@graphty/graph-io 0.3.28 → 0.3.29
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/chunks/{choose-DrXtu_96.js → choose-DT5da6OC.js} +2 -2
- package/dist/chunks/{choose-DrXtu_96.js.map → choose-DT5da6OC.js.map} +1 -1
- package/dist/chunks/{constants-ikG85dT8.js → constants-DowRD9ai.js} +2 -2
- package/dist/chunks/{constants-ikG85dT8.js.map → constants-DowRD9ai.js.map} +1 -1
- package/dist/chunks/{escape-D1HPTUrP.js → escape-DQC5HWqF.js} +2 -2
- package/dist/chunks/{escape-D1HPTUrP.js.map → escape-DQC5HWqF.js.map} +1 -1
- package/dist/chunks/{export-CHd4tQE2.js → export-CVi12U7J.js} +81 -60
- package/dist/chunks/{export-CHd4tQE2.js.map → export-CVi12U7J.js.map} +1 -1
- package/dist/chunks/{exporter-D23CKNqF.js → exporter-C3Pa2PSd.js} +5 -5
- package/dist/chunks/{exporter-D23CKNqF.js.map → exporter-C3Pa2PSd.js.map} +1 -1
- package/dist/chunks/{exporter-DfWTgrti.js → exporter-CgsO2nSl.js} +4 -4
- package/dist/chunks/{exporter-DfWTgrti.js.map → exporter-CgsO2nSl.js.map} +1 -1
- package/dist/chunks/{exporter-Cl021ZIE.js → exporter-Cy_1da4c.js} +4 -4
- package/dist/chunks/{exporter-Cl021ZIE.js.map → exporter-Cy_1da4c.js.map} +1 -1
- package/dist/chunks/{exporter-DhtW6FxK.js → exporter-JubAlNWi.js} +34 -34
- package/dist/chunks/exporter-JubAlNWi.js.map +1 -0
- package/dist/chunks/{importer-CIAzt-wo.js → importer-BA_hZKo7.js} +4 -4
- package/dist/chunks/{importer-CIAzt-wo.js.map → importer-BA_hZKo7.js.map} +1 -1
- package/dist/chunks/{importer-BZB7iP9r.js → importer-CDXlxXlS.js} +5 -5
- package/dist/chunks/{importer-BZB7iP9r.js.map → importer-CDXlxXlS.js.map} +1 -1
- package/dist/chunks/{importer-BVRE--Un.js → importer-DLz2Vb4q.js} +3 -3
- package/dist/chunks/{importer-BVRE--Un.js.map → importer-DLz2Vb4q.js.map} +1 -1
- package/dist/chunks/{importer-B2W_58pz.js → importer-DVxzzibh.js} +4 -4
- package/dist/chunks/{importer-B2W_58pz.js.map → importer-DVxzzibh.js.map} +1 -1
- package/dist/chunks/{importer-BSALvkui.js → importer-Dej72hIF.js} +6 -6
- package/dist/chunks/{importer-BSALvkui.js.map → importer-Dej72hIF.js.map} +1 -1
- package/dist/chunks/{importer-z_FL4VMb.js → importer-lLH9gQF_.js} +5 -5
- package/dist/chunks/{importer-z_FL4VMb.js.map → importer-lLH9gQF_.js.map} +1 -1
- package/dist/chunks/{importer-DpEW5zeG.js → importer-q-R-Q98w.js} +4 -4
- package/dist/chunks/{importer-DpEW5zeG.js.map → importer-q-R-Q98w.js.map} +1 -1
- package/dist/chunks/{json-elements-BAmNBZok.js → json-elements-1IUzkRNy.js} +3 -3
- package/dist/chunks/{json-elements-BAmNBZok.js.map → json-elements-1IUzkRNy.js.map} +1 -1
- package/dist/chunks/{ontology-export-Bab4eUA8.js → ontology-export-b0GLNIj-.js} +2 -2
- package/dist/chunks/{ontology-export-Bab4eUA8.js.map → ontology-export-b0GLNIj-.js.map} +1 -1
- package/dist/chunks/{records-CdlvL4RO.js → records-CdyqwXeY.js} +2 -2
- package/dist/chunks/{records-CdlvL4RO.js.map → records-CdyqwXeY.js.map} +1 -1
- package/dist/chunks/{text-DzXjAiTl.js → text-CDgjbkLC.js} +2 -2
- package/dist/chunks/{text-DzXjAiTl.js.map → text-CDgjbkLC.js.map} +1 -1
- package/dist/csv.js +22 -15
- package/dist/csv.js.map +1 -1
- package/dist/cx.js +1 -1
