@graphty/graph-io 0.3.25 → 0.3.27

package/dist/src/formats/obo/syntax.js

@@ -19,6 +19,7 @@ const ESCAPES = Object.freeze({
  * backslash at the very end is dropped.
  * @param text - raw text
  * @returns the unescaped text
+ * @category Plugin helpers
  */
 export function unescapeObo(text) {
     if (!text.includes("\\")) {
@@ -52,10 +53,38 @@ function isEscaped(text, index) {
     }
     return run % 2 === 1;
 }
+/**
+ * Split a line at the form feeds outside quotes (the 1.4 grammar counts a form feed as a line end;
+ * one inside a quoted value is text).
+ * @param line - the raw line
+ * @returns the pieces, the line itself when it holds no such form feed
+ * @category Plugin helpers
+ */
+export function splitFormFeeds(line) {
+    if (!line.includes("\f")) {
+        return [line];
+    }
+    const pieces = [];
+    let quoted = false;
+    let start = 0;
+    for (let i = 0; i < line.length; i += line[i] === "\\" ? 2 : 1) {
+        const ch = line[i];
+        if (ch === '"') {
+            quoted = !quoted;
+        }
+        else if (ch === "\f" && !quoted) {
+            pieces.push(line.slice(start, i));
+            start = i + 1;
+        }
+    }
+    pieces.push(line.slice(start));
+    return pieces;
+}
 /**
  * Whether a raw line ends with an unescaped backslash (the 1.0 / 1.2 line continuation).
  * @param line - the raw line, trailing whitespace included
  * @returns true when the line continues on the next one
+ * @category Plugin helpers
  */
 export function endsWithContinuation(line) {
     return line.endsWith("\\") && !isEscaped(line, line.length - 1);
@@ -64,6 +93,7 @@ export function endsWithContinuation(line) {
  * Split a line at its first unescaped colon (values contain colons freely: `is_a: GO:0000001`).
  * @param line - the raw line, trimmed
  * @returns the tag and the rest, or null when the line has no colon
+ * @category Plugin helpers
  */
 export function splitTagValue(line) {
     for (let i = 0; i < line.length; i++) {
@@ -85,6 +115,7 @@ export function splitTagValue(line) {
  * hide the comment after it.
  * @param rest - the raw value
  * @returns the value before the comment, trailing whitespace removed
+ * @category Plugin helpers
  */
 export function stripComment(rest) {
     let quoted = false;
@@ -107,36 +138,54 @@ export function stripComment(rest) {
 /**
  * Split the trailing qualifier blocks off a value: a `{...}` is a block only when it closes the
  * value (after the comment was stripped); several blocks (`{a="1"}{b="2"}`, 1.2 examples) are
- * merged. A closing brace whose block does not parse is left in the value and reported.
+ * merged. A closing brace whose block does not parse is left in the value and reported. The value
+ * is scanned once, so a value of many blocks costs its length, not its length times its blocks.
  * @param value - the raw value without its comment
  * @returns the value and its qualifiers
+ * @category Plugin helpers
  */
 export function splitQualifiers(value) {
-    let rest = value;
+    if (!value.endsWith("}")) {
+        return { value, qualifiers: null, badBlock: null };
+    }
+    const blocks = braceBlocks(value);
+    // the blocks read right to left, merged left to right below
+    const parsed = [];
+    let end = value.length;
+    let badBlock = null;
+    while (end > 0 && value[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) {
+            badBlock = value.slice(Math.max(open, 0), end);
+            break;
+        }
+        parsed.push(block);
+        end = open;
+        while (end > 0 && /\s/.test(value[end - 1])) {
+            end--;
+        }
+    }
     let qualifiers = null;
-    for (;;) {
-        if (!rest.endsWith("}") || isEscaped(rest, rest.length - 1)) {
-            return { value: rest, qualifiers, badBlock: null };
-        }
-        const open = openingBrace(rest);
-        const parsed = open < 0 ? null : parseQualifiers(rest.slice(open + 1, -1));
-        if (parsed === null) {
-            return { value: rest, qualifiers, badBlock: open < 0 ? rest : rest.slice(open) };
-        }
-        // a block read right to left: an earlier block's names come first
-        qualifiers = qualifiers === null ? parsed : mergeQualifiers(parsed, qualifiers);
-        rest = rest.slice(0, open).trimEnd();
+    for (let i = parsed.length - 1; i >= 0; i--) {
+        qualifiers ?? (qualifiers = Object.create(null));
+        for (const [name, v] of Object.entries(parsed[i])) {
+            addQualifier(qualifiers, name, v);
+        }
     }
+    return { value: value.slice(0, end), qualifiers, badBlock };
 }
 /**
- * The index of the unescaped `{` outside quotes that opens the block closing the value.
