@graphty/graph-io 0.3.19 → 0.3.21

package/dist/src/common/zip.js

@@ -0,0 +1,399 @@
+/**
+ * A zip reader with no dependency (design `design/graph-io/cytoscape-and-obo/design.md` section
+ * 3.3; PKWARE APPNOTE 6.3.10, https://pkware.cachefly.net/webdocs/casestudies/APPNOTE.TXT), for
+ * the Cytoscape session importer.
+ *
+ * The whole archive is in memory: every Cytoscape-written entry has a data descriptor and zero
+ * sizes in its local header, so the sizes come from the central directory at the end. The end
+ * record is searched in the last 65,557 bytes (a comment can be 65,535 bytes long); the zip64
+ * locator and the `0x0001` extra field are followed; bytes prepended to the archive (a
+ * self-extracting stub) are tolerated by the shift between the directory's stated and actual
+ * offsets. Deflate (method 8) is inflated by wrapping the raw deflate bytes in a gzip member
+ * (header, data, the directory's CRC-32 and size) and passing it to `DecompressionStream("gzip")`,
+ * which every supported runtime has (Node 18, unlike `"deflate-raw"`) and which checks the CRC and
+ * the length itself; stored entries (method 0) are checked against a CRC-32 table here. Every
+ * other method, and encryption, is refused by name. Entry names are decoded by `decodeEntryName()`
+ * (the one place bytes become text) and are matching keys only, never paths.
+ */
+import { decodeEntryName, throwIfAborted } from "./input.js";
+/** A zip that cannot be read, or an entry that cannot be inflated. */
+export class ZipError extends Error {
+    /**
+     * Create the error.
+     * @param kind - what went wrong
+     * @param message - a plain-ASCII message
+     */
+    constructor(kind, message) {
+        super(message);
+        this.name = "ZipError";
+        this.kind = kind;
+    }
+}
+/** A per-entry size under which the ratio limit does not apply (tiny entries compress well). */
+export const RATIO_FLOOR = 1024 * 1024;
+const EOCD_SIGNATURE = 0x06054b50;
+const ZIP64_LOCATOR_SIGNATURE = 0x07064b50;
+const ZIP64_EOCD_SIGNATURE = 0x06064b50;
+const CENTRAL_SIGNATURE = 0x02014b50;
+const LOCAL_SIGNATURE = 0x04034b50;
+const EOCD_SIZE = 22;
+const MAX_COMMENT = 65535;
+const CENTRAL_SIZE = 46;
+const LOCAL_SIZE = 30;
+const ZIP64_EOCD_SIZE = 56;
+const ZIP64_LOCATOR_SIZE = 20;
+const U16_MAX = 0xffff;
+const U32_MAX = 0xffffffff;
+/** Bytes between two cancellation checks while a stored entry's CRC is computed. */
+const CRC_SLICE = 1024 * 1024;
+/** The compression methods other tools write, by number, for the refusal message. */
+const METHOD_NAMES = {
+    1: "shrink",
+    6: "implode",
+    9: "deflate64",
+    12: "bzip2",
+    14: "LZMA",
+    93: "zstd",
+    95: "xz",
+    96: "JPEG",
+    97: "WavPack",
+    98: "PPMd",
+    99: "AES encryption",
+};
+/**
+ * Whether bytes start with a local file header signature (`PK\x03\x04`).
+ * @param bytes - the bytes
+ * @returns true for the start of a zip
+ */
+export function startsLikeZip(bytes) {
+    return bytes.byteLength >= 4 && bytes[0] === 0x50 && bytes[1] === 0x4b && bytes[2] === 3 && bytes[3] === 4;
+}
+/**
+ * Read the central directory.
+ * @param bytes - the whole archive
+ * @returns the entries in directory order; ZipError "not-zip" when there is no end record and the
+ * bytes do not start like a zip, "corrupt" for an end record or directory that does not fit,
+ * "unsupported" for a split archive
+ */
+export function readZipDirectory(bytes) {
+    const view = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
+    const eocd = findEndRecord(bytes, view);
+    if (eocd < 0) {
+        throw startsLikeZip(bytes)
+            ? new ZipError("corrupt", "the archive has no end of central directory record (truncated?)")
