@graphty/graph-io 0.3.18 → 0.3.20

package/dist/chunks/importer-DD-xv9_Y.js.map

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+{"version":3,"file":"importer-DD-xv9_Y.js","sources":["../../src/formats/cys/constants.ts","../../src/common/zip.ts","../../src/formats/cys/session.ts","../../src/formats/cys/tables.ts","../../src/formats/cys/importer.ts"],"sourcesContent":["/**\n * What the Cytoscape session importer's modules share: the format facts, the column and metadata\n * names it adds, and its issue code table (design `design/graph-io/cytoscape-and-obo/design.md`\n * sections 1.4 and 3).\n */\n\nimport {\n    AMBIGUOUS_GRAPH_NAME_CODE,\n    DANGLING_REFERENCE_CODE,\n    EMPTY_INPUT_CODE,\n    GRAPH_NOT_FOUND_CODE,\n    MULTIPLE_GRAPHS_CODE,\n    NO_GRAPH_CODE,\n    STYLES_NOT_IMPORTED_CODE,\n    TOO_LARGE_CODE,\n} from \"../../common/codes.js\";\nimport { XGMML_ISSUE } from \"../xgmml/constants.js\";\n\n/** The format name. */\nexport const FORMAT = \"cys\";\n\n/** File extensions. */\nexport const EXTENSIONS: readonly string[] = Object.freeze([\".cys\"]);\n\n/** MIME types: Cytoscape declares none, so the generic zip type. */\nexport const MIME_TYPES: readonly string[] = Object.freeze([\"application/zip\"]);\n\n/** The `meta.extra` key of the session facts. */\nexport const META_KEY = \"cytoscape\";\n\n/** The origin namespace of the columns the session importer adds (selection, hidden state). */\nexport const CYTOSCAPE_NAMESPACE = \"cytoscape\";\n\n/** The 2.x selected state (bool node and edge column). */\nexport const SELECTED_COLUMN = \"cytoscape.selected\";\n\n/** The 2.x hidden state (bool node and edge column). */\nexport const HIDDEN_COLUMN = \"cytoscape.hidden\";\n\n/** The prefix of the node columns of a second and further view's positions (`position@2`). */\nexport const VIEW_POSITION_PREFIX = \"position@\";\n\n/** The default total of uncompressed bytes one import may inflate (2 GiB). */\nexport const DEFAULT_MAX_UNCOMPRESSED = 2 * 1024 * 1024 * 1024;\n\n/** The largest uncompressed-to-compressed ratio an entry may have (real sessions reach 30:1). */\nexport const MAX_RATIO = 1000;\n\n/**\n * The XGMML codes the session importer relays from the network and view files inside, keyed as\n * every table is (the code without its `E_` / `W_` prefix).\n */\nconst RELAYED: Readonly<Record<string, string>> = Object.fromEntries(\n    Object.values(XGMML_ISSUE).map((code) => [code.replace(/^[EW]_/, \"\"), code]),\n);\n\n/**\n * Issue codes of the Cytoscape session importer: its own, the shared ones it records and the\n * XGMML codes it relays from the files inside (with the entry name in the message).\n */\nexport const CYS_ISSUE = Object.freeze({\n    ...RELAYED,\n    /** The input is not a zip archive (or is text). */\n    NOT_ZIP: \"E_CYS_NOT_ZIP\",\n    /** The archive is damaged: no end record, offsets outside the file, a bad CRC, truncated data. */\n    CORRUPT: \"E_CYS_CORRUPT\",\n    /** A zip without a session marker (`<x.y.z>.version` or `cysession.xml`). */\n    NOT_SESSION: \"E_CYS_NOT_SESSION\",\n    /** A zip feature the reader does not support: encryption, a compression method, split archives. */\n    UNSUPPORTED: \"E_CYS_UNSUPPORTED\",\n    /** A session version graph-io cannot read: a major above 3, or the 2011 3.0 pre-release layout. */\n    VERSION: \"E_CYS_VERSION\",\n    /** A table or a virtual column that cannot be read at all; it is skipped. */\n    TABLE: \"E_CYS_TABLE\",\n    /** Table rows with too few or too many cells, a repeated key, or a key matching no element. */\n    TABLE_ROW: \"W_CYS_TABLE_ROW\",\n    /** A collapsed group's members are not in the network; they are recorded in meta.extra. */\n    COLLAPSED_GROUP: \"W_CYS_COLLAPSED_GROUP\",\n    /** Entries the importer does not read (apps, global tables, properties, images, thumbnails). */\n    ENTRY_SKIPPED: \"W_CYS_ENTRY_SKIPPED\",\n    /** Two entries with one name; the first is read. */\n    DUPLICATE_ENTRY: \"W_CYS_DUPLICATE_ENTRY\",\n    /** The archive inflates beyond maxUncompressedBytes, or an entry beyond the ratio limit. */\n    TOO_LARGE: TOO_LARGE_CODE,\n    /** The session's styles are not applied (issue #706). */\n    STYLES_NOT_IMPORTED: STYLES_NOT_IMPORTED_CODE,\n    /** A view, table or network the session names but does not hold. */\n    DANGLING_REFERENCE: DANGLING_REFERENCE_CODE,\n    /** The input is empty. */\n    EMPTY_INPUT: EMPTY_INPUT_CODE,\n    /** The session holds no network. */\n    NO_GRAPH: NO_GRAPH_CODE,\n    /** The session holds several networks; one was read. */\n    MULTIPLE_GRAPHS: MULTIPLE_GRAPHS_CODE,\n    /** graphIndex / graphName names no network (fatal). */\n    GRAPH_NOT_FOUND: GRAPH_NOT_FOUND_CODE,\n    /** graphName names several networks (fatal). */\n    AMBIGUOUS_GRAPH_NAME: AMBIGUOUS_GRAPH_NAME_CODE,\n});\n","/**\n * A zip reader with no dependency (design `design/graph-io/cytoscape-and-obo/design.md` section\n * 3.3; PKWARE APPNOTE 6.3.10, https://pkware.cachefly.net/webdocs/casestudies/APPNOTE.TXT), for\n * the Cytoscape session importer.\n *\n * The whole archive is in memory: every Cytoscape-written entry has a data descriptor and zero\n * sizes in its local header, so the sizes come from the central directory at the end. The end\n * record is searched in the last 65,557 bytes (a comment can be 65,535 bytes long); the zip64\n * locator and the `0x0001` extra field are followed; bytes prepended to the archive (a\n * self-extracting stub) are tolerated by the shift between the directory's stated and actual\n * offsets. Deflate (method 8) is inflated by wrapping the raw deflate bytes in a gzip member\n * (header, data, the directory's CRC-32 and size) and passing it to `DecompressionStream(\"gzip\")`,\n * which every supported runtime has (Node 18, unlike `\"deflate-raw\"`) and which checks the CRC and\n * the length itself; stored entries (method 0) are checked against a CRC-32 table here. Every\n * other method, and encryption, is refused by name. Entry names are decoded by `decodeEntryName()`\n * (the one place bytes become text) and are matching keys only, never paths.\n */\n\nimport { decodeEntryName, throwIfAborted } from \"./input.js\";\n\n/** Why a zip could not be read; the importer maps each kind to its own issue code. */\ntype ZipErrorKind = \"not-zip\" | \"corrupt\" | \"unsupported\" | \"too-large\";\n\n/** A zip that cannot be read, or an entry that cannot be inflated. */\nexport class ZipError extends Error {\n    /** What went wrong. */\n    readonly kind: ZipErrorKind;\n\n    /**\n     * Create the error.\n     * @param kind - what went wrong\n     * @param message - a plain-ASCII message\n     */\n    constructor(kind: ZipErrorKind, message: string) {\n        super(message);\n        this.name = \"ZipError\";\n        this.kind = kind;\n    }\n}\n\n/** One entry of the central directory. */\nexport interface ZipEntry {\n    /** The name, decoded, as the central directory spells it. */\n    readonly name: string;\n    /** The compression method (0 stored, 8 deflate, ...). */\n    readonly method: number;\n    /** The general purpose bit flags. */\n    readonly flags: number;\n    /** The CRC-32 of the uncompressed data. */\n    readonly crc32: number;\n    /** The compressed size in bytes. */\n    readonly compressedSize: number;\n    /** The uncompressed size in bytes. */\n    readonly size: number;\n    /** The offset of the local header in the archive bytes (the prepended-data shift applied). */\n    readonly localOffset: number;\n    /** The name ends in `/`: a directory entry, which holds no data. */\n    readonly directory: boolean;\n}\n\n/** How one entry is read. */\nexport interface ReadEntryOptions {\n    /** The cancellation signal. */\n    readonly signal?: AbortSignal | null | undefined;\n    /** Called with the bytes inflated so far by this call. */\n    readonly onBytes?: ((inflated: number) => void) | undefined;\n    /** The most uncompressed bytes this entry may have (the import's remaining budget). */\n    readonly maxBytes: number;\n    /** The largest uncompressed-to-compressed ratio allowed (above `RATIO_FLOOR` bytes). */\n    readonly maxRatio: number;\n}\n\n/** A per-entry size under which the ratio limit does not apply (tiny entries compress well). */\nexport const RATIO_FLOOR = 1024 * 1024;\n\nconst EOCD_SIGNATURE = 0x06054b50;\nconst ZIP64_LOCATOR_SIGNATURE = 0x07064b50;\nconst ZIP64_EOCD_SIGNATURE = 0x06064b50;\nconst CENTRAL_SIGNATURE = 0x02014b50;\nconst LOCAL_SIGNATURE = 0x04034b50;\nconst EOCD_SIZE = 22;\nconst MAX_COMMENT = 65535;\nconst CENTRAL_SIZE = 46;\nconst LOCAL_SIZE = 30;\nconst ZIP64_EOCD_SIZE = 56;\nconst ZIP64_LOCATOR_SIZE = 20;\nconst U16_MAX = 0xffff;\nconst U32_MAX = 0xffffffff;\n/** Bytes between two cancellation checks while a stored entry's CRC is computed. */\nconst CRC_SLICE = 1024 * 1024;\n\n/** The compression methods other tools write, by number, for the refusal message. */\nconst METHOD_NAMES: Readonly<Record<number, string>> = {\n    1: \"shrink\",\n    6: \"implode\",\n    9: \"deflate64\",\n    12: \"bzip2\",\n    14: \"LZMA\",\n    93: \"zstd\",\n    95: \"xz\",\n    96: \"JPEG\",\n    97: \"WavPack\",\n    98: \"PPMd\",\n    99: \"AES encryption\",\n};\n\n/**\n * Whether bytes start with a local file header signature (`PK\\x03\\x04`).\n * @param bytes - the bytes\n * @returns true for the start of a zip\n */\nexport function startsLikeZip(bytes: Uint8Array): boolean {\n    return bytes.byteLength >= 4 && bytes[0] === 0x50 && bytes[1] === 0x4b && bytes[2] === 3 && bytes[3] === 4;\n}\n\n/**\n * Read the central directory.\n * @param bytes - the whole archive\n * @returns the entries in directory order; ZipError \"not-zip\" when there is no end record and the\n * bytes do not start like a zip, \"corrupt\" for an end record or directory that does not fit,\n * \"unsupported\" for a split archive\n */\nexport function readZipDirectory(bytes: Uint8Array): ZipEntry[] {\n    const view = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);\n    const eocd = findEndRecord(bytes, view);\n    if (eocd < 0) {\n        throw startsLikeZip(bytes)\n            ? new ZipError(\"corrupt\", \"the archive has no end of central directory record (truncated?)\")\n            : new ZipError(\"not-zip\", \"the input is not a zip archive\");\n    }\n    let disk = view.getUint16(eocd + 4, true);\n    let directoryDisk = view.getUint16(eocd + 6, true);\n    let count = view.getUint16(eocd + 10, true);\n    let directorySize = view.getUint32(eocd + 12, true);\n    let directoryOffset = view.getUint32(eocd + 16, true);\n    let directoryEnd = eocd;\n    const locator = eocd - ZIP64_LOCATOR_SIZE;\n    if (locator >= 0 && view.getUint32(locator, true) === ZIP64_LOCATOR_SIGNATURE) {\n        const record = zip64EndRecord(view, locator);\n        disk = view.getUint32(record + 16, true);\n        directoryDisk = view.getUint32(record + 20, true);\n        count = readU64(view, record + 32);\n        directorySize = readU64(view, record + 40);\n        directoryOffset = readU64(view, record + 48);\n        directoryEnd = record;\n    } else if (count === U16_MAX || directorySize === U32_MAX || directoryOffset === U32_MAX) {\n        throw new ZipError(\"corrupt\", \"the end record needs a zip64 record the archive does not have\");\n    }\n    if (disk !== 0 || directoryDisk !