- package/dist/cx2.js +2 -2
- package/dist/cys.js +1 -1
- package/dist/dot.js +1 -1
- package/dist/gexf.js +2 -2
- package/dist/gml.js +3 -3
- package/dist/graph-io.js +26 -26
- package/dist/graphml.js +2 -2
- package/dist/json.js +1 -1
- package/dist/neo4j.js +3 -3
- package/dist/obo.js +1 -1
- package/dist/pajek.js +1 -1
- package/dist/src/common/export.d.ts +6 -0
- package/dist/src/common/export.d.ts.map +1 -1
- package/dist/src/common/export.js +62 -28
- package/dist/src/common/export.js.map +1 -1
- package/dist/src/formats/csv/exporter.d.ts.map +1 -1
- package/dist/src/formats/csv/exporter.js +18 -7
- package/dist/src/formats/csv/exporter.js.map +1 -1
- package/dist/src/formats/obo/syntax.d.ts +4 -0
- package/dist/src/formats/obo/syntax.d.ts.map +1 -1
- package/dist/src/formats/obo/syntax.js +35 -31
- package/dist/src/formats/obo/syntax.js.map +1 -1
- package/dist/src/types.d.ts +6 -0
- package/dist/src/types.d.ts.map +1 -1
- package/dist/src/types.js.map +1 -1
- package/dist/xgmml.js +2 -2
- package/package.json +1 -1
- package/src/common/export.ts +105 -62
- package/src/formats/csv/exporter.ts +19 -15
- package/src/formats/obo/syntax.ts +35 -31
- package/src/types.ts +6 -0
- package/dist/chunks/exporter-DhtW6FxK.js.map +0 -1
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1
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+
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OAAO,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC,CAAC,CAAC;IACjE,CAAC;CACJ,CAAC,CAAC"}
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@@ -6,6 +6,10 @@
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|
|
6
6
|
*
|
|
7
7
|
* Every function works on the RAW text (escapes still in place) and unescapes only the pieces it
|
|
8
8
|
* hands back, so an escaped quote, colon, comma, brace or `!` never ends a construct.
|
|
9
|
+
*
|
|
10
|
+
* The scanners read characters with charAt(), never `text[i]`: the importer's linear-time tests
|
|
11
|
+
* count the characters the import reads through the string methods, and an index read is
|
|
12
|
+
* invisible to them, so a quadratic scan written with it would pass unnoticed.
|
|
9
13
|
*/
|
|
10
14
|
/**
|
|
11
15
|
* Remove the OBO escapes: `\n` newline, `\t` tab, `\W` space, any other `\x` the character x; a
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"syntax.d.ts","sourceRoot":"","sources":["../../../../src/formats/obo/syntax.ts"],"names":[],"mappings":"AAAA
|
|
1
|
+
{"version":3,"file":"syntax.d.ts","sourceRoot":"","sources":["../../../../src/formats/obo/syntax.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAUH;;;;;;GAMG;AACH,wBAAgB,WAAW,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAkBhD;AAgBD;;;;;;GAMG;AACH,wBAAgB,cAAc,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,EAAE,CAkBrD;AAED;;;;;GAKG;AACH,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAE1D;AAED,2DAA2D;AAC3D,UAAU,QAAQ;IACd,sCAAsC;IACtC,QAAQ,CAAC,GAAG,EAAE,MAAM,CAAC;IACrB,gEAAgE;IAChE,QAAQ,CAAC,IAAI,EAAE,MAAM,CAAC;CACzB;AAED;;;;;GAKG;AACH,wBAAgB,aAAa,CAAC,IAAI,EAAE,MAAM,GAAG,QAAQ,GAAG,IAAI,CAW3D;AAED;;;