@graphty/graph-io 0.3.18 → 0.3.20

package/dist/obo.js

@@ -1,4 +1,4 @@
-import { O, o } from "./chunks/importer-aNJfe0qu.js";
+import { O, o } from "./chunks/importer-DEcKhsmQ.js";
 export {
   O as OBO_ISSUE,
   o as oboImporter

package/dist/pajek.js

@@ -1,4 +1,4 @@
-import { P, a, p, b } from "./chunks/importer-d0uQxFp6.js";
+import { P, a, p, b } from "./chunks/importer-zGLo8Dg_.js";
 export {
   P as PAJEK_ISSUE,
   a as PAJEK_LOSS,

package/dist/src/common/cell-budget.d.ts

@@ -0,0 +1,84 @@
+/**
+ * A memory guard for the builder importGraph() fills. graph-format stores every attribute as a dense
+ * column, one slot per node (or edge) whether or not that element has a value, so a file whose nodes
+ * each carry a differently named attribute holds n values but allocates n x n slots: a few hundred
+ * kilobytes of input can need gigabytes. The guard counts the slots that hold no value and stops the
+ * import once they pass a limit. A dense file has almost no empty slots, so it is never stopped
+ * however large it is.
+ */
+import { type ColumnDecl, type ColumnHandle, GraphBuilder, type GraphBuilderOptions, type NodeId } from "@graphty/graph-format";
+/** The issue code of an import stopped for allocating too many empty attribute slots. */
+export declare const TOO_MANY_EMPTY_CELLS_CODE = "E_TOO_MANY_EMPTY_CELLS";
+/**
+ * Resolve the maxEmptyCells option.
+ * @param value - the caller's value
+ * @returns a non-negative integer or Infinity
+ * @throws GraphFormatError E_UNSUPPORTED for anything else
+ */
+export declare function maxEmptyCellsOption(value: unknown): number;
+/** A GraphBuilder that throws an ImportError once its attribute columns hold too many empty slots. */
+export declare class CellBudgetBuilder extends GraphBuilder {
+    private readonly format;
+    private readonly maxEmptyCells;
+    private readonly nodeColumns;
+    private readonly edgeColumns;
+    private values;
+    /**
+     * Create a builder with a limit.
+     * @param options - the builder options
+     * @param format - the format being read, for the error's report
+     * @param maxEmptyCells - the most empty slots allowed
+     */
+    constructor(options: GraphBuilderOptions, format: string, maxEmptyCells: number);
+    /**
+     * Add a node, then check the limit (its row adds a slot to every node column).
+     * @param id - the node id
+     * @returns the node index
+     */
+    addNode(id: NodeId): number;
+    /**
+     * Add an edge, then check the limit (its row adds a slot to every edge column).
+     * @param source - source id
+     * @param target - target id
+     * @param weight - the weight
+     * @returns the edge index
+     */
+    addEdge(source: NodeId, target: NodeId, weight?: number): number;
+    /**
+     * Declare a node column, then check the limit.
+     * @param decl - the declaration
+     * @returns the column handle
+     */
+    declareNodeColumn(decl: ColumnDecl): ColumnHandle;
+    /**
+     * Declare an edge column, then check the limit.
+     * @param decl - the declaration
+     * @returns the column handle
+     */
+    declareEdgeColumn(decl: ColumnDecl): ColumnHandle;
+    /**
+     * Set a node cell (a new name declares a column), then check the limit.
+     * @param column - the handle or name
+     * @param index - the node index
+     * @param value - the value
+     */
+    setNodeValue(column: ColumnHandle | string, index: number, value: unknown): void;
+    /**
+     * Set an edge cell (a new name declares a column), then check the limit.
+     * @param column - the handle or name
+     * @param edge - the edge index
+     * @param value - the value
+     */
+    setEdgeValue(column: ColumnHandle | string, edge: number, value: unknown): void;
+    /**
+     * Count a written value and check the budget.
+     * @param value - the value; null and undefined unset a slot and do not count
+     */
+    private count;
+    /**
+     * Throw when the columns' slots minus the values written pass the limit.
+     * @throws ImportError E_TOO_MANY_EMPTY_CELLS
+     */
+    private checkBudget;
+}
+//# sourceMappingURL=cell-budget.d.ts.map

package/dist/src/common/cell-budget.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/common/cell-budget.js

