@nfdi4plants/arctrl 3.0.0-beta.8 → 3.0.0

package/dist/ts/ts/Contract/Datamap.js

@@ -4,8 +4,7 @@ import { defaultOf, safeHash } from '../../node_modules/@fable-org/fable-library
 import { value } from '../../node_modules/@fable-org/fable-library-js/Option.js';
 import { Assay_datamapFileNameFromIdentifier, Study_datamapFileNameFromIdentifier, Workflow_datamapFileNameFromIdentifier, Run_datamapFileNameFromIdentifier } from '../Core/Helper/Identifier.js';
 import { Contract } from './Contract.js';
-import { toFsWorkbook, fromFsWorkbook } from '../Spreadsheet/DataMap.js';
-import { DataMap__set_StaticHash_Z524259A4 } from '../Core/DataMap.js';
+import { toFsWorkbook, fromFsWorkbook } from '../Spreadsheet/Datamap.js';
 
 function $007CDatamapPath$007C_$007C(input) {
   let matchResult;
@@ -14,19 +13,31 @@ function $007CDatamapPath$007C_$007C(input) {
       if (item(2, input) === "isa.datamap.xlsx") {
         matchResult = 0;
       } else {
-        matchResult = 2;
+        matchResult = 4;
       }
     } else if (item(0, input) === "studies") {
       if (item(2, input) === "isa.datamap.xlsx") {
         matchResult = 1;
       } else {
+        matchResult = 4;
+      }
+    } else if (item(0, input) === "workflows") {
+      if (item(2, input) === "isa.datamap.xlsx") {
         matchResult = 2;
+      } else {
+        matchResult = 4;
+      }
+    } else if (item(0, input) === "runs") {
+      if (item(2, input) === "isa.datamap.xlsx") {
+        matchResult = 3;
+      } else {
+        matchResult = 4;
       }
     } else {
-      matchResult = 2;
+      matchResult = 4;
     }
   } else {
-    matchResult = 2;
+    matchResult = 4;
   }
   switch (matchResult) {
     case 0: {
@@ -37,29 +48,37 @@ function $007CDatamapPath$007C_$007C(input) {
       const anyStudyName = item(1, input);
       return combineMany(input);
     }
+    case 2: {
+      const anyWorkflowName = item(1, input);
+      return combineMany(input);
+    }
+    case 3: {
+      const anyRunName = item(1, input);
+      return combineMany(input);
+    }
     default:
       return void 0;
   }
 }
-function ARCtrl_DataMap__DataMap_ToCreateContractForAssay_Z721C83C5(this$, assayIdentifier) {
+function ARCtrl_Datamap__Datamap_ToCreateContractForAssay_Z721C83C5(this$, assayIdentifier) {
   const path = Assay_datamapFileNameFromIdentifier(assayIdentifier);
   return Contract.createCreate(path, "ISA_Datamap", toFsWorkbook(this$));
 }
-function ARCtrl_DataMap__DataMap_ToUpdateContractForAssay_Z721C83C5(this$, assayIdentifier) {
+function ARCtrl_Datamap__Datamap_ToUpdateContractForAssay_Z721C83C5(this$, assayIdentifier) {
   const path = Assay_datamapFileNameFromIdentifier(assayIdentifier);
   return Contract.createUpdate(path, "ISA_Datamap", toFsWorkbook(this$));
 }
-function ARCtrl_DataMap__DataMap_ToDeleteContractForAssay_Z721C83C5(this$, assayIdentifier) {
+function ARCtrl_Datamap__Datamap_ToDeleteContractForAssay_Z721C83C5(this$, assayIdentifier) {
   const path = Assay_datamapFileNameFromIdentifier(assayIdentifier);
   return Contract.createDelete(path);
 }
-function ARCtrl_DataMap__DataMap_toDeleteContractForAssay_Static_Z721C83C5(assayIdentifier) {
-  return (dataMap) => ARCtrl_DataMap__DataMap_ToDeleteContractForAssay_Z721C83C5(dataMap, assayIdentifier);
+function ARCtrl_Datamap__Datamap_toDeleteContractForAssay_Static_Z721C83C5(assayIdentifier) {
+  return (datamap) => ARCtrl_Datamap__Datamap_ToDeleteContractForAssay_Z721C83C5(datamap, assayIdentifier);
 }
-function ARCtrl_DataMap__DataMap_toUpdateContractForAssay_Static_Z721C83C5(assayIdentifier) {
-  return (dataMap) => ARCtrl_DataMap__DataMap_ToUpdateContractForAssay_Z721C83C5(dataMap, assayIdentifier);
+function ARCtrl_Datamap__Datamap_toUpdateContractForAssay_Static_Z721C83C5(assayIdentifier) {
+  return (datamap) => ARCtrl_Datamap__Datamap_ToUpdateContractForAssay_Z721C83C5(datamap, assayIdentifier);
 }
-function ARCtrl_DataMap__DataMap_tryFromReadContractForAssay_Static(assayIdentifier, c) {
