@nfdi4plants/arctrl 3.0.0-alpha.3 → 3.0.0-beta.1

package/dist/ts/esm/ts/ARC.js

@@ -8,15 +8,16 @@ import { PromiseBuilder__Delay_62FBFDE1, PromiseBuilder__Run_212F1D4B } from "./
 import { promise } from "./fable_modules/Fable.Promise.3.2.0/PromiseImpl.fs.js";
 import { getAllFilePathsAsync } from "./ContractIO/FileSystemHelper.js";
 import { toList, collect, empty, find, tryFind, iterate, map, singleton, append, delay, contains, toArray } from "@fable-org/fable-library-js/Seq.js";
-import { defaultOf, disposeSafe, getEnumerator, safeHash, curry2, comparePrimitives, stringHash } from "@fable-org/fable-library-js/Util.js";
+import { equals, defaultOf, disposeSafe, getEnumerator, safeHash, curry2, comparePrimitives, stringHash } from "@fable-org/fable-library-js/Util.js";
 import { getStudyFolderPath, getAssayFolderPath } from "./FileSystem/Path.js";
 import { ARCtrl_ArcAssay__ArcAssay_tryFromReadContract_Static_7570923F, ARCtrl_ArcAssay__ArcAssay_ToUpdateContract, ARCtrl_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49, ARCtrl_ArcAssay__ArcAssay_ToDeleteContract } from "./Contract/ArcAssay.js";
 import { ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F, ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract } from "./Contract/ArcInvestigation.js";
 import { ARCtrl_ArcStudy__ArcStudy_tryFromReadContract_Static_7570923F, ARCtrl_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49, ARCtrl_ArcStudy__ArcStudy_ToUpdateContract } from "./Contract/ArcStudy.js";
-import { exactlyOne, tryPick, append as append_1, contains as contains_2, concat, fold, choose, map as map_1 } from "@fable-org/fable-library-js/Array.js";
+import { item, equalsWith, tryPick, append as append_1, contains as contains_2, concat, fold, choose, map as map_1 } from "@fable-org/fable-library-js/Array.js";
 import { toText, printf, toFail, join, replace } from "@fable-org/fable-library-js/String.js";
 import { Run_datamapFileNameFromIdentifier, Run_fileNameFromIdentifier, Workflow_datamapFileNameFromIdentifier, Workflow_fileNameFromIdentifier, Assay_datamapFileNameFromIdentifier, Assay_fileNameFromIdentifier, Study_datamapFileNameFromIdentifier, Study_fileNameFromIdentifier, createMissingIdentifier } from "./Core/Helper/Identifier.js";
 import { FSharpSet__Contains, unionMany, contains as contains_1, ofSeq } from "@fable-org/fable-library-js/Set.js";
+import { ResizeArray_map, ResizeArray_iter } from "./Core/Helper/Collections.js";
 import { DataMap__get_StaticHash, DataMap__set_StaticHash_Z524259A4, DataMap__get_DataContexts } from "./Core/DataMap.js";
 import { FileSystemTree_Folder, FileSystemTree } from "./FileSystem/FileSystemTree.js";
 import { tryISAReadContractFromPath } from "./Contract/ARC.js";
@@ -33,8 +34,7 @@ import { Dictionary_tryGet } from "./fable_modules/FsSpreadsheet.6.3.1/Cells/FsC
 import { ARCtrl_DataMap__DataMap_tryFromReadContractForRun_Static, ARCtrl_DataMap__DataMap_tryFromReadContractForWorkflow_Static, ARCtrl_DataMap__DataMap_tryFromReadContractForStudy_Static, ARCtrl_DataMap__DataMap_tryFromReadContractForAssay_Static, ARCtrl_DataMap__DataMap_ToUpdateContractForRun_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForRun_Z721C83C5, ARCtrl_DataMap__DataMap_ToUpdateContractForWorkflow_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForWorkflow_Z721C83C5, ARCtrl_DataMap__DataMap_ToUpdateContractForAssay_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForAssay_Z721C83C5, ARCtrl_DataMap__DataMap_ToUpdateContractForStudy_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForStudy_Z721C83C5 } from "./Contract/Datamap.js";
 import { ARCtrl_ArcWorkflow__ArcWorkflow_tryFromReadContract_Static_7570923F, ARCtrl_ArcWorkflow__ArcWorkflow_ToUpdateContract, ARCtrl_ArcWorkflow__ArcWorkflow_ToCreateContract_6FCE9E49 } from "./Contract/ArcWorkflow.js";
 import { ARCtrl_ArcRun__ArcRun_tryFromReadContract_Static_7570923F, ARCtrl_ArcRun__ArcRun_ToUpdateContract, ARCtrl_ArcRun__ArcRun_ToCreateContract_6FCE9E49 } from "./Contract/ArcRun.js";
-import { Clone_createCloneContract_5000466F, Init_createAddRemoteContract_Z721C83C5, gitignoreContract, gitattributesContract, Init_createInitContract_6DFDD678 } from "./Contract/Git.js";
-import { ResizeArray_map } from "./Core/Helper/Collections.js";
+import { Clone_createCloneContract_5000466F, Init_createAddRemoteContract_Z721C83C5, gitattributesContract, gitignoreContract, Init_createInitContract_6DFDD678 } from "./Contract/Git.js";
 import { ofSeq as ofSeq_1 } from "@fable-org/fable-library-js/Map.js";
 import { fromString } from "./fable_modules/Thoth.Json.JavaScript.0.3.0/Decode.fs.js";
 import { ROCrate_encoder_8A8D439, ROCrate_get_decoder, ROCrate_get_decoderDeprecated } from "./ROCrateIO.js";
@@ -53,7 +53,7 @@ export class ARC extends ArcInvestigation {
         this._fs = ((fs_1 = defaultArg(fs, FileSystem.create({
             tree: FileSystemTree_Folder("", []),
         })), ARCAux_updateFSByISA(this$.contents, fs_1)));
-        this["init@89"] = 1;
+        this["init@90"] = 1;
     }
     get FileSystem() {
         const this$ = this;
@@ -287,12 +287,12 @@ export class ARC extends ArcInvestigation {
             }
             switch (matchResult) {
                 case 0: {
