@nfdi4plants/arctrl 3.0.0-alpha.4 → 3.0.0-beta.2

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

@@ -73,7 +73,8 @@ const ProcessOutput_js_1 = require("./Process/ProcessOutput.js");
 const Util_js_1 = require("@fable-org/fable-library-js/Util.js");
 const Regex_js_1 = require("./Helper/Regex.js");
 const ColumnIndex_js_1 = require("./Process/ColumnIndex.js");
-const MapUtil_js_1 = require("@fable-org/fable-library-js/MapUtil.js");
+const ArcTableAux_js_1 = require("./Table/ArcTableAux.js");
+const ArcTable_js_1 = require("./Table/ArcTable.js");
 const List_js_1 = require("@fable-org/fable-library-js/List.js");
 const Source_js_1 = require("./Process/Source.js");
 const Sample_js_1 = require("./Process/Sample.js");
@@ -82,10 +83,7 @@ const Protocol_js_1 = require("./Process/Protocol.js");
 const Seq2_js_1 = require("@fable-org/fable-library-js/Seq2.js");
 const Identifier_js_1 = require("./Helper/Identifier.js");
 const HashCodes_js_1 = require("./Helper/HashCodes.js");
-const ArcTable_js_1 = require("./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("./Table/ArcTableAux.js");
 const ArcTables_js_1 = require("./Table/ArcTables.js");
 exports.Person_orcidKey = "ORCID";
 exports.Person_AssayIdentifierPrefix = "performer (ARC:00000168)";
@@ -486,7 +484,11 @@ function ProcessParsing_tryComponentGetter(generalI, valueI, valueHeader) {
         const oa = valueHeader.fields[0];
         const newOA = oa.Copy();
         (0, ColumnIndex_js_1.ARCtrl_OntologyAnnotation__OntologyAnnotation_SetColumnIndex_Z524259A4)(newOA, valueI);
-        return (matrix) => ((i) => JsonTypes_composeComponent((0, CompositeHeader_js_1.CompositeHeader_Component)(newOA), (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i])));
+        const cat = (0, CompositeHeader_js_1.CompositeHeader_Component)(newOA);
+        return (table) => ((i) => {
+            let matchValue;
+            return JsonTypes_composeComponent(cat, (matchValue = (0, ArcTableAux_js_1.Unchecked_tryGetCellAt)(generalI, i, table.Values), (matchValue == null) ? (0, ArcTableAux_js_1.getEmptyCellForHeader)(cat, undefined) : (0, Option_js_1.value)(matchValue)));
+        });
     }
     else {
         return undefined;
@@ -498,7 +500,10 @@ function ProcessParsing_tryComponentGetter(generalI, valueI, valueHeader) {
 function ProcessParsing_tryParameterGetter(generalI, valueI, valueHeader) {
     if (valueHeader.tag === /* Parameter */ 3) {
         const cat = (0, CompositeHeader_js_1.CompositeHeader_Parameter)((0, ColumnIndex_js_1.ARCtrl_OntologyAnnotation__OntologyAnnotation_setColumnIndex_Static)(valueI, valueHeader.fields[0]));
-        return (matrix) => ((i_1) => JsonTypes_composeParameterValue(cat, (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i_1])));
+        return (table) => ((i_1) => {
+            let matchValue;
+            return JsonTypes_composeParameterValue(cat, (matchValue = (0, ArcTableAux_js_1.Unchecked_tryGetCellAt)(generalI, i_1, table.Values), (matchValue == null) ? (0, ArcTableAux_js_1.getEmptyCellForHeader)(cat, undefined) : (0, Option_js_1.value)(matchValue)));
+        });
     }
     else {
         return undefined;
@@ -510,7 +515,10 @@ function ProcessParsing_tryParameterGetter(generalI, valueI, valueHeader) {
 function ProcessParsing_tryFactorGetter(generalI, valueI, valueHeader) {
     if (valueHeader.tag === /* Factor */ 2) {
         const cat = (0, CompositeHeader_js_1.CompositeHeader_Factor)((0, ColumnIndex_js_1.ARCtrl_OntologyAnnotation__OntologyAnnotation_setColumnIndex_Static)(valueI, valueHeader.fields[0]));
-        return (matrix) => ((i_1) => JsonTypes_composeFactorValue(cat, (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i_1])));
+        return (table) => ((i_1) => {
+            let matchValue;
+            return JsonTypes_composeFactorValue(cat, (matchValue = (0, ArcTableAux_js_1.Unchecked_tryGetCellAt)(generalI, i_1, table.Values), (matchValue == null) ? (0, ArcTableAux_js_1.getEmptyCellForHeader)(cat, undefined) : (0, Option_js_1.value)(matchValue)));
