@graphty/graph-io 0.3.16 → 0.3.18

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

@@ -1 +1 @@
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package/dist/src/formats/json/dialect.d.ts

@@ -19,11 +19,12 @@ export type JsonDialect = "node-link" | "d3" | "jgf" | "cytoscape" | "graphology
 /** Every dialect name, for option checking and messages. */
 export declare const JSON_DIALECTS: readonly JsonDialect[];
 /**
- * The dialects the importer reads: every JsonDialect plus two it only reads, NetworkX
- * adjacency_data (`nodes` plus one neighbour list per node under `adjacency`) and tree_data (a
- * nested `id` / `children` record). The exporter writes neither; write node-link instead.
+ * The dialects the importer reads: every JsonDialect plus three it only reads, NetworkX
+ * adjacency_data (`nodes` plus one neighbour list per node under `adjacency`), tree_data (a
+ * nested `id` / `children` record) and OBO Graphs (`graphs[]` of `sub` / `pred` / `obj` edges, the
+ * JSON form of the Gene Ontology and the OBO Foundry ontologies). The exporter writes none of them.
  */
-export type JsonImportDialect = JsonDialect | "adjacency" | "tree";
+export type JsonImportDialect = JsonDialect | "adjacency" | "tree" | "obographs";
 /** Every dialect the importer reads, for option checking and messages. */
 export declare const JSON_IMPORT_DIALECTS: readonly JsonImportDialect[];
 /** The key under `meta.extra` that holds the shape record (design section 8.5). */
@@ -83,8 +84,9 @@ export declare function isJsonDialect(value: unknown): value is JsonDialect;
 export declare function isJsonImportDialect(value: unknown): value is JsonImportDialect;
 /**
  * The dialect of a parsed JSON document, by the shape rules of design section 8.2 (Cytoscape:
- * `elements` or a top-level array of `{ data }` elements; JGF: `graph.nodes` / `graph.edges` or
- * `graphs[]`; graphology: `options.type` / `options.multi`, `key` nodes without `id`, edges with
+ * `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
  * `directed` / `multigraph` / `graph`; NetworkX adjacency_data: `nodes` and `adjacency` without
  * `links` / `edges`; NetworkX tree_data: `children` without `nodes` / `links` / `edges`; else

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

@@ -1 +1 @@
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package/dist/src/formats/json/dialect.js

@@ -27,6 +27,7 @@ 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). */
 export const META_KEY = "json";
@@ -66,8 +67,9 @@ export function isJsonImportDialect(value) {
 }
 /**
  * The dialect of a parsed JSON document, by the shape rules of design section 8.2 (Cytoscape:
- * `elements` or a top-level array of `{ data }` elements; JGF: `graph.nodes` / `graph.edges` or
- * `graphs[]`; graphology: `options.type` / `options.multi`, `key` nodes without `id`, edges with
+ * `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
  * `directed` / `multigraph` / `graph`; NetworkX adjacency_data: `nodes` and `adjacency` without
  * `links` / `edges`; NetworkX tree_data: `children` without `nodes` / `links` / `edges`; else
@@ -91,7 +93,7 @@ export function sniffJsonDialect(root) {
         return "jgf";
     }
     if (Array.isArray(root.graphs)) {
-        return "jgf";
+        return isOboGraph(firstJsonObject(root.graphs)) ? "obographs" : "jgf";
     }
     if (!hasKey(root, "edges") && !hasKey(root, "links")) {
         if (hasKey(root, "nodes") && hasKey(root, "adjacency")) {
@@ -120,6 +122,25 @@ export function sniffJsonDialect(root) {
     const bare = !hasKey(root, "directed") && !hasKey(root, "multigraph") && !hasKey(root, "graph");
     return bare && hasKey(root, "links") ? "d3" : "node-link";
 }
+/** The node types of OBO Graphs (the OWL entity kinds). */
+const OBOGRAPHS_NODE_TYPES = new Set(["CLASS", "INDIVIDUAL", "PROPERTY"]);
+/**
+ * Whether a graph of a `graphs[]` document is an OBO Graphs graph rather than JGF: anywhere in its
+ * nodes or edges, an edge with `sub` (or the outdated `subj`) and `obj`, or a `pred`, or a node
+ * with `lbl`, `meta` or a `type` of CLASS / INDIVIDUAL / PROPERTY (design 1.6: looking only at the
+ * first node and edge misses graphs with no edges and graphs whose first node has no `lbl`).
