@graphty/graph-io 0.3.18 → 0.3.20

package/dist/src/formats/xgmml/document.js.map

@@ -0,0 +1 @@
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package/dist/src/formats/xgmml/emit.d.ts

@@ -0,0 +1,341 @@
+/**
+ * Resolving a parsed XGMML document (document.ts) into a sink: which nodes and edges a graph
+ * holds, their ids, endpoints, direction, weights, containment, positions, graphics and attribute
+ * columns. The `.cys` importer calls the same code with the session's tables and views merged into
+ * the records first, so both readers share every rule.
+ */
+import { type ColumnDecl, type ColumnHandle, type GraphSink } from "@graphty/graph-format";
+import { type ResolvedImportOptions } from "../../common/options.js";
+import { type ImportReportBuilder } from "../../common/report.js";
+import { type EdgeRec, type GraphRec, type NodeRec, type XgmmlDocument } from "./document.js";
+/** The XGMML-specific options, resolved. */
+export interface XgmmlSettings {
+    /** Resolve missing or unknown endpoints through `"a (pp) b"` edge labels. */
+    readonly labelAliases: boolean;
+    /** Decode Cytoscape's `\n` / `\t` in strings. */
+    readonly cytoscapeEscapes: boolean;
+    /** Where Cytoscape's z goes. */
+    readonly zAs: "column" | "position";
+}
+/** What a session adds to the document's own rules. */
+export interface EmitExtras {
+    /** Ids of nodes the session's group bookkeeping lists as groups. */
+    readonly groupNodes?: ReadonlySet<string> | undefined;
+    /** The network name a cross-file pointer (`file.xgmml#id`) names, or null when unknown. */
+    readonly resolvePointer?: ((href: string) => string | null) | undefined;
+    /** Graph-level attributes and the graph name come from elsewhere: skip the graph's own. */
+    readonly graphName?: string | null | undefined;
+    /** Extra json graph columns. */
+    readonly graphJson?: Readonly<Record<string, unknown>> | undefined;
+    /** Extra entries of `meta.extra`. */
+    readonly metaExtra?: Readonly<Record<string, unknown>> | undefined;
+    /** The format name the report and metadata carry ("cys"). */
+    readonly sourceFormat?: string | undefined;
+    /** Prefix of every issue message (the session entry name). */
+    readonly entry?: string | undefined;
+    /**
+     * A group member that is not in the graph being read (a collapsed group's member in a
+     * session): the session records it instead of E_UNKNOWN_PARENT.
+     */
+    readonly onMissingMember?: ((group: string, member: string) => void) | undefined;
+}
+/** The dialect facts the rules depend on. */
+export interface Dialect {
+    /** The documentVersion as written, or null. */
+    readonly versionText: string | null;
+    /** The parsed version, or 0 when absent or unparseable. */
+    readonly version: number;
+    /** Cytoscape wrote the file (the `cy` namespace is in use). */
+    readonly cytoscape: boolean;
+    /** A Cytoscape 2.x document (Cytoscape dialect with a version below 3). */
+    readonly cy2: boolean;
+    /** The 3.x session network dialect (root `cy:registered="0"` with registered subnetworks). */
+    readonly session: boolean;
+    /** A session view document (root `cy:view="1"`). */
+    readonly view: boolean;
+}
+/**
+ * The dialect of a document (`research-xgmml.md` section 2).
+ * @param doc - the document
+ * @param report - the report the unparseable-version warning goes to
+ * @returns the dialect
+ */
+export declare function dialectOf(doc: XgmmlDocument, report: ImportReportBuilder): Dialect;
+/**
+ * The graphs a document offers: the registered subnetworks of a session network document, else
+ * the root.
+ * @param doc - the document
+ * @param dialect - its dialect
+ * @returns the graphs, in document order
+ */
+export declare function graphsOf(doc: XgmmlDocument, dialect: Dialect): GraphRec[];
+/**
+ * The nodes and edges a graph holds: its direct members, references resolved.
+ * @param doc - the document
+ * @param graph - the graph (a registered subnetwork), or null for the whole document
+ * @returns the declared node and edge records it holds, references resolved, in order
+ */
+export declare function membersOf(doc: XgmmlDocument, graph: GraphRec | null): {
+    readonly nodes: NodeRec[];
+    readonly edges: EdgeRec[];
+    readonly dangling: number;
+};
+/** Per-node state while emitting. */
+interface NodeRow {
+    readonly id: string;
+    readonly records: NodeRec[];
+    index: number;
+    readonly row: number;
+}
+/**
+ * Pushes one graph of a document into a sink.
+ */
+export declare class XgmmlEmitter {
+    private readonly doc;