+        });
     }
     else {
         return undefined;
@@ -522,7 +530,10 @@ function ProcessParsing_tryFactorGetter(generalI, valueI, valueHeader) {
 function ProcessParsing_tryCharacteristicGetter(generalI, valueI, valueHeader) {
     if (valueHeader.tag === /* Characteristic */ 1) {
         const cat = (0, CompositeHeader_js_1.CompositeHeader_Characteristic)((0, ColumnIndex_js_1.ARCtrl_OntologyAnnotation__OntologyAnnotation_setColumnIndex_Static)(valueI, valueHeader.fields[0]));
-        return (matrix) => ((i_1) => JsonTypes_composeCharacteristicValue(cat, (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i_1])));
+        return (table) => ((i_1) => {
+            let matchValue;
+            return JsonTypes_composeCharacteristicValue(cat, (matchValue = (0, ArcTableAux_js_1.Unchecked_tryGetCellAt)(generalI, i_1, table.Values), (matchValue == null) ? (0, ArcTableAux_js_1.getEmptyCellForHeader)(cat, undefined) : (0, Option_js_1.value)(matchValue)));
+        });
     }
     else {
         return undefined;
@@ -533,7 +544,16 @@ function ProcessParsing_tryCharacteristicGetter(generalI, valueI, valueHeader) {
  */
 function ProcessParsing_tryGetProtocolTypeGetter(generalI, header) {
     if (header.tag === /* ProtocolType */ 4) {
-        return (matrix) => ((i) => (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i]).AsTerm);
+        return (table) => ((i) => {
+            const matchValue = (0, ArcTableAux_js_1.Unchecked_tryGetCellAt)(generalI, i, table.Values);
+            if (matchValue == null) {
+                return new OntologyAnnotation_js_1.OntologyAnnotation();
+            }
+            else {
+                const cell = (0, Option_js_1.value)(matchValue);
+                return cell.AsTerm;
+            }
+        });
     }
     else {
         return undefined;
@@ -544,7 +564,16 @@ function ProcessParsing_tryGetProtocolTypeGetter(generalI, header) {
  */
 function ProcessParsing_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;
@@ -555,7 +584,16 @@ function ProcessParsing_tryGetProtocolREFGetter(generalI, header) {
  */
 function ProcessParsing_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;
@@ -566,7 +604,16 @@ function ProcessParsing_tryGetProtocolDescriptionGetter(generalI, header) {
  */
 function ProcessParsing_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;
@@ -577,7 +624,16 @@ function ProcessParsing_tryGetProtocolURIGetter(generalI, header) {
  */
 function ProcessParsing_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;
@@ -589,7 +645,10 @@ function ProcessParsing_tryGetProtocolVersionGetter(generalI, header) {
 function ProcessParsing_tryGetInputGetter(generalI, header) {
     if (header.tag === /* Input */ 11) {
         const io = header.fields[0];
-        return (matrix) => ((i) => JsonTypes_composeProcessInput(header, (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i])));
+        return (table) => ((i) => {
+            let matchValue;
+            return JsonTypes_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;
@@ -601,7 +660,10 @@ function ProcessParsing_tryGetInputGetter(generalI, header) {
 function ProcessParsing_tryGetOutputGetter(generalI, header) {
     if (header.tag === /* Output */ 12) {
         const io = header.fields[0];
-        return (matrix) => ((i) => JsonTypes_composeProcessOutput(header, (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i])));
+        return (table) => ((i) => {
+            let matchValue;
+            return JsonTypes_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;
@@ -613,7 +675,16 @@ function ProcessParsing_tryGetOutputGetter(generalI, header) {
 function ProcessParsing_tryGetCommentGetter(generalI, header) {
     if (header.tag === /* Comment */ 14) {
         const c = header.fields[0];
-        return (matrix) => ((i) => (new Comment_js_1.Comment$(c, (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i]).AsFreeText)));
+        return (table) => ((i) => {
+            const matchValue = (0, ArcTableAux_js_1.Unchecked_tryGetCellAt)(generalI, i, table.Values);
