@graphty/graph-io 0.3.30 → 0.3.31

package/dist/chunks/exporter-DEk_XLLs.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"exporter-DEk_XLLs.js","sources":["../../src/formats/cx2/exporter.ts"],"sourcesContent":["/**\n * The CX2 exporter (design/graph-io/cytoscape-and-obo/design.md section 1.3; graphty issue #307):\n * writes a snapshot as one CX2 document -- the descriptor, the pre-metadata, one\n * `attributeDeclarations` block (aliases from `origin.id`, defaults from `meta.default`),\n * `networkAttributes`, `nodes` (x / y from the position with y flipped back to screen coordinates,\n * `z` from the `z` column), `edges`, the `cx2.bypass` columns as `nodeBypasses` / `edgeBypasses`,\n * the opaque aspects a CX2 import kept (which returns its own style rules) and `status`.\n *\n * What CX2 cannot hold is announced by check() before anything is written: every edge is\n * directed (W_CX2_UNDIRECTED_AS_DIRECTED, W_MUTUAL_EXPANDED), node ids are integers (E_ID_CHARSET\n * unless `sanitizeIds: \"mangle\"`, which keeps the original in the `graphty:originalId` attribute\n * the importer restores), nested values are written as JSON text (W_CX2_JSON_AS_STRING), NaN and\n * the infinities as null (W_CX2_NONFINITE_AS_NULL), and the generic notes of checkCapabilities().\n */\n\nimport { type Column, GraphFormatError, type GraphSnapshot } from \"@graphty/graph-format\";\n\nimport {\n    aspectBlock,\n    declaredType,\n    directionNotes,\n    nonFinitePositions,\n    planEdgeIds,\n    planNodeIds,\n    stringify,\n    type WrittenIds,\n} from \"../../common/cx-export.js\";\nimport { type PairFolding, pairFolding } from \"../../common/direction.js\";\nimport { capabilities, checkCapabilities, LOSS } from \"../../common/export.js\";\nimport { isRecord, POSITION_COLUMN } from \"../../common/json-elements.js\";\nimport { type ResolvedExportOptions, resolveExportOptions } from \"../../common/options.js\";\nimport { plural } from \"../../common/plural.js\";\nimport { type ExplicitWeights, explicitWeights } from \"../../common/weights.js\";\nimport { encodeChunks, joinText } from \"../../common/writer.js\";\nimport { type CommonExportOptions, type ExportCapabilities, type GraphExporter, type LossNote } from \"../../types.js\";\nimport { BYPASS_NAMESPACE, CX2_FORMAT, cx2Type, ORIGINAL_ID_ATTRIBUTE } from \"./importer.js\";\n\n/**\n * The options of the CX2 exporter: the common export options; it has none of its own.\n * @category Built-in formats\n */\nexport type Cx2ExportOptions = CommonExportOptions;\n\n/**\n * The loss notes the CX2 exporter's check() returns, by name. A key is the\n * code without its severity and format prefixes.\n * @category Built-in formats\n */\nexport const CX2_LOSS = Object.freeze({\n    /**\n     * Every edge is written as directed, so an undirected graph, or the undirected edges of a mixed graph, read back\n     * as directed.\n     */\n    UNDIRECTED_AS_DIRECTED: \"W_CX2_UNDIRECTED_AS_DIRECTED\",\n    /** A nested (json) column is written as a string attribute holding its JSON text. */\n    JSON_AS_STRING: \"W_CX2_JSON_AS_STRING\",\n    /** NaN and the infinities cannot be written; they are written as null and read back unset. */\n    NONFINITE_AS_NULL: \"W_CX2_NONFINITE_AS_NULL\",\n    /** A mutual pair is written as two directed edges without its mark. */\n    MUTUAL_EXPANDED: LOSS.MUTUAL_EXPANDED,\n    /**\n     * An attribute without the weight role is named like the key weights are written under; it reads back as the edge\n     * weight, or is not written when the graph has weights of its own.\n     */\n    WEIGHT_KEY_CLASH: LOSS.WEIGHT_KEY_CLASH,\n    /** A parent / parents column: CX2 has no containment. */\n    HIERARCHY_DROPPED: LOSS.HIERARCHY,\n    /** A start / end / timestamp column: CX2 has no time. */\n    TEMPORAL_DROPPED: LOSS.TEMPORAL,\n    /** An attribute with a role the format has no place for is written as a plain attribute; the role is lost. */\n    ROLE_DROPPED: LOSS.ROLE,\n    /**\n     * An attribute type CX2 stores as another (a 32-bit float as double, an unsigned integer as long, a dictionary as\n     * string); it reads back with that type.\n     */\n    DTYPE_UNSUPPORTED: LOSS.DTYPE,\n    /**\n     * Node ids the format cannot write, under `sanitizeIds: \"error\"`; the save fails with E_INVALID_ID. Pass\n     * `sanitizeIds: \"mangle\"` to rewrite them.\n     */\n    ID_CHARSET: LOSS.ID_CHARSET,\n    /** Node ids that are not integers under sanitizeIds \"mangle\": renumbered, originals kept. */\n    ID_MANGLED: LOSS.ID_MANGLED,\n    /** Edges without a usable id get generated integer ids. */\n    EDGE_IDS_GENERATED: LOSS.EDGE_IDS_GENERATED,\n});\n\n/**\n * What CX2 keeps: directed multigraphs with self-loops, integer node ids,\n * required integer edge ids, declared string / double / integer / boolean columns and lists of\n * them, declared defaults, network attributes and the position role. f32, u32, u8 and dict columns\n * are written as the nearest declared type and read back as it.\n * @category Built-in formats\n */\nexport const CX2_CAPABILITIES: ExportCapabilities = capabilities({\n    mixedDirection: false,\n    multiEdges: true,\n    selfLoops: true,\n    edgeIds: \"required\",\n    idCharset: \"integer\",\n    dtypes: [\"string\", \"f64\", \"i32\", \"bool\"],\n    components: false,\n    lists: true,\n    json: false,\n    defaults: true,\n    options: false,\n    hierarchy: false,\n    temporal: \"none\",\n    graphAttributes: true,\n    positions: true,\n    viz: false,\n});\n\n/** The roles CX2 has a slot for, and the column names its importer gives them. */\nconst SLOT_ROLES: ReadonlySet<string> = new Set([\"label\", \"position\", \"id\"]);\nconst ROLE_NAMES: Readonly<Record<string, string>> = Object.freeze({\n    label: \"name\",\n    position: POSITION_COLUMN,\n});\n\n/** Roles whose columns are never written as attributes. */\nconst SKIPPED_ROLES: ReadonlySet<string> = new Set([\n    \"directed\",\n    \"pair\",\n    \"mutual\",\n    \"weight\",\n    \"timeText\",\n    \"originalId\",\n    \"parent\",\n    \"parents\",\n    \"start\",\n    \"end\",\n    \"timestamp\",\n    \"timestamps\",\n    \"spells\",\n    \"open\",\n    \"spellsOpen\",\n    \"position\",\n    \"color\",\n    \"size\",\n    \"shape\",\n    \"thickness\",\n]);\n\n/** The aspects the exporter writes itself; an opaque aspect of the same name is not written again. */\nconst CORE_ASPECTS: ReadonlySet<string> = new Set([\n    \"nodes\",\n    \"edges\",\n    \"attributeDeclarations\",\n    \"networkAttributes\",\n    \"nodeBypasses\",\n    \"edgeBypasses\",\n    \"metaData\",\n    \"status\",\n]);\n\n/** The weight attribute name. */\nconst WEIGHT_ATTRIBUTE = \"weight\";\n\n/** One attribute column as it will be written. */\ninterface AttributePlan {\n    readonly column: Column;\n    /** The full attribute name. */\n    readonly name: string;\n    /** The key used in v (the alias, or the name). */\n    readonly key: string;\n    /** The declared type text. */\n    readonly d: string;\n    /** Whether values are written as their JSON text (a json column). */\n    readonly jsonText: boolean;\n}\n\n/** Everything export() and check() need, computed once. */\ninterface Plan {\n    readonly notes: LossNote[];\n    readonly fatal: GraphFormatError | null;\n    readonly ids: WrittenIds | null;\n    readonly folding: PairFolding;\n    readonly weights: ExplicitWeights;\n    readonly nodeAttrs: readonly AttributePlan[];\n    readonly edgeAttrs: readonly AttributePlan[];\n    readonly graphAttrs: readonly AttributePlan[];\n    readonly nodeBypasses: readonly Column[];\n    readonly edgeBypasses: readonly Column[];\n    readonly position: Column | null;\n    readonly positionZ: boolean;\n    readonly z: Column | null;\n    readonly edgeIds: readonly number[];\n    readonly originalIds: boolean;\n}\n\n/**\n * Whether a column is a bypass column of a CX2 import.