@nfdi4plants/arctrl 3.0.0-beta.11 → 3.0.0-beta.13

package/dist/ts/ts/ROCrateIO.js

@@ -1,17 +1,17 @@
 import { class_type } from '../node_modules/@fable-org/fable-library-js/Reflection.js';
 import { LDNode, LDRef } from './ROCrate/LDObject.js';
-import { LDCreativeWork } from './ROCrate/Generic/CreativeWork.js';
+import { LDCreativeWork } from './ROCrate/LDTypes/CreativeWork.js';
 import { value, unwrap, bind } from '../node_modules/@fable-org/fable-library-js/Option.js';
 import { License } from './License.js';
 import { LDContext } from './ROCrate/LDContext.js';
 import { ARCtrl_ArcInvestigation__ArcInvestigation_ToROCrateInvestigation_1695DD5C, ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateInvestigation_Static_Z6839B9E8 } from './Conversion.js';
-import { LDDataset } from './ROCrate/Generic/Dataset.js';
+import { LDDataset } from './ROCrate/LDTypes/Dataset.js';
 import { now } from '../node_modules/@fable-org/fable-library-js/Date.js';
-import { initV1_1, initBioschemasContext } from './ROCrate/ROCrateContext.js';
+import { initV1_2, initBioschemasContext, initV1_1 } from './ROCrate/ROCrateContext.js';
 import { encoder, decoder } from './Json/ROCrate/LDGraph.js';
 import { map } from './fable_modules/Thoth.Json.Core.0.7.0/Decode.fs.js';
 import { ResizeArray_choose } from './Core/Helper/Collections.js';
-import { LDFile } from './ROCrate/Generic/File.js';
+import { LDFile } from './ROCrate/LDTypes/File.js';
 import { exactlyOne } from '../node_modules/@fable-org/fable-library-js/Seq.js';
 import { decoder as decoder$1 } from './Json/ROCrate/LDNode.js';
 
@@ -24,7 +24,7 @@ function ROCrate_$reflection() {
 }
 function ROCrate_get_metadataFileDescriptor() {
   const node = new LDNode("ro-crate-metadata.json", ["http://schema.org/CreativeWork"]);
-  node.SetProperty("http://purl.org/dc/terms/conformsTo", new LDRef("https://w3id.org/ro/crate/1.1"));
+  node.SetProperty("http://purl.org/dc/terms/conformsTo", new LDRef("https://w3id.org/ro/crate/1.2"));
   node.SetProperty("http://schema.org/about", new LDRef("./"));
   return node;
 }
@@ -79,7 +79,7 @@ function ROCrate_encoder_1E8A3F74(isa, license, fs) {
   LDDataset.setSDDatePublishedAsDateTime(isa_1, now());
   LDDataset.setLicenseAsCreativeWork(isa_1, license_1);
   const graph = isa_1.Flatten();
-  const context = new LDContext(void 0, [initV1_1(), initBioschemasContext()]);
+  const context = new LDContext(void 0, [initV1_2(), initBioschemasContext()]);
   graph.SetContext(context);
   graph.AddNode(ROCrate_get_metadataFileDescriptor());
   graph.Compact_InPlace();

package/dist/ts/ts/Spreadsheet/Metadata/Run.js

@@ -38,7 +38,7 @@ function fromString(identifier, title, description, workflowIdentifiers, measure
   const measurementType_2 = Option_fromValueWithDefault(new OntologyAnnotation(), measurementType_1);
   const technologyType_2 = Option_fromValueWithDefault(new OntologyAnnotation(), technologyType_1);
   const technologyPlatform_1 = map(JsonTypes_decomposeTechnologyPlatform, technologyPlatform);
-  return ArcRun.make(identifier_4, title, description, measurementType_2, technologyType_2, technologyPlatform_1, workflowIdentifiers_1, [], void 0, [], comments);
+  return ArcRun.make(identifier_4, title, description, measurementType_2, technologyType_2, technologyPlatform_1, workflowIdentifiers_1, [], void 0, [], void 0, [], comments);
 }
 function fromSparseTable(matrix) {
   let comments;

