@nfdi4plants/arctrl 2.0.0-alpha.6 → 2.0.0-alpha.8

package/Spreadsheet/DataMapTable/DataMapHeader.js

@@ -1,16 +1,36 @@
-import { singleton, ofArray, tryFindIndex, tail, head, isEmpty, map } from "../../fable_modules/fable-library-js.4.16.0/List.js";
-import { dataFromFsCells, freeTextFromFsCells, termFromFsCells } from "../AnnotationTable/CompositeCell.js";
-import { DataMapAux_generatedByHeader, DataMapAux_descriptionHeader, DataMapAux_objectTypeHeader, DataMapAux_unitHeader, DataMapAux_explicationHeader } from "../../Core/Table/DataMap.js";
+import { tryFindIndex, tail, head, isEmpty, item, map } from "../../fable_modules/fable-library-js.4.16.0/List.js";
 import { map as map_1 } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
-import { CompositeHeader, IOType } from "../../Core/Table/CompositeHeader.js";
-import { printf, toFail } from "../../fable_modules/fable-library-js.4.16.0/String.js";
+import { OntologyAnnotation } from "../../Core/OntologyAnnotation.js";
+import { Data } from "../../Core/Data.js";
+import { DataContext__set_GeneratedBy_6DFDD678, DataContext__set_Description_6DFDD678, DataContext__set_ObjectType_279AAFF2, DataContext__set_Unit_279AAFF2, DataContext__set_Explication_279AAFF2 } from "../../Core/DataContext.js";
+import { Comment$ } from "../../Core/Comment.js";
+import { ActivePatterns_$007CComment$007C_$007C } from "../../Core/Helper/Regex.js";
+import { printf, toFail, join } from "../../fable_modules/fable-library-js.4.16.0/String.js";
+import { map as map_2, append, delay, toList } from "../../fable_modules/fable-library-js.4.16.0/Seq.js";
 import { FsCell } from "../../fable_modules/FsSpreadsheet.6.1.2/Cells/FsCell.fs.js";
-import { equals } from "../../fable_modules/fable-library-js.4.16.0/Util.js";
 
-export function ActivePattern_$007CTerm$007C_$007C(categoryString, categoryHeader, cells) {
+export function ActivePattern_ontologyAnnotationFromFsCells(tsrCol, tanCol, cells) {
+    const cellValues = map((c) => c.ValueAsString(), cells);
+    const tsr = map_1((i) => item(i, cellValues), tsrCol);
+    const tan = map_1((i_1) => item(i_1, cellValues), tanCol);
+    return new OntologyAnnotation(item(0, cellValues), tsr, tan);
+}
+
+export function ActivePattern_freeTextFromFsCells(cells) {
+    return item(0, map((c) => c.ValueAsString(), cells));
+}
+
+export function ActivePattern_dataFromFsCells(format, selectorFormat, cells) {
+    const cellValues = map((c) => c.ValueAsString(), cells);
+    const format_1 = map_1((i) => item(i, cellValues), format);
+    const selectorFormat_1 = map_1((i_1) => item(i_1, cellValues), selectorFormat);
+    return new Data(void 0, item(0, cellValues), void 0, format_1, selectorFormat_1);
+}
+
+export function ActivePattern_$007CTerm$007C_$007C(categoryString, cells) {
     const $007CAC$007C_$007C = (s) => {
         if (s === categoryString) {
-            return categoryHeader;
+            return 1;
         }
         else {
             return void 0;
@@ -54,7 +74,7 @@ export function ActivePattern_$007CTerm$007C_$007C(categoryString, categoryHeade
     }
     switch (matchResult) {
         case 0:
-            return [header, (cells_1) => termFromFsCells(void 0, void 0, cells_1)];
+            return (cells_1) => ActivePattern_ontologyAnnotationFromFsCells(void 0, void 0, cells_1);
         default: {
             let matchResult_1, header_1;
             if (!isEmpty(cellValues)) {
@@ -97,7 +117,7 @@ export function ActivePattern_$007CTerm$007C_$007C(categoryString, categoryHeade
             }
             switch (matchResult_1) {
                 case 0:
-                    return [header_1, (cells_2) => termFromFsCells(1, 2, cells_2)];
+                    return (cells_2) => ActivePattern_ontologyAnnotationFromFsCells(1, 2, cells_2);
                 default: {
                     let matchResult_2, header_2;
                     if (!isEmpty(cellValues)) {
@@ -140,7 +160,7 @@ export function ActivePattern_$007CTerm$007C_$007C(categoryString, categoryHeade
                     }
                     switch (matchResult_2) {
                         case 0:
-                            return [header_2, (cells_3) => termFromFsCells(2, 1, cells_3)];
+                            return (cells_3) => ActivePattern_ontologyAnnotationFromFsCells(2, 1, cells_3);
                         default:
                             return void 0;
                     }
@@ -151,10 +171,13 @@ export function ActivePattern_$007CTerm$007C_$007C(categoryString, categoryHeade
 }
 
