@nfdi4plants/arctrl 3.2.2 → 3.3.0

package/dist/ts/ts/Conversion/Process.js

@@ -3,22 +3,24 @@ import { LDLabProtocol } from '../ROCrate/LDTypes/LabProtocol.js';
 import { unwrap, value, defaultArg } from '../../node_modules/@fable-org/fable-library-ts/Option.js';
 import { OntologyAnnotation } from '../Core/OntologyAnnotation.js';
 import { BaseTypes_decomposeDefinedTerm_Z2F770004, BaseTypes_composeComponent, BaseTypes_composeParameterValue, BaseTypes_composeFactorValue, BaseTypes_composeCharacteristicValue, BaseTypes_composeDefinedTerm_ZDED3A0F, BaseTypes_composeProcessInput, BaseTypes_composeProcessOutput, BaseTypes_decomposeParameterValue_Z2F770004, BaseTypes_decomposeComponent_Z2F770004, BaseTypes_decomposeCharacteristicValue_Z2F770004, BaseTypes_decomposeFactorValue_Z2F770004, BaseTypes_decomposeProcessInput_Z2F770004, BaseTypes_decomposeProcessOutput_Z2F770004 } from './Basic.js';
-import { parse } from '../../node_modules/@fable-org/fable-library-ts/Int32.js';
-import { ActivePatterns_$007CRegex$007C_$007C } from '../Core/Helper/Regex.js';
+import { tryParse } from '../../node_modules/@fable-org/fable-library-ts/Int32.js';
+import { match, create } from '../../node_modules/@fable-org/fable-library-ts/RegExp.js';
+import { Pattern_handleGroupPatterns } from '../Core/Helper/Regex.js';
+import { FSharpRef, toString } from '../../node_modules/@fable-org/fable-library-ts/Types.js';
 import { Unchecked_tryGetCellAt, getEmptyCellForHeader } from '../Core/Table/ArcTableAux.js';
-import { ARCtrl_ROCrate_LDNode__LDNode_SetColumnIndex_Z524259A4, tryGetIndex } from './ColumnIndex.js';
 import { CompositeCell_FreeText, CompositeCell_Term } from '../Core/Table/CompositeCell.js';
+import { ARCtrl_ROCrate_LDNode__LDNode_SetColumnIndex_Z524259A4, tryGetIndex } from './ColumnIndex.js';
 import { CompositeHeader, CompositeHeader_Comment$ } from '../Core/Table/CompositeHeader.js';
-import { toString } from '../../node_modules/@fable-org/fable-library-ts/Types.js';
 import { Comment$ } from '../Core/Comment.js';
 import { LDPerson } from '../ROCrate/LDTypes/Person.js';
 import { indexed, toList, filter, tryPick, choose as choose$1, map, delay, append, empty as empty$1, singleton } from '../../node_modules/@fable-org/fable-library-ts/Seq.js';
-import { choose, length, empty, map as map$1, sortBy } from '../../node_modules/@fable-org/fable-library-ts/List.js';
+import { choose, ofSeq, forAll, length, empty, map as map$1, sortBy } from '../../node_modules/@fable-org/fable-library-ts/List.js';
 import { ResizeArray_singleton, Option_fromValueWithDefault, ResizeArray_map, ResizeArray_create, ResizeArray_zip } from '../Core/Helper/Collections.js';
 import { LDSample } from '../ROCrate/LDTypes/Sample.js';
 import { LDLabProcess } from '../ROCrate/LDTypes/LabProcess.js';
 import { List_groupBy } from '../../node_modules/@fable-org/fable-library-ts/Seq2.js';
 import { createMissingIdentifier } from '../Core/Helper/Identifier.js';
+import { isNullOrWhiteSpace } from '../../node_modules/@fable-org/fable-library-ts/String.js';
 import { stringHash, comparePrimitives } from '../../node_modules/@fable-org/fable-library-ts/Util.js';
 
 class ProcessConversion {
@@ -35,21 +37,29 @@ function ProcessConversion_tryGetProtocolType_Z6839B9E8(pv, graph, context) {
     if (matchValue_1 == null) {
       return void 0;
     } else {
-      const s = value(matchValue_1);
+      const s = matchValue_1;
       return OntologyAnnotation.create(s);
     }
   } else {
-    return BaseTypes_decomposeDefinedTerm_Z2F770004(value(matchValue), unwrap(context));
+    return BaseTypes_decomposeDefinedTerm_Z2F770004(matchValue, unwrap(context));
   }
 }
 function ProcessConversion_composeProcessName(processNameRoot, i) {
   return `${processNameRoot}_${i}`;
 }
 function ProcessConversion_decomposeProcessName_Z721C83C5(name) {
-  const activePatternResult = ActivePatterns_$007CRegex$007C_$007C("(?<name>.+)_(?<num>\\d+)", name);
-  if (activePatternResult != null) {
-    const r = value(activePatternResult);
-    return [r.groups && r.groups.name || "", parse(r.groups && r.groups.num || "", 511, false, 32)];
