@nfdi4plants/arctrl 1.2.0 → 2.0.0-alpha.2

package/{ISA/ISA.Spreadsheet → Spreadsheet}/Metadata/Factors.js

@@ -1,13 +1,13 @@
-import { reverse, cons, iterateIndexed, empty, map, toArray, initialize, singleton, length, ofArray } from "../../../fable_modules/fable-library-js.4.13.0/List.js";
-import { OntologyAnnotation } from "../../ISA/JsonTypes/OntologyAnnotation.js";
-import { Option_fromValueWithDefault } from "./Conversions.js";
-import { Factor } from "../../ISA/JsonTypes/Factor.js";
-import { SparseTable_ToRows_6A3D4534, SparseTable_FromRows_Z5579EC29, SparseTable, SparseTable_Create_Z2192E64B, SparseTable__TryGetValue_11FD62A8, SparseTable__TryGetValueDefault_5BAE6133, SparseTable_GetEmptyComments_651559CC } from "./SparseTable.js";
+import { reverse, cons, iterateIndexed, empty, map, initialize, singleton, length, ofArray } from "../../fable_modules/fable-library-js.4.16.0/List.js";
+import { OntologyAnnotation } from "../../Core/OntologyAnnotation.js";
+import { ResizeArray_iter, Option_fromValueWithDefault } from "../../Core/Helper/Collections.js";
+import { Factor } from "../../Core/Process/Factor.js";
+import { SparseTable_ToRows_759CAFC1, SparseTable_FromRows_Z5579EC29, SparseTable, SparseTable_Create_Z2192E64B, SparseTable__TryGetValue_11FD62A8, SparseTable__TryGetValueDefault_5BAE6133, SparseTable_GetEmptyComments_3ECCA699 } from "./SparseTable.js";
 import { Comment_toString, Comment_fromString } from "./Comment.js";
-import { defaultArg } from "../../../fable_modules/fable-library-js.4.13.0/Option.js";
-import { addToDict } from "../../../fable_modules/fable-library-js.4.13.0/MapUtil.js";
-import { List_distinct } from "../../../fable_modules/fable-library-js.4.13.0/Seq2.js";
-import { stringHash } from "../../../fable_modules/fable-library-js.4.13.0/Util.js";
+import { defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
+import { addToDict } from "../../fable_modules/fable-library-js.4.16.0/MapUtil.js";
+import { List_distinct } from "../../fable_modules/fable-library-js.4.16.0/Seq2.js";
+import { stringHash } from "../../fable_modules/fable-library-js.4.16.0/Util.js";
 
 export const nameLabel = "Name";
 
@@ -20,20 +20,22 @@ export const typeTermSourceREFLabel = "Type Term Source REF";
 export const labels = ofArray([nameLabel, factorTypeLabel, typeTermAccessionNumberLabel, typeTermSourceREFLabel]);
 
 export function fromString(name, designType, typeTermSourceREF, typeTermAccessionNumber, comments) {
-    const factorType = OntologyAnnotation.fromString(designType, typeTermSourceREF, typeTermAccessionNumber);
-    const factorType_1 = Option_fromValueWithDefault(OntologyAnnotation.empty, factorType);
+    const factorType = OntologyAnnotation.create(designType, typeTermSourceREF, typeTermAccessionNumber);
+    const factorType_1 = Option_fromValueWithDefault(new OntologyAnnotation(), factorType);
     const comments_1 = Option_fromValueWithDefault([], comments);
-    return Factor.make(void 0, name, factorType_1, comments_1);
+    return Factor.make(name, factorType_1, comments_1);
 }
 