+            if (matchValue == null) {
+                return new Comment_js_1.Comment$(c);
+            }
+            else {
+                const cell = (0, Option_js_1.value)(matchValue);
+                return new Comment_js_1.Comment$(c, cell.AsFreeText);
+            }
+        });
     }
     else {
         return undefined;
@@ -650,36 +721,36 @@ function ProcessParsing_getProcessGetter(processNameRoot, headers) {
     let inputGetter_1;
     const matchValue = (0, Seq_js_1.tryPick)((tupledArg_10) => ProcessParsing_tryGetInputGetter(tupledArg_10[0], tupledArg_10[1]), headers_1);
     if (matchValue == null) {
-        inputGetter_1 = ((matrix_1) => ((i_1) => (0, List_js_1.singleton)((0, ProcessInput_js_1.ProcessInput_Source)((0, Source_js_1.Source_create_Z5CA08497)(undefined, `${processNameRoot}_Input_${i_1}`, (0, Seq_js_1.toList)((0, Seq_js_1.map)((f_1) => f_1(matrix_1)(i_1), charGetters)))))));
+        inputGetter_1 = ((table_1) => ((i_1) => (0, List_js_1.singleton)((0, ProcessInput_js_1.ProcessInput_Source)((0, Source_js_1.Source_create_Z5CA08497)(undefined, `${processNameRoot}_Input_${i_1}`, (0, Seq_js_1.toList)((0, Seq_js_1.map)((f_1) => f_1(table_1)(i_1), charGetters)))))));
     }
     else {
         const inputGetter = (0, Option_js_1.value)(matchValue);
-        inputGetter_1 = ((matrix) => ((i) => {
-            const chars = (0, Seq_js_1.toList)((0, Seq_js_1.map)((f) => f(matrix)(i), charGetters));
-            const input = inputGetter(matrix)(i);
+        inputGetter_1 = ((table) => ((i) => {
+            const chars = (0, Seq_js_1.toList)((0, Seq_js_1.map)((f) => f(table)(i), charGetters));
+            const input = inputGetter(table)(i);
             return (!((0, ProcessInput_js_1.ProcessInput__isSample)(input) ? true : (0, ProcessInput_js_1.ProcessInput__isSource)(input)) && !(0, List_js_1.isEmpty)(chars)) ? (0, List_js_1.ofArray)([input, (0, ProcessInput_js_1.ProcessInput_createSample_Z598187B7)((0, ProcessInput_js_1.ProcessInput__get_Name)(input), chars)]) : (0, List_js_1.singleton)(((0, List_js_1.length)(chars) > 0) ? (0, ProcessInput_js_1.ProcessInput_setCharacteristicValues)(chars, input) : input);
         }));
     }
     let outputGetter_1;
     const matchValue_1 = (0, Seq_js_1.tryPick)((tupledArg_11) => ProcessParsing_tryGetOutputGetter(tupledArg_11[0], tupledArg_11[1]), headers_1);
     if (matchValue_1 == null) {
-        outputGetter_1 = ((matrix_3) => ((i_3) => (0, List_js_1.singleton)((0, ProcessOutput_js_1.ProcessOutput_Sample)((0, Sample_js_1.Sample_create_62424AD2)(undefined, `${processNameRoot}_Output_${i_3}`, undefined, (0, Seq_js_1.toList)((0, Seq_js_1.map)((f_3) => f_3(matrix_3)(i_3), factorValueGetters)))))));
+        outputGetter_1 = ((table_3) => ((i_3) => (0, List_js_1.singleton)((0, ProcessOutput_js_1.ProcessOutput_Sample)((0, Sample_js_1.Sample_create_62424AD2)(undefined, `${processNameRoot}_Output_${i_3}`, undefined, (0, Seq_js_1.toList)((0, Seq_js_1.map)((f_3) => f_3(table_3)(i_3), factorValueGetters)))))));
     }
     else {
         const outputGetter = (0, Option_js_1.value)(matchValue_1);
-        outputGetter_1 = ((matrix_2) => ((i_2) => {
-            const factors = (0, Seq_js_1.toList)((0, Seq_js_1.map)((f_2) => f_2(matrix_2)(i_2), factorValueGetters));
-            const output = outputGetter(matrix_2)(i_2);
+        outputGetter_1 = ((table_2) => ((i_2) => {
+            const factors = (0, Seq_js_1.toList)((0, Seq_js_1.map)((f_2) => f_2(table_2)(i_2), factorValueGetters));
+            const output = outputGetter(table_2)(i_2);
             return (!(0, ProcessOutput_js_1.ProcessOutput__isSample)(output) && !(0, List_js_1.isEmpty)(factors)) ? (0, List_js_1.ofArray)([output, (0, ProcessOutput_js_1.ProcessOutput_createSample_Z598187B7)((0, ProcessOutput_js_1.ProcessOutput__get_Name)(output), undefined, factors)]) : (0, List_js_1.singleton)(((0, List_js_1.length)(factors) > 0) ? (0, ProcessOutput_js_1.ProcessOutput_setFactorValues)(factors, output) : output);
         }));