@@ -0,0 +1,138 @@
+/**
+ * A memory guard for the builder importGraph() fills. graph-format stores every attribute as a dense
+ * column, one slot per node (or edge) whether or not that element has a value, so a file whose nodes
+ * each carry a differently named attribute holds n values but allocates n x n slots: a few hundred
+ * kilobytes of input can need gigabytes. The guard counts the slots that hold no value and stops the
+ * import once they pass a limit. A dense file has almost no empty slots, so it is never stopped
+ * however large it is.
+ */
+import { GraphBuilder, GraphFormatError, } from "@graphty/graph-format";
+import { describe } from "./options.js";
+import { ImportReportBuilder } from "./report.js";
+/** The issue code of an import stopped for allocating too many empty attribute slots. */
+export const TOO_MANY_EMPTY_CELLS_CODE = "E_TOO_MANY_EMPTY_CELLS";
+/** The default limit: 2^24 empty slots, about 130 MB of f64 columns. */
+const DEFAULT_MAX_EMPTY_CELLS = 2 ** 24;
+/**
+ * Resolve the maxEmptyCells option.
+ * @param value - the caller's value
+ * @returns a non-negative integer or Infinity
+ * @throws GraphFormatError E_UNSUPPORTED for anything else
+ */
+export function maxEmptyCellsOption(value) {
+    if (value === undefined) {
+        return DEFAULT_MAX_EMPTY_CELLS;
+    }
+    if (typeof value === "number" && value >= 0 && (Number.isInteger(value) || value === Infinity)) {
+        return value;
+    }
+    throw new GraphFormatError("E_UNSUPPORTED", `option maxEmptyCells: ${describe(value)} is not a non-negative integer or Infinity`, { option: "maxEmptyCells", found: value });
+}
+/** A GraphBuilder that throws an ImportError once its attribute columns hold too many empty slots. */
+export class CellBudgetBuilder extends GraphBuilder {
+    /**
+     * Create a builder with a limit.
+     * @param options - the builder options
+     * @param format - the format being read, for the error's report
+     * @param maxEmptyCells - the most empty slots allowed
+     */
+    constructor(options, format, maxEmptyCells) {
+        super(options);
+        this.format = format;
+        this.maxEmptyCells = maxEmptyCells;
+        this.nodeColumns = new Set();
+        this.edgeColumns = new Set();
+        this.values = 0;
+    }
+    /**
+     * Add a node, then check the limit (its row adds a slot to every node column).
+     * @param id - the node id
+     * @returns the node index
+     */
+    addNode(id) {
+        const index = super.addNode(id);
+        this.checkBudget();
+        return index;
+    }
+    /**
+     * Add an edge, then check the limit (its row adds a slot to every edge column).
+     * @param source - source id
+     * @param target - target id
+     * @param weight - the weight
+     * @returns the edge index
+     */
+    addEdge(source, target, weight) {
+        const edge = super.addEdge(source, target, weight);
+        this.checkBudget();
+        return edge;
+    }
+    /**
+     * Declare a node column, then check the limit.
+     * @param decl - the declaration
+     * @returns the column handle
+     */
+    declareNodeColumn(decl) {
+        const handle = super.declareNodeColumn(decl);
+        this.nodeColumns.add(handle);
+        this.checkBudget();
+        return handle;
+    }
+    /**
+     * Declare an edge column, then check the limit.
+     * @param decl - the declaration
+     * @returns the column handle
+     */
+    declareEdgeColumn(decl) {
+        const handle = super.declareEdgeColumn(decl);
+        this.edgeColumns.add(handle);
+        this.checkBudget();
+        return handle;
+    }
+    /**
+     * Set a node cell (a new name declares a column), then check the limit.
+     * @param column - the handle or name
+     * @param index - the node index
+     * @param value - the value
+     */
+    setNodeValue(column, index, value) {
+        super.setNodeValue(column, index, value);
+        this.nodeColumns.add(typeof column === "string" ? this.nodeColumn(column) : column);
+        this.count(value);
+    }
+    /**
+     * Set an edge cell (a new name declares a column), then check the limit.
+     * @param column - the handle or name
+     * @param edge - the edge index
+     * @param value - the value
+     */
+    setEdgeValue(column, edge, value) {
+        super.setEdgeValue(column, edge, value);
+        this.edgeColumns.add(typeof column === "string" ? this.edgeColumn(column) : column);
+        this.count(value);
+    }
+    /**
+     * Count a written value and check the budget.
+     * @param value - the value; null and undefined unset a slot and do not count
+     */
+    count(value) {
+        if (value !== null && value !== undefined) {
+            this.values++;
+        }
+        this.checkBudget();
+    }
+    /**
+     * Throw when the columns' slots minus the values written pass the limit.
+     * @throws ImportError E_TOO_MANY_EMPTY_CELLS
+     */
+    checkBudget() {
+        const slots = this.nodeColumns.size * this.nodeBound + this.edgeColumns.size * this.edgeBound;
+        const empty = slots - this.values;
+        if (empty > this.maxEmptyCells) {
+            new ImportReportBuilder(this.format, Infinity).fail(TOO_MANY_EMPTY_CELLS_CODE, `the attributes are too sparse: ${this.nodeColumns.size} node and ${this.edgeColumns.size} edge ` +
+                `attribute column(s) over ${this.nodeBound} node(s) and ${this.edgeBound} edge(s) would ` +
+                `allocate more than ${this.maxEmptyCells} slots that hold no value; pass a larger ` +
+                `maxEmptyCells (or Infinity) to read the file anyway`, undefined, { emptyCells: empty, maxEmptyCells: this.maxEmptyCells });
+        }
+    }
+}
+//# sourceMappingURL=cell-budget.js.map

