@graphty/graph-io 0.3.20 → 0.3.21

package/README.md

@@ -8,8 +8,9 @@
 Importers and exporters for the [@graphty/graph-format](https://www.npmjs.com/package/@graphty/graph-format)
 snapshot: GEXF, GraphML, GML, DOT (Graphviz), Pajek NET, CSV / TSV, JSON (NetworkX node-link, d3,
 JSON Graph Format, Cytoscape, graphology, vis.js; NetworkX adjacency_data and tree_data and OBO
-Graphs are read only), Neo4j (`neo4j-admin import` CSV), CX2 (the NDEx / Cytoscape exchange format;
-its version 1, CX, is read only) and OBO, the ontology format of the Gene Ontology (read only).
+Graphs are read only), Neo4j (`neo4j-admin import` CSV), XGMML (Cytoscape's XML format), CX2 (the
+NDEx / Cytoscape exchange format; its version 1, CX, is read only), Cytoscape sessions (`.cys`, read
+only) and OBO, the ontology format of the Gene Ontology (read only).
 
 Every importer streams its input into a `GraphSink` (a `GraphBuilder` or your own sink) one scalar at
 a time and reports what it could not represent instead of dropping it; every exporter says what it
@@ -154,10 +155,10 @@ reports every column or feature outside it):
 | CSV     | `@graphty/graph-io/csv`     | `.csv` `.tsv` `.edges` `.edgelist` | yes         | yes         | optional    | any           | bool i32 f64 string dict               | no    | no   | no       | no        | none           | no          | no        | no  |
 | JSON    | `@graphty/graph-io/json`    | `.json`                            | per dialect | yes         | per dialect | any           | f64 i32 bool string (no declarations)  | no    | yes  | no       | Cytoscape | none           | per dialect | Cytoscape | no  |
 | Neo4j   | `@graphty/graph-io/neo4j`   | `.csv` `.tsv`                      | no          | yes         | none        | any           | f32 f64 i32 bool string                | yes   | no   | no       | no        | none           | no          | no        | no  |
-| OBO     | `@graphty/graph-io/obo`     | `.obo`                             | read only   | -           | -           | -             | -                                      | -     | -    | -        | -         | -              | -           | -         | -   |
-| CX2     | `@graphty/graph-io/cx2`     | `.cx2`                             | no          | yes         | required    | integer       | f64 i32 bool string                    | yes   | no   | yes      | no        | none           | yes         | yes       | no  |
 | XGMML   | `@graphty/graph-io/xgmml`   | `.xgmml` `.xml`                    | yes         | yes         | optional    | any           | f64 i32 bool string (long as Long)     | yes   | no   | no       | yes       | none           | yes         | yes       | no  |
+| CX2     | `@graphty/graph-io/cx2`     | `.cx2`                             | no          | yes         | required    | integer       | f64 i32 bool string                    | yes   | no   | yes      | no        | none           | yes         | yes       | no  |
 | Session | `@graphty/graph-io/cys`     | `.cys`                             | read only   | read only   | read only   | read only     | read only                              | -     | -    | -        | -         | -              | -           | -         | -   |
+| OBO     | `@graphty/graph-io/obo`     | `.obo`                             | read only   | -           | -           | -             | -                                      | -     | -    | -        | -         | -              | -           | -         | -   |
 
 Every importer reads the whole corpus of research note 07 with the manifest counts and every
 exporter round-trips it (import -> export -> import gives the same ids, topology, orientation,
@@ -260,7 +261,8 @@ losses and format rules, in addition to the table:
   lists the inferred dtypes only, and `check()` names every f32 / u32 / u8 / dict / list / vector
   column (they come back f64 / i32 / string / json), integral f64 columns (i32) and every role the
   dialect has no slot for. Edge ids exist in JGF, Cytoscape, graphology and vis only; positions in
-  Cytoscape only. A repeated node id is merged with `W_DUPLICATE_NODE`, a repeated edge id skipped
+  Cytoscape only, stored y-up as for every Cytoscape-family format (Cytoscape's y grows downward,
+  so it is negated at import and negated back on export). A repeated node id is merged with `W_DUPLICATE_NODE`, a repeated edge id skipped
   with `E_DUPLICATE_EDGE_ID`; an out-of-range d3 index link is `E_BAD_INDEX`. Non-finite numbers
   are written as `null` and reported. NetworkX `adjacency_data` (`nodes` plus an `adjacency` list
   per node; an undirected file lists each edge from both ends and it is read once) and `tree_data`

package/dist/chunks/{importer-BaQpCEcJ.js → importer-DET1tg6s.js}

@@ -775,6 +775,15 @@ 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.
@@ -1070,7 +1079,7 @@ class CxReader {
           continue;
         }
         const target = refId(value.po);
-        const row = target === null ? void 0 : rows.get(this.options.ids === "keep" ? target : this.coercer.value(target));
+        const row = target === null ? void 0 : rows.get(this.key(target));
         if (row === void 0) {
           if (target === null || !root.has(target)) {
             this.dangle(`${domain} attribute target`);
@@ -1248,7 +1257,7 @@ class CxReader {
         report.counts.skippedNodes++;
         continue;
       }
-      if (!this.inGraph(id)) {
+      if (!this.inGraph(refId(value["@id"]) ?? id)) {
         continue;
       }
       let row = this.nodeRows.get(id);
@@ -1337,18 +1346,18 @@ class CxReader {
         });
         continue;
       }
-      let groupRow = this.nodeRows.get(id);
+      let groupRow = this.nodeRows.get(this.key(id));
       if (groupRow === void 0) {
         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",
@@ -1365,7 +1374,7 @@ class CxReader {
       }
       for (const raw of Array.isArray(value.nodes) ? value.nodes : []) {
         const member = refId(raw);
-        const row = member === null ? void 0 : this.nodeRows.get(member);
+        const row = member === null ? void 0 : this.nodeRows.get(this.key(member));
         if (row === void 0) {
           if (member === null || !this.rootNodes.has(member)) {
             this.report.error(
@@ -1419,7 +1428,7 @@ class CxReader {
   hasMemberIn(raw) {
     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));
     });
   }
   /**
@@ -1501,7 +1510,7 @@ class CxReader {
         continue;
       }
       const node = refId(value.node);
-      const row = node === null ? void 0 : this.nodeRows.get(node);
+      const row = node === null ? void 0 : this.nodeRows.get(this.key(node));
       if (row === void 0) {
         if (node === null || !this.rootNodes.has(node)) {
           this.dangle("layout entry");
@@ -1606,7 +1615,7 @@ 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 === void 0 || value.s === null || value.t === void 0 || value.t === null) {
@@ -1719,7 +1728,7 @@ class CxReader {
         if (isRecord(value) && this.scopePeek(value.s) !== 0) {
           const po = refId(value.po);
           if (po !== null && value.v !== void 0 && value.v !== null) {
-            this.weights.set(po, plainJson(value.v));
+            this.weights.set(this.key(po), plainJson(value.v));
           }
         }
       }
@@ -1820,7 +1829,8 @@ class CxReader {
         case "edges": {
           const domain = value.properties_of === "nodes" ? "node" : "edge";
           const target = refId(value.applies_to);
-          const row = target === null ? void 0 : (domain === "node" ? this.nodeRows : this.edgeRows).get(target);
+          const rows = domain === "node" ? this.nodeRows : this.edgeRows;
+          const row = target === null ? void 0 : rows.get(this.key(target));
           if (row === void 0) {
             if (target === null || !(domain === "node" ? this.rootNodes : this.rootEdges).has(target)) {
               this.dangle(`${domain} visual property entry`);
@@ -1914,7 +1924,7 @@ class CxReader {
         continue;
       }
       const po = refId(value.po);
-      const row = po === null ? void 0 : this.nodeRows.get(po);
+      const row = po === null ? void 0 : this.nodeRows.get(this.key(po));
       if (row === void 0) {
         if (po === null || !this.rootNodes.has(po)) {
           this.dangle("functionTerms entry");
@@ -1932,8 +1942,8 @@ class CxReader {
       }
       const node = refId(value.node);
       const edge = refId(value.edge);
-      const row = node === null ? void 0 : this.nodeRows.get(node);
-      const edgeRow = edge === null ? void 0 : this.edgeRows.get(edge);
+      const row = node === null ? void 0 : this.nodeRows.get(this.key(node));
+      const edgeRow = edge === null ? void 0 : this.edgeRows.get(this.key(edge));
       if (row === void 0 || edgeRow === void 0) {
         if (node === null || !this.rootNodes.has(node) || edge === null || !this.rootEdges.has(edge)) {
           this.dangle("reifiedEdges entry");
@@ -2002,7 +2012,7 @@ class CxReader {
       const ids = (Array.isArray(value[column]) ? value[column] : []).map(refId).filter((id) => id !== null).map(Number);
       for (const raw of targets) {
         const target = refId(raw);
-        const row = target === null ? void 0 : rows.get(target);
+        const row = target === null ? void 0 : rows.get(this.key(target));
         if (row === void 0) {
           if (target === null || !root.has(target)) {
             this.dangle(`${aspectName} entry`);
@@ -2191,4 +2201,4 @@ export {
   CX_ISSUE as C,
   cxImporter as c
 };
-//# sourceMappingURL=importer-BaQpCEcJ.js.map
+//# sourceMappingURL=importer-DET1tg6s.js.map

package/dist/chunks/importer-DET1tg6s.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"importer-DET1tg6s.js","sources":["../../src/formats/cx/importer.ts"],"sourcesContent":["/**\n * The CX version 1 importer (design/graph-io/cytoscape-and-obo/design.md section 1.2; the feature\n * and error inventory is research-cx.md): the JSON exchange format of NDEx and Cytoscape's CX\n * support. A CX document is an array of aspect fragments (`nodes`, `edges`, `nodeAttributes`,\n * `cartesianLayout`, `cySubNetworks`, `cyGroups`, `cyVisualProperties`, ...) that refer to each\n * other by integer ids, in any order.\n *\n * The document is read through the streaming scanner of common/json-elements.ts, so its text is\n * never held as one string; the parsed aspect elements are collected and each graph is built at the\n * end, because a reference may precede what it names.\n *\n * Mapping: every edge is directed; ids follow the CX id rule (design section 1.0.2); `n` is the\n * `name` column (the label), `r` is `represents`, `i` is `interaction`; attributes become columns\n * typed by their `d` (Cytoscape's value rule: \"\" and \"null\" are unset, \"NaN\" is NaN in a double); a\n * subnetwork's values are the unscoped ones and its own (`s`), its own winning. A collection (several\n * `cySubNetworks`) holds one graph per subnetwork: `importAll()` returns them, `import()` reads the\n * one `graphIndex` / `graphName` picks, `listGraphs()` lists them. Positions come from the\n * subnetwork's view, y flipped to y-up, `z` into the `z` column; `cyGroups` give `parent` (or\n * `parents`); per-element visual properties are one column per property (origin namespace\n * \"cx.bypass\") and style rules are kept verbatim in `meta.extra.cx` and not applied\n * (W_STYLES_NOT_IMPORTED, issue #706); provenance aspects become extension tables and list columns.\n */\n\nimport {\n    type ColumnDecl,\n    type ColumnHandle,\n    type Dtype,\n    type GraphMetaPatch,\n    type GraphSink,\n    INVALID_INDEX,\n    type NodeId,\n    type ScalarDtype,\n} from \"@graphty/graph-format\";\n\nimport { declareResolved, uniqueColumnName } from \"../../common/attributes.js\";\nimport {\n    AMBIGUOUS_GRAPH_NAME_CODE,\n    ASPECT_ORDER_CODE,\n    BAD_ASPECT_BLOCK_CODE,\n    BAD_VALUE_CODE,\n    COLUMN_RENAMED_CODE,\n    COUNT_MISMATCH_CODE,\n    DANGLING_REFERENCE_CODE,\n    DIRECTION_FORCED_CODE,\n    DIRECTION_REFUSED_CODE,\n    DUPLICATE_ATTRIBUTE_CODE,\n    DUPLICATE_EDGE_ID_CODE,\n    DUPLICATE_NODE_CODE,\n    EMPTY_INPUT_CODE,\n    ENCODING_FALLBACK_CODE,\n    GRAPH_NOT_FOUND_CODE,\n    ID_MERGED_CODE,\n    ID_TEXT_TYPE_CODE,\n    INVALID_ENCODING_CODE,\n    INVALID_UTF8_CODE,\n    MISSING_ENDPOINT_CODE,\n    MISSING_ID_CODE,\n    MULTIPLE_GRAPHS_CODE,\n    NO_GRAPH_CODE,\n    OPTION_IGNORED_CODE,\n    PARENT_CYCLE_CODE,\n    PRECISION_CODE,\n    ROLE_TAKEN_CODE,\n    SINK_OPTION_CODE,\n    STATUS_FAILED_CODE,\n    STATUS_WARNING_CODE,\n    STYLES_NOT_IMPORTED_CODE,\n    SYNTAX_CODE,\n    TOO_LARGE_CODE,\n    UNKNOWN_ATTR_TYPE_CODE,\n    UNKNOWN_ENCODING_CODE,\n    UNKNOWN_PARENT_CODE,\n    WIDENED_CODE,\n} from \"../../common/codes.js\";\nimport { DirectionResolver } from \"../../common/direction.js\";\nimport { IdCoercer } from \"../../common/ids.js\";\nimport { textChunks, throwIfAborted } from \"../../common/input.js\";\nimport {\n    cxId,\n    CxStructure,\n    declareFresh,\n    ExactInteger,\n    flipY,\n    inexactLiteral,\n    isRecord,\n    JsonScanError,\n    plainJson,\n    positionDecl,\n    reportTooDeep,\n    scanAspects,\n    zDecl,\n} from \"../../common/json-elements.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 { weightFromValue } from \"../../common/weights.js\";\nimport {\n    type CommonImportOptions,\n    type GraphChoiceOptions,\n    type GraphImporter,\n    type GraphListing,\n    type ImportInput,\n    type ImportReport,\n} from \"../../types.js\";\nimport { zAsOption } from \"../cx2/importer.js\";\n\n/** The format name. */\nconst CX_FORMAT = \"cx\";\n\n/** The origin namespace of the per-element visual property columns. */\nconst CX_BYPASS_NAMESPACE = \"cx.bypass\";\n\n/** The format-specific options of the CX importer. */\nexport interface CxImportOptions extends GraphChoiceOptions {\n    /**\n     * Where a node's `z` goes: \"column\" (default) keeps it in the f64 node column `z` (Cytoscape\n     * writes a stacking order there); \"position\" makes it the third component of the position.\n     */\n    zAs?: \"column\" | \"position\" | undefined;\n}\n\n/**\n * The issue codes the CX importer records (design section 1.2), by name: the codes shared with\n * the other importers (src/common/codes.ts) and the CX-specific ones. A key is the code without\n * its severity and format prefixes.