@graphty/graph-io 0.3.17 → 0.3.18

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

@@ -1 +1 @@
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+{"version":3,"file":"importer.d.ts","sourceRoot":"","sources":["../../../../src/formats/json/importer.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+BG;AAEH,OAAO,EACH,KAAK,UAAU,EACf,KAAK,YAAY,EAEjB,KAAK,cAAc,EACnB,KAAK,SAAS,EAEd,KAAK,MAAM,EACd,MAAM,uBAAuB,CAAC;AAwB/B,OAAO,EAAE,iBAAiB,EAAE,KAAK,QAAQ,EAAE,MAAM,2BAA2B,CAAC;AAC7E,OAAO,EAAkB,SAAS,EAAE,MAAM,qBAAqB,CAAC;AAEhE,OAAO,EAKH,KAAK,qBAAqB,EAG7B,MAAM,yBAAyB,CAAC;AACjC,OAAO,EAAE,mBAAmB,EAAE,MAAM,wBAAwB,CAAC;AAE7D,OAAO,EAEH,KAAK,kBAAkB,EACvB,KAAK,aAAa,EAIrB,MAAM,gBAAgB,CAAC;AACxB,OAAO,EASH,KAAK,iBAAiB,EACtB,KAAK,aAAa,EAQrB,MAAM,cAAc,CAAC;AAGtB;;;;GAIG;AACH,MAAM,WAAW,iBAAkB,SAAQ,kBAAkB;IACzD,wEAAwE;IACxE,OAAO,CAAC,EAAE,iBAAiB,GAAG,MAAM,GAAG,SAAS,CAAC;IACjD;;;OAGG;IACH,SAAS,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAC/B,qGAAqG;IACrG,QAAQ,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAC9B,4GAA4G;IAC5G,SAAS,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAC/B,wGAAwG;IACxG,SAAS,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAC/B;;;OAGG;IACH,UAAU,CAAC,EAAE,OAAO,GAAG,MAAM,GAAG,SAAS,CAAC;IAC1C;;;;OAIG;IACH,MAAM,CAAC,EAAE,OAAO,GAAG,KAAK,GAAG,SAAS,CAAC;IACrC;;;;OAIG;IACH,QAAQ,CAAC,EAAE,UAAU,GAAG,OAAO,GAAG,SAAS,CAAC;IAC5C;;;;;OAKG;IACH,SAAS,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAC/B;;;;;OAKG;IACH,SAAS,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;CAClC;AAED;;;;GAIG;AACH,eAAO,MAAM,UAAU;IACnB,+CAA+C;;IAE/C,2CAA2C;;IAE3C,yDAAyD;;IAEzD,yEAAyE;;IAEzE,qGAAqG;;IAErG,oDAAoD;;IAEpD,+BAA+B;;IAE/B,8GAA8G;;IAE9G,iDAAiD;;IAEjD,yFAAyF;;IAEzF,gHAAgH;;IAEhH,mHAAmH;;IAEnH,uDAAuD;;IAEvD,+FAA+F;;IAE/F,4GAA4G;;IAE5G,uEAAuE;;IAEvE,wDAAwD;;IAExD,iGAAiG;;IAEjG,kGAAkG;;IAElG,2EAA2E;;IAE3E,qGAAqG;;IAErG,sIAAsI;;IAEtI,gGAAgG;;IAEhG,+CAA+C;;IAE/C,8DAA8D;;IAE9D,6EAA6E;;IAE7E,uEAAuE;;IAEvE,6HAA6H;;IAE7H,4IAA4I;;IAE5I,0GAA0G;;IAE1G,6CAA6C;;IAE7C,+FAA+F;;IAE/F,kFAAkF;;IAElF,yHAAyH;;IAEzH,sGAAsG;;IAEtG,kEAAkE;;EAEpE,CAAC;AA2DH,MAAM,MAAM,UAAU,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;AAEjD,qEAAqE;AACrE,UAAU,YAAY;IAClB,QAAQ,CAAC,MAAM,EAAE,YAAY,CAAC;IAC9B,mFAAmF;IACnF,QAAQ,CAAC,SAAS,EAAE,OAAO,CAAC;IAC5B,gFAAgF;IAChF,QAAQ,CAAC,IAAI,EAAE,GAAG,CAAC,MAAM,CAAC,GAAG,IAAI,CAAC;CACrC;AAUD,4CAA4C;AAC5C,UAAU,mBAAmB;IACzB,QAAQ,CAAC,OAAO,EAAE,iBAAiB,GAAG,MAAM,CAAC;IAC7C,QAAQ,CAAC,SAAS,EAAE,MAAM,GAAG,IAAI,CAAC;IAClC,QAAQ,CAAC,QAAQ,EAAE,MAAM,GAAG,IAAI,CAAC;IACjC,QAAQ,CAAC,SAAS,EAAE,MAAM,GAAG,IAAI,CAAC;IAClC,QAAQ,CAAC,SAAS,EAAE,MAAM,GAAG,IAAI,CAAC;IAClC,QAAQ,CAAC,UAAU,EAAE,OAAO,GAAG,MAAM,CAAC;IACtC,QAAQ,CAAC,UAAU,EAAE,MAAM,CAAC;IAC5B,wEAAwE;IACxE,QAAQ,CAAC,MAAM,EAAE,kBAAkB,CAAC;IACpC,mCAAmC;IACnC,QAAQ,CAAC,MAAM,EAAE,OAAO,GAAG,KAAK,CAAC;IACjC,yDAAyD;IACzD,QAAQ,CAAC,QAAQ,EAAE,UAAU,GAAG,OAAO,CAAC;IACxC,wFAAwF;IACxF,QAAQ,CAAC,SAAS,EAAE,SAAS,MAAM,EAAE,GAAG,IAAI,CAAC;IAC7C,sGAAsG;IACtG,QAAQ,CAAC,SAAS,EAAE,SAAS,MAAM,EAAE,GAAG,IAAI,CAAC;IAC7C,mGAAmG;IACnG,QAAQ,CAAC,GAAG,CAAC,EAAE,OAAO,CAAC;CAC1B;AAqRD;;;;GAIG;AACH,cAAM,eAAe;IACjB,OAAO,CAAC,QAAQ,CAAC,IAAI,CAAY;IAEjC,OAAO,CAAC,QAAQ,CAAC,MAAM,CAAkB;IAEzC,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAmC;IAE3D,OAAO,CAAC,QAAQ,CAAC,aAAa,CAAqB;IAEnD;;;;OAIG;gBACS,IAAI,EAAE,SAAS,EAAE,MAAM,EAAE,MAAM,GAAG,MAAM;IAKpD;;;;OAIG;IACH,OAAO,CAAC,IAAI,EAAE,UAAU,GAAG,YAAY;IAOvC;;;;;OAKG;IACH,SAAS,CAAC,IAAI,EAAE,UAAU,EAAE,OAAO,EAAE,OAAO,GAAG,YAAY;IAI3D;;;;OAIG;IACH,KAAK,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO;IAI5B;;;;;;OAMG;IACH,KAAK,CAAC,GAAG,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,EAAE,KAAK,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,GAAG,IAAI;IAiBrE;;;;;OAKG;IACH,GAAG,CAAC,MAAM,EAAE,YAAY,GAAG,MAAM,EAAE,GAAG,EAAE,MAAM,EAAE,KAAK,EAAE,OAAO,GAAG,IAAI;IAQrE;;;;OAIG;IACH,OAAO,CAAC,MAAM;CAGjB;AAID;;GAEG;AACH,qBAAa,aAAa;IACtB,QAAQ,CAAC,IAAI,EAAE,SAAS,CAAC;IAEzB,QAAQ,CAAC,MAAM,EAAE,mBAAmB,CAAC;IAErC,QAAQ,CAAC,OAAO,EAAE,qBAAqB,CAAC;IAExC,QAAQ,CAAC,IAAI,EAAE,mBAAmB,CAAC;IAEnC,QAAQ,CAAC,GAAG,EAAE,SAAS,CAAC;IAExB,QAAQ,CAAC,SAAS,EAAE,iBAAiB,CAAC;IAEtC,QAAQ,CAAC,KAAK,EAAE,eAAe,CAAC;IAEhC,QAAQ,CAAC,KAAK,EAAE,eAAe,CAAC;IAEhC,uGAAuG;IACvG,QAAQ,CAAC,uBAAuB,EAAE,OAAO,CAAC;IAE1C,gEAAgE;IAChE,OAAO,CAAC,kBAAkB,CAAK;IAE/B;;;;;;;OAOG;gBAEC,IAAI,EAAE,SAAS,EACf,MAAM,EAAE,mBAAmB,EAC3B,OAAO,EAAE,qBAAqB,EAC9B,IAAI,EAAE,mBAAmB,EACzB,uBAAuB,EAAE,OAAO;IAapC;;;;OAIG;IACH,gBAAgB,CAAC,OAAO,EAAE,iBAAiB,EAAE,OAAO,EAAE,MAAM,GAAG,IAAI;IAWnE;;;;;OAKG;IACH,eAAe,CAAC,OAAO,EAAE,iBAAiB,GAAG,OAAO;IAIpD,4EAA4E;IAC5E,OAAO,CAAC,YAAY,CAAS;IAE7B;;;;OAIG;IACH,SAAS,CAAC,QAAQ,EAAE,OAAO,GAAG,IAAI;IAKlC;;;;OAIG;IACH,WAAW,IAAI,QAAQ;IAIvB;;;;;;;OAOG;IACH,QAAQ,CAAC,GAAG,EAAE,OAAO,EAAE,OAAO,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI;IAkCtD;;;;;;OAMG;IACH,SAAS,CAAC,GAAG,EAAE,OAAO,EAAE,OAAO,EAAE,MAAM,GAAG,MAAM;IAUhD;;;;;OAKG;IACH,QAAQ,CAAC,EAAE,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,GAAG,MAAM;IAuB7C;;;;;;;;;OASG;IACH,QAAQ,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,EAAE,MAAM,GAAG,SAAS,EAAE,OAAO,EAAE,MAAM,GAAG,MAAM;IAc7G;;;OAGG;IACH,UAAU,IAAI,IAAI;IAOlB;;;;;OAKG;IACH,IAAI,CAAC,GAAG,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,GAAG,MAAM,EAAE,OAAO,EAAE,MAAM,GAAG,IAAI;IASlE;;;;;OAKG;IACH,UAAU,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,IAAI,SAAc,GAAG,IAAI;IAK9E;;;OAGG;IACH,YAAY,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI;IAQ3C;;;;OAIG;IACH,eAAe,CAAC,OAAO,EAAE,MAAM,EAAE,KAAK,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package/dist/src/formats/json/importer.js

@@ -32,14 +32,15 @@
  */
 import { GraphFormatError, INVALID_INDEX, } from "@graphty/graph-format";
 import { uniqueColumnName } from "../../common/attributes.js";
-import { BAD_VALUE_CODE, DUPLICATE_EDGE_ID_CODE, DUPLICATE_NODE_CODE, EMPTY_INPUT_CODE, ENCODING_FALLBACK_CODE, HYPEREDGE_CODE, INVALID_ENCODING_CODE, INVALID_UTF8_CODE, MISSING_ENDPOINT_CODE, MISSING_ID_CODE, MULTIPLE_GRAPHS_CODE, OPTION_IGNORED_CODE, SYNTAX_CODE, UNKNOWN_ENCODING_CODE, UNKNOWN_PARENT_CODE, } from "../../common/codes.js";
+import { AMBIGUOUS_GRAPH_NAME_CODE, BAD_VALUE_CODE, DANGLING_REFERENCE_CODE, DUPLICATE_EDGE_ID_CODE, DUPLICATE_NODE_CODE, EMPTY_INPUT_CODE, ENCODING_FALLBACK_CODE, GRAPH_NOT_FOUND_CODE, HYPEREDGE_CODE, INVALID_ENCODING_CODE, INVALID_UTF8_CODE, MISSING_ENDPOINT_CODE, MISSING_ID_CODE, MULTIPLE_GRAPHS_CODE, OPTION_IGNORED_CODE, SYNTAX_CODE, TOO_LARGE_CODE, UNKNOWN_ENCODING_CODE, UNKNOWN_PARENT_CODE, } from "../../common/codes.js";
 import { DirectionResolver } from "../../common/direction.js";
 import { ID_MERGED_CODE, IdCoercer } from "../../common/ids.js";
-import { readText, throwIfAborted } from "../../common/input.js";
-import { reportSinkOptions, reportUnusedOptions, resolveImportOptions, SINK_OPTION_CODE, } from "../../common/options.js";
+import { readText, textChunks, throwIfAborted } from "../../common/input.js";
+import { chooseGraph, reportSinkOptions, reportUnusedOptions, resolveImportOptions, SINK_OPTION_CODE, } from "../../common/options.js";
 import { ImportReportBuilder } from "../../common/report.js";
 import { weightFromValue } from "../../common/weights.js";
 import { CLASSES_COLUMN, CYTOSCAPE_ELEMENT_KEYS, CYTOSCAPE_STRUCTURAL_KEYS, DIALECT_DEFAULT_DIRECTED, hasKey, isJsonImportDialect, isJsonObject, JSON_IMPORT_DIALECTS, META_KEY, NODE_LINK_SOURCE_KEYS, NODE_LINK_TARGET_KEYS, PARENT_COLUMN, POSITION_COLUMN, sniffJsonDialect, SUFFIX, } from "./dialect.js";
+import { importObographs } from "./obographs.js";
 /**
  * The issue codes the JSON importer records (design section 8.6), by name: the codes shared with
  * the other importers (src/common/codes.ts) and the JSON-specific ones. A key is the code without
