@graphty/graph-io 0.3.25 → 0.3.27

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

@@ -0,0 +1,1217 @@
+/**
+ * The CX version 1 exporter (design/graph-io/cytoscape-and-obo/design.md section 1.2): writes a
+ * snapshot as the NDEx form of a CX document -- one network with at most one view, no
+ * `cySubNetworks` -- which NDEx, ndex2 and Cytoscape's CX import all read.
+ *
+ * Aspects, in the order Cytoscape and NDEx write them: `numberVerification`, the pre-`metaData`
+ * (element counts, `idCounter` on nodes, edges, citations and supports), `nodes` (`n` the label,
+ * `r` the `represents` column), `edges` (`i` the `interaction` column), `nodeAttributes`,
+ * `edgeAttributes` and `networkAttributes` (values as JSON strings, the spec's form), `cyTableColumn`
+ * (so a column no element fills is still declared), `cartesianLayout` (y negated back to screen
+ * coordinates), `cyGroups` from the parent / parents column, `cyVisualProperties` from the
+ * `cx.bypass` columns, the provenance aspects a CX import created, the style rules and unknown
+ * aspects a CX import kept, and `status`.
+ *
+ * What CX cannot hold is announced by check() before anything is written: every edge is directed
+ * (W_CX_UNDIRECTED_AS_DIRECTED, W_MUTUAL_EXPANDED), node ids are integers (E_ID_CHARSET unless
+ * `sanitizeIds: "mangle"`, which keeps the original in the `graphty:originalId` attribute the
+ * importer restores), nested values are written as JSON text (W_CX_JSON_AS_STRING), and the generic
+ * notes of checkCapabilities(). NaN and the infinities are written as "NaN" / "Infinity" in double
+ * attributes, which read back as they were.
+ */
+import { GraphFormatError } from "@graphty/graph-format";
+import { childrenCsr } from "../../children.js";
+import { aspectBlock, declaredType, directionNotes, nextNodeId, noteList, planEdgeIds, planNodeIds, stringify, } from "../../common/cx-export.js";
+import { pairFolding } from "../../common/direction.js";
+import { capabilities, checkCapabilities, LOSS } from "../../common/export.js";
+import { isRecord, POSITION_COLUMN } from "../../common/json-elements.js";
+import { resolveExportOptions } from "../../common/options.js";
+import { plural } from "../../common/plural.js";
+import { explicitWeights } from "../../common/weights.js";
+import { encodeChunks, joinText } from "../../common/writer.js";
+import { ORIGINAL_ID_ATTRIBUTE } from "../cx2/importer.js";
+/** The format name. */
+const CX_FORMAT = "cx";
+/**
+ * The loss notes the CX exporter's check() returns, by name. A key is the code without its
+ * severity and format prefixes.
+ * @category Built-in formats
+ */
+export const CX_LOSS = Object.freeze({
+    /**
+     * Every edge is written as directed, so an undirected graph, or the undirected edges of a mixed graph, read back
+     * as directed.
+     */
+    UNDIRECTED_AS_DIRECTED: "W_CX_UNDIRECTED_AS_DIRECTED",
+    /** A nested (json) column is written as a string attribute holding its JSON text. */
+    JSON_AS_STRING: "W_CX_JSON_AS_STRING",
+    /** A mutual pair is written as two directed edges without its mark. */
+    MUTUAL_EXPANDED: LOSS.MUTUAL_EXPANDED,
+    /**
+     * An attribute named `weight` without the weight role reads back as the edge weight, or is not written when the
+     * graph has weights of its own.
+     */
+    WEIGHT_KEY_CLASH: LOSS.WEIGHT_KEY_CLASH,
+    /** A start / end / timestamp column: CX has no time. */
+    TEMPORAL_DROPPED: LOSS.TEMPORAL,
+    /** An attribute with a role the format has no place for is written as a plain attribute; the role is lost. */
+    ROLE_DROPPED: LOSS.ROLE,
+    /**
+     * An attribute without a role is written where the format keeps a role (for example, a `name` column as the label), and
+     * reads back with that role.
+     */
+    ROLE_ASSUMED: LOSS.ROLE_ASSUMED,
+    /**
+     * An attribute type CX stores as another (a 32-bit float as double, an unsigned integer as long, a byte as
+     * integer, a dictionary as string); it reads back with that type.
+     */
+    DTYPE_UNSUPPORTED: LOSS.DTYPE,
+    /** A multi-component column (a second view's `position@2`, a vector) is written as a list of doubles. */
+    COMPONENTS_FLATTENED: LOSS.COMPONENTS,
+    /** A declared default: CX has none. */
+    DEFAULT_DROPPED: LOSS.DEFAULT,
+    /** Declared options: CX has no enumerations. */
+    OPTIONS_DROPPED: LOSS.OPTIONS,
+    /**
+     * Node ids the format cannot write, under `sanitizeIds: "error"`; the save fails with E_INVALID_ID. Pass
+     * `sanitizeIds: "mangle"` to rewrite them.
+     */
+    ID_CHARSET: LOSS.ID_CHARSET,
+    /** Node ids that are not integers under sanitizeIds "mangle": renumbered, originals kept. */
+    ID_MANGLED: LOSS.ID_MANGLED,
+    /** Edges without a usable integer id get generated ids. */
+    EDGE_IDS_GENERATED: LOSS.EDGE_IDS_GENERATED,
+    /**
+     * An attribute with a role (for example, the label) is written where the format keeps that role, and reads back under the
+     * name the format's importer gives it.
+     */
+    COLUMN_NAME_CHANGED: LOSS.COLUMN_NAME_CHANGED,
+    /** An extension table other than the `cx:citations` / `cx:supports` tables a CX import creates. */
+    EXTENSION_TABLE_DROPPED: LOSS.EXTENSION_TABLE,
+    /** A position, stacking order or weight that is NaN or infinite: CX spells no such number there. */
+    NONFINITE_AS_NULL: LOSS.NONFINITE_AS_NULL,
+    /** Visual columns (color, size, shape, thickness roles): CX keeps style as visual properties, not roles. */
+    VIZ_DROPPED: LOSS.VIZ,
+});
+/**
+ * What CX version 1 keeps: directed multigraphs with self-loops, integer node ids, required
+ * integer edge ids, typed string / double / integer / boolean attributes and lists of them, network
+ * attributes, the position role (one view), and containment as `cyGroups`. f32, u32, u8 and dict
+ * columns are written as the nearest declared type and read back as it.
