@graphty/graph-io 0.3.18 → 0.3.19

package/dist/src/formats/cx/importer.js

@@ -0,0 +1,2220 @@
+/**
+ * The CX version 1 importer (design/graph-io/cytoscape-and-obo/design.md section 1.2; the feature
+ * and error inventory is research-cx.md): the JSON exchange format of NDEx and Cytoscape's CX
+ * support. A CX document is an array of aspect fragments (`nodes`, `edges`, `nodeAttributes`,
+ * `cartesianLayout`, `cySubNetworks`, `cyGroups`, `cyVisualProperties`, ...) that refer to each
+ * other by integer ids, in any order.
+ *
+ * The document is read through the streaming scanner of common/json-elements.ts, so its text is
+ * never held as one string; the parsed aspect elements are collected and each graph is built at the
+ * end, because a reference may precede what it names.
+ *
+ * Mapping: every edge is directed; ids follow the CX id rule (design section 1.0.2); `n` is the
+ * `name` column (the label), `r` is `represents`, `i` is `interaction`; attributes become columns
+ * typed by their `d` (Cytoscape's value rule: "" and "null" are unset, "NaN" is NaN in a double); a
+ * subnetwork's values are the unscoped ones and its own (`s`), its own winning. A collection (several
+ * `cySubNetworks`) holds one graph per subnetwork: `importAll()` returns them, `import()` reads the
+ * one `graphIndex` / `graphName` picks, `listGraphs()` lists them. Positions come from the
+ * subnetwork's view, y flipped to y-up, `z` into the `z` column; `cyGroups` give `parent` (or
+ * `parents`); per-element visual properties are one column per property (origin namespace
+ * "cx.bypass") and style rules are kept verbatim in `meta.extra.cx` and not applied
+ * (W_STYLES_NOT_IMPORTED, issue #706); provenance aspects become extension tables and list columns.
+ */
+import { INVALID_INDEX, } from "@graphty/graph-format";
+import { declareResolved, uniqueColumnName } from "../../common/attributes.js";
+import { AMBIGUOUS_GRAPH_NAME_CODE, ASPECT_ORDER_CODE, BAD_ASPECT_BLOCK_CODE, BAD_VALUE_CODE, COLUMN_RENAMED_CODE, COUNT_MISMATCH_CODE, DANGLING_REFERENCE_CODE, DIRECTION_FORCED_CODE, DIRECTION_REFUSED_CODE, DUPLICATE_ATTRIBUTE_CODE, DUPLICATE_EDGE_ID_CODE, DUPLICATE_NODE_CODE, EMPTY_INPUT_CODE, ENCODING_FALLBACK_CODE, GRAPH_NOT_FOUND_CODE, ID_MERGED_CODE, ID_TEXT_TYPE_CODE, INVALID_ENCODING_CODE, INVALID_UTF8_CODE, MISSING_ENDPOINT_CODE, MISSING_ID_CODE, MULTIPLE_GRAPHS_CODE, NO_GRAPH_CODE, OPTION_IGNORED_CODE, PARENT_CYCLE_CODE, PRECISION_CODE, ROLE_TAKEN_CODE, SINK_OPTION_CODE, STATUS_FAILED_CODE, STATUS_WARNING_CODE, STYLES_NOT_IMPORTED_CODE, SYNTAX_CODE, TOO_LARGE_CODE, UNKNOWN_ATTR_TYPE_CODE, UNKNOWN_ENCODING_CODE, UNKNOWN_PARENT_CODE, WIDENED_CODE, } from "../../common/codes.js";
+import { DirectionResolver } from "../../common/direction.js";
+import { IdCoercer } from "../../common/ids.js";
+import { textChunks, throwIfAborted } from "../../common/input.js";
+import { cxId, CxStructure, declareFresh, ExactInteger, flipY, inexactLiteral, isRecord, JsonScanError, plainJson, positionDecl, reportTooDeep, scanAspects, zDecl, } from "../../common/json-elements.js";
+import { chooseGraph, reportSinkOptions, reportUnusedOptions, resolveImportOptions, } from "../../common/options.js";
+import { ImportReportBuilder } from "../../common/report.js";
+import { weightFromValue } from "../../common/weights.js";
+import { zAsOption } from "../cx2/importer.js";
+/** The format name. */
+const CX_FORMAT = "cx";
+/** The origin namespace of the per-element visual property columns. */
+const CX_BYPASS_NAMESPACE = "cx.bypass";
+/**
+ * The issue codes the CX importer records (design section 1.2), by name: the codes shared with
+ * the other importers (src/common/codes.ts) and the CX-specific ones. A key is the code without
+ * its severity and format prefixes.
+ */
+export const CX_ISSUE = Object.freeze({
+    /** The input is empty (fatal). */
+    EMPTY_INPUT: EMPTY_INPUT_CODE,
+    /** The text is not JSON (fatal). */
+    SYNTAX: SYNTAX_CODE,
+    /** Invalid UTF-8 (fatal). */
+    INVALID_UTF8: INVALID_UTF8_CODE,
+    /** Invalid bytes in the encoding a BOM or the encoding option chose (fatal). */
+    INVALID_ENCODING: INVALID_ENCODING_CODE,
+    /** Bytes that are not UTF-8 were read as windows-1252. */
+    ENCODING_FALLBACK: ENCODING_FALLBACK_CODE,
+    /** An encoding the platform cannot decode was ignored. */
+    UNKNOWN_ENCODING: UNKNOWN_ENCODING_CODE,
+    /** The document is not a CX array, or it is CX2 (fatal; the message names CX2). */
+    NOT_CX: "E_CX_NOT_CX",
+    /** numberVerification holds another value than 2^48 - 1, or comes twice. */
+    NUMBER_VERIFICATION: "W_CX_NUMBER_VERIFICATION",
+    /** An old Cytoscape aspect name (visualProperties, subNetworks, ...) read under its cy name. */
+    OLD_ASPECT_NAME: "W_CX_OLD_ASPECT_NAME",
+    /** A cyGroups group whose id is not a node: the group node is added. */
+    GROUP_NODE_ADDED: "W_CX_GROUP_NODE_ADDED",
+    /** Nodes or edges of the root network that no subnetwork holds: Cytoscape shows them in no network; not read. */
+    ROOT_ONLY: "W_CX_ROOT_ONLY",
+    /** The producer marked the document as failed (fatal). */
+    STATUS_FAILED: STATUS_FAILED_CODE,
+    /** The producer marked the document as successful with an error text. */
+    STATUS_WARNING: STATUS_WARNING_CODE,
+    /** A member of the array that is not a one-key aspect block, or an element that is not an object. */
+    BAD_ASPECT_BLOCK: BAD_ASPECT_BLOCK_CODE,
+    /** An aspect after the post-metadata or after the status, a third metaData. */
+    ASPECT_ORDER: ASPECT_ORDER_CODE,
+    /** A metaData element count disagrees with what was read. */
+    COUNT_MISMATCH: COUNT_MISMATCH_CODE,
+    /** A value that does not parse as its data type; the cell is unset. */
+    BAD_VALUE: BAD_VALUE_CODE,
+    /** One attribute name with several data types: the column takes the wider one. */
+    WIDENED: WIDENED_CODE,
+    /** A data type CX does not define; the value is kept as text. */
+    UNKNOWN_ATTR_TYPE: UNKNOWN_ATTR_TYPE_CODE,
+    /** An attribute, layout, bypass, subnetwork member, view or provenance entry naming nothing. */
+    DANGLING_REFERENCE: DANGLING_REFERENCE_CODE,
+    /** The same attribute twice on one element (or n and a different name attribute); the later wins. */
+    DUPLICATE_ATTRIBUTE: DUPLICATE_ATTRIBUTE_CODE,
+    /** A group member naming no node. */
+    UNKNOWN_PARENT: UNKNOWN_PARENT_CODE,
+    /** A group membership that would close a parent cycle; dropped. */
+    PARENT_CYCLE: PARENT_CYCLE_CODE,
+    /** The style rules of cyVisualProperties are not applied (issue #706). */
+    STYLES_NOT_IMPORTED: STYLES_NOT_IMPORTED_CODE,
+    /** A node without an @id. */
+    MISSING_ID: MISSING_ID_CODE,
+    /** An edge without s or t. */
+    MISSING_ENDPOINT: MISSING_ENDPOINT_CODE,
+    /** A node id declared twice; the second merges into the first. */
+    DUPLICATE_NODE: DUPLICATE_NODE_CODE,
+    /** An edge id declared twice; the second edge is skipped. */
+    DUPLICATE_EDGE_ID: DUPLICATE_EDGE_ID_CODE,
+    /** An id that is not an integer. */
+    INVALID_ID: "E_INVALID_ID",
+    /** An edge endpoint naming no node of the graph (addMissingNodes false, the default). */
+    UNKNOWN_NODE: "E_UNKNOWN_NODE",
+    /** A weight that is not a number. */
+    INVALID_WEIGHT: "E_INVALID_WEIGHT",
+    /** An id spelled as a string or a non-integer literal; read as the integer. */
+    ID_TEXT_TYPE: ID_TEXT_TYPE_CODE,
+    /** An integer beyond 2^53: an id kept as its digits, a value stored as the nearest f64. */
+    PRECISION: PRECISION_CODE,
+    /** Two id texts merged under `ids: "number"`. */
+    ID_MERGED: ID_MERGED_CODE,
+    /** A collection read by import(): the other subnetworks are skipped. */
+    MULTIPLE_GRAPHS: MULTIPLE_GRAPHS_CODE,
+    /** graphIndex or graphName names no subnetwork (fatal). */
+    GRAPH_NOT_FOUND: GRAPH_NOT_FOUND_CODE,
+    /** graphName names several subnetworks (fatal). */
+    AMBIGUOUS_GRAPH_NAME: AMBIGUOUS_GRAPH_NAME_CODE,
+    /** The input holds no graph (fatal). */
+    NO_GRAPH: NO_GRAPH_CODE,
+    /** A column renamed because its name was taken. */
+    COLUMN_RENAMED: COLUMN_RENAMED_CODE,
+    /** A column that lost its role because another column holds it. */
+    ROLE_TAKEN: ROLE_TAKEN_CODE,
+    /** The sink refused the direction. */
+    DIRECTION_REFUSED: DIRECTION_REFUSED_CODE,
+    /** Edges forced to the policy's direction. */
+    DIRECTION_FORCED: DIRECTION_FORCED_CODE,
+    /** A common option CX has no use for. */
+    OPTION_IGNORED: OPTION_IGNORED_CODE,
+    /** A builder option the caller's sink does not honour. */
+    SINK_OPTION: SINK_OPTION_CODE,
+    /** The input is beyond a size limit (fatal). */
+    TOO_LARGE: TOO_LARGE_CODE,
+});
+const USED_OPTIONS = new Set([
+    "ids",
+    "addMissingNodes",
+    "duplicateEdges",
+    "selfLoops",
+    "onMixedDirection",
+    "weightFrom",
+    "weightDtype",
+    "long",
+    "errorLimit",
+    "signal",
+    "onProgress",
+]);
+/** CX has no undirected edge: defaultDirected never applies (reported W_OPTION_IGNORED). */
+const FORMAT_DEFAULTS = {
+    ids: "keep",
+    defaultDirected: true,
+    weightFrom: "weight",
+    addMissingNodes: false,
+};
+const ABORT_CHECK_INTERVAL = 64;
+/** The numberVerification values a reader accepts: 2^48 - 1 and Java's Long.MAX_VALUE. */
+const NUMBER_VERIFICATION_VALUES = new Set(["281474976710655", "9223372036854775807"]);
+/** Old Cytoscape aspect names and the names they are read under. */
+const OLD_ASPECT_NAMES = {
+    visualProperties: "cyVisualProperties",
+    subNetworks: "cySubNetworks",
+    networkRelations: "cyNetworkRelations",
+    hiddenAttributes: "cyHiddenAttributes",
+};
+/** The aspects the importer reads into the graph (everything else is kept verbatim). */
