@nfdi4plants/arctrl 2.1.0-alpha.1 → 2.1.0-alpha.3

package/Spreadsheet/ArcAssay.js

@@ -1,113 +1,136 @@
-import { FsWorksheet } from "../fable_modules/FsSpreadsheet.6.3.0-alpha.4/FsWorksheet.fs.js";
-import { iterate, isEmpty as isEmpty_1, tryPick, choose, tryFind, tryHead, head, exists, map, singleton, append, delay, iterateIndexed } from "../fable_modules/fable-library-js.4.22.0/Seq.js";
-import { SparseRowModule_tryGetValueAt, SparseRowModule_fromFsRow, SparseRowModule_fromValues, SparseRowModule_writeToSheet } from "./Metadata/SparseTable.js";
-import { fromRows as fromRows_1, toRows as toRows_1 } from "./Metadata/Assays.js";
-import { empty, isEmpty, ofSeq, singleton as singleton_1 } from "../fable_modules/fable-library-js.4.22.0/List.js";
-import { fromRows as fromRows_2, toRows as toRows_2 } from "./Metadata/Contacts.js";
-import { toConsole, printf, toFail } from "../fable_modules/fable-library-js.4.22.0/String.js";
+import { iterate, isEmpty as isEmpty_1, tryPick, choose, tryFind, map, iterateIndexed, singleton, append, delay, tryHead, head, exists } from "../fable_modules/fable-library-js.4.22.0/Seq.js";
 import { getEnumerator } from "../fable_modules/fable-library-js.4.22.0/Util.js";
+import { toRows, fromRows } from "./Metadata/Assays.js";
+import { toRows as toRows_1, fromRows as fromRows_1 } from "./Metadata/Contacts.js";
 import { ArcAssay } from "../Core/ArcTypes.js";
 import { createMissingIdentifier } from "../Core/Helper/Identifier.js";
 import { unwrap, toArray, defaultArg } from "../fable_modules/fable-library-js.4.22.0/Option.js";
+import { ofSeq, singleton as singleton_1, empty, isEmpty } from "../fable_modules/fable-library-js.4.22.0/List.js";
+import { SparseRowModule_fromAllValues, SparseRowModule_getAllValues, SparseRowModule_fromFsRow, SparseRowModule_writeToSheet, SparseRowModule_fromValues, SparseRowModule_tryGetValueAt } from "./Metadata/SparseTable.js";
+import { FsWorksheet } from "../fable_modules/FsSpreadsheet.6.3.0-alpha.4/FsWorksheet.fs.js";
+import { toConsole, printf, toFail } from "../fable_modules/fable-library-js.4.22.0/String.js";
 import { toFsWorksheet as toFsWorksheet_1, tryFromFsWorksheet } from "./AnnotationTable/ArcTable.js";
 import { toFsWorksheet, tryFromFsWorksheet as tryFromFsWorksheet_1 } from "./DataMapTable/DataMapTable.js";
 import { FsWorkbook } from "../fable_modules/FsSpreadsheet.6.3.0-alpha.4/FsWorkbook.fs.js";
 