+ * @param graph - the first graph, or null
+ * @returns true for OBO Graphs
+ */
+function isOboGraph(graph) {
+    if (graph === null) {
+        return false;
+    }
+    const isEdge = (e) => isJsonObject(e) && ((hasKey(e, "obj") && (hasKey(e, "sub") || hasKey(e, "subj"))) || hasKey(e, "pred"));
+    const isNode = (n) => isJsonObject(n) && (hasKey(n, "lbl") || hasKey(n, "meta") || OBOGRAPHS_NODE_TYPES.has(n.type));
+    return ((Array.isArray(graph.edges) && graph.edges.some(isEdge)) ||
+        (Array.isArray(graph.nodes) && graph.nodes.some(isNode)));
+}
 /**
  * The first object of an array, or null.
  * @param value - maybe an array
@@ -170,6 +191,8 @@ export const DIALECT_DEFAULT_DIRECTED = Object.freeze({
     // networkx adjacency_data declares `directed`; tree_graph always builds a DiGraph
     adjacency: false,
     tree: true,
+    // OBO Graphs edges point from the subject (child) to the object (parent)
+    obographs: true,
 });
 /**
  * The dtypes a JSON dialect keeps as declared: JSON declares no types, so a value reads back as

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

@@ -1 +1 @@
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+{"version":3,"file":"dialect.js","sourceRoot":"","sources":["../../../../src/formats/json/dialect.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAIH,OAAO,EAAE,YAAY,EAAE,MAAM,wBAAwB,CAAC;AAMtD,4DAA4D;AAC5D,MAAM,CAAC,MAAM,aAAa,GAA2B,MAAM,CAAC,MAAM,CAAC;IAC/D,WAAW;IACX,IAAI;IACJ,KAAK;IACL,WAAW;IACX,YAAY;IACZ,KAAK;CACR,CAAC,CAAC;AAUH,0EAA0E;AAC1E,MAAM,CAAC,MAAM,oBAAoB,GAAiC,MAAM,CAAC,MAAM,CAAC;IAC5E,GAAG,aAAa;IAChB,WAAW;IACX,MAAM;IACN,WAAW;CACd,CAAC,CAAC;AAEH,mFAAmF;AACnF,MAAM,CAAC,MAAM,QAAQ,GAAG,MAAM,CAAC;AA8B/B;;;;GAIG;AACH,MAAM,UAAU,YAAY,CAAC,KAAc;IACvC,OAAO,OAAO,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC;AAChF,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,MAAM,CAAC,MAAyC,EAAE,GAAW;IACzE,OAAO,MAAM,CAAC,SAAS,CAAC,cAAc,CAAC,IAAI,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC;AAC7D,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,aAAa,CAAC,KAAc;IACxC,OAAO,OAAO,KAAK,KAAK,QAAQ,IAAK,aAAmC,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC;AAC7F,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,mBAAmB,CAAC,KAAc;IAC9C,OAAO,OAAO,KAAK,KAAK,QAAQ,IAAK,oBAA0C,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC;AACpG,CAAC;AAED;;;;;;;;;;;;GAYG;AACH,MAAM,UAAU,gBAAgB,CAAC,IAAa;IAC1C,IAAI,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;QACtB,MAAM,KAAK,GAAG,eAAe,CAAC,IAAI,CAAC,CAAC;QACpC,OAAO,IAAI,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,KAAK,KAAK,IAAI,IAAI,YAAY,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,IAAI,CAAC;IAClG,CAAC;IACD,IAAI,CAAC,YAAY,CAAC,IAAI,CAAC,EAAE,CAAC;QACtB,OAAO,IAAI,CAAC;IAChB,CAAC;IACD,IAAI,MAAM,CAAC,IAAI,EAAE,UAAU,CAAC,EAAE,CAAC;QAC3B,OAAO,WAAW,CAAC;IACvB,CAAC;IACD,IAAI,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,EAAE,OAAO,CAAC,IAAI,MAAM,CAAC,IAAI,CAAC,KAAK,EAAE,OAAO,CAAC,CAAC,EAAE,CAAC;QAC3F,OAAO,KAAK,CAAC;IACjB,CAAC;IACD,IAAI,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,EAAE,CAAC;QAC7B,OAAO,UAAU,CAAC,eAAe,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,CAAC;IAC1E,CAAC;IACD,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,EAAE,CAAC;QACnD,IAAI,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,IAAI,MAAM,CAAC,IAAI,EAAE,WAAW,CAAC,EAAE,CAAC;YACrD,OAAO,WAAW,CAAC;QACvB,CAAC;QACD,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,EAAE,CAAC;YACzB,OAAO,MAAM,CAAC,IAAI,EAAE,UAAU,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC;QACpD,CAAC;IACL,CAAC;IACD,MAAM,SAAS,GAAG,eAAe,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;IAC9C,MAAM,SAAS,GAAG,eAAe,CAAC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;IACnF,IAAI,YAAY,CAAC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,EAAE,MAAM,CAAC,IAAI,MAAM,CAAC,IAAI,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC,EAAE,CAAC;QAChG,OAAO,YAAY,CAAC;IACxB,CAAC;IACD,IAAI,SAAS,KAAK,IAAI,IAAI,MAAM,CAAC,SAAS,EAAE,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,IAAI,CAAC,EAAE,CAAC;QAC7E,OAAO,YAAY,CAAC;IACxB,CAAC;IACD,IAAI,SAAS,KAAK,IAAI,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,MAAM,CAAC,EAAE,CAAC;QACnD,IAAI,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,IAAI,YAAY,CAAC,SAAS,CAAC,UAAU,CAAC,EAAE,CAAC;YACxE,OAAO,YAAY,CAAC;QACxB,CAAC;IACL,CAAC;IACD,IAAI,SAAS,KAAK,IAAI,IAAI,MAAM,CAAC,SAAS,EAAE,MAAM,CAAC,IAAI,MAAM,CAAC,SAAS,EAAE,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,QAAQ,CAAC,EAAE,CAAC;QAC7G,OAAO,KAAK,CAAC;IACjB,CAAC;IACD,MAAM,IAAI,GAAG,CAAC,MAAM,CAAC,IAAI,EAAE,UAAU,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,YAAY,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC;IAChG,OAAO,IAAI,IAAI,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,WAAW,CAAC;AAC9D,CAAC;AAED,2DAA2D;AAC3D,MAAM,oBAAoB,GAAyB,IAAI,GAAG,CAAC,CAAC,OAAO,EAAE,YAAY,EAAE,UAAU,CAAC,CAAC,CAAC;AAEhG;;;;;;;GAOG;AACH,SAAS,UAAU,CAAC,KAAqC;IACrD,IAAI,KAAK,KAAK,IAAI,EAAE,CAAC;QACjB,OAAO,KAAK,CAAC;IACjB,CAAC;IACD,MAAM,MAAM,GAAG,CAAC,CAAU,EAAW,EAAE,CACnC,YAAY,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC,CAAC,EAAE,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC,CAAC,IAAI,MAAM,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC,CAAC;IAC5G,MAAM,MAAM,GAAG,CAAC,CAAU,EAAW,EAAE,CACnC,YAAY,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,CAAC,EAAE,MAAM,CAAC,IAAI,oBAAoB,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC;IACnG,OAAO,CACH,CAAC,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,IAAI,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;QACxD,CAAC,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,IAAI,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAC3D,CAAC;AACN,CAAC;AAED;;;;GAIG;AACH,SAAS,eAAe,CAAC,KAAc;IACnC,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC;QACxB,OAAO,IAAI,CAAC;IAChB,CAAC;IACD,MAAM,KAAK,GAAY,KAAK,CAAC,IAAI,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,YAAY,CAAC,IAAI,CAAC,CAAC,CAAC;IAChE,OAAO,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC;AAC9C,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,WAAW,CAAC,IAAe;IACvC,MAAM,GAAG,GAAY,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC;IAC1C,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,EAAE,CAAC;QACrB,OAAO,EAAE,CAAC;IACd,CAAC;IACD,MAAM,IAAI,GAAG,CAAC,GAAW,EAAsB,EAAE,CAAC,CAAC,OAAO,GAAG,CAAC,GAAG,CAAC,KAAK,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IACxG,MAAM,IAAI,GAAG,CAAC,GAAW,EAAuB,EAAE,CAAC,CAAC,OAAO,GAAG,CAAC,GAAG,CAAC,KAAK,SAAS,C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package/dist/src/formats/json/importer.d.ts

@@ -30,10 +30,19 @@
  * endpoint, a declared field of the wrong type, an unknown Cytoscape parent, an id the coercion rule
  * rejects.