- * @param value - a raw value ending with `}`
- * @returns the index, or -1 when there is none
+ * The qualifier blocks of a value in one scan: for every unescaped `}` outside quotes, the index of
+ * the unescaped `{` outside quotes that opens it (-1 when a `}` came after that `{`, or none did).
+ * @param value - a raw value
+ * @returns the opening index by closing index
  */
-function openingBrace(value) {
+function braceBlocks(value) {
+    const blocks = new Map();
     let quoted = false;
     let open = -1;
-    for (let i = 0; i < value.length - 1; i++) {
+    for (let i = 0; i < value.length; i++) {
         const ch = value[i];
         if (ch === "\\") {
             i++;
@@ -149,37 +198,61 @@ function openingBrace(value) {
             open = i;
         }
         else if (!quoted && ch === "}") {
+            blocks.set(i, open);
             open = -1;
         }
     }
-    return quoted ? -1 : open;
+    return blocks;
 }
 /**
- * Merge two qualifier records, a repeated name becoming a list.
- * @param first - the earlier record
- * @param second - the later record
- * @returns the merged record
+ * The index of an unescaped `{` outside quotes that no `}` closes: a qualifier block cut short (a
+ * file truncated inside it).
+ * @param value - a raw value, closing blocks already split off
+ * @returns the index, or -1 when every brace is closed
+ * @category Plugin helpers
  */
-function mergeQualifiers(first, second) {
-    const out = { ...first };
-    for (const [name, value] of Object.entries(second)) {
-        addQualifier(out, name, value);
+export function unclosedBlock(value) {
+    let quoted = false;
+    let open = -1;
+    for (let i = 0; i < value.length; i += value[i] === "\\" ? 2 : 1) {
+        const ch = value[i];
+        if (ch === "\\") {
+            continue;
+        }
+        if (ch === '"' && open < 0) {
+            quoted = !quoted;
+        }
+        else if (!quoted && ch === "{") {
+            open = i;
+        }
+        else if (!quoted && ch === "}") {
+            open = -1;
+        }
     }
-    return out;
+    return open;
 }
 /**
- * Add one qualifier, turning a repeated name into a list.
+ * Add one qualifier, turning a repeated name into a list (a list the record owns, appended to in
+ * place). The record must have a null prototype, so a name such as `__proto__` is an own key.
  * @param record - the record
  * @param name - the name
  * @param value - the value (or values)
  */
 function addQualifier(record, name, value) {
+    const values = Array.isArray(value) ? value : [value];
     if (!Object.prototype.hasOwnProperty.call(record, name)) {
-        record[name] = value;
+        record[name] = Array.isArray(value) ? [...value] : value;
         return;
     }
     const before = record[name];
-    record[name] = [...(Array.isArray(before) ? before : [before]), ...(Array.isArray(value) ? value : [value])];
+    if (Array.isArray(before)) {
+        for (const v of values) {
+            before.push(v);
+        }
+    }
+    else {
+        record[name] = [before, ...values];
+    }
 }
 /**
  * Parse the inside of a qualifier block: `name="value"` pairs separated by commas, the 1.2
@@ -187,6 +260,7 @@ function addQualifier(record, name, value) {
  * (qualifier names may be IRIs with colons).
  * @param inner - the text between the braces
  * @returns the qualifiers, or null when the block does not parse (a pair without `=`, an unclosed quote)
+ * @category Plugin helpers
  */
 export function parseQualifiers(inner) {
     const out = Object.create(null);
@@ -232,7 +306,7 @@ export function parseQualifiers(inner) {
         addQualifier(out, name, value);
         any = true;
     }
-    return any ? { ...out } : null;
+    return any ? out : null;
 }
 /**
  * The index of the unescaped closing quote.
