@graphty/graph-io 0.0.0 → 0.2.1

package/dist/tsconfig.build.tsbuildinfo

@@ -0,0 +1 @@
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package/package.json

@@ -1,10 +1,125 @@
 {
   "name": "@graphty/graph-io",
-  "version": "0.0.0",
-  "description": "OIDC trusted publishing setup package for @graphty/graph-io",
+  "version": "0.2.1",
+  "description": "Importers and exporters (GEXF, GraphML, GML, DOT, Pajek, CSV, JSON, Neo4j) for the @graphty/graph-format snapshot",
+  "author": "Adam Powers <apowers@ato.ms>",
+  "type": "module",
+  "main": "dist/graph-io.js",
+  "types": "dist/graph-io.d.ts",
+  "exports": {
+    ".": {
+      "types": "./dist/graph-io.d.ts",
+      "import": "./dist/graph-io.js",
+      "default": "./dist/graph-io.js"
+    },
+    "./gexf": {
+      "types": "./dist/gexf.d.ts",
+      "import": "./dist/gexf.js",
+      "default": "./dist/gexf.js"
+    },
+    "./graphml": {
+      "types": "./dist/graphml.d.ts",
+      "import": "./dist/graphml.js",
+      "default": "./dist/graphml.js"
+    },
+    "./gml": {
+      "types": "./dist/gml.d.ts",
+      "import": "./dist/gml.js",
+      "default": "./dist/gml.js"
+    },
+    "./dot": {
+      "types": "./dist/dot.d.ts",
+      "import": "./dist/dot.js",
+      "default": "./dist/dot.js"
+    },
+    "./pajek": {
+      "types": "./dist/pajek.d.ts",
+      "import": "./dist/pajek.js",
+      "default": "./dist/pajek.js"
+    },
+    "./csv": {
+      "types": "./dist/csv.d.ts",
+      "import": "./dist/csv.js",
+      "default": "./dist/csv.js"
+    },
+    "./json": {
+      "types": "./dist/json.d.ts",
+      "import": "./dist/json.js",
+      "default": "./dist/json.js"
+    },
+    "./neo4j": {
+      "types": "./dist/neo4j.d.ts",
+      "import": "./dist/neo4j.js",
+      "default": "./dist/neo4j.js"
+    }
+  },
+  "sideEffects": false,
+  "files": [
+    "dist/",
+    "src/",
+    "README.md",
+    "LICENSE"
+  ],
+  "publishConfig": {
+    "access": "public",
+    "provenance": true
+  },
+  "engines": {
+    "node": ">=18.19.0"
+  },
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/graphty-org/graphty-monorepo.git",
+    "directory": "graph-io"
+  },
   "keywords": [
-    "oidc",
-    "trusted-publishing",
-    "setup"
-  ]
-}
+    "graph",
+    "gexf",
+    "graphml",
+    "gml",
+    "dot",
+    "graphviz",
+    "pajek",
+    "csv",
+    "json",
+    "neo4j",
+    "graph-format"
+  ],
+  "license": "MIT",
+  "bugs": {
+    "url": "https://github.com/graphty-org/graphty-monorepo/issues"
+  },
+  "homepage": "https://github.com/graphty-org/graphty-monorepo/tree/master/graph-io#readme",
+  "dependencies": {
+    "@graphty/graph-format": "0.2.1"
+  },
+  "peerDependencies": {
+    "@graphty/graph-format": "^0.2.0"
+  },
+  "devDependencies": {
+    "@vitest/coverage-v8": "^3.2.4",
+    "@vitest/ui": "^3.2.4",
+    "fast-check": "^4.2.0",
+    "fast-xml-parser": "^5.11.1",
+    "tsx": "^4.20.3",
+    "typescript": "^5.9.3",
+    "vite": "^7.0.5",
+    "vitest": "^3.2.4"
+  },
+  "scripts": {
+    "build": "tsc -p tsconfig.build.json",
+    "build:bundle": "node scripts/build-bundle.js",
+    "build:all": "npm run build && npm run build:bundle",
+    "lint": "eslint && tsc --noEmit -p tsconfig.json",
+    "lint:fix": "eslint --fix",
+    "typecheck": "tsc --noEmit -p tsconfig.json",
+    "typecheck:strict-consumer": "tsc -p tsconfig.strict-consumer.json",
+    "test": "vitest",
+    "test:ui": "vitest --ui",
+    "test:run": "vitest run",
+    "coverage": "vitest run --coverage",
+    "coverage:preview": "npx serve coverage -p 9057",
+    "benchmark": "tsx benchmarks/run.ts",
+    "ready:commit": "npm run build:all && npm run lint && npm run typecheck:strict-consumer && npm run test:run"
+  }
+}

package/src/children.ts