+  const m = match(create(Pattern_handleGroupPatterns("^(?<name>.*)_(?<num>\\d+)$")), name);
+  if (m != null) {
+    const nameGroup = m.groups && m.groups.name || "";
+    const numGroup = m.groups && m.groups.num || "";
+    let matchValue;
+    const cell = new FSharpRef(0);
+    matchValue = [tryParse(numGroup, 511, false, 32, cell), cell.contents];
+    if (matchValue[0]) {
+      return [nameGroup, matchValue[1]];
+    } else {
+      return [name, void 0];
+    }
   } else {
     return [name, void 0];
   }
@@ -60,7 +70,7 @@ function ProcessConversion_tryComponentGetter(generalI, valueI, valueHeader) {
     valueHeader.fields[0];
     return (table) => (i) => {
       let matchValue = void 0;
-      const c = BaseTypes_composeComponent(valueHeader, (matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), matchValue == null ? getEmptyCellForHeader(valueHeader, void 0) : value(matchValue)));
+      const c = BaseTypes_composeComponent(valueHeader, (matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), matchValue == null ? getEmptyCellForHeader(valueHeader, void 0) : matchValue));
       ARCtrl_ROCrate_LDNode__LDNode_SetColumnIndex_Z524259A4(c, valueI);
       return c;
     };
@@ -74,7 +84,7 @@ function ProcessConversion_tryParameterGetter(generalI, valueI, valueHeader) {
     valueHeader.fields[0];
     return (table) => (i) => {
       let matchValue = void 0;
-      const p = BaseTypes_composeParameterValue(valueHeader, (matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), matchValue == null ? getEmptyCellForHeader(valueHeader, void 0) : value(matchValue)));
+      const p = BaseTypes_composeParameterValue(valueHeader, (matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), matchValue == null ? getEmptyCellForHeader(valueHeader, void 0) : matchValue));
       ARCtrl_ROCrate_LDNode__LDNode_SetColumnIndex_Z524259A4(p, valueI);
       return p;
     };
@@ -88,7 +98,7 @@ function ProcessConversion_tryFactorGetter(generalI, valueI, valueHeader) {
     valueHeader.fields[0];
     return (table) => (i) => {
       let matchValue = void 0;
-      const f = BaseTypes_composeFactorValue(valueHeader, (matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), matchValue == null ? getEmptyCellForHeader(valueHeader, void 0) : value(matchValue)));
+      const f = BaseTypes_composeFactorValue(valueHeader, (matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), matchValue == null ? getEmptyCellForHeader(valueHeader, void 0) : matchValue));
       ARCtrl_ROCrate_LDNode__LDNode_SetColumnIndex_Z524259A4(f, valueI);
       return f;
     };
@@ -102,7 +112,7 @@ function ProcessConversion_tryCharacteristicGetter(generalI, valueI, valueHeader
     valueHeader.fields[0];
     return (table) => (i) => {
       let matchValue = void 0;
-      const c = BaseTypes_composeCharacteristicValue(valueHeader, (matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), matchValue == null ? getEmptyCellForHeader(valueHeader, void 0) : value(matchValue)));
+      const c = BaseTypes_composeCharacteristicValue(valueHeader, (matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), matchValue == null ? getEmptyCellForHeader(valueHeader, void 0) : matchValue));
       ARCtrl_ROCrate_LDNode__LDNode_SetColumnIndex_Z524259A4(c, valueI);
       return c;
     };
@@ -115,7 +125,7 @@ function ProcessConversion_tryGetProtocolTypeGetter(generalI, header) {
   4) {
     return (table) => (i) => {
       let matchValue = void 0, cell = void 0;
-      return BaseTypes_composeDefinedTerm_ZDED3A0F((matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), matchValue == null ? new OntologyAnnotation() : (cell = value(matchValue), cell.AsTerm)));
+      return BaseTypes_composeDefinedTerm_ZDED3A0F((matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), matchValue == null ? new OntologyAnnotation() : (cell = matchValue, cell.AsTerm)));
     };
   } else {
     return void 0;
@@ -129,7 +139,7 @@ function ProcessConversion_tryGetProtocolREFGetter(generalI, header) {
       if (matchValue == null) {
         return "";
       } else {
-        const cell = value(matchValue);
