@opencodehub/ingestion 0.1.0

package/dist/pipeline/phases/coverage-parsers/jacoco.js

@@ -0,0 +1,98 @@
+/**
+ * JaCoCo XML parser.
+ *
+ * JaCoCo's XML report tree:
+ *   <report>
+ *     <package name="com/foo">
+ *       <sourcefile name="Bar.java">
+ *         <line nr="12" mi="0" ci="3" mb="0" cb="0"/>
+ *         ...
+ *       </sourcefile>
+ *
+ * Per the JaCoCo DTD, `mi` is missed-instructions, `ci` is covered-
+ * instructions. We treat a line as covered when `ci > 0`. Total is the
+ * count of `<line>` elements for the sourcefile.
+ *
+ * Path assembly: the JaCoCo `name` attribute on `<package>` is slash-joined
+ * (e.g. `com/foo`), and the `<sourcefile>` name is the basename. We join
+ * them into a single POSIX path for graph matching. Callers may additionally
+ * set a project-source-root prefix via `options.sourceRoot` so the returned
+ * path aligns with the scan output.
+ */
+import { XMLParser } from "fast-xml-parser";
+import { canonLines, ratio } from "./types.js";
+export function parseJacoco(raw, _repoRoot, options = {}) {
+    const parser = new XMLParser({
+        ignoreAttributes: false,
+        attributeNamePrefix: "@_",
+        isArray: (name) => name === "package" || name === "sourcefile" || name === "line",
+    });
+    let parsed;
+    try {
+        parsed = parser.parse(raw);
+    }
+    catch {
+        return new Map();
+    }
+    const out = new Map();
+    const report = parsed?.report;
+    const packages = report?.package;
+    if (!Array.isArray(packages))
+        return out;
+    const sourceRoot = options.sourceRoot ?? "";
+    for (const pkg of packages) {
+        const pkgName = typeof pkg["@_name"] === "string"
+            ? String(pkg["@_name"])
+            : "";
+        const sourcefiles = pkg?.sourcefile;
+        if (!Array.isArray(sourcefiles))
+            continue;
+        for (const sf of sourcefiles) {
+            const sfName = sf["@_name"];
+            if (typeof sfName !== "string" || sfName.length === 0)
+                continue;
+            const lines = sf?.line;
+            if (!Array.isArray(lines) || lines.length === 0)
+                continue;
+            let covered = 0;
+            const coveredLines = [];
+            let total = 0;
+            for (const l of lines) {
+                const rec = l;
+                const nr = numberAttr(rec["@_nr"]);
+                const ci = numberAttr(rec["@_ci"]) ?? 0;
+                if (nr === undefined)
+                    continue;
+                total += 1;
+                if (ci > 0) {
+                    covered += 1;
+                    coveredLines.push(nr);
+                }
+            }
+            if (total === 0)
+                continue;
+            const relPath = joinPath(sourceRoot, pkgName, sfName);
+            out.set(relPath, {
+                filePath: relPath,
+                coveredLines: canonLines(coveredLines),
+                totalLines: total,
+                coveragePercent: ratio(covered, total),
+            });
+        }
+    }
+    return out;
+}
+function numberAttr(v) {
+    if (typeof v === "number")
+        return Number.isFinite(v) ? v : undefined;
+    if (typeof v === "string") {
+        const n = Number.parseInt(v, 10);
+        return Number.isInteger(n) ? n : undefined;
+    }
+    return undefined;
+}
+function joinPath(root, pkg, file) {
+    const segs = [root, pkg, file].filter((s) => s.length > 0);
+    return segs.join("/").replace(/\/+/g, "/");
+}
+//# sourceMappingURL=jacoco.js.map

package/dist/pipeline/phases/coverage-parsers/jacoco.js.map

@@ -0,0 +1 @@
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package/dist/pipeline/phases/coverage-parsers/lcov.d.ts

