/ComputationalWorkflow.js';
 import { ARCtrl_ArcTables__ArcTables_GetProcesses_5E660E5C, ARCtrl_ArcTables__ArcTables_fromProcesses_Static_Z27F0B586 } from './Table.js';
 import { ArcTables } from '../Core/Table/ArcTables.js';
@@ -26,6 +26,7 @@ import { DatamapConversion_composeFragmentDescriptors_Z892BFC3, DatamapConversio
 import { Datamap } from '../Core/Datamap.js';
 import { AssayConversion_getDataFilesFromProcesses_6BABD1B0 } from './Assay.js';
 import { LDDataset } from '../ROCrate/LDTypes/Dataset.js';
+import { LDWorkflowProtocol } from '../ROCrate/LDTypes/WorkflowProtocol.js';
 
 class RunConversion {
   constructor() {
@@ -128,7 +129,7 @@ function RunConversion_composeWorkflowInvocationFromArcRun_Z8CC08AC(run, fs) {
       }
     }, run.CWLInput);
     if (paramRef == null) {
-      throw new Error(`Could not create workflow invocation for run "${run.Identifier}": Workflow parameter "name" had no assigned value.`);
+      throw new Error(`Could not create workflow invocation for run "${run.Identifier}": Workflow parameter "${name}" had no assigned value.`);
     } else {
       return RunConversion_composeCWLInputValue_70DD9184(value(paramRef), ldI, tupledArg[0], run.Identifier);
     }
@@ -173,7 +174,27 @@ function RunConversion_composeRun_Z8CC08AC(run, fs) {
   return LDDataset.createARCRun(run.Identifier, void 0, unwrap(run.Title), unwrap(run.Description), unwrap(creators), unwrap(dataFiles), unwrap(measurementMethod), unwrap(measurementTechnique), unwrap(variableMeasureds), unwrap(workflowInvocations), unwrap(workflowInvocations), unwrap(comments));
 }
 function RunConversion_decomposeRun_Z6839B9E8(run, graph, context) {
-  const mainWorkflowInvocation = find((wi) => exists((i) => LDFile.tryGetExampleOfWorkAsFormalParameter(i, unwrap(graph), unwrap(context)) != null, LDLabProcess.getObjects(wi, unwrap(graph), unwrap(context))), LDDataset.getAboutsAsWorkflowInvocation(run, unwrap(graph), unwrap(context)));
+  const mainWorkflowInvocation = find((wi) => {
+    let lp;
+    const matchValue = LDLabProcess.tryGetExecutesLabProtocol(wi, unwrap(graph), unwrap(context));
+    let matchResult, lp_1;
+    if (matchValue != null) {
+      if (lp = value(matchValue), LDWorkflowProtocol.validate(lp, unwrap(context))) {
+        matchResult = 0;
+        lp_1 = value(matchValue);
+      } else {
+        matchResult = 1;
+      }
+    } else {
+      matchResult = 1;
+    }
+    switch (matchResult) {
+      case 0:
+        return true;
+      default:
+        return false;
+    }
+  }, LDDataset.getAboutsAsWorkflowInvocation(run, unwrap(graph), unwrap(context)));
   const patternInput = RunConversion_decomposeMainWorkflowInvocation_Z1346FE9D(mainWorkflowInvocation, LDDataset.getIdentifierAsString(run, unwrap(context)), unwrap(context), unwrap(graph));
   const measurementMethod = map((m) => BaseTypes_decomposeDefinedTerm_Z2F770004(m, unwrap(context)), LDDataset.tryGetMeasurementMethodAsDefinedTerm(run, unwrap(graph), unwrap(context)));
   const measurementTechnique = map((m_1) => BaseTypes_decomposeDefinedTerm_Z2F770004(m_1, unwrap(context)), LDDataset.tryGetMeasurementTechniqueAsDefinedTerm(run, unwrap(graph), unwrap(context)));

