@graphty/graph-io 0.3.40 → 0.3.42

package/dist/src/formats/xgmml/importer.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"importer.d.ts","sourceRoot":"","sources":["../../../../src/formats/xgmml/importer.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAKH,OAAO,EAMH,KAAK,qBAAqB,EAE7B,MAAM,yBAAyB,CAAC;AAEjC,OAAO,EAAE,mBAAmB,EAAE,MAAM,wBAAwB,CAAC;AAE7D,OAAO,EACH,KAAK,mBAAmB,EACxB,KAAK,kBAAkB,EACvB,KAAK,aAAa,EAElB,KAAK,WAAW,EAEnB,MAAM,gBAAgB,CAAC;AAExB,OAAO,EAAiB,KAAK,aAAa,EAAe,MAAM,eAAe,CAAC;AAC/E,OAAO,EAOH,KAAK,aAAa,EACrB,MAAM,WAAW,CAAC;AAEnB;;;GAGG;AACH,MAAM,WAAW,kBAAmB,SAAQ,kBAAkB,EAAE,mBAAmB;IAC/E;;;;;OAKG;IACH,YAAY,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IACnC;;;;OAIG;IACH,gBAAgB,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IACvC;;;;OAIG;IACH,oBAAoB,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IAC3C;;;;OAIG;IACH,uBAAuB,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IAC9C;;;;OAIG;IACH,GAAG,CAAC,EAAE,QAAQ,GAAG,UAAU,GAAG,SAAS,CAAC;CAC3C;AA8BD;;;;;;GAMG;AACH,wBAAgB,eAAe,CAAC,OAAO,EAAE,kBAAkB,GAAG,SAAS,EAAE,SAAS,EAAE,OAAO,GAAG,aAAa,CAiB1G;AAsBD;;;;;;;;GAQG;AACH,wBAAsB,UAAU,CAC5B,KAAK,EAAE,WAAW,EAClB,MAAM,EAAE,mBAAmB,EAC3B,MAAM,EAAE,qBAAqB,EAC7B,OAAO,EAAE,kBAAkB,GAAG,SAAS,GACxC,OAAO,CAAC,aAAa,CAAC,CA6CxB;AAqOD;;;GAGG;AACH,eAAO,MAAM,aAAa,EAAE,aAAa,CAAC,kBAAkB,CAe1D,CAAC"}
+{"version":3,"file":"importer.d.ts","sourceRoot":"","sources":["../../../../src/formats/xgmml/importer.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAKH,OAAO,EAMH,KAAK,qBAAqB,EAE7B,MAAM,yBAAyB,CAAC;AAEjC,OAAO,EAAE,mBAAmB,EAAE,MAAM,wBAAwB,CAAC;AAE7D,OAAO,EACH,KAAK,mBAAmB,EACxB,KAAK,kBAAkB,EACvB,KAAK,aAAa,EAElB,KAAK,WAAW,EAEnB,MAAM,gBAAgB,CAAC;AAExB,OAAO,EAAiB,KAAK,aAAa,EAAe,MAAM,eAAe,CAAC;AAC/E,OAAO,EAOH,KAAK,aAAa,EACrB,MAAM,WAAW,CAAC;AAEnB;;;GAGG;AACH,MAAM,WAAW,kBAAmB,SAAQ,kBAAkB,EAAE,mBAAmB;IAC/E;;;;;OAKG;IACH,YAAY,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IACnC;;;;OAIG;IACH,gBAAgB,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IACvC;;;;OAIG;IACH,oBAAoB,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IAC3C;;;;OAIG;IACH,uBAAuB,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IAC9C;;;;OAIG;IACH,GAAG,CAAC,EAAE,QAAQ,GAAG,UAAU,GAAG,SAAS,CAAC;CAC3C;AA8BD;;;;;;GAMG;AACH,wBAAgB,eAAe,CAAC,OAAO,EAAE,kBAAkB,GAAG,SAAS,EAAE,SAAS,EAAE,OAAO,GAAG,aAAa,CAiB1G;AAsBD;;;;;;;;GAQG;AACH,wBAAsB,UAAU,CAC5B,KAAK,EAAE,WAAW,EAClB,MAAM,EAAE,mBAAmB,EAC3B,MAAM,EAAE,qBAAqB,EAC7B,OAAO,EAAE,kBAAkB,GAAG,SAAS,GACxC,OAAO,CAAC,aAAa,CAAC,CAwBxB;AAgRD;;;GAGG;AACH,eAAO,MAAM,aAAa,EAAE,aAAa,CAAC,kBAAkB,CAe1D,CAAC"}