  */
-import { type GraphImporter } from "../../types.js";
-import { type JsonImportDialect } from "./dialect.js";
-/** The format-specific options of the JSON importer. */
-export interface JsonImportOptions {
+import { type ColumnDecl, type ColumnHandle, type GraphMetaPatch, type GraphSink, type NodeId } from "@graphty/graph-format";
+import { DirectionResolver, type EdgeKind } from "../../common/direction.js";
+import { IdCoercer } from "../../common/ids.js";
+import { type ResolvedImportOptions } from "../../common/options.js";
+import { ImportReportBuilder } from "../../common/report.js";
+import { type GraphChoiceOptions, type GraphImporter } from "../../types.js";
+import { type JsonImportDialect, type JsonShapeMeta } from "./dialect.js";
+/**
+ * The format-specific options of the JSON importer. `graphIndex` / `graphName` choose one graph of
+ * a JGF or OBO Graphs `graphs` array (the first by default); a graph's name is its `id`, else its
+ * label.
+ */
+export interface JsonImportOptions extends GraphChoiceOptions {
     /** The dialect to read; "auto" (default) sniffs the parsed document. */
     dialect?: JsonImportDialect | "auto" | undefined;
     /**
@@ -52,8 +61,18 @@ export interface JsonImportOptions {
      * every endpoint is an integer below the node count and no node id is a number.
      */
     indexLinks?: boolean | "auto" | undefined;
-    /** jgf: which graph of a `graphs` array to read; 0 by default. */
-    graphIndex?: number | undefined;
+    /**
+     * obographs: "curie" (default) reads `http://purl.obolibrary.org/obo/GO_0008150` as `GO:0008150`
+     * and `.../obo/go#regulates` as `regulates`, the identifiers the `.obo` file of the same ontology
+     * writes; "iri" keeps every IRI as written.
+     */
+    oboIds?: "curie" | "iri" | undefined;
+    /**
+     * obographs: "metadata" (default) keeps PROPERTY nodes and their subPropertyOf / inverseOf edges
+     * in `meta.extra.obographs`, as the OBO importer keeps `[Typedef]` frames; "nodes" makes them
+     * nodes and edges.
+     */
+    typedefs?: "metadata" | "nodes" | undefined;
     /**
      * node-link / d3 / vis / graphology: where the node array is, as a dotted path of object keys
      * from the document root (`"data.nodes"`); the object holding it is read as the graph record
@@ -109,8 +128,18 @@ export declare const JSON_ISSUE: Readonly<{
     ID_MERGED: "W_ID_MERGED";
     /** Edge ids of mixed JSON types were stored as text. */
     EDGE_ID_STRINGIFIED: "W_EDGE_ID_STRINGIFIED";
-    /** A JGF `graphs` array holds more than one graph; only `graphIndex` is read. */
+    /** A JGF or OBO Graphs `graphs` array holds more than one graph; only the chosen one is read. */
     MULTIPLE_GRAPHS: "W_MULTIPLE_GRAPHS";
+    /** `graphIndex` is beyond the `graphs` array, or `graphName` names none of its graphs (fatal). */
+    GRAPH_NOT_FOUND: "E_GRAPH_NOT_FOUND";
+    /** `graphName` names more than one graph of the `graphs` array (fatal). */
+    AMBIGUOUS_GRAPH_NAME: "E_AMBIGUOUS_GRAPH_NAME";
+    /** obographs: an edge uses the outdated `subj` key of the OBO Graphs README; it is read as `sub`. */
+    OBOGRAPHS_SUBJ: "W_JSON_OBOGRAPHS_SUBJ";
+    /** obographs: an edge endpoint missing from `nodes` (a placeholder node is made, or the edge dropped under addMissingNodes false). */
+    DANGLING_REFERENCE: "W_DANGLING_REFERENCE";
+    /** The document is longer than one JavaScript string can hold (fatal; category unsupported). */
+    TOO_LARGE: "E_TOO_LARGE";
     /** JGF hyperedges under the "error" policy. */
     HYPEREDGE: "E_HYPEREDGE";
     /** JGF hyperedges skipped under the default "skip" policy. */
@@ -138,8 +167,296 @@ export declare const JSON_ISSUE: Readonly<{
     /** A declared encoding the platform cannot decode was ignored. */
     UNKNOWN_ENCODING: "W_UNKNOWN_ENCODING";
 }>;
+export type JsonRecord = Record<string, unknown>;
+/** An edge id column declared from a scan of the file's edge ids. */
+interface EdgeIdColumn {
+    readonly handle: ColumnHandle;
+    /** Whether numeric ids are stored as text (the file mixes numbers and strings). */
+    readonly stringify: boolean;
