@graphty/graph-io 0.3.25 → 0.3.27

package/dist/src/common/compare.d.ts

@@ -0,0 +1,81 @@
+/**
+ * Compare two snapshots node by node, edge by edge and value by value, for testing a format plugin:
+ * read a file, save it, read the saved file back, and compare. Every difference should be one that
+ * the save's checkExport() notes announced.
+ */
+import { type GraphSnapshot } from "@graphty/graph-format";
+/**
+ * One difference between two snapshots.
+ * @category Plugin helpers
+ */
+export interface SnapshotDiff {
+    /** Where: "directed", "ids[3]", "nodes.label[4]", "edges.weight[0]", "extensions.temporal:node:price.rowCount"... */
+    readonly path: string;
+    /** The value in the expected snapshot. */
+    readonly expected: unknown;
+    /** The value in the actual snapshot. */
+    readonly actual: unknown;
+    /** A one-line description. */
+    readonly message: string;
+}
+/**
+ * What compareSnapshots() compares.
+ * @category Plugin helpers
+ */
+export interface CompareOptions {
+    /** Column names to skip in every table (format-owned helpers an exporter adds, for instance). */
+    readonly ignoreColumns?: readonly string[] | undefined;
+    /** Column roles to skip in every table. */
+    readonly ignoreRoles?: readonly string[] | undefined;
+    /** Whether the actual snapshot may hold columns the expected one lacks (default true). */
+    readonly allowExtraColumns?: boolean | undefined;
+    /** Whether dtypes must match (default true); false compares values only. */
+    readonly dtypes?: boolean | undefined;
+    /** Whether roles must match (default true). */
+    readonly roles?: boolean | undefined;
+    /** Whether origin.type must match (default false). */
+    readonly originType?: boolean | undefined;
+    /** Absolute tolerance for numeric cell and weight comparisons (default 0: Object.is). */
+    readonly tolerance?: number | undefined;
+    /** Whether the explicit / defaulted status of weights must match (default true). */
+    readonly weightExplicitness?: boolean | undefined;
+    /** Whether extension tables are compared (default true). */
+    readonly extensions?: boolean | undefined;
+    /** Stop after this many differences (default 50). */
+    readonly limit?: number | undefined;
+}
+/**
+ * Compare two snapshots: the direction, the node ids, the edges, the weights and every attribute
+ * value. Use it to test a format plugin: read a file, save it in your format, read the saved file
+ * back, and compare the two graphs. Each difference has a `path` ("ids[3]", "nodes.label[4]",
+ * "edges.weight[0]") and a one-line `message`; every one should match a note that `checkExport()`
+ * returned for the save.
+ * @example
+ * ```ts
+ * const notes = checkExport(original, "pairs");
+ * const readBack = (await importGraph(await exportGraphToString(original, "pairs"), { format: "pairs" })).snapshot;
+ * console.log(describeDiffs(compareSnapshots(original, readBack)));
+ * ```
+ * @param expected - the graph you saved
+ * @param actual - the graph read back from the saved file
+ * @param options - what to compare
+ * @returns the differences, empty when the graphs are the same
+ * @category Plugin helpers
+ */
+export declare function compareSnapshots(expected: GraphSnapshot, actual: GraphSnapshot, options?: CompareOptions): SnapshotDiff[];
+/**
+ * Deep equality with a numeric tolerance (for the tests).
+ * @param e - expected
+ * @param a - actual
+ * @param tolerance - absolute tolerance for numbers
+ * @returns true when equal
+ */
+export declare function valuesEqual(e: unknown, a: unknown, tolerance: number): boolean;
+/**
+ * The differences compareSnapshots() found, one per line, for printing.
+ * @param diffs - the differences
+ * @returns one line per difference, "no differences" when empty
+ * @category Plugin helpers
+ */
+export declare function describeDiffs(diffs: readonly SnapshotDiff[]): string;
+//# sourceMappingURL=compare.d.ts.map

package/dist/src/common/compare.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/common/compare.js

@@ -0,0 +1,394 @@
+/**
+ * Compare two snapshots node by node, edge by edge and value by value, for testing a format plugin:
+ * read a file, save it, read the saved file back, and compare. Every difference should be one that
+ * the save's checkExport() notes announced.