 export function fromSparseTable(matrix) {
     if ((matrix.ColumnCount === 0) && (length(matrix.CommentKeys) !== 0)) {
-        const comments = SparseTable_GetEmptyComments_651559CC(matrix);
-        return singleton(Factor.create(void 0, void 0, void 0, comments));
+        const comments = SparseTable_GetEmptyComments_3ECCA699(matrix);
+        return singleton(Factor.create(void 0, void 0, comments));
     }
     else {
         return initialize(matrix.ColumnCount, (i) => {
-            const comments_1 = toArray(map((k) => Comment_fromString(k, SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [k, i])), matrix.CommentKeys));
+            let comments_1;
+            const collection = map((k) => Comment_fromString(k, SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [k, i])), matrix.CommentKeys);
+            comments_1 = Array.from(collection);
             return fromString(SparseTable__TryGetValue_11FD62A8(matrix, [nameLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [factorTypeLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [typeTermSourceREFLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [typeTermAccessionNumberLabel, i]), comments_1);
         });
     }
@@ -45,21 +47,20 @@ export function toSparseTable(factors) {
     iterateIndexed((i, f) => {
         const i_1 = (i + 1) | 0;
         let ft;
-        const f_1 = defaultArg(f.FactorType, OntologyAnnotation.empty);
-        ft = OntologyAnnotation.toString(f_1, true);
+        const f_1 = defaultArg(f.FactorType, new OntologyAnnotation());
+        ft = OntologyAnnotation.toStringObject(f_1, true);
         addToDict(matrix.Matrix, [nameLabel, i_1], defaultArg(f.Name, ""));
         addToDict(matrix.Matrix, [factorTypeLabel, i_1], ft.TermName);
         addToDict(matrix.Matrix, [typeTermAccessionNumberLabel, i_1], ft.TermAccessionNumber);
         addToDict(matrix.Matrix, [typeTermSourceREFLabel, i_1], ft.TermSourceREF);
         const matchValue = f.Comments;
         if (matchValue != null) {
-            const array = matchValue;
-            array.forEach((comment) => {
+            ResizeArray_iter((comment) => {
                 const patternInput = Comment_toString(comment);
                 const n = patternInput[0];
                 commentKeys = cons(n, commentKeys);
                 addToDict(matrix.Matrix, [n, i_1], patternInput[1]);
-            });
+            }, matchValue);
         }
     }, factors);
     return new SparseTable(matrix.Matrix, matrix.Keys, reverse(List_distinct(commentKeys, {
@@ -76,10 +77,10 @@ export function fromRows(prefix, lineNumber, rows) {
 export function toRows(prefix, factors) {
     const m = toSparseTable(factors);
     if (prefix == null) {
-        return SparseTable_ToRows_6A3D4534(m);
+        return SparseTable_ToRows_759CAFC1(m);
     }
     else {
-        return SparseTable_ToRows_6A3D4534(m, prefix);
+        return SparseTable_ToRows_759CAFC1(m, prefix);
     }
 }
 

package/Spreadsheet/Metadata/OntologyAnnotation.js

@@ -0,0 +1,64 @@
+import { reverse, cons, iterateIndexed, empty, ofArray, map, initialize, singleton, length } from "../../fable_modules/fable-library-js.4.16.0/List.js";
+import { SparseTable_ToRows_759CAFC1, SparseTable_FromRows_Z5579EC29, SparseTable, SparseTable_Create_Z2192E64B, SparseTable__TryGetValue_11FD62A8, SparseTable__TryGetValueDefault_5BAE6133, SparseTable_GetEmptyComments_3ECCA699 } from "./SparseTable.js";
+import { OntologyAnnotation } from "../../Core/OntologyAnnotation.js";
+import { Comment_toString, Comment_fromString } from "./Comment.js";
+import { unwrap } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
+import { addToDict } from "../../fable_modules/fable-library-js.4.16.0/MapUtil.js";
+import { ResizeArray_iter } from "../../Core/Helper/Collections.js";
+import { List_distinct } from "../../fable_modules/fable-library-js.4.16.0/Seq2.js";
+import { stringHash } from "../../fable_modules/fable-library-js.4.16.0/Util.js";
+
+export function fromSparseTable(label, labelTSR, labelTAN, matrix) {
+    let returnVal;
+    if ((matrix.ColumnCount === 0) && (length(matrix.CommentKeys) !== 0)) {
+        const comments = SparseTable_GetEmptyComments_3ECCA699(matrix);
+        return singleton((returnVal = OntologyAnnotation.create(), (returnVal.Comments = comments, returnVal)));
+    }
+    else {
+        return initialize(matrix.ColumnCount, (i) => {
+            let comments_1;
+            const collection = map((k) => Comment_fromString(k, SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [k, i])), matrix.CommentKeys);
+            comments_1 = Array.from(collection);
+            return new OntologyAnnotation(unwrap(SparseTable__TryGetValue_11FD62A8(matrix, [label, i])), unwrap(SparseTable__TryGetValue_11FD62A8(matrix, [labelTSR, i])), unwrap(SparseTable__TryGetValue_11FD62A8(matrix, [labelTAN, i])), comments_1);
+        });
+    }
+}
+
+export function toSparseTable(label, labelTSR, labelTAN, designs) {
+    const matrix = SparseTable_Create_Z2192E64B(void 0, ofArray([label, labelTAN, labelTSR]), void 0, length(designs) + 1);
+    let commentKeys = empty();
+    iterateIndexed((i, d) => {
+        const i_1 = (i + 1) | 0;
+        const oa = OntologyAnnotation.toStringObject(d, true);
+        addToDict(matrix.Matrix, [label, i_1], oa.TermName);
+        addToDict(matrix.Matrix, [labelTAN, i_1], oa.TermAccessionNumber);
+        addToDict(matrix.Matrix, [labelTSR, i_1], oa.TermSourceREF);
+        ResizeArray_iter((comment) => {
+            const patternInput = Comment_toString(comment);
+            const n = patternInput[0];
+            commentKeys = cons(n, commentKeys);
+            addToDict(matrix.Matrix, [n, i_1], patternInput[1]);
+        }, d.Comments);
+    }, designs);
+    return new SparseTable(matrix.Matrix, matrix.Keys, reverse(List_distinct(commentKeys, {
+        Equals: (x, y) => (x === y),
+        GetHashCode: stringHash,
+    })), matrix.ColumnCount);
+}
+
+export function fromRows(prefix, label, labelTSR, labelTAN, lineNumber, rows) {
+    const labels = ofArray([label, labelTAN, labelTSR]);
+    const tupledArg = (prefix == null) ? SparseTable_FromRows_Z5579EC29(rows, labels, lineNumber) : SparseTable_FromRows_Z5579EC29(rows, labels, lineNumber, prefix);
+    return [tupledArg[0], tupledArg[1], tupledArg[2], fromSparseTable(label, labelTSR, labelTAN, tupledArg[3])];
+}
+
+export function toRows(prefix, label, labelTSR, labelTAN, designs) {
+    const m = toSparseTable(label, labelTSR, labelTAN, designs);
+    if (prefix == null) {
+        return SparseTable_ToRows_759CAFC1(m);
+    }
+    else {
+        return SparseTable_ToRows_759CAFC1(m, prefix);
+    }
+}
+

