@nfdi4plants/arctrl 1.0.0-alpha8 → 1.0.0-beta.1

package/ARC.js

@@ -11,11 +11,11 @@ import { FileSystemTree } from "./FileSystem/FileSystemTree.js";
 import { FileSystem } from "./FileSystem/FileSystem.js";
 import { bind, map as map_1, value as value_2, defaultArg, unwrap } from "./fable_modules/fable-library.4.1.4/Option.js";
 import { tryISAReadContractFromPath } from "./Contracts/Contracts.ARCtrl.js";
-import { ArcTables__get_Tables, ArcTables_$ctor_Z18C2F36D, ArcTables_updateReferenceTablesBySheets_Z2EE88E97 } from "./ISA/ISA/ArcTypes/ArcTables.js";
+import { ArcTables } from "./ISA/ISA/ArcTypes/ArcTables.js";
 import { addToDict } from "./fable_modules/fable-library.4.1.4/MapUtil.js";
 import { ArcInvestigation } from "./ISA/ISA/ArcTypes/ArcTypes.js";
 import { Assay_fileNameFromIdentifier, Study_fileNameFromIdentifier } from "./ISA/ISA/Identifier.js";
-import { Dictionary_tryGet } from "./fable_modules/FsSpreadsheet.4.1.0/Cells/FsCellsCollection.fs.js";
+import { Dictionary_tryGet } from "./fable_modules/FsSpreadsheet.5.0.0/Cells/FsCellsCollection.fs.js";
 import { Contract } from "./Contract/Contract.js";
 import { Clone_createCloneContract_5000466F, Init_createAddRemoteContract_Z721C83C5, gitignoreContract, Init_createInitContract_6DFDD678 } from "./Contracts/Contracts.Git.js";
 import { FSharpSet__Contains, ofSeq, unionMany } from "./fable_modules/fable-library.4.1.4/Set.js";
@@ -99,9 +99,8 @@ export class ARC {
         const this$ = this;
         return choose(tryISAReadContractFromPath, this$._fs.Tree.ToFilePaths());
     }
-    SetISAFromContracts(contracts, enableLogging) {
+    SetISAFromContracts(contracts) {
         const this$ = this;
-        const enableLogging_1 = defaultArg(enableLogging, false);
         const investigation = ARCAux_getArcInvestigationFromContracts(contracts);
         const studies = map((tuple) => tuple[0], ARCAux_getArcStudiesFromContracts(contracts));
         const assays = ARCAux_getArcAssaysFromContracts(contracts);
@@ -127,8 +126,8 @@ export class ARC {
             const assay_1 = find((a_1) => (a_1.Identifier === assay.Identifier), investigation.Assays);
             let updatedTables;
             const array_2 = assay_1.StudiesRegisteredIn;
-            updatedTables = fold((tables, study_1) => ArcTables_updateReferenceTablesBySheets_Z2EE88E97(ArcTables_$ctor_Z18C2F36D(study_1.Tables), tables, false), ArcTables_$ctor_Z18C2F36D(assay_1.Tables), array_2);
-            assay_1.Tables = ArcTables__get_Tables(updatedTables);
+            updatedTables = fold((tables, study_1) => ArcTables.updateReferenceTablesBySheets(new ArcTables(study_1.Tables), tables, false), new ArcTables(assay_1.Tables), array_2);
+            assay_1.Tables = updatedTables.Tables;
         });
         this$.ISA = investigation;
     }