;;;;;;GASG;AACH,wBAAgB,YAAY,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAgBjD;AAED;;;GAGG;AACH,MAAM,MAAM,UAAU,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC,CAAC;AAE3D,4DAA4D;AAC5D,UAAU,cAAc;IACpB,iDAAiD;IACjD,QAAQ,CAAC,KAAK,EAAE,MAAM,CAAC;IACvB,uDAAuD;IACvD,QAAQ,CAAC,UAAU,EAAE,UAAU,GAAG,IAAI,CAAC;IACvC,iFAAiF;IACjF,QAAQ,CAAC,QAAQ,EAAE,MAAM,GAAG,IAAI,CAAC;CACpC;AAED;;;;;;;;GAQG;AACH,wBAAgB,eAAe,CAAC,KAAK,EAAE,MAAM,GAAG,cAAc,CA8B7D;AA8BD;;;;;;GAMG;AACH,wBAAgB,aAAa,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAiBnD;AAyBD;;;;;;;GAOG;AACH,wBAAgB,eAAe,CAAC,KAAK,EAAE,MAAM,GAAG,UAAU,GAAG,IAAI,CA4ChE;AAmBD;;;GAGG;AACH,MAAM,WAAW,KAAK;IAClB,wDAAwD;IACxD,QAAQ,CAAC,IAAI,EAAE,MAAM,GAAG,QAAQ,GAAG,MAAM,CAAC;IAC1C,qGAAqG;IACrG,QAAQ,CAAC,IAAI,EAAE,MAAM,CAAC;IACtB,8FAA8F;IAC9F,QAAQ,CAAC,YAAY,EAAE,OAAO,CAAC;CAClC;AAED;;;;;;GAMG;AACH,wBAAgB,QAAQ,CAAC,KAAK,EAAE,MAAM,GAAG,KAAK,EAAE,CA6C/C;AAuBD;;;GAGG;AACH,MAAM,WAAW,IAAI;IACjB,uFAAuF;IACvF,QAAQ,CAAC,EAAE,EAAE,MAAM,CAAC;IACpB,gCAAgC;IAChC,QAAQ,CAAC,WAAW,EAAE,MAAM,GAAG,IAAI,CAAC;IACpC,4DAA4D;IAC5D,QAAQ,CAAC,UAAU,EAAE,UAAU,GAAG,IAAI,CAAC;IACvC,6EAA6E;IAC7E,QAAQ,CAAC,YAAY,EAAE,OAAO,CAAC;CAClC;AAED;;;;;;GAMG;AACH,wBAAgB,SAAS,CAAC,GAAG,EAAE,MAAM,GAAG,IAAI,GAAG,IAAI,CAuBlD;AAED;;;;;;GAMG;AACH,wBAAgB,aAAa,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI,EAAE,CA4BnD;AAED;;;;;;;GAOG;AACH,wBAAgB,aAAa,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAiBpD;AAOD;;;;;;GAMG;AACH,wBAAgB,UAAU,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAEhD;AAED;;;;;;;GAOG;AACH,wBAAgB,eAAe,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAWpD;AAED;;;;;;;;GAQG;AACH,wBAAgB,cAAc,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAEnD;AAED;;;;;;;;GAQG;AACH,wBAAgB,SAAS,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAE/C;AAED;;;GAGG;AACH,eAAO,MAAM,WAAW,QAAmB,CAAC;AAE5C;;;;;;GAMG;AACH,wBAAgB,aAAa,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAGlD;AAED;;;;;;;GAOG;AACH,wBAAgB,eAAe,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAErD;AAED;;;;;GAKG;AACH,wBAAgB,cAAc,CAAC,KAAK,EAAE,SAAS,CAAC,SAAS,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,EAAE,GAAG,MAAM,CAMpF"}
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@@ -6,6 +6,10 @@
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6
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*
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* Every function works on the RAW text (escapes still in place) and unescapes only the pieces it
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* hands back, so an escaped quote, colon, comma, brace or `!` never ends a construct.
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*
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* The scanners read characters with charAt(), never `text[i]`: the importer's linear-time tests
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* count the characters the import reads through the string methods, and an index read is
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* invisible to them, so a quadratic scan written with it would pass unnoticed.
