@graphty/graph-io 0.3.25 → 0.3.26

package/dist/src/common/cx-export.js

@@ -0,0 +1,334 @@
+/**
+ * The exporter machinery CX version 1 and CX2 share (design/graph-io/cytoscape-and-obo/design.md
+ * sections 1.2 and 1.3): integer node ids (safe integers, or the digits of an integer beyond 2^53
+ * written raw), sanitizeIds "mangle" renumbering, edge ids from the id role column, the declared
+ * type of a column, the direction notes (every CX edge is directed) and the JSON writer that keeps
+ * -0 and raw big integers.
+ */
+import { GraphFormatError } from "@graphty/graph-format";
+import { LOSS } from "./export.js";
+import { agree, plural } from "./plural.js";
+/**
+ * The prefix of a string that stands for a raw number literal in the output: -0 (which
+ * JSON.stringify writes as 0) and an integer id beyond 2^53 (kept as its digits).
+ */
+const RAW = `${String.fromCodePoint(0)}cx:`;
+/** A raw literal as JSON.stringify writes it, to be unquoted. */
+const RAW_JSON = /"\\u0000cx:(-?\d+)"/g;
+/** An integer literal beyond 2^53 as text: a CX id graph-io keeps as its digits. */
+const BIG_INTEGER_TEXT = /^-?[1-9]\d{15,}$/;
+/**
+ * Whether an id can be written as a CX id unchanged: a safe integer, or the digits of an integer
+ * beyond 2^53 (the CX importers read those back as the same digits).
+ * @param id - the id
+ * @returns true when writable
+ */
+function writableId(id) {
+    return typeof id === "number"
+        ? Number.isSafeInteger(id)
+        : BIG_INTEGER_TEXT.test(id) && !Number.isSafeInteger(Number(id));
+}
+/**
+ * The written node ids; under "error" an id that is not writable throws E_INVALID_ID, under
+ * "mangle" it gets the next unused integer.
+ * @param snapshot - the snapshot
+ * @param mode - the sanitizeIds option
+ * @param format - the format's display name, for the message
+ * @returns the ids
+ */
+function writtenIds(snapshot, mode, format) {
+    const { ids } = snapshot;
+    const bad = [];
+    const used = new Set();
+    for (let i = 0; i < ids.size; i++) {
+        const id = ids.idOf(i);
+        if (!writableId(id)) {
+            bad.push(i);
+        }
+        else if (typeof id === "number") {
+            used.add(id);
+        }
+    }
+    if (bad.length > 0 && mode === "error") {
+        const first = ids.idOf(bad[0]);
+        throw new GraphFormatError("E_INVALID_ID", `${bad.length} node id${plural(bad.length)} cannot be written as ${format} integers (first: ${JSON.stringify(first)} at index ${bad[0]}); pass sanitizeIds: "mangle" to rewrite them`, { reason: "charset", charset: "integer", count: bad.length, index: bad[0] });
+    }
+    const renumbered = new Map();
+    let next = 0;
+    for (const i of bad) {
+        while (used.has(next)) {
+            next++;
+        }
+        used.add(next);
+        renumbered.set(i, next);
+    }
+    return {
+        changed: bad.length,
+        idAt: (i) => {
+            const id = renumbered.get(i) ?? ids.idOf(i);
+            return typeof id === "string" ? `${RAW}${id}` : id;
+        },
+        isChanged: (i) => renumbered.has(i),
+        originalAt: (i) => ids.idOf(i),
+    };
+}
+/**
+ * The `idCounter` of the node ids as written (the largest id plus one, NDEx's next free id).
+ * @param ids - the written ids
+ * @param count - the node count
+ * @returns the counter: a number, or a raw big integer for stringify()
+ * @category Plugin helpers
+ */
+export function nextNodeId(ids, count) {
+    let max = -1n;
+    for (let i = 0; i < count; i++) {
+        const id = ids.idAt(i);
+        const value = typeof id === "number" ? BigInt(id) : BigInt(id.slice(RAW.length));
+        if (value > max) {
+            max = value;
+        }
+    }
+    const next = max + 1n;
+    return next <= BigInt(Number.MAX_SAFE_INTEGER) ? Number(next) : `${RAW}${next.toString()}`;
+}
+/**
+ * How many node ids are not writable unchanged.
+ * @param snapshot - the snapshot
+ * @returns the count
+ */
+function unwritableIds(snapshot) {
+    let count = 0;
+    for (let i = 0; i < snapshot.ids.size; i++) {
+        if (!writableId(snapshot.ids.idOf(i))) {
+            count++;
+        }
+    }
+    return count;
+}
+/**
+ * The id notes and the written ids of a CX export: E_ID_CHARSET (export() throws) or
+ * W_ID_MANGLED for the ids that are not integers.
+ * @param snapshot - the snapshot