@@ -256,6 +330,7 @@ function closingQuote(text, from) {
  * Whitespace separates tokens; an escaped space belongs to its word.
  * @param value - the raw value
  * @returns the tokens
+ * @category Plugin helpers
  */
 export function tokenize(value) {
     const tokens = [];
@@ -330,6 +405,7 @@ function closingBracket(text, from) {
  * string its description, a closing block its qualifiers.
  * @param raw - the raw text of one xref
  * @returns the xref, or null when it has no id
+ * @category Plugin helpers
  */
 export function parseXref(raw) {
     const { value, qualifiers } = splitQualifiers(raw.trim());
@@ -348,17 +424,20 @@ export function parseXref(raw) {
         return null;
     }
     let description = null;
+    let unterminated = false;
     if (quote >= 0) {
         const end = closingQuote(value, quote + 1);
+        unterminated = end < 0;
         description = unescapeObo(value.slice(quote + 1, end < 0 ? value.length : end));
     }
-    return { id, description, qualifiers };
+    return { id, description, qualifiers, unterminated };
 }
 /**
  * Split the inside of a bracketed list into xrefs at the unescaped commas outside quotes and
  * braces (a solitary xref needs no escaping of its commas only outside a list).
  * @param inner - the raw text between the brackets
  * @returns the xrefs, in order
+ * @category Plugin helpers
  */
 export function parseXrefList(inner) {
     const out = [];
@@ -399,6 +478,7 @@ export function parseXrefList(inner) {
  * have escaped).
  * @param value - the raw value, qualifiers already split off
  * @returns true when a stray brace is present
+ * @category Plugin helpers
  */
 export function hasStrayBrace(value) {
     let quoted = false;
@@ -421,4 +501,101 @@ export function hasStrayBrace(value) {
     }
     return false;
 }
+// ============================================================ the writer side
+/** A carriage return, a CRLF pair or a form feed: line ends OBO text cannot carry. */
+const LINE_ENDS = /\r\n|\r|\f/g;
+/**
+ * Whether a text holds a carriage return or a form feed, which the OBO line grammar reads as a line
+ * end wherever it stands and no escape can spell; the writers turn them into `\n`.
+ * @param text - the text
+ * @returns true when the text loses a character on the way through an OBO file
+ * @category Plugin helpers
+ */
+export function hasLineEnd(text) {
+    return text.includes("\r") || text.includes("\f");
+}
+/**
+ * Escape text for a quoted OBO string (`def: "..."`, a synonym, a qualifier value): backslash,
+ * quote, newline and tab. A carriage return or form feed becomes a newline (see hasLineEnd()).
+ * `\W` is never written: graph-io reads it as a space, fastobo and the 1.4 BNF as the letter W.
+ * @param text - the text
+ * @returns the escaped text, without the quotes
+ * @category Plugin helpers
+ */
+export function escapeOboQuoted(text) {
+    return text.replaceAll(LINE_ENDS, "\n").replaceAll(/[\\"\n\t]/g, (ch) => {
+        switch (ch) {
+            case "\n":
+                return String.raw `\n`;
+            case "\t":
+                return String.raw `\t`;
+            default:
+                return `\\${ch}`;
+        }
+    });
+}
+/**
+ * Escape text for an unquoted OBO value (`name:`, `comment:`, an xref id, an unknown tag): what
+ * escapeOboQuoted() escapes plus `!` (a comment), `{` and `}` (a qualifier block), `[`, `]` and `,`
+ * (an xref list) and `"` (a quoted string). The reader trims an unquoted value, so its leading
+ * and trailing spaces cannot be kept.
+ * @param text - the text
+ * @returns the escaped text
+ * @category Plugin helpers
+ */
+export function escapeOboValue(text) {
+    return escapeOboQuoted(text).replaceAll(/[!{}[\],]/g, (ch) => `\\${ch}`);
+}
+/**
+ * Whether a text can stand as one OBO word (an id, a relation, a subset or synonym type name): not
+ * empty, no whitespace, no control character (the importer refuses an id holding one), no `!`, `{`
+ * or `}`. escapeOboWord() escapes what else would end it or turn
+ * it into another token (a backslash, a quote, a leading `[`).