+function ARCtrl_Datamap__Datamap_tryFromReadContractForAssay_Static(assayIdentifier, c) {
   let fsworkbook;
   const path = Assay_datamapFileNameFromIdentifier(assayIdentifier);
   let matchResult, fsworkbook_1, p_1;
@@ -89,32 +108,32 @@ function ARCtrl_DataMap__DataMap_tryFromReadContractForAssay_Static(assayIdentif
   switch (matchResult) {
     case 0: {
       const dm = fromFsWorkbook(fsworkbook_1);
-      DataMap__set_StaticHash_Z524259A4(dm, safeHash(dm));
+      dm.StaticHash = safeHash(dm) | 0;
       return dm;
     }
     default:
       return void 0;
   }
 }
-function ARCtrl_DataMap__DataMap_ToCreateContractForStudy_Z721C83C5(this$, studyIdentifier) {
+function ARCtrl_Datamap__Datamap_ToCreateContractForStudy_Z721C83C5(this$, studyIdentifier) {
   const path = Study_datamapFileNameFromIdentifier(studyIdentifier);
   return Contract.createCreate(path, "ISA_Datamap", toFsWorkbook(this$));
 }
-function ARCtrl_DataMap__DataMap_ToUpdateContractForStudy_Z721C83C5(this$, studyIdentifier) {
+function ARCtrl_Datamap__Datamap_ToUpdateContractForStudy_Z721C83C5(this$, studyIdentifier) {
   const path = Study_datamapFileNameFromIdentifier(studyIdentifier);
   return Contract.createUpdate(path, "ISA_Datamap", toFsWorkbook(this$));
 }
-function ARCtrl_DataMap__DataMap_ToDeleteContractForStudy_Z721C83C5(this$, studyIdentifier) {
+function ARCtrl_Datamap__Datamap_ToDeleteContractForStudy_Z721C83C5(this$, studyIdentifier) {
   const path = Study_datamapFileNameFromIdentifier(studyIdentifier);
   return Contract.createDelete(path);
 }
-function ARCtrl_DataMap__DataMap_toDeleteContractForStudy_Static_Z721C83C5(studyIdentifier) {
-  return (dataMap) => ARCtrl_DataMap__DataMap_ToDeleteContractForStudy_Z721C83C5(dataMap, studyIdentifier);
+function ARCtrl_Datamap__Datamap_toDeleteContractForStudy_Static_Z721C83C5(studyIdentifier) {
+  return (datamap) => ARCtrl_Datamap__Datamap_ToDeleteContractForStudy_Z721C83C5(datamap, studyIdentifier);
 }
-function ARCtrl_DataMap__DataMap_toUpdateContractForStudy_Static_Z721C83C5(studyIdentifier) {
-  return (dataMap) => ARCtrl_DataMap__DataMap_ToUpdateContractForStudy_Z721C83C5(dataMap, studyIdentifier);
+function ARCtrl_Datamap__Datamap_toUpdateContractForStudy_Static_Z721C83C5(studyIdentifier) {
+  return (datamap) => ARCtrl_Datamap__Datamap_ToUpdateContractForStudy_Z721C83C5(datamap, studyIdentifier);
 }
-function ARCtrl_DataMap__DataMap_tryFromReadContractForStudy_Static(studyIdentifier, c) {
+function ARCtrl_Datamap__Datamap_tryFromReadContractForStudy_Static(studyIdentifier, c) {
   let fsworkbook;
   const path = Study_datamapFileNameFromIdentifier(studyIdentifier);
   let matchResult, fsworkbook_1, p_1;
@@ -144,32 +163,32 @@ function ARCtrl_DataMap__DataMap_tryFromReadContractForStudy_Static(studyIdentif
   switch (matchResult) {
     case 0: {
       const dm = fromFsWorkbook(fsworkbook_1);
-      DataMap__set_StaticHash_Z524259A4(dm, safeHash(dm));
+      dm.StaticHash = safeHash(dm) | 0;
       return dm;
     }
     default:
       return void 0;
   }
 }
-function ARCtrl_DataMap__DataMap_ToCreateContractForWorkflow_Z721C83C5(this$, workflowIdentifier) {
+function ARCtrl_Datamap__Datamap_ToCreateContractForWorkflow_Z721C83C5(this$, workflowIdentifier) {
   const path = Workflow_datamapFileNameFromIdentifier(workflowIdentifier);
   return Contract.createCreate(path, "ISA_Datamap", toFsWorkbook(this$));
 }
-function ARCtrl_DataMap__DataMap_ToUpdateContractForWorkflow_Z721C83C5(this$, workflowIdentifier) {
+function ARCtrl_Datamap__Datamap_ToUpdateContractForWorkflow_Z721C83C5(this$, workflowIdentifier) {
   const path = Workflow_datamapFileNameFromIdentifier(workflowIdentifier);
   return Contract.createUpdate(path, "ISA_Datamap", toFsWorkbook(this$));
 }
-function ARCtrl_DataMap__DataMap_ToDeleteContractForWorkflow_Z721C83C5(this$, workflowIdentifier) {
+function ARCtrl_Datamap__Datamap_ToDeleteContractForWorkflow_Z721C83C5(this$, workflowIdentifier) {
   const path = Workflow_datamapFileNameFromIdentifier(workflowIdentifier);
   return Contract.createDelete(path);