+        const cell = matchValue;
         return cell.AsFreeText;
       }
     };
@@ -145,7 +155,7 @@ function ProcessConversion_tryGetProtocolDescriptionGetter(generalI, header) {
       if (matchValue == null) {
         return "";
       } else {
-        const cell = value(matchValue);
+        const cell = matchValue;
         return cell.AsFreeText;
       }
     };
@@ -161,7 +171,7 @@ function ProcessConversion_tryGetProtocolURIGetter(generalI, header) {
       if (matchValue == null) {
         return "";
       } else {
-        const cell = value(matchValue);
+        const cell = matchValue;
         return cell.AsFreeText;
       }
     };
@@ -177,7 +187,7 @@ function ProcessConversion_tryGetProtocolVersionGetter(generalI, header) {
       if (matchValue == null) {
         return "";
       } else {
-        const cell = value(matchValue);
+        const cell = matchValue;
         return cell.AsFreeText;
       }
     };
@@ -191,7 +201,7 @@ function ProcessConversion_tryGetInputGetter(generalI, header, fs) {
     header.fields[0];
     return (table) => (i) => {
       let matchValue = void 0;
-      return BaseTypes_composeProcessInput(header, (matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), matchValue == null ? getEmptyCellForHeader(header, void 0) : value(matchValue)), fs);
+      return BaseTypes_composeProcessInput(header, (matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), matchValue == null ? getEmptyCellForHeader(header, void 0) : matchValue), fs);
     };
   } else {
     return void 0;
@@ -203,7 +213,7 @@ function ProcessConversion_tryGetOutputGetter(generalI, header, fs) {
     header.fields[0];
     return (table) => (i) => {
       let matchValue = void 0;
-      return BaseTypes_composeProcessOutput(header, (matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), matchValue == null ? getEmptyCellForHeader(header, void 0) : value(matchValue)), fs);
+      return BaseTypes_composeProcessOutput(header, (matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), matchValue == null ? getEmptyCellForHeader(header, void 0) : matchValue), fs);
     };
   } else {
     return void 0;
@@ -215,7 +225,7 @@ function ProcessConversion_tryGetCommentGetter(generalI, header) {
     const c = header.fields[0];
     return (table) => (i) => {
       let matchValue = void 0, cell = void 0;
-      return toString((matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), matchValue == null ? new Comment$(c) : (cell = value(matchValue), new Comment$(c, cell.AsFreeText))));
+      return toString((matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), matchValue == null ? new Comment$(c) : (cell = matchValue, new Comment$(c, cell.AsFreeText))));
     };
   } else {
     return void 0;
@@ -230,7 +240,7 @@ function ProcessConversion_tryGetPerformerGetter(generalI, header) {
       if (matchValue == null) {
         performer = "";
       } else {
-        const cell = value(matchValue);
+        const cell = matchValue;
         performer = cell.AsFreeText;
       }
       return LDPerson.create(performer);
@@ -265,75 +275,97 @@ function ProcessConversion_getProcessGetter(assayName, studyName, processNameRoo
   const protocolVersionGetter = tryPick((tupledArg_8) => ProcessConversion_tryGetProtocolVersionGetter(tupledArg_8[0], tupledArg_8[1]), headers_1);
   const performerGetter = tryPick((tupledArg_9) => ProcessConversion_tryGetPerformerGetter(tupledArg_9[0], tupledArg_9[1]), headers_1);
   const commentGetters = toList(choose$1((tupledArg_10) => ProcessConversion_tryGetCommentGetter(tupledArg_10[0], tupledArg_10[1]), headers_1));
+  const areCellsEmpty = (isColumn) => {
+    const columnIndices = ofSeq(map((tuple_2) => tuple_2[0] | 0, filter((arg_1) => isColumn(arg_1[1]), headers_1)));
+    return (table) => (i) => forAll((generalI_22) => {
+      const matchValue = Unchecked_tryGetCellAt(generalI_22, i, table.Values);
+      if (matchValue == null) {
+        return true;
+      } else {
+        const cell = matchValue;
+        return cell.isEmpty();
+      }
+    }, columnIndices);
+  };
