@graphty/graph-io 0.3.25 → 0.3.26

package/dist/src/formats/json/dialect.js

@@ -8,12 +8,16 @@
  * / `graph`), the d3 lineage of the same shape (`links`, `name` ids, integer index endpoints),
  * JSON Graph Format v2 (`graph.nodes` keyed by id, per-edge `directed`, hyperedges), Cytoscape.js
  * elements (`data.id` / `data.source` / `data.target`, `position`, `classes`, `data.parent`),
- * graphology serialisation (`key` / `attributes`, `undirected` edges, `options.type` / `multi`) and
+ * graphology serialization (`key` / `attributes`, `undirected` edges, `options.type` / `multi`) and
  * vis.js (`from` / `to`); read only: NetworkX adjacency_data (`nodes` + `adjacency`) and tree_data
  * (nested `id` / `children`).
  */
 import { capabilities } from "../../common/export.js";
-/** Every dialect name, for option checking and messages. */
+import { trimTrailingZeros } from "../../common/text.js";
+/**
+ * Every dialect name, for option checking and messages.
+ * @category Built-in formats
+ */
 export const JSON_DIALECTS = Object.freeze([
     "node-link",
     "d3",
@@ -21,20 +25,39 @@ export const JSON_DIALECTS = Object.freeze([
     "cytoscape",
     "graphology",
     "vis",
+    "obographs",
 ]);
-/** Every dialect the importer reads, for option checking and messages. */
+/**
+ * Every dialect the importer reads, for option checking and messages.
+ * @category Plugin helpers
+ */
 export const JSON_IMPORT_DIALECTS = Object.freeze([
     ...JSON_DIALECTS,
     "adjacency",
     "tree",
-    "obographs",
 ]);
-/** The key under `meta.extra` that holds the shape record (design section 8.5). */
+/**
+ * The key under `meta.extra` that holds the shape record (design section 8.5).
+ * @category Plugin helpers
+ */
 export const META_KEY = "json";
+/**
+ * What a JSON import recorded about the document's shape: the dialect it was read as
+ * (`jsonShapeOf(snapshot)?.dialect`), the keys it used, and so on. A JSON export with default
+ * options writes the same shape back.
+ * @param snapshot - a graph read from a JSON document
+ * @returns the shape, or null for a graph that was not read from JSON
+ * @category Built-in formats
+ */
+export function jsonShapeOf(snapshot) {
+    const shape = snapshot.meta.extra[META_KEY];
+    return isJsonObject(shape) ? shape : null;
+}
 /**
  * Whether a value is a plain JSON object (not null, not an array).
  * @param value - any value
  * @returns true for an object that is not an array
+ * @category Plugin helpers
  */
 export function isJsonObject(value) {
     return typeof value === "object" && value !== null && !Array.isArray(value);
@@ -45,6 +68,7 @@ export function isJsonObject(value) {
  * @param record - the record
  * @param key - the key
  * @returns true when the key is an own property
+ * @category Plugin helpers
  */
 export function hasKey(record, key) {
     return Object.prototype.hasOwnProperty.call(record, key);
@@ -53,6 +77,7 @@ export function hasKey(record, key) {
  * Whether a text names a dialect.
  * @param value - any value
  * @returns true for one of JSON_DIALECTS
+ * @category Plugin helpers
  */
 export function isJsonDialect(value) {
     return typeof value === "string" && JSON_DIALECTS.includes(value);
@@ -61,6 +86,7 @@ export function isJsonDialect(value) {
  * Whether a text names a dialect the importer reads.
