@graphty/graph-io 0.3.39 → 0.3.41

package/dist/chunks/{importer-B7Ir269L.js → importer-DviEsHy4.js}

@@ -1,7 +1,7 @@
 import { INVALID_INDEX, GraphFormatError } from "@graphty/graph-format";
-import { M as MIXED_DIRECTION_CODE, D as DIRECTION_FORCED_CODE, d as DIRECTION_REFUSED_CODE, S as SINK_OPTION_CODE, O as OPTION_IGNORED_CODE, I as ID_MERGED_CODE, R as ROLE_TAKEN_CODE, C as COLUMN_RENAMED_CODE, ae as AMBIGUOUS_GRAPH_NAME_CODE, af as GRAPH_NOT_FOUND_CODE, l as MULTIPLE_GRAPHS_CODE, f as STRAY_TEXT_CODE, g as UNKNOWN_ELEMENT_CODE, U as UNKNOWN_ATTR_TYPE_CODE, b6 as EQUATION_AS_TEXT_CODE, ai as PARENT_CYCLE_CODE, q as UNKNOWN_PARENT_CODE, o as DUPLICATE_ATTRIBUTE_CODE, i as DANGLING_REFERENCE_CODE, P as PRECISION_CODE, aj as WIDENED_CODE, a3 as BAD_VALUE_CODE, m as DUPLICATE_EDGE_ID_CODE, n as DUPLICATE_NODE_CODE, s as MISSING_ENDPOINT_CODE, t as MISSING_ID_CODE, N as NO_GRAPH_CODE, v as ENCODING_CONFLICT_CODE, w as UNKNOWN_ENCODING_CODE, x as ENCODING_FALLBACK_CODE, y as INVALID_ENCODING_CODE, z as INVALID_UTF8_CODE, E as EMPTY_INPUT_CODE, X as XML_SYNTAX_CODE, F as ELEMENT_ISSUE, G as INPUT_ISSUE, bj as STORAGE_CLASS_CODE, bp as WEIGHT_KEY_CLASH_CODE, au as ROLE_ASSUMED_CODE, a$ as COLUMN_RENAMED_LOSS_CODE, J as ID_TEXT_TYPE_CODE, bc as MUTUAL_EXPANDED_CODE, Q as PARENTS_DROPPED_CODE, K as ROLE_DROPPED_CODE, bl as TEMPORAL_TEXT_DROPPED_CODE, bk as TEMPORAL_DROPPED_CODE, ax as XML_ILLEGAL_CHAR_CODE, a0 as uniqueColumnName, a1 as declareResolved, ac as DictHeuristic, ar as IdCoercer, aq as DirectionResolver, b as plural, $ as agree, am as throwIfAborted, aK as parseWeightText, ao as reportSinkOptions, an as reportUnusedOptions, a7 as chooseGraph, ap as graphChosen, al as resolveImportOptions, a8 as ImportReportBuilder, a4 as textChunks, c0 as elementCount } from "./export-B-aVCwyG.js";
-import { l as localName, a as escapeXmlText, j as isWhitespace, e as escapeXmlAttribute, t as tokenizeXml, f as xmlDeclaredEncoding, X as XmlSyntaxError } from "./escape-BpYMQZVa.js";
-import { p as parseTextCell, i as inferTextDtype } from "./text-Bjfa1xYL.js";
+import { M as MIXED_DIRECTION_CODE, D as DIRECTION_FORCED_CODE, d as DIRECTION_REFUSED_CODE, S as SINK_OPTION_CODE, O as OPTION_IGNORED_CODE, I as ID_MERGED_CODE, R as ROLE_TAKEN_CODE, C as COLUMN_RENAMED_CODE, ae as AMBIGUOUS_GRAPH_NAME_CODE, af as GRAPH_NOT_FOUND_CODE, l as MULTIPLE_GRAPHS_CODE, f as STRAY_TEXT_CODE, g as UNKNOWN_ELEMENT_CODE, U as UNKNOWN_ATTR_TYPE_CODE, b6 as EQUATION_AS_TEXT_CODE, ai as PARENT_CYCLE_CODE, q as UNKNOWN_PARENT_CODE, o as DUPLICATE_ATTRIBUTE_CODE, i as DANGLING_REFERENCE_CODE, P as PRECISION_CODE, aj as WIDENED_CODE, a3 as BAD_VALUE_CODE, m as DUPLICATE_EDGE_ID_CODE, n as DUPLICATE_NODE_CODE, s as MISSING_ENDPOINT_CODE, t as MISSING_ID_CODE, N as NO_GRAPH_CODE, v as ENCODING_CONFLICT_CODE, w as UNKNOWN_ENCODING_CODE, x as ENCODING_FALLBACK_CODE, y as INVALID_ENCODING_CODE, z as INVALID_UTF8_CODE, E as EMPTY_INPUT_CODE, X as XML_SYNTAX_CODE, F as ELEMENT_ISSUE, G as INPUT_ISSUE, bj as STORAGE_CLASS_CODE, bp as WEIGHT_KEY_CLASH_CODE, au as ROLE_ASSUMED_CODE, a$ as COLUMN_RENAMED_LOSS_CODE, J as