@graphty/graph-io 0.3.25 → 0.3.26

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

@@ -4,7 +4,7 @@
  * `directed` / `multigraph` / `graph`), the d3 lineage of the same shape (`name` ids, integer
  * index endpoints), JSON Graph Format v2 (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`)
+ * `data.parent`), graphology serialization (`key` / `attributes`, `undirected` edges, `options`)
  * vis.js (`from` / `to`), and NetworkX adjacency_data (`nodes` + `adjacency`) and tree_data (nested
  * `id` / `children`) -- and pushes it scalar by scalar into the sink.
  *
@@ -35,80 +35,112 @@ 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 CommonImportOptions, 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.
+ * @category Built-in formats
  */
-export interface JsonImportOptions extends GraphChoiceOptions {
-    /** The dialect to read; "auto" (default) sniffs the parsed document. */
+export interface JsonImportOptions extends GraphChoiceOptions, CommonImportOptions {
+    /**
+     * The dialect to read; "auto" detects it from the document. `jsonShapeOf(snapshot).dialect` is
+     * the dialect that was read.
+     * @defaultValue "auto"
+     */
     dialect?: JsonImportDialect | "auto" | undefined;
     /**
-     * node-link / d3 / vis / adjacency / tree: the node key holding the id; auto: "id" (node-link /
-     * d3: "id" when any node has it, else "name").
+     * node-link, d3, vis, adjacency and tree documents: the node key that holds the id. The default
+     * is "id" (for node-link and d3, "name" when no node has an "id").
+     * @defaultValue "id"
      */
     nodeIdKey?: string | undefined;
-    /** node-link / d3: the top-level key holding the edges; auto: "edges" when present, else "links". */
+    /**
+     * node-link and d3 documents: the top-level key that holds the edges. The default is "edges"
+     * when the document has it, else "links".
+     * @defaultValue "edges" or "links"
+     */
     edgesKey?: string | undefined;
-    /** node-link / d3 / vis: the edge key holding the source; auto: "source", "src" or "from" (vis: "from"). */
+    /**
+     * node-link, d3 and vis documents: the edge key that holds the source. The default is the first
+     * of "source", "src" and "from" the edges use (vis: "from").
+     * @defaultValue "source"
+     */
     sourceKey?: string | undefined;
-    /** node-link / d3 / vis: the edge key holding the target; auto: "target", "dst" or "to" (vis: "to"). */
+    /**
+     * node-link, d3 and vis documents: the edge key that holds the target. The default is the first
+     * of "target", "dst" and "to" the edges use (vis: "to").
+     * @defaultValue "target"
+     */
     targetKey?: string | undefined;
     /**
-     * node-link / d3: whether edge endpoints are node array positions; "auto" (default) says yes when
-     * every endpoint is an integer below the node count and no node id is a number.
+     * node-link and d3 documents: whether edge ends are positions in the node array rather than
+     * ids; "auto" says yes when every end is an integer below the number of nodes and no node id is
+     * a number.
+     * @defaultValue "auto"
      */
     indexLinks?: boolean | "auto" | 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.
+     * OBO Graphs documents: "curie" reads `http://purl.obolibrary.org/obo/GO_0008150` as
+     * `GO:0008150` and `.../obo/go#regulates` as `regulates`, the ids the `.obo` file of the same
+     * ontology uses; "iri" keeps every IRI as written.
+     * @defaultValue "curie"
      */
     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.
+     * OBO Graphs documents: "metadata" keeps the relation definitions (PROPERTY nodes, with their
+     * subPropertyOf and inverseOf edges) in `snapshot.meta.extra.obographs`, the way the OBO
+     * importer keeps `[Typedef]` frames; "nodes" makes them nodes and edges of the graph.
+     * @defaultValue "metadata"
      */
     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
-     * (its `directed`, `multigraph`, `graph` and edge keys). "nodes" by default. A path that names
-     * nothing is an E_MISSING_SECTION issue and the graph has no node records.
+     * node-link, d3, vis and graphology documents: where the node array is, as a dotted path of
+     * keys and array positions from the top of the document (`"data.nodes"`, `"graphs.0.nodes"`).
+     * The object that holds the array is read as the graph (its `directed`, `multigraph`, `graph`
+     * and edge keys). A path that leads nowhere is reported as E_MISSING_SECTION and the graph has
+     * no nodes.
+     * @defaultValue "nodes"
      */
     nodesPath?: string | undefined;
     /**
-     * node-link / d3 / vis / graphology: where the edge array is, as a dotted path of object keys
-     * from the document root (`"data.links"`); by default the edges or links key of the object
-     * holding the nodes. A path that names nothing is an E_MISSING_SECTION issue and the graph has
-     * no edge records.