+ * @category Built-in formats
+ */
+export const CX_CAPABILITIES = capabilities({
+    mixedDirection: false,
+    multiEdges: true,
+    selfLoops: true,
+    edgeIds: "required",
+    idCharset: "integer",
+    dtypes: ["string", "f64", "i32", "bool"],
+    components: false,
+    lists: true,
+    json: false,
+    defaults: false,
+    options: false,
+    hierarchy: true,
+    temporal: "none",
+    graphAttributes: true,
+    positions: true,
+    viz: false,
+});
+/** The roles CX has a slot for, and the column names its importer gives them. */
+const SLOT_ROLES = new Set(["label", "position", "id"]);
+const ROLE_NAMES = Object.freeze({
+    label: "name",
+    position: POSITION_COLUMN,
+    id: "id",
+    parent: "parent",
+});
+/** Roles whose columns are never written as attributes. */
+const SKIPPED_ROLES = new Set([
+    "directed",
+    "pair",
+    "mutual",
+    "weight",
+    "timeText",
+    "originalId",
+    "parent",
+    "parents",
+    "start",
+    "end",
+    "timestamp",
+    "timestamps",
+    "spells",
+    "open",
+    "spellsOpen",
+    "position",
+    "color",
+    "size",
+    "shape",
+    "thickness",
+    "id",
+]);
+/** The origin namespace of the per-element visual property columns of a CX import. */
+const BYPASS_NAMESPACE = "cx.bypass";
+/** The extension tables a CX import creates from the citations and supports aspects. */
+const PROVENANCE_TABLES = Object.freeze({
+    "cx:citations": "citations",
+    "cx:supports": "supports",
+});
+/**
+ * Kept aspects never written back: they describe the collection, views and SUIDs of the file the
+ * snapshot came from, or are written by the exporter itself.
+ */
+const NEVER_WRITTEN = new Set([
+    "nodes",
+    "edges",
+    "nodeAttributes",
+    "edgeAttributes",
+    "networkAttributes",
+    "cartesianLayout",
+    "cyGroups",
+    "cyVisualProperties",
+    "cyTableColumn",
+    "cySubNetworks",
+    "cyNetworkRelations",
+    "cyViews",
+    "CX Element ID",
+    "citations",
+    "supports",
+    "nodeCitations",
+    "edgeCitations",
+    "nodeSupports",
+    "edgeSupports",
+    "functionTerms",
+    "reifiedEdges",
+    "numberVerification",
+    "metaData",
+    "status",
+    "groups",
+    "subnetwork",
+]);
+/** The weight attribute name (the CX importer's weightFrom default). */
+const WEIGHT_ATTRIBUTE = "weight";
+/** The dtypes a plain `weight` column may have to be written as the weight. */
+const NUMERIC_DTYPES = new Set(["f32", "f64", "i32", "u32", "u8"]);
+/**
+ * Whether a column was created by the CX importer in an origin namespace.
+ * @param column - the column
+ * @param namespace - the namespace
+ * @returns true when it was
+ */
+function fromCx(column, namespace) {
+    return column.meta.origin?.format === CX_FORMAT && column.meta.origin.namespace === namespace;
+}
+/**
+ * Whether a column is a bypass column of a CX import.
+ * @param column - the column
+ * @returns true for the cx.bypass namespace
+ */
+function isBypass(column) {
+    return column.meta.origin?.namespace === BYPASS_NAMESPACE;
+}
+/**
+ * Whether a column is the z (stacking order) column.
+ * @param column - the column
+ * @returns true for the column marked by a Cytoscape-family importer
+ */
+function isZ(column) {
+    return column.meta.extra.cytoscape === "z";
+}
+/**
+ * Whether a column is a provenance list column (citations / supports) of a CX import.
+ * @param column - the column
+ * @returns true for one
+ */
+function isLink(column) {
+    return (fromCx(column, "provenance") &&
+        column.meta.dtype === "list" &&
+        (column.meta.name === "citations" || column.meta.name === "supports"));
+}
+/**
+ * Whether a column holds a text the core fields (n, r, i) cannot hold as itself.
+ * @param column - the column
+ * @returns true for every dtype but string (dict and json have their own notes)
+ */
+function coreNeedsText(column) {
+    const { dtype } = column.meta;
+    return dtype !== "string" && dtype !== "dict" && dtype !== "json";
+}
+/**
+ * The notes of checkCapabilities(), adapted to CX: json columns are written as JSON text, the id
+ * notes are counted by planNodeIds(), the provenance tables and columns a CX import made are
+ * written back.
+ * @param snapshot - the snapshot
+ * @param common - the resolved common options
+ * @param several - whether the parents column gives some node several parents
+ * @param own - the functionTerm and reifiedEdge columns written as their own aspects
+ * @param notes - the notes so far
+ * @param note - records a note
+ * @returns the error export() throws for mixed direction, or null
+ */
+function genericNotes(snapshot, common, several, own, notes, note) {
+    let fatal = null;
+    const edgeLabel = snapshot.edges.byRole("label")?.meta.name;
+    const ownNames = new Set(own.filter((c) => c !== null).map((c) => c.meta.name));
+    for (const gen of checkCapabilities(snapshot, CX_CAPABILITIES, common, {
+        roles: SLOT_ROLES,
+        // a parents column reads back as parents only when some node has several parents
+        roleNames: several ? { ...ROLE_NAMES, parents: "parents" } : ROLE_NAMES,
+    })) {
+        if (writtenOtherwise(gen, ownNames)) {
+            continue;
+        }
+        if (gen.code === LOSS.JSON) {
+            const which = gen.column === null ? "a column" : `column "${gen.column}"`;
+            note(CX_LOSS.JSON_AS_STRING, `${which} holds nested values; written as a string attribute holding their JSON text`, gen.column, gen.count);
+            continue;
+        }
+        if (isEdgeLabelRename(gen, edgeLabel)) {
+            // only nodes have a label slot (n); an edge label is a plain attribute
+            note(LOSS.ROLE, `edge column "${edgeLabel ?? ""}" (label) is written as a plain attribute; CX edges have no label slot and the role is lost`, gen.column, gen.count);
+            continue;
+        }
+        if (gen.code === LOSS.MIXED_DIRECTION_ERROR && fatal === null) {
+            fatal = new GraphFormatError("E_DIRECTED", gen.message, { reason: "mixed direction" });
+        }
+        notes.push(gen);
+    }
+    if (edgeLabel === "name") {
+        note(LOSS.ROLE, `edge column "name" (label) is written as a plain attribute; CX edges have no label slot and the role is lost`, "name", null);
+    }
+    return fatal;
+}
+/**
+ * Whether a generic note is about something CX writes another way: the functionTerm and
+ * reifiedEdge columns (their own aspects), ids (counted by planNodeIds(), since CX also keeps
+ * integer ids beyond 2^53, which the generic rule refuses) and the provenance tables.