\n * @param column - the column\n * @returns true for the cx2.bypass namespace\n */\nfunction isBypass(column: Column): boolean {\n    return column.meta.origin?.namespace === BYPASS_NAMESPACE;\n}\n\n/**\n * Whether a column is the z (stacking order) column.\n * @param column - the column\n * @returns true for the column marked by a Cytoscape-family importer\n */\nfunction isZ(column: Column): boolean {\n    return column.meta.extra.cytoscape === \"z\";\n}\n\n/**\n * Count the non-finite numbers of a column.\n * @param column - the column\n * @returns how many set cells (or list items) are NaN or infinite\n */\nfunction nonFiniteCount(column: Column): number {\n    const { dtype, itemDtype } = column.meta;\n    const numeric =\n        dtype === \"f32\" || dtype === \"f64\" || (dtype === \"list\" && (itemDtype === \"f32\" || itemDtype === \"f64\"));\n    if (!numeric) {\n        return 0;\n    }\n    let count = 0;\n    for (let i = 0; i < column.length; i++) {\n        if (!column.isSet(i)) {\n            continue;\n        }\n        const value = column.value(i);\n        if (dtype === \"list\") {\n            if ((value as readonly number[]).some((v) => !Number.isFinite(v))) {\n                count++;\n            }\n        } else if (!Number.isFinite(value)) {\n            count++;\n        }\n    }\n    return count;\n}\n\n/**\n * Plan the attribute columns of one table.\n * @param table - the table\n * @param skip - columns not written as attributes\n * @param rename - the written name of a column, when it differs (the label as `name`)\n * @param reserved - keys already used in v\n * @returns the plans\n */\nfunction planAttributes(\n    table: Iterable<Column>,\n    skip: (column: Column) => boolean,\n    rename: (column: Column) => string,\n    reserved: ReadonlySet<string> = new Set(),\n): AttributePlan[] {\n    const plans: AttributePlan[] = [];\n    const used = new Set<string>(reserved);\n    const candidates = [...table].filter((c) => !skip(c));\n    for (const column of candidates) {\n        used.add(rename(column));\n    }\n    for (const column of candidates) {\n        const name = rename(column);\n        const { origin } = column.meta;\n        let key = name;\n        const alias = origin?.format === CX2_FORMAT && typeof origin.id === \"string\" ? origin.id : null;\n        if (alias !== null && alias.length > 0 && alias !== name && !used.has(alias)) {\n            key = alias;\n            used.add(alias);\n        }\n        plans.push({ column, name, key, d: declaredType(column), jsonText: column.meta.dtype === \"json\" });\n    }\n    return plans;\n}\n\n/** A note-recording callback. */\ntype Note = (code: string, message: string, column?: string | null, count?: number | null) => void;\n\n/**\n * The generic notes of checkCapabilities(), adapted to CX2: bypass columns hold any JSON value,\n * ids are counted by planNodeIds(), nested values are written as JSON text, and only the node\n * label is written into the \"n\" slot (an edge label keeps its own name but loses its role).\n * @param snapshot - the snapshot\n * @param common - the resolved common options\n * @param notes - the notes so far, appended to\n * @param note - the recorder\n * @returns the fatal condition, or null\n */\nfunction capabilityNotes(\n    snapshot: GraphSnapshot,\n    common: ResolvedExportOptions,\n    notes: LossNote[],\n    note: Note,\n): GraphFormatError | null {\n    let fatal: GraphFormatError | null = null;\n    // bypass columns are written as bypasses, which hold any JSON value\n    const bypassNames = new Set(\n        [...snapshot.nodes, ...snapshot.edges].filter((c) => isBypass(c) || isZ(c)).map((c) => c.meta.name),\n    );\n    for (const gen of checkCapabilities(snapshot, CX2_CAPABILITIES, common, {\n        roles: SLOT_ROLES,\n        roleNames: ROLE_NAMES,\n    })) {\n        if (!keepGenericNote(gen, bypassNames)) {\n            continue;\n        }\n        if (gen.code === LOSS.JSON) {\n            note(\n                CX2_LOSS.JSON_AS_STRING,\n                `${gen.column === null ? \"a column\" : `column \"${gen.column}\"`} holds nested values; written as a string attribute holding their JSON text`,\n                gen.column,\n                gen.count,\n            );\n            continue;\n        }\n        if (gen.code === LOSS.MIXED_DIRECTION_ERROR && fatal === null) {\n            fatal = new GraphFormatError(\"E_DIRECTED\", gen.message, { reason: \"mixed direction\" });\n        }\n        notes.push(gen);\n    }\n    const edgeLabel = snapshot.edges.byRole(\"label\");\n    if (edgeLabel !== null) {\n        note(\n            LOSS.ROLE,\n            `edge column \"${edgeLabel.meta.name}\" (label) is written as a plain attribute; CX2 edges have no label slot and the role is lost`,\n            edgeLabel.meta.name,\n            edgeLabel.length - edgeLabel.nullCount,\n        );\n    }\n    return fatal;\n}\n\n/**\n * Whether a generic note applies to CX2 as it stands.\n * @param gen - the generic note\n * @param bypassNames - the names of the columns written as bypasses\n * @returns false for a note CX2 drops or replaces\n */\nfunction keepGenericNote(gen: LossNote, bypassNames: ReadonlySet<string>): boolean {\n    if (gen.column !== null && bypassNames.has(gen.column) && (gen.code === LOSS.JSON || gen.code === LOSS.DTYPE)) {\n        return false;\n    }\n    if (gen.code === LOSS.COLUMN_NAME_CHANGED && gen.message.startsWith(\"edge column\")) {\n        // only the node label is written into the \"n\" slot; an edge label keeps its own name\n        return false;\n    }\n    // ids are counted by planNodeIds(): CX2 also keeps integer ids beyond 2^53, which the generic rule refuses\n    return gen.code !== LOSS.ID_CHARSET && gen.code !== LOSS.ID_MANGLED;\n}\n\n/**\n * Note the NaN and infinite values written as null: attribute cells, explicit weights, positions.\n * @param snapshot - the snapshot\n * @param attrs - every planned attribute\n * @param weights - the explicit weights\n * @param position - the position column, or null\n * @param note - the recorder\n */\nfunction nonFiniteNote(\n    snapshot: GraphSnapshot,\n    attrs: readonly AttributePlan[],\n    weights: ExplicitWeights,\n    position: Column | null,\n    note: Note,\n): void {\n    let nonfinite = 0;\n    for (const p of attrs) {\n        nonfinite += nonFiniteCount(p.column);\n    }\n    for (let e = 0; e < snapshot.edgeCount; e++) {\n        if (weights.isExplicit(e) && !Number.isFinite(weights.value(e))) {\n            nonfinite++;\n        }\n    }\n    if (position !