 export function ActivePattern_$007CExplication$007C_$007C(cells) {
-    const activePatternResult = ActivePattern_$007CTerm$007C_$007C("Explication", DataMapAux_explicationHeader, cells);
+    const activePatternResult = ActivePattern_$007CTerm$007C_$007C("Explication", cells);
     if (activePatternResult != null) {
         const r = activePatternResult;
-        return r;
+        return (dc) => ((cells_1) => {
+            DataContext__set_Explication_279AAFF2(dc, r(cells_1));
+            return dc;
+        });
     }
     else {
         return void 0;
@@ -162,10 +185,13 @@ export function ActivePattern_$007CExplication$007C_$007C(cells) {
 }
 
 export function ActivePattern_$007CUnit$007C_$007C(cells) {
-    const activePatternResult = ActivePattern_$007CTerm$007C_$007C("Unit", DataMapAux_unitHeader, cells);
+    const activePatternResult = ActivePattern_$007CTerm$007C_$007C("Unit", cells);
     if (activePatternResult != null) {
         const r = activePatternResult;
-        return r;
+        return (dc) => ((cells_1) => {
+            DataContext__set_Unit_279AAFF2(dc, r(cells_1));
+            return dc;
+        });
     }
     else {
         return void 0;
@@ -173,10 +199,13 @@ export function ActivePattern_$007CUnit$007C_$007C(cells) {
 }
 