+            : new ZipError("not-zip", "the input is not a zip archive");
+    }
+    let disk = view.getUint16(eocd + 4, true);
+    let directoryDisk = view.getUint16(eocd + 6, true);
+    let count = view.getUint16(eocd + 10, true);
+    let directorySize = view.getUint32(eocd + 12, true);
+    let directoryOffset = view.getUint32(eocd + 16, true);
+    let directoryEnd = eocd;
+    const locator = eocd - ZIP64_LOCATOR_SIZE;
+    if (locator >= 0 && view.getUint32(locator, true) === ZIP64_LOCATOR_SIGNATURE) {
+        const record = zip64EndRecord(view, locator);
+        disk = view.getUint32(record + 16, true);
+        directoryDisk = view.getUint32(record + 20, true);
+        count = readU64(view, record + 32);
+        directorySize = readU64(view, record + 40);
+        directoryOffset = readU64(view, record + 48);
+        directoryEnd = record;
+    }
+    else if (count === U16_MAX || directorySize === U32_MAX || directoryOffset === U32_MAX) {
+        throw new ZipError("corrupt", "the end record needs a zip64 record the archive does not have");
+    }
+    if (disk !== 0 || directoryDisk !== 0) {
+        throw new ZipError("unsupported", "a split (multi-disk) archive cannot be read");
+    }
+    const start = directoryEnd - directorySize;
+    if (start < 0 || directoryOffset > bytes.byteLength) {
+        throw new ZipError("corrupt", "the central directory lies outside the archive");
+    }
+    // data prepended to the archive moves every offset by the same amount
+    const shift = start - directoryOffset;
+    if (shift < 0) {
+        throw new ZipError("corrupt", "the central directory offset does not match its position");
+    }
+    const entries = [];
+    let at = start;
+    for (let i = 0; i < count; i++) {
+        if (at + CENTRAL_SIZE > directoryEnd || view.getUint32(at, true) !== CENTRAL_SIGNATURE) {
+            throw new ZipError("corrupt", `central directory entry ${i + 1} of ${count} is damaged`);
+        }
+        const nameLength = view.getUint16(at + 28, true);
+        const extraLength = view.getUint16(at + 30, true);
+        const commentLength = view.getUint16(at + 32, true);
+        const next = at + CENTRAL_SIZE + nameLength + extraLength + commentLength;
+        if (next > directoryEnd) {
+            throw new ZipError("corrupt", `central directory entry ${i + 1} runs past the directory`);
+        }
+        const name = decodeEntryName(bytes.subarray(at + CENTRAL_SIZE, at + CENTRAL_SIZE + nameLength));
+        let compressedSize = view.getUint32(at + 20, true);
+        let size = view.getUint32(at + 24, true);
+        let localOffset = view.getUint32(at + 42, true);
+        if (compressedSize === U32_MAX || size === U32_MAX || localOffset === U32_MAX) {
+            ({ compressedSize, size, localOffset } = zip64Extra(view, at + CENTRAL_SIZE + nameLength, extraLength, {
+                compressedSize,
+                size,
+                localOffset,
+            }));
+        }
+        entries.push(Object.freeze({
+            name,
+            method: view.getUint16(at + 10, true),
+            flags: view.getUint16(at + 8, true),
+            crc32: view.getUint32(at + 16, true),
+            compressedSize,
+            size,
+            localOffset: localOffset + shift,
+            directory: name.endsWith("/"),
+        }));
+        at = next;
+    }
+    return entries;
+}
+/**
+ * The position of the end of central directory record: the last signature whose comment length
+ * fits the archive, else the last signature at all (an archive with bytes after its comment).
+ * @param bytes - the archive
+ * @param view - a view of it
+ * @returns the offset, or -1
+ */
+function findEndRecord(bytes, view) {
+    const lowest = Math.max(0, bytes.byteLength - EOCD_SIZE - MAX_COMMENT);
+    let fallback = -1;
+    for (let at = bytes.byteLength - EOCD_SIZE; at >= lowest; at--) {
+        if (view.getUint32(at, true) !== EOCD_SIGNATURE) {
+            continue;
+        }
+        if (at + EOCD_SIZE + view.getUint16(at + 20, true) === bytes.byteLength) {
+            return at;
+        }
+        if (fallback < 0) {
+            fallback = at;
+        }
+    }
+    return fallback;
+}
+/**
+ * The zip64 end of central directory record a locator points at (or, when the archive has bytes
+ * prepended, the one right before the locator).