+     * node-link, d3, vis and graphology documents: where the edge array is, as a dotted path
+     * (`"data.links"`). The default is the edges or links key next to the node array. A path that
+     * leads nowhere is reported as E_MISSING_SECTION and the graph has no edges.
+     * @defaultValue next to the nodes
      */
     edgesPath?: string | undefined;
 }
 /**
- * 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
+ * The issue codes the JSON importer records, by name: the codes shared with
+ * the other importers and the JSON-specific ones. A key is the code without
  * its severity and format prefixes.
+ * @category Built-in formats
  */
 export declare const JSON_ISSUE: Readonly<{
-    /** The text is empty or whitespace (fatal). */
+    /** The text is empty or whitespace. The import stops. */
     EMPTY_INPUT: "E_EMPTY_INPUT";
-    /** JSON.parse refused the text (fatal). */
+    /** The text is not valid JSON. The import stops. */
     SYNTAX: "E_SYNTAX";
-    /** No dialect matches the document's top-level shape. */
+    /** No dialect matches the document's top-level shape. The import stops. */
     DIALECT: "E_JSON_DIALECT";
     /** A section (nodes, edges, elements, graph) has the wrong JSON type. */
     SHAPE: "E_JSON_SHAPE";
-    /** A node-link document lacks its nodes or its edges array, or a Cytoscape document its elements. */
-    MISSING_SECTION: "E_MISSING_SECTION";
+    /**
+     * A section the dialect expects is not there: a node-link document without its nodes or its edges array, an
+     * adjacency document without lists for some nodes, or a `nodesPath` / `edgesPath` that names nothing. Nothing is
+     * skipped: the graph is read without that section (nodes come from the edges, or there are no edges).
+     */
+    MISSING_SECTION: "W_MISSING_SECTION";
     /** A node record or an element is not an object. */
     BAD_ELEMENT: "E_BAD_ELEMENT";
     /** A node record has no id. */
     MISSING_ID: "E_MISSING_ID";
-    /** A node id is a JSON boolean or null (legal in NetworkX, not a NodeId); coerced only under ids "string". */
+    /**
+     * A node id is a JSON boolean or null, which graph-io cannot use as an id; the node is skipped. With `ids:
+     * "string"` it is read as the text "true", "false" or "null".
+     */
     UNSUPPORTED_ID: "E_UNSUPPORTED_ID";
     /** An edge record has no source or no target. */
     MISSING_ENDPOINT: "E_MISSING_ENDPOINT";
@@ -124,25 +156,35 @@ export declare const JSON_ISSUE: Readonly<{
     DUPLICATE_NODE: "W_DUPLICATE_NODE";
     /** An edge id (Cytoscape data.id, graphology key, vis id) repeated by a later edge; the edge is skipped. */
     DUPLICATE_EDGE_ID: "E_DUPLICATE_EDGE_ID";
-    /** Two distinct id texts merged into one number under ids "number". */
+    /** Two different id texts became the same number because `ids` is "number", so their nodes were merged. */
     ID_MERGED: "W_ID_MERGED";
     /** Edge ids of mixed JSON types were stored as text. */
     EDGE_ID_STRINGIFIED: "W_EDGE_ID_STRINGIFIED";
-    /** A JGF or OBO Graphs `graphs` array holds more than one graph; only the chosen one is read. */
+    /**
+     * The file holds several graphs and only the first was read. It is not added when `graphIndex` or `graphName` chose the graph.
+     * `importAllGraphs()` reads every one.
+     */
     MULTIPLE_GRAPHS: "W_MULTIPLE_GRAPHS";
-    /** `graphIndex` is beyond the `graphs` array, or `graphName` names none of its graphs (fatal). */
+    /**
+     * `graphIndex` is past the end of the `graphs` array, or `graphName` matches none of its graphs. The import stops.
+     */
     GRAPH_NOT_FOUND: "E_GRAPH_NOT_FOUND";
-    /** `graphName` names more than one graph of the `graphs` array (fatal). */
+    /** `graphName` matches more than one graph of the `graphs` array. The import stops. */
     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: 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). */
+    /**
+     * 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). */
+    /** The document is longer than a JavaScript string can hold. The import stops. */
     TOO_LARGE: "E_TOO_LARGE";
-    /** JGF hyperedges under the "error" policy. */
+    /** A JGF hyperedge (an edge with more than two ends) while `hyperedges` is "error". */
     HYPEREDGE: "E_HYPEREDGE";
-    /** JGF hyperedges skipped under the default "skip" policy. */
+    /**
+     * JGF hyperedges were skipped, because `hyperedges` is "skip" (the default). Pass "star" or "clique" to keep them.