@@ -80,8 +81,18 @@ export const JSON_ISSUE = Object.freeze({
     ID_MERGED: ID_MERGED_CODE,
     /** 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: MULTIPLE_GRAPHS_CODE,
+    /** `graphIndex` is beyond the `graphs` array, or `graphName` names none of its graphs (fatal). */
+    GRAPH_NOT_FOUND: GRAPH_NOT_FOUND_CODE,
+    /** `graphName` names more than one graph of the `graphs` array (fatal). */
+    AMBIGUOUS_GRAPH_NAME: AMBIGUOUS_GRAPH_NAME_CODE,
+    /** 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: DANGLING_REFERENCE_CODE,
+    /** The document is longer than one JavaScript string can hold (fatal; category unsupported). */
+    TOO_LARGE: TOO_LARGE_CODE,
     /** JGF hyperedges under the "error" policy. */
     HYPEREDGE: HYPEREDGE_CODE,
     /** JGF hyperedges skipped under the default "skip" policy. */
@@ -180,6 +191,14 @@ function resolveJsonOptions(options) {
     if (!Number.isInteger(graphIndex) || graphIndex < 0) {
         throw unsupportedOption("graphIndex", graphIndex, ["a non-negative integer"]);
     }
+    const oboIds = o.oboIds ?? "curie";
+    if (oboIds !== "curie" && oboIds !== "iri") {
+        throw unsupportedOption("oboIds", oboIds, ["curie", "iri"]);
+    }
+    const typedefs = o.typedefs ?? "metadata";
+    if (typedefs !== "metadata" && typedefs !== "nodes") {
+        throw unsupportedOption("typedefs", typedefs, ["metadata", "nodes"]);
+    }
     const nodesPath = pathOption("nodesPath", o.nodesPath);
     const edgesPath = pathOption("edgesPath", o.edgesPath);
     if ((nodesPath !== null || edgesPath !== null) && dialect !== "auto" && !PATH_DIALECTS.has(dialect)) {
@@ -193,6 +212,9 @@ function resolveJsonOptions(options) {
         targetKey: keyOption("targetKey", o.targetKey),
         indexLinks,
         graphIndex,
+        choice: { graphIndex: o.graphIndex, graphName: o.graphName },
+        oboIds,
+        typedefs,
         nodesPath,
         edgesPath,
     };
@@ -493,7 +515,7 @@ class AttributeWriter {
 /**
  * Everything one import call shares between the dialect readers.
  */
-class ImportContext {
+export class ImportContext {
     /**
      * Create the context.
      * @param sink - the sink
@@ -1906,32 +1928,123 @@ function importJgf(ctx, root) {
     ctx.setMeta(shape, { name: label, ...ctx.weightOriginPatch() });
 }
 /**
- * The graph object of a JGF document: `graph`, or `graphs[graphIndex]`.
+ * The graph object of a JGF document: `graph`, or the graph of `graphs` that graphIndex /
+ * graphName choose (chooseGraph()).