package/{ISA/ISA.Spreadsheet → Spreadsheet}/Metadata/OntologySourceReference.js

@@ -1,12 +1,12 @@
-import { reverse, cons, iterateIndexed, empty, map, toArray, initialize, singleton, length, ofArray } from "../../../fable_modules/fable-library-js.4.13.0/List.js";
-import { Option_fromValueWithDefault } from "./Conversions.js";
-import { OntologySourceReference } from "../../ISA/JsonTypes/OntologySourceReference.js";
-import { SparseTable_ToRows_6A3D4534, SparseTable_FromRows_Z5579EC29, SparseTable, SparseTable_Create_Z2192E64B, SparseTable__TryGetValue_11FD62A8, SparseTable__TryGetValueDefault_5BAE6133, SparseTable_GetEmptyComments_651559CC } from "./SparseTable.js";
+import { reverse, cons, iterateIndexed, empty, map, initialize, singleton, length, ofArray } from "../../fable_modules/fable-library-js.4.16.0/List.js";
+import { OntologySourceReference } from "../../Core/OntologySourceReference.js";
+import { SparseTable_ToRows_759CAFC1, SparseTable_FromRows_Z5579EC29, SparseTable, SparseTable_Create_Z2192E64B, SparseTable__TryGetValue_11FD62A8, SparseTable__TryGetValueDefault_5BAE6133, SparseTable_GetEmptyComments_3ECCA699 } from "./SparseTable.js";
 import { Comment_toString, Comment_fromString } from "./Comment.js";
-import { addToDict } from "../../../fable_modules/fable-library-js.4.13.0/MapUtil.js";
-import { defaultArg } from "../../../fable_modules/fable-library-js.4.13.0/Option.js";
-import { List_distinct } from "../../../fable_modules/fable-library-js.4.13.0/Seq2.js";
-import { stringHash } from "../../../fable_modules/fable-library-js.4.13.0/Util.js";
+import { addToDict } from "../../fable_modules/fable-library-js.4.16.0/MapUtil.js";
+import { defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
+import { ResizeArray_iter } from "../../Core/Helper/Collections.js";
+import { List_distinct } from "../../fable_modules/fable-library-js.4.16.0/Seq2.js";
+import { stringHash } from "../../fable_modules/fable-library-js.4.16.0/Util.js";
 
 export const nameLabel = "Term Source Name";
 
@@ -19,18 +19,20 @@ export const descriptionLabel = "Term Source Description";
 export const labels = ofArray([nameLabel, fileLabel, versionLabel, descriptionLabel]);
 
 export function fromString(description, file, name, version, comments) {
-    const comments_1 = Option_fromValueWithDefault([], comments);
-    return OntologySourceReference.make(description, file, name, version, comments_1);
+    return OntologySourceReference.make(description, file, name, version, comments);
 }
 