+     */
     HYPEREDGES_SKIPPED: "W_HYPEREDGES_SKIPPED";
     /** A JGF hyperedge with neither a nodes array nor source / target arrays. */
     HYPEREDGE_SHAPE: "E_HYPEREDGE_SHAPE";
@@ -150,13 +192,19 @@ export declare const JSON_ISSUE: Readonly<{
     POSITIONAL_NODES: "W_POSITIONAL_NODES";
     /** A node-link / d3 top-level key the importer does not read (the other of edges / links, an unknown key); it is dropped. */
     UNREAD_KEY: "W_JSON_UNREAD_KEY";
-    /** A builder-policy option (addMissingNodes, duplicateEdges, selfLoops, weightDtype) differs from the sink's (the shared W_SINK_OPTION). */
+    /**
+     * You read into your own graph builder, which was created with a different `addMissingNodes`, `duplicateEdges`,
+     * `selfLoops` or `weightDtype` than the option you passed; the builder's setting applies.
+     */
     SINK_OPTION: "W_SINK_OPTION";
-    /** A common option the dialect has no use for (nodeIdFrom outside node-link, long, restoreMangledIds). */
+    /** You set an option this format does not use; it had no effect. The message names the option. */
     OPTION_IGNORED: "W_OPTION_IGNORED";
-    /** The input holds invalid UTF-8 (fatal). */
+    /** The input is not valid UTF-8. The import stops. */
     INVALID_UTF8: "E_INVALID_UTF8";
-    /** Invalid bytes in the encoding a BOM, a declaration or the encoding option chose (fatal). */
+    /**
+     * Some bytes are not valid in the encoding that was chosen (by a byte order mark, the file's declaration or the
+     * `encoding` option). The import stops.
+     */
     INVALID_ENCODING: "E_INVALID_ENCODING";
     /** Bytes that are not UTF-8 and declare no encoding were read as windows-1252. */
     ENCODING_FALLBACK: "W_ENCODING_FALLBACK";
@@ -166,6 +214,46 @@ export declare const JSON_ISSUE: Readonly<{
     BIG_INTEGER: "W_JSON_BIG_INTEGER";
     /** A declared encoding the platform cannot decode was ignored. */
     UNKNOWN_ENCODING: "W_UNKNOWN_ENCODING";
+    /** An integer beyond 2^53 was stored as the nearest 64-bit float; pass `long: "string"` to keep every digit. */
+    PRECISION: "W_PRECISION";
+    /**
+     * The document contradicts itself: a declared option its edges break (multigraph false with
+     * parallel links, graphology's options), a record whose section disagrees with its shape, a
+     * JGF inner id other than its key, the two listings of one adjacency edge.
+     */
+    INCONSISTENT: "W_JSON_INCONSISTENT";
+    /** IndexLinks "auto" read integer endpoints as array positions although they also name node ids. */
+    INDEX_LINKS: "W_JSON_INDEX_LINKS";
+    /** A Cytoscape parent link that would close a cycle; that link is dropped. */
+    PARENT_CYCLE: "E_PARENT_CYCLE";
+    /** An attribute key that is null on every element makes no column (NetworkX writes None as null). */
+    EMPTY_COLUMN_DROPPED: "W_EMPTY_COLUMN_DROPPED";
+    /** OBO Graphs: a node type or synonym predicate outside the schema's set; kept as written, once per name. */
+    UNKNOWN_ELEMENT: "W_UNKNOWN_ELEMENT";
+    /**
+     * A key repeated in one JSON object (JSON.parse keeps the last value, the earlier is dropped),
+     * or, in OBO Graphs, a single-valued OBO tag given twice in basicPropertyValues (the first is kept).
+     */
+    DUPLICATE_ATTRIBUTE: "W_DUPLICATE_ATTRIBUTE";
+    /**
+     * An attribute was renamed `<name>#<suffix>` because another attribute already has its name, for example
+     * two attributes declared with the same name.
+     */
+    COLUMN_RENAMED: "W_COLUMN_RENAMED";
+    /**
+     * You read into a graph builder that already has an id, label or position attribute, so this file's one is kept as
+     * a plain attribute.
