@graphty/graph-io 0.3.19 → 0.3.21

package/dist/chunks/importer-D_e7e7LX.js.map

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+{"version":3,"file":"importer-D_e7e7LX.js","sources":["../../src/formats/xgmml/constants.ts","../../src/formats/xgmml/document.ts","../../src/formats/xgmml/values.ts","../../src/formats/xgmml/columns.ts","../../src/formats/xgmml/emit.ts","../../src/formats/xgmml/importer.ts"],"sourcesContent":["/**\n * What the XGMML importer and exporter share: the namespaces, the format facts, the fixed column\n * names, the `meta.extra` key, and the issue and loss code tables (design\n * `design/graph-io/cytoscape-and-obo/design.md` section 1.1).\n */\n\nimport {\n    AMBIGUOUS_GRAPH_NAME_CODE,\n    BAD_VALUE_CODE,\n    COLUMN_RENAMED_CODE,\n    COLUMN_RENAMED_LOSS_CODE,\n    DANGLING_REFERENCE_CODE,\n    DIRECTION_FORCED_CODE,\n    DIRECTION_REFUSED_CODE,\n    DUPLICATE_ATTRIBUTE_CODE,\n    DUPLICATE_EDGE_ID_CODE,\n    DUPLICATE_NODE_CODE,\n    EMPTY_INPUT_CODE,\n    ENCODING_FALLBACK_CODE,\n    EQUATION_AS_TEXT_CODE,\n    GRAPH_NOT_FOUND_CODE,\n    ID_MERGED_CODE,\n    ID_TEXT_TYPE_CODE,\n    INVALID_ENCODING_CODE,\n    INVALID_UTF8_CODE,\n    MISSING_ENDPOINT_CODE,\n    MISSING_ID_CODE,\n    MIXED_DIRECTION_CODE,\n    MULTIPLE_GRAPHS_CODE,\n    MUTUAL_EXPANDED_CODE,\n    NO_GRAPH_CODE,\n    OPTION_IGNORED_CODE,\n    PARENT_CYCLE_CODE,\n    PARENTS_DROPPED_CODE,\n    PRECISION_CODE,\n    ROLE_ASSUMED_CODE,\n    ROLE_DROPPED_CODE,\n    ROLE_TAKEN_CODE,\n    SINK_OPTION_CODE,\n    STORAGE_CLASS_CODE,\n    STRAY_TEXT_CODE,\n    TEMPORAL_DROPPED_CODE,\n    TEMPORAL_TEXT_DROPPED_CODE,\n    UNKNOWN_ATTR_TYPE_CODE,\n    UNKNOWN_ELEMENT_CODE,\n    UNKNOWN_ENCODING_CODE,\n    UNKNOWN_PARENT_CODE,\n    WEIGHT_KEY_CLASH_CODE,\n    WIDENED_CODE,\n    XML_ILLEGAL_CHAR_CODE,\n    XML_SYNTAX_CODE,\n} from \"../../common/codes.js\";\n\n/** The format name. */\nexport const FORMAT = \"xgmml\";\n\n/** File extensions (never `.gr`, which DIMACS owns). */\nexport const EXTENSIONS: readonly string[] = Object.freeze([\".xgmml\", \".xml\"]);\n\n/** MIME types: the draft's (appendix E) and Cytoscape's. */\nexport const MIME_TYPES: readonly string[] = Object.freeze([\"application/xgmml\", \"text/xgmml\", \"text/xgmml+xml\"]);\n\n/** The XGMML namespace. */\nexport const XGMML_NAMESPACE = \"http://www.cs.rpi.edu/XGMML\";\n\n/** Cytoscape's namespace, bound to the `cy` prefix. */\nexport const CY_NAMESPACE = \"http://www.cytoscape.org\";\n\n/** The XLink namespace. */\nexport const XLINK_NAMESPACE = \"http://www.w3.org/1999/xlink\";\n\n/** The `meta.extra` key the importer writes and the exporter reads. */\nexport const META_KEY = \"xgmml\";\n\n/** The label column (role label) of node and edge `label` attributes. */\nexport const LABEL_COLUMN = \"label\";\n\n/** The edge `id` column (role id, unique). */\nexport const EDGE_ID_COLUMN = \"id\";\n\n/** The node position (f32 x3, role position, y up). */\nexport const POSITION_COLUMN = \"position\";\n\n/** Cytoscape's stacking order (`NODE_Z_LOCATION`), kept out of the position. */\nexport const Z_COLUMN = \"z\";\n\n/** The node, edge and graph json column of a `<graphics>` element's values as written. */\nexport const GRAPHICS_COLUMN = \"graphics\";\n\n/** The containing group node (u32, role parent). */\nexport const PARENT_COLUMN = \"parent\";\n\n/** Every containing group node of a node that is in several groups (list of u32, role parents). */\nexport const PARENTS_COLUMN = \"parents\";\n\n/** The json node column of a group's nested graph id, label and atts. */\nexport const SUBGRAPH_COLUMN = \"xgmml.subgraph\";\n\n/** The string node column naming the network a node's nested-network pointer points to. */\nexport const NESTED_NETWORK_COLUMN = \"cytoscape.nestedNetwork\";\n\n/** The string node column of a nested-network pointer into another file (`file.xgmml#id`). */\nexport const NETWORK_POINTER_COLUMN = \"xgmml.networkPointer\";\n\n/** The list node column of the root-level subgraphs a node belongs to, in a generic document. */\nexport const NETWORKS_COLUMN = \"xgmml.networks\";\n\n/** The edge column of Cytoscape's interaction type. */\nexport const INTERACTION_COLUMN = \"interaction\";\n\n/** The `origin.namespace` of the columns the importer derives from XGMML structure. */\nexport const XGMML_ORIGIN_NAMESPACE = \"xgmml\";\n\n/** The `origin.namespace` of the columns that hold Cytoscape-only data (z, nested networks). */\nexport const CYTOSCAPE_ORIGIN_NAMESPACE = \"cytoscape\";\n\n/**\n * The issue codes the XGMML importer records (design section 8.6), by name: the codes shared with\n * the other importers (src/common/codes.ts) and the XGMML-specific ones. A key is the code without\n * its severity and format prefixes.\n */\nexport const XGMML_ISSUE = Object.freeze({\n    /** Fatal: the input is not well-formed XML. */\n    XML_SYNTAX: XML_SYNTAX_CODE,\n    /** Fatal: the input is empty or whitespace only. */\n    EMPTY_INPUT: EMPTY_INPUT_CODE,\n    /** Fatal: the input holds invalid UTF-8. */\n    INVALID_UTF8: INVALID_UTF8_CODE,\n    /** Fatal: bytes invalid in the encoding a BOM, a declaration or the option chose. */\n    INVALID_ENCODING: INVALID_ENCODING_CODE,\n    /** Undeclared non-UTF-8 bytes were read as windows-1252. */\n    ENCODING_FALLBACK: ENCODING_FALLBACK_CODE,\n    /** A declared encoding the platform cannot decode was ignored. */\n    UNKNOWN_ENCODING: UNKNOWN_ENCODING_CODE,\n    /** Fatal: the root element is not `<graph>` (an XHTML page embedding one, a GraphML file). */\n    NO_GRAPH: NO_GRAPH_CODE,\n    /** Fatal: a session view document (`cy:view=\"1\"`): view SUIDs and no topology. */\n    VIEW_DOCUMENT: \"E_XGMML_VIEW_DOCUMENT\",\n    /** A node with neither an id nor a label; it is skipped with its subtree. */\n    MISSING_ID: MISSING_ID_CODE,\n    /** A node without an id; its label is used as the id. */\n    ID_FROM_LABEL: \"W_XGMML_ID_FROM_LABEL\",\n    /** An edge without a source or a target that no label alias resolves. */\n    MISSING_ENDPOINT: MISSING_ENDPOINT_CODE,\n    /** An edge endpoint that names no node (addMissingNodes false); the edge is skipped. */\n    UNKNOWN_NODE: \"E_UNKNOWN_NODE\",\n    /** Endpoints resolved through Cytoscape's `\"a (pp) b\"` label aliases; interactions filled from labels. */\n    LABEL_ALIAS: \"W_XGMML_LABEL_ALIAS\",\n    /** A node id declared twice; the declarations are merged. */\n    DUPLICATE_NODE: DUPLICATE_NODE_CODE,\n    /** An edge id used twice; the second edge is skipped. */\n    DUPLICATE_EDGE_ID: DUPLICATE_EDGE_ID_CODE,\n    /** A meta-edge the 2.x writer repeats inside a group; the copy is dropped. */\n    GROUP_DUPLICATE_EDGE: \"W_XGMML_GROUP_DUPLICATE_EDGE\",\n    /** A `directed` or `cy:directed` value other than 0 / 1. */\n    BAD_DIRECTED: \"W_XGMML_BAD_DIRECTED\",\n    /** A `documentVersion` that does not parse; the dialect is chosen from the content. */\n    DOCUMENT_VERSION: \"W_XGMML_DOCUMENT_VERSION\",\n    /** A root `<graph>` with neither the XGMML namespace nor an XGMML DOCTYPE. */\n    NO_NAMESPACE: \"W_XGMML_NO_NAMESPACE\",\n    /** A malformed `<att>`: a list with a value, a scalar with child atts, an att with no name. */\n    BAD_ATT: \"W_XGMML_BAD_ATT\",\n    /** A bare `&` read as `&amp;` under repairBareAmpersands. */\n    AMPERSAND_REPAIRED: \"W_XGMML_AMPERSAND_REPAIRED\",\n    /** Two surrogate character references joined under pairSurrogateReferences. */\n    SURROGATE_PAIRED: \"W_XGMML_SURROGATE_PAIRED\",\n    /** An empty list whose element type nothing states; a list of strings is assumed. */\n    EMPTY_LIST_TYPE: \"W_XGMML_EMPTY_LIST_TYPE\",\n    /** A record list, a list of lists, a 2.x map or foreign XML in an att, kept as json. */\n    RECORD_LIST: \"W_XGMML_RECORD_LIST\",\n    /** A pointer into another file (`file.xgmml#id`); kept as text. */\n    CROSS_FILE_REFERENCE: \"W_XGMML_CROSS_FILE_REFERENCE\",\n    /** A graph nested in an edge's att; there is no model for it. */\n    EDGE_NESTED_GRAPH: \"W_XGMML_EDGE_NESTED_GRAPH\",\n    /** Elements of a session network declared outside every registered subnetwork. */\n    ROOT_ONLY_ELEMENTS: \"W_XGMML_ROOT_ONLY_ELEMENTS\",\n    /** A value that does not parse as its declared type; the cell is unset. */\n    BAD_VALUE: BAD_VALUE_CODE,\n    /** A column widened because its values or declared types disagree. */\n    WIDENED: WIDENED_CODE,\n    /** A long or real beyond what a double holds exactly. */\n    PRECISION: PRECISION_CODE,\n    /** A reference (xlink:href, nested-network pointer) that names nothing. */\n    DANGLING_REFERENCE: DANGLING_REFERENCE_CODE,\n    /** The same attribute twice on one element; the later value wins. */\n    DUPLICATE_ATTRIBUTE: DUPLICATE_ATTRIBUTE_CODE,\n    /** A group membership naming no node. */\n    UNKNOWN_PARENT: UNKNOWN_PARENT_CODE,\n    /** A group membership that would close a parent cycle; that link is dropped. */\n    PARENT_CYCLE: PARENT_CYCLE_CODE,\n    /** A Cytoscape formula kept as its text. */\n    EQUATION_AS_TEXT: EQUATION_AS_TEXT_CODE,\n    /** An att type XGMML and Cytoscape do not define; kept as text. */\n    UNKNOWN_ATTR_TYPE: UNKNOWN_ATTR_TYPE_CODE,\n    /** An element XGMML does not define at that place; skipped with its subtree. */\n    UNKNOWN_ELEMENT: UNKNOWN_ELEMENT_CODE,\n    /** Character data where XGMML allows only elements, or inside an att. */\n    STRAY_TEXT: STRAY_TEXT_CODE,\n    /** A session network document holds several registered networks; one was read. */\n    MULTIPLE_GRAPHS: MULTIPLE_GRAPHS_CODE,\n    /** graphIndex / graphName names no network (fatal). */\n    GRAPH_NOT_FOUND: GRAPH_NOT_FOUND_CODE,\n    /** graphName names several networks (fatal). */\n    AMBIGUOUS_GRAPH_NAME: AMBIGUOUS_GRAPH_NAME_CODE,\n    /** A column renamed `<name>#<n>` because its name was taken. */\n    COLUMN_RENAMED: COLUMN_RENAMED_CODE,\n    /** A column declared without its role because the table already holds it. */\n    ROLE_TAKEN: ROLE_TAKEN_CODE,\n    /** Two id texts merged into one number under ids \"number\". */\n    ID_MERGED: ID_MERGED_CODE,\n    /** An option the format has no use for. */\n    OPTION_IGNORED: OPTION_IGNORED_CODE,\n    /** A builder-policy option the sink does not honour. */\n    SINK_OPTION: SINK_OPTION_CODE,\n    /** The sink refused the file's direction. */\n    DIRECTION_REFUSED: DIRECTION_REFUSED_CODE,\n    /** Edges forced to the policy's direction. */\n    DIRECTION_FORCED: DIRECTION_FORCED_CODE,\n    /** A mixed file under onMixedDirection \"error\" (fatal). */\n    MIXED_DIRECTION: MIXED_DIRECTION_CODE,\n});\n\n/**\n * Loss note codes of the XGMML exporter (check()): the XGMML ones and the shared ones its notes\n * can carry. The generic notes of `checkCapabilities()` (dtypes, components, temporal and visual\n * roles, extension tables) are those of `LOSS`.\n */\nexport const XGMML_LOSS = Object.freeze({\n    /** A json or nested-list column written as a string att. */\n    JSON_AS_STRING: \"W_XGMML_JSON_AS_STRING\",\n    /** A dtype written as a wider Cytoscape type (f32 as Double, u32 above i32 as Long, u8 as Integer, dict as String). */\n    WIDENED_TYPE: \"W_XGMML_WIDENED_TYPE\",\n    /** A string holding a character XML 1.0 cannot carry; export() throws. */\n    XML_ILLEGAL_CHAR: XML_ILLEGAL_CHAR_CODE,\n    /** A temporal column written as plain numbers. */\n    TEMPORAL_DROPPED: TEMPORAL_DROPPED_CODE,\n    /** A temporal text companion written as a plain string att. */\n    TEMPORAL_TEXT_DROPPED: TEMPORAL_TEXT_DROPPED_CODE,\n    /** A role the format has no slot for, written as a plain att. */\n    ROLE_DROPPED: ROLE_DROPPED_CODE,\n    /** A parents column not written because the snapshot also has a parent column. */\n    PARENTS_DROPPED: PARENTS_DROPPED_CODE,\n    /** A mutual pair written as two directed edges. */\n    MUTUAL_EXPANDED: MUTUAL_EXPANDED_CODE,\n    /** Node ids whose text reads back as the other type. */\n    ID_TEXT_TYPE: ID_TEXT_TYPE_CODE,\n    /** An edge id column of another dtype written as text; it reads back as strings. */\n    EDGE_ID_TEXT: \"W_XGMML_EDGE_ID_TEXT\",\n    /** Strings holding a literal backslash-n or backslash-t read back as newline / tab (Cytoscape's escapes). */\n    BACKSLASH_ESCAPE: \"W_XGMML_BACKSLASH_ESCAPE\",\n    /** A position that cannot be written as it is: another shape, a non-finite coordinate, a z read back in the z column. */\n    POSITION: \"W_XGMML_POSITION\",\n    /** Nodes whose parent chain never reaches a root are written at the top level. */\n    PARENT_CYCLE: \"W_XGMML_PARENT_CYCLE\",\n    /** A column named like a column the importer owns reads back renamed. */\n    COLUMN_NAME_CHANGED: COLUMN_RENAMED_LOSS_CODE,\n    /** A role-less column written into a slot reads back with the slot's role. */\n    ROLE_ASSUMED: ROLE_ASSUMED_CODE,\n    /** A plain `weight` edge column reads back as THE weight. */\n    WEIGHT_KEY_CLASH: WEIGHT_KEY_CLASH_CODE,\n    /** A string / dict column that reads back as the other storage class. */\n    STORAGE_CLASS_CHANGED: STORAGE_CLASS_CODE,\n    /** Edge labels shaped `a (i) b` read back with an `interaction` column (Cytoscape's label alias). */\n    INTERACTION_FROM_LABEL: \"W_XGMML_INTERACTION_FROM_LABEL\",\n});\n","/**\n * The XGMML document model: one pass of the shared XML tokenizer turns an XGMML document into\n * plain records (graphs, nodes, edges, atts, graphics) that keep everything the file says, with\n * forward references (`xlink:href`, an edge before its nodes) left as ids. The importer\n * (importer.ts) resolves the records into a sink once the outermost `</graph>` has closed, as\n * Cytoscape does, and the `.cys` importer reuses the same records for the network and view files\n * of a session.\n *\n * It recognises the five shapes of `research-xgmml.md` section 2: the 1.0 draft, the Cytoscape\n * 2.x export and session, the 3.x export, the 3.x session network file (root `cy:registered=\"0\"`)\n * and the 3.x session view file (root `cy:view=\"1\"`).\n */\n\nimport { escapeXmlAttribute, escapeXmlText } from \"../../common/escape.js\";\nimport { type ImportReportBuilder } from \"../../common/report.js\";\nimport { isWhitespace, localName, type XmlHandler } from \"../../common/xml.js\";\nimport { XGMML_ISSUE, XGMML_NAMESPACE } from \"./constants.js\";\n\n/** One `<att>` and what it holds. */\nexport interface AttRec {\n    /** The `name` (else `label`) attribute, or null. */\n    name: string | null;\n    /** The XGMML `type` as written, or null. */\n    readonly type: string | null;\n    /** Cytoscape's `cy:type`, or null. */\n    readonly cyType: string | null;\n    /** Cytoscape's `cy:elementType` of a list, or null. */\n    readonly elementType: string | null;\n    /** The `value` attribute, or null when absent. */\n    readonly value: string | null;\n    /** `cy:hidden` is 1, true or yes. */\n    readonly hidden: boolean;\n    /** `cy:equation` is 1, true or yes: the value is a formula. */\n    readonly equation: boolean;\n    /** The child atts (list items, record fields, graphics properties). */\n    readonly children: AttRec[];\n    /** The XML attributes besides the ones above (a 2.x bend handle's `x` and `y`). */\n    readonly extra: Record<string, string>;\n    /** Foreign XML inside the att (RDF), serialized, or null. */\n    xml: string | null;\n    /** Whether the att held a `<graph>`. */\n    hasGraph: boolean;\n    /** Non-whitespace character data inside the att. */\n    text: string;\n    /** The line of the `<att`. */\n    readonly line: number;\n    /** The table namespace of a `.cys` column, or null for an att of the document. */\n    readonly namespace?: string | null | undefined;\n}\n\n/** A `<node>`. */\nexport interface NodeRec {\n    readonly kind: \"node\";\n    /** The id (the label when the id is missing), or null for an `xlink:href` reference. */\n    readonly id: string | null;\n    /** The `xlink:href` of a reference to a node declared elsewhere, or null. */\n    readonly href: string | null;\n    /** The `label` attribute (else `name`), or null. */\n    readonly label: string | null;\n    /** The `name` attribute when a label is also given, or null. */\n    readonly name: string | null;\n    /** The other XML attributes, as written. */\n    readonly xmlAttrs: [string, string][];\n    /** The atts, in document order. */\n    readonly atts: AttRec[];\n    /** The graphics values besides x, y and z, or null without `<graphics>`. */\n    graphics: Record<string, unknown> | null;\n    /** The x, y and z texts of the graphics (or its `<center>`), or null. */\n    x: string | null;\n    y: string | null;\n    z: string | null;\n    /** The graphs nested in the node's atts. */\n    readonly nested: GraphRec[];\n    /** The graph that declares (or references) the node. */\n    readonly graph: GraphRec;\n    /** The line of the `<node`. */\n    readonly line: number;\n    /** A session view's `cy:nodeId`, or null. */\n    readonly viewId: string | null;\n}\n\n/** An `<edge>`. */\nexport interface EdgeRec {\n    readonly kind: \"edge\";\n    /** The id attribute, or null. */\n    readonly id: string | null;\n    /** The `xlink:href` of a reference to an edge declared elsewhere, or null. */\n    readonly href: string | null;\n    /** The source and target texts, or null when missing. */\n    readonly source: string | null;\n    readonly target: string | null;\n    /** The label attribute, or null. */\n    readonly label: string | null;\n    /** The `name` attribute, or null. */\n    readonly name: string | null;\n    /** The `weight` attribute, or null. */\n    readonly weight: string | null;\n    /** The `cy:directed` attribute, or null. */\n    readonly directed: string | null;\n    /** The other XML attributes, as written. */\n    readonly xmlAttrs: [string, string][];\n    /** The atts, in document order. */\n    readonly atts: AttRec[];\n    /** The graphics values, or null. */\n    graphics: Record<string, unknown> | null;\n    /** The graph that declares (or references) the edge. */\n    readonly graph: GraphRec;\n    /** The line of the `<edge`. */\n    readonly line: number;\n    /** A session view's `cy:edgeId`, or null. */\n    readonly viewId: string | null;\n}\n\n/** A `<graph>`: the root, a subnetwork, a group or a nested-network pointer. */\nexport interface GraphRec {\n    /** The id attribute, or null. */\n    readonly id: string | null;\n    /** The label attribute, or null. */\n    readonly label: string | null;\n    /** The `xlink:href` of a pointer to a graph written elsewhere, or null. */\n    readonly href: string | null;\n    /** `cy:registered` as written, or null. */\n    readonly registered: string | null;\n    /** Every XML attribute, as written. */\n    readonly attrs: ReadonlyMap<string, string>;\n    /** The graph-level atts. */\n    readonly atts: AttRec[];\n    /** The graph's `<graphics>` values, or null. */\n    graphics: Record<string, unknown> | null;\n    /** The node whose att holds this graph, or null. */\n    readonly owner: NodeRec | null;\n    /** The graph this one is nested in, or null for the root. */\n    readonly parent: GraphRec | null;\n    /** The nodes and edges directly in this graph (declared or referenced), in document order. */\n    readonly members: (NodeRec | EdgeRec)[];\n    /** The graphs held by this graph's own atts (subnetworks of the root). */\n    readonly subgraphs: GraphRec[];\n    /** The line of the `<graph`. */\n    readonly line: number;\n}\n\n/** A parsed document. */\nexport interface XgmmlDocument {\n    /** The root graph. */\n    readonly root: GraphRec;\n    /** Every declared node (not references), in document order. */\n    readonly nodes: NodeRec[];\n    /** Every declared edge, in document order. */\n    readonly edges: EdgeRec[];\n    /** Every graph, root first. */\n    readonly graphs: GraphRec[];\n    /** The `cy` prefix is bound, or a `cy:` attribute is used: Cytoscape wrote the file. */\n    readonly cytoscape: boolean;\n    /** The root is in the XGMML namespace (default or prefixed). */\n    readonly xgmmlNamespace: boolean;\n    /** The RDF network metadata fields (`dc:title`, ...) by local name. */\n    readonly rdf: Record<string, string>;\n    /** The serialized `networkMetadata` RDF, or null. */\n    readonly rdfXml: string | null;\n}\n\n/** What the parser keeps about one open element. */\ntype Frame =\n    | { readonly kind: \"graph\"; readonly graph: GraphRec }\n    | { readonly kind: \"node\"; readonly node: NodeRec }\n    | { readonly kind: \"edge\"; readonly edge: EdgeRec }\n    | { readonly kind: \"att\"; readonly att: AttRec; readonly owner: \"graph\" | \"node\" | \"edge\" | \"graphics\" | \"att\" }\n    | { readonly kind: \"graphics\"; readonly target: GraphicsTarget }\n    | { readonly kind: \"line\"; readonly points: Record<string, string>[] }\n    | { readonly kind: \"capture\"; readonly att: AttRec; depth: number }\n    | { readonly kind: \"skip\" };\n\n/** What a `<graphics>` writes into. */\ninterface GraphicsTarget {\n    graphics: Record<string, unknown> | null;\n    x?: string | null;\n    y?: string | null;\n    z?: string | null;\n}\n\n/** The XML attributes the parser reads on `<node>`. */\nconst NODE_READ: ReadonlySet<string> = new Set([\"id\", \"label\", \"name\", \"xlink:href\", \"cy:nodeId\"]);\n\n/** The XML attributes the parser reads on `<edge>`. */\nconst EDGE_READ: ReadonlySet<string> = new Set([\n    \"id\",\n    \"label\",\n    \"name\",\n    \"source\",\n    \"target\",\n    \"weight\",\n    \"cy:directed\",\n    \"xlink:href\",\n    \"cy:edgeId\",\n]);\n\n/** The XML attributes an `<att>` uses as its own; any other is kept in `extra`. */\nconst ATT_READ: ReadonlySet<string> = new Set([\n    \"name\",\n    \"label\",\n    \"type\",\n    \"value\",\n    \"cy:type\",\n    \"cy:elementType\",\n    \"cy:hidden\",\n    \"cy:equation\",\n    \"cy:editable\",\n]);\n\n/** Cytoscape's spellings of true (`1`, `true`, `yes`, any case). */\nconst TRUE_TEXT = /^(1|true|yes)$/i;\n\n/**\n * Whether a Cytoscape flag text is true.