+const READ_ASPECTS = new Set([
+    "nodes",
+    "edges",
+    "nodeAttributes",
+    "edgeAttributes",
+    "networkAttributes",
+    "cartesianLayout",
+    "cySubNetworks",
+    "cyNetworkRelations",
+    "cyViews",
+    "cyGroups",
+    "cyVisualProperties",
+    "cyTableColumn",
+    "citations",
+    "supports",
+    "nodeCitations",
+    "edgeCitations",
+    "nodeSupports",
+    "edgeSupports",
+    "functionTerms",
+    "reifiedEdges",
+    "numberVerification",
+    "metaData",
+    "status",
+]);
+/** The aspects also kept verbatim in meta.extra.cx although they are read. */
+const ALSO_KEPT = new Set([
+    "cySubNetworks",
+    "cyNetworkRelations",
+    "cyViews",
+    "cyVisualProperties",
+    "cyTableColumn",
+    "numberVerification",
+    "metaData",
+]);
+/** Cytoscape's table-cell style aspects (both spellings): style rules, kept and reported, never read. */
+const TABLE_STYLE_ASPECTS = ["tableVisualProperties", "cyTableVisualProperties"];
+/** The first keys that make a head CX for sure, and the other aspect names a CX document may start with. */
+const CX_FIRST_KEYS = ["numberVerification", "metaData"];
+const CX_ASPECT_KEYS = [
+    "nodes",
+    "edges",
+    "nodeAttributes",
+    "edgeAttributes",
+    "networkAttributes",
+    "cartesianLayout",
+    "@context",
+    "cySubNetworks",
+    "subNetworks",
+    "cyNetworkRelations",
+    "networkRelations",
+    "cyVisualProperties",
+    "visualProperties",
+    "cyHiddenAttributes",
+    "hiddenAttributes",
+    "cyTableColumn",
+    "cyGroups",
+    "cyViews",
+    "ndexStatus",
+    "provenanceHistory",
+    "citations",
+    "supports",
+    "functionTerms",
+];
+/** The CX data types, with the Java reader's float aliases. */
+const SCALARS = {
+    string: "string",
+    boolean: "boolean",
+    integer: "integer",
+    long: "long",
+    double: "double",
+    float: "double",
+};
+/**
+ * Resolve a `d` value.
+ * @param d - the data type (undefined: string)
+ * @returns the type, or null when CX does not define it
+ */
+function cxType(d) {
+    if (d === undefined || d === null) {
+        return { scalar: "string", list: false };
+    }
+    if (typeof d !== "string") {
+        return null;
+    }
+    const list = d.startsWith("list_of_");
+    const scalar = SCALARS[list ? d.slice("list_of_".length) : d];
+    return scalar === undefined ? null : { scalar, list };
+}
+/**
+ * The type text of a type.
+ * @param type - the type
+ * @returns `list_of_double`, `string`, ...
+ */
+function typeText(type) {
+    return type.list ? `list_of_${type.scalar}` : type.scalar;
+}
+/** The widening rank of the scalar types (design 5.1 order; boolean and numbers widen to string). */
+const RANK = { boolean: 0, integer: 1, long: 2, double: 3, string: 4 };
+/**
+ * Widen two types to one that holds both.
+ * @param a - the type so far
+ * @param b - another type
+ * @returns the wider type, or null when they cannot share a column (a list and a scalar)
+ */
+function widenType(a, b) {
+    if (a.list !== b.list) {
+        return null;
+    }
+    if (a.scalar === b.scalar) {
+        return a;
+    }
+    const numeric = (s) => s === "integer" || s === "long" || s === "double";
+    if (numeric(a.scalar) && numeric(b.scalar)) {
+        return RANK[a.scalar] > RANK[b.scalar] ? a : b;
+    }
+    return { scalar: "string", list: a.list };
+}
+/** What parseValue() returns for a value that does not parse. */
+const BAD = Symbol("bad");
+/** What parseValue() returns for a value Cytoscape reads as null ("", "null"). */
+const UNSET = Symbol("unset");
+const I32_MIN = -2147483648;
+const I32_MAX = 2147483647;
+const INTEGER_TEXT = /^-?[0-9]+$/;
+const DECIMAL_TEXT = /^-?([0-9]+(\.[0-9]*)?|\.[0-9]+)([eE][+-]?[0-9]+)?$/;
+/**
+ * Whether a text is Cytoscape's null: the empty string or "null" in any case.
+ * @param text - the text
+ * @returns true for a null text
+ */
+function isNullText(text) {
+    return text === "" || text.toLowerCase() === "null";
+}
+/**
+ * Parse one scalar value (or list item) of a CX attribute by its type, with Cytoscape's value
+ * rule: "" and "null" are unset, "NaN" is NaN in a double (unset in an integer or long), native JSON
+ * numbers and booleans are accepted, anything else that does not parse is BAD.
+ * @param value - the value (never null)
+ * @param scalar - the type
+ * @param long - the importer's `long` option
+ * @param onPrecision - called for a long beyond 2^53
+ * @returns the value, UNSET or BAD
+ */
+function parseScalar(value, scalar, long, onPrecision) {
+    if (value instanceof ExactInteger) {
+        if (scalar === "string" || (scalar === "long" && long === "string")) {
+            return value.digits;
+        }
+        if (scalar === "long" || scalar === "double") {
+            if (scalar === "long") {
+                onPrecision(value.digits);
+            }
+            return Number(value.digits);
+        }
+        return BAD;
+    }
+    if (typeof value === "number" || typeof value === "boolean") {
+        return parseNative(value, scalar, long);
+    }
+    if (typeof value !== "string") {
+        return BAD;
+    }
+    if (scalar === "string") {
+        return value;
+    }
+    if (isNullText(value)) {
+        return UNSET;
+    }
+    switch (scalar) {
+        case "boolean": {
+            const lower = value.toLowerCase();
+            if (lower === "true" || lower === "false") {
+                return lower === "true";
+            }
+            return BAD;
+        }
+        case "integer":
+        case "long": {
+            if (value === "NaN") {
+                return UNSET;
+            }
+            if (!INTEGER_TEXT.test(value)) {
+                return BAD;
+            }
+            const n = Number(value);
+            if (scalar === "integer") {
+                return n >= I32_MIN && n <= I32_MAX ? n : BAD;
+            }
+            if (long === "string") {
+                return value;
+            }
+            if (!Number.isSafeInteger(n)) {
+                onPrecision(value);
+            }
+            return n;
+        }
+        default: {
+            if (value === "NaN" || value === "nan") {
+                return NaN;
+            }
+            if (value === "Infinity" || value === "-Infinity") {
+                return Number(value);
+            }
+            return DECIMAL_TEXT.test(value) ? Number(value) : BAD;
+        }
+    }
+}
+/**
+ * Parse a native JSON number or boolean by a type.
+ * @param value - the value
+ * @param scalar - the type
+ * @param long - the importer's `long` option
+ * @returns the value or BAD
+ */
+function parseNative(value, scalar, long) {
+    switch (scalar) {
+        case "string":
+            return String(value);
+        case "boolean":
+            return typeof value === "boolean" ? value : BAD;
+        case "integer":
+            return typeof value === "number" && Number.isInteger(value) && value >= I32_MIN && value <= I32_MAX
+                ? value
+                : BAD;
+        case "long":
+            if (typeof value !== "number" || !Number.isInteger(value)) {
+                return BAD;
+            }
+            return long === "string" ? String(value) : value;
+        default:
+            return typeof value === "number" ? value : BAD;
+    }
+}
+/**
+ * Parse an attribute value by its type: a scalar, or a list whose items parse one by one (a null
+ * item is NaN in a double list and BAD elsewhere).
+ * @param value - the value (never null)
+ * @param type - the type
+ * @param long - the importer's `long` option
+ * @param onPrecision - called for a long beyond 2^53
+ * @returns the value, UNSET or BAD
+ */
+function parseValue(value, type, long, onPrecision) {
+    if (Array.isArray(value) !== type.list) {
+        return BAD;
+    }
+    if (!type.list) {
+        return parseScalar(value, type.scalar, long, onPrecision);
+    }
+    const out = [];
+    for (const item of value) {
+        let parsed = item === null ? UNSET : parseScalar(item, type.scalar, long, onPrecision);
+        if (parsed === UNSET) {
+            parsed = type.scalar === "double" ? NaN : BAD;
+        }
+        if (parsed === BAD) {
+            return BAD;
+        }
+        out.push(parsed);
+    }
+    return out;
+}
+/**
+ * The column dtype of a type.
+ * @param scalar - the scalar type
+ * @param long - the importer's `long` option
+ * @returns the dtype
+ */
+function scalarDtype(scalar, long) {
+    switch (scalar) {
+        case "boolean":
+            return "bool";
+        case "integer":
+            return "i32";
+        case "long":
+            return long === "string" ? "string" : "f64";
+        case "double":
+            return "f64";
+        default:
+            return "string";
+    }
+}
+/**
+ * A parsed value converted to the column's type (a narrower value in a widened column).
+ * @param value - the parsed value
+ * @param type - the column's type
+ * @returns the value to store
+ */
+function toColumn(value, type) {
+    if (type.scalar !== "string") {
+        return value;
+    }
+    if (type.list) {
+        return value.map((item) => (typeof item === "string" ? item : String(item)));
+    }
+    return typeof value === "string" ? value : String(value);
+}
+/**
+ * A short JSON rendering of a value for a message.
+ * @param value - the value
+ * @returns the text, at most 60 characters
+ */
+function shown(value) {
+    if (value instanceof ExactInteger) {
+        return value.digits;
+    }
+    let text;
+    try {
+        text = JSON.stringify(value) ?? String(value);
+    }
+    catch {
+        text = String(value);
+    }
+    return text.length > 60 ? `${text.slice(0, 57)}...` : text;
+}
+/**
+ * The elements of a read aspect.