== 0) {\n        throw new ZipError(\"unsupported\", \"a split (multi-disk) archive cannot be read\");\n    }\n    const start = directoryEnd - directorySize;\n    if (start < 0 || directoryOffset > bytes.byteLength) {\n        throw new ZipError(\"corrupt\", \"the central directory lies outside the archive\");\n    }\n    // data prepended to the archive moves every offset by the same amount\n    const shift = start - directoryOffset;\n    if (shift < 0) {\n        throw new ZipError(\"corrupt\", \"the central directory offset does not match its position\");\n    }\n    const entries: ZipEntry[] = [];\n    let at = start;\n    for (let i = 0; i < count; i++) {\n        if (at + CENTRAL_SIZE > directoryEnd || view.getUint32(at, true) !== CENTRAL_SIGNATURE) {\n            throw new ZipError(\"corrupt\", `central directory entry ${i + 1} of ${count} is damaged`);\n        }\n        const nameLength = view.getUint16(at + 28, true);\n        const extraLength = view.getUint16(at + 30, true);\n        const commentLength = view.getUint16(at + 32, true);\n        const next = at + CENTRAL_SIZE + nameLength + extraLength + commentLength;\n        if (next > directoryEnd) {\n            throw new ZipError(\"corrupt\", `central directory entry ${i + 1} runs past the directory`);\n        }\n        const name = decodeEntryName(bytes.subarray(at + CENTRAL_SIZE, at + CENTRAL_SIZE + nameLength));\n        let compressedSize = view.getUint32(at + 20, true);\n        let size = view.getUint32(at + 24, true);\n        let localOffset = view.getUint32(at + 42, true);\n        if (compressedSize === U32_MAX || size === U32_MAX || localOffset === U32_MAX) {\n            ({ compressedSize, size, localOffset } = zip64Extra(view, at + CENTRAL_SIZE + nameLength, extraLength, {\n                compressedSize,\n                size,\n                localOffset,\n            }));\n        }\n        entries.push(\n            Object.freeze({\n                name,\n                method: view.getUint16(at + 10, true),\n                flags: view.getUint16(at + 8, true),\n                crc32: view.getUint32(at + 16, true),\n                compressedSize,\n                size,\n                localOffset: localOffset + shift,\n                directory: name.endsWith(\"/\"),\n            }),\n        );\n        at = next;\n    }\n    return entries;\n}\n\n/**\n * The position of the end of central directory record: the last signature whose comment length\n * fits the archive, else the last signature at all (an archive with bytes after its comment).\n * @param bytes - the archive\n * @param view - a view of it\n * @returns the offset, or -1\n */\nfunction findEndRecord(bytes: Uint8Array, view: DataView): number {\n    const lowest = Math.max(0, bytes.byteLength - EOCD_SIZE - MAX_COMMENT);\n    let fallback = -1;\n    for (let at = bytes.byteLength - EOCD_SIZE; at >= lowest; at--) {\n        if (view.getUint32(at, true) !== EOCD_SIGNATURE) {\n            continue;\n        }\n        if (at + EOCD_SIZE + view.getUint16(at + 20, true) === bytes.byteLength) {\n            return at;\n        }\n        if (fallback < 0) {\n            fallback = at;\n        }\n    }\n    return fallback;\n}\n\n/**\n * The zip64 end of central directory record a locator points at (or, when the archive has bytes\n * prepended, the one right before the locator).\n * @param view - the archive\n * @param locator - the locator's offset\n * @returns the record's offset\n */\nfunction zip64EndRecord(view: DataView, locator: number): number {\n    const stated = readU64(view, locator + 8);\n    for (const at of [stated, locator - ZIP64_EOCD_SIZE]) {\n        if (at >= 0 && at + ZIP64_EOCD_SIZE <= locator && view.getUint32(at, true) === ZIP64_EOCD_SIGNATURE) {\n            return at;\n        }\n    }\n    throw new ZipError(\"corrupt\", \"the zip64 end record the locator names is missing\");\n}\n\n/**\n * The zip64 extended information extra field (header id 0x0001) of a central entry: the 64-bit\n * values of the fields whose 32-bit slot is 0xFFFFFFFF, in the order APPNOTE 4.5.3 gives.\n * @param view - the archive\n * @param at - the start of the extra field\n * @param length - its length\n * @param fields - the 32-bit values\n * @param fields.compressedSize - the compressed size slot\n * @param fields.size - the uncompressed size slot\n * @param fields.localOffset - the local header offset slot\n * @returns the resolved values\n */\nfunction zip64Extra(\n    view: DataView,\n    at: number,\n    length: number,\n    fields: { compressedSize: number; size: number; localOffset: number },\n): { compressedSize: number; size: number; localOffset: number } {\n    const out = { ...fields };\n    for (let p = at; p + 4 <= at + length; ) {\n        const id = view.getUint16(p, true);\n        const dataLength = view.getUint16(p + 2, true);\n        if (id === 1) {\n            let q = p + 4;\n            const end = q + dataLength;\n            for (const key of [\"size\", \"compressedSize\", \"localOffset\"] as const) {\n                if (fields[key] === U32_MAX) {\n                    if (q + 8 > end) {\n                        throw new ZipError(\"corrupt\", \"a zip64 extra field is too short\");\n                    }\n                    out[key] = readU64(view, q);\n                    q += 8;\n                }\n            }\n            return out;\n        }\n        p += 4 + dataLength;\n    }\n    throw new ZipError(\"corrupt\", \"an entry needs a zip64 extra field it does not have\");\n}\n\n/**\n * An unsigned 64-bit little-endian integer as a number (exact up to 2^53).\n * @param view - the bytes\n * @param at - the offset\n * @returns the value; ZipError \"unsupported\" beyond 2^53\n */\nfunction readU64(view: DataView, at: number): number {\n    const high = view.getUint32(at + 4, true);\n    if (high >= 0x200000) {\n        throw new ZipError(\"unsupported\", \"a zip64 size or offset beyond 2^53 cannot be read\");\n    }\n    return high * 0x100000000 + view.getUint32(at, true);\n}\n\n/**\n * Read one entry's data: stored entries are sliced and CRC-checked, deflated ones inflated.\n * @param bytes - the whole archive\n * @param entry - the entry\n * @param options - cancellation, progress and the size limits\n * @returns the uncompressed bytes; ZipError for a damaged, encrypted, unsupported or oversized entry\n */\nexport async function readZipEntry(bytes: Uint8Array, entry: ZipEntry, options: ReadEntryOptions): Promise<Uint8Array> {\n    if ((entry.flags & 1) !== 0 || entry.method === 99) {\n        throw new ZipError(\"unsupported\", `${entry.name}: the entry is encrypted`);\n    }\n    if (entry.method !== 0 && entry.method !== 8) {\n        const name = METHOD_NAMES[entry.method] ?? `method ${entry.method}`;\n        throw new ZipError(\n            \"unsupported\",\n            `${entry.name}: compression ${name} is not supported (only stored and deflate)`,\n        );\n    }\n    if (entry.size > options.maxBytes) {\n        throw new ZipError(\n            \"too-large\",\n            `${entry.name}: ${entry.size} uncompressed bytes exceed the limit of ${options.maxBytes}`,\n        );\n    }\n    if (entry.size > RATIO_FLOOR && entry.size > options.maxRatio * Math.max(entry.compressedSize, 1)) {\n        throw new ZipError(\n            \"too-large\",\n            `${entry.name}: ${entry.size} bytes from ${entry.compressedSize} is a compression ratio above ${options.maxRatio}:1`,\n        );\n    }\n    const data = entryData(bytes, entry);\n    if (entry.method === 0) {\n        if (data.byteLength !== entry.size) {\n            throw new ZipError(\"corrupt\", `${entry.name}: a stored entry's sizes disagree`);\n        }\n        let crc = 0xffffffff;\n        for (let at = 0; at < data.byteLength; at += CRC_SLICE) {\n            throwIfAborted(options.signal);\n            crc = crcUpdate(crc, data.subarray(at, Math.min(at + CRC_SLICE, data.byteLength)));\n            options.onBytes?.(Math.min(at + CRC_SLICE, data.byteLength));\n        }\n        if ((crc ^ 0xffffffff) >>> 0 !== entry.crc32) {\n            throw new ZipError(\"corrupt\", `${entry.name}: the data does not match its CRC-32`);\n        }\n        return data;\n    }\n    return inflate(data, entry, options);\n}\n\n/**\n * The compressed bytes of an entry, located through its local header (whose name and extra\n * lengths can differ from the central directory's).\n * @param bytes - the archive\n * @param entry - the entry\n * @returns exactly compressedSize bytes\n */\nfunction entryData(bytes: Uint8Array, entry: ZipEntry): Uint8Array {\n    const view = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);\n    const at = entry.localOffset;\n    if (at + LOCAL_SIZE > bytes.byteLength || view.getUint32(at, true) !== LOCAL_SIGNATURE) {\n        throw new ZipError(\"corrupt\", `${entry.name}: the local header is missing`);\n    }\n    const start = at + LOCAL_SIZE + view.getUint16(at + 26, true) + view.getUint16(at + 28, true);\n    const end = start + entry.compressedSize;\n    if (end > bytes.byteLength) {\n        throw new ZipError(\"corrupt\", `${entry.name}: the entry's data runs past the end of the archive (truncated?)`);\n    }\n    return bytes.subarray(start, end);\n}\n\n/**\n * Inflate a deflate stream through `DecompressionStream(\"gzip\")`, wrapped in a gzip member that\n * carries the directory's CRC-32 and size, so the platform checks both.\n * @param data - the raw deflate bytes\n * @param entry - the entry\n * @param options - cancellation, progress and limits\n * @returns the bytes\n */\nasync function inflate(data: Uint8Array, entry: ZipEntry, options: ReadEntryOptions): Promise<Uint8Array> {\n    if (typeof DecompressionStream !== \"function\") {\n        throw new ZipError(\n            \"unsupported\",\n            \"this runtime has no DecompressionStream, so deflated entries cannot be read\",\n        );\n    }\n    const member = new Uint8Array(10 + data.byteLength + 8);\n    member.set([0x1f, 0x8b, 8, 0, 0, 0, 0, 0, 0, 0xff]);\n    member.set(data, 10);\n    const trailer = new DataView(member.buffer, 10 + data.byteLength, 8);\n    trailer.setUint32(0, entry.crc32, true);\n    trailer.setUint32(4, entry.size % 0x100000000, true);\n    const source = new ReadableStream<BufferSource>({\n        start(controller): void {\n            controller.enqueue(member);\n            controller.close();\n        },\n    });\n    const reader = source.pipeThrough(new DecompressionStream(\"gzip\")).getReader();\n    const parts: Uint8Array[] = [];\n    let total = 0;\n    try {\n        for (;;) {\n            throwIfAborted(options.signal);\n            let chunk: ReadableStreamReadResult<Uint8Array>;\n            try {\n                chunk = await reader.read();\n            } catch {\n                throw new ZipError(\n                    \"corrupt\",\n                    `${entry.name}: the deflate data is damaged or does not match its CRC-32 and size`,\n                );\n            }\n            if (chunk.done) {\n                break;\n            }\n            total += chunk.value.byteLength;\n            if (total > entry.size) {\n                throw new ZipError(\"corrupt\", `${entry.name}: the data is longer than its directory size`);\n            }\n            parts.push(chunk.value);\n            options.onBytes?.(total);\n        }\n    } finally {\n        await reader.cancel().catch(() => undefined);\n    }\n    if (total !== entry.size) {\n        throw new ZipError(\"corrupt\", `${entry.name}: the data is shorter than its directory size`);\n    }\n    if (parts.length === 1) {\n        return parts[0];\n    }\n    const out = new Uint8Array(total);\n    let at = 0;\n    for (const part of parts) {\n        out.set(part, at);\n        at += part.byteLength;\n    }\n    return out;\n}\n\n/** The CRC-32 table (polynomial 0xEDB88320). */\nconst CRC_TABLE = ((): Uint32Array => {\n    const table = new Uint32Array(256);\n    for (let n = 0; n < 256; n++) {\n        let c = n;\n        for (let k = 0; k < 8; k++) {\n            c = (c & 1) === 1 ? 