@nfdi4plants/arctrl 3.0.0-alpha.4 → 3.0.0-beta.1

package/README.md

@@ -90,11 +90,19 @@ Measured on 13th Gen Intel(R) Core(TM) i7-13800H
 
 | Name | Description | FSharp Time (ms) | JavaScript Time (ms) | Python Time (ms) |
 | --- | --- | --- | --- | --- |
-| Table_GetHashCode | From a table with 1 column and 10000 rows, retrieve the Hash Code |  2 ± 0 | 9 ± 7 | 133 ± 7 |
-| Table_AddRows | Add 10000 rows to a table with 4 columns. |  40 ± 9 | 20 ± 8 | 309 ± 26 |
-| Table_fillMissingCells | For a table 6 columns and 20000 rows, where each row has one missing value, fill those values with default values. | 55 ± 31 | 101 ± 11 | 3375 ± 221 |
-| Table_ToJson | Serialize a table with 5 columns and 10000 rows to json. |  1027 ± 200 | 293 ± 56 | 17990 ± 1482 |
-| Table_ToCompressedJson | Serialize a table with 5 columns and 10000 rows to compressed json. |  216 ± 19 |  4552 ± 326 | 6188 ± 839 |
-| Assay_toJson | Parse an assay with one table with 10000 rows and 6 columns to json |  856 ± 42 | 271 ± 55 | 19278 ± 1289 |
-| Study_FromWorkbook | Parse a workbook with one study with 10000 rows and 6 columns to an ArcStudy |  84 ± 29 | 96 ± 12 | 1787 ± 1410 |
-| Investigation_ToWorkbook_ManyStudies | Parse an investigation with 1500 studies to a workbook |  387 ± 71 | 442 ± 61 | 6305 ± 660 |
+| Table_GetHashCode | From a table with 1 column and 10000 rows, retrieve the Hash Code | 0 ± 0 | 0 ± 1 | 91 ± 12 |
+| Table_AddDistinctRows | Add 10000 distinct rows to a table with 4 columns. | 13 ± 2 | 14 ± 4 | 119 ± 12 |
+| Table_AddIdenticalRows | Add 10000 identical rows to a table with 4 columns. | 6 ± 2 | 6 ± 1 | 104 ± 6 |
+| Table_AddColumnsWithDistinctValues | Add 4 columns with 10000 distinct values each. | 8 ± 3 | 10 ± 1 | 53 ± 1 |
+| Table_AddColumnsWithIdenticalValues | Add 4 columns with 10000 identical values each. | 5 ± 1 | 4 ± 0 | 47 ± 1 |
+| Table_fillMissingCells | For a table 6 columns and 20000 rows, where each row has one missing value, fill those values with default values. | 0 ± 0 |  2 ± 1 | 6 ± 4 |
+| Table_ToJson | Serialize a table with 5 columns and 10000 rows to json, with 3 fixed and 2 variable columns. | 227 ± 64 | 68 ± 18 | 7851 ± 1411 |
+| Table_ToCompressedJson | Serialize a table with 5 columns and 10000 rows to compressed json, with 3 fixed and 2 variable columns. | 147 ± 15 | 2878 ± 135 | 6303 ± 1798 |
+| Assay_toJson | Parse an assay with one table with 10000 rows and 6 columns to json, with 3 fixed and 3 variable columns. | 330 ± 36 | 88 ± 9 | 12644 ± 550 |
+| Assay_fromJson | Parse an assay with one table with 10000 rows and 6 columns from json, with 3 fixed and 3 variable columns. | 355 ± 66 | 61 ± 6 | 6499 ± 1068 |
+| Assay_toISAJson | Parse an assay with one table with 10000 rows and 6 columns to json, with 3 fixed and 3 variable columns | 487 ± 36 | 959 ± 36 | 15618 ± 482 |
+| Assay_fromISAJson | Parse an assay with one table with 10000 rows and 6 columns from json, with 3 fixed and 3 variable columns | 359 ± 29 | 706 ± 46 | 9587 ± 621 |
+| Study_FromWorkbook | Parse a workbook with one study with 10000 rows and 6 columns to an ArcStudy | 29 ± 14 | 62 ± 5 | 818 ± 36 |
+| Investigation_ToWorkbook_ManyStudies | Parse an investigation with 1500 studies to a workbook | 240 ± 31 | 284 ± 24 | 3657 ± 199 |
+| Investigation_FromWorkbook_ManyStudies | Parse a workbook with 1500 studies to an ArcInvestigation | 127 ± 20 | 498 ± 21 | 9469 ± 412 |
+| ARC_ToROCrate | Parse an ARC with one assay with 10000 rows and 6 columns to a RO-Crate metadata file. | 1431 ± 99 | 3526 ± 264 | 61224 ± 728 |

package/dist/ts/cjs/ts/ARC.js

@@ -33,6 +33,7 @@ const Array_js_1 = require("@fable-org/fable-library-js/Array.js");
 const String_js_1 = require("@fable-org/fable-library-js/String.js");
 const Identifier_js_1 = require("./Core/Helper/Identifier.js");
 const Set_js_1 = require("@fable-org/fable-library-js/Set.js");
+const Collections_js_1 = require("./Core/Helper/Collections.js");
 const DataMap_js_1 = require("./Core/DataMap.js");
 const FileSystemTree_js_1 = require("./FileSystem/FileSystemTree.js");
 const ARC_js_1 = require("./Contract/ARC.js");
@@ -50,7 +51,6 @@ const Datamap_js_1 = require("./Contract/Datamap.js");
 const ArcWorkflow_js_2 = require("./Contract/ArcWorkflow.js");
 const ArcRun_js_2 = require("./Contract/ArcRun.js");
 const Git_js_1 = require("./Contract/Git.js");
-const Collections_js_1 = require("./Core/Helper/Collections.js");
 const Map_js_1 = require("@fable-org/fable-library-js/Map.js");
 const Decode_fs_js_1 = require("./fable_modules/Thoth.Json.JavaScript.0.3.0/Decode.fs.js");
 const ROCrateIO_js_1 = require("./ROCrateIO.js");