+ * @param doc - the document
+ * @param name - the aspect
+ * @returns the elements, empty when absent
+ */
+function aspect(doc, name) {
+    return doc.aspects.get(name) ?? [];
+}
+/**
+ * The inexact-literal bits of an element.
+ * @param text - the element's JSON text
+ * @param keys - the id keys to check, bit 1, 2, 4 in order
+ * @returns the bits
+ */
+function inexactBits(text, keys) {
+    if (!/[0-9][.eE]/.test(text)) {
+        return 0;
+    }
+    let bits = 0;
+    keys.forEach((key, i) => {
+        if (inexactLiteral(text, key)) {
+            bits |= 1 << i;
+        }
+    });
+    return bits;
+}
+/**
+ * The attribute map of an attribute aspect.
+ * @param doc - the document
+ * @param name - the aspect name
+ * @returns the map, or null for another aspect
+ */
+function attributeTable(doc, name) {
+    switch (name) {
+        case "nodeAttributes":
+            return doc.attributes.node;
+        case "edgeAttributes":
+            return doc.attributes.edge;
+        case "networkAttributes":
+            return doc.attributes.network;
+        default:
+            return null;
+    }
+}
+/**
+ * Check a numberVerification element: 2^48 - 1 (or Java's Long.MAX_VALUE), and only one.
+ * @param value - the element
+ * @param count - how many numberVerification elements were read, this one included
+ * @param report - the report
+ * @param line - its line
+ */
+function checkNumberVerification(value, count, report, line) {
+    const raw = isRecord(value) ? value.longNumber : undefined;
+    const digits = raw instanceof ExactInteger ? raw.digits : String(raw);
+    if (count > 1 || !NUMBER_VERIFICATION_VALUES.has(digits)) {
+        report.warning("validation-error", CX_ISSUE.NUMBER_VERIFICATION, count > 1
+            ? "a second numberVerification element; ignored"
+            : `numberVerification holds ${shown(raw === undefined ? null : digits)}, not 281474976710655`, { line, element: "numberVerification" });
+    }
+}
+/**
+ * Read the whole document through the streaming scanner, checking its structure.
+ * @param input - the input
+ * @param report - the report
+ * @param options - the resolved options
+ * @returns what was read
+ */
+async function readDocument(input, report, options) {
+    const structure = new CxStructure(report);
+    const doc = {
+        aspects: new Map(),
+        attributes: { node: new Map(), edge: new Map(), network: new Map() },
+        kept: new Map(),
+        structure,
+    };
+    let sinceCheck = 0;
+    let verifications = 0;
+    const canonical = (name, line) => {
+        const renamed = OLD_ASPECT_NAMES[name];
+        if (renamed === undefined) {
+            return name;
+        }
+        report.warnOnce("coercion", CX_ISSUE.OLD_ASPECT_NAME, `the old aspect name "${name}" is read as "${renamed}"`, { line, element: name }, `${CX_ISSUE.OLD_ASPECT_NAME}:${name}`);
+        return renamed;
+    };
+    const collect = (name, value, text, line, exact) => {
+        structure.element(name, value, line);
+        if (ALSO_KEPT.has(name) || !READ_ASPECTS.has(name)) {
+            if (!doc.kept.has(name)) {
+                doc.kept.set(name, []);
+            }
+            doc.kept.get(name)?.push(exact ? plainJson(value) : value);
+        }
+        if (!READ_ASPECTS.has(name) || name === "metaData" || name === "status") {
+            return;
+        }
+        if (name === "numberVerification") {
+            checkNumberVerification(value, ++verifications, report, line);
+            return;
+        }
+        let inexact = 0;
+        if (name === "nodes") {
+            inexact = inexactBits(text, ["@id"]);
+        }
+        else if (name === "edges") {
+            inexact = inexactBits(text, ["@id", "s", "t"]);
+        }
+        const held = { value, line, inexact };
+        const table = attributeTable(doc, name);
+        if (table !== null) {
+            if (!isRecord(value) || typeof value.n !== "string") {
+                report.error("missing-value", MISSING_ID_CODE, `a ${name} element has no attribute name n; skipped`, {
+                    line,
+                    element: name,
+                });
+                return;
+            }
+            const key = value.n;
+            if (!table.has(key)) {
+                table.set(key, []);
+            }
+            table.get(key)?.push(held);
+            return;
+        }
+        if (!doc.aspects.has(name)) {
+            doc.aspects.set(name, []);
+        }
+        doc.aspects.get(name)?.push(held);
+    };
+    try {
+        for await (const event of scanAspects(textChunks(input, report, options))) {
+            if (++sinceCheck >= ABORT_CHECK_INTERVAL) {
+                sinceCheck = 0;
+                throwIfAborted(options.signal);
+            }
+            switch (event.kind) {
+                case "root":
+                    report.fail(CX_ISSUE.NOT_CX, `a CX document is a JSON array of aspects; found ${isRecord(event.value) ? "an object" : shown(event.value)}`, { line: event.line });
+                    break;
+                case "member": {
+                    const { value } = event;
+                    if (isRecord(value) && "CXVersion" in value) {
+                        report.fail(CX_ISSUE.NOT_CX, `the document is CX2 (CXVersion ${shown(value.CXVersion)}), not CX version 1; read it with the cx2 importer`, { line: event.line });
+                    }
+                    const keys = isRecord(value) ? Object.keys(value) : [];
+                    if (isRecord(value) && keys.length === 1 && isRecord(value[keys[0]])) {
+                        const name = canonical(keys[0], event.line);
+                        structure.block(name, event.line);
+                        collect(name, value[keys[0]], "", event.line, event.exact);
+                        break;
+                    }
+                    report.error("parse-error", BAD_ASPECT_BLOCK_CODE, `a member of the document is ${keys.length > 1 ? `an object with ${keys.length} keys (${keys.join(", ")})` : shown(value)}, not a one-key aspect fragment; skipped`, { line: event.line, element: keys[0] ?? null });
+                    break;
+                }
+                case "block":
+                    structure.block(canonical(event.aspect, event.line), event.line);
+                    break;
+                case "element": {
+                    const name = OLD_ASPECT_NAMES[event.aspect] ?? event.aspect;
+                    collect(name, event.value, event.text, event.line, event.exact);
+                    break;
+                }
+                case "deep":
+                    reportTooDeep(report, event);
+                    break;
+                case "extraKeys":
+                    report.error("parse-error", BAD_ASPECT_BLOCK_CODE, `the "${event.aspect}" fragment holds more keys (${event.keys.join(", ")}); a fragment has one key, the others are skipped`, { line: event.line, element: event.aspect });
+                    break;
+                default:
+                    break;
+            }
+        }
+    }
+    catch (err) {
+        if (err instanceof JsonScanError) {
+            report.fail(err.empty ? EMPTY_INPUT_CODE : SYNTAX_CODE, err.message, { line: err.line });
+        }
+        throw err;
+    }
+    structure.checkCounts();
+    return doc;
+}
+/**
+ * An id of a reference, or null when it is not one.
+ * @param raw - the parsed reference
+ * @returns the id
+ */
+function refId(raw) {
+    try {
+        return cxId(raw).id;
+    }
+    catch {
+        return null;
+    }
+}
+/**
+ * A member list: the ids of an array, or null for "all".
+ * @param raw - the list
+ * @returns the set, or null for every element
+ */
+function memberSet(raw) {
+    if (raw === "all") {
+        return null;
+    }
+    const out = new Set();
+    if (Array.isArray(raw)) {
+        for (const item of raw) {
+            const id = refId(item);
+            if (id !== null) {
+                out.add(id);
+            }
+        }
+    }
+    return out;
+}
+/**
+ * The graphs of a document, in the order Cytoscape opens them.
+ * @param doc - the document
+ * @returns one plan per graph (at least one)
+ */
+function graphPlans(doc) {
+    const subs = new Map();
+    for (const { value } of aspect(doc, "cySubNetworks")) {
+        const id = isRecord(value) ? refId(value["@id"]) : null;
+        if (id !== null && isRecord(value) && !subs.has(id)) {
+            subs.set(id, { nodes: memberSet(value.nodes), edges: memberSet(value.edges) });
+        }
+    }
+    const relationNames = new Map();
+    const order = [];
+    const views = new Map();
+    const addView = (sub, view) => {
+        const list = views.get(sub) ?? [];
+        if (!list.includes(view)) {
+            list.push(view);
+        }
+        views.set(sub, list);
+    };
+    for (const { value } of aspect(doc, "cyNetworkRelations")) {
+        if (!isRecord(value)) {
+            continue;
+        }
+        const child = refId(value.c);
+        if (child === null) {
+            continue;
+        }
+        if (value.r === "view") {
+            const parent = refId(value.p);
+            if (parent !== null) {
+                addView(parent, child);
+            }
+            continue;
+        }
+        if (typeof value.name === "string") {
+            relationNames.set(child, value.name);
+        }
+        if (subs.has(child) && !order.includes(child)) {
+            order.push(child);
+        }
+    }
+    for (const { value } of aspect(doc, "cyViews")) {
+        const view = isRecord(value) ? refId(value["@id"]) : null;
+        const sub = isRecord(value) ? refId(value.s) : null;
+        if (view !== null && sub !== null) {
+            addView(sub, view);
+        }
+    }
+    for (const id of subs.keys()) {
+        if (!order.includes(id)) {
+            order.push(id);
+        }
+    }
+    const networkName = (sub) => {
+        let found = null;
+        for (const { value } of doc.attributes.network.get("name") ?? []) {
+            if (!isRecord(value) || typeof value.v !== "string") {
+                continue;
+            }
+            const scope = value.s === undefined ? null : refId(value.s);
+            if (scope === sub) {
+                return value.v;
+            }
+            if (scope === null) {
+                found ?? (found = value.v);
+            }
+        }
+        return found;
+    };
+    if (order.length <= 1) {
+        const sub = order.length === 1 ? order[0] : null;
+        const members = sub === null ? undefined : subs.get(sub);
+        let graphViews = sub === null ? [] : (views.get(sub) ?? []);
+        if (graphViews.length === 0) {
+            graphViews = [...new Set([...views.values()].flat())];
+        }
+        if (graphViews.length === 0) {
+            graphViews = layoutViews(doc);
+        }
+        return [
+            {
+                index: 0,
+                name: (sub === null ? null : (relationNames.get(sub) ?? null)) ?? networkName(sub),
+                subnetwork: sub,
+                nodes: members?.nodes ?? null,
+                edges: members?.edges ?? null,
+                views: graphViews,
+            },
+        ];
+    }
+    return order.map((sub, index) => ({
+        index,
+        name: relationNames.get(sub) ?? networkName(sub),
+        subnetwork: sub,
+        nodes: subs.get(sub)?.nodes ?? null,
+        edges: subs.get(sub)?.edges ?? null,
+        views: views.get(sub) ?? [],
+    }));
+}
+/**
+ * The distinct views the layout entries name, in order of appearance.