\n * @param text - the text, or undefined\n * @returns true for 1, true or yes in any case\n */\nexport function isCyTrue(text: string | null | undefined): boolean {\n    return text !== null && text !== undefined && TRUE_TEXT.test(text.trim());\n}\n\n/**\n * The name an XML attribute is known by, its `xlink` prefix normalised whatever prefix the file\n * binds XLink to (galFiltered.xgmml uses `ns1`).\n * @param name - the attribute name as written\n * @param xlinkPrefixes - the prefixes bound to the XLink namespace\n * @returns the name with `xlink:` for XLink attributes\n */\nfunction normaliseName(name: string, xlinkPrefixes: ReadonlySet<string>): string {\n    const colon = name.indexOf(\":\");\n    if (colon > 0 && xlinkPrefixes.has(name.slice(0, colon))) {\n        return `xlink:${name.slice(colon + 1)}`;\n    }\n    return name;\n}\n\n/**\n * The tokenizer handler that builds an XgmmlDocument.\n */\nexport class XgmmlParser implements XmlHandler {\n    private readonly report: ImportReportBuilder;\n\n    private readonly frames: Frame[] = [];\n\n    private readonly xlinkPrefixes = new Set<string>([\"xlink\"]);\n\n    private rootGraph: GraphRec | null = null;\n\n    private readonly nodes: NodeRec[] = [];\n\n    private readonly edges: EdgeRec[] = [];\n\n    private readonly graphs: GraphRec[] = [];\n\n    private cytoscape = false;\n\n    private xgmmlNamespace = false;\n\n    /** The prefix of the root element (`xgmml` in `<xgmml:graph>`), or null when it has none. */\n    private rootPrefix: string | null = null;\n\n    private readonly rdf: Record<string, string> = {};\n\n    private rdfXml: string | null = null;\n\n    /**\n     * Create a parser.\n     * @param report - the report issues are recorded in\n     */\n    constructor(report: ImportReportBuilder) {\n        this.report = report;\n    }\n\n    /**\n     * The parsed document.\n     * @returns the document; E_NO_GRAPH (fatal) when no root graph was read\n     */\n    document(): XgmmlDocument {\n        const root = this.rootGraph;\n        if (root === null) {\n            return this.report.fail(XGMML_ISSUE.NO_GRAPH, \"the document has no <graph> element\");\n        }\n        return {\n            root,\n            nodes: this.nodes,\n            edges: this.edges,\n            graphs: this.graphs,\n            cytoscape: this.cytoscape,\n            xgmmlNamespace: this.xgmmlNamespace,\n            rdf: this.rdf,\n            rdfXml: this.rdfXml,\n        };\n    }\n\n    /**\n     * An element starts.\n     * @param rawName - the element name as written\n     * @param rawAttrs - its attributes\n     * @param line - the line\n     */\n    start(rawName: string, rawAttrs: ReadonlyMap<string, string>, line: number): void {\n        const top = this.frames.length === 0 ? null : this.frames[this.frames.length - 1];\n        if (top === null) {\n            this.startRoot(rawName, rawAttrs, line);\n            return;\n        }\n        if (top.kind === \"skip\") {\n            this.frames.push(top);\n            return;\n        }\n        if (top.kind === \"capture\") {\n            this.capture(top, rawName, rawAttrs);\n            return;\n        }\n        const attrs = this.normalise(rawAttrs);\n        const name = localName(rawName);\n        switch (top.kind) {\n            case \"graph\":\n                this.startInGraph(top.graph, rawName, name, attrs, line);\n                return;\n            case \"node\":\n                this.startInElement(top.node, rawName, name, attrs, line);\n                return;\n            case \"edge\":\n                this.startInElement(top.edge, rawName, name, attrs, line);\n                return;\n            case \"att\":\n                this.startInAtt(top, rawName, name, attrs, line);\n                return;\n            case \"graphics\":\n                this.startInGraphics(top.target, rawName, name, attrs, line);\n                return;\n            case \"line\":\n                if (name === \"point\") {\n                    top.points.push(Object.fromEntries(attrs));\n                    this.frames.push({ kind: \"skip\" });\n                    return;\n                }\n                this.unknownElement(rawName, line);\n                return;\n            default: {\n                const kind: never = top;\n                throw new Error(`unknown XGMML frame ${String(kind)}`);\n            }\n        }\n    }\n\n    /**\n     * An element ends.\n     * @param name - the element name\n     * @param _line - the line\n     */\n    end(name: string, _line: number): void {\n        const frame = this.frames.pop();\n        const below = this.frames.length === 0 ? null : this.frames[this.frames.length - 1];\n        switch (frame?.kind) {\n            case \"capture\":\n                frame.att.xml = `${frame.att.xml ?? \"\"}</${name}>`;\n                frame.depth--;\n                if (frame.depth > 0) {\n                    this.frames.push(frame);\n                } else if (frame.att.name === \"networkMetadata\") {\n                    this.rdfXml = frame.att.xml;\n                }\n                this.rdfElement = null;\n                return;\n            case \"att\":\n                if (below?.kind === \"graphics\") {\n                    this.graphicsAtt(below.target, frame.att);\n                }\n                return;\n            case \"line\":\n                if (below?.kind === \"graphics\") {\n                    below.target.graphics = { ...(below.target.graphics ?? {}), Line: frame.points };\n                }\n                return;\n            default:\n        }\n    }\n\n    /**\n     * Character data.\n     * @param text - the text\n     * @param line - the line\n     */\n    text(text: string, line: number): void {\n        const top = this.frames.length === 0 ? null : this.frames[this.frames.length - 1];\n        if (top === null || top.kind === \"skip\") {\n            return;\n        }\n        if (top.kind === \"capture\") {\n            top.att.xml = `${top.att.xml ?? \"\"}${escapeXmlText(text)}`;\n            this.captureRdfText(text);\n            return;\n        }\n        if (isWhitespace(text)) {\n            return;\n        }\n        if (top.kind === \"att\") {\n            top.att.text += text;\n        }\n        this.report.warnOnce(\n            \"validation-error\",\n            XGMML_ISSUE.STRAY_TEXT,\n            top.kind === \"att\"\n                ? \"text inside <att> is ignored; an XGMML value is the value attribute\"\n                : \"text where XGMML allows only elements was ignored\",\n            { line },\n        );\n    }\n\n    // ------------------------------------------------------------------ structure\n\n    /**\n     * The XML attribute map with every XLink prefix written `xlink:`.\n     * @param attrs - the attributes as written\n     * @returns the normalised map\n     */\n    private normalise(attrs: ReadonlyMap<string, string>): Map<string, string> {\n        const out = new Map<string, string>();\n        for (const [key, value] of attrs) {\n            out.set(normaliseName(key, this.xlinkPrefixes), value);\n        }\n        return out;\n    }\n\n    /**\n     * The root element: a `<graph>`, else the document is not XGMML.\n     * @param rawName - the name as written\n     * @param rawAttrs - its attributes\n     * @param line - the line\n     */\n    private startRoot(rawName: string, rawAttrs: ReadonlyMap<string, string>, line: number): void {\n        const local = localName(rawName);\n        const prefix = rawName.includes(\":\") ? rawName.slice(0, rawName.indexOf(\":\")) : null;\n        for (const [key, value] of rawAttrs) {\n            if (key.startsWith(\"xmlns:\") && value === \"http://www.w3.org/1999/xlink\") {\n                this.xlinkPrefixes.add(key.slice(6));\n            }\n            if (key === \"xmlns:cy\" || key.startsWith(\"cy:\")) {\n                this.cytoscape = true;\n            }\n        }\n        this.rootPrefix = prefix;\n        const nsKey = prefix === null ? \"xmlns\" : `xmlns:${prefix}`;\n        this.xgmmlNamespace = rawAttrs.get(nsKey) === XGMML_NAMESPACE;\n        if (local !== \"graph\") {\n            this.report.fail(\n                XGMML_ISSUE.NO_GRAPH,\n                `the root element is <${rawName}>, not <graph>; an XGMML graph embedded in another document is not read`,\n                { line },\n            );\n        }\n        const graph = this.newGraph(this.normalise(rawAttrs), line, null, null);\n        this.rootGraph = graph;\n        this.frames.push({ kind: \"graph\", graph });\n    }\n\n    /**\n     * A graph record, registered in the document.\n     * @param attrs - its attributes\n     * @param line - the line\n     * @param owner - the node whose att holds it, or null\n     * @param parent - the graph it is nested in, or null\n     * @returns the record\n     */\n    private newGraph(\n        attrs: ReadonlyMap<string, string>,\n        line: number,\n        owner: NodeRec | null,\n        parent: GraphRec | null,\n    ): GraphRec {\n        const graph: GraphRec = {\n            id: attrs.get(\"id\") ?? null,\n            label: attrs.get(\"label\") ?? null,\n            href: attrs.get(\"xlink:href\") ?? null,\n            registered: attrs.get(\"cy:registered\") ?? null,\n            attrs,\n            atts: [],\n            graphics: null,\n            owner,\n            parent,\n            members: [],\n            subgraphs: [],\n            line,\n        };\n        if (!this.cytoscape) {\n            for (const key of attrs.keys()) {\n                if (key.startsWith(\"cy:\")) {\n                    this.cytoscape = true;\n                }\n            }\n        }\n        this.graphs.push(graph);\n        return graph;\n    }\n\n    /**\n     * A child of `<graph>`.\n     * @param graph - the graph\n     * @param rawName - the name as written\n     * @param name - its local name\n     * @param attrs - its attributes\n     * @param line - the line\n     */\n    private startInGraph(\n        graph: GraphRec,\n        rawName: string,\n        name: string,\n        attrs: Map<string, string>,\n        line: number,\n    ): void {\n        switch (name) {\n            case \"node\":\n                this.beginNode(graph, attrs, line);\n                return;\n            case \"edge\":\n                this.beginEdge(graph, attrs, line);\n                return;\n            case \"att\": {\n                const att = this.newAtt(attrs, line);\n                graph.atts.push(att);\n                this.beginAtt(att, attrs, \"graph\");\n                return;\n            }\n            case \"graphics\":\n                this.beginGraphics(graph, attrs);\n                return;\n            default:\n                this.unknownElement(rawName, line);\n        }\n    }\n\n    /**\n     * A child of `<node>` or `<edge>`.\n     * @param element - the node or edge\n     * @param rawName - the name as written\n     * @param name - its local name\n     * @param attrs - its attributes\n     * @param line - the line\n     */\n    private startInElement(\n        element: NodeRec | EdgeRec,\n        rawName: string,\n        name: string,\n        attrs: Map<string, string>,\n        line: number,\n    ): void {\n        switch (name) {\n            case \"att\": {\n                const att = this.newAtt(attrs, line);\n                element.atts.push(att);\n                this.beginAtt(att, attrs, element.kind);\n                return;\n            }\n            case \"graphics\":\n                this.beginGraphics(element, attrs);\n                return;\n            default:\n                this.unknownElement(rawName, line);\n        }\n    }\n\n    /**\n     * A child of `<att>`: a child att, a nested graph, or foreign XML.\n     * @param frame - the att frame\n     * @param rawName - the name as written\n     * @param name - its local name\n     * @param attrs - its attributes\n     * @param line - the line\n     */\n    private startInAtt(\n        frame: Extract<Frame, { kind: \"att\" }>,\n        rawName: string,\n        name: string,\n        attrs: Map<string, string>,\n        line: number,\n    ): void {\n        const { att } = frame;\n        const xgmml = this.isXgmmlName(rawName);\n        if (name === \"att\" && xgmml) {\n            const child = this.newAtt(attrs, line);\n            att.children.push(child);\n            this.beginAtt(child, attrs, frame.owner === \"graphics\" ? \"graphics\" : \"att\");\n            return;\n        }\n        if (name === \"graph\" && xgmml) {\n            att.hasGraph = true;\n            this.beginNestedGraph(frame, attrs, line);\n            return;\n        }\n        // a second foreign element of the same att is appended to the first\n        att.xml ??= \"\";\n        const capture: Extract<Frame, { kind: \"capture\" }> = { kind: \"capture\", att, depth: 0 };\n        this.frames.push(capture);\n        this.capture(capture, rawName, attrs);\n    }\n\n    /**\n     * Whether an element name inside an att is XGMML's own (unprefixed, or with the root's prefix,\n     * as in a document whose root is `<xgmml:graph>`) rather than foreign XML such as `rdf:RDF`.\n     * @param rawName - the name as written\n     * @returns true for an XGMML element name\n     */\n    private isXgmmlName(rawName: string): boolean {\n        const colon = rawName.indexOf(\":\");\n        return colon < 0 || (this.rootPrefix !== null && rawName.slice(0, colon) === this.rootPrefix);\n    }\n\n    /**\n     * A `<graph>` inside an `<att>`: a subnetwork of the root, a group or nested-network pointer\n     * of a node, or (in an edge) a graph with no model.\n     * @param frame - the att frame\n     * @param attrs - the graph's attributes\n     * @param line - the line\n     */\n    private beginNestedGraph(frame: Extract<Frame, { kind: \"att\" }>, attrs: Map<string, string>, line: number): void {\n        const holder = this.attHolder();\n        if (holder === null || holder.kind === \"edge\" || frame.owner === \"graphics\") {\n            this.report.warnOnce(\n                \"unsupported\",\n                XGMML_ISSUE.EDGE_NESTED_GRAPH,\n                \"a graph nested in an edge's (or a graphics) att has no model and was skipped with its content\",\n                { line },\n            );\n            this.frames.push({ kind: \"skip\" });\n            return;\n        }\n        if (holder.kind === \"node\") {\n            const graph = this.newGraph(attrs, line, holder.node, holder.node.graph);\n            holder.node.nested.push(graph);\n            this.frames.push({ kind: \"graph\", graph });\n            return;\n        }\n        const graph = this.newGraph(attrs, line, null, holder.graph);\n        holder.graph.subgraphs.push(graph);\n        this.frames.push({ kind: \"graph\", graph });\n    }\n\n    /**\n     * The innermost node, edge or graph frame below the open atts.\n     * @returns the frame, or null\n     */\n    private attHolder(): Extract<Frame, { kind: \"graph\" | \"node\" | \"edge\" }> | null {\n        for (let i = this.frames.length - 1; i >= 0; i--) {\n            const frame = this.frames[i];\n            if (frame.kind === \"graph\" || frame.kind === \"node\" || frame.kind === \"edge\") {\n                return frame;\n            }\n        }\n        return null;\n    }\n\n    /**\n     * Report an element XGMML does not define here and skip its subtree.\n     * @param rawName - the name as written\n     * @param line - the line\n     */\n    private unknownElement(rawName: string, line: number): void {\n        this.report.warnOnce(\n            \"unsupported\",\n            XGMML_ISSUE.UNKNOWN_ELEMENT,\n            `element <${rawName}> is not XGMML here and was skipped with its content`,\n            { line, element: rawName },\n            `${XGMML_ISSUE.UNKNOWN_ELEMENT}:${rawName}`,\n        );\n        this.frames.push({ kind: \"skip\" });\n    }\n\n    // ------------------------------------------------------------------ nodes and edges\n\n    /**\n     * Open a `<node>`.\n     * @param graph - the graph it is in\n     * @param attrs - its attributes\n     * @param line - the line\n     */\n    private beginNode(graph: GraphRec, attrs: Map<string, string>, line: number): void {\n        const href = attrs.get(\"xlink:href\") ?? null;\n        let id = attrs.get(\"id\") ?? null;\n        const labelAttr = attrs.get(\"label\") ?? null;\n        const nameAttr = attrs.get(\"name\") ?? null;\n        const label = labelAttr ?? nameAttr;\n        if (href === null && id === null) {\n            if (label === null || label.length === 0) {\n                this.report.counts.skippedNodes++;\n                this.report.error(\"missing-value\", XGMML_ISSUE.MISSING_ID, \"<node> without an id or a label\", {\n                    line,\n                });\n                this.frames.push({ kind: \"skip\" });\n                return;\n            }\n            this.report.warning(\n                \"validation-error\",\n                XGMML_ISSUE.ID_FROM_LABEL,\n                `<node> without an id: its label \"${label}\" is used as the id`,\n                { line, element: label },\n            );\n            id = label;\n        }\n        const node: NodeRec = {\n            kind: \"node\",\n            id: href === null ? id : null,\n            href,\n            label,\n            name: labelAttr !== null ? nameAttr : null,\n            xmlAttrs: otherAttributes(attrs, NODE_READ),\n            atts: [],\n            graphics: null,\n            x: null,\n            y: null,\n            z: null,\n            nested: [],\n            graph,\n            line,\n            viewId: attrs.get(\"cy:nodeId\") ?? null,\n        };\n        graph.members.push(node);\n        if (href === null) {\n            this.nodes.push(node);\n        }\n        this.frames.push({ kind: \"node\", node });\n    }\n\n    /**\n     * Open an `<edge>`.\n     * @param graph - the graph it is in\n     * @param attrs - its attributes\n     * @param line - the line\n     */\n    private beginEdge(graph: GraphRec, attrs: Map<string, string>, line: number): void {\n        const href = attrs.get(\"xlink:href\") ?? null;\n        const edge: EdgeRec = {\n            kind: \"edge\",\n            id: href === null ? (attrs.get(\"id\") ?? null) : null,\n            href,\n            source: attrs.get(\"source\") ?? null,\n            target: attrs.get(\"target\") ?? null,\n            label: attrs.get(\"label\") ?? null,\n            name: attrs.get(\"name\") ?? null,\n            weight: attrs.get(\"weight\") ?? null,\n            directed: attrs.get(\"cy:directed\") ?? null,\n            xmlAttrs: otherAttributes(attrs, EDGE_READ),\n            atts: [],\n            graphics: null,\n            graph,\n            line,\n            viewId: attrs.get(\"cy:edgeId\") ?? null,\n        };\n        graph.members.push(edge);\n        if (href === null) {\n            this.edges.push(edge);\n        }\n        this.frames.push({ kind: \"edge\", edge });\n    }\n\n    // ------------------------------------------------------------------ atts\n\n    /**\n     * An att record from its XML attributes.