@nfdi4plants/arctrl 2.0.0-alpha.5 → 2.0.0-alpha.7

package/Core/Data.js

@@ -1,15 +1,39 @@
+import { printf, toText } from "../fable_modules/fable-library-js.4.16.0/String.js";
+import { item } from "../fable_modules/fable-library-js.4.16.0/Array.js";
 import { defaultArg, unwrap } from "../fable_modules/fable-library-js.4.16.0/Option.js";
 import { ResizeArray_map } from "./Helper/Collections.js";
 import { hash, boxHashSeq, boxHashOption, boxHashArray } from "./Helper/HashCodes.js";
 import { toString } from "../fable_modules/fable-library-js.4.16.0/Types.js";
-import { printf, toText } from "../fable_modules/fable-library-js.4.16.0/String.js";
 import { DataFile__get_AsString } from "./DataFile.js";
 import { class_type } from "../fable_modules/fable-library-js.4.16.0/Reflection.js";
 
+export function DataAux_nameFromPathAndSelector(path, selector) {
+    return toText(printf("%s#%s"))(path)(selector);
+}
+
+export function DataAux_pathAndSelectorFromName(name) {
+    const parts = name.split("#");
+    if (parts.length === 2) {
+        return [item(0, parts), item(1, parts)];
+    }
+    else {
+        return [name, void 0];
+    }
+}
+
 export class Data {
     constructor(id, name, dataType, format, selectorFormat, comments) {
         this._id = id;
-        this._name = name;
+        let patternInput_1;
+        if (name == null) {
+            patternInput_1 = [void 0, void 0];
+        }
+        else {
+            const patternInput = DataAux_pathAndSelectorFromName(name);
+            patternInput_1 = [patternInput[0], patternInput[1]];
+        }
+        this._selector = patternInput_1[1];
+        this._filePath = patternInput_1[0];
         this._dataType = dataType;
         this._format = format;
         this._selectorFormat = selectorFormat;
@@ -24,12 +48,37 @@ export class Data {
         this$._id = id;
     }
     get Name() {
+        let matchValue, matchValue_1, p_1, p, s;
         const this$ = this;
-        return unwrap(this$._name);
+        return unwrap((matchValue = this$._filePath, (matchValue_1 = this$._selector, (matchValue == null) ? void 0 : ((matchValue_1 == null) ? ((p_1 = matchValue, p_1)) : ((p = matchValue, (s = matchValue_1, DataAux_nameFromPathAndSelector(p, s))))))));
     }
     set Name(name) {
         const this$ = this;
-        this$._name = name;
+        if (name == null) {
+            this$._filePath = void 0;
+            this$._selector = void 0;
+        }
+        else {
+            const patternInput = DataAux_pathAndSelectorFromName(name);
+            this$._filePath = patternInput[0];
+            this$._selector = patternInput[1];
+        }
+    }
+    get FilePath() {
+        const this$ = this;
+        return unwrap(this$._filePath);
+    }
+    set FilePath(filePath) {
+        const this$ = this;
+        this$._filePath = filePath;
+    }
+    get Selector() {
+        const this$ = this;
+        return unwrap(this$._selector);
+    }
+    set Selector(selector) {
+        const this$ = this;
+        this$._selector = selector;
     }
     get DataType() {
         const this$ = this;