== null) {\n        nonfinite += nonFinitePositions(position);\n    }\n    if (nonfinite > 0) {\n        note(\n            CX2_LOSS.NONFINITE_AS_NULL,\n            `${nonfinite} NaN or infinite value${plural(nonfinite)} cannot be written in CX2; written as null, they read back unset`,\n            null,\n            nonfinite,\n        );\n    }\n}\n\n/**\n * Plan the edge attributes, noting a plain `weight` column that clashes with the weight key.\n * @param snapshot - the snapshot\n * @param weights - the explicit weights\n * @param note - the recorder\n * @returns the edge attribute plans\n */\nfunction planEdgeAttributes(snapshot: GraphSnapshot, weights: ExplicitWeights, note: Note): AttributePlan[] {\n    const plainWeight = snapshot.edges.get(WEIGHT_ATTRIBUTE);\n    if (plainWeight !== null && plainWeight.meta.role === null) {\n        note(\n            LOSS.WEIGHT_KEY_CLASH,\n            weights.weighted\n                ? `edge column \"${WEIGHT_ATTRIBUTE}\" is not written: the explicit weights are written under that name`\n                : `edge column \"${WEIGHT_ATTRIBUTE}\" reads back as the edge weight`,\n            WEIGHT_ATTRIBUTE,\n            null,\n        );\n    }\n    return planAttributes(\n        snapshot.edges,\n        (c) =>\n            (c.meta.role !== null && (SKIPPED_ROLES.has(c.meta.role) || c.meta.role === \"id\")) ||\n            isBypass(c) ||\n            (weights.weighted && c === plainWeight),\n        (c) => c.meta.name,\n        weights.weighted ? new Set([WEIGHT_ATTRIBUTE]) : new Set(),\n    );\n}\n\n/**\n * Plan an export: the notes, the fatal condition and what is written.\n * @param snapshot - the snapshot\n * @param common - the resolved common options\n * @returns the plan\n */\nfunction plan(snapshot: GraphSnapshot, common: ResolvedExportOptions): Plan {\n    const notes: LossNote[] = [];\n    const note: Note = (code, message, column = null, count = null) => {\n        notes.push(Object.freeze({ code, message, column, count }));\n    };\n    let fatal = capabilityNotes(snapshot, common, notes, note);\n\n    const folding = pairFolding(snapshot);\n    directionNotes(snapshot, folding, common, CX2_LOSS.UNDIRECTED_AS_DIRECTED, note);\n\n    const planned = planNodeIds(snapshot, common, \"CX2\", ORIGINAL_ID_ATTRIBUTE, note);\n    const ids = planned instanceof GraphFormatError ? null : planned;\n    if (planned instanceof GraphFormatError) {\n        fatal ??= planned;\n    }\n\n    const weights = explicitWeights(snapshot);\n    const label = snapshot.nodes.byRole(\"label\");\n    const nodeAttrs = planAttributes(\n        snapshot.nodes,\n        (c) => (c.meta.role !== null && SKIPPED_ROLES.has(c.meta.role)) || isBypass(c) || isZ(c),\n        (c) => (c === label && !snapshot.nodes.has(\"name\") ? \"name\" : c.meta.name),\n        ids !== null && ids.changed > 0 ? new Set([ORIGINAL_ID_ATTRIBUTE]) : new Set(),\n    );\n    const edgeAttrs = planEdgeAttributes(snapshot, weights, note);\n    const graphAttrs = planAttributes(\n        snapshot.graph,\n        () => false,\n        (c) => c.meta.name,\n    ).map((p) => ({ ...p, key: p.name }));\n\n    const position = snapshot.nodes.byRole(\"position\");\n    nonFiniteNote(snapshot, [...nodeAttrs, ...edgeAttrs, ...graphAttrs], weights, position, note);\n\n    const edgeIds = planEdgeIds(snapshot, note);\n    const z = [...snapshot.nodes].find(isZ) ?? null;\n    const positionZ = position !== null && z === null && position.meta.extra.sourceDims === 3;\n    return {\n        notes,\n        fatal,\n        ids,\n        folding,\n        weights,\n        nodeAttrs,\n        edgeAttrs,\n        graphAttrs,\n        nodeBypasses: [...snapshot.nodes].filter(isBypass),\n        edgeBypasses: [...snapshot.edges].filter(isBypass),\n        position,\n        positionZ,\n        z,\n        edgeIds,\n        originalIds: ids !== null && ids.changed > 0,\n    };\n}\n\n// ============================================================ writing\n\n/**\n * The value written for one cell.\n * @param p - the attribute plan\n * @param row - the row\n * @returns the value, or undefined for an unset cell\n */\nfunction cellValue(p: AttributePlan, row: number): unknown {\n    const { column } = p;\n    if (!column.isSet(row)) {\n        return undefined;\n    }\n    const value = column.value(row);\n    if (p.jsonText) {\n        return JSON.stringify(value);\n    }\n    if (column.meta.dtype === \"list\" || column.meta.components > 1) {\n        const items = Array.from(value as ArrayLike<unknown>);\n        if (p.d === \"string\") {\n            return JSON.stringify(items);\n        }\n        return items.some((v) => typeof v === \"number\" && !Number.isFinite(v)) ? null : items;\n    }\n    if (typeof value === \"number\" && !Number.isFinite(value)) {\n        return null;\n    }\n    return value;\n}\n\n/**\n * The declarations of one table.\n * @param plans - the attribute plans\n * @param defaults - whether defaults and aliases may be written (not for network attributes)\n * @returns the declaration object\n */\nfunction declarations(plans: readonly AttributePlan[], defaults: boolean): Record<string, unknown> {\n    const out: Record<string, unknown> = {};\n    for (const p of plans) {\n        const decl: Record<string, unknown> = { d: p.d };\n        if (defaults && p.key !== p.name) {\n            decl.a = p.key;\n        }\n        const fallback = p.column.meta.default;\n        if (defaults && fallback !== undefined && fallback !== null) {\n            if (defaultFits(cx2Type(p.d), fallback)) {\n                decl.v = fallback;\n            }\n        }\n        out[p.name] = decl;\n    }\n    return out;\n}\n\n/**\n * Whether a declared default can be written as the value of a declared type.\n * @param type - the type\n * @param fallback - the default\n * @returns true when it matches\n */\nfunction defaultFits(type: ReturnType<typeof cx2Type>, fallback: unknown): boolean {\n    if (type === null) {\n        return false;\n    }\n    if (type.list) {\n        return Array.isArray(fallback);\n    }\n    switch (type.scalar) {\n        case \"string\":\n            return typeof fallback === \"string\";\n        case \"boolean\":\n            return typeof fallback === \"boolean\";\n        default:\n            return typeof fallback === \"number\" && Number.isFinite(fallback);\n    }\n}\n\n/**\n * The v object of one element.\n * @param plans - the attribute plans\n * @param row - the row\n * @returns the object, or null when empty\n */\nfunction attributesOf(plans: readonly AttributePlan[], row: number): Record<string, unknown> | null {\n    let out: Record<string, unknown> | null = null;\n    for (const p of plans) {\n        const value = cellValue(p, row);\n        if (value !== undefined) {\n            out ??= {};\n            out[p.key] = value;\n        }\n    }\n    return out;\n}\n\n/**\n * Write the document as text parts.\n * @param snapshot - the snapshot\n * @param p - the plan\n * @yields the document's text\n * @returns nothing\n */\nfunction* write(snapshot: GraphSnapshot, p: Plan): Generator<string, void, undefined> {\n    if (p.fatal !