@@ -69,7 +69,7 @@ class ARC extends ArcTypes_js_1.ArcInvestigation {
         this._fs = ((fs_1 = (0, Option_js_1.defaultArg)(fs, FileSystem_js_1.FileSystem.create({
             tree: (0, FileSystemTree_js_1.FileSystemTree_Folder)("", []),
         })), ARCAux_updateFSByISA(this$.contents, fs_1)));
-        this["init@89"] = 1;
+        this["init@90"] = 1;
     }
     get FileSystem() {
         const this$ = this;
@@ -303,12 +303,12 @@ class ARC extends ArcTypes_js_1.ArcInvestigation {
             }
             switch (matchResult) {
                 case 0: {
-                    col_2.Cells.forEach((c) => {
+                    (0, Collections_js_1.ResizeArray_iter)((c) => {
                         if (c.AsData.FilePath != null) {
                             const newFilePath = dataNameFunction(c.AsData);
                             c.AsData.FilePath = newFilePath;
                         }
-                    });
+                    }, col_2.Cells);
                     break;
                 }
                 case 1: {
@@ -329,19 +329,19 @@ class ARC extends ArcTypes_js_1.ArcInvestigation {
             }, (0, DataMap_js_1.DataMap__get_DataContexts)(dm));
         };
         (0, Seq_js_1.iterate)((s) => {
-            const f = (d) => d.GetAbsolutePathForStudy(s.Identifier, checkExistenceFromRoot);
+            const f_1 = (d) => d.GetAbsolutePathForStudy(s.Identifier, checkExistenceFromRoot);
             const source_1 = s.Tables;
-            (0, Seq_js_1.iterate)((0, Util_js_1.curry2)(updateTable)(f), source_1);
+            (0, Seq_js_1.iterate)((0, Util_js_1.curry2)(updateTable)(f_1), source_1);
             if (s.DataMap != null) {
-                updateDataMap(f, (0, Option_js_1.value)(s.DataMap));
+                updateDataMap(f_1, (0, Option_js_1.value)(s.DataMap));
             }
         }, this$.Studies);
-        (0, Seq_js_1.iterate)((a) => {
-            const f_1 = (d_1) => d_1.GetAbsolutePathForAssay(a.Identifier, checkExistenceFromRoot);
-            const source_3 = a.Tables;
-            (0, Seq_js_1.iterate)((0, Util_js_1.curry2)(updateTable)(f_1), source_3);
-            if (a.DataMap != null) {
-                updateDataMap(f_1, (0, Option_js_1.value)(a.DataMap));
+        (0, Seq_js_1.iterate)((a_1) => {
+            const f_2 = (d_1) => d_1.GetAbsolutePathForAssay(a_1.Identifier, checkExistenceFromRoot);
+            const source_3 = a_1.Tables;
+            (0, Seq_js_1.iterate)((0, Util_js_1.curry2)(updateTable)(f_2), source_3);
+            if (a_1.DataMap != null) {
+                updateDataMap(f_2, (0, Option_js_1.value)(a_1.DataMap));
             }
         }, this$.Assays);
     }
@@ -397,7 +397,7 @@ class ARC extends ArcTypes_js_1.ArcInvestigation {
                 const registeredStudy = (0, Option_js_1.value)(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;
             }
@@ -679,9 +679,10 @@ class ARC extends ArcTypes_js_1.ArcInvestigation {
             }));
         }
     }
-    GetGitInitContracts(branch, repositoryAddress, defaultGitignore) {
+    GetGitInitContracts(branch, repositoryAddress, defaultGitignore, defaultGitattributes) {
         const defaultGitignore_1 = (0, Option_js_1.defaultArg)(defaultGitignore, false);
-        return (0, Seq_js_1.toArray)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Git_js_1.Init_createInitContract_6DFDD678)((0, Option_js_1.unwrap)(branch))), (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)(Git_js_1.gitattributesContract), (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)(defaultGitignore_1 ? (0, Seq_js_1.singleton)(Git_js_1.gitignoreContract) : (0, Seq_js_1.empty)(), (0, Seq_js_1.delay)(() => ((repositoryAddress != null) ? (0, Seq_js_1.singleton)((0, Git_js_1.Init_createAddRemoteContract_Z721C83C5)((0, Option_js_1.value)(repositoryAddress))) : (0, Seq_js_1.empty)())))))))));
+        const defaultGitattributes_1 = (0, Option_js_1.defaultArg)(defaultGitattributes, false);
+        return (0, Seq_js_1.toArray)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, Git_js_1.Init_createInitContract_6DFDD678)((0, Option_js_1.unwrap)(branch))), (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)(defaultGitignore_1 ? (0, Seq_js_1.singleton)(Git_js_1.gitignoreContract) : (0, Seq_js_1.empty)(), (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)(defaultGitattributes_1 ? (0, Seq_js_1.singleton)(Git_js_1.gitattributesContract) : (0, Seq_js_1.empty)(), (0, Seq_js_1.delay)(() => ((repositoryAddress != null) ? (0, Seq_js_1.singleton)((0, Git_js_1.Init_createAddRemoteContract_Z721C83C5)((0, Option_js_1.value)(repositoryAddress))) : (0, Seq_js_1.empty)())))))))));