0xedb88320 ^ (c >>> 1) : c >>> 1;\n        }\n        table[n] = c >>> 0;\n    }\n    return table;\n})();\n\n/**\n * Continue a CRC-32 over more bytes.\n * @param crc - the running value (start with 0xFFFFFFFF)\n * @param bytes - the bytes\n * @returns the running value (XOR with 0xFFFFFFFF to finish)\n */\nfunction crcUpdate(crc: number, bytes: Uint8Array): number {\n    let c = crc;\n    for (const byte of bytes) {\n        c = CRC_TABLE[(c ^ byte) & 0xff] ^ (c >>> 8);\n    }\n    return c >>> 0;\n}\n\n/**\n * The CRC-32 of bytes.\n * @param bytes - the bytes\n * @returns the checksum\n */\nexport function crc32(bytes: Uint8Array): number {\n    return (crcUpdate(0xffffffff, bytes) ^ 0xffffffff) >>> 0;\n}\n","/**\n * The layout of a Cytoscape session archive (`research-session-and-style.md` sections 2.1 to 2.3;\n * Cytoscape's `Cy3SessionReaderImpl`, `Cy2SessionReaderImpl` and `SessionUtil`): which entries\n * are the version marker, the networks, views, tables, styles and the rest, read from the central\n * directory alone. Entries are inflated one at a time, only when asked for, within the import's\n * byte budget.\n */\n\nimport { readBytes, textChunks } from \"../../common/input.js\";\nimport { type ResolvedImportOptions } from \"../../common/options.js\";\nimport { ImportReportBuilder } from \"../../common/report.js\";\nimport { tokenizeXml, xmlDeclaredEncoding, XmlSyntaxError } from \"../../common/xml.js\";\nimport { readZipDirectory, readZipEntry, type ZipEntry, ZipError } from \"../../common/zip.js\";\nimport { ImportError, type ImportInput } from \"../../types.js\";\nimport { CYS_ISSUE, FORMAT, MAX_RATIO } from \"./constants.js\";\n\n/** An entry of the session, by its path under the session's root folder. */\nexport interface SessionEntry {\n    /** The path under the root folder, as the archive spells it (URL-encoded parts). */\n    readonly path: string;\n    /** The full entry name, for messages. */\n    readonly name: string;\n    /** The zip entry. */\n    readonly zip: ZipEntry;\n}\n\n/** A 3.x network file: one root network (a collection). */\nexport interface NetworkEntry extends SessionEntry {\n    /** The root network's saved SUID. */\n    readonly suid: string;\n    /** The file name's network name, decoded. */\n    readonly title: string;\n}\n\n/** A 3.x view file. */\ninterface ViewEntry extends SessionEntry {\n    /** The SUID of the network the view shows. */\n    readonly network: string;\n    /** The view's SUID. */\n    readonly view: string;\n}\n\n/** A 3.x table file. */\nexport interface TableEntry extends SessionEntry {\n    /** The path under `tables/` (what `cytables.xml` names). */\n    readonly tablePath: string;\n    /** The SUID of the network the table belongs to. */\n    readonly network: string;\n    /** The namespace: LOCAL_ATTRS, SHARED_ATTRS, HIDDEN or an app's. */\n    readonly namespace: string;\n    /** The element class: CyNode, CyEdge or CyNetwork. */\n    readonly element: \"node\" | \"edge\" | \"network\" | null;\n}\n\n/** What a session archive holds, by kind. */\ninterface SessionLayout {\n    /** \"3\" for a 3.x session, \"2\" for a 2.x one. */\n    readonly era: \"2\" | \"3\";\n    /** The version marker as written (`3.0.0`), or the 2.x cysession.xml documentVersion. */\n    readonly version: string;\n    /** The root folder, with its trailing slash (\"\" when the entries have none). */\n    readonly root: string;\n    readonly networks: readonly NetworkEntry[];\n    readonly views: readonly ViewEntry[];\n    readonly tables: readonly TableEntry[];\n    /** `tables/cytables.xml`, if present. */\n    readonly cytables: SessionEntry | null;\n    /** `apps/org.cytoscape.swing-application/network_list.xml`, if present. */\n    readonly networkList: SessionEntry | null;\n    /** 2.x: `cysession.xml`. */\n    readonly cysession: SessionEntry | null;\n    /** 2.x: the network files by their path. */\n    readonly files: ReadonlyMap<string, SessionEntry>;\n    /** The style entries (`session_vizmap.xml`, `session_vizmap.props`). */\n    readonly styles: readonly SessionEntry[];\n    /** Every entry the importer does not read. */\n    readonly skipped: readonly string[];\n}\n\n/** An opened session: its bytes, its layout and an entry reader within the byte budget. */\nexport interface Session {\n    readonly layout: SessionLayout;\n    /**\n     * Inflate one entry.\n     * @param entry - the entry\n     * @returns its bytes\n     */\n    read(entry: SessionEntry): Promise<Uint8Array>;\n}\n\n/**\n * Java's `URLDecoder.decode` (UTF-8): `+` is a space, `%XX` a byte; a malformed escape leaves the\n * text as it is.\n * @param text - the encoded text\n * @returns the decoded text\n */\nexport function urlDecode(text: string): string {\n    const plus = text.replace(/\\+/g, \" \");\n    try {\n        return decodeURIComponent(plus);\n    } catch {\n        return plus;\n    }\n}\n\n/**\n * Read the input as a zip and lay out its session entries. Fatal: text input or not a zip\n * (E_CYS_NOT_ZIP), an empty input, a damaged archive (E_CYS_CORRUPT), a split archive\n * (E_CYS_UNSUPPORTED), no session marker (E_CYS_NOT_SESSION), a version graph-io cannot read\n * (E_CYS_VERSION).\n * @param input - the input\n * @param report - the report\n * @param common - cancellation and progress\n * @param maxBytes - the import's uncompressed byte budget\n * @returns the session\n */\nexport async function openSession(\n    input: ImportInput,\n    report: ImportReportBuilder,\n    common: ResolvedImportOptions,\n    maxBytes: number,\n): Promise<Session> {\n    const bytes = await readBytes(input, common);\n    if (bytes === null) {\n        report.fail(\n            CYS_ISSUE.NOT_ZIP,\n            \"a Cytoscape session is a zip archive; text input cannot hold one (pass the bytes)\",\n        );\n    }\n    if (bytes.byteLength === 0) {\n        report.fail(CYS_ISSUE.EMPTY_INPUT, \"the input is empty\");\n    }\n    let zipEntries: ZipEntry[];\n    try {\n        zipEntries = readZipDirectory(bytes);\n    } catch (err) {\n        return zipFailure(err, report);\n    }\n    const layout = layoutOf(zipEntries, report);\n    let budget = maxBytes;\n    let inflated = 0;\n    const total = zipEntries.reduce((sum, e) => sum + e.size, 0);\n    return {\n        layout,\n        read: async (entry: SessionEntry): Promise<Uint8Array> => {\n            const before = inflated;\n            try {\n                const data = await readZipEntry(bytes, entry.zip, {\n                    signal: common.signal,\n                    maxBytes: budget,\n                    maxRatio: MAX_RATIO,\n                    onBytes: (n) => common.onProgress?.(before + n, total),\n                });\n                budget -= data.byteLength;\n                inflated += data.byteLength;\n                return data;\n            } catch (err) {\n                return zipFailure(err, report);\n            }\n        },\n    };\n}\n\n/**\n * Fail the import with the fatal issue of a zip error (any other error is rethrown).\n * @param err - the error\n * @param report - the report\n */\nfunction zipFailure(err: unknown, report: ImportReportBuilder): never {\n    if (!(err instanceof ZipError)) {\n        throw err;\n    }\n    const code = {\n        \"not-zip\": CYS_ISSUE.NOT_ZIP,\n        corrupt: CYS_ISSUE.CORRUPT,\n        unsupported: CYS_ISSUE.UNSUPPORTED,\n        \"too-large\": CYS_ISSUE.TOO_LARGE,\n    }[err.kind];\n    if (err.kind === \"too-large\") {\n        // the size limits are not a parse error: graph-io records E_TOO_LARGE as unsupported\n        report.error(\"unsupported\", code, err.message);\n        throw report.abort(err.message, { code });\n    }\n    report.fail(code, err.message);\n}\n\n/** A 3.x network entry name: `<SUID>[-<name>].xgmml`. */\nconst NETWORK_FILE = /^networks\\/(\\d+)(?:-([^/]*))?\\.xgmml$/;\n/** A 3.x view entry name: `<networkSUID>-<viewSUID>[-<title>].xgmml`. */\nconst VIEW_FILE = /^views\\/(\\d+)-(\\d+)(?:-[^/]*)?\\.xgmml$/;\n/** A 3.x table: `tables/<networkSUID>[-<name>]/<namespace>-<class>-<title>.cytable`. */\nconst TABLE_FILE = /^tables\\/((\\d+)(?:-[^/]*)?\\/([^/-]+)-([^/-]+)-[^/]*\\.cytable)$/;\n\n/** Entries of other tools that carry nothing: macOS resource forks and folder metadata. */\nconst NOISE = /(^|\\/)(__MACOSX\\/|\\.DS_Store$)/;\n\n/**\n * Lay out the entries: drop directory entries and macOS noise, keep the first of a repeated name\n * (W_CYS_DUPLICATE_ENTRY), find the session marker and its root folder, classify what is under\n * it, and list what is not read.\n * @param zipEntries - the central directory\n * @param report - the report\n * @returns the layout\n */\nfunction layoutOf(zipEntries: readonly ZipEntry[], report: ImportReportBuilder): SessionLayout {\n    const byName = new Map<string, ZipEntry>();\n    const repeated: string[] = [];\n    for (const entry of zipEntries) {\n        if (entry.directory || NOISE.test(entry.name)) {\n            continue;\n        }\n        if (byName.has(entry.name)) {\n            repeated.push(entry.name);\n            continue;\n        }\n        byName.set(entry.name, entry);\n    }\n    if (repeated.length > 0) {\n        report.warning(\n            \"unsupported\",\n            CYS_ISSUE.DUPLICATE_ENTRY,\n            `${repeated.length} entry name(s) appear more than once; the first of each is read: ${listed(repeated)}`,\n        );\n    }\n    const names = [...byName.keys()];\n    const marker = names.find((n) => /^([^/]*\\/)?[^/]+\\.version$/.test(n));\n    const cysession = names.find((n) => /^([^/]*\\/)?cysession\\.xml$/.test(n));\n    if (marker === undefined && cysession === undefined) {\n        report.fail(\n            CYS_ISSUE.NOT_SESSION,\n            \"the zip holds neither a session version marker (<x.y.z>.version) nor cysession.xml: it is not a Cytoscape session\",\n        );\n    }\n    const anchor = marker ?? (cysession as string);\n    const root = anchor.slice(0, anchor.lastIndexOf(\"/\") + 1);\n    let era: \"2\" | \"3\" = \"2\";\n    let version = \"2.0.0\";\n    if (marker !== undefined) {\n        version = marker.slice(root.length, -\".version\".length);\n        const major = Number(version.split(\".\")[0]);\n        if (!Number.isInteger(major) || major > 3) {\n            report.fail(\n                CYS_ISSUE.VERSION,\n                `the session version ${version} is newer than the Cytoscape 3 sessions graph-io reads`,\n            );\n        }\n        era = major === 3 ? \"3\" : \"2\";\n    }\n    const layout = {\n        era,\n        version,\n        root,\n        networks: [] as NetworkEntry[],\n        views: [] as ViewEntry[],\n        tables: [] as TableEntry[],\n        cytables: null as SessionEntry | null,\n        networkList: null as SessionEntry | null,\n        cysession: null as SessionEntry | null,\n        files: new Map<string, SessionEntry>(),\n        styles: [] as SessionEntry[],\n        skipped: [] as string[],\n    };\n    for (const [name, zip] of byName) {\n        if (!name.startsWith(root) || name === marker) {\n            if (name !== marker) {\n                layout.skipped.push(name);\n            }\n            continue;\n        }\n        const path = name.slice(root.length);\n        const entry: SessionEntry = { path, name, zip };\n        if (era === \"3\") {\n            classify3(entry, layout);\n        } else {\n            classify2(entry, layout);\n        }\n    }\n    return layout;\n}\n\n/**\n * Classify one entry of a 3.x session.