package/Core/DataContext.js

@@ -0,0 +1,92 @@
+import { hash, boxHashSeq, boxHashOption, boxHashArray } from "./Helper/HashCodes.js";
+import { Data_$reflection, Data } from "./Data.js";
+import { unwrap } from "../fable_modules/fable-library-js.4.16.0/Option.js";
+import { class_type } from "../fable_modules/fable-library-js.4.16.0/Reflection.js";
+
+export class DataContext extends Data {
+    constructor(id, name, dataType, format, selectorFormat, explication, unit, objectType, description, generatedBy, comments) {
+        super(unwrap(id), unwrap(name), unwrap(dataType), unwrap(format), unwrap(selectorFormat), unwrap(comments));
+        this._explication = explication;
+        this._unit = unit;
+        this._objectType = objectType;
+        this._description = description;
+        this._generatedBy = generatedBy;
+    }
+    GetHashCode() {
+        const this$ = this;
+        return boxHashArray([boxHashOption(this$.ID), boxHashOption(this$.Name), boxHashOption(this$.DataType), boxHashOption(this$.Format), boxHashOption(this$.SelectorFormat), boxHashSeq(this$.Comments), boxHashOption(DataContext__get_Explication(this$)), boxHashOption(DataContext__get_Unit(this$)), boxHashOption(DataContext__get_ObjectType(this$)), boxHashOption(DataContext__get_Description(this$)), boxHashOption(DataContext__get_GeneratedBy(this$))]) | 0;
+    }
+    Equals(obj) {
+        const this$ = this;
+        return hash(this$) === hash(obj);
+    }
+}
+
+export function DataContext_$reflection() {
+    return class_type("ARCtrl.DataContext", void 0, DataContext, Data_$reflection());
+}
+
+export function DataContext_$ctor_Z2FD70A12(id, name, dataType, format, selectorFormat, explication, unit, objectType, description, generatedBy, comments) {
+    return new DataContext(id, name, dataType, format, selectorFormat, explication, unit, objectType, description, generatedBy, comments);
+}
+
+export function DataContext__get_Explication(this$) {
+    return this$._explication;
+}
+
+export function DataContext__set_Explication_279AAFF2(this$, explication) {
+    this$._explication = explication;
+}
+
+export function DataContext__get_Unit(this$) {
+    return this$._unit;
+}
+
+export function DataContext__set_Unit_279AAFF2(this$, unit) {
+    this$._unit = unit;
+}
+
+export function DataContext__get_ObjectType(this$) {
+    return this$._objectType;
+}
+
+export function DataContext__set_ObjectType_279AAFF2(this$, objectType) {
+    this$._objectType = objectType;
+}
+
+export function DataContext__get_Description(this$) {
+    return this$._description;
+}
+
+export function DataContext__set_Description_6DFDD678(this$, description) {
+    this$._description = description;
+}
+
+export function DataContext__get_GeneratedBy(this$) {
+    return this$._generatedBy;
+}
+
+export function DataContext__set_GeneratedBy_6DFDD678(this$, generatedBy) {
+    this$._generatedBy = generatedBy;
+}
+
+export function DataContext__AsData(this$) {
+    return new Data(unwrap(this$.ID), unwrap(this$.Name), unwrap(this$.DataType), unwrap(this$.Format), unwrap(this$.SelectorFormat), this$.Comments);
+}
+
+export function DataContext__Copy(this$) {
+    const copy = DataContext_$ctor_Z2FD70A12();
+    copy.ID = this$.ID;
+    copy.Name = this$.Name;
+    copy.DataType = this$.DataType;
+    copy.Format = this$.Format;
+    copy.SelectorFormat = this$.SelectorFormat;
+    DataContext__set_Explication_279AAFF2(copy, DataContext__get_Explication(this$));
+    DataContext__set_Unit_279AAFF2(copy, DataContext__get_Unit(this$));
+    DataContext__set_ObjectType_279AAFF2(copy, DataContext__get_ObjectType(this$));
+    DataContext__set_Description_6DFDD678(copy, DataContext__get_Description(this$));
+    DataContext__set_GeneratedBy_6DFDD678(copy, DataContext__get_GeneratedBy(this$));
+    copy.Comments = this$.Comments;
+    return copy;
+}
+

package/Core/Helper/Regex.js

@@ -14,13 +14,15 @@ export const Pattern_TermAnnotationURIPattern = `http://purl.obolibrary.org/obo/
 
 export const Pattern_TermAnnotationURIPattern_lessRestrictive = `.*\\/(?<${"idspace"}>\\w+?)[:_](?<${"localid"}>\\w+)`;
 
-export const Pattern_IOTypePattern = `(Input|Output)\\s\\[(?<${"iotype"}>.+)\\]`;
+export const Pattern_TermAnnotationURIPattern_MS_RO_PO = `.*252F(?<${"idspace"}>\\w+?)_(?<${"localid"}>\\w+)`;
 
-export const Pattern_InputPattern = `Input\\s\\[(?<${"iotype"}>.+)\\]`;
+export const Pattern_IOTypePattern = `(Input|Output)\\s*\\[(?<${"iotype"}>.+)\\]`;
 