\n */\nexport const CX_ISSUE = Object.freeze({\n    /** The input is empty (fatal). */\n    EMPTY_INPUT: EMPTY_INPUT_CODE,\n    /** The text is not JSON (fatal). */\n    SYNTAX: SYNTAX_CODE,\n    /** Invalid UTF-8 (fatal). */\n    INVALID_UTF8: INVALID_UTF8_CODE,\n    /** Invalid bytes in the encoding a BOM or the encoding option chose (fatal). */\n    INVALID_ENCODING: INVALID_ENCODING_CODE,\n    /** Bytes that are not UTF-8 were read as windows-1252. */\n    ENCODING_FALLBACK: ENCODING_FALLBACK_CODE,\n    /** An encoding the platform cannot decode was ignored. */\n    UNKNOWN_ENCODING: UNKNOWN_ENCODING_CODE,\n    /** The document is not a CX array, or it is CX2 (fatal; the message names CX2). */\n    NOT_CX: \"E_CX_NOT_CX\",\n    /** numberVerification holds another value than 2^48 - 1, or comes twice. */\n    NUMBER_VERIFICATION: \"W_CX_NUMBER_VERIFICATION\",\n    /** An old Cytoscape aspect name (visualProperties, subNetworks, ...) read under its cy name. */\n    OLD_ASPECT_NAME: \"W_CX_OLD_ASPECT_NAME\",\n    /** A cyGroups group whose id is not a node: the group node is added. */\n    GROUP_NODE_ADDED: \"W_CX_GROUP_NODE_ADDED\",\n    /** Nodes or edges of the root network that no subnetwork holds: Cytoscape shows them in no network; not read. */\n    ROOT_ONLY: \"W_CX_ROOT_ONLY\",\n    /** The producer marked the document as failed (fatal). */\n    STATUS_FAILED: STATUS_FAILED_CODE,\n    /** The producer marked the document as successful with an error text. */\n    STATUS_WARNING: STATUS_WARNING_CODE,\n    /** A member of the array that is not a one-key aspect block, or an element that is not an object. */\n    BAD_ASPECT_BLOCK: BAD_ASPECT_BLOCK_CODE,\n    /** An aspect after the post-metadata or after the status, a third metaData. */\n    ASPECT_ORDER: ASPECT_ORDER_CODE,\n    /** A metaData element count disagrees with what was read. */\n    COUNT_MISMATCH: COUNT_MISMATCH_CODE,\n    /** A value that does not parse as its data type; the cell is unset. */\n    BAD_VALUE: BAD_VALUE_CODE,\n    /** One attribute name with several data types: the column takes the wider one. */\n    WIDENED: WIDENED_CODE,\n    /** A data type CX does not define; the value is kept as text. */\n    UNKNOWN_ATTR_TYPE: UNKNOWN_ATTR_TYPE_CODE,\n    /** An attribute, layout, bypass, subnetwork member, view or provenance entry naming nothing. */\n    DANGLING_REFERENCE: DANGLING_REFERENCE_CODE,\n    /** The same attribute twice on one element (or n and a different name attribute); the later wins. */\n    DUPLICATE_ATTRIBUTE: DUPLICATE_ATTRIBUTE_CODE,\n    /** A group member naming no node. */\n    UNKNOWN_PARENT: UNKNOWN_PARENT_CODE,\n    /** A group membership that would close a parent cycle; dropped. */\n    PARENT_CYCLE: PARENT_CYCLE_CODE,\n    /** The style rules of cyVisualProperties are not applied (issue #706). */\n    STYLES_NOT_IMPORTED: STYLES_NOT_IMPORTED_CODE,\n    /** A node without an @id. */\n    MISSING_ID: MISSING_ID_CODE,\n    /** An edge without s or t. */\n    MISSING_ENDPOINT: MISSING_ENDPOINT_CODE,\n    /** A node id declared twice; the second merges into the first. */\n    DUPLICATE_NODE: DUPLICATE_NODE_CODE,\n    /** An edge id declared twice; the second edge is skipped. */\n    DUPLICATE_EDGE_ID: DUPLICATE_EDGE_ID_CODE,\n    /** An id that is not an integer. */\n    INVALID_ID: \"E_INVALID_ID\",\n    /** An edge endpoint naming no node of the graph (addMissingNodes false, the default). */\n    UNKNOWN_NODE: \"E_UNKNOWN_NODE\",\n    /** A weight that is not a number. */\n    INVALID_WEIGHT: \"E_INVALID_WEIGHT\",\n    /** An id spelled as a string or a non-integer literal; read as the integer. */\n    ID_TEXT_TYPE: ID_TEXT_TYPE_CODE,\n    /** An integer beyond 2^53: an id kept as its digits, a value stored as the nearest f64. */\n    PRECISION: PRECISION_CODE,\n    /** Two id texts merged under `ids: \"number\"`. */\n    ID_MERGED: ID_MERGED_CODE,\n    /** A collection read by import(): the other subnetworks are skipped. */\n    MULTIPLE_GRAPHS: MULTIPLE_GRAPHS_CODE,\n    /** graphIndex or graphName names no subnetwork (fatal). */\n    GRAPH_NOT_FOUND: GRAPH_NOT_FOUND_CODE,\n    /** graphName names several subnetworks (fatal). */\n    AMBIGUOUS_GRAPH_NAME: AMBIGUOUS_GRAPH_NAME_CODE,\n    /** The input holds no graph (fatal). */\n    NO_GRAPH: NO_GRAPH_CODE,\n    /** A column renamed because its name was taken. */\n    COLUMN_RENAMED: COLUMN_RENAMED_CODE,\n    /** A column that lost its role because another column holds it. */\n    ROLE_TAKEN: ROLE_TAKEN_CODE,\n    /** The sink refused the direction. */\n    DIRECTION_REFUSED: DIRECTION_REFUSED_CODE,\n    /** Edges forced to the policy's direction. */\n    DIRECTION_FORCED: DIRECTION_FORCED_CODE,\n    /** A common option CX has no use for. */\n    OPTION_IGNORED: OPTION_IGNORED_CODE,\n    /** A builder option the caller's sink does not honour. */\n    SINK_OPTION: SINK_OPTION_CODE,\n    /** The input is beyond a size limit (fatal). */\n    TOO_LARGE: TOO_LARGE_CODE,\n});\n\nconst USED_OPTIONS: ReadonlySet<keyof CommonImportOptions> = new Set<keyof CommonImportOptions>([\n    \"ids\",\n    \"addMissingNodes\",\n    \"duplicateEdges\",\n    \"selfLoops\",\n    \"onMixedDirection\",\n    \"weightFrom\",\n    \"weightDtype\",\n    \"long\",\n    \"errorLimit\",\n    \"signal\",\n    \"onProgress\",\n]);\n\n/** CX has no undirected edge: defaultDirected never applies (reported W_OPTION_IGNORED). */\nconst FORMAT_DEFAULTS: ImportFormatDefaults = {\n    ids: \"keep\",\n    defaultDirected: true,\n    weightFrom: \"weight\",\n    addMissingNodes: false,\n};\n\nconst ABORT_CHECK_INTERVAL = 64;\n\n/** The numberVerification values a reader accepts: 2^48 - 1 and Java's Long.MAX_VALUE. */\nconst NUMBER_VERIFICATION_VALUES: ReadonlySet<string> = new Set([\"281474976710655\", \"9223372036854775807\"]);\n\n/** Old Cytoscape aspect names and the names they are read under. */\nconst OLD_ASPECT_NAMES: Readonly<Record<string, string>> = {\n    visualProperties: \"cyVisualProperties\",\n    subNetworks: \"cySubNetworks\",\n    networkRelations: \"cyNetworkRelations\",\n    hiddenAttributes: \"cyHiddenAttributes\",\n};\n\n/** The aspects the importer reads into the graph (everything else is kept verbatim). */\nconst READ_ASPECTS: ReadonlySet<string> = new Set([\n    \"nodes\",\n    \"edges\",\n    \"nodeAttributes\",\n    \"edgeAttributes\",\n    \"networkAttributes\",\n    \"cartesianLayout\",\n    \"cySubNetworks\",\n    \"cyNetworkRelations\",\n    \"cyViews\",\n    \"cyGroups\",\n    \"cyVisualProperties\",\n    \"cyTableColumn\",\n    \"citations\",\n    \"supports\",\n    \"nodeCitations\",\n    \"edgeCitations\",\n    \"nodeSupports\",\n    \"edgeSupports\",\n    \"functionTerms\",\n    \"reifiedEdges\",\n    \"numberVerification\",\n    \"metaData\",\n    \"status\",\n]);\n\n/** The aspects also kept verbatim in meta.extra.cx although they are read. */\nconst ALSO_KEPT: ReadonlySet<string> = new Set([\n    \"cySubNetworks\",\n    \"cyNetworkRelations\",\n    \"cyViews\",\n    \"cyVisualProperties\",\n    \"cyTableColumn\",\n    \"numberVerification\",\n    \"metaData\",\n]);\n\n/** Cytoscape's table-cell style aspects (both spellings): style rules, kept and reported, never read. */\nconst TABLE_STYLE_ASPECTS: readonly string[] = [\"tableVisualProperties\", \"cyTableVisualProperties\"];\n\n/** The first keys that make a head CX for sure, and the other aspect names a CX document may start with. */\nconst CX_FIRST_KEYS: readonly string[] = [\"numberVerification\", \"metaData\"];\nconst CX_ASPECT_KEYS: readonly string[] = [\n    \"nodes\",\n    \"edges\",\n    \"nodeAttributes\",\n    \"edgeAttributes\",\n    \"networkAttributes\",\n    \"cartesianLayout\",\n    \"@context\",\n    \"cySubNetworks\",\n    \"subNetworks\",\n    \"cyNetworkRelations\",\n    \"networkRelations\",\n    \"cyVisualProperties\",\n    \"visualProperties\",\n    \"cyHiddenAttributes\",\n    \"hiddenAttributes\",\n    \"cyTableColumn\",\n    \"cyGroups\",\n    \"cyViews\",\n    \"ndexStatus\",\n    \"provenanceHistory\",\n    \"citations\",\n    \"supports\",\n    \"functionTerms\",\n];\n\n// ============================================================ values\n\n/** The canonical CX scalar types. */\ntype CxScalar = \"string\" | \"boolean\" | \"integer\" | \"long\" | \"double\";\n\n/** A CX data type. */\ninterface CxType {\n    readonly scalar: CxScalar;\n    readonly list: boolean;\n}\n\n/** The CX data types, with the Java reader's float aliases. */\nconst SCALARS: Readonly<Record<string, CxScalar>> = {\n    string: \"string\",\n    boolean: \"boolean\",\n    integer: \"integer\",\n    long: \"long\",\n    double: \"double\",\n    float: \"double\",\n};\n\n/**\n * Resolve a `d` value.\n * @param d - the data type (undefined: string)\n * @returns the type, or null when CX does not define it\n */\nfunction cxType(d: unknown): CxType | null {\n    if (d === undefined || d === null) {\n        return { scalar: \"string\", list: false };\n    }\n    if (typeof d !== \"string\") {\n        return null;\n    }\n    const list = d.startsWith(\"list_of_\");\n    const scalar = SCALARS[list ? d.slice(\"list_of_\".length) : d] as CxScalar | undefined;\n    return scalar === undefined ? null : { scalar, list };\n}\n\n/**\n * The type text of a type.\n * @param type - the type\n * @returns `list_of_double`, `string`, ...\n */\nfunction typeText(type: CxType): string {\n    return type.list ? `list_of_${type.scalar}` : type.scalar;\n}\n\n/** The widening rank of the scalar types (design 5.1 order; boolean and numbers widen to string). */\nconst RANK: Readonly<Record<CxScalar, number>> = { boolean: 0, integer: 1, long: 2, double: 3, string: 4 };\n\n/**\n * Widen two types to one that holds both.\n * @param a - the type so far\n * @param b - another type\n * @returns the wider type, or null when they cannot share a column (a list and a scalar)\n */\nfunction widenType(a: CxType, b: CxType): CxType | null {\n    if (a.list !== b.list) {\n        return null;\n    }\n    if (a.scalar === b.scalar) {\n        return a;\n    }\n    const numeric = (s: CxScalar): boolean => s === \"integer\" || s === \"long\" || s === \"double\";\n    if (numeric(a.scalar) && numeric(b.scalar)) {\n        return RANK[a.scalar] > RANK[b.scalar] ? a : b;\n    }\n    return { scalar: \"string\", list: a.list };\n}\n\n/** What parseValue() returns for a value that does not parse. */\nconst BAD = Symbol(\"bad\");\n\n/** What parseValue() returns for a value Cytoscape reads as null (\"\", \"null\"). */\nconst UNSET = Symbol(\"unset\");\n\nconst I32_MIN = -2147483648;\nconst I32_MAX = 2147483647;\nconst INTEGER_TEXT = /^-?[0-9]+$/;\nconst DECIMAL_TEXT = /^-?([0-9]+(\\.[0-9]*)?|\\.[0-9]+)([eE][+-]?[0-9]+)?$/;\n\n/**\n * Whether a text is Cytoscape's null: the empty string or \"null\" in any case.\n * @param text - the text\n * @returns true for a null text\n */\nfunction isNullText(text: string): boolean {\n    return text === \"\" || text.toLowerCase() === \"null\";\n}\n\n/**\n * Parse one scalar value (or list item) of a CX attribute by its type, with Cytoscape's value\n * rule: \"\" and \"null\" are unset, \"NaN\" is NaN in a double (unset in an integer or long), native JSON\n * numbers and booleans are accepted, anything else that does not parse is BAD.\n * @param value - the value (never null)\n * @param scalar - the type\n * @param long - the importer's `long` option\n * @param onPrecision - called for a long beyond 2^53\n * @returns the value, UNSET or BAD\n */\nfunction parseScalar(\n    value: unknown,\n    scalar: CxScalar,\n    long: \"f64\" | \"string\",\n    onPrecision: (digits: string) => void,\n): unknown {\n    if (value instanceof ExactInteger) {\n        if (scalar === \"string\" || (scalar === \"long\" && long === \"string\")) {\n            return value.digits;\n        }\n        if (scalar === \"long\" || scalar === \"double\") {\n            if (scalar === \"long\") {\n                onPrecision(value.digits);\n            }\n            return Number(value.digits);\n        }\n        return BAD;\n    }\n    if (typeof value === \"number\" || typeof value === \"boolean\") {\n        return parseNative(value, scalar, long);\n    }\n    if (typeof value !== \"string\") {\n        return BAD;\n    }\n    if (scalar === \"string\") {\n        return value;\n    }\n    if (isNullText(value)) {\n        return UNSET;\n    }\n    switch (scalar) {\n        case \"boolean\": {\n            const lower = value.toLowerCase();\n            if (lower === \"true\" || lower === \"false\") {\n                return lower === \"true\";\n            }\n            return BAD;\n        }\n        case \"integer\":\n        case \"long\": {\n            if (value === \"NaN\") {\n                return UNSET;\n            }\n            if (!INTEGER_TEXT.test(value)) {\n                return BAD;\n            }\n            const n = Number(value);\n            if (scalar === \"integer\") {\n                return n >= I32_MIN && n <= I32_MAX ? n : BAD;\n            }\n            if (long === \"string\") {\n                return value;\n            }\n            if (!Number.isSafeInteger(n)) {\n                onPrecision(value);\n            }\n            return n;\n        }\n        default: {\n            if (value === \"NaN\" || value === \"nan\") {\n                return NaN;\n            }\n            if (value === \"Infinity\" || value === \"-Infinity\") {\n                return Number(value);\n            }\n            return DECIMAL_TEXT.test(value) ? Number(value) : BAD;\n        }\n    }\n}\n\n/**\n * Parse a native JSON number or boolean by a type.\n * @param value - the value\n * @param scalar - the type\n * @param long - the importer's `long` option\n * @returns the value or BAD\n */\nfunction parseNative(value: number | boolean, scalar: CxScalar, long: \"f64\" | \"string\"): unknown {\n    switch (scalar) {\n        case \"string\":\n            return String(value);\n        case \"boolean\":\n            return typeof value === \"boolean\" ? value : BAD;\n        case \"integer\":\n            return typeof value === \"number\" && Number.isInteger(value) && value >= I32_MIN && value <= I32_MAX\n                ? value\n                : BAD;\n        case \"long\":\n            if (typeof value !== \"number\" || !Number.isInteger(value)) {\n                return BAD;\n            }\n            return long === \"string\" ? String(value) : value;\n        default:\n            return typeof value === \"number\" ? value : BAD;\n    }\n}\n\n/**\n * Parse an attribute value by its type: a scalar, or a list whose items parse one by one (a null\n * item is NaN in a double list and BAD elsewhere).\n * @param value - the value (never null)\n * @param type - the type\n * @param long - the importer's `long` option\n * @param onPrecision - called for a long beyond 2^53\n * @returns the value, UNSET or BAD\n */\nfunction parseValue(\n    value: unknown,\n    type: CxType,\n    long: \"f64\" | \"string\",\n    onPrecision: (digits: string) => void,\n): unknown {\n    if (Array.isArray(value) !