 }
-function ARCtrl_DataMap__DataMap_toDeleteContractForWorkflow_Static_Z721C83C5(workflowIdentifier) {
-  return (dataMap) => ARCtrl_DataMap__DataMap_ToDeleteContractForWorkflow_Z721C83C5(dataMap, workflowIdentifier);
+function ARCtrl_Datamap__Datamap_toDeleteContractForWorkflow_Static_Z721C83C5(workflowIdentifier) {
+  return (datamap) => ARCtrl_Datamap__Datamap_ToDeleteContractForWorkflow_Z721C83C5(datamap, workflowIdentifier);
 }
-function ARCtrl_DataMap__DataMap_toUpdateContractForWorkflow_Static_Z721C83C5(workflowIdentifier) {
-  return (dataMap) => ARCtrl_DataMap__DataMap_ToUpdateContractForWorkflow_Z721C83C5(dataMap, workflowIdentifier);
+function ARCtrl_Datamap__Datamap_toUpdateContractForWorkflow_Static_Z721C83C5(workflowIdentifier) {
+  return (datamap) => ARCtrl_Datamap__Datamap_ToUpdateContractForWorkflow_Z721C83C5(datamap, workflowIdentifier);
 }
-function ARCtrl_DataMap__DataMap_tryFromReadContractForWorkflow_Static(workflowIdentifier, c) {
+function ARCtrl_Datamap__Datamap_tryFromReadContractForWorkflow_Static(workflowIdentifier, c) {
   let fsworkbook;
   const path = Workflow_datamapFileNameFromIdentifier(workflowIdentifier);
   let matchResult, fsworkbook_1, p_1;
@@ -199,32 +218,32 @@ function ARCtrl_DataMap__DataMap_tryFromReadContractForWorkflow_Static(workflowI
   switch (matchResult) {
     case 0: {
       const dm = fromFsWorkbook(fsworkbook_1);
-      DataMap__set_StaticHash_Z524259A4(dm, safeHash(dm));
+      dm.StaticHash = safeHash(dm) | 0;
       return dm;
     }
     default:
       return void 0;
   }
 }
-function ARCtrl_DataMap__DataMap_ToCreateContractForRun_Z721C83C5(this$, runIdentifier) {
+function ARCtrl_Datamap__Datamap_ToCreateContractForRun_Z721C83C5(this$, runIdentifier) {
   const path = Run_datamapFileNameFromIdentifier(runIdentifier);
   return Contract.createCreate(path, "ISA_Datamap", toFsWorkbook(this$));
 }
-function ARCtrl_DataMap__DataMap_ToUpdateContractForRun_Z721C83C5(this$, runIdentifier) {
+function ARCtrl_Datamap__Datamap_ToUpdateContractForRun_Z721C83C5(this$, runIdentifier) {
   const path = Run_datamapFileNameFromIdentifier(runIdentifier);
   return Contract.createUpdate(path, "ISA_Datamap", toFsWorkbook(this$));
 }
-function ARCtrl_DataMap__DataMap_ToDeleteContractForRun_Z721C83C5(this$, runIdentifier) {
+function ARCtrl_Datamap__Datamap_ToDeleteContractForRun_Z721C83C5(this$, runIdentifier) {
   const path = Run_datamapFileNameFromIdentifier(runIdentifier);
   return Contract.createDelete(path);
 }
-function ARCtrl_DataMap__DataMap_toDeleteContractForRun_Static_Z721C83C5(runIdentifier) {
-  return (dataMap) => ARCtrl_DataMap__DataMap_ToDeleteContractForRun_Z721C83C5(dataMap, runIdentifier);
+function ARCtrl_Datamap__Datamap_toDeleteContractForRun_Static_Z721C83C5(runIdentifier) {
+  return (datamap) => ARCtrl_Datamap__Datamap_ToDeleteContractForRun_Z721C83C5(datamap, runIdentifier);
 }
-function ARCtrl_DataMap__DataMap_toUpdateContractForRun_Static_Z721C83C5(runIdentifier) {
-  return (dataMap) => ARCtrl_DataMap__DataMap_ToUpdateContractForRun_Z721C83C5(dataMap, runIdentifier);
+function ARCtrl_Datamap__Datamap_toUpdateContractForRun_Static_Z721C83C5(runIdentifier) {
+  return (datamap) => ARCtrl_Datamap__Datamap_ToUpdateContractForRun_Z721C83C5(datamap, runIdentifier);
 }
-function ARCtrl_DataMap__DataMap_tryFromReadContractForRun_Static(runIdentifier, c) {
+function ARCtrl_Datamap__Datamap_tryFromReadContractForRun_Static(runIdentifier, c) {
   let fsworkbook;
   const path = Run_datamapFileNameFromIdentifier(runIdentifier);
   let matchResult, fsworkbook_1, p_1;
@@ -254,7 +273,7 @@ function ARCtrl_DataMap__DataMap_tryFromReadContractForRun_Static(runIdentifier,
   switch (matchResult) {
     case 0: {
       const dm = fromFsWorkbook(fsworkbook_1);
-      DataMap__set_StaticHash_Z524259A4(dm, safeHash(dm));
+      dm.StaticHash = safeHash(dm) | 0;
       return dm;
     }
     default:
@@ -262,4 +281,4 @@ function ARCtrl_DataMap__DataMap_tryFromReadContractForRun_Static(runIdentifier,
   }
 }
 