+ * @param text - the text
+ * @returns true when the text is a word
+ * @category Plugin helpers
+ */
+export function isOboWord(text) {
+    return text.length > 0 && !NOT_IN_WORD.test(text);
+}
+/**
+ * A character an OBO word cannot hold: whitespace, a control character, `!`, `{` or `}`.
+ * @category Plugin helpers
+ */
+export const NOT_IN_WORD = /[\s!{}\p{Cc}]/u;
+/**
+ * Write a word (see isOboWord()): a backslash and a quote escaped, and a leading `[` (which would
+ * open an xref list).
+ * @param word - a text isOboWord() accepts
+ * @returns the text to write
+ * @category Plugin helpers
+ */
+export function escapeOboWord(word) {
+    const out = word.replaceAll(/[\\"]/g, (ch) => `\\${ch}`);
+    return out.startsWith("[") ? `\\${out}` : out;
+}
+/**
+ * Whether a text can be a qualifier name: not empty, no surrounding space, none of `=`, `"`, `,`,
+ * `{`, `}`, `[`, `]`, `!`, a backslash or a line end (the reader takes a name as everything up to
+ * the first `=`, unescaped only after the split).
+ * @param name - the name
+ * @returns true when the name is written as it is
+ * @category Plugin helpers
+ */
+export function isQualifierName(name) {
+    return name.length > 0 && name === name.trim() && !/[=",{}[\]!\\\n\r\t\f]/.test(name);
+}
+/**
+ * A qualifier block: `{name="value", ...}`, a list value as one pair per item.
+ * @param pairs - the name / value pairs, in order (names isQualifierName() accepts)
+ * @returns the block with a leading space, or "" when there are no pairs
+ * @category Plugin helpers
+ */
+export function qualifierBlock(pairs) {
+    if (pairs.length === 0) {
+        return "";
+    }
+    const items = pairs.map(([name, value]) => `${name}="${escapeOboQuoted(value)}"`);
+    return ` {${items.join(", ")}}`;
+}
 //# sourceMappingURL=syntax.js.map

package/dist/src/formats/obo/syntax.js.map

@@ -1 +1 @@
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package/dist/src/formats/pajek/exporter.d.ts

@@ -11,50 +11,88 @@
  * attributes from the primary half, so a mixed file round-trips in its original edge order. The
  * weight is written for edges whose weight was explicit (the role-weight column's validity).
  */
-import { type GraphExporter } from "../../types.js";
-/** The format-specific options of the Pajek exporter. */
-export interface PajekExportOptions {
+import { type CommonExportOptions, type GraphExporter } from "../../types.js";
+/**
+ * The format-specific options of the Pajek exporter.
+ * @category Built-in formats
+ */
+export interface PajekExportOptions extends CommonExportOptions {
     /**
-     * Write a `*Network <name>` header line (the .paj project-file convention) when the snapshot's
-     * meta.name is set; default false, since plain .net readers do not expect it.
+     * Write a `*Network <name>` line first, as Pajek project files (.paj) have. The name is the `name`
+     * option, else the graph's name (`snapshot.meta.name`); a graph with neither gets a bare
+     * `*Network` line. Plain .net readers do not expect the line. An explicit `false` wins over
+     * `name`: `{ networkHeader: false, name: "x" }` writes no line.
+     * @defaultValue false, or true when `name` is given
      */
     networkHeader?: boolean | undefined;
+    /**
+     * The network name written on the `*Network` line. Giving one writes the line, unless
+     * `networkHeader` is `false`. The default is the graph's name (`snapshot.meta.name`), which a
+     * Pajek, DOT, GML or GEXF import keeps; a graph read from CSV has none.
+     * @defaultValue the graph's name
+     */
+    name?: string | undefined;
 }
 /**
  * The LossNote codes of the Pajek exporter's check(): the Pajek-specific ones and, aliased, the
  * shared ones it records itself (`LOSS` holds the rest of the generic pre-flight's codes). A key
  * is the code without its severity and format prefixes.