@@ -0,0 +1,21 @@
+/**
+ * lcov.info parser.
+ *
+ * lcov trace files are newline-delimited records grouped into per-file blocks:
+ *   SF:<source file path>
+ *   DA:<line>,<hit count>[,<md5>]
+ *   ...
+ *   end_of_record
+ *
+ * A file's covered-lines set is every DA line whose hit count > 0. We ignore
+ * the optional line-hash trailing field because it is irrelevant to the
+ * coverage ratio.
+ *
+ * Path resolution: lcov records may carry either relative or absolute paths.
+ * When the path is absolute and starts with `repoRoot`, we strip the prefix
+ * so the phase can match against scan output (repo-relative POSIX paths).
+ * Otherwise we pass the path through unchanged.
+ */
+import { type FileCoverage } from "./types.js";
+export declare function parseLcov(raw: string, repoRoot: string): ReadonlyMap<string, FileCoverage>;
+//# sourceMappingURL=lcov.d.ts.map

package/dist/pipeline/phases/coverage-parsers/lcov.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"lcov.d.ts","sourceRoot":"","sources":["../../../../src/pipeline/phases/coverage-parsers/lcov.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;GAiBG;AAGH,OAAO,EAAc,KAAK,YAAY,EAAS,MAAM,YAAY,CAAC;AAElE,wBAAgB,SAAS,CAAC,GAAG,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,WAAW,CAAC,MAAM,EAAE,YAAY,CAAC,CAsE1F"}

package/dist/pipeline/phases/coverage-parsers/lcov.js

@@ -0,0 +1,104 @@
+/**
+ * lcov.info parser.
+ *
+ * lcov trace files are newline-delimited records grouped into per-file blocks:
+ *   SF:<source file path>
+ *   DA:<line>,<hit count>[,<md5>]
+ *   ...
+ *   end_of_record
+ *
+ * A file's covered-lines set is every DA line whose hit count > 0. We ignore
+ * the optional line-hash trailing field because it is irrelevant to the
+ * coverage ratio.
+ *
+ * Path resolution: lcov records may carry either relative or absolute paths.
+ * When the path is absolute and starts with `repoRoot`, we strip the prefix
+ * so the phase can match against scan output (repo-relative POSIX paths).
+ * Otherwise we pass the path through unchanged.
+ */
+import path from "node:path";
+import { canonLines, ratio } from "./types.js";
+export function parseLcov(raw, repoRoot) {
+    const out = new Map();
+    let currentFile;
+    let covered = 0;
+    let total = 0;
+    let lines = [];
+    const reset = () => {
+        currentFile = undefined;
+        covered = 0;
+        total = 0;
+        lines = [];
+    };
+    for (const rawLine of raw.split(/\r?\n/)) {
+        const line = rawLine.trim();
+        if (line.length === 0)
+            continue;
+        if (line.startsWith("SF:")) {
+            currentFile = normalisePath(line.slice(3).trim(), repoRoot);
+            covered = 0;
+            total = 0;
+            lines = [];
+            continue;
+        }
+        if (line.startsWith("DA:")) {
+            if (currentFile === undefined)
+                continue;
+            const rest = line.slice(3);
+            const comma = rest.indexOf(",");
+            if (comma === -1)
+                continue;
+            const lineNum = Number.parseInt(rest.slice(0, comma), 10);
+            // Hit count may be followed by an extra `,md5`. Parse only up to the
+            // next comma or end-of-line.
+            const tail = rest.slice(comma + 1);
+            const nextComma = tail.indexOf(",");
+            const hitStr = nextComma === -1 ? tail : tail.slice(0, nextComma);
+            const hits = Number.parseInt(hitStr, 10);
+            if (!Number.isInteger(lineNum) || !Number.isInteger(hits))
+                continue;
+            total += 1;
+            if (hits > 0) {
+                covered += 1;
+                lines.push(lineNum);
+            }
+            continue;
+        }
+        if (line === "end_of_record") {
+            if (currentFile !== undefined && total > 0) {
+                const clean = canonLines(lines);
+                out.set(currentFile, {
+                    filePath: currentFile,
+                    coveredLines: clean,
+                    totalLines: total,
+                    coveragePercent: ratio(covered, total),
+                });
+            }
+            reset();
+        }
+    }
+    // Trailing block without `end_of_record` still matters — flush it.
+    if (currentFile !== undefined && total > 0) {
+        const clean = canonLines(lines);
+        out.set(currentFile, {
+            filePath: currentFile,
+            coveredLines: clean,
+            totalLines: total,
+            coveragePercent: ratio(covered, total),
+        });
+    }
+    return out;
+}
+function normalisePath(raw, repoRoot) {
+    // Always emit POSIX forward slashes so downstream matching against scan
+    // output (which uses POSIX separators) works on every platform.
+    const posix = raw.replace(/\\/g, "/");
+    if (!path.isAbsolute(posix))
+        return posix;
+    const rootPosix = repoRoot.replace(/\\/g, "/");
+    const prefix = rootPosix.endsWith("/") ? rootPosix : `${rootPosix}/`;
+    if (posix.startsWith(prefix))
+        return posix.slice(prefix.length);
+    return posix;
+}
+//# sourceMappingURL=lcov.js.map