     }
     static getCloneContract(remoteUrl, merge, branch, token, nolfs) {
         return (0, Git_js_1.Clone_createCloneContract_5000466F)(remoteUrl, (0, Option_js_1.unwrap)(merge), (0, Option_js_1.unwrap)(branch), (0, Option_js_1.unwrap)(token), (0, Option_js_1.unwrap)(nolfs));
@@ -930,7 +931,14 @@ function ARCAux_getRunDataMapFromContracts(runIdentifier, contracts) {
     return (0, Array_js_1.tryPick)((c) => (0, Datamap_js_1.ARCtrl_DataMap__DataMap_tryFromReadContractForRun_Static)(runIdentifier, c), contracts);
 }
 function ARCAux_getArcInvestigationFromContracts(contracts) {
-    return (0, Array_js_1.exactlyOne)((0, Array_js_1.choose)(ArcInvestigation_js_1.ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F, contracts));
+    const matchValue = (0, Array_js_1.choose)(ArcInvestigation_js_1.ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F, contracts);
+    if (!(0, Array_js_1.equalsWith)(Util_js_1.equals, matchValue, (0, Util_js_1.defaultOf)()) && (matchValue.length === 1)) {
+        return (0, Array_js_1.item)(0, matchValue);
+    }
+    else {
+        const arg = matchValue.length | 0;
+        return (0, String_js_1.toFail)((0, String_js_1.printf)("Could not find investigation in contracts. Expected exactly one investigation, but found %d."))(arg);
+    }
 }
 function ARCAux_updateFSByISA(isa, fs) {
     let assaysFolder;

package/dist/ts/cjs/ts/Conversion.js

@@ -135,17 +135,15 @@ const DataContext_js_1 = require("./Core/DataContext.js");
 const Sample_js_1 = require("./ROCrate/Generic/Sample.js");
 const Regex_js_1 = require("./Core/Helper/Regex.js");
 const LabProtocol_js_1 = require("./ROCrate/Generic/LabProtocol.js");
-const MapUtil_js_1 = require("@fable-org/fable-library-js/MapUtil.js");
+const ArcTableAux_js_1 = require("./Core/Table/ArcTableAux.js");
+const ArcTable_js_1 = require("./Core/Table/ArcTable.js");
 const Person_js_1 = require("./ROCrate/Generic/Person.js");
 const Seq_js_1 = require("@fable-org/fable-library-js/Seq.js");
 const List_js_1 = require("@fable-org/fable-library-js/List.js");
 const LabProcess_js_1 = require("./ROCrate/Generic/LabProcess.js");
 const Seq2_js_1 = require("@fable-org/fable-library-js/Seq2.js");
 const Identifier_js_1 = require("./Core/Helper/Identifier.js");
-const ArcTable_js_1 = require("./Core/Table/ArcTable.js");
-const Array_js_1 = require("@fable-org/fable-library-js/Array.js");
 const Range_js_1 = require("@fable-org/fable-library-js/Range.js");
-const ArcTableAux_js_1 = require("./Core/Table/ArcTableAux.js");
 const ArcTables_js_1 = require("./Core/Table/ArcTables.js");
 const DataMap_js_1 = require("./Core/DataMap.js");
 const Organization_js_1 = require("./ROCrate/Generic/Organization.js");
@@ -717,8 +715,9 @@ function ProcessConversion_decomposeProcessName_Z721C83C5(name) {
 function ProcessConversion_tryComponentGetter(generalI, valueI, valueHeader) {
     if (valueHeader.tag === /* Component */ 0) {
         const oa = valueHeader.fields[0];
-        return (matrix) => ((i) => {
-            const c = BaseTypes_composeComponent(valueHeader, (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i]));
+        return (table) => ((i) => {
+            let matchValue;
+            const c = BaseTypes_composeComponent(valueHeader, (matchValue = (0, ArcTableAux_js_1.Unchecked_tryGetCellAt)(generalI, i, table.Values), (matchValue == null) ? (0, ArcTableAux_js_1.getEmptyCellForHeader)(valueHeader, undefined) : (0, Option_js_1.value)(matchValue)));
             ARCtrl_ROCrate_LDNode__LDNode_SetColumnIndex_Z524259A4(c, valueI);
             return c;
         });
@@ -733,8 +732,9 @@ function ProcessConversion_tryComponentGetter(generalI, valueI, valueHeader) {
 function ProcessConversion_tryParameterGetter(generalI, valueI, valueHeader) {
     if (valueHeader.tag === /* Parameter */ 3) {
         const oa = valueHeader.fields[0];
-        return (matrix) => ((i) => {
-            const p = BaseTypes_composeParameterValue(valueHeader, (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i]));
+        return (table) => ((i) => {
+            let matchValue;
+            const p = BaseTypes_composeParameterValue(valueHeader, (matchValue = (0, ArcTableAux_js_1.Unchecked_tryGetCellAt)(generalI, i, table.Values), (matchValue == null) ? (0, ArcTableAux_js_1.getEmptyCellForHeader)(valueHeader, undefined) : (0, Option_js_1.value)(matchValue)));
             ARCtrl_ROCrate_LDNode__LDNode_SetColumnIndex_Z524259A4(p, valueI);
             return p;
         });
@@ -749,8 +749,9 @@ function ProcessConversion_tryParameterGetter(generalI, valueI, valueHeader) {