-export function ArcAssay_toMetadataSheet(assay) {
-    let assay_1;
-    const sheet = new FsWorksheet("isa_assay");
-    iterateIndexed((rowI, r) => {
-        SparseRowModule_writeToSheet(rowI + 1, r, sheet);
-    }, (assay_1 = assay, delay(() => append(singleton(SparseRowModule_fromValues(["ASSAY"])), delay(() => append(toRows_1("Assay", singleton_1(assay_1)), delay(() => append(singleton(SparseRowModule_fromValues(["ASSAY PERFORMERS"])), delay(() => toRows_2("Assay Person", ofSeq(assay_1.Performers)))))))))));
-    return sheet;
-}
-
-export function ArcAssay_fromMetadataSheet(sheet) {
-    try {
-        const rows_1 = map(SparseRowModule_fromFsRow, sheet.Rows);
-        const patternInput = exists((row) => {
-            const s = head(row)[1];
-            return s.startsWith("Assay");
-        }, rows_1) ? ["Assay", "Assay Person"] : [undefined, undefined];
-        const en = getEnumerator(rows_1);
-        const loop = (lastLine_mut, assays_mut, contacts_mut, lineNumber_mut) => {
-            let k;
-            loop:
-            while (true) {
-                const lastLine = lastLine_mut, assays = assays_mut, contacts = contacts_mut, lineNumber = lineNumber_mut;
-                let matchResult, k_2, k_3, k_4;
-                if (lastLine != null) {
-                    if ((k = lastLine, (k === "ASSAY") ? true : (k === "ASSAY METADATA"))) {
-                        matchResult = 0;
-                        k_2 = lastLine;
-                    }
-                    else if (lastLine === "ASSAY PERFORMERS") {
-                        matchResult = 1;
-                        k_3 = lastLine;
-                    }
-                    else {
-                        matchResult = 2;
-                        k_4 = lastLine;
-                    }
+export function ArcAssay_fromRows(rows) {
+    const patternInput = exists((row) => {
+        const s = head(row)[1];
+        return s.startsWith("Assay");
+    }, rows) ? ["Assay", "Assay Person"] : [undefined, undefined];
+    const en = getEnumerator(rows);
+    const loop = (lastRow_mut, assays_mut, contacts_mut, rowNumber_mut) => {
+        let prefix;
+        loop:
+        while (true) {
+            const lastRow = lastRow_mut, assays = assays_mut, contacts = contacts_mut, rowNumber = rowNumber_mut;
+            let matchResult, prefix_2, prefix_3;
+            if (lastRow != null) {
+                if ((prefix = lastRow, (prefix === "ASSAY") ? true : (prefix === "ASSAY METADATA"))) {
+                    matchResult = 0;
+                    prefix_2 = lastRow;
+                }
+                else if (lastRow === "ASSAY PERFORMERS") {
+                    matchResult = 1;
+                    prefix_3 = lastRow;
                 }
                 else {
                     matchResult = 2;
-                    k_4 = lastLine;
                 }
-                switch (matchResult) {
-                    case 0: {
-                        const patternInput_1 = fromRows_1(patternInput[0], lineNumber + 1, en);
-                        lastLine_mut = patternInput_1[0];
-                        assays_mut = patternInput_1[3];
-                        contacts_mut = contacts;
-                        lineNumber_mut = patternInput_1[1];
-                        continue loop;
-                    }
-                    case 1: {
-                        const patternInput_2 = fromRows_2(patternInput[1], lineNumber + 1, en);
-                        lastLine_mut = patternInput_2[0];
-                        assays_mut = assays;
-                        contacts_mut = patternInput_2[3];
-                        lineNumber_mut = patternInput_2[1];
-                        continue loop;
-                    }
-                    default: {
-                        let matchResult_1, assays_2, contacts_2;
-                        if (isEmpty(assays)) {
-                            if (isEmpty(contacts)) {
-                                matchResult_1 = 0;
-                            }
-                            else {
-                                matchResult_1 = 1;
-                                assays_2 = assays;
-                                contacts_2 = contacts;
-                            }
+            }
+            else {
+                matchResult = 2;
+            }
+            switch (matchResult) {
+                case 0: {
+                    const patternInput_1 = fromRows(patternInput[0], rowNumber + 1, en);