== type.list) {\n        return BAD;\n    }\n    if (!type.list) {\n        return parseScalar(value, type.scalar, long, onPrecision);\n    }\n    const out: unknown[] = [];\n    for (const item of value as unknown[]) {\n        let parsed = item === null ? UNSET : parseScalar(item, type.scalar, long, onPrecision);\n        if (parsed === UNSET) {\n            parsed = type.scalar === \"double\" ? NaN : BAD;\n        }\n        if (parsed === BAD) {\n            return BAD;\n        }\n        out.push(parsed);\n    }\n    return out;\n}\n\n/**\n * The column dtype of a type.\n * @param scalar - the scalar type\n * @param long - the importer's `long` option\n * @returns the dtype\n */\nfunction scalarDtype(scalar: CxScalar, long: \"f64\" | \"string\"): ScalarDtype {\n    switch (scalar) {\n        case \"boolean\":\n            return \"bool\";\n        case \"integer\":\n            return \"i32\";\n        case \"long\":\n            return long === \"string\" ? \"string\" : \"f64\";\n        case \"double\":\n            return \"f64\";\n        default:\n            return \"string\";\n    }\n}\n\n/**\n * A parsed value converted to the column's type (a narrower value in a widened column).\n * @param value - the parsed value\n * @param type - the column's type\n * @returns the value to store\n */\nfunction toColumn(value: unknown, type: CxType): unknown {\n    if (type.scalar !== \"string\") {\n        return value;\n    }\n    if (type.list) {\n        return (value as unknown[]).map((item) => (typeof item === \"string\" ? item : String(item)));\n    }\n    return typeof value === \"string\" ? value : String(value);\n}\n\n/**\n * A short JSON rendering of a value for a message.\n * @param value - the value\n * @returns the text, at most 60 characters\n */\nfunction shown(value: unknown): string {\n    if (value instanceof ExactInteger) {\n        return value.digits;\n    }\n    let text: string;\n    try {\n        text = JSON.stringify(value) ?? String(value);\n    } catch {\n        text = String(value);\n    }\n    return text.length > 60 ? `${text.slice(0, 57)}...` : text;\n}\n\n// ============================================================ the document as read\n\n/** A parsed aspect element with where it came from. */\ninterface Held {\n    readonly value: unknown;\n    readonly line: number;\n    /** Bit 1: @id, bit 2: s, bit 4: t was written as a non-integer literal. */\n    readonly inexact: number;\n}\n\n/** Everything the scan collects. */\ninterface CxDocument {\n    /** The read aspects by their (cy) name. */\n    readonly aspects: Map<string, Held[]>;\n    /** Attribute elements by table and attribute name. */\n    readonly attributes: {\n        readonly node: Map<string, Held[]>;\n        readonly edge: Map<string, Held[]>;\n        readonly network: Map<string, Held[]>;\n    };\n    /** Aspects kept verbatim in meta.extra.cx. */\n    readonly kept: Map<string, unknown[]>;\n    readonly structure: CxStructure;\n}\n\n/**\n * The elements of a read aspect.\n * @param doc - the document\n * @param name - the aspect\n * @returns the elements, empty when absent\n */\nfunction aspect(doc: CxDocument, name: string): readonly Held[] {\n    return doc.aspects.get(name) ?? [];\n}\n\n/**\n * The inexact-literal bits of an element.\n * @param text - the element's JSON text\n * @param keys - the id keys to check, bit 1, 2, 4 in order\n * @returns the bits\n */\nfunction inexactBits(text: string, keys: readonly string[]): number {\n    if (!/[0-9][.eE]/.test(text)) {\n        return 0;\n    }\n    let bits = 0;\n    keys.forEach((key, i) => {\n        if (inexactLiteral(text, key)) {\n            bits |= 1 << i;\n        }\n    });\n    return bits;\n}\n\n/**\n * The attribute map of an attribute aspect.\n * @param doc - the document\n * @param name - the aspect name\n * @returns the map, or null for another aspect\n */\nfunction attributeTable(doc: CxDocument, name: string): Map<string, Held[]> | null {\n    switch (name) {\n        case \"nodeAttributes\":\n            return doc.attributes.node;\n        case \"edgeAttributes\":\n            return doc.attributes.edge;\n        case \"networkAttributes\":\n            return doc.attributes.network;\n        default:\n            return null;\n    }\n}\n\n/**\n * Check a numberVerification element: 2^48 - 1 (or Java's Long.MAX_VALUE), and only one.\n * @param value - the element\n * @param count - how many numberVerification elements were read, this one included\n * @param report - the report\n * @param line - its line\n */\nfunction checkNumberVerification(value: unknown, count: number, report: ImportReportBuilder, line: number): void {\n    const raw = isRecord(value) ? value.longNumber : undefined;\n    const digits = raw instanceof ExactInteger ? raw.digits : String(raw);\n    if (count > 1 || !NUMBER_VERIFICATION_VALUES.has(digits)) {\n        report.warning(\n            \"validation-error\",\n            CX_ISSUE.NUMBER_VERIFICATION,\n            count > 1\n                ? \"a second numberVerification element; ignored\"\n                : `numberVerification holds ${shown(raw === undefined ? null : digits)}, not 281474976710655`,\n            { line, element: \"numberVerification\" },\n        );\n    }\n}\n\n/**\n * Read the whole document through the streaming scanner, checking its structure.\n * @param input - the input\n * @param report - the report\n * @param options - the resolved options\n * @returns what was read\n */\nasync function readDocument(\n    input: ImportInput,\n    report: ImportReportBuilder,\n    options: ResolvedImportOptions,\n): Promise<CxDocument> {\n    const structure = new CxStructure(report);\n    const doc: CxDocument = {\n        aspects: new Map(),\n        attributes: { node: new Map(), edge: new Map(), network: new Map() },\n        kept: new Map(),\n        structure,\n    };\n    let sinceCheck = 0;\n    let verifications = 0;\n    const canonical = (name: string, line: number): string => {\n        const renamed = OLD_ASPECT_NAMES[name] as string | undefined;\n        if (renamed === undefined) {\n            return name;\n        }\n        report.warnOnce(\n            \"coercion\",\n            CX_ISSUE.OLD_ASPECT_NAME,\n            `the old aspect name \"${name}\" is read as \"${renamed}\"`,\n            { line, element: name },\n            `${CX_ISSUE.OLD_ASPECT_NAME}:${name}`,\n        );\n        return renamed;\n    };\n    const collect = (name: string, value: unknown, text: string, line: number, exact: boolean): void => {\n        structure.element(name, value, line);\n        if (ALSO_KEPT.has(name) || !READ_ASPECTS.has(name)) {\n            if (!doc.kept.has(name)) {\n                doc.kept.set(name, []);\n            }\n            doc.kept.get(name)?.push(exact ? plainJson(value) : value);\n        }\n        if (!READ_ASPECTS.has(name) || name === \"metaData\" || name === \"status\") {\n            return;\n        }\n        if (name === \"numberVerification\") {\n            checkNumberVerification(value, ++verifications, report, line);\n            return;\n        }\n        let inexact = 0;\n        if (name === \"nodes\") {\n            inexact = inexactBits(text, [\"@id\"]);\n        } else if (name === \"edges\") {\n            inexact = inexactBits(text, [\"@id\", \"s\", \"t\"]);\n        }\n        const held: Held = { value, line, inexact };\n        const table = attributeTable(doc, name);\n        if (table !== null) {\n            if (!isRecord(value) || typeof value.n !== \"string\") {\n                report.error(\"missing-value\", MISSING_ID_CODE, `a ${name} element has no attribute name n; skipped`, {\n                    line,\n                    element: name,\n                });\n                return;\n            }\n            const key = value.n;\n            if (!table.has(key)) {\n                table.set(key, []);\n            }\n            table.get(key)?.push(held);\n            return;\n        }\n        if (!doc.aspects.has(name)) {\n            doc.aspects.set(name, []);\n        }\n        doc.aspects.get(name)?.push(held);\n    };\n    try {\n        for await (const event of scanAspects(textChunks(input, report, options))) {\n            if (++sinceCheck >= ABORT_CHECK_INTERVAL) {\n                sinceCheck = 0;\n                throwIfAborted(options.signal);\n            }\n            switch (event.kind) {\n                case \"root\":\n                    report.fail(\n                        CX_ISSUE.NOT_CX,\n                        `a CX document is a JSON array of aspects; found ${isRecord(event.value) ? \"an object\" : shown(event.value)}`,\n                        { line: event.line },\n                    );\n                    break;\n                case \"member\": {\n                    const { value } = event;\n                    if (isRecord(value) && \"CXVersion\" in value) {\n                        report.fail(\n                            CX_ISSUE.NOT_CX,\n                            `the document is CX2 (CXVersion ${shown(value.CXVersion)}), not CX version 1; read it with the cx2 importer`,\n                            { line: event.line },\n                        );\n                    }\n                    const keys = isRecord(value) ? Object.keys(value) : [];\n                    if (isRecord(value) && keys.length === 1 && isRecord(value[keys[0]])) {\n                        const name = canonical(keys[0], event.line);\n                        structure.block(name, event.line);\n                        collect(name, value[keys[0]], \"\", event.line, event.exact);\n                        break;\n                    }\n                    report.error(\n                        \"parse-error\",\n                        BAD_ASPECT_BLOCK_CODE,\n                        `a member of the document is ${keys.length > 1 ? `an object with ${keys.length} keys (${keys.join(\", \")})` : shown(value)}, not a one-key aspect fragment; skipped`,\n                        { line: event.line, element: keys[0] ?? null },\n                    );\n                    break;\n                }\n                case \"block\":\n                    structure.block(canonical(event.aspect, event.line), event.line);\n                    break;\n                case \"element\": {\n                    const name = OLD_ASPECT_NAMES[event.aspect] ?? event.aspect;\n                    collect(name, event.value, event.text, event.line, event.exact);\n                    break;\n                }\n                case \"deep\":\n                    reportTooDeep(report, event);\n                    break;\n                case \"extraKeys\":\n                    report.error(\n                        \"parse-error\",\n                        BAD_ASPECT_BLOCK_CODE,\n                        `the \"${event.aspect}\" fragment holds more keys (${event.keys.join(\", \")}); a fragment has one key, the others are skipped`,\n                        { line: event.line, element: event.aspect },\n                    );\n                    break;\n                default:\n                    break;\n            }\n        }\n    } catch (err) {\n        if (err instanceof JsonScanError) {\n            report.fail(err.empty ? EMPTY_INPUT_CODE : SYNTAX_CODE, err.message, { line: err.line });\n        }\n        throw err;\n    }\n    structure.checkCounts();\n    return doc;\n}\n\n// ============================================================ graphs (subnetworks)\n\n/** One graph of a document: the root network, or one subnetwork of a collection. */\ninterface GraphPlan {\n    readonly index: number;\n    readonly name: string | null;\n    /** The subnetwork's id, or null for the root network. */\n    readonly subnetwork: NodeId | null;\n    /** The member node ids, or null for every node. */\n    readonly nodes: ReadonlySet<NodeId> | null;\n    /** The member edge ids, or null for every edge. */\n    readonly edges: ReadonlySet<NodeId> | null;\n    /** The views of the graph, the first one first. */\n    readonly views: readonly NodeId[];\n}\n\n/**\n * An id of a reference, or null when it is not one.\n * @param raw - the parsed reference\n * @returns the id\n */\nfunction refId(raw: unknown): NodeId | null {\n    try {\n        return cxId(raw).id;\n    } catch {\n        return null;\n    }\n}\n\n/**\n * A member list: the ids of an array, or null for \"all\".\n * @param raw - the list\n * @returns the set, or null for every element\n */\nfunction memberSet(raw: unknown): Set<NodeId> | null {\n    if (raw === \"all\") {\n        return null;\n    }\n    const out = new Set<NodeId>();\n    if (Array.isArray(raw)) {\n        for (const item of raw) {\n            const id = refId(item);\n            if (id !== null) {\n                out.add(id);\n            }\n        }\n    }\n    return out;\n}\n\n/**\n * The graphs of a document, in the order Cytoscape opens them.\n * @param doc - the document\n * @returns one plan per graph (at least one)\n */\nfunction graphPlans(doc: CxDocument): GraphPlan[] {\n    const subs = new Map<NodeId, { nodes: Set<NodeId> | null; edges: Set<NodeId> | null }>();\n    for (const { value } of aspect(doc, \"cySubNetworks\")) {\n        const id = isRecord(value) ? refId(value[\"@id\"]) : null;\n        if (id !== null && isRecord(value) && !subs.has(id)) {\n            subs.set(id, { nodes: memberSet(value.nodes), edges: memberSet(value.edges) });\n        }\n    }\n    const relationNames = new Map<NodeId, string>();\n    const order: NodeId[] = [];\n    const views = new Map<NodeId, NodeId[]>();\n    const addView = (sub: NodeId, view: NodeId): void => {\n        const list = views.get(sub) ?? [];\n        if (!list.includes(view)) {\n            list.push(view);\n        }\n        views.set(sub, list);\n    };\n    for (const { value } of aspect(doc, \"cyNetworkRelations\")) {\n        if (!isRecord(value)) {\n            continue;\n        }\n        const child = refId(value.c);\n        if (child === null) {\n            continue;\n        }\n        if (value.r === \"view\") {\n            const parent = refId(value.p);\n            if (parent !== null) {\n                addView(parent, child);\n            }\n            continue;\n        }\n        if (typeof value.name === \"string\") {\n            relationNames.set(child, value.name);\n        }\n        if (subs.has(child) && !order.includes(child)) {\n            order.push(child);\n        }\n    }\n    for (const { value } of aspect(doc, \"cyViews\")) {\n        const view = isRecord(value) ? refId(value[\"@id\"]) : null;\n        const sub = isRecord(value) ? refId(value.s) : null;\n        if (view !== null && sub !== null) {\n            addView(sub, view);\n        }\n    }\n    for (const id of subs.keys()) {\n        if (!order.includes(id)) {\n            order.push(id);\n        }\n    }\n    const networkName = (sub: NodeId | null): string | null => {\n        let found: string | null = null;\n        for (const { value } of doc.attributes.network.get(\"name\") ?? []) {\n            if (!isRecord(value) || typeof value.v !