+ * @param view - the archive
+ * @param locator - the locator's offset
+ * @returns the record's offset
+ */
+function zip64EndRecord(view, locator) {
+    const stated = readU64(view, locator + 8);
+    for (const at of [stated, locator - ZIP64_EOCD_SIZE]) {
+        if (at >= 0 && at + ZIP64_EOCD_SIZE <= locator && view.getUint32(at, true) === ZIP64_EOCD_SIGNATURE) {
+            return at;
+        }
+    }
+    throw new ZipError("corrupt", "the zip64 end record the locator names is missing");
+}
+/**
+ * The zip64 extended information extra field (header id 0x0001) of a central entry: the 64-bit
+ * values of the fields whose 32-bit slot is 0xFFFFFFFF, in the order APPNOTE 4.5.3 gives.
+ * @param view - the archive
+ * @param at - the start of the extra field
+ * @param length - its length
+ * @param fields - the 32-bit values
+ * @param fields.compressedSize - the compressed size slot
+ * @param fields.size - the uncompressed size slot
+ * @param fields.localOffset - the local header offset slot
+ * @returns the resolved values
+ */
+function zip64Extra(view, at, length, fields) {
+    const out = { ...fields };
+    for (let p = at; p + 4 <= at + length;) {
+        const id = view.getUint16(p, true);
+        const dataLength = view.getUint16(p + 2, true);
+        if (id === 1) {
+            let q = p + 4;
+            const end = q + dataLength;
+            for (const key of ["size", "compressedSize", "localOffset"]) {
+                if (fields[key] === U32_MAX) {
+                    if (q + 8 > end) {
+                        throw new ZipError("corrupt", "a zip64 extra field is too short");
+                    }
+                    out[key] = readU64(view, q);
+                    q += 8;
+                }
+            }
+            return out;
+        }
+        p += 4 + dataLength;
+    }
+    throw new ZipError("corrupt", "an entry needs a zip64 extra field it does not have");
+}
+/**
+ * An unsigned 64-bit little-endian integer as a number (exact up to 2^53).
+ * @param view - the bytes
+ * @param at - the offset
+ * @returns the value; ZipError "unsupported" beyond 2^53
+ */
+function readU64(view, at) {
+    const high = view.getUint32(at + 4, true);
+    if (high >= 0x200000) {
+        throw new ZipError("unsupported", "a zip64 size or offset beyond 2^53 cannot be read");
+    }
+    return high * 0x100000000 + view.getUint32(at, true);
+}
+/**
+ * Read one entry's data: stored entries are sliced and CRC-checked, deflated ones inflated.
+ * @param bytes - the whole archive
+ * @param entry - the entry
+ * @param options - cancellation, progress and the size limits
+ * @returns the uncompressed bytes; ZipError for a damaged, encrypted, unsupported or oversized entry
+ */
+export async function readZipEntry(bytes, entry, options) {
+    if ((entry.flags & 1) !== 0 || entry.method === 99) {
+        throw new ZipError("unsupported", `${entry.name}: the entry is encrypted`);
+    }
+    if (entry.method !== 0 && entry.method !== 8) {
+        const name = METHOD_NAMES[entry.method] ?? `method ${entry.method}`;
+        throw new ZipError("unsupported", `${entry.name}: compression ${name} is not supported (only stored and deflate)`);
+    }
+    if (entry.size > options.maxBytes) {
+        throw new ZipError("too-large", `${entry.name}: ${entry.size} uncompressed bytes exceed the limit of ${options.maxBytes}`);
+    }
+    if (entry.size > RATIO_FLOOR && entry.size > options.maxRatio * Math.max(entry.compressedSize, 1)) {
+        throw new ZipError("too-large", `${entry.name}: ${entry.size} bytes from ${entry.compressedSize} is a compression ratio above ${options.maxRatio}:1`);
+    }
+    const data = entryData(bytes, entry);
+    if (entry.method === 0) {
+        if (data.byteLength !== entry.size) {
+            throw new ZipError("corrupt", `${entry.name}: a stored entry's sizes disagree`);
+        }
+        let crc = 0xffffffff;
+        for (let at = 0; at < data.byteLength; at += CRC_SLICE) {
+            throwIfAborted(options.signal);
+            crc = crcUpdate(crc, data.subarray(at, Math.min(at + CRC_SLICE, data.byteLength)));
+            options.onBytes?.(Math.min(at + CRC_SLICE, data.byteLength));
+        }
+        if ((crc ^ 0xffffffff) >>> 0 !== entry.crc32) {
+            throw new ZipError("corrupt", `${entry.name}: the data does not match its CRC-32`);
+        }
+        return data;
+    }
+    return inflate(data, entry, options);
+}
+/**
+ * The compressed bytes of an entry, located through its local header (whose name and extra
+ * lengths can differ from the central directory's).