 function ProcessConversion_tryFactorGetter(generalI, valueI, valueHeader) {
     if (valueHeader.tag === /* Factor */ 2) {
         const oa = valueHeader.fields[0];
-        return (matrix) => ((i) => {
-            const f = BaseTypes_composeFactorValue(valueHeader, (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i]));
+        return (table) => ((i) => {
+            let matchValue;
+            const f = BaseTypes_composeFactorValue(valueHeader, (matchValue = (0, ArcTableAux_js_1.Unchecked_tryGetCellAt)(generalI, i, table.Values), (matchValue == null) ? (0, ArcTableAux_js_1.getEmptyCellForHeader)(valueHeader, undefined) : (0, Option_js_1.value)(matchValue)));
             ARCtrl_ROCrate_LDNode__LDNode_SetColumnIndex_Z524259A4(f, valueI);
             return f;
         });
@@ -765,8 +766,9 @@ function ProcessConversion_tryFactorGetter(generalI, valueI, valueHeader) {
 function ProcessConversion_tryCharacteristicGetter(generalI, valueI, valueHeader) {
     if (valueHeader.tag === /* Characteristic */ 1) {
         const oa = valueHeader.fields[0];
-        return (matrix) => ((i) => {
-            const c = BaseTypes_composeCharacteristicValue(valueHeader, (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i]));
+        return (table) => ((i) => {
+            let matchValue;
+            const c = BaseTypes_composeCharacteristicValue(valueHeader, (matchValue = (0, ArcTableAux_js_1.Unchecked_tryGetCellAt)(generalI, i, table.Values), (matchValue == null) ? (0, ArcTableAux_js_1.getEmptyCellForHeader)(valueHeader, undefined) : (0, Option_js_1.value)(matchValue)));
             ARCtrl_ROCrate_LDNode__LDNode_SetColumnIndex_Z524259A4(c, valueI);
             return c;
         });
@@ -780,7 +782,10 @@ function ProcessConversion_tryCharacteristicGetter(generalI, valueI, valueHeader
  */
 function ProcessConversion_tryGetProtocolTypeGetter(generalI, header) {
     if (header.tag === /* ProtocolType */ 4) {
-        return (matrix) => ((i) => BaseTypes_composeDefinedTerm_ZDED3A0F((0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i]).AsTerm));
+        return (table) => ((i) => {
+            let matchValue, cell;
+            return BaseTypes_composeDefinedTerm_ZDED3A0F((matchValue = (0, ArcTableAux_js_1.Unchecked_tryGetCellAt)(generalI, i, table.Values), (matchValue == null) ? (new OntologyAnnotation_js_1.OntologyAnnotation()) : ((cell = (0, Option_js_1.value)(matchValue), cell.AsTerm))));
+        });
     }
     else {
         return undefined;
@@ -791,7 +796,16 @@ function ProcessConversion_tryGetProtocolTypeGetter(generalI, header) {
  */
 function ProcessConversion_tryGetProtocolREFGetter(generalI, header) {
     if (header.tag === /* ProtocolREF */ 8) {
-        return (matrix) => ((i) => (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i]).AsFreeText);
+        return (table) => ((i) => {
+            const matchValue = (0, ArcTableAux_js_1.Unchecked_tryGetCellAt)(generalI, i, table.Values);
+            if (matchValue == null) {
+                return "";
+            }
+            else {
+                const cell = (0, Option_js_1.value)(matchValue);
+                return cell.AsFreeText;
+            }
+        });
     }
     else {
         return undefined;
@@ -802,7 +816,16 @@ function ProcessConversion_tryGetProtocolREFGetter(generalI, header) {
  */
 function ProcessConversion_tryGetProtocolDescriptionGetter(generalI, header) {
     if (header.tag === /* ProtocolDescription */ 5) {
-        return (matrix) => ((i) => (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i]).AsFreeText);
+        return (table) => ((i) => {
+            const matchValue = (0, ArcTableAux_js_1.Unchecked_tryGetCellAt)(generalI, i, table.Values);
+            if (matchValue == null) {
+                return "";
+            }
+            else {
+                const cell = (0, Option_js_1.value)(matchValue);
+                return cell.AsFreeText;
+            }
+        });
     }
     else {
         return undefined;
@@ -813,7 +836,16 @@ function ProcessConversion_tryGetProtocolDescriptionGetter(generalI, header) {
  */
 function ProcessConversion_tryGetProtocolURIGetter(generalI, header) {
     if (header.tag === /* ProtocolUri */ 6) {
-        return (matrix) => ((i) => (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i]).AsFreeText);
+        return (table) => ((i) => {
+            const matchValue = (0, ArcTableAux_js_1.Unchecked_tryGetCellAt)(generalI, i, table.Values);
+            if (matchValue == null) {
+                return "";
+            }
+            else {
+                const cell = (0, Option_js_1.value)(matchValue);