-                    col_2.Cells.forEach((c) => {
+                    ResizeArray_iter((c) => {
                         if (c.AsData.FilePath != null) {
                             const newFilePath = dataNameFunction(c.AsData);
                             c.AsData.FilePath = newFilePath;
                         }
-                    });
+                    }, col_2.Cells);
                     break;
                 }
                 case 1: {
@@ -313,19 +313,19 @@ export class ARC extends ArcInvestigation {
             }, DataMap__get_DataContexts(dm));
         };
         iterate((s) => {
-            const f = (d) => d.GetAbsolutePathForStudy(s.Identifier, checkExistenceFromRoot);
+            const f_1 = (d) => d.GetAbsolutePathForStudy(s.Identifier, checkExistenceFromRoot);
             const source_1 = s.Tables;
-            iterate(curry2(updateTable)(f), source_1);
+            iterate(curry2(updateTable)(f_1), source_1);
             if (s.DataMap != null) {
-                updateDataMap(f, value_3(s.DataMap));
+                updateDataMap(f_1, value_3(s.DataMap));
             }
         }, this$.Studies);
-        iterate((a) => {
-            const f_1 = (d_1) => d_1.GetAbsolutePathForAssay(a.Identifier, checkExistenceFromRoot);
-            const source_3 = a.Tables;
-            iterate(curry2(updateTable)(f_1), source_3);
-            if (a.DataMap != null) {
-                updateDataMap(f_1, value_3(a.DataMap));
+        iterate((a_1) => {
+            const f_2 = (d_1) => d_1.GetAbsolutePathForAssay(a_1.Identifier, checkExistenceFromRoot);
+            const source_3 = a_1.Tables;
+            iterate(curry2(updateTable)(f_2), source_3);
+            if (a_1.DataMap != null) {
+                updateDataMap(f_2, value_3(a_1.DataMap));
             }
         }, this$.Assays);
     }
@@ -381,7 +381,7 @@ export class ARC extends ArcInvestigation {
                 const registeredStudy = value_3(registeredStudyOpt);
                 registeredStudy.UpdateReferenceByStudyFile(study, true);
             }
-            const datamap = ARCAux_getAssayDataMapFromContracts(study.Identifier, contracts);
+            const datamap = ARCAux_getStudyDataMapFromContracts(study.Identifier, contracts);
             if (study.DataMap == null) {
                 study.DataMap = datamap;
             }
@@ -663,9 +663,10 @@ export class ARC extends ArcInvestigation {
             }));
         }
     }
-    GetGitInitContracts(branch, repositoryAddress, defaultGitignore) {
+    GetGitInitContracts(branch, repositoryAddress, defaultGitignore, defaultGitattributes) {
         const defaultGitignore_1 = defaultArg(defaultGitignore, false);
-        return toArray(delay(() => append(singleton(Init_createInitContract_6DFDD678(unwrap(branch))), delay(() => append(singleton(gitattributesContract), delay(() => append(defaultGitignore_1 ? singleton(gitignoreContract) : empty(), delay(() => ((repositoryAddress != null) ? singleton(Init_createAddRemoteContract_Z721C83C5(value_3(repositoryAddress))) : empty())))))))));
+        const defaultGitattributes_1 = defaultArg(defaultGitattributes, false);
+        return toArray(delay(() => append(singleton(Init_createInitContract_6DFDD678(unwrap(branch))), delay(() => append(defaultGitignore_1 ? singleton(gitignoreContract) : empty(), delay(() => append(defaultGitattributes_1 ? singleton(gitattributesContract) : empty(), delay(() => ((repositoryAddress != null) ? singleton(Init_createAddRemoteContract_Z721C83C5(value_3(repositoryAddress))) : empty())))))))));
     }
     static getCloneContract(remoteUrl, merge, branch, token, nolfs) {
         return Clone_createCloneContract_5000466F(remoteUrl, unwrap(merge), unwrap(branch), unwrap(token), unwrap(nolfs));
@@ -913,7 +914,14 @@ export function ARCAux_getRunDataMapFromContracts(runIdentifier, contracts) {
     return tryPick((c) => ARCtrl_DataMap__DataMap_tryFromReadContractForRun_Static(runIdentifier, c), contracts);
 }
 export function ARCAux_getArcInvestigationFromContracts(contracts) {
-    return exactlyOne(choose(ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F, contracts));
+    const matchValue = choose(ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F, contracts);
+    if (!equalsWith(equals, matchValue, defaultOf()) && (matchValue.length === 1)) {
+        return item(0, matchValue);
+    }
+    else {
+        const arg = matchValue.length | 0;
+        return toFail(printf("Could not find investigation in contracts. Expected exactly one investigation, but found %d."))(arg);
+    }
 }
 export function ARCAux_updateFSByISA(isa, fs) {
     let assaysFolder;

package/dist/ts/esm/ts/Conversion.js

@@ -1,13 +1,13 @@
 import { fromString } from "./fable_modules/Thoth.Json.JavaScript.0.3.0/Decode.fs.js";
 import { Decode_datetime } from "./Json/Decode.js";
-import { join, remove, toFail, printf, toText } from "@fable-org/fable-library-js/String.js";
+import { join, toFail, printf, toText } from "@fable-org/fable-library-js/String.js";
 import { bind, defaultArg, map, unwrap, value as value_4 } from "@fable-org/fable-library-js/Option.js";
 import { toString } from "./fable_modules/Thoth.Json.JavaScript.0.3.0/Encode.fs.js";
 import { dateTime } from "./Json/Encode.js";