+                    lastRow_mut = patternInput_1[0];
+                    assays_mut = patternInput_1[3];
+                    contacts_mut = contacts;
+                    rowNumber_mut = patternInput_1[1];
+                    continue loop;
+                }
+                case 1: {
+                    const patternInput_2 = fromRows_1(patternInput[1], rowNumber + 1, en);
+                    lastRow_mut = patternInput_2[0];
+                    assays_mut = assays;
+                    contacts_mut = patternInput_2[3];
+                    rowNumber_mut = patternInput_2[1];
+                    continue loop;
+                }
+                default: {
+                    let matchResult_1, assays_2, contacts_2;
+                    if (isEmpty(assays)) {
+                        if (isEmpty(contacts)) {
+                            matchResult_1 = 0;
                         }
                         else {
                             matchResult_1 = 1;
                             assays_2 = assays;
                             contacts_2 = contacts;
                         }
-                        switch (matchResult_1) {
-                            case 0:
-                                return ArcAssay.create(createMissingIdentifier());
-                            default: {
-                                const performers = Array.from(contacts_2);
-                                const assay = defaultArg(tryHead(assays_2), ArcAssay.create(createMissingIdentifier()));
-                                return ArcAssay.setPerformers(performers, assay);
-                            }
+                    }
+                    else {
+                        matchResult_1 = 1;
+                        assays_2 = assays;
+                        contacts_2 = contacts;
+                    }
+                    switch (matchResult_1) {
+                        case 0:
+                            return ArcAssay.create(createMissingIdentifier());
+                        default: {
+                            const performers = Array.from(contacts_2);
+                            const assay = defaultArg(tryHead(assays_2), ArcAssay.create(createMissingIdentifier()));
+                            return ArcAssay.setPerformers(performers, assay);
                         }
                     }
                 }
-                break;
             }
-        };
-        if (en["System.Collections.IEnumerator.MoveNext"]()) {
-            return loop(SparseRowModule_tryGetValueAt(0, en["System.Collections.Generic.IEnumerator`1.get_Current"]()), empty(), empty(), 1);
-        }
-        else {
-            throw new Error("empty assay metadata sheet");
+            break;
         }
+    };
+    if (en["System.Collections.IEnumerator.MoveNext"]()) {
+        return loop(SparseRowModule_tryGetValueAt(0, en["System.Collections.Generic.IEnumerator`1.get_Current"]()), empty(), empty(), 1);
+    }
+    else {
+        throw new Error("empty assay metadata sheet");
+    }
+}
+
+export function ArcAssay_toRows(assay) {
+    return delay(() => append(singleton(SparseRowModule_fromValues(["ASSAY"])), delay(() => append(toRows("Assay", singleton_1(assay)), delay(() => append(singleton(SparseRowModule_fromValues(["ASSAY PERFORMERS"])), delay(() => toRows_1("Assay Person", ofSeq(assay.Performers)))))))));
+}
+
+export function ArcAssay_toMetadataSheet(assay) {
+    const sheet = new FsWorksheet("isa_assay");
+    iterateIndexed((rowI, r) => {
+        SparseRowModule_writeToSheet(rowI + 1, r, sheet);
+    }, ArcAssay_toRows(assay));
+    return sheet;
+}
+
+export function ArcAssay_fromMetadataSheet(sheet) {
+    try {
+        const rows = map(SparseRowModule_fromFsRow, sheet.Rows);
+        const hasPrefix = exists((row) => {
+            const s = head(row)[1];
+            return s.startsWith("Assay");
+        }, rows);
+        return ArcAssay_fromRows(rows);
+    }
+    catch (err) {
+        const arg = err.message;
+        return toFail(printf("Failed while parsing metadatasheet: %s"))(arg);
+    }
+}
+
+export function ArcAssay_toMetadataCollection(assay) {
+    return map(SparseRowModule_getAllValues, ArcAssay_toRows(assay));
+}
+
+export function ArcAssay_fromMetadataCollection(collection) {
+    try {
+        return ArcAssay_fromRows(map(SparseRowModule_fromAllValues, collection));
     }
     catch (err) {
         const arg = err.message;