-export { $007CDatamapPath$007C_$007C, ARCtrl_DataMap__DataMap_ToCreateContractForAssay_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForRun_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForStudy_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForWorkflow_Z721C83C5, ARCtrl_DataMap__DataMap_ToDeleteContractForAssay_Z721C83C5, ARCtrl_DataMap__DataMap_ToDeleteContractForRun_Z721C83C5, ARCtrl_DataMap__DataMap_ToDeleteContractForStudy_Z721C83C5, ARCtrl_DataMap__DataMap_ToDeleteContractForWorkflow_Z721C83C5, ARCtrl_DataMap__DataMap_ToUpdateContractForAssay_Z721C83C5, ARCtrl_DataMap__DataMap_ToUpdateContractForRun_Z721C83C5, ARCtrl_DataMap__DataMap_ToUpdateContractForStudy_Z721C83C5, ARCtrl_DataMap__DataMap_ToUpdateContractForWorkflow_Z721C83C5, ARCtrl_DataMap__DataMap_toDeleteContractForAssay_Static_Z721C83C5, ARCtrl_DataMap__DataMap_toDeleteContractForRun_Static_Z721C83C5, ARCtrl_DataMap__DataMap_toDeleteContractForStudy_Static_Z721C83C5, ARCtrl_DataMap__DataMap_toDeleteContractForWorkflow_Static_Z721C83C5, ARCtrl_DataMap__DataMap_toUpdateContractForAssay_Static_Z721C83C5, ARCtrl_DataMap__DataMap_toUpdateContractForRun_Static_Z721C83C5, ARCtrl_DataMap__DataMap_toUpdateContractForStudy_Static_Z721C83C5, ARCtrl_DataMap__DataMap_toUpdateContractForWorkflow_Static_Z721C83C5, ARCtrl_DataMap__DataMap_tryFromReadContractForAssay_Static, ARCtrl_DataMap__DataMap_tryFromReadContractForRun_Static, ARCtrl_DataMap__DataMap_tryFromReadContractForStudy_Static, ARCtrl_DataMap__DataMap_tryFromReadContractForWorkflow_Static };
+export { $007CDatamapPath$007C_$007C, ARCtrl_Datamap__Datamap_ToCreateContractForAssay_Z721C83C5, ARCtrl_Datamap__Datamap_ToCreateContractForRun_Z721C83C5, ARCtrl_Datamap__Datamap_ToCreateContractForStudy_Z721C83C5, ARCtrl_Datamap__Datamap_ToCreateContractForWorkflow_Z721C83C5, ARCtrl_Datamap__Datamap_ToDeleteContractForAssay_Z721C83C5, ARCtrl_Datamap__Datamap_ToDeleteContractForRun_Z721C83C5, ARCtrl_Datamap__Datamap_ToDeleteContractForStudy_Z721C83C5, ARCtrl_Datamap__Datamap_ToDeleteContractForWorkflow_Z721C83C5, ARCtrl_Datamap__Datamap_ToUpdateContractForAssay_Z721C83C5, ARCtrl_Datamap__Datamap_ToUpdateContractForRun_Z721C83C5, ARCtrl_Datamap__Datamap_ToUpdateContractForStudy_Z721C83C5, ARCtrl_Datamap__Datamap_ToUpdateContractForWorkflow_Z721C83C5, ARCtrl_Datamap__Datamap_toDeleteContractForAssay_Static_Z721C83C5, ARCtrl_Datamap__Datamap_toDeleteContractForRun_Static_Z721C83C5, ARCtrl_Datamap__Datamap_toDeleteContractForStudy_Static_Z721C83C5, ARCtrl_Datamap__Datamap_toDeleteContractForWorkflow_Static_Z721C83C5, ARCtrl_Datamap__Datamap_toUpdateContractForAssay_Static_Z721C83C5, ARCtrl_Datamap__Datamap_toUpdateContractForRun_Static_Z721C83C5, ARCtrl_Datamap__Datamap_toUpdateContractForStudy_Static_Z721C83C5, ARCtrl_Datamap__Datamap_toUpdateContractForWorkflow_Static_Z721C83C5, ARCtrl_Datamap__Datamap_tryFromReadContractForAssay_Static, ARCtrl_Datamap__Datamap_tryFromReadContractForRun_Static, ARCtrl_Datamap__Datamap_tryFromReadContractForStudy_Static, ARCtrl_Datamap__Datamap_tryFromReadContractForWorkflow_Static };