package/dist/pipeline/phases/coverage-parsers/lcov.js.map

@@ -0,0 +1 @@
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package/dist/pipeline/phases/coverage-parsers/types.d.ts

@@ -0,0 +1,27 @@
+/**
+ * Shared coverage-parser contract.
+ *
+ * Every format-specific parser ingests a raw payload (plus the repo root,
+ * which the parser may need to resolve absolute → relative paths) and
+ * returns a map keyed by repo-relative POSIX file path. `FileCoverage`
+ * carries the minimal information needed to populate
+ * `FileNode.coveragePercent` + `FileNode.coveredLines` downstream.
+ *
+ * Invariants the phase relies on:
+ *   - `coveredLines` is sorted ascending with duplicates removed.
+ *   - `totalLines` is the count of instrumented lines (hit or miss), NOT
+ *     the file's raw line count — a partial-coverage report must still
+ *     compute a sensible ratio.
+ *   - `coveragePercent` is in `[0, 1]`. Parsers are free to return their
+ *     own ratio; the phase validates + clamps before writing to the graph.
+ */
+export interface FileCoverage {
+    readonly filePath: string;
+    readonly coveredLines: readonly number[];
+    readonly totalLines: number;
+    readonly coveragePercent: number;
+}
+/** Sort ascending + dedupe. Used by every parser before construction. */
+export declare function canonLines(raw: readonly number[]): readonly number[];
+export declare function ratio(covered: number, total: number): number;
+//# sourceMappingURL=types.d.ts.map

package/dist/pipeline/phases/coverage-parsers/types.d.ts.map

@@ -0,0 +1 @@
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package/dist/pipeline/phases/coverage-parsers/types.js

@@ -0,0 +1,39 @@
+/**
+ * Shared coverage-parser contract.
+ *
+ * Every format-specific parser ingests a raw payload (plus the repo root,
+ * which the parser may need to resolve absolute → relative paths) and
+ * returns a map keyed by repo-relative POSIX file path. `FileCoverage`
+ * carries the minimal information needed to populate
+ * `FileNode.coveragePercent` + `FileNode.coveredLines` downstream.
+ *
+ * Invariants the phase relies on:
+ *   - `coveredLines` is sorted ascending with duplicates removed.
+ *   - `totalLines` is the count of instrumented lines (hit or miss), NOT
+ *     the file's raw line count — a partial-coverage report must still
+ *     compute a sensible ratio.
+ *   - `coveragePercent` is in `[0, 1]`. Parsers are free to return their
+ *     own ratio; the phase validates + clamps before writing to the graph.
+ */
+/** Sort ascending + dedupe. Used by every parser before construction. */
+export function canonLines(raw) {
+    const seen = new Set();
+    for (const n of raw) {
+        if (Number.isInteger(n) && n > 0)
+            seen.add(n);
+    }
+    return [...seen].sort((a, b) => a - b);
+}
+export function ratio(covered, total) {
+    if (total <= 0)
+        return 0;
+    const r = covered / total;
+    if (!Number.isFinite(r))
+        return 0;
+    if (r < 0)
+        return 0;
+    if (r > 1)
+        return 1;
+    return r;
+}
+//# sourceMappingURL=types.js.map

package/dist/pipeline/phases/coverage-parsers/types.js.map

@@ -0,0 +1 @@
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package/dist/pipeline/phases/coverage.d.ts