 export function ActivePattern_$007CObjectType$007C_$007C(cells) {
-    const activePatternResult = ActivePattern_$007CTerm$007C_$007C("Object Type", DataMapAux_objectTypeHeader, cells);
+    const activePatternResult = ActivePattern_$007CTerm$007C_$007C("Object Type", cells);
     if (activePatternResult != null) {
         const r = activePatternResult;
-        return r;
+        return (dc) => ((cells_1) => {
+            DataContext__set_ObjectType_279AAFF2(dc, r(cells_1));
+            return dc;
+        });
     }
     else {
         return void 0;
@@ -204,7 +233,10 @@ export function ActivePattern_$007CDescription$007C_$007C(cells) {
     }
     switch (matchResult) {
         case 0:
-            return [DataMapAux_descriptionHeader, freeTextFromFsCells];
+            return (dc) => ((cells_1) => {
+                DataContext__set_Description_6DFDD678(dc, ActivePattern_freeTextFromFsCells(cells_1));
+                return dc;
+            });
         default:
             return void 0;
     }
@@ -231,7 +263,10 @@ export function ActivePattern_$007CGeneratedBy$007C_$007C(cells) {
     }
     switch (matchResult) {
         case 0:
-            return [DataMapAux_generatedByHeader, freeTextFromFsCells];
+            return (dc) => ((cells_1) => {
+                DataContext__set_GeneratedBy_6DFDD678(dc, ActivePattern_freeTextFromFsCells(cells_1));
+                return dc;
+            });
         default:
             return void 0;
     }
@@ -253,23 +288,60 @@ export function ActivePattern_$007CData$007C_$007C(cells) {
         matchResult = 1;
     }
     switch (matchResult) {
-        case 0: {
-            const format = map_1((y) => (1 + y), tryFindIndex((s) => (s.indexOf("Data Format") === 0), cols));
-            const selectorFormat = map_1((y_1) => (1 + y_1), tryFindIndex((s_1) => (s_1.indexOf("Data Selector Format") === 0), cols));
-            return [new CompositeHeader(11, [new IOType(2, [])]), (cells_1) => dataFromFsCells(format, selectorFormat, cells_1)];
+        case 0:
+            return (dc) => ((cells_1) => {
+                const d = ActivePattern_dataFromFsCells(map_1((y) => (1 + y), tryFindIndex((s) => (s.indexOf("Data Format") === 0), cols)), map_1((y_1) => (1 + y_1), tryFindIndex((s_1) => (s_1.indexOf("Data Selector Format") === 0), cols)), cells_1);
+                dc.FilePath = d.FilePath;
+                dc.Selector = d.Selector;
+                dc.Format = d.Format;
+                dc.SelectorFormat = d.SelectorFormat;
+                return dc;
+            });
+        default:
+            return void 0;
+    }
+}
+
+export function ActivePattern_$007CComment$007C_$007C(cells) {
+    const cellValues = map((c) => c.ValueAsString(), cells);
+    let matchResult, key;
+    if (!isEmpty(cellValues)) {
+        const activePatternResult = ActivePatterns_$007CComment$007C_$007C(head(cellValues));
+        if (activePatternResult != null) {
+            if (isEmpty(tail(cellValues))) {
+                matchResult = 0;
+                key = activePatternResult;
+            }
+            else {
+                matchResult = 1;
+            }
+        }
+        else {
+            matchResult = 1;
         }
+    }
+    else {
+        matchResult = 1;
+    }
+    switch (matchResult) {
+        case 0:
+            return (dc) => ((cells_1) => {
+                const comment = item(0, map((c_1) => c_1.ValueAsString(), cells_1));
+                void (dc.Comments.push(Comment$.create(key, comment)));
+                return dc;
+            });
         default:
             return void 0;
     }
 }
 
-export function ActivePattern_$007CFreeText$007C_$007C(cells) {
+export function ActivePattern_$007CFreetext$007C_$007C(cells) {
     const cellValues = map((c) => c.ValueAsString(), cells);
-    let matchResult, text;
+    let matchResult, key;
     if (!isEmpty(cellValues)) {
         if (isEmpty(tail(cellValues))) {
             matchResult = 0;
-            text = head(cellValues);
+            key = head(cellValues);
         }
         else {
             matchResult = 1;
@@ -280,56 +352,68 @@ export function ActivePattern_$007CFreeText$007C_$007C(cells) {
     }
     switch (matchResult) {
         case 0:
-            return [new CompositeHeader(13, [text]), freeTextFromFsCells];
+            return (dc) => ((cells_1) => {
+                const comment = item(0, map((c_1) => c_1.ValueAsString(), cells_1));
+                void (dc.Comments.push(Comment$.create(key, comment)));
+                return dc;
+            });
         default:
             return void 0;
     }
 }
 