+    /** The id texts seen so far when the dialect requires unique ids, else null. */
+    readonly seen: Set<string> | null;
+}
+/** The resolved format-specific options. */
+interface ResolvedJsonOptions {
+    readonly dialect: JsonImportDialect | "auto";
+    readonly nodeIdKey: string | null;
+    readonly edgesKey: string | null;
+    readonly sourceKey: string | null;
+    readonly targetKey: string | null;
+    readonly indexLinks: boolean | "auto";
+    readonly graphIndex: number;
+    /** The caller's graphIndex / graphName, as given, for chooseGraph(). */
+    readonly choice: GraphChoiceOptions;
+    /** obographs: CURIE or IRI ids. */
+    readonly oboIds: "curie" | "iri";
+    /** obographs: PROPERTY nodes as metadata or as nodes. */
+    readonly typedefs: "metadata" | "nodes";
+    /** The dotted path segments of the node array, or null for the root's own nodes key. */
+    readonly nodesPath: readonly string[] | null;
+    /** The dotted path segments of the edge array, or null for the edges / links key beside the nodes. */
+    readonly edgesPath: readonly string[] | null;
+    /** Set by importAll(): every graph of a `graphs` array is read, so none is reported as skipped. */
+    readonly all?: boolean;
+}
+/**
+ * Writes inferred attribute cells for one table, caching the handle of every column after its
+ * first write so the hot loop never looks a column up by name twice. Names that collide with a
+ * structural column declared up front are suffixed deterministically (design section 5.6).
+ */
+declare class AttributeWriter {
+    private readonly sink;
+    private readonly domain;
+    private readonly handles;
+    private readonly reservedNames;
+    /**
+     * Create a writer.
+     * @param sink - the sink
+     * @param domain - node or edge
+     */
+    constructor(sink: GraphSink, domain: "node" | "edge");
+    /**
+     * Declare a structural column up front; attribute keys with its name are suffixed from now on.
+     * @param decl - the declaration
+     * @returns the handle
+     */
+    declare(decl: ColumnDecl): ColumnHandle;
+    /**
+     * Declare a structural column only when the file uses it.
+     * @param decl - the declaration
+     * @param present - whether any element carries the field
+     * @returns the handle, or INVALID_INDEX when not declared
+     */
+    declareIf(decl: ColumnDecl, present: boolean): ColumnHandle;
+    /**
+     * Whether a name is taken in the sink's table (for the deterministic rename rule).
+     * @param name - the column name
+     * @returns true when a column of that name exists
+     */
+    taken(name: string): boolean;
+    /**
+     * Write one attribute cell by its source key; null and undefined leave the row unset.
+     * @param row - the node or edge index
+     * @param key - the source key
+     * @param value - the JSON value
+     * @param suffix - the suffix applied when the key collides with a structural column
+     */
+    write(row: number, key: string, value: unknown, suffix: string): void;
+    /**
+     * Write through a handle or a name.
+     * @param column - the handle or name
+     * @param row - the row
+     * @param value - the value
+     */
+    set(column: ColumnHandle | string, row: number, value: unknown): void;
+    /**
+     * Look a column up by name.
+     * @param name - the column name
+     * @returns the handle, or INVALID_INDEX
+     */
+    private lookup;
+}
+/**
+ * Everything one import call shares between the dialect readers.
+ */
+export declare class ImportContext {
+    readonly sink: GraphSink;
+    readonly report: ImportReportBuilder;
+    readonly options: ResolvedImportOptions;
+    readonly json: ResolvedJsonOptions;
+    readonly ids: IdCoercer;
+    readonly direction: DirectionResolver;
+    readonly nodes: AttributeWriter;
+    readonly edges: AttributeWriter;
+    /** Whether the caller passed `defaultDirected` explicitly (then it beats the dialect's convention). */
+    readonly explicitDefaultDirected: boolean;
+    /** Nodes and edges pushed since the signal was last checked. */
+    private elementsSinceCheck;
+    /**
+     * Create the context.