+ * @param common - the resolved common options
+ * @param format - the format's display name
+ * @param attribute - the attribute the originals are kept in
+ * @param note - records a note
+ * @returns the ids, or the error export() throws
+ * @category Plugin helpers
+ */
+export function planNodeIds(snapshot, common, format, attribute, note) {
+    const unwritable = unwritableIds(snapshot);
+    if (unwritable > 0) {
+        note(common.sanitizeIds === "mangle" ? LOSS.ID_MANGLED : LOSS.ID_CHARSET, common.sanitizeIds === "mangle"
+            ? `${unwritable} node id${plural(unwritable)} ${agree(unwritable, "is", "are")} not integers, so they are renumbered; the original ids are written to the ${attribute} attribute, and an import with restoreMangledIds: true reads them back`
+            : `${unwritable} node id${plural(unwritable)} ${agree(unwritable, "is", "are")} not integers, so the save fails unless sanitizeIds is "mangle"`, null, unwritable);
+    }
+    try {
+        return writtenIds(snapshot, common.sanitizeIds, format);
+    }
+    catch (err) {
+        if (err instanceof GraphFormatError) {
+            return err;
+        }
+        throw err;
+    }
+}
+/**
+ * The CX type of a scalar dtype.
+ * @param dtype - the dtype
+ * @param longOrigin - whether the source declared the column long
+ * @returns the type text
+ */
+function scalarType(dtype, longOrigin) {
+    switch (dtype) {
+        case "f64":
+            return longOrigin ? "long" : "double";
+        case "f32":
+            return "double";
+        case "i32":
+        case "u8":
+            return "integer";
+        case "u32":
+            return "long";
+        case "bool":
+            return "boolean";
+        default:
+            return "string";
+    }
+}
+/**
+ * Whether every set value of an f64 column is integral (so a declared long stays long).
+ * @param column - the column
+ * @returns true when every set value is a safe integer
+ */
+function allIntegral(column) {
+    for (let i = 0; i < column.length; i++) {
+        if (column.isSet(i) && !Number.isSafeInteger(column.value(i))) {
+            return false;
+        }
+    }
+    return true;
+}
+/**
+ * The declared CX type of a column: string / double / long / integer / boolean or a list of one;
+ * a json column (and a list of json items) is a string holding JSON text.
+ * @param column - the column
+ * @returns the type text
+ * @category Plugin helpers
+ */
+export function declaredType(column) {
+    const { meta } = column;
+    const origin = meta.origin?.type ?? null;
+    const longOrigin = origin !== null && origin.endsWith("long") && (meta.dtype !== "f64" || allIntegral(column));
+    if (meta.dtype === "list") {
+        return meta.itemDtype === null || meta.itemDtype === "json"
+            ? "string"
+            : `list_of_${scalarType(meta.itemDtype, longOrigin)}`;
+    }
+    // a multi-component column (a color, a 3D vector) is written as a list of its components
+    return meta.components > 1 ? `list_of_${scalarType(meta.dtype, false)}` : scalarType(meta.dtype, longOrigin);
+}
+/**
+ * Count the positions with a non-finite x or y.
+ * @param position - the position column
+ * @returns the count
+ * @category Plugin helpers
+ */
+export function nonFinitePositions(position) {
+    let count = 0;
+    for (let i = 0; i < position.length; i++) {
+        if (position.isSet(i)) {
+            const p = position.value(i);
+            if (!Number.isFinite(p[0]) || !Number.isFinite(p[1])) {
+                count++;
+            }
+        }
+    }
+    return count;
+}
+/**
+ * The edge ids to write: the id role column's values when they are distinct safe integers, next
+ * unused integers for edges without one (W_EDGE_IDS_GENERATED).
+ * @param snapshot - the snapshot
+ * @param note - records a note
+ * @returns one id per edge
+ * @category Plugin helpers
+ */
+export function planEdgeIds(snapshot, note) {
+    const column = snapshot.edges.byRole("id");
+    const used = new Set();
+    let generated = 0;
+    const ids = keptEdgeIds(column, snapshot.edgeCount, used);
+    let next = 0;
+    const out = [];
+    for (let e = 0; e < snapshot.edgeCount; e++) {
+        let id = ids[e];
+        if (id === null) {
+            while (used.has(next)) {
+                next++;
+            }
+            id = next;
+            used.add(next);