ID_TEXT_TYPE_CODE, bc as MUTUAL_EXPANDED_CODE, Q as PARENTS_DROPPED_CODE, K as ROLE_DROPPED_CODE, bl as TEMPORAL_TEXT_DROPPED_CODE, bk as TEMPORAL_DROPPED_CODE, ax as XML_ILLEGAL_CHAR_CODE, a0 as uniqueColumnName, a1 as declareResolved, ac as DictHeuristic, ar as IdCoercer, aq as DirectionResolver, b as plural, $ as agree, am as throwIfAborted, aK as parseWeightText, ao as reportSinkOptions, an as reportUnusedOptions, a7 as chooseGraph, ap as graphChosen, al as resolveImportOptions, a8 as ImportReportBuilder, a4 as textChunks, c0 as elementCount } from "./export-DD3Lvw-F.js";
+import { l as localName, a as escapeXmlText, j as isWhitespace, e as escapeXmlAttribute, t as tokenizeXml, f as xmlDeclaredEncoding, X as XmlSyntaxError } from "./escape-DBb8zuNE.js";
+import { p as parseTextCell, i as inferTextDtype } from "./text-Bh9SaAob.js";
 const FORMAT = "xgmml";
 const EXTENSIONS = Object.freeze([".xgmml", ".xml"]);
 const MIME_TYPES = Object.freeze(["application/xgmml", "text/xgmml", "text/xgmml+xml"]);
@@ -1747,6 +1747,9 @@ function parseCoordinate(text) {
 function localRef(href) {
   return href.startsWith("#") ? href.slice(1) : null;
 }
+function memberRef(id, href) {
+  return id ?? (href === null ? null : localRef(href));
+}
 function membersOf(doc, graph) {
   if (graph === null) {
     return { nodes: doc.nodes, edges: doc.edges, dangling: 0 };
@@ -1757,19 +1760,7 @@ function membersOf(doc, graph) {
   const edges = [];
   let dangling = 0;
   for (const member of graph.members) {
-    if (member.href === null) {
-      if (member.kind === "node") {
-        nodes.push(member);
-      } else {
-        edges.push(member);
-      }
-      continue;
-    }
-    const id = localRef(member.href);
-    let target;
-    if (id !== null) {
-      target = member.kind === "node" ? nodeById.get(id) : edgeById.get(id);
-    }
+    const target = resolveMember(member, nodeById, edgeById);
     if (target === void 0) {
       dangling++;
     } else if (target.kind === "node") {
@@ -1780,6 +1771,16 @@ function membersOf(doc, graph) {
   }
   return { nodes, edges, dangling };
 }
+function resolveMember(member, nodeById, edgeById) {
+  if (member.href === null) {
+    return member;
+  }
+  const id = localRef(member.href);
+  if (id === null) {
+    return void 0;
+  }
+  return member.kind === "node" ? nodeById.get(id) : edgeById.get(id);
+}
 function indexById(records) {
   const out = /* @__PURE__ */ new Map();
   for (const record of records) {
@@ -1789,6 +1790,26 @@ function indexById(records) {
   }
   return out;
 }
+function isRepeat(seen, record) {
+  if (seen === null) {
+    return false;
+  }
+  const key2 = record.id ?? (record.label === null ? null : JSON.stringify([record.label, record.source, record.target]));
+  if (key2 === null) {
+    return false;
+  }
+  if (seen.has(key2)) {
+    return true;
+  }
+  seen.add(key2);
+  return false;
+}
+function isGraphValueAtt(att) {
+  if (att.name !== null && META_ATTS.has(att.name)) {
+    return false;
+  }
+  return !(att.hasGraph && att.name === null);
+}
 class XgmmlEmitter {
   /**
    * Create an emitter for one graph.
