@graphty/graph-io 0.3.27 → 0.3.29

package/src/formats/gml/exporter.ts

@@ -305,6 +305,25 @@ function versionText(text: string): string {
     return NUMBER_TEXT.test(text) ? text : quoteGmlString(text);
 }
 
+/**
+ * A node or edge table's label role column, which is written under "label" (the key the importer
+ * gives the role back to): the key is marked used so a plain column of that name cannot have it.
+ * @param columns - the written columns
+ * @param label - the table name
+ * @param used - the keys already taken, gaining "label" when there is a label role column
+ * @returns the label role column, or undefined
+ */
+function labelRoleColumn(columns: readonly Column[], label: string, used: Set<string>): Column | undefined {
+    if (label !== "node" && label !== "edge") {
+        return undefined;
+    }
+    const column = columns.find((c) => c.meta.role === "label");
+    if (column !== undefined) {
+        used.add("label");
+    }
+    return column;
+}
+
 /**
  * Select the written columns of a table and assign their keys, recording invalid and reserved
  * keys as notes (or rewriting them under mangle).
@@ -326,14 +345,13 @@ function selectColumns(
 ): WrittenColumn[] {
     const used = new Set<string>(reserved);
     const out: WrittenColumn[] = [];
-    for (const column of table) {
-        if (!isWritten(column) || !filter(column)) {
-            continue;
-        }
-        const preferred = preferredKey(column.meta);
+    const columns = [...table].filter((c) => isWritten(c) && filter(c));
+    const labelRole = labelRoleColumn(columns, label, used);
+    for (const column of columns) {
+        const preferred = column === labelRole ? "label" : preferredKey(column.meta);
         let key = preferred;
         const valid = isGmlKey(preferred);
-        const taken = used.has(preferred);
+        const taken = column !== labelRole && used.has(preferred);
         if (!valid || taken) {
             const code = valid ? RESERVED_KEY_CODE : INVALID_KEY_CODE;
             let why = "is not a GML key";

package/src/formats/obo/syntax.ts

@@ -6,6 +6,10 @@
  *
  * Every function works on the RAW text (escapes still in place) and unescapes only the pieces it
  * hands back, so an escaped quote, colon, comma, brace or `!` never ends a construct.
+ *
+ * The scanners read characters with charAt(), never `text[i]`: the importer's linear-time tests
+ * count the characters the import reads through the string methods, and an index read is
+ * invisible to them, so a quadratic scan written with it would pass unnoticed.
  */
 