== \"string\") {\n                continue;\n            }\n            const scope = value.s === undefined ? null : refId(value.s);\n            if (scope === sub) {\n                return value.v;\n            }\n            if (scope === null) {\n                found ??= value.v;\n            }\n        }\n        return found;\n    };\n    if (order.length <= 1) {\n        const sub = order.length === 1 ? order[0] : null;\n        const members = sub === null ? undefined : subs.get(sub);\n        let graphViews = sub === null ? [] : (views.get(sub) ?? []);\n        if (graphViews.length === 0) {\n            graphViews = [...new Set([...views.values()].flat())];\n        }\n        if (graphViews.length === 0) {\n            graphViews = layoutViews(doc);\n        }\n        return [\n            {\n                index: 0,\n                name: (sub === null ? null : (relationNames.get(sub) ?? null)) ?? networkName(sub),\n                subnetwork: sub,\n                nodes: members?.nodes ?? null,\n                edges: members?.edges ?? null,\n                views: graphViews,\n            },\n        ];\n    }\n    return order.map((sub, index) => ({\n        index,\n        name: relationNames.get(sub) ?? networkName(sub),\n        subnetwork: sub,\n        nodes: subs.get(sub)?.nodes ?? null,\n        edges: subs.get(sub)?.edges ?? null,\n        views: views.get(sub) ?? [],\n    }));\n}\n\n/**\n * The distinct views the layout entries name, in order of appearance.\n * @param doc - the document\n * @returns the view ids\n */\nfunction layoutViews(doc: CxDocument): NodeId[] {\n    const out: NodeId[] = [];\n    for (const { value } of aspect(doc, \"cartesianLayout\")) {\n        const view = isRecord(value) && value.view !== undefined ? refId(value.view) : null;\n        if (view !== null && !out.includes(view)) {\n            out.push(view);\n        }\n    }\n    return out;\n}\n\n/**\n * How many elements a member set holds.\n * @param members - the set, or null for every element\n * @param total - the element count of the root network\n * @returns the count\n */\nfunction memberCount(members: ReadonlySet<NodeId> | null, total: number): number {\n    return members === null ? total : members.size;\n}\n\n// ============================================================ the build\n\n/** One attribute column of the graph being built. */\ninterface AttributeColumn {\n    readonly name: string;\n    readonly type: CxType | null;\n    /** null: values are kept as text (an unknown or conflicting type). */\n    handle: ColumnHandle;\n}\n\n/** Reads one graph of a collected document into a sink. */\nclass CxReader {\n    private readonly sink: GraphSink;\n\n    private readonly report: ImportReportBuilder;\n\n    private readonly options: ResolvedImportOptions;\n\n    private readonly zAs: \"column\" | \"position\";\n\n    private readonly doc: CxDocument;\n\n    private readonly plan: GraphPlan;\n\n    private readonly direction: DirectionResolver;\n\n    private readonly coercer: IdCoercer;\n\n    /** Every node id of the root network. */\n    private readonly rootNodes = new Set<NodeId>();\n\n    /** Every edge id of the root network. */\n    private readonly rootEdges = new Set<NodeId>();\n\n    /** CX node id -> sink node index, for this graph. */\n    private readonly nodeRows = new Map<NodeId, number>();\n\n    /** CX edge id -> sink edge index, for this graph. */\n    private readonly edgeRows = new Map<NodeId, number>();\n\n    /** The subnetwork ids of the document. */\n    private readonly subnetworks = new Set<NodeId>();\n\n    private readonly dangling = new Map<string, number>();\n\n    private nameHandle: ColumnHandle = INVALID_INDEX as ColumnHandle;\n\n    private representsHandle: ColumnHandle = INVALID_INDEX as ColumnHandle;\n\n    private interactionHandle: ColumnHandle = INVALID_INDEX as ColumnHandle;\n\n    private edgeIdHandle: ColumnHandle = INVALID_INDEX as ColumnHandle;\n\n    private sinceCheck = 0;\n\n    private idType: \"integer\" | \"mixed\" = \"integer\";\n\n    private weighted = false;\n\n    /**\n     * Create the reader.\n     * @param sink - the sink\n     * @param report - the report\n     * @param options - the resolved options\n     * @param zAs - where z goes\n     * @param doc - the collected document\n     * @param plan - the graph to read\n     */\n    constructor(\n        sink: GraphSink,\n        report: ImportReportBuilder,\n        options: ResolvedImportOptions,\n        zAs: \"column\" | \"position\",\n        doc: CxDocument,\n        plan: GraphPlan,\n    ) {\n        this.sink = sink;\n        this.report = report;\n        this.options = options;\n        this.zAs = zAs;\n        this.doc = doc;\n        this.plan = plan;\n        this.direction = new DirectionResolver(sink, report, options.onMixedDirection);\n        this.coercer = new IdCoercer(options.ids);\n        for (const { value } of aspect(doc, \"nodes\")) {\n            const id = isRecord(value) ? refId(value[\"@id\"]) : null;\n            if (id !== null) {\n                this.rootNodes.add(id);\n            }\n        }\n        for (const { value } of aspect(doc, \"edges\")) {\n            const id = isRecord(value) ? refId(value[\"@id\"]) : null;\n            if (id !== null) {\n                this.rootEdges.add(id);\n            }\n        }\n        for (const { value } of aspect(doc, \"cySubNetworks\")) {\n            const id = isRecord(value) ? refId(value[\"@id\"]) : null;\n            if (id !== null) {\n                this.subnetworks.add(id);\n            }\n        }\n    }\n\n    /** Build the graph. */\n    build(): void {\n        const { report } = this;\n        this.direction.setHeader(true);\n        this.checkMembers();\n        this.checkRootOnly();\n        const nodeColumns = this.declareAttributes(\"node\");\n        this.readNodes();\n        this.readGroups();\n        this.writeAttributes(\"node\", nodeColumns);\n        this.readLayout();\n        const edgeColumns = this.declareAttributes(\"edge\");\n        this.readEdges();\n        this.writeAttributes(\"edge\", edgeColumns);\n        this.readNetworkAttributes();\n        this.readVisualProperties();\n        this.readProvenance();\n        for (const [kind, count] of this.dangling) {\n            report.warning(\"validation-error\", DANGLING_REFERENCE_CODE, `${count} ${kind}(s) name nothing; ignored`, {\n                element: kind,\n            });\n        }\n        this.setMeta();\n    }\n\n    // ------------------------------------------------------------ helpers\n\n    /**\n     * Count a reference that names nothing.\n     * @param kind - what referred\n     */\n    private dangle(kind: string): void {\n        this.dangling.set(kind, (this.dangling.get(kind) ?? 0) + 1);\n    }\n\n    /** Check the cancellation signal every ABORT_CHECK_INTERVAL elements. */\n    private checkAbort(): void {\n        if (++this.sinceCheck >= ABORT_CHECK_INTERVAL) {\n            this.sinceCheck = 0;\n            throwIfAborted(this.options.signal);\n        }\n    }\n\n    /**\n     * Whether a node id belongs to this graph.\n     * @param id - the CX id\n     * @returns true for a member\n     */\n    private inGraph(id: NodeId): boolean {\n        return this.plan.nodes === null || this.plan.nodes.has(id);\n    }\n\n    /**\n     * The key of the node and edge row maps for a CX id as an aspect writes it: the id the `ids`\n     * option makes of it, which is what idOf() stored the element under.\n     * @param raw - the CX id\n     * @returns the row key\n     */\n    private key(raw: NodeId): NodeId {\n        return this.options.ids === \"keep\" ? raw : this.coercer.value(raw);\n    }\n\n    /**\n     * Whether a scoped value applies to this graph: unscoped, or scoped to its subnetwork. A scope\n     * naming no subnetwork is counted as dangling.\n     * @param scope - the element's s\n     * @returns 1 for an unscoped value, 2 for this graph's own, 0 for another graph's\n     */\n    private scopeOf(scope: unknown): 0 | 1 | 2 {\n        if (scope === undefined || scope === null) {\n            return 1;\n        }\n        const id = refId(scope);\n        if (id !== null && id === this.plan.subnetwork) {\n            return 2;\n        }\n        if (id === null || !this.subnetworks.has(id)) {\n            this.dangle(\"attribute subnetwork reference\");\n        }\n        return 0;\n    }\n\n    /**\n     * The id of an element, by the CX id rule and the `ids` option.\n     * @param raw - the parsed id\n     * @param inexact - whether the literal was not a plain integer\n     * @param element - the element name for issues\n     * @param edgeId - whether this is an edge's own id (stored in the f64 id column, not kept as digits)\n     * @returns the id, or null when it was reported\n     */\n    private idOf(raw: unknown, inexact: boolean, element: string, edgeId = false): NodeId | null {\n        try {\n            const parsed = cxId(raw, inexact);\n            if (parsed.note === \"text\") {\n                this.report.warnOnce(\n                    \"coercion\",\n                    ID_TEXT_TYPE_CODE,\n                    `${element}: the id ${shown(raw)} is not written as an integer; read as ${String(parsed.id)}`,\n                    { element },\n                );\n            } else if (parsed.note === \"precision\" && edgeId) {\n                // the edge is told apart by its digits, but the id column is f64\n                this.report.warnOnce(\n                    \"precision\",\n                    PRECISION_CODE,\n                    `${element}: the edge id ${String(parsed.id)} is beyond 2^53; the id column holds the nearest double`,\n                    { element },\n                    `${PRECISION_CODE}:edge`,\n                );\n            } else if (parsed.note === \"precision\") {\n                this.idType = \"mixed\";\n                this.report.warnOnce(\n                    \"precision\",\n                    PRECISION_CODE,\n                    `${element}: the id ${String(parsed.id)} is beyond 2^53; kept as its digits (a string id)`,\n                    { element },\n                );\n            }\n            return this.options.ids === \"keep\" ? parsed.id : this.coercer.value(parsed.id);\n        } catch (err) {\n            this.report.recordError(err, { element });\n            return null;\n        }\n    }\n\n    /**\n     * Record a long value beyond 2^53 (once).\n     * @param name - the attribute\n     * @param digits - the value\n     */\n    private precision(name: string, digits: string): void {\n        this.report.warnOnce(\n            \"precision\",\n            PRECISION_CODE,\n            `\"${name}\": ${digits} is beyond 2^53; stored as the nearest double`,\n            { element: name },\n            `${PRECISION_CODE}:value`,\n        );\n    }\n\n    /** Count the subnetwork members that name no node or edge. */\n    private checkMembers(): void {\n        for (const id of this.plan.nodes ?? []) {\n            if (!this.rootNodes.has(id)) {\n                this.dangle(\"subnetwork node member\");\n            }\n        }\n        for (const id of this.plan.edges ?? []) {\n            if (!this.rootEdges.has(id)) {\n                this.dangle(\"subnetwork edge member\");\n            }\n        }\n    }\n\n    /**\n     * Report the root network's nodes and edges that no subnetwork holds (W_CX_ROOT_ONLY): they\n     * belong to no graph Cytoscape opens, so no graph of this file reads them.\n     */\n    private checkRootOnly(): void {\n        const subs = aspect(this.doc, \"cySubNetworks\");\n        if (subs.length === 0) {\n            return;\n        }\n        const held = { nodes: new Set<NodeId>(), edges: new Set<NodeId>() };\n        const all = { nodes: false, edges: false };\n        for (const { value } of subs) {\n            if (!isRecord(value)) {\n                continue;\n            }\n            for (const key of [\"nodes\", \"edges\"] as const) {\n                const members = memberSet(value[key]);\n                if (members === null) {\n                    all[key] = true;\n                } else {\n                    members.forEach((id) => held[key].add(id));\n                }\n            }\n        }\n        const lost = (key: \"nodes\" | \"edges\", root: ReadonlySet<NodeId>): number =>\n            all[key] ? 0 : [...root].filter((id) => !held[key].has(id)).length;\n        const nodes = lost(\"nodes\", this.rootNodes);\n        const edges = lost(\"edges\", this.rootEdges);\n        if (nodes + edges > 0) {\n            this.report.warning(\n                \"unsupported\",\n                CX_ISSUE.ROOT_ONLY,\n                `${nodes} node(s) and ${edges} edge(s) of the root network belong to no subnetwork (cySubNetworks); they are not read`,\n                { element: \"cySubNetworks\" },\n            );\n        }\n    }\n\n    /**\n     * The handle of a structural column, declared on first use.\n     * @param domain - node or edge\n     * @param current - the handle so far\n     * @param decl - the declaration\n     * @returns the handle\n     */\n    private structural(domain: \"node\" | \"edge\", current: ColumnHandle, decl: ColumnDecl): ColumnHandle {\n        return current === INVALID_INDEX ? declareResolved(this.sink, domain, decl, this.report).handle : current;\n    }\n\n    // ------------------------------------------------------------ attribute columns\n\n    /**\n     * Type and declare the attribute columns of a table for this graph: each name's type is the\n     * wider of the types its applicable elements and its cyTableColumn entries give (W_WIDENED when\n     * they differ); a name with a type CX does not define keeps its values as text.\n     * @param domain - node or edge\n     * @returns the columns by attribute name\n     */\n    private declareAttributes(domain: \"node\" | \"edge\"): Map<string, AttributeColumn> {\n        const columns = new Map<string, AttributeColumn>();\n        const declared = this.tableColumns(domain === \"node\" ? \"node_table\" : \"edge_table\");\n        const names = new Set<string>([...declared.keys(), ...this.doc.attributes[domain].keys()]);\n        for (const name of names) {\n            if (name === \"\" || (domain === \"edge\" && name === this.options.weightFrom)) {\n                continue;\n            }\n            const types: CxType[] = [];\n            let unknown = false;\n            const tableType = declared.get(name);\n            if (tableType !