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

@@ -95,30 +95,14 @@ function booleanOption(name, value, fallback) {
  * @returns the document
  */
 export 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 });
-            }
-            : undefined,
-        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 });
-            }
-            : undefined,
-    };
+    const repairs = repairsOf(options, report);
     const parser = new XgmmlParser(report);
     const seen = { content: false };
     try {
         await tokenizeXml(watch(textChunks(input, report, { ...common, declaredEncoding: xmlDeclaredEncoding, xml: true }), seen), parser, 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();
@@ -127,6 +111,42 @@ export async function parseXgmml(input, report, common, options) {
     }
     return doc;
 }
+/**
+ * The XML repairs the options switch on, each reporting where it repaired.
+ * @param options - the XGMML options
+ * @param report - the report
+ * @returns the repairs
+ */
+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 });
+            }
+            : undefined,
+        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 });
+            }
+            : undefined,
+    };
+}
+/**
+ * Fail the report on an XML syntax error: an input with no content is empty, any other is
+ * malformed. Any other error is left to the caller.
+ * @param err - the error the tokenizer threw
+ * @param content - whether non-whitespace text was seen
+ * @param report - the report
+ */
+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 });
+}
 /**
  * Pass text chunks through while noting non-whitespace content.
  * @param chunks - the chunks

package/dist/src/formats/xgmml/importer.js.map

@@ -1 +1 @@
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package/dist/src/sniff.js