@@ -0,0 +1,335 @@
+/**
+ * The children CSR over a containment column (design sections 5.10, 7.1 and 8.2): containment
+ * (GEXF `pid` / `<parents>`, Cytoscape `parent`, DOT clusters, GraphML nested graphs) is a node
+ * column with the `parent` role (u32, refersTo node) or the `parents` role (list of u32) and never
+ * enters the CSR of the snapshot. Importers and exporters that need to walk containers top-down
+ * (nested subgraphs, cluster blocks, parent lists) build this inverse index once: for every node
+ * `u`, `children[rowPtr[u] .. rowPtr[u + 1])` are its children in ascending index order, `roots`
+ * are the nodes with no parent, and `depthFirst()` is the pre-order the nested writers use.
+ *
+ * The helper is deliberately outside the core (7.1: it computes a property the arrays do not
+ * already imply and only io needs it). A reference is ignored when it is unset, INVALID_INDEX, out
+ * of range, or the node itself; a cycle (a parent chain that never reaches a root) is reported
+ * through `unreachable` and its members are appended to the depth-first order in index order so
+ * every node is written exactly once.
+ */
+
+import { type Column, type GraphSnapshot, INVALID_INDEX } from "@graphty/graph-format";
+
+/** The role of the column a children CSR is built over. */
+export type ContainmentRole = "parent" | "parents";
+
+/** How the CSR is built: from a role column of the snapshot (default `parent`, then `parents`) or an explicit column. */
+export interface ChildrenOptions {
+    /**
+     * The column to read: a role name (`parent` for the u32 single-parent column, `parents` for
+     * the list column) or a column object of either shape; "auto" (default) takes the `parent`
+     * role column when the snapshot has one, else `parents`, else no containment; null builds
+     * the empty CSR (every node a root) whatever the snapshot holds.
+     */
+    readonly column?: ContainmentRole | Column | "auto" | null | undefined;
+}
+
+/** One depth-first traversal of the containment forest. */
+export interface DepthFirstOrder {
+    /** Every node index exactly once: roots in index order, each followed by its descendants, cycle members last. */
+    readonly order: Uint32Array;
+    /** The depth of every node in the traversal (0 for a root or a cycle member forced to the top). */
+    readonly depth: Uint32Array;
+    /** Whether `order` differs from `0..n-1`. */
+    readonly reordered: boolean;
+}
+
+/**
+ * The children CSR of a snapshot's containment column (design sections 5.10 and 7.1): the inverse
+ * of the parent relation as a compressed sparse row structure over node indices.
+ */
+export class ChildrenCsr {
+    /** The number of nodes (the row count of the CSR). */
+    readonly nodeCount: number;
+    /** `rowPtr[u] .. rowPtr[u + 1]` is the range of `children` holding the children of `u`; length nodeCount + 1. */
+    readonly rowPtr: Uint32Array;
+    /** Child node indices, ascending within each parent's range. */
+    readonly children: Uint32Array;
+    /** The nodes with no (valid) parent, in index order. */
+    readonly roots: Uint32Array;
+    /** Every (child, parent) reference kept; equal to `children.length`. */
+    readonly edgeCount: number;
+    /** References dropped because they were INVALID_INDEX, out of range or self-references. */
+    readonly dropped: number;
+    /** Nodes whose parent chain never reaches a root (members of a cycle), counted once each. */
+    readonly unreachable: number;
+    /** The column the CSR was built from, or null when the snapshot has no containment. */
+    readonly column: Column | null;
+
+    private readonly parentCount: Uint32Array;
+
+    /**
+     * Build the CSR; use childrenCsr() rather than the constructor.