     }
-    return (matrix_4) => ((i_4) => {
+    return (table_4) => ((i_4) => {
         const pn = (0, Option_js_1.map)((p) => (0, Process_js_1.Process_composeName)(p, i_4), (0, Collections_js_1.Option_fromValueWithDefault)("", processNameRoot));
-        const paramvalues = (0, Collections_js_1.Option_fromValueWithDefault)((0, List_js_1.empty)(), (0, List_js_1.map)((f_4) => f_4(matrix_4)(i_4), parameterValueGetters));
+        const paramvalues = (0, Collections_js_1.Option_fromValueWithDefault)((0, List_js_1.empty)(), (0, List_js_1.map)((f_4) => f_4(table_4)(i_4), parameterValueGetters));
         const parameters = (0, Option_js_1.map)((list_5) => (0, List_js_1.map)((pv) => (0, Option_js_1.value)(pv.Category), list_5), paramvalues);
-        const comments = (0, Collections_js_1.Option_fromValueWithDefault)((0, List_js_1.empty)(), (0, List_js_1.map)((f_5) => f_5(matrix_4)(i_4), commentGetters));
+        const comments = (0, Collections_js_1.Option_fromValueWithDefault)((0, List_js_1.empty)(), (0, List_js_1.map)((f_5) => f_5(table_4)(i_4), commentGetters));
         let protocol;
-        const p_1 = (0, Protocol_js_1.Protocol_make)(undefined, (0, Option_js_1.map)((f_6) => f_6(matrix_4)(i_4), protocolREFGetter), (0, Option_js_1.map)((f_7) => f_7(matrix_4)(i_4), protocolTypeGetter), (0, Option_js_1.map)((f_8) => f_8(matrix_4)(i_4), protocolDescriptionGetter), (0, Option_js_1.map)((f_9) => f_9(matrix_4)(i_4), protocolURIGetter), (0, Option_js_1.map)((f_10) => f_10(matrix_4)(i_4), protocolVersionGetter), parameters, (0, Collections_js_1.Option_fromValueWithDefault)((0, List_js_1.empty)(), (0, List_js_1.map)((f_11) => f_11(matrix_4)(i_4), componentGetters)), undefined);
+        const p_1 = (0, Protocol_js_1.Protocol_make)(undefined, (0, Option_js_1.map)((f_6) => f_6(table_4)(i_4), protocolREFGetter), (0, Option_js_1.map)((f_7) => f_7(table_4)(i_4), protocolTypeGetter), (0, Option_js_1.map)((f_8) => f_8(table_4)(i_4), protocolDescriptionGetter), (0, Option_js_1.map)((f_9) => f_9(table_4)(i_4), protocolURIGetter), (0, Option_js_1.map)((f_10) => f_10(table_4)(i_4), protocolVersionGetter), parameters, (0, Collections_js_1.Option_fromValueWithDefault)((0, List_js_1.empty)(), (0, List_js_1.map)((f_11) => f_11(table_4)(i_4), componentGetters)), undefined);
         let matchResult;
         if (p_1.Name == null) {
             if (p_1.ProtocolType == null) {
@@ -721,8 +792,8 @@ function ProcessParsing_getProcessGetter(processNameRoot, headers) {
                 protocol = p_1;
         }
         let patternInput;
-        const inputs = inputGetter_1(matrix_4)(i_4);
-        const outputs = outputGetter_1(matrix_4)(i_4);
+        const inputs = inputGetter_1(table_4)(i_4);
+        const outputs = outputGetter_1(table_4)(i_4);
         patternInput = ((((0, List_js_1.length)(inputs) === 1) && ((0, List_js_1.length)(outputs) === 2)) ? [(0, List_js_1.ofArray)([(0, List_js_1.item)(0, inputs), (0, List_js_1.item)(0, inputs)]), outputs] : ((((0, List_js_1.length)(inputs) === 2) && ((0, List_js_1.length)(outputs) === 1)) ? [inputs, (0, List_js_1.ofArray)([(0, List_js_1.item)(0, outputs), (0, List_js_1.item)(0, outputs)])] : [inputs, outputs]));
         return (0, Process_js_1.Process_make)(undefined, pn, protocol, paramvalues, undefined, undefined, undefined, undefined, patternInput[0], patternInput[1], comments);
     });
@@ -742,10 +813,6 @@ function ProcessParsing_groupProcesses(ps) {
         else if ((x.ExecutesProtocol != null) && ((0, Option_js_1.value)(x.ExecutesProtocol).Name != null)) {
             return (0, Option_js_1.value)((0, Option_js_1.value)(x.ExecutesProtocol).Name);
         }
-        else if ((x.Name != null) && ((0, Option_js_1.value)(x.Name).indexOf("_") >= 0)) {
-            const lastUnderScoreIndex = (0, Option_js_1.value)(x.Name).lastIndexOf("_") | 0;
-            return (0, String_js_1.remove)((0, Option_js_1.value)(x.Name), lastUnderScoreIndex);
-        }
         else if (x.Name != null) {
             return (0, Option_js_1.value)(x.Name);