package/dist/ts/ts/Spreadsheet/Metadata/Workflow.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"Workflow.d.ts","sourceRoot":"","sources":["../../../../../src/ARCtrl/ts/Spreadsheet/Metadata/Workflow.ts"],"names":[],"mappings":"AAAA,OAAO,EAA6C,UAAU,EAAW,MAAM,qCAAqC,CAAC;AACrH,OAAO,EAAsB,MAAM,EAAS,MAAM,uCAAuC,CAAC;AAQ1F,OAAO,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,uBAAuB,CAAC;AAEzD,OAAO,EAA6F,WAAW,EAA+E,MAAM,kBAAkB,CAAC;AACvN,OAAO,EAAE,KAAK,EAAE,MAAM,sCAAsC,CAAC;AAI7D,OAAO,EAAE,WAAW,EAAc,MAAM,qCAAqC,CAAC;AAE9E,eAAO,MAAM,eAAe,eAAe,CAAC;AAE5C,eAAO,MAAM,UAAU,UAAU,CAAC;AAElC,eAAO,MAAM,gBAAgB,gBAAgB,CAAC;AAE9C,eAAO,MAAM,iBAAiB,SAAS,CAAC;AAExC,eAAO,MAAM,4BAA4B,+BAA+B,CAAC;AAEzE,eAAO,MAAM,sBAAsB,yBAAyB,CAAC;AAE7D,eAAO,MAAM,2BAA2B,6BAA6B,CAAC;AAEtE,eAAO,MAAM,QAAQ,QAAQ,CAAC;AAE9B,eAAO,MAAM,YAAY,YAAY,CAAC;AAEtC,eAAO,MAAM,mBAAmB,oBAAoB,CAAC;AAErD,eAAO,MAAM,kCAAkC,qCAAqC,CAAC;AAErF,eAAO,MAAM,4BAA4B,+BAA+B,CAAC;AAEzE,eAAO,MAAM,mBAAmB,oBAAoB,CAAC;AAErD,eAAO,MAAM,mBAAmB,oBAAoB,CAAC;AAErD,eAAO,MAAM,sCAAsC,0CAA0C,CAAC;AAE9F,eAAO,MAAM,gCAAgC,oCAAoC,CAAC;AAElF,eAAO,MAAM,aAAa,cAAc,CAAC;AAEzC,eAAO,MAAM,MAAM,EAAE,UAAU,CAAC,MAAM,CAAoZ,CAAC;AAE3b,wBAAgB,UAAU,CAAC,UAAU,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,WAAW,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,YAAY,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,+BAA+B,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,yBAAyB,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,sBAAsB,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,GAAG,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,cAAc,EAAE,MAAM,EAAE,6BAA6B,EAAE,MAAM,EAAE,uBAAuB,EAAE,MAAM,EAAE,cAAc,EAAE,MAAM,EAAE,cAAc,EAAE,MAAM,EAAE,iCAAiC,EAAE,MAAM,EAAE,2BAA2B,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,QAAQ,EAAE,QAAQ,EAAE,GAAG,WAAW,CAiCtlB;AAED,wBAAgB,eAAe,CAAC,MAAM,EAAE,WAAW,GAAG,WAAW,CAGhE;AAED,wBAAgB,aAAa,CAAC,QAAQ,EAAE,WAAW,GAAG,WAAW,CAqChE;AAED,wBAAgB,QAAQ,CAAC,UAAU,EAAE,KAAK,EAAE,IAAI,EAAE,WAAW,CAAC,QAAQ,CAAC,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,KAAK,EAAE,UAAU,CAAC,MAAM,CAAC,EAAE,WAAW,CAAC,CAGlJ;AAED,wBAAgB,MAAM,CAAC,QAAQ,EAAE,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC,CAAC,CAEjF"}