+ * @param gen - the generic note
+ * @param ownNames - the names of the columns written as their own aspects
+ * @returns true when the note does not apply
+ */
+function writtenOtherwise(gen, ownNames) {
+    if (gen.column !== null && ownNames.has(gen.column) && (gen.code === LOSS.JSON || gen.code === LOSS.DTYPE)) {
+        return true;
+    }
+    if (gen.code === LOSS.ID_CHARSET || gen.code === LOSS.ID_MANGLED) {
+        return true;
+    }
+    return gen.code === LOSS.EXTENSION_TABLE && gen.column !== null && gen.column in PROVENANCE_TABLES;
+}
+/**
+ * Whether a generic note is the rename of the edge label column.
+ * @param gen - the generic note
+ * @param edgeLabel - the edge label column's name, if any
+ * @returns true when it is
+ */
+function isEdgeLabelRename(gen, edgeLabel) {
+    return gen.code === LOSS.COLUMN_NAME_CHANGED && gen.column === edgeLabel && gen.message.startsWith("edge column");
+}
+/**
+ * The node positions to write: the position column, the z column (when it fits the layout), whether
+ * the position's third coordinate is written as z, and the count of non-finite values left out.
+ * @param snapshot - the snapshot
+ * @param note - records a note
+ * @returns the position plan
+ */
+function planPositions(snapshot, note) {
+    const position = snapshot.nodes.byRole("position");
+    const zColumn = [...snapshot.nodes].find(isZ) ?? null;
+    const z = zColumn !== null && zFitsLayout(zColumn, position) ? zColumn : null;
+    if (position === null) {
+        return { position, z, positionZ: false, nonfinite: 0 };
+    }
+    let nonfinite = nonFiniteCells(position, (v) => [v[0], v[1]]);
+    const depth = nonFiniteCells(position, (v) => (v[2] === 0 ? [] : [Number.NaN]));
+    const positionZ = zColumn === null && (position.meta.extra.sourceDims === 3 || depth > 0);
+    if (positionZ) {
+        nonfinite += nonFiniteCells(position, (v) => (Number.isFinite(v[0]) && Number.isFinite(v[1]) ? [v[2]] : []));
+        note(LOSS.COMPONENTS, `node column "${position.meta.name}" (position) has a third coordinate; CX writes it as the layout's z, which reads back in the z column (a stacking order), not in the position`, position.meta.name, depth);
+    }
+    return { position, z, positionZ, nonfinite };
+}
+/**
+ * Note the graph columns that read back as the graph's name or description.
+ * @param snapshot - the snapshot
+ * @param note - records a note
+ */
+function graphColumnNotes(snapshot, note) {
+    for (const c of snapshot.graph) {
+        const named = c.meta.name === "name" || c.meta.name === "description";
+        if (!isBypass(c) && named && (c.dtype === "string" || c.dtype === "dict")) {
+            note(LOSS.ROLE_ASSUMED, `graph column "${c.meta.name}" is written as the network attribute ${c.meta.name}, which reads back as the graph's ${c.meta.name}, not as a column`, c.meta.name, null);
+        }
+    }
+}
+/**
+ * Plan an export: the notes, the fatal condition and what is written.
+ * @param snapshot - the snapshot
+ * @param common - the resolved common options
+ * @returns the plan
+ */
+function plan(snapshot, common) {
+    const { notes, note } = noteList();
+    const functionTerm = [...snapshot.nodes].find((c) => fromCx(c, "provenance") && c.meta.name === "functionTerm") ?? null;
+    const reifiedEdge = [...snapshot.nodes].find((c) => fromCx(c, "reifiedEdges") && c.dtype === "u32") ?? null;
+    const children = childrenCsr(snapshot);
+    const several = children.column?.meta.role === "parents" && severalParents(children.column);
+    let fatal = genericNotes(snapshot, common, several, [functionTerm, reifiedEdge], notes, note);
+    const folding = pairFolding(snapshot);
+    directionNotes(snapshot, folding, common, CX_LOSS.UNDIRECTED_AS_DIRECTED, note);
+    const planned = planNodeIds(snapshot, common, "CX", ORIGINAL_ID_ATTRIBUTE, note);
+    const ids = planned instanceof GraphFormatError ? null : planned;
+    if (planned instanceof GraphFormatError) {
+        fatal ?? (fatal = planned);
+    }
+    const edgeIds = planEdgeIds(snapshot, note);
+    if (snapshot.nodes.has(ORIGINAL_ID_ATTRIBUTE)) {
+        note(LOSS.ROLE_ASSUMED, `node column "${ORIGINAL_ID_ATTRIBUTE}" is the importer's record of mangled ids: it reads back as the node ids unless restoreMangledIds is false`, ORIGINAL_ID_ATTRIBUTE, null);
+    }
+    // nodes: n, r, the z column, the groups' collapsed flags, provenance
+    const positions = planPositions(snapshot, note);
+    const { position, z, positionZ } = positions;
+    let { nonfinite } = positions;
+    const collapsed = [...snapshot.nodes].find((c) => fromCx(c, "cyGroups") && c.dtype === "bool") ?? null;
+    const nodeCore = corePlans(snapshot, note);
+    const edgeCore = [];
+    const interaction = snapshot.edges.get("interaction");
+    if (interaction !== null && (interaction.meta.role === null || !SKIPPED_ROLES.has(interaction.meta.role))) {
+        edgeCore.push({ key: "i", column: interaction });
+        coreTextNote(interaction, "edge", note);
+    }
+    const coreColumns = new Set([...nodeCore, ...edgeCore].map((c) => c.column));
+    const special = (c) => coreColumns.has(c) ||
+        isBypass(c) ||
+        isLink(c) ||
+        c === z ||
+        c === collapsed ||
+        c === functionTerm ||
+        c === reifiedEdge ||
+        (c.meta.role !== null && SKIPPED_ROLES.has(c.meta.role));
+    const label = snapshot.nodes.byRole("label");
+    const renamedName = label !== null && label.meta.name !== "name" ? snapshot.nodes.get("name") : null;
+    if (renamedName !== null) {