== undefined) {\n                types.push(tableType);\n            }\n            for (const { value } of this.doc.attributes[domain].get(name) ?? []) {\n                if (!isRecord(value) || this.scopePeek(value.s) === 0) {\n                    continue;\n                }\n                const type = cxType(value.d);\n                if (type === null) {\n                    unknown = true;\n                    continue;\n                }\n                if (!types.some((t) => t.scalar === type.scalar && t.list === type.list)) {\n                    types.push(type);\n                }\n            }\n            if (unknown) {\n                this.report.warnOnce(\n                    \"unsupported\",\n                    UNKNOWN_ATTR_TYPE_CODE,\n                    `a ${domain} attribute \"${name}\" declares a data type CX does not define; its values are kept as text`,\n                    { element: name },\n                    `${UNKNOWN_ATTR_TYPE_CODE}:${domain}:${name}`,\n                );\n                types.push({ scalar: \"string\", list: false });\n            }\n            let type: CxType | null = types[0] ?? { scalar: \"string\", list: false };\n            for (const other of types.slice(1)) {\n                type = type === null ? null : widenType(type, other);\n            }\n            if (types.length > 1) {\n                this.report.warnOnce(\n                    \"coercion\",\n                    WIDENED_CODE,\n                    `the ${domain} attribute \"${name}\" has the data types ${types.map(typeText).join(\", \")}; the column holds ${type === null ? \"their values as JSON\" : typeText(type)}`,\n                    { element: name },\n                    `${WIDENED_CODE}:${domain}:${name}`,\n                );\n            }\n            if (this.isStructural(domain, name)) {\n                columns.set(name, {\n                    name,\n                    type: { scalar: \"string\", list: false },\n                    handle: INVALID_INDEX as ColumnHandle,\n                });\n                continue;\n            }\n            columns.set(name, { name, type, handle: this.declareColumn(domain, name, type) });\n        }\n        return columns;\n    }\n\n    /**\n     * Whether an attribute name is the column of a core field (n / r on nodes, i on edges).\n     * @param domain - node or edge\n     * @param name - the attribute name\n     * @returns true for name, represents and interaction\n     */\n    private isStructural(domain: \"node\" | \"edge\", name: string): boolean {\n        return domain === \"node\" ? name === \"name\" || name === \"represents\" : name === \"interaction\";\n    }\n\n    /**\n     * The scope of a value without counting a dangling one (for typing, which runs before the values).\n     * @param scope - the element's s\n     * @returns as scopeOf()\n     */\n    private scopePeek(scope: unknown): 0 | 1 | 2 {\n        if (scope === undefined || scope === null) {\n            return 1;\n        }\n        const id = refId(scope);\n        return id !== null && id === this.plan.subnetwork ? 2 : 0;\n    }\n\n    /**\n     * The column types cyTableColumn declares for one table and this graph.\n     * @param table - node_table, edge_table or network_table\n     * @returns name -> type\n     */\n    private tableColumns(table: string): Map<string, CxType> {\n        const out = new Map<string, CxType>();\n        for (const { value } of aspect(this.doc, \"cyTableColumn\")) {\n            if (!isRecord(value) || value.applies_to !== table || typeof value.n !== \"string\") {\n                continue;\n            }\n            if (this.scopePeek(value.s) === 0) {\n                continue;\n            }\n            const type = cxType(value.d);\n            if (type !== null) {\n                out.set(value.n, type);\n            }\n        }\n        return out;\n    }\n\n    /**\n     * Declare one attribute column.\n     * @param domain - node or edge\n     * @param name - the attribute name\n     * @param type - the type, or null for a json column\n     * @returns the handle\n     */\n    private declareColumn(domain: \"node\" | \"edge\", name: string, type: CxType | null): ColumnHandle {\n        const { long } = this.options;\n        const decl: ColumnDecl =\n            type === null\n                ? { name, dtype: \"json\", nullable: true, origin: { format: CX_FORMAT, id: null } }\n                : {\n                      name,\n                      dtype: type.list ? \"list\" : scalarDtype(type.scalar, long),\n                      ...(type.list ? { itemDtype: scalarDtype(type.scalar, long) } : {}),\n                      nullable: true,\n                      origin: { format: CX_FORMAT, id: null, type: typeText(type) },\n                  };\n        return declareResolved(this.sink, domain, decl, this.report).handle;\n    }\n\n    /**\n     * Write the attribute values of a table: per element, its own subnetwork's value beats the\n     * unscoped one; a repeated value of the same scope is the later one (W_DUPLICATE_ATTRIBUTE\n     * when they differ).\n     * @param domain - node or edge\n     * @param columns - the columns from declareAttributes()\n     */\n    private writeAttributes(domain: \"node\" | \"edge\", columns: ReadonlyMap<string, AttributeColumn>): void {\n        const rows = domain === \"node\" ? this.nodeRows : this.edgeRows;\n        const root = domain === \"node\" ? this.rootNodes : this.rootEdges;\n        for (const column of columns.values()) {\n            const chosen = new Map<number, { scope: 1 | 2; value: unknown; d: unknown; line: number }>();\n            for (const held of this.doc.attributes[domain].get(column.name) ?? []) {\n                this.checkAbort();\n                const { value, line } = held;\n                if (!isRecord(value)) {\n                    this.report.error(\n                        \"parse-error\",\n                        BAD_ASPECT_BLOCK_CODE,\n                        `a ${domain}Attributes element is not an object`,\n                        {\n                            line,\n                            element: `${domain}Attributes`,\n                        },\n                    );\n                    continue;\n                }\n                const scope = this.scopeOf(value.s);\n                if (scope === 0) {\n                    continue;\n                }\n                const target = refId(value.po);\n                const row = target === null ? undefined : rows.get(this.key(target));\n                if (row === undefined) {\n                    if (target === null || !root.has(target)) {\n                        this.dangle(`${domain} attribute target`);\n                    }\n                    continue;\n                }\n                if (value.v === undefined) {\n                    this.report.error(\n                        \"missing-value\",\n                        BAD_VALUE_CODE,\n                        `a ${domain}Attributes element for \"${column.name}\" has no v; skipped`,\n                        {\n                            line,\n                            element: column.name,\n                        },\n                    );\n                    continue;\n                }\n                if (value.v === null) {\n                    continue;\n                }\n                const previous = chosen.get(row);\n                if (previous !== undefined && previous.scope > scope) {\n                    continue;\n                }\n                if (\n                    previous?.scope === scope &&\n                    JSON.stringify(previous.value) !== JSON.stringify(plainJson(value.v))\n                ) {\n                    this.report.warnOnce(\n                        \"validation-error\",\n                        DUPLICATE_ATTRIBUTE_CODE,\n                        `${domain} ${shown(value.po)} has the attribute \"${column.name}\" twice; the later value wins`,\n                        { line, element: column.name },\n                        `${DUPLICATE_ATTRIBUTE_CODE}:${domain}:${column.name}`,\n                    );\n                }\n                chosen.set(row, { scope, value: value.v, d: value.d, line });\n            }\n            for (const [row, { value, d, line }] of chosen) {\n                this.writeCell(domain, column, row, value, d, line);\n            }\n        }\n    }\n\n    /**\n     * Parse and write one attribute cell. The core fields' attributes (name, represents,\n     * interaction) go into their columns; a name attribute that differs from n wins with\n     * W_DUPLICATE_ATTRIBUTE.\n     * @param domain - node or edge\n     * @param column - the column\n     * @param row - the row\n     * @param raw - the value\n     * @param d - the data type the value was written with\n     * @param line - its line\n     */\n    private writeCell(\n        domain: \"node\" | \"edge\",\n        column: AttributeColumn,\n        row: number,\n        raw: unknown,\n        d: unknown,\n        line: number,\n    ): void {\n        const element = `${domain} attribute \"${column.name}\"`;\n        let value: unknown;\n        if (column.type === null) {\n            value = plainJson(raw, (digits) => {\n                this.precision(column.name, digits);\n            });\n        } else {\n            const own = cxType(d) ?? { scalar: \"string\", list: false };\n            const parsed = parseValue(raw, own, this.options.long, (digits) => {\n                this.precision(column.name, digits);\n            });\n            if (parsed === UNSET) {\n                return;\n            }\n            if (parsed === BAD) {\n                this.report.error(\n                    \"validation-error\",\n                    BAD_VALUE_CODE,\n                    `${element}: ${shown(raw)} is not a ${typeText(own)}; the cell is unset`,\n                    { line, element: column.name },\n                );\n                return;\n            }\n            value = toColumn(parsed, column.type);\n        }\n        let { handle } = column;\n        if (this.isStructural(domain, column.name)) {\n            handle = this.coreColumn(domain, column.name);\n            const prior = this.coreValue(domain, row, column.name);\n            if (prior !== undefined && prior !== value) {\n                this.report.warnOnce(\n                    \"validation-error\",\n                    DUPLICATE_ATTRIBUTE_CODE,\n                    `a ${domain} has \"${column.name}\" both as its core field and as an attribute with another value; the attribute wins`,\n                    { line, element: column.name },\n                    `${DUPLICATE_ATTRIBUTE_CODE}:core:${column.name}`,\n                );\n            }\n        }\n        try {\n            if (domain === \"node\") {\n                this.sink.setNodeValue(handle, row, value);\n            } else {\n                this.sink.setEdgeValue(handle, row, value);\n            }\n        } catch (err) {\n            this.report.recordError(err, { line, element: column.name });\n        }\n    }\n\n    /** The core field values written per row (n, r), to detect a differing name attribute. */\n    private readonly coreValues = new Map<string, Map<number, string>>();\n\n    /**\n     * The core field value of a row.\n     * @param domain - node or edge\n     * @param row - the row\n     * @param name - name, represents or interaction\n     * @returns the value, or undefined\n     */\n    private coreValue(domain: \"node\" | \"edge\", row: number, name: string): string | undefined {\n        return this.coreValues.get(`${domain}:${name}`)?.get(row);\n    }\n\n    /**\n     * The column of a core field.\n     * @param domain - node or edge\n     * @param name - name, represents or interaction\n     * @returns the handle\n     */\n    private coreColumn(domain: \"node\" | \"edge\", name: string): ColumnHandle {\n        if (domain === \"edge\") {\n            this.interactionHandle = this.structural(\"edge\", this.interactionHandle, {\n                name: \"interaction\",\n                dtype: \"string\",\n                nullable: true,\n                origin: { format: CX_FORMAT, id: \"i\", type: \"string\" },\n            });\n            return this.interactionHandle;\n        }\n        if (name === \"name\") {\n            this.nameHandle = this.structural(\"node\", this.nameHandle, {\n                name: \"name\",\n                dtype: \"string\",\n                role: \"label\",\n                nullable: true,\n                origin: { format: CX_FORMAT, id: \"n\", type: \"string\" },\n            });\n            return this.nameHandle;\n        }\n        this.representsHandle = this.structural(\"node\", this.representsHandle, {\n            name: \"represents\",\n            dtype: \"string\",\n            nullable: true,\n            origin: { format: CX_FORMAT, id: \"r\", type: \"string\" },\n        });\n        return this.representsHandle;\n    }\n\n    // ------------------------------------------------------------ nodes, groups, layout\n\n    /** Read the nodes of this graph. */\n    private readNodes(): void {\n        const { report, sink } = this;\n        for (const held of aspect(this.doc, \"nodes\")) {\n            this.checkAbort();\n            const { value, line } = held;\n            if (!isRecord(value)) {\n                report.error(\n                    \"parse-error\",\n                    BAD_ASPECT_BLOCK_CODE,\n                    `a nodes element is ${shown(value)}, not an object`,\n                    {\n                        line,\n                        element: \"nodes\",\n                    },\n                );\n                report.counts.skippedNodes++;\n                continue;\n            }\n            if (value[\"@id\"] === undefined || value[\"@id\"] === null) {\n                report.error(\"missing-value\", MISSING_ID_CODE, \"a node has no @id\", { line, element: \"nodes\" });\n                report.counts.skippedNodes++;\n                continue;\n            }\n            const element = `node ${shown(value[\"@id\"])}`;\n            const id = this.idOf(value[\"@id\"], (held.inexact & 1) !== 0, element);\n            if (id === null) {\n                report.counts.skippedNodes++;\n                continue;\n            }\n            // membership lists hold CX ids as written, before the ids option coerces them\n            if (!this.inGraph(refId(value[\"@id\"]) ?? id)) {\n                continue;\n            }\n            let row = this.nodeRows.get(id);\n            if (row !== undefined) {\n                report.warning(\n                    \"merged\",\n                    DUPLICATE_NODE_CODE,\n                    `${element} is declared more than once; its fields are merged (the later values win)`,\n                    { line, element },\n                );\n            } else {\n                try {\n                    row = sink.addNode(id);\n                } catch (err) {\n                    report.recordError(err, { line, element });\n                    report.counts.skippedNodes++;\n                    continue;\n                }\n                this.nodeRows.set(id, row);\n                report.counts.nodes++;\n            }\n            this.writeCore(\"node\", row, \"name\", value.n, element, line);\n            this.writeCore(\"node\", row, \"represents\", value.r, element, line);\n        }\n    }\n\n    /**\n     * Write a core string field (n, r, i).