+ * @param doc - the document
+ * @returns the view ids
+ */
+function layoutViews(doc) {
+    const out = [];
+    for (const { value } of aspect(doc, "cartesianLayout")) {
+        const view = isRecord(value) && value.view !== undefined ? refId(value.view) : null;
+        if (view !== null && !out.includes(view)) {
+            out.push(view);
+        }
+    }
+    return out;
+}
+/**
+ * How many elements a member set holds.
+ * @param members - the set, or null for every element
+ * @param total - the element count of the root network
+ * @returns the count
+ */
+function memberCount(members, total) {
+    return members === null ? total : members.size;
+}
+/** Reads one graph of a collected document into a sink. */
+class CxReader {
+    /**
+     * Create the reader.
+     * @param sink - the sink
+     * @param report - the report
+     * @param options - the resolved options
+     * @param zAs - where z goes
+     * @param doc - the collected document
+     * @param plan - the graph to read
+     */
+    constructor(sink, report, options, zAs, doc, plan) {
+        /** Every node id of the root network. */
+        this.rootNodes = new Set();
+        /** Every edge id of the root network. */
+        this.rootEdges = new Set();
+        /** CX node id -> sink node index, for this graph. */
+        this.nodeRows = new Map();
+        /** CX edge id -> sink edge index, for this graph. */
+        this.edgeRows = new Map();
+        /** The subnetwork ids of the document. */
+        this.subnetworks = new Set();
+        this.dangling = new Map();
+        this.nameHandle = INVALID_INDEX;
+        this.representsHandle = INVALID_INDEX;
+        this.interactionHandle = INVALID_INDEX;
+        this.edgeIdHandle = INVALID_INDEX;
+        this.sinceCheck = 0;
+        this.idType = "integer";
+        this.weighted = false;
+        /** The core field values written per row (n, r), to detect a differing name attribute. */
+        this.coreValues = new Map();
+        /** The weight attribute values of the edges, by edge id (built once). */
+        this.weights = null;
+        this.sink = sink;
+        this.report = report;
+        this.options = options;
+        this.zAs = zAs;
+        this.doc = doc;
+        this.plan = plan;
+        this.direction = new DirectionResolver(sink, report, options.onMixedDirection);
+        this.coercer = new IdCoercer(options.ids);
+        for (const { value } of aspect(doc, "nodes")) {
+            const id = isRecord(value) ? refId(value["@id"]) : null;
+            if (id !== null) {
+                this.rootNodes.add(id);
+            }
+        }
+        for (const { value } of aspect(doc, "edges")) {
+            const id = isRecord(value) ? refId(value["@id"]) : null;
+            if (id !== null) {
+                this.rootEdges.add(id);
+            }
+        }
+        for (const { value } of aspect(doc, "cySubNetworks")) {
+            const id = isRecord(value) ? refId(value["@id"]) : null;
+            if (id !== null) {
+                this.subnetworks.add(id);
+            }
+        }
+    }
+    /** Build the graph. */
+    build() {
+        const { report } = this;
+        this.direction.setHeader(true);
+        this.checkMembers();
+        this.checkRootOnly();
+        const nodeColumns = this.declareAttributes("node");
+        this.readNodes();
+        this.readGroups();
+        this.writeAttributes("node", nodeColumns);
+        this.readLayout();
+        const edgeColumns = this.declareAttributes("edge");
+        this.readEdges();
+        this.writeAttributes("edge", edgeColumns);
+        this.readNetworkAttributes();
+        this.readVisualProperties();
+        this.readProvenance();
+        for (const [kind, count] of this.dangling) {
+            report.warning("validation-error", DANGLING_REFERENCE_CODE, `${count} ${kind}(s) name nothing; ignored`, {
+                element: kind,
+            });
+        }
+        this.setMeta();
+    }
+    // ------------------------------------------------------------ helpers
+    /**
+     * Count a reference that names nothing.
+     * @param kind - what referred
+     */
+    dangle(kind) {
+        this.dangling.set(kind, (this.dangling.get(kind) ?? 0) + 1);
+    }
+    /** Check the cancellation signal every ABORT_CHECK_INTERVAL elements. */
+    checkAbort() {
+        if (++this.sinceCheck >= ABORT_CHECK_INTERVAL) {
+            this.sinceCheck = 0;
+            throwIfAborted(this.options.signal);
+        }
+    }
+    /**
+     * Whether a node id belongs to this graph.
+     * @param id - the CX id
+     * @returns true for a member
+     */
+    inGraph(id) {
+        return this.plan.nodes === null || this.plan.nodes.has(id);
+    }
+    /**
+     * Whether a scoped value applies to this graph: unscoped, or scoped to its subnetwork. A scope
+     * naming no subnetwork is counted as dangling.
+     * @param scope - the element's s
+     * @returns 1 for an unscoped value, 2 for this graph's own, 0 for another graph's
+     */
+    scopeOf(scope) {
+        if (scope === undefined || scope === null) {
+            return 1;
+        }
+        const id = refId(scope);
+        if (id !== null && id === this.plan.subnetwork) {
+            return 2;
+        }
+        if (id === null || !this.subnetworks.has(id)) {
+            this.dangle("attribute subnetwork reference");
+        }
+        return 0;
+    }
+    /**
+     * The id of an element, by the CX id rule and the `ids` option.
+     * @param raw - the parsed id
+     * @param inexact - whether the literal was not a plain integer
+     * @param element - the element name for issues
+     * @param edgeId - whether this is an edge's own id (stored in the f64 id column, not kept as digits)
+     * @returns the id, or null when it was reported
+     */
+    idOf(raw, inexact, element, edgeId = false) {
+        try {
+            const parsed = cxId(raw, inexact);
+            if (parsed.note === "text") {
+                this.report.warnOnce("coercion", ID_TEXT_TYPE_CODE, `${element}: the id ${shown(raw)} is not written as an integer; read as ${String(parsed.id)}`, { element });
+            }
+            else if (parsed.note === "precision" && edgeId) {
+                // the edge is told apart by its digits, but the id column is f64
+                this.report.warnOnce("precision", PRECISION_CODE, `${element}: the edge id ${String(parsed.id)} is beyond 2^53; the id column holds the nearest double`, { element }, `${PRECISION_CODE}:edge`);
+            }
+            else if (parsed.note === "precision") {
+                this.idType = "mixed";
+                this.report.warnOnce("precision", PRECISION_CODE, `${element}: the id ${String(parsed.id)} is beyond 2^53; kept as its digits (a string id)`, { element });
+            }
+            return this.options.ids === "keep" ? parsed.id : this.coercer.value(parsed.id);
+        }
+        catch (err) {
+            this.report.recordError(err, { element });
+            return null;
+        }
+    }
+    /**
+     * Record a long value beyond 2^53 (once).
+     * @param name - the attribute
+     * @param digits - the value
+     */
+    precision(name, digits) {
+        this.report.warnOnce("precision", PRECISION_CODE, `"${name}": ${digits} is beyond 2^53; stored as the nearest double`, { element: name }, `${PRECISION_CODE}:value`);
+    }
+    /** Count the subnetwork members that name no node or edge. */
+    checkMembers() {
+        for (const id of this.plan.nodes ?? []) {
+            if (!this.rootNodes.has(id)) {
+                this.dangle("subnetwork node member");
+            }
+        }
+        for (const id of this.plan.edges ?? []) {
+            if (!this.rootEdges.has(id)) {
+                this.dangle("subnetwork edge member");
+            }
+        }
+    }
+    /**
+     * Report the root network's nodes and edges that no subnetwork holds (W_CX_ROOT_ONLY): they
+     * belong to no graph Cytoscape opens, so no graph of this file reads them.
+     */
+    checkRootOnly() {
+        const subs = aspect(this.doc, "cySubNetworks");
+        if (subs.length === 0) {
+            return;
+        }
+        const held = { nodes: new Set(), edges: new Set() };
+        const all = { nodes: false, edges: false };
+        for (const { value } of subs) {
+            if (!isRecord(value)) {
+                continue;
+            }
+            for (const key of ["nodes", "edges"]) {
+                const members = memberSet(value[key]);
+                if (members === null) {
+                    all[key] = true;
+                }
+                else {
+                    members.forEach((id) => held[key].add(id));
+                }
+            }
+        }
+        const lost = (key, root) => all[key] ? 0 : [...root].filter((id) => !held[key].has(id)).length;
+        const nodes = lost("nodes", this.rootNodes);
+        const edges = lost("edges", this.rootEdges);
+        if (nodes + edges > 0) {
+            this.report.warning("unsupported", CX_ISSUE.ROOT_ONLY, `${nodes} node(s) and ${edges} edge(s) of the root network belong to no subnetwork (cySubNetworks); they are not read`, { element: "cySubNetworks" });
+        }
+    }
+    /**
+     * The handle of a structural column, declared on first use.
+     * @param domain - node or edge
+     * @param current - the handle so far
+     * @param decl - the declaration
+     * @returns the handle
+     */
+    structural(domain, current, decl) {
+        return current === INVALID_INDEX ? declareResolved(this.sink, domain, decl, this.report).handle : current;
+    }
+    // ------------------------------------------------------------ attribute columns
+    /**
+     * Type and declare the attribute columns of a table for this graph: each name's type is the
+     * wider of the types its applicable elements and its cyTableColumn entries give (W_WIDENED when
+     * they differ); a name with a type CX does not define keeps its values as text.