  * @param value - any value
  * @returns true for one of JSON_IMPORT_DIALECTS
+ * @category Plugin helpers
  */
 export function isJsonImportDialect(value) {
     return typeof value === "string" && JSON_IMPORT_DIALECTS.includes(value);
@@ -70,13 +96,15 @@ export function isJsonImportDialect(value) {
  * `elements` or a top-level array of `{ data }` elements; OBO Graphs: `graphs[]` whose first graph
  * has an edge with `sub` (or `subj`) and `obj` or a `pred`, or a node with `lbl`, `meta` or an OWL
  * `type`; JGF: `graph.nodes` / `graph.edges` or any other `graphs[]`; graphology: `options.type` / `options.multi`, `key` nodes without `id`, edges with
- * `undirected` or an `attributes` record; vis: edges with `from` / `to`; d3: `links` without
+ * `undirected` or an `attributes` record, and vis: edges with `from` / `to`, both only without
+ * NetworkX's `links` / `directed` / `multigraph` / `graph` keys; d3: `links` without
  * `directed` / `multigraph` / `graph`; NetworkX adjacency_data: `nodes` and `adjacency` without
  * `links` / `edges`; NetworkX tree_data: `children` without `nodes` / `links` / `edges`; else
  * node-link). Pure: the importer wraps it with its issue
  * codes, the registry's sniff() uses it on a head that parses as a whole document.
  * @param root - the parsed document
  * @returns the dialect, or null when the document is not a graph document in any dialect
+ * @category Plugin helpers
  */
 export function sniffJsonDialect(root) {
     if (Array.isArray(root)) {
@@ -93,7 +121,8 @@ export function sniffJsonDialect(root) {
         return "jgf";
     }
     if (Array.isArray(root.graphs)) {
-        return isOboGraph(firstJsonObject(root.graphs)) ? "obographs" : "jgf";
+        // any graph decides: an ontology's first graph may be an empty stub before its imports
+        return root.graphs.some((g) => isJsonObject(g) && isOboGraph(g)) ? "obographs" : "jgf";
     }
     if (!hasKey(root, "edges") && !hasKey(root, "links")) {
         if (hasKey(root, "nodes") && hasKey(root, "adjacency")) {
@@ -108,15 +137,22 @@ export function sniffJsonDialect(root) {
     if (isJsonObject(root.options) && (hasKey(root.options, "type") || hasKey(root.options, "multi"))) {
         return "graphology";
     }
-    if (firstNode !== null && hasKey(firstNode, "key") && !hasKey(firstNode, "id")) {
+    // NetworkX's own keys (links, directed, multigraph, graph) settle node-link: one attribute named
+    // like a graphology or vis field (`attributes`, `undirected`, `key`, `from`) must not re-route it
+    const networkx = hasKey(root, "links") || hasKey(root, "directed") || hasKey(root, "multigraph") || hasKey(root, "graph");
+    if (!networkx && firstNode !== null && hasKey(firstNode, "key") && !hasKey(firstNode, "id")) {
         return "graphology";
     }
-    if (firstEdge !== null && !hasKey(firstEdge, "from")) {
+    if (!networkx && firstEdge !== null && !hasKey(firstEdge, "from")) {
         if (hasKey(firstEdge, "undirected") || isJsonObject(firstEdge.attributes)) {
             return "graphology";
         }
     }
-    if (firstEdge !== null && hasKey(firstEdge, "from") && hasKey(firstEdge, "to") && !hasKey(firstEdge, "source")) {
+    if (!networkx &&
+        firstEdge !== null &&
+        hasKey(firstEdge, "from") &&
+        hasKey(firstEdge, "to") &&
+        !hasKey(firstEdge, "source")) {
         return "vis";
     }
     const bare = !hasKey(root, "directed") && !hasKey(root, "multigraph") && !hasKey(root, "graph");
@@ -158,6 +194,7 @@ function firstJsonObject(value) {
  * from the JSON importer.
  * @param meta - the snapshot's metadata
  * @returns the fields found under `meta.extra.json`, each only when it has the expected type
+ * @category Plugin helpers
  */
 export function shapeMetaOf(meta) {
     const raw = meta.extra[META_KEY];
@@ -180,7 +217,10 @@ export function shapeMetaOf(meta) {
         cytoscape: isJsonObject(raw.cytoscape) ? raw.cytoscape : undefined,
     };
 }
-/** The direction a dialect assumes when the file declares none (design section 8.4, `defaultDirected`). */
+/**
+ * The direction a dialect assumes when the file declares none (design section 8.4, `defaultDirected`).