+        note(LOSS.COLUMN_NAME_CHANGED, `node column "name" is written as the attribute "name#2": the label column "${label?.meta.name ?? ""}" is written as n, which reads back as "name"`, "name", renamedName.length - renamedName.nullCount);
+    }
+    const nodeAttrs = attributePlans(snapshot.nodes, special, (c) => (c === renamedName ? "name#2" : c.meta.name));
+    const weight = planWeight(snapshot, folding, note);
+    const plainWeight = snapshot.edges.get(WEIGHT_ATTRIBUTE);
+    const edgeAttrs = attributePlans(snapshot.edges, (c) => special(c) || (c === plainWeight && c.meta.role === null), (c) => c.meta.name);
+    nonfinite += weight.nonfinite;
+    graphColumnNotes(snapshot, note);
+    const graphAttrs = attributePlans(snapshot.graph, isBypass, (c) => c.meta.name);
+    if (children.column !== null && children.column.meta.role === "parents" && !several) {
+        note(LOSS.COLUMN_NAME_CHANGED, `node column "${children.column.meta.name}" (parents) holds at most one parent per node; it reads back as the single-parent column "parent"`, children.column.meta.name, children.column.length - children.column.nullCount);
+    }
+    if (nonfinite > 0) {
+        note(LOSS.NONFINITE_AS_NULL, `${nonfinite} NaN or infinite position${plural(nonfinite)}, stacking orders or weights cannot be written in CX; they read back unset`, null, nonfinite);
+    }
+    return {
+        notes,
+        fatal,
+        ids,
+        folding,
+        edgeIds,
+        weight: weight.plan,
+        nodeCore,
+        edgeCore,
+        nodeAttrs,
+        edgeAttrs,
+        graphAttrs,
+        position,
+        positionZ,
+        z,
+        bypass: {
+            node: [...snapshot.nodes].filter(isBypass),
+            edge: [...snapshot.edges].filter(isBypass),
+            graph: [...snapshot.graph].filter(isBypass),
+        },
+        collapsed,
+        links: linkPlans(snapshot),
+        functionTerm,
+        reifiedEdge,
+    };
+}
+/**
+ * The node core fields: n from the label column (else a plain `name` column, which then reads back
+ * as the label), r from a `represents` column.
+ * @param snapshot - the snapshot
+ * @param note - records a note
+ * @returns the plans
+ */
+function corePlans(snapshot, note) {
+    const out = [];
+    const label = snapshot.nodes.byRole("label");
+    const plainName = snapshot.nodes.get("name");
+    const n = label ?? (plainName !== null && plainName.meta.role === null ? plainName : null);
+    if (n !== null) {
+        out.push({ key: "n", column: n });
+        coreTextNote(n, "node", note);
+        if (n !== label) {
+            note(LOSS.ROLE_ASSUMED, `node column "name" is written as n and reads back as the label`, "name", n.length - n.nullCount);
+        }
+    }
+    const represents = snapshot.nodes.get("represents");
+    if (represents !== null &&
+        represents !== n &&
+        (represents.meta.role === null || !SKIPPED_ROLES.has(represents.meta.role))) {
+        out.push({ key: "r", column: represents });
+        coreTextNote(represents, "node", note);
+    }
+    return out;
+}
+/**
+ * The note of a core field column that is not text: n, r and i are strings in CX.
+ * @param column - the column
+ * @param domain - node or edge
+ * @param note - records a note
+ */
+function coreTextNote(column, domain, note) {
+    if (coreNeedsText(column)) {
+        note(LOSS.DTYPE, `${domain} column "${column.meta.name}" is ${column.dtype}; CX writes it as text and it reads back as string`, column.meta.name, column.length - column.nullCount);
+    }
+}
+/**
+ * The attribute plans of one table.
+ * @param table - the table
+ * @param skip - columns not written as attributes
+ * @param rename - the written name of a column
+ * @returns the plans
+ */
+function attributePlans(table, skip, rename) {
+    return [...table]
+        .filter((c) => !skip(c))
+        .map((column) => ({ column, name: rename(column), d: declaredType(column) }));
+}
+/**
+ * The weights to write: the explicit weights, else a plain numeric `weight` column (which then
+ * reads back as THE weight); a plain `weight` column that is not written is noted.
+ * @param snapshot - the snapshot
+ * @param folding - the pair folding
+ * @param note - records a note
+ * @returns the plan, or null for no weight attribute, and the count of non-finite weights skipped
+ */
+function planWeight(snapshot, folding, note) {
+    const weights = explicitWeights(snapshot);
+    const plain = snapshot.edges.get(WEIGHT_ATTRIBUTE);
+    const clash = plain !== null && plain.meta.role === null;
+    let plan = null;
+    if (weights.weighted) {
+        plan = { value: (e) => (weights.isExplicit(e) ? weights.value(e) : undefined) };
+        if (clash) {
+            note(LOSS.WEIGHT_KEY_CLASH, `edge column "${WEIGHT_ATTRIBUTE}" is not written: the explicit weights are written under that name`, WEIGHT_ATTRIBUTE, null);
+        }
+    }
+    else if (clash) {
+        const numeric = NUMERIC_DTYPES.has(plain.dtype);
+        note(LOSS.WEIGHT_KEY_CLASH, numeric
+            ? `edge column "${WEIGHT_ATTRIBUTE}" is written as the weight attribute and reads back as the edge weight`
+            : `edge column "${WEIGHT_ATTRIBUTE}" is ${plain.dtype}, and CX reads that attribute as the edge weight; it is not written`, WEIGHT_ATTRIBUTE, null);
+        if (numeric) {
+            plan = { value: (e) => (plain.isSet(e) ? plain.value(e) : undefined) };
+        }
+    }
+    return { plan, nonfinite: plan === null ? 0 : nanWeights(snapshot.edgeCount, plan, folding) };
+}
+/**
+ * The written weights that are NaN, which is not a weight on re-import (the infinities are).