@@ -2036,10 +2057,16 @@ class XgmmlEmitter {
     }
     const lower = t.toLowerCase();
     const readable = lower === "true" || lower === "yes" || lower === "false" || lower === "no";
+    let readAs;
+    if (readable) {
+      readAs = lower === "true" || lower === "yes" ? "1" : "0";
+    } else {
+      readAs = fallback ? "directed" : "undirected";
+    }
     this.report.warnOnce(
       "validation-error",
       XGMML_ISSUE.BAD_DIRECTED,
-      readable ? `${this.prefix()}directed="${text}" is not 0 or 1; read as ${lower === "true" || lower === "yes" ? "1" : "0"}` : `${this.prefix()}directed="${text}" is not 0 or 1; read as ${fallback ? "directed" : "undirected"}`,
+      `${this.prefix()}directed="${text}" is not 0 or 1; read as ${readAs}`,
       where,
       `${XGMML_ISSUE.BAD_DIRECTED}:${text}`
     );
@@ -2156,16 +2183,7 @@ class XgmmlEmitter {
       if (graph.owner !== null && isGroup(graph.owner)) {
         continue;
       }
-      for (const member of graph.members) {
-        if (member.href === null) {
-          continue;
-        }
-        const id = localRef(member.href);
-        const known = id !== null && (member.kind === "node" ? this.rows.has(id) : edgeIds.has(id));
-        if (!known) {
-          dangling++;
-        }
-      }
+      dangling += this.danglingReferences(graph, edgeIds);
     }
     if (dangling > 0) {
       this.report.warning(
@@ -2175,6 +2193,26 @@ class XgmmlEmitter {
       );
     }
   }
+  /**
+   * How many `xlink:href` members of a graph name no node or edge of the document.
+   * @param graph - the graph
+   * @param edgeIds - the id of every edge
+   * @returns the count
+   */
+  danglingReferences(graph, edgeIds) {
+    let dangling = 0;
+    for (const member of graph.members) {
+      if (member.href === null) {
+        continue;
+      }
+      const id = localRef(member.href);
+      const known = id !== null && (member.kind === "node" ? this.rows.has(id) : edgeIds.has(id));
+      if (!known) {
+        dangling++;
+      }
+    }
+    return dangling;
+  }
   /**
    * Write the per-node values: label, attributes, XML attributes, graphics, positions, nested
    * network pointers and subgraph memberships.
@@ -2305,17 +2343,17 @@ class XgmmlEmitter {
       }
     });
   }
-  /** The `xgmml.networks` membership of nodes in root-level subgraphs of a generic document. */
-  writeNetworks() {
-    const { subgraphs } = this.doc.root;
-    if (subgraphs.length === 0) {
-      return;
-    }
+  /**
+   * The names of the subgraphs each node row is a member of.
+   * @param subgraphs - the root-level subgraphs
+   * @returns the subgraph names by node row index
+   */
+  networkMembership(subgraphs) {
     const member = /* @__PURE__ */ new Map();
     for (const graph of subgraphs) {
       const name = graph.id ?? graph.label ?? "";
       for (const m of graph.members) {
-        const id = m.kind === "node" ? m.id ?? (m.href === null ? null : localRef(m.href)) : null;
+        const id = m.kind === "node" ? memberRef(m.id, m.href) : null;
         const row = id === null ? void 0 : this.rows.get(id);
         if (row !== void 0 && row.index >= 0) {
           const list = member.get(row.index) ?? [];
@@ -2324,6 +2362,15 @@ class XgmmlEmitter {
         }
       }
     }
+    return member;
+  }
+  /** The `xgmml.networks` membership of nodes in root-level subgraphs of a generic document. */
+  writeNetworks() {
+    const { subgraphs } = this.doc.root;
+    if (subgraphs.length === 0) {
+      return;
+    }
+    const member = this.networkMembership(subgraphs);
     if (member.size === 0) {
       return;
     }
@@ -2358,14 +2405,10 @@ class XgmmlEmitter {
     this.decideNameLabel("edge", records);
     for (const record of records) {
       const where = { line: record.line, element: record.id ?? record.label };
-      const key2 = record.id ?? (record.label === null ? null : JSON.stringify([record.label, record.source, record.target]));