+  const isInputEmpty = areCellsEmpty((h_1) => h_1.isInput ? true : h_1.isCharacteristic);
+  const isOutputEmpty = areCellsEmpty((h_2) => h_2.isOutput ? true : h_2.isFactor);
   let inputGetter_1;
-  const matchValue = tryPick((tupledArg_11) => ProcessConversion_tryGetInputGetter(tupledArg_11[0], tupledArg_11[1], fs), headers_1);
-  if (matchValue == null) {
-    inputGetter_1 = length(charGetters) !== 0 ? (table_1) => (i_1) => {
+  const matchValue_1 = tryPick((tupledArg_11) => ProcessConversion_tryGetInputGetter(tupledArg_11[0], tupledArg_11[1], fs), headers_1);
+  if (matchValue_1 == null) {
+    inputGetter_1 = length(charGetters) !== 0 ? (table_2) => (i_2) => {
       let chars_1;
-      const collection_1 = map((f_1) => f_1(table_1)(i_1), charGetters);
+      const collection_1 = map((f_1) => f_1(table_2)(i_2), charGetters);
       chars_1 = Array.from(collection_1);
-      return ResizeArray_singleton(LDSample.createSample(`${processNameRoot}_Input_${i_1}`, void 0, chars_1));
-    } : (table_2) => (i_2) => [];
+      return ResizeArray_singleton(LDSample.createSample(`${processNameRoot}_Input_${i_2}`, void 0, chars_1));
+    } : (table_3) => (i_3) => [];
   } else {
-    const inputGetter = value(matchValue);
-    inputGetter_1 = (table) => (i) => {
-      let chars;
-      const collection = map((f) => f(table)(i), charGetters);
-      chars = Array.from(collection);
-      const input = inputGetter(table)(i);
-      if (chars.length > 0) {
-        LDSample.setAdditionalProperties(input, chars);
+    const inputGetter = value(matchValue_1);
+    inputGetter_1 = (table_1) => (i_1) => {
+      if (isInputEmpty(table_1)(i_1)) {
+        return [];
+      } else {
+        let chars;
+        const collection = map((f) => f(table_1)(i_1), charGetters);
+        chars = Array.from(collection);
+        const input = inputGetter(table_1)(i_1);
+        if (chars.length > 0) {
+          LDSample.setAdditionalProperties(input, chars);
+        }
+        return ResizeArray_singleton(input);
       }
-      return ResizeArray_singleton(input);
     };
   }
   let outputGetter_1;
-  const matchValue_1 = tryPick((tupledArg_12) => ProcessConversion_tryGetOutputGetter(tupledArg_12[0], tupledArg_12[1], fs), headers_1);
-  if (matchValue_1 == null) {
-    outputGetter_1 = length(factorValueGetters) !== 0 ? (table_4) => (i_4) => {
+  const matchValue_2 = tryPick((tupledArg_12) => ProcessConversion_tryGetOutputGetter(tupledArg_12[0], tupledArg_12[1], fs), headers_1);
+  if (matchValue_2 == null) {
+    outputGetter_1 = length(factorValueGetters) !== 0 ? (table_5) => (i_5) => {
       let factors_1;
-      const collection_3 = map((f_3) => f_3(table_4)(i_4), factorValueGetters);
+      const collection_3 = map((f_3) => f_3(table_5)(i_5), factorValueGetters);
       factors_1 = Array.from(collection_3);
-      return ResizeArray_singleton(LDSample.createSample(`${processNameRoot}_Output_${i_4}`, void 0, factors_1));
-    } : (table_5) => (i_5) => [];
+      return ResizeArray_singleton(LDSample.createSample(`${processNameRoot}_Output_${i_5}`, void 0, factors_1));
+    } : (table_6) => (i_6) => [];
   } else {
-    const outputGetter = value(matchValue_1);
-    outputGetter_1 = (table_3) => (i_3) => {
-      let factors;
-      const collection_2 = map((f_2) => f_2(table_3)(i_3), factorValueGetters);
-      factors = Array.from(collection_2);
-      const output = outputGetter(table_3)(i_3);
-      if (factors.length > 0) {
-        LDSample.setAdditionalProperties(output, factors);
+    const outputGetter = value(matchValue_2);
+    outputGetter_1 = (table_4) => (i_4) => {
+      if (isOutputEmpty(table_4)(i_4)) {
+        return [];
+      } else {
+        let factors;
+        const collection_2 = map((f_2) => f_2(table_4)(i_4), factorValueGetters);
+        factors = Array.from(collection_2);
+        const output = outputGetter(table_4)(i_4);
+        if (factors.length > 0) {
+          LDSample.setAdditionalProperties(output, factors);
+        }
+        return ResizeArray_singleton(output);
       }
-      return ResizeArray_singleton(output);
     };
   }