\n     * @param attrs - the attributes\n     * @param line - the line\n     * @returns the record\n     */\n    private newAtt(attrs: Map<string, string>, line: number): AttRec {\n        const extra: Record<string, string> = {};\n        for (const [key, value] of attrs) {\n            if (!ATT_READ.has(key) && key !== \"xmlns\" && !key.startsWith(\"xmlns:\")) {\n                extra[key] = value;\n            }\n        }\n        return {\n            name: attrs.get(\"name\") ?? attrs.get(\"label\") ?? null,\n            type: attrs.get(\"type\") ?? null,\n            cyType: attrs.get(\"cy:type\") ?? null,\n            elementType: attrs.get(\"cy:elementType\") ?? null,\n            value: attrs.get(\"value\") ?? null,\n            hidden: isCyTrue(attrs.get(\"cy:hidden\")),\n            equation: isCyTrue(attrs.get(\"cy:equation\")),\n            children: [],\n            extra,\n            xml: null,\n            hasGraph: false,\n            text: \"\",\n            line,\n        };\n    }\n\n    /**\n     * Open an `<att>`.\n     * @param att - the record\n     * @param _attrs - its attributes\n     * @param owner - what holds it\n     */\n    private beginAtt(\n        att: AttRec,\n        _attrs: Map<string, string>,\n        owner: \"graph\" | \"node\" | \"edge\" | \"graphics\" | \"att\",\n    ): void {\n        this.frames.push({ kind: \"att\", att, owner });\n    }\n\n    /**\n     * Serialize one start tag of foreign XML into the capturing att.\n     * @param frame - the capture frame\n     * @param rawName - the name as written\n     * @param attrs - its attributes\n     */\n    private capture(\n        frame: Extract<Frame, { kind: \"capture\" }>,\n        rawName: string,\n        attrs: ReadonlyMap<string, string>,\n    ): void {\n        let tag = `<${rawName}`;\n        for (const [key, value] of attrs) {\n            tag += ` ${key}=\"${escapeXmlAttribute(value)}\"`;\n        }\n        frame.att.xml = `${frame.att.xml ?? \"\"}${tag}>`;\n        frame.depth++;\n        if (frame.att.name === \"networkMetadata\") {\n            this.rdfElement = localName(rawName);\n        }\n    }\n\n    /** The local name of the RDF element whose text is being read, or null. */\n    private rdfElement: string | null = null;\n\n    /**\n     * Keep the text of an RDF metadata field.\n     * @param text - the text\n     */\n    private captureRdfText(text: string): void {\n        if (this.rdfElement !== null && !isWhitespace(text)) {\n            this.rdf[this.rdfElement] = (this.rdf[this.rdfElement] ?? \"\") + text;\n        }\n    }\n\n    // ------------------------------------------------------------------ graphics\n\n    /**\n     * Open a `<graphics>`: x, y and z (draft and Cytoscape) are read as coordinates; every other\n     * attribute is kept as written, merged key by key with an earlier `<graphics>`.\n     * @param target - the node, edge or graph\n     * @param attrs - its attributes\n     */\n    private beginGraphics(target: GraphicsTarget, attrs: Map<string, string>): void {\n        const graphics: Record<string, unknown> = { ...(target.graphics ?? {}) };\n        for (const [key, value] of attrs) {\n            if (\"x\" in target && (key === \"x\" || key === \"y\" || key === \"z\")) {\n                target[key] = value;\n            } else if (key !== \"xmlns\" && !key.startsWith(\"xmlns:\")) {\n                graphics[key] = value;\n            }\n        }\n        target.graphics = graphics;\n        this.frames.push({ kind: \"graphics\", target });\n    }\n\n    /**\n     * A child of `<graphics>`: a visual-property att, a `<center>` or a `<Line>`.\n     * @param target - the graphics target\n     * @param rawName - the name as written\n     * @param name - its local name\n     * @param attrs - its attributes\n     * @param line - the line\n     */\n    private startInGraphics(\n        target: GraphicsTarget,\n        rawName: string,\n        name: string,\n        attrs: Map<string, string>,\n        line: number,\n    ): void {\n        switch (name) {\n            case \"att\": {\n                this.frames.push({ kind: \"att\", att: this.newAtt(attrs, line), owner: \"graphics\" });\n                return;\n            }\n            case \"center\":\n                if (\"x\" in target) {\n                    target.x ??= attrs.get(\"x\") ?? null;\n                    target.y ??= attrs.get(\"y\") ?? null;\n                    target.z ??= attrs.get(\"z\") ?? null;\n                }\n                this.frames.push({ kind: \"skip\" });\n                return;\n            case \"Line\":\n            case \"line\":\n                this.frames.push({ kind: \"line\", points: [] });\n                return;\n            default:\n                this.unknownElement(rawName, line);\n        }\n    }\n\n    /**\n     * Keep a visual-property att of a `<graphics>` in its record, as written. A session view's\n     * `<att name=\"z\">` repeats z and is read as z when the attributes gave none.\n     * @param target - the graphics target\n     * @param att - the att\n     */\n    private graphicsAtt(target: GraphicsTarget, att: AttRec): void {\n        if (att.name === \"z\" && \"z\" in target && att.children.length === 0) {\n            target.z ??= att.value;\n            return;\n        }\n        if (att.name === null) {\n            this.report.warnOnce(\n                \"validation-error\",\n                XGMML_ISSUE.BAD_ATT,\n                \"a graphics <att> without a name was skipped\",\n                { line: att.line },\n                `${XGMML_ISSUE.BAD_ATT}:graphics-name`,\n            );\n            return;\n        }\n        target.graphics = { ...(target.graphics ?? {}), [att.name]: attJson(att) };\n    }\n}\n\n/**\n * Whether an att's children are list items rather than named fields: they have no names, repeat\n * the parent's name (Cytoscape 3 lists), or are several that share one name (2.x bend handles).\n * @param att - the att\n * @returns true for a list\n */\nexport function isListLike(att: AttRec): boolean {\n    const names = new Set(att.children.map((c) => c.name));\n    if (names.size !== 1) {\n        return false;\n    }\n    const [only] = names;\n    return only === null || only === att.name || att.children.length > 1;\n}\n\n/**\n * A graphics att as plain data, values as written: an att with children is an array when they\n * are list items (isListLike), else a record by name; a childless att is its value,\n * else its other XML attributes (a 2.x bend handle's x and y), else null.\n * @param att - the att\n * @returns the value\n */\nexport function attJson(att: AttRec): unknown {\n    if (att.children.length === 0) {\n        if (att.value !== null) {\n            return att.value;\n        }\n        return Object.keys(att.extra).length > 0 ? { ...att.extra } : null;\n    }\n    if (isListLike(att)) {\n        return att.children.map(attJson);\n    }\n    const out: Record<string, unknown> = {};\n    for (const child of att.children) {\n        out[child.name ?? \"\"] = attJson(child);\n    }\n    return out;\n}\n\n/**\n * The XML attributes of an element the parser does not read itself, without namespace\n * declarations.\n * @param attrs - the attributes\n * @param read - the names the parser reads\n * @returns the others, in document order\n */\nfunction otherAttributes(attrs: ReadonlyMap<string, string>, read: ReadonlySet<string>): [string, string][] {\n    const out: [string, string][] = [];\n    for (const [key, value] of attrs) {\n        if (!read.has(key) && key !== \"xmlns\" && !key.startsWith(\"xmlns:\")) {\n            out.push([key, value]);\n        }\n    }\n    return out;\n}\n","/**\n * XGMML attribute types and values (`research-xgmml.md` sections 3.6, 3.8 and 4.3): which kind an\n * `<att>` declares (Cytoscape's `cy:type` before the draft's `type`, case-insensitively), and the\n * lexical rules of each kind as Cytoscape writes them. A value that does not parse is never\n * guessed at: the caller records E_BAD_VALUE and leaves the cell unset.\n */\n\nimport { type AttRec } from \"./document.js\";\n\n/** The scalar kinds of a column, in widening order (string beats everything). */\nexport type ScalarKind = \"bool\" | \"int\" | \"long\" | \"real\" | \"string\";\n\n/** What one att declares. */\ntype DeclaredKind = ScalarKind | \"list\" | \"map\";\n\n/** The declared kind of an att and the type text to keep in `origin.type`. */\ninterface AttType {\n    /** The kind. */\n    readonly kind: DeclaredKind;\n    /** The type as declared (`cy:type` when given, else `type`), or null for an untyped att. */\n    readonly declared: string | null;\n    /** The type text no kind matched (kept as text, W_UNKNOWN_ATTR_TYPE), or null. */\n    readonly unknown: string | null;\n}\n\n/** Cytoscape's `cy:type` names (3.3+), lower-cased. */\nconst CY_TYPES: Readonly<Record<string, DeclaredKind>> = {\n    string: \"string\",\n    double: \"real\",\n    integer: \"int\",\n    long: \"long\",\n    boolean: \"bool\",\n    list: \"list\",\n};\n\n/** The XGMML draft's types, Cytoscape's `boolean` and the 2.x `map`, lower-cased. */\nconst XGMML_TYPES: Readonly<Record<string, DeclaredKind>> = {\n    string: \"string\",\n    real: \"real\",\n    integer: \"int\",\n    boolean: \"bool\",\n    list: \"list\",\n    map: \"map\",\n};\n\n/**\n * The kind an att declares: `cy:type` first, then `type`, both case-insensitive; no type is a\n * string; an unknown type is a string the caller reports. An untyped-by-Cytoscape `integer` att\n * whose name ends in `.SUID` is a long (Cytoscape keeps SUID references as Long).\n * @param att - the att\n * @returns the declared kind\n */\nexport function attType(att: AttRec): AttType {\n    let kind: DeclaredKind | undefined;\n    let declared: string | null = null;\n    if (att.cyType !== null && att.cyType.length > 0) {\n        kind = CY_TYPES[att.cyType.trim().toLowerCase()];\n        declared = att.cyType;\n    }\n    if (kind === undefined && att.type !== null && att.type.length > 0) {\n        kind = XGMML_TYPES[att.type.trim().toLowerCase()];\n        declared = att.type;\n    }\n    if (kind === undefined) {\n        const unknown = declared ?? null;\n        return { kind: \"string\", declared, unknown };\n    }\n    if (kind === \"int\" && att.cyType === null && att.name?.endsWith(\".SUID\") === true) {\n        // pre-3.3 Cytoscape wrote its Long SUID references as \"integer\"; a real one stays real\n        // (Cytoscape writes Double.toString forms such as \"21.0\", which no integer rule reads)\n        kind = \"long\";\n    }\n    return { kind, declared, unknown: null };\n}\n\n/**\n * The scalar kind a list element type names (`cy:elementType`), or null when it names none.\n * @param text - the element type text\n * @returns the kind, or null\n */\nexport function elementKind(text: string | null): ScalarKind | null {\n    if (text === null) {\n        return null;\n    }\n    const kind = CY_TYPES[text.trim().toLowerCase()] ?? XGMML_TYPES[text.trim().toLowerCase()];\n    return kind === undefined || kind === \"list\" || kind === \"map\" ? null : kind;\n}\n\n/**\n * The wider of two scalar kinds (design section 5.1): int and long widen to long, any two numbers\n * to real, a boolean and a number to string, anything and a string to string.\n * @param a - one kind\n * @param b - the other\n * @returns the kind both fit\n */\nexport function widenScalar(a: ScalarKind, b: ScalarKind): ScalarKind {\n    if (a === b) {\n        return a;\n    }\n    if (a === \"string\" || b === \"string\" || a === \"bool\" || b === \"bool\") {\n        return \"string\";\n    }\n    if (a === \"real\" || b === \"real\") {\n        return \"real\";\n    }\n    return \"long\";\n}\n\nconst INTEGER_TEXT = /^[+-]?[0-9]+$/;\n\n/** Java's Double.valueOf forms that Cytoscape writes: no hex, no `d` / `f` suffix. */\nconst REAL_TEXT = /^[+-]?(NaN|Infinity|([0-9]+\\.?[0-9]*|\\.[0-9]+)([eE][+-]?[0-9]+)?)$/;\n\nconst I32_MIN = -2147483648;\nconst I32_MAX = 2147483647;\n\n/** A parsed scalar and what parsing it found. */\ninterface ParsedScalar {\n    /** The value. */\n    readonly value: boolean | number | string;\n    /** An integer beyond i32 (the column widens), or a long / real beyond what a double holds exactly. */\n    readonly overflow?: \"i32\" | \"precision\" | undefined;\n}\n\n/**\n * Parse one value text by its declared scalar kind. Numbers and booleans are trimmed; strings\n * never are. Booleans accept 1 / 0 / true / false / yes / no in any case.\n * @param text - the value text\n * @param kind - the declared kind\n * @param unescape - decode Cytoscape's two-character `\\n` and `\\t` in strings\n * @returns the value, or null when the text does not parse as the kind\n */\nexport function parseScalar(text: string, kind: ScalarKind, unescape: boolean): ParsedScalar | null {\n    switch (kind) {\n        case \"string\":\n            return { value: unescape ? unescapeCytoscape(text) : text };\n        case \"bool\": {\n            const t = text.trim().toLowerCase();\n            if (t === \"1\" || t === \"true\" || t === \"yes\") {\n                return { value: true };\n            }\n            if (t === \"0\" || t === \"false\" || t === \"no\") {\n                return { value: false };\n            }\n            return null;\n        }\n        case \"int\":\n        case \"long\": {\n            const t = text.trim();\n            if (!INTEGER_TEXT.test(t)) {\n                return null;\n            }\n            const n = Number(t);\n            if (kind === \"int\" && (n < I32_MIN || n > I32_MAX)) {\n                return { value: n, overflow: Number.isSafeInteger(n) ? \"i32\" : \"precision\" };\n            }\n            return { value: n, overflow: Number.isSafeInteger(n) ? undefined : \"precision\" };\n        }\n        case \"real\": {\n            const t = text.trim();\n            if (!REAL_TEXT.test(t)) {\n                return null;\n            }\n            const n = Number(t);\n            // only a finite spelling that overflows (1e400) loses precision; NaN and the infinities are exact\n            const overflow = !Number.isFinite(n) && !/Infinity|NaN/.test(t) ? \"precision\" : undefined;\n            return { value: n, overflow };\n        }\n        default: {\n            const name: never = kind;\n            throw new Error(`unknown scalar kind ${String(name)}`);\n        }\n    }\n}\n\n/**\n * Decode the two-character escapes the Cytoscape writer uses for newline and tab.\n * @param text - the text\n * @returns the text with `\\n` and `\\t` decoded\n */\nfunction unescapeCytoscape(text: string): string {\n    return text.includes(\"\\\\\") ? text.replace(/\\\\t/g, \"\\t\").replace(/\\\\n/g, \"\\n\") : text;\n}\n","/**\n * The attribute columns of one XGMML (or `.cys`) import: every att and every untyped XML\n * attribute is parsed by its own declared kind when it is read, then each column's dtype is\n * decided once over all its values (design section 5.1 widening: int and long to f64, numbers\n * and booleans to string, lists and scalars to json), and only then declared on the sink, so a\n * column is never re-typed after rows were written and a caller's sink needs no widening call.\n */\n\nimport { type ColumnDecl, type Dtype, type GraphSink, type ScalarDtype } from \"@graphty/graph-format\";\n\nimport { declareResolved, DictHeuristic, uniqueColumnName } from \"../../common/attributes.js\";\nimport { type ImportReportBuilder, type IssueLocation } from \"../../common/report.js\";\nimport { inferTextDtype, parseTextCell } from \"../../common/text.js\";\nimport { CYTOSCAPE_ORIGIN_NAMESPACE, FORMAT, XGMML_ISSUE } from \"./constants.js\";\nimport { type AttRec, isListLike } from \"./document.js\";\nimport { attType, elementKind, parseScalar, type ScalarKind, widenScalar } from \"./values.js\";\n\n/** A table of the snapshot. */\ntype Domain = \"node\" | \"edge\" | \"graph\";\n\n/** One item of a list cell. */\ninterface Item {\n    readonly value: boolean | number | string;\n    readonly text: string;\n}\n\n/** One parsed value. */\ninterface Cell {\n    /** The kind the value was parsed as. */\n    readonly kind: ScalarKind | \"list\" | \"json\";\n    /** A scalar's value, a json value, or null for a list. */\n    readonly value: unknown;\n    /** A scalar's text as written (what a column widened to string keeps). */\n    readonly text: string;\n    /** A list's items. */\n    readonly items: readonly Item[];\n    /** A list's item kind, or null for an empty list whose type nothing states. */\n    readonly itemKind: ScalarKind | null;\n    /** The kind came from a declared type (not the text grammar of an XML attribute). */\n    readonly typed: boolean;\n}\n\n/** One column being collected. */\ninterface Plan {\n    readonly name: string;\n    readonly namespace: string | null;\n    readonly cells: Map<number, Cell>;\n    readonly declared: Set<string>;\n    readonly lines: Map<number, number>;\n    declaredType: string | null;\n    hidden: boolean;\n    equation: boolean;\n    suid: boolean;\n    overflow: boolean;\n    precision: boolean;\n}\n\n/** Options of a column set. */\ninterface ColumnSetOptions {\n    /** Decode Cytoscape's `\\n` / `\\t` escapes in string values. */\n    readonly unescape: boolean;\n    /** The importer's `long` option. */\n    readonly long: \"f64\" | \"string\";\n    /** The column names the importer's own columns hold; an att of one of these names is renamed. */\n    readonly reserved: ReadonlySet<string>;\n}\n\n/** The dtype of each scalar kind. */\nconst DTYPES: Readonly<Record<ScalarKind, ScalarDtype>> = {\n    bool: \"bool\",\n    int: \"i32\",\n    long: \"f64\",\n    real: \"f64\",\n    string: \"string\",\n};\n\n/**\n * Collects the attribute values of one table, then declares and writes the columns.\n */\nexport class ColumnSet {\n    private readonly domain: Domain;\n\n    private readonly report: ImportReportBuilder;\n\n    private readonly options: ColumnSetOptions;\n\n    private readonly plans = new Map<string, Plan>();\n\n    /**\n     * Create a column set.\n     * @param domain - the table\n     * @param report - the report\n     * @param options - the options\n     */\n    constructor(domain: Domain, report: ImportReportBuilder, options: ColumnSetOptions) {\n        this.domain = domain;\n        this.report = report;\n        this.options = options;\n    }\n\n    /**\n     * Whether a column of that name (any namespace) was collected.\n     * @param name - the name\n     * @returns true when some row has a value or the column was declared\n     */\n    has(name: string): boolean {\n        return this.plans.has(key(null, name));\n    }\n\n    /**\n     * Add one att of a row: parse it by its declared kind (E_BAD_VALUE for a value that does not\n     * parse; the cell stays unset). A second value of the same column on one row wins with\n     * W_DUPLICATE_ATTRIBUTE.\n     * @param row - the row\n     * @param att - the att\n     * @param where - the element, for issues\n     */\n    addAtt(row: number, att: AttRec, where: IssueLocation): void {\n        const { name } = att;\n        if (name === null || name.length === 0) {\n            this.badAtt(\"an <att> without a name was skipped\", att, \"name\");\n            return;\n        }\n        const plan = this.plan(name, att.namespace ?? null);\n        const type = attType(att);\n        plan.hidden ||= att.hidden;\n        plan.suid ||= name.endsWith(\".SUID\");\n        if (type.declared !== null) {\n            plan.declaredType ??= type.declared;\n        }\n        const at = { line: att.line, element: where.element ?? name };\n        if (type.unknown !== null) {\n            this.report.warnOnce(\n                \"unsupported\",\n                XGMML_ISSUE.UNKNOWN_ATTR_TYPE,\n                `att type \"${type.unknown}\" of \"${name}\" is not an XGMML or Cytoscape type; its values are kept as text`,\n                at,\n                `${XGMML_ISSUE.UNKNOWN_ATTR_TYPE}:${this.domain}:${name}`,\n            );\n        }\n        let cell: Cell | null;\n        if (att.equation) {\n            plan.equation = true;\n            this.report.warnOnce(\n                \"unsupported\",\n                XGMML_ISSUE.EQUATION_AS_TEXT,\n                `\"${name}\" holds Cytoscape formulas; each is kept as its text, never evaluated`,\n                at,\n                `${XGMML_ISSUE.EQUATION_AS_TEXT}:${this.domain}:${name}`,\n            );\n            cell = att.value === null ? null : scalarCell(\"string\", att.value, att.value, true);\n            if (cell !