+            generated++;
+        }
+        out.push(id);
+    }
+    if (column !== null && generated > 0) {
+        note(LOSS.EDGE_IDS_GENERATED, `${generated} edge${plural(generated)} ${agree(generated, "has", "have")} no distinct integer id in "${column.meta.name}"; they are written with generated ids`, column.meta.name, generated);
+    }
+    if (column !== null && column.dtype !== "f64") {
+        note(LOSS.DTYPE, `edge id column "${column.meta.name}" is ${column.dtype}; CX edge ids are integers and read back as f64`, column.meta.name, snapshot.edgeCount - column.nullCount);
+    }
+    return out;
+}
+/**
+ * The edge ids an id column can keep: its distinct safe integers (numbers, or text that reads as one).
+ * @param column - the edge id column, or null
+ * @param edgeCount - the number of edges
+ * @param used - receives the kept ids
+ * @returns the kept id per edge, null where it cannot be kept
+ */
+function keptEdgeIds(column, edgeCount, used) {
+    const ids = new Array(edgeCount).fill(null);
+    if (column === null) {
+        return ids;
+    }
+    for (let e = 0; e < edgeCount; e++) {
+        const value = column.isSet(e) ? column.value(e) : undefined;
+        const n = typeof value === "number" || typeof value === "string" ? Number(value) : Number.NaN;
+        if (Number.isSafeInteger(n) && !used.has(n)) {
+            ids[e] = n === 0 ? 0 : n;
+            used.add(n);
+        }
+    }
+    return ids;
+}
+/**
+ * The direction notes: every CX edge is directed, so an undirected snapshot (or the undirected
+ * pairs of a mixed one, folded under onMixedDirection) is written directed, and a mutual pair as
+ * two edges without its mark.
+ * @param snapshot - the snapshot
+ * @param folding - the pair folding
+ * @param common - the resolved common options
+ * @param undirectedCode - the format's "undirected written as directed" code
+ * @param note - records a note
+ * @category Plugin helpers
+ */
+export function directionNotes(snapshot, folding, common, undirectedCode, note) {
+    if (!snapshot.directed) {
+        note(undirectedCode, `the snapshot is undirected; every edge is written as a directed edge (${snapshot.edgeCount} edge${plural(snapshot.edgeCount)})`, null, snapshot.edgeCount);
+    }
+    else if (common.onMixedDirection !== "error") {
+        let undirected = 0;
+        for (let e = 0; e < snapshot.edgeCount; e++) {
+            if (!folding.folded(e) && !folding.sourceDirected(e)) {
+                undirected++;
+            }
+        }
+        if (undirected > 0) {
+            note(undirectedCode, `${undirected} undirected edge${plural(undirected)} ${agree(undirected, "is", "are")} written as one directed edge each (a pair folded to its primary); CX has no undirected edge`, null, undirected);
+        }
+    }
+    if (folding.mutualCount > 0) {
+        note(LOSS.MUTUAL_EXPANDED, `${folding.mutualCount} mutual pair${plural(folding.mutualCount)} ${agree(folding.mutualCount, "is", "are")} written as two directed edges; the mutual mark is lost`, null, folding.mutualCount);
+    }
+}
+/**
+ * The note recorder of a plan and its notes.
+ * @returns the notes and the recorder
+ * @category Plugin helpers
+ */
+export function noteList() {
+    const notes = [];
+    const note = (code, message, column = null, count = null) => {
+        notes.push(Object.freeze({ code, message, column, count }));
+    };
+    return { notes, note };
+}
+/**
+ * The JSON text of a value, keeping -0 and writing the raw big-integer ids of idAt() as numbers.
+ * @param value - the value
+ * @returns the text
+ * @category Plugin helpers
+ */
+export function stringify(value) {
+    const text = JSON.stringify(value, (_key, v) => (Object.is(v, -0) ? `${RAW}-0` : v));
+    return text.includes(String.raw `\u0000cx:`) ? text.replaceAll(RAW_JSON, "$1") : text;
+}
+/**
+ * The text of one aspect block, element by element.
+ * @param aspect - the aspect name
+ * @param elements - the JSON texts of its elements
+ * @yields the block's text
+ * @returns nothing
+ */
+export function* aspectBlock(aspect, elements) {
+    yield `{${JSON.stringify(aspect)}:[`;
+    let first = true;
+    for (const element of elements) {
+        yield first ? `\n${element}` : `,\n${element}`;
+        first = false;
+    }
+    yield "]},\n";
+}
+//# sourceMappingURL=cx-export.js.map