+     * @param nodeCount - the node count
+     * @param rowPtr - the row pointers
+     * @param children - the child list
+     * @param parentCount - parents per node (0 for a root)
+     * @param dropped - references ignored
+     * @param column - the source column, or null
+     */
+    constructor(
+        nodeCount: number,
+        rowPtr: Uint32Array,
+        children: Uint32Array,
+        parentCount: Uint32Array,
+        dropped: number,
+        column: Column | null,
+    ) {
+        this.nodeCount = nodeCount;
+        this.rowPtr = rowPtr;
+        this.children = children;
+        this.parentCount = parentCount;
+        this.edgeCount = children.length;
+        this.dropped = dropped;
+        this.column = column;
+        let rootCount = 0;
+        for (let u = 0; u < nodeCount; u++) {
+            if (parentCount[u] === 0) {
+                rootCount++;
+            }
+        }
+        const roots = new Uint32Array(rootCount);
+        let r = 0;
+        for (let u = 0; u < nodeCount; u++) {
+            if (parentCount[u] === 0) {
+                roots[r++] = u;
+            }
+        }
+        this.roots = roots;
+        this.unreachable = nodeCount - this.reachableCount();
+    }
+
+    /**
+     * The children of a node, as a view into `children` (do not modify).
+     * @param node - the node index
+     * @returns the child indices in ascending order; empty for a leaf
+     */
+    childrenOf(node: number): Uint32Array {
+        return this.children.subarray(this.rowPtr[node], this.rowPtr[node + 1]);
+    }
+
+    /**
+     * How many children a node has.
+     * @param node - the node index
+     * @returns the count
+     */
+    childCount(node: number): number {
+        return this.rowPtr[node + 1] - this.rowPtr[node];
+    }
+
+    /**
+     * Whether a node is a container (has at least one child).
+     * @param node - the node index
+     * @returns true when it has children
+     */
+    hasChildren(node: number): boolean {
+        return this.rowPtr[node + 1] > this.rowPtr[node];
+    }
+
+    /**
+     * How many parents a node has: 0 for a root, 1 under a `parent` column, any number under `parents`.
+     * @param node - the node index
+     * @returns the parent count
+     */
+    parentCountOf(node: number): number {
+        return this.parentCount[node];
+    }
+
+    /**
+     * Whether a node has no parent.
+     * @param node - the node index
+     * @returns true for a root
+     */
+    isRoot(node: number): boolean {
+        return this.parentCount[node] === 0;
+    }
+
+    /**
+     * Whether the snapshot has any containment at all.
+     * @returns true when at least one child reference was kept
+     */
+    isEmpty(): boolean {
+        return this.edgeCount === 0;
+    }
+
+    /**
+     * A pre-order depth-first traversal from the roots in index order (children in ascending
+     * order), then every node not yet visited (a cycle member, or a multi-parent node reached
+     * only through a cycle) in index order at depth 0. Each node appears exactly once, so nested
+     * writers emit every element once even for a `parents` column that shares a child.
+     * @returns the order, the depth of every node and whether the order differs from index order
+     */
+    depthFirst(): DepthFirstOrder {
+        const n = this.nodeCount;
+        const order = new Uint32Array(n);
+        const depth = new Uint32Array(n);
+        const visited = new Uint8Array(n);
+        const stackNode: number[] = [];
+        const stackCursor: number[] = [];
+        let position = 0;
+        let reordered = false;
+        const place = (u: number, d: number): void => {
+            visited[u] = 1;
+            if (u !== position) {
+                reordered = true;
+            }
+            order[position++] = u;
+            depth[u] = d;
+        };
+        const visit = (root: number): void => {
+            place(root, 0);
+            stackNode.push(root);
+            stackCursor.push(this.rowPtr[root]);
+            while (stackNode.length > 0) {
+                const top = stackNode.length - 1;
+                const u = stackNode[top];
+                const cursor = stackCursor[top];
+                if (cursor >= this.rowPtr[u + 1]) {
+                    stackNode.pop();
+                    stackCursor.pop();
+                    continue;
+                }
+                stackCursor[top] = cursor + 1;
+                const v = this.children[cursor];
+                if (visited[v] === 1) {
+                    continue;
+                }
+                place(v, stackNode.length);
+                stackNode.push(v);
+                stackCursor.push(this.rowPtr[v]);
+            }
+        };
+        for (const root of this.roots) {
+            visit(root);
+        }
+        for (let u = 0; u < n; u++) {
+            if (visited[u] === 0) {
+                visit(u);
+            }
+        }
+        return { order, depth, reordered };
+    }
+
+    /**
+     * The nodes reachable from the roots by following child references.