+ */
+/**
+ * Compare two snapshots: the direction, the node ids, the edges, the weights and every attribute
+ * value. Use it to test a format plugin: read a file, save it in your format, read the saved file
+ * back, and compare the two graphs. Each difference has a `path` ("ids[3]", "nodes.label[4]",
+ * "edges.weight[0]") and a one-line `message`; every one should match a note that `checkExport()`
+ * returned for the save.
+ * @example
+ * ```ts
+ * const notes = checkExport(original, "pairs");
+ * const readBack = (await importGraph(await exportGraphToString(original, "pairs"), { format: "pairs" })).snapshot;
+ * console.log(describeDiffs(compareSnapshots(original, readBack)));
+ * ```
+ * @param expected - the graph you saved
+ * @param actual - the graph read back from the saved file
+ * @param options - what to compare
+ * @returns the differences, empty when the graphs are the same
+ * @category Plugin helpers
+ */
+export function compareSnapshots(expected, actual, options = {}) {
+    const diffs = [];
+    const limit = options.limit ?? 50;
+    const tolerance = options.tolerance ?? 0;
+    const ctx = {
+        options,
+        diff: (path, e, a, message) => {
+            diffs.push({
+                path,
+                expected: e,
+                actual: a,
+                message: message ?? `${path}: expected ${show(e)}, got ${show(a)}`,
+            });
+            if (diffs.length >= limit) {
+                throw new LimitReached();
+            }
+        },
+        same: (e, a) => valuesEqual(e, a, tolerance),
+    };
+    try {
+        compareGraphs(expected, actual, ctx);
+    }
+    catch (err) {
+        if (!(err instanceof LimitReached)) {
+            throw err;
+        }
+    }
+    return diffs;
+}
+/** Thrown by the recorder once the limit of differences is reached, to end the walk. */
+class LimitReached extends Error {
+}
+/**
+ * Compare two snapshots step by step: the counts, the ids, the topology, the weights, the tables.
+ * @param expected - the reference
+ * @param actual - the snapshot under test
+ * @param ctx - the comparison context
+ */
+function compareGraphs(expected, actual, ctx) {
+    const { diff } = ctx;
+    if (expected.directed !== actual.directed) {
+        diff("directed", expected.directed, actual.directed);
+    }
+    if (expected.nodeCount !== actual.nodeCount) {
+        diff("nodeCount", expected.nodeCount, actual.nodeCount);
+    }
+    if (expected.edgeCount !== actual.edgeCount) {
+        diff("edgeCount", expected.edgeCount, actual.edgeCount);
+    }
+    compareIds(expected, actual, diff);
+    if (expected.nodeCount !== actual.nodeCount || expected.edgeCount !== actual.edgeCount) {
+        return;
+    }
+    compareTopology(expected, actual, diff);
+    compareWeights(expected, actual, ctx);
+    compareTables("nodes", expected.nodes, actual.nodes, ctx);
+    compareTables("edges", expected.edges, actual.edges, ctx);
+    compareTables("graph", expected.graph, actual.graph, ctx);
+    if (ctx.options.extensions !== false) {
+        compareExtensions(expected, actual, ctx);
+    }
+}
+/**
+ * Compare the node ids in index order.
+ * @param expected - the reference
+ * @param actual - the snapshot under test
+ * @param diff - the recorder
+ */
+function compareIds(expected, actual, diff) {
+    const expectedIds = expected.ids.toArray();
+    const actualIds = actual.ids.toArray();
+    const n = Math.min(expectedIds.length, actualIds.length);
+    for (let i = 0; i < n; i++) {
+        if (!Object.is(expectedIds[i], actualIds[i])) {
+            diff(`ids[${i}]`, expectedIds[i], actualIds[i]);
+        }
+    }
+}
+/**
+ * Compare the topology: the CSR arrays (identical when node order and edge order survived), then the
+ * orientation of every logical edge.