 export function fromFsCells(cells) {
-    const activePatternResult = ActivePattern_$007CData$007C_$007C(cells);
+    let matchResult, r;
+    const activePatternResult = ActivePattern_$007CExplication$007C_$007C(cells);
     if (activePatternResult != null) {
-        const d = activePatternResult;
-        return d;
+        matchResult = 0;
+        r = activePatternResult;
     }
     else {
-        const activePatternResult_1 = ActivePattern_$007CExplication$007C_$007C(cells);
+        const activePatternResult_1 = ActivePattern_$007CUnit$007C_$007C(cells);
         if (activePatternResult_1 != null) {
-            const e = activePatternResult_1;
-            return e;
+            matchResult = 0;
+            r = activePatternResult_1;
         }
         else {
-            const activePatternResult_2 = ActivePattern_$007CUnit$007C_$007C(cells);
+            const activePatternResult_2 = ActivePattern_$007CObjectType$007C_$007C(cells);
             if (activePatternResult_2 != null) {
-                const u = activePatternResult_2;
-                return u;
+                matchResult = 0;
+                r = activePatternResult_2;
             }
             else {
-                const activePatternResult_3 = ActivePattern_$007CObjectType$007C_$007C(cells);
+                const activePatternResult_3 = ActivePattern_$007CDescription$007C_$007C(cells);
                 if (activePatternResult_3 != null) {
-                    const ot = activePatternResult_3;
-                    return ot;
+                    matchResult = 0;
+                    r = activePatternResult_3;
                 }
                 else {
-                    const activePatternResult_4 = ActivePattern_$007CDescription$007C_$007C(cells);
+                    const activePatternResult_4 = ActivePattern_$007CGeneratedBy$007C_$007C(cells);
                     if (activePatternResult_4 != null) {
-                        const d_1 = activePatternResult_4;
-                        return d_1;
+                        matchResult = 0;
+                        r = activePatternResult_4;
                     }
                     else {
-                        const activePatternResult_5 = ActivePattern_$007CGeneratedBy$007C_$007C(cells);
+                        const activePatternResult_5 = ActivePattern_$007CData$007C_$007C(cells);
                         if (activePatternResult_5 != null) {
-                            const gb = activePatternResult_5;
-                            return gb;
+                            matchResult = 0;
+                            r = activePatternResult_5;
                         }
                         else {
-                            const activePatternResult_6 = ActivePattern_$007CFreeText$007C_$007C(cells);
+                            const activePatternResult_6 = ActivePattern_$007CComment$007C_$007C(cells);
                             if (activePatternResult_6 != null) {
-                                const ft = activePatternResult_6;
-                                return ft;
+                                matchResult = 0;
+                                r = activePatternResult_6;
                             }
                             else {
-                                return toFail(printf("Could not parse header group %O"))(cells);
+                                const activePatternResult_7 = ActivePattern_$007CFreetext$007C_$007C(cells);
+                                if (activePatternResult_7 != null) {
+                                    matchResult = 0;
+                                    r = activePatternResult_7;
+                                }
+                                else {
+                                    matchResult = 1;
+                                }
                             }
                         }
                     }
@@ -337,81 +421,21 @@ export function fromFsCells(cells) {
             }
         }
     }
-}
-
-export function toFsCells(header) {
-    let matchResult, h_9, h_10, h_11, text;
-    switch (header.tag) {
-        case 11: {
-            if (header.fields[0].tag === 2) {
-                matchResult = 0;
-            }
-            else if (equals(header, DataMapAux_explicationHeader)) {
-                matchResult = 1;
-                h_9 = header;
-            }
-            else if (equals(header, DataMapAux_unitHeader)) {
-                matchResult = 2;
-                h_10 = header;
-            }
-            else if (equals(header, DataMapAux_objectTypeHeader)) {
-                matchResult = 3;
-                h_11 = header;
-            }
-            else {
-                matchResult = 5;
-            }
-            break;
-        }
-        case 13: {
-            if (equals(header, DataMapAux_explicationHeader)) {
-                matchResult = 1;
-                h_9 = header;
-            }
-            else if (equals(header, DataMapAux_unitHeader)) {
-                matchResult = 2;
-                h_10 = header;
-            }
-            else if (equals(header, DataMapAux_objectTypeHeader)) {
-                matchResult = 3;
-                h_11 = header;
-            }
-            else {
-                matchResult = 4;
-                text = header.fields[0];
-            }
-            break;
-        }
-        default:
-            if (equals(header, DataMapAux_explicationHeader)) {
-                matchResult = 1;
-                h_9 = header;
-            }
-            else if (equals(header, DataMapAux_unitHeader)) {
-                matchResult = 2;
-                h_10 = header;
-            }
-            else if (equals(header, DataMapAux_objectTypeHeader)) {
-                matchResult = 3;
-                h_11 = header;
-            }
-            else {
-                matchResult = 5;
-            }
-    }
     switch (matchResult) {
         case 0:
-            return ofArray([new FsCell("Data"), new FsCell("Data Format"), new FsCell("Data Selector Format")]);
-        case 1:
-            return ofArray([new FsCell("Explication"), new FsCell("Term Source REF"), new FsCell("Term Accession Number")]);
-        case 2:
-            return ofArray([new FsCell("Unit"), new FsCell("Term Source REF"), new FsCell("Term Accession Number")]);
-        case 3:
-            return ofArray([new FsCell("Object Type"), new FsCell("Term Source REF"), new FsCell("Term Accession Number")]);
-        case 4:
-            return singleton(new FsCell(text));
-        default:
-            return toFail(printf("Could not parse DataMap header %O."))(header);
+            return (dc) => ((cells_1) => r(dc)(cells_1));
+        default: {
+            const arg = join(", ", map((c) => c.ValueAsString(), cells));
+            const clo_1 = toFail(printf("Could not parse data map column: %s"))(arg);
+            return (arg_1) => {
+                const clo_2 = clo_1(arg_1);
+                return clo_2;
+            };
+        }
     }
 }
 