+ * @category Built-in formats
  */
 export declare const PAJEK_LOSS: Readonly<{
-    /** A label or text value holds a double quote or a line break; export() will throw E_UNSUPPORTED. */
+    /**
+     * A label or text value holds a double quote or a line break, which Pajek cannot write; the save fails with
+     * E_UNSUPPORTED.
+     */
     TEXT: "E_PAJEK_TEXT";
     /** A column whose name cannot be a parameter key (whitespace, a quote, numeric, a shape keyword); skipped. */
     KEY_DROPPED: "W_PAJEK_KEY_DROPPED";
-    /** A label role column that is not text; its values are written as text and re-import as string. */
+    /**
+     * The node label attribute holds numbers or other values that are not text; they are written as text and read back
+     * as text.
+     */
     LABEL_AS_TEXT: "W_PAJEK_LABEL_AS_TEXT";
-    /** A non-finite f64 value; written as Infinity / NaN text, which re-imports as string. */
+    /** NaN or an infinity is written as the text Infinity or NaN, which reads back as text. */
     NONFINITE_AS_TEXT: "W_PAJEK_NONFINITE_AS_TEXT";
     /** A mutual pair; written as one undirected edge, the mark lost. */
     MUTUAL_AS_UNDIRECTED: "W_MUTUAL_AS_UNDIRECTED";
     /** A start / end / timestamp role column; Pajek intervals are written from the spells role only. */
     TEMPORAL_DROPPED: "W_TEMPORAL_DROPPED";
-    /** A position column with a stride other than 2 or 3. */
+    /** A position with other than 2 or 3 coordinates is not written. */
     POSITION_STRIDE: "W_PAJEK_POSITION_STRIDE";
-    /** meta.extra.pajek.firstMode is not a count within 0..N; the two-mode header is not written. */
+    /**
+     * The graph's two-mode vertex count (`meta.extra.pajek.firstMode`) is not between 0 and the number of nodes, so
+     * the file is written as a one-mode network.
+     */
     FIRST_MODE_DROPPED: "W_PAJEK_FIRST_MODE_DROPPED";
-    /** A role column Pajek has no slot for (kind, ...) written as a plain parameter; the role is lost. */
+    /** An attribute with a role the format has no place for is written as a plain attribute; the role is lost. */
     ROLE_DROPPED: "W_ROLE_DROPPED";
-    /** A `shape` column with a value outside the shape keywords is written as a parameter (a string on re-import). */
+    /**
+     * A `shape` attribute whose value is not one of Pajek's shape names is written as a parameter, and reads back as a
+     * plain text attribute.
+     */
     SHAPE_AS_PARAMETER: "W_PAJEK_SHAPE_AS_PARAMETER";
     /** A vertex line with coordinates, a shape or parameters needs a label: the id text is written and reads back as a label. */
     LABEL_GAINED: "W_PAJEK_LABEL_GAINED";
-    /** A role-less node column named `label` reads back with the label role (its values become the vertex labels). */
+    /**
+     * An attribute without a role is written where the format keeps a role (for example, a `name` column as the label), and
+     * reads back with that role.
+     */
     ROLE_ASSUMED: "W_ROLE_ASSUMED";
-    /** Under sanitizeIds "mangle": an original id whose text reads back as the other type under ids "canonical". */
+    /**
+     * With `sanitizeIds: "mangle"`: an original id that reads back as a different type, such as the text "7" as the
+     * number 7.
+     */
     ID_TEXT_TYPE: "W_ID_TEXT_TYPE";
-    /** Parameter text that looks like a number or a boolean reads back as one (parameters are untyped, design 5.1). */
+    /**
+     * A text value that reads back as a number or a boolean, because the format does not record that it was text (the
+     * text "42" reads back as the number 42).
+     */
     TEXT_INFERRED: "W_TEXT_INFERRED";
 }>;
-/** The Pajek NET exporter. */
+/**
+ * The Pajek NET exporter.
+ * @category Built-in formats
+ */
 export declare const pajekExporter: GraphExporter<PajekExportOptions>;
 //# sourceMappingURL=exporter.d.ts.map

package/dist/src/formats/pajek/exporter.d.ts.map

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