+     * @param domain - node or edge
+     * @returns the columns by attribute name
+     */
+    declareAttributes(domain) {
+        const columns = new Map();
+        const declared = this.tableColumns(domain === "node" ? "node_table" : "edge_table");
+        const names = new Set([...declared.keys(), ...this.doc.attributes[domain].keys()]);
+        for (const name of names) {
+            if (name === "" || (domain === "edge" && name === this.options.weightFrom)) {
+                continue;
+            }
+            const types = [];
+            let unknown = false;
+            const tableType = declared.get(name);
+            if (tableType !== undefined) {
+                types.push(tableType);
+            }
+            for (const { value } of this.doc.attributes[domain].get(name) ?? []) {
+                if (!isRecord(value) || this.scopePeek(value.s) === 0) {
+                    continue;
+                }
+                const type = cxType(value.d);
+                if (type === null) {
+                    unknown = true;
+                    continue;
+                }
+                if (!types.some((t) => t.scalar === type.scalar && t.list === type.list)) {
+                    types.push(type);
+                }
+            }
+            if (unknown) {
+                this.report.warnOnce("unsupported", UNKNOWN_ATTR_TYPE_CODE, `a ${domain} attribute "${name}" declares a data type CX does not define; its values are kept as text`, { element: name }, `${UNKNOWN_ATTR_TYPE_CODE}:${domain}:${name}`);
+                types.push({ scalar: "string", list: false });
+            }
+            let type = types[0] ?? { scalar: "string", list: false };
+            for (const other of types.slice(1)) {
+                type = type === null ? null : widenType(type, other);
+            }
+            if (types.length > 1) {
+                this.report.warnOnce("coercion", WIDENED_CODE, `the ${domain} attribute "${name}" has the data types ${types.map(typeText).join(", ")}; the column holds ${type === null ? "their values as JSON" : typeText(type)}`, { element: name }, `${WIDENED_CODE}:${domain}:${name}`);
+            }
+            if (this.isStructural(domain, name)) {
+                columns.set(name, {
+                    name,
+                    type: { scalar: "string", list: false },
+                    handle: INVALID_INDEX,
+                });
+                continue;
+            }
+            columns.set(name, { name, type, handle: this.declareColumn(domain, name, type) });
+        }
+        return columns;
+    }
+    /**
+     * Whether an attribute name is the column of a core field (n / r on nodes, i on edges).
+     * @param domain - node or edge
+     * @param name - the attribute name
+     * @returns true for name, represents and interaction
+     */
+    isStructural(domain, name) {
+        return domain === "node" ? name === "name" || name === "represents" : name === "interaction";
+    }
+    /**
+     * The scope of a value without counting a dangling one (for typing, which runs before the values).
+     * @param scope - the element's s
+     * @returns as scopeOf()
+     */
+    scopePeek(scope) {
+        if (scope === undefined || scope === null) {
+            return 1;
+        }
+        const id = refId(scope);
+        return id !== null && id === this.plan.subnetwork ? 2 : 0;
+    }
+    /**
+     * The column types cyTableColumn declares for one table and this graph.
+     * @param table - node_table, edge_table or network_table
+     * @returns name -> type
+     */
+    tableColumns(table) {
+        const out = new Map();
+        for (const { value } of aspect(this.doc, "cyTableColumn")) {
+            if (!isRecord(value) || value.applies_to !== table || typeof value.n !== "string") {
+                continue;
+            }
+            if (this.scopePeek(value.s) === 0) {
+                continue;
+            }
+            const type = cxType(value.d);
+            if (type !== null) {
+                out.set(value.n, type);
+            }
+        }
+        return out;
+    }
+    /**
+     * Declare one attribute column.
+     * @param domain - node or edge
+     * @param name - the attribute name
+     * @param type - the type, or null for a json column
+     * @returns the handle
+     */
+    declareColumn(domain, name, type) {
+        const { long } = this.options;
+        const decl = type === null
+            ? { name, dtype: "json", nullable: true, origin: { format: CX_FORMAT, id: null } }
+            : {
+                name,
+                dtype: type.list ? "list" : scalarDtype(type.scalar, long),
+                ...(type.list ? { itemDtype: scalarDtype(type.scalar, long) } : {}),
+                nullable: true,
+                origin: { format: CX_FORMAT, id: null, type: typeText(type) },
+            };
+        return declareResolved(this.sink, domain, decl, this.report).handle;
+    }
+    /**
+     * Write the attribute values of a table: per element, its own subnetwork's value beats the
+     * unscoped one; a repeated value of the same scope is the later one (W_DUPLICATE_ATTRIBUTE
+     * when they differ).
+     * @param domain - node or edge
+     * @param columns - the columns from declareAttributes()
+     */
+    writeAttributes(domain, columns) {
+        const rows = domain === "node" ? this.nodeRows : this.edgeRows;
+        const root = domain === "node" ? this.rootNodes : this.rootEdges;
+        for (const column of columns.values()) {
+            const chosen = new Map();
+            for (const held of this.doc.attributes[domain].get(column.name) ?? []) {
+                this.checkAbort();
+                const { value, line } = held;
+                if (!isRecord(value)) {
+                    this.report.error("parse-error", BAD_ASPECT_BLOCK_CODE, `a ${domain}Attributes element is not an object`, {
+                        line,
+                        element: `${domain}Attributes`,
+                    });
+                    continue;
+                }
+                const scope = this.scopeOf(value.s);
+                if (scope === 0) {
+                    continue;
+                }
+                const target = refId(value.po);
+                const row = target === null
+                    ? undefined
+                    : rows.get(this.options.ids === "keep" ? target : this.coercer.value(target));
+                if (row === undefined) {
+                    if (target === null || !root.has(target)) {
+                        this.dangle(`${domain} attribute target`);
+                    }
+                    continue;
+                }
+                if (value.v === undefined) {
+                    this.report.error("missing-value", BAD_VALUE_CODE, `a ${domain}Attributes element for "${column.name}" has no v; skipped`, {
+                        line,
+                        element: column.name,
+                    });
+                    continue;
+                }
+                if (value.v === null) {
+                    continue;
+                }
+                const previous = chosen.get(row);
+                if (previous !== undefined && previous.scope > scope) {
+                    continue;
+                }
+                if (previous?.scope === scope &&
+                    JSON.stringify(previous.value) !== JSON.stringify(plainJson(value.v))) {
+                    this.report.warnOnce("validation-error", DUPLICATE_ATTRIBUTE_CODE, `${domain} ${shown(value.po)} has the attribute "${column.name}" twice; the later value wins`, { line, element: column.name }, `${DUPLICATE_ATTRIBUTE_CODE}:${domain}:${column.name}`);
+                }
+                chosen.set(row, { scope, value: value.v, d: value.d, line });
+            }
+            for (const [row, { value, d, line }] of chosen) {
+                this.writeCell(domain, column, row, value, d, line);
+            }
+        }
+    }
+    /**
+     * Parse and write one attribute cell. The core fields' attributes (name, represents,
+     * interaction) go into their columns; a name attribute that differs from n wins with
+     * W_DUPLICATE_ATTRIBUTE.
+     * @param domain - node or edge
+     * @param column - the column
+     * @param row - the row
+     * @param raw - the value
+     * @param d - the data type the value was written with
+     * @param line - its line
+     */
+    writeCell(domain, column, row, raw, d, line) {
+        const element = `${domain} attribute "${column.name}"`;
+        let value;
+        if (column.type === null) {
+            value = plainJson(raw, (digits) => {
+                this.precision(column.name, digits);
+            });
+        }
+        else {
+            const own = cxType(d) ?? { scalar: "string", list: false };
+            const parsed = parseValue(raw, own, this.options.long, (digits) => {
+                this.precision(column.name, digits);
+            });
+            if (parsed === UNSET) {
+                return;
+            }
+            if (parsed === BAD) {
+                this.report.error("validation-error", BAD_VALUE_CODE, `${element}: ${shown(raw)} is not a ${typeText(own)}; the cell is unset`, { line, element: column.name });
+                return;
+            }
+            value = toColumn(parsed, column.type);
+        }
+        let { handle } = column;
+        if (this.isStructural(domain, column.name)) {
+            handle = this.coreColumn(domain, column.name);
+            const prior = this.coreValue(domain, row, column.name);
+            if (prior !== undefined && prior !== value) {
+                this.report.warnOnce("validation-error", DUPLICATE_ATTRIBUTE_CODE, `a ${domain} has "${column.name}" both as its core field and as an attribute with another value; the attribute wins`, { line, element: column.name }, `${DUPLICATE_ATTRIBUTE_CODE}:core:${column.name}`);
+            }
+        }
+        try {
+            if (domain === "node") {
+                this.sink.setNodeValue(handle, row, value);
+            }
+            else {
+                this.sink.setEdgeValue(handle, row, value);
+            }
+        }
+        catch (err) {
+            this.report.recordError(err, { line, element: column.name });
+        }
+    }
+    /**
+     * The core field value of a row.
+     * @param domain - node or edge
+     * @param row - the row
+     * @param name - name, represents or interaction
+     * @returns the value, or undefined
+     */
+    coreValue(domain, row, name) {
+        return this.coreValues.get(`${domain}:${name}`)?.get(row);
+    }
+    /**
+     * The column of a core field.
+     * @param domain - node or edge
+     * @param name - name, represents or interaction
+     * @returns the handle
+     */
+    coreColumn(domain, name) {
+        if (domain === "edge") {
+            this.interactionHandle = this.structural("edge", this.interactionHandle, {
+                name: "interaction",
+                dtype: "string",
+                nullable: true,
+                origin: { format: CX_FORMAT, id: "i", type: "string" },
+            });
+            return this.interactionHandle;
+        }
+        if (name === "name") {
+            this.nameHandle = this.structural("node", this.nameHandle, {
+                name: "name",
+                dtype: "string",
+                role: "label",
+                nullable: true,
+                origin: { format: CX_FORMAT, id: "n", type: "string" },
+            });
+            return this.nameHandle;
+        }
+        this.representsHandle = this.structural("node", this.representsHandle, {
+            name: "represents",
+            dtype: "string",
+            nullable: true,
+            origin: { format: CX_FORMAT, id: "r", type: "string" },
+        });
+        return this.representsHandle;
+    }
+    // ------------------------------------------------------------ nodes, groups, layout
+    /** Read the nodes of this graph. */
+    readNodes() {
+        const { report, sink } = this;
+        for (const held of aspect(this.doc, "nodes")) {
+            this.checkAbort();
+            const { value, line } = held;
+            if (!isRecord(value)) {
+                report.error("parse-error", BAD_ASPECT_BLOCK_CODE, `a nodes element is ${shown(value)}, not an object`, {
+                    line,
+                    element: "nodes",
+                });
+                report.counts.skippedNodes++;
+                continue;
+            }
+            if (value["@id"] === undefined || value["@id"] === null) {
+                report.error("missing-value", MISSING_ID_CODE, "a node has no @id", { line, element: "nodes" });
+                report.counts.skippedNodes++;
+                continue;
+            }
+            const element = `node ${shown(value["@id"])}`;
+            const id = this.idOf(value["@id"], (held.inexact & 1) !== 0, element);
+            if (id === null) {
+                report.counts.skippedNodes++;
+                continue;
+            }
+            if (!this.inGraph(id)) {
+                continue;
+            }
+            let row = this.nodeRows.get(id);
+            if (row !== undefined) {
+                report.warning("merged", DUPLICATE_NODE_CODE, `${element} is declared more than once; its fields are merged (the later values win)`, { line, element });
+            }
+            else {
+                try {
+                    row = sink.addNode(id);
+                }
+                catch (err) {
+                    report.recordError(err, { line, element });
+                    report.counts.skippedNodes++;
+                    continue;
+                }
+                this.nodeRows.set(id, row);
+                report.counts.nodes++;
+            }
+            this.writeCore("node", row, "name", value.n, element, line);
+            this.writeCore("node", row, "represents", value.r, element, line);
+        }
+    }
+    /**
+     * Write a core string field (n, r, i).