+ * @param bytes - the archive
+ * @param entry - the entry
+ * @returns exactly compressedSize bytes
+ */
+function entryData(bytes, entry) {
+    const view = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
+    const at = entry.localOffset;
+    if (at + LOCAL_SIZE > bytes.byteLength || view.getUint32(at, true) !== LOCAL_SIGNATURE) {
+        throw new ZipError("corrupt", `${entry.name}: the local header is missing`);
+    }
+    const start = at + LOCAL_SIZE + view.getUint16(at + 26, true) + view.getUint16(at + 28, true);
+    const end = start + entry.compressedSize;
+    if (end > bytes.byteLength) {
+        throw new ZipError("corrupt", `${entry.name}: the entry's data runs past the end of the archive (truncated?)`);
+    }
+    return bytes.subarray(start, end);
+}
+/**
+ * Inflate a deflate stream through `DecompressionStream("gzip")`, wrapped in a gzip member that
+ * carries the directory's CRC-32 and size, so the platform checks both.
+ * @param data - the raw deflate bytes
+ * @param entry - the entry
+ * @param options - cancellation, progress and limits
+ * @returns the bytes
+ */
+async function inflate(data, entry, options) {
+    if (typeof DecompressionStream !== "function") {
+        throw new ZipError("unsupported", "this runtime has no DecompressionStream, so deflated entries cannot be read");
+    }
+    const member = new Uint8Array(10 + data.byteLength + 8);
+    member.set([0x1f, 0x8b, 8, 0, 0, 0, 0, 0, 0, 0xff]);
+    member.set(data, 10);
+    const trailer = new DataView(member.buffer, 10 + data.byteLength, 8);
+    trailer.setUint32(0, entry.crc32, true);
+    trailer.setUint32(4, entry.size % 0x100000000, true);
+    const source = new ReadableStream({
+        start(controller) {
+            controller.enqueue(member);
+            controller.close();
+        },
+    });
+    const reader = source.pipeThrough(new DecompressionStream("gzip")).getReader();
+    const parts = [];
+    let total = 0;
+    try {
+        for (;;) {
+            throwIfAborted(options.signal);
+            let chunk;
+            try {
+                chunk = await reader.read();
+            }
+            catch {
+                throw new ZipError("corrupt", `${entry.name}: the deflate data is damaged or does not match its CRC-32 and size`);
+            }
+            if (chunk.done) {
+                break;
+            }
+            total += chunk.value.byteLength;
+            if (total > entry.size) {
+                throw new ZipError("corrupt", `${entry.name}: the data is longer than its directory size`);
+            }
+            parts.push(chunk.value);
+            options.onBytes?.(total);
+        }
+    }
+    finally {
+        await reader.cancel().catch(() => undefined);
+    }
+    if (total !== entry.size) {
+        throw new ZipError("corrupt", `${entry.name}: the data is shorter than its directory size`);
+    }
+    if (parts.length === 1) {
+        return parts[0];
+    }
+    const out = new Uint8Array(total);
+    let at = 0;
+    for (const part of parts) {
+        out.set(part, at);
+        at += part.byteLength;
+    }
+    return out;
+}
+/** The CRC-32 table (polynomial 0xEDB88320). */
+const CRC_TABLE = (() => {
+    const table = new Uint32Array(256);
+    for (let n = 0; n < 256; n++) {
+        let c = n;
+        for (let k = 0; k < 8; k++) {
+            c = (c & 1) === 1 ? 0xedb88320 ^ (c >>> 1) : c >>> 1;
+        }
+        table[n] = c >>> 0;
+    }
+    return table;
+})();
+/**
+ * Continue a CRC-32 over more bytes.