-  return (table_6) => (i_6) => {
+  return (table_7) => (i_7) => {
     let collection_4 = void 0, collection_5 = void 0, collection_6 = void 0, option_9 = void 0, option_11 = void 0, option_13 = void 0, option_15 = void 0;
-    const pn = table_6.RowCount === 1 ? processNameRoot : ProcessConversion_composeProcessName(processNameRoot, i_6);
+    const pn = ProcessConversion_composeProcessName(processNameRoot, i_7);
     let paramvalues;
-    const option_1 = Option_fromValueWithDefault(empty(), map$1((f_4) => f_4(table_6)(i_6), parameterValueGetters));
-    paramvalues = option_1 != null ? (collection_4 = value(option_1), Array.from(collection_4)) : void 0;
+    const option_1 = Option_fromValueWithDefault(empty(), map$1((f_4) => f_4(table_7)(i_7), parameterValueGetters));
+    paramvalues = option_1 != null ? (collection_4 = option_1, Array.from(collection_4)) : void 0;
     let comments;
-    const option_3 = Option_fromValueWithDefault(empty(), map$1((f_5) => f_5(table_6)(i_6), commentGetters));
-    comments = option_3 != null ? (collection_5 = value(option_3), Array.from(collection_5)) : void 0;
+    const option_3 = Option_fromValueWithDefault(empty(), map$1((f_5) => f_5(table_7)(i_7), commentGetters));
+    comments = option_3 != null ? (collection_5 = option_3, Array.from(collection_5)) : void 0;
     let components;
-    const option_5 = Option_fromValueWithDefault(empty(), map$1((f_6) => f_6(table_6)(i_6), componentGetters));
-    components = option_5 != null ? (collection_6 = value(option_5), Array.from(collection_6)) : void 0;
-    const id = LDLabProcess.genId(processNameRoot, unwrap(assayName), unwrap(studyName)) + `_${i_6}`;
+    const option_5 = Option_fromValueWithDefault(empty(), map$1((f_6) => f_6(table_7)(i_7), componentGetters));
+    components = option_5 != null ? (collection_6 = option_5, Array.from(collection_6)) : void 0;
+    const id = LDLabProcess.genId(processNameRoot, unwrap(assayName), unwrap(studyName)) + `_${i_7}`;
     let protocol;
     let name;
     const option_7 = protocolREFGetter;
-    name = option_7 != null ? value(option_7)(table_6)(i_6) : void 0;
+    name = option_7 != null ? value(option_7)(table_7)(i_7) : void 0;
     const protocolId = LDLabProtocol.genId(unwrap(name), processNameRoot);
-    protocol = LDLabProtocol.create(protocolId, unwrap(name), unwrap((option_9 = protocolDescriptionGetter, option_9 != null ? value(option_9)(table_6)(i_6) : void 0)), unwrap((option_11 = protocolTypeGetter, option_11 != null ? value(option_11)(table_6)(i_6) : void 0)), void 0, void 0, unwrap(components), void 0, unwrap((option_13 = protocolURIGetter, option_13 != null ? value(option_13)(table_6)(i_6) : void 0)), unwrap((option_15 = protocolVersionGetter, option_15 != null ? value(option_15)(table_6)(i_6) : void 0)));
-    const matchValue_2 = inputGetter_1(table_6)(i_6);
-    const matchValue_3 = outputGetter_1(table_6)(i_6);
+    protocol = LDLabProtocol.create(protocolId, unwrap(name), unwrap((option_9 = protocolDescriptionGetter, option_9 != null ? value(option_9)(table_7)(i_7) : void 0)), unwrap((option_11 = protocolTypeGetter, option_11 != null ? value(option_11)(table_7)(i_7) : void 0)), void 0, void 0, unwrap(components), void 0, unwrap((option_13 = protocolURIGetter, option_13 != null ? value(option_13)(table_7)(i_7) : void 0)), unwrap((option_15 = protocolVersionGetter, option_15 != null ? value(option_15)(table_7)(i_7) : void 0)));
+    const matchValue_3 = inputGetter_1(table_7)(i_7);
+    const matchValue_4 = outputGetter_1(table_7)(i_7);
     let agent;
     const option_17 = performerGetter;
-    agent = option_17 != null ? value(option_17)(table_6)(i_6) : void 0;
-    return LDLabProcess.create(pn, matchValue_2, matchValue_3, id, unwrap(agent), unwrap(protocol), unwrap(paramvalues), void 0, unwrap(comments));
+    agent = option_17 != null ? value(option_17)(table_7)(i_7) : void 0;
+    return LDLabProcess.create(pn, matchValue_3, matchValue_4, id, unwrap(agent), unwrap(protocol), unwrap(paramvalues), void 0, unwrap(comments));
   };
 }
 function ProcessConversion_groupProcesses_Z27F0B586(processes, graph, context) {