+     * @param domain - node or edge
+     * @param row - the row
+     * @param name - the column
+     * @param raw - the value
+     * @param element - the element name
+     * @param line - its line
+     */
+    writeCore(domain, row, name, raw, element, line) {
+        if (raw === undefined || raw === null) {
+            return;
+        }
+        if (typeof raw !== "string") {
+            this.report.error("validation-error", BAD_VALUE_CODE, `${element}: ${name} is ${shown(raw)}, not a string`, {
+                line,
+                element,
+            });
+            return;
+        }
+        const handle = this.coreColumn(domain, name);
+        if (domain === "node") {
+            this.sink.setNodeValue(handle, row, raw);
+        }
+        else {
+            this.sink.setEdgeValue(handle, row, raw);
+        }
+        const key = `${domain}:${name}`;
+        let values = this.coreValues.get(key);
+        if (values === undefined) {
+            values = new Map();
+            this.coreValues.set(key, values);
+        }
+        values.set(row, raw);
+    }
+    /**
+     * Read cyGroups: a group's members get the group node as their parent (parents when a node is in
+     * several groups); a group whose id is not a node gets one (W_CX_GROUP_NODE_ADDED); collapsed is
+     * a bool column on the group node.
+     */
+    readGroups() {
+        const groups = aspect(this.doc, "cyGroups");
+        if (groups.length === 0) {
+            return;
+        }
+        const parents = new Map();
+        const collapsed = [];
+        for (const { value, line } of groups) {
+            if (!isRecord(value)) {
+                continue;
+            }
+            const id = refId(value["@id"]);
+            if (id === null) {
+                this.report.error("missing-value", MISSING_ID_CODE, "a cyGroups element has no @id", {
+                    line,
+                    element: "cyGroups",
+                });
+                continue;
+            }
+            let groupRow = this.nodeRows.get(id);
+            if (groupRow === undefined) {
+                if (this.rootNodes.has(id) || !this.hasMemberIn(value.nodes)) {
+                    continue;
+                }
+                try {
+                    groupRow = this.sink.addNode(id);
+                }
+                catch (err) {
+                    this.report.recordError(err, { line, element: String(id) });
+                    continue;
+                }
+                this.nodeRows.set(id, groupRow);
+                this.report.counts.nodes++;
+                this.report.warning("coercion", CX_ISSUE.GROUP_NODE_ADDED, `group ${String(id)} is not a node; its group node is added`, { line, element: String(id) });
+            }
+            if (typeof value.n === "string" && this.coreValue("node", groupRow, "name") === undefined) {
+                this.writeCore("node", groupRow, "name", value.n, `group ${String(id)}`, line);
+            }
+            if (typeof value.collapsed === "boolean") {
+                collapsed.push([groupRow, value.collapsed]);
+            }
+            for (const raw of Array.isArray(value.nodes) ? value.nodes : []) {
+                const member = refId(raw);
+                const row = member === null ? undefined : this.nodeRows.get(member);
+                if (row === undefined) {
+                    if (member === null || !this.rootNodes.has(member)) {
+                        this.report.error("missing-value", UNKNOWN_PARENT_CODE, `group ${String(id)}: the member ${shown(raw)} is not a node`, { line, element: String(id) });
+                    }
+                    continue;
+                }
+                if (this.closesCycle(parents, row, groupRow)) {
+                    this.report.error("validation-error", PARENT_CYCLE_CODE, `group ${String(id)}: making ${shown(raw)} a member would close a parent cycle; that membership is dropped`, { line, element: String(id) });
+                    continue;
+                }
+                const list = parents.get(row) ?? [];
+                if (!list.includes(groupRow)) {
+                    list.push(groupRow);
+                }
+                parents.set(row, list);
+            }
+        }
+        this.writeParents(parents);
+        if (collapsed.length > 0) {
+            const { handle } = declareResolved(this.sink, "node", {
+                name: "collapsed",
+                dtype: "bool",
+                nullable: true,
+                origin: { format: CX_FORMAT, namespace: "cyGroups" },
+            }, this.report);
+            for (const [row, flag] of collapsed) {
+                this.sink.setNodeValue(handle, row, flag);
+            }
+        }
+    }
+    /**
+     * Whether a member list names a node of this graph.
+     * @param raw - the list
+     * @returns true when one member is in the graph
+     */
+    hasMemberIn(raw) {
+        return (Array.isArray(raw) &&
+            raw.some((item) => {
+                const id = refId(item);
+                return id !== null && this.nodeRows.has(id);
+            }));
+    }
+    /**
+     * Whether making `child` a member of `group` closes a cycle: the group already is, through its
+     * own parents, below the child.
+     * @param parents - the memberships so far
+     * @param child - the member row
+     * @param group - the group row
+     * @returns true for a cycle
+     */
+    closesCycle(parents, child, group) {
+        const stack = [group];
+        const seen = new Set();
+        while (stack.length > 0) {
+            const row = stack.pop();
+            if (row === child) {
+                return true;
+            }
+            if (seen.has(row)) {
+                continue;
+            }
+            seen.add(row);
+            stack.push(...(parents.get(row) ?? []));
+        }
+        return false;
+    }
+    /**
+     * Write the group memberships: a parent column, or a parents list column when a node is in
+     * several groups.
+     * @param parents - member row -> group rows
+     */
+    writeParents(parents) {
+        if (parents.size === 0) {
+            return;
+        }
+        const several = [...parents.values()].some((list) => list.length > 1);
+        const decl = several
+            ? { name: "parents", dtype: "list", itemDtype: "u32", role: "parents", refersTo: "node", nullable: true }
+            : { name: "parent", dtype: "u32", role: "parent", refersTo: "node", nullable: true };
+        const { handle } = declareResolved(this.sink, "node", decl, this.report);
+        for (const [row, list] of parents) {
+            this.sink.setNodeValue(handle, row, several ? list : list[0]);
+        }
+    }
+    /**
+     * Read cartesianLayout for this graph's views: the first view is the position (y flipped), z the
+     * z column, every other view a position@n column.
+     */
+    readLayout() {
+        const entries = aspect(this.doc, "cartesianLayout");
+        if (entries.length === 0) {
+            return;
+        }
+        const { views } = this.plan;
+        const knownViews = this.allViews();
+        const columns = new Map();
+        const zHandle = { current: INVALID_INDEX };
+        const seen = new Set();
+        const point = [0, 0, 0];
+        for (const { value, line } of entries) {
+            this.checkAbort();
+            if (!isRecord(value)) {
+                continue;
+            }
+            const view = value.view === undefined || value.view === null ? null : refId(value.view);
+            if (view !== null && knownViews.size > 0 && !knownViews.has(view)) {
+                this.dangle("layout view reference");
+                continue;
+            }
+            const slot = view === null ? 0 : views.indexOf(view);
+            if (slot < 0) {
+                continue;
+            }
+            if (typeof value.x !== "number" || typeof value.y !== "number") {
+                this.report.error("validation-error", BAD_VALUE_CODE, `a cartesianLayout element for node ${shown(value.node)} has no numeric x and y; skipped`, { line, element: "cartesianLayout" });
+                continue;
+            }
+            const node = refId(value.node);
+            const row = node === null ? undefined : this.nodeRows.get(node);
+            if (row === undefined) {
+                if (node === null || !this.rootNodes.has(node)) {
+                    this.dangle("layout entry");
+                }
+                continue;
+            }
+            const key = `${slot}:${row}`;
+            if (seen.has(key)) {
+                this.report.warnOnce("validation-error", DUPLICATE_ATTRIBUTE_CODE, `node ${shown(value.node)} has two layout entries for one view; the later wins`, { line, element: "cartesianLayout" }, `${DUPLICATE_ATTRIBUTE_CODE}:layout`);
+            }
+            seen.add(key);
+            const z = typeof value.z === "number" ? value.z : null;
+            point[0] = value.x;
+            point[1] = flipY(value.y);
+            point[2] = slot === 0 && this.zAs === "position" && z !== null ? z : 0;
+            this.sink.setNodeValue(this.layoutColumn(columns, slot, views), row, point);
+            if (slot === 0 && z !== null && this.zAs === "column") {
+                zHandle.current = this.structural("node", zHandle.current, zDecl(CX_FORMAT));
+                this.sink.setNodeValue(zHandle.current, row, z);
+            }
+        }
+    }
+    /**
+     * Every view id the document names.
+     * @returns the set (empty when the document names none)
+     */
+    allViews() {
+        const out = new Set();
+        for (const { value } of aspect(this.doc, "cyNetworkRelations")) {
+            if (isRecord(value) && value.r === "view") {
+                const id = refId(value.c);
+                if (id !== null) {
+                    out.add(id);
+                }
+            }
+        }
+        for (const { value } of aspect(this.doc, "cyViews")) {
+            const id = isRecord(value) ? refId(value["@id"]) : null;
+            if (id !== null) {
+                out.add(id);
+            }
+        }
+        return out;
+    }
+    /**
+     * The position column of a view slot, declared on first use.