+ * @param crc - the running value (start with 0xFFFFFFFF)
+ * @param bytes - the bytes
+ * @returns the running value (XOR with 0xFFFFFFFF to finish)
+ */
+function crcUpdate(crc, bytes) {
+    let c = crc;
+    for (const byte of bytes) {
+        c = CRC_TABLE[(c ^ byte) & 0xff] ^ (c >>> 8);
+    }
+    return c >>> 0;
+}
+/**
+ * The CRC-32 of bytes.
+ * @param bytes - the bytes
+ * @returns the checksum
+ */
+export function crc32(bytes) {
+    return (crcUpdate(0xffffffff, bytes) ^ 0xffffffff) >>> 0;
+}
+//# sourceMappingURL=zip.js.map

package/dist/src/common/zip.js.map

@@ -0,0 +1 @@
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package/dist/src/formats/cx/importer.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"importer.d.ts","sourceRoot":"","sources":["../../../../src/formats/cx/importer.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;GAqBG;AAiFH,OAAO,EAEH,KAAK,kBAAkB,EACvB,KAAK,aAAa,EAIrB,MAAM,gBAAgB,CAAC;AASxB,sDAAsD;AACtD,MAAM,WAAW,eAAgB,SAAQ,kBAAkB;IACvD;;;OAGG;IACH,GAAG,CAAC,EAAE,QAAQ,GAAG,UAAU,GAAG,SAAS,CAAC;CAC3C;AAED;;;;GAIG;AACH,eAAO,MAAM,QAAQ;IACjB,kCAAkC;;IAElC,oCAAoC;;IAEpC,6BAA6B;;IAE7B,gFAAgF;;IAEhF,0DAA0D;;IAE1D,0DAA0D;;IAE1D,mFAAmF;;IAEnF,4EAA4E;;IAE5E,gGAAgG;;IAEhG,wEAAwE;;IAExE,iHAAiH;;IAEjH,0DAA0D;;IAE1D,yEAAyE;;IAEzE,qGAAqG;;IAErG,+EAA+E;;IAE/E,6DAA6D;;IAE7D,uEAAuE;;IAEvE,kFAAkF;;IAElF,iEAAiE;;IAEjE,gGAAgG;;IAEhG,qGAAqG;;IAErG,qCAAqC;;IAErC,mEAAmE;;IAEnE,0EAA0E;;IAE1E,6BAA6B;;IAE7B,8BAA8B;;IAE9B,kEAAkE;;IAElE,6DAA6D;;IAE7D,oCAAoC;;IAEpC,yFAAyF;;IAEzF,qCAAqC;;IAErC,+EAA+E;;IAE/E,2FAA2F;;IAE3F,iDAAiD;;IAEjD,wEAAwE;;IAExE,2DAA2D;;IAE3D,mDAAmD;;IAEnD,wCAAwC;;IAExC,mDAAmD;;IAEnD,mEAAmE;;IAEnE,sCAAsC;;IAEtC,8CAA8C;;IAE9C,yCAAyC;;IAEzC,0DAA0D;;IAE1D,gDAAgD;;EAElD,CAAC;AAs2EH;;GAEG;AACH,eAAO,MAAM,UAAU,EAAE,aAAa,CAAC,eAAe,CAoGpD,CAAC"}
+{"version":3,"file":"importer.d.ts","sourceRoot":"","sources":["../../../../src/formats/cx/importer.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;GAqBG;AAiFH,OAAO,EAEH,KAAK,kBAAkB,EACvB,KAAK,aAAa,EAIrB,MAAM,gBAAgB,CAAC;AASxB,sDAAsD;AACtD,MAAM,WAAW,eAAgB,SAAQ,kBAAkB;IACvD;;;OAGG;IACH,GAAG,CAAC,EAAE,QAAQ,GAAG,UAAU,GAAG,SAAS,CAAC;CAC3C;AAED;;;;GAIG;AACH,eAAO,MAAM,QAAQ;IACjB,kCAAkC;;IAElC,oCAAoC;;IAEpC,6BAA6B;;IAE7B,gFAAgF;;IAEhF,0DAA0D;;IAE1D,0DAA0D;;IAE1D,mFAAmF;;IAEnF,4EAA4E;;IAE5E,gGAAgG;;IAEhG,wEAAwE;;IAExE,iHAAiH;;IAEjH,0DAA0D;;IAE1D,yEAAyE;;IAEzE,qGAAqG;;IAErG,+EAA+E;;IAE/E,6DAA6D;;IAE7D,uEAAuE;;IAEvE,kFAAkF;;IAElF,iEAAiE;;IAEjE,gGAAgG;;IAEhG,qGAAqG;;IAErG,qCAAqC;;IAErC,mEAAmE;;IAEnE,0EAA0E;;IAE1E,6BAA6B;;IAE7B,8BAA8B;;IAE9B,kEAAkE;;IAElE,6DAA6D;;IAE7D,oCAAoC;;IAEpC,yFAAyF;;IAEzF,qCAAqC;;IAErC,+EAA+E;;IAE/E,2FAA2F;;IAE3F,iDAAiD;;IAEjD,wEAAwE;;IAExE,2DAA2D;;IAE3D,mDAAmD;;IAEnD,wCAAwC;;IAExC,mDAAmD;;IAEnD,mEAAmE;;IAEnE,sCAAsC;;IAEtC,8CAA8C;;IAE9C,yCAAyC;;IAEzC,0DAA0D;;IAE1D,gDAAgD;;EAElD,CAAC;AA82EH;;GAEG;AACH,eAAO,MAAM,UAAU,EAAE,aAAa,CAAC,eAAe,CAoGpD,CAAC"}

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

@@ -930,6 +930,15 @@ class CxReader {
     inGraph(id) {
         return this.plan.nodes === null || this.plan.nodes.has(id);
     }
+    /**
+     * The key of the node and edge row maps for a CX id as an aspect writes it: the id the `ids`
+     * option makes of it, which is what idOf() stored the element under.
+     * @param raw - the CX id
+     * @returns the row key
+     */
+    key(raw) {
+        return this.options.ids === "keep" ? raw : this.coercer.value(raw);
+    }
     /**