package/dist/ts/ts/ContractIO/ContractIO.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"ContractIO.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/ContractIO/ContractIO.ts"],"names":[],"mappings":"AAEA,OAAO,EAAqB,qBAAqB,EAAwB,MAAM,uCAAuC,CAAC;AACvH,OAAO,EAAoC,QAAQ,EAAE,MAAM,yBAAyB,CAAC;AAWrF,wBAAgB,wBAAwB,CAAC,QAAQ,EAAE,MAAM,EAAE,CAAC,EAAE,QAAQ,GAAG,OAAO,CAAC,qBAAqB,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC,CAkDxH;AAED,wBAAgB,4BAA4B,CAAC,SAAS,EAAE,CAAC,CAAC,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,QAAQ,KAAK,OAAO,CAAC,qBAAqB,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC,CAAC,EAAE,QAAQ,EAAE,MAAM,EAAE,EAAE,EAAE,QAAQ,EAAE,GAAG,OAAO,CAAC,qBAAqB,CAAC,QAAQ,EAAE,EAAE,MAAM,EAAE,CAAC,CAAC,CA+BpO;AAED,wBAAgB,yBAAyB,CAAC,QAAQ,EAAE,MAAM,EAAE,CAAC,EAAE,QAAQ,GAAG,OAAO,CAAC,qBAAqB,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC,CAwBzH;AAED,wBAAgB,0BAA0B,CAAC,QAAQ,EAAE,MAAM,EAAE,CAAC,EAAE,QAAQ,GAAG,OAAO,CAAC,qBAAqB,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC,CAwB1H;AAED,wBAAgB,2BAA2B,CAAC,QAAQ,EAAE,MAAM,EAAE,CAAC,EAAE,QAAQ,GAAG,OAAO,CAAC,qBAAqB,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC,CAwC3H;AAED,wBAAgB,2BAA2B,CAAC,QAAQ,EAAE,MAAM,EAAE,CAAC,EAAE,QAAQ,GAAG,OAAO,CAAC,qBAAqB,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC,CAW3H;AAED,wBAAgB,gBAAgB,CAAC,QAAQ,EAAE,MAAM,EAAE,CAAC,EAAE,QAAQ,GAAG,OAAO,CAAC,qBAAqB,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC,CAQhH;AAED,wBAAgB,0BAA0B,CAAC,QAAQ,EAAE,MAAM,EAAE,EAAE,EAAE,QAAQ,EAAE,GAAG,OAAO,CAAC,qBAAqB,CAAC,QAAQ,EAAE,EAAE,MAAM,EAAE,CAAC,CAAC,CAEjI"}