\n * @param entry - the entry\n * @param layout - the layout being built\n */\nfunction classify3(entry: SessionEntry, layout: Mutable): void {\n    const { path } = entry;\n    const network = NETWORK_FILE.exec(path);\n    const view = VIEW_FILE.exec(path);\n    const table = TABLE_FILE.exec(path);\n    if (network !== null) {\n        layout.networks.push({ ...entry, suid: network[1], title: urlDecode(network[2] ?? \"\") });\n    } else if (view !== null) {\n        layout.views.push({ ...entry, network: view[1], view: view[2] });\n    } else if (path === \"tables/cytables.xml\") {\n        layout.cytables = entry;\n    } else if (table !== null) {\n        const element = {\n            \"org.cytoscape.model.CyNode\": \"node\",\n            \"org.cytoscape.model.CyEdge\": \"edge\",\n            \"org.cytoscape.model.CyNetwork\": \"network\",\n        }[urlDecode(table[4])] as TableEntry[\"element\"] | undefined;\n        layout.tables.push({\n            ...entry,\n            tablePath: table[1],\n            network: table[2],\n            namespace: urlDecode(table[3]),\n            element: element ?? null,\n        });\n    } else if (path === \"apps/org.cytoscape.swing-application/network_list.xml\") {\n        layout.networkList = entry;\n    } else if (/(^|\\/)session_vizmap\\.(xml|props)$/.test(path)) {\n        layout.styles.push(entry);\n    } else {\n        layout.skipped.push(entry.name);\n    }\n}\n\n/**\n * Classify one entry of a 2.x session.\n * @param entry - the entry\n * @param layout - the layout being built\n */\nfunction classify2(entry: SessionEntry, layout: Mutable): void {\n    const { path } = entry;\n    if (path === \"cysession.xml\") {\n        layout.cysession = entry;\n    } else if (/^[^/]+\\.xgmml$/.test(path)) {\n        layout.files.set(path, entry);\n    } else if (/^session_vizmap\\.(props|xml)$/.test(path)) {\n        layout.styles.push(entry);\n    } else {\n        layout.skipped.push(entry.name);\n    }\n}\n\n/** The layout while it is built. */\ntype Mutable = {\n    -readonly [K in keyof SessionLayout]: SessionLayout[K] extends readonly (infer T)[] ? T[] : SessionLayout[K];\n} & { files: Map<string, SessionEntry> };\n\n/**\n * A list of names for a message: the first ten, then a count.\n * @param names - the names\n * @returns the text\n */\nexport function listed(names: readonly string[]): string {\n    const head = names.slice(0, 10).join(\", \");\n    return names.length > 10 ? `${head} and ${names.length - 10} more` : head;\n}\n\n/** One element of a small XML document, as a tree. */\nexport interface XmlNode {\n    /** The local name. */\n    readonly name: string;\n    /** The attributes by name as written (prefix included). */\n    readonly attrs: ReadonlyMap<string, string>;\n    /** The child elements. */\n    readonly children: XmlNode[];\n}\n\n/**\n * Read a small XML entry (`cytables.xml`, `network_list.xml`, `cysession.xml`) as a tree. A\n * document that is not well-formed is E_CYS_CORRUPT naming the entry.\n * @param bytes - the entry's bytes\n * @param entry - the entry name\n * @param report - the report\n * @param common - cancellation\n * @returns the root element\n */\nexport async function readXmlTree(\n    bytes: Uint8Array,\n    entry: string,\n    report: ImportReportBuilder,\n    common: ResolvedImportOptions,\n): Promise<XmlNode> {\n    const scratch = new ImportReportBuilder(FORMAT, 0);\n    const stack: XmlNode[] = [{ name: \"\", attrs: new Map(), children: [] }];\n    try {\n        await tokenizeXml(\n            textChunks(bytes, scratch, { signal: common.signal, declaredEncoding: xmlDeclaredEncoding }),\n            {\n                start(name, attrs): void {\n                    const node: XmlNode = { name: name.slice(name.lastIndexOf(\":\") + 1), attrs, children: [] };\n                    stack[stack.length - 1].children.push(node);\n                    stack.push(node);\n                },\n                end(): void {\n                    stack.pop();\n                },\n                text(): void {\n                    // the session documents keep everything in attributes\n                },\n            },\n        );\n    } catch (err) {\n        if (err instanceof XmlSyntaxError || err instanceof ImportError) {\n            report.fail(CYS_ISSUE.CORRUPT, `${entry}: ${err.message}`);\n        }\n        throw err;\n    }\n    const [root] = stack[0].children;\n    if (root === undefined) {\n        report.fail(CYS_ISSUE.CORRUPT, `${entry}: the document is empty`);\n    }\n    return root;\n}\n\n/**\n * Every element of a tree with a local name, depth first.\n * @param node - the tree\n * @param name - the local name\n * @returns the elements\n */\nexport function elementsNamed(node: XmlNode, name: string): XmlNode[] {\n    const out: XmlNode[] = [];\n    const stack = [node];\n    while (stack.length > 0) {\n        const n = stack.pop() as XmlNode;\n        if (n.name === name) {\n            out.push(n);\n        }\n        for (let i = n.children.length - 1; i >= 0; i--) {\n            stack.push(n.children[i]);\n        }\n    }\n    return out;\n}\n","/**\n * The tables of a Cytoscape 3 session: the CyCSV `.cytable` files (`research-session-and-style.md`\n * section 2.4; Cytoscape's `CSVCyReader`) and the virtual columns `tables/cytables.xml` joins into\n * them. Cells become XGMML att records, typed by the column's Java class, so the XGMML emitter\n * applies the same column rules (types, widening, equations, hidden columns, renames) to a\n * session's tables as to an XGMML file's atts.\n */\n\nimport { type ResolvedImportOptions } from \"../../common/options.js\";\nimport { ImportReportBuilder } from \"../../common/report.js\";\nimport { ImportError } from \"../../types.js\";\nimport { CsvRecordReader } from \"../csv/records.js\";\nimport { type AttRec } from \"../xgmml/document.js\";\nimport { CYS_ISSUE, FORMAT } from \"./constants.js\";\n\n/** The Cytoscape type names of the Java classes a CyCSV column can hold. */\nconst JAVA_TYPES: Readonly<Record<string, string>> = {\n    \"java.lang.String\": \"String\",\n    \"java.lang.Long\": \"Long\",\n    \"java.lang.Integer\": \"Integer\",\n    \"java.lang.Double\": \"Double\",\n    \"java.lang.Boolean\": \"Boolean\",\n};\n\n/** A list column's class: `java.util.List<java.lang.X>`. */\nconst LIST_CLASS = /^java\\.util\\.List<\\s*([\\w.]+)\\s*>$/;\n\n/** One column of a table. */\ninterface CyColumn {\n    /** The name. */\n    readonly name: string;\n    /** The Cytoscape type of a scalar column, or of a list's items. */\n    readonly type: string;\n    /** A list column. */\n    readonly list: boolean;\n}\n\n/** One table, read. */\nexport interface CyTable {\n    /** The table's path under `tables/` as the archive spells it (what cytables.xml names). */\n    readonly path: string;\n    /** The entry name, for messages. */\n    readonly entry: string;\n    /** The columns; the first is the primary key. */\n    readonly columns: readonly CyColumn[];\n    /** The rows by key text, in file order (the first row of a repeated key). */\n    readonly rows: ReadonlyMap<string, readonly string[]>;\n    /** The line each row starts on, by key. */\n    readonly lines: ReadonlyMap<string, number>;\n}\n\n/** What a table read reports besides its rows. */\ninterface RowProblems {\n    short: number;\n    long: number;\n    repeated: number;\n}\n\n/**\n * Read one CyCSV table. A table that cannot be read at all (an unknown CyCSV version or column\n * class, a malformed header, broken CSV) is recorded as E_CYS_TABLE and skipped (null); rows with\n * the wrong number of cells or a repeated key are counted in one W_CYS_TABLE_ROW.\n * @param bytes - the entry's bytes\n * @param path - the table's path under `tables/`\n * @param entry - the entry name, for messages\n * @param report - the import's report\n * @param common - cancellation\n * @returns the table, or null\n */\nexport async function readCyTable(\n    bytes: Uint8Array,\n    path: string,\n    entry: string,\n    report: ImportReportBuilder,\n    common: ResolvedImportOptions,\n): Promise<CyTable | null> {\n    const scratch = new ImportReportBuilder(FORMAT, 0);\n    const reader = new CsvRecordReader(bytes, scratch, { delimiter: \",\", encoding: \"utf-8\", signal: common.signal });\n    const records: { readonly cells: string[]; readonly line: number }[] = [];\n    try {\n        for await (const cells of reader) {\n            records.push({ cells, line: reader.line });\n        }\n    } catch (err) {\n        if (err instanceof ImportError) {\n            return tableError(report, entry, scratch.issues.at(-1)?.message ?? err.message);\n        }\n        throw err;\n    }\n    let at = 0;\n    let version = 0;\n    if (records[0]?.cells.length === 2 && records[0].cells[0] === \"CyCSV-Version\") {\n        version = Number(records[0].cells[1]);\n        at = 1;\n    }\n    if (version !== 0 && version !== 1) {\n        return tableError(report, entry, `CyCSV version \"${records[0].cells[1]}\" is not 0 or 1`);\n    }\n    // version 1: names, types, column options, table title; version 0: names, types, table title\n    const headerLines = version === 1 ? 4 : 3;\n    if (records.length < at + headerLines) {\n        return tableError(report, entry, \"the table header is incomplete\");\n    }\n    const names = records[at].cells;\n    const classes = records[at + 1].cells;\n    if (names.length === 0 || classes.length !== names.length) {\n        return tableError(report, entry, `${names.length} column name(s) but ${classes.length} column class(es)`);\n    }\n    const columns: CyColumn[] = [];\n    for (let i = 0; i < names.length; i++) {\n        const column = columnOf(names[i], classes[i]);\n        if (column === null) {\n            return tableError(\n                report,\n                entry,\n                `column \"${names[i]}\" has the class \"${classes[i]}\", which graph-io cannot read`,\n            );\n        }\n        columns.push(column);\n    }\n    const rows = new Map<string, readonly string[]>();\n    const lines = new Map<string, number>();\n    const problems: RowProblems = { short: 0, long: 0, repeated: 0 };\n    for (const record of records.slice(at + headerLines)) {\n        const { cells } = record;\n        if (cells.length < columns.length) {\n            problems.short++;\n        } else if (cells.length > columns.length) {\n            problems.long++;\n        }\n        const key = cells[0];\n        if (rows.has(key)) {\n            problems.repeated++;\n            continue;\n        }\n        rows.set(key, cells.slice(0, columns.length));\n        lines.set(key, record.line);\n    }\n    if (problems.short + problems.long + problems.repeated > 0) {\n        report.warning(\n            \"parse-error\",\n            CYS_ISSUE.TABLE_ROW,\n            `${entry}: ${problems.short} row(s) with too few cells (the rest are unset), ${problems.long} with too many (the extra cells are ignored), ${problems.repeated} repeating a key (the first row is read)`,\n        );\n    }\n    return { path, entry, columns, rows, lines };\n}\n\n/**\n * The column of a name and a Java class.\n * @param name - the name\n * @param javaClass - the class text\n * @returns the column, or null for a class graph-io cannot read\n */\nfunction columnOf(name: string, javaClass: string): CyColumn | null {\n    const scalar = JAVA_TYPES[javaClass.trim()];\n    if (scalar !== undefined) {\n        return { name, type: scalar, list: false };\n    }\n    const list = LIST_CLASS.exec(javaClass.trim());\n    const item = list === null ? undefined : JAVA_TYPES[list[1]];\n    return item === undefined ? null : { name, type: item, list: true };\n}\n\n/**\n * Record E_CYS_TABLE for a table that is skipped.