+    private readonly dialect;
+    private readonly sink;
+    private readonly report;
+    private readonly options;
+    private readonly settings;
+    private readonly extras;
+    private readonly coercer;
+    private readonly direction;
+    private readonly nodeColumns;
+    private readonly edgeColumns;
+    private readonly graphColumns;
+    private readonly rows;
+    private readonly rowList;
+    private readonly edgeIndex;
+    private sinceCheck;
+    private aliasResolved;
+    private aliasInteractions;
+    private weighted;
+    /**
+     * Create an emitter for one graph.
+     * @param doc - the document
+     * @param dialect - its dialect
+     * @param sink - the sink
+     * @param report - the report
+     * @param options - the resolved common options
+     * @param settings - the XGMML options
+     * @param extras - what a session adds
+     */
+    constructor(doc: XgmmlDocument, dialect: Dialect, sink: GraphSink, report: ImportReportBuilder, options: ResolvedImportOptions, settings: XgmmlSettings, extras?: EmitExtras);
+    /**
+     * Push the graph: nodes, containment, positions, edges, columns, metadata.
+     * @param graph - the subnetwork, or null for the whole document
+     */
+    emit(graph: GraphRec | null): void;
+    /**
+     * The sink.
+     * @returns the sink
+     */
+    get target(): GraphSink;
+    /**
+     * The report.
+     * @returns the report
+     */
+    get issues(): ImportReportBuilder;
+    /**
+     * The row of a node id in this graph.
+     * @param id - the id text
+     * @returns the row, or undefined
+     */
+    rowOf(id: string): NodeRow | undefined;
+    /**
+     * The network name a cross-file pointer names, when a session can tell.
+     * @param href - the pointer
+     * @returns the name, or null
+     */
+    resolvePointer(href: string): string | null;
+    /**
+     * Hand a group member the graph does not hold to the session, when one is reading.
+     * @param group - the group node's id
+     * @param member - the member's id
+     * @returns true when the session took it
+     */
+    missingMember(group: string, member: string): boolean;
+    /**
+     * The first graph of the document with an id.
+     * @param id - the id
+     * @returns the graph, or undefined
+     */
+    graphById(id: string): GraphRec | undefined;
+    /**
+     * The prefix of every message (the session entry), or "".
+     * @returns the prefix
+     */
+    prefix(): string;
+    /**
+     * Check the cancellation signal every few dozen elements.
+     */
+    checkAbort(): void;
+    /**
+     * Declare a column the importer owns on first use (the 5.6 rename rule applies).
+     * @param domain - node or edge
+     * @param decl - the declaration
+     * @returns the handle, or null when the sink refused it (recorded)
+     */
+    declare(domain: "node" | "edge", decl: ColumnDecl): ColumnHandle | null;
+    /**
+     * The header direction: the root's `directed` (0 by the DTD), else the defaultDirected option.
+     * @returns whether the graph is directed by default
+     */
+    private headerDirected;
+    /** The direction of each edge, decided once (its warning is recorded once). */
+    private readonly directions;
+    /**
+     * The direction of one edge: its cy:directed, else the header.
+     * @param record - the edge
+     * @param header - the header direction
+     * @returns whether the edge is directed
+     */
+    private edgeDirection;
+    /**
+     * The direction the sink starts with: the one every edge has when they all agree (a
+     * Cytoscape file writes cy:directed on every edge and may omit the root attribute), else the
+     * header, so a graph of one direction is never expanded into a mixed one.
+     * @param edges - the edges of the graph
+     * @param header - the header direction
+     * @returns the sink direction
+     */
+    private sinkDirection;
+    /**
+     * A 0 / 1 direction flag: true, false, yes and no are accepted with a warning; anything else
+     * falls back.
+     * @param text - the text
+     * @param fallback - the direction for an unreadable value
+     * @param where - the location
+     * @returns the direction
+     */
+    private flag;
+    /**
+     * Add every node record to the sink (one node per id; later declarations merge).
+     * @param records - the node records
+     */
+    private addNodes;
+    /**
+     * The coerced id of a node text.
+     * @param text - the id text
+     * @param line - the line
+     * @returns the id
+     */
+    private nodeId;
+    /**
+     * Whether a node's nested graph is a group (containment) rather than a nested-network