@@ -275,39 +275,54 @@ function skeletonOf(text) {
     }
     const root = {};
     for (const key of rootKeys) {
-        switch (key) {
-            case "graph":
-            case "options":
-                root[key] = objectOf(keys.get(key));
-                break;
-            case "graphs": {
-                // the keys of any node or edge of the first graph: OBO Graphs or JGF (design 1.6)
-                const nodes = keys.get("graphs[0].nodes[]");
-                const edges = keys.get("graphs[0].edges[]");
-                const graph = {};
-                if (nodes !== undefined) {
-                    graph.nodes = [objectOf(nodes)];
-                }
-                if (edges !== undefined) {
-                    graph.edges = [objectOf(edges)];
-                }
-                root[key] = nodes === undefined && edges === undefined ? [] : [graph];
-                break;
-            }
-            case "nodes":
-            case "edges":
-            case "links": {
-                const first = keys.get(`${key}[0]`);
-                root[key] = first === undefined ? [] : [objectOf(first)];
-                break;
-            }
-            default:
-                root[key] = true;
-                break;
-        }
+        root[key] = placeholderOf(key, keys);
     }
     return root;
 }
+/**
+ * The placeholder value of a root key: the shape the dialect rule tests that key for.
+ * @param key - the root key
+ * @param keys - the key sets by path
+ * @returns the placeholder
+ */
+function placeholderOf(key, keys) {
+    switch (key) {
+        case "graph":
+        case "options":
+            return objectOf(keys.get(key));
+        case "graphs":
+            return graphsPlaceholder(keys);
+        case "nodes":
+        case "edges":
+        case "links": {
+            const first = keys.get(`${key}[0]`);
+            return first === undefined ? [] : [objectOf(first)];
+        }
+        default:
+            return true;
+    }
+}
+/**
+ * The placeholder of `graphs`: the keys of any node or edge of the first graph, which tell OBO
+ * Graphs from JGF (design 1.6).
+ * @param keys - the key sets by path
+ * @returns `[]` when neither was seen, else one graph holding them
+ */
+function graphsPlaceholder(keys) {
+    const nodes = keys.get("graphs[0].nodes[]");
+    const edges = keys.get("graphs[0].edges[]");
+    if (nodes === undefined && edges === undefined) {
+        return [];
+    }
+    const graph = {};
+    if (nodes !== undefined) {
+        graph.nodes = [objectOf(nodes)];
+    }
+    if (edges !== undefined) {
+        graph.edges = [objectOf(edges)];
+    }
+    return [graph];
+}
 /**
  * An object holding placeholder values for a key set: `{}` for the keys the rule tests with
  * isJsonObject (`attributes`, `data`), `true` otherwise.
@@ -341,32 +356,6 @@ function scanKeys(text) {
     const counts = [];
     let pendingKey = null;
     let expectingKey = false;
-    const pathOf = () => {
-        const depth = kinds.length;
-        if (depth === 1) {
-            return kinds[0] === "object" ? "" : null;
-        }
-        if (depth === 2 && kinds[0] === "array" && kinds[1] === "object" && labels[1] === "0") {
-            return "nodes[0]";
-        }
-        if (depth === 2 && kinds[0] === "object" && kinds[1] === "object") {
-            return labels[1] === "graph" || labels[1] === "options" ? labels[1] : null;
-        }
-        if (depth === 5 &&
-            kinds.join() === "object,array,object,array,object" &&
-            labels[1] === "graphs" &&
-            labels[2] === "0" &&
-            (labels[3] === "nodes" || labels[3] === "edges")) {
-            return labels[3] === "nodes" ? "graphs[0].nodes[]" : "graphs[0].edges[]";
-        }
-        if (depth === 3 && kinds[0] === "object" && kinds[1] === "array" && kinds[2] === "object") {
-            const section = labels[1];
-            if ((section === "nodes" || section === "edges" || section === "links") && labels[2] === "0") {
-                return `${section}[0]`;
-            }
-        }
-        return null;
-    };
     let i = 0;
     const n = text.length;
     while (i < n) {
@@ -404,7 +393,7 @@ function scanKeys(text) {
         }
         else if (ch === ":") {
             if (pendingKey !== null) {
-                const path = pathOf();
+                const path = keyPathOf(kinds, labels);
                 if (path !== null) {
                     let set = found.get(path);
                     if (set === undefined) {
@@ -427,6 +416,69 @@ function scanKeys(text) {
     }
     return found;
 }
+/**
+ * The watched path of the innermost open object, from the container stack.
+ * @param kinds - the kind of each open container, outermost first
+ * @param labels - the key or index each open container sits under
+ * @returns the path, or null when keys there are not watched
+ */
+function keyPathOf(kinds, labels) {
+    switch (kinds.length) {
+        case 1:
+            return kinds[0] === "object" ? "" : null;
+        case 2:
+            return nestedObjectPath(kinds, labels);
+        case 3:
+            return sectionElementPath(kinds, labels);
+        case 5:
+            return graphsMemberPath(kinds, labels);
+        default:
+            return null;
+    }
+}
+/**
+ * At depth 2: the first element of a top-level array, or the `graph` / `options` object.
+ * @param kinds - the kind of each open container, outermost first
+ * @param labels - the key or index each open container sits under
+ * @returns the path, or null
+ */
+function nestedObjectPath(kinds, labels) {
+    if (kinds[0] === "array" && kinds[1] === "object" && labels[1] === "0") {
+        return "nodes[0]";
+    }
+    if (kinds[0] === "object" && kinds[1] === "object") {
+        return labels[1] === "graph" || labels[1] === "options" ? labels[1] : null;
+    }
+    return null;
+}
+/**
+ * At depth 3: the first element of the root's `nodes`, `edges` or `links` array.
+ * @param kinds - the kind of each open container, outermost first
+ * @param labels - the key or index each open container sits under
+ * @returns the path, or null
+ */
+function sectionElementPath(kinds, labels) {
+    if (kinds[0] !== "object" || kinds[1] !== "array" || kinds[2] !== "object" || labels[2] !== "0") {
+        return null;
+    }
+    const section = labels[1];
+    return section === "nodes" || section === "edges" || section === "links" ? `${section}[0]` : null;
+}
+/**
+ * At depth 5: any node or edge of the first graph of the root's `graphs` array.
+ * @param kinds - the kind of each open container, outermost first
+ * @param labels - the key or index each open container sits under
+ * @returns the path, or null
+ */
+function graphsMemberPath(kinds, labels) {
+    if (kinds.join() !== "object,array,object,array,object" || labels[1] !== "graphs" || labels[2] !== "0") {
+        return null;
+    }
+    if (labels[3] === "nodes") {
+        return "graphs[0].nodes[]";
+    }
+    return labels[3] === "edges" ? "graphs[0].edges[]" : null;
+}
 /**
  * The index of the closing quote of a JSON string starting after its opening quote.
  * @param text - the text

package/dist/src/sniff.js.map

@@ -1 +1 @@
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package/dist/xgmml.js