+ * @category Plugin helpers
+ */
 export const DIALECT_DEFAULT_DIRECTED = Object.freeze({
     "node-link": false,
     d3: false,
@@ -259,9 +299,18 @@ const TABLES = Object.freeze({
         hierarchy: false,
         graphAttributes: false,
     }),
+    // the OBO flat file's table: no column of the snapshot's own reads back as a column (the
+    // vocabulary columns have their places; every other one becomes property values or edge meta)
+    obographs: capabilities({
+        mixedDirection: false,
+        multiEdges: true,
+        selfLoops: true,
+        edgeIds: "none",
+        idCharset: "any",
+    }),
 });
 /**
- * What one dialect can express (design section 8.5): positions and visual columns are written as
+ * What one dialect can express: positions and visual columns are written as
  * plain attributes (an array for a multi-component column) and read back without their role,
  * except Cytoscape's `position` object; containment only as the Cytoscape `data.parent`; mixed
  * direction only where the dialect carries a per-edge flag (JGF `directed`, graphology
@@ -269,11 +318,15 @@ const TABLES = Object.freeze({
  * graph attributes everywhere but d3 (the bare shape) and vis.
  * @param dialect - the dialect
  * @returns its frozen capability table
+ * @category Built-in formats
  */
 export function dialectCapabilities(dialect) {
     return TABLES[dialect];
 }
-/** The Cytoscape element-level keys (everything else on an element lives under `data`). */
+/**
+ * The Cytoscape element-level keys (everything else on an element lives under `data`).
+ * @category Plugin helpers
+ */
 export const CYTOSCAPE_ELEMENT_KEYS = new Set([
     "selected",
     "selectable",
@@ -284,12 +337,16 @@ export const CYTOSCAPE_ELEMENT_KEYS = new Set([
     "scratch",
     "renderedPosition",
 ]);
-/** The Cytoscape element keys the importer maps structurally rather than to columns. */
+/**
+ * The Cytoscape element keys the importer maps structurally rather than to columns.
+ * @category Plugin helpers
+ */
 export const CYTOSCAPE_STRUCTURAL_KEYS = new Set(["data", "group", "position", "classes"]);
 /**
  * The suffix the importer appends to a column name that collides with a structural column or a
  * reserved key of its dialect (design section 5.6 names collisions deterministically); the exporter
  * strips it when the value goes back to the level the suffix names.
+ * @category Plugin helpers
  */
 export const SUFFIX = Object.freeze({
     /** A Cytoscape `data` key or a JGF / graphology attribute that collides with a structural column. */
@@ -297,14 +354,47 @@ export const SUFFIX = Object.freeze({
     /** An element-level key the dialect does not define (Cytoscape, JGF, graphology). */
     element: "#element",
 });
-/** The default source keys of a node-link edge record, tried in order (as fromRecords does). */
+/**
+ * The default source keys of a node-link edge record, tried in order (as fromRecords does).
+ * @category Plugin helpers
+ */
 export const NODE_LINK_SOURCE_KEYS = Object.freeze(["source", "src", "from"]);
-/** The default target keys of a node-link edge record, tried in order. */
+/**
+ * The default target keys of a node-link edge record, tried in order.
+ * @category Plugin helpers
+ */
 export const NODE_LINK_TARGET_KEYS = Object.freeze(["target", "dst", "to"]);
-/** The name of the position column every JSON dialect writes / reads (design section 5.2). */
+/**
+ * The name of the position column every JSON dialect writes / reads (design section 5.2).
+ * @category Plugin helpers
+ */
 export const POSITION_COLUMN = "position";
-/** The name of the Cytoscape classes column (a list of strings with role "classes"). */
+/**
+ * The name of the Cytoscape classes column (a list of strings with role "classes").
+ * @category Plugin helpers
+ */
 export const CLASSES_COLUMN = "classes";
-/** The name of the Cytoscape parent column (u32 refersTo node, role "parent"). */
+/**
+ * The name of the Cytoscape parent column (u32 refersTo node, role "parent").
+ * @category Plugin helpers
+ */
 export const PARENT_COLUMN = "parent";
+/**
+ * An integer text beyond 2^53 in exponent form (`100000000000000000000` -> `1e+20`, the same
+ * digits): the importer reads an integer literal that large as its exact digits (a string), so
+ * a number must not be written as one.