+{"version":3,"file":"Workflow.d.ts","sourceRoot":"","sources":["../../../../../src/ARCtrl/ts/Spreadsheet/Metadata/Workflow.ts"],"names":[],"mappings":"AAAA,OAAO,EAA6C,UAAU,EAAW,MAAM,qCAAqC,CAAC;AACrH,OAAO,EAAsB,MAAM,EAAS,MAAM,uCAAuC,CAAC;AAO1F,OAAO,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,uBAAuB,CAAC;AAEzD,OAAO,EAA6F,WAAW,EAA+E,MAAM,kBAAkB,CAAC;AACvN,OAAO,EAAE,KAAK,EAAE,MAAM,sCAAsC,CAAC;AAI7D,OAAO,EAAE,WAAW,EAAc,MAAM,qCAAqC,CAAC;AAE9E,eAAO,MAAM,eAAe,eAAe,CAAC;AAE5C,eAAO,MAAM,UAAU,UAAU,CAAC;AAElC,eAAO,MAAM,gBAAgB,gBAAgB,CAAC;AAE9C,eAAO,MAAM,iBAAiB,SAAS,CAAC;AAExC,eAAO,MAAM,4BAA4B,+BAA+B,CAAC;AAEzE,eAAO,MAAM,sBAAsB,yBAAyB,CAAC;AAE7D,eAAO,MAAM,2BAA2B,6BAA6B,CAAC;AAEtE,eAAO,MAAM,QAAQ,QAAQ,CAAC;AAE9B,eAAO,MAAM,YAAY,YAAY,CAAC;AAEtC,eAAO,MAAM,mBAAmB,oBAAoB,CAAC;AAErD,eAAO,MAAM,kCAAkC,qCAAqC,CAAC;AAErF,eAAO,MAAM,4BAA4B,+BAA+B,CAAC;AAEzE,eAAO,MAAM,mBAAmB,oBAAoB,CAAC;AAErD,eAAO,MAAM,mBAAmB,oBAAoB,CAAC;AAErD,eAAO,MAAM,sCAAsC,0CAA0C,CAAC;AAE9F,eAAO,MAAM,gCAAgC,oCAAoC,CAAC;AAElF,eAAO,MAAM,aAAa,cAAc,CAAC;AAEzC,eAAO,MAAM,MAAM,EAAE,UAAU,CAAC,MAAM,CAAoZ,CAAC;AAE3b,wBAAgB,UAAU,CAAC,UAAU,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,WAAW,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,YAAY,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,+BAA+B,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,yBAAyB,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,sBAAsB,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,GAAG,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,cAAc,EAAE,MAAM,EAAE,6BAA6B,EAAE,MAAM,EAAE,uBAAuB,EAAE,MAAM,EAAE,cAAc,EAAE,MAAM,EAAE,cAAc,EAAE,MAAM,EAAE,iCAAiC,EAAE,MAAM,EAAE,2BAA2B,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,QAAQ,EAAE,QAAQ,EAAE,GAAG,WAAW,CAiCtlB;AAED,wBAAgB,eAAe,CAAC,MAAM,EAAE,WAAW,GAAG,WAAW,CAGhE;AAED,wBAAgB,aAAa,CAAC,QAAQ,EAAE,WAAW,GAAG,WAAW,CAqChE;AAED,wBAAgB,QAAQ,CAAC,UAAU,EAAE,KAAK,EAAE,IAAI,EAAE,WAAW,CAAC,QAAQ,CAAC,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,KAAK,EAAE,UAAU,CAAC,MAAM,CAAC,EAAE,WAAW,CAAC,CAGlJ;AAED,wBAAgB,MAAM,CAAC,QAAQ,EAAE,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC,CAAC,CAEjF"}