 /** The OBO escapes with a meaning of their own; any other `\x` is `x` (the guides). */
@@ -29,14 +33,14 @@ export function unescapeObo(text: string): string {
     }
     let out = "";
     for (let i = 0; i < text.length; i++) {
-        const ch = text[i];
+        const ch = text.charAt(i);
         if (ch !== "\\") {
             out += ch;
             continue;
         }
         i++;
         if (i < text.length) {
-            const next = text[i];
+            const next = text.charAt(i);
             out += ESCAPES[next] ?? next;
         }
     }
@@ -51,7 +55,7 @@ export function unescapeObo(text: string): string {
  */
 function isEscaped(text: string, index: number): boolean {
     let run = 0;
-    for (let i = index - 1; i >= 0 && text[i] === "\\"; i--) {
+    for (let i = index - 1; i >= 0 && text.charAt(i) === "\\"; i--) {
         run++;
     }
     return run % 2 === 1;
@@ -71,8 +75,8 @@ export function splitFormFeeds(line: string): string[] {
     const pieces: string[] = [];
     let quoted = false;
     let start = 0;
-    for (let i = 0; i < line.length; i += line[i] === "\\" ? 2 : 1) {
-        const ch = line[i];
+    for (let i = 0; i < line.length; i += line.charAt(i) === "\\" ? 2 : 1) {
+        const ch = line.charAt(i);
         if (ch === '"') {
             quoted = !quoted;
         } else if (ch === "\f" && !quoted) {
@@ -110,11 +114,11 @@ interface TagValue {
  */
 export function splitTagValue(line: string): TagValue | null {
     for (let i = 0; i < line.length; i++) {
-        if (line[i] === "\\") {
+        if (line.charAt(i) === "\\") {
             i++;
             continue;
         }
-        if (line[i] === ":") {
+        if (line.charAt(i) === ":") {
             return { tag: unescapeObo(line.slice(0, i).trim()), rest: line.slice(i + 1).trimStart() };
         }
     }
@@ -134,12 +138,12 @@ export function splitTagValue(line: string): TagValue | null {
 export function stripComment(rest: string): string {
     let quoted = false;
     for (let i = 0; i < rest.length; i++) {
-        const ch = rest[i];
+        const ch = rest.charAt(i);
         if (ch === "\\") {
             i++;
             continue;
         }
-        const atStart = i === 0 || rest[i - 1] === " " || rest[i - 1] === "\t";
+        const atStart = i === 0 || rest.charAt(i - 1) === " " || rest.charAt(i - 1) === "\t";
         if (ch === '"' && (quoted || atStart)) {
             quoted = !quoted;
         } else if (ch === "!" && !quoted && atStart) {
@@ -183,7 +187,7 @@ export function splitQualifiers(value: string): QualifiedValue {
     const parsed: Qualifiers[] = [];
     let end = value.length;
     let badBlock: string | null = null;
-    while (end > 0 && value[end - 1] === "}" && !isEscaped(value, end - 1)) {
+    while (end > 0 && value.charAt(end - 1) === "}" && !isEscaped(value, end - 1)) {
         const open = blocks.get(end - 1) ?? -1;
         const block = open < 0 ? null : parseQualifiers(value.slice(open + 1, end - 1));
         if (block === null) {
@@ -192,7 +196,7 @@ export function splitQualifiers(value: string): QualifiedValue {
         }
         parsed.push(block);
         end = open;
-        while (end > 0 && /\s/.test(value[end - 1])) {
+        while (end > 0 && /\s/.test(value.charAt(end - 1))) {
             end--;
         }
     }
@@ -217,7 +221,7 @@ function braceBlocks(value: string): Map<number, number> {
     let quoted = false;
     let open = -1;
     for (let i = 0; i < value.length; i++) {
-        const ch = value[i];
+        const ch = value.charAt(i);
         if (ch === "\\") {
             i++;
             continue;
@@ -244,8 +248,8 @@ function braceBlocks(value: string): Map<number, number> {
 export function unclosedBlock(value: string): number {
     let quoted = false;
     let open = -1;
-    for (let i = 0; i < value.length; i += value[i] === "\\" ? 2 : 1) {
-        const ch = value[i];
+    for (let i = 0; i < value.length; i += value.charAt(i) === "\\" ? 2 : 1) {
+        const ch = value.charAt(i);
         if (ch === "\\") {
             continue;
         }
@@ -297,7 +301,7 @@ export function parseQualifiers(inner: string): Qualifiers | null {
     const n = inner.length;
     let any = false;
     while (i < n) {
-        while (i < n && (inner[i] === " " || inner[i] === "\t" || inner[i] === ",")) {
+        while (i < n && (inner.charAt(i) === " " || inner.charAt(i) === "\t" || inner.charAt(i) === ",")) {