+     * pointer: any graph in the 1.0 draft dialect, a 2.x node with `__groupState`, a 3.x node with
+     * `__isGroup` true, or a node the session lists.
+     * @returns the test
+     */
+    private groupTest;
+    /**
+     * W_DANGLING_REFERENCE for the `xlink:href` members of a generic document's non-group graphs
+     * that name no node or edge (a group's are E_UNKNOWN_PARENT, reported by the containment).
+     */
+    private checkReferences;
+    /**
+     * Write the per-node values: label, attributes, XML attributes, graphics, positions, nested
+     * network pointers and subgraph memberships.
+     * @param graph - the subnetwork, or null
+     */
+    private writeNodeExtras;
+    /**
+     * Add an element's XML attributes (text grammar) and atts to a column set; atts of a later
+     * duplicate declaration only fill names the earlier ones left unset.
+     * @param columns - the column set
+     * @param row - the row
+     * @param record - the node or edge
+     * @param seen - the names set by earlier declarations of the same node
+     * @param where - the location
+     */
+    private addElementColumns;
+    /**
+     * Whether an att is not a column: an edge's weight att under weightFrom.
+     * @param record - the element
+     * @param att - the att
+     * @returns true to skip it
+     */
+    private skipAtt;
+    /**
+     * Write a label column (role label).
+     * @param domain - node or edge
+     * @param labels - the label of each row
+     * @param index - the sink index of a row
+     */
+    private writeLabels;
+    /** The `xgmml.networks` membership of nodes in root-level subgraphs of a generic document. */
+    private writeNetworks;
+    /**
+     * Push every edge record.
+     * @param records - the edge records
+     * @param header - the header direction
+     */
+    private addEdges;
+    /**
+     * Push one edge: endpoints (with label aliases), duplicate id check, direction and weight.
+     * @param record - the edge
+     * @param header - the header direction
+     * @param ids - the edge ids used so far
+     * @param where - the location
+     * @returns the edge index, or -1 when it was skipped
+     */
+    private addEdge;
+    /**
+     * The weight of an edge: its `weight` XML attribute (or the att weightFrom names).
+     * @param record - the edge
+     * @returns the weight, or undefined
+     */
+    private weightOf;
+    /**
+     * Resolve one endpoint: a node of this graph by id, else (under labelAliases) the label alias
+     * by id or by unique node label; a missing endpoint is E_MISSING_ENDPOINT, an unknown one
+     * E_UNKNOWN_NODE unless addMissingNodes adds it.
+     * @param text - the source or target text, or null
+     * @param alias - the label alias, or null
+     * @param side - which end
+     * @param where - the location
+     * @returns the node id, or null when the edge cannot be added
+     */
+    private endpoint;
+    /** Node labels to rows, for label aliases; null marks a label two nodes share. */
+    private labelRows;
+    /**
+     * The node a label alias names: by id, else by a label only one node has.
+     * @param alias - the alias
+     * @returns the row, or null
+     */
+    private aliasRow;
+    /**
+     * Fill the interaction of an edge without one from its label alias, as Cytoscape does.
+     * @param record - the edge
+     * @param row - the edge row
+     * @param where - the location
+     */
+    private fillInteraction;
+    /** Report the label alias uses, once. */
+    private finishAliases;
+    /**
+     * Write the edge `id` column (role id, unique).
+     * @param ids - the id of each row
+     */
+    private writeEdgeIds;
+    /**
+     * The graph table: the graph's atts and other XML attributes, and its graphics.
+     * @param graph - the subnetwork, or null for the root
+     */
+    private writeGraph;
+    /**
+     * The graph metadata: name, description and date from the RDF metadata, the format, version
+     * and what the exporter needs.
+     * @param graph - the subnetwork, or null
+     */
+    private writeMeta;
+}
+/**
+ * The three parts of a Cytoscape edge label (`source (interaction) target`).
+ * @param label - the label, or null
+ * @returns source alias, interaction, target alias; null when the label has another shape
+ */
+export declare function aliasesOf(label: string | null): [string, string, string] | null;
+export {};
+//# sourceMappingURL=emit.d.ts.map

package/dist/src/formats/xgmml/emit.d.ts.map

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