package/Spreadsheet/ArcInvestigation.js

@@ -3,7 +3,7 @@ import { record_type, list_type, string_type } from "../fable_modules/fable-libr
 import { Remark, Comment$_$reflection } from "../Core/Comment.js";
 import { head, tail, isEmpty, ofSeq, concat, unzip, append, reverse, cons, empty, map, ofArray } from "../fable_modules/fable-library-js.4.22.0/List.js";
 import { Remark_wrapRemark, Comment_toString, Comment_fromString } from "./Metadata/Comment.js";
-import { SparseRowModule_writeToSheet, SparseRowModule_fromFsRow, SparseRowModule_fromValues, SparseRowModule_tryGetValueAt, SparseTable_ToRows_759CAFC1, SparseTable_FromRows_Z5579EC29, SparseTable, SparseTable_Create_Z2192E64B, SparseTable__TryGetValueDefault_5BAE6133 } from "./Metadata/SparseTable.js";
+import { SparseRowModule_writeToSheet, SparseRowModule_fromFsRow, SparseRowModule_fromAllValues, SparseRowModule_getAllValues, SparseRowModule_fromValues, SparseRowModule_tryGetValueAt, SparseTable_ToRows_759CAFC1, SparseTable_FromRows_Z5579EC29, SparseTable, SparseTable_Create_Z2192E64B, SparseTable__TryGetValueDefault_5BAE6133 } from "./Metadata/SparseTable.js";
 import { addToDict } from "../fable_modules/fable-library-js.4.22.0/MapUtil.js";
 import { value as value_1, defaultArg } from "../fable_modules/fable-library-js.4.22.0/Option.js";
 import { Option_fromValueWithDefault, ResizeArray_iter } from "../Core/Helper/Collections.js";
@@ -14,7 +14,7 @@ import { toRows, fromRows } from "./Metadata/OntologySourceReference.js";
 import { toRows as toRows_1, fromRows as fromRows_1 } from "./Metadata/Publication.js";
 import { toRows as toRows_2, fromRows as fromRows_2 } from "./Metadata/Contacts.js";
 import { toRows as toRows_3, fromRows as fromRows_3 } from "./Metadata/Study.js";
-import { iterateIndexed, map as map_1, tryFind as tryFind_1, toList, collect, singleton, append as append_1, delay } from "../fable_modules/fable-library-js.4.22.0/Seq.js";
+import { iterateIndexed, tryFind as tryFind_1, map as map_1, toList, collect, singleton, append as append_1, delay } from "../fable_modules/fable-library-js.4.22.0/Seq.js";
 import { tryFind, ofList } from "../fable_modules/fable-library-js.4.22.0/Map.js";
 import { printf, toFail } from "../fable_modules/fable-library-js.4.22.0/String.js";
 import { FsWorksheet } from "../fable_modules/FsSpreadsheet.6.3.0-alpha.4/FsWorksheet.fs.js";
@@ -102,7 +102,7 @@ export function ArcInvestigation_fromRows(rows) {
         loop:
         while (true) {
             const lastLine = lastLine_mut, ontologySourceReferences = ontologySourceReferences_mut, investigationInfo = investigationInfo_mut, publications = publications_mut, contacts = contacts_mut, studies = studies_mut, remarks = remarks_mut, lineNumber = lineNumber_mut;
-            let matchResult, k_5, k_6, k_7, k_8, k_9, k_10;
+            let matchResult, k_5, k_6, k_7, k_8, k_9;
             if (lastLine != null) {
                 switch (lastLine) {
                     case "ONTOLOGY SOURCE REFERENCE": {
@@ -130,15 +130,12 @@ export function ArcInvestigation_fromRows(rows) {
                         k_9 = lastLine;
                         break;
                     }
-                    default: {
+                    default:
                         matchResult = 5;
-                        k_10 = lastLine;
-                    }
                 }
             }
             else {
                 matchResult = 5;
-                k_10 = lastLine;
             }
             switch (matchResult) {
                 case 0: {
@@ -283,6 +280,14 @@ export function ArcInvestigation_toRows(investigation) {
     })()));
 }
 
+export function ArcInvestigation_toMetadataCollection(investigation) {
+    return map_1(SparseRowModule_getAllValues, ArcInvestigation_toRows(investigation));
+}
+
+export function ArcInvestigation_fromMetadataCollection(collection) {
+    return ArcInvestigation_fromRows(map_1(SparseRowModule_fromAllValues, collection));
+}
+
 export function ArcInvestigation_isMetadataSheetName(name) {
     if (name === "isa_investigation") {
         return true;

package/Spreadsheet/ArcStudy.js

@@ -1,10 +1,10 @@
 import { FsWorksheet } from "../fable_modules/FsSpreadsheet.6.3.0-alpha.4/FsWorksheet.fs.js";
 import { iterate, tryPick, tryFind, map, append, iterateIndexed } from "../fable_modules/fable-library-js.4.22.0/Seq.js";
-import { SparseRowModule_fromFsRow, SparseRowModule_fromValues, SparseRowModule_writeToSheet } from "./Metadata/SparseTable.js";
-import { fromRows as fromRows_1, toRows } from "./Metadata/Study.js";
+import { SparseRowModule_fromAllValues, SparseRowModule_getAllValues, SparseRowModule_fromFsRow, SparseRowModule_fromValues, SparseRowModule_writeToSheet } from "./Metadata/SparseTable.js";
+import { fromRows, toRows } from "./Metadata/Study.js";
+import { getEnumerator } from "../fable_modules/fable-library-js.4.22.0/Util.js";
 import { toConsole, printf, toFail } from "../fable_modules/fable-library-js.4.22.0/String.js";
 import { unwrap, toArray, defaultArg } from "../fable_modules/fable-library-js.4.22.0/Option.js";
-import { getEnumerator } from "../fable_modules/fable-library-js.4.22.0/Util.js";
 import { ArcStudy } from "../Core/ArcTypes.js";
 import { createMissingIdentifier } from "../Core/Helper/Identifier.js";
 import { empty } from "../fable_modules/fable-library-js.4.22.0/List.js";
@@ -22,10 +22,30 @@ export function ArcStudy_toMetadataSheet(study, assays) {
     return sheet;
 }
 