package/dist/src/common/cx-export.js.map

@@ -0,0 +1 @@
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package/dist/src/common/declared-types.d.ts

@@ -14,11 +14,17 @@
  */
 import { type Dtype, type ScalarDtype } from "@graphty/graph-format";
 import { type TemporalKind } from "./temporal.js";
-/** The formats whose declarations this table covers. */
+/**
+ * The formats whose declarations this table covers.
+ * @category Plugin helpers
+ */
 export type DeclaringFormat = "gexf" | "graphml" | "gml" | "neo4j";
 /** How the text of one scalar value (or one list item) is parsed. */
 type ValueKind = "boolean" | "integer" | "long" | "float" | "double" | "string" | "temporal" | "duration" | "point" | "json";
-/** The resolved storage of a declared type. */
+/**
+ * The resolved storage of a declared type.
+ * @category Plugin helpers
+ */
 export interface DeclaredTypeSpec {
     /** The declared type text as given by the file (origin.type). */
     readonly declared: string;
@@ -41,12 +47,14 @@ export interface DeclaredTypeSpec {
  * @param type - the type text as written (matched case-insensitively; GEXF `list*` and Neo4j `[]` denote lists)
  * @param long - how declared long / integer-64 columns are stored (the importer option)
  * @returns the spec, or null when the format does not define the type (the importer reports it and keeps the text)
+ * @category Plugin helpers
  */
 export declare function mapDeclaredType(format: DeclaringFormat, type: string, long: "f64" | "string"): DeclaredTypeSpec | null;
 /**
  * The spec of an untyped attribute: a string column with the given (or absent) type text.
  * @param declared - the type text to record in origin.type, or null
  * @returns a string spec
+ * @category Plugin helpers
  */
 export declare function stringSpec(declared: string | null): DeclaredTypeSpec;
 /**
@@ -57,12 +65,14 @@ export declare function stringSpec(declared: string | null): DeclaredTypeSpec;
  * @param kind - the value kind
  * @param temporal - the temporal kind when `kind` is "temporal"
  * @returns a boolean, a number, a string or (point / json) a JSON value; E_COLUMN_TYPE when the text is not of the kind
+ * @category Plugin helpers
  */
 export declare function parseScalarText(text: string, kind: ValueKind, temporal?: TemporalKind | null): unknown;
 /**
  * Parse a boolean text the way the formats write it: `true` / `false` in any case, or `1` / `0`.
  * @param text - the value text
  * @returns the boolean, or null when the text is neither
+ * @category Plugin helpers
  */
 export declare function parseBooleanText(text: string): boolean | null;
 /**
@@ -71,13 +81,23 @@ export declare function parseBooleanText(text: string): boolean | null;
  * @param text - the value text
  * @param kind - float or double, for the error
  * @returns the number
+ * @category Plugin helpers
  */
 export declare function parseDecimalText(text: string, kind?: ValueKind): number;
+/**
+ * Whether a number text is finite as written but too large for a double (`1e400`, a 400-digit
+ * integer), so it parses as Infinity: a value the importer should report, unlike `INF`.
+ * @param text - the value text
+ * @returns true when the text overflows
+ * @category Plugin helpers
+ */
+export declare function overflowsToInfinity(text: string): boolean;
 /**
  * Parse a Neo4j point literal `{x:1.0, y:2.0, crs:'cartesian'}` (also `latitude` / `longitude` /
  * `height` / `z` / `srid`) into a JSON object; a JSON object text is accepted as well.
  * @param text - the value text
  * @returns an object with numeric coordinates and string crs
+ * @category Plugin helpers
  */
 export declare function parsePointText(text: string): Readonly<Record<string, number | string>>;
 export {};

package/dist/src/common/declared-types.d.ts.map

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package/dist/src/common/declared-types.js