         }
@@ -1016,7 +1083,7 @@ function ARCtrl_ArcTable__ArcTable_fromProtocol_Static_3BF20962(p) {
     try {
         while (enumerator_1["System.Collections.IEnumerator.MoveNext"]()) {
             const c = enumerator_1["System.Collections.Generic.IEnumerator`1.get_Current"]();
-            const v_1 = (0, Option_js_1.map)((arg) => (0, Array_js_1.singleton)(ARCtrl_CompositeCell__CompositeCell_fromValue_Static_Z6986DF18(arg, (0, Option_js_1.unwrap)(c.ComponentUnit))), c.ComponentValue);
+            const v_1 = (0, Option_js_1.map)((arg) => (0, Collections_js_1.ResizeArray_singleton)(ARCtrl_CompositeCell__CompositeCell_fromValue_Static_Z6986DF18(arg, (0, Option_js_1.unwrap)(c.ComponentUnit))), c.ComponentValue);
             t.AddColumn((0, CompositeHeader_js_1.CompositeHeader_Parameter)((0, Option_js_1.value)(c.ComponentType)), (0, Option_js_1.unwrap)(v_1), (0, Option_js_1.unwrap)((0, ColumnIndex_js_1.ARCtrl_Process_Component__Component_TryGetColumnIndex)(c)));
         }
     }
@@ -1024,19 +1091,19 @@ function ARCtrl_ArcTable__ArcTable_fromProtocol_Static_3BF20962(p) {
         (0, Util_js_1.disposeSafe)(enumerator_1);
     }
     (0, Option_js_1.map)((d) => {
-        t.AddProtocolDescriptionColumn([d]);
+        t.AddProtocolDescriptionColumn((0, Collections_js_1.ResizeArray_singleton)(d));
     }, p.Description);
     (0, Option_js_1.map)((d_1) => {
-        t.AddProtocolVersionColumn([d_1]);
+        t.AddProtocolVersionColumn((0, Collections_js_1.ResizeArray_singleton)(d_1));
     }, p.Version);
     (0, Option_js_1.map)((d_2) => {
-        t.AddProtocolTypeColumn([d_2]);
+        t.AddProtocolTypeColumn((0, Collections_js_1.ResizeArray_singleton)(d_2));
     }, p.ProtocolType);
     (0, Option_js_1.map)((d_3) => {
-        t.AddProtocolUriColumn([d_3]);
+        t.AddProtocolUriColumn((0, Collections_js_1.ResizeArray_singleton)(d_3));
     }, p.Uri);
     (0, Option_js_1.map)((d_4) => {
-        t.AddProtocolNameColumn([d_4]);
+        t.AddProtocolNameColumn((0, Collections_js_1.ResizeArray_singleton)(d_4));
     }, p.Name);
     return t;
 }
@@ -1095,7 +1162,7 @@ function ARCtrl_ArcTable__ArcTable_GetProcesses(this$) {
             const clo_1 = clo(arg);
             return clo_1;
         });
-        return ProcessParsing_mergeIdenticalProcesses((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 ProcessParsing_mergeIdenticalProcesses((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)))));
     }
 }
 /**
@@ -1107,7 +1174,7 @@ function ARCtrl_ArcTable__ArcTable_GetProcesses(this$) {
  */
 function ARCtrl_ArcTable__ArcTable_fromProcesses_Static(name, ps) {
     const tupledArg = (0, ArcTableAux_js_1.Unchecked_alignByHeaders)(true, (0, List_js_1.collect)(ProcessParsing_processToRows, 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.
@@ -1126,6 +1193,6 @@ function ARCtrl_ArcTables__ArcTables_fromProcesses_Static_62A3309D(ps) {
     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)(ProcessParsing_processToRows, 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]);
     }, ProcessParsing_groupProcesses(ps)), Array.from(collection)));
 }

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

@@ -139,8 +139,10 @@ class Data {
             throw new Error("Data does not have a file path");
         }
         else {
-            const p_2 = (0, Option_js_1.value)(matchValue);
-            return ((checkExistenceFromRoot_1(p_2) ? true : ((p = p_2, ((p.startsWith("assays/") ? true : p.startsWith("studies/")) ? true : p.startsWith("workflows/")) ? true : p.startsWith("runs/")))) ? true : ((p_1 = p_2, p_1.startsWith("http:") ? true : p_1.startsWith("https:")))) ? p_2 : f(p_2);
+            let p_3;
+            const s = (0, String_js_1.trimStart)((0, Option_js_1.value)(matchValue), "/");
+            p_3 = (s.startsWith("./") ? (0, String_js_1.substring)(s, "./".length) : s);
+            return ((checkExistenceFromRoot_1(p_3) ? true : ((p = p_3, ((p.startsWith("assays/") ? true : p.startsWith("studies/")) ? true : p.startsWith("workflows/")) ? true : p.startsWith("runs/")))) ? true : ((p_1 = p_3, p_1.startsWith("http:") ? true : p_1.startsWith("https:")))) ? p_3 : f(p_3);