+export function toFsCells(commentKeys) {
+    return toList(delay(() => append([new FsCell("Data"), new FsCell("Data Format"), new FsCell("Data Selector Format")], delay(() => append([new FsCell("Explication"), new FsCell("Term Source REF"), new FsCell("Term Accession Number")], delay(() => append([new FsCell("Unit"), new FsCell("Term Source REF"), new FsCell("Term Accession Number")], delay(() => append([new FsCell("Object Type"), new FsCell("Term Source REF"), new FsCell("Term Accession Number")], delay(() => append([new FsCell("Description")], delay(() => append([new FsCell("Generated By")], delay(() => map_2((ck) => (new FsCell(ck)), commentKeys)))))))))))))));
+}
+

package/Spreadsheet/DataMapTable/DataMapTable.js

@@ -1,11 +1,12 @@
-import { iterateIndexed, head, length, sortBy, collect, map, toArray, exists, ofArray } from "../../fable_modules/fable-library-js.4.16.0/List.js";
-import { classifyColumnOrder, Aux_List_groupWhen } from "../AnnotationTable/ArcTable.js";
-import { toList, tryFind } from "../../fable_modules/fable-library-js.4.16.0/Seq.js";
-import { toFsColumns, fromFsColumns } from "./DataMapColumn.js";
+import { iterateIndexed, head, length, iterate, exists, ofArray } from "../../fable_modules/fable-library-js.4.16.0/List.js";
+import { Aux_List_groupWhen } from "../AnnotationTable/ArcTable.js";
+import { toList, map, delay, toArray, item, tryFind } from "../../fable_modules/fable-library-js.4.16.0/Seq.js";
+import { DataContext_$ctor_Z2FD70A12 } from "../../Core/DataContext.js";
+import { rangeDouble } from "../../fable_modules/fable-library-js.4.16.0/Range.js";
+import { toFsColumns, setFromFsColumns } from "./DataMapColumn.js";
 import { printf, toFail } from "../../fable_modules/fable-library-js.4.16.0/String.js";
-import { DataMap__get_Table, DataMap_init, DataMap_addColumns_6369C010 } from "../../Core/Table/DataMap.js";
+import { DataMap__get_DataContexts, DataMap_$ctor_4E3220A7 } from "../../Core/Table/DataMap.js";
 import { FsWorksheet } from "../../fable_modules/FsSpreadsheet.6.1.2/FsWorksheet.fs.js";
-import { comparePrimitives } from "../../fable_modules/fable-library-js.4.16.0/Util.js";
 import { FsRangeAddress_$ctor_7E77A4A0 } from "../../fable_modules/FsSpreadsheet.6.1.2/Ranges/FsRangeAddress.fs.js";
 import { FsAddress_$ctor_Z37302880 } from "../../fable_modules/FsSpreadsheet.6.1.2/FsAddress.fs.js";
 import { Dictionary_tryGet } from "../../fable_modules/FsSpreadsheet.6.1.2/Cells/FsCellsCollection.fs.js";
@@ -32,7 +33,12 @@ export function tryDataMapTable(sheet) {
  * Groups and parses a collection of single columns into the according ISA composite columns
  */
 export function composeColumns(columns) {
-    return toArray(map(fromFsColumns, groupColumnsByHeader(toList(columns))));
+    const l = (item(0, columns).MaxRowIndex - 1) | 0;
+    const dc = Array.from(toArray(delay(() => map((i) => DataContext_$ctor_Z2FD70A12(), rangeDouble(0, 1, l - 1)))));
+    iterate((arg) => {
+        setFromFsColumns(dc, arg);
+    }, groupColumnsByHeader(toList(columns)));
+    return dc;
 }
 