\n * @param report - the report\n * @param entry - the entry name\n * @param reason - why\n * @returns null\n */\nfunction tableError(report: ImportReportBuilder, entry: string, reason: string): null {\n    report.error(\"parse-error\", CYS_ISSUE.TABLE, `${entry}: ${reason}; the table is not read`);\n    return null;\n}\n\n/**\n * The att record of one cell, or null for an unset cell. CyCSV's rules: an empty cell is unset\n * except in a String column, where it is the empty string; a list cell holds its items separated\n * by newlines (Java's `split`, so trailing empty items vanish; an empty String-list cell is one\n * empty item, any other empty list cell unset); a cell starting with `=` is an equation.\n * @param column - the column\n * @param text - the cell text\n * @param line - the row's line\n * @param namespace - the table namespace the column belongs to (null for the network's own table)\n * @param hidden - whether the column is hidden (HIDDEN and app tables)\n * @returns the att, or null\n */\nexport function cellAtt(\n    column: CyColumn,\n    text: string,\n    line: number,\n    namespace: string | null,\n    hidden: boolean,\n): AttRec | null {\n    if (text.startsWith(\"=\")) {\n        return att(column.name, column.list ? \"List\" : column.type, null, text, line, namespace, hidden, true);\n    }\n    if (!column.list) {\n        if (text.length === 0 && column.type !== \"String\") {\n            return null;\n        }\n        return att(column.name, column.type, null, text, line, namespace, hidden, false);\n    }\n    if (text.length === 0 && column.type !== \"String\") {\n        return null;\n    }\n    const list = att(column.name, \"List\", column.type, null, line, namespace, hidden, false);\n    for (const item of javaSplitLines(text)) {\n        if (item.length === 0 && column.type !== \"String\") {\n            continue;\n        }\n        list.children.push(att(column.name, column.type, null, item, line, namespace, hidden, false));\n    }\n    return list;\n}\n\n/**\n * Java's `String.split(\"\\n\")`: trailing empty strings are removed, and a text without a newline\n * is itself (so `\"\"` is one empty item).\n * @param text - the cell\n * @returns the items\n */\nfunction javaSplitLines(text: string): string[] {\n    if (!text.includes(\"\\n\")) {\n        return [text];\n    }\n    const items = text.split(\"\\n\");\n    while (items.length > 0 && items[items.length - 1].length === 0) {\n        items.pop();\n    }\n    return items;\n}\n\n/**\n * An att record.\n * @param name - the name\n * @param cyType - the Cytoscape type\n * @param elementType - a list's item type, or null\n * @param value - the value, or null\n * @param line - the line\n * @param namespace - the table namespace, or null\n * @param hidden - a hidden column\n * @param equation - the value is a formula\n * @returns the record\n */\nfunction att(\n    name: string,\n    cyType: string,\n    elementType: string | null,\n    value: string | null,\n    line: number,\n    namespace: string | null,\n    hidden: boolean,\n    equation: boolean,\n): AttRec {\n    return {\n        name,\n        type: null,\n        cyType,\n        elementType,\n        value,\n        hidden,\n        equation,\n        children: [],\n        extra: {},\n        xml: null,\n        hasGraph: false,\n        text: \"\",\n        line,\n        namespace,\n    };\n}\n\n/** One virtual column of `tables/cytables.xml`. */\nexport interface VirtualColumn {\n    /** The column name in the target table. */\n    readonly name: string;\n    /** The target table's path under `tables/`. */\n    readonly targetTable: string;\n    /** The source table's path. */\n    readonly sourceTable: string;\n    /** The source column's name. */\n    readonly sourceColumn: string;\n    /** The join column of the source (normally SUID). */\n    readonly sourceJoinKey: string;\n    /** The join column of the target (normally SUID). */\n    readonly targetJoinKey: string;\n}\n\n/** A resolved virtual column: its type and its value per target row key. */\ninterface VirtualValues {\n    readonly column: CyColumn;\n    readonly values: ReadonlyMap<string, string>;\n}\n\n/**\n * Resolve the virtual columns of one table: each one's values joined from its source table,\n * following a source that is itself a virtual column. A column whose source table or column is\n * missing, or whose sources form a cycle, is E_CYS_TABLE and skipped.\n * @param target - the table\n * @param virtuals - every virtual column of the session\n * @param tableOf - reads (and caches) a table by path, null when it cannot be read or is absent\n * @param report - the report\n * @returns the virtual columns of the table, in cytables.xml order\n */\nexport async function virtualColumnsOf(\n    target: CyTable,\n    virtuals: readonly VirtualColumn[],\n    tableOf: (path: string) => Promise<CyTable | null>,\n    report: ImportReportBuilder,\n): Promise<VirtualValues[]> {\n    const out: VirtualValues[] = [];\n    for (const virtual of virtuals) {\n        if (virtual.targetTable !== target.path) {\n            continue;\n        }\n        const resolved = await resolve(virtual, virtuals, tableOf, new Set());\n        if (typeof resolved === \"string\") {\n            report.error(\n                \"parse-error\",\n                CYS_ISSUE.TABLE,\n                `${target.entry}: the virtual column \"${virtual.name}\" ${resolved}; the column is not read`,\n            );\n            continue;\n        }\n        const targetKey = target.columns.findIndex((c) => c.name === virtual.targetJoinKey);\n        const values = new Map<string, string>();\n        for (const [key, cells] of target.rows) {\n            const join = targetKey <= 0 ? key : cells[targetKey];\n            const value = join === undefined ? undefined : resolved.values.get(join);\n            if (value !== undefined) {\n                values.set(key, value);\n            }\n        }\n        out.push({ column: { ...resolved.column, name: virtual.name }, values });\n    }\n    return out;\n}\n\n/**\n * The values of a virtual column's source, by the source's join key.\n * @param virtual - the virtual column\n * @param virtuals - every virtual column\n * @param tableOf - the table reader\n * @param seen - the virtual columns on the current chain (a cycle check)\n * @returns the values, or the reason they cannot be read\n */\nasync function resolve(\n    virtual: VirtualColumn,\n    virtuals: readonly VirtualColumn[],\n    tableOf: (path: string) => Promise<CyTable | null>,\n    seen: Set<VirtualColumn>,\n): Promise<VirtualValues | string> {\n    if (seen.has(virtual)) {\n        return \"is part of a cycle of virtual columns\";\n    }\n    seen.add(virtual);\n    const source = await tableOf(virtual.sourceTable);\n    if (source === null) {\n        return `names the source table \"${virtual.sourceTable}\", which the session does not hold or cannot read`;\n    }\n    const joinIndex = source.columns.findIndex((c) => c.name === virtual.sourceJoinKey);\n    if (joinIndex < 0) {\n        return `joins on the column \"${virtual.sourceJoinKey}\", which its source table does not have`;\n    }\n    const joinOf = (key: string, cells: readonly string[]): string | undefined =>\n        joinIndex === 0 ? key : cells[joinIndex];\n    const own = source.columns.findIndex((c) => c.name === virtual.sourceColumn);\n    if (own >= 0) {\n        const values = new Map<string, string>();\n        for (const [key, cells] of source.rows) {\n            const join = joinOf(key, cells);\n            if (join !== undefined && cells[own] !== undefined) {\n                values.set(join, cells[own]);\n            }\n        }\n        return { column: source.columns[own], values };\n    }\n    const chained = virtuals.find((v) => v.targetTable === source.path && v.name === virtual.sourceColumn);\n    if (chained === undefined) {\n        return `names the source column \"${virtual.sourceColumn}\", which its source table does not have`;\n    }\n    const inner = await resolve(chained, virtuals, tableOf, seen);\n    if (typeof inner === \"string\") {\n        return inner;\n    }\n    // re-key the chained values (by the chained source's join key) to this source's join key\n    const values = new Map<string, string>();\n    const chainedJoin = source.columns.findIndex((c) => c.name === chained.targetJoinKey);\n    for (const [key, cells] of source.rows) {\n        const lookup = chainedJoin <= 0 ? key : cells[chainedJoin];\n        const value = lookup === undefined ? undefined : inner.values.get(lookup);\n        const join = joinOf(key, cells);\n        if (value !== undefined && join !== undefined) {\n            values.set(join, value);\n        }\n    }\n    return { column: inner.column, values };\n}\n","/**\n * The Cytoscape session importer (design `design/graph-io/cytoscape-and-obo/design.md` sections\n * 1.4 and 3; `research-session-and-style.md`). A session is a zip of every network of a Cytoscape\n * desktop; the unit of import is the registered subnetwork (3.x) or the network (2.x), one\n * snapshot each: `import()` reads the one `graphIndex` / `graphName` picks (the first by default),\n * `importAll()` every one, and `listGraphs()` lists them from the network files alone.\n *\n * 3.x: the network file gives the topology (shared nodes through `xlink:href`, per-edge direction,\n * groups, nested-network pointers); the subnetwork's CyCSV tables give its columns (LOCAL_ATTRS as\n * they are, the SHARED_ATTRS columns `cytables.xml` joins in, HIDDEN and app tables as hidden\n * columns under their namespace); its first view gives positions (y flipped) and the `graphics`\n * column, further views `position@<n>` columns. 2.x: one full XGMML file per network, with\n * selection and hidden state from `cysession.xml`. Everything is resolved by the XGMML emitter, so\n * both readers share every column rule. Styles are not read (issue #706): W_STYLES_NOT_IMPORTED.\n */\n\nimport { GraphFormatError, type GraphSink, INVALID_INDEX } from \"@graphty/graph-format\";\n\nimport { declareResolved } from \"../../common/attributes.js\";\nimport { IdCoercer } from \"../../common/ids.js\";\nimport { decodeEntryName, readBytes, throwIfAborted } from \"../../common/input.js\";\nimport {\n    chooseGraph,\n    type ImportFormatDefaults,\n    reportSinkOptions,\n    reportUnusedOptions,\n    type ResolvedImportOptions,\n    resolveImportOptions,\n} from \"../../common/options.js\";\nimport { ImportReportBuilder } from \"../../common/report.js\";\nimport { startsLikeZip } from \"../../common/zip.js\";\nimport {\n    type CommonImportOptions,\n    type GraphChoiceOptions,\n    type GraphImporter,\n    type GraphListing,\n    ImportError,\n    type ImportInput,\n    type ImportReport,\n} from \"../../types.js\";\nimport { XGMML_ISSUE, XGMML_ORIGIN_NAMESPACE } from \"../xgmml/constants.js\";\nimport {\n    type AttRec,\n    type EdgeRec,\n    type GraphRec,\n    isCyTrue,\n    type NodeRec,\n    type XgmmlDocument,\n} from \"../xgmml/document.js\";\nimport {\n    type Dialect,\n    dialectOf,\n    type EmitExtras,\n    membersOf,\n    XgmmlEmitter,\n    type XgmmlSettings,\n} from \"../xgmml/emit.js\";\nimport { parseXgmml, resolveSettings } from \"../xgmml/importer.js\";\nimport {\n    CYS_ISSUE,\n    CYTOSCAPE_NAMESPACE,\n    DEFAULT_MAX_UNCOMPRESSED,\n    EXTENSIONS,\n    FORMAT,\n    HIDDEN_COLUMN,\n    META_KEY,\n    MIME_TYPES,\n    SELECTED_COLUMN,\n    VIEW_POSITION_PREFIX,\n} from \"./constants.js\";\nimport {\n    elementsNamed,\n    listed,\n    type NetworkEntry,\n    openSession,\n    readXmlTree,\n    type Session,\n    type SessionEntry,\n    type TableEntry,\n    urlDecode,\n    type XmlNode,\n} from \"./session.js\";\nimport { cellAtt, type CyTable, readCyTable, type VirtualColumn, virtualColumnsOf } from \"./tables.js\";\n\n/** The format-specific options of the session importer. */\nexport interface CysImportOptions extends GraphChoiceOptions {\n    /** Where Cytoscape's z (a stacking order) goes: the `z` column (default) or the position. */\n    zAs?: \"column\" | \"position\" | undefined;\n    /**\n     * The most bytes one import may inflate, in total (default 2 GiB); an entry beyond it, or one\n     * whose compression ratio is above 1000:1, is E_TOO_LARGE.