package/dist/ts/ts/ContractIO/ContractIO.js

@@ -28,7 +28,9 @@ function fulfillReadContractAsync(basePath, c) {
           matchResult = 0;
           break;
         }
-        case "PlainText": {
+        case "PlainText":
+        case "CWL":
+        case "YAML": {
           matchResult = 1;
           break;
         }

package/dist/ts/ts/Conversion/Assay.d.ts

@@ -0,0 +1,13 @@
+import { TypeInfo } from '@fable-org/fable-library-js/Reflection.js';
+import { LDGraph, LDNode } from '../ROCrate/LDObject.js';
+import { LDContext } from '../ROCrate/LDContext.js';
+import { ArcAssay } from '../Core/ArcTypes.js';
+import { FileSystem } from '../FileSystem/FileSystem.js';
+export declare class AssayConversion {
+    constructor();
+}
+export declare function AssayConversion_$reflection(): TypeInfo;
+export declare function AssayConversion_getDataFilesFromProcesses_6BABD1B0(processes: LDNode[], fragmentDescriptors?: LDNode[], graph?: LDGraph, context?: LDContext): LDNode[];
+export declare function AssayConversion_composeAssay_Z5C53FD5C(assay: ArcAssay, fs?: FileSystem): LDNode;
+export declare function AssayConversion_decomposeAssay_Z6839B9E8(assay: LDNode, graph?: LDGraph, context?: LDContext): ArcAssay;
+//# sourceMappingURL=Assay.d.ts.map

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

@@ -0,0 +1 @@
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package/dist/ts/ts/Conversion/Assay.js