 import { parse, tryParse } from "@fable-org/fable-library-js/Int32.js";
 import { toString as toString_1, FSharpRef } from "@fable-org/fable-library-js/Types.js";
 import { LDRef, LDNode } from "./ROCrate/LDObject.js";
-import { safeHash, equals, disposeSafe, getEnumerator, stringHash, comparePrimitives, int32ToString } from "@fable-org/fable-library-js/Util.js";
+import { safeHash, equals, disposeSafe, getEnumerator, comparePrimitives, stringHash, int32ToString } from "@fable-org/fable-library-js/Util.js";
 import { class_type } from "@fable-org/fable-library-js/Reflection.js";
 import { LDComment } from "./ROCrate/Generic/Comment.js";
 import { Comment$ } from "./Core/Comment.js";
@@ -24,17 +24,15 @@ import { DataContext_$ctor_Z780A8A2A, DataContext__get_Label, DataContext__get_D
 import { LDSample } from "./ROCrate/Generic/Sample.js";
 import { ActivePatterns_$007CRegex$007C_$007C } from "./Core/Helper/Regex.js";
 import { LDLabProtocol } from "./ROCrate/Generic/LabProtocol.js";
-import { getItemFromDict } from "@fable-org/fable-library-js/MapUtil.js";
+import { Unchecked_alignByHeaders, getEmptyCellForHeader, Unchecked_tryGetCellAt } from "./Core/Table/ArcTableAux.js";
+import { ArcTable } from "./Core/Table/ArcTable.js";
 import { LDPerson } from "./ROCrate/Generic/Person.js";
-import { isEmpty, zip, fold, singleton, empty as empty_1, append, delay, max, map as map_1, choose as choose_1, tryPick, filter, toList, indexed } from "@fable-org/fable-library-js/Seq.js";
-import { ofSeq, collect, initialize, singleton as singleton_2, sortBy, map as map_2, empty, length, choose } from "@fable-org/fable-library-js/List.js";
+import { isEmpty, zip, fold, singleton, empty as empty_1, append, delay, map as map_1, choose as choose_1, tryPick, filter, toList, indexed } from "@fable-org/fable-library-js/Seq.js";
+import { ofSeq, collect, initialize, singleton as singleton_1, sortBy, map as map_2, empty, length, choose } from "@fable-org/fable-library-js/List.js";
 import { LDLabProcess } from "./ROCrate/Generic/LabProcess.js";
 import { List_distinct, List_groupBy } from "@fable-org/fable-library-js/Seq2.js";
 import { createMissingIdentifier } from "./Core/Helper/Identifier.js";
-import { ArcTable } from "./Core/Table/ArcTable.js";
-import { singleton as singleton_1 } from "@fable-org/fable-library-js/Array.js";
 import { rangeDouble } from "@fable-org/fable-library-js/Range.js";
-import { Unchecked_alignByHeaders } from "./Core/Table/ArcTableAux.js";
 import { ArcTables } from "./Core/Table/ArcTables.js";
 import { DataMap_init, DataMap_$ctor_4E3220A7, DataMap__get_DataContexts } from "./Core/DataMap.js";
 import { LDOrganization } from "./ROCrate/Generic/Organization.js";
@@ -604,8 +602,9 @@ export function ProcessConversion_decomposeProcessName_Z721C83C5(name) {
 export function ProcessConversion_tryComponentGetter(generalI, valueI, valueHeader) {
     if (valueHeader.tag === /* Component */ 0) {
         const oa = valueHeader.fields[0];
-        return (matrix) => ((i) => {
-            const c = BaseTypes_composeComponent(valueHeader, getItemFromDict(matrix, [generalI, i]));
+        return (table) => ((i) => {
+            let matchValue;
+            const c = BaseTypes_composeComponent(valueHeader, (matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), (matchValue == null) ? getEmptyCellForHeader(valueHeader, undefined) : value_4(matchValue)));
             ARCtrl_ROCrate_LDNode__LDNode_SetColumnIndex_Z524259A4(c, valueI);
             return c;
         });
@@ -620,8 +619,9 @@ export function ProcessConversion_tryComponentGetter(generalI, valueI, valueHead
 export function ProcessConversion_tryParameterGetter(generalI, valueI, valueHeader) {
     if (valueHeader.tag === /* Parameter */ 3) {
         const oa = valueHeader.fields[0];
-        return (matrix) => ((i) => {
-            const p = BaseTypes_composeParameterValue(valueHeader, getItemFromDict(matrix, [generalI, i]));
+        return (table) => ((i) => {
+            let matchValue;
+            const p = BaseTypes_composeParameterValue(valueHeader, (matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), (matchValue == null) ? getEmptyCellForHeader(valueHeader, undefined) : value_4(matchValue)));
             ARCtrl_ROCrate_LDNode__LDNode_SetColumnIndex_Z524259A4(p, valueI);
             return p;
         });
@@ -636,8 +636,9 @@ export function ProcessConversion_tryParameterGetter(generalI, valueI, valueHead
 export function ProcessConversion_tryFactorGetter(generalI, valueI, valueHeader) {
     if (valueHeader.tag === /* Factor */ 2) {
         const oa = valueHeader.fields[0];
-        return (matrix) => ((i) => {
-            const f = BaseTypes_composeFactorValue(valueHeader, getItemFromDict(matrix, [generalI, i]));
+        return (table) => ((i) => {
+            let matchValue;
+            const f = BaseTypes_composeFactorValue(valueHeader, (matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), (matchValue == null) ? getEmptyCellForHeader(valueHeader, undefined) : value_4(matchValue)));
             ARCtrl_ROCrate_LDNode__LDNode_SetColumnIndex_Z524259A4(f, valueI);
             return f;
         });
@@ -652,8 +653,9 @@ export function ProcessConversion_tryFactorGetter(generalI, valueI, valueHeader)