+     * @param sink - the sink
+     * @param report - the report
+     * @param options - the resolved common options
+     * @param json - the resolved format options
+     * @param explicitDefaultDirected - whether the caller passed defaultDirected
+     */
+    constructor(sink: GraphSink, report: ImportReportBuilder, options: ResolvedImportOptions, json: ResolvedJsonOptions, explicitDefaultDirected: boolean);
+    /**
+     * Report a `nodeIdFrom` other than "id" for a dialect whose ids are unambiguous.
+     * @param dialect - the dialect
+     * @param idField - where the dialect's ids come from, for the message
+     */
+    reportNodeIdFrom(dialect: JsonImportDialect, idField: string): void;
+    /**
+     * The direction assumed when the file declares none: the caller's `defaultDirected` when given,
+     * else the dialect's convention.
+     * @param dialect - the dialect
+     * @returns the direction
+     */
+    defaultDirected(dialect: JsonImportDialect): boolean;
+    /** The direction the file declares (or the default), set by setHeader(). */
+    private fileDirected;
+    /**
+     * Rule 1 of design section 8.4: set the sink's direction from the file's header (or the
+     * dialect's default) before the first edge, remembering the file's direction for uniformKind().
+     * @param directed - the file's direction
+     */
+    setHeader(directed: boolean): void;
+    /**
+     * The edge kind every edge of a dialect without per-edge direction has: the file's direction
+     * (the resolver expands it when the sink's direction differs).
+     * @returns the kind
+     */
+    uniformKind(): EdgeKind;
+    /**
+     * Coerce a node id value per the `ids` option, reporting what cannot be an id. A JSON boolean or
+     * null is `unsupported` unless `ids` is "string" (design section 8.5); anything the rule rejects
+     * is recorded through the per-element catch.
+     * @param raw - the JSON value; undefined when the record has no id key
+     * @param element - the element name for the issue
+     * @returns the id, or null when the value was reported and the element must be skipped
+     */
+    coerceId(raw: unknown, element: string): NodeId | null;
+    /**
+     * Coerce an id that must be valid for the caller to proceed (hyperedge members): the rejections
+     * of coerceId() are thrown instead of recorded.
+     * @param raw - the JSON value
+     * @param element - the element name
+     * @returns the id
+     */
+    requireId(raw: unknown, element: string): NodeId;
+    /**
+     * Add a node, counting it or recording the failure.
+     * @param id - the node id
+     * @param element - the element name
+     * @returns the node index, or -1 when the sink refused the node
+     */
+    pushNode(id: NodeId, element: string): number;
+    /**
+     * Push one edge through the direction resolver, counting every logical edge the sink gained
+     * (both halves of an expanded edge, and the mirrors of an in-place expansion).
+     * @param source - the source id
+     * @param target - the target id
+     * @param kind - the edge's direction in the file
+     * @param weight - the weight, or undefined
+     * @param element - the element name for issues
+     * @returns the primary edge index
+     */
+    pushEdge(source: NodeId, target: NodeId, kind: EdgeKind, weight: number | undefined, element: string): number;
+    /**
+     * Check the cancellation signal every ABORT_CHECK_INTERVAL pushed elements, so an abort raised
+     * while the whole in-memory document is being walked rejects promptly.
+     */
+    checkAbort(): void;
+    /**
+     * Record a per-element failure and count the skipped element.
+     * @param err - the thrown value
+     * @param domain - which counter to bump
+     * @param element - the element name
+     */
+    skip(err: unknown, domain: "node" | "edge", element: string): void;
+    /**
+     * Report an element that is not an object and count it as skipped.
+     * @param domain - node or edge
+     * @param element - the element name
+     * @param what - what was expected
+     */
+    badElement(domain: "node" | "edge", element: string, what?: string): void;
+    /**
+     * Count a skipped element whose issue was already recorded.
+     * @param domain - node or edge
+     */
+    countSkipped(domain: "node" | "edge"): void;
+    /**
+     * Report an edge record without an endpoint and count it as skipped.