\n     * @param domain - node or edge\n     * @param row - the row\n     * @param name - the column\n     * @param raw - the value\n     * @param element - the element name\n     * @param line - its line\n     */\n    private writeCore(\n        domain: \"node\" | \"edge\",\n        row: number,\n        name: string,\n        raw: unknown,\n        element: string,\n        line: number,\n    ): void {\n        if (raw === undefined || raw === null) {\n            return;\n        }\n        if (typeof raw !== \"string\") {\n            this.report.error(\n                \"validation-error\",\n                BAD_VALUE_CODE,\n                `${element}: ${name} is ${shown(raw)}, not a string`,\n                {\n                    line,\n                    element,\n                },\n            );\n            return;\n        }\n        const handle = this.coreColumn(domain, name);\n        if (domain === \"node\") {\n            this.sink.setNodeValue(handle, row, raw);\n        } else {\n            this.sink.setEdgeValue(handle, row, raw);\n        }\n        const key = `${domain}:${name}`;\n        let values = this.coreValues.get(key);\n        if (values === undefined) {\n            values = new Map();\n            this.coreValues.set(key, values);\n        }\n        values.set(row, raw);\n    }\n\n    /**\n     * Read cyGroups: a group's members get the group node as their parent (parents when a node is in\n     * several groups); a group whose id is not a node gets one (W_CX_GROUP_NODE_ADDED); collapsed is\n     * a bool column on the group node.\n     */\n    private readGroups(): void {\n        const groups = aspect(this.doc, \"cyGroups\");\n        if (groups.length === 0) {\n            return;\n        }\n        const parents = new Map<number, number[]>();\n        const collapsed: [number, boolean][] = [];\n        for (const { value, line } of groups) {\n            if (!isRecord(value)) {\n                continue;\n            }\n            const id = refId(value[\"@id\"]);\n            if (id === null) {\n                this.report.error(\"missing-value\", MISSING_ID_CODE, \"a cyGroups element has no @id\", {\n                    line,\n                    element: \"cyGroups\",\n                });\n                continue;\n            }\n            let groupRow = this.nodeRows.get(this.key(id));\n            if (groupRow === undefined) {\n                if (this.rootNodes.has(id) || !this.hasMemberIn(value.nodes)) {\n                    continue;\n                }\n                try {\n                    groupRow = this.sink.addNode(this.key(id));\n                } catch (err) {\n                    this.report.recordError(err, { line, element: String(id) });\n                    continue;\n                }\n                this.nodeRows.set(this.key(id), groupRow);\n                this.report.counts.nodes++;\n                this.report.warning(\n                    \"coercion\",\n                    CX_ISSUE.GROUP_NODE_ADDED,\n                    `group ${String(id)} is not a node; its group node is added`,\n                    { line, element: String(id) },\n                );\n            }\n            if (typeof value.n === \"string\" && this.coreValue(\"node\", groupRow, \"name\") === undefined) {\n                this.writeCore(\"node\", groupRow, \"name\", value.n, `group ${String(id)}`, line);\n            }\n            if (typeof value.collapsed === \"boolean\") {\n                collapsed.push([groupRow, value.collapsed]);\n            }\n            for (const raw of Array.isArray(value.nodes) ? (value.nodes as unknown[]) : []) {\n                const member = refId(raw);\n                const row = member === null ? undefined : this.nodeRows.get(this.key(member));\n                if (row === undefined) {\n                    if (member === null || !this.rootNodes.has(member)) {\n                        this.report.error(\n                            \"missing-value\",\n                            UNKNOWN_PARENT_CODE,\n                            `group ${String(id)}: the member ${shown(raw)} is not a node`,\n                            { line, element: String(id) },\n                        );\n                    }\n                    continue;\n                }\n                if (this.closesCycle(parents, row, groupRow)) {\n                    this.report.error(\n                        \"validation-error\",\n                        PARENT_CYCLE_CODE,\n                        `group ${String(id)}: making ${shown(raw)} a member would close a parent cycle; that membership is dropped`,\n                        { line, element: String(id) },\n                    );\n                    continue;\n                }\n                const list = parents.get(row) ?? [];\n                if (!list.includes(groupRow)) {\n                    list.push(groupRow);\n                }\n                parents.set(row, list);\n            }\n        }\n        this.writeParents(parents);\n        if (collapsed.length > 0) {\n            const { handle } = declareResolved(\n                this.sink,\n                \"node\",\n                {\n                    name: \"collapsed\",\n                    dtype: \"bool\",\n                    nullable: true,\n                    origin: { format: CX_FORMAT, namespace: \"cyGroups\" },\n                },\n                this.report,\n            );\n            for (const [row, flag] of collapsed) {\n                this.sink.setNodeValue(handle, row, flag);\n            }\n        }\n    }\n\n    /**\n     * Whether a member list names a node of this graph.\n     * @param raw - the list\n     * @returns true when one member is in the graph\n     */\n    private hasMemberIn(raw: unknown): boolean {\n        return (\n            Array.isArray(raw) &&\n            raw.some((item) => {\n                const id = refId(item);\n                return id !== null && this.nodeRows.has(this.key(id));\n            })\n        );\n    }\n\n    /**\n     * Whether making `child` a member of `group` closes a cycle: the group already is, through its\n     * own parents, below the child.\n     * @param parents - the memberships so far\n     * @param child - the member row\n     * @param group - the group row\n     * @returns true for a cycle\n     */\n    private closesCycle(parents: ReadonlyMap<number, readonly number[]>, child: number, group: number): boolean {\n        const stack = [group];\n        const seen = new Set<number>();\n        while (stack.length > 0) {\n            const row = stack.pop() as number;\n            if (row === child) {\n                return true;\n            }\n            if (seen.has(row)) {\n                continue;\n            }\n            seen.add(row);\n            stack.push(...(parents.get(row) ?? []));\n        }\n        return false;\n    }\n\n    /**\n     * Write the group memberships: a parent column, or a parents list column when a node is in\n     * several groups.\n     * @param parents - member row -> group rows\n     */\n    private writeParents(parents: ReadonlyMap<number, readonly number[]>): void {\n        if (parents.size === 0) {\n            return;\n        }\n        const several = [...parents.values()].some((list) => list.length > 1);\n        const decl: ColumnDecl = several\n            ? { name: \"parents\", dtype: \"list\", itemDtype: \"u32\", role: \"parents\", refersTo: \"node\", nullable: true }\n            : { name: \"parent\", dtype: \"u32\", role: \"parent\", refersTo: \"node\", nullable: true };\n        const { handle } = declareResolved(this.sink, \"node\", decl, this.report);\n        for (const [row, list] of parents) {\n            this.sink.setNodeValue(handle, row, several ? list : list[0]);\n        }\n    }\n\n    /**\n     * Read cartesianLayout for this graph's views: the first view is the position (y flipped), z the\n     * z column, every other view a position@n column.\n     */\n    private readLayout(): void {\n        const entries = aspect(this.doc, \"cartesianLayout\");\n        if (entries.length === 0) {\n            return;\n        }\n        const { views } = this.plan;\n        const knownViews = this.allViews();\n        const columns = new Map<number, ColumnHandle>();\n        const zHandle = { current: INVALID_INDEX as ColumnHandle };\n        const seen = new Set<string>();\n        const point: [number, number, number] = [0, 0, 0];\n        for (const { value, line } of entries) {\n            this.checkAbort();\n            if (!isRecord(value)) {\n                continue;\n            }\n            const view = value.view === undefined || value.view === null ? null : refId(value.view);\n            if (view !== null && knownViews.size > 0 && !knownViews.has(view)) {\n                this.dangle(\"layout view reference\");\n                continue;\n            }\n            const slot = view === null ? 0 : views.indexOf(view);\n            if (slot < 0) {\n                continue;\n            }\n            if (typeof value.x !== \"number\" || typeof value.y !== \"number\") {\n                this.report.error(\n                    \"validation-error\",\n                    BAD_VALUE_CODE,\n                    `a cartesianLayout element for node ${shown(value.node)} has no numeric x and y; skipped`,\n                    { line, element: \"cartesianLayout\" },\n                );\n                continue;\n            }\n            const node = refId(value.node);\n            const row = node === null ? undefined : this.nodeRows.get(this.key(node));\n            if (row === undefined) {\n                if (node === null || !this.rootNodes.has(node)) {\n                    this.dangle(\"layout entry\");\n                }\n                continue;\n            }\n            const key = `${slot}:${row}`;\n            if (seen.has(key)) {\n                this.report.warnOnce(\n                    \"validation-error\",\n                    DUPLICATE_ATTRIBUTE_CODE,\n                    `node ${shown(value.node)} has two layout entries for one view; the later wins`,\n                    { line, element: \"cartesianLayout\" },\n                    `${DUPLICATE_ATTRIBUTE_CODE}:layout`,\n                );\n            }\n            seen.add(key);\n            const z = typeof value.z === \"number\" ? value.z : null;\n            point[0] = value.x;\n            point[1] = flipY(value.y);\n            point[2] = slot === 0 && this.zAs === \"position\" && z !== null ? z : 0;\n            this.sink.setNodeValue(this.layoutColumn(columns, slot, views), row, point);\n            if (slot === 0 && z !== null && this.zAs === \"column\") {\n                zHandle.current = this.structural(\"node\", zHandle.current, zDecl(CX_FORMAT));\n                this.sink.setNodeValue(zHandle.current, row, z);\n            }\n        }\n    }\n\n    /**\n     * Every view id the document names.\n     * @returns the set (empty when the document names none)\n     */\n    private allViews(): Set<NodeId> {\n        const out = new Set<NodeId>();\n        for (const { value } of aspect(this.doc, \"cyNetworkRelations\")) {\n            if (isRecord(value) && value.r === \"view\") {\n                const id = refId(value.c);\n                if (id !== null) {\n                    out.add(id);\n                }\n            }\n        }\n        for (const { value } of aspect(this.doc, \"cyViews\")) {\n            const id = isRecord(value) ? refId(value[\"@id\"]) : null;\n            if (id !== null) {\n                out.add(id);\n            }\n        }\n        return out;\n    }\n\n    /**\n     * The position column of a view slot, declared on first use.\n     * @param columns - slot -> handle\n     * @param slot - 0 for the position, n - 1 for position@n\n     * @param views - the graph's views\n     * @returns the handle\n     */\n    private layoutColumn(columns: Map<number, ColumnHandle>, slot: number, views: readonly NodeId[]): ColumnHandle {\n        let handle = columns.get(slot);\n        if (handle === undefined) {\n            const base = positionDecl(CX_FORMAT, this.zAs === \"position\" && slot === 0 ? 3 : 2);\n            const decl: ColumnDecl =\n                slot === 0\n                    ? base\n                    : {\n                          ...base,\n                          name: `position@${slot + 1}`,\n                          role: undefined,\n                          origin: { format: CX_FORMAT, namespace: \"cytoscape\", id: String(views[slot]) },\n                      };\n            ({ handle } = declareResolved(this.sink, \"node\", decl, this.report));\n            columns.set(slot, handle);\n        }\n        return handle;\n    }\n\n    // ------------------------------------------------------------ edges\n\n    /** Read the edges of this graph. */\n    private readEdges(): void {\n        const { report, sink } = this;\n        const members = this.plan.edges;\n        for (const held of aspect(this.doc, \"edges\")) {\n            this.checkAbort();\n            const { value, line } = held;\n            if (!isRecord(value)) {\n                report.error(\n                    \"parse-error\",\n                    BAD_ASPECT_BLOCK_CODE,\n                    `an edges element is ${shown(value)}, not an object`,\n                    {\n                        line,\n                        element: \"edges\",\n                    },\n                );\n                report.counts.skippedEdges++;\n                continue;\n            }\n            if (value[\"@id\"] === undefined || value[\"@id\"] === null) {\n                report.error(\"missing-value\", MISSING_ID_CODE, \"an edge has no @id\", { line, element: \"edges\" });\n                report.counts.skippedEdges++;\n                continue;\n            }\n            const element = `edge ${shown(value[\"@id\"])}`;\n            const id = this.idOf(value[\"@id\"], (held.inexact & 1) !== 0, element, true);\n            if (id === null) {\n                report.counts.skippedEdges++;\n                continue;\n            }\n            if (members !== null && !members.has(refId(value[\"@id\"]) ?? id)) {\n                continue;\n            }\n            if (value.s === undefined || value.s === null || value.t === undefined || value.t === null) {\n                report.error(\n                    \"missing-value\",\n                    MISSING_ENDPOINT_CODE,\n                    `${element} has no ${value.s === undefined || value.s === null ? \"s\" : \"t\"}`,\n                    {\n                        line,\n                        element,\n                    },\n                );\n                report.counts.skippedEdges++;\n                continue;\n            }\n            const s = this.idOf(value.s, (held.inexact & 2) !