 export function ProcessConversion_tryCharacteristicGetter(generalI, valueI, valueHeader) {
     if (valueHeader.tag === /* Characteristic */ 1) {
         const oa = valueHeader.fields[0];
-        return (matrix) => ((i) => {
-            const c = BaseTypes_composeCharacteristicValue(valueHeader, getItemFromDict(matrix, [generalI, i]));
+        return (table) => ((i) => {
+            let matchValue;
+            const c = BaseTypes_composeCharacteristicValue(valueHeader, (matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), (matchValue == null) ? getEmptyCellForHeader(valueHeader, undefined) : value_4(matchValue)));
             ARCtrl_ROCrate_LDNode__LDNode_SetColumnIndex_Z524259A4(c, valueI);
             return c;
         });
@@ -667,7 +669,10 @@ export function ProcessConversion_tryCharacteristicGetter(generalI, valueI, valu
  */
 export function ProcessConversion_tryGetProtocolTypeGetter(generalI, header) {
     if (header.tag === /* ProtocolType */ 4) {
-        return (matrix) => ((i) => BaseTypes_composeDefinedTerm_ZDED3A0F(getItemFromDict(matrix, [generalI, i]).AsTerm));
+        return (table) => ((i) => {
+            let matchValue, cell;
+            return BaseTypes_composeDefinedTerm_ZDED3A0F((matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), (matchValue == null) ? (new OntologyAnnotation()) : ((cell = value_4(matchValue), cell.AsTerm))));
+        });
     }
     else {
         return undefined;
@@ -678,7 +683,16 @@ export function ProcessConversion_tryGetProtocolTypeGetter(generalI, header) {
  */
 export function ProcessConversion_tryGetProtocolREFGetter(generalI, header) {
     if (header.tag === /* ProtocolREF */ 8) {
-        return (matrix) => ((i) => getItemFromDict(matrix, [generalI, i]).AsFreeText);
+        return (table) => ((i) => {
+            const matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values);
+            if (matchValue == null) {
+                return "";
+            }
+            else {
+                const cell = value_4(matchValue);
+                return cell.AsFreeText;
+            }
+        });
     }
     else {
         return undefined;
@@ -689,7 +703,16 @@ export function ProcessConversion_tryGetProtocolREFGetter(generalI, header) {
  */
 export function ProcessConversion_tryGetProtocolDescriptionGetter(generalI, header) {
     if (header.tag === /* ProtocolDescription */ 5) {
-        return (matrix) => ((i) => getItemFromDict(matrix, [generalI, i]).AsFreeText);
+        return (table) => ((i) => {
+            const matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values);
+            if (matchValue == null) {
+                return "";
+            }
+            else {
+                const cell = value_4(matchValue);
+                return cell.AsFreeText;
+            }
+        });
     }
     else {
         return undefined;
@@ -700,7 +723,16 @@ export function ProcessConversion_tryGetProtocolDescriptionGetter(generalI, head
  */
 export function ProcessConversion_tryGetProtocolURIGetter(generalI, header) {
     if (header.tag === /* ProtocolUri */ 6) {
-        return (matrix) => ((i) => getItemFromDict(matrix, [generalI, i]).AsFreeText);
+        return (table) => ((i) => {
+            const matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values);
+            if (matchValue == null) {
+                return "";
+            }
+            else {
+                const cell = value_4(matchValue);
+                return cell.AsFreeText;
+            }
+        });
     }
     else {
         return undefined;
@@ -711,7 +743,16 @@ export function ProcessConversion_tryGetProtocolURIGetter(generalI, header) {
  */
 export function ProcessConversion_tryGetProtocolVersionGetter(generalI, header) {
     if (header.tag === /* ProtocolVersion */ 7) {
-        return (matrix) => ((i) => getItemFromDict(matrix, [generalI, i]).AsFreeText);
+        return (table) => ((i) => {
+            const matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values);
+            if (matchValue == null) {
+                return "";
+            }
+            else {
+                const cell = value_4(matchValue);
+                return cell.AsFreeText;
+            }
+        });
     }
     else {
         return undefined;
@@ -723,7 +764,10 @@ export function ProcessConversion_tryGetProtocolVersionGetter(generalI, header)
 export function ProcessConversion_tryGetInputGetter(generalI, header) {
     if (header.tag === /* Input */ 11) {
         const io = header.fields[0];
-        return (matrix) => ((i) => BaseTypes_composeProcessInput(header, getItemFromDict(matrix, [generalI, i])));
+        return (table) => ((i) => {
+            let matchValue;
+            return BaseTypes_composeProcessInput(header, (matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), (matchValue == null) ? getEmptyCellForHeader(header, undefined) : value_4(matchValue)));
+        });
     }
     else {
         return undefined;
@@ -735,7 +779,10 @@ export function ProcessConversion_tryGetInputGetter(generalI, header) {
 export function ProcessConversion_tryGetOutputGetter(generalI, header) {
     if (header.tag === /* Output */ 12) {