\n     */\n    maxUncompressedBytes?: number | undefined;\n}\n\n/** The per-format defaults: SUIDs as written, edges directed unless they say otherwise, no weight. */\nconst FORMAT_DEFAULTS: ImportFormatDefaults = {\n    ids: \"keep\",\n    defaultDirected: true,\n    weightFrom: null,\n    addMissingNodes: false,\n};\n\n/** The common options the session importer reads. */\nconst USED_OPTIONS: ReadonlySet<keyof CommonImportOptions> = new Set<keyof CommonImportOptions>([\n    \"ids\",\n    \"addMissingNodes\",\n    \"duplicateEdges\",\n    \"selfLoops\",\n    \"onMixedDirection\",\n    \"defaultDirected\",\n    \"weightFrom\",\n    \"weightDtype\",\n    \"long\",\n    \"errorLimit\",\n    \"signal\",\n    \"onProgress\",\n]);\n\n/** One network the session holds: a registered subnetwork of a 3.x network file, or a 2.x network. */\ntype Choice = Choice3 | Choice2;\n\n/** A registered subnetwork of a 3.x network file. */\ninterface Choice3 {\n    readonly era: \"3\";\n    readonly network: NetworkEntry;\n    readonly graphId: string;\n    readonly name: string | null;\n    readonly nodes: number;\n    readonly edges: number;\n}\n\n/** A 2.x network and its `cysession.xml` record. */\ninterface Choice2 {\n    readonly era: \"2\";\n    readonly file: SessionEntry;\n    readonly name: string;\n    readonly record: XmlNode;\n    readonly parent: string | null;\n}\n\n/** What every import call sets up. */\ninterface Prepared {\n    readonly report: ImportReportBuilder;\n    readonly common: ResolvedImportOptions;\n    /** The options the entries inside are read with: no progress, no encoding override. */\n    readonly inner: ResolvedImportOptions;\n    readonly zAs: \"column\" | \"position\";\n    readonly session: Session;\n    readonly choices: readonly Choice[];\n    /** The network file documents parsed for the listing, by entry name (3.x). */\n    readonly docs: Map<string, Parsed>;\n}\n\n/** A parsed XGMML entry. */\ninterface Parsed {\n    readonly doc: XgmmlDocument;\n    readonly dialect: Dialect;\n}\n\n/**\n * The maxUncompressedBytes option, checked.\n * @param value - the caller's value\n * @returns the byte budget; E_UNSUPPORTED for anything but a positive number\n */\nfunction budgetOption(value: unknown): number {\n    if (value === undefined) {\n        return DEFAULT_MAX_UNCOMPRESSED;\n    }\n    if (typeof value !== \"number\" || !(value > 0)) {\n        throw new GraphFormatError(\n            \"E_UNSUPPORTED\",\n            `option maxUncompressedBytes: ${JSON.stringify(value)} is not a positive number`,\n            {\n                option: \"maxUncompressedBytes\",\n                found: value,\n            },\n        );\n    }\n    return value;\n}\n\n/**\n * Resolve the options, open the archive and list its networks.\n * @param input - the input\n * @param sink - the sink, or null for listGraphs\n * @param options - the options\n * @returns what the import needs\n */\nasync function prepare(\n    input: ImportInput,\n    sink: GraphSink | null,\n    options: (CysImportOptions & CommonImportOptions) | undefined,\n): Promise<Prepared> {\n    const common = resolveImportOptions(options, FORMAT_DEFAULTS);\n    const report = new ImportReportBuilder(FORMAT, common.errorLimit);\n    if (sink !== null) {\n        reportSinkOptions(sink, options, report, true);\n        reportUnusedOptions(options, report, USED_OPTIONS);\n    }\n    const { zAs } = resolveSettings({ zAs: options?.zAs }, false);\n    const maxBytes = budgetOption(options?.maxUncompressedBytes);\n    const session = await openSession(input, report, common, maxBytes);\n    const inner: ResolvedImportOptions = Object.freeze({ ...common, onProgress: null, encoding: null });\n    const docs = new Map<string, Parsed>();\n    const choices =\n        session.layout.era === \"3\"\n            ? await networks3(session, report, inner, docs)\n            : await networks2(session, report, inner);\n    return { report, common, inner, zAs, session, choices, docs };\n}\n\n/**\n * Read an XGMML entry. Its issues are relayed into the import's report with the entry name in\n * the message; a fatal one fails the import.\n * @param session - the session\n * @param entry - the entry\n * @param report - the import's report\n * @param inner - the options entries are read with\n * @returns the document and its dialect\n */\nasync function parseEntry(\n    session: Session,\n    entry: SessionEntry,\n    report: ImportReportBuilder,\n    inner: ResolvedImportOptions,\n): Promise<Parsed> {\n    const bytes = await session.read(entry);\n    const scratch = new ImportReportBuilder(FORMAT, Number.MAX_SAFE_INTEGER);\n    try {\n        const doc = await parseXgmml(bytes, scratch, inner, undefined);\n        const dialect = dialectOf(doc, scratch);\n        relay(scratch.issues, report, entry.name);\n        return { doc, dialect };\n    } catch (err) {\n        if (!(err instanceof ImportError)) {\n            throw err;\n        }\n        const { issues } = scratch;\n        const fatal = issues.at(-1);\n        relay(issues.slice(0, -1), report, entry.name);\n        return report.fail(fatal?.code ?? CYS_ISSUE.CORRUPT, `${entry.name}: ${fatal?.message ?? err.message}`, {\n            line: fatal?.line ?? null,\n        });\n    }\n}\n\n/**\n * Record issues of an entry in the import's report, the entry name before each message.\n * @param issues - the issues\n * @param report - the import's report\n * @param entry - the entry name\n */\nfunction relay(issues: ImportReport[\"issues\"], report: ImportReportBuilder, entry: string): void {\n    for (const issue of issues) {\n        const where = { line: issue.line, element: issue.element };\n        if (issue.severity === \"error\") {\n            report.error(issue.category, issue.code, `${entry}: ${issue.message}`, where);\n        } else {\n            report.warning(issue.category, issue.code, `${entry}: ${issue.message}`, where);\n        }\n    }\n}\n\n// ---------------------------------------------------------------------------------------- 3.x\n\n/**\n * The registered subnetworks of a 3.x session, in `network_list.xml` order (else entry order).\n * @param session - the session\n * @param report - the report\n * @param inner - the options entries are read with\n * @param docs - where the parsed network files are kept\n * @returns the networks\n */\nasync function networks3(\n    session: Session,\n    report: ImportReportBuilder,\n    inner: ResolvedImportOptions,\n    docs: Map<string, Parsed>,\n): Promise<Choice3[]> {\n    const { layout } = session;\n    const choices: Choice3[] = [];\n    for (const network of layout.networks) {\n        const parsed = await parseEntry(session, network, report, inner);\n        docs.set(network.name, parsed);\n        for (const graph of registeredGraphs(parsed)) {\n            const members = membersOf(parsed.doc, graph);\n            choices.push({\n                era: \"3\",\n                network,\n                graphId: graph.id ?? \"\",\n                name: graph.label ?? graph.id,\n                nodes: new Set(members.nodes).size,\n                edges: members.edges.length,\n            });\n        }\n    }\n    const known = new Set(choices.map((c) => c.graphId));\n    const strayViews = layout.views.filter((v) => !known.has(v.network)).map((v) => v.name);\n    const strayTables = layout.tables.filter(\n        (t) =>\n            !known.has(t.network) &&\n            !layout.networks.some((n) => n.suid === t.network) &&\n            !isGroupTable(t, session, docs),\n    );\n    if (strayViews.length > 0 || strayTables.length > 0) {\n        report.warning(\n            \"validation-error\",\n            CYS_ISSUE.DANGLING_REFERENCE,\n            `${strayViews.length + strayTables.length} view(s) or table(s) belong to a network the session does not hold and were not read: ${listed([...strayViews, ...strayTables.map((t) => t.name)])}`,\n        );\n    }\n    if (layout.networkList === null) {\n        return choices;\n    }\n    const tree = await readXmlTree(await session.read(layout.networkList), layout.networkList.name, report, inner);\n    const order = new Map<string, number>();\n    for (const node of elementsNamed(tree, \"network\")) {\n        const id = node.attrs.get(\"id\");\n        const position = Number(node.attrs.get(\"order\"));\n        if (id !== undefined && Number.isFinite(position)) {\n            order.set(id, position);\n        }\n    }\n    return choices\n        .map((choice, index) => ({ choice, index }))\n        .sort(\n            (a, b) =>\n                (order.get(a.choice.graphId) ?? Infinity) - (order.get(b.choice.graphId) ?? Infinity) ||\n                a.index - b.index,\n        )\n        .map((c) => c.choice);\n}\n\n/**\n * Whether a table belongs to a graph declared in some network file (a group's network): those are\n * read with their network, not reported.\n * @param table - the table\n * @param session - the session\n * @param docs - the parsed network files\n * @returns true for a table of a known graph\n */\nfunction isGroupTable(table: TableEntry, session: Session, docs: ReadonlyMap<string, Parsed>): boolean {\n    for (const network of session.layout.networks) {\n        if (docs.get(network.name)?.doc.graphs.some((g) => g.id === table.network) === true) {\n            return true;\n        }\n    }\n    return false;\n}\n\n/**\n * The registered subnetworks of a network file (`cy:registered` true under the root).\n * @param parsed - the network file\n * @returns the graphs\n */\nfunction registeredGraphs(parsed: Parsed): GraphRec[] {\n    return parsed.doc.root.subgraphs.filter((g) => isCyTrue(g.registered));\n}\n\n/**\n * Import one registered subnetwork of a 3.x session.\n * @param prepared - the prepared import\n * @param choice - the subnetwork\n * @param sink - the sink\n * @param parsed - its network file, parsed for this import (its records are filled in)\n */\nasync function import3(prepared: Prepared, choice: Choice3, sink: GraphSink, parsed: Parsed): Promise<void> {\n    const { report, inner, session } = prepared;\n    const { layout } = session;\n    const { doc, dialect } = parsed;\n    const graph = doc.root.subgraphs.find((g) => g.id === choice.graphId) as GraphRec;\n    const members = membersOf(doc, graph);\n    const nodes = byId(members.nodes);\n    const edges = byId(members.edges);\n    const cache = new Map<string, Promise<CyTable | null>>();\n    const tableOf = (path: string): Promise<CyTable | null> => {\n        let pending = cache.get(path);\n        if (pending === undefined) {\n            const entry = layout.tables.find((t) => t.tablePath === path);\n            pending =\n                entry === undefined\n                    ? Promise.resolve(null)\n                    : session.read(entry).then((bytes) => readCyTable(bytes, path, entry.name, report, inner));\n            cache.set(path, pending);\n        }\n        return pending;\n    };\n    const virtuals = layout.cytables === null ? [] : await readVirtuals(session, layout.cytables, report, inner);\n    // a row of an element the file declares outside this network (a collapsed group's member, a\n    // meta-edge) is Cytoscape's bookkeeping, not a stale row\n    const declared = new Set<string>([\n        ...doc.nodes.flatMap((n) => (n.id === null ? [] : [n.id])),\n        ...doc.edges.flatMap((e) => (e.id === null ? [] : [e.id])),\n    ]);\n    let unmatched = 0;\n    for (const entry of layout.tables.filter((t) => t.network === choice.graphId && t.element !