== 0, element);\n            const t = s === null ? null : this.idOf(value.t, (held.inexact & 4) !== 0, element);\n            if (s === null || t === null) {\n                report.counts.skippedEdges++;\n                continue;\n            }\n            if (this.edgeRows.has(id)) {\n                report.error(\n                    \"validation-error\",\n                    DUPLICATE_EDGE_ID_CODE,\n                    `${element} is declared more than once; the later edge is skipped`,\n                    { line, element },\n                );\n                report.counts.skippedEdges++;\n                continue;\n            }\n            if (!this.endpoint(s, element, line) || !this.endpoint(t, element, line)) {\n                report.counts.skippedEdges++;\n                continue;\n            }\n            let weight: number | undefined;\n            try {\n                weight = this.weightOf(id);\n            } catch (err) {\n                report.recordError(err, { line, element });\n                report.counts.skippedEdges++;\n                continue;\n            }\n            const before = sink.edgeCount;\n            let edge: number;\n            try {\n                edge = this.direction.addEdge(s, t, \"directed\", weight, { line, element });\n            } catch (err) {\n                report.recordError(err, { line, element });\n                report.counts.skippedEdges++;\n                continue;\n            }\n            if (weight !== undefined) {\n                this.weighted = true;\n            }\n            report.counts.edges += sink.edgeCount - before;\n            this.edgeRows.set(id, edge);\n            this.edgeIdHandle = this.structural(\"edge\", this.edgeIdHandle, {\n                name: uniqueColumnName(\"id\", \"cx\", (n) => sink.edgeColumn(n) !== INVALID_INDEX),\n                dtype: \"f64\",\n                role: \"id\",\n                nullable: true,\n            });\n            sink.setEdgeValue(this.edgeIdHandle, edge, typeof id === \"number\" ? id : Number(id));\n            this.writeCore(\"edge\", edge, \"interaction\", value.i, element, line);\n        }\n    }\n\n    /**\n     * Whether an endpoint is a node of this graph; under addMissingNodes it is created.\n     * @param id - the endpoint\n     * @param element - the edge name\n     * @param line - its line\n     * @returns false when the edge is to be skipped (reported)\n     */\n    private endpoint(id: NodeId, element: string, line: number): boolean {\n        if (this.nodeRows.has(id)) {\n            return true;\n        }\n        if (!this.options.addMissingNodes) {\n            this.report.error(\n                \"missing-value\",\n                CX_ISSUE.UNKNOWN_NODE,\n                `${element}: the endpoint ${String(id)} is not a node of the graph; the edge is skipped`,\n                { line, element },\n            );\n            return false;\n        }\n        try {\n            this.nodeRows.set(id, this.sink.addNode(id));\n        } catch (err) {\n            this.report.recordError(err, { line, element });\n            return false;\n        }\n        this.report.counts.nodes++;\n        return true;\n    }\n\n    /** The weight attribute values of the edges, by edge id (built once). */\n    private weights: Map<NodeId, unknown> | null = null;\n\n    /**\n     * The weight of an edge: its weightFrom attribute, parsed as a number.\n     * @param id - the edge id\n     * @returns the weight, or undefined; E_INVALID_WEIGHT for a non-number\n     */\n    private weightOf(id: NodeId): number | undefined {\n        const { weightFrom } = this.options;\n        if (weightFrom === null) {\n            return undefined;\n        }\n        if (this.weights === null) {\n            this.weights = new Map();\n            for (const { value } of this.doc.attributes.edge.get(weightFrom) ?? []) {\n                if (isRecord(value) && this.scopePeek(value.s) !== 0) {\n                    const po = refId(value.po);\n                    if (po !== null && value.v !== undefined && value.v !== null) {\n                        this.weights.set(this.key(po), plainJson(value.v));\n                    }\n                }\n            }\n        }\n        const raw = this.weights.get(id);\n        if (typeof raw === \"string\" && isNullText(raw)) {\n            return undefined;\n        }\n        return weightFromValue(raw);\n    }\n\n    // ------------------------------------------------------------ network, visual properties, provenance\n\n    /** Write the network attributes (unscoped and this subnetwork's, its own winning) as graph columns. */\n    private readNetworkAttributes(): void {\n        for (const [name, elements] of this.doc.attributes.network) {\n            let chosen: Record<string, unknown> | null = null;\n            let chosenScope = 0;\n            for (const { value } of elements) {\n                if (!isRecord(value)) {\n                    continue;\n                }\n                const scope = this.scopeOf(value.s);\n                if (scope !== 0 && scope >= chosenScope) {\n                    chosen = value;\n                    chosenScope = scope;\n                }\n            }\n            if (chosen === null || chosen.v === undefined || chosen.v === null || name === \"\") {\n                continue;\n            }\n            const type = cxType(chosen.d);\n            if (type === null) {\n                this.report.warnOnce(\n                    \"unsupported\",\n                    UNKNOWN_ATTR_TYPE_CODE,\n                    `the network attribute \"${name}\" declares a data type CX does not define; kept as text`,\n                    { element: name },\n                    `${UNKNOWN_ATTR_TYPE_CODE}:network:${name}`,\n                );\n            }\n            const effective = type ?? { scalar: \"string\", list: false };\n            const parsed = parseValue(chosen.v, effective, this.options.long, (digits) => {\n                this.precision(name, digits);\n            });\n            if (parsed === UNSET) {\n                continue;\n            }\n            if (parsed === BAD) {\n                this.report.error(\n                    \"validation-error\",\n                    BAD_VALUE_CODE,\n                    `the network attribute \"${name}\" is ${shown(chosen.v)}, not a ${typeText(effective)}; unset`,\n                    { element: name },\n                );\n                continue;\n            }\n            if ((name === \"name\" || name === \"description\") && typeof parsed === \"string\") {\n                continue;\n            }\n            const scalar = scalarDtype(effective.scalar, this.options.long);\n            try {\n                this.sink.setGraphValue(name, parsed, {\n                    dtype: effective.list ? \"list\" : scalar,\n                    ...(effective.list ? { itemDtype: scalar } : {}),\n                    origin: { format: CX_FORMAT, id: null, type: typeText(effective) },\n                });\n            } catch (err) {\n                this.report.recordError(err, { element: name });\n            }\n        }\n    }\n\n    /**\n     * Read cyVisualProperties for this graph's views: per-element and network values become columns\n     * (origin namespace cx.bypass); defaults, mappings and dependencies are style rules, kept and not\n     * applied.\n     */\n    private readVisualProperties(): void {\n        const entries = aspect(this.doc, \"cyVisualProperties\");\n        // Cytoscape's table-cell styles: a visual property aspect graph-io keeps but does not read\n        const tableStyles = TABLE_STYLE_ASPECTS.reduce((n, name) => n + (this.doc.kept.get(name)?.length ?? 0), 0);\n        // the graph's own view (its first): the one its positions come from; the others stay in meta.extra.cx\n        const views = new Set(this.plan.views.slice(0, 1));\n        const columns = { node: new Map<string, [number, string][]>(), edge: new Map<string, [number, string][]>() };\n        const network = new Map<string, string>();\n        let defaults = 0;\n        let mappings = 0;\n        let dependencies = 0;\n        for (const { value } of entries) {\n            if (!isRecord(value)) {\n                continue;\n            }\n            const view = value.view === undefined || value.view === null ? null : refId(value.view);\n            if (view !== null && views.size > 0 && !views.has(view)) {\n                continue;\n            }\n            const properties = isRecord(value.properties) ? value.properties : {};\n            mappings += isRecord(value.mappings) ? Object.keys(value.mappings).length : 0;\n            dependencies += isRecord(value.dependencies) ? Object.keys(value.dependencies).length : 0;\n            switch (value.properties_of) {\n                case \"nodes\":\n                case \"edges\": {\n                    const domain = value.properties_of === \"nodes\" ? \"node\" : \"edge\";\n                    const target = refId(value.applies_to);\n                    const rows = domain === \"node\" ? this.nodeRows : this.edgeRows;\n                    const row = target === null ? undefined : rows.get(this.key(target));\n                    if (row === undefined) {\n                        if (target === null || !(domain === \"node\" ? this.rootNodes : this.rootEdges).has(target)) {\n                            this.dangle(`${domain} visual property entry`);\n                        }\n                        continue;\n                    }\n                    for (const [property, raw] of Object.entries(properties)) {\n                        const list = columns[domain].get(property) ?? [];\n                        list.push([row, typeof raw === \"string\" ? raw : JSON.stringify(raw)]);\n                        columns[domain].set(property, list);\n                    }\n                    break;\n                }\n                case \"network\":\n                    for (const [property, raw] of Object.entries(properties)) {\n                        network.set(property, typeof raw === \"string\" ? raw : JSON.stringify(raw));\n                    }\n                    break;\n                default:\n                    defaults += Object.keys(properties).length;\n                    break;\n            }\n        }\n        for (const domain of [\"node\", \"edge\"] as const) {\n            for (const [property, cells] of columns[domain]) {\n                const handle = declareFresh(\n                    this.sink,\n                    domain,\n                    {\n                        name: property,\n                        dtype: \"string\",\n                        nullable: true,\n                        origin: { format: CX_FORMAT, id: null, namespace: CX_BYPASS_NAMESPACE },\n                    },\n                    this.report,\n                );\n                for (const [row, text] of cells) {\n                    if (domain === \"node\") {\n                        this.sink.setNodeValue(handle, row, text);\n                    } else {\n                        this.sink.setEdgeValue(handle, row, text);\n                    }\n                }\n            }\n        }\n        for (const [property, text] of network) {\n            try {\n                this.sink.setGraphValue(property, text, {\n                    dtype: \"string\",\n                    origin: { format: CX_FORMAT, id: null, namespace: CX_BYPASS_NAMESPACE },\n                });\n            } catch (err) {\n                this.report.recordError(err, { element: property });\n            }\n        }\n        if (defaults + mappings + dependencies + tableStyles > 0) {\n            const parts = [\n                `cyVisualProperties: ${defaults} default(s), ${mappings} mapping(s), ${dependencies} dependenc(ies)`,\n            ];\n            if (tableStyles > 0) {\n                parts.push(`${tableStyles} table style element(s)`);\n            }\n            this.report.warning(\n                \"unsupported\",\n                STYLES_NOT_IMPORTED_CODE,\n                `the file's style rules are not applied (${parts.join(\"; \")}); they are kept in meta.extra.cx (style import is issue #706)`,\n                { element: \"cyVisualProperties\" },\n            );\n        }\n    }\n\n    /**\n     * Read the provenance aspects: citations and supports as extension tables cx:citations and\n     * cx:supports, the node / edge links to them as list columns, functionTerms as a json column,\n     * reifiedEdges as a u32 column referring to edges.\n     */\n    private readProvenance(): void {\n        for (const name of [\"citations\", \"supports\"] as const) {\n            this.extensionTable(`cx:${name}`, aspect(this.doc, name));\n        }\n        for (const [aspectName, domain, column] of [\n            [\"nodeCitations\", \"node\", \"citations\"],\n            [\"edgeCitations\", \"edge\", \"citations\"],\n            [\"nodeSupports\", \"node\", \"supports\"],\n            [\"edgeSupports\", \"edge\", \"supports\"],\n        ] as const) {\n            this.linkColumn(aspectName, domain, column);\n        }\n        const terms: [number, unknown][] = [];\n        for (const { value } of aspect(this.doc, \"functionTerms\")) {\n            if (!isRecord(value)) {\n                continue;\n            }\n            const po = refId(value.po);\n            const row = po === null ? undefined : this.nodeRows.get(this.key(po));\n            if (row === undefined) {\n                if (po === null || !this.rootNodes.has(po)) {\n                    this.dangle(\"functionTerms entry\");\n                }\n                continue;\n            }\n            const { po: _po, ...term } = value;\n            terms.push([row, plainJson(term)]);\n        }\n        this.writeColumn(\"node\", \"functionTerm\", \"json\", null, terms);\n        const reified: [number, number][] = [];\n        for (const { value } of aspect(this.doc, \"reifiedEdges\")) {\n            if (!isRecord(value)) {\n                continue;\n            }\n            const node = refId(value.node);\n            const edge = refId(value.edge);\n            const row = node === null ? undefined : this.nodeRows.get(this.key(node));\n            const edgeRow = edge === null ? undefined : this.edgeRows.get(this.key(edge));\n            if (row === undefined || edgeRow === undefined) {\n                if (node === null || !this.rootNodes.has(node) || edge === null || !this.rootEdges.has(edge)) {\n                    this.dangle(\"reifiedEdges entry\");\n                }\n                continue;\n            }\n            reified.push([row, edgeRow]);\n        }\n        if (reified.length > 0) {\n            const { handle } = declareResolved(\n                this.sink,\n                \"node\",\n                {\n                    name: \"reifiedEdge\",\n                    dtype: \"u32\",\n                    refersTo: \"edge\",\n                    nullable: true,\n                    origin: { format: CX_FORMAT, namespace: \"reifiedEdges\" },\n                },\n                this.report,\n            );\n            for (const [row, edge] of reified) {\n                this.sink.setNodeValue(handle, row, edge);\n            }\n        }\n    }\n\n    /**\n     * An extension table of a provenance aspect: an f64 `id` column and one json column per field.