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*/
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/** The OBO escapes with a meaning of their own; any other `\x` is `x` (the guides). */
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const ESCAPES = Object.freeze({
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@@ -27,14 +31,14 @@ export function unescapeObo(text) {
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}
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const ch = text.charAt(i);
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const next = text.charAt(i);
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out += ESCAPES[next] ?? next;
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}
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*/
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function isEscaped(text, index) {
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for (let i = index - 1; i >= 0 && text
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for (let i = index - 1; i >= 0 && text.charAt(i) === "\\"; i--) {
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run++;
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return run % 2 === 1;
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const pieces = [];
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let quoted = false;
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const ch = line
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for (let i = 0; i < line.length; i += line.charAt(i) === "\\" ? 2 : 1) {
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const ch = line.charAt(i);
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*/
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export function splitTagValue(line) {
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if (line
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if (line.charAt(i) === ":") {
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return { tag: unescapeObo(line.slice(0, i).trim()), rest: line.slice(i + 1).trimStart() };
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export function stripComment(rest) {
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const ch = rest.charAt(i);
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const atStart = i === 0 || rest
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while (end > 0 && value
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while (end > 0 && value.charAt(end - 1) === "}" && !isEscaped(value, end - 1)) {
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while (end > 0 && /\s/.test(value
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while (end > 0 && /\s/.test(value.charAt(end - 1))) {
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}
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const ch = value.charAt(i);
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if (ch === "\\") {
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continue;
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@@ -214,8 +218,8 @@ function braceBlocks(value) {
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export function unclosedBlock(value) {
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|
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let open = -1;
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|
-
for (let i = 0; i < value.length; i += value
|
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|
-
const ch = value
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+
for (let i = 0; i < value.length; i += value.charAt(i) === "\\" ? 2 : 1) {
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|
+
const ch = value.charAt(i);
|
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|
if (ch === "\\") {
|
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224
|
continue;
|
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|
}
|
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@@ -268,7 +272,7 @@ export function parseQualifiers(inner) {
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|
const n = inner.length;
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|
let any = false;
|
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|
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|
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while (i < n && (inner
|
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|
+
while (i < n && (inner.charAt(i) === " " || inner.charAt(i) === "\t" || inner.charAt(i) === ",")) {
|
|
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|
i++;
|
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277
|
}
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278
|
if (i >= n) {
|
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@@ -283,11 +287,11 @@ export function parseQualifiers(inner) {
|
|
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283
287
|
return null;
|
|
284
288
|
}
|
|
285
289
|
i = eq + 1;
|
|
286
|
-
while (i < n && (inner
|
|
290
|
+
while (i < n && (inner.charAt(i) === " " || inner.charAt(i) === "\t")) {
|
|
287
291
|
i++;
|
|
288
292
|
}
|
|
289
293
|
let value;
|
|
290
|
-
if (inner
|
|
294
|
+
if (inner.charAt(i) === '"') {
|
|
291
295
|
const end = closingQuote(inner, i + 1);
|
|
292
296
|
if (end < 0) {
|
|
293
297
|
return null;
|
|
@@ -297,8 +301,8 @@ export function parseQualifiers(inner) {
|
|
|
297
301