 export function fromSparseTable(matrix) {
+    let returnVal;
     if ((matrix.ColumnCount === 0) && (length(matrix.CommentKeys) !== 0)) {
-        const comments = SparseTable_GetEmptyComments_651559CC(matrix);
-        return singleton(OntologySourceReference.create(void 0, void 0, void 0, void 0, comments));
+        const comments = SparseTable_GetEmptyComments_3ECCA699(matrix);
+        return singleton((returnVal = OntologySourceReference.create(), (returnVal.Comments = comments, returnVal)));
     }
     else {
         return initialize(matrix.ColumnCount, (i) => {
-            const comments_1 = toArray(map((k) => Comment_fromString(k, SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [k, i])), matrix.CommentKeys));
+            let comments_1;
+            const collection = map((k) => Comment_fromString(k, SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [k, i])), matrix.CommentKeys);
+            comments_1 = Array.from(collection);
             return fromString(SparseTable__TryGetValue_11FD62A8(matrix, [descriptionLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [fileLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [nameLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [versionLabel, i]), comments_1);
         });
     }
@@ -45,16 +47,12 @@ export function toSparseTable(ontologySources) {
         addToDict(matrix.Matrix, [fileLabel, i_1], defaultArg(o.File, ""));
         addToDict(matrix.Matrix, [versionLabel, i_1], defaultArg(o.Version, ""));
         addToDict(matrix.Matrix, [descriptionLabel, i_1], defaultArg(o.Description, ""));
-        const matchValue = o.Comments;
-        if (matchValue != null) {
-            const array = matchValue;
-            array.forEach((comment) => {
-                const patternInput = Comment_toString(comment);
-                const n = patternInput[0];
-                commentKeys = cons(n, commentKeys);
-                addToDict(matrix.Matrix, [n, i_1], patternInput[1]);
-            });
-        }
+        ResizeArray_iter((comment) => {
+            const patternInput = Comment_toString(comment);
+            const n = patternInput[0];
+            commentKeys = cons(n, commentKeys);
+            addToDict(matrix.Matrix, [n, i_1], patternInput[1]);
+        }, o.Comments);
     }, ontologySources);
     return new SparseTable(matrix.Matrix, matrix.Keys, reverse(List_distinct(commentKeys, {
         Equals: (x, y) => (x === y),
@@ -68,6 +66,6 @@ export function fromRows(lineNumber, rows) {
 }
 
 export function toRows(termSources) {
-    return SparseTable_ToRows_6A3D4534(toSparseTable(termSources));
+    return SparseTable_ToRows_759CAFC1(toSparseTable(termSources));
 }
 

package/{ISA/ISA.Spreadsheet → Spreadsheet}/Metadata/Protocols.js

@@ -1,14 +1,14 @@
-import { reverse, cons, iterate, iterateIndexed, map as map_1, initialize, singleton, length, empty, ofArray } from "../../../fable_modules/fable-library-js.4.13.0/List.js";
-import { OntologyAnnotation } from "../../ISA/JsonTypes/OntologyAnnotation.js";
+import { reverse, cons, iterate, iterateIndexed, map as map_1, initialize, singleton, length, empty, ofSeq, ofArray } from "../../fable_modules/fable-library-js.4.16.0/List.js";
+import { OntologyAnnotation } from "../../Core/OntologyAnnotation.js";
 import { Component_toAggregatedStrings, ProtocolParameter_toAggregatedStrings, Option_fromValueWithDefault, Component_fromAggregatedStrings, ProtocolParameter_fromAggregatedStrings } from "./Conversions.js";
-import { Protocol_create_Z7DFD6E67, Protocol_make } from "../../ISA/JsonTypes/Protocol.js";
-import { defaultArg, map } from "../../../fable_modules/fable-library-js.4.13.0/Option.js";
-import { URIModule_fromString } from "../../ISA/JsonTypes/URI.js";
-import { SparseTable_ToRows_6A3D4534, SparseTable_FromRows_Z5579EC29, SparseTable, SparseTable_Create_Z2192E64B, SparseTable__TryGetValue_11FD62A8, SparseTable__TryGetValueDefault_5BAE6133, SparseTable_GetEmptyComments_651559CC } from "./SparseTable.js";
+import { Protocol_create_Z414665E7, Protocol_make } from "../../Core/Process/Protocol.js";
+import { defaultArg, map } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
+import { URIModule_fromString } from "../../Core/URI.js";
+import { SparseTable_ToRows_759CAFC1, SparseTable_FromRows_Z5579EC29, SparseTable, SparseTable_Create_Z2192E64B, SparseTable__TryGetValue_11FD62A8, SparseTable__TryGetValueDefault_5BAE6133, SparseTable_GetEmptyComments_3ECCA699 } from "./SparseTable.js";
 import { Comment_toString, Comment_fromString } from "./Comment.js";
-import { addToDict } from "../../../fable_modules/fable-library-js.4.13.0/MapUtil.js";
-import { List_distinct } from "../../../fable_modules/fable-library-js.4.13.0/Seq2.js";
-import { stringHash } from "../../../fable_modules/fable-library-js.4.13.0/Util.js";
+import { addToDict } from "../../fable_modules/fable-library-js.4.16.0/MapUtil.js";
+import { List_distinct } from "../../fable_modules/fable-library-js.4.16.0/Seq2.js";
+import { stringHash } from "../../fable_modules/fable-library-js.4.16.0/Util.js";
 
 export const nameLabel = "Name";
 