         }
     }
     GetAbsolutePathForAssay(assayIdentifier, checkExistenceFromRoot) {

package/dist/ts/cjs/ts/Core/Helper/Collections.js

@@ -12,20 +12,28 @@ exports.Dictionary_ofSeqWithMerge = Dictionary_ofSeqWithMerge;
 exports.Dictionary_init = Dictionary_init;
 exports.Dictionary_items = Dictionary_items;
 exports.StringDictionary_ofSeq = StringDictionary_ofSeq;
+exports.IntDictionary_ofSeq = IntDictionary_ofSeq;
 exports.ResizeArray_create = ResizeArray_create;
 exports.ResizeArray_singleton = ResizeArray_singleton;
 exports.ResizeArray_map = ResizeArray_map;
+exports.ResizeArray_mapi = ResizeArray_mapi;
+exports.ResizeArray_map2 = ResizeArray_map2;
 exports.ResizeArray_choose = ResizeArray_choose;
 exports.ResizeArray_filter = ResizeArray_filter;
 exports.ResizeArray_fold = ResizeArray_fold;
 exports.ResizeArray_foldBack = ResizeArray_foldBack;
 exports.ResizeArray_iter = ResizeArray_iter;
+exports.ResizeArray_iteri = ResizeArray_iteri;
+exports.ResizeArray_init = ResizeArray_init;
 exports.ResizeArray_reduce = ResizeArray_reduce;
 exports.ResizeArray_collect = ResizeArray_collect;
 exports.ResizeArray_distinct = ResizeArray_distinct;
 exports.ResizeArray_isEmpty = ResizeArray_isEmpty;
 exports.ResizeArray_append = ResizeArray_append;
 exports.ResizeArray_appendSingleton = ResizeArray_appendSingleton;
+exports.ResizeArray_indexed = ResizeArray_indexed;
+exports.ResizeArray_rev = ResizeArray_rev;
+exports.ResizeArray_take = ResizeArray_take;
 exports.ResizeArray_groupBy = ResizeArray_groupBy;
 exports.ResizeArray_tryPick = ResizeArray_tryPick;
 exports.ResizeArray_zip = ResizeArray_zip;
@@ -37,9 +45,10 @@ const List_js_1 = require("@fable-org/fable-library-js/List.js");
 const MapUtil_js_1 = require("@fable-org/fable-library-js/MapUtil.js");
 const MutableMap_js_1 = require("@fable-org/fable-library-js/MutableMap.js");
 const Types_js_1 = require("@fable-org/fable-library-js/Types.js");
+const Double_js_1 = require("@fable-org/fable-library-js/Double.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 Seq2_js_1 = require("@fable-org/fable-library-js/Seq2.js");
-const Double_js_1 = require("@fable-org/fable-library-js/Double.js");
 /**
  * If the value matches the default, a None is returned, else a Some is returned
  */
@@ -167,6 +176,9 @@ function Dictionary_items(dict) {
 function StringDictionary_ofSeq(s) {
     return new Map(s);
 }
+function IntDictionary_ofSeq(s) {
+    return new Map(s);
+}
 function ResizeArray_create(i, v) {
     const a = [];
     if (i > 0) {
@@ -195,6 +207,21 @@ function ResizeArray_map(f, a) {
     }
     return b;
 }
+function ResizeArray_mapi(f, a) {
+    const b = [];
+    for (let i = 0; i <= (a.length - 1); i++) {
+        void (b.push(f(i, a[i])));
+    }
+    return b;
+}
+function ResizeArray_map2(f, a, b) {
+    const c = [];
+    const n = (0, Double_js_1.min)(a.length, b.length) | 0;
+    for (let i = 0; i <= (n - 1); i++) {
+        void (c.push(f(a[i], b[i])));
+    }
+    return c;
+}
 function ResizeArray_choose(f, a) {
     const b = [];
     let enumerator = (0, Util_js_1.getEnumerator)(a);
@@ -269,6 +296,18 @@ function ResizeArray_iter(f, a) {
         (0, Util_js_1.disposeSafe)(enumerator);
     }
 }
+function ResizeArray_iteri(f, a) {
+    for (let i = 0; i <= (a.length - 1); i++) {
+        f(i, a[i]);
+    }
+}
+function ResizeArray_init(n, f) {
+    const a = [];
+    for (let i = 0; i <= (n - 1); i++) {
+        void (a.push(f(i)));
+    }
+    return a;
+}
 function ResizeArray_reduce(f, a) {
     switch (a.length) {
         case 0:
@@ -374,6 +413,35 @@ function ResizeArray_appendSingleton(b, a) {
     void (c.push(b));
     return c;
 }
+function ResizeArray_indexed(a) {
+    const b = [];
+    for (let i = 0; i <= (a.length - 1); i++) {
+        void (b.push([i, a[i]]));
+    }
+    return b;
+}
+function ResizeArray_rev(a) {
+    const b = [];