+ * @param expected - the reference
+ * @param actual - the snapshot under test, with as many nodes and edges
+ * @param diff - the recorder
+ */
+function compareTopology(expected, actual, diff) {
+    if (!typedEqual(expected.rowPtr, actual.rowPtr)) {
+        diff("rowPtr", expected.rowPtr, actual.rowPtr, "rowPtr differs");
+    }
+    if (!typedEqual(expected.colIdx, actual.colIdx)) {
+        diff("colIdx", expected.colIdx, actual.colIdx, "colIdx differs");
+    }
+    const el = expected.edgeList();
+    const al = actual.edgeList();
+    for (let e = 0; e < expected.edgeCount; e++) {
+        if (el.src[e] !== al.src[e] || el.dst[e] !== al.dst[e]) {
+            diff(`edge[${e}]`, `${el.src[e]}->${el.dst[e]}`, `${al.src[e]}->${al.dst[e]}`);
+        }
+    }
+}
+/**
+ * Compare the weights of two snapshots: the exact weight column when both have one, the 32-bit
+ * weights otherwise.
+ * @param expected - the reference
+ * @param actual - the snapshot under test
+ * @param ctx - the comparison context
+ */
+function compareWeights(expected, actual, ctx) {
+    if (expected.flags.weighted !== actual.flags.weighted) {
+        ctx.diff("flags.weighted", expected.flags.weighted, actual.flags.weighted);
+        return;
+    }
+    if (!expected.flags.weighted) {
+        return;
+    }
+    const eShadow = expected.edges.byRole("weight");
+    const aShadow = actual.edges.byRole("weight");
+    if (eShadow !== null && aShadow !== null) {
+        compareExactWeights(expected.edgeCount, eShadow, aShadow, ctx);
+        return;
+    }
+    if (ctx.options.weightExplicitness !== false && (eShadow === null) !== (aShadow === null)) {
+        ctx.diff("weightColumn", eShadow !== null, aShadow !== null, "one snapshot has a role-weight column, the other does not");
+    }
+    const ew = expected.edgeList().weights;
+    const aw = actual.edgeList().weights;
+    for (let e = 0; e < expected.edgeCount; e++) {
+        const ev = ew === null ? 1 : ew[e];
+        const av = aw === null ? 1 : aw[e];
+        if (!ctx.same(ev, av)) {
+            ctx.diff(`weight[${e}]`, ev, av);
+        }
+    }
+}
+/**
+ * Compare the exact weight columns of two snapshots: which edges have an explicit weight, and its value.
+ * @param edgeCount - the number of edges
+ * @param expected - the reference's weight column
+ * @param actual - the weight column under test
+ * @param ctx - the comparison context
+ */
+function compareExactWeights(edgeCount, expected, actual, ctx) {
+    for (let e = 0; e < edgeCount; e++) {
+        const eSet = expected.isSet(e);
+        const aSet = actual.isSet(e);
+        if (ctx.options.weightExplicitness !== false && eSet !== aSet) {
+            ctx.diff(`weightExplicit[${e}]`, eSet, aSet);
+        }
+        else if (eSet && aSet && !ctx.same(expected.value(e), actual.value(e))) {
+            ctx.diff(`weight[${e}]`, expected.value(e), actual.value(e));
+        }
+    }
+}
+/**
+ * Compare the extension tables: which exist, their row counts and their columns.
+ * @param expected - the reference
+ * @param actual - the snapshot under test
+ * @param ctx - the comparison context
+ */
+function compareExtensions(expected, actual, ctx) {
+    for (const [name, table] of expected.extensions) {
+        const other = actual.extensions.get(name);
+        if (other === undefined) {
+            ctx.diff(`extensions.${name}`, "present", "absent");
+        }
+        else if (table.rowCount === other.rowCount) {
+            compareTables(`extensions.${name}`, table, other, ctx);
+        }
+        else {
+            ctx.diff(`extensions.${name}.rowCount`, table.rowCount, other.rowCount);
+        }
+    }
+    if (ctx.options.allowExtraColumns === false) {
+        for (const name of actual.extensions.keys()) {
+            if (!expected.extensions.has(name)) {
+                ctx.diff(`extensions.${name}`, "absent", "present");
+            }
+        }
+    }
+}
+/**
+ * Compare the columns of one table.