+ * @param edgeCount - the number of edges
+ * @param plan - the weight plan
+ * @param folding - the pair folding
+ * @returns the count
+ */
+function nanWeights(edgeCount, plan, folding) {
+    let nan = 0;
+    for (let e = 0; e < edgeCount; e++) {
+        const w = plan.value(e);
+        if (!folding.folded(e) && w !== undefined && Number.isNaN(w)) {
+            nan++;
+        }
+    }
+    return nan;
+}
+/**
+ * Whether the z column can go into cartesianLayout: every set z is finite and its node has a
+ * finite position (a layout entry needs x and y). Otherwise it is written as an ordinary attribute.
+ * @param z - the z column
+ * @param position - the position column
+ * @returns true when every z fits a layout entry
+ */
+function zFitsLayout(z, position) {
+    for (let i = 0; i < z.length; i++) {
+        if (!z.isSet(i)) {
+            continue;
+        }
+        const value = z.value(i);
+        const point = position?.isSet(i) === true ? position.value(i) : null;
+        if (typeof value !== "number" ||
+            !Number.isFinite(value) ||
+            point === null ||
+            !Number.isFinite(point[0]) ||
+            !Number.isFinite(point[1])) {
+            return false;
+        }
+    }
+    return true;
+}
+/**
+ * Count the set cells of a multi-component column with a non-finite component among those picked.
+ * @param column - the column
+ * @param pick - the components that are written
+ * @returns the count
+ */
+function nonFiniteCells(column, pick) {
+    let count = 0;
+    for (let i = 0; i < column.length; i++) {
+        if (column.isSet(i) && pick(column.value(i)).some((v) => !Number.isFinite(v))) {
+            count++;
+        }
+    }
+    return count;
+}
+/**
+ * Whether a parents column gives some node more than one parent.
+ * @param column - the parents list column
+ * @returns true when one does
+ */
+function severalParents(column) {
+    for (let i = 0; i < column.length; i++) {
+        if (column.isSet(i) && column.value(i).length > 1) {
+            return true;
+        }
+    }
+    return false;
+}
+/**
+ * The citations / supports list columns of a CX import and the aspects they go to.
+ * @param snapshot - the snapshot
+ * @returns the plans
+ */
+function linkPlans(snapshot) {
+    const out = [];
+    for (const [domain, table] of [
+        ["node", snapshot.nodes],
+        ["edge", snapshot.edges],
+    ]) {
+        for (const column of table) {
+            if (isLink(column)) {
+                const key = column.meta.name;
+                out.push({ aspect: `${domain}${key === "citations" ? "Citations" : "Supports"}`, key, domain, column });
+            }
+        }
+    }
+    return out;
+}
+// ============================================================ writing
+/**
+ * The text of a scalar the way Cytoscape writes CX values: numbers by their shortest decimal
+ * ("-0", "NaN", "Infinity" included), booleans as "true" / "false".
+ * @param value - the value
+ * @returns the text
+ */
+function scalarText(value) {
+    if (typeof value === "number") {
+        return Object.is(value, -0) ? "-0" : String(value);
+    }
+    if (typeof value === "string") {
+        return value;
+    }
+    return typeof value === "boolean" ? String(value) : JSON.stringify(value);
+}
+/**
+ * The v of one cell: a JSON string, or an array of strings for a list type.
+ * @param column - the column
+ * @param d - its declared type
+ * @param row - the row
+ * @returns the value, or undefined for an unset cell
+ */
+function cellValue(column, d, row) {
+    if (!column.isSet(row)) {
+        return undefined;
+    }
+    const value = column.value(row);
+    if (column.meta.dtype === "json") {
+        return JSON.stringify(value);
+    }
+    if (column.meta.dtype === "list" || column.meta.components > 1) {
+        const items = Array.from(value);
+        return d === "string" ? JSON.stringify(items) : items.map(scalarText);
+    }
+    return scalarText(value);
+}
+/**
+ * The text a core field (n, r, i) holds for one row.
+ * @param column - the column
+ * @param row - the row
+ * @returns the text, or undefined for an unset cell
+ */
+function coreText(column, row) {
+    if (!column.isSet(row)) {
+        return undefined;
+    }
+    const value = column.value(row);
+    if (column.meta.dtype === "json" || column.meta.dtype === "list" || column.meta.components > 1) {
+        return JSON.stringify(column.meta.dtype === "json" ? value : Array.from(value));
+    }
+    return scalarText(value);
+}
+/**
+ * The written edges: every logical edge but the folded halves of pairs.
+ * @param snapshot - the snapshot
+ * @param folding - the pair folding
+ * @returns the edge indexes
+ */
+function writtenEdges(snapshot, folding) {
+    const out = [];
+    for (let e = 0; e < snapshot.edgeCount; e++) {
+        if (!folding.folded(e)) {
+            out.push(e);
+        }
+    }
+    return out;
+}
+/**
+ * Build every aspect of the document, in the order Cytoscape and NDEx write them.