== null) {\n                plan.declared.add(\"string\");\n            }\n        } else if (type.kind === \"list\") {\n            cell = this.listCell(att, name, plan, at);\n            plan.declared.add(\"list\");\n        } else if (type.kind === \"map\") {\n            cell = jsonCell(recordOf(att));\n            this.recordList(`\"${name}\" is a 2.x map; it is kept as a json record`, at);\n            plan.declared.add(\"json\");\n        } else {\n            cell = this.scalarAtt(att, type.kind, plan, at);\n        }\n        if (cell !== null) {\n            this.set(plan, row, cell, at);\n        }\n    }\n\n    /**\n     * Add one value read by the 5.1 text grammar (an XML attribute of an element).\n     * @param row - the row\n     * @param name - the column name\n     * @param text - the text\n     * @param where - the element, for issues\n     */\n    addText(row: number, name: string, text: string, where: IssueLocation): void {\n        const plan = this.plan(name, null);\n        const value = parseTextCell(text);\n        const kind = textKind(inferTextDtype(text));\n        this.set(plan, row, { kind, value, text, items: [], itemKind: null, typed: false }, where);\n    }\n\n    /**\n     * Add one value of a known kind (a typed table cell of a session).\n     * @param row - the row\n     * @param name - the column name\n     * @param value - the value\n     * @param where - the element, for issues\n     */\n    addJson(row: number, name: string, value: unknown, where: IssueLocation): void {\n        this.set(this.plan(name, null), row, jsonCell(value), where);\n    }\n\n    /**\n     * Declare every collected column on the sink and write its values.\n     * @param sink - the sink\n     * @param rowIndex - the sink index of a row (node or edge index), or -1 when the row was not added\n     */\n    write(sink: GraphSink, rowIndex: (row: number) => number): void {\n        const taken = new Set<string>(this.options.reserved);\n        const ordered = [...this.plans.values()].sort(\n            (a, b) => Number(a.namespace !== null) - Number(b.namespace !== null),\n        );\n        for (const plan of ordered) {\n            let { name } = plan;\n            if (taken.has(name)) {\n                name = uniqueColumnName(plan.name, plan.namespace, (n) => taken.has(n));\n                this.report.warning(\n                    \"coercion\",\n                    XGMML_ISSUE.COLUMN_RENAMED,\n                    `${this.domain} attribute \"${plan.name}\" renamed to \"${name}\": the name was taken`,\n                    { element: plan.name },\n                );\n            }\n            taken.add(name);\n            this.writePlan(sink, plan, name, rowIndex);\n        }\n    }\n\n    // ------------------------------------------------------------------ cells\n\n    /**\n     * The plan of a column, created on first use.\n     * @param name - the attribute name\n     * @param namespace - the table namespace, or null\n     * @returns the plan\n     */\n    private plan(name: string, namespace: string | null): Plan {\n        const k = key(namespace, name);\n        let plan = this.plans.get(k);\n        if (plan === undefined) {\n            plan = {\n                name,\n                namespace,\n                cells: new Map(),\n                declared: new Set(),\n                lines: new Map(),\n                declaredType: null,\n                hidden: false,\n                equation: false,\n                suid: false,\n                overflow: false,\n                precision: false,\n            };\n            this.plans.set(k, plan);\n        }\n        return plan;\n    }\n\n    /**\n     * Store a cell, reporting a second value on the same row.\n     * @param plan - the column\n     * @param row - the row\n     * @param cell - the cell\n     * @param where - the location\n     */\n    private set(plan: Plan, row: number, cell: Cell, where: IssueLocation): void {\n        if (plan.cells.has(row)) {\n            this.report.warning(\n                \"validation-error\",\n                XGMML_ISSUE.DUPLICATE_ATTRIBUTE,\n                `\"${plan.name}\" is given twice on one ${this.domain}; the later value is kept`,\n                { line: where.line ?? null, element: where.element ?? plan.name },\n            );\n        }\n        plan.cells.set(row, cell);\n        if (where.line !== undefined && where.line !== null) {\n            plan.lines.set(row, where.line);\n        }\n    }\n\n    /**\n     * Parse a scalar att.\n     * @param att - the att\n     * @param kind - the declared kind\n     * @param plan - the column\n     * @param at - the location\n     * @returns the cell, or null when unset or invalid\n     */\n    private scalarAtt(att: AttRec, kind: ScalarKind, plan: Plan, at: IssueLocation): Cell | null {\n        if (att.children.length > 0) {\n            this.badAtt(`the ${kind} att \"${att.name ?? \"\"}\" holds child atts; they are ignored`, att, \"children\");\n        }\n        if (att.xml !== null) {\n            this.recordList(`\"${att.name ?? \"\"}\" holds foreign XML; it is kept as text in a json column`, at);\n            plan.declared.add(\"json\");\n            return jsonCell(att.xml);\n        }\n        if (att.value === null) {\n            plan.declared.add(kind);\n            return null;\n        }\n        const parsed = parseScalar(att.value, kind, this.options.unescape);\n        if (parsed === null || (parsed.overflow !== undefined && kind === \"int\" && exactInteger(att.cyType))) {\n            this.badValue(att.value, kind, at);\n            return null;\n        }\n        plan.declared.add(kind);\n        if (parsed.overflow === \"i32\") {\n            plan.overflow = true;\n        } else if (parsed.overflow === \"precision\") {\n            plan.precision = true;\n            plan.overflow ||= kind === \"int\";\n        }\n        return scalarCell(kind, parsed.value, att.value, true);\n    }\n\n    /**\n     * Parse a list att: items by `cy:elementType`, else by the widened kinds of the children.\n     * A list of lists, a list with records, or a list of named fields is a json value.\n     * @param att - the att\n     * @param name - the column name\n     * @param plan - the column (an item beyond i32 widens it, as a scalar does)\n     * @param at - the location\n     * @returns the cell\n     */\n    private listCell(att: AttRec, name: string, plan: Plan, at: IssueLocation): Cell | null {\n        if (att.value !== null) {\n            this.badAtt(`the list att \"${name}\" has a value; it is ignored`, att, \"list-value\");\n        }\n        const { children } = att;\n        const names = new Set(children.map((c) => c.name).filter((n): n is string => n !== null && n !== name));\n        if (names.size > 1 || children.some((c) => c.children.length > 0 || c.xml !== null)) {\n            this.recordList(`\"${name}\" is a record or a list of lists; it is kept as json`, at);\n            return jsonCell(names.size > 1 ? recordOf(att) : children.map(jsonOfAtt));\n        }\n        let itemKind = elementKind(att.elementType);\n        if (itemKind === null) {\n            const kinds = new Set<ScalarKind>();\n            for (const child of children) {\n                const type = attType(child);\n                const kind: ScalarKind = type.kind === \"list\" || type.kind === \"map\" ? \"string\" : type.kind;\n                kinds.add(kind);\n                itemKind = itemKind === null ? kind : widenScalar(itemKind, kind);\n            }\n            if (kinds.size > 1) {\n                this.report.warnOnce(\n                    \"coercion\",\n                    XGMML_ISSUE.WIDENED,\n                    `the items of list \"${name}\" declare different types; they are read as ${itemKind ?? \"string\"}`,\n                    at,\n                    `${XGMML_ISSUE.WIDENED}:${this.domain}:${name}`,\n                );\n            }\n        }\n        const items: Item[] = [];\n        for (const child of children) {\n            if (child.value === null) {\n                continue;\n            }\n            const parsed = parseScalar(child.value, itemKind ?? \"string\", this.options.unescape);\n            const exact = exactInteger(att.elementType) || exactInteger(child.cyType);\n            if (parsed === null || (parsed.overflow !== undefined && itemKind === \"int\" && exact)) {\n                this.badValue(child.value, itemKind ?? \"string\", { line: child.line, element: at.element });\n                continue;\n            }\n            if (parsed.overflow === \"i32\") {\n                plan.overflow = true;\n            } else if (parsed.overflow === \"precision\") {\n                plan.precision = true;\n                plan.overflow ||= itemKind === \"int\";\n            }\n            items.push({ value: parsed.value, text: child.value });\n        }\n        return { kind: \"list\", value: null, text: \"\", items, itemKind, typed: true };\n    }\n\n    // ------------------------------------------------------------------ decision and writing\n\n    /**\n     * Decide one column's dtype, declare it and write its values.\n     * @param sink - the sink\n     * @param plan - the column\n     * @param name - the name to declare it under\n     * @param rowIndex - the row to sink index map\n     */\n    private writePlan(sink: GraphSink, plan: Plan, name: string, rowIndex: (row: number) => number): void {\n        const cells = [...plan.cells.values()];\n        const decision = this.decide(plan, cells);\n        const decl: ColumnDecl = {\n            name,\n            dtype: decision.dtype,\n            nullable: true,\n            origin: {\n                format: FORMAT,\n                id: null,\n                title: name === plan.name ? null : plan.name,\n                type: originType(plan, decision),\n                namespace: plan.namespace ?? (plan.hidden ? CYTOSCAPE_ORIGIN_NAMESPACE : null),\n            },\n        };\n        if (decision.itemDtype !== null) {\n            decl.itemDtype = decision.itemDtype;\n        }\n        const extra: Record<string, unknown> = {};\n        if (plan.hidden) {\n            extra.hidden = true;\n        }\n        if (plan.suid) {\n            extra.suidReference = true;\n        }\n        if (plan.equation) {\n            extra.equation = true;\n        }\n        if (Object.keys(extra).length > 0) {\n            decl.extra = extra;\n        }\n        const where = { element: name };\n        if (this.domain === \"graph\") {\n            const cell = plan.cells.get(0);\n            try {\n                sink.setGraphValue(name, cell === undefined ? undefined : convert(cell, decision), decl);\n            } catch (err) {\n                this.report.recordError(err, where);\n            }\n            return;\n        }\n        let handle;\n        try {\n            ({ handle } = declareResolved(sink, this.domain, decl, this.report, where));\n        } catch (err) {\n            this.report.recordError(err, where);\n            return;\n        }\n        for (const [row, cell] of plan.cells) {\n            const index = rowIndex(row);\n            if (index < 0) {\n                continue;\n            }\n            const value = convert(cell, decision);\n            try {\n                if (this.domain === \"node\") {\n                    sink.setNodeValue(handle, index, value);\n                } else {\n                    sink.setEdgeValue(handle, index, value);\n                }\n            } catch (err) {\n                this.report.recordError(err, { line: plan.lines.get(row) ?? null, element: name });\n            }\n        }\n    }\n\n    /**\n     * The dtype of a column from its cells, with the widening and precision warnings.\n     * @param plan - the column\n     * @param cells - its cells\n     * @returns the decision\n     */\n    private decide(plan: Plan, cells: readonly Cell[]): Decision {\n        const where = { element: plan.name };\n        const typedKinds = new Set(cells.filter((c) => c.typed).map((c) => c.kind));\n        let widened = typedKinds.size > 1 || plan.declared.size > 1;\n        let decision: Decision;\n        if (\n            cells.some((c) => c.kind === \"json\") ||\n            (cells.some((c) => c.kind === \"list\") && cells.some((c) => c.kind !== \"list\"))\n        ) {\n            decision = { dtype: \"json\", itemDtype: null, scalar: null, item: null, long: false };\n        } else if (cells.length > 0 && cells.every((c) => c.kind === \"list\")) {\n            let item: ScalarKind | null = null;\n            for (const cell of cells) {\n                if (cell.itemKind !== null) {\n                    widened ||= item !== null && item !== cell.itemKind;\n                    item = item === null ? cell.itemKind : widenScalar(item, cell.itemKind);\n                }\n            }\n            if (item === null) {\n                this.report.warnOnce(\n                    \"coercion\",\n                    XGMML_ISSUE.EMPTY_LIST_TYPE,\n                    `list \"${plan.name}\" has no element type and no items; it is a list of strings`,\n                    where,\n                    `${XGMML_ISSUE.EMPTY_LIST_TYPE}:${this.domain}:${plan.name}`,\n                );\n                item = \"string\";\n            }\n            if (plan.overflow && item === \"int\") {\n                item = \"real\";\n                widened = true;\n            }\n            decision = { dtype: \"list\", itemDtype: DTYPES[item], scalar: null, item, long: item === \"long\" };\n        } else {\n            decision = this.decideScalar(plan, cells);\n            widened ||= plan.overflow && decision.scalar === \"real\" && plan.declared.has(\"int\");\n        }\n        if (widened) {\n            this.report.warnOnce(\n                \"coercion\",\n                XGMML_ISSUE.WIDENED,\n                `${this.domain} column \"${plan.name}\" was widened to ${decision.dtype}: its values or declared types disagree`,\n                where,\n                `${XGMML_ISSUE.WIDENED}:${this.domain}:${plan.name}`,\n            );\n        }\n        if (plan.precision) {\n            this.report.warnOnce(\n                \"precision\",\n                XGMML_ISSUE.PRECISION,\n                `values of \"${plan.name}\" beyond what a double holds exactly are stored as the nearest double (or infinity)`,\n                where,\n                `${XGMML_ISSUE.PRECISION}:${this.domain}:${plan.name}`,\n            );\n        }\n        return decision;\n    }\n\n    /**\n     * The scalar decision of a column.\n     * @param plan - the column\n     * @param cells - its cells\n     * @returns the decision\n     */\n    private decideScalar(plan: Plan, cells: readonly Cell[]): Decision {\n        let scalar: ScalarKind | null = null;\n        for (const cell of cells) {\n            const kind = cell.kind as ScalarKind;\n            scalar = scalar === null ? kind : widenScalar(scalar, kind);\n        }\n        if (scalar === null) {\n            const declared = [...plan.declared].find((k): k is ScalarKind => k in DTYPES);\n            scalar = declared ?? \"string\";\n        }\n        if (scalar === \"int\" && plan.overflow) {\n            scalar = \"real\";\n        }\n        const long = scalar === \"long\";\n        if (long && this.options.long === \"string\") {\n            return { dtype: \"string\", itemDtype: null, scalar: \"string\", item: null, long: true };\n        }\n        let dtype: Dtype = DTYPES[scalar];\n        if (scalar === \"string\") {\n            const heuristic = new DictHeuristic();\n            for (const cell of cells) {\n                if (heuristic.observe(cell.text)) {\n                    break;\n                }\n            }\n            dtype = heuristic.decide();\n        }\n        return { dtype, itemDtype: null, scalar, item: null, long };\n    }\n\n    /**\n     * Report a malformed att, once per kind of defect.\n     * @param message - the message\n     * @param att - the att\n     * @param kind - the defect, for the once key\n     */\n    private badAtt(message: string, att: AttRec, kind: string): void {\n        this.report.warnOnce(\n            \"parse-error\",\n            XGMML_ISSUE.BAD_ATT,\n            message,\n            { line: att.line, element: att.name },\n            `${XGMML_ISSUE.BAD_ATT}:${kind}`,\n        );\n    }\n\n    /**\n     * Report a value that does not parse as its declared kind (an error; the cell stays unset).\n     * @param text - the value\n     * @param kind - the kind\n     * @param at - the location\n     */\n    private badValue(text: string, kind: ScalarKind, at: IssueLocation): void {\n        this.report.error(\n            \"validation-error\",\n            XGMML_ISSUE.BAD_VALUE,\n            `value ${JSON.stringify(text)} is not a valid ${KIND_NAMES[kind]}; the cell is left unset`,\n            at,\n        );\n    }\n\n    /**\n     * Report a record list, list of lists, map or foreign XML kept as json, once.\n     * @param message - the message\n     * @param at - the location\n     */\n    private recordList(message: string, at: IssueLocation): void {\n        this.report.warnOnce(\"coercion\", XGMML_ISSUE.RECORD_LIST, message, at);\n    }\n}\n\n/**\n * Whether a Cytoscape type names Java's Integer exactly (`cy:type=\"Integer\"`, a CyCSV\n * `java.lang.Integer` column): a value beyond i32 is then not an Integer at all (Cytoscape cannot\n * write one), where the XGMML `integer` of pre-3.3 Cytoscape also carried Longs and widens.\n * @param cyType - the Cytoscape type, or null\n * @returns true for Integer\n */\nfunction exactInteger(cyType: string | null): boolean {\n    return cyType?.trim().toLowerCase() === \"integer\";\n}\n\n/** A column's decided storage. */\ninterface Decision {\n    readonly dtype: Dtype;\n    readonly itemDtype: ScalarDtype | null;\n    readonly scalar: ScalarKind | null;\n    readonly item: ScalarKind | null;\n    /** The column is a declared long (origin.type \"long\"). */\n    readonly long: boolean;\n}\n\n/**\n * The `origin.type` of a column: \"equation\" for formulas, \"long\" for a declared long, else the\n * declared type text.\n * @param plan - the column\n * @param decision - its decision\n * @returns the type text, or null\n */\nfunction originType(plan: Plan, decision: Decision): string | null {\n    if (plan.equation) {\n        return \"equation\";\n    }\n    return decision.long ? \"long\" : plan.declaredType;\n}\n\n/** How a kind is named in messages. */\nconst KIND_NAMES: Readonly<Record<ScalarKind, string>> = {\n    bool: \"boolean (1, 0, true, false, yes, no)\",\n    int: \"integer\",\n    long: \"long integer\",\n    real: \"real number\",\n    string: \"string\",\n};\n\n/**\n * The plans key of a column.\n * @param namespace - the namespace, or null\n * @param name - the name\n * @returns the key\n */\nfunction key(namespace: string | null, name: string): string {\n    return namespace === null ? name : `${namespace}\\u0000${name}`;\n}\n\n/**\n * The scalar kind of a text grammar dtype.\n * @param dtype - the dtype\n * @returns the kind\n */\nfunction textKind(dtype: \"bool\" | \"i32\" | \"f64\" | \"string\"): ScalarKind {\n    switch (dtype) {\n        case \"bool\":\n            return \"bool\";\n        case \"i32\":\n            return \"int\";\n        case \"f64\":\n            return \"real\";\n        default:\n            return \"string\";\n    }\n}\n\n/**\n * A scalar cell.\n * @param kind - its kind\n * @param value - its value\n * @param text - its text as written\n * @param typed - whether a declared type gave the kind\n * @returns the cell\n */\nfunction scalarCell(kind: ScalarKind, value: unknown, text: string, typed: boolean): Cell {\n    return { kind, value, text, items: [], itemKind: null, typed };\n}\n\n/**\n * A json cell.\n * @param value - the value\n * @returns the cell\n */\nfunction jsonCell(value: unknown): Cell {\n    return { kind: \"json\", value, text: JSON.stringify(value), items: [], itemKind: null, typed: true };\n}\n\n/**\n * An att with named children as a record of name to value.