@nfdi4plants/arctrl 1.1.0 → 2.0.0-alpha.1

package/{ISA/ISA/ArcTypes → Core/Table}/ArcTable.js

@@ -1,59 +1,54 @@
-import { Dictionary } from "../../../fable_modules/fable-library.4.5.0/MutableMap.js";
-import { compareArrays, safeHash, disposeSafe, getEnumerator, comparePrimitives, equals, arrayHash, equalArrays } from "../../../fable_modules/fable-library.4.5.0/Util.js";
-import { value as value_9, map as map_2, defaultArg, unwrap } from "../../../fable_modules/fable-library.4.5.0/Option.js";
-import { boxHashValues, Unchecked_extendToRowCount, ProcessParsing_processToRows, ProcessParsing_alignByHeaders, ProcessParsing_mergeIdenticalProcesses, ProcessParsing_getProcessGetter, Unchecked_removeRowCells_withIndexChange, Unchecked_addRows, Unchecked_addRow, Unchecked_getEmptyCellForHeader, Unchecked_removeColumnCells_withIndexChange, tryFindDuplicateUniqueInArray, Unchecked_removeColumnCells, Unchecked_removeHeader, Unchecked_fillMissingCells, Unchecked_addColumn, tryFindDuplicateUnique, Unchecked_setCellAt, SanityChecks_validateColumn, SanityChecks_validateRowIndex, SanityChecks_validateColumnIndex, Unchecked_tryGetCellAt, getRowCount, getColumnCount } from "./ArcTableAux.js";
-import { item, append as append_1, indexed as indexed_1, choose, toList, zip, fold, filter, length, tryFindIndex, empty, singleton, collect, removeAt, map, delay, toArray } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
-import { rangeDouble } from "../../../fable_modules/fable-library.4.5.0/Range.js";
+import { boxHashValues, Unchecked_alignByHeaders, Unchecked_extendToRowCount, Unchecked_removeRowCells_withIndexChange, Unchecked_addRows, Unchecked_addRow, Unchecked_getEmptyCellForHeader, Unchecked_removeColumnCells_withIndexChange, tryFindDuplicateUniqueInArray, Unchecked_removeColumnCells, Unchecked_removeHeader, Unchecked_fillMissingCells, Unchecked_addColumn, tryFindDuplicateUnique, Unchecked_setCellAt, SanityChecks_validateColumn, SanityChecks_validateRowIndex, SanityChecks_validateColumnIndex, Unchecked_tryGetCellAt, getRowCount, getColumnCount, SanityChecks_validate } from "./ArcTableAux.js";
+import { Dictionary } from "../../fable_modules/fable-library-js.4.16.0/MutableMap.js";
+import { compareArrays, safeHash, comparePrimitives, equals, arrayHash, equalArrays } from "../../fable_modules/fable-library-js.4.16.0/Util.js";
+import { value as value_3, map as map_2, unwrap, defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
+import { item as item_1, fold, append as append_1, toList, indexed as indexed_1, choose, filter, length, tryFindIndex, empty, singleton, collect, removeAt, map, delay, toArray } from "../../fable_modules/fable-library-js.4.16.0/Seq.js";
+import { rangeDouble } from "../../fable_modules/fable-library-js.4.16.0/Range.js";
 import { CompositeColumn } from "./CompositeColumn.js";
-import { sortBy, indexed, mapIndexed, singleton as singleton_1, initialize, sortDescending, iterateIndexed, map as map_1 } from "../../../fable_modules/fable-library.4.5.0/Array.js";
-import { append, collect as collect_1, initialize as initialize_1, singleton as singleton_2, empty as empty_1, iterate, isEmpty } from "../../../fable_modules/fable-library.4.5.0/List.js";
-import { StringBuilder__AppendLine_Z721C83C5, StringBuilder_$ctor } from "../../../fable_modules/fable-library.4.5.0/System.Text.js";
-import { toString } from "../../../fable_modules/fable-library.4.5.0/Types.js";
-import { join, printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
+import { sortBy, indexed, mapIndexed, initialize, item, sortDescending, iterateIndexed, map as map_1 } from "../../fable_modules/fable-library-js.4.16.0/Array.js";
+import { append, iterate, isEmpty } from "../../fable_modules/fable-library-js.4.16.0/List.js";
+import { StringBuilder__AppendLine_Z721C83C5, StringBuilder_$ctor } from "../../fable_modules/fable-library-js.4.16.0/System.Text.js";
+import { toString } from "../../fable_modules/fable-library-js.4.16.0/Types.js";
+import { join, printf, toFail } from "../../fable_modules/fable-library-js.4.16.0/String.js";
 import { CompositeCell } from "./CompositeCell.js";