+    const enumerator = (0, Util_js_1.getEnumerator)((0, Range_js_1.rangeDouble)(a.length - 1, -1, 0));
+    try {
+        while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
+            const i = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]() | 0;
+            void (b.push(a[i]));
+        }
+    }
+    finally {
+        (0, Util_js_1.disposeSafe)(enumerator);
+    }
+    return b;
+}
+function ResizeArray_take(n, a) {
+    const b = [];
+    const n_1 = (0, Double_js_1.min)(n, a.length) | 0;
+    for (let i = 0; i <= (n_1 - 1); i++) {
+        void (b.push(a[i]));
+    }
+    return b;
+}
 function ResizeArray_groupBy(f, a) {
     const collection = (0, Seq_js_1.map)((tupledArg) => [tupledArg[0], Array.from(tupledArg[1])], (0, Seq2_js_1.groupBy)(f, a, {
         Equals: Util_js_1.equals,

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

@@ -4,15 +4,15 @@ exports.OntologyAnnotation = void 0;
 exports.OntologyAnnotation_$reflection = OntologyAnnotation_$reflection;
 exports.OntologyAnnotation_$ctor_Z54349580 = OntologyAnnotation_$ctor_Z54349580;
 const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
-const Regex_js_1 = require("./Helper/Regex.js");
 const Url_js_1 = require("./Helper/Url.js");
+const Regex_js_1 = require("./Helper/Regex.js");
 const System_Text_js_1 = require("@fable-org/fable-library-js/System.Text.js");
 const String_js_1 = require("@fable-org/fable-library-js/String.js");
 const Seq_js_1 = require("@fable-org/fable-library-js/Seq.js");
 const Types_js_1 = require("@fable-org/fable-library-js/Types.js");
 const HashCodes_js_1 = require("./Helper/HashCodes.js");
-const Collections_js_1 = require("./Helper/Collections.js");
 const Util_js_1 = require("@fable-org/fable-library-js/Util.js");
+const Collections_js_1 = require("./Helper/Collections.js");
 const Reflection_js_1 = require("@fable-org/fable-library-js/Reflection.js");
 class OntologyAnnotation {
     constructor(name, tsr, tan, comments) {
@@ -20,6 +20,7 @@ class OntologyAnnotation {
         this._termSourceREF = ((tsr == null) ? undefined : (((0, Option_js_1.value)(tsr) === "") ? undefined : tsr));
         this._termAccessionNumber = ((tan == null) ? undefined : (((0, Option_js_1.value)(tan) === "") ? undefined : (((0, Option_js_1.value)(tan) === ":") ? undefined : tan)));
         this._comments = (0, Option_js_1.defaultArg)(comments, []);
+        this._tanInfo = OntologyAnnotation.computeTanInfo((0, Option_js_1.unwrap)(this._termAccessionNumber), (0, Option_js_1.unwrap)(this._termSourceREF));
     }
     get Name() {
         const this$ = this;
@@ -36,6 +37,7 @@ class OntologyAnnotation {
     set TermSourceREF(tsr) {
         const this$ = this;
         this$._termSourceREF = tsr;
+        this$.recomputeTanInfo();
     }
     get TermAccessionNumber() {
         const this$ = this;
@@ -44,6 +46,7 @@ class OntologyAnnotation {
     set TermAccessionNumber(tan) {
         const this$ = this;
         this$._termAccessionNumber = tan;
+        this$.recomputeTanInfo();
     }
     get Comments() {
         const this$ = this;
@@ -61,12 +64,8 @@ class OntologyAnnotation {
         return OntologyAnnotation.make(name, tsr, tan, comments_1);
     }
     get TANInfo() {
-        let matchValue, tan, matchValue_1, matchValue_2, tsr;
         const this$ = this;
-        return (0, Option_js_1.unwrap)((matchValue = this$.TermAccessionNumber, (matchValue == null) ? undefined : ((tan = (0, Option_js_1.value)(matchValue), (matchValue_1 = (0, Regex_js_1.tryParseTermAnnotation)(tan), (matchValue_1 == null) ? ((matchValue_2 = this$.TermSourceREF, (matchValue_2 == null) ? undefined : (((0, Option_js_1.value)(matchValue_2) === "") ? undefined : ((tsr = (0, Option_js_1.value)(matchValue_2), {
-            IDSpace: tsr,
-            LocalID: tan,
-        }))))) : (0, Option_js_1.value)(matchValue_1))))));
+        return (0, Option_js_1.unwrap)(this$._tanInfo);
     }
     get NameText() {
         const this$ = this;
@@ -155,23 +154,9 @@ class OntologyAnnotation {