\n * @param att - the att\n * @returns the record\n */\nfunction recordOf(att: AttRec): Record<string, unknown> {\n    const out: Record<string, unknown> = {};\n    for (const child of att.children) {\n        out[child.name ?? \"\"] = jsonOfAtt(child);\n    }\n    return out;\n}\n\n/**\n * An att as a json value: its value text, its children as an array or a record, or its XML.\n * @param att - the att\n * @returns the value\n */\nfunction jsonOfAtt(att: AttRec): unknown {\n    if (att.xml !== null) {\n        return att.xml;\n    }\n    if (att.children.length === 0) {\n        return att.value;\n    }\n    return isListLike(att) ? att.children.map(jsonOfAtt) : recordOf(att);\n}\n\n/**\n * A cell as the value its column's dtype stores.\n * @param cell - the cell\n * @param decision - the column's decision\n * @returns the value\n */\nfunction convert(cell: Cell, decision: Decision): unknown {\n    if (decision.dtype === \"json\") {\n        if (cell.kind === \"json\") {\n            return cell.value;\n        }\n        return cell.kind === \"list\" ? cell.items.map((i) => i.value) : cell.value;\n    }\n    if (decision.dtype === \"list\") {\n        return cell.items.map((item) => convertScalar(item.value, item.text, decision.item ?? \"string\"));\n    }\n    return convertScalar(\n        cell.value,\n        cell.text,\n        decision.long && decision.dtype === \"string\" ? \"string\" : (decision.scalar ?? \"string\"),\n    );\n}\n\n/**\n * A scalar as the kind its column stores.\n * @param value - the parsed value\n * @param text - its text as written\n * @param kind - the column's kind\n * @returns the value\n */\nfunction convertScalar(value: unknown, text: string, kind: ScalarKind): unknown {\n    switch (kind) {\n        case \"bool\":\n            return value;\n        case \"int\":\n        case \"long\":\n        case \"real\":\n            return Number(value);\n        default:\n            return typeof value === \"string\" ? value : text;\n    }\n}\n","/**\n * Resolving a parsed XGMML document (document.ts) into a sink: which nodes and edges a graph\n * holds, their ids, endpoints, direction, weights, containment, positions, graphics and attribute\n * columns. The `.cys` importer calls the same code with the session's tables and views merged into\n * the records first, so both readers share every rule.\n */\n\nimport { type ColumnDecl, type ColumnHandle, type GraphSink, INVALID_INDEX, type NodeId } from \"@graphty/graph-format\";\n\nimport { declareResolved } from \"../../common/attributes.js\";\nimport { DirectionResolver, type EdgeKind } from \"../../common/direction.js\";\nimport { IdCoercer } from \"../../common/ids.js\";\nimport { throwIfAborted } from \"../../common/input.js\";\nimport { type ResolvedImportOptions } from \"../../common/options.js\";\nimport { type ImportReportBuilder, type IssueLocation } from \"../../common/report.js\";\nimport { parseWeightText } from \"../../common/weights.js\";\nimport { ColumnSet } from \"./columns.js\";\nimport {\n    CYTOSCAPE_ORIGIN_NAMESPACE,\n    EDGE_ID_COLUMN,\n    FORMAT,\n    GRAPHICS_COLUMN,\n    INTERACTION_COLUMN,\n    LABEL_COLUMN,\n    META_KEY,\n    NESTED_NETWORK_COLUMN,\n    NETWORK_POINTER_COLUMN,\n    NETWORKS_COLUMN,\n    PARENT_COLUMN,\n    PARENTS_COLUMN,\n    POSITION_COLUMN,\n    SUBGRAPH_COLUMN,\n    XGMML_ISSUE,\n    XGMML_ORIGIN_NAMESPACE,\n    Z_COLUMN,\n} from \"./constants.js\";\nimport {\n    attJson,\n    type AttRec,\n    type EdgeRec,\n    type GraphRec,\n    isCyTrue,\n    type NodeRec,\n    type XgmmlDocument,\n} from \"./document.js\";\n\n/** The XGMML-specific options, resolved. */\nexport interface XgmmlSettings {\n    /** Resolve missing or unknown endpoints through `\"a (pp) b\"` edge labels. */\n    readonly labelAliases: boolean;\n    /** Decode Cytoscape's `\\n` / `\\t` in strings. */\n    readonly cytoscapeEscapes: boolean;\n    /** Where Cytoscape's z goes. */\n    readonly zAs: \"column\" | \"position\";\n}\n\n/** What a session adds to the document's own rules. */\nexport interface EmitExtras {\n    /** Ids of nodes the session's group bookkeeping lists as groups. */\n    readonly groupNodes?: ReadonlySet<string> | undefined;\n    /** The network name a cross-file pointer (`file.xgmml#id`) names, or null when unknown. */\n    readonly resolvePointer?: ((href: string) => string | null) | undefined;\n    /** Graph-level attributes and the graph name come from elsewhere: skip the graph's own. */\n    readonly graphName?: string | null | undefined;\n    /** Extra json graph columns. */\n    readonly graphJson?: Readonly<Record<string, unknown>> | undefined;\n    /** Extra entries of `meta.extra`. */\n    readonly metaExtra?: Readonly<Record<string, unknown>> | undefined;\n    /** The format name the report and metadata carry (\"cys\"). */\n    readonly sourceFormat?: string | undefined;\n    /** Prefix of every issue message (the session entry name). */\n    readonly entry?: string | undefined;\n    /**\n     * A group member that is not in the graph being read (a collapsed group's member in a\n     * session): the session records it instead of E_UNKNOWN_PARENT.\n     */\n    readonly onMissingMember?: ((group: string, member: string) => void) | undefined;\n}\n\n/** The dialect facts the rules depend on. */\nexport interface Dialect {\n    /** The documentVersion as written, or null. */\n    readonly versionText: string | null;\n    /** The parsed version, or 0 when absent or unparseable. */\n    readonly version: number;\n    /** Cytoscape wrote the file (the `cy` namespace is in use). */\n    readonly cytoscape: boolean;\n    /** A Cytoscape 2.x document (Cytoscape dialect with a version below 3). */\n    readonly cy2: boolean;\n    /** The 3.x session network dialect (root `cy:registered=\"0\"` with registered subnetworks). */\n    readonly session: boolean;\n    /** A session view document (root `cy:view=\"1\"`). */\n    readonly view: boolean;\n}\n\n/** The graph atts that are document metadata, not columns. */\nconst META_ATTS: ReadonlySet<string> = new Set([\"documentVersion\", \"networkMetadata\"]);\n\n/** The root XML attributes that are structure, not graph columns. */\nconst GRAPH_STRUCTURE: ReadonlySet<string> = new Set([\n    \"id\",\n    \"label\",\n    \"directed\",\n    \"xlink:href\",\n    \"cy:documentVersion\",\n    \"cy:view\",\n    \"cy:registered\",\n    \"cy:networkId\",\n    \"cy:visualStyle\",\n    \"cy:rendererId\",\n]);\n\n/** Elements between two checks of the cancellation signal. */\nconst ABORT_CHECK_INTERVAL = 64;\n\n/** Cytoscape's label alias shape: `source (interaction) target`. */\nconst ALIAS_SPLIT = /[()]/;\n\n/**\n * The dialect of a document (`research-xgmml.md` section 2).\n * @param doc - the document\n * @param report - the report the unparseable-version warning goes to\n * @returns the dialect\n */\nexport function dialectOf(doc: XgmmlDocument, report: ImportReportBuilder): Dialect {\n    const { root } = doc;\n    let versionText = root.attrs.get(\"cy:documentVersion\") ?? null;\n    for (const att of root.atts) {\n        if (att.name === \"documentVersion\" && att.value !== null) {\n            versionText ??= att.value;\n        }\n    }\n    let version = 0;\n    if (versionText !== null) {\n        version = Number(versionText.trim());\n        if (!Number.isFinite(version) || versionText.trim().length === 0) {\n            report.warning(\n                \"validation-error\",\n                XGMML_ISSUE.DOCUMENT_VERSION,\n                `documentVersion \"${versionText}\" does not parse; the dialect is chosen from the content`,\n                { line: root.line },\n            );\n            version = 0;\n        }\n    }\n    const registered = root.subgraphs.some((g) => isCyTrue(g.registered));\n    return {\n        versionText,\n        version,\n        cytoscape: doc.cytoscape,\n        cy2: doc.cytoscape && version < 3,\n        session: root.registered !== null && !isCyTrue(root.registered) && registered,\n        view: isCyTrue(root.attrs.get(\"cy:view\")),\n    };\n}\n\n/**\n * The graphs a document offers: the registered subnetworks of a session network document, else\n * the root.\n * @param doc - the document\n * @param dialect - its dialect\n * @returns the graphs, in document order\n */\nexport function graphsOf(doc: XgmmlDocument, dialect: Dialect): GraphRec[] {\n    return dialect.session ? doc.root.subgraphs.filter((g) => isCyTrue(g.registered)) : [doc.root];\n}\n\n/**\n * The id a `#id` reference names, or null for a cross-file or malformed reference.\n * @param href - the xlink:href text\n * @returns the id\n */\nfunction localRef(href: string): string | null {\n    return href.startsWith(\"#\") ? href.slice(1) : null;\n}\n\n/**\n * The nodes and edges a graph holds: its direct members, references resolved.\n * @param doc - the document\n * @param graph - the graph (a registered subnetwork), or null for the whole document\n * @returns the declared node and edge records it holds, references resolved, in order\n */\nexport function membersOf(\n    doc: XgmmlDocument,\n    graph: GraphRec | null,\n): { readonly nodes: NodeRec[]; readonly edges: EdgeRec[]; readonly dangling: number } {\n    if (graph === null) {\n        return { nodes: doc.nodes, edges: doc.edges, dangling: 0 };\n    }\n    const nodeById = indexById(doc.nodes);\n    const edgeById = indexById(doc.edges);\n    const nodes: NodeRec[] = [];\n    const edges: EdgeRec[] = [];\n    let dangling = 0;\n    for (const member of graph.members) {\n        if (member.href === null) {\n            if (member.kind === \"node\") {\n                nodes.push(member);\n            } else {\n                edges.push(member);\n            }\n            continue;\n        }\n        const id = localRef(member.href);\n        let target: NodeRec | EdgeRec | undefined;\n        if (id !== null) {\n            target = member.kind === \"node\" ? nodeById.get(id) : edgeById.get(id);\n        }\n        if (target === undefined) {\n            dangling++;\n        } else if (target.kind === \"node\") {\n            nodes.push(target);\n        } else {\n            edges.push(target);\n        }\n    }\n    return { nodes, edges, dangling };\n}\n\n/**\n * The first declaration of each id.\n * @param records - node or edge records\n * @returns id to record\n */\nfunction indexById<T extends NodeRec | EdgeRec>(records: readonly T[]): Map<string, T> {\n    const out = new Map<string, T>();\n    for (const record of records) {\n        if (record.id !== null && !out.has(record.id)) {\n            out.set(record.id, record);\n        }\n    }\n    return out;\n}\n\n/** Per-node state while emitting. */\ninterface NodeRow {\n    readonly id: string;\n    readonly records: NodeRec[];\n    index: number;\n    readonly row: number;\n}\n\n/**\n * Pushes one graph of a document into a sink.\n */\nexport class XgmmlEmitter {\n    private readonly doc: XgmmlDocument;\n\n    private readonly dialect: Dialect;\n\n    private readonly sink: GraphSink;\n\n    private readonly report: ImportReportBuilder;\n\n    private readonly options: ResolvedImportOptions;\n\n    private readonly settings: XgmmlSettings;\n\n    private readonly extras: EmitExtras;\n\n    private readonly coercer: IdCoercer;\n\n    private readonly direction: DirectionResolver;\n\n    private readonly nodeColumns: ColumnSet;\n\n    private readonly edgeColumns: ColumnSet;\n\n    private readonly graphColumns: ColumnSet;\n\n    private readonly rows = new Map<string, NodeRow>();\n\n    private readonly rowList: NodeRow[] = [];\n\n    private readonly edgeIndex: number[] = [];\n\n    private sinceCheck = 0;\n\n    private aliasResolved = 0;\n\n    private aliasInteractions = 0;\n\n    private weighted = false;\n\n    /**\n     * Create an emitter for one graph.\n     * @param doc - the document\n     * @param dialect - its dialect\n     * @param sink - the sink\n     * @param report - the report\n     * @param options - the resolved common options\n     * @param settings - the XGMML options\n     * @param extras - what a session adds\n     */\n    constructor(\n        doc: XgmmlDocument,\n        dialect: Dialect,\n        sink: GraphSink,\n        report: ImportReportBuilder,\n        options: ResolvedImportOptions,\n        settings: XgmmlSettings,\n        extras: EmitExtras = {},\n    ) {\n        this.doc = doc;\n        this.dialect = dialect;\n        this.sink = sink;\n        this.report = report;\n        this.options = options;\n        this.settings = settings;\n        this.extras = extras;\n        this.coercer = new IdCoercer(options.ids);\n        this.direction = new DirectionResolver(sink, report, options.onMixedDirection);\n        const base = { unescape: settings.cytoscapeEscapes, long: options.long };\n        this.nodeColumns = new ColumnSet(\"node\", report, {\n            ...base,\n            reserved: new Set([\n                LABEL_COLUMN,\n                POSITION_COLUMN,\n                Z_COLUMN,\n                GRAPHICS_COLUMN,\n                PARENT_COLUMN,\n                PARENTS_COLUMN,\n                SUBGRAPH_COLUMN,\n                NESTED_NETWORK_COLUMN,\n                NETWORK_POINTER_COLUMN,\n                NETWORKS_COLUMN,\n            ]),\n        });\n        this.edgeColumns = new ColumnSet(\"edge\", report, {\n            ...base,\n            reserved: new Set([EDGE_ID_COLUMN, LABEL_COLUMN, GRAPHICS_COLUMN]),\n        });\n        this.graphColumns = new ColumnSet(\"graph\", report, { ...base, reserved: new Set([GRAPHICS_COLUMN]) });\n    }\n\n    /**\n     * Push the graph: nodes, containment, positions, edges, columns, metadata.\n     * @param graph - the subnetwork, or null for the whole document\n     */\n    emit(graph: GraphRec | null): void {\n        const members = membersOf(this.doc, graph);\n        if (members.dangling > 0) {\n            this.report.warning(\n                \"validation-error\",\n                XGMML_ISSUE.DANGLING_REFERENCE,\n                `${this.prefix()}${members.dangling} xlink:href member reference(s) name no node or edge of the document`,\n                { line: graph?.line ?? null },\n            );\n        }\n        const header = this.headerDirected();\n        this.direction.setHeader(this.sinkDirection(members.edges, header), { line: this.doc.root.line });\n        this.addNodes(members.nodes);\n        if (graph === null) {\n            this.checkReferences();\n        }\n        const containment = new Containment(this);\n        containment.resolve(this.rowList, this.groupTest());\n        this.writeNodeExtras(graph);\n        this.addEdges(members.edges, header);\n        this.finishAliases();\n        this.writeGraph(graph);\n        const nodeIndex = (row: number): number => this.rowList[row].index;\n        this.nodeColumns.write(this.sink, nodeIndex);\n        this.edgeColumns.write(this.sink, (row) => this.edgeIndex[row] ?? -1);\n        containment.write();\n        this.writeMeta(graph);\n        throwIfAborted(this.options.signal);\n    }\n\n    // ------------------------------------------------------------------ shared helpers (also used by Containment)\n\n    /**\n     * The sink.\n     * @returns the sink\n     */\n    get target(): GraphSink {\n        return this.sink;\n    }\n\n    /**\n     * The report.\n     * @returns the report\n     */\n    get issues(): ImportReportBuilder {\n        return this.report;\n    }\n\n    /**\n     * The row of a node id in this graph.\n     * @param id - the id text\n     * @returns the row, or undefined\n     */\n    rowOf(id: string): NodeRow | undefined {\n        return this.rows.get(id);\n    }\n\n    /**\n     * The network name a cross-file pointer names, when a session can tell.\n     * @param href - the pointer\n     * @returns the name, or null\n     */\n    resolvePointer(href: string): string | null {\n        return this.extras.resolvePointer?.(href) ?? null;\n    }\n\n    /**\n     * Hand a group member the graph does not hold to the session, when one is reading.\n     * @param group - the group node's id\n     * @param member - the member's id\n     * @returns true when the session took it\n     */\n    missingMember(group: string, member: string): boolean {\n        if (this.extras.onMissingMember === undefined) {\n            return false;\n        }\n        this.extras.onMissingMember(group, member);\n        return true;\n    }\n\n    /**\n     * The first graph of the document with an id.\n     * @param id - the id\n     * @returns the graph, or undefined\n     */\n    graphById(id: string): GraphRec | undefined {\n        return this.doc.graphs.find((g) => g.id === id);\n    }\n\n    /**\n     * The prefix of every message (the session entry), or \"\".\n     * @returns the prefix\n     */\n    prefix(): string {\n        return this.extras.entry === undefined ? \"\" : `${this.extras.entry}: `;\n    }\n\n    /**\n     * Check the cancellation signal every few dozen elements.\n     */\n    checkAbort(): void {\n        if (++this.sinceCheck >= ABORT_CHECK_INTERVAL) {\n            this.sinceCheck = 0;\n            throwIfAborted(this.options.signal);\n        }\n    }\n\n    /**\n     * Declare a column the importer owns on first use (the 5.6 rename rule applies).\n     * @param domain - node or edge\n     * @param decl - the declaration\n     * @returns the handle, or null when the sink refused it (recorded)\n     */\n    declare(domain: \"node\" | \"edge\", decl: ColumnDecl): ColumnHandle | null {\n        try {\n            return declareResolved(this.sink, domain, decl, this.report, { element: decl.name }).handle;\n        } catch (err) {\n            this.report.recordError(err, { element: decl.name });\n            return null;\n        }\n    }\n\n    // ------------------------------------------------------------------ nodes\n\n    /**\n     * The header direction: the root's `directed` (0 by the DTD), else the defaultDirected option.\n     * @returns whether the graph is directed by default\n     */\n    private headerDirected(): boolean {\n        const text = this.doc.root.attrs.get(\"directed\");\n        if (text === undefined) {\n            return this.options.defaultDirected;\n        }\n        return this.flag(text, this.options.defaultDirected, { line: this.doc.root.line, element: \"directed\" });\n    }\n\n    /** The direction of each edge, decided once (its warning is recorded once). */\n    private readonly directions = new Map<EdgeRec, boolean>();\n\n    /**\n     * The direction of one edge: its cy:directed, else the header.\n     * @param record - the edge\n     * @param header - the header direction\n     * @returns whether the edge is directed\n     */\n    private edgeDirection(record: EdgeRec, header: boolean): boolean {\n        let directed = this.directions.get(record);\n        if (directed === undefined) {\n            directed =\n                record.directed === null\n                    ? header\n                    : this.flag(record.directed, header, { line: record.line, element: record.id ?? record.label });\n            this.directions.set(record, directed);\n        }\n        return directed;\n    }\n\n    /**\n     * The direction the sink starts with: the one every edge has when they all agree (a\n     * Cytoscape file writes cy:directed on every edge and may omit the root attribute), else the\n     * header, so a graph of one direction is never expanded into a mixed one.\n     * @param edges - the edges of the graph\n     * @param header - the header direction\n     * @returns the sink direction\n     */\n    private sinkDirection(edges: readonly EdgeRec[], header: boolean): boolean {\n        let first: boolean | null = null;\n        for (const edge of edges) {\n            const directed = this.edgeDirection(edge, header);\n            if (first === null) {\n                first = directed;\n            } else if (first !== directed) {\n                return header;\n            }\n        }\n        return first ?? header;\n    }\n\n    /**\n     * A 0 / 1 direction flag: true, false, yes and no are accepted with a warning; anything else\n     * falls back.