         const io = header.fields[0];
-        return (matrix) => ((i) => BaseTypes_composeProcessOutput(header, getItemFromDict(matrix, [generalI, i])));
+        return (table) => ((i) => {
+            let matchValue;
+            return BaseTypes_composeProcessOutput(header, (matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), (matchValue == null) ? getEmptyCellForHeader(header, undefined) : value_4(matchValue)));
+        });
     }
     else {
         return undefined;
@@ -747,7 +794,10 @@ export function ProcessConversion_tryGetOutputGetter(generalI, header) {
 export function ProcessConversion_tryGetCommentGetter(generalI, header) {
     if (header.tag === /* Comment */ 14) {
         const c = header.fields[0];
-        return (matrix) => ((i) => toString_1(new Comment$(c, getItemFromDict(matrix, [generalI, i]).AsFreeText)));
+        return (table) => ((i) => {
+            let matchValue, cell;
+            return toString_1((matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values), (matchValue == null) ? (new Comment$(c)) : ((cell = value_4(matchValue), new Comment$(c, cell.AsFreeText)))));
+        });
     }
     else {
         return undefined;
@@ -755,8 +805,16 @@ export function ProcessConversion_tryGetCommentGetter(generalI, header) {
 }
 export function ProcessConversion_tryGetPerformerGetter(generalI, header) {
     if (header.tag === /* Performer */ 9) {
-        return (matrix) => ((i) => {
-            const performer = getItemFromDict(matrix, [generalI, i]).AsFreeText;
+        return (table) => ((i) => {
+            let performer;
+            const matchValue = Unchecked_tryGetCellAt(generalI, i, table.Values);
+            if (matchValue == null) {
+                performer = "";
+            }
+            else {
+                const cell = value_4(matchValue);
+                performer = cell.AsFreeText;
+            }
             return LDPerson.create(performer);
         });
     }
@@ -767,7 +825,7 @@ export function ProcessConversion_tryGetPerformerGetter(generalI, header) {
 /**
  * Given the header sequence of an ArcTable, returns a function for parsing each row of the table to a process
  */
-export function ProcessConversion_getProcessGetter(processNameRoot, headers) {
+export function ProcessConversion_getProcessGetter(assayName, studyName, processNameRoot, headers) {
     const headers_1 = indexed(headers);
     const valueHeaders = toList(indexed(filter((arg) => arg[1].IsCvParamColumn, headers_1)));
     const charGetters = choose((tupledArg) => {
@@ -796,20 +854,20 @@ export function ProcessConversion_getProcessGetter(processNameRoot, headers) {
     let inputGetter_1;
     const matchValue = tryPick((tupledArg_11) => ProcessConversion_tryGetInputGetter(tupledArg_11[0], tupledArg_11[1]), headers_1);
     if (matchValue == null) {
-        inputGetter_1 = ((length(charGetters) !== 0) ? ((matrix_1) => ((i_1) => {
+        inputGetter_1 = ((length(charGetters) !== 0) ? ((table_1) => ((i_1) => {
             let chars_1;
-            const collection_1 = map_1((f_1) => f_1(matrix_1)(i_1), charGetters);
+            const collection_1 = map_1((f_1) => f_1(table_1)(i_1), charGetters);
             chars_1 = Array.from(collection_1);
             return ResizeArray_singleton(LDSample.createSample(`${processNameRoot}_Input_${i_1}`, undefined, chars_1));
-        })) : ((matrix_2) => ((i_2) => [])));
+        })) : ((table_2) => ((i_2) => [])));
     }
     else {
         const inputGetter = value_4(matchValue);
-        inputGetter_1 = ((matrix) => ((i) => {
+        inputGetter_1 = ((table) => ((i) => {
             let chars;
-            const collection = map_1((f) => f(matrix)(i), charGetters);
+            const collection = map_1((f) => f(table)(i), charGetters);
             chars = Array.from(collection);
-            const input = inputGetter(matrix)(i);
+            const input = inputGetter(table)(i);
             if (chars.length > 0) {
                 LDSample.setAdditionalProperties(input, chars);
             }
@@ -819,41 +877,40 @@ export function ProcessConversion_getProcessGetter(processNameRoot, headers) {
     let outputGetter_1;
     const matchValue_1 = tryPick((tupledArg_12) => ProcessConversion_tryGetOutputGetter(tupledArg_12[0], tupledArg_12[1]), headers_1);
     if (matchValue_1 == null) {
-        outputGetter_1 = ((length(factorValueGetters) !== 0) ? ((matrix_4) => ((i_4) => {
+        outputGetter_1 = ((length(factorValueGetters) !== 0) ? ((table_4) => ((i_4) => {
             let factors_1;
-            const collection_3 = map_1((f_3) => f_3(matrix_4)(i_4), factorValueGetters);
+            const collection_3 = map_1((f_3) => f_3(table_4)(i_4), factorValueGetters);
             factors_1 = Array.from(collection_3);
             return ResizeArray_singleton(LDSample.createSample(`${processNameRoot}_Output_${i_4}`, undefined, factors_1));
-        })) : ((matrix_5) => ((i_5) => [])));
+        })) : ((table_5) => ((i_5) => [])));
     }
     else {
         const outputGetter = value_4(matchValue_1);
-        outputGetter_1 = ((matrix_3) => ((i_3) => {
+        outputGetter_1 = ((table_3) => ((i_3) => {
             let factors;