== null)) {\n        throwIfAborted(inner.signal);\n        const table = await tableOf(entry.tablePath);\n        if (table === null) {\n            continue;\n        }\n        const local = entry.namespace === \"LOCAL_ATTRS\";\n        const shared = entry.namespace === \"SHARED_ATTRS\";\n        const namespace = local ? null : entry.namespace;\n        const hidden = !local && !shared;\n        const target = (key: string): AttRec[] | undefined => {\n            if (entry.element === \"network\") {\n                return key === choice.graphId ? graph.atts : undefined;\n            }\n            return (entry.element === \"node\" ? nodes : edges).get(key)?.atts;\n        };\n        for (const [key, cells] of table.rows) {\n            const atts = target(key);\n            if (atts === undefined) {\n                if (!declared.has(key)) {\n                    unmatched++;\n                }\n                continue;\n            }\n            const line = table.lines.get(key) ?? 0;\n            for (let i = 1; i < table.columns.length && i < cells.length; i++) {\n                const att = cellAtt(table.columns[i], cells[i], line, namespace, hidden);\n                if (att !== null) {\n                    atts.push(att);\n                }\n            }\n        }\n        for (const virtual of await virtualColumnsOf(table, virtuals, tableOf, report)) {\n            // a shared column named like a local one is renamed; the local one keeps the name\n            const owned = table.columns.some((c) => c.name === virtual.column.name);\n            let ns = namespace;\n            if (local) {\n                ns = owned ? \"SHARED_ATTRS\" : null;\n            }\n            for (const [key, text] of virtual.values) {\n                const att = cellAtt(virtual.column, text, table.lines.get(key) ?? 0, ns, hidden);\n                if (att !== null) {\n                    target(key)?.push(att);\n                }\n            }\n        }\n    }\n    if (unmatched > 0) {\n        report.warning(\n            \"parse-error\",\n            CYS_ISSUE.TABLE_ROW,\n            `${unmatched} table row(s) of network ${choice.graphId} name no node, edge or network of it (stale rows); they are not read`,\n        );\n    }\n    const views = layout.views.filter((v) => v.network === choice.graphId);\n    let visualStyle: string | null = null;\n    const extraViews: Map<string, [number, number, number]>[] = [];\n    for (const [i, view] of views.entries()) {\n        const viewDoc = (await parseEntry(session, view, report, inner)).doc;\n        if (i === 0) {\n            visualStyle = viewDoc.root.attrs.get(\"cy:visualStyle\") ?? null;\n            applyView(viewDoc, graph, nodes, edges, report, view.name);\n        } else {\n            extraViews.push(viewPositions(viewDoc, prepared.zAs));\n        }\n    }\n    const cyMeta = sessionMeta(prepared, {\n        collection: doc.root.label ?? choice.network.title,\n        network: choice.graphId,\n        parentNetwork: parentNetwork(graph, prepared.choices),\n        visualStyle,\n    });\n    const groups: { group: string; members: string[] }[] = [];\n    cyMeta.groups = groups;\n    const extras: EmitExtras = {\n        sourceFormat: FORMAT,\n        entry: choice.network.name,\n        graphName: localName(graph) ?? choice.name,\n        metaExtra: { [META_KEY]: cyMeta },\n        groupNodes: new Set(\n            members.nodes\n                .filter((n) => n.atts.some((a) => a.name === \"__isGroup\" && isCyTrue(a.value)))\n                .flatMap((n) => (n.id === null ? [] : [n.id])),\n        ),\n        resolvePointer: pointerResolver(prepared, doc),\n        onMissingMember: (group, member): void => {\n            const record = groups.find((g) => g.group === group);\n            if (record === undefined) {\n                groups.push({ group, members: [member] });\n            } else if (!record.members.includes(member)) {\n                record.members.push(member);\n            }\n        },\n    };\n    const settings: XgmmlSettings = { labelAliases: false, cytoscapeEscapes: false, zAs: prepared.zAs };\n    new XgmmlEmitter(doc, dialect, sink, report, prepared.inner, settings, extras).emit(graph);\n    if (groups.length > 0) {\n        report.warning(\n            \"unsupported\",\n            CYS_ISSUE.COLLAPSED_GROUP,\n            `${groups.length} collapsed group(s) hold ${groups.reduce((n, g) => n + g.members.length, 0)} member(s) that are not in the network; they are listed in meta.extra.cytoscape.groups`,\n        );\n    }\n    reportRootOnly(parsed, report, choice.network.name);\n    writeViewPositions(\n        sink,\n        extraViews,\n        views.slice(1).map((v) => v.view),\n        report,\n        prepared.inner,\n    );\n}\n\n/**\n * The virtual columns of `tables/cytables.xml`.\n * @param session - the session\n * @param entry - the cytables.xml entry\n * @param report - the report\n * @param inner - the options entries are read with\n * @returns the virtual columns in document order\n */\nasync function readVirtuals(\n    session: Session,\n    entry: SessionEntry,\n    report: ImportReportBuilder,\n    inner: ResolvedImportOptions,\n): Promise<VirtualColumn[]> {\n    const tree = await readXmlTree(await session.read(entry), entry.name, report, inner);\n    const out: VirtualColumn[] = [];\n    for (const node of elementsNamed(tree, \"virtualColumn\")) {\n        const a = (key: string): string => node.attrs.get(key) ?? \"\";\n        out.push({\n            name: a(\"name\"),\n            targetTable: a(\"targetTable\"),\n            sourceTable: a(\"sourceTable\"),\n            sourceColumn: a(\"sourceColumn\"),\n            sourceJoinKey: node.attrs.get(\"sourceJoinKey\") ?? \"SUID\",\n            targetJoinKey: node.attrs.get(\"targetJoinKey\") ?? \"SUID\",\n        });\n    }\n    return out;\n}\n\n/**\n * Records by id.\n * @param records - node or edge records\n * @returns the first record of each id\n */\nfunction byId<T extends NodeRec | EdgeRec>(records: readonly T[]): Map<string, T> {\n    const out = new Map<string, T>();\n    for (const record of records) {\n        if (record.id !== null && !out.has(record.id)) {\n            out.set(record.id, record);\n        }\n    }\n    return out;\n}\n\n/**\n * Copy a view's coordinates and graphics onto the network's records (by `cy:nodeId` and\n * `cy:edgeId`), and its network graphics onto the graph. A view element naming nothing of the\n * network is counted in one W_DANGLING_REFERENCE.\n * @param view - the view document\n * @param graph - the subnetwork\n * @param nodes - its node records by id\n * @param edges - its edge records by id\n * @param report - the report\n * @param entry - the view entry name\n */\nfunction applyView(\n    view: XgmmlDocument,\n    graph: GraphRec,\n    nodes: ReadonlyMap<string, NodeRec>,\n    edges: ReadonlyMap<string, EdgeRec>,\n    report: ImportReportBuilder,\n    entry: string,\n): void {\n    let dangling = 0;\n    for (const node of view.nodes) {\n        const target = node.viewId === null ? undefined : nodes.get(node.viewId);\n        if (target === undefined) {\n            dangling++;\n            continue;\n        }\n        target.x = node.x;\n        target.y = node.y;\n        target.z = node.z;\n        if (node.graphics !== null) {\n            target.graphics = { ...(target.graphics ?? {}), ...node.graphics };\n        }\n    }\n    for (const edge of view.edges) {\n        const target = edge.viewId === null ? undefined : edges.get(edge.viewId);\n        if (target === undefined) {\n            dangling++;\n            continue;\n        }\n        if (edge.graphics !== null) {\n            target.graphics = { ...(target.graphics ?? {}), ...edge.graphics };\n        }\n    }\n    if (view.root.graphics !== null) {\n        graph.graphics = { ...(graph.graphics ?? {}), ...view.root.graphics };\n    }\n    if (dangling > 0) {\n        report.warning(\n            \"validation-error\",\n            CYS_ISSUE.DANGLING_REFERENCE,\n            `${entry}: ${dangling} view element(s) name no node or edge of the network; they are not read`,\n        );\n    }\n}\n\n/**\n * The positions of a further view, by model node id: y flipped to y-up, z in the position only\n * under zAs \"position\".\n * @param view - the view document\n * @param zAs - where z goes\n * @returns the positions\n */\nfunction viewPositions(view: XgmmlDocument, zAs: \"column\" | \"position\"): Map<string, [number, number, number]> {\n    const out = new Map<string, [number, number, number]>();\n    for (const node of view.nodes) {\n        const x = Number(node.x);\n        const y = Number(node.y);\n        const z = zAs === \"position\" ? Number(node.z ?? 0) : 0;\n        if (node.viewId !== null && node.x !== null && node.y !== null && Number.isFinite(x) && Number.isFinite(y)) {\n            out.set(node.viewId, [x, y === 0 ? 0 : -y, Number.isFinite(z) ? z : 0]);\n        }\n    }\n    return out;\n}\n\n/**\n * Write each further view's positions as a `position@<n>` column (n from 2), no role.\n * @param sink - the sink\n * @param views - the positions of each further view\n * @param viewIds - each view's SUID\n * @param report - the report\n * @param common - the id rule\n */\nfunction writeViewPositions(\n    sink: GraphSink,\n    views: readonly Map<string, [number, number, number]>[],\n    viewIds: readonly string[],\n    report: ImportReportBuilder,\n    common: ResolvedImportOptions,\n): void {\n    const coercer = new IdCoercer(common.ids);\n    views.forEach((positions, i) => {\n        const name = `${VIEW_POSITION_PREFIX}${i + 2}`;\n        const { handle } = declareResolved(\n            sink,\n            \"node\",\n            {\n                name,\n                dtype: \"f32\",\n                components: 3,\n                nullable: true,\n                origin: {\n                    format: FORMAT,\n                    id: viewIds[i],\n                    title: null,\n                    type: \"graphics\",\n                    namespace: XGMML_ORIGIN_NAMESPACE,\n                },\n                extra: { sourceDims: 2, units: \"file\" },\n            },\n            report,\n            { element: name },\n        );\n        for (const [id, xyz] of positions) {\n            let index: number;\n            try {\n                index = sink.indexOf(coercer.text(id));\n            } catch {\n                continue; // an id the id rule refuses was refused, and recorded, as a node already\n            }\n            if (index !== INVALID_INDEX) {\n                sink.setNodeValue(handle, index, xyz);\n            }\n        }\n    });\n}\n\n/**\n * The network's name from its own table (the LOCAL `name` att), else null.