      * Whether a scoped value applies to this graph: unscoped, or scoped to its subnetwork. A scope
      * naming no subnetwork is counted as dangling.
@@ -1188,9 +1197,7 @@ class CxReader {
                     continue;
                 }
                 const target = refId(value.po);
-                const row = target === null
-                    ? undefined
-                    : rows.get(this.options.ids === "keep" ? target : this.coercer.value(target));
+                const row = target === null ? undefined : rows.get(this.key(target));
                 if (row === undefined) {
                     if (target === null || !root.has(target)) {
                         this.dangle(`${domain} attribute target`);
@@ -1345,7 +1352,8 @@ class CxReader {
                 report.counts.skippedNodes++;
                 continue;
             }
-            if (!this.inGraph(id)) {
+            // membership lists hold CX ids as written, before the ids option coerces them
+            if (!this.inGraph(refId(value["@id"]) ?? id)) {
                 continue;
             }
             let row = this.nodeRows.get(id);
@@ -1427,19 +1435,19 @@ class CxReader {
                 });
                 continue;
             }
-            let groupRow = this.nodeRows.get(id);
+            let groupRow = this.nodeRows.get(this.key(id));
             if (groupRow === undefined) {
                 if (this.rootNodes.has(id) || !this.hasMemberIn(value.nodes)) {
                     continue;
                 }
                 try {
-                    groupRow = this.sink.addNode(id);
+                    groupRow = this.sink.addNode(this.key(id));
                 }
                 catch (err) {
                     this.report.recordError(err, { line, element: String(id) });
                     continue;
                 }
-                this.nodeRows.set(id, groupRow);
+                this.nodeRows.set(this.key(id), groupRow);
                 this.report.counts.nodes++;
                 this.report.warning("coercion", CX_ISSUE.GROUP_NODE_ADDED, `group ${String(id)} is not a node; its group node is added`, { line, element: String(id) });
             }
@@ -1451,7 +1459,7 @@ class CxReader {
             }
             for (const raw of Array.isArray(value.nodes) ? value.nodes : []) {
                 const member = refId(raw);
-                const row = member === null ? undefined : this.nodeRows.get(member);
+                const row = member === null ? undefined : this.nodeRows.get(this.key(member));
                 if (row === undefined) {
                     if (member === null || !this.rootNodes.has(member)) {
                         this.report.error("missing-value", UNKNOWN_PARENT_CODE, `group ${String(id)}: the member ${shown(raw)} is not a node`, { line, element: String(id) });
@@ -1491,7 +1499,7 @@ class CxReader {
         return (Array.isArray(raw) &&
             raw.some((item) => {
                 const id = refId(item);
-                return id !== null && this.nodeRows.has(id);
+                return id !== null && this.nodeRows.has(this.key(id));
             }));
     }
     /**
@@ -1570,7 +1578,7 @@ class CxReader {
                 continue;
             }
             const node = refId(value.node);
-            const row = node === null ? undefined : this.nodeRows.get(node);
+            const row = node === null ? undefined : this.nodeRows.get(this.key(node));