+ * @param snapshot - the snapshot
+ * @param p - the plan
+ * @param ids - the written node ids
+ * @returns the aspects (those without elements included; the writer skips them)
+ */
+function aspects(snapshot, p, ids) {
+    const { src, dst } = snapshot.edgeList();
+    const edges = writtenEdges(snapshot, p.folding);
+    const nodeRange = () => Array.from({ length: snapshot.nodeCount }, (_, i) => i);
+    const nodeCore = (key) => p.nodeCore.find((c) => c.key === key)?.column ?? null;
+    const n = nodeCore("n");
+    const r = nodeCore("r");
+    const i = p.edgeCore[0]?.column ?? null;
+    const kept = snapshot.meta.sourceFormat === CX_FORMAT && isRecord(snapshot.meta.extra.cx) ? snapshot.meta.extra.cx : {};
+    const out = [
+        {
+            name: "nodes",
+            idCounter: nextNodeId(ids, snapshot.nodeCount),
+            *elements() {
+                for (let row = 0; row < snapshot.nodeCount; row++) {
+                    const element = { "@id": ids.idAt(row) };
+                    const name = n === null ? undefined : coreText(n, row);
+                    const represents = r === null ? undefined : coreText(r, row);
+                    if (name !== undefined) {
+                        element.n = name;
+                    }
+                    if (represents !== undefined) {
+                        element.r = represents;
+                    }
+                    yield element;
+                }
+            },
+        },
+        {
+            name: "edges",
+            idCounter: edges.reduce((max, e) => Math.max(max, p.edgeIds[e] + 1), 0),
+            *elements() {
+                for (const e of edges) {
+                    const element = {
+                        "@id": p.edgeIds[e],
+                        s: ids.idAt(src[e]),
+                        t: ids.idAt(dst[e]),
+                    };
+                    const interaction = i === null ? undefined : coreText(i, e);
+                    if (interaction !== undefined) {
+                        element.i = interaction;
+                    }
+                    yield element;
+                }
+            },
+        },
+        {
+            name: "nodeAttributes",
+            *elements() {
+                for (const a of p.nodeAttrs) {
+                    for (let row = 0; row < snapshot.nodeCount; row++) {
+                        const v = cellValue(a.column, a.d, row);
+                        if (v !== undefined) {
+                            yield { po: ids.idAt(row), n: a.name, v, d: a.d };
+                        }
+                    }
+                }
+                for (let row = 0; row < snapshot.nodeCount; row++) {
+                    if (ids.isChanged(row)) {
+                        yield {
+                            po: ids.idAt(row),
+                            n: ORIGINAL_ID_ATTRIBUTE,
+                            v: String(ids.originalAt(row)),
+                            d: "string",
+                        };
+                    }
+                }
+            },
+        },
+        {
+            name: "edgeAttributes",
+            *elements() {
+                for (const a of p.edgeAttrs) {
+                    for (const e of edges) {
+                        const v = cellValue(a.column, a.d, e);
+                        if (v !== undefined) {
+                            yield { po: p.edgeIds[e], n: a.name, v, d: a.d };
+                        }
+                    }
+                }
+                if (p.weight !== null) {
+                    for (const e of edges) {
+                        const w = p.weight.value(e);
+                        if (w !== undefined && !Number.isNaN(w)) {
+                            yield { po: p.edgeIds[e], n: WEIGHT_ATTRIBUTE, v: scalarText(w), d: "double" };
+                        }
+                    }
+                }
+            },
+        },
+        {
+            name: "networkAttributes",
+            *elements() {
+                for (const a of p.graphAttrs) {
+                    const v = cellValue(a.column, a.d, 0);
+                    if (v !== undefined) {
+                        yield { n: a.name, v, d: a.d };
+                    }
+                }
+                const { meta } = snapshot;
+                for (const [key, value] of [
+                    ["name", meta.name],
+                    ["description", meta.description],
+                ]) {
+                    if (value !== null && !p.graphAttrs.some((a) => a.name === key)) {
+                        yield { n: key, v: value, d: "string" };
+                    }
+                }
+            },
+        },
+        { name: "cyTableColumn", elements: () => tableColumns(p, ids) },
+        { name: "cartesianLayout", elements: () => layoutElements(p, ids, nodeRange()) },
+        { name: "cyGroups", elements: () => groupElements(snapshot, p, ids, edges) },
+        { name: "cyVisualProperties", elements: () => visualProperties(p, ids, nodeRange(), edges, kept) },
+    ];
+    out.push(...provenanceAspects(snapshot, p, ids, edges));
+    for (const [name, value] of Object.entries(kept)) {
+        if (!NEVER_WRITTEN.has(name) && Array.isArray(value)) {
+            out.push({ name, elements: () => keptElements(value, kept.subnetwork, STYLE_ASPECTS.has(name)) });
+        }
+    }
+    return out;
+}
+/**
+ * The cyTableColumn entries: every written column with its type, so a column no element fills is
+ * still declared on re-import.
+ * @param p - the plan
+ * @param ids - the written ids
+ * @yields the entries
+ */
+function* tableColumns(p, ids) {
+    for (const { key, column } of [...p.nodeCore, ...p.edgeCore]) {
+        const n = { n: "name", r: "represents", i: "interaction" }[key];
+        if (n !== undefined && column !== null) {
+            yield { applies_to: key === "i" ? "edge_table" : "node_table", n, d: "string" };
+        }
+    }
+    for (const a of p.nodeAttrs) {
+        yield { applies_to: "node_table", n: a.name, d: a.d };
+    }
+    if (ids.changed > 0) {
+        yield { applies_to: "node_table", n: ORIGINAL_ID_ATTRIBUTE, d: "string" };
+    }
+    for (const a of p.edgeAttrs) {
+        yield { applies_to: "edge_table", n: a.name, d: a.d };
+    }
+    if (p.weight !== null) {
+        yield { applies_to: "edge_table", n: WEIGHT_ATTRIBUTE, d: "double" };
+    }
+    for (const a of p.graphAttrs) {
+        yield { applies_to: "network_table", n: a.name, d: a.d };
+    }
+}
+/** Kept aspects whose view references are rewritten to the one view of the written file. */
+const STYLE_ASPECTS = new Set(["tableVisualProperties", "cyTableVisualProperties"]);
+/**
+ * The elements of a kept aspect: those of the snapshot's own subnetwork (or unscoped), with the
+ * scope dropped; style elements get their view references rewritten to view 0.
+ * @param elements - the kept elements
+ * @param subnetwork - the subnetwork the snapshot was read from, if any
+ * @param style - whether the aspect is a style aspect
+ * @yields the elements to write
+ */
+function* keptElements(elements, subnetwork, style) {
+    for (const element of elements) {
+        if (!isRecord(element)) {
+            yield element;
+            continue;
+        }
+        if (element.s !== undefined && element.s !== null && element.s !== subnetwork) {
+            continue;
+        }
+        const { s: _scope, ...rest } = element;
+        yield style ? rewriteView(rest) : rest;
+    }
+}
+/**
+ * A style element with its view and subnetwork references rewritten to 0, the written network.