+ * @param label - the table name for paths
+ * @param expected - the reference table
+ * @param actual - the table under test
+ * @param ctx - the comparison context
+ */
+function compareTables(label, expected, actual, ctx) {
+    const ignoreNames = new Set(ctx.options.ignoreColumns ?? []);
+    const ignoreRoles = new Set(ctx.options.ignoreRoles ?? []);
+    // the role-weight shadow column is compared by the weights step, not as a declared column
+    const skip = (column) => {
+        const { name, role } = column.meta;
+        return (ignoreNames.has(name) ||
+            (role !== null && (ignoreRoles.has(role) || (label === "edges" && role === "weight"))));
+    };
+    for (const column of expected) {
+        if (skip(column)) {
+            continue;
+        }
+        const path = `${label}.${column.meta.name}`;
+        const other = actual.get(column.meta.name);
+        if (other === null) {
+            ctx.diff(path, "present", "absent", `${path}: column missing after round trip`);
+        }
+        else {
+            compareColumn(path, column, other, ctx);
+        }
+    }
+    if (ctx.options.allowExtraColumns === false) {
+        for (const column of actual) {
+            if (!skip(column) && expected.get(column.meta.name) === null) {
+                const path = `${label}.${column.meta.name}`;
+                ctx.diff(path, "absent", "present", `${path}: extra column after round trip`);
+            }
+        }
+    }
+}
+/**
+ * Compare one column: its declaration, then every cell.
+ * @param path - the column's path for messages
+ * @param column - the reference column
+ * @param other - the column under test
+ * @param ctx - the comparison context
+ */
+function compareColumn(path, column, other, ctx) {
+    compareDeclaration(path, column, other, ctx);
+    if (column.length !== other.length) {
+        ctx.diff(`${path}.length`, column.length, other.length);
+        return;
+    }
+    for (let r = 0; r < column.length; r++) {
+        const eSet = column.isSet(r);
+        const aSet = other.isSet(r);
+        if (eSet !== aSet) {
+            ctx.diff(`${path}[${r}]`, eSet ? column.value(r) : undefined, aSet ? other.value(r) : undefined);
+        }
+        else if (eSet) {
+            const ev = cellValue(column, r);
+            const av = cellValue(other, r);
+            if (!ctx.same(ev, av)) {
+                ctx.diff(`${path}[${r}]`, ev, av);
+            }
+        }
+    }
+}
+/**
+ * Compare what two columns declare: dtype, item dtype, components, role and origin type, as the
+ * options ask.
+ * @param path - the column's path for messages
+ * @param column - the reference column
+ * @param other - the column under test
+ * @param ctx - the comparison context
+ */
+function compareDeclaration(path, column, other, ctx) {
+    const { options, diff } = ctx;
+    const e = column.meta;
+    const a = other.meta;
+    if (options.dtypes !== false) {
+        for (const key of ["dtype", "itemDtype", "components"]) {
+            if (e[key] !== a[key]) {
+                diff(`${path}.${key}`, e[key], a[key]);
+            }
+        }
+    }
+    if (options.roles !== false && e.role !== a.role) {
+        diff(`${path}.role`, e.role, a.role);
+    }
+    const eType = e.origin?.type ?? null;
+    const aType = a.origin?.type ?? null;
+    if (options.originType === true && eType !== aType) {
+        diff(`${path}.origin.type`, eType, aType);
+    }
+}
+/**
+ * The comparable value of a set cell: list rows through sliceOf, json rows through values, the
+ * typed accessor otherwise (a components > 1 subarray becomes a plain array).