\n * @param graph - the subnetwork with its table atts\n * @returns the name\n */\nfunction localName(graph: GraphRec): string | null {\n    const att = graph.atts.find((a) => a.name === \"name\" && (a.namespace ?? null) === null);\n    return att?.value ?? null;\n}\n\n/**\n * The name of the network a subnetwork was made from: the hidden `__parentNetwork.SUID` (or the\n * pre-3.4 `Cy2 Parent Network.SUID`), named when the session holds it.\n * @param graph - the subnetwork with its table atts\n * @param choices - the session's networks\n * @returns the parent's name, its SUID when unnamed, or null\n */\nfunction parentNetwork(graph: GraphRec, choices: readonly Choice[]): string | null {\n    const att = graph.atts.find((a) => a.name === \"__parentNetwork.SUID\" || a.name === \"Cy2 Parent Network.SUID\");\n    if (att?.value === undefined || att.value === null || att.value.length === 0) {\n        return null;\n    }\n    const suid = att.value;\n    const named = choices.find((c) => c.era === \"3\" && c.graphId === suid);\n    return named?.name ?? suid;\n}\n\n/**\n * The resolver of nested-network pointers into other network files of the session\n * (`207-Set+2.xgmml#223`): the target graph's label. Only the files a pointer names are read.\n * @param prepared - the prepared import\n * @param doc - the network file being read\n * @returns the resolver\n */\nfunction pointerResolver(prepared: Prepared, doc: XgmmlDocument): (href: string) => string | null {\n    const names = new Map<string, string>();\n    for (const graph of doc.graphs) {\n        const { href } = graph;\n        const hash = href?.indexOf(\"#\") ?? -1;\n        if (href === null || hash <= 0 || names.has(href)) {\n            continue;\n        }\n        const file = urlDecode(href.slice(0, hash));\n        const id = href.slice(hash + 1);\n        const network = prepared.session.layout.networks.find(\n            (n) => urlDecode(n.path.slice(\"networks/\".length)) === file,\n        );\n        const parsed = network === undefined ? undefined : prepared.docs.get(network.name);\n        const target = parsed?.doc.graphs.find((g) => g.id === id);\n        if (target !== undefined) {\n            names.set(href, target.label ?? id);\n        }\n    }\n    return (href) => names.get(href) ?? null;\n}\n\n/**\n * W_XGMML_ROOT_ONLY_ELEMENTS for elements of a network file no registered subnetwork holds.\n * @param parsed - the network file\n * @param report - the report\n * @param entry - the entry name\n */\nfunction reportRootOnly(parsed: Parsed, report: ImportReportBuilder, entry: string): void {\n    const held = new Set<unknown>();\n    for (const graph of registeredGraphs(parsed)) {\n        const members = membersOf(parsed.doc, graph);\n        members.nodes.forEach((n) => held.add(n));\n        members.edges.forEach((e) => held.add(e));\n    }\n    const nodes = parsed.doc.nodes.filter((n) => !held.has(n)).length;\n    const edges = parsed.doc.edges.filter((e) => !held.has(e)).length;\n    if (nodes + edges > 0) {\n        report.warning(\n            \"unsupported\",\n            XGMML_ISSUE.ROOT_ONLY_ELEMENTS,\n            `${entry}: ${nodes} node(s) and ${edges} edge(s) belong to no registered network (group meta-edges, collapsed group members) and were not read`,\n        );\n    }\n}\n\n// ---------------------------------------------------------------------------------------- 2.x\n\n/**\n * The networks of a 2.x session: every network of `cysession.xml`'s tree except `Network Root`,\n * in the order of their files in the archive.\n * @param session - the session\n * @param report - the report\n * @param inner - the options entries are read with\n * @returns the networks\n */\nasync function networks2(\n    session: Session,\n    report: ImportReportBuilder,\n    inner: ResolvedImportOptions,\n): Promise<Choice2[]> {\n    const { layout } = session;\n    if (layout.cysession === null) {\n        return report.fail(CYS_ISSUE.NOT_SESSION, \"the session has no cysession.xml\");\n    }\n    const tree = await readXmlTree(await session.read(layout.cysession), layout.cysession.name, report, inner);\n    const documentVersion = tree.attrs.get(\"documentVersion\") ?? \"\";\n    if (documentVersion.startsWith(\"3\")) {\n        report.fail(\n            CYS_ISSUE.VERSION,\n            `cysession.xml has documentVersion ${documentVersion} and no version marker: the 2011 Cytoscape 3.0 pre-release layout, which no released Cytoscape reads`,\n        );\n    }\n    const byDecoded = new Map<string, SessionEntry>();\n    for (const [path, entry] of layout.files) {\n        byDecoded.set(path, entry);\n        byDecoded.set(urlDecode(path), entry);\n    }\n    const order = [...layout.files.values()];\n    const choices: Choice2[] = [];\n    const missing: string[] = [];\n    const named = new Set<SessionEntry>();\n    for (const record of elementsNamed(tree, \"network\")) {\n        const id = record.attrs.get(\"id\") ?? \"\";\n        const filename = record.attrs.get(\"filename\") ?? `${id}.xgmml`;\n        if (id === \"Network Root\") {\n            continue;\n        }\n        const file = byDecoded.get(filename);\n        if (file === undefined) {\n            missing.push(filename);\n            continue;\n        }\n        named.add(file);\n        const parent = record.children.find((c) => c.name === \"parent\")?.attrs.get(\"id\") ?? null;\n        choices.push({\n            era: \"2\",\n            file,\n            name: id,\n            record,\n            parent: parent === \"Network Root\" || parent === \"NULL\" ? null : parent,\n        });\n    }\n    if (missing.length > 0) {\n        report.warning(\n            \"validation-error\",\n            CYS_ISSUE.DANGLING_REFERENCE,\n            `cysession.xml names ${missing.length} network file(s) the session does not hold: ${listed(missing)}`,\n        );\n    }\n    const unnamed = order.filter((e) => !named.has(e)).map((e) => e.name);\n    if (unnamed.length > 0) {\n        report.warning(\n            \"unsupported\",\n            CYS_ISSUE.ENTRY_SKIPPED,\n            `${unnamed.length} network file(s) are not in cysession.xml's network tree and were not read: ${listed(unnamed)}`,\n        );\n    }\n    return choices.sort((a, b) => order.indexOf(a.file) - order.indexOf(b.file));\n}\n\n/**\n * Import one network of a 2.x session.\n * @param prepared - the prepared import\n * @param choice - the network\n * @param sink - the sink\n */\nasync function import2(prepared: Prepared, choice: Choice2, sink: GraphSink): Promise<void> {\n    const { report, inner, session } = prepared;\n    const { doc, dialect } = await parseEntry(session, choice.file, report, inner);\n    for (const [list, column] of [\n        [\"selectedNodes\", SELECTED_COLUMN],\n        [\"hiddenNodes\", HIDDEN_COLUMN],\n    ] as const) {\n        mark(doc.nodes, idsIn(choice.record, list), column);\n    }\n    for (const [list, column] of [\n        [\"selectedEdges\", SELECTED_COLUMN],\n        [\"hiddenEdges\", HIDDEN_COLUMN],\n    ] as const) {\n        mark(doc.edges, idsIn(choice.record, list), column);\n    }\n    const cyMeta = sessionMeta(prepared, {\n        collection: null,\n        network: choice.name,\n        parentNetwork: choice.parent,\n        visualStyle: choice.record.attrs.get(\"visualStyle\") ?? null,\n    });\n    const extras: EmitExtras = {\n        sourceFormat: FORMAT,\n        entry: choice.file.name,\n        graphName: choice.name,\n        metaExtra: { [META_KEY]: cyMeta },\n    };\n    const settings: XgmmlSettings = { labelAliases: true, cytoscapeEscapes: true, zAs: prepared.zAs };\n    new XgmmlEmitter(doc, dialect, sink, report, inner, settings, extras).emit(null);\n}\n\n/**\n * The element ids a `cysession.xml` network record lists under one key (`selectedNodes`, ...).\n * @param record - 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1} were not read (use importAll, graphIndex or graphName)`,\n        );\n    }\n    return importChoice(prepared, index, sink);\n}\n\n/**\n * Import every network of a session, each into its own sink with its own report.\n * @param input - the session bytes\n * @param sinkFor - a sink per network\n * @param options - format-specific and common options\n * @returns one report per network\n */\nasync function importAllCys(\n    input: ImportInput,\n    sinkFor: (index: number) => GraphSink,\n    options?: CysImportOptions & CommonImportOptions,\n): Promise<ImportReport[]> {\n    const bytes = (await readBytes(input, { signal: options?.signal ?? null })) ?? input;\n    const first = await prepare(bytes, null, options);\n    const reports: ImportReport[] = [];\n    for (let i = 0; i < first.choices.length; i++) {\n        const sink = sinkFor(i);\n        // every network gets fresh records and a fresh report\n        const prepared = i === 0 ? first : await prepare(bytes, null, options);\n        reportSinkOptions(sink, options, prepared.report, true);\n        reportUnusedOptions(options, prepared.report, USED_OPTIONS);\n        reports.push(await importChoice(prepared, i, sink));\n    }\n    return reports;\n}\n\n/**\n * List the networks of a session from its network files, without reading tables or views.\n * @param input - 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The zip may\n * start after a short stub (a self-extracting archive) within the head.\n * @param head - the first bytes\n * @returns the confidence\n */\nexport function sniffCys(head: Uint8Array): number {\n    for (let at = 0; at + 4 <= head.byteLength; at++) {\n        if (startsLikeZip(head.subarray(at))) {\n            return SESSION_NAME.test(decodeEntryName(head.subarray(at))) ? 0.95 : 0;\n        }\n    }\n    return 0;\n}\n\n/** The Cytoscape session importer. */\nexport const cysImporter: GraphImporter<CysImportOptions> = Object.freeze({\n    format: FORMAT,\n    extensions: EXTENSIONS,\n    mimeTypes: MIME_TYPES,\n    sniff: sniffCys,\n    import: importCys,\n    importAll: importAllCys,\n    listGraphs: 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package/dist/chunks/{importer-aNJfe0qu.js → importer-DEcKhsmQ.js}

@@ -1,5 +1,5 @@
 import { GraphFormatError, INVALID_INDEX } from "@graphty/graph-format";
-import { a3 as SINK_OPTION_CODE, V as OPTION_IGNORED_CODE, a2 as ROLE_TAKEN_CODE, $ as RENAMED_CODE, v as ID_MERGED_CODE, D as DANGLING_REFERENCE_CODE, af as UNKNOWN_ELEMENT_CODE, m as DUPLICATE_ATTRIBUTE_CODE, p as DUPLICATE_NODE_CODE, e as BAD_VALUE_CODE, N as MISSING_ID_CODE, ag as UNKNOWN_ENCODING_CODE, s as ENCODING_FALLBACK_CODE, z as INVALID_ENCODING_CODE, F as INVALID_UTF8_CODE, r as EMPTY_INPUT_CODE, aD as resolveImportOptions, I as ImportReportBuilder, aA as reportSinkOptions, aB as reportUnusedOptions, L as LineReader, a as throwIfAborted, as as declareResolved, J as IdCoercer, q as DirectionResolver } from "./report-BOk0p5y8.js";
+import { S as SINK_OPTION_CODE, O as OPTION_IGNORED_CODE, R as ROLE_TAKEN_CODE, at as RENAMED_CODE, I as ID_MERGED_CODE, j as DANGLING_REFERENCE_CODE, Y as UNKNOWN_ELEMENT_CODE, i as DUPLICATE_ATTRIBUTE_CODE, d as DUPLICATE_NODE_CODE, B as BAD_VALUE_CODE, f as MISSING_ID_CODE, q as UNKNOWN_ENCODING_CODE, E as ENCODING_FALLBACK_CODE, r as INVALID_ENCODING_CODE, s as INVALID_UTF8_CODE, u as EMPTY_INPUT_CODE, v as resolveImportOptions, w as ImportReportBuilder, F as reportSinkOptions, z as reportUnusedOptions, ap as LineReader, y as throwIfAborted, L as declareResolved, K as IdCoercer, J as DirectionResolver } from "./report-B1z4WT9e.js";
 import { S as SYNONYM_SCOPES, O as OBO_NODE_COLUMNS, o as oboColumnDecl, P as PLACEHOLDER_COLUMN } from "./ontology-BnrJ4I98.js";
 const ESCAPES = Object.freeze({
   n: "\n",
@@ -1611,4 +1611,4 @@ export {
   OBO_ISSUE as O,
   oboImporter as o
 };
-//# sourceMappingURL=importer-aNJfe0qu.js.map
+//# sourceMappingURL=importer-DEcKhsmQ.js.map