+ * @param element - the element
+ * @returns the rewritten element
+ */
+function rewriteView(element) {
+    const out = { ...element };
+    if ("view" in out) {
+        out.view = 0;
+    }
+    if (typeof out.applies_to === "number") {
+        out.applies_to = 0;
+    }
+    return out;
+}
+/**
+ * The cartesianLayout entries: x / y (y negated back to screen coordinates) and z.
+ * @param p - the plan
+ * @param ids - the written ids
+ * @param rows - every node row
+ * @yields the entries
+ */
+function* layoutElements(p, ids, rows) {
+    const { position } = p;
+    if (position === null) {
+        return;
+    }
+    for (const row of rows) {
+        if (!position.isSet(row)) {
+            continue;
+        }
+        const point = position.value(row);
+        if (!Number.isFinite(point[0]) || !Number.isFinite(point[1])) {
+            continue;
+        }
+        const entry = { node: ids.idAt(row), x: point[0], y: point[1] === 0 ? 0 : -point[1] };
+        if (p.z?.isSet(row) === true) {
+            entry.z = p.z.value(row);
+        }
+        else if (p.positionZ && Number.isFinite(point[2])) {
+            entry.z = point[2];
+        }
+        yield entry;
+    }
+}
+/**
+ * The cyGroups entries: one per node that has members (or a collapsed flag), its members, and the
+ * edges with both ends (internal) or one end (external) among them.
+ * @param snapshot - the snapshot
+ * @param p - the plan
+ * @param ids - the written ids
+ * @param edges - the written edges
+ * @yields the entries
+ */
+function* groupElements(snapshot, p, ids, edges) {
+    const children = childrenCsr(snapshot);
+    const groupsOf = new Map();
+    const groups = [];
+    for (let g = 0; g < snapshot.nodeCount; g++) {
+        const members = children.childrenOf(g);
+        if (members.length > 0 || p.collapsed?.isSet(g) === true) {
+            groups.push(g);
+        }
+        for (const c of members) {
+            groupsOf.set(c, [...(groupsOf.get(c) ?? []), g]);
+        }
+    }
+    if (groups.length === 0) {
+        return;
+    }
+    const { internal, external } = groupEdges(snapshot, p, groupsOf, edges);
+    const label = p.nodeCore.find((c) => c.key === "n")?.column ?? null;
+    for (const g of groups) {
+        const entry = { "@id": ids.idAt(g) };
+        const name = label === null ? undefined : coreText(label, g);
+        if (name !== undefined) {
+            entry.n = name;
+        }
+        entry.nodes = Array.from(children.childrenOf(g), (c) => ids.idAt(c));
+        entry.internal_edges = internal.get(g) ?? [];
+        entry.external_edges = external.get(g) ?? [];
+        if (p.collapsed?.isSet(g) === true) {
+            entry.collapsed = p.collapsed.value(g);
+        }
+        yield entry;
+    }
+}
+/**
+ * The written edges of each group: internal (both ends among its members) and external (one end).
+ * @param snapshot - the snapshot
+ * @param p - the plan
+ * @param groupsOf - the groups each member node is in
+ * @param edges - the written edges
+ * @returns the edge ids by group
+ */
+function groupEdges(snapshot, p, groupsOf, edges) {
+    const internal = new Map();
+    const external = new Map();
+    const add = (table, g, id) => {
+        table.set(g, [...(table.get(g) ?? []), id]);
+    };
+    const { src, dst } = snapshot.edgeList();
+    for (const e of edges) {
+        const ofSource = groupsOf.get(src[e]) ?? [];
+        const ofTarget = groupsOf.get(dst[e]) ?? [];
+        for (const g of ofSource) {
+            add(ofTarget.includes(g) ? internal : external, g, p.edgeIds[e]);
+        }
+        for (const g of ofTarget.filter((t) => !ofSource.includes(t))) {
+            add(external, g, p.edgeIds[e]);
+        }
+    }
+    return { internal, external };
+}
+/**
+ * The visual property values of one row: property -> value text.
+ * @param columns - the bypass columns
+ * @param row - the row
+ * @returns the properties, or null when none is set
+ */
+function bypassValues(columns, row) {
+    let out = null;
+    for (const column of columns) {
+        if (column.isSet(row)) {
+            // the visual property's own name: a column renamed for a clash with an attribute keeps it in origin.id
+            const property = column.meta.origin?.id;
+            out ?? (out = {});
+            out[typeof property === "string" && property.length > 0 ? property : column.meta.name] = scalarText(column.value(row));
+        }
+    }
+    return out;
+}
+/**
+ * The cyVisualProperties entries: the network values, the style rules a CX import kept (its own
+ * view's, rewritten to view 0) and the per-element values.
+ * @param p - the plan
+ * @param ids - the written ids
+ * @param rows - every node row
+ * @param edges - the written edges
+ * @param kept - meta.extra.cx of a CX import, else empty
+ * @yields the entries
+ */
+function* visualProperties(p, ids, rows, edges, kept) {
+    const network = bypassValues(p.bypass.graph, 0);
+    if (network !== null) {
+        yield { properties_of: "network", properties: network };
+    }
+    const view = ownView(kept);
+    for (const entry of Array.isArray(kept.cyVisualProperties) ? kept.cyVisualProperties : []) {
+        if (isRecord(entry) &&
+            !["nodes", "edges", "network"].includes(String(entry.properties_of)) &&
+            (view === null || entry.view === undefined || entry.view === null || entry.view === view)) {
+            yield rewriteView(entry);
+        }
+    }
+    for (const row of rows) {
+        const properties = bypassValues(p.bypass.node, row);
+        if (properties !== null) {
+            yield { properties_of: "nodes", applies_to: ids.idAt(row), properties };
+        }
+    }
+    for (const e of edges) {
+        const properties = bypassValues(p.bypass.edge, e);
+        if (properties !== null) {
+            yield { properties_of: "edges", applies_to: p.edgeIds[e], properties };
+        }
+    }
+}
+/**
+ * The view of the subnetwork a CX import read (the one its style rules belong to).