  * @param ctx - the context
  * @param root - the document
  * @returns the graph object; the import fails when there is none
  */
 function jgfGraphOf(ctx, root) {
+    return isJsonObject(root.graph) ? root.graph : chosenGraph(ctx, root, "JGF");
+}
+/**
+ * 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 function chosenGraph(ctx, root, what) {
     const { report } = ctx;
-    if (isJsonObject(root.graph)) {
-        return root.graph;
-    }
     const graphs = arraySection(root.graphs, "graphs", report) ?? [];
     if (graphs.length === 0) {
-        report.fail(JSON_ISSUE.SHAPE, "a JGF document needs a graph object or a non-empty graphs array");
+        report.fail(JSON_ISSUE.SHAPE, `a ${what} document needs a graph object or a non-empty graphs array`);
     }
+    const index = ctx.json.all === true ? ctx.json.graphIndex : chooseGraph(graphs.map(graphNameOf), ctx.json.choice, report);
     if (graphs.length > 1 && ctx.json.all !== true) {
-        report.warning("unsupported", JSON_ISSUE.MULTIPLE_GRAPHS, `the document holds ${graphs.length} graphs; only graphs[${ctx.json.graphIndex}] is read (${graphs.length - 1} skipped), importAll() reads every one`, { element: "graphs" });
+        report.warning("unsupported", JSON_ISSUE.MULTIPLE_GRAPHS, `the document holds ${graphs.length} graphs; only graphs[${index}] is read (${graphs.length - 1} skipped), importAll() reads every one`, { element: "graphs" });
     }
-    if (ctx.json.graphIndex >= graphs.length) {
-        report.fail(JSON_ISSUE.SHAPE, `graphIndex ${ctx.json.graphIndex} is beyond the ${graphs.length} graph(s)`);
-    }
-    const graph = graphs[ctx.json.graphIndex];
+    const graph = graphs[index];
     if (!isJsonObject(graph)) {
-        return report.fail(JSON_ISSUE.SHAPE, `graphs[${ctx.json.graphIndex}] is not an object`);
+        return report.fail(JSON_ISSUE.SHAPE, `graphs[${index}] is not an object`);
     }
     return graph;
 }
+/**
+ * The name a graph of a `graphs` array is listed and chosen by: its `id`, else its `label` (JGF)
+ * or `lbl` (OBO Graphs).
+ * @param graph - the graph
+ * @returns the name, or null
+ */
+function graphNameOf(graph) {
+    if (!isJsonObject(graph)) {
+        return null;
+    }
+    for (const key of ["id", "label", "lbl"]) {
+        if (typeof graph[key] === "string") {
+            return graph[key];
+        }
+    }
+    return null;
+}
+/**
+ * How many elements a nodes or edges section holds: an array's length, an object's key count, 0
+ * when absent, null for anything else.
+ * @param section - the section
+ * @returns the count, or null
+ */
+function countOf(section) {
+    if (section === undefined || section === null) {
+        return 0;
+    }
+    if (Array.isArray(section)) {
+        return section.length;
+    }
+    return isJsonObject(section) ? Object.keys(section).length : null;
+}
+/**
+ * The graphs of a parsed document, for listGraphs(): each entry of a JGF or OBO Graphs `graphs`
+ * array with its name and counts; any other document holds one graph.
+ * @param root - the parsed document
+ * @param dialect - its dialect
+ * @returns the listings
+ */
+function listingsOf(root, dialect) {
+    if ((dialect === "jgf" || dialect === "obographs") && isJsonObject(root)) {
+        if (Array.isArray(root.graphs) && !isJsonObject(root.graph)) {
+            return root.graphs.map((graph, index) => ({
+                index,
+                name: graphNameOf(graph),
+                nodes: isJsonObject(graph) ? countOf(graph.nodes) : null,
+                edges: isJsonObject(graph) ? countOf(graph.edges) : null,
+            }));
+        }
+        if (isJsonObject(root.graph)) {
+            const { graph } = root;
+            return [{ index: 0, name: graphNameOf(graph), nodes: countOf(graph.nodes), edges: countOf(graph.edges) }];
+        }
+    }
+    return [{ index: 0, name: null, nodes: null, edges: null }];
+}
+/** The longest string V8 makes (2^29 - 24 UTF-16 code units); a longer document cannot be one JSON.parse input. */
+const MAX_TEXT_LENGTH = 2 ** 29 - 24;
+/**
+ * Read the whole input as one string, failing with E_TOO_LARGE (category unsupported) before the
+ * join when it is longer than one JavaScript string can hold (OBO Graphs files such as
+ * ncbitaxon.json are; design 7.1 defers streaming the JSON reader).