+export function ArcStudy_fromRows(rows) {
+    const en = getEnumerator(rows);
+    en["System.Collections.IEnumerator.MoveNext"]();
+    return fromRows(2, en)[3];
+}
+
 export function ArcStudy_fromMetadataSheet(sheet) {
-    let en;
     try {
-        return defaultArg((en = getEnumerator(map(SparseRowModule_fromFsRow, sheet.Rows)), (void en["System.Collections.IEnumerator.MoveNext"](), fromRows_1(2, en)[3])), [ArcStudy.create(createMissingIdentifier()), empty()]);
+        return defaultArg(ArcStudy_fromRows(map(SparseRowModule_fromFsRow, sheet.Rows)), [ArcStudy.create(createMissingIdentifier()), empty()]);
+    }
+    catch (err) {
+        const arg = err.message;
+        return toFail(printf("Failed while parsing metadatasheet: %s"))(arg);
+    }
+}
+
+export function ArcStudy_toMetadataCollection(study, assays) {
+    let source_1;
+    return map(SparseRowModule_getAllValues, (source_1 = toRows(study, assays), append([SparseRowModule_fromValues(["STUDY"])], source_1)));
+}
+
+export function ArcStudy_fromMetadataCollection(collection) {
+    try {
+        return defaultArg(ArcStudy_fromRows(map(SparseRowModule_fromAllValues, collection)), [ArcStudy.create(createMissingIdentifier()), empty()]);
     }
     catch (err) {
         const arg = err.message;

package/Spreadsheet/Template.js

@@ -4,7 +4,7 @@ import { ofSeq, append as append_1, reverse, map, empty, ofArray } from "../fabl
 import { toRows, fromRows, toSparseTable, fromSparseTable } from "./Metadata/OntologyAnnotation.js";
 import { Comment$_$reflection } from "../Core/Comment.js";
 import { Comment_fromString } from "./Metadata/Comment.js";
-import { SparseRowModule_fromFsRow, SparseRowModule_writeToSheet, SparseRowModule_fromValues, SparseRowModule_tryGetValueAt, SparseTable_ToRows_759CAFC1, SparseTable_FromRows_Z5579EC29, SparseTable, SparseTable_Create_Z2192E64B, SparseTable__TryGetValueDefault_5BAE6133 } from "./Metadata/SparseTable.js";
+import { SparseRowModule_fromAllValues, SparseRowModule_getAllValues, SparseRowModule_fromFsRow, SparseRowModule_writeToSheet, SparseRowModule_fromValues, SparseRowModule_tryGetValueAt, SparseTable_ToRows_759CAFC1, SparseTable_FromRows_Z5579EC29, SparseTable, SparseTable_Create_Z2192E64B, SparseTable__TryGetValueDefault_5BAE6133 } from "./Metadata/SparseTable.js";
 import { createMissingIdentifier } from "../Core/Helper/Identifier.js";
 import { addToDict } from "../fable_modules/fable-library-js.4.22.0/MapUtil.js";
 import { List_distinct } from "../fable_modules/fable-library-js.4.22.0/Seq2.js";
@@ -281,6 +281,14 @@ export function Template_fromMetadataSheet(sheet) {
     return Metadata_Template_fromRows(map_1(SparseRowModule_fromFsRow, sheet.Rows));
 }
 
+export function Template_toMetadataCollection(template) {
+    return map_1(SparseRowModule_getAllValues, Metadata_Template_toRows(template));
+}
+
+export function Template_fromMetadataCollection(collection) {
+    return Metadata_Template_fromRows(map_1(SparseRowModule_fromAllValues, collection));
+}
+
 /**
  * Reads an assay from a spreadsheet
  */

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@nfdi4plants/arctrl",
-  "version": "2.1.0-alpha.1",
+  "version": "2.1.0-alpha.3",
   "description": "Top level ARC DataModel and API function descriptions.",
   "type": "module",
   "main": "index.js",