== null) {\n        throw p.fatal;\n    }\n    const { ids } = p;\n    if (ids === null) {\n        throw new GraphFormatError(\"E_INVALID_ID\", \"node ids cannot be written as CX2 integers\", { reason: \"charset\" });\n    }\n    const { src, dst } = snapshot.edgeList();\n    const edges: number[] = [];\n    for (let e = 0; e < snapshot.edgeCount; e++) {\n        if (!p.folding.folded(e)) {\n            edges.push(e);\n        }\n    }\n\n    const nodeDecls = declarations(p.nodeAttrs, true);\n    if (p.originalIds) {\n        nodeDecls[ORIGINAL_ID_ATTRIBUTE] = { d: \"string\" };\n    }\n    const edgeDecls = declarations(p.edgeAttrs, true);\n    if (p.weights.weighted) {\n        edgeDecls[WEIGHT_ATTRIBUTE] = { d: \"double\" };\n    }\n    const networkDecls = declarations(p.graphAttrs, false);\n    const network: Record<string, unknown> = {};\n    for (const a of p.graphAttrs) {\n        const value = cellValue(a, 0);\n        if (value !== undefined) {\n            network[a.name] = value;\n        }\n    }\n    const { meta } = snapshot;\n    for (const [key, value] of [\n        [\"name\", meta.name],\n        [\"description\", meta.description],\n    ] as const) {\n        if (value !== null && !(key in network) && !(key in networkDecls)) {\n            network[key] = value;\n            networkDecls[key] = { d: \"string\" };\n        }\n    }\n    const kept = isRecord(meta.extra.cx2) ? meta.extra.cx2 : {};\n    const otherDecls = isRecord(kept.declarations) ? kept.declarations : {};\n    const opaque = meta.sourceFormat === CX2_FORMAT && isRecord(kept.opaque) ? kept.opaque : {};\n    const declarationsElement: Record<string, unknown> = { ...otherDecls };\n    for (const [key, table] of [\n        [\"networkAttributes\", networkDecls],\n        [\"nodes\", nodeDecls],\n        [\"edges\", edgeDecls],\n    ] as const) {\n        if (Object.keys(table).length > 0) {\n            declarationsElement[key] = table;\n        }\n    }\n    const nodeBypassRows = bypassRows(p.nodeBypasses, snapshot.nodeCount);\n    const edgeBypassRows = bypassRows(p.edgeBypasses, snapshot.edgeCount).filter((e) => !p.folding.folded(e));\n    const opaqueAspects = Object.entries(opaque).filter(\n        (entry): entry is [string, unknown[]] => !CORE_ASPECTS.has(entry[0]) && Array.isArray(entry[1]),\n    );\n\n    const counts: [string, number][] = [];\n    const hasDeclarations = Object.keys(declarationsElement).length > 0;\n    if (hasDeclarations) {\n        counts.push([\"attributeDeclarations\", 1]);\n    }\n    if (Object.keys(network).length > 0) {\n        counts.push([\"networkAttributes\", 1]);\n    }\n    counts.push([\"nodes\", snapshot.nodeCount], [\"edges\", edges.length]);\n    if (nodeBypassRows.length > 0) {\n        counts.push([\"nodeBypasses\", nodeBypassRows.length]);\n    }\n    if (edgeBypassRows.length > 0) {\n        counts.push([\"edgeBypasses\", edgeBypassRows.length]);\n    }\n    for (const [name, elements] of opaqueAspects) {\n        counts.push([name, elements.length]);\n    }\n\n    yield '[{\"CXVersion\":\"2.0\",\"hasFragments\":false},\\n';\n    yield `{\"metaData\":${stringify(counts.map(([name, elementCount]) => ({ name, elementCount })))}},\\n`;\n    if (hasDeclarations) {\n        yield `{\"attributeDeclarations\":[${stringify(declarationsElement)}]},\\n`;\n    }\n    if (Object.keys(network).length > 0) {\n        yield `{\"networkAttributes\":[${stringify(network)}]},\\n`;\n    }\n    yield* block(\"nodes\", snapshot.nodeCount, (i) => stringify(nodeElement(p, ids, i)));\n    yield* block(\"edges\", edges.length, (k) => {\n        const e = edges[k];\n        const element: Record<string, unknown> = {\n            id: p.edgeIds[e],\n            s: ids.idAt(src[e]),\n            t: ids.idAt(dst[e]),\n        };\n        let v = attributesOf(p.edgeAttrs, e);\n        if (p.weights.isExplicit(e)) {\n            const w = p.weights.value(e);\n            v ??= {};\n            v[WEIGHT_ATTRIBUTE] = Number.isFinite(w) ? w : null;\n        }\n        if (v !== null) {\n            element.v = v;\n        }\n        return stringify(element);\n    });\n    if (nodeBypassRows.length > 0) {\n        yield* block(\"nodeBypasses\", nodeBypassRows.length, (k) => {\n            const i = nodeBypassRows[k];\n            return stringify({ id: ids.idAt(i), v: bypassValues(p.nodeBypasses, i) });\n        });\n    }\n    if (edgeBypassRows.length > 0) {\n        yield* block(\"edgeBypasses\", edgeBypassRows.length, (k) => {\n         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origin.id\n            const property = column.meta.origin?.id;\n            out[typeof property === \"string\" && property.length > 0 ? property : column.meta.name] = column.value(row);\n        }\n    }\n    return out;\n}\n\n/**\n * The CX2 exporter plugin.\n * @category Built-in formats\n */\nexport const cx2Exporter: GraphExporter<Cx2ExportOptions> = Object.freeze({\n    format: CX2_FORMAT,\n    options: Object.freeze([]),\n    capabilities: CX2_CAPABILITIES,\n\n    /**\n     * Pre-flight: what export() would lose, without writing anything.\n     * @param snapshot - the snapshot\n     * @param options - the common options\n     * @returns the notes, empty when the export is exact\n     */\n    check(snapshot: GraphSnapshot, options?: Cx2ExportOptions): readonly LossNote[] {\n        return Object.freeze([...plan(snapshot, resolveExportOptions(options)).notes]);\n    },\n\n    /**\n     * Write the document as UTF-8 chunks.\n     * @param snapshot - the snapshot\n     * @param 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package/dist/chunks/ontology-export-C5Xd3W-7.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"ontology-export-C5Xd3W-7.js","sources":["../../src/common/ontology.ts","../../src/common/ontology-export.ts"],"sourcesContent":["/**\n * What the OBO importer and the JSON importer's `obographs` dialect share (design section 1.0, the\n * `ontology.ts` building block): the OBO column vocabulary (names, dtypes, roles), so the `.obo` and\n * the `.json` of one ontology give the same columns, and the OBO 1.4 rule for turning the IRIs\n * OBO Graphs writes back into the identifiers the `.obo` file writes (section 4.6).\n */\n\nimport { type ColumnDecl } from \"@graphty/graph-format\";\n\n/** The dtypes the OBO vocabulary uses. */\ntype OboDtype = \"string\" | \"dict\" | \"bool\" | \"list\" | \"json\";\n\n/** One column of the OBO vocabulary. */\ninterface OboColumnSpec {\n    /** The dtype. */\n    readonly dtype: OboDtype;\n    /** The role, when the column carries one. */\n    readonly role?: \"label\" | \"kind\" | undefined;\n}\n\n/**\n * The node columns of the OBO vocabulary, keyed by column name (design section 4.2). The names are\n * the OBO tag names, so a Gene Ontology user finds `namespace`, `def` and `is_obsolete` under the\n * names the GO documentation uses.