+     * @param columns - slot -> handle
+     * @param slot - 0 for the position, n - 1 for position@n
+     * @param views - the graph's views
+     * @returns the handle
+     */
+    layoutColumn(columns, slot, views) {
+        let handle = columns.get(slot);
+        if (handle === undefined) {
+            const base = positionDecl(CX_FORMAT, this.zAs === "position" && slot === 0 ? 3 : 2);
+            const decl = slot === 0
+                ? base
+                : {
+                    ...base,
+                    name: `position@${slot + 1}`,
+                    role: undefined,
+                    origin: { format: CX_FORMAT, namespace: "cytoscape", id: String(views[slot]) },
+                };
+            ({ handle } = declareResolved(this.sink, "node", decl, this.report));
+            columns.set(slot, handle);
+        }
+        return handle;
+    }
+    // ------------------------------------------------------------ edges
+    /** Read the edges of this graph. */
+    readEdges() {
+        const { report, sink } = this;
+        const members = this.plan.edges;
+        for (const held of aspect(this.doc, "edges")) {
+            this.checkAbort();
+            const { value, line } = held;
+            if (!isRecord(value)) {
+                report.error("parse-error", BAD_ASPECT_BLOCK_CODE, `an edges element is ${shown(value)}, not an object`, {
+                    line,
+                    element: "edges",
+                });
+                report.counts.skippedEdges++;
+                continue;
+            }
+            if (value["@id"] === undefined || value["@id"] === null) {
+                report.error("missing-value", MISSING_ID_CODE, "an edge has no @id", { line, element: "edges" });
+                report.counts.skippedEdges++;
+                continue;
+            }
+            const element = `edge ${shown(value["@id"])}`;
+            const id = this.idOf(value["@id"], (held.inexact & 1) !== 0, element, true);
+            if (id === null) {
+                report.counts.skippedEdges++;
+                continue;
+            }
+            if (members !== null && !members.has(id)) {
+                continue;
+            }
+            if (value.s === undefined || value.s === null || value.t === undefined || value.t === null) {
+                report.error("missing-value", MISSING_ENDPOINT_CODE, `${element} has no ${value.s === undefined || value.s === null ? "s" : "t"}`, {
+                    line,
+                    element,
+                });
+                report.counts.skippedEdges++;
+                continue;
+            }
+            const s = this.idOf(value.s, (held.inexact & 2) !== 0, element);
+            const t = s === null ? null : this.idOf(value.t, (held.inexact & 4) !== 0, element);
+            if (s === null || t === null) {
+                report.counts.skippedEdges++;
+                continue;
+            }
+            if (this.edgeRows.has(id)) {
+                report.error("validation-error", DUPLICATE_EDGE_ID_CODE, `${element} is declared more than once; the later edge is skipped`, { line, element });
+                report.counts.skippedEdges++;
+                continue;
+            }
+            if (!this.endpoint(s, element, line) || !this.endpoint(t, element, line)) {
+                report.counts.skippedEdges++;
+                continue;
+            }
+            let weight;
+            try {
+                weight = this.weightOf(id);
+            }
+            catch (err) {
+                report.recordError(err, { line, element });
+                report.counts.skippedEdges++;
+                continue;
+            }
+            const before = sink.edgeCount;
+            let edge;
+            try {
+                edge = this.direction.addEdge(s, t, "directed", weight, { line, element });
+            }
+            catch (err) {
+                report.recordError(err, { line, element });
+                report.counts.skippedEdges++;
+                continue;
+            }
+            if (weight !== undefined) {
+                this.weighted = true;
+            }
+            report.counts.edges += sink.edgeCount - before;
+            this.edgeRows.set(id, edge);
+            this.edgeIdHandle = this.structural("edge", this.edgeIdHandle, {
+                name: uniqueColumnName("id", "cx", (n) => sink.edgeColumn(n) !== INVALID_INDEX),
+                dtype: "f64",
+                role: "id",
+                nullable: true,
+            });
+            sink.setEdgeValue(this.edgeIdHandle, edge, typeof id === "number" ? id : Number(id));
+            this.writeCore("edge", edge, "interaction", value.i, element, line);
+        }
+    }
+    /**
+     * Whether an endpoint is a node of this graph; under addMissingNodes it is created.
+     * @param id - the endpoint
+     * @param element - the edge name
+     * @param line - its line
+     * @returns false when the edge is to be skipped (reported)
+     */
+    endpoint(id, element, line) {
+        if (this.nodeRows.has(id)) {
+            return true;
+        }
+        if (!this.options.addMissingNodes) {
+            this.report.error("missing-value", CX_ISSUE.UNKNOWN_NODE, `${element}: the endpoint ${String(id)} is not a node of the graph; the edge is skipped`, { line, element });
+            return false;
+        }
+        try {
+            this.nodeRows.set(id, this.sink.addNode(id));
+        }
+        catch (err) {
+            this.report.recordError(err, { line, element });
+            return false;
+        }
+        this.report.counts.nodes++;
+        return true;
+    }
+    /**
+     * The weight of an edge: its weightFrom attribute, parsed as a number.
+     * @param id - the edge id
+     * @returns the weight, or undefined; E_INVALID_WEIGHT for a non-number
+     */
+    weightOf(id) {
+        const { weightFrom } = this.options;
+        if (weightFrom === null) {
+            return undefined;
+        }
+        if (this.weights === null) {
+            this.weights = new Map();
+            for (const { value } of this.doc.attributes.edge.get(weightFrom) ?? []) {
+                if (isRecord(value) && this.scopePeek(value.s) !== 0) {
+                    const po = refId(value.po);
+                    if (po !== null && value.v !== undefined && value.v !== null) {
+                        this.weights.set(po, plainJson(value.v));
+                    }
+                }
+            }
+        }
+        const raw = this.weights.get(id);
+        if (typeof raw === "string" && isNullText(raw)) {
+            return undefined;
+        }
+        return weightFromValue(raw);
+    }
+    // ------------------------------------------------------------ network, visual properties, provenance
+    /** Write the network attributes (unscoped and this subnetwork's, its own winning) as graph columns. */
+    readNetworkAttributes() {
+        for (const [name, elements] of this.doc.attributes.network) {
+            let chosen = null;
+            let chosenScope = 0;
+            for (const { value } of elements) {
+                if (!isRecord(value)) {
+                    continue;
+                }
+                const scope = this.scopeOf(value.s);
+                if (scope !== 0 && scope >= chosenScope) {
+                    chosen = value;
+                    chosenScope = scope;
+                }
+            }
+            if (chosen === null || chosen.v === undefined || chosen.v === null || name === "") {
+                continue;
+            }
+            const type = cxType(chosen.d);
+            if (type === null) {
+                this.report.warnOnce("unsupported", UNKNOWN_ATTR_TYPE_CODE, `the network attribute "${name}" declares a data type CX does not define; kept as text`, { element: name }, `${UNKNOWN_ATTR_TYPE_CODE}:network:${name}`);
+            }
+            const effective = type ?? { scalar: "string", list: false };
+            const parsed = parseValue(chosen.v, effective, this.options.long, (digits) => {
+                this.precision(name, digits);
+            });
+            if (parsed === UNSET) {
+                continue;
+            }
+            if (parsed === BAD) {
+                this.report.error("validation-error", BAD_VALUE_CODE, `the network attribute "${name}" is ${shown(chosen.v)}, not a ${typeText(effective)}; unset`, { element: name });
+                continue;
+            }
+            if ((name === "name" || name === "description") && typeof parsed === "string") {
+                continue;
+            }
+            const scalar = scalarDtype(effective.scalar, this.options.long);
+            try {
+                this.sink.setGraphValue(name, parsed, {
+                    dtype: effective.list ? "list" : scalar,
+                    ...(effective.list ? { itemDtype: scalar } : {}),
+                    origin: { format: CX_FORMAT, id: null, type: typeText(effective) },
+                });
+            }
+            catch (err) {
+                this.report.recordError(err, { element: name });
+            }
+        }
+    }
+    /**
+     * Read cyVisualProperties for this graph's views: per-element and network values become columns
+     * (origin namespace cx.bypass); defaults, mappings and dependencies are style rules, kept and not
+     * applied.
+     */
+    readVisualProperties() {
+        const entries = aspect(this.doc, "cyVisualProperties");
+        // Cytoscape's table-cell styles: a visual property aspect graph-io keeps but does not read
+        const tableStyles = TABLE_STYLE_ASPECTS.reduce((n, name) => n + (this.doc.kept.get(name)?.length ?? 0), 0);
+        // the graph's own view (its first): the one its positions come from; the others stay in meta.extra.cx
+        const views = new Set(this.plan.views.slice(0, 1));
+        const columns = { node: new Map(), edge: new Map() };
+        const network = new Map();
+        let defaults = 0;
+        let mappings = 0;
+        let dependencies = 0;
+        for (const { value } of entries) {
+            if (!isRecord(value)) {
+                continue;
+            }
+            const view = value.view === undefined || value.view === null ? null : refId(value.view);
+            if (view !== null && views.size > 0 && !views.has(view)) {
+                continue;
+            }
+            const properties = isRecord(value.properties) ? value.properties : {};
+            mappings += isRecord(value.mappings) ? Object.keys(value.mappings).length : 0;
+            dependencies += isRecord(value.dependencies) ? Object.keys(value.dependencies).length : 0;
+            switch (value.properties_of) {
+                case "nodes":
+                case "edges": {
+                    const domain = value.properties_of === "nodes" ? "node" : "edge";
+                    const target = refId(value.applies_to);
+                    const row = target === null ? undefined : (domain === "node" ? this.nodeRows : this.edgeRows).get(target);
+                    if (row === undefined) {
+                        if (target === null || !(domain === "node" ? this.rootNodes : this.rootEdges).has(target)) {
+                            this.dangle(`${domain} visual property entry`);
+                        }
+                        continue;
+                    }
+                    for (const [property, raw] of Object.entries(properties)) {
+                        const list = columns[domain].get(property) ?? [];
+                        list.push([row, typeof raw === "string" ? raw : JSON.stringify(raw)]);
+                        columns[domain].set(property, list);
+                    }
+                    break;
+                }
+                case "network":
+                    for (const [property, raw] of Object.entries(properties)) {
+                        network.set(property, typeof raw === "string" ? raw : JSON.stringify(raw));
+                    }
+                    break;
+                default:
+                    defaults += Object.keys(properties).length;
+                    break;
+            }
+        }
+        for (const domain of ["node", "edge"]) {
+            for (const [property, cells] of columns[domain]) {
+                const handle = declareFresh(this.sink, domain, {
+                    name: property,
+                    dtype: "string",
+                    nullable: true,
+                    origin: { format: CX_FORMAT, id: null, namespace: CX_BYPASS_NAMESPACE },
+                }, this.report);
+                for (const [row, text] of cells) {
+                    if (domain === "node") {
+                        this.sink.setNodeValue(handle, row, text);
+                    }
+                    else {
+                        this.sink.setEdgeValue(handle, row, text);
+                    }
+                }
+            }
+        }
+        for (const [property, text] of network) {
+            try {
+                this.sink.setGraphValue(property, text, {
+                    dtype: "string",
+                    origin: { format: CX_FORMAT, id: null, namespace: CX_BYPASS_NAMESPACE },
+                });
+            }
+            catch (err) {
+                this.report.recordError(err, { element: property });
+            }
+        }
+        if (defaults + mappings + dependencies + tableStyles > 0) {
+            const parts = [
+                `cyVisualProperties: ${defaults} default(s), ${mappings} mapping(s), ${dependencies} dependenc(ies)`,
+            ];
+            if (tableStyles > 0) {
+                parts.push(`${tableStyles} table style element(s)`);
+            }
+            this.report.warning("unsupported", STYLES_NOT_IMPORTED_CODE, `the file's style rules are not applied (${parts.join("; ")}); they are kept in meta.extra.cx (style import is issue #706)`, { element: "cyVisualProperties" });
+        }
+    }
+    /**
+     * Read the provenance aspects: citations and supports as extension tables cx:citations and
+     * cx:supports, the node / edge links to them as list columns, functionTerms as a json column,
+     * reifiedEdges as a u32 column referring to edges.