@@ -41,15 +41,15 @@ export const componentsTypeTermSourceREFLabel = "Components Type Term Source REF
 export const labels = ofArray([nameLabel, protocolTypeLabel, typeTermAccessionNumberLabel, typeTermSourceREFLabel, descriptionLabel, uriLabel, versionLabel, parametersNameLabel, parametersTermAccessionNumberLabel, parametersTermSourceREFLabel, componentsNameLabel, componentsTypeLabel, componentsTypeTermAccessionNumberLabel, componentsTypeTermSourceREFLabel]);
 
 export function fromString(name, protocolType, typeTermAccessionNumber, typeTermSourceREF, description, uri, version, parametersName, parametersTermAccessionNumber, parametersTermSourceREF, componentsName, componentsType, componentsTypeTermAccessionNumber, componentsTypeTermSourceREF, comments) {
-    const protocolType_1 = OntologyAnnotation.fromString(protocolType, typeTermSourceREF, typeTermAccessionNumber);
-    const parameters = ofArray(ProtocolParameter_fromAggregatedStrings(";", parametersName, parametersTermSourceREF, parametersTermAccessionNumber));
+    const protocolType_1 = OntologyAnnotation.create(protocolType, typeTermSourceREF, typeTermAccessionNumber);
+    const parameters = ofSeq(ProtocolParameter_fromAggregatedStrings(";", parametersName, parametersTermSourceREF, parametersTermAccessionNumber));
     const components = Component_fromAggregatedStrings(";", componentsName, componentsType, componentsTypeTermSourceREF, componentsTypeTermAccessionNumber);
-    return Protocol_make(void 0, map(URIModule_fromString, name), Option_fromValueWithDefault(OntologyAnnotation.empty, protocolType_1), description, map(URIModule_fromString, uri), version, Option_fromValueWithDefault(empty(), parameters), Option_fromValueWithDefault(empty(), components), Option_fromValueWithDefault(empty(), comments));
+    return Protocol_make(void 0, map(URIModule_fromString, name), Option_fromValueWithDefault(new OntologyAnnotation(), protocolType_1), description, map(URIModule_fromString, uri), version, Option_fromValueWithDefault(empty(), parameters), Option_fromValueWithDefault(empty(), components), Option_fromValueWithDefault(empty(), comments));
 }
 
 export function fromSparseTable(matrix) {
     if ((matrix.ColumnCount === 0) && (length(matrix.CommentKeys) !== 0)) {
-        return singleton(Protocol_create_Z7DFD6E67(void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, ofArray(SparseTable_GetEmptyComments_651559CC(matrix))));
+        return singleton(Protocol_create_Z414665E7(void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, ofSeq(SparseTable_GetEmptyComments_3ECCA699(matrix))));
     }
     else {
         return initialize(matrix.ColumnCount, (i) => {
@@ -65,8 +65,8 @@ export function toSparseTable(protocols) {
     iterateIndexed((i, p) => {
         const i_1 = (i + 1) | 0;
         let pt_1;
-        const pt = defaultArg(p.ProtocolType, OntologyAnnotation.empty);
-        pt_1 = OntologyAnnotation.toString(pt, true);
+        const pt = defaultArg(p.ProtocolType, new OntologyAnnotation());
+        pt_1 = OntologyAnnotation.toStringObject(pt, true);
         const pAgg = ProtocolParameter_toAggregatedStrings(";", defaultArg(p.Parameters, empty()));
         const cAgg = Component_toAggregatedStrings(";", defaultArg(p.Components, empty()));
         addToDict(matrix.Matrix, [nameLabel, i_1], defaultArg(p.Name, ""));
@@ -107,10 +107,10 @@ export function fromRows(prefix, lineNumber, rows) {
 export function toRows(prefix, protocols) {
     const m = toSparseTable(protocols);
     if (prefix == null) {
-        return SparseTable_ToRows_6A3D4534(m);
+        return SparseTable_ToRows_759CAFC1(m);
     }
     else {
-        return SparseTable_ToRows_6A3D4534(m, prefix);
+        return SparseTable_ToRows_759CAFC1(m, prefix);
     }
 }
 