 import { CompositeHeader } from "./CompositeHeader.js";
-import { createMissingIdentifier } from "../Identifier.js";
-import { ARCtrl_ISA_Component__Component_TryGetColumnIndex, ARCtrl_ISA_ProtocolParameter__ProtocolParameter_TryGetColumnIndex } from "../JsonTypes/ColumnIndex.js";
-import { Protocol_create_Z7DFD6E67, Protocol_addComponent, Protocol_addParameter, Protocol_setName, Protocol_setDescription, Protocol_setUri, Protocol_setVersion, Protocol_setProtocolType } from "../JsonTypes/Protocol.js";
-import { OntologyAnnotation } from "../JsonTypes/OntologyAnnotation.js";
-import { ProtocolParameter } from "../JsonTypes/ProtocolParameter.js";
-import { Component_create_61502994 } from "../JsonTypes/Component.js";
-import { Array_groupBy, List_distinct } from "../../../fable_modules/fable-library.4.5.0/Seq2.js";
-import { toProtocol } from "./CompositeRow.js";
-import { Process_create_Z42860F3E } from "../JsonTypes/Process.js";
-import { getItemFromDict } from "../../../fable_modules/fable-library.4.5.0/MapUtil.js";
-import { HashCodes_boxHashSeq, HashCodes_boxHashArray } from "../Helper.js";
-import { class_type } from "../../../fable_modules/fable-library.4.5.0/Reflection.js";
+import { Array_groupBy } from "../../fable_modules/fable-library-js.4.16.0/Seq2.js";
+import { getItemFromDict } from "../../fable_modules/fable-library-js.4.16.0/MapUtil.js";
+import { boxHashSeq, boxHashArray } from "../Helper/HashCodes.js";
+import { class_type } from "../../fable_modules/fable-library-js.4.16.0/Reflection.js";
 
 export class ArcTable {
     constructor(name, headers, values) {
-        this["name@20"] = name;
-        this["headers@21"] = headers;
-        this["values@22"] = values;
+        const valid = SanityChecks_validate(headers, values, true);
+        this["name@21"] = name;
+        this["headers@22"] = headers;
+        this["values@23"] = values;
     }
     get Headers() {
         const this$ = this;
-        return this$["headers@21"];
+        return this$["headers@22"];
     }
     set Headers(newHeaders) {
         const this$ = this;
-        this$["headers@21"] = newHeaders;
+        SanityChecks_validate(newHeaders, this$["values@23"], true);
+        this$["headers@22"] = newHeaders;
     }
     get Values() {
         const this$ = this;
-        return this$["values@22"];
+        return this$["values@23"];
     }
     set Values(newValues) {
         const this$ = this;
-        this$["values@22"] = newValues;
+        SanityChecks_validate(this$["headers@22"], newValues, true);
+        this$["values@23"] = newValues;
     }
     get Name() {
         const this$ = this;
-        return this$["name@20"];
+        return this$["name@21"];
     }
     set Name(newName) {
         const this$ = this;
-        this$["name@20"] = newName;
+        this$["name@21"] = newName;
     }
     static create(name, headers, values) {
         return new ArcTable(name, headers, values);
@@ -77,12 +72,8 @@ export class ArcTable {
     }
     Validate(raiseException) {
         const this$ = this;
-        let isValid = true;
-        for (let columnIndex = 0; columnIndex <= (this$.ColumnCount - 1); columnIndex++) {
-            const column = this$.GetColumn(columnIndex);
-            isValid = column.Validate(unwrap(raiseException));
-        }
-        return isValid;
+        const raiseException_1 = defaultArg(raiseException, true);
+        return SanityChecks_validate(this$.Headers, this$.Values, raiseException_1);
     }
     static validate(raiseException) {
         return (table) => table.Validate(unwrap(raiseException));
@@ -189,7 +180,7 @@ export class ArcTable {
             return newTable;
         };
     }
-    AddColumn(header, cells, index, forceReplace, SkipFillMissing) {
+    AddColumn(header, cells, index, forceReplace, skipFillMissing) {
         const this$ = this;
         const index_1 = defaultArg(index, this$.ColumnCount) | 0;
         const cells_1 = defaultArg(cells, []);
@@ -197,7 +188,7 @@ export class ArcTable {
         SanityChecks_validateColumnIndex(index_1, this$.ColumnCount, true);