\n * @category Plugin helpers\n */\nexport const OBO_NODE_COLUMNS: Readonly<Record<string, OboColumnSpec>> = Object.freeze({\n    type: { dtype: \"dict\" },\n    name: { dtype: \"string\", role: \"label\" },\n    namespace: { dtype: \"dict\" },\n    def: { dtype: \"string\" },\n    \"def.xrefs\": { dtype: \"list\" },\n    comment: { dtype: \"string\" },\n    synonym: { dtype: \"json\" },\n    xref: { dtype: \"list\" },\n    \"xref.descriptions\": { dtype: \"json\" },\n    alt_id: { dtype: \"list\" },\n    subset: { dtype: \"list\" },\n    replaced_by: { dtype: \"list\" },\n    consider: { dtype: \"list\" },\n    is_obsolete: { dtype: \"bool\" },\n    is_anonymous: { dtype: \"bool\" },\n    builtin: { dtype: \"bool\" },\n    created_by: { dtype: \"string\" },\n    creation_date: { dtype: \"string\" },\n    intersection_of: { dtype: \"json\" },\n    union_of: { dtype: \"list\" },\n    equivalent_to: { dtype: \"list\" },\n    disjoint_from: { dtype: \"list\" },\n    property_value: { dtype: \"json\" },\n    // Typedef frames, under typedefs: \"nodes\"\n    domain: { dtype: \"string\" },\n    range: { dtype: \"string\" },\n    inverse_of: { dtype: \"string\" },\n    transitive_over: { dtype: \"list\" },\n    disjoint_over: { dtype: \"list\" },\n    holds_over_chain: { dtype: \"json\" },\n    equivalent_to_chain: { dtype: \"json\" },\n    expand_assertion_to: { dtype: \"json\" },\n    expand_expression_to: { dtype: \"json\" },\n    is_cyclic: { dtype: \"bool\" },\n    is_reflexive: { dtype: \"bool\" },\n    is_symmetric: { dtype: \"bool\" },\n    is_anti_symmetric: { dtype: \"bool\" },\n    is_asymmetric: { dtype: \"bool\" },\n    is_transitive: { dtype: \"bool\" },\n    is_functional: { dtype: \"bool\" },\n    is_inverse_functional: { dtype: \"bool\" },\n    is_metadata_tag: { dtype: \"bool\" },\n    is_class_level: { dtype: \"bool\" },\n    // OBO Graphs only\n    propertyType: { dtype: \"dict\" },\n    // what has no column of its own\n    \"obo.qualifiers\": { dtype: \"json\" },\n    \"obo.unrecognized\": { dtype: \"json\" },\n});\n\n/** The edge columns of the OBO vocabulary. */\nconst OBO_EDGE_COLUMNS: Readonly<Record<string, OboColumnSpec>> = Object.freeze({\n    relation: { dtype: \"dict\", role: \"kind\" },\n    qualifiers: { dtype: \"json\" },\n    meta: { dtype: \"json\" },\n});\n\n/**\n * The node column that marks a node made for an undeclared reference (design section 4.2).\n * @category Plugin helpers\n */\nexport const PLACEHOLDER_COLUMN = \"graphty.placeholder\";\n\n/**\n * The declaration of an OBO vocabulary column.\n * @param domain - node or edge\n * @param name - the column name (a key of OBO_NODE_COLUMNS / OBO_EDGE_COLUMNS, or the placeholder column)\n * @returns the declaration, nullable, with origin `{ format: \"obo\", id: name }`\n * @category Plugin helpers\n */\nexport function oboColumnDecl(domain: \"node\" | \"edge\", name: string): ColumnDecl {\n    if (name === PLACEHOLDER_COLUMN) {\n        return { name, dtype: \"bool\", nullable: true, origin: { format: \"graphty\", id: \"placeholder\" } };\n    }\n    const spec = (domain === \"node\" ? OBO_NODE_COLUMNS : OBO_EDGE_COLUMNS)[name];\n    const decl: ColumnDecl = { name, dtype: spec.dtype, nullable: true, origin: { format: \"obo\", id: name } };\n    if (spec.dtype === \"list\") {\n        decl.itemDtype = \"string\";\n    }\n    if (spec.role !== undefined) {\n        decl.role = spec.role;\n    }\n    return decl;\n}\n\n/**\n * The OBO PURL base every OBO Foundry IRI starts with.\n * @category Plugin helpers\n */\nexport const OBO_PURL = \"http://purl.obolibrary.org/obo/\"; // NOSONAR(S5332): an identifier the OBO standard fixes, never fetched\n\n/** The same base under https, which newer OBO Graphs writers use. */\nconst OBO_PURL_HTTPS = \"https://purl.obolibrary.org/obo/\";\n\n/**\n * The oboInOwl namespace of the OBO-to-OWL mapping's annotation properties.\n * @category Plugin helpers\n */\nexport const OBO_IN_OWL = \"http://www.geneontology.org/formats/oboInOwl#\"; // NOSONAR(S5332): an identifier the OBO standard fixes, never fetched\n\n/**\n * An IRI as the identifier the `.obo` file writes (the OBO 1.4 mapping, section 5.9, read\n * backwards): `http://purl.obolibrary.org/obo/GO_0008150` is `GO:0008150` (the prefix is the text\n * before the first underscore), and `http://purl.obolibrary.org/obo/go#regulates` (how the OWL\n * translation writes an unprefixed OBO id: subsets, relations, synonym types) is `regulates`; the\n * same under `https://purl.obolibrary.org/obo/`.\n * Every other IRI, and an OBO PURL that fits neither form (`.../obo/T/Female`), is kept.\n * @param iri - the IRI\n * @returns the CURIE or local id, or the IRI unchanged\n * @category Plugin helpers\n */\nexport function compactOboIri(iri: string): string {\n    const base = [OBO_PURL, OBO_PURL_HTTPS].find((b) => iri.startsWith(b));\n    if (base === undefined) {\n        return iri;\n    }\n    const rest = iri.slice(base.length);\n    const hash = rest.indexOf(\"#\");\n    if (hash > 0) {\n        const local = rest.slice(hash + 1);\n        return local.length > 0 && !rest.slice(0, hash).includes(\"/\") ? local : iri;\n    }\n    const underscore = rest.indexOf(\"_\");\n    if (underscore <= 0 || rest.includes(\"/\") || underscore === rest.length - 1) {\n        return iri;\n    }\n    return `${rest.slice(0, underscore)}:${rest.slice(underscore + 1)}`;\n}\n\n/**\n * The OBO synonym scopes.\n * @category Plugin helpers\n */\nexport const SYNONYM_SCOPES: ReadonlySet<string> = new Set([\"EXACT\", \"BROAD\", \"NARROW\", \"RELATED\"]);\n\n/**\n * The OBO synonym scope of an OBO Graphs synonym predicate (`hasExactSynonym`, with or without the\n * oboInOwl namespace).\n * @param pred - the predicate\n * @returns the scope, or null for a predicate that is not one of the four\n * @category Plugin helpers\n */\nexport function synonymScopeOf(pred: string): string | null {\n    const local = pred.startsWith(OBO_IN_OWL) ? pred.slice(OBO_IN_OWL.length) : pred;\n    const match = /^has(Exact|Broad|Narrow|Related)Synonym$/.exec(local);\n    return match === null ? null : match[1].toUpperCase();\n}\n\n/**\n * The OBO tag a `basicPropertyValues` predicate of OBO Graphs came from (the OBO-to-OWL mapping of\n * the tags that are annotations), so the `.json` of an ontology fills the same columns as its\n * `.obo`. `shorthand` is the relation's short name; every predicate not listed is a\n * `property_value`.\n * @category Plugin helpers\n */\nexport const OBOGRAPHS_PREDICATE_TAGS: ReadonlyMap<string, string> = new Map([\n    [`${OBO_IN_OWL}hasOBONamespace`, \"namespace\"],\n    [`${OBO_IN_OWL}hasAlternativeId`, \"alt_id\"],\n    [`${OBO_IN_OWL}created_by`, \"created_by\"],\n    [`${OBO_IN_OWL}creation_date`, \"creation_date\"],\n    [`${OBO_PURL}IAO_0100001`, \"replaced_by\"],\n    [`${OBO_IN_OWL}consider`, \"consider\"],\n    [`${OBO_IN_OWL}shorthand`, \"shorthand\"],\n]);\n","/**\n * What the two ontology exporters share (the OBO flat file and the JSON exporter's `obographs`\n * dialect): the snapshot columns that fill the OBO slots (the label as `name`, the edge kind as\n * `relation`), the placeholder nodes a re-import makes again by itself, the order a re-import gives\n * the nodes, and the text of a cell. Both read the snapshot through the column vocabulary of\n * ontology.ts, so a column means the same thing in both files.