+ * @param column - the column
+ * @param row - the row
+ * @returns the value
+ */
+function cellValue(column, row) {
+    switch (column.dtype) {
+        case "list":
+            return [...column.sliceOf(row)];
+        case "json":
+            return column.values[row];
+        default: {
+            const value = column.value(row);
+            return ArrayBuffer.isView(value) ? Array.from(value) : value;
+        }
+    }
+}
+/**
+ * Deep equality with a numeric tolerance (for the tests).
+ * @param e - expected
+ * @param a - actual
+ * @param tolerance - absolute tolerance for numbers
+ * @returns true when equal
+ */
+export function valuesEqual(e, a, tolerance) {
+    if (typeof e === "number" && typeof a === "number") {
+        if (Object.is(e, a)) {
+            return true;
+        }
+        return Number.isFinite(e) && Number.isFinite(a) && Math.abs(e - a) <= tolerance;
+    }
+    if (Array.isArray(e) || ArrayBuffer.isView(e)) {
+        const ea = Array.from(e);
+        if (!(Array.isArray(a) || ArrayBuffer.isView(a))) {
+            return false;
+        }
+        const aa = Array.from(a);
+        return ea.length === aa.length && ea.every((v, i) => valuesEqual(v, aa[i], tolerance));
+    }
+    if (typeof e === "object" && e !== null && typeof a === "object" && a !== null) {
+        const eo = e;
+        const ao = a;
+        const keys = Object.keys(eo);
+        if (keys.length !== Object.keys(ao).length) {
+            return false;
+        }
+        return keys.every((k) => Object.hasOwn(ao, k) && valuesEqual(eo[k], ao[k], tolerance));
+    }
+    return Object.is(e, a);
+}
+/**
+ * Element-wise equality of two typed arrays.
+ * @param a - one array
+ * @param b - the other
+ * @returns true when same length and contents
+ */
+function typedEqual(a, b) {
+    if (a.length !== b.length) {
+        return false;
+    }
+    for (let i = 0; i < a.length; i++) {
+        if (a[i] !== b[i]) {
+            return false;
+        }
+    }
+    return true;
+}
+/**
+ * A short text of a value for messages.
+ * @param v - the value
+ * @returns JSON when possible, else String()
+ */
+function show(v) {
+    if (ArrayBuffer.isView(v)) {
+        const items = Array.from(v);
+        return `[${items.slice(0, 8).join(", ")}${items.length > 8 ? ", ..." : ""}]`;
+    }
+    try {
+        const text = JSON.stringify(v);
+        return text ?? String(v);
+    }
+    catch {
+        return String(v);
+    }
+}
+/**
+ * The differences compareSnapshots() found, one per line, for printing.
+ * @param diffs - the differences
+ * @returns one line per difference, "no differences" when empty
+ * @category Plugin helpers
+ */
+export function describeDiffs(diffs) {
+    return diffs.length === 0 ? "no differences" : diffs.map((d) => `  - ${d.message}`).join("\n");
+}
+//# sourceMappingURL=compare.js.map

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

@@ -0,0 +1 @@
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package/dist/src/common/cx-export.d.ts

@@ -0,0 +1,123 @@
+/**
+ * The exporter machinery CX version 1 and CX2 share (design/graph-io/cytoscape-and-obo/design.md
+ * sections 1.2 and 1.3): integer node ids (safe integers, or the digits of an integer beyond 2^53
+ * written raw), sanitizeIds "mangle" renumbering, edge ids from the id role column, the declared
+ * type of a column, the direction notes (every CX edge is directed) and the JSON writer that keeps
+ * -0 and raw big integers.
+ */
+import { type Column, GraphFormatError, type GraphSnapshot, type NodeId } from "@graphty/graph-format";
+import { type LossNote } from "../types.js";
+import { type PairFolding } from "./direction.js";
+import { type ResolvedExportOptions } from "./options.js";
+/**
+ * Records a loss note.
+ * @category Plugin helpers
+ */
+export type CxNoteFn = (code: string, message: string, column?: string | null, count?: number | null) => void;
+/**
+ * The node ids as written: the original, a renumbered one, or a raw big integer.
+ * @category Plugin helpers
+ */
+export interface WrittenIds {
+    /** How many ids were renumbered (sanitizeIds "mangle"). */
+    readonly changed: number;
+    /**
+     * The written id of a node.