package/ISA/ISA/ArcTypes/ArcTable.js

@@ -1,14 +1,15 @@
 import { Dictionary } from "../../../fable_modules/fable-library.4.1.4/MutableMap.js";
-import { stringHash, compareArrays, safeHash, disposeSafe, getEnumerator, equals, comparePrimitives, arrayHash, equalArrays } from "../../../fable_modules/fable-library.4.1.4/Util.js";
-import { map as map_2, value as value_9, defaultArg, unwrap } from "../../../fable_modules/fable-library.4.1.4/Option.js";
+import { compareArrays, safeHash, disposeSafe, getEnumerator, equals, comparePrimitives, arrayHash, equalArrays } from "../../../fable_modules/fable-library.4.1.4/Util.js";
+import { value as value_9, map as map_2, defaultArg, unwrap } from "../../../fable_modules/fable-library.4.1.4/Option.js";
 import { Unchecked_extendToRowCount, ProcessParsing_processToRows, ProcessParsing_alignByHeaders, ProcessParsing_mergeIdenticalProcesses, ProcessParsing_getProcessGetter, Unchecked_removeRowCells_withIndexChange, 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 { sortBy, item, append as append_1, indexed as indexed_1, choose, zip, fold, filter, length, singleton, collect, tryFindIndex, findIndex, toArray, removeAt, map, delay, toList } from "../../../fable_modules/fable-library.4.1.4/Seq.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.4.1.4/Seq.js";
 import { rangeDouble } from "../../../fable_modules/fable-library.4.1.4/Range.js";
 import { CompositeColumn } from "./CompositeColumn.js";
-import { indexed, mapIndexed, singleton as singleton_1, initialize, sortDescending, iterateIndexed, map as map_1 } from "../../../fable_modules/fable-library.4.1.4/Array.js";
-import { append, collect as collect_1, initialize as initialize_1, singleton as singleton_2, empty, iterate, isEmpty } from "../../../fable_modules/fable-library.4.1.4/List.js";
+import { sortBy, indexed, mapIndexed, singleton as singleton_1, initialize, sortDescending, iterateIndexed, map as map_1 } from "../../../fable_modules/fable-library.4.1.4/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.4.1.4/List.js";
 import { StringBuilder__AppendLine_Z721C83C5, StringBuilder_$ctor } from "../../../fable_modules/fable-library.4.1.4/System.Text.js";
 import { toString } from "../../../fable_modules/fable-library.4.1.4/Types.js";
+import { join, printf, toFail } from "../../../fable_modules/fable-library.4.1.4/String.js";
 import { CompositeCell } from "./CompositeCell.js";
 import { CompositeHeader } from "./CompositeHeader.js";
 import { createMissingIdentifier } from "../Identifier.js";
@@ -21,7 +22,7 @@ import { Array_groupBy, List_distinct } from "../../../fable_modules/fable-libra
 import { toProtocol } from "./CompositeRow.js";
 import { Process_create_Z42860F3E } from "../JsonTypes/Process.js";
 import { getItemFromDict } from "../../../fable_modules/fable-library.4.1.4/MapUtil.js";
-import { join } from "../../../fable_modules/fable-library.4.1.4/String.js";
+import { HashCodes_boxHashArray } from "../Helper.js";
 import { class_type } from "../../../fable_modules/fable-library.4.1.4/Reflection.js";
 