@@ -341,42 +373,47 @@ function ProcessConversion_groupProcesses_Z27F0B586(processes, graph, context) {
     let protocol = void 0, protocol_1 = void 0;
     const matchValue = LDLabProcess.tryGetNameAsString(p, unwrap(context));
     const matchValue_1 = LDLabProcess.tryGetExecutesLabProtocol(p, unwrap(graph), unwrap(context));
-    let matchResult = void 0, name_1 = void 0, protocol_2 = void 0, name_2 = void 0, protocol_3 = void 0;
+    let matchResult = void 0, name_2 = void 0, name_3 = void 0, protocol_2 = void 0, name_4 = void 0, protocol_3 = void 0;
     if (matchValue != null) {
-      if (ProcessConversion_decomposeProcessName_Z721C83C5(value(matchValue))[1] != null) {
+      if (ProcessConversion_decomposeProcessName_Z721C83C5(matchValue)[1] != null) {
         matchResult = 0;
-        name_1 = value(matchValue);
+        name_2 = matchValue;
+      } else if (!isNullOrWhiteSpace(matchValue)) {
+        matchResult = 1;
+        name_3 = matchValue;
       } else if (matchValue_1 != null) {
-        if (protocol = value(matchValue_1), LDLabProtocol.tryGetNameAsString(protocol, unwrap(context)) != null) {
-          matchResult = 1;
-          protocol_2 = value(matchValue_1);
-        } else {
+        if (protocol = matchValue_1, LDLabProtocol.tryGetNameAsString(protocol, unwrap(context)) != null) {
           matchResult = 2;
-          name_2 = value(matchValue);
+          protocol_2 = matchValue_1;
+        } else {
+          matchResult = 3;
+          name_4 = matchValue;
         }
       } else {
-        matchResult = 2;
-        name_2 = value(matchValue);
+        matchResult = 3;
+        name_4 = matchValue;
       }
     } else if (matchValue_1 != null) {
-      if (protocol_1 = value(matchValue_1), LDLabProtocol.tryGetNameAsString(protocol_1, unwrap(context)) != null) {
-        matchResult = 1;
-        protocol_2 = value(matchValue_1);
+      if (protocol_1 = matchValue_1, LDLabProtocol.tryGetNameAsString(protocol_1, unwrap(context)) != null) {
+        matchResult = 2;
+        protocol_2 = matchValue_1;
       } else {
-        matchResult = 3;
-        protocol_3 = value(matchValue_1);
+        matchResult = 4;
+        protocol_3 = matchValue_1;
       }
     } else {
-      matchResult = 4;
+      matchResult = 5;
     }
     switch (matchResult) {
       case 0:
-        return ProcessConversion_decomposeProcessName_Z721C83C5(name_1)[0];
+        return ProcessConversion_decomposeProcessName_Z721C83C5(name_2)[0];
       case 1:
-        return defaultArg(LDLabProtocol.tryGetNameAsString(protocol_2, unwrap(context)), "");
+        return name_3;
       case 2:
-        return name_2;
+        return defaultArg(LDLabProtocol.tryGetNameAsString(protocol_2, unwrap(context)), "");
       case 3:
+        return name_4;
+      case 4:
         return protocol_3.Id;
       default:
         return createMissingIdentifier();
@@ -393,7 +430,7 @@ function ProcessConversion_processToRows_Z6839B9E8(p, graph, context) {
   if (matchValue == null) {
     components = [];
   } else {
-    const prot = value(matchValue);
+    const prot = matchValue;
     components = ResizeArray_map((ppv_1) => [BaseTypes_decomposeComponent_Z2F770004(ppv_1, unwrap(context)), tryGetIndex(ppv_1)], LDLabProtocol.getComponents(prot, unwrap(graph), unwrap(context)));
   }
   let protVals;
@@ -401,21 +438,21 @@ function ProcessConversion_processToRows_Z6839B9E8(p, graph, context) {
   if (matchValue_1 == null) {
     protVals = empty();
   } else {
-    const prot_1 = value(matchValue_1);
+    const prot_1 = matchValue_1;
     protVals = toList(delay(() => {
       let matchValue_2 = void 0;
-      return append((matchValue_2 = LDLabProtocol.tryGetNameAsString(prot_1, unwrap(context)), matchValue_2 == null ? empty$1() : singleton([CompositeHeader.ProtocolREF, CompositeCell_FreeText(value(matchValue_2))])), delay(() => {
+      return append((matchValue_2 = LDLabProtocol.tryGetNameAsString(prot_1, unwrap(context)), matchValue_2 == null ? empty$1() : singleton([CompositeHeader.ProtocolREF, CompositeCell_FreeText(matchValue_2)])), delay(() => {