\n     * @param text - the text\n     * @param fallback - the direction for an unreadable value\n     * @param where - the location\n     * @returns the direction\n     */\n    private flag(text: string, fallback: boolean, where: IssueLocation): boolean {\n        const t = text.trim();\n        if (t === \"1\" || t === \"0\") {\n            return t === \"1\";\n        }\n        const lower = t.toLowerCase();\n        const readable = lower === \"true\" || lower === \"yes\" || lower === \"false\" || lower === \"no\";\n        this.report.warnOnce(\n            \"validation-error\",\n            XGMML_ISSUE.BAD_DIRECTED,\n            readable\n                ? `${this.prefix()}directed=\"${text}\" is not 0 or 1; read as ${lower === \"true\" || lower === \"yes\" ? \"1\" : \"0\"}`\n                : `${this.prefix()}directed=\"${text}\" is not 0 or 1; read as ${fallback ? \"directed\" : \"undirected\"}`,\n            where,\n            `${XGMML_ISSUE.BAD_DIRECTED}:${text}`,\n        );\n        return readable ? lower === \"true\" || lower === \"yes\" : fallback;\n    }\n\n    /**\n     * Add every node record to the sink (one node per id; later declarations merge).\n     * @param records - the node records\n     */\n    private addNodes(records: readonly NodeRec[]): void {\n        for (const record of records) {\n            const { id } = record;\n            if (id === null) {\n                continue;\n            }\n            const existing = this.rows.get(id);\n            if (existing !== undefined) {\n                existing.records.push(record);\n                this.report.warning(\n                    \"validation-error\",\n                    XGMML_ISSUE.DUPLICATE_NODE,\n                    `${this.prefix()}node \"${id}\" is declared twice; the declarations are merged`,\n                    { line: record.line, element: id },\n                );\n                continue;\n            }\n            // -1 (not INVALID_INDEX, which is positive) marks a node the sink refused\n            const row: NodeRow = { id, records: [record], index: -1, row: this.rowList.length };\n            try {\n                row.index = this.sink.addNode(this.nodeId(id, record.line));\n                this.report.counts.nodes++;\n            } catch (err) {\n                this.report.counts.skippedNodes++;\n                this.report.recordError(err, { line: record.line, element: id });\n            }\n            this.rows.set(id, row);\n            this.rowList.push(row);\n            this.checkAbort();\n        }\n    }\n\n    /**\n     * The coerced id of a node text.\n     * @param text - the id text\n     * @param line - the line\n     * @returns the id\n     */\n    private nodeId(text: string, line: number): NodeId {\n        const id = this.coercer.text(text);\n        const merge = this.coercer.lastMerge;\n        if (merge !== null) {\n            this.report.warning(\n                \"coercion\",\n                XGMML_ISSUE.ID_MERGED,\n                `id \"${merge.text}\" merged with \"${merge.previousText}\" as ${merge.id} under ids: \"number\"`,\n                { line, element: text },\n            );\n        }\n        return id;\n    }\n\n    /**\n     * Whether a node's nested graph is a group (containment) rather than a nested-network\n     * pointer: any graph in the 1.0 draft dialect, a 2.x node with `__groupState`, a 3.x node with\n     * `__isGroup` true, or a node the session lists.\n     * @returns the test\n     */\n    private groupTest(): (node: NodeRec) => boolean {\n        const { groupNodes } = this.extras;\n        const { cytoscape } = this.dialect;\n        return (node: NodeRec): boolean => {\n            if (!cytoscape) {\n                return true;\n            }\n            if (node.id !== null && groupNodes?.has(node.id) === true) {\n                return true;\n            }\n            return node.atts.some((a) => a.name === \"__groupState\" || (a.name === \"__isGroup\" && isCyTrue(a.value)));\n        };\n    }\n\n    /**\n     * W_DANGLING_REFERENCE for the `xlink:href` members of a generic document's non-group graphs\n     * that name no node or edge (a group's are E_UNKNOWN_PARENT, reported by the containment).\n     */\n    private checkReferences(): void {\n        const isGroup = this.groupTest();\n        const edgeIds = new Set(this.doc.edges.map((e) => e.id));\n        let dangling = 0;\n        for (const graph of this.doc.graphs) {\n            if (graph.owner !== null && isGroup(graph.owner)) {\n                continue;\n            }\n            for (const member of graph.members) {\n                if (member.href === null) {\n                    continue;\n                }\n                const id = localRef(member.href);\n                const known = id !== null && (member.kind === \"node\" ? this.rows.has(id) : edgeIds.has(id));\n                if (!known) {\n                    dangling++;\n                }\n            }\n        }\n        if (dangling > 0) {\n            this.report.warning(\n                \"validation-error\",\n                XGMML_ISSUE.DANGLING_REFERENCE,\n                `${this.prefix()}${dangling} xlink:href reference(s) name no node or edge of the document`,\n            );\n        }\n    }\n\n    /**\n     * Write the per-node values: label, attributes, XML attributes, graphics, positions, nested\n     * network pointers and subgraph memberships.\n     * @param graph - the subnetwork, or null\n     */\n    private writeNodeExtras(graph: GraphRec | null): void {\n        const labels: (string | undefined)[] = [];\n        const positions = new Positions(this, this.dialect.cytoscape ? this.settings.zAs : \"position\");\n        const graphics = new JsonColumn(this, \"node\", GRAPHICS_COLUMN, XGMML_ORIGIN_NAMESPACE, \"graphics\");\n        const pointers = new Pointers(this, this.groupTest());\n        for (const row of this.rowList) {\n            const where = { line: row.records[0].line, element: row.id };\n            const seen = new Set<string>();\n            for (const record of row.records) {\n                labels[row.row] ??= record.label ?? undefined;\n                this.addElementColumns(this.nodeColumns, row.row, record, seen, where);\n                positions.add(row, record);\n                if (record.graphics !== null && Object.keys(record.graphics).length > 0) {\n                    graphics.set(row.index, record.graphics);\n                }\n                pointers.add(row, record);\n            }\n            this.checkAbort();\n        }\n        this.writeLabels(\"node\", labels, (row) => this.rowList[row].index);\n        positions.write();\n        pointers.write();\n        if (graph === null) {\n            this.writeNetworks();\n        }\n    }\n\n    /**\n     * Add an element's XML attributes (text grammar) and atts to a column set; atts of a later\n     * duplicate declaration only fill names the earlier ones left unset.\n     * @param columns - the column set\n     * @param row - the row\n     * @param record - the node or edge\n     * @param seen - the names set by earlier declarations of the same node\n     * @param where - the location\n     */\n    private addElementColumns(\n        columns: ColumnSet,\n        row: number,\n        record: NodeRec | EdgeRec,\n        seen: Set<string>,\n        where: IssueLocation,\n    ): void {\n        const merging = seen.size > 0;\n        const names = new Set<string>();\n        if (record.name !== null) {\n            if (!(merging && seen.has(\"name\"))) {\n                columns.addText(row, \"name\", record.name, where);\n            }\n            names.add(\"name\");\n        }\n        for (const [key, value] of record.xmlAttrs) {\n            if (!(merging && seen.has(key))) {\n                columns.addText(row, key, value, where);\n            }\n            names.add(key);\n        }\n        for (const att of record.atts) {\n            if (this.skipAtt(record, att) || (merging && att.name !== null && seen.has(att.name))) {\n                continue;\n            }\n            if (record.kind === \"node\" && att.name === \"__isGroup\" && record.nested.length > 0 && isCyTrue(att.value)) {\n                // the group is the containment itself (parent / parents and xgmml.subgraph)\n                continue;\n            }\n            if (att.hasGraph && att.name === null) {\n                continue;\n            }\n            columns.addAtt(row, att, where);\n            if (att.name !== null) {\n                names.add(att.name);\n            }\n        }\n        for (const name of names) {\n            seen.add(name);\n        }\n    }\n\n    /**\n     * Whether an att is not a column: an edge's weight att under weightFrom.\n     * @param record - the element\n     * @param att - the att\n     * @returns true to skip it\n     */\n    private skipAtt(record: NodeRec | EdgeRec, att: AttRec): boolean {\n        return record.kind === \"edge\" && record.weight === null && att.name === this.options.weightFrom;\n    }\n\n    /**\n     * Write a label column (role label).\n     * @param domain - node or edge\n     * @param labels - the label of each row\n     * @param index - the sink index of a row\n     */\n    private writeLabels(\n        domain: \"node\" | \"edge\",\n        labels: readonly (string | undefined)[],\n        index: (row: number) => number,\n    ): void {\n        if (!labels.some((l) => l !== undefined)) {\n            return;\n        }\n        const handle = this.declare(domain, {\n            name: LABEL_COLUMN,\n            dtype: \"string\",\n            role: \"label\",\n            nullable: true,\n            origin: { format: FORMAT, id: null, title: null, type: \"label\", namespace: null },\n        });\n        if (handle === null) {\n            return;\n        }\n        labels.forEach((label, row) => {\n            const i = index(row);\n            if (label !== undefined && i >= 0) {\n                if (domain === \"node\") {\n                    this.sink.setNodeValue(handle, i, label);\n                } else {\n                    this.sink.setEdgeValue(handle, i, label);\n                }\n            }\n        });\n    }\n\n    /** The `xgmml.networks` membership of nodes in root-level subgraphs of a generic document. */\n    private writeNetworks(): void {\n        const { subgraphs } = this.doc.root;\n        if (subgraphs.length === 0) {\n            return;\n        }\n        const member = new Map<number, string[]>();\n        for (const graph of subgraphs) {\n            const name = graph.id ?? graph.label ?? \"\";\n            for (const m of graph.members) {\n                const id = m.kind === \"node\" ? (m.id ?? (m.href === null ? null : localRef(m.href))) : null;\n                const row = id === null ? undefined : this.rows.get(id);\n                if (row !== undefined && row.index >= 0) {\n                    const list = member.get(row.index) ?? [];\n                    list.push(name);\n                    member.set(row.index, list);\n                }\n            }\n        }\n        if (member.size === 0) {\n            return;\n        }\n        const handle = this.declare(\"node\", {\n            name: NETWORKS_COLUMN,\n            dtype: \"list\",\n            itemDtype: \"string\",\n            nullable: true,\n            origin: { format: FORMAT, id: null, title: null, type: \"graph\", namespace: XGMML_ORIGIN_NAMESPACE },\n        });\n        if (handle !== null) {\n            for (const [index, list] of member) {\n                this.sink.setNodeValue(handle, index, list);\n            }\n        }\n    }\n\n    // ------------------------------------------------------------------ edges\n\n    /**\n     * Push every edge record.\n     * @param records - the edge records\n     * @param header - the header direction\n     */\n    private addEdges(records: readonly EdgeRec[], header: boolean): void {\n        const ids = new Set<string>();\n        const dedupe = this.dialect.cy2 && this.doc.nodes.some((n) => n.nested.length > 0) ? new Set<string>() : null;\n        const labels: (string | undefined)[] = [];\n        const edgeIds: (string | undefined)[] = [];\n        const graphics: [number, Record<string, unknown>][] = [];\n        let row = 0;\n        for (const record of records) {\n            const where = { line: record.line, element: record.id ?? record.label };\n            const key = record.id ?? record.label;\n            if (dedupe !== null && key !== null) {\n                if (dedupe.has(key)) {\n                    this.report.warnOnce(\n                        \"merged\",\n                        XGMML_ISSUE.GROUP_DUPLICATE_EDGE,\n                        `${this.prefix()}the Cytoscape 2.x writer repeats the edges of a group; each repeat is dropped`,\n                        where,\n                    );\n                    continue;\n                }\n                dedupe.add(key);\n            }\n            const index = this.addEdge(record, header, ids, where);\n            this.checkAbort();\n            if (index < 0) {\n                continue;\n            }\n            this.edgeIndex[row] = index;\n            labels[row] = record.label ?? undefined;\n            edgeIds[row] = record.id ?? undefined;\n            this.addElementColumns(this.edgeColumns, row, record, new Set(), where);\n            this.fillInteraction(record, row, where);\n            if (record.graphics !== null && Object.keys(record.graphics).length > 0) {\n                graphics.push([index, record.graphics]);\n            }\n            row++;\n        }\n        this.writeEdgeIds(edgeIds);\n        this.writeLabels(\"edge\", labels, (r) => this.edgeIndex[r] ?? -1);\n        const column = new JsonColumn(this, \"edge\", GRAPHICS_COLUMN, XGMML_ORIGIN_NAMESPACE, \"graphics\");\n        for (const [index, value] of graphics) {\n            column.set(index, value);\n        }\n    }\n\n    /**\n     * Push one edge: endpoints (with label aliases), duplicate id check, direction and weight.\n     * @param record - the edge\n     * @param header - the header direction\n     * @param ids - the edge ids used so far\n     * @param where - the location\n     * @returns the edge index, or -1 when it was skipped\n     */\n    private addEdge(record: EdgeRec, header: boolean, ids: Set<string>, where: IssueLocation): number {\n        const alias = this.settings.labelAliases ? aliasesOf(record.label) : null;\n        let source: NodeId | null;\n        let target: NodeId | null;\n        try {\n            source = this.endpoint(record.source, alias?.[0] ?? null, \"source\", where);\n            target = this.endpoint(record.target, alias?.[2] ?? null, \"target\", where);\n        } catch (err) {\n            // an endpoint the id rule or the sink refuses (ids: \"number\", a caller's sink)\n            this.report.counts.skippedEdges++;\n            this.report.recordError(err, where);\n            return -1;\n        }\n        if (source === null || target === null) {\n            this.report.counts.skippedEdges++;\n            return -1;\n        }\n        if (record.id !== null && ids.has(record.id)) {\n            this.report.counts.skippedEdges++;\n            this.report.error(\n                \"validation-error\",\n                XGMML_ISSUE.DUPLICATE_EDGE_ID,\n                `${this.prefix()}edge id \"${record.id}\" is used twice; the second edge is skipped`,\n                where,\n            );\n            return -1;\n        }\n        const directed = this.edgeDirection(record, header);\n        const kind: EdgeKind = directed ? \"directed\" : \"undirected\";\n        let weight: number | undefined;\n        try {\n            weight = this.weightOf(record);\n            const before = this.sink.edgeCount;\n            const e = this.direction.addEdge(source, target, kind, weight, where);\n            this.report.counts.edges += this.sink.edgeCount - before;\n            if (record.id !== null) {\n                ids.add(record.id);\n            }\n            return e;\n        } catch (err) {\n            this.report.counts.skippedEdges++;\n            this.report.recordError(err, where);\n            return -1;\n        }\n    }\n\n    /**\n     * The weight of an edge: its `weight` XML attribute (or the att weightFrom names).\n     * @param record - the edge\n     * @returns the weight, or undefined\n     */\n    private weightOf(record: EdgeRec): number | undefined {\n        const from = this.options.weightFrom;\n        if (from === null) {\n            return undefined;\n        }\n        let text: string | null = from === \"weight\" ? record.weight : null;\n        if (text === null) {\n            text = record.atts.find((a) => a.name === from && a.children.length === 0)?.value ?? null;\n        }\n        if (text === null) {\n            return undefined;\n        }\n        const weight = parseWeightText(text);\n        this.weighted ||= weight !== undefined;\n        return weight;\n    }\n\n    /**\n     * Resolve one endpoint: a node of this graph by id, else (under labelAliases) the label alias\n     * by id or by unique node label; a missing endpoint is E_MISSING_ENDPOINT, an unknown one\n     * E_UNKNOWN_NODE unless addMissingNodes adds it.\n     * @param text - the source or target text, or null\n     * @param alias - the label alias, or null\n     * @param side - which end\n     * @param where - the location\n     * @returns the node id, or null when the edge cannot be added\n     */\n    private endpoint(text: string | null, alias: string | null, side: string, where: IssueLocation): NodeId | null {\n        if (text !== null) {\n            const row = this.rows.get(text);\n            if (row !== undefined && row.index >= 0) {\n                return this.coercer.text(text);\n            }\n        }\n        if (alias !== null) {\n            const resolved = this.aliasRow(alias);\n            if (resolved !== null) {\n                this.aliasResolved++;\n                return this.coercer.text(resolved.id);\n            }\n        }\n        if (text === null) {\n            this.report.error(\n                \"missing-value\",\n                XGMML_ISSUE.MISSING_ENDPOINT,\n                `${this.prefix()}<edge> without a ${side}`,\n                where,\n            );\n            return null;\n        }\n        if (this.options.addMissingNodes) {\n            const id = this.coercer.text(text);\n            if (this.sink.indexOf(id) === INVALID_INDEX) {\n                this.sink.addNode(id);\n                this.report.counts.nodes++;\n            }\n            return id;\n        }\n        this.report.error(\n            \"validation-error\",\n            XGMML_ISSUE.UNKNOWN_NODE,\n            `${this.prefix()}edge ${side} \"${text}\" is not a node of this graph; the edge is skipped`,\n            where,\n        );\n        return null;\n    }\n\n    /** Node labels to rows, for label aliases; null marks a label two nodes share. */\n    private labelRows: Map<string, NodeRow | null> | null = null;\n\n    /**\n     * The node a label alias names: by id, else by a label only one node has.\n     * @param alias - the alias\n     * @returns the row, or null\n     */\n    private aliasRow(alias: string): NodeRow | null {\n        const byId = this.rows.get(alias);\n        if (byId !== undefined && byId.index >= 0) {\n            return byId;\n        }\n        if (this.labelRows === null) {\n            this.labelRows = new Map();\n            for (const row of this.rowList) {\n                const { label } = row.records[0];\n                if (label !== null && row.index >= 0) {\n                    this.labelRows.set(label, this.labelRows.has(label) ? null : row);\n                }\n            }\n        }\n        return this.labelRows.get(alias) ?? null;\n    }\n\n    /**\n     * Fill the interaction of an edge without one from its label alias, as Cytoscape does.\n     * @param record - the edge\n     * @param row - the edge row\n     * @param where - the location\n     */\n    private fillInteraction(record: EdgeRec, row: number, where: IssueLocation): void {\n        if (\n            !this.settings.labelAliases ||\n            this.dialect.session ||\n            record.atts.some((a) => a.name === INTERACTION_COLUMN)\n        ) {\n            return;\n        }\n        const alias = aliasesOf(record.label);\n        if (alias !== null) {\n            this.edgeColumns.addText(row, INTERACTION_COLUMN, alias[1], where);\n            this.aliasInteractions++;\n        }\n    }\n\n    /** Report the label alias uses, once. */\n    private finishAliases(): void {\n        if (this.aliasResolved === 0 && this.aliasInteractions === 0) {\n            return;\n        }\n        this.report.warning(\n            \"coercion\",\n            XGMML_ISSUE.LABEL_ALIAS,\n            `${this.prefix()}Cytoscape label aliases (\"a (pp) b\"): ${this.aliasResolved} endpoint(s) resolved, ${this.aliasInteractions} interaction(s) filled from edge labels`,\n        );\n    }\n\n    /**\n     * Write the edge `id` column (role id, unique).