 export class ArcTable {
@@ -79,7 +80,7 @@ export class ArcTable {
         let isValid = true;
         for (let columnIndex = 0; columnIndex <= (this$.ColumnCount - 1); columnIndex++) {
             const column = this$.GetColumn(columnIndex);
-            isValid = column.validate(unwrap(raiseException));
+            isValid = column.Validate(unwrap(raiseException));
         }
         return isValid;
     }
@@ -96,7 +97,7 @@ export class ArcTable {
     }
     get Columns() {
         const this$ = this;
-        return toList(delay(() => map((i) => this$.GetColumn(i), rangeDouble(0, 1, this$.ColumnCount - 1))));
+        return toArray(delay(() => map((i) => this$.GetColumn(i), rangeDouble(0, 1, this$.ColumnCount - 1))));
     }
     Copy() {
         const this$ = this;
@@ -136,7 +137,7 @@ export class ArcTable {
             throw new Error(`Invalid input. Tried setting unique header \`${header}\`, but header of same type already exists at index ${matchValue}.`);
         }
         const c = new CompositeColumn(newHeader, this$.GetColumn(index).Cells);
-        if (c.validate()) {
+        if (c.Validate()) {
             let setHeader;
             setHeader = (this$.Headers[index] = newHeader);
         }
@@ -169,7 +170,7 @@ export class ArcTable {
         const forceReplace_1 = defaultArg(forceReplace, false);
         SanityChecks_validateColumnIndex(index_1, this$.ColumnCount, true);
         SanityChecks_validateColumn(CompositeColumn.create(header, cells_1));
-        Unchecked_addColumn(header, cells_1, index_1, forceReplace_1, this$.Headers, this$.Values);
+        Unchecked_addColumn(header, cells_1, index_1, forceReplace_1, false, this$.Headers, this$.Values);
         Unchecked_fillMissingCells(this$.Headers, this$.Values);
     }
     static addColumn(header, cells, index, forceReplace) {
@@ -245,7 +246,7 @@ export class ArcTable {
         });
         columns.forEach((col) => {
             const prevHeadersCount = this$.Headers.length | 0;
-            Unchecked_addColumn(col.Header, col.Cells, index_1, forceReplace_1, this$.Headers, this$.Values);
+            Unchecked_addColumn(col.Header, col.Cells, index_1, forceReplace_1, false, this$.Headers, this$.Values);
             if (this$.Headers.length > prevHeadersCount) {
                 index_1 = ((index_1 + 1) | 0);
             }
@@ -296,26 +297,83 @@ export class ArcTable {
         const this$ = this;
         SanityChecks_validateColumnIndex(columnIndex, this$.ColumnCount, false);
         const h = this$.Headers[columnIndex];
-        const cells = toArray(delay(() => map((i) => value_9(this$.TryGetCellAt(columnIndex, i)), rangeDouble(0, 1, this$.RowCount - 1))));
+        const cells = toArray(delay(() => collect((i) => {
+            const matchValue = this$.TryGetCellAt(columnIndex, i);
+            if (matchValue != null) {
+                return singleton(matchValue);
+            }
+            else {
+                toFail(printf("Unable to find cell for index: (%i, %i)"))(columnIndex)(i);
+                return empty();
+            }
+        }, rangeDouble(0, 1, this$.RowCount - 1))));
         return CompositeColumn.create(h, cells);
     }
     static getColumn(index) {
         return (table) => table.GetColumn(index);
     }
+    TryGetColumnByHeader(header) {
+        const this$ = this;
+        return map_2((i) => this$.GetColumn(i), tryFindIndex((x) => equals(x, header), this$.Headers));
+    }
+    static tryGetColumnByHeader(header) {
+        return (table) => table.TryGetColumnByHeader(header);
+    }
     GetColumnByHeader(header) {
         const this$ = this;
-        const index = findIndex((x) => equals(x, header), this$.Headers) | 0;
-        return this$.GetColumn(index);
+        const matchValue = this$.TryGetColumnByHeader(header);
+        if (matchValue == null) {
+            const arg = this$.Name;
+            return toFail(printf("Unable to find column with header in table %s: %O"))(arg)(header);
+        }
+        else {
+            return matchValue;
+        }
     }
     static getColumnByHeader(header) {
         return (table) => table.GetColumnByHeader(header);
     }
-    TryGetColumnByHeader(header) {
+    TryGetInputColumn() {
         const this$ = this;
-        return map_2((i) => this$.GetColumn(i), tryFindIndex((x) => equals(x, header), this$.Headers));
+        return map_2((i) => this$.GetColumn(i), tryFindIndex((x) => x.isInput, this$.Headers));
     }
-    static tryGetColumnByHeader(header) {
-        return (table) => table.TryGetColumnByHeader(header);
+    static tryGetInputColumn() {
+        return (table) => table.TryGetInputColumn();
+    }
+    GetInputColumn() {
+        const this$ = this;
+        const matchValue = this$.TryGetInputColumn();
+        if (matchValue == null) {
+            const arg = this$.Name;
+            return toFail(printf("Unable to find input column in table %s"))(arg);
+        }
+        else {
+            return matchValue;
+        }
+    }
+    static getInputColumn() {
+        return (table) => table.GetInputColumn();
+    }
+    TryGetOutputColumn() {
+        const this$ = this;
+        return map_2((i) => this$.GetColumn(i), tryFindIndex((x) => x.isOutput, this$.Headers));
+    }
+    static tryGetOutputColumn() {
+        return (table) => table.TryGetOutputColumn();
+    }
+    GetOutputColumn() {
+        const this$ = this;
+        const matchValue = this$.TryGetOutputColumn();
+        if (matchValue == null) {
+            const arg = this$.Name;
+            return toFail(printf("Unable to find output column in table %s"))(arg);
+        }
+        else {
+            return matchValue;
+        }
+    }
+    static getOutputColumn() {
+        return (table) => table.GetOutputColumn();
     }
     AddRow(cells, index) {
         const this$ = this;