package/dist/src/common/cell-budget.js.map

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

@@ -85,6 +85,16 @@ export declare function throwIfAborted(signal: AbortSignal | null | undefined):
  * @returns nothing
  */
 export declare function textChunks(input: ImportInput, report: ImportReportBuilder, options?: ReadOptions): AsyncGenerator<string, void, undefined>;
+/**
+ * Read the whole input as bytes, for a binary format (a zip): nothing is decoded. The signal is
+ * checked before every chunk and progress reported after it; a stream is cancelled when the read
+ * stops early.
+ * @param input - the input
+ * @param options - cancellation and progress (the encoding is ignored)
+ * @returns the bytes, or null when the input is text (a string, or a chunk that is a string),
+ * which a binary format cannot read
+ */
+export declare function readBytes(input: ImportInput, options?: ReadOptions): Promise<Uint8Array | null>;
 /**
  * Read the whole input as one string (the GML / DOT / JSON path, design section 8.4).
  * @param input - the input

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@@ -1 +1 @@
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+{"version":3,"file":"input.d.ts","sourceRoot":"","sources":["../../../src/common/input.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;GAeG;AAIH,OAAO,EAAE,KAAK,WAAW,EAAE,MAAM,aAAa,CAAC;AAC/C,OAAO,EAAiD,iBAAiB,EAAyB,MAAM,YAAY,CAAC;AACrH,OAAO,EAAE,KAAK,mBAAmB,EAAE,MAAM,aAAa,CAAC;AAEvD,OAAO,EAAE,iBAAiB,EAAE,CAAC;AAE7B;;;;GAIG;AACH,MAAM,WAAW,WAAW;IACxB,6DAA6D;IAC7D,QAAQ,CAAC,MAAM,CAAC,EAAE,WAAW,GAAG,IAAI,GAAG,SAAS,CAAC;IACjD,2DAA2D;IAC3D,QAAQ,CAAC,UAAU,CAAC,EAAE,CAAC,CAAC,SAAS,EAAE,MAAM,EAAE,UAAU,CAAC,EAAE,MAAM,KAAK,IAAI,CAAC,GAAG,IAAI,GAAG,SAAS,CAAC;IAC5F,qGAAqG;IACrG,QAAQ,CAAC,QAAQ,CAAC,EAAE,MAAM,GAAG,IAAI,GAAG,SAAS,CAAC;IAC9C;;;OAGG;IACH,QAAQ,CAAC,gBAAgB,CAAC,EAAE,CAAC,CAAC,IAAI,EAAE,MAAM,KAAK,MAAM,GAAG,IAAI,CAAC,GAAG,SAAS,CAAC;CAC7E;AAQD;;;;GAIG;AACH,wBAAgB,iBAAiB,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAM9D;AA2MD;;;;;;;GAOG;AACH,wBAAgB,eAAe,CAAC,KAAK,EAAE,UAAU,GAAG,MAAM,CAMzD;AA8BD;;;;GAIG;AACH,wBAAgB,aAAa,CAAC,KAAK,EAAE,OAAO,GAAG,KAAK,IAAI,WAAW,CAQlE;AAED;;;;;GAKG;AACH,wBAAgB,WAAW,CAAC,KAAK,EAAE,WAAW,GAAG,MAAM,GAAG,IAAI,CAQ7D;AAED;;;;;;;GAOG;AACH,wBAAgB,cAAc,CAAC,MAAM,EAAE,WAAW,GAAG,IAAI,GAAG,SAAS,GAAG,IAAI,CAU3E;AAgBD;;;;;;;;;;GAUG;AACH,wBAAuB,UAAU,CAC7B,KAAK,EAAE,WAAW,EAClB,MAAM,EAAE,mBAAmB,EAC3B,OAAO,GAAE,WAAgB,GAC1B,cAAc,CAAC,MAAM,EAAE,IAAI,EAAE,SAAS,CAAC,CAmGzC;AA4CD;;;;;;;;GAQG;AACH,wBAAsB,SAAS,CAAC,KAAK,