\n     * @param ids - the id of each row\n     */\n    private writeEdgeIds(ids: readonly (string | undefined)[]): void {\n        if (!ids.some((id) => id !== undefined)) {\n            return;\n        }\n        const handle = this.declare(\"edge\", {\n            name: EDGE_ID_COLUMN,\n            dtype: \"string\",\n            role: \"id\",\n            unique: true,\n            nullable: true,\n            origin: { format: FORMAT, id: null, title: null, type: \"id\", namespace: null },\n        });\n        if (handle === null) {\n            return;\n        }\n        ids.forEach((id, row) => {\n            const e = this.edgeIndex[row];\n            if (id !== undefined && e !== undefined) {\n                try {\n                    this.sink.setEdgeValue(handle, e, id);\n                } catch (err) {\n                    this.report.recordError(err, { element: id });\n                }\n            }\n        });\n    }\n\n    // ------------------------------------------------------------------ graph and metadata\n\n    /**\n     * The graph table: the graph's atts and other XML attributes, and its graphics.\n     * @param graph - the subnetwork, or null for the root\n     */\n    private writeGraph(graph: GraphRec | null): void {\n        const g = graph ?? this.doc.root;\n        const where = { line: g.line, element: g.id };\n        if (graph === null) {\n            for (const [key, value] of g.attrs) {\n                if (!GRAPH_STRUCTURE.has(key) && key !== \"xmlns\" && !key.startsWith(\"xmlns:\")) {\n                    this.graphColumns.addText(0, key, value, where);\n                }\n            }\n        }\n        for (const att of g.atts) {\n            if (att.name !== null && META_ATTS.has(att.name)) {\n                continue;\n            }\n            if (att.hasGraph && att.name === null) {\n                continue;\n            }\n            this.graphColumns.addAtt(0, att, where);\n        }\n        this.graphColumns.write(this.sink, () => 0);\n        const json: Record<string, unknown> = { ...(this.extras.graphJson ?? {}) };\n        if (g.graphics !== null && Object.keys(g.graphics).length > 0) {\n            json[GRAPHICS_COLUMN] = g.graphics;\n        }\n        for (const [name, value] of Object.entries(json)) {\n            this.sink.setGraphValue(name, value, {\n                name,\n                dtype: \"json\",\n                nullable: true,\n                origin: { format: FORMAT, id: null, title: null, type: name, namespace: XGMML_ORIGIN_NAMESPACE },\n            });\n        }\n    }\n\n    /**\n     * The graph metadata: name, description and date from the RDF metadata, the format, version\n     * and what the exporter needs.\n     * @param graph - the subnetwork, or null\n     */\n    private writeMeta(graph: GraphRec | null): void {\n        const g = graph ?? this.doc.root;\n        const { rdf } = this.doc;\n        const name = this.extras.graphName ?? g.label ?? rdf.title ?? g.id ?? undefined;\n        this.sink.setMeta({\n            name: name ?? undefined,\n            description: rdf.description ?? undefined,\n            created: rdf.date ?? undefined,\n            sourceFormat: this.extras.sourceFormat ?? FORMAT,\n            sourceVersion: this.dialect.versionText ?? undefined,\n            weightOrigin: this.weighted\n                ? { format: FORMAT, id: \"weight\", title: null, type: \"weight\", namespace: null }\n                : undefined,\n            extra: {\n                [META_KEY]: {\n                    graphId: g.id,\n                    directed: this.doc.root.attrs.get(\"directed\") ?? null,\n                    rdf: Object.keys(rdf).length > 0 ? { ...rdf } : null,\n                },\n                ...(this.extras.metaExtra ?? {}),\n            },\n        });\n    }\n}\n\n/**\n * The three parts of a Cytoscape edge label (`source (interaction) target`).\n * @param label - the label, or null\n * @returns source alias, interaction, target alias; null when the label has another shape\n */\nexport function aliasesOf(label: string | null): [string, string, string] | null {\n    if (label === null) {\n        return null;\n    }\n    const parts = label.split(ALIAS_SPLIT);\n    return parts.length === 3 ? [parts[0].trim(), parts[1], parts[2].trim()] : null;\n}\n\n/**\n * A json column the importer owns, declared on first value.\n */\nclass JsonColumn {\n    private handle: ColumnHandle | null | undefined;\n\n    /**\n     * Create the column.\n     * @param emitter - the emitter\n     * @param domain - node or edge\n     * @param name - the column name\n     * @param namespace - its origin namespace\n     * @param type - its origin type\n     * @param dtype - json (default) or string\n     */\n    constructor(\n        private readonly emitter: XgmmlEmitter,\n        private readonly domain: \"node\" | \"edge\",\n        private readonly name: string,\n        private readonly namespace: string,\n        private readonly type: string,\n        private readonly dtype: \"json\" | \"string\" = \"json\",\n    ) {}\n\n    /**\n     * Set one value.\n     * @param index - the node or edge index\n     * @param value - the value\n     */\n    set(index: number, value: unknown): void {\n        if (index < 0) {\n            return;\n        }\n        if (this.handle === undefined) {\n            this.handle = this.emitter.declare(this.domain, {\n                name: this.name,\n                dtype: this.dtype,\n                nullable: true,\n                origin: { format: FORMAT, id: null, title: null, type: this.type, namespace: this.namespace },\n            });\n        }\n        if (this.handle === null) {\n            return;\n        }\n        const sink = this.emitter.target;\n        if (this.domain === \"node\") {\n            sink.setNodeValue(this.handle, index, value);\n        } else {\n            sink.setEdgeValue(this.handle, index, value);\n        }\n    }\n}\n\n/**\n * Node positions: x and y (y negated: Cytoscape's screen y grows down, graph-io's grows up), z\n * as a coordinate in the draft dialect or under zAs \"position\", else as the `z` column.\n */\nclass Positions {\n    private readonly values = new Map<number, [number, number, number]>();\n\n    private readonly zValues = new Map<number, number>();\n\n    private hasZ = false;\n\n    /**\n     * Create the collector.\n     * @param emitter - the emitter\n     * @param zAs - where z goes\n     */\n    constructor(\n        private readonly emitter: XgmmlEmitter,\n        private readonly zAs: \"column\" | \"position\",\n    ) {}\n\n    /**\n     * Read one node record's coordinates.\n     * @param row - the node row\n     * @param record - the record\n     */\n    add(row: NodeRow, record: NodeRec): void {\n        if (row.index < 0 || (record.x === null && record.y === null && record.z === null)) {\n            return;\n        }\n        const where = { line: record.line, element: row.id };\n        const x = this.number(record.x, where);\n        const y = this.number(record.y, where);\n        const z = this.number(record.z, where);\n        if (z !== null) {\n            this.hasZ = true;\n            if (this.zAs === \"column\") {\n                this.zValues.set(row.index, z);\n            }\n        }\n        if (x !== null && y !== null) {\n            const flipped = y === 0 ? 0 : -y;\n            this.values.set(row.index, [x, flipped, this.zAs === \"position\" ? (z ?? 0) : 0]);\n        }\n    }\n\n    /**\n     * A coordinate.\n     * @param text - the text, or null\n     * @param where - the location\n     * @returns the number, or null when absent or invalid (recorded)\n     */\n    private number(text: string | null, where: IssueLocation): number | null {\n        if (text === null) {\n            return null;\n        }\n        const n = Number(text.trim());\n        if (text.trim().length === 0 || !Number.isFinite(n)) {\n            this.emitter.issues.error(\n                \"validation-error\",\n                XGMML_ISSUE.BAD_VALUE,\n                `${this.emitter.prefix()}graphics coordinate \"${text}\" is not a number`,\n                where,\n            );\n            return null;\n        }\n        return n;\n    }\n\n    /** Declare and write the position and z columns. */\n    write(): void {\n        const sink = this.emitter.target;\n        if (this.values.size > 0) {\n            const handle = this.emitter.declare(\"node\", {\n                name: POSITION_COLUMN,\n                dtype: \"f32\",\n                components: 3,\n                role: \"position\",\n                nullable: true,\n                origin: { format: FORMAT, id: null, title: null, type: \"graphics\", namespace: XGMML_ORIGIN_NAMESPACE },\n                extra: { sourceDims: this.zAs === \"position\" && this.hasZ ? 3 : 2, units: \"file\" },\n            });\n            if (handle !== null) {\n                for (const [index, xyz] of this.values) {\n                    sink.setNodeValue(handle, index, xyz);\n                }\n            }\n        }\n        if (this.zValues.size > 0) {\n            const handle = this.emitter.declare(\"node\", {\n                name: Z_COLUMN,\n                dtype: \"f64\",\n                nullable: true,\n                origin: {\n                    format: FORMAT,\n                    id: null,\n                    title: null,\n                    type: \"graphics\",\n                    namespace: CYTOSCAPE_ORIGIN_NAMESPACE,\n                },\n            });\n            if (handle !== null) {\n                for (const [index, z] of this.zValues) {\n                    sink.setNodeValue(handle, index, z);\n                }\n            }\n        }\n    }\n}\n\n/**\n * Nested-network pointers: a node-nested graph that is not a group names a network.\n */\nclass Pointers {\n    private readonly names = new Map<number, string>();\n\n    private readonly crossFile = new Map<number, string>();\n\n    private dangling = 0;\n\n    /**\n     * Create the collector.\n     * @param emitter - the emitter\n     * @param isGroup - the group test\n     */\n    constructor(\n        private readonly emitter: XgmmlEmitter,\n        private readonly isGroup: (node: NodeRec) => boolean,\n    ) {}\n\n    /**\n     * Read one node record's pointers.\n     * @param row - the node row\n     * @param record - the record\n     */\n    add(row: NodeRow, record: NodeRec): void {\n        if (record.nested.length === 0 || this.isGroup(record) || row.index < 0) {\n            return;\n        }\n        for (const graph of record.nested) {\n            if (graph.href === null) {\n                this.names.set(row.index, graph.label ?? graph.id ?? \"\");\n                continue;\n            }\n            const id = localRef(graph.href);\n            if (id === null) {\n                const resolved = this.emitter.resolvePointer(graph.href);\n                if (resolved !== null) {\n                    this.names.set(row.index, resolved);\n                } else {\n                    this.crossFile.set(row.index, graph.href);\n                }\n                continue;\n            }\n            const target = this.emitter.graphById(id);\n            if (target === undefined) {\n                this.dangling++;\n            } else {\n                this.names.set(row.index, target.label ?? target.id ?? id);\n            }\n        }\n    }\n\n    /** Write the pointer columns and their warnings. */\n    write(): void {\n        const prefix = this.emitter.prefix();\n        if (this.dangling > 0) {\n            this.emitter.issues.warning(\n                \"validation-error\",\n                XGMML_ISSUE.DANGLING_REFERENCE,\n                `${prefix}${this.dangling} nested-network pointer(s) name no graph of the document`,\n            );\n        }\n        const names = new JsonColumn(\n            this.emitter,\n            \"node\",\n            NESTED_NETWORK_COLUMN,\n            CYTOSCAPE_ORIGIN_NAMESPACE,\n            \"nestedNetwork\",\n            \"string\",\n        );\n        for (const [index, name] of this.names) {\n            names.set(index, name);\n        }\n        if (this.crossFile.size > 0) {\n            this.emitter.issues.warning(\n                \"unsupported\",\n                XGMML_ISSUE.CROSS_FILE_REFERENCE,\n                `${prefix}${this.crossFile.size} nested-network pointer(s) point into another file; each is kept as text in ${NETWORK_POINTER_COLUMN}`,\n            );\n            const column = new JsonColumn(\n                this.emitter,\n                \"node\",\n                NETWORK_POINTER_COLUMN,\n                XGMML_ORIGIN_NAMESPACE,\n                \"xlink:href\",\n                \"string\",\n            );\n            for (const [index, href] of this.crossFile) {\n                column.set(index, href);\n            }\n        }\n    }\n}\n\n/**\n * Group containment: every node (declared or referenced) in a group's nested graph has the group\n * node as a parent; a node in several groups gets the `parents` list instead of `parent`.\n */\nclass Containment {\n    private readonly parents = new Map<number, number[]>();\n\n    private readonly subgraphs = new Map<number, Record<string, unknown>>();\n\n    /**\n     * Create the resolver.\n     * @param emitter - the emitter\n     */\n    constructor(private readonly emitter: XgmmlEmitter) {}\n\n    /**\n     * Collect the memberships of every group node of the graph.\n     * @param rows - the node rows\n     * @param isGroup - the group test\n     */\n    resolve(rows: readonly NodeRow[], isGroup: (node: NodeRec) => boolean): void {\n        let unknown = 0;\n        for (const row of rows) {\n            for (const record of row.records) {\n                if (row.index < 0 || record.nested.length === 0 || !isGroup(record)) {\n                    continue;\n                }\n                for (const graph of record.nested) {\n                    const atts = graph.atts.filter((a) => a.name !== null);\n                    if (graph.id !== null || graph.label !== null || atts.length > 0) {\n                        this.subgraphs.set(row.index, {\n                            id: graph.id,\n                            label: graph.label,\n                            atts: Object.fromEntries(atts.map((a) => [a.name, attJson(a)])),\n                        });\n                    }\n                    for (const member of graph.members) {\n                        if (member.kind !== \"node\") {\n                            continue;\n                        }\n                        const id = member.id ?? (member.href === null ? null : localRef(member.href));\n                        const child = id === null ? undefined : this.emitter.rowOf(id);\n                        if (child === undefined) {\n                            if (id === null || !this.emitter.missingMember(row.id, id)) {\n                                unknown++;\n                            }\n                            continue;\n                        }\n                        if (child.index >= 0) {\n                            this.link(child.index, row.index, member.line);\n                        }\n                    }\n                }\n            }\n        }\n        if (unknown > 0) {\n            this.emitter.issues.error(\n                \"missing-value\",\n                XGMML_ISSUE.UNKNOWN_PARENT,\n                `${this.emitter.prefix()}${unknown} group member(s) name no node of this graph`,\n            );\n        }\n    }\n\n    /**\n     * Add one membership unless it closes a parent cycle.\n     * @param child - the member's index\n     * @param parent - the group node's index\n     * @param line - the line\n     */\n    private link(child: number, parent: number, line: number): void {\n        if (child === parent || this.isAncestor(child, parent)) {\n            this.emitter.issues.error(\n                \"validation-error\",\n                XGMML_ISSUE.PARENT_CYCLE,\n                `${this.emitter.prefix()}a group membership would make a node its own ancestor; that membership is dropped`,\n                { line },\n            );\n            return;\n        }\n        const list = this.parents.get(child) ?? [];\n        if (!list.includes(parent)) {\n            list.push(parent);\n        }\n        this.parents.set(child, list);\n    }\n\n    /**\n     * Whether a node is an ancestor of another through the memberships so far.\n     * @param ancestor - the candidate ancestor\n     * @param node - the node\n     * @returns true when following parents from node reaches ancestor\n     */\n    private isAncestor(ancestor: number, node: number): boolean {\n        const stack = [node];\n        const seen = new Set<number>();\n        while (stack.length > 0) {\n            const n = stack.pop() as number;\n            if (n === ancestor) {\n                return true;\n            }\n            if (seen.has(n)) {\n                continue;\n            }\n            seen.add(n);\n            stack.push(...(this.parents.get(n) ?? []));\n        }\n        return false;\n    }\n\n    /** Declare and write the parent (or parents) and subgraph columns. */\n    write(): void {\n        const sink = this.emitter.target;\n        if (this.parents.size > 0) {\n            const multi = [...this.parents.values()].some((list) => list.length > 1);\n            const handle = this.emitter.declare(\"node\", {\n                name: multi ? PARENTS_COLUMN : PARENT_COLUMN,\n                dtype: multi ? \"list\" : \"u32\",\n                itemDtype: multi ? \"u32\" : undefined,\n                role: multi ? \"parents\" : \"parent\",\n                refersTo: \"node\",\n                nullable: true,\n                origin: { format: FORMAT, id: null, title: null, type: \"graph\", namespace: null },\n            });\n            if (handle !== null) {\n                for (const [child, list] of this.parents) {\n                    sink.setNodeValue(handle, child, multi ? list : list[0]);\n                }\n            }\n        }\n        if (this.subgraphs.size > 0) {\n            const column = new JsonColumn(this.emitter, \"node\", SUBGRAPH_COLUMN, XGMML_ORIGIN_NAMESPACE, \"graph\");\n            for (const [index, value] of this.subgraphs) {\n                column.set(index, value);\n            }\n        }\n    }\n}\n","/**\n * The XGMML importer (design `design/graph-io/cytoscape-and-obo/design.md` section 1.1;\n * `research-xgmml.md`): one reader for the 1.0 draft, the Cytoscape 2.x and 3.x exports and the\n * Cytoscape 3 session network files. The document is read in one pass of the shared XML tokenizer\n * into records (document.ts), and resolved into the sink once the outermost `</graph>` closes\n * (emit.ts), so forward references and edges before their nodes need nothing special.\n *\n * Direction follows the specification: the root `directed` (0 by the DTD, else the\n * `defaultDirected` option), then `cy:directed` per edge, overruling Cytoscape, which ignores the\n * root attribute. Ids are kept as written (`ids: \"keep\"`), so `\"1\"`, `\"01\"` and `\" 1 \"` stay three\n * nodes. Positions are stored y-up (Cytoscape writes screen coordinates). Graphics values are kept\n * as a json column, never interpreted (style import is issue #706).\n */\n\nimport { GraphFormatError, type GraphSink } from \"@graphty/graph-format\";\n\nimport { textChunks, throwIfAborted } from \"../../common/input.js\";\nimport {\n    chooseGraph,\n    type ImportFormatDefaults,\n    reportSinkOptions,\n    reportUnusedOptions,\n    type ResolvedImportOptions,\n    resolveImportOptions,\n} from \"../../common/options.js\";\nimport { ImportReportBuilder } from \"../../common/report.js\";\nimport { isWhitespace, tokenizeXml, xmlDeclaredEncoding, type XmlRepairs, XmlSyntaxError } from \"../../common/xml.js\";\nimport {\n    type CommonImportOptions,\n    type GraphChoiceOptions,\n    type GraphImporter,\n    type GraphListing,\n    type ImportInput,\n    type ImportReport,\n} from \"../../types.js\";\nimport { EXTENSIONS, FORMAT, MIME_TYPES, XGMML_ISSUE } from \"./constants.js\";\nimport { type GraphRec, type XgmmlDocument, XgmmlParser } from \"./document.js\";\nimport {\n    type Dialect,\n    dialectOf,\n    type EmitExtras,\n    graphsOf,\n    membersOf,\n    XgmmlEmitter,\n    type XgmmlSettings,\n} from \"./emit.js\";\n\n/** The format-specific options of the XGMML importer. */\nexport interface XgmmlImportOptions extends GraphChoiceOptions {\n    /**\n     * Resolve an edge endpoint that is missing or names no node through Cytoscape's\n     * `\"source (interaction) target\"` edge label, and fill a missing interaction from it. Default:\n     * on for files that use the Cytoscape (`cy`) namespace, off otherwise.