         let matchValue_3 = void 0;
-        return append((matchValue_3 = LDLabProtocol.tryGetDescriptionAsString(prot_1, unwrap(context)), matchValue_3 == null ? empty$1() : singleton([CompositeHeader.ProtocolDescription, CompositeCell_FreeText(value(matchValue_3))])), delay(() => {
+        return append((matchValue_3 = LDLabProtocol.tryGetDescriptionAsString(prot_1, unwrap(context)), matchValue_3 == null ? empty$1() : singleton([CompositeHeader.ProtocolDescription, CompositeCell_FreeText(matchValue_3)])), delay(() => {
           let matchValue_4 = void 0;
-          return append((matchValue_4 = LDLabProtocol.tryGetUrl(prot_1, unwrap(context)), matchValue_4 == null ? empty$1() : singleton([CompositeHeader.ProtocolUri, CompositeCell_FreeText(value(matchValue_4))])), delay(() => {
+          return append((matchValue_4 = LDLabProtocol.tryGetUrl(prot_1, unwrap(context)), matchValue_4 == null ? empty$1() : singleton([CompositeHeader.ProtocolUri, CompositeCell_FreeText(matchValue_4)])), delay(() => {
             let matchValue_5 = void 0;
-            return append((matchValue_5 = LDLabProtocol.tryGetVersionAsString(prot_1, unwrap(context)), matchValue_5 == null ? empty$1() : singleton([CompositeHeader.ProtocolVersion, CompositeCell_FreeText(value(matchValue_5))])), delay(() => {
+            return append((matchValue_5 = LDLabProtocol.tryGetVersionAsString(prot_1, unwrap(context)), matchValue_5 == null ? empty$1() : singleton([CompositeHeader.ProtocolVersion, CompositeCell_FreeText(matchValue_5)])), delay(() => {
               const matchValue_6 = ProcessConversion_tryGetProtocolType_Z6839B9E8(prot_1, unwrap(graph), unwrap(context));
               if (matchValue_6 == null) {
                 return empty$1();
               } else {
-                return singleton([CompositeHeader.ProtocolType, CompositeCell_Term(value(matchValue_6))]);
+                return singleton([CompositeHeader.ProtocolType, CompositeCell_Term(matchValue_6)]);
               }
             }));
           }));
@@ -445,14 +482,14 @@ function ProcessConversion_processToRows_Z6839B9E8(p, graph, context) {
       if (i == null) {
         chars = [];
       } else {
-        const i_1 = value(i);
+        const i_1 = i;
         chars = ResizeArray_map((cv) => [BaseTypes_decomposeCharacteristicValue_Z2F770004(cv, unwrap(context)), tryGetIndex(cv)], LDSample.getCharacteristics(i_1, unwrap(graph), unwrap(context)));
       }
       let factors;
       if (o == null) {
         factors = [];
       } else {
-        const o_1 = value(o);
+        const o_1 = o;
         factors = ResizeArray_map((fv) => [BaseTypes_decomposeFactorValue_Z2F770004(fv, unwrap(context)), tryGetIndex(fv)], LDSample.getFactors(o_1, unwrap(graph), unwrap(context)));
       }
       const vals_1 = map$1((tuple_3) => tuple_3[0], sortBy((arg_1) => defaultArg(arg_1[1], 1e4) | 0, toList(delay(() => append(chars, delay(() => append(components, delay(() => append(pvs, delay(() => factors)))))))), {

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

@@ -1,13 +1,13 @@
 import { TypeInfo } from '@fable-org/fable-library-ts/Reflection.ts';
+import { LDGraph, LDNode } from '../ROCrate/LDObject.ts';
+import { FileSystem } from '../FileSystem/FileSystem.ts';
+import { LDContext } from '../ROCrate/LDContext.ts';
 import { CWLType_$union } from '../CWL/CWLTypes.ts';
 import { CWLParameterValue_$union } from '../CWL/ParameterValue.ts';
-import { LDContext } from '../ROCrate/LDContext.ts';
 import { CWLParameterReference } from '../CWL/ParameterReference.ts';
-import { LDGraph, LDNode } from '../ROCrate/LDObject.ts';
 import { CWLInput } from '../CWL/Inputs.ts';
 import { CWLProcessingUnit_$union } from '../CWL/CWLProcessingUnit.ts';
 import { ArcRun } from '../Core/ArcTypes.ts';
-import { FileSystem } from '../FileSystem/FileSystem.ts';
 export declare class RunConversion {
     constructor();
 }
@@ -16,15 +16,45 @@ export declare function RunConversion_$reflection(): TypeInfo;
  * File paths in CWL files are relative to the file itself. In RO-Crate, we use relative paths from the root of the crate.