+ * @param input - the input
+ * @param report - the report
+ * @param options - cancellation, progress and encoding
+ * @returns the text
+ */
+async function readJsonText(input, report, options) {
+    if (typeof input === "string") {
+        return readText(input, report, options);
+    }
+    const parts = [];
+    let length = 0;
+    for await (const chunk of textChunks(input, report, options)) {
+        length += chunk.length;
+        if (length > MAX_TEXT_LENGTH) {
+            const message = `the document is longer than ${MAX_TEXT_LENGTH} characters, the most one JavaScript string holds`;
+            report.error("unsupported", JSON_ISSUE.TOO_LARGE, message);
+            throw report.abort(message, { code: JSON_ISSUE.TOO_LARGE });
+        }
+        parts.push(chunk);
+    }
+    return parts.length === 1 ? parts[0] : parts.join("");
+}
 /**
  * Push a JGF node: `label` into the declared column, `metadata` as attributes.
  * @param ctx - the context
@@ -2321,11 +2434,27 @@ export const jsonImporter = Object.freeze({
         const resolved = resolveImportOptions(options, FORMAT_DEFAULTS);
         const json = resolveJsonOptions(options);
         const report = new ImportReportBuilder("json", resolved.errorLimit);
-        const text = await readText(input, report, resolved);
+        const text = await readJsonText(input, report, resolved);
         const { root, dialect } = documentOf(parseDocument(text, report), json, report);
         readGraph(root, dialect, sink, report, resolved, json, options);
         return report.finish();
     },
+    /**
+     * List the graphs of a JSON document without importing them: each entry of a JGF or OBO
+     * Graphs `graphs` array with its name (`id`, else its label) and node and edge counts; any
+     * other document holds one graph.
+     * @param input - the text, bytes or stream
+     * @param options - format-specific and common options
+     * @returns one listing per graph
+     */
+    async listGraphs(input, options) {
+        const resolved = resolveImportOptions(options, FORMAT_DEFAULTS);
+        const json = resolveJsonOptions(options);
+        const report = new ImportReportBuilder("json", resolved.errorLimit);
+        const text = await readJsonText(input, report, resolved);
+        const { root, dialect } = documentOf(parseDocument(text, report), json, report);
+        return listingsOf(root, dialect);
+    },
     /**
      * Read every graph of a JSON document: each entry of a JGF `graphs` array into its own sink;
      * any other document holds one graph.
@@ -2338,11 +2467,9 @@ export const jsonImporter = Object.freeze({
         const resolved = resolveImportOptions(options, FORMAT_DEFAULTS);
         const json = resolveJsonOptions(options);
         const first = new ImportReportBuilder("json", resolved.errorLimit);
-        const text = await readText(input, first, resolved);
+        const text = await readJsonText(input, first, resolved);
         const { root, dialect } = documentOf(parseDocument(text, first), json, first);
-        const graphs = dialect === "jgf" && isJsonObject(root) && !isJsonObject(root.graph) && Array.isArray(root.graphs)
-            ? root.graphs.length
-            : 1;
+        const graphs = listingsOf(root, dialect).length;
         const reports = [];
         for (let i = 0; i < Math.max(graphs, 1); i++) {
             const report = i === 0 ? first : new ImportReportBuilder("json", resolved.errorLimit);
@@ -2364,7 +2491,8 @@ export const jsonImporter = Object.freeze({
  */
 function readGraph(root, dialect, sink, report, resolved, json, options) {
     const ctx = new ImportContext(sink, report, resolved, json, options?.defaultDirected !== undefined);
-    reportSinkOptions(sink, options, report);
+    // the obographs reader refuses missing endpoints itself, so addMissingNodes false holds on any sink
+    reportSinkOptions(sink, options, report, dialect === "obographs");
     reportUnusedOptions(options, report, USED_OPTIONS);
     if (dialect === "cytoscape") {
         importCytoscape(ctx, root);
@@ -2394,6 +2522,9 @@ function readGraph(root, dialect, sink, report, resolved, json, options) {
         case "tree":
             importTree(ctx, doc);
             break;
+        case "obographs":
+            importObographs(ctx, doc);
+            break;
         default: {
             const name = dialect;
             throw new GraphFormatError("E_UNSUPPORTED", `unknown dialect ${name}`, {