|
}
|
|
298
302
|
else {
|
|
299
303
|
let end = i;
|
|
300
|
-
while (end < n && inner
|
|
301
|
-
end += inner
|
|
304
|
+
while (end < n && inner.charAt(end) !== ",") {
|
|
305
|
+
end += inner.charAt(end) === "\\" ? 2 : 1;
|
|
302
306
|
}
|
|
303
307
|
value = unescapeObo(inner.slice(i, end).trim());
|
|
304
308
|
i = end;
|
|
@@ -316,10 +320,10 @@ export function parseQualifiers(inner) {
|
|
|
316
320
|
*/
|
|
317
321
|
function closingQuote(text, from) {
|
|
318
322
|
for (let i = from; i < text.length; i++) {
|
|
319
|
-
if (text
|
|
323
|
+
if (text.charAt(i) === "\\") {
|
|
320
324
|
i++;
|
|
321
325
|
}
|
|
322
|
-
else if (text
|
|
326
|
+
else if (text.charAt(i) === '"') {
|
|
323
327
|
return i;
|
|
324
328
|
}
|
|
325
329
|
}
|
|
@@ -337,7 +341,7 @@ export function tokenize(value) {
|
|
|
337
341
|
const n = value.length;
|
|
338
342
|
let i = 0;
|
|
339
343
|
while (i < n) {
|
|
340
|
-
const ch = value
|
|
344
|
+
const ch = value.charAt(i);
|
|
341
345
|
if (ch === " " || ch === "\t") {
|
|
342
346
|
i++;
|
|
343
347
|
continue;
|
|
@@ -348,8 +352,8 @@ export function tokenize(value) {
|
|
|
348
352
|
// a 1.4 language tag glued to the closing quote ("chat"@fr) is kept with the text, as an
|
|
349
353
|
// unquoted chat@fr is (research-obo.md 4.1: no language is split out)
|
|
350
354
|
let after = stop + 1;
|
|
351
|
-
if (end >= 0 && value
|
|
352
|
-
while (after < n && value
|
|
355
|
+
if (end >= 0 && value.charAt(after) === "@") {
|
|
356
|
+
while (after < n && value.charAt(after) !== " " && value.charAt(after) !== "\t") {
|
|
353
357
|
after++;
|
|
354
358
|
}
|
|
355
359
|
}
|
|
@@ -370,8 +374,8 @@ export function tokenize(value) {
|
|
|
370
374
|
continue;
|
|
371
375
|
}
|
|
372
376
|
let end = i;
|
|
373
|
-
while (end < n && value
|
|
374
|
-
end += value
|
|
377
|
+
while (end < n && value.charAt(end) !== " " && value.charAt(end) !== "\t") {
|
|
378
|
+
end += value.charAt(end) === "\\" ? 2 : 1;
|
|
375
379
|
}
|
|
376
380
|
tokens.push({ kind: "word", text: unescapeObo(value.slice(i, Math.min(end, n))), unterminated: false });
|
|
377
381
|
i = end;
|
|
@@ -387,7 +391,7 @@ export function tokenize(value) {
|
|
|
387
391
|
function closingBracket(text, from) {
|
|
388
392
|
let quoted = false;
|
|
389
393
|
for (let i = from; i < text.length; i++) {
|
|
390
|
-
const ch = text
|
|
394
|
+
const ch = text.charAt(i);
|
|
391
395
|
if (ch === "\\") {
|
|
392
396
|
i++;
|
|
393
397
|
}
|
|
@@ -411,10 +415,10 @@ export function parseXref(raw) {
|
|
|
411
415
|
const { value, qualifiers } = splitQualifiers(raw.trim());
|
|
412
416
|
let quote = -1;
|
|
413
417
|
for (let i = 0; i < value.length; i++) {
|
|
414
|
-
if (value
|
|
418
|
+
if (value.charAt(i) === "\\") {
|
|
415
419
|
i++;
|
|
416
420
|
}
|
|
417
|
-
else if (value
|
|
421
|
+
else if (value.charAt(i) === '"') {
|
|
418
422
|
quote = i;
|
|
419
423
|
break;
|
|
420
424
|
}
|
|
@@ -451,7 +455,7 @@ export function parseXrefList(inner) {
|
|
|
451
455
|
}
|
|
452
456
|
};
|
|
453
457
|
for (let i = 0; i < inner.length; i++) {
|
|
454
|
-
const ch = inner
|
|
458
|
+
const ch = inner.charAt(i);
|
|
455
459
|
if (ch === "\\") {
|
|
456
460
|
i++;
|
|
457
461
|
}
|
|
@@ -484,7 +488,7 @@ export function hasStrayBrace(value) {
|
|
|
484
488
|
let quoted = false;
|
|
485
489
|
let listed = false;
|
|
486
490
|
for (let i = 0; i < value.length; i++) {
|
|
487
|
-
const ch = value
|
|
491
|
+
const ch = value.charAt(i);
|
|
488
492
|
if (ch === "\\") {
|
|
489
493
|
i++;
|
|
490
494
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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|
package/dist/src/types.d.ts
CHANGED
|
@@ -349,6 +349,12 @@ export interface LossNote {
|
|
|
349
349
|
readonly column: string | null;
|
|
350
350
|
/** How many nodes, edges or values are affected, or null when not counted. */
|
|
351
351
|
readonly count: number | null;
|
|
352
|
+
/**
|
|
353
|
+
* Every column the note is about, when it is about several and `column` is null: the graph
|
|
354
|
+
* attributes a format has no place for, or the node columns a CSV edge table leaves for the node
|
|
355
|
+
* table. Absent on a note about one column or none.
|
|
356
|
+
*/
|
|
357
|
+
readonly columns?: readonly string[];
|
|
352
358
|
}
|
|
353
359
|
/**
|
|
354
360
|
* The options every exporter accepts next to its format-specific ones.
|
package/dist/src/types.d.ts.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
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|
package/dist/src/types.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
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|
package/dist/xgmml.js
CHANGED
|
@@ -1,5 +1,5 @@
|
|
|
1
|
-
import { X, a, x } from "./chunks/importer-
|
|
2
|
-
import { x as x2 } from "./chunks/exporter-
|
|
1
|
+
import { X, a, x } from "./chunks/importer-DVxzzibh.js";
|
|
2
|
+
import { x as x2 } from "./chunks/exporter-CgsO2nSl.js";
|
|
3
3
|
export {
|
|
4
4
|
X as XGMML_ISSUE,
|
|
5
5
|
a as XGMML_LOSS,
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@graphty/graph-io",
|
|
3
|
-
"version": "0.3.
|
|
3
|
+
"version": "0.3.29",
|
|
4
4
|
"description": "Read and write 13 graph file formats (JSON, GraphML, GEXF, CSV, GML, DOT, Pajek, Neo4j CSV, XGMML, CX2, CX, OBO, Cytoscape sessions) as @graphty/graph-format snapshots",
|
|
5
5
|
"author": "Adam Powers <apowers@ato.ms>",
|
|
6
6
|
"type": "module",
|