package/dist/ts/ts/Spreadsheet/Metadata/Workflow.js

@@ -3,7 +3,7 @@ import { value, unwrap, defaultArg } from '../../../node_modules/@fable-org/fabl
 import { map } from '../../../node_modules/@fable-org/fable-library-js/Seq.js';
 import { OntologyAnnotation } from '../../Core/OntologyAnnotation.js';
 import { Option_fromValueWithDefault, ResizeArray_iter } from '../../Core/Helper/Collections.js';
-import { ProtocolParameter_fromAggregatedStrings, Component_fromAggregatedStrings, ProtocolParameter_toAggregatedStrings, Component_toAggregatedStrings } from './Conversions.js';
+import { OntologyAnnotation_fromAggregatedStrings, Component_fromAggregatedStrings, OntologyAnnotation_toAggregatedStrings, Component_toAggregatedStrings } from './Conversions.js';
 import { createMissingIdentifier, Workflow_tryIdentifierFromFileName, Workflow_fileNameFromIdentifier } from '../../Core/Helper/Identifier.js';
 import { ArcWorkflow } from '../../Core/ArcTypes.js';
 import { Comment_fromString, Comment_toString } from './Comment.js';
@@ -44,7 +44,7 @@ function fromString(identifier, title, description, workflowType, workflowTypeTe
   const v = OntologyAnnotation.create(unwrap(workflowType), unwrap(workflowTypeTermSourceREF), unwrap(workflowTypeTermAccessionNumber));
   workflowType_1 = Option_fromValueWithDefault(new OntologyAnnotation(), v);
   let parameters;
-  const collection_1 = ProtocolParameter_fromAggregatedStrings(";", parametersName, parametersTermSourceREF, parametersTermAccessionNumber);
+  const collection_1 = OntologyAnnotation_fromAggregatedStrings(";", parametersName, parametersTermSourceREF, parametersTermAccessionNumber);
   parameters = Array.from(collection_1);
   let components;
   const collection_2 = Component_fromAggregatedStrings(";", componentsName, componentsType, componentsTypeTermSourceREF, componentsTypeTermAccessionNumber);
@@ -60,7 +60,7 @@ function fromString(identifier, title, description, workflowType, workflowTypeTe
   } else {
     identifier_4 = value(identifier);
   }
-  return ArcWorkflow.make(identifier_4, title, description, workflowType_1, uri, version, subworkflowIdentifiers_2, parameters, components, void 0, [], comments);
+  return ArcWorkflow.make(identifier_4, title, description, workflowType_1, uri, version, subworkflowIdentifiers_2, parameters, components, void 0, [], void 0, comments);
 }
 function fromSparseTable(matrix) {
   const comments = map$1((k) => Comment_fromString(k, SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [k, 0])), matrix.CommentKeys);
@@ -73,7 +73,7 @@ function toSparseTable(workflow) {
   let wt;
   const tt = defaultArg(workflow.WorkflowType, new OntologyAnnotation());
   wt = OntologyAnnotation.toStringObject(tt, true);
-  const pAgg = ProtocolParameter_toAggregatedStrings(";", ofSeq(workflow.Parameters));
+  const pAgg = OntologyAnnotation_toAggregatedStrings(";", Array.from(workflow.Parameters));
   const cAgg = Component_toAggregatedStrings(";", ofSeq(workflow.Components));
   const subWorkflowsAgg = join(";", workflow.SubWorkflowIdentifiers);
   addToDict(matrix.Matrix, [identifierLabel, 1], patternInput[0]);