             if (row === undefined) {
                 if (node === null || !this.rootNodes.has(node)) {
                     this.dangle("layout entry");
@@ -1666,7 +1674,7 @@ class CxReader {
                 report.counts.skippedEdges++;
                 continue;
             }
-            if (members !== null && !members.has(id)) {
+            if (members !== null && !members.has(refId(value["@id"]) ?? id)) {
                 continue;
             }
             if (value.s === undefined || value.s === null || value.t === undefined || value.t === null) {
@@ -1767,7 +1775,7 @@ class CxReader {
                 if (isRecord(value) && this.scopePeek(value.s) !== 0) {
                     const po = refId(value.po);
                     if (po !== null && value.v !== undefined && value.v !== null) {
-                        this.weights.set(po, plainJson(value.v));
+                        this.weights.set(this.key(po), plainJson(value.v));
                     }
                 }
             }
@@ -1860,7 +1868,8 @@ class CxReader {
                 case "edges": {
                     const domain = value.properties_of === "nodes" ? "node" : "edge";
                     const target = refId(value.applies_to);
-                    const row = target === null ? undefined : (domain === "node" ? this.nodeRows : this.edgeRows).get(target);
+                    const rows = domain === "node" ? this.nodeRows : this.edgeRows;
+                    const row = target === null ? undefined : rows.get(this.key(target));
                     if (row === undefined) {
                         if (target === null || !(domain === "node" ? this.rootNodes : this.rootEdges).has(target)) {
                             this.dangle(`${domain} visual property entry`);
@@ -1946,7 +1955,7 @@ class CxReader {
                 continue;
             }
             const po = refId(value.po);
-            const row = po === null ? undefined : this.nodeRows.get(po);
+            const row = po === null ? undefined : this.nodeRows.get(this.key(po));
             if (row === undefined) {
                 if (po === null || !this.rootNodes.has(po)) {
                     this.dangle("functionTerms entry");
@@ -1964,8 +1973,8 @@ class CxReader {
             }
             const node = refId(value.node);
             const edge = refId(value.edge);
-            const row = node === null ? undefined : this.nodeRows.get(node);
-            const edgeRow = edge === null ? undefined : this.edgeRows.get(edge);
+            const row = node === null ? undefined : this.nodeRows.get(this.key(node));
+            const edgeRow = edge === null ? undefined : this.edgeRows.get(this.key(edge));
             if (row === undefined || edgeRow === undefined) {
                 if (node === null || !this.rootNodes.has(node) || edge === null || !this.rootEdges.has(edge)) {
                     this.dangle("reifiedEdges entry");
@@ -2032,7 +2041,7 @@ class CxReader {
                 .map(Number);
             for (const raw of targets) {
                 const target = refId(raw);
-                const row = target === null ? undefined : rows.get(target);
+                const row = target === null ? undefined : rows.get(this.key(target));
                 if (row === undefined) {
                     if (target === null || !root.has(target)) {
                         this.dangle(`${aspectName} entry`);