             i++;
         }
         if (i >= n) {
@@ -312,11 +316,11 @@ export function parseQualifiers(inner: string): Qualifiers | null {
             return null;
         }
         i = eq + 1;
-        while (i < n && (inner[i] === " " || inner[i] === "\t")) {
+        while (i < n && (inner.charAt(i) === " " || inner.charAt(i) === "\t")) {
             i++;
         }
         let value: string;
-        if (inner[i] === '"') {
+        if (inner.charAt(i) === '"') {
             const end = closingQuote(inner, i + 1);
             if (end < 0) {
                 return null;
@@ -325,8 +329,8 @@ export function parseQualifiers(inner: string): Qualifiers | null {
             i = end + 1;
         } else {
             let end = i;
-            while (end < n && inner[end] !== ",") {
-                end += inner[end] === "\\" ? 2 : 1;
+            while (end < n && inner.charAt(end) !== ",") {
+                end += inner.charAt(end) === "\\" ? 2 : 1;
             }
             value = unescapeObo(inner.slice(i, end).trim());
             i = end;
@@ -345,9 +349,9 @@ export function parseQualifiers(inner: string): Qualifiers | null {
  */
 function closingQuote(text: string, from: number): number {
     for (let i = from; i < text.length; i++) {
-        if (text[i] === "\\") {
+        if (text.charAt(i) === "\\") {
             i++;
-        } else if (text[i] === '"') {
+        } else if (text.charAt(i) === '"') {
             return i;
         }
     }
@@ -379,7 +383,7 @@ export function tokenize(value: string): Token[] {
     const n = value.length;
     let i = 0;
     while (i < n) {
-        const ch = value[i];
+        const ch = value.charAt(i);
         if (ch === " " || ch === "\t") {
             i++;
             continue;
@@ -390,8 +394,8 @@ export function tokenize(value: string): Token[] {
             // a 1.4 language tag glued to the closing quote ("chat"@fr) is kept with the text, as an
             // unquoted chat@fr is (research-obo.md 4.1: no language is split out)
             let after = stop + 1;
-            if (end >= 0 && value[after] === "@") {
-                while (after < n && value[after] !== " " && value[after] !== "\t") {
+            if (end >= 0 && value.charAt(after) === "@") {
+                while (after < n && value.charAt(after) !== " " && value.charAt(after) !== "\t") {
                     after++;
                 }
             }
@@ -412,8 +416,8 @@ export function tokenize(value: string): Token[] {
             continue;
         }
         let end = i;
-        while (end < n && value[end] !== " " && value[end] !== "\t") {
-            end += value[end] === "\\" ? 2 : 1;
+        while (end < n && value.charAt(end) !== " " && value.charAt(end) !== "\t") {
+            end += value.charAt(end) === "\\" ? 2 : 1;
         }
         tokens.push({ kind: "word", text: unescapeObo(value.slice(i, Math.min(end, n))), unterminated: false });
         i = end;
@@ -430,7 +434,7 @@ export function tokenize(value: string): Token[] {
 function closingBracket(text: string, from: number): number {
     let quoted = false;
     for (let i = from; i < text.length; i++) {
-        const ch = text[i];
+        const ch = text.charAt(i);
         if (ch === "\\") {
             i++;
         } else if (ch === '"') {
@@ -468,9 +472,9 @@ export function parseXref(raw: string): Xref | null {
     const { value, qualifiers } = splitQualifiers(raw.trim());
     let quote = -1;
     for (let i = 0; i < value.length; i++) {
-        if (value[i] === "\\") {
+        if (value.charAt(i) === "\\") {
             i++;
-        } else if (value[i] === '"') {
+        } else if (value.charAt(i) === '"') {
             quote = i;
             break;
         }
@@ -508,7 +512,7 @@ export function parseXrefList(inner: string): Xref[] {
         }
     };
     for (let i = 0; i < inner.length; i++) {
-        const ch = inner[i];
+        const ch = inner.charAt(i);
         if (ch === "\\") {
             i++;
         } else if (ch === '"') {
@@ -538,7 +542,7 @@ export function hasStrayBrace(value: string): boolean {
     let quoted = false;
     let listed = false;
     for (let i = 0; i < value.length; i++) {
-        const ch = value[i];
+        const ch = value.charAt(i);
         if (ch === "\\") {
             i++;
         } else if (ch === '"') {