+     */
+    readProvenance() {
+        for (const name of ["citations", "supports"]) {
+            this.extensionTable(`cx:${name}`, aspect(this.doc, name));
+        }
+        for (const [aspectName, domain, column] of [
+            ["nodeCitations", "node", "citations"],
+            ["edgeCitations", "edge", "citations"],
+            ["nodeSupports", "node", "supports"],
+            ["edgeSupports", "edge", "supports"],
+        ]) {
+            this.linkColumn(aspectName, domain, column);
+        }
+        const terms = [];
+        for (const { value } of aspect(this.doc, "functionTerms")) {
+            if (!isRecord(value)) {
+                continue;
+            }
+            const po = refId(value.po);
+            const row = po === null ? undefined : this.nodeRows.get(po);
+            if (row === undefined) {
+                if (po === null || !this.rootNodes.has(po)) {
+                    this.dangle("functionTerms entry");
+                }
+                continue;
+            }
+            const { po: _po, ...term } = value;
+            terms.push([row, plainJson(term)]);
+        }
+        this.writeColumn("node", "functionTerm", "json", null, terms);
+        const reified = [];
+        for (const { value } of aspect(this.doc, "reifiedEdges")) {
+            if (!isRecord(value)) {
+                continue;
+            }
+            const node = refId(value.node);
+            const edge = refId(value.edge);
+            const row = node === null ? undefined : this.nodeRows.get(node);
+            const edgeRow = edge === null ? undefined : this.edgeRows.get(edge);
+            if (row === undefined || edgeRow === undefined) {
+                if (node === null || !this.rootNodes.has(node) || edge === null || !this.rootEdges.has(edge)) {
+                    this.dangle("reifiedEdges entry");
+                }
+                continue;
+            }
+            reified.push([row, edgeRow]);
+        }
+        if (reified.length > 0) {
+            const { handle } = declareResolved(this.sink, "node", {
+                name: "reifiedEdge",
+                dtype: "u32",
+                refersTo: "edge",
+                nullable: true,
+                origin: { format: CX_FORMAT, namespace: "reifiedEdges" },
+            }, this.report);
+            for (const [row, edge] of reified) {
+                this.sink.setNodeValue(handle, row, edge);
+            }
+        }
+    }
+    /**
+     * An extension table of a provenance aspect: an f64 `id` column and one json column per field.
+     * @param name - the table name
+     * @param elements - the elements
+     */
+    extensionTable(name, elements) {
+        const records = elements.map((h) => h.value).filter(isRecord);
+        if (records.length === 0) {
+            return;
+        }
+        const fields = [...new Set(records.flatMap((r) => Object.keys(r)).filter((k) => k !== "@id"))];
+        const decls = [
+            { name: "id", dtype: "f64", nullable: true },
+            ...fields.map((field) => ({ name: field, dtype: "json", nullable: true })),
+        ];
+        const table = this.sink.addExtensionTable(name, decls);
+        for (const record of records) {
+            const id = refId(record["@id"]);
+            this.sink.addExtensionRow(table, [
+                id === null ? null : Number(id),
+                ...fields.map((field) => (record[field] === undefined ? null : plainJson(record[field]))),
+            ]);
+        }
+    }
+    /**
+     * A list column of the citation or support ids a node or edge links to.
+     * @param aspectName - nodeCitations, edgeCitations, nodeSupports or edgeSupports
+     * @param domain - node or edge
+     * @param column - citations or supports
+     */
+    linkColumn(aspectName, domain, column) {
+        const rows = domain === "node" ? this.nodeRows : this.edgeRows;
+        const root = domain === "node" ? this.rootNodes : this.rootEdges;
+        const links = new Map();
+        for (const { value } of aspect(this.doc, aspectName)) {
+            if (!isRecord(value)) {
+                continue;
+            }
+            const targets = Array.isArray(value.po) ? value.po : [value.po];
+            const ids = (Array.isArray(value[column]) ? value[column] : [])
+                .map(refId)
+                .filter((id) => id !== null)
+                .map(Number);
+            for (const raw of targets) {
+                const target = refId(raw);
+                const row = target === null ? undefined : rows.get(target);
+                if (row === undefined) {
+                    if (target === null || !root.has(target)) {
+                        this.dangle(`${aspectName} entry`);
+                    }
+                    continue;
+                }
+                links.set(row, [...(links.get(row) ?? []), ...ids]);
+            }
+        }
+        this.writeColumn(domain, column, "list", "f64", [...links]);
+    }
+    /**
+     * Declare a column and write its cells (nothing when there are none).
+     * @param domain - node or edge
+     * @param name - the column name
+     * @param dtype - the dtype
+     * @param itemDtype - the list item dtype, or null
+     * @param cells - row and value pairs
+     */
+    writeColumn(domain, name, dtype, itemDtype, cells) {
+        if (cells.length === 0) {
+            return;
+        }
+        const decl = {
+            name,
+            dtype,
+            ...(itemDtype === null ? {} : { itemDtype }),
+            nullable: true,
+            origin: { format: CX_FORMAT, namespace: "provenance" },
+        };
+        const { handle } = declareResolved(this.sink, domain, decl, this.report);
+        for (const [row, value] of cells) {
+            if (domain === "node") {
+                this.sink.setNodeValue(handle, row, value);
+            }
+            else {
+                this.sink.setEdgeValue(handle, row, value);
+            }
+        }
+    }
+    /** Record the metadata: source format, name, description, id type, the kept aspects. */
+    setMeta() {
+        const describe = (key) => {
+            let found = null;
+            for (const { value } of this.doc.attributes.network.get(key) ?? []) {
+                if (isRecord(value) && typeof value.v === "string") {
+                    const scope = this.scopePeek(value.s);
+                    if (scope === 2) {
+                        return value.v;
+                    }
+                    if (scope === 1) {
+                        found ?? (found = value.v);
+                    }
+                }
+            }
+            return found;
+        };
+        const extra = Object.fromEntries(this.doc.kept);
+        const groups = aspect(this.doc, "cyGroups").map((h) => plainJson(h.value));
+        if (groups.length > 0) {
+            extra.groups = groups;
+        }
+        if (this.plan.subnetwork !== null) {
+            extra.subnetwork = this.plan.subnetwork;
+        }
+        const { weightFrom } = this.options;
+        const name = this.plan.name ?? describe("name");
+        const description = describe("description");
+        const patch = {
+            sourceFormat: CX_FORMAT,
+            sourceVersion: "1",
+            idType: this.idType,
+            ...(name === null ? {} : { name }),
+            ...(description === null ? {} : { description }),
+            ...(this.weighted && weightFrom !== null
+                ? { weightOrigin: { format: CX_FORMAT, id: null, title: weightFrom, type: "double", namespace: null } }
+                : {}),
+            extra: { cx: extra },
+        };
+        this.sink.setMeta(patch);
+    }
+}
+// ============================================================ the plugin
+/**
+ * Read a document, then build the graphs `pick` selects.
+ * @param input - the input
+ * @param options - the caller's options
+ * @param sinkFor - the sink of graph i, or null to skip it
+ * @param pick - which graph indexes to build, given the plans and the first report
+ * @returns one report per built graph
+ */
+async function run(input, options, sinkFor, pick) {
+    const resolved = resolveImportOptions(options, FORMAT_DEFAULTS);
+    const zAs = zAsOption(options?.zAs);
+    const first = new ImportReportBuilder(CX_FORMAT, resolved.errorLimit);
+    reportUnusedOptions(options, first, USED_OPTIONS);
+    const doc = await readDocument(input, first, resolved);
+    const plans = graphPlans(doc);
+    const chosen = pick(plans, first);
+    const reports = [];
+    chosen.forEach((index, k) => {
+        const report = k === 0 ? first : new ImportReportBuilder(CX_FORMAT, resolved.errorLimit);
+        const sink = sinkFor(index);
+        reportSinkOptions(sink, options, report, true);
+        new CxReader(sink, report, resolved, zAs, doc, plans[index]).build();
+        throwIfAborted(resolved.signal);
+        reports.push(report.finish());
+    });
+    return reports;
+}
+/**
+ * The CX version 1 importer plugin (design section 1.2).
+ */
+export const cxImporter = Object.freeze({
+    format: CX_FORMAT,
+    extensions: Object.freeze([".cx"]),
+    mimeTypes: Object.freeze(["application/json"]),
+    /**
+     * Confidence that the head is CX version 1: 0.95 when a top-level array starts with an object
+     * whose first key is numberVerification or metaData (Cytoscape's file filter), 0.7 for another
+     * CX aspect name.
+     * @param head - the first bytes
+     * @returns the confidence
+     */
+    sniff(head) {
+        const text = new TextDecoder("utf-8").decode(head.subarray(0, 1024)).replace(/^\uFEFF/, "");
+        const match = /^\s*\[\s*\{\s*"((?:[^"\\]|\\.)*)"\s*:/.exec(text);
+        if (match === null) {
+            return 0;
+        }
+        if (CX_FIRST_KEYS.includes(match[1])) {
+            return 0.95;
+        }
+        return CX_ASPECT_KEYS.includes(match[1]) ? 0.7 : 0;
+    },
+    /**
+     * Read one graph of a CX document into the sink: the root network, or the subnetwork
+     * graphIndex / graphName picks (the first by default; W_MULTIPLE_GRAPHS names the others).
+     * @param input - the text, bytes or stream
+     * @param sink - the sink
+     * @param options - format-specific and common options
+     * @returns the import report; ImportError on a fatal error or beyond the error limit
+     */
+    async import(input, sink, options) {
+        const [report] = await run(input, options, () => sink, (plans, first) => {
+            const index = chooseGraph(plans.map((p) => p.name), options, first);
+            if (plans.length > 1) {
+                first.warning("unsupported", MULTIPLE_GRAPHS_CODE, `the collection holds ${plans.length} subnetworks; graph ${index} is read and ${plans.length - 1} skipped (importAll() reads every one)`);
+            }
+            return [index];
+        });
+        return report;
+    },
+    /**
+     * Read every graph of a CX document: one per subnetwork of a collection, in the order of
+     * cyNetworkRelations; the root network for any other document.
+     * @param input - the text, bytes or stream
+     * @param sinkFor - the sink of the graph with this index, called before its first push
+     * @param options - format-specific and common options
+     * @returns one report per graph
+     */
+    importAll(input, sinkFor, options) {
+        return run(input, options, sinkFor, (plans) => plans.map((p) => p.index));
+    },
+    /**
+     * List the graphs of a CX document with their names and member counts.
+     * @param input - the text, bytes or stream
+     * @param options - format-specific and common options
+     * @returns one listing per graph
+     */
+    async listGraphs(input, options) {
+        const resolved = resolveImportOptions(options, FORMAT_DEFAULTS);
+        const report = new ImportReportBuilder(CX_FORMAT, resolved.errorLimit);
+        const doc = await readDocument(input, report, resolved);
+        const nodes = aspect(doc, "nodes").length;
+        const edges = aspect(doc, "edges").length;
+        return graphPlans(doc).map((plan) => Object.freeze({
+            index: plan.index,
+            name: plan.name,
+            nodes: memberCount(plan.nodes, nodes),
+            edges: memberCount(plan.edges, edges),
+        }));
+    },
+});
+//# sourceMappingURL=importer.js.map