-export const Pattern_OutputPattern = `Output\\s\\[(?<${"iotype"}>.+)\\]`;
+export const Pattern_InputPattern = `Input\\s*\\[(?<${"iotype"}>.+)\\]`;
 
-export const Pattern_CommentPattern = `Comment\\s\\[(?<${"commentKey"}>.+)\\]`;
+export const Pattern_OutputPattern = `Output\\s*\\[(?<${"iotype"}>.+)\\]`;
+
+export const Pattern_CommentPattern = `Comment\\s*\\[(?<${"commentKey"}>.+)\\]`;
 
 /**
  * Matches, if the input string matches the given regex pattern.
@@ -39,7 +41,7 @@ export function ActivePatterns_$007CRegex$007C_$007C(pattern, input) {
  * Matches any column header starting with some text, followed by one whitespace and a term name inside squared brackets.
  */
 export function ActivePatterns_$007CReferenceColumnHeader$007C_$007C(input) {
-    const activePatternResult = ActivePatterns_$007CRegex$007C_$007C("(Term Source REF|Term Accession Number)\\s\\((?<id>.*)\\)", input);
+    const activePatternResult = ActivePatterns_$007CRegex$007C_$007C("(Term Source REF|Term Accession Number)\\s*\\((?<id>.*)\\)", input);
     if (activePatternResult != null) {
         const r = activePatternResult;
         return {
@@ -55,7 +57,7 @@ export function ActivePatterns_$007CReferenceColumnHeader$007C_$007C(input) {
  * Matches any column header starting with some text, followed by one whitespace and a term name inside squared brackets.
  */
 export function ActivePatterns_$007CTermColumn$007C_$007C(input) {
-    const activePatternResult = ActivePatterns_$007CRegex$007C_$007C("(?<termcolumntype>.+?)\\s\\[(?<termname>.+)\\]", input);
+    const activePatternResult = ActivePatterns_$007CRegex$007C_$007C("(?<termcolumntype>.+?)\\s*\\[(?<termname>.+)\\]", input);
     if (activePatternResult != null) {
         const r = activePatternResult;
         return {
@@ -213,7 +215,14 @@ export function ActivePatterns_$007CTermAnnotation$007C_$007C(input) {
                 value = activePatternResult_2;
             }
             else {
-                matchResult = 1;
+                const activePatternResult_3 = ActivePatterns_$007CRegex$007C_$007C(Pattern_TermAnnotationURIPattern_MS_RO_PO, input);
+                if (activePatternResult_3 != null) {
+                    matchResult = 0;
+                    value = activePatternResult_3;
+                }
+                else {
+                    matchResult = 1;
+                }
             }
         }
     }
@@ -234,7 +243,7 @@ export function ActivePatterns_$007CTermAnnotation$007C_$007C(input) {
  * Example: "Term Source REF (MS:1003022)" --> term source ref: "MS"; annotation number: "1003022"
  */
 export function ActivePatterns_$007CTSRColumnHeader$007C_$007C(input) {
-    const activePatternResult = ActivePatterns_$007CRegex$007C_$007C("Term Source REF\\s\\((?<id>.*)\\)", input);
+    const activePatternResult = ActivePatterns_$007CRegex$007C_$007C("Term Source REF\\s*\\((?<id>.*)\\)", input);
     if (activePatternResult != null) {
         const r = activePatternResult;
         const matchValue = (r.groups && r.groups.id) || "";
@@ -261,7 +270,7 @@ export function ActivePatterns_$007CTSRColumnHeader$007C_$007C(input) {
  * Example: "Term Accession Number (MS:1003022)" --> term source ref: "MS"; annotation number: "1003022"
  */
 export function ActivePatterns_$007CTANColumnHeader$007C_$007C(input) {
-    const activePatternResult = ActivePatterns_$007CRegex$007C_$007C("Term Accession Number\\s\\((?<id>.*)\\)", input);
+    const activePatternResult = ActivePatterns_$007CRegex$007C_$007C("Term Accession Number\\s*\\((?<id>.*)\\)", input);
     if (activePatternResult != null) {
         const r = activePatternResult;
         const matchValue = (r.groups && r.groups.id) || "";
@@ -392,7 +401,14 @@ export function tryParseTermAnnotation(str) {
                 value = activePatternResult_2;
             }
             else {
-                matchResult = 1;
+                const activePatternResult_3 = ActivePatterns_$007CRegex$007C_$007C(Pattern_TermAnnotationURIPattern_MS_RO_PO, matchValue);
+                if (activePatternResult_3 != null) {
+                    matchResult = 0;
+                    value = activePatternResult_3;
+                }
+                else {
+                    matchResult = 1;
+                }
             }
         }
     }