package/src/formats/pajek/importer.ts

@@ -1607,7 +1607,7 @@ class PajekParser {
     private extras(tokens: readonly string[], start: number, domain: "node" | "edge", line: number): RowExtras {
         const extras: RowExtras = { keys: [], values: [], spells: null };
         const seen = new Set<string>();
-        for (let i = start; i < tokens.length; ) {
+        for (let i = start; i < tokens.length;) {
             const token = tokens[i];
             if (token.startsWith("[")) {
                 extras.spells = this.intervals(token, domain);

package/src/registry.ts

@@ -421,16 +421,15 @@ export class FormatRegistry {
     ): Promise<ImportGraphResult> {
         const opts = options as ImportGraphOptions;
         const picked = await this.choose(input, opts);
-        const unknown = this.unknownOptions(opts).map(
-            (name): ImportIssue =>
-                Object.freeze({
-                    category: "unsupported",
-                    severity: "warning",
-                    code: UNKNOWN_OPTION_CODE,
-                    message: unknownOptionText(name),
-                    line: null,
-                    element: name,
-                }),
+        const unknown = this.unknownOptions(opts).map((name): ImportIssue =>
+            Object.freeze({
+                category: "unsupported",
+                severity: "warning",
+                code: UNKNOWN_OPTION_CODE,
+                message: unknownOptionText(name),
+                line: null,
+                element: name,
+            }),
         );
         const chosen = unknown.length === 0 ? picked : { ...picked, warnings: [...picked.warnings, ...unknown] };
         const { importer } = chosen;

package/src/sniff.ts

@@ -32,19 +32,7 @@ import { type GraphImporter } from "./types.js";
  * @category Formats and detection
  */
 export type GraphFormatName =
-    | "gexf"
-    | "graphml"
-    | "gml"
-    | "dot"
-    | "pajek"
-    | "csv"
-    | "json"
-    | "neo4j"
-    | "xgmml"
-    | "cx2"
-    | "cx"
-    | "obo"
-    | "cys";
+    "gexf" | "graphml" | "gml" | "dot" | "pajek" | "csv" | "json" | "neo4j" | "xgmml" | "cx2" | "cx" | "obo" | "cys";
 
 /**
  * A format name: one of the built-in names (with editor autocomplete) or the name of a format you
@@ -345,14 +333,7 @@ export function sniffJsonDialectHead(head: Uint8Array | string): JsonImportDiale
 
 /** Where a key was seen while scanning a truncated head. */
 type KeyPath =
-    | ""
-    | "graph"
-    | "options"
-    | "nodes[0]"
-    | "edges[0]"
-    | "links[0]"
-    | "graphs[0].nodes[]"
-    | "graphs[0].edges[]";
+    "" | "graph" | "options" | "nodes[0]" | "edges[0]" | "links[0]" | "graphs[0].nodes[]" | "graphs[0].edges[]";
 
 /**
  * A partial document rebuilt from the keys a truncated head reveals: every key gets a placeholder

package/src/types.ts

@@ -368,6 +368,12 @@ export interface LossNote {
     readonly column: string | null;
     /** How many nodes, edges or values are affected, or null when not counted. */
     readonly count: number | null;
+    /**
+     * Every column the note is about, when it is about several and `column` is null: the graph
+     * attributes a format has no place for, or the node columns a CSV edge table leaves for the node
+     * table. Absent on a note about one column or none.
+     */
+    readonly columns?: readonly string[];
 }
 
 /**
@@ -458,13 +464,7 @@ export interface GraphExporter<Opts = unknown> {
  * @category Reports and errors
  */
 export type IssueCategory =
-    | "parse-error"
-    | "missing-value"
-    | "validation-error"
-    | "unsupported"
-    | "precision"
-    | "coercion"
-    | "merged";
+    "parse-error" | "missing-value" | "validation-error" | "unsupported" | "precision" | "coercion" | "merged";
 
 /**
  * One problem found while importing.