package/{ISA/ISA.Spreadsheet → Spreadsheet}/Metadata/Publication.js

@@ -1,14 +1,14 @@
-import { reverse, cons, iterateIndexed, empty, map as map_1, toArray, initialize, singleton, length, ofArray } from "../../../fable_modules/fable-library-js.4.13.0/List.js";
-import { OntologyAnnotation } from "../../ISA/JsonTypes/OntologyAnnotation.js";
-import { defaultArg, map } from "../../../fable_modules/fable-library-js.4.13.0/Option.js";
-import { URIModule_fromString } from "../../ISA/JsonTypes/URI.js";
-import { Option_fromValueWithDefault } from "./Conversions.js";
-import { Publication } from "../../ISA/JsonTypes/Publication.js";
-import { SparseTable_ToRows_6A3D4534, SparseTable_FromRows_Z5579EC29, SparseTable, SparseTable_Create_Z2192E64B, SparseTable__TryGetValue_11FD62A8, SparseTable__TryGetValueDefault_5BAE6133, SparseTable_GetEmptyComments_651559CC } from "./SparseTable.js";
+import { reverse, cons, iterateIndexed, empty, map as map_1, initialize, singleton, length, ofArray } from "../../fable_modules/fable-library-js.4.16.0/List.js";
+import { OntologyAnnotation } from "../../Core/OntologyAnnotation.js";
+import { defaultArg, map } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
+import { URIModule_fromString } from "../../Core/URI.js";
+import { ResizeArray_iter, Option_fromValueWithDefault } from "../../Core/Helper/Collections.js";
+import { Publication } from "../../Core/Publication.js";
+import { SparseTable_ToRows_759CAFC1, SparseTable_FromRows_Z5579EC29, SparseTable, SparseTable_Create_Z2192E64B, SparseTable__TryGetValue_11FD62A8, SparseTable__TryGetValueDefault_5BAE6133, SparseTable_GetEmptyComments_3ECCA699 } from "./SparseTable.js";
 import { Comment_toString, Comment_fromString } from "./Comment.js";
-import { addToDict } from "../../../fable_modules/fable-library-js.4.13.0/MapUtil.js";
-import { List_distinct } from "../../../fable_modules/fable-library-js.4.13.0/Seq2.js";
-import { stringHash } from "../../../fable_modules/fable-library-js.4.13.0/Util.js";
+import { addToDict } from "../../fable_modules/fable-library-js.4.16.0/MapUtil.js";
+import { List_distinct } from "../../fable_modules/fable-library-js.4.16.0/Seq2.js";
+import { stringHash } from "../../fable_modules/fable-library-js.4.16.0/Util.js";
 
 export const pubMedIDLabel = "PubMed ID";
 
@@ -27,21 +27,23 @@ export const statusTermSourceREFLabel = "Status Term Source REF";
 export const labels = ofArray([pubMedIDLabel, doiLabel, authorListLabel, titleLabel, statusLabel, statusTermAccessionNumberLabel, statusTermSourceREFLabel]);
 
 export function fromString(pubMedID, doi, author, title, status, statusTermSourceREF, statusTermAccessionNumber, comments) {
-    const status_1 = OntologyAnnotation.fromString(status, statusTermSourceREF, statusTermAccessionNumber);
+    const status_1 = new OntologyAnnotation(status, statusTermSourceREF, statusTermAccessionNumber);
     const pubMedID_1 = map(URIModule_fromString, pubMedID);
-    const status_2 = Option_fromValueWithDefault(OntologyAnnotation.empty, status_1);
-    const comments_1 = Option_fromValueWithDefault([], comments);
-    return Publication.make(pubMedID_1, doi, author, title, status_2, comments_1);
+    const status_2 = Option_fromValueWithDefault(new OntologyAnnotation(), status_1);
+    return Publication.make(pubMedID_1, doi, author, title, status_2, comments);
 }
 