-            const collection_2 = map_1((f_2) => f_2(matrix_3)(i_3), factorValueGetters);
+            const collection_2 = map_1((f_2) => f_2(table_3)(i_3), factorValueGetters);
             factors = Array.from(collection_2);
-            const output = outputGetter(matrix_3)(i_3);
+            const output = outputGetter(table_3)(i_3);
             if (factors.length > 0) {
                 LDSample.setAdditionalProperties(output, factors);
             }
             return ResizeArray_singleton(output);
         }));
     }
-    return (matrix_6) => ((i_6) => {
-        const pn = ((1 + max(map_1((tuple_1) => tuple_1[1], matrix_6.keys()), {
-            Compare: comparePrimitives,
-        })) === 1) ? processNameRoot : ProcessConversion_composeProcessName(processNameRoot, i_6);
-        const paramvalues = map((collection_4) => Array.from(collection_4), Option_fromValueWithDefault(empty(), map_2((f_4) => f_4(matrix_6)(i_6), parameterValueGetters)));
-        const comments = map((collection_5) => Array.from(collection_5), Option_fromValueWithDefault(empty(), map_2((f_5) => f_5(matrix_6)(i_6), commentGetters)));
-        const components = map((collection_6) => Array.from(collection_6), Option_fromValueWithDefault(empty(), map_2((f_6) => f_6(matrix_6)(i_6), componentGetters)));
+    return (table_6) => ((i_6) => {
+        const pn = (table_6.RowCount === 1) ? processNameRoot : ProcessConversion_composeProcessName(processNameRoot, i_6);
+        const paramvalues = map((collection_4) => Array.from(collection_4), Option_fromValueWithDefault(empty(), map_2((f_4) => f_4(table_6)(i_6), parameterValueGetters)));
+        const comments = map((collection_5) => Array.from(collection_5), Option_fromValueWithDefault(empty(), map_2((f_5) => f_5(table_6)(i_6), commentGetters)));
+        const components = map((collection_6) => Array.from(collection_6), Option_fromValueWithDefault(empty(), map_2((f_6) => f_6(table_6)(i_6), componentGetters)));
+        const id = LDLabProcess.genId(processNameRoot, unwrap(assayName), unwrap(studyName)) + (`_${i_6}`);
         let protocol;
-        const name = map((f_7) => f_7(matrix_6)(i_6), protocolREFGetter);
+        const name = map((f_7) => f_7(table_6)(i_6), protocolREFGetter);
         const protocolId = LDLabProtocol.genId(unwrap(name), processNameRoot);
-        protocol = LDLabProtocol.create(protocolId, unwrap(name), unwrap(map((f_8) => f_8(matrix_6)(i_6), protocolDescriptionGetter)), unwrap(map((f_9) => f_9(matrix_6)(i_6), protocolTypeGetter)), undefined, undefined, unwrap(components), undefined, unwrap(map((f_10) => f_10(matrix_6)(i_6), protocolURIGetter)), unwrap(map((f_11) => f_11(matrix_6)(i_6), protocolVersionGetter)));
-        const matchValue_2 = inputGetter_1(matrix_6)(i_6);
-        const matchValue_3 = outputGetter_1(matrix_6)(i_6);
-        const agent = map((f_12) => f_12(matrix_6)(i_6), performerGetter);
-        return LDLabProcess.create(pn, matchValue_2, matchValue_3, undefined, unwrap(agent), unwrap(protocol), unwrap(paramvalues), undefined, unwrap(comments));
+        protocol = LDLabProtocol.create(protocolId, unwrap(name), unwrap(map((f_8) => f_8(table_6)(i_6), protocolDescriptionGetter)), unwrap(map((f_9) => f_9(table_6)(i_6), protocolTypeGetter)), undefined, undefined, unwrap(components), undefined, unwrap(map((f_10) => f_10(table_6)(i_6), protocolURIGetter)), unwrap(map((f_11) => f_11(table_6)(i_6), protocolVersionGetter)));
+        const matchValue_2 = inputGetter_1(table_6)(i_6);
+        const matchValue_3 = outputGetter_1(table_6)(i_6);
+        const agent = map((f_12) => f_12(table_6)(i_6), performerGetter);
+        return LDLabProcess.create(pn, matchValue_2, matchValue_3, id, unwrap(agent), unwrap(protocol), unwrap(paramvalues), undefined, unwrap(comments));
     });
 }
 /**
@@ -865,36 +922,28 @@ export function ProcessConversion_getProcessGetter(processNameRoot, headers) {
  */
 export function ProcessConversion_groupProcesses_Z27F0B586(processes, graph, context) {
     return List_groupBy((p) => {
-        let protocol, name_1, name_2, protocol_1;
+        let protocol, protocol_1;
         const matchValue = LDLabProcess.tryGetNameAsString(p, unwrap(context));
         const matchValue_1 = LDLabProcess.tryGetExecutesLabProtocol(p, unwrap(graph), unwrap(context));
-        let matchResult, name_3, protocol_2, name_4, name_5, protocol_3;
+        let matchResult, name_1, protocol_2, name_2, protocol_3;
         if (matchValue != null) {
             if (ProcessConversion_decomposeProcessName_Z721C83C5(value_4(matchValue))[1] != null) {
                 matchResult = 0;
-                name_3 = value_4(matchValue);
+                name_1 = value_4(matchValue);
             }
             else if (matchValue_1 != null) {
                 if ((protocol = value_4(matchValue_1), LDLabProtocol.tryGetNameAsString(protocol, unwrap(context)) != null)) {
                     matchResult = 1;
                     protocol_2 = value_4(matchValue_1);
                 }
-                else if ((name_1 = value_4(matchValue), name_1.indexOf("_") >= 0)) {
-                    matchResult = 2;
-                    name_4 = value_4(matchValue);
-                }
                 else {
-                    matchResult = 3;