@@ -0,0 +1,69 @@
+import { class_type } from '../../node_modules/@fable-org/fable-library-js/Reflection.js';
+import { ResizeArray_distinct, ResizeArray_append, ResizeArray_choose, ResizeArray_collect, ResizeArray_filter, ResizeArray_map, ResizeArray_tryFind, Option_fromSeq, ResizeArray_groupBy, ResizeArray_singleton, ResizeArray_appendSingleton, Option_fromValueWithDefault } from '../Core/Helper/Collections.js';
+import { LDPropertyValue } from '../ROCrate/LDTypes/PropertyValue.js';
+import { unwrap, defaultArg, value, map } from '../../node_modules/@fable-org/fable-library-js/Option.js';
+import { LDLabProcess } from '../ROCrate/LDTypes/LabProcess.js';
+import { DataAux_pathAndSelectorFromName } from '../Core/Data.js';
+import { LDFile } from '../ROCrate/LDTypes/File.js';
+import { LDDataset } from '../ROCrate/LDTypes/Dataset.js';
+import { BaseTypes_composeDefinedTerm_ZDED3A0F, BaseTypes_composePropertyValueFromOA_ZDED3A0F, BaseTypes_composeComment_Z13201A7E, BaseTypes_decomposeDefinedTerm_Z2F770004, BaseTypes_decomposePropertyValueToOA_Z2F770004, BaseTypes_decomposeComment_Z2F770004 } from './Basic.js';
+import { PersonConversion_composePerson_Z64D846DC, PersonConversion_decomposePerson_Z6839B9E8 } from './Person.js';
+import { ARCtrl_ArcTables__ArcTables_GetProcesses_5E660E5C, ARCtrl_ArcTables__ArcTables_fromProcesses_Static_Z27F0B586 } from './Table.js';
+import { ArcTables } from '../Core/Table/ArcTables.js';
+import { DatamapConversion_composeFragmentDescriptors_Z892BFC3, DatamapConversion_decomposeFragmentDescriptors_Z6E59645F } from './Datamap.js';
+import { Datamap } from '../Core/Datamap.js';
+import { ArcAssay } from '../Core/ArcTypes.js';
+import { ofSeq } from '../../node_modules/@fable-org/fable-library-js/List.js';
+
+class AssayConversion {
+  constructor() {
+  }
+}
+function AssayConversion_$reflection() {
+  return class_type("ARCtrl.Conversion.AssayConversion", void 0, AssayConversion);
+}
+function AssayConversion_getDataFilesFromProcesses_6BABD1B0(processes, fragmentDescriptors, graph, context) {
+  const data = ResizeArray_distinct(ResizeArray_append(ResizeArray_choose((df) => LDPropertyValue.tryGetSubjectOf(df, unwrap(graph), unwrap(context)), defaultArg(fragmentDescriptors, [])), ResizeArray_collect((p) => ResizeArray_append(LDLabProcess.getObjectsAsData(p, unwrap(graph), unwrap(context)), LDLabProcess.getResultsAsData(p, unwrap(graph), unwrap(context))), processes)));
+  const files = ResizeArray_filter((d) => DataAux_pathAndSelectorFromName(d.Id)[1] == null, data);
+  return ResizeArray_append(files, ResizeArray_map((tupledArg) => {
+    const path = tupledArg[0];
+    const fragments = tupledArg[1];
+    let file;
+    const matchValue = ResizeArray_tryFind((d_3) => d_3.Id === path, files);
+    if (matchValue == null) {
+      const comments = Option_fromSeq(LDFile.getComments(fragments[0], unwrap(graph), unwrap(context)));
+      file = LDFile.create(path, path, unwrap(comments), unwrap(LDFile.tryGetDisambiguatingDescriptionAsString(fragments[0], unwrap(context))), unwrap(LDFile.tryGetEncodingFormatAsString(fragments[0], unwrap(context))), void 0, unwrap(fragments[0].TryGetContext()));
+    } else {
+      file = value(matchValue);
+    }
+    LDDataset.setHasParts(file, fragments, unwrap(context));
+    return file;
+  }, ResizeArray_groupBy((d_2) => DataAux_pathAndSelectorFromName(d_2.Id)[0], ResizeArray_filter((d_1) => DataAux_pathAndSelectorFromName(d_1.Id)[1] != null, data))));
+}
+function AssayConversion_composeAssay_Z5C53FD5C(assay, fs) {
+  let collection, fds_1, vm_1, fds, vm;
+  const measurementMethod = map(BaseTypes_composeDefinedTerm_ZDED3A0F, assay.TechnologyType);
+  const measurementTechnique = map(BaseTypes_composeDefinedTerm_ZDED3A0F, assay.TechnologyPlatform);
+  const variableMeasured = map(BaseTypes_composePropertyValueFromOA_ZDED3A0F, assay.MeasurementType);
+  const creators = Option_fromSeq(ResizeArray_map(PersonConversion_composePerson_Z64D846DC, assay.Performers));
+  const processSequence = Option_fromSeq((collection = ARCtrl_ArcTables__ArcTables_GetProcesses_5E660E5C(new ArcTables(assay.Tables), assay.Identifier, void 0, unwrap(fs)), Array.from(collection)));
+  const fragmentDescriptors = map(DatamapConversion_composeFragmentDescriptors_Z892BFC3, assay.Datamap);
+  const dataFiles = map((ps) => AssayConversion_getDataFilesFromProcesses_6BABD1B0(ps, unwrap(fragmentDescriptors)), processSequence);
+  const variableMeasureds = variableMeasured == null ? fragmentDescriptors == null ? void 0 : (fds_1 = value(fragmentDescriptors), fds_1) : fragmentDescriptors == null ? (vm_1 = value(variableMeasured), ResizeArray_singleton(vm_1)) : (fds = value(fragmentDescriptors), vm = value(variableMeasured), ResizeArray_appendSingleton(vm, fds));
+  const comments = Option_fromSeq(ResizeArray_map(BaseTypes_composeComment_Z13201A7E, assay.Comments));
+  return LDDataset.createAssay(assay.Identifier, void 0, unwrap(assay.Title), unwrap(assay.Description), unwrap(creators), unwrap(dataFiles), unwrap(measurementMethod), unwrap(measurementTechnique), unwrap(variableMeasureds), unwrap(processSequence), unwrap(comments));
+}
+function AssayConversion_decomposeAssay_Z6839B9E8(assay, graph, context) {
+  const measurementMethod = map((m) => BaseTypes_decomposeDefinedTerm_Z2F770004(m, unwrap(context)), LDDataset.tryGetMeasurementMethodAsDefinedTerm(assay, unwrap(graph), unwrap(context)));
+  const measurementTechnique = map((m_1) => BaseTypes_decomposeDefinedTerm_Z2F770004(m_1, unwrap(context)), LDDataset.tryGetMeasurementTechniqueAsDefinedTerm(assay, unwrap(graph), unwrap(context)));
+  const variableMeasured = map((v) => BaseTypes_decomposePropertyValueToOA_Z2F770004(v, unwrap(context)), LDDataset.tryGetVariableMeasuredAsMeasurementType(assay, unwrap(graph), unwrap(context)));
+  const perfomers = ResizeArray_map((c) => PersonConversion_decomposePerson_Z6839B9E8(c, unwrap(graph), unwrap(context)), LDDataset.getCreators(assay, unwrap(graph), unwrap(context)));
+  let datamap;
+  const v_1 = DatamapConversion_decomposeFragmentDescriptors_Z6E59645F(LDDataset.getVariableMeasuredAsFragmentDescriptors(assay, unwrap(graph), unwrap(context)), unwrap(graph), unwrap(context));
+  datamap = Option_fromValueWithDefault(Datamap.init(), v_1);
+  const tables = ARCtrl_ArcTables__ArcTables_fromProcesses_Static_Z27F0B586(ofSeq(LDDataset.getAboutsAsLabProcess(assay, unwrap(graph), unwrap(context))), unwrap(graph), unwrap(context));
+  const comments = ResizeArray_map((c_1) => BaseTypes_decomposeComment_Z2F770004(c_1, unwrap(context)), LDDataset.getComments(assay, unwrap(graph), unwrap(context)));
+  return ArcAssay.create(LDDataset.getIdentifierAsString(assay, unwrap(context)), unwrap(LDDataset.tryGetNameAsString(assay, unwrap(context))), unwrap(LDDataset.tryGetDescriptionAsString(assay, unwrap(context))), unwrap(variableMeasured), unwrap(measurementMethod), unwrap(measurementTechnique), tables.Tables, unwrap(datamap), perfomers, comments);
+}
+
+export { AssayConversion, AssayConversion_$reflection, AssayConversion_composeAssay_Z5C53FD5C, AssayConversion_decomposeAssay_Z6839B9E8, AssayConversion_getDataFilesFromProcesses_6BABD1B0 };