+ * @param kept - meta.extra.cx
+ * @returns the view id, or null when the file named none
+ */
+function ownView(kept) {
+    const sub = kept.subnetwork;
+    for (const r of Array.isArray(kept.cyNetworkRelations) ? kept.cyNetworkRelations : []) {
+        if (isRecord(r) && r.r === "view" && (sub === undefined || r.p === sub)) {
+            return r.c;
+        }
+    }
+    for (const v of Array.isArray(kept.cyViews) ? kept.cyViews : []) {
+        if (isRecord(v) && (sub === undefined || v.s === sub)) {
+            return v["@id"];
+        }
+    }
+    return null;
+}
+/**
+ * The provenance aspects a CX import turned into extension tables and columns, written back:
+ * citations, supports, their node / edge links, functionTerms and reifiedEdges.
+ * @param snapshot - the snapshot
+ * @param p - the plan
+ * @param ids - the written ids
+ * @param edges - the written edges
+ * @returns the aspects
+ */
+function provenanceAspects(snapshot, p, ids, edges) {
+    const out = [];
+    for (const [table, aspect] of Object.entries(PROVENANCE_TABLES)) {
+        const ext = snapshot.extensions.get(table);
+        if (ext === undefined) {
+            continue;
+        }
+        const idColumn = ext.get("id");
+        const fields = [...ext].filter((c) => c !== idColumn);
+        let max = -1;
+        for (let row = 0; row < ext.rowCount; row++) {
+            if (idColumn?.isSet(row) === true) {
+                max = Math.max(max, Number(idColumn.value(row)));
+            }
+        }
+        out.push({
+            name: aspect,
+            idCounter: max + 1,
+            *elements() {
+                for (let row = 0; row < ext.rowCount; row++) {
+                    const element = {};
+                    if (idColumn?.isSet(row) === true) {
+                        element["@id"] = idColumn.value(row);
+                    }
+                    for (const field of fields) {
+                        if (field.isSet(row)) {
+                            element[field.meta.name] = field.value(row);
+                        }
+                    }
+                    yield element;
+                }
+            },
+        });
+    }
+    for (const link of p.links) {
+        out.push({
+            name: link.aspect,
+            *elements() {
+                const rows = link.domain === "node" ? Array.from({ length: snapshot.nodeCount }, (_, i) => i) : edges;
+                for (const row of rows) {
+                    if (link.column.isSet(row)) {
+                        const po = link.domain === "node" ? ids.idAt(row) : p.edgeIds[row];
+                        yield { po: [po], [link.key]: Array.from(link.column.value(row)) };
+                    }
+                }
+            },
+        });
+    }
+    const terms = p.functionTerm;
+    if (terms !== null) {
+        out.push({
+            name: "functionTerms",
+            *elements() {
+                for (let row = 0; row < snapshot.nodeCount; row++) {
+                    const term = terms.isSet(row) ? terms.value(row) : null;
+                    if (isRecord(term)) {
+                        yield { po: ids.idAt(row), ...term };
+                    }
+                }
+            },
+        });
+    }
+    const reified = p.reifiedEdge;
+    if (reified !== null) {
+        out.push({
+            name: "reifiedEdges",
+            *elements() {
+                for (let row = 0; row < snapshot.nodeCount; row++) {
+                    const edge = reified.isSet(row) ? reified.value(row) : -1;
+                    if (edge >= 0 && edge < snapshot.edgeCount) {
+                        yield { node: ids.idAt(row), edge: p.edgeIds[edge] };
+                    }
+                }
+            },
+        });
+    }
+    return out;
+}
+/**
+ * Write the document as text parts.
+ * @param snapshot - the snapshot
+ * @param p - the plan
+ * @yields the document's text
+ * @returns nothing
+ */
+function* write(snapshot, p) {
+    if (p.fatal !== null) {
+        throw p.fatal;
+    }
+    const { ids } = p;
+    if (ids === null) {
+        throw new GraphFormatError("E_INVALID_ID", "node ids cannot be written as CX integers", { reason: "charset" });
+    }
+    const all = aspects(snapshot, p, ids);
+    const written = [];
+    for (const aspect of all) {
+        let count = 0;
+        for (const _ of aspect.elements()) {
+            count++;
+        }
+        if (count > 0 || aspect.name === "nodes") {
+            written.push({ aspect, count });
+        }
+    }
+    const metaData = written.map(({ aspect, count }) => ({
+        name: aspect.name,
+        version: "1.0",
+        ...(aspect.idCounter === undefined ? {} : { idCounter: aspect.idCounter }),
+        elementCount: count,
+        consistencyGroup: 1,
+    }));
+    yield '[{"numberVerification":[{"longNumber":281474976710655}]},\n';
+    yield `{"metaData":${stringify(metaData)}},\n`;
+    for (const { aspect } of written) {
+        yield* aspectBlock(aspect.name, mapIterable(aspect.elements(), stringify));
+    }
+    yield '{"status":[{"error":"","success":true}]}]\n';
+}
+/**
+ * Map an iterable lazily.
+ * @param items - the items
+ * @param fn - the mapping
+ * @yields the mapped items
+ */
+function* mapIterable(items, fn) {
+    for (const item of items) {
+        yield fn(item);
+    }
+}
+/**
+ * The CX version 1 exporter plugin.
+ * @category Built-in formats
+ */
+export const cxExporter = Object.freeze({
+    format: CX_FORMAT,
+    options: Object.freeze([]),
+    capabilities: CX_CAPABILITIES,
+    /**
+     * Pre-flight: what export() would lose, without writing anything.
+     * @param snapshot - the snapshot
+     * @param options - the common options
+     * @returns the notes, empty when the export is exact
+     */
+    check(snapshot, options) {
+        return Object.freeze([...plan(snapshot, resolveExportOptions(options)).notes]);
+    },
+    /**
+     * Write the document as UTF-8 chunks.
+     * @param snapshot - the snapshot
+     * @param options - the common options
+     * @returns the chunks
+     */
+    export(snapshot, options) {
+        return encodeChunks(write(snapshot, plan(snapshot, resolveExportOptions(options))));
+    },
+    /**
+     * Write the document as one string.
+     * @param snapshot - the snapshot
+     * @param options - the common options
+     * @returns the document
+     */
+    exportToString(snapshot, options) {
+        return joinText(write(snapshot, plan(snapshot, resolveExportOptions(options))));
+    },
+});
+//# sourceMappingURL=exporter.js.map