-      if (dedupe !== null && key2 !== null) {
-        if (dedupe.has(key2)) {
-          repeats++;
-          firstRepeat ??= where;
-          continue;
-        }
-        dedupe.add(key2);
+      if (isRepeat(dedupe, record)) {
+        repeats++;
+        firstRepeat ??= where;
+        continue;
       }
       const index = this.addEdge(record, header, ids, where);
       this.checkAbort();
@@ -2614,13 +2657,9 @@ class XgmmlEmitter {
       }
     }
     for (const att of g.atts) {
-      if (att.name !== null && META_ATTS.has(att.name)) {
-        continue;
-      }
-      if (att.hasGraph && att.name === null) {
-        continue;
+      if (isGraphValueAtt(att)) {
+        this.graphColumns.addAtt(0, att, where);
       }
-      this.graphColumns.addAtt(0, att, where);
     }
     this.graphColumns.write(this.sink, () => 0);
     const json = { ...this.extras.graphJson };
@@ -3089,19 +3128,7 @@ function booleanOption(name, value, fallback) {
   return value;
 }
 async function parseXgmml(input, report, common, options) {
-  const repairs = {
-    bareAmpersand: booleanOption("repairBareAmpersands", options?.repairBareAmpersands, false) ? (line) => {
-      report.warning("parse-error", XGMML_ISSUE.AMPERSAND_REPAIRED, "a bare & was read as &", { line });
-    } : void 0,
-    surrogatePair: booleanOption("pairSurrogateReferences", options?.pairSurrogateReferences, false) ? (line) => {
-      report.warning(
-        "parse-error",
-        XGMML_ISSUE.SURROGATE_PAIRED,
-        "two surrogate character references were joined into one character",
-        { line }
-      );
-    } : void 0
-  };
+  const repairs = repairsOf(options, report);
   const parser = new XgmmlParser(report);
   const seen = { content: false };
   try {
@@ -3111,12 +3138,7 @@ async function parseXgmml(input, report, common, options) {
       repairs
     );
   } catch (err) {
-    if (err instanceof XmlSyntaxError) {
-      if (!seen.content) {
-        report.fail(XGMML_ISSUE.EMPTY_INPUT, "the input is empty");
-      }
-      report.fail(XGMML_ISSUE.XML_SYNTAX, err.message, { line: err.line });
-    }
+    failOnSyntax(err, seen.content, report);
     throw err;
   }
   const doc = parser.document();
@@ -3130,6 +3152,30 @@ async function parseXgmml(input, report, common, options) {
   }
   return doc;
 }
+function repairsOf(options, report) {
+  return {
+    bareAmpersand: booleanOption("repairBareAmpersands", options?.repairBareAmpersands, false) ? (line) => {
+      report.warning("parse-error", XGMML_ISSUE.AMPERSAND_REPAIRED, "a bare & was read as &", { line });
+    } : void 0,
+    surrogatePair: booleanOption("pairSurrogateReferences", options?.pairSurrogateReferences, false) ? (line) => {
+      report.warning(
+        "parse-error",
+        XGMML_ISSUE.SURROGATE_PAIRED,
+        "two surrogate character references were joined into one character",
+        { line }
+      );
+    } : void 0
+  };
+}
+function failOnSyntax(err, content, report) {
+  if (!(err instanceof XmlSyntaxError)) {
+    return;
+  }
+  if (!content) {
+    report.fail(XGMML_ISSUE.EMPTY_INPUT, "the input is empty");
+  }
+  report.fail(XGMML_ISSUE.XML_SYNTAX, err.message, { line: err.line });
+}
 async function* watch(chunks, seen) {
   for await (const chunk of chunks) {
     seen.content ||= !isWhitespace(chunk);
@@ -3290,10 +3336,10 @@ export {
   XLINK_NAMESPACE as b,
   XGMML_NAMESPACE as c,
   aliasesOf as d,
-  NETWORK_POINTER_COLUMN as e,
-  NETWORKS_COLUMN as f,
-  PARENT_COLUMN as g,
-  PARENTS_COLUMN as h,
+  PARENT_COLUMN as e,
+  PARENTS_COLUMN as f,
+  NETWORK_POINTER_COLUMN as g,
+  NETWORKS_COLUMN as h,
   XGMML_ORIGIN_NAMESPACE as i,
   CYTOSCAPE_ORIGIN_NAMESPACE as j,
   XgmmlEmitter as k,
@@ -3305,4 +3351,4 @@ export {
   resolveSettings as r,
   xgmmlImporter as x
 };
-//# sourceMappingURL=importer-B7Ir269L.js.map
+//# sourceMappingURL=importer-DviEsHy4.js.map