package/dist/ts/ts/fable_modules/DynamicObj.7.1.0/DynObj.fs.js

@@ -0,0 +1,109 @@
+import { DynamicObj, CopyUtils_tryDeepCopyObj_75B3D832 } from './DynamicObj.fs.js';
+import { getEnumerator, disposeSafe } from '../../../node_modules/@fable-org/fable-library-js/Util.js';
+import { isEmpty, tail, head, cons, ofSeq as ofSeq$1, empty, reverse } from '../../../node_modules/@fable-org/fable-library-js/List.js';
+import { value } from '../../../node_modules/@fable-org/fable-library-js/Option.js';
+import { join, toConsole, printf } from '../../../node_modules/@fable-org/fable-library-js/String.js';
+import { toList, delay, map } from '../../../node_modules/@fable-org/fable-library-js/Seq.js';
+import { rangeDouble } from '../../../node_modules/@fable-org/fable-library-js/Range.js';
+
+function ofDict(dynamicProperties) {
+  return DynamicObj.ofDict(dynamicProperties);
+}
+function ofSeq(dynamicProperties) {
+  const dynamicProperties_1 = new Map(new Map(dynamicProperties));
+  return DynamicObj.ofDict(dynamicProperties_1);
+}
+function ofList(dynamicProperties) {
+  return ofSeq(dynamicProperties);
+}
+function ofArray(dynamicProperties) {
+  return ofSeq(dynamicProperties);
+}
+function combine(first, second) {
+  const enumerator = getEnumerator(second.GetProperties(true));
+  try {
+    while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
+      const kv = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
+      const matchValue = kv[1];
+      if (matchValue instanceof DynamicObj) {
+        const valueS = matchValue;
+        const matchValue_1 = first.TryGetPropertyValue(kv[0]);
+        if (matchValue_1 == null) {
+          first.SetProperty(kv[0], valueS);
+        } else {
+          const tmp = combine(value(matchValue_1), valueS);
+          first.SetProperty(kv[0], tmp);
+        }
+      } else {
+        first.SetProperty(kv[0], kv[1]);
+      }
+    }
+  } finally {
+    disposeSafe(enumerator);
+  }
+  return first;
+}
+function setProperty(propertyName, propertyValue, dynObj) {
+  dynObj.SetProperty(propertyName, propertyValue);
+}
+function setOptionalProperty(propertyName, propertyValue, dynObj) {
+  if (propertyValue == null) {
+  } else {
+    setProperty(propertyName, value(propertyValue), dynObj);
+  }
+}
+function setOptionalPropertyBy(propertyName, propertyValue, mapping, dynObj) {
+  if (propertyValue == null) {
+  } else {
+    setProperty(propertyName, mapping(value(propertyValue)), dynObj);
+  }
+}
+function tryGetPropertyValue(propertyName, dynObj) {
+  return dynObj.TryGetPropertyValue(propertyName);
+}
+function removeProperty(propertyName, dynObj) {
+  dynObj.RemoveProperty(propertyName);
+}
+function format(dynObj) {
+  const loop = (object_mut, indentationLevel_mut, membersLeft_mut, acc_mut) => {
+    loop:
+      while (true) {
+        const object = object_mut, indentationLevel = indentationLevel_mut, membersLeft = membersLeft_mut, acc = acc_mut;
+        const indent = join("", toList(delay(() => map((i) => "    ", rangeDouble(0, 1, indentationLevel - 1)))));
+        if (!isEmpty(membersLeft)) {
+          const rest = tail(membersLeft);
+          const m = head(membersLeft);
+          const item = m.GetValue(object);
+          const dynamicIndicator = m.IsDynamic ? "?" : "";
+          const name = m.Name;
+          if (item instanceof DynamicObj) {
+            const item_1 = item;
+            object_mut = object;
+            indentationLevel_mut = indentationLevel;
+            membersLeft_mut = rest;
+            acc_mut = cons(`${indent}${dynamicIndicator}${name}:${"\n"}${loop(item_1, indentationLevel + 1, ofSeq$1(item_1.GetPropertyHelpers(true)), empty())}`, acc);
+            continue loop;
+          } else {
+            object_mut = object;
+            indentationLevel_mut = indentationLevel;
+            membersLeft_mut = rest;
+            acc_mut = cons(`${indent}${dynamicIndicator}${name}: ${item}`, acc);
+            continue loop;
+          }
+        } else {
+          return join("\n", reverse(acc));
+        }
+        break;
+      }
+  };
+  return loop(dynObj, 0, ofSeq$1(dynObj.GetPropertyHelpers(true)), empty());
+}
+function print(dynObj) {
+  const arg = format(dynObj);
+  toConsole(printf("%s"))(arg);
+}
+function tryDeepCopyObj(includeInstanceProperties, o) {
+  return CopyUtils_tryDeepCopyObj_75B3D832(o, includeInstanceProperties);
+}
+
+export { combine, format, ofArray, ofDict, ofList, ofSeq, print, removeProperty, setOptionalProperty, setOptionalPropertyBy, setProperty, tryDeepCopyObj, tryGetPropertyValue };

package/package.json

@@ -1,7 +1,7 @@
 {
   "type": "module",
   "name": "@nfdi4plants/arctrl",
-  "version": "3.0.0-beta.11",
+  "version": "3.0.0-beta.13",
   "description": "Top level ARC DataModel and API function descriptions.",
   "repository": {
     "type": "git",

package/dist/ts/ts/ROCrate/Generic/Dataset.d.ts.map

@@ -1 +0,0 @@
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package/dist/ts/ts/ROCrate/Generic/File.d.ts.map

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package/dist/ts/ts/ROCrate/Generic/LabProcess.d.ts.map

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package/dist/ts/ts/ROCrate/Generic/LabProtocol.d.ts.map

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package/dist/ts/ts/ROCrate/Generic/PropertyValue.d.ts.map

@@ -1 +0,0 @@
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