+                return cell.AsFreeText;
+            }
+        });
     }
     else {
         return undefined;
@@ -824,7 +856,16 @@ function ProcessConversion_tryGetProtocolURIGetter(generalI, header) {
  */
 function ProcessConversion_tryGetProtocolVersionGetter(generalI, header) {
     if (header.tag === /* ProtocolVersion */ 7) {
-        return (matrix) => ((i) => (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i]).AsFreeText);
+        return (table) => ((i) => {
+            const matchValue = (0, ArcTableAux_js_1.Unchecked_tryGetCellAt)(generalI, i, table.Values);
+            if (matchValue == null) {
+                return "";
+            }
+            else {
+                const cell = (0, Option_js_1.value)(matchValue);
+                return cell.AsFreeText;
+            }
+        });
     }
     else {
         return undefined;
@@ -836,7 +877,10 @@ function ProcessConversion_tryGetProtocolVersionGetter(generalI, header) {
 function ProcessConversion_tryGetInputGetter(generalI, header) {
     if (header.tag === /* Input */ 11) {
         const io = header.fields[0];
-        return (matrix) => ((i) => BaseTypes_composeProcessInput(header, (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i])));
+        return (table) => ((i) => {
+            let matchValue;
+            return BaseTypes_composeProcessInput(header, (matchValue = (0, ArcTableAux_js_1.Unchecked_tryGetCellAt)(generalI, i, table.Values), (matchValue == null) ? (0, ArcTableAux_js_1.getEmptyCellForHeader)(header, undefined) : (0, Option_js_1.value)(matchValue)));
+        });
     }
     else {
         return undefined;
@@ -848,7 +892,10 @@ function ProcessConversion_tryGetInputGetter(generalI, header) {
 function ProcessConversion_tryGetOutputGetter(generalI, header) {
     if (header.tag === /* Output */ 12) {
         const io = header.fields[0];
-        return (matrix) => ((i) => BaseTypes_composeProcessOutput(header, (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i])));
+        return (table) => ((i) => {
+            let matchValue;
+            return BaseTypes_composeProcessOutput(header, (matchValue = (0, ArcTableAux_js_1.Unchecked_tryGetCellAt)(generalI, i, table.Values), (matchValue == null) ? (0, ArcTableAux_js_1.getEmptyCellForHeader)(header, undefined) : (0, Option_js_1.value)(matchValue)));
+        });
     }
     else {
         return undefined;
@@ -860,7 +907,10 @@ function ProcessConversion_tryGetOutputGetter(generalI, header) {
 function ProcessConversion_tryGetCommentGetter(generalI, header) {
     if (header.tag === /* Comment */ 14) {
         const c = header.fields[0];
-        return (matrix) => ((i) => (0, Types_js_1.toString)(new Comment_js_2.Comment$(c, (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i]).AsFreeText)));
+        return (table) => ((i) => {
+            let matchValue, cell;
+            return (0, Types_js_1.toString)((matchValue = (0, ArcTableAux_js_1.Unchecked_tryGetCellAt)(generalI, i, table.Values), (matchValue == null) ? (new Comment_js_2.Comment$(c)) : ((cell = (0, Option_js_1.value)(matchValue), new Comment_js_2.Comment$(c, cell.AsFreeText)))));
+        });
     }
     else {
         return undefined;
@@ -868,8 +918,16 @@ function ProcessConversion_tryGetCommentGetter(generalI, header) {
 }
 function ProcessConversion_tryGetPerformerGetter(generalI, header) {
     if (header.tag === /* Performer */ 9) {
-        return (matrix) => ((i) => {
-            const performer = (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i]).AsFreeText;
+        return (table) => ((i) => {
+            let performer;
+            const matchValue = (0, ArcTableAux_js_1.Unchecked_tryGetCellAt)(generalI, i, table.Values);
+            if (matchValue == null) {
+                performer = "";
+            }
+            else {
+                const cell = (0, Option_js_1.value)(matchValue);
+                performer = cell.AsFreeText;
+            }
             return Person_js_1.LDPerson.create(performer);
         });
     }
@@ -909,20 +967,20 @@ function ProcessConversion_getProcessGetter(assayName, studyName, processNameRoo
     let inputGetter_1;
     const matchValue = (0, Seq_js_1.tryPick)((tupledArg_11) => ProcessConversion_tryGetInputGetter(tupledArg_11[0], tupledArg_11[1]), headers_1);
     if (matchValue == null) {
-        inputGetter_1 = (((0, List_js_1.length)(charGetters) !== 0) ? ((matrix_1) => ((i_1) => {
+        inputGetter_1 = (((0, List_js_1.length)(charGetters) !== 0) ? ((table_1) => ((i_1) => {
             let chars_1;
-            const collection_1 = (0, Seq_js_1.map)((f_1) => f_1(matrix_1)(i_1), charGetters);