+     * @param i - the node index
+     * @returns a number, or a raw string for a big integer
+     */
+    idAt(i: number): NodeId;
+    /**
+     * Whether a node was renumbered.
+     * @param i - the node index
+     * @returns true when its original goes into graphty:originalId
+     */
+    isChanged(i: number): boolean;
+    /**
+     * The original id of a node.
+     * @param i - the node index
+     * @returns the snapshot's id
+     */
+    originalAt(i: number): NodeId;
+}
+/**
+ * The `idCounter` of the node ids as written (the largest id plus one, NDEx's next free id).
+ * @param ids - the written ids
+ * @param count - the node count
+ * @returns the counter: a number, or a raw big integer for stringify()
+ * @category Plugin helpers
+ */
+export declare function nextNodeId(ids: WrittenIds, count: number): NodeId;
+/**
+ * The id notes and the written ids of a CX export: E_ID_CHARSET (export() throws) or
+ * W_ID_MANGLED for the ids that are not integers.
+ * @param snapshot - the snapshot
+ * @param common - the resolved common options
+ * @param format - the format's display name
+ * @param attribute - the attribute the originals are kept in
+ * @param note - records a note
+ * @returns the ids, or the error export() throws
+ * @category Plugin helpers
+ */
+export declare function planNodeIds(snapshot: GraphSnapshot, common: ResolvedExportOptions, format: string, attribute: string, note: CxNoteFn): WrittenIds | GraphFormatError;
+/**
+ * The declared CX type of a column: string / double / long / integer / boolean or a list of one;
+ * a json column (and a list of json items) is a string holding JSON text.
+ * @param column - the column
+ * @returns the type text
+ * @category Plugin helpers
+ */
+export declare function declaredType(column: Column): string;
+/**
+ * Count the positions with a non-finite x or y.
+ * @param position - the position column
+ * @returns the count
+ * @category Plugin helpers
+ */
+export declare function nonFinitePositions(position: Column): number;
+/**
+ * The edge ids to write: the id role column's values when they are distinct safe integers, next
+ * unused integers for edges without one (W_EDGE_IDS_GENERATED).
+ * @param snapshot - the snapshot
+ * @param note - records a note
+ * @returns one id per edge
+ * @category Plugin helpers
+ */
+export declare function planEdgeIds(snapshot: GraphSnapshot, note: CxNoteFn): number[];
+/**
+ * The direction notes: every CX edge is directed, so an undirected snapshot (or the undirected
+ * pairs of a mixed one, folded under onMixedDirection) is written directed, and a mutual pair as
+ * two edges without its mark.
+ * @param snapshot - the snapshot
+ * @param folding - the pair folding
+ * @param common - the resolved common options
+ * @param undirectedCode - the format's "undirected written as directed" code
+ * @param note - records a note
+ * @category Plugin helpers
+ */
+export declare function directionNotes(snapshot: GraphSnapshot, folding: PairFolding, common: ResolvedExportOptions, undirectedCode: string, note: CxNoteFn): void;
+/**
+ * The note recorder of a plan and its notes.
+ * @returns the notes and the recorder
+ * @category Plugin helpers
+ */
+export declare function noteList(): {
+    notes: LossNote[];
+    note: CxNoteFn;
+};
+/**
+ * The JSON text of a value, keeping -0 and writing the raw big-integer ids of idAt() as numbers.
+ * @param value - the value
+ * @returns the text
+ * @category Plugin helpers
+ */
+export declare function stringify(value: unknown): string;
+/**
+ * The text of one aspect block, element by element.
+ * @param aspect - the aspect name
+ * @param elements - the JSON texts of its elements
+ * @yields the block's text
+ * @returns nothing
+ */
+export declare function aspectBlock(aspect: string, elements: Iterable<string>): Generator<string, void, undefined>;
+//# sourceMappingURL=cx-export.d.ts.map

package/dist/src/common/cx-export.d.ts.map

@@ -0,0 +1 @@
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