package/Core/Helper/Url.js

@@ -0,0 +1,38 @@
+import { Dictionary_tryFind, Dictionary_ofSeq } from "./Collections.js";
+
+export function OntobeeParser(tsr, localTan) {
+    return `${"http://purl.obolibrary.org/obo/"}${tsr}_${localTan}`;
+}
+
+export function BioregistryParser(tsr, localTan) {
+    return `${"https://bioregistry.io/"}${tsr}:${localTan}`;
+}
+
+export function OntobeeDPBOParser(tsr, localTan) {
+    return `${"http://purl.org/nfdi4plants/ontology/dpbo/"}${tsr}_${localTan}`;
+}
+
+export function MSParser(tsr, localTan) {
+    return `${"https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252F"}${tsr}_${localTan}`;
+}
+
+export function POParser(tsr, localTan) {
+    return `${"https://www.ebi.ac.uk/ols4/ontologies/po/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252F"}${tsr}_${localTan}`;
+}
+
+export function ROParser(tsr, localTan) {
+    return `${"https://www.ebi.ac.uk/ols4/ontologies/ro/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252F"}${tsr}_${localTan}`;
+}
+
+export const uriParserCollection = Dictionary_ofSeq([["DPBO", (tsr) => ((localTan) => OntobeeDPBOParser(tsr, localTan))], ["MS", (tsr_1) => ((localTan_1) => MSParser(tsr_1, localTan_1))], ["PO", (tsr_2) => ((localTan_2) => POParser(tsr_2, localTan_2))], ["RO", (tsr_3) => ((localTan_3) => ROParser(tsr_3, localTan_3))], ["ENVO", (tsr_4) => ((localTan_4) => BioregistryParser(tsr_4, localTan_4))], ["CHEBI", (tsr_5) => ((localTan_5) => BioregistryParser(tsr_5, localTan_5))], ["GO", (tsr_6) => ((localTan_6) => BioregistryParser(tsr_6, localTan_6))], ["OBI", (tsr_7) => ((localTan_7) => BioregistryParser(tsr_7, localTan_7))], ["PATO", (tsr_8) => ((localTan_8) => BioregistryParser(tsr_8, localTan_8))], ["PECO", (tsr_9) => ((localTan_9) => BioregistryParser(tsr_9, localTan_9))], ["TO", (tsr_10) => ((localTan_10) => BioregistryParser(tsr_10, localTan_10))], ["UO", (tsr_11) => ((localTan_11) => BioregistryParser(tsr_11, localTan_11))], ["EFO", (tsr_12) => ((localTan_12) => BioregistryParser(tsr_12, localTan_12))], ["NCIT", (tsr_13) => ((localTan_13) => BioregistryParser(tsr_13, localTan_13))], ["OMP", (tsr_14) => ((localTan_14) => BioregistryParser(tsr_14, localTan_14))]]);
+
+export function createOAUri(tsr, localTan) {
+    const matchValue = Dictionary_tryFind(tsr, uriParserCollection);
+    if (matchValue == null) {
+        return OntobeeParser(tsr, localTan);
+    }
+    else {
+        return matchValue(tsr)(localTan);
+    }
+}
+