         SanityChecks_validateColumn(CompositeColumn.create(header, cells_1));
         Unchecked_addColumn(header, cells_1, index_1, forceReplace_1, false, this$.Headers, this$.Values);
-        if (!equals(SkipFillMissing, true)) {
+        if (!equals(skipFillMissing, true)) {
             Unchecked_fillMissingCells(this$.Headers, this$.Values);
         }
     }
@@ -208,7 +199,7 @@ export class ArcTable {
             return newTable;
         };
     }
-    UpdateColumn(columnIndex, header, cells, SkipFillMissing) {
+    UpdateColumn(columnIndex, header, cells, skipFillMissing) {
         const this$ = this;
         SanityChecks_validateColumnIndex(columnIndex, this$.ColumnCount, false);
         const column = CompositeColumn.create(header, unwrap(cells));
@@ -224,7 +215,7 @@ export class ArcTable {
         iterateIndexed((rowIndex, v) => {
             Unchecked_setCellAt(columnIndex, rowIndex, v, this$.Values);
         }, column.Cells);
-        if (!equals(SkipFillMissing, true)) {
+        if (!equals(skipFillMissing, true)) {
             Unchecked_fillMissingCells(this$.Headers, this$.Values);
         }
     }
@@ -257,7 +248,7 @@ export class ArcTable {
             return newTable;
         };
     }
-    AddColumns(columns, index, forceReplace, SkipFillMissing) {
+    AddColumns(columns, index, forceReplace, skipFillMissing) {
         const this$ = this;
         let index_1 = defaultArg(index, this$.ColumnCount);
         const forceReplace_1 = defaultArg(forceReplace, false);
@@ -281,14 +272,14 @@ export class ArcTable {
                 index_1 = ((index_1 + 1) | 0);
             }
         });
-        if (!equals(SkipFillMissing, true)) {
+        if (!equals(skipFillMissing, true)) {
             Unchecked_fillMissingCells(this$.Headers, this$.Values);
         }
     }
-    static addColumns(columns, index, SkipFillMissing) {
+    static addColumns(columns, index, skipFillMissing) {
         return (table) => {
             const newTable = table.Copy();
-            newTable.AddColumns(columns, unwrap(index), void 0, unwrap(SkipFillMissing));
+            newTable.AddColumns(columns, unwrap(index), void 0, unwrap(skipFillMissing));
             return newTable;
         };
     }
@@ -410,7 +401,7 @@ export class ArcTable {
     AddRow(cells, index) {
         const this$ = this;
         const index_1 = defaultArg(index, this$.RowCount) | 0;
-        const cells_1 = (cells == null) ? toArray(delay(() => collect((columnIndex) => singleton(Unchecked_getEmptyCellForHeader(this$.Headers[columnIndex], Unchecked_tryGetCellAt(columnIndex, 0, this$.Values))), rangeDouble(0, 1, this$.ColumnCount - 1)))) : value_9(cells);
+        const cells_1 = (cells == null) ? toArray(delay(() => collect((columnIndex) => singleton(Unchecked_getEmptyCellForHeader(this$.Headers[columnIndex], Unchecked_tryGetCellAt(columnIndex, 0, this$.Values))), rangeDouble(0, 1, this$.ColumnCount - 1)))) : value_3(cells);
         SanityChecks_validateRowIndex(index_1, this$.RowCount, true);
         const columnCount = this$.ColumnCount | 0;
         const newCellsCount = length(cells_1) | 0;
@@ -422,7 +413,7 @@ export class ArcTable {
         }
         for (let columnIndex_1 = 0; columnIndex_1 <= (this$.ColumnCount - 1); columnIndex_1++) {
             const h_1 = this$.Headers[columnIndex_1];
-            SanityChecks_validateColumn(CompositeColumn.create(h_1, [cells_1[columnIndex_1]]));
+            SanityChecks_validateColumn(CompositeColumn.create(h_1, [item(columnIndex_1, cells_1)]));
         }
         Unchecked_addRow(index_1, cells_1, this$.Headers, this$.Values);
     }
@@ -496,10 +487,10 @@ export class ArcTable {
             }
         });
         for (let idx = 0; idx <= (rows.length - 1); idx++) {
-            const row_1 = rows[idx];
+            const row_1 = item(idx, rows);
             for (let columnIndex = 0; columnIndex <= (this$.ColumnCount - 1); columnIndex++) {
                 const h = this$.Headers[columnIndex];
-                SanityChecks_validateColumn(CompositeColumn.create(h, [row_1[columnIndex]]));