 export function fromSparseTable(matrix) {
+    let returnVal;
     if ((matrix.ColumnCount === 0) && (length(matrix.CommentKeys) !== 0)) {
-        const comments = SparseTable_GetEmptyComments_651559CC(matrix);
-        return singleton(Publication.create(void 0, void 0, void 0, void 0, void 0, comments));
+        const comments = SparseTable_GetEmptyComments_3ECCA699(matrix);
+        return singleton((returnVal = Publication.create(), (returnVal.Comments = comments, returnVal)));
     }
     else {
         return initialize(matrix.ColumnCount, (i) => {
-            const comments_1 = toArray(map_1((k) => Comment_fromString(k, SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [k, i])), matrix.CommentKeys));
+            let comments_1;
+            const collection = map_1((k) => Comment_fromString(k, SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [k, i])), matrix.CommentKeys);
+            comments_1 = Array.from(collection);
             return fromString(SparseTable__TryGetValue_11FD62A8(matrix, [pubMedIDLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [doiLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [authorListLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [titleLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [statusLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [statusTermSourceREFLabel, i]), SparseTable__TryGetValue_11FD62A8(matrix, [statusTermAccessionNumberLabel, i]), comments_1);
         });
     }
@@ -53,8 +55,8 @@ export function toSparseTable(publications) {
     iterateIndexed((i, p) => {
         const i_1 = (i + 1) | 0;
         let s_1;
-        const s = defaultArg(p.Status, OntologyAnnotation.empty);
-        s_1 = OntologyAnnotation.toString(s, true);
+        const s = defaultArg(p.Status, new OntologyAnnotation());
+        s_1 = OntologyAnnotation.toStringObject(s, true);
         addToDict(matrix.Matrix, [pubMedIDLabel, i_1], defaultArg(p.PubMedID, ""));
         addToDict(matrix.Matrix, [doiLabel, i_1], defaultArg(p.DOI, ""));
         addToDict(matrix.Matrix, [authorListLabel, i_1], defaultArg(p.Authors, ""));
@@ -62,16 +64,12 @@ export function toSparseTable(publications) {
         addToDict(matrix.Matrix, [statusLabel, i_1], s_1.TermName);
         addToDict(matrix.Matrix, [statusTermAccessionNumberLabel, i_1], s_1.TermAccessionNumber);
         addToDict(matrix.Matrix, [statusTermSourceREFLabel, i_1], s_1.TermSourceREF);
-        const matchValue = p.Comments;
-        if (matchValue != null) {
-            const array = matchValue;
-            array.forEach((comment) => {
-                const patternInput = Comment_toString(comment);
-                const n = patternInput[0];
-                commentKeys = cons(n, commentKeys);
-                addToDict(matrix.Matrix, [n, i_1], patternInput[1]);
-            });
-        }
+        ResizeArray_iter((comment) => {
+            const patternInput = Comment_toString(comment);
+            const n = patternInput[0];
+            commentKeys = cons(n, commentKeys);
+            addToDict(matrix.Matrix, [n, i_1], patternInput[1]);
+        }, p.Comments);
     }, publications);
     return new SparseTable(matrix.Matrix, matrix.Keys, reverse(List_distinct(commentKeys, {
         Equals: (x, y) => (x === y),
@@ -87,10 +85,10 @@ export function fromRows(prefix, lineNumber, rows) {
 export function toRows(prefix, publications) {
     const m = toSparseTable(publications);
     if (prefix == null) {
-        return SparseTable_ToRows_6A3D4534(m);
+        return SparseTable_ToRows_759CAFC1(m);
     }
     else {
-        return SparseTable_ToRows_6A3D4534(m, prefix);
+        return SparseTable_ToRows_759CAFC1(m, prefix);
     }
 }
 

package/{ISA/ISA.Spreadsheet → Spreadsheet}/Metadata/SparseTable.js

@@ -1,22 +1,22 @@
-import { append as append_1, delay, tryItem, length as length_1, isEmpty, iterate, fold, tryPick, maxBy, initialize, choose, map, indexed } from "../../../fable_modules/fable-library-js.4.13.0/Seq.js";
-import { defaultArg, map as map_1 } from "../../../fable_modules/fable-library-js.4.13.0/Option.js";
-import { tryFind, ofSeq } from "../../../fable_modules/fable-library-js.4.13.0/Map.js";
-import { arrayHash, equalArrays, equals, comparePrimitives } from "../../../fable_modules/fable-library-js.4.13.0/Util.js";
-import { RowBuilder_get_Empty, RowBuilder__Combine_19F30600, RowBuilder_$ctor } from "../../../fable_modules/FsSpreadsheet.5.1.3/DSL/RowBuilder.fs.js";
-import { CellBuilder_$ctor, CellBuilder__AsCellElement_6F87C2ED } from "../../../fable_modules/FsSpreadsheet.5.1.3/DSL/CellBuilder.fs.js";
-import { Messages_format, SheetEntity$1_some_2B595 } from "../../../fable_modules/FsSpreadsheet.5.1.3/DSL/Types.fs.js";
-import { DataType } from "../../../fable_modules/FsSpreadsheet.5.1.3/Cells/FsCell.fs.js";
-import { map as map_2, toArray, initialize as initialize_1, exists, find, cons, append, empty, singleton } from "../../../fable_modules/fable-library-js.4.13.0/List.js";
-import { ColumnIndex, RowElement } from "../../../fable_modules/FsSpreadsheet.5.1.3/DSL/Types.fs.js";
-import { FsRangeAddress_$ctor_7E77A4A0 } from "../../../fable_modules/FsSpreadsheet.5.1.3/Ranges/FsRangeAddress.fs.js";
-import { FsAddress_$ctor_Z37302880 } from "../../../fable_modules/FsSpreadsheet.5.1.3/FsAddress.fs.js";
-import { Record } from "../../../fable_modules/fable-library-js.4.13.0/Types.js";
-import { record_type, list_type, class_type, tuple_type, int32_type, string_type } from "../../../fable_modules/fable-library-js.4.13.0/Reflection.js";
+import { append as append_1, delay, tryItem, length as length_1, isEmpty, iterate, fold, tryPick, maxBy, initialize, choose, map, indexed } from "../../fable_modules/fable-library-js.4.16.0/Seq.js";
+import { defaultArg, map as map_1 } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
+import { tryFind, ofSeq } from "../../fable_modules/fable-library-js.4.16.0/Map.js";
+import { arrayHash, equalArrays, equals, comparePrimitives } from "../../fable_modules/fable-library-js.4.16.0/Util.js";
+import { RowBuilder_get_Empty, RowBuilder__Combine_19F30600, RowBuilder_$ctor } from "../../fable_modules/FsSpreadsheet.5.1.3/DSL/RowBuilder.fs.js";
+import { CellBuilder_$ctor, CellBuilder__AsCellElement_6F87C2ED } from "../../fable_modules/FsSpreadsheet.5.1.3/DSL/CellBuilder.fs.js";
+import { Messages_format, SheetEntity$1_some_2B595 } from "../../fable_modules/FsSpreadsheet.5.1.3/DSL/Types.fs.js";
+import { DataType } from "../../fable_modules/FsSpreadsheet.5.1.3/Cells/FsCell.fs.js";
+import { map as map_2, initialize as initialize_1, exists, find, cons, append, empty, singleton } from "../../fable_modules/fable-library-js.4.16.0/List.js";
+import { ColumnIndex, RowElement } from "../../fable_modules/FsSpreadsheet.5.1.3/DSL/Types.fs.js";
+import { FsRangeAddress_$ctor_7E77A4A0 } from "../../fable_modules/FsSpreadsheet.5.1.3/Ranges/FsRangeAddress.fs.js";
+import { FsAddress_$ctor_Z37302880 } from "../../fable_modules/FsSpreadsheet.5.1.3/FsAddress.fs.js";
+import { Record } from "../../fable_modules/fable-library-js.4.16.0/Types.js";
+import { record_type, list_type, class_type, tuple_type, int32_type, string_type } from "../../fable_modules/fable-library-js.4.16.0/Reflection.js";
 import { Seq_trySkip, Dictionary_tryGetValue } from "../CollectionAux.js";
-import { addToDict, getItemFromDict } from "../../../fable_modules/fable-library-js.4.13.0/MapUtil.js";
-import { Dictionary } from "../../../fable_modules/fable-library-js.4.13.0/MutableMap.js";
-import { printf, toFail } from "../../../fable_modules/fable-library-js.4.13.0/String.js";
-import { Comment$, Remark } from "../../ISA/JsonTypes/Comment.js";
+import { addToDict, getItemFromDict } from "../../fable_modules/fable-library-js.4.16.0/MapUtil.js";
+import { Dictionary } from "../../fable_modules/fable-library-js.4.16.0/MutableMap.js";
+import { printf, toFail } from "../../fable_modules/fable-library-js.4.16.0/String.js";
+import { Comment$, Remark } from "../../Core/Comment.js";
 import { Comment_wrapCommentKey, Comment_$007CComment$007C_$007C, Remark_$007CRemark$007C_$007C } from "./Comment.js";
 