-                    name_5 = value_4(matchValue);
+                    matchResult = 2;
+                    name_2 = value_4(matchValue);
                 }
             }
-            else if ((name_2 = value_4(matchValue), name_2.indexOf("_") >= 0)) {
-                matchResult = 2;
-                name_4 = value_4(matchValue);
-            }
             else {
-                matchResult = 3;
-                name_5 = value_4(matchValue);
+                matchResult = 2;
+                name_2 = value_4(matchValue);
             }
         }
         else if (matchValue_1 != null) {
@@ -903,23 +952,21 @@ export function ProcessConversion_groupProcesses_Z27F0B586(processes, graph, con
                 protocol_2 = value_4(matchValue_1);
             }
             else {
-                matchResult = 4;
+                matchResult = 3;
                 protocol_3 = value_4(matchValue_1);
             }
         }
         else {
-            matchResult = 5;
+            matchResult = 4;
         }
         switch (matchResult) {
             case 0:
-                return ProcessConversion_decomposeProcessName_Z721C83C5(name_3)[0];
+                return ProcessConversion_decomposeProcessName_Z721C83C5(name_1)[0];
             case 1:
                 return defaultArg(LDLabProtocol.tryGetNameAsString(protocol_2, unwrap(context)), "");
             case 2:
-                return remove(name_4, name_4.lastIndexOf("_"));
+                return name_2;
             case 3:
-                return name_5;
-            case 4:
                 return protocol_3.Id;
             default:
                 return createMissingIdentifier();
@@ -1126,25 +1173,25 @@ export function ARCtrl_ArcTable__ArcTable_fromProtocol_Static_Z6839B9E8(p, graph
         while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
             const c = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
             const patternInput = BaseTypes_decomposeComponent_Z2F770004(c, unwrap(context));
-            t.AddColumn(patternInput[0], singleton_1(patternInput[1]), unwrap(ARCtrl_ROCrate_LDNode__LDNode_TryGetColumnIndex(c)));
+            t.AddColumn(patternInput[0], ResizeArray_singleton(patternInput[1]), unwrap(ARCtrl_ROCrate_LDNode__LDNode_TryGetColumnIndex(c)));
         }
     }
     finally {
         disposeSafe(enumerator);
     }
     map((d) => {
-        t.AddProtocolDescriptionColumn([d]);
+        t.AddProtocolDescriptionColumn(ResizeArray_singleton(d));
     }, LDLabProtocol.tryGetDescriptionAsString(p, unwrap(context)));
     map((d_1) => {
-        t.AddProtocolVersionColumn([d_1]);
+        t.AddProtocolVersionColumn(ResizeArray_singleton(d_1));
     }, LDLabProtocol.tryGetVersionAsString(p, unwrap(context)));
     map((d_2) => {
-        t.AddProtocolTypeColumn([d_2]);
+        t.AddProtocolTypeColumn(ResizeArray_singleton(d_2));
     }, ProcessConversion_tryGetProtocolType_Z6839B9E8(p, undefined, unwrap(context)));
     map((d_3) => {
-        t.AddProtocolUriColumn([d_3]);
+        t.AddProtocolUriColumn(ResizeArray_singleton(d_3));
     }, LDLabProtocol.tryGetUrl(p, unwrap(context)));
-    t.AddProtocolNameColumn([name]);
+    t.AddProtocolNameColumn(ResizeArray_singleton(name));
     return t;
 }
 /**
@@ -1153,7 +1200,7 @@ export function ARCtrl_ArcTable__ArcTable_fromProtocol_Static_Z6839B9E8(p, graph
 export function ARCtrl_ArcTable__ArcTable_GetProtocols(this$) {
     let source;
     if (this$.RowCount === 0) {
-        return singleton_2((source = this$.Headers, fold((p, h) => {
+        return singleton_1((source = this$.Headers, fold((p, h) => {
             if (h.tag === /* Component */ 0) {
                 const oa = h.fields[0];
                 const matchValue = oa.NameText;
@@ -1179,13 +1226,13 @@ export function ARCtrl_ArcTable__ArcTable_GetProtocols(this$) {
 /**
  * Returns the list of processes specidified in this ArcTable
  */
-export function ARCtrl_ArcTable__ArcTable_GetProcesses(this$) {
+export function ARCtrl_ArcTable__ArcTable_GetProcesses_40457300(this$, assayName, studyName) {
     if (this$.RowCount === 0) {
-        return singleton_2(LDLabProcess.create(this$.Name));
+        return singleton_1(LDLabProcess.create(this$.Name));
     }
     else {
-        const getter = ProcessConversion_getProcessGetter(this$.Name, this$.Headers);
-        return toList(delay(() => map_1((i) => getter(this$.Values)(i), rangeDouble(0, 1, this$.RowCount - 1))));
+        const getter = ProcessConversion_getProcessGetter(assayName, studyName, this$.Name, this$.Headers);
+        return toList(delay(() => map_1((i) => getter(this$)(i), rangeDouble(0, 1, this$.RowCount - 1))));
     }
 }
 /**
@@ -1197,13 +1244,13 @@ export function ARCtrl_ArcTable__ArcTable_GetProcesses(this$) {
  */
 export function ARCtrl_ArcTable__ArcTable_fromProcesses_Static_Z3575FB5F(name, ps, graph, context) {
     const tupledArg = Unchecked_alignByHeaders(true, collect((p) => ofSeq(ProcessConversion_processToRows_Z6839B9E8(p, unwrap(graph), unwrap(context))), ps));
-    return ArcTable.create(name, tupledArg[0], tupledArg[1]);
+    return ArcTable.fromArcTableValues(name, tupledArg[0], tupledArg[1]);
 }
 /**
  * Return a list of all the processes in all the tables.