\n     */\n    labelAliases?: boolean | undefined;\n    /**\n     * Decode Cytoscape's two-character `\\n` and `\\t` escapes in string values. Default: on for\n     * files that use the Cytoscape namespace, off otherwise.\n     */\n    cytoscapeEscapes?: boolean | undefined;\n    /** Read an `&` not followed by `;` within 7 characters as `&amp;` (warned per occurrence). Default false. */\n    repairBareAmpersands?: boolean | undefined;\n    /** Join two surrogate character references into one character (warned per pair). Default false. */\n    pairSurrogateReferences?: boolean | undefined;\n    /** Where Cytoscape's z (a stacking order) goes: the `z` column (default) or the position. */\n    zAs?: \"column\" | \"position\" | undefined;\n}\n\n/** The per-format defaults: ids as written, undirected by the DTD, the edge `weight` attribute. */\nconst FORMAT_DEFAULTS: ImportFormatDefaults = {\n    ids: \"keep\",\n    defaultDirected: false,\n    weightFrom: \"weight\",\n    addMissingNodes: false,\n};\n\n/** The common options the XGMML importer reads. */\nconst USED_OPTIONS: ReadonlySet<keyof CommonImportOptions> = new Set<keyof CommonImportOptions>([\n    \"ids\",\n    \"addMissingNodes\",\n    \"duplicateEdges\",\n    \"selfLoops\",\n    \"onMixedDirection\",\n    \"defaultDirected\",\n    \"weightFrom\",\n    \"weightDtype\",\n    \"long\",\n    \"errorLimit\",\n    \"signal\",\n    \"onProgress\",\n    \"encoding\",\n]);\n\n/** Bytes inspected by sniff(). */\nconst SNIFF_BYTES = 4096;\n\n/** The head of the document kept for the DOCTYPE check. */\nconst HEAD_CHARS = 2048;\n\n/** An XGMML DOCTYPE (Cytoscape's file filter tests the same). */\nconst XGMML_DOCTYPE = /<!DOCTYPE\\s+graph\\s[^<>]*xgmml\\.dtd/i;\n\n/**\n * The XGMML option values, checked.\n * @param options - the caller's options\n * @param cytoscape - whether the document uses the Cytoscape namespace\n * @returns the settings; E_UNSUPPORTED for a value of the wrong type\n */\nexport function resolveSettings(options: XgmmlImportOptions | undefined, cytoscape: boolean): XgmmlSettings {\n    const zAs = options?.zAs ?? \"column\";\n    if (zAs !== \"column\" && zAs !== \"position\") {\n        throw new GraphFormatError(\n            \"E_UNSUPPORTED\",\n            `option zAs: ${JSON.stringify(zAs)} is not \"column\" or \"position\"`,\n            {\n                option: \"zAs\",\n                found: zAs,\n            },\n        );\n    }\n    return {\n        labelAliases: booleanOption(\"labelAliases\", options?.labelAliases, cytoscape),\n        cytoscapeEscapes: booleanOption(\"cytoscapeEscapes\", options?.cytoscapeEscapes, cytoscape),\n        zAs,\n    };\n}\n\n/**\n * One boolean option.\n * @param name - the option name\n * @param value - the caller's value\n * @param fallback - the default\n * @returns the value; E_UNSUPPORTED when not a boolean\n */\nfunction booleanOption(name: string, value: unknown, fallback: boolean): boolean {\n    if (value === undefined) {\n        return fallback;\n    }\n    if (typeof value !== \"boolean\") {\n        throw new GraphFormatError(\"E_UNSUPPORTED\", `option ${name}: ${JSON.stringify(value)} is not a boolean`, {\n            option: name,\n            found: value,\n        });\n    }\n    return value;\n}\n\n/**\n * Read an XGMML document into records. Fatal conditions (not XML, not a graph, empty) fail the\n * report.\n * @param input - the input\n * @param report - the report\n * @param common - the resolved common options\n * @param options - the XGMML options (for the repairs)\n * @returns the document\n */\nexport async function parseXgmml(\n    input: ImportInput,\n    report: ImportReportBuilder,\n    common: ResolvedImportOptions,\n    options: XgmmlImportOptions | undefined,\n): Promise<XgmmlDocument> {\n    const repairs: XmlRepairs = {\n        bareAmpersand: booleanOption(\"repairBareAmpersands\", options?.repairBareAmpersands, false)\n            ? (line): void => {\n                  report.warning(\"parse-error\", XGMML_ISSUE.AMPERSAND_REPAIRED, \"a bare & was read as &amp;\", { line });\n              }\n            : undefined,\n        surrogatePair: booleanOption(\"pairSurrogateReferences\", options?.pairSurrogateReferences, false)\n            ? (line): void => {\n                  report.warning(\n                      \"parse-error\",\n                      XGMML_ISSUE.SURROGATE_PAIRED,\n                      \"two surrogate character references were joined into one character\",\n                      { line },\n                  );\n              }\n            : undefined,\n    };\n    const parser = new XgmmlParser(report);\n    const seen = { head: \"\", content: false };\n    try {\n        await tokenizeXml(\n            watch(textChunks(input, report, { ...common, declaredEncoding: xmlDeclaredEncoding }), seen),\n            parser,\n            repairs,\n        );\n    } catch (err) {\n        if (err instanceof XmlSyntaxError) {\n            if (!seen.content) {\n                report.fail(XGMML_ISSUE.EMPTY_INPUT, \"the input is empty\");\n            }\n            report.fail(XGMML_ISSUE.XML_SYNTAX, err.message, { line: err.line });\n        }\n        throw err;\n    }\n    const doc = parser.document();\n    if (!doc.xgmmlNamespace && !XGMML_DOCTYPE.test(seen.head)) {\n        report.warning(\n            \"validation-error\",\n            XGMML_ISSUE.NO_NAMESPACE,\n            \"the root <graph> has neither the XGMML namespace nor an XGMML DOCTYPE; it is read as XGMML\",\n            { line: doc.root.line },\n        );\n    }\n    return doc;\n}\n\n/**\n * Pass text chunks through while keeping the head and noting non-whitespace content.\n * @param chunks - the chunks\n * @param seen - where the head and the content flag are kept\n * @param seen.head - the first characters of the document\n * @param seen.content - whether non-whitespace text was seen\n * @yields the chunks unchanged\n * @returns nothing\n */\nasync function* watch(\n    chunks: AsyncIterable<string>,\n    seen: { head: string; content: boolean },\n): AsyncGenerator<string, void, undefined> {\n    for await (const chunk of chunks) {\n        if (seen.head.length < HEAD_CHARS) {\n            seen.head += chunk.slice(0, HEAD_CHARS - seen.head.length);\n        }\n        seen.content ||= !isWhitespace(chunk);\n        yield chunk;\n    }\n}\n\n/** What an import call sets up before it emits. */\ninterface Prepared {\n    readonly report: ImportReportBuilder;\n    readonly common: ResolvedImportOptions;\n    readonly doc: XgmmlDocument;\n    readonly dialect: Dialect;\n    readonly settings: XgmmlSettings;\n    readonly graphs: readonly GraphRec[];\n}\n\n/**\n * Resolve the options, read the document and check it is a graph document.\n * @param input - the input\n * @param sink - the sink, or null for listGraphs\n * @param options - the options\n * @returns what the import needs\n */\nasync function prepare(\n    input: ImportInput,\n    sink: GraphSink | null,\n    options: (XgmmlImportOptions & CommonImportOptions) | undefined,\n): Promise<Prepared> {\n    const common = resolveImportOptions(options, FORMAT_DEFAULTS);\n    const report = new ImportReportBuilder(FORMAT, common.errorLimit);\n    if (sink !== null) {\n        reportSinkOptions(sink, options, report, true);\n        reportUnusedOptions(options, report, USED_OPTIONS);\n    }\n    resolveSettings(options, false);\n    const doc = await parseXgmml(input, report, common, options);\n    const dialect = dialectOf(doc, report);\n    if (dialect.view) {\n        report.fail(\n            XGMML_ISSUE.VIEW_DOCUMENT,\n            \"this is a Cytoscape session view file (cy:view): it holds positions keyed by view ids and no topology; open the session (.cys) instead\",\n            { line: doc.root.line },\n        );\n    }\n    return {\n        report,\n        common,\n        doc,\n        dialect,\n        settings: resolveSettings(options, doc.cytoscape),\n        graphs: graphsOf(doc, dialect),\n    };\n}\n\n/**\n * Emit one graph of a prepared document.\n * @param prepared - the prepared import\n * @param graph - the graph to read\n * @param sink - the sink\n * @param extras - what a session adds\n * @returns the report\n */\nfunction emitOne(prepared: Prepared, graph: GraphRec, sink: GraphSink, extras?: EmitExtras): ImportReport {\n    const { doc, dialect, report, common, settings } = prepared;\n    const emitter = new XgmmlEmitter(doc, dialect, sink, report, common, settings, extras);\n    emitter.emit(dialect.session ? graph : null);\n    if (dialect.session) {\n        reportRootOnly(prepared);\n    }\n    throwIfAborted(common.signal);\n    return report.finish();\n}\n\n/**\n * W_XGMML_ROOT_ONLY_ELEMENTS: elements of a session network document no registered subnetwork\n * holds (group meta-edges, members of collapsed groups).\n * @param prepared - the prepared import\n */\nfunction reportRootOnly(prepared: Prepared): void {\n    const held = new Set<unknown>();\n    for (const graph of prepared.graphs) {\n        const members = membersOf(prepared.doc, graph);\n        members.nodes.forEach((n) => held.add(n));\n        members.edges.forEach((e) => held.add(e));\n    }\n    const nodes = prepared.doc.nodes.filter((n) => !held.has(n)).length;\n    const edges = prepared.doc.edges.filter((e) => !held.has(e)).length;\n    if (nodes + edges > 0) {\n        prepared.report.warning(\n            \"unsupported\",\n            XGMML_ISSUE.ROOT_ONLY_ELEMENTS,\n            `${nodes} node(s) and ${edges} edge(s) belong to no registered network (group meta-edges, collapsed group members) and were not read`,\n        );\n    }\n}\n\n/**\n * Import one graph of an XGMML document.\n * @param input - the document\n * @param sink - the sink\n * @param options - format-specific and common options\n * @returns the report; ImportError when the document cannot be read or the error limit is exceeded\n */\nasync function importXgmml(\n    input: ImportInput,\n    sink: GraphSink,\n    options?: XgmmlImportOptions & CommonImportOptions,\n): Promise<ImportReport> {\n    const prepared = await prepare(input, sink, options);\n    const index = chooseGraph(\n        prepared.graphs.map((g) => graphName(g, prepared.doc)),\n        options,\n        prepared.report,\n    );\n    if (prepared.graphs.length > 1) {\n        prepared.report.warning(\n            \"unsupported\",\n            XGMML_ISSUE.MULTIPLE_GRAPHS,\n            `the session network document holds ${prepared.graphs.length} registered networks; ${prepared.graphs.length - 1} were not read (use importAll, graphIndex or graphName)`,\n        );\n    }\n    return emitOne(prepared, prepared.graphs[index], sink);\n}\n\n/**\n * Import every graph of an XGMML document: each registered subnetwork of a session network\n * document, else the one graph.\n * @param input - the document\n * @param sinkFor - a sink per graph\n * @param options - format-specific and common options\n * @returns one report per graph\n */\nasync function importAllXgmml(\n    input: ImportInput,\n    sinkFor: (index: number) => GraphSink,\n    options?: XgmmlImportOptions & CommonImportOptions,\n): Promise<ImportReport[]> {\n    const bytes = await reread(input);\n    const first = await prepare(bytes, null, options);\n    const reports: ImportReport[] = [];\n    for (let i = 0; i < first.graphs.length; i++) {\n        const sink = sinkFor(i);\n        const prepared = i === 0 ? first : await prepare(bytes, null, options);\n        reportSinkOptions(sink, options, prepared.report, true);\n        reportUnusedOptions(options, prepared.report, USED_OPTIONS);\n        reports.push(emitOne(prepared, prepared.graphs[i], sink));\n    }\n    return reports;\n}\n\n/**\n * List the graphs of an XGMML document without importing them.\n * @param input - the document\n * @param options - the options\n * @returns one listing per graph\n */\nasync function listXgmmlGraphs(\n    input: ImportInput,\n    options?: XgmmlImportOptions & CommonImportOptions,\n): Promise<readonly GraphListing[]> {\n    const prepared = await prepare(input, null, options);\n    return prepared.graphs.map((graph, index) => {\n        const members = membersOf(prepared.doc, prepared.dialect.session ? graph : null);\n        return Object.freeze({\n            index,\n            name: graphName(graph, prepared.doc),\n            nodes: new Set(members.nodes.map((n) => n.id)).size,\n            edges: members.edges.length,\n        });\n    });\n}\n\n/**\n * The name of a graph: its label, else the RDF title (root only), else its id.\n * @param graph - the graph\n * @param doc - the document\n * @returns the name, or null\n */\nfunction graphName(graph: GraphRec, doc: XgmmlDocument): string | null {\n    return graph.label ?? (graph === doc.root ? (doc.rdf.title ?? null) : null) ?? graph.id ?? null;\n}\n\n/**\n * The input in a form that can be read more than once (a stream is read into bytes).\n * @param input - the input\n * @returns the same input when it is a string or bytes, else the collected bytes\n */\nasync function reread(input: ImportInput): Promise<string | Uint8Array> {\n    if (typeof input === \"string\" || input instanceof Uint8Array) {\n        return input;\n    }\n    const parts: (string | Uint8Array)[] = [];\n    const iterable: AsyncIterable<string | Uint8Array> =\n        typeof (input as { getReader?: unknown }).getReader === \"function\"\n            ? streamIterable(input as ReadableStream<Uint8Array>)\n            : (input as AsyncIterable<string | Uint8Array>);\n    for await (const chunk of iterable) {\n        parts.push(chunk);\n    }\n    if (parts.every((p) => typeof p === \"string\")) {\n        return parts.join(\"\");\n    }\n    const bytes = parts.map((p) => (typeof p === \"string\" ? new TextEncoder().encode(p) : p));\n    const out = new Uint8Array(bytes.reduce((n, b) => n + b.byteLength, 0));\n    let at = 0;\n    for (const b of bytes) {\n        out.set(b, at);\n        at += b.byteLength;\n    }\n    return out;\n}\n\n/**\n * A ReadableStream as an async iterable.\n * @param stream - the stream\n * @yields its chunks\n * @returns nothing\n */\nasync function* streamIterable(stream: ReadableStream<Uint8Array>): AsyncGenerator<Uint8Array, void, undefined> {\n    const reader = stream.getReader();\n    try {\n        for (;;) {\n            const { done, value } = await reader.read();\n            if (done) {\n                return;\n            }\n            yield value;\n        }\n    } finally {\n        reader.releaseLock();\n    }\n}\n\n/**\n * Confidence that a head of bytes is XGMML: 0.95 for a root `graph` in the XGMML namespace or an\n * XGMML DOCTYPE (Cytoscape's file filter tests the same two things, and a session view file still\n * scores so its failure names it), 0.5 for a root local name `graph` without either.\n * @param head - the first bytes\n * @returns the confidence\n */\nfunction sniffXgmml(head: Uint8Array): number {\n    const text = new TextDecoder(\"utf-8\", { fatal: false }).decode(head.subarray(0, SNIFF_BYTES));\n    if (!/^\\uFEFF?\\s*</.test(text)) {\n        return 0;\n    }\n    if (XGMML_DOCTYPE.test(text)) {\n        return 0.95;\n    }\n    const root = /<(?!\\?|!)([A-Za-z_][\\w.-]*:)?([A-Za-z_][\\w.-]*)[\\s/>]/.exec(text.replace(/<!--[\\s\\S]*?-->/g, \"\"));\n    if (root === null || root[2] !== \"graph\") {\n        return 0;\n    }\n    const tagEnd = text.indexOf(\">\", root.index);\n    const tag = text.slice(root.index, tagEnd < 0 ? undefined : tagEnd);\n    return tag.includes(\"http://www.cs.rpi.edu/XGMML\") ? 0.95 : 0.5;\n}\n\n/** The XGMML importer. */\nexport const xgmmlImporter: GraphImporter<XgmmlImportOptions> = Object.freeze({\n    format: FORMAT,\n    extensions: EXTENSIONS,\n    mimeTypes: MIME_TYPES,\n    sniff: sniffXgmml,\n    import: importXgmml,\n    importAll: importAllXgmml,\n    listGraphs: 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package/dist/chunks/{importer-Bm1_5vPS.js → importer-eUREhBGj.js}

@@ -1,8 +1,9 @@
 import { GraphFormatError, INVALID_INDEX } from "@graphty/graph-format";
-import { aB as resolveExportOptions, ax as pairFolding, ar as declareResolved, af as UNKNOWN_ENCODING_CODE, r as ENCODING_FALLBACK_CODE, y as INVALID_ENCODING_CODE, z as INVALID_UTF8_CODE, U as OPTION_IGNORED_CODE, a2 as SINK_OPTION_CODE, H as HYPEREDGE_CODE, ac as TOO_LARGE_CODE, D as DANGLING_REFERENCE_CODE, A as AMBIGUOUS_GRAPH_NAME_CODE, G as GRAPH_NOT_FOUND_CODE, O as MULTIPLE_GRAPHS_CODE, u as ID_MERGED_CODE, m as DUPLICATE_EDGE_ID_CODE, o as DUPLICATE_NODE_CODE, ag as UNKNOWN_PARENT_CODE, d as BAD_VALUE_CODE, M as MISSING_ENDPOINT_CODE, K as MISSING_ID_CODE, a8 as SYNTAX_CODE, q as EMPTY_INPUT_CODE, aC as resolveImportOptions, I as ImportReportBuilder, ay as readText, aD as textChunks, az as reportSinkOptions, aA as reportUnusedOptions, t as throwIfAborted, F as IdCoercer, p as DirectionResolver, aE as uniqueColumnName, an as chooseGraph } from "./report-BcWboivV.js";
-import { c as capabilities, L as LOSS, j as joinText, e as encodeChunks, a as checkCapabilities, g as countMixedEdges } from "./writer-DQiKgQJc.js";
-import { e as explicitWeights, a as formatF32, b as formatF64, w as weightFromValue } from "./weights-CwISIpCP.js";
-import { M as MAYBE_UNSAFE_INTEGER, e as rewriteNumbers, g as reviveNonstandard } from "./json-elements-CZY1wiZh.js";
+import { V as resolveExportOptions, X as pairFolding, L as declareResolved, q as UNKNOWN_ENCODING_CODE, E as ENCODING_FALLBACK_CODE, r as INVALID_ENCODING_CODE, s as INVALID_UTF8_CODE, O as OPTION_IGNORED_CODE, S as SINK_OPTION_CODE, an as HYPEREDGE_CODE, T as TOO_LARGE_CODE, j as DANGLING_REFERENCE_CODE, A as AMBIGUOUS_GRAPH_NAME_CODE, G as GRAPH_NOT_FOUND_CODE, M as MULTIPLE_GRAPHS_CODE, I as ID_MERGED_CODE, c as DUPLICATE_EDGE_ID_CODE, d as DUPLICATE_NODE_CODE, U as UNKNOWN_PARENT_CODE, B as BAD_VALUE_CODE, e as MISSING_ENDPOINT_CODE, f as MISSING_ID_CODE, t as SYNTAX_CODE, u as EMPTY_INPUT_CODE, v as resolveImportOptions, w as ImportReportBuilder, aG as readText, x as textChunks, F as reportSinkOptions, z as reportUnusedOptions, y as throwIfAborted, K as IdCoercer, J as DirectionResolver, Q as uniqueColumnName, H as chooseGraph } from "./report-B1z4WT9e.js";
+import { c as capabilities, L as LOSS, a as checkCapabilities, d as countMixedEdges } from "./export-Bh60Dv-n.js";
+import { e as explicitWeights, f as formatF32, a as formatF64, w as weightFromValue } from "./weights-Dzba96G3.js";
+import { f as flipY, M as MAYBE_UNSAFE_INTEGER, e as rewriteNumbers, g as reviveNonstandard } from "./json-elements-DDS8N2Dd.js";
+import { j as joinText, e as encodeChunks } from "./writer-C7flM-Ih.js";
 import { a as OBOGRAPHS_PREDICATE_TAGS, c as compactOboIri, o as oboColumnDecl, P as PLACEHOLDER_COLUMN, s as synonymScopeOf, O as OBO_NODE_COLUMNS } from "./ontology-BnrJ4I98.js";
 const JSON_DIALECTS = Object.freeze([
   "node-link",
@@ -1265,7 +1266,7 @@ function* writeCytoscape(snapshot, p) {
         w.key("position");
         w.open("{");
         w.member("x", numberText(value[0], f32, c.nonfinite));
-        w.member("y", numberText(value[1], f32, c.nonfinite));
+        w.member("y", numberText(flipY(value[1]), f32, c.nonfinite));
         w.close("}");
       }
     }
@@ -1381,9 +1382,11 @@ const GRAPH_FORMATS = Object.freeze([
   "dot",
   "pajek",
   "neo4j",
+  "xgmml",
   "cx2",
   "cx",
-  "obo"
+  "obo",
+  "cys"
 ]);
 const SNIFF_HEAD_BYTES = 8192;
 function extensionOf(filename) {
@@ -3895,7 +3898,7 @@ function importCytoscape(ctx, root) {
       if (position !== void 0 && position !== null) {
         if (isJsonObject(position) && typeof position.x === "number" && typeof position.y === "number") {
           point[0] = position.x;
-          point[1] = position.y;
+          point[1] = flipY(position.y);
           ctx.nodes.set(positionColumn, index, point);
         } else {
           report.error(
@@ -4164,4 +4167,4 @@ export {
   rankFormats as r,
   sniffFormat as s
 };
-//# sourceMappingURL=importer-Bm1_5vPS.js.map
+//# sourceMappingURL=importer-eUREhBGj.js.map