 export function SparseRowModule_fromValues(v) {
@@ -293,7 +293,7 @@ export class SparseTable extends Record {
 }
 
 export function SparseTable_$reflection() {
-    return record_type("ARCtrl.ISA.Spreadsheet.SparseTable", [], SparseTable, () => [["Matrix", class_type("System.Collections.Generic.Dictionary`2", [tuple_type(string_type, int32_type), string_type])], ["Keys", list_type(string_type)], ["CommentKeys", list_type(string_type)], ["ColumnCount", int32_type]]);
+    return record_type("ARCtrl.Spreadsheet.SparseTable", [], SparseTable, () => [["Matrix", class_type("System.Collections.Generic.Dictionary`2", [tuple_type(string_type, int32_type), string_type])], ["Keys", list_type(string_type)], ["CommentKeys", list_type(string_type)], ["ColumnCount", int32_type]]);
 }
 
 export function SparseTable__TryGetValue_11FD62A8(this$, key) {
@@ -447,12 +447,13 @@ export function SparseTable_FromRows_Z5579EC29(en, labels, lineNumber, prefix) {
     }
 }
 
-export function SparseTable_ToRows_6A3D4534(matrix, prefix) {
+export function SparseTable_ToRows_759CAFC1(matrix, prefix) {
     const prefix_1 = (prefix == null) ? "" : (prefix + " ");
     return delay(() => append_1(map((key) => SparseRowModule_fromValues(cons(prefix_1 + key, initialize_1(matrix.ColumnCount - 1, (i) => SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [key, i + 1])))), matrix.Keys), delay(() => map((key_1) => SparseRowModule_fromValues(cons(Comment_wrapCommentKey(key_1), initialize_1(matrix.ColumnCount - 1, (i_1) => SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [key_1, i_1 + 1])))), matrix.CommentKeys))));
 }
 
-export function SparseTable_GetEmptyComments_651559CC(matrix) {
-    return toArray(map_2((key) => Comment$.create(void 0, key), matrix.CommentKeys));
+export function SparseTable_GetEmptyComments_3ECCA699(matrix) {
+    const collection = map_2((key) => Comment$.create(key), matrix.CommentKeys);
+    return Array.from(collection);
 }