+            const collection_1 = (0, Seq_js_1.map)((f_1) => f_1(table_1)(i_1), charGetters);
             chars_1 = Array.from(collection_1);
             return (0, Collections_js_1.ResizeArray_singleton)(Sample_js_1.LDSample.createSample(`${processNameRoot}_Input_${i_1}`, undefined, chars_1));
-        })) : ((matrix_2) => ((i_2) => [])));
+        })) : ((table_2) => ((i_2) => [])));
     }
     else {
         const inputGetter = (0, Option_js_1.value)(matchValue);
-        inputGetter_1 = ((matrix) => ((i) => {
+        inputGetter_1 = ((table) => ((i) => {
             let chars;
-            const collection = (0, Seq_js_1.map)((f) => f(matrix)(i), charGetters);
+            const collection = (0, Seq_js_1.map)((f) => f(table)(i), charGetters);
             chars = Array.from(collection);
-            const input = inputGetter(matrix)(i);
+            const input = inputGetter(table)(i);
             if (chars.length > 0) {
                 Sample_js_1.LDSample.setAdditionalProperties(input, chars);
             }
@@ -932,41 +990,39 @@ function ProcessConversion_getProcessGetter(assayName, studyName, processNameRoo
     let outputGetter_1;
     const matchValue_1 = (0, Seq_js_1.tryPick)((tupledArg_12) => ProcessConversion_tryGetOutputGetter(tupledArg_12[0], tupledArg_12[1]), headers_1);
     if (matchValue_1 == null) {
-        outputGetter_1 = (((0, List_js_1.length)(factorValueGetters) !== 0) ? ((matrix_4) => ((i_4) => {
+        outputGetter_1 = (((0, List_js_1.length)(factorValueGetters) !== 0) ? ((table_4) => ((i_4) => {
             let factors_1;
-            const collection_3 = (0, Seq_js_1.map)((f_3) => f_3(matrix_4)(i_4), factorValueGetters);
+            const collection_3 = (0, Seq_js_1.map)((f_3) => f_3(table_4)(i_4), factorValueGetters);
             factors_1 = Array.from(collection_3);
             return (0, Collections_js_1.ResizeArray_singleton)(Sample_js_1.LDSample.createSample(`${processNameRoot}_Output_${i_4}`, undefined, factors_1));
-        })) : ((matrix_5) => ((i_5) => [])));
+        })) : ((table_5) => ((i_5) => [])));
     }
     else {
         const outputGetter = (0, Option_js_1.value)(matchValue_1);
-        outputGetter_1 = ((matrix_3) => ((i_3) => {
+        outputGetter_1 = ((table_3) => ((i_3) => {
             let factors;
-            const collection_2 = (0, Seq_js_1.map)((f_2) => f_2(matrix_3)(i_3), factorValueGetters);
+            const collection_2 = (0, Seq_js_1.map)((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) {
                 Sample_js_1.LDSample.setAdditionalProperties(output, factors);
             }
             return (0, Collections_js_1.ResizeArray_singleton)(output);
         }));
     }
-    return (matrix_6) => ((i_6) => {
-        const pn = ((1 + (0, Seq_js_1.max)((0, Seq_js_1.map)((tuple_1) => tuple_1[1], matrix_6.keys()), {
-            Compare: Util_js_1.comparePrimitives,
-        })) === 1) ? processNameRoot : ProcessConversion_composeProcessName(processNameRoot, i_6);
-        const paramvalues = (0, Option_js_1.map)((collection_4) => Array.from(collection_4), (0, Collections_js_1.Option_fromValueWithDefault)((0, List_js_1.empty)(), (0, List_js_1.map)((f_4) => f_4(matrix_6)(i_6), parameterValueGetters)));
-        const comments = (0, Option_js_1.map)((collection_5) => Array.from(collection_5), (0, Collections_js_1.Option_fromValueWithDefault)((0, List_js_1.empty)(), (0, List_js_1.map)((f_5) => f_5(matrix_6)(i_6), commentGetters)));
-        const components = (0, Option_js_1.map)((collection_6) => Array.from(collection_6), (0, Collections_js_1.Option_fromValueWithDefault)((0, List_js_1.empty)(), (0, List_js_1.map)((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 = (0, Option_js_1.map)((collection_4) => Array.from(collection_4), (0, Collections_js_1.Option_fromValueWithDefault)((0, List_js_1.empty)(), (0, List_js_1.map)((f_4) => f_4(table_6)(i_6), parameterValueGetters)));
+        const comments = (0, Option_js_1.map)((collection_5) => Array.from(collection_5), (0, Collections_js_1.Option_fromValueWithDefault)((0, List_js_1.empty)(), (0, List_js_1.map)((f_5) => f_5(table_6)(i_6), commentGetters)));
+        const components = (0, Option_js_1.map)((collection_6) => Array.from(collection_6), (0, Collections_js_1.Option_fromValueWithDefault)((0, List_js_1.empty)(), (0, List_js_1.map)((f_6) => f_6(table_6)(i_6), componentGetters)));
         const id = LabProcess_js_1.LDLabProcess.genId(processNameRoot, (0, Option_js_1.unwrap)(assayName), (0, Option_js_1.unwrap)(studyName)) + (`_${i_6}`);
         let protocol;