@@ -13,6 +13,7 @@
  * recorded in `origin.type` in every case so the exporter can restore the declaration.
  */
 import { GraphFormatError } from "@graphty/graph-format";
+import { withArticle } from "./plural.js";
 import { parseTemporal } from "./temporal.js";
 const BOOLEAN = { dtype: "bool", kind: "boolean" };
 const INTEGER = { dtype: "i32", kind: "integer" };
@@ -97,6 +98,7 @@ const I32_MAX = 2147483647;
  * @param type - the type text as written (matched case-insensitively; GEXF `list*` and Neo4j `[]` denote lists)
  * @param long - how declared long / integer-64 columns are stored (the importer option)
  * @returns the spec, or null when the format does not define the type (the importer reports it and keeps the text)
+ * @category Plugin helpers
  */
 export function mapDeclaredType(format, type, long) {
     const table = TABLES[format];
@@ -142,6 +144,7 @@ export function mapDeclaredType(format, type, long) {
  * The spec of an untyped attribute: a string column with the given (or absent) type text.
  * @param declared - the type text to record in origin.type, or null
  * @returns a string spec
+ * @category Plugin helpers
  */
 export function stringSpec(declared) {
     return {
@@ -162,6 +165,7 @@ export function stringSpec(declared) {
  * @param kind - the value kind
  * @param temporal - the temporal kind when `kind` is "temporal"
  * @returns a boolean, a number, a string or (point / json) a JSON value; E_COLUMN_TYPE when the text is not of the kind
+ * @category Plugin helpers
  */
 export function parseScalarText(text, kind, temporal = null) {
     switch (kind) {
@@ -219,6 +223,7 @@ export function parseScalarText(text, kind, temporal = null) {
  * Parse a boolean text the way the formats write it: `true` / `false` in any case, or `1` / `0`.
  * @param text - the value text
  * @returns the boolean, or null when the text is neither
+ * @category Plugin helpers
  */
 export function parseBooleanText(text) {
     switch (text.trim().toLowerCase()) {
@@ -238,6 +243,7 @@ export function parseBooleanText(text) {
  * @param text - the value text
  * @param kind - float or double, for the error
  * @returns the number
+ * @category Plugin helpers
  */
 export function parseDecimalText(text, kind = "double") {
     const trimmed = text.trim();
@@ -259,11 +265,23 @@ export function parseDecimalText(text, kind = "double") {
             throw typeError(text, kind);
     }
 }
+/**
+ * Whether a number text is finite as written but too large for a double (`1e400`, a 400-digit
+ * integer), so it parses as Infinity: a value the importer should report, unlike `INF`.
+ * @param text - the value text
+ * @returns true when the text overflows
+ * @category Plugin helpers
+ */
+export function overflowsToInfinity(text) {
+    const trimmed = text.trim();
+    return /^[+-]?[0-9.]/.test(trimmed) && Number(trimmed) === (trimmed.startsWith("-") ? -Infinity : Infinity);
+}
 /**
  * Parse a Neo4j point literal `{x:1.0, y:2.0, crs:'cartesian'}` (also `latitude` / `longitude` /
  * `height` / `z` / `srid`) into a JSON object; a JSON object text is accepted as well.
  * @param text - the value text
  * @returns an object with numeric coordinates and string crs
+ * @category Plugin helpers
  */
 export function parsePointText(text) {
     const trimmed = text.trim();
@@ -321,6 +339,6 @@ function parseJsonText(text) {
  */
 function typeError(text, kind) {
     const shown = text.length > 40 ? `${text.slice(0, 40)}...` : text;
-    return new GraphFormatError("E_COLUMN_TYPE", `"${shown}" is not a ${kind}`, { value: text, kind });
+    return new GraphFormatError("E_COLUMN_TYPE", `"${shown}" is not ${withArticle(kind)}`, { value: text, kind });
 }
 //# sourceMappingURL=declared-types.js.map

package/dist/src/common/declared-types.js.map

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