@@ -1,5 +1,5 @@
-import { X, a, x } from "./chunks/importer-DEp_fYjf.js";
-import { x as x2 } from "./chunks/exporter-BVXnV9-9.js";
+import { X, a, x } from "./chunks/importer-Ht7LNg8L.js";
+import { x as x2 } from "./chunks/exporter-BWwEuOPT.js";
 export {
   X as XGMML_ISSUE,
   a as XGMML_LOSS,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@graphty/graph-io",
-  "version": "0.3.40",
+  "version": "0.3.42",
   "description": "Read and write 13 graph file formats (JSON, GraphML, GEXF, CSV, GML, DOT, Pajek, Neo4j CSV, XGMML, CX2, CX, OBO, Cytoscape sessions) as @graphty/graph-format snapshots",
   "author": "Adam Powers <apowers@ato.ms>",
   "type": "module",
@@ -121,7 +121,7 @@
   },
   "homepage": "https://graphty.app/docs/graph-io/",
   "dependencies": {
-    "@graphty/graph-format": "^1.4.1"
+    "@graphty/graph-format": "^1.4.3"
   },
   "peerDependencies": {
     "@graphty/graph-format": "^1.0.0"

package/src/children.ts

@@ -14,7 +14,7 @@
  * every node is written exactly once.
  */
 
-import { type Column, type GraphSnapshot, INVALID_INDEX } from "@graphty/graph-format";
+import { type Column, type GraphSnapshot, INVALID_INDEX, type ListColumn } from "@graphty/graph-format";
 
 /**
  * The role of the column a children CSR is built over.
@@ -282,7 +282,6 @@ export function childrenFromColumn(nodeCount: number, column: Column | null): Ch
     let dropped = 0;
     const references: number[] = [];
     if (column !== null) {
-        const rows = Math.min(column.length, nodeCount);
         const keep = (child: number, parent: number): void => {
             if (!Number.isInteger(parent) || parent === INVALID_INDEX || parent >= nodeCount || parent === child) {
                 dropped++;
@@ -292,31 +291,9 @@ export function childrenFromColumn(nodeCount: number, column: Column | null): Ch
             rowPtr[parent + 1]++;
             parentCount[child]++;
         };
-        if (column.dtype === "u32") {
-            const { data } = column;
-            for (let i = 0; i < rows; i++) {
-                if (column.isSet(i)) {
-                    keep(i, data[i]);
-                }
-            }
-        } else if (column.dtype === "list") {
-            for (let i = 0; i < rows; i++) {
-                if (!column.isSet(i)) {
-                    continue;
-                }
-                for (const item of column.sliceOf(i)) {
-                    if (typeof item === "number") {
-                        keep(i, item);
-                    } else {
-                        dropped++;
-                    }
-                }
-            }
-        } else {
-            throw new TypeError(
-                `a containment column must be u32 or a list of u32, found ${column.dtype} column "${column.meta.name}"`,
-            );
-        }
+        // keep() counts into `dropped` while it runs, so add the non-numeric items after the call
+        const nonNumeric = readContainment(column, Math.min(column.length, nodeCount), keep);
+        dropped += nonNumeric;
     }
     for (let u = 0; u < nodeCount; u++) {
         rowPtr[u + 1] += rowPtr[u];
@@ -330,6 +307,56 @@ export function childrenFromColumn(nodeCount: number, column: Column | null): Ch
     return new ChildrenCsr(nodeCount, rowPtr, children, parentCount, dropped, column);
 }
 
+/**
+ * Hand every (child, parent) reference of the first `rows` rows of a containment column to `keep`,
+ * in ascending child order.
+ * @param column - a u32 `parent`-shaped column or a list-of-u32 `parents`-shaped column
+ * @param rows - how many rows to read
+ * @param keep - receives each reference
+ * @returns how many list items were dropped for not being a number
+ */
+function readContainment(column: Column, rows: number, keep: (child: number, parent: number) => void): number {
+    if (column.dtype === "u32") {
+        const { data } = column;
+        for (let i = 0; i < rows; i++) {
+            if (column.isSet(i)) {
+                keep(i, data[i]);
+            }
+        }
+        return 0;
+    }
+    if (column.dtype === "list") {
+        return readParentLists(column, rows, keep);
+    }
+    throw new TypeError(
+        `a containment column must be u32 or a list of u32, found ${column.dtype} column "${column.meta.name}"`,
+    );
+}
+
+/**
+ * Hand every numeric item of a `parents`-shaped list column to `keep`.
+ * @param column - the list column
+ * @param rows - how many rows to read
+ * @param keep - receives each reference
+ * @returns how many items were not numbers
+ */
+function readParentLists(column: ListColumn, rows: number, keep: (child: number, parent: number) => void): number {
+    let dropped = 0;
+    for (let i = 0; i < rows; i++) {
+        if (!column.isSet(i)) {
+            continue;
+        }
+        for (const item of column.sliceOf(i)) {
+            if (typeof item === "number") {
+                keep(i, item);
+            } else {
+                dropped++;
+            }
+        }
+    }
+    return dropped;
+}
+
 /**
  * The column a ChildrenOptions selects.
  * @param snapshot - the snapshot