+ * @param text - the shortest decimal text of a finite number
+ * @returns the text, or its exponent form for an integer literal of 16 or more digits
+ * @category Plugin helpers
+ */
+export function exponentIfUnsafe(text) {
+    const match = /^(-?)(\d{16,})$/.exec(text);
+    if (match === null || Number.isSafeInteger(Number(text))) {
+        return text;
+    }
+    const [, sign, digits] = match;
+    const mantissa = trimTrailingZeros(digits);
+    const fraction = mantissa.length > 1 ? `.${mantissa.slice(1)}` : "";
+    return `${sign}${mantissa[0]}${fraction}e+${digits.length - 1}`;
+}
 //# sourceMappingURL=dialect.js.map

package/dist/src/formats/json/dialect.js.map

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package/dist/src/formats/json/exporter.d.ts

@@ -1,7 +1,7 @@
 /**
  * The JSON exporter (design section 8.5): one GraphExporter with a `dialect` option writing
  * NetworkX node-link (the default), d3 (`links`, optional index endpoints), JSON Graph Format v2,
- * Cytoscape.js elements, graphology serialisation or vis.js. The dialect defaults to the one the
+ * Cytoscape.js elements, graphology serialization or vis.js. The dialect defaults to the one the
  * importer recorded under `meta.extra.json` so a JSON file re-exported as JSON keeps its shape,
  * and to node-link for a snapshot from any other source.
  *
@@ -17,48 +17,113 @@
  * value is its JSON text; an unset row writes no key (design section 5.3). Non-finite numbers,
  * which JSON cannot carry, become null and are reported.
  */
-import { type ExportCapabilities, type GraphExporter } from "../../types.js";
+import { type CommonExportOptions, type ExportCapabilities, type GraphExporter } from "../../types.js";
 import { type JsonDialect } from "./dialect.js";
-/** The format-specific options of the JSON exporter. */
-export interface JsonExportOptions {
-    /** The dialect to write; default: the dialect the importer recorded, else "node-link". */
+/**
+ * The format-specific options of the JSON exporter.
+ * @category Built-in formats
+ */
+export interface JsonExportOptions extends CommonExportOptions {
+    /**
+     * The dialect to write. The default is the dialect a JSON import read, else "node-link".
+     * Attributes are written under their own names; vis.js shows the `label` attribute, so rename
+     * the attribute you want shown to `label` first (`snapshot.nodes.rename("name", "label")`). A CSV
+     * dialect name ("gephi", "generic"), from an options object shared with CSV saves, is ignored.
+     * @defaultValue as read, else "node-link"
+     */
     dialect?: JsonDialect | undefined;
-    /** Spaces per indentation level; 0 (default) writes compact JSON. */
-    indent?: number | undefined;
-    /** node-link / d3: the key of the edge array; default: the recorded key, else "edges" (d3: "links"). */
+    /**
+     * The indentation of one level: a number of spaces, or the text itself (spaces or tabs, such as
+     * "\t"). 0 or "" writes compact JSON on one line.
+     * @defaultValue 0
+     */
+    indent?: number | string | undefined;
+    /**
+     * node-link and d3: the key of the edge array. The default is the key a JSON import read, else
+     * "edges" ("links" for d3).
+     * @defaultValue as read, else "edges"
+     */
     edgesKey?: string | undefined;
-    /** node-link / d3 / vis: the node id key; default: the recorded key, else "id". */
+    /**
+     * node-link, d3 and vis: the node id key. The default is the key a JSON import read, else "id".
+     * @defaultValue as read, else "id"
+     */
     nodeIdKey?: string | undefined;
-    /** node-link / d3: write endpoints as node array positions; default: the recorded flag, else false. */
+    /**
+     * node-link and d3: write edge ends as positions in the node array instead of ids. The default
+     * is what a JSON import read, else false.
+     * @defaultValue as read, else false
+     */
     indexLinks?: boolean | undefined;
-    /** node-link / d3 / vis: the source key; default: the recorded key, else "source" (vis: "from"). */
+    /**
+     * node-link, d3 and vis: the source key. The default is the key a JSON import read, else
+     * "source" ("from" for vis). graph-io finds "source", "src" and "from" by itself; for another
+     * key, read the file back with the same `sourceKey` import option. Without it every edge is an
+     * `E_MISSING_ENDPOINT` error and is skipped, and a file with more edges than `errorLimit` (100 by
+     * default) fails to load with an `ImportError`. `checkExport()` does not warn about this.