+                SanityChecks_validateColumn(CompositeColumn.create(h, [item(columnIndex, row_1)]));
             }
         }
         Unchecked_addRows(index_1, rows, this$.Headers, this$.Values);
@@ -560,7 +551,7 @@ export class ArcTable {
         if (!equals(SkipValidation, true)) {
             SanityChecks_validateRowIndex(rowIndex, this$.RowCount, false);
         }
-        return toArray(delay(() => map((columnIndex) => value_9(this$.TryGetCellAt(columnIndex, rowIndex)), rangeDouble(0, 1, this$.ColumnCount - 1))));
+        return toArray(delay(() => map((columnIndex) => value_3(this$.TryGetCellAt(columnIndex, rowIndex)), rangeDouble(0, 1, this$.ColumnCount - 1))));
     }
     static getRow(index) {
         return (table) => table.GetRow(index);
@@ -615,12 +606,6 @@ export class ArcTable {
             return copy;
         };
     }
-    static insertParameterValue(t, p) {
-        throw new Error();
-    }
-    static getParameterValues(t) {
-        throw new Error();
-    }
     AddProtocolTypeColumn(types, index) {
         const this$ = this;
         const cells = map_2((array) => map_1((Item) => (new CompositeCell(0, [Item])), array), types);
@@ -674,97 +659,6 @@ export class ArcTable {
         const this$ = this;
         return map_1((h_1) => this$.GetColumnByHeader(h_1), toArray(filter((h) => h.isComponent, this$.Headers)));
     }
-    static fromProtocol(p) {
-        const t = ArcTable.init(defaultArg(p.Name, createMissingIdentifier()));
-        const enumerator = getEnumerator(defaultArg(p.Parameters, empty_1()));
-        try {
-            while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
-                const pp = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
-                t.AddColumn(new CompositeHeader(3, [value_9(pp.ParameterName)]), void 0, ARCtrl_ISA_ProtocolParameter__ProtocolParameter_TryGetColumnIndex(pp));
-            }
-        }
-        finally {
-            disposeSafe(enumerator);
-        }
-        const enumerator_1 = getEnumerator(defaultArg(p.Components, empty_1()));
-        try {
-            while (enumerator_1["System.Collections.IEnumerator.MoveNext"]()) {
-                const c = enumerator_1["System.Collections.Generic.IEnumerator`1.get_Current"]();
-                const v_1 = map_2((arg) => singleton_1(CompositeCell.fromValue(arg, unwrap(c.ComponentUnit))), c.ComponentValue);
-                t.AddColumn(new CompositeHeader(3, [value_9(c.ComponentType)]), v_1, ARCtrl_ISA_Component__Component_TryGetColumnIndex(c));
-            }
-        }
-        finally {
-            disposeSafe(enumerator_1);
-        }
-        map_2((d) => {
-            t.AddProtocolDescriptionColumn([d]);
-        }, p.Description);
-        map_2((d_1) => {
-            t.AddProtocolVersionColumn([d_1]);
-        }, p.Version);
-        map_2((d_2) => {
-            t.AddProtocolTypeColumn([d_2]);
-        }, p.ProtocolType);
-        map_2((d_3) => {
-            t.AddProtocolUriColumn([d_3]);
-        }, p.Uri);
-        map_2((d_4) => {
-            t.AddProtocolNameColumn([d_4]);
-        }, p.Name);
-        return t;
-    }
-    GetProtocols() {
-        let source;
-        const this$ = this;
-        return (this$.RowCount === 0) ? singleton_2((source = this$.Headers, fold((p, h) => {
-            switch (h.tag) {
-                case 4:
-                    return Protocol_setProtocolType(p, OntologyAnnotation.empty);
-                case 7:
-                    return Protocol_setVersion(p, "");
-                case 6:
-                    return Protocol_setUri(p, "");
-                case 5:
-                    return Protocol_setDescription(p, "");
-                case 8:
-                    return Protocol_setName(p, "");
-                case 3:
-                    return Protocol_addParameter(ProtocolParameter.create(void 0, h.fields[0]), p);
-                case 0:
-                    return Protocol_addComponent(Component_create_61502994(void 0, void 0, void 0, h.fields[0]), p);
-                default:
-                    return p;