@@ -476,6 +534,51 @@ export class ArcTable {
     static getRow(index) {
         return (table) => table.GetRow(index);
     }
+    Join(table, joinOptions, forceReplace) {
+        const this$ = this;
+        const joinOptions_1 = defaultArg(joinOptions, "headers");
+        const forceReplace_1 = defaultArg(forceReplace, false);
+        const onlyHeaders = joinOptions_1 === "headers";
+        let columns;
+        const pre = table.Columns;
+        columns = ((joinOptions_1 === "withUnit") ? map_1((c_1) => {
+            const unitsOpt = c_1.TryGetColumnUnits();
+            if (unitsOpt == null) {
+                return new CompositeColumn(c_1.Header, []);
+            }
+            else {
+                return new CompositeColumn(c_1.Header, map_1((u) => CompositeCell.createUnitized("", u), unitsOpt));
+            }
+        }, pre) : ((joinOptions_1 === "withValues") ? pre : map_1((c) => (new CompositeColumn(c.Header, [])), pre)));
+        const duplicates = tryFindDuplicateUniqueInArray(map((x) => x.Header, columns));
+        if (!isEmpty(duplicates)) {
+            const sb = StringBuilder_$ctor();
+            StringBuilder__AppendLine_Z721C83C5(sb, "Found duplicate unique columns in `columns`.");
+            iterate((x_1) => {
+                StringBuilder__AppendLine_Z721C83C5(sb, `Duplicate \`${x_1.HeaderType}\` at index ${x_1.Index1} and ${x_1.Index2}.`);
+            }, duplicates);
+            throw new Error(toString(sb));
+        }
+        columns.forEach((x_2) => {
+            SanityChecks_validateColumn(x_2);
+        });
+        let index = this$.ColumnCount;
+        columns.forEach((col) => {
+            const prevHeadersCount = this$.Headers.length | 0;
+            Unchecked_addColumn(col.Header, col.Cells, index, forceReplace_1, onlyHeaders, this$.Headers, this$.Values);
+            if (this$.Headers.length > prevHeadersCount) {
+                index = ((index + 1) | 0);
+            }
+        });
+        Unchecked_fillMissingCells(this$.Headers, this$.Values);
+    }
+    static join(table, joinOptions, forceReplace) {
+        return (this$) => {
+            const copy = this$.Copy();
+            copy.Join(table, unwrap(joinOptions), unwrap(forceReplace));
+            return copy;
+        };
+    }
     static insertParameterValue(t, p) {
         throw new Error();
     }
@@ -537,7 +640,7 @@ export class ArcTable {
     }
     static fromProtocol(p) {
         const t = ArcTable.init(defaultArg(p.Name, createMissingIdentifier()));
-        const enumerator = getEnumerator(defaultArg(p.Parameters, empty()));
+        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"]();
@@ -547,7 +650,7 @@ export class ArcTable {
         finally {
             disposeSafe(enumerator);
         }
-        const enumerator_1 = getEnumerator(defaultArg(p.Components, empty()));
+        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"]();
@@ -666,15 +769,10 @@ export class ArcTable {
         }, indexed_1(refTable_1.Headers)));
         refTable_1.RemoveColumns(nonProtocolColumns);
         Unchecked_extendToRowCount(annotationTable_1.RowCount, refTable_1.Headers, refTable_1.Values);
-        const enumerator = getEnumerator(annotationTable_1.Columns);
-        try {
-            while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
-                const c = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
-                refTable_1.AddColumn(c.Header, c.Cells, void 0, true);
-            }
-        }
-        finally {
-            disposeSafe(enumerator);
+        const arr = annotationTable_1.Columns;
+        for (let idx = 0; idx <= (arr.length - 1); idx++) {
+            const c = arr[idx];
+            refTable_1.AddColumn(c.Header, c.Cells, void 0, true);
         }
         return refTable_1;
     }
@@ -690,6 +788,9 @@ export class ArcTable {
     StructurallyEquals(other) {
         let a, b;
         const this$ = this;
+        const sort = (arg) => sortBy((_arg) => _arg[0], Array.from(arg), {
+            Compare: compareArrays,
+        });
         if ((this$.Name === other.Name) && ((a = this$.Headers, (b = other.Headers, (length(a) === length(b)) && fold((acc, e) => {
             if (acc) {
                 return e;
@@ -698,12 +799,8 @@ export class ArcTable {
                 return false;
             }
         }, true, toList(delay(() => map((i) => equals(item(i, a), item(i, b)), rangeDouble(0, 1, length(a) - 1))))))))) {
-            const a_1 = sortBy((x) => x[0], this$.Values, {
-                Compare: compareArrays,
-            });
-            const b_1 = sortBy((x_2) => x_2[0], other.Values, {
-                Compare: compareArrays,
-            });
+            const a_1 = sort(this$.Values);
+            const b_1 = sort(other.Values);
             return (length(a_1) === length(b_1)) && fold((acc_1, e_1) => {
                 if (acc_1) {
                     return e_1;
@@ -728,9 +825,16 @@ export class ArcTable {
     }
     GetHashCode() {
         const this$ = this;
-        return ((stringHash(this$.Name) + fold((state, ele) => (state + safeHash(ele)), 0, this$.Headers)) + fold((state_2, ele_1) => (state_2 + safeHash(ele_1)), 0, sortBy((x) => x[0], this$.Values, {
+        const v_2 = map_1((tupledArg) => {
+            const _arg = tupledArg[0];
+            return HashCodes_boxHashArray([_arg[0], _arg[1], tupledArg[1]]);
+        }, sortBy((tuple) => tuple[0], toArray(delay(() => collect((matchValue) => {
+            const activePatternResult = matchValue;
+            return singleton([activePatternResult[0], activePatternResult[1]]);
+        }, this$.Values))), {
             Compare: compareArrays,
-        }))) | 0;
+        }));
+        return HashCodes_boxHashArray([this$.Name, HashCodes_boxHashArray(Array.from(this$.Headers)), HashCodes_boxHashArray(Array.from(v_2))]) | 0;
     }
 }
 