package/Core/OntologyAnnotation.js

@@ -1,5 +1,6 @@
 import { value as value_4, defaultArg, unwrap } from "../fable_modules/fable-library-js.4.16.0/Option.js";
 import { Pattern_TermAnnotationShortPattern, ActivePatterns_$007CRegex$007C_$007C, tryParseTermAnnotation } from "./Helper/Regex.js";
+import { createOAUri } from "./Helper/Url.js";
 import { StringBuilder__Append_Z721C83C5, StringBuilder_$ctor } from "../fable_modules/fable-library-js.4.16.0/System.Text.js";
 import { printf, toText, join } from "../fable_modules/fable-library-js.4.16.0/String.js";
 import { toArray, empty, singleton, append, delay, toList } from "../fable_modules/fable-library-js.4.16.0/Seq.js";
@@ -65,7 +66,7 @@ export class OntologyAnnotation {
         return defaultArg(this$.Name, "");
     }
     static createUriAnnotation(termSourceRef, localTAN) {
-        return `${"http://purl.obolibrary.org/obo/"}${termSourceRef}_${localTAN}`;
+        return createOAUri(termSourceRef, localTAN);
     }
     static fromTermAnnotation(tan, name) {
         const matchValue = tryParseTermAnnotation(tan);

package/Core/Table/ArcTableAux.js

@@ -387,7 +387,7 @@ export function Unchecked_fillMissingCells(headers, values) {
         if (matchValue == null) {
             const defaultCell_1 = Unchecked_getEmptyCellForHeader(header, void 0);
             for (let rowIndex_1 = 0; rowIndex_1 <= (rowCount - 1); rowIndex_1++) {
-                Unchecked_addCellAt(columnIndex, rowIndex_1, defaultCell_1, values);
+                Unchecked_addCellAt(columnIndex, rowIndex_1, defaultCell_1.Copy(), values);
             }
         }
         else if ((col = matchValue, col.length === rowCount)) {
@@ -401,7 +401,7 @@ export function Unchecked_fillMissingCells(headers, values) {
             });
             for (let rowIndex = 0; rowIndex <= (rowCount - 1); rowIndex++) {
                 if (!FSharpSet__Contains(rowKeys, rowIndex)) {
-                    Unchecked_addCellAt(columnIndex, rowIndex, defaultCell, values);
+                    Unchecked_addCellAt(columnIndex, rowIndex, defaultCell.Copy(), values);
                 }
             }
         }

package/Core/Table/CompositeCell.js

@@ -172,6 +172,10 @@ export class CompositeCell extends Union {
         const this$ = this;
         return (this$.tag === 1) ? this$.fields[0] : ((this$.tag === 2) ? (`${this$.fields[0]} ${this$.fields[1].NameText}`) : ((this$.tag === 3) ? (`${this$.fields[0].NameText}`) : (`${this$.fields[0].NameText}`)));
     }
+    Copy() {
+        const this$ = this;
+        return (this$.tag === 1) ? (new CompositeCell(1, [this$.fields[0]])) : ((this$.tag === 2) ? (new CompositeCell(2, [this$.fields[0], this$.fields[1].Copy()])) : ((this$.tag === 3) ? (new CompositeCell(3, [this$.fields[0].Copy()])) : (new CompositeCell(0, [this$.fields[0].Copy()]))));
+    }
     static term(oa) {
         return new CompositeCell(0, [oa]);
     }

package/Core/Table/DataMap.js

@@ -1,14 +1,11 @@
 import { CompositeHeader, IOType } from "./CompositeHeader.js";
 import { OntologyAnnotation } from "../OntologyAnnotation.js";
-import { exists as exists_1, ofArray } from "../../fable_modules/fable-library-js.4.16.0/List.js";
-import { exists } from "../../fable_modules/fable-library-js.4.16.0/Seq.js";
-import { arrayHash, equalArrays, safeHash, equals } from "../../fable_modules/fable-library-js.4.16.0/Util.js";
-import { printf, toFail } from "../../fable_modules/fable-library-js.4.16.0/String.js";
-import { SanityChecks_validate } from "./ArcTableAux.js";
-import { ArcTable } from "./ArcTable.js";
+import { ofArray } from "../../fable_modules/fable-library-js.4.16.0/List.js";
+import { iterateIndexed, map } from "../../fable_modules/fable-library-js.4.16.0/Seq.js";
+import { CompositeCell } from "./CompositeCell.js";
+import { boxHashSeq, hash } from "../Helper/HashCodes.js";
 import { class_type } from "../../fable_modules/fable-library-js.4.16.0/Reflection.js";
-import { Dictionary } from "../../fable_modules/fable-library-js.4.16.0/MutableMap.js";
-import { unwrap } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
+import { DataContext__Copy, DataContext__set_Description_6DFDD678, DataContext__get_Description, DataContext__set_ObjectType_279AAFF2, DataContext__get_ObjectType, DataContext__set_Unit_279AAFF2, DataContext__get_Unit, DataContext__set_Explication_279AAFF2, DataContext__get_Explication } from "../DataContext.js";
 
 export const DataMapAux_dataHeader = new CompositeHeader(11, [new IOType(2, [])]);
 