+     */
+    ROLE_TAKEN: "W_ROLE_TAKEN";
+    INVALID_ID: "E_INVALID_ID";
+    UNKNOWN_NODE: "E_UNKNOWN_NODE";
+    INVALID_WEIGHT: "E_INVALID_WEIGHT";
+    DUPLICATE_EDGE: "E_DUPLICATE_EDGE";
+    SELF_LOOP: "E_SELF_LOOP";
+    ENCODING_CONFLICT: "W_ENCODING_CONFLICT";
+    CONTROL_CHARACTER: "W_CONTROL_CHARACTER";
+    FOREIGN_FORMAT: "E_FOREIGN_FORMAT";
+    ISSUES_SUPPRESSED: "W_ISSUES_SUPPRESSED";
 }>;
 export type JsonRecord = Record<string, unknown>;
 /** An edge id column declared from a scan of the file's edge ids. */
@@ -208,12 +296,16 @@ declare class AttributeWriter {
     private readonly domain;
     private readonly handles;
     private readonly reservedNames;
+    private readonly report;
+    /** Column names written only with null so far (NetworkX writes None as null). */
+    private readonly nullOnly;
     /**
      * Create a writer.
      * @param sink - the sink
      * @param domain - node or edge
+     * @param report - where a refused cell is recorded
      */
-    constructor(sink: GraphSink, domain: "node" | "edge");
+    constructor(sink: GraphSink, domain: "node" | "edge", report: ImportReportBuilder);
     /**
      * Declare a structural column up front; attribute keys with its name are suffixed from now on.
      * @param decl - the declaration
@@ -234,13 +326,20 @@ declare class AttributeWriter {
      */
     taken(name: string): boolean;
     /**
-     * Write one attribute cell by its source key; null and undefined leave the row unset.
+     * Write one attribute cell by its source key; null and undefined leave the row unset. A cell the
+     * sink refuses is recorded and skipped, so the element's other keys are still written.
      * @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
+     * @param element - the element name for an issue
      */
-    write(row: number, key: string, value: unknown, suffix: string): void;
+    write(row: number, key: string, value: unknown, suffix: string, element: string): void;
+    /**
+     * Report the keys that were null on every element that had them: they made no column, so a
+     * round trip loses them (W_EMPTY_COLUMN_DROPPED, one warning per table).
+     */
+    reportNullOnly(): void;
     /**
      * Write through a handle or a name.
      * @param column - the handle or name
@@ -257,6 +356,7 @@ declare class AttributeWriter {
 }
 /**
  * Everything one import call shares between the dialect readers.
+ * @category Plugin helpers
  */
 export declare class ImportContext {
     readonly sink: GraphSink;
@@ -328,9 +428,10 @@ export declare class ImportContext {
      * Add a node, counting it or recording the failure.
      * @param id - the node id
      * @param element - the element name
+     * @param why - more about a repeated id, for the duplicate warning
      * @returns the node index, or -1 when the sink refused the node
      */
-    pushNode(id: NodeId, element: string): number;
+    pushNode(id: NodeId, element: string, why?: 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).
@@ -342,6 +443,23 @@ export declare class ImportContext {
      * @returns the primary edge index
      */
     pushEdge(source: NodeId, target: NodeId, kind: EdgeKind, weight: number | undefined, element: string): number;
+    /** Endpoints that named no node and became placeholder nodes, the first few kept for the message. */
+    private readonly danglingIds;
+    private danglingCount;
+    /** Set when the document has no node section: every node comes from an edge (E_MISSING_SECTION says so). */
+    nodesFromEdges: boolean;
+    /** Dangling endpoints whose id, as the other JSON type, is a node (`"1"` next to the node 1). */
+    private readonly nearMatches;
+    /**
+     * Count a placeholder node an edge endpoint created.
+     * @param id - the endpoint
+     */
+    private dangling;
+    /**
+     * Report the edge endpoints that named no node (the shared W_DANGLING_REFERENCE, once with the
+     * count): each became a placeholder node, which is rarely what the file meant.
+     */
+    reportDangling(): void;
     /**
      * 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.
@@ -407,8 +525,9 @@ export declare class ImportContext {
      * @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
+     * @param element - the element name for issues
      */
-    writeNested(writer: AttributeWriter, row: number, record: JsonRecord, dict: JsonRecord, structural: ReadonlySet<string>, weightFrom: string | null): void;
+    writeNested(writer: AttributeWriter, row: number, record: JsonRecord, dict: JsonRecord, structural: ReadonlySet<string>, weightFrom: string | null, element: string): void;
     /**
      * Write a spec-typed string field (JGF label / relation), reporting a value of another type.
      * @param writer - the table writer
@@ -452,10 +571,12 @@ export declare class ImportContext {
  * @param root - the document
  * @param what - the dialect's name, for the messages
  * @returns the graph object; the import fails when there is none
+ * @category Plugin helpers
  */
 export declare function chosenGraph(ctx: ImportContext, root: JsonRecord, what: string): JsonRecord;
 /**
- * The JSON importer plugin (design section 8.4).
+ * The JSON importer plugin.
+ * @category Built-in formats
  */
 export declare const jsonImporter: GraphImporter<JsonImportOptions>;
 export {};

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

@@ -1 +1 @@
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