 /**
@@ -46,7 +52,7 @@ export function tryFromFsWorksheet(sheet) {
         }
         else {
             const t = matchValue;
-            return DataMap_addColumns_6369C010(composeColumns(t.GetColumns(sheet.CellCollection)), true)(DataMap_init());
+            return DataMap_$ctor_4E3220A7(composeColumns(t.GetColumns(sheet.CellCollection)));
         }
     }
     catch (err) {
@@ -59,13 +65,11 @@ export function tryFromFsWorksheet(sheet) {
 export function toFsWorksheet(table) {
     const stringCount = new Map([]);
     const ws = new FsWorksheet("isa_datamap");
-    if (DataMap__get_Table(table).Columns.length === 0) {
+    if (DataMap__get_DataContexts(table).length === 0) {
         return ws;
     }
     else {
-        const columns = collect(toFsColumns, sortBy(classifyColumnOrder, ofArray(DataMap__get_Table(table).Columns), {
-            Compare: comparePrimitives,
-        }));
+        const columns = toFsColumns(DataMap__get_DataContexts(table));
         const maxRow = length(head(columns)) | 0;
         const maxCol = length(columns) | 0;
         const fsTable = ws.Table("datamapTable", FsRangeAddress_$ctor_7E77A4A0(FsAddress_$ctor_Z37302880(1, 1), FsAddress_$ctor_Z37302880(maxRow, maxCol)));
@@ -92,6 +96,7 @@ export function toFsWorksheet(table) {
                 FsRangeBase__Cell_Z3407A44B(fsTable, address, ws.CellCollection).SetValueAs(value);
             }, col);
         }, columns);
+        ws.RescanRows();
         return ws;
     }
 }

package/Template.Web.js

@@ -6,7 +6,7 @@ import { startAsPromise } from "./fable_modules/fable-library-js.4.16.0/Async.js
 import { class_type } from "./fable_modules/fable-library-js.4.16.0/Reflection.js";
 
 export function getTemplates(url) {
-    const url_1 = defaultArg(url, "https://github.com/nfdi4plants/Swate-templates/releases/download/latest/templates.json");
+    const url_1 = defaultArg(url, "https://github.com/nfdi4plants/Swate-templates/releases/download/latest/templates_v2.0.0.json");
     return singleton.Delay(() => singleton.Bind(downloadFile(url_1), (_arg) => {
         const mapResult = Templates_fromJsonString(_arg);
         return singleton.Return(mapResult);