@@ -0,0 +1,39 @@
+/**
+ * Coverage overlay phase.
+ *
+ * Consumes a coverage report produced by an external test runner and
+ * annotates each `File` node with:
+ *   - `coveragePercent`  — covered / total, clamped to [0, 1].
+ *   - `coveredLines`     — sorted, deduped list of covered 1-based line
+ *                          numbers.
+ *
+ * Format auto-detection looks at a fixed set of well-known paths (in
+ * priority order):
+ *   1. `coverage/lcov.info`                                 → lcov.
+ *   2. `lcov.info`                                          → lcov.
+ *   3. `coverage.xml`                                       → cobertura.
+ *   4. `build/reports/jacoco/test/jacocoTestReport.xml`     → jacoco.
+ *   5. `coverage.json`                                      → coverage.py.
+ *
+ * The phase is a silent no-op unless `options.coverage === true`; runs after
+ * `scan` and `profile` so a later framework-aware detection tier can refine
+ * search paths per-language if needed (e.g. pytest vs Jest).
+ *
+ * Failure posture: parse errors and missing reports log a warning via
+ * `ctx.onProgress` and still return a zero-result envelope — coverage is an
+ * optional overlay and must never crash analyze.
+ */
+import type { PipelinePhase } from "../types.js";
+export declare const COVERAGE_PHASE_NAME: "coverage";
+export type CoverageFormat = "lcov" | "cobertura" | "jacoco" | "coverage-py";
+export interface CoverageOutput {
+    readonly ran: boolean;
+    readonly format?: CoverageFormat;
+    readonly reportPath?: string;
+    /** Count of File nodes that received a coverage annotation. */
+    readonly annotatedFileCount: number;
+    /** Count of entries in the report that did not match any File node. */
+    readonly unmatchedFileCount: number;
+}
+export declare const coveragePhase: PipelinePhase<CoverageOutput>;
+//# sourceMappingURL=coverage.d.ts.map

package/dist/pipeline/phases/coverage.d.ts.map

@@ -0,0 +1 @@
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package/dist/pipeline/phases/coverage.js

@@ -0,0 +1,154 @@
+/**
+ * Coverage overlay phase.
+ *
+ * Consumes a coverage report produced by an external test runner and
+ * annotates each `File` node with:
+ *   - `coveragePercent`  — covered / total, clamped to [0, 1].
+ *   - `coveredLines`     — sorted, deduped list of covered 1-based line
+ *                          numbers.
+ *
+ * Format auto-detection looks at a fixed set of well-known paths (in
+ * priority order):
+ *   1. `coverage/lcov.info`                                 → lcov.
+ *   2. `lcov.info`                                          → lcov.
+ *   3. `coverage.xml`                                       → cobertura.
+ *   4. `build/reports/jacoco/test/jacocoTestReport.xml`     → jacoco.
+ *   5. `coverage.json`                                      → coverage.py.
+ *
+ * The phase is a silent no-op unless `options.coverage === true`; runs after
+ * `scan` and `profile` so a later framework-aware detection tier can refine
+ * search paths per-language if needed (e.g. pytest vs Jest).
+ *
+ * Failure posture: parse errors and missing reports log a warning via
+ * `ctx.onProgress` and still return a zero-result envelope — coverage is an
+ * optional overlay and must never crash analyze.
+ */
+import { promises as fs } from "node:fs";
+import path from "node:path";
+import { parseCobertura } from "./coverage-parsers/cobertura.js";
+import { parseCoveragePy } from "./coverage-parsers/coverage-py.js";
+import { parseJacoco } from "./coverage-parsers/jacoco.js";
+import { parseLcov } from "./coverage-parsers/lcov.js";
+import { PROFILE_PHASE_NAME } from "./profile.js";
+import { SCAN_PHASE_NAME } from "./scan.