@@ -30,35 +27,75 @@ export const DataMapAux_generatedByHeader = new CompositeHeader(13, ["Generated
 
 export const DataMapAux_allowedHeaders = ofArray([DataMapAux_dataHeader, DataMapAux_explicationHeader, DataMapAux_unitHeader, DataMapAux_objectTypeHeader, DataMapAux_descriptionHeader, DataMapAux_generatedByHeader]);
 
-export function DataMapAux_validate(headers, values, raiseException) {
-    if (exists((h) => {
-        const hasForeignHeader = !exists_1((ah) => equals(ah, h), DataMapAux_allowedHeaders);
-        if (raiseException && hasForeignHeader) {
-            toFail(printf("Header %O is not allowed in DataMap"))(h);
+export function DataMapAux_getOntologyColumn(f, dataContexts) {
+    const collection = map((dc) => {
+        const matchValue = f(dc);
+        if (matchValue == null) {
+            return CompositeCell.emptyTerm;
         }
-        return hasForeignHeader;
-    }, headers)) {
-        return SanityChecks_validate(headers, values, raiseException);
+        else {
+            return new CompositeCell(0, [matchValue]);
+        }
+    }, dataContexts);
+    return Array.from(collection);
+}
+
+export function DataMapAux_getStringColumn(f, dataContexts) {
+    const collection = map((dc) => {
+        const matchValue = f(dc);
+        if (matchValue == null) {
+            return CompositeCell.emptyFreeText;
+        }
+        else {
+            return new CompositeCell(1, [matchValue]);
+        }
+    }, dataContexts);
+    return Array.from(collection);
+}
+
+export function DataMapAux_setOntologyColumn(f, column, dataContexts) {
+    iterateIndexed((i, cell) => {
+        if (cell.tag === 0) {
+            f(dataContexts[i], cell.fields[0]);
+        }
+    }, column);
+}
+
+export function DataMapAux_setStringColumn(f, column, dataContexts) {
+    iterateIndexed((i, cell) => {
+        if (cell.tag === 1) {
+            f(dataContexts[i], cell.fields[0]);
+        }
+    }, column);
+}
+
+export function DataMapAux_SanityChecks_rowIndexInBoundaries(row, dataContexts) {
+    if (row < 0) {
+        throw new Error("Row index must be greater or equal to 0.");
+    }
+    if (row >= dataContexts.length) {
+        throw new Error("Row index must be less than the number of rows.");
     }
-    else {
-        return false;
+}
+
+export function DataMapAux_SanityChecks_lengthOfNewColumn(newColumn, dataContexts) {
+    if (newColumn.length !== dataContexts.length) {
+        throw new Error("Length of new column does not match length of data contexts.");
     }
 }
 
 export class DataMap {
-    constructor(headers, values) {
-        DataMapAux_validate(headers, values, true);
-        this.table = (new ArcTable("DataMap", headers, values));
+    constructor(dataContexts) {
         this.staticHash = 0;
+        this["dataContexts@103"] = dataContexts;
     }
     Equals(obj) {
-        let dm;
         const this$ = this;
-        return (obj instanceof DataMap) && ((dm = obj, equals(DataMap__get_Table(this$), DataMap__get_Table(dm))));
+        return hash(this$) === hash(obj);
     }
     GetHashCode() {
         const this$ = this;
-        return safeHash(DataMap__get_Table(this$)) | 0;
+        return boxHashSeq(this$["dataContexts@103"]) | 0;
     }
 }
 
@@ -66,16 +103,8 @@ export function DataMap_$reflection() {
     return class_type("ARCtrl.DataMap", void 0, DataMap);
 }
 