+     * @defaultValue as read, else "source"
+     */
     sourceKey?: string | undefined;
-    /** node-link / d3 / vis: the target key; default: the recorded key, else "target" (vis: "to"). */
+    /**
+     * node-link, d3 and vis: the target key. The default is the key a JSON import read, else
+     * "target" ("to" for vis). graph-io finds "target", "dst" and "to" by itself; for another key,
+     * read the file back with the same `targetKey` import option, as for `sourceKey`.
+     * @defaultValue as read, else "target"
+     */
     targetKey?: string | undefined;
-    /** The key the weight is written under; default: the key the JSON importer read it from, else "weight". */
+    /**
+     * The key the weight is written under, in every dialect but OBO Graphs, which always writes the
+     * weight as "weight" in each edge's `meta` (checkExport() then returns W_OBOGRAPHS_EDGE_COLUMN_AS_META).
+     * The default is the key a JSON import read the weights from, else "weight". For another key,
+     * read the file back with `weightFrom` set to it, or the weights come back as a plain edge
+     * attribute.
+     * @defaultValue as read, else "weight"
+     */
     weightKey?: string | undefined;
+    /**
+     * OBO Graphs: the graph id written when the graph has none. A graph read from an OBO Graphs
+     * document keeps its own graph id, which this option does not change. Node ids are written in
+     * the form graph-io reads back as the same id: an IRI as it is, a prefixed id such as
+     * `GO:0008150` as its OBO address, and an id without a prefix (`a`) under the default OBO
+     * address (`http://purl.obolibrary.org/obo/graph.owl#a`), or as it is when you pass another IRI
+     * here. The default is `http://purl.obolibrary.org/obo/<ontology>.owl`.
+     * @defaultValue the ontology's OBO address
+     */
+    ontologyIri?: string | undefined;
 }
 /**
  * The LossNote codes of the JSON exporter's check(): the dialect-specific ones and, aliased, the
  * shared ones it records (`LOSS` holds the rest of the generic pre-flight's codes). A key is the
  * code without its severity prefix.
+ * @category Built-in formats
  */
 export declare const JSON_LOSS: Readonly<{
     /** Non-finite numbers (columns, weights) are written as null. */
     NONFINITE_AS_NULL: "W_NONFINITE_AS_NULL";
-    /** Cytoscape, vis and d3 carry no direction; the file re-imports with the dialect's default direction. */
+    /**
+     * The file cannot record direction: an undirected graph's edges read back as directed, or the whole graph reads
+     * back with the importer's default direction.
+     */
     DIRECTION_DROPPED: "W_DIRECTION_DROPPED";
     /** GEXF mutual pairs are written as two directed edges. */
     MUTUAL_EXPANDED: "W_MUTUAL_EXPANDED";
-    /** JGF keys its nodes by string; numeric ids re-import as text unless ids: "canonical". */
+    /**
+     * JGF keys its nodes by text, so number ids read back as text, unless you read the file with `ids: "canonical"`.
+     */
     NUMERIC_IDS_STRINGIFIED: "W_NUMERIC_IDS_STRINGIFIED";
-    /** JGF: two ids have the same text; export() throws E_INVALID_ID. */
+    /**
+     * Two node ids would be written as the same text (the number 5 and the text "5"); the save fails with
+     * E_INVALID_ID.
+     */
     ID_TEXT_COLLISION: "E_ID_TEXT_COLLISION";
-    /** JGF: integer-like id keys are enumerated first and ascending by JSON parsers; node order changes on re-import. */
+    /** The nodes read back in a different order. */
     NODE_ORDER: "W_NODE_ORDER";
     /** A column named like a reserved key of the dialect (id, source, target, ...) is skipped. */
     RESERVED_KEY: "W_RESERVED_KEY";
-    /** A plain edge column named like the weight key reads back as THE weight (or is skipped when weights are written). */
+    /**
+     * An attribute without the weight role is named like the key weights are written under; it reads back as the edge
+     * weight, or is not written when the graph has weights of its own.