package/dist/ts/ts/Json/ROCrate/LDNode.d.ts

@@ -2,6 +2,7 @@ import { Decoder$1, IEncodable } from '../../fable_modules/Thoth.Json.Core.0.7.0
 import { LDNode } from '../../ROCrate/LDObject.js';
 export declare function genericEncoder(obj: any): IEncodable;
 export declare function encoder(obj: LDNode): IEncodable;
+export declare const nullDecoder: Decoder$1<void>;
 /**
  * Returns a decoder
  *

package/dist/ts/ts/Json/ROCrate/LDNode.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"LDNode.d.ts","sourceRoot":"","sources":["../../../../../src/ARCtrl/ts/Json/ROCrate/LDNode.ts"],"names":[],"mappings":"AAAA,OAAO,EAA+F,SAAS,EAAE,UAAU,EAAqB,MAAM,uDAAuD,CAAC;AAG9M,OAAO,EAAE,MAAM,EAAkB,MAAM,2BAA2B,CAAC;AAgBnE,wBAAgB,cAAc,CAAC,GAAG,EAAE,GAAG,GAAG,UAAU,CA+DnD;AAED,wBAAgB,OAAO,CAAC,GAAG,EAAE,MAAM,GAAG,UAAU,CA6B/C;AAED;;;;GAIG;AACH,wBAAgB,UAAU,CAAC,YAAY,EAAE,OAAO,GAAG,SAAS,CAAC,GAAG,CAAC,CA0FhE;AAED,eAAO,MAAM,OAAO,EAAE,SAAS,CAAC,MAAM,CAAuE,CAAC;AAE9G,eAAO,MAAM,cAAc,EAAE,SAAS,CAAC,GAAG,CAAqB,CAAC"}
+{"version":3,"file":"LDNode.d.ts","sourceRoot":"","sources":["../../../../../src/ARCtrl/ts/Json/ROCrate/LDNode.ts"],"names":[],"mappings":"AAAA,OAAO,EAA0B,SAAS,EAAuE,UAAU,EAAqB,MAAM,uDAAuD,CAAC;AAG9M,OAAO,EAAE,MAAM,EAAkB,MAAM,2BAA2B,CAAC;AAgBnE,wBAAgB,cAAc,CAAC,GAAG,EAAE,GAAG,GAAG,UAAU,CA+DnD;AAED,wBAAgB,OAAO,CAAC,GAAG,EAAE,MAAM,GAAG,UAAU,CA6B/C;AAED,eAAO,MAAM,WAAW,EAAE,SAAS,CAAC,IAAI,CAIvC,CAAC;AAEF;;;;GAIG;AACH,wBAAgB,UAAU,CAAC,YAAY,EAAE,OAAO,GAAG,SAAS,CAAC,GAAG,CAAC,CAgGhE;AAED,eAAO,MAAM,OAAO,EAAE,SAAS,CAAC,MAAM,CAAuE,CAAC;AAE9G,eAAO,MAAM,cAAc,EAAE,SAAS,CAAC,GAAG,CAAqB,CAAC"}

package/dist/ts/ts/Json/ROCrate/LDNode.js

@@ -1,4 +1,4 @@
-import { ErrorReason$1_BadOneOf, ErrorReason$1_BadPrimitive } from '../../fable_modules/Thoth.Json.Core.0.7.0/Types.fs.js';
+import { ErrorReason$1_BadPrimitive, ErrorReason$1_BadOneOf } from '../../fable_modules/Thoth.Json.Core.0.7.0/Types.fs.js';
 import { dateTime, resizeArrayOrSingleton } from '../Encode.js';
 import { LDValue, LDRef, LDNode } from '../../ROCrate/LDObject.js';
 import { encoder as encoder$1, decoder as decoder$2 } from './LDValue.js';
@@ -8,10 +8,10 @@ import { list } from '../../fable_modules/Thoth.Json.Core.0.7.0/Encode.fs.js';
 import { toList, delay, map, enumerateFromFunctions, append, singleton, empty, collect } from '../../../node_modules/@fable-org/fable-library-js/Seq.js';
 import { encoder as encoder$3, decoder as decoder$1 } from './LDContext.js';
 import { value, unwrap } from '../../../node_modules/@fable-org/fable-library-js/Option.js';
+import { FSharpResult$2_Ok, FSharpResult$2_Error } from '../../../node_modules/@fable-org/fable-library-js/Result.js';
 import { Getters$2_$ctor_Z4BE6C149, string, Getters$2__get_Errors, map as map$1, oneOf, int, decimal, bool } from '../../fable_modules/Thoth.Json.Core.0.7.0/Decode.fs.js';
 import { Decode_resizeArrayOrSingleton, Helpers_prependPath } from '../Decode.js';
 import { isEmpty, length, head, ofArray } from '../../../node_modules/@fable-org/fable-library-js/List.js';
-import { FSharpResult$2_Error, FSharpResult$2_Ok } from '../../../node_modules/@fable-org/fable-library-js/Result.js';
 import { fold } from '../../../node_modules/@fable-org/fable-library-js/Array.js';
 