  */
-export function ARCtrl_ArcTables__ArcTables_GetProcesses(this$) {
-    return collect(ARCtrl_ArcTable__ArcTable_GetProcesses, toList(this$.Tables));
+export function ARCtrl_ArcTables__ArcTables_GetProcesses_40457300(this$, assayName, studyName) {
+    return collect((t) => ARCtrl_ArcTable__ArcTable_GetProcesses_40457300(t, unwrap(assayName), unwrap(studyName)), toList(this$.Tables));
 }
 /**
  * Create a collection of tables from a list of processes.
@@ -1216,7 +1263,7 @@ export function ARCtrl_ArcTables__ArcTables_fromProcesses_Static_Z27F0B586(ps, g
     let collection;
     return new ArcTables((collection = map_2((tupledArg) => {
         const tupledArg_1 = Unchecked_alignByHeaders(true, collect((p) => ofSeq(ProcessConversion_processToRows_Z6839B9E8(p, unwrap(graph), unwrap(context))), tupledArg[1]));
-        return ArcTable.create(tupledArg[0], tupledArg_1[0], tupledArg_1[1]);
+        return ArcTable.fromArcTableValues(tupledArg[0], tupledArg_1[0], tupledArg_1[1]);
     }, ProcessConversion_groupProcesses_Z27F0B586(ps, unwrap(graph), unwrap(context))), Array.from(collection)));
 }
 export class DatamapConversion {
@@ -1453,7 +1500,7 @@ export function AssayConversion_composeAssay_1501C0F8(assay) {
     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(new ArcTables(assay.Tables)), Array.from(collection)));
+    const processSequence = Option_fromSeq((collection = ARCtrl_ArcTables__ArcTables_GetProcesses_40457300(new ArcTables(assay.Tables), assay.Identifier), Array.from(collection)));
     const fragmentDescriptors = map(DatamapConversion_composeFragmentDescriptors_Z8923FA3, assay.DataMap);
     const dataFiles = map((ps) => AssayConversion_getDataFilesFromProcesses_6BABD1B0(ps, unwrap(fragmentDescriptors)), processSequence);
     const variableMeasureds = (variableMeasured == null) ? ((fragmentDescriptors == null) ? undefined : ((fds_1 = value_4(fragmentDescriptors), fds_1))) : ((fragmentDescriptors == null) ? ((vm_1 = value_4(variableMeasured), ResizeArray_singleton(vm_1))) : ((fds = value_4(fragmentDescriptors), (vm = value_4(variableMeasured), ResizeArray_appendSingleton(vm, fds)))));
@@ -1486,7 +1533,7 @@ export function StudyConversion_composeStudy_1680536E(study) {
     const dateModified = now();
     const publications = Option_fromSeq(ResizeArray_map(ScholarlyArticleConversion_composeScholarlyArticle_D324A6D, study.Publications));
     const creators = Option_fromSeq(ResizeArray_map(PersonConversion_composePerson_Z64D846DC, study.Contacts));
-    const processSequence = Option_fromSeq((collection = ARCtrl_ArcTables__ArcTables_GetProcesses(new ArcTables(study.Tables)), Array.from(collection)));
+    const processSequence = Option_fromSeq((collection = ARCtrl_ArcTables__ArcTables_GetProcesses_40457300(new ArcTables(study.Tables), undefined, study.Identifier), Array.from(collection)));
     const fragmentDescriptors = map(DatamapConversion_composeFragmentDescriptors_Z8923FA3, study.DataMap);
     const dataFiles = map((ps) => AssayConversion_getDataFilesFromProcesses_6BABD1B0(ps, unwrap(fragmentDescriptors)), processSequence);
     const comments = Option_fromSeq(ResizeArray_map(BaseTypes_composeComment_Z13201A7E, study.Comments));

package/dist/ts/esm/ts/Core/ArcTypes.js

@@ -1607,7 +1607,7 @@ export class ArcRun extends ArcTables {
             return newRun;
         };
     }
-    static updateTable(name, updateFun) {
+    static mapTable(name, updateFun) {
         return (run) => {
             const newRun = run.Copy();
             newRun.MapTable(name, updateFun);