-        const name = (0, Option_js_1.map)((f_7) => f_7(matrix_6)(i_6), protocolREFGetter);
+        const name = (0, Option_js_1.map)((f_7) => f_7(table_6)(i_6), protocolREFGetter);
         const protocolId = LabProtocol_js_1.LDLabProtocol.genId((0, Option_js_1.unwrap)(name), processNameRoot);
-        protocol = LabProtocol_js_1.LDLabProtocol.create(protocolId, (0, Option_js_1.unwrap)(name), (0, Option_js_1.unwrap)((0, Option_js_1.map)((f_8) => f_8(matrix_6)(i_6), protocolDescriptionGetter)), (0, Option_js_1.unwrap)((0, Option_js_1.map)((f_9) => f_9(matrix_6)(i_6), protocolTypeGetter)), undefined, undefined, (0, Option_js_1.unwrap)(components), undefined, (0, Option_js_1.unwrap)((0, Option_js_1.map)((f_10) => f_10(matrix_6)(i_6), protocolURIGetter)), (0, Option_js_1.unwrap)((0, Option_js_1.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 = (0, Option_js_1.map)((f_12) => f_12(matrix_6)(i_6), performerGetter);
+        protocol = LabProtocol_js_1.LDLabProtocol.create(protocolId, (0, Option_js_1.unwrap)(name), (0, Option_js_1.unwrap)((0, Option_js_1.map)((f_8) => f_8(table_6)(i_6), protocolDescriptionGetter)), (0, Option_js_1.unwrap)((0, Option_js_1.map)((f_9) => f_9(table_6)(i_6), protocolTypeGetter)), undefined, undefined, (0, Option_js_1.unwrap)(components), undefined, (0, Option_js_1.unwrap)((0, Option_js_1.map)((f_10) => f_10(table_6)(i_6), protocolURIGetter)), (0, Option_js_1.unwrap)((0, Option_js_1.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 = (0, Option_js_1.map)((f_12) => f_12(table_6)(i_6), performerGetter);
         return LabProcess_js_1.LDLabProcess.create(pn, matchValue_2, matchValue_3, id, (0, Option_js_1.unwrap)(agent), (0, Option_js_1.unwrap)(protocol), (0, Option_js_1.unwrap)(paramvalues), undefined, (0, Option_js_1.unwrap)(comments));
     });
 }
@@ -979,36 +1035,28 @@ function ProcessConversion_getProcessGetter(assayName, studyName, processNameRoo
  */
 function ProcessConversion_groupProcesses_Z27F0B586(processes, graph, context) {
     return (0, Seq2_js_1.List_groupBy)((p) => {
-        let protocol, name_1, name_2, protocol_1;
+        let protocol, protocol_1;
         const matchValue = LabProcess_js_1.LDLabProcess.tryGetNameAsString(p, (0, Option_js_1.unwrap)(context));
         const matchValue_1 = LabProcess_js_1.LDLabProcess.tryGetExecutesLabProtocol(p, (0, Option_js_1.unwrap)(graph), (0, Option_js_1.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((0, Option_js_1.value)(matchValue))[1] != null) {
                 matchResult = 0;
-                name_3 = (0, Option_js_1.value)(matchValue);
+                name_1 = (0, Option_js_1.value)(matchValue);
             }
             else if (matchValue_1 != null) {
                 if ((protocol = (0, Option_js_1.value)(matchValue_1), LabProtocol_js_1.LDLabProtocol.tryGetNameAsString(protocol, (0, Option_js_1.unwrap)(context)) != null)) {
                     matchResult = 1;
                     protocol_2 = (0, Option_js_1.value)(matchValue_1);
                 }
-                else if ((name_1 = (0, Option_js_1.value)(matchValue), name_1.indexOf("_") >= 0)) {
-                    matchResult = 2;
-                    name_4 = (0, Option_js_1.value)(matchValue);
-                }
                 else {
-                    matchResult = 3;
-                    name_5 = (0, Option_js_1.value)(matchValue);
+                    matchResult = 2;
+                    name_2 = (0, Option_js_1.value)(matchValue);
                 }
             }
-            else if ((name_2 = (0, Option_js_1.value)(matchValue), name_2.indexOf("_") >= 0)) {
-                matchResult = 2;
-                name_4 = (0, Option_js_1.value)(matchValue);
-            }
             else {
-                matchResult = 3;
-                name_5 = (0, Option_js_1.value)(matchValue);
+                matchResult = 2;
+                name_2 = (0, Option_js_1.value)(matchValue);
             }
         }
         else if (matchValue_1 != null) {
@@ -1017,23 +1065,21 @@ function ProcessConversion_groupProcesses_Z27F0B586(processes, graph, context) {
                 protocol_2 = (0, Option_js_1.value)(matchValue_1);
             }
             else {
-                matchResult = 4;
+                matchResult = 3;
                 protocol_3 = (0, Option_js_1.value)(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 (0, Option_js_1.defaultArg)(LabProtocol_js_1.LDLabProtocol.tryGetNameAsString(protocol_2, (0, Option_js_1.unwrap)(context)), "");
             case 2:
-                return (0, String_js_1.remove)(name_4, name_4.lastIndexOf("_"));
+                return name_2;
             case 3:
-                return name_5;
-            case 4:
                 return protocol_3.Id;
             default:
                 return (0, Identifier_js_1.createMissingIdentifier)();
@@ -1240,25 +1286,25 @@ function ARCtrl_ArcTable__ArcTable_fromProtocol_Static_Z6839B9E8(p, graph, conte
         while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
             const c = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
             const patternInput = BaseTypes_decomposeComponent_Z2F770004(c, (0, Option_js_1.unwrap)(context));
-            t.AddColumn(patternInput[0], (0, Array_js_1.singleton)(patternInput[1]), (0, Option_js_1.unwrap)(ARCtrl_ROCrate_LDNode__LDNode_TryGetColumnIndex(c)));
+            t.AddColumn(patternInput[0], (0, Collections_js_1.ResizeArray_singleton)(patternInput[1]), (0, Option_js_1.unwrap)(ARCtrl_ROCrate_LDNode__LDNode_TryGetColumnIndex(c)));
         }
     }
     finally {
         (0, Util_js_1.disposeSafe)(enumerator);
     }
     (0, Option_js_1.map)((d) => {
-        t.AddProtocolDescriptionColumn([d]);
+        t.AddProtocolDescriptionColumn((0, Collections_js_1.ResizeArray_singleton)(d));
     }, LabProtocol_js_1.LDLabProtocol.tryGetDescriptionAsString(p, (0, Option_js_1.unwrap)(context)));
     (0, Option_js_1.map)((d_1) => {
-        t.AddProtocolVersionColumn([d_1]);
+        t.AddProtocolVersionColumn((0, Collections_js_1.ResizeArray_singleton)(d_1));
     }, LabProtocol_js_1.LDLabProtocol.tryGetVersionAsString(p, (0, Option_js_1.unwrap)(context)));
     (0, Option_js_1.map)((d_2) => {
-        t.AddProtocolTypeColumn([d_2]);
+        t.AddProtocolTypeColumn((0, Collections_js_1.ResizeArray_singleton)(d_2));
     }, ProcessConversion_tryGetProtocolType_Z6839B9E8(p, undefined, (0, Option_js_1.unwrap)(context)));
     (0, Option_js_1.map)((d_3) => {
-        t.AddProtocolUriColumn([d_3]);
+        t.AddProtocolUriColumn((0, Collections_js_1.ResizeArray_singleton)(d_3));
     }, LabProtocol_js_1.LDLabProtocol.tryGetUrl(p, (0, Option_js_1.unwrap)(context)));
-    t.AddProtocolNameColumn([name]);
+    t.AddProtocolNameColumn((0, Collections_js_1.ResizeArray_singleton)(name));
     return t;
 }
 /**
@@ -1299,7 +1345,7 @@ function ARCtrl_ArcTable__ArcTable_GetProcesses_40457300(this$, assayName, study
     }
     else {
         const getter = ProcessConversion_getProcessGetter(assayName, studyName, this$.Name, this$.Headers);
-        return (0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((i) => getter(this$.Values)(i), (0, Range_js_1.rangeDouble)(0, 1, this$.RowCount - 1))));
+        return (0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((i) => getter(this$)(i), (0, Range_js_1.rangeDouble)(0, 1, this$.RowCount - 1))));
     }
 }
 /**
@@ -1311,7 +1357,7 @@ function ARCtrl_ArcTable__ArcTable_GetProcesses_40457300(this$, assayName, study
  */
 function ARCtrl_ArcTable__ArcTable_fromProcesses_Static_Z3575FB5F(name, ps, graph, context) {
     const tupledArg = (0, ArcTableAux_js_1.Unchecked_alignByHeaders)(true, (0, List_js_1.collect)((p) => (0, List_js_1.ofSeq)(ProcessConversion_processToRows_Z6839B9E8(p, (0, Option_js_1.unwrap)(graph), (0, Option_js_1.unwrap)(context))), ps));
-    return ArcTable_js_1.ArcTable.create(name, tupledArg[0], tupledArg[1]);
+    return ArcTable_js_1.ArcTable.fromArcTableValues(name, tupledArg[0], tupledArg[1]);
 }
 /**
  * Return a list of all the processes in all the tables.
@@ -1330,7 +1376,7 @@ function ARCtrl_ArcTables__ArcTables_fromProcesses_Static_Z27F0B586(ps, graph, c
     let collection;
     return new ArcTables_js_1.ArcTables((collection = (0, List_js_1.map)((tupledArg) => {
         const tupledArg_1 = (0, ArcTableAux_js_1.Unchecked_alignByHeaders)(true, (0, List_js_1.collect)((p) => (0, List_js_1.ofSeq)(ProcessConversion_processToRows_Z6839B9E8(p, (0, Option_js_1.unwrap)(graph), (0, Option_js_1.unwrap)(context))), tupledArg[1]));
-        return ArcTable_js_1.ArcTable.create(tupledArg[0], tupledArg_1[0], tupledArg_1[1]);
+        return ArcTable_js_1.ArcTable.fromArcTableValues(tupledArg[0], tupledArg_1[0], tupledArg_1[1]);
     }, ProcessConversion_groupProcesses_Z27F0B586(ps, (0, Option_js_1.unwrap)(graph), (0, Option_js_1.unwrap)(context))), Array.from(collection)));
 }
 class DatamapConversion {

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

@@ -1680,7 +1680,7 @@ class ArcRun extends ArcTables_js_1.ArcTables {
             return newRun;
         };
     }
-    static updateTable(name, updateFun) {
+    static mapTable(name, updateFun) {
         return (run) => {
             const newRun = run.Copy();
             newRun.MapTable(name, updateFun);