\n */\n\nimport { type Column, GraphFormatError, type GraphSnapshot } from \"@graphty/graph-format\";\n\nimport { type ExportCapabilities, type LossNote } from \"../types.js\";\nimport { COLUMN_AS_PROPERTY_VALUE_CODE, ROLE_ASSUMED_CODE } from \"./codes.js\";\nimport { checkCapabilities, LOSS } from \"./export.js\";\nimport { formatNumber } from \"./format.js\";\nimport { PLACEHOLDER_COLUMN } from \"./ontology.js\";\nimport { type ResolvedExportOptions } from \"./options.js\";\n\n/**\n * A note recorder.\n * @category Plugin helpers\n */\nexport type NoteFn = (code: string, message: string, column?: string | null, count?: number | null) => void;\n\n/** The generic notes the ontology formats replace with their own (see capabilityNotes()). */\nconst SUPERSEDED: ReadonlySet<string> = new Set([\n    LOSS.DTYPE,\n    LOSS.LIST,\n    LOSS.JSON,\n    LOSS.COMPONENTS,\n    LOSS.GRAPH_ATTRIBUTES,\n]);\n\n/** The roles the ontology formats have a slot for, and the column names their importers give them. */\nconst SLOT_ROLES: ReadonlySet<string> = new Set([\"label\", \"kind\"]);\nconst ROLE_NAMES: Readonly<Record<string, string>> = Object.freeze({ label: \"name\", kind: \"relation\" });\n\n/**\n * The roles whose columns are never written as values (their loss notes come from checkCapabilities()).\n * @category Plugin helpers\n */\nexport const UNWRITTEN_ROLES: ReadonlySet<string> = new Set([\n    \"directed\",\n    \"pair\",\n    \"mutual\",\n    \"weight\",\n    \"timeText\",\n    \"originalId\",\n    \"parent\",\n    \"parents\",\n    \"start\",\n    \"end\",\n    \"timestamp\",\n    \"timestamps\",\n    \"spells\",\n    \"open\",\n    \"spellsOpen\",\n    \"position\",\n    \"color\",\n    \"size\",\n    \"shape\",\n    \"thickness\",\n]);\n\n/**\n * The OBO frame types.\n * @category Plugin helpers\n */\nexport type FrameKind = \"Term\" | \"Instance\" | \"Typedef\";\n\n/**\n * The frame types as a set, for checking a `type` cell.\n * @category Plugin helpers\n */\nexport const FRAME_KINDS: ReadonlySet<string> = new Set([\"Term\", \"Instance\", \"Typedef\"]);\n\n/**\n * The value of a set cell (a multi-component value as a plain array), or undefined when unset; a\n * declared default is not a value here (the formats have no defaults and say so).\n * @param column - the column\n * @param row - the row\n * @returns the value or undefined\n * @category Plugin helpers\n */\nexport function cellOf(column: Column, row: number): unknown {\n    if (!column.isSet(row)) {\n        return undefined;\n    }\n    const value: unknown = column.value(row);\n    return ArrayBuffer.isView(value) ? Array.from(value as unknown as ArrayLike<number>) : value;\n}\n\n/**\n * The text of a scalar value: a number by its dtype's shortest round-tripping form (`-0` kept), a\n * boolean as `true` / `false`, a string as it is, anything else as its JSON text.\n * @param value - the value\n * @param dtype - the dtype it came from (the item dtype for a list item)\n * @returns the text\n * @category Plugin helpers\n */\nexport function textOf(value: unknown, dtype: string): string {\n    switch (typeof value) {\n        case \"string\":\n            return value;\n        case \"boolean\":\n            return value ? \"true\" : \"false\";\n        case \"number\":\n            return formatNumber(\n                value,\n                dtype === \"f32\" || dtype === \"i32\" || dtype === \"u32\" || dtype === \"u8\" ? dtype : \"f64\",\n            );\n        default:\n            return JSON.stringify(value) ?? \"null\";\n    }\n}\n\n/**\n * Whether a column has the dtype of a vocabulary column (string and dict both fit a text column;\n * the other text dtype is reported, not refused).\n * @param want - the vocabulary dtype\n * @param column - the column\n * @returns true when the column can be written into the vocabulary slot\n * @category Plugin helpers\n */\nexport function fitsVocabulary(want: string, column: Column): boolean {\n    switch (want) {\n        case \"list\":\n        case \"bool\":\n        case \"json\":\n            return column.dtype === want;\n        default:\n            return isText(column);\n    }\n}\n\n/**\n * The values of a cell that may hold one value or a list of them.\n * @param value - the cell value, or undefined\n * @returns the values\n * @category Plugin helpers\n */\nexport function valuesOf(value: unknown): readonly unknown[] {\n    if (value === undefined) {\n        return [];\n    }\n    return Array.isArray(value) ? value : [value];\n}\n\n/** A column chosen for an OBO slot. */\ninterface Slot {\n    /** The column, or null when the snapshot has none for the slot. */\n    readonly column: Column | null;\n    /** Whether a role-less column was chosen by its name; it reads back with the role (W_ROLE_ASSUMED). */\n    readonly assumed: boolean;\n}\n\n/**\n * The column of a slot: the column with the role when it holds text, else a role-less text column\n * of the slot's name (which the importer reads back with the role).\n * @param table - the node or edge table\n * @param role - the role (`label` for `name`, `kind` for `relation`)\n * @param name - the name the importer gives the slot\n * @returns the column and whether its role is assumed\n * @category Plugin helpers\n */\nexport function slotColumn(table: GraphSnapshot[\"nodes\"], role: \"label\" | \"kind\", name: string): Slot {\n    const byRole = table.byRole(role);\n    if (byRole !== null) {\n        return { column: isText(byRole) ? byRole : null, assumed: false };\n    }\n    const byName = table.get(name);\n    if (byName !== null && byName.meta.role === null && isText(byName)) {\n        return { column: byName, assumed: true };\n    }\n    return { column: null, assumed: false };\n}\n\n/**\n * Whether a column holds text (string or dict).\n * @param column - the column\n * @returns true for string and dict\n */\nfunction isText(column: Column): boolean {\n    return column.dtype === \"string\" || column.dtype === \"dict\";\n}\n\n/**\n * The placeholder column (`graphty.placeholder`, a bool), or null.\n * @param snapshot - the snapshot\n * @returns the column\n */\nfunction placeholderColumn(snapshot: GraphSnapshot): Column | null {\n    const column = snapshot.nodes.get(PLACEHOLDER_COLUMN);\n    return column !== null && column.dtype === \"bool\" ? column : null;\n}\n\n/**\n * The nodes written without a frame (OBO) or a node record (OBO Graphs) because the re-import makes\n * them again as placeholders: a `graphty.placeholder` true cell, no other set cell, an id written\n * as it is, an edge that references it, and (in the flat file, where an edge is written on its\n * source's frame) no edge of its own.\n * @param snapshot - the snapshot\n * @param written - the logical edges written\n * @param options - `outgoingAllowed`: whether a placeholder may be an edge's source; `changed`: whether a node's id is rewritten\n * @param options.outgoingAllowed - whether a placeholder may be an edge's source\n * @param options.changed - whether a node's id is rewritten\n * @returns one flag per node, 1 for a node written without a frame\n * @category Plugin helpers\n */\nexport function framelessNodes(\n    snapshot: GraphSnapshot,\n    written: readonly number[],\n    options: { readonly outgoingAllowed: boolean; readonly changed: (i: number) => boolean },\n): Uint8Array {\n    const flags = new Uint8Array(snapshot.nodeCount);\n    const placeholder = placeholderColumn(snapshot);\n    if (placeholder === null) {\n        return flags;\n    }\n    const { src, dst } = snapshot.edgeList();\n    const referenced = new Uint8Array(snapshot.nodeCount);\n    const sources = new Uint8Array(snapshot.nodeCount);\n    for (const e of written) {\n        referenced[dst[e]] = 1;\n        if (options.outgoingAllowed) {\n            referenced[src[e]] = 1;\n        } else {\n            sources[src[e]] = 1;\n        }\n    }\n    const others = [...snapshot.nodes].filter((c) => c !