  *
  * This function replaces the relative paths in the CWL input file with paths relative to the root of the crate.
+ * The path is joined to the run folder, and its "." and ".." segments are resolved. A path that names the root of
+ * the ARC is ".". A path with a URI scheme is a URL and stays as it is.
  */
 export declare function RunConversion_composeCWLInputFilePath_Z384F8060(path: string, runName: string): string;
+/**
+ * Turns the id of a file in the crate back into a path relative to the run folder. The run folder is compared by
+ * whole segments, so runs/R does not contain runs/R2, and the run folder itself is ".". An id with a URI scheme is a
+ * URL and stays as it is.
+ */
 export declare function RunConversion_decomposeCWLInputFilePath_Z384F8060(path: string, runName: string): string;
-export declare function RunConversion_composeCWLParameterValue_6CF93391(value: CWLParameterValue_$union, runName: string, context?: LDContext): any;
-export declare function RunConversion_composeCWLInputValue_70DD9184(inputValue: CWLParameterReference, exampleOfWork: LDNode, inputParam: CWLInput, runName: string): LDNode;
+/**
+ * The Dataset entity of a directory that a job value names. The id of a local directory ends with "/", and its
+ * files in the file system are its parts. A directory with a URI scheme keeps the URL as its id.
+ */
+export declare function RunConversion_composeDirectoryDataset_111D9870(path: string, fs?: FileSystem, context?: LDContext): LDNode;
+export declare function RunConversion_composeCWLParameterValue_1A8A78ED(value: CWLParameterValue_$union, runName: string, context?: LDContext, fs?: FileSystem): any;
+/**
+ * The entity of the value of a job file for an input. A File or a Directory, alone or in a list, has to fit the type
+ * of the input, and the error names the run.
+ */
+export declare function RunConversion_composeCWLInputValue_Z65E5E0A8(inputValue: CWLParameterReference, exampleOfWork: LDNode, inputParam: CWLInput, runName: string, fs?: FileSystem): LDNode;
 export declare function RunConversion_decomposeCWLParameterValue_Z3524B680(value: any, runName: string, expectedType?: CWLType_$union, graph?: LDGraph): CWLParameterValue_$union;
 export declare function RunConversion_decomposeCWLInputValue_Z1346FE9D(inputValue: LDNode, runName: string, context?: LDContext, graph?: LDGraph): CWLParameterReference;
+/**
+ * The invocations of a run. An input without a value or with a null value in the job file takes its CWL default.
+ */
 export declare function RunConversion_composeWorkflowInvocationFromArcRun_Z8CC08AC(run: ArcRun, fs?: FileSystem): LDNode[];
 export declare function RunConversion_decomposeMainWorkflowInvocation_Z1346FE9D(workflowInvocation: LDNode, runName: string, context?: LDContext, graph?: LDGraph): [CWLProcessingUnit_$union, CWLParameterReference[]];
-export declare function RunConversion_composeRun_Z8CC08AC(run: ArcRun, fs?: FileSystem): LDNode;
+/**
+ * The dataset of a run. Its workflow is created at the given time, in UTC, and now when none is given. A time of kind
+ * Unspecified counts as local time, as in .NET. An input without a value or with a null value in the job file takes
+ * its CWL default. With a file system, the local files that the CWL file of the run needs are parts of the dataset.
+ * When the run is the root of its crate, its folder is a part like any other folder.
+ */
+export declare function RunConversion_composeRun_3F79BD1(run: ArcRun, fs?: FileSystem, dateCreated?: Date, isCrateRoot?: boolean): LDNode;
+/**
+ * Reads a run from its dataset. The crate holds neither the CWL file nor the job file of the run, so the run comes
+ * back with no CWL description and no job values. The tables skip the main workflow invocation, which stands for
+ * the CWL run.
+ */
 export declare function RunConversion_decomposeRun_Z6839B9E8(run: LDNode, graph?: LDGraph, context?: LDContext): ArcRun;
 //# sourceMappingURL=Run.d.ts.map

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