+     */
     WEIGHT_KEY_CLASH: "W_WEIGHT_KEY_CLASH";
     /** A position column without a slot (every dialect but Cytoscape) is a plain array attribute; the role is lost. */
     POSITIONS_DROPPED: "W_POSITIONS_DROPPED";
@@ -66,24 +131,71 @@ export declare const JSON_LOSS: Readonly<{
     POSITION_Z_DROPPED: "W_POSITION_Z_DROPPED";
     /** Cytoscape has a single parent; a `parents` list column cannot be written. */
     PARENTS_DROPPED: "W_PARENTS_DROPPED";
-    /** node-link / d3 have no edge id slot; the id column is written as a plain attribute. */
+    /** Node-link / d3 have no edge id slot; the id column is written as a plain attribute. */
     EDGE_IDS_DROPPED: "W_EDGE_IDS_DROPPED";
-    /** An f64 column of integral values reads back as i32 (JSON declares no types). */
+    /**
+     * A number attribute whose values are all whole numbers reads back as integers, because the format does not record
+     * the type.
+     */
     INTEGRAL_F64_AS_I32: "W_INTEGRAL_F64_AS_I32";
-    /** A role column the dialect has no slot for is a plain attribute; 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 column without a set cell is not written (JSON declares no columns). */
     EMPTY_COLUMN_DROPPED: "W_EMPTY_COLUMN_DROPPED";
+    /**
+     * Obographs: an edge column (or the explicit weights) is written into each edge's meta and reads back inside the
+     * meta column.
+     */
+    OBOGRAPHS_EDGE_COLUMN_AS_META: "W_OBOGRAPHS_EDGE_COLUMN_AS_META";
+    /**
+     * Obographs: a node id or relation is written as an IRI the importer's default oboIds "curie" reads back as
+     * another id.
+     */
+    OBOGRAPHS_ID_CHANGED: "W_OBOGRAPHS_ID_CHANGED";
+    /** Obographs: a property_value's xsd datatype has no place in basicPropertyValues and reads back unset. */
+    OBOGRAPHS_DATATYPE_DROPPED: "W_OBOGRAPHS_DATATYPE_DROPPED";
+    /** Obographs: a node column outside the OBO vocabulary reads back inside the property_value column. */
+    COLUMN_AS_PROPERTY_VALUE: "W_COLUMN_AS_PROPERTY_VALUE";
+    /** Obographs: an edge without a relation is written with the pred is_a. */
+    RELATION_ASSUMED: "W_RELATION_ASSUMED";
+    /**
+     * Obographs: Typedef nodes are written as PROPERTY nodes, which read back as nodes only under typedefs: "nodes".
+     */
+    TYPEDEF_NODES: "W_TYPEDEF_NODES";
+    /**
+     * OBO Graphs: a graph attribute is written into the graph's `meta` and reads back in
+     * `snapshot.meta.extra.obographs`.
+     */
+    GRAPH_COLUMN_AS_METADATA: "W_GRAPH_COLUMN_AS_METADATA";
+    /** Obographs: numeric node ids are written as text and read back as strings. */
+    ID_TEXT_TYPE: "W_ID_TEXT_TYPE";
+    /**
+     * 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";
+    /**
+     * An attribute with a role (for example, the label) is written where the format keeps that role, and reads back under the
+     * name the format's importer gives it.
+     */
+    COLUMN_NAME_CHANGED: "W_COLUMN_NAME_CHANGED";
+    /**
+     * OBO Graphs: an OBO attribute stored as text where graph-io uses a dictionary (or the other way round); it reads
+     * back with graph-io's usual type. The values are the same.
+     */
+    DTYPE_UNSUPPORTED: "W_DTYPE_UNSUPPORTED";
 }>;
 /**
- * The JSON exporter plugin (design section 8.5). `capabilities` is the node-link table (the
+ * The JSON exporter plugin. `capabilities` is the node-link table (the
  * default dialect); check() applies the table of the dialect actually selected.
+ * @category Built-in formats
  */
 export declare const jsonExporter: GraphExporter<JsonExportOptions>;
 /**
  * The capability table of one dialect, for callers that pick a dialect before check().
  * @param dialect - the dialect
  * @returns the frozen table
+ * @category Built-in formats
  */
 export declare function jsonCapabilities(dialect: JsonDialect): ExportCapabilities;
 //# sourceMappingURL=exporter.d.ts.map

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

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