package/dist/ts/ts/Conversion/Basic.d.ts

@@ -0,0 +1,105 @@
+import { TypeInfo } from '@fable-org/fable-library-js/Reflection.js';
+import { Option } from '@fable-org/fable-library-js/Option.js';
+import { Comment$ } from '../Core/Comment.js';
+import { LDGraph, LDNode } from '../ROCrate/LDObject.js';
+import { LDContext } from '../ROCrate/LDContext.js';
+import { OntologyAnnotation } from '../Core/OntologyAnnotation.js';
+import { Data } from '../Core/Data.js';
+import { CompositeCell_$union } from '../Core/Table/CompositeCell.js';
+import { CompositeHeader_$union } from '../Core/Table/CompositeHeader.js';
+import { FileSystem } from '../FileSystem/FileSystem.js';
+import { DataContext } from '../Core/DataContext.js';
+import { Value_$union } from '../Core/Value.js';
+export declare class BaseTypes {
+    constructor();
+}
+export declare function BaseTypes_$reflection(): TypeInfo;
+export declare function BaseTypes_composeComment_Z13201A7E(comment: Comment$): LDNode;
+export declare function BaseTypes_decomposeComment_Z2F770004(comment: LDNode, context?: LDContext): Comment$;
+export declare function BaseTypes_ontologyTermFromNameAndID_40457300(name?: string, id?: string): OntologyAnnotation;
+export declare function BaseTypes_tryOntologyTermFromNameAndID_40457300(name?: string, id?: string): Option<OntologyAnnotation>;
+export declare function BaseTypes_composeDefinedTerm_ZDED3A0F(term: OntologyAnnotation): LDNode;
+export declare function BaseTypes_decomposeDefinedTerm_Z2F770004(term: LDNode, context?: LDContext): OntologyAnnotation;
+export declare function BaseTypes_composePropertyValueFromOA_ZDED3A0F(term: OntologyAnnotation): LDNode;
+export declare function BaseTypes_decomposePropertyValueToOA_Z2F770004(term: LDNode, context?: LDContext): OntologyAnnotation;
+/**
+ * Convert a CompositeCell to a ISA Value and Unit tuple.
+ */
+export declare function BaseTypes_valuesOfCell_Z436420FE(value: CompositeCell_$union): [Option<string>, Option<string>, Option<string>, Option<string>];
+export declare function BaseTypes_termOfHeader_6CAF647B(header: CompositeHeader_$union): [string, Option<string>];
+/**
+ * Convert a CompositeHeader and Cell tuple to a ISA Component
+ */
+export declare function BaseTypes_composeComponent(header: CompositeHeader_$union, value: CompositeCell_$union): LDNode;
+/**
+ * Convert a CompositeHeader and Cell tuple to a ISA ProcessParameterValue
+ */
+export declare function BaseTypes_composeParameterValue(header: CompositeHeader_$union, value: CompositeCell_$union): LDNode;
+/**
+ * Convert a CompositeHeader and Cell tuple to a ISA FactorValue
+ */
+export declare function BaseTypes_composeFactorValue(header: CompositeHeader_$union, value: CompositeCell_$union): LDNode;
+/**
+ * Convert a CompositeHeader and Cell tuple to a ISA MaterialAttributeValue
+ */
+export declare function BaseTypes_composeCharacteristicValue(header: CompositeHeader_$union, value: CompositeCell_$union): LDNode;
+export declare function BaseTypes_composeFreetextMaterialName(headerFT: string, name: string): string;
+export declare function BaseTypes_composeFile_6CE21C7D(d: Data, fs?: FileSystem): LDNode;
+export declare function BaseTypes_decomposeFile_Z2F770004(f: LDNode, context?: LDContext): Data;
+export declare function BaseTypes_composeFragmentDescriptor_Z4C0BEF62(dc: DataContext): LDNode;
+export declare function BaseTypes_decomposeFragmentDescriptor_Z6839B9E8(fd: LDNode, graph?: LDGraph, context?: LDContext): DataContext;
+/**
+ * Convert a CompositeHeader and Cell tuple to a ISA ProcessInput
+ */
+export declare function BaseTypes_composeProcessInput(header: CompositeHeader_$union, value: CompositeCell_$union, fs: Option<FileSystem>): LDNode;
+/**
+ * Convert a CompositeHeader and Cell tuple to a ISA ProcessOutput
+ */
+export declare function BaseTypes_composeProcessOutput(header: CompositeHeader_$union, value: CompositeCell_$union, fs: Option<FileSystem>): LDNode;
+export declare function BaseTypes_headerOntologyOfPropertyValue_Z2F770004(pv: LDNode, context?: LDContext): OntologyAnnotation;
+/**
+ * Convert an ISA Value and Unit tuple to a CompositeCell
+ */
+export declare function BaseTypes_cellOfPropertyValue_Z2F770004(pv: LDNode, context?: LDContext): CompositeCell_$union;
+/**
+ * Convert an ISA Component to a CompositeHeader and Cell tuple
+ */
+export declare function BaseTypes_decomposePropertyValue_Z2F770004(pv: LDNode, context?: LDContext): [OntologyAnnotation, Option<Value_$union>, Option<OntologyAnnotation>];
+/**
+ * Convert an ISA Component to a CompositeHeader and Cell tuple
+ */
+export declare function BaseTypes_decomposeComponent_Z2F770004(c: LDNode, context?: LDContext): [CompositeHeader_$union, CompositeCell_$union];
+/**
+ * Convert an ISA ProcessParameterValue to a CompositeHeader and Cell tuple
+ */
+export declare function BaseTypes_decomposeParameterValue_Z2F770004(c: LDNode, context?: LDContext): [CompositeHeader_$union, CompositeCell_$union];
+/**
+ * Convert an ISA FactorValue to a CompositeHeader and Cell tuple
+ */
+export declare function BaseTypes_decomposeFactorValue_Z2F770004(c: LDNode, context?: LDContext): [CompositeHeader_$union, CompositeCell_$union];
+/**
+ * Convert an ISA MaterialAttributeValue to a CompositeHeader and Cell tuple
+ */
+export declare function BaseTypes_decomposeCharacteristicValue_Z2F770004(c: LDNode, context?: LDContext): [CompositeHeader_$union, CompositeCell_$union];
+/**
+ * Convert an ISA ProcessOutput to a CompositeHeader and Cell tuple
+ */
+export declare function BaseTypes_decomposeProcessInput_Z2F770004(pn: LDNode, context?: LDContext): [CompositeHeader_$union, CompositeCell_$union];
+export declare function BaseTypes_decomposeProcessOutput_Z2F770004(pn: LDNode, context?: LDContext): [CompositeHeader_$union, CompositeCell_$union];
+/**
+ * This function creates a string containing the name and the ontology short-string of the given ontology annotation term
+ *
+ * TechnologyPlatforms are plain strings in ISA-JSON.
+ *
+ * This function allows us, to parse them as an ontology term.
+ */
+export declare function BaseTypes_composeTechnologyPlatform_ZDED3A0F(tp: OntologyAnnotation): string;
+/**
+ * This function parses the given string containing the name and the ontology short-string of the given ontology annotation term
+ *
+ * TechnologyPlatforms are plain strings in ISA-JSON.
+ *
+ * This function allows us, to parse them as an ontology term.
+ */
+export declare function BaseTypes_decomposeTechnologyPlatform_Z721C83C5(name: string): OntologyAnnotation;
+//# sourceMappingURL=Basic.d.ts.map

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

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