-            }
-        }, Protocol_create_Z7DFD6E67(void 0, this$.Name), source))) : List_distinct(initialize_1(this$.RowCount, (i) => {
-            let row;
-            const source_2 = this$.GetRow(i, true);
-            row = zip(this$.Headers, source_2);
-            return toProtocol(this$.Name, row);
-        }), {
-            Equals: equals,
-            GetHashCode: safeHash,
-        });
-    }
-    GetProcesses() {
-        const this$ = this;
-        if (this$.RowCount === 0) {
-            return singleton_2(Process_create_Z42860F3E(void 0, this$.Name));
-        }
-        else {
-            let getter;
-            const clo = ProcessParsing_getProcessGetter(this$.Name, this$.Headers);
-            getter = ((arg) => {
-                const clo_1 = clo(arg);
-                return clo_1;
-            });
-            return ProcessParsing_mergeIdenticalProcesses(toList(delay(() => map((i) => getter(this$.Values)(i), rangeDouble(0, 1, this$.RowCount - 1)))));
-        }
-    }
-    static fromProcesses(name, ps) {
-        const tupledArg = ProcessParsing_alignByHeaders(true, collect_1(ProcessParsing_processToRows, ps));
-        return ArcTable.create(name, tupledArg[0], tupledArg[1]);
-    }
     static SplitByColumnValues(columnIndex) {
         return (table) => mapIndexed((i, indexGroup) => {
             let headers;
@@ -807,14 +701,14 @@ export class ArcTable {
         Unchecked_extendToRowCount(annotationTable_1.RowCount, refTable_1.Headers, refTable_1.Values);
         const arr = annotationTable_1.Columns;
         for (let idx = 0; idx <= (arr.length - 1); idx++) {
-            const c = arr[idx];
+            const c = item(idx, arr);
             refTable_1.AddColumn(c.Header, c.Cells, void 0, true);
         }
         return refTable_1;
     }
     static append(table1, table2) {
         const getList = (t) => toList(delay(() => map((row) => toList(delay(() => map((col) => [t.Headers[col], getItemFromDict(t.Values, [col, row])], rangeDouble(0, 1, t.ColumnCount - 1)))), rangeDouble(0, 1, t.RowCount - 1))));
-        const patternInput = ProcessParsing_alignByHeaders(false, append(getList(table1), getList(table2)));
+        const patternInput = Unchecked_alignByHeaders(false, append(getList(table1), getList(table2)));
         return ArcTable.create(table1.Name, patternInput[0], patternInput[1]);
     }
     toString() {
@@ -834,7 +728,7 @@ export class ArcTable {
             else {
                 return false;
             }
-        }, true, toList(delay(() => map((i) => equals(item(i, a), item(i, b)), rangeDouble(0, 1, length(a) - 1))))))))) {
+        }, true, toList(delay(() => map((i) => equals(item_1(i, a), item_1(i, b)), rangeDouble(0, 1, length(a) - 1))))))))) {
             const a_1 = sort(this$.Values);
             const b_1 = sort(other.Values);
             return (length(a_1) === length(b_1)) && fold((acc_1, e_1) => {
@@ -844,7 +738,7 @@ export class ArcTable {
                 else {
                     return false;
                 }
-            }, true, toList(delay(() => map((i_1) => equals(item(i_1, a_1), item(i_1, b_1)), rangeDouble(0, 1, length(a_1) - 1)))));
+            }, true, toList(delay(() => map((i_1) => equals(item_1(i_1, a_1), item_1(i_1, b_1)), rangeDouble(0, 1, length(a_1) - 1)))));
         }
         else {
             return false;
@@ -862,15 +756,15 @@ export class ArcTable {
     GetHashCode() {
         const this$ = this;
         const vHash = boxHashValues(this$.ColumnCount, this$.Values);
-        return HashCodes_boxHashArray([this$.Name, HashCodes_boxHashSeq(this$.Headers), vHash]) | 0;
+        return boxHashArray([this$.Name, boxHashSeq(this$.Headers), vHash]) | 0;
     }
 }
 
 export function ArcTable_$reflection() {
-    return class_type("ARCtrl.ISA.ArcTable", void 0, ArcTable);
+    return class_type("ARCtrl.ArcTable", void 0, ArcTable);
 }
 
-export function ArcTable_$ctor_474CDC4E(name, headers, values) {
+export function ArcTable_$ctor_76CAD84E(name, headers, values) {
     return new ArcTable(name, headers, values);
 }