         return (((this$.Name == null) && (this$.TermSourceREF == null)) && (this$.TermAccessionNumber == null)) && (this$.Comments.length === 0);
     }
     GetHashCode() {
+        let matchValue, matchValue_1, matchValue_2, tsr_1, matchValue_4, tan, taninfo_1, tsr, taninfo;
         const this$ = this;
-        return (0, HashCodes_js_1.boxHashArray)((0, Seq_js_1.toArray)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)((0, HashCodes_js_1.boxHashOption)(this$.Name)), (0, Seq_js_1.delay)(() => {
-            let tsr_1, taninfo_1, tsr;
-            const matchValue = this$.TermSourceREF;
-            const matchValue_1 = this$.TANInfo;
-            if (matchValue != null) {
-                return (matchValue_1 == null) ? ((tsr_1 = (0, Option_js_1.value)(matchValue), (0, Seq_js_1.singleton)((0, HashCodes_js_1.boxHashArray)([tsr_1, (0, Option_js_1.defaultArg)(this$.TermAccessionNumber, "")])))) : ((taninfo_1 = (0, Option_js_1.value)(matchValue_1), (tsr = (0, Option_js_1.value)(matchValue), (0, Seq_js_1.singleton)((0, HashCodes_js_1.boxHashArray)([tsr, (taninfo_1.IDSpace + ":") + taninfo_1.LocalID])))));
-            }
-            else if (matchValue_1 == null) {
-                const tan_1 = (0, Option_js_1.defaultArg)(this$.TermAccessionNumber, "");
-                return (0, Seq_js_1.singleton)((0, HashCodes_js_1.boxHashArray)([(0, Option_js_1.defaultArg)(this$.TermAccessionNumber, ""), tan_1]));
-            }
-            else {
-                const taninfo = (0, Option_js_1.value)(matchValue_1);
-                return (0, Seq_js_1.singleton)((0, HashCodes_js_1.boxHashArray)([taninfo.IDSpace, (taninfo.IDSpace + ":") + taninfo.LocalID]));
-            }
-        }))))) | 0;
+        return (0, HashCodes_js_1.mergeHashes)((matchValue = this$.Name, (matchValue == null) ? 0 : (0, Util_js_1.stringHash)((0, Option_js_1.value)(matchValue))), (matchValue_1 = this$.TermSourceREF, (matchValue_2 = this$.TANInfo, (matchValue_1 != null) ? ((matchValue_2 == null) ? ((tsr_1 = (0, Option_js_1.value)(matchValue_1), (matchValue_4 = this$.TermAccessionNumber, (matchValue_4 == null) ? (0, Util_js_1.stringHash)(tsr_1) : ((tan = (0, Option_js_1.value)(matchValue_4), (0, HashCodes_js_1.mergeHashes)((0, Util_js_1.stringHash)(tsr_1), (0, Util_js_1.stringHash)(tan))))))) : ((taninfo_1 = (0, Option_js_1.value)(matchValue_2), (tsr = (0, Option_js_1.value)(matchValue_1), (0, HashCodes_js_1.mergeHashes)((0, Util_js_1.stringHash)(tsr), (0, Util_js_1.stringHash)(taninfo_1.LocalID)))))) : ((matchValue_2 == null) ? 0 : ((taninfo = (0, Option_js_1.value)(matchValue_2), (0, HashCodes_js_1.mergeHashes)((0, Util_js_1.stringHash)(taninfo.IDSpace), (0, Util_js_1.stringHash)(taninfo.LocalID)))))))) | 0;
     }
     Equals(obj) {
         const this$ = this;
@@ -185,6 +170,20 @@ class OntologyAnnotation {
         const tan = this$.TermAccessionNumber;
         return OntologyAnnotation.make(name, tsr, tan, nextComments);
     }
+    static computeTanInfo(tan, tsr) {
+        let tsr_1;
+        if (tan == null) {
+            return undefined;
+        }
+        else {
+            const tan_1 = (0, Option_js_1.value)(tan);
+            const matchValue = (0, Regex_js_1.tryParseTermAnnotation)(tan_1);
+            return (matchValue == null) ? ((tsr == null) ? undefined : (((0, Option_js_1.value)(tsr) === "") ? undefined : ((tsr_1 = (0, Option_js_1.value)(tsr), {
+                IDSpace: tsr_1,
+                LocalID: tan_1,
+            })))) : (0, Option_js_1.value)(matchValue);
+        }
+    }
     Print() {
         const this$ = this;
         return (0, Types_js_1.toString)(this$);
@@ -205,6 +204,11 @@ class OntologyAnnotation {
             return 1;
         }
     }
+    recomputeTanInfo() {
+        const this$ = this;
+        const newTanInfo = OntologyAnnotation.computeTanInfo((0, Option_js_1.unwrap)(this$._termAccessionNumber), (0, Option_js_1.unwrap)(this$._termSourceREF));
+        this$._tanInfo = newTanInfo;
+    }
 }
 exports.OntologyAnnotation = OntologyAnnotation;
 function OntologyAnnotation_$reflection() {