\n     * @param name - the table name\n     * @param elements - the elements\n     */\n    private extensionTable(name: string, elements: readonly Held[]): void {\n        const records = elements.map((h) => h.value).filter(isRecord);\n        if (records.length === 0) {\n            return;\n        }\n        const fields = [...new Set(records.flatMap((r) => Object.keys(r)).filter((k) => k !== \"@id\"))];\n        const decls: ColumnDecl[] = [\n            { name: \"id\", dtype: \"f64\", nullable: true },\n            ...fields.map((field): ColumnDecl => ({ name: field, dtype: \"json\", nullable: true })),\n        ];\n        const table = this.sink.addExtensionTable(name, decls);\n        for (const record of records) {\n            const id = refId(record[\"@id\"]);\n            this.sink.addExtensionRow(table, [\n                id === null ? null : Number(id),\n                ...fields.map((field) => (record[field] === undefined ? null : plainJson(record[field]))),\n            ]);\n        }\n    }\n\n    /**\n     * A list column of the citation or support ids a node or edge links to.\n     * @param aspectName - nodeCitations, edgeCitations, nodeSupports or edgeSupports\n     * @param domain - node or edge\n     * @param column - citations or supports\n     */\n    private linkColumn(aspectName: string, domain: \"node\" | \"edge\", column: \"citations\" | \"supports\"): void {\n        const rows = domain === \"node\" ? this.nodeRows : this.edgeRows;\n        const root = domain === \"node\" ? this.rootNodes : this.rootEdges;\n        const links = new Map<number, number[]>();\n        for (const { value } of aspect(this.doc, aspectName)) {\n            if (!isRecord(value)) {\n                continue;\n            }\n            const targets = Array.isArray(value.po) ? (value.po as unknown[]) : [value.po];\n            const ids = (Array.isArray(value[column]) ? (value[column] as unknown[]) : [])\n                .map(refId)\n                .filter((id): id is NodeId => id !== null)\n                .map(Number);\n            for (const raw of targets) {\n                const target = refId(raw);\n                const row = target === null ? undefined : rows.get(this.key(target));\n                if (row === undefined) {\n                    if (target === null || !root.has(target)) {\n                        this.dangle(`${aspectName} entry`);\n                    }\n                    continue;\n                }\n                links.set(row, [...(links.get(row) ?? []), ...ids]);\n            }\n        }\n        this.writeColumn(domain, column, \"list\", \"f64\", [...links]);\n    }\n\n    /**\n     * Declare a column and write its cells (nothing when there are none).\n     * @param domain - node or edge\n     * @param name - the column name\n     * @param dtype - the dtype\n     * @param itemDtype - the list item dtype, or null\n     * @param cells - row and value pairs\n     */\n    private writeColumn(\n        domain: \"node\" | \"edge\",\n        name: string,\n        dtype: Dtype,\n        itemDtype: ScalarDtype | null,\n        cells: readonly (readonly [number, unknown])[],\n    ): void {\n        if (cells.length === 0) {\n            return;\n        }\n        const decl: ColumnDecl = {\n            name,\n            dtype,\n            ...(itemDtype === null ? {} : { itemDtype }),\n            nullable: true,\n            origin: { format: CX_FORMAT, namespace: \"provenance\" },\n        };\n        const { handle } = declareResolved(this.sink, domain, decl, this.report);\n        for (const [row, value] of cells) {\n            if (domain === \"node\") {\n                this.sink.setNodeValue(handle, row, value);\n            } else {\n                this.sink.setEdgeValue(handle, row, value);\n            }\n        }\n    }\n\n    /** Record the metadata: source format, name, description, id type, the kept aspects. */\n    private setMeta(): void {\n        const describe = (key: string): string | null => {\n            let found: string | null = null;\n            for (const { value } of this.doc.attributes.network.get(key) ?? []) {\n                if (isRecord(value) && typeof value.v === \"string\") {\n                    const scope = this.scopePeek(value.s);\n                    if (scope === 2) {\n                        return value.v;\n                    }\n                    if (scope === 1) {\n                        found ??= value.v;\n                    }\n                }\n            }\n            return found;\n        };\n        const extra: Record<string, unknown> = Object.fromEntries(this.doc.kept);\n        const groups = aspect(this.doc, \"cyGroups\").map((h) => plainJson(h.value));\n        if (groups.length > 0) {\n            extra.groups = groups;\n        }\n        if (this.plan.subnetwork !== null) {\n            extra.subnetwork = this.plan.subnetwork;\n        }\n        const { weightFrom } = this.options;\n        const name = this.plan.name ?? describe(\"name\");\n        const description = describe(\"description\");\n        const patch: GraphMetaPatch = {\n            sourceFormat: CX_FORMAT,\n            sourceVersion: \"1\",\n            idType: this.idType,\n            ...(name === null ? {} : { name }),\n            ...(description === null ? {} : { description }),\n            ...(this.weighted && weightFrom !== null\n                ? { weightOrigin: { format: CX_FORMAT, id: null, title: weightFrom, type: \"double\", namespace: null } }\n                : {}),\n            extra: { cx: extra },\n        };\n        this.sink.setMeta(patch);\n    }\n}\n\n// ============================================================ the plugin\n\n/**\n * Read a document, then build the graphs `pick` selects.\n * @param input - the input\n * @param options - the caller's options\n * @param sinkFor - the sink of graph i, or null to skip it\n * @param pick - which graph indexes to build, given the plans and the first report\n * @returns one report per built graph\n */\nasync function run(\n    input: ImportInput,\n    options: (CxImportOptions & CommonImportOptions) | undefined,\n    sinkFor: (index: number) => GraphSink,\n    pick: (plans: readonly GraphPlan[], report: ImportReportBuilder) => readonly number[],\n): Promise<ImportReport[]> {\n    const resolved = resolveImportOptions(options, FORMAT_DEFAULTS);\n    const zAs = zAsOption(options?.zAs);\n    const first = new ImportReportBuilder(CX_FORMAT, resolved.errorLimit);\n    reportUnusedOptions(options, first, USED_OPTIONS);\n    const doc = await readDocument(input, first, resolved);\n    const plans = graphPlans(doc);\n    const chosen = pick(plans, first);\n    const reports: ImportReport[] = [];\n    chosen.forEach((index, k) => {\n        const report = k === 0 ? first : new ImportReportBuilder(CX_FORMAT, resolved.errorLimit);\n        const sink = sinkFor(index);\n        reportSinkOptions(sink, options, report, true);\n        new CxReader(sink, report, resolved, zAs, doc, plans[index]).build();\n        throwIfAborted(resolved.signal);\n        reports.push(report.finish());\n    });\n    return reports;\n}\n\n/**\n * The CX version 1 importer plugin (design section 1.2).\n */\nexport const cxImporter: GraphImporter<CxImportOptions> = Object.freeze({\n    format: CX_FORMAT,\n    extensions: Object.freeze([\".cx\"]),\n    mimeTypes: Object.freeze([\"application/json\"]),\n\n    /**\n     * Confidence that the head is CX version 1: 0.95 when a top-level array starts with an object\n     * whose first key is numberVerification or metaData (Cytoscape's file filter), 0.7 for another\n     * CX aspect name.\n     * @param head - the first bytes\n     * @returns the confidence\n     */\n    sniff(head: Uint8Array): number {\n        const text = new TextDecoder(\"utf-8\").decode(head.subarray(0, 1024)).replace(/^\\uFEFF/, \"\");\n        const match = /^\\s*\\[\\s*\\{\\s*\"((?:[^\"\\\\]|\\\\.)*)\"\\s*:/.exec(text);\n        if (match === null) {\n            return 0;\n        }\n        if (CX_FIRST_KEYS.includes(match[1])) {\n            return 0.95;\n        }\n        return CX_ASPECT_KEYS.includes(match[1]) ? 0.7 : 0;\n    },\n\n    /**\n     * Read one graph of a CX document into the sink: the root network, or the subnetwork\n     * graphIndex / graphName picks (the first by default; W_MULTIPLE_GRAPHS names the others).\n     * @param input - the text, bytes or stream\n     * @param sink - the sink\n     * @param options - format-specific and common options\n     * @returns the import report; ImportError on a fatal error or beyond the error limit\n     */\n    async import(\n        input: ImportInput,\n        sink: GraphSink,\n        options?: CxImportOptions & CommonImportOptions,\n    ): Promise<ImportReport> {\n        const [report] = await run(\n            input,\n            options,\n            () => sink,\n            (plans, first) => {\n                const index = chooseGraph(\n                    plans.map((p) => p.name),\n                    options,\n                    first,\n                );\n                if (plans.length > 1) {\n                    first.warning(\n                        \"unsupported\",\n                        MULTIPLE_GRAPHS_CODE,\n                        `the collection holds ${plans.length} subnetworks; graph ${index} is read and ${plans.length - 1} skipped (importAll() reads every one)`,\n                    );\n                }\n                return [index];\n            },\n        );\n        return report;\n    },\n\n    /**\n     * Read every graph of a CX document: one per subnetwork of a collection, in the order of\n     * cyNetworkRelations; the root network for any other document.\n     * @param input - the text, bytes or stream\n     * @param sinkFor - the sink of the graph with this index, called before its first push\n     * @param options - format-specific and common options\n     * @returns one report per graph\n     */\n    importAll(\n        input: ImportInput,\n        sinkFor: (index: number) => GraphSink,\n        options?: CxImportOptions & CommonImportOptions,\n    ): Promise<ImportReport[]> {\n        return run(input, options, sinkFor, (plans) => plans.map((p) => p.index));\n    },\n\n    /**\n     * List the graphs of a CX document with their names and member counts.\n     * @param input - the text, bytes or stream\n     * @param options - format-specific and common options\n     * @returns one listing per graph\n     */\n    async listGraphs(\n        input: ImportInput,\n        options?: CxImportOptions & CommonImportOptions,\n    ): Promise<readonly GraphListing[]> {\n        const resolved = resolveImportOptions(options, FORMAT_DEFAULTS);\n        const report = new ImportReportBuilder(CX_FORMAT, resolved.errorLimit);\n        const doc = await readDocument(input, report, resolved);\n        const nodes = aspect(doc, \"nodes\").length;\n        const edges = aspect(doc, \"edges\").length;\n        return graphPlans(doc).map((plan) =>\n            Object.freeze({\n                index: plan.index,\n                name: plan.name,\n                nodes: memberCount(plan.nodes, nodes),\n                edges: memberCount(plan.edges, edges),\n            }),\n        );\n    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package/dist/chunks/{importer-Wv4C4gaF.js → importer-eUREhBGj.js}

@@ -2,8 +2,8 @@ import { GraphFormatError, INVALID_INDEX } from "@graphty/graph-format";
 import { V as resolveExportOptions, X as pairFolding, L as declareResolved, q as UNKNOWN_ENCODING_CODE, E as ENCODING_FALLBACK_CODE, r as INVALID_ENCODING_CODE, s as INVALID_UTF8_CODE, O as OPTION_IGNORED_CODE, S as SINK_OPTION_CODE, an as HYPEREDGE_CODE, T as TOO_LARGE_CODE, j as DANGLING_REFERENCE_CODE, A as AMBIGUOUS_GRAPH_NAME_CODE, G as GRAPH_NOT_FOUND_CODE, M as MULTIPLE_GRAPHS_CODE, I as ID_MERGED_CODE, c as DUPLICATE_EDGE_ID_CODE, d as DUPLICATE_NODE_CODE, U as UNKNOWN_PARENT_CODE, B as BAD_VALUE_CODE, e as MISSING_ENDPOINT_CODE, f as MISSING_ID_CODE, t as SYNTAX_CODE, u as EMPTY_INPUT_CODE, v as resolveImportOptions, w as ImportReportBuilder, aG as readText, x as textChunks, F as reportSinkOptions, z as reportUnusedOptions, y as throwIfAborted, K as IdCoercer, J as DirectionResolver, Q as uniqueColumnName, H as chooseGraph } from "./report-B1z4WT9e.js";
 import { c as capabilities, L as LOSS, a as checkCapabilities, d as countMixedEdges } from "./export-Bh60Dv-n.js";
 import { e as explicitWeights, f as formatF32, a as formatF64, w as weightFromValue } from "./weights-Dzba96G3.js";
+import { f as flipY, M as MAYBE_UNSAFE_INTEGER, e as rewriteNumbers, g as reviveNonstandard } from "./json-elements-DDS8N2Dd.js";
 import { j as joinText, e as encodeChunks } from "./writer-C7flM-Ih.js";
-import { M as MAYBE_UNSAFE_INTEGER, e as rewriteNumbers, g as reviveNonstandard } from "./json-elements-DDS8N2Dd.js";
 import { a as OBOGRAPHS_PREDICATE_TAGS, c as compactOboIri, o as oboColumnDecl, P as PLACEHOLDER_COLUMN, s as synonymScopeOf, O as OBO_NODE_COLUMNS } from "./ontology-BnrJ4I98.js";
 const JSON_DIALECTS = Object.freeze([
   "node-link",
@@ -1266,7 +1266,7 @@ function* writeCytoscape(snapshot, p) {
         w.key("position");
         w.open("{");
         w.member("x", numberText(value[0], f32, c.nonfinite));
-        w.member("y", numberText(value[1], f32, c.nonfinite));
+        w.member("y", numberText(flipY(value[1]), f32, c.nonfinite));
         w.close("}");
       }
     }
@@ -3898,7 +3898,7 @@ function importCytoscape(ctx, root) {
       if (position !== void 0 && position !== null) {
         if (isJsonObject(position) && typeof position.x === "number" && typeof position.y === "number") {
           point[0] = position.x;
-          point[1] = position.y;
+          point[1] = flipY(position.y);
           ctx.nodes.set(positionColumn, index, point);
         } else {
           report.error(
@@ -4167,4 +4167,4 @@ export {
   rankFormats as r,
   sniffFormat as s
 };
-//# sourceMappingURL=importer-Wv4C4gaF.js.map
+//# sourceMappingURL=importer-eUREhBGj.js.map