-export function DataMap_$ctor_ZD0829CB(headers, values) {
-    return new DataMap(headers, values);
-}
-
-export function DataMap__get_Headers(this$) {
-    return this$.table.Headers;
-}
-
-export function DataMap__get_Values(this$) {
-    return this$.table.Values;
+export function DataMap_$ctor_4E3220A7(dataContexts) {
+    return new DataMap(dataContexts);
 }
 
 export function DataMap__get_StaticHash(this$) {
@@ -86,81 +115,65 @@ export function DataMap__set_StaticHash_Z524259A4(this$, value) {
     this$.staticHash = (value | 0);
 }
 
-export function DataMap_init() {
-    return DataMap_$ctor_ZD0829CB([], new Dictionary([], {
-        Equals: equalArrays,
-        GetHashCode: arrayHash,
-    }));
-}
-
-export function DataMap__AddColumns_6369C010(this$, columns, skipFillMissing) {
-    columns.forEach((c) => {
-        c.Validate(true);
-    });
-    this$.table.AddColumns(columns, void 0, void 0, unwrap(skipFillMissing));
-    DataMapAux_validate(this$.table.Headers, this$.table.Values, true);
-}
-
-export function DataMap_addColumns_6369C010(columns, skipFillMissing) {
-    return (dm) => {
-        const dm_1 = DataMap__Copy(dm);
-        DataMap__AddColumns_6369C010(dm_1, columns, unwrap(skipFillMissing));
-        return dm_1;
-    };
+export function DataMap__get_DataContexts(this$) {
+    return this$["dataContexts@103"];
 }
 
-export function DataMap__get_Table(this$) {
-    return this$.table;
-}
-
-export function DataMap__TryGetCellAt_Z37302880(this$, row, column) {
-    return this$.table.TryGetCellAt(row, column);
+export function DataMap_init() {
+    return DataMap_$ctor_4E3220A7([]);
 }
 
 export function DataMap__GetExplicationColumn(this$) {
-    return this$.table.GetColumnByHeader(DataMapAux_explicationHeader);
+    return DataMapAux_getOntologyColumn(DataContext__get_Explication, this$["dataContexts@103"]);
 }
 
-export function DataMap__AddExplicationColumn_C98E589(this$, cells) {
-    this$.table.AddColumn(DataMapAux_explicationHeader, cells);
+export function DataMap__SetExplicationColumn_C98E589(this$, cells) {
+    DataMapAux_setOntologyColumn((dc, oa) => {
+        DataContext__set_Explication_279AAFF2(dc, oa);
+    }, cells, this$["dataContexts@103"]);
 }
 
 export function DataMap__GetUnitColumn(this$) {
-    return this$.table.GetColumnByHeader(DataMapAux_unitHeader);
+    return DataMapAux_getOntologyColumn(DataContext__get_Unit, this$["dataContexts@103"]);
 }
 
-export function DataMap__AddUnitColumn_C98E589(this$, cells) {
-    this$.table.AddColumn(DataMapAux_unitHeader, cells);
+export function DataMap__SetUnitColumn_C98E589(this$, cells) {
+    DataMapAux_setOntologyColumn((dc, oa) => {
+        DataContext__set_Unit_279AAFF2(dc, oa);
+    }, cells, this$["dataContexts@103"]);
 }
 
-export function DataMap__GetDataTypeColumn(this$) {
-    return this$.table.GetColumnByHeader(DataMapAux_objectTypeHeader);
+export function DataMap__GetObjectTypeColumn(this$) {
+    return DataMapAux_getOntologyColumn(DataContext__get_ObjectType, this$["dataContexts@103"]);
 }
 
-export function DataMap__AddDataTypeColumn_C98E589(this$, cells) {
-    this$.table.AddColumn(DataMapAux_objectTypeHeader, cells);
+export function DataMap__SetDataTypeColumn_C98E589(this$, cells) {
+    DataMapAux_setOntologyColumn((dc, oa) => {
+        DataContext__set_ObjectType_279AAFF2(dc, oa);
+    }, cells, this$["dataContexts@103"]);
 }
 
 export function DataMap__GetDescriptionColumn(this$) {
-    return this$.table.GetColumnByHeader(DataMapAux_descriptionHeader);
+    return DataMapAux_getStringColumn(DataContext__get_Description, this$["dataContexts@103"]);
 }
 