== placeholder);\n    for (let i = 0; i < snapshot.nodeCount; i++) {\n        if (\n            placeholder.isSet(i) &&\n            placeholder.value(i) === true &&\n            referenced[i] === 1 &&\n            sources[i] === 0 &&\n            !options.changed(i) &&\n            others.every((c) => !c.isSet(i))\n        ) {\n            flags[i] = 1;\n        }\n    }\n    return flags;\n}\n\n/**\n * How many nodes a re-import puts at another index: the written nodes keep their order and the\n * placeholders follow in the order the edges first reference them.\n * @param frameless - the framelessNodes() flags\n * @param references - the node indices in the order the written edges reference them\n * @returns the number of nodes whose index changes\n * @category Plugin helpers\n */\nexport function movedNodes(frameless: Uint8Array, references: Iterable<number>): number {\n    const order: number[] = [];\n    for (let i = 0; i < frameless.length; i++) {\n        if (frameless[i] === 0) {\n            order.push(i);\n        }\n    }\n    const seen = new Uint8Array(frameless.length);\n    for (const i of references) {\n        if (frameless[i] === 1 && seen[i] === 0) {\n            seen[i] = 1;\n            order.push(i);\n        }\n    }\n    let moved = 0;\n    for (let k = 0; k < order.length; k++) {\n        if (order[k] !== k) {\n            moved++;\n        }\n    }\n    return moved;\n}\n\n/**\n * Whether a value is a qualifier record as the importers make it: a non-empty object of names to a\n * text or a list of two or more texts (a name given once reads back as a text, never as a\n * one-item list), every name passing `nameOk`.\n * @param value - the value\n * @param nameOk - the name rule\n * @returns true when the record is written and read back unchanged\n * @category Plugin helpers\n */\nexport function isQualifierRecord(value: unknown, nameOk: (name: string) => boolean): boolean {\n    if (typeof value !== \"object\" || value === null || Array.isArray(value)) {\n        return false;\n    }\n    const entries = Object.entries(value);\n    return (\n        entries.length > 0 &&\n        entries.every(\n            ([name, v]) =>\n                nameOk(name) &&\n                (typeof v === \"string\" ||\n                    (Array.isArray(v) && v.length >= 2 && v.every((item) => typeof item === \"string\"))),\n        )\n    );\n}\n\n/** What capabilityNotes() needs to know about the export. */\ninterface CapabilityNoteSpec {\n    /** The format's capabilities. */\n    readonly caps: ExportCapabilities;\n    /** The label column written as the name, or null. */\n    readonly label: Column | null;\n    /** Whether the label is a role-less `name` column. */\n    readonly labelAssumed: boolean;\n    /** Where an edge column without a slot goes, for messages (\"a qualifier\"). */\n    readonly edgeSlot: string;\n    /** Records a note. */\n    readonly note: NoteFn;\n}\n\n/**\n * The generic notes of checkCapabilities() as the ontology formats see them. No column of the\n * snapshot's own survives as a column (the formats keep only the OBO vocabulary), so the generic\n * dtype, list, json, strides and graph-attribute notes give way to the formats' own, which say\n * where each column goes (a vocabulary column written into its slot needs no note; any other\n * becomes property values, edge qualifiers or metadata). The name-change notes stand only for the\n * label and kind columns actually written into their slot. Added: the roles without a slot (a\n * node kind, an edge label) and a role-less `name` column taking the label role.\n * @param snapshot - the snapshot\n * @param common - the common options\n * @param spec - the export's facts\n * @returns the fatal error of a mixed graph under onMixedDirection \"error\", or null\n * @category Plugin helpers\n */\nexport function capabilityNotes(\n    snapshot: GraphSnapshot,\n    common: ResolvedExportOptions,\n    spec: CapabilityNoteSpec,\n): GraphFormatError | null {\n    const { label, note } = spec;\n    let fatal: GraphFormatError | null = null;\n    const kind = snapshot.edges.byRole(\"kind\");\n    for (const gen of checkCapabilities(snapshot, spec.caps, common, { roles: SLOT_ROLES, roleNames: ROLE_NAMES })) {\n        if (SUPERSEDED.has(gen.code) || (gen.code === LOSS.COLUMN_NAME_CHANGED && !isSlotRename(gen, label, kind))) {\n            continue;\n        }\n        if (gen.code === LOSS.MIXED_DIRECTION_ERROR && fatal === null) {\n            fatal = new GraphFormatError(\"E_DIRECTED\", gen.message, { reason: \"mixed direction\" });\n        }\n        note(gen.code, gen.message, gen.column, gen.count);\n    }\n    slotlessRoleNotes(snapshot, spec);\n    return fatal;\n}\n\n/**\n * Note the roles the ontology formats have no slot for (a node kind, an edge label), and a\n * role-less `name` column taking the label role.\n * @param snapshot - the snapshot\n * @param spec - the export's facts\n */\nfunction slotlessRoleNotes(snapshot: GraphSnapshot, spec: CapabilityNoteSpec): void {\n    const { label, note } = spec;\n    const nodeKind = snapshot.nodes.byRole(\"kind\");\n    if (nodeKind !== null) {\n        note(\n            LOSS.ROLE,\n            `node column \"${nodeKind.meta.name}\" (kind) is written as property values; the format has no node kind slot`,\n            nodeKind.meta.name,\n            nodeKind.length - nodeKind.nullCount,\n        );\n    }\n    const edgeLabel = snapshot.edges.byRole(\"label\");\n    if (edgeLabel !== null) {\n        note(\n            LOSS.ROLE,\n            `edge column \"${edgeLabel.meta.name}\" (label) is written as ${spec.edgeSlot}; the format has no edge label slot`,\n            edgeLabel.meta.name,\n            edgeLabel.length - edgeLabel.nullCount,\n        );\n    }\n    if (label !== null && spec.labelAssumed) {\n        note(\n            ROLE_ASSUMED_CODE,\n            `node column \"name\" is written as each node's name and reads back as the label`,\n            \"name\",\n            label.length - label.nullCount,\n        );\n    }\n}\n\n/**\n * Whether a name-change note is about a column written into its slot: the node label, or a text\n * edge kind column.\n * @param gen - the note\n * @param label - the node label column, or null\n * @param kind - the edge kind column, or null\n * @returns true when it is\n */\nfunction isSlotRename(gen: LossNote, label: Column | null, kind: Column | null): boolean {\n    const isLabel = label !== null && gen.column === label.meta.name;\n    return isLabel || (kind !