+     * @returns how many nodes a traversal from the roots reaches
+     */
+    private reachableCount(): number {
+        const visited = new Uint8Array(this.nodeCount);
+        // every node is pushed at most once, so a stack of nodeCount entries never overflows
+        const stack = new Uint32Array(this.nodeCount);
+        let top = 0;
+        let count = 0;
+        for (const root of this.roots) {
+            visited[root] = 1;
+            count++;
+            stack[top++] = root;
+            while (top > 0) {
+                const u = stack[--top];
+                for (let k = this.rowPtr[u]; k < this.rowPtr[u + 1]; k++) {
+                    const v = this.children[k];
+                    if (visited[v] === 0) {
+                        visited[v] = 1;
+                        count++;
+                        stack[top++] = v;
+                    }
+                }
+            }
+        }
+        return count;
+    }
+}
+
+/**
+ * Build the children CSR of a snapshot (design section 7.1: a graph-io helper, not a core view).
+ * @param snapshot - the snapshot
+ * @param options - which column to read; the `parent` role, then `parents`, by default
+ * @returns the CSR; empty (every node a root) when the snapshot has no containment column
+ */
+export function childrenCsr(snapshot: GraphSnapshot, options: ChildrenOptions = {}): ChildrenCsr {
+    const column = resolveColumn(snapshot, options.column === undefined ? "auto" : options.column);
+    return childrenFromColumn(snapshot.nodeCount, column);
+}
+
+/**
+ * Build the children CSR over one containment column without a snapshot (an importer that holds
+ * the column before freezing, a test).
+ * @param nodeCount - the node count the references index into
+ * @param column - a u32 `parent`-shaped column, a list-of-u32 `parents`-shaped column, or null for none
+ * @returns the CSR
+ */
+export function childrenFromColumn(nodeCount: number, column: Column | null): ChildrenCsr {
+    const rowPtr = new Uint32Array(nodeCount + 1);
+    const parentCount = new Uint32Array(nodeCount);
+    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++;
+                return;
+            }
+            references.push(child, parent);
+            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}"`,
+            );
+        }
+    }
+    for (let u = 0; u < nodeCount; u++) {
+        rowPtr[u + 1] += rowPtr[u];
+    }
+    const children = new Uint32Array(rowPtr[nodeCount]);
+    const fill = rowPtr.slice(0, nodeCount);
+    // references were collected in ascending child order, so each parent's range fills ascending
+    for (let k = 0; k < references.length; k += 2) {
+        children[fill[references[k + 1]]++] = references[k];
+    }
+    return new ChildrenCsr(nodeCount, rowPtr, children, parentCount, dropped, column);
+}
+
+/**
+ * The column a ChildrenOptions selects.
+ * @param snapshot - the snapshot
+ * @param choice - the option value
+ * @returns the column, or null when the snapshot has none of that shape
+ */
+function resolveColumn(snapshot: GraphSnapshot, choice: ContainmentRole | Column | "auto" | null): Column | null {
+    if (typeof choice !== "string") {
+        return choice;
+    }
+    if (choice === "parent" || choice === "parents") {
+        return snapshot.nodes.byRole(choice);
+    }
+    return snapshot.nodes.byRole("parent") ?? snapshot.nodes.byRole("parents");
+}