-export function DataMap__AddDescriptionColumn_C98E589(this$, cells) {
-    this$.table.AddColumn(DataMapAux_descriptionHeader, cells);
+export function DataMap__SetDescriptionColumn_C98E589(this$, cells) {
+    DataMapAux_setStringColumn((dc, s) => {
+        DataContext__set_Description_6DFDD678(dc, s);
+    }, cells, this$["dataContexts@103"]);
 }
 
-export function DataMap__GetRow_ABCEF95(this$, row, SkipValidation) {
-    return this$.table.GetRow(row, unwrap(SkipValidation));
+export function DataMap__GetDataContext_Z58338566(this$, row, SkipValidation) {
+    DataMapAux_SanityChecks_rowIndexInBoundaries(row, this$["dataContexts@103"]);
+    return this$["dataContexts@103"][row];
 }
 
-export function DataMap_getRow_ABCEF95(row, SkipValidation) {
-    return (dm) => DataMap__GetRow_ABCEF95(dm, row, unwrap(SkipValidation));
+export function DataMap_getDataContext_Z58338566(row, SkipValidation) {
+    return (dm) => DataMap__GetDataContext_Z58338566(dm, row, SkipValidation);
 }
 
 export function DataMap__Copy(this$) {
-    return DataMap_$ctor_ZD0829CB(Array.from(DataMap__get_Headers(this$)), new Dictionary(DataMap__get_Values(this$), {
-        Equals: equalArrays,
-        GetHashCode: arrayHash,
-    }));
+    let collection;
+    return DataMap_$ctor_4E3220A7((collection = map(DataContext__Copy, this$["dataContexts@103"]), Array.from(collection)));
 }
 

package/Json/Assay.js

@@ -143,6 +143,10 @@ export function ARCtrl_ArcAssay__ArcAssay_toJsonString_Static_71136F3F(spaces) {
     };
 }
 
+export function ARCtrl_ArcAssay__ArcAssay_ToJsonString_71136F3F(this$, spaces) {
+    return ARCtrl_ArcAssay__ArcAssay_toJsonString_Static_71136F3F(unwrap(spaces))(this$);
+}
+
 export function ARCtrl_ArcAssay__ArcAssay_fromCompressedJsonString_Static_Z721C83C5(s) {
     try {
         const matchValue = fromString(decode(Assay_decoderCompressed), s);
@@ -163,6 +167,10 @@ export function ARCtrl_ArcAssay__ArcAssay_toCompressedJsonString_Static_71136F3F
     return (obj) => toString(defaultArg(spaces, 0), encode(Assay_encoderCompressed, obj));
 }
 
+export function ARCtrl_ArcAssay__ArcAssay_ToCompressedJsonString_71136F3F(this$, spaces) {
+    return ARCtrl_ArcAssay__ArcAssay_toCompressedJsonString_Static_71136F3F(unwrap(spaces))(this$);
+}
+
 export function ARCtrl_ArcAssay__ArcAssay_fromROCrateJsonString_Static_Z721C83C5(s) {
     const matchValue = fromString(Assay_ROCrate_decoder, s);
     if (matchValue.tag === 1) {
@@ -183,6 +191,10 @@ export function ARCtrl_ArcAssay__ArcAssay_toROCrateJsonString_Static_5CABCA47(st
     };
 }
 
+export function ARCtrl_ArcAssay__ArcAssay_ToROCrateJsonString_5CABCA47(this$, studyName, spaces) {
+    return ARCtrl_ArcAssay__ArcAssay_toROCrateJsonString_Static_5CABCA47(unwrap(studyName), unwrap(spaces))(this$);
+}
+
 export function ARCtrl_ArcAssay__ArcAssay_toISAJsonString_Static_71136F3F(spaces) {
     return (obj) => {
         const value = Assay_ISAJson_encoder(obj);
@@ -200,3 +212,7 @@ export function ARCtrl_ArcAssay__ArcAssay_fromISAJsonString_Static_Z721C83C5(s)
     }
 }
 
+export function ARCtrl_ArcAssay__ArcAssay_ToISAJsonString_71136F3F(this$, spaces) {
+    return ARCtrl_ArcAssay__ArcAssay_toISAJsonString_Static_71136F3F(unwrap(spaces))(this$);
+}
+