== null && gen.column === kind.meta.name && isText(kind));\n}\n\n/**\n * Record the columns that read back absent: a node or edge column without a set cell on a written\n * element (the importers declare a column when a value needs it).\n * @param snapshot - the snapshot\n * @param rows - the written nodes\n * @param frameless - the frameless flags (a placeholder column set only there reads back)\n * @param written - the written edges\n * @param note - records a note\n * @category Plugin helpers\n */\nexport function emptyColumnNotes(\n    snapshot: GraphSnapshot,\n    rows: readonly number[],\n    frameless: Uint8Array,\n    written: readonly number[],\n    note: NoteFn,\n): void {\n    const tables = [\n        [\n            \"node\",\n            snapshot.nodes,\n            (c: Column): boolean =>\n                rows.some((i) => c.isSet(i)) ||\n                (c.meta.name === PLACEHOLDER_COLUMN && frameless.some((f, i) => f === 1 && c.isSet(i))),\n        ],\n        [\"edge\", snapshot.edges, (c: Column): boolean => written.some((e) => c.isSet(e))],\n    ] as const;\n    for (const [domain, table, used] of tables) {\n        for (const column of table) {\n            const { role, name } = column.meta;\n            if (\n                (role !== null && (UNWRITTEN_ROLES.has(role) || (domain === \"edge\" && role === \"id\"))) ||\n                used(column)\n            ) {\n                continue;\n            }\n            note(LOSS.EMPTY_COLUMN, `${domain} column \"${name}\" has no value to write; it reads back absent`, name, 0);\n        }\n    }\n}\n\n/**\n * Record the note of a node column written as property values.\n * @param note - the recorder\n * @param column - the column\n * @param rows - the written nodes\n * @param how - how the values are written, for the message\n * @category Plugin helpers\n */\nexport function notePropertyColumn(note: NoteFn, column: Column, rows: readonly number[], how: string): void {\n    const count = rows.filter((i) => column.isSet(i)).length;\n    if (count === 0) {\n        return;\n    }\n    const role = column.meta.role === null ? \"\" : ` (its ${column.meta.role} role is lost)`;\n    note(\n        COLUMN_AS_PROPERTY_VALUE_CODE,\n        `node column \"${column.meta.name}\" is written as ${how} and reads back inside the property_value column, not as its own column${role}`,\n        column.meta.name,\n        count,\n    );\n}\n"],"names":[],"mappings":";;AA0BO,MAAM,mBAA4D,OAAO,OAAO;AAAA,EACnF,MAAM,EAAE,OAAO,OAAA;AAAA,EACf,MAAM,EAAE,OAAO,UAAU,MAAM,QAAA;AAAA,EAC/B,WAAW,EAAE,OAAO,OAAA;AAAA,EACpB,KAAK,EAAE,OAAO,SAAA;AAAA,EACd,aAAa,EAAE,OAAO,OAAA;AAAA,EACtB,SAAS,EAAE,OAAO,SAAA;AAAA,EAClB,SAAS,EAAE,OAAO,OAAA;AAAA,EAClB,MAAM,EAAE,OAAO,OAAA;AAAA,EACf,qBAAqB,EAAE,OAAO,OAAA;AAAA,EAC9B,QAAQ,EAAE,OAAO,OAAA;AAAA,EACjB,QAAQ,EAAE,OAAO,OAAA;AAAA,EACjB,aAAa,EAAE,OAAO,OAAA;AAAA,EACtB,UAAU,EAAE,OAAO,OAAA;AAAA,EACnB,aAAa,EAAE,OAAO,OAAA;AAAA,EACtB,cAAc,EAAE,OAAO,OAAA;AAAA,EACvB,SAAS,EAAE,OAAO,OAAA;AAAA,EAClB,YAAY,EAAE,OAAO,SAAA;AAAA,EACrB,eAAe,EAAE,OAAO,SAAA;AAAA,EACxB,iBAAiB,EAAE,OAAO,OAAA;AAAA,EAC1B,UAAU,EAAE,OAAO,OAAA;AAAA,EACnB,eAAe,EAAE,OAAO,OAAA;AAAA,EACxB,eAAe,EAAE,OAAO,OAAA;AAAA,EACxB,gBAAgB,EAAE,OAAO,OAAA;AAAA;AAAA,EAEzB,QAAQ,EAAE,OAAO,SAAA;AAAA,EACjB,OAAO,EAAE,OAAO,SAAA;AAAA,EAChB,YAAY,EAAE,OAAO,SAAA;AAAA,EACrB,iBAAiB,EAAE,OAAO,OAAA;AAAA,EAC1B,eAAe,EAAE,OAAO,OAAA;AAAA,EACxB,kBAAkB,EAAE,OAAO,OAAA;AAAA,EAC3B,qBAAqB,EAAE,OAAO,OAAA;AAAA,EAC9B,qBAAqB,EAAE,OAAO,OAAA;AAAA,EAC9B,sBAAsB,EAAE,OAAO,OAAA;AAAA,EAC/B,WAAW,EAAE,OAAO,OAAA;AAAA,EACpB,cAAc,EAAE,OAAO,OAAA;AAAA,EACvB,cAAc,EAAE,OAAO,OAAA;AAAA,EACvB,mBAAmB,EAAE,OAAO,OAAA;AAAA,EAC5B,eAAe,EAAE,OAAO,OAAA;AAAA,EACxB,eAAe,EAAE,OAAO,OAAA;AAAA,EACxB,eAAe,EAAE,OAAO,OAAA;AAAA,EACxB,uBAAuB,EAAE,OAAO,OAAA;AAAA,EAChC,iBAAiB,EAAE,OAAO,OAAA;AAAA,EAC1B,gBAAgB,EAAE,OAAO,OAAA;AAAA;AAAA,EAEzB,cAAc,EAAE,OAAO,OAAA;AAAA;AAAA,EAEvB,kBAAkB,EAAE,OAAO,OAAA;AAAA,EAC3B,oBAAoB,EAAE,OAAO,OAAA;AACjC,CAAC;AAGD,MAAM,mBAA4D,OAAO,OAAO;AAAA,EAC5E,UAAU,EAAE,OAAO,QAAQ,MAAM,OAAA;AAAA,EACjC,YAAY,EAAE,OAAO,OAAA;AAAA,EACrB,MAAM,EAAE,OAAO,OAAA;AACnB,CAAC;AAMM,MAAM,qBAAqB;AAS3B,SAAS,cAAc,QAAyB,MAA0B;AAC7E,MAAI,SAAS,oBAAoB;AAC7B,WAAO,EAAE,MAAM,OAAO,QAAQ,UAAU,MAAM,QAAQ,EAAE,QAAQ,WAAW,IAAI,cAAA,EAAc;AAAA,EACjG;AACA,QAAM,QAAQ,WAAW,SAAS,mBAAmB,kBAAkB,IAAI;AAC3E,QAAM,OAAmB,EAAE,MAAM,OAAO,KAAK,OAAO,UAAU,MAAM,QAAQ,EAAE,QAAQ,OAAO,IAAI,OAAK;AACtG,MAAI,KAAK,UAAU,QAAQ;AACvB,SAAK,YAAY;AAAA,EACrB;AACA,MAAI,KAAK,SAAS,QAAW;AACzB,SAAK,OAAO,KAAK;AAAA,EACrB;AACA,SAAO;AACX;AAMO,MAAM,WAAW;AAGxB,MAAM,iBAAiB;AAMhB,MAAM,aAAa;AAanB,SAAS,cAAc,KAAqB;AAC/C,QAAM,OAAO,CAAC,UAAU,cAAc,EAAE,KAAK,CAAC,MAAM,IAAI,WAAW,CAAC,CAAC;AACrE,MAAI,SAAS,QAAW;AACpB,WAAO;AAAA,EACX;AACA,QAAM,OAAO,IAAI,MAAM,KAAK,MAAM;AAClC,QAAM,OAAO,KAAK,QAAQ,GAAG;AAC7B,MAAI,OAAO,GAAG;AACV,UAAM,QAAQ,KAAK,MAAM,OAAO,CAAC;AACjC,WAAO,MAAM,SAAS,KAAK,CAAC,KAAK,MAAM,GAAG,IAAI,EAAE,SAAS,GAAG,IAAI,QAAQ;AAAA,EAC5E;AACA,QAAM,aAAa,KAAK,QAAQ,GAAG;AACnC,MAAI,cAAc,KAAK,KAAK,SAAS,GAAG,KAAK,eAAe,KAAK,SAAS,GAAG;AACzE,WAAO;AAAA,EACX;AACA,SAAO,GAAG,KAAK,MAAM,GAAG,UAAU,CAAC,IAAI,KAAK,MAAM,aAAa,CAAC,CAAC;AACrE;AAMO,MAAM,qCAA0C,IAAI,CAAC,SAAS,SAAS,UAAU,SAAS,CAAC;AAS3F,SAAS,eAAe,MAA6B;AACxD,QAAM,QAAQ,KAAK,WAAW,UAAU,IAAI,KAAK,MAAM,WAAW,MAAM,IAAI;AAC5E,QAAM,QAAQ,2CAA2C,KAAK,KAAK;AACnE,SAAO,UAAU,OAAO,OAAO,MAAM,CAAC,EAAE,YAAA;AAC5C;AASO,MAAM,+CAA4D,IAAI;AAAA,EACzE,CAAC,GAAG,UAAU,mBAAmB,WAAW;AAAA,EAC5C,CAAC,GAAG,UAAU,oBAAoB,QAAQ;AAAA,EAC1C,CAAC,GAAG,UAAU,cAAc,YAAY;AAAA,EACxC,CAAC,GAAG,UAAU,iBAAiB,eAAe;AAAA,EAC9C,CAAC,GAAG,QAAQ,eAAe,aAAa;AAAA,EACxC,CAAC,GAAG,UAAU,YAAY,UAAU;AAAA,EACpC,CAAC,GAAG,UAAU,aAAa,WAAW;AAC1C,CAAC;ACtKD,MAAM,iCAAsC,IAAI;AAAA,EAC5C,KAAK;AAAA,EACL,KAAK;AAAA,EACL,KAAK;AAAA,EACL,KAAK;AAAA,EACL,KAAK;AACT,CAAC;AAGD,MAAM,aAAkC,oBAAI,IAAI,CAAC,SAAS,MAAM,CAAC;AACjE,MAAM,aAA+C,OAAO,OAAO,EAAE,OAAO,QAAQ,MAAM,YAAY;AAM/F,MAAM,sCAA2C,IAAI;AAAA,EACxD;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AACJ,CAAC;AAYM,MAAM,cAAmC,oBAAI,IAAI,CAAC,QAAQ,YAAY,SAAS,CAAC;AAUhF,SAAS,OAAO,QAAgB,KAAsB;AACzD,MAAI,CAAC,OAAO,MAAM,GAAG,GAAG;AACpB,WAAO;AAAA,EACX;AACA,QAAM,QAAiB,OAAO,MAAM,GAAG;AACvC,SAAO,YAAY,OAAO,KAAK,IAAI,MAAM,KAAK,KAAqC,IAAI;AAC3F;AAUO,SAAS,OAAO,OAAgB,OAAuB;AAC1D,UAAQ,OAAO,OAAA;AAAA,IACX,KAAK;AACD,aAAO;AAAA,IACX,KAAK;AACD,aAAO,QAAQ,SAAS;AAAA,IAC5B,KAAK;AACD,aAAO;AAAA,QACH;AAAA,QACA,UAAU,SAAS,UAAU,SAAS,UAAU,SAAS,UAAU,OAAO,QAAQ;AAAA,MAAA;AAAA,IAE1F;AACI,aAAO,KAAK,UAAU,KAAK,KAAK;AAAA,EAAA;AAE5C;AAUO,SAAS,eAAe,MAAc,QAAyB;AAClE,UAAQ,MAAA;AAAA,IACJ,KAAK;AAAA,IACL,KAAK;AAAA,IACL,KAAK;AACD,aAAO,OAAO,UAAU;AAAA,IAC5B;AACI,aAAO,OAAO,MAAM;AAAA,EAAA;AAEhC;AAQO,SAAS,SAAS,OAAoC;AACzD,MAAI,UAAU,QAAW;AACrB,WAAO,CAAA;AAAA,EACX;AACA,SAAO,MAAM,QAAQ,KAAK,IAAI,QAAQ,CAAC,KAAK;AAChD;AAmBO,SAAS,WAAW,OAA+B,MAAwB,MAAoB;AAClG,QAAM,SAAS,MAAM,OAAO,IAAI;AAChC,MAAI,WAAW,MAAM;AACjB,WAAO,EAAE,QAAQ,OAAO,MAAM,IAAI,SAAS,MAAM,SAAS,MAAA;AAAA,EAC9D;AACA,QAAM,SAAS,MAAM,IAAI,IAAI;AAC7B,MAAI,WAAW,QAAQ,OAAO,KAAK,SAAS,QAAQ,OAAO,MAAM,GAAG;AAChE,WAAO,EAAE,QAAQ,QAAQ,SAAS,KAAA;AAAA,EACtC;AACA,SAAO,EAAE,QAAQ,MAAM,SAAS,MAAA;AACpC;AAOA,SAAS,OAAO,QAAyB;AACrC,SAAO,OAAO,UAAU,YAAY,OAAO,UAAU;AACzD;AAOA,SAAS,kBAAkB,UAAwC;AAC/D,QAAM,SAAS,SAAS,MAAM,IAAI,kBAAkB;AACpD,SAAO,WAAW,QAAQ,OAAO,UAAU,SAAS,SAAS;AACjE;AAeO,SAAS,eACZ,UACA,SACA,SACU;AACV,QAAM,QAAQ,IAAI,WAAW,SAAS,SAAS;AAC/C,QAAM,cAAc,kBAAkB,QAAQ;AAC9C,MAAI,gBAAgB,MAAM;AACtB,WAAO;AAAA,EACX;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