package/ISA/ISA/ArcTypes/ArcTableAux.js

@@ -179,7 +179,7 @@ export function SanityChecks_validateRowIndex(index, rowCount, allowAppend) {
 }
 
 export function SanityChecks_validateColumn(column) {
-    column.validate(true);
+    column.Validate(true);
 }
 
 export function Unchecked_tryGetCellAt(column, row, cells) {
@@ -312,7 +312,10 @@ export function Unchecked_getEmptyCellForHeader(header, columCellOption) {
     }
 }
 
-export function Unchecked_addColumn(newHeader, newCells, index, forceReplace, headers, values) {
+/**
+ * 
+ */
+export function Unchecked_addColumn(newHeader, newCells, index, forceReplace, onlyHeaders, headers, values) {
     let numberOfNewColumns = 1;
     let index_1 = index;
     const hasDuplicateUnique = tryFindDuplicateUnique(newHeader, headers);
@@ -326,12 +329,10 @@ export function Unchecked_addColumn(newHeader, newCells, index, forceReplace, he
     const matchValue = getColumnCount(headers) | 0;
     const matchValue_1 = getRowCount(values) | 0;
     const startColCount = matchValue | 0;
-    let setNewHeader;
     if (hasDuplicateUnique != null) {
         Unchecked_removeHeader(index_1, headers);
     }
-    setNewHeader = headers.splice(index_1, 0, newHeader);
-    let increaseColumnIndices;
+    headers.splice(index_1, 0, newHeader);
     if ((index_1 < startColCount) && (hasDuplicateUnique == null)) {
         const lastColumnIndex = max(startColCount - 1, 0) | 0;
         for (let columnIndex = lastColumnIndex; columnIndex >= index_1; columnIndex--) {
@@ -340,16 +341,14 @@ export function Unchecked_addColumn(newHeader, newCells, index, forceReplace, he
             }
         }
     }
-    else {
-        increaseColumnIndices = void 0;
-    }
-    let setNewCells;
-    if (hasDuplicateUnique != null) {
-        Unchecked_removeColumnCells(index_1, values);
+    if (!onlyHeaders) {
+        if (hasDuplicateUnique != null) {
+            Unchecked_removeColumnCells(index_1, values);
+        }
+        iterateIndexed((rowIndex_1, cell) => {
+            Unchecked_setCellAt(index_1, rowIndex_1, cell, values);
+        }, newCells);
     }
-    setNewCells = iterateIndexed((rowIndex_1, cell) => {
-        Unchecked_setCellAt(index_1, rowIndex_1, cell, values);
-    }, newCells);
 }
 
 export function Unchecked_fillMissingCells(headers, values) {