+     * @param element - the element name
+     * @param field - the missing field
+     */
+    missingEndpoint(element: string, field: string): void;
+    /**
+     * Record the shape metadata, the source format and further metadata fields in one setMeta()
+     * call (the sink replaces `extra` as a whole).
+     * @param shape - the shape record
+     * @param patch - further metadata fields
+     */
+    setMeta(shape: JsonShapeMeta, patch?: GraphMetaPatch): void;
+    /**
+     * Record which source field the weight came from, so the exporter writes it back under the same
+     * key (design section 3.7, `meta.weightOrigin`).
+     * @returns the metadata patch, empty for an unweighted import
+     */
+    weightOriginPatch(): GraphMetaPatch;
+    /**
+     * Write the graph-level attributes of a dict (NetworkX `graph`, JGF `metadata`, graphology
+     * `attributes`, Cytoscape `data`), one column per key.
+     * @param dict - the dict, or anything else (then reported)
+     * @param what - the dict's name for the issue
+     */
+    writeGraphDict(dict: unknown, what: string): void;
+    /**
+     * Read the weight field of an edge record.
+     * @param record - the record holding the attributes
+     * @returns the weight, or undefined when absent or null; E_INVALID_WEIGHT otherwise
+     */
+    weightOf(record: JsonRecord): number | undefined;
+    /**
+     * Write the attributes of a nested dict plus the element-level keys the dialect does not
+     * define (kept with the `#element` suffix).
+     * @param writer - the table writer
+     * @param row - the row
+     * @param record - the element record
+     * @param dict - the nested attribute dict
+     * @param structural - the element keys that are not attributes
+     * @param weightFrom - the weight key to skip in the dict, or null
+     */
+    writeNested(writer: AttributeWriter, row: number, record: JsonRecord, dict: JsonRecord, structural: ReadonlySet<string>, weightFrom: string | null): void;
+    /**
+     * Write a spec-typed string field (JGF label / relation), reporting a value of another type.
+     * @param writer - the table writer
+     * @param column - the declared column, or INVALID_INDEX when the file has no such field
+     * @param row - the row
+     * @param value - the value
+     * @param field - the field name
+     * @param element - the element name
+     */
+    writeStringField(writer: AttributeWriter, column: ColumnHandle, row: number, value: unknown, field: string, element: string): void;
+    /**
+     * Declare an edge id column with role "id" from a scan of the file's edge ids: f64 when every
+     * id is a number, string otherwise (numbers are then stored as their text and reported once).
+     * @param edges - the edge records
+     * @param read - how to read an edge's raw id
+     * @param name - the column name
+     * @param unique - whether uniqueness is enforced at freeze
+     * @returns the column, or null when no edge has an id
+     */
+    declareEdgeIds(edges: readonly unknown[], read: (edge: JsonRecord) => unknown, name: string, unique: boolean): EdgeIdColumn | null;
+    /**
+     * The value an edge id column stores for a raw id, checked BEFORE the edge is pushed so a bad
+     * id skips the edge without touching the sink (design section 11.1).
+     * @param column - the column, or null when the file has no edge ids
+     * @param raw - the raw id value
+     * @returns the value to store, or null when there is nothing to store
+     */
+    edgeIdValue(column: EdgeIdColumn | null, raw: unknown): string | number | null;
+    /**
+     * Write an edge id value from edgeIdValue().
+     * @param column - the column, or null
+     * @param edge - the edge index
+     * @param value - the value, or null for none
+     */
+    setEdgeId(column: EdgeIdColumn | null, edge: number, value: string | number | null): void;
+}
+/**
+ * The graph of a `graphs` array (JGF, OBO Graphs) that graphIndex / graphName choose, with
+ * W_MULTIPLE_GRAPHS when the others are skipped; importAll() reads graphs[graphIndex].
+ * @param ctx - the context
+ * @param root - the document
+ * @param what - the dialect's name, for the messages
+ * @returns the graph object; the import fails when there is none
+ */
+export declare function chosenGraph(ctx: ImportContext, root: JsonRecord, what: string): JsonRecord;
 /**
  * The JSON importer plugin (design section 8.4).
  */
 export declare const jsonImporter: GraphImporter<JsonImportOptions>;
+export {};
 //# sourceMappingURL=importer.d.ts.map

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

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