EAAE,WAAW,EAAE,OAAO,GAAE,WAAgB,GAAG,OAAO,CAAC,UAAU,GAAG,IAAI,CAAC,CA6BzG;AAED;;;;;;GAMG;AACH,wBAAsB,QAAQ,CAC1B,KAAK,EAAE,WAAW,EAClB,MAAM,EAAE,mBAAmB,EAC3B,OAAO,GAAE,WAAgB,GAC1B,OAAO,CAAC,MAAM,CAAC,CAWjB;AAED;;;;;;GAMG;AACH,qBAAa,UAAW,YAAW,aAAa,CAAC,MAAM,CAAC;IACpD,OAAO,CAAC,QAAQ,CAAC,KAAK,CAAc;IAEpC,OAAO,CAAC,QAAQ,CAAC,MAAM,CAAsB;IAE7C,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAc;IAEtC,OAAO,CAAC,UAAU,CAAK;IAEvB;;;;;OAKG;gBACS,KAAK,EAAE,WAAW,EAAE,MAAM,EAAE,mBAAmB,EAAE,OAAO,GAAE,WAAgB;IAMtF;;;OAGG;IACH,IAAI,IAAI,IAAI,MAAM,CAEjB;IAED;;;;OAIG;IACI,CAAC,MAAM,CAAC,aAAa,CAAC,IAAI,cAAc,CAAC,MAAM,EAAE,IAAI,EAAE,SAAS,CAAC;CAoE3E"}

package/dist/src/common/input.js

@@ -462,6 +462,45 @@ async function* streamChunks(stream, signal) {
         reader.releaseLock();
     }
 }
+/**
+ * Read the whole input as bytes, for a binary format (a zip): nothing is decoded. The signal is
+ * checked before every chunk and progress reported after it; a stream is cancelled when the read
+ * stops early.
+ * @param input - the input
+ * @param options - cancellation and progress (the encoding is ignored)
+ * @returns the bytes, or null when the input is text (a string, or a chunk that is a string),
+ * which a binary format cannot read
+ */
+export async function readBytes(input, options = {}) {
+    const signal = options.signal ?? null;
+    throwIfAborted(signal);
+    if (typeof input === "string") {
+        return null;
+    }
+    if (input instanceof Uint8Array) {
+        options.onProgress?.(input.byteLength, input.byteLength);
+        return input;
+    }
+    const parts = [];
+    let done = 0;
+    for await (const chunk of isReadableStream(input) ? streamChunks(input, signal) : input) {
+        throwIfAborted(signal);
+        if (typeof chunk === "string") {
+            return null;
+        }
+        if (!(chunk instanceof Uint8Array)) {
+            throw new GraphFormatError("E_UNSUPPORTED", "an input chunk must be a string or a Uint8Array", {
+                reason: "chunk type",
+                found: typeof chunk,
+            });
+        }
+        parts.push(chunk);
+        done += chunk.byteLength;
+        options.onProgress?.(done);
+    }
+    options.onProgress?.(done, done);
+    return parts.length === 0 ? new Uint8Array(0) : concatBytes(parts);
+}
 /**
  * Read the whole input as one string (the GML / DOT / JSON path, design section 8.4).
  * @param input - the input

package/dist/src/common/input.js.map

@@ -1 +1 @@
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