 function genericEncoder(obj) {
@@ -98,11 +98,16 @@ function encoder(obj) {
     }
   };
 }
+const nullDecoder = {
+  Decode(helpers, value) {
+    return helpers.isNullValue(value) ? FSharpResult$2_Ok(void 0) : FSharpResult$2_Error(["", ErrorReason$1_BadPrimitive("null", value)]);
+  }
+};
 function getDecoder(expectObject) {
   const decode = (expectObject_1) => {
     const decodeObject = {
       Decode(helpers, value$1) {
-        let arg_7, objectArg_3, arg_9, objectArg_4;
+        let arg_7, objectArg_3;
         if (helpers.isObject(value$1)) {
           const getters = Getters$2_$ctor_Z4BE6C149(helpers, value$1);
           const properties = helpers.getProperties(value$1);
@@ -124,7 +129,13 @@ function getDecoder(expectObject) {
             while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
               const property = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
               if (property !== "@id" && property !== "@type" && property !== "@context") {
-                o.SetProperty(property, (arg_9 = decode(false), objectArg_4 = get$.Required, objectArg_4.Field(property, arg_9)));
+                let r;
+                const arg_9 = decode(false);
+                const objectArg_4 = get$.Required;
+                r = objectArg_4.Field(property, arg_9);
+                if (!equals(r, defaultOf())) {
+                  o.SetProperty(property, r);
+                }
               }
             }
           } finally {
@@ -179,7 +190,7 @@ function getDecoder(expectObject) {
     if (expectObject_1) {
       return map$1((value_4) => value_4, decodeObject);
     } else {
-      return oneOf(ofArray([map$1((value_5) => value_5, decoder$2), map$1((value_6) => value_6, decodeObject), map$1((value_7) => value_7, decoder$3), map$1((value_8) => value_8, resizeArray), map$1((value_9) => value_9, string), map$1((value_10) => value_10, int), map$1((value_11) => value_11, decimal), map$1((value_12) => value_12, bool)]));
+      return oneOf(ofArray([map$1((value_5) => value_5, decoder$2), map$1((value_6) => value_6, decodeObject), map$1((value_7) => value_7, decoder$3), map$1((value_8) => value_8, resizeArray), map$1((value_9) => value_9, string), map$1((value_10) => value_10, int), map$1((value_11) => value_11, decimal), map$1((value_12) => value_12, bool), map$1(() => void 0, nullDecoder)]));
     }
   };
   return decode(expectObject);
@@ -187,4 +198,4 @@ function getDecoder(expectObject) {
 const decoder = map$1((value) => value, getDecoder(true));
 const genericDecoder = getDecoder(false);
 
-export { decoder, encoder, genericDecoder, genericEncoder, getDecoder };
+export { decoder, encoder, genericDecoder, genericEncoder, getDecoder, nullDecoder };

package/package.json

@@ -1,7 +1,7 @@
 {
   "type": "module",
   "name": "@nfdi4plants/arctrl",
-  "version": "3.0.0-beta.14",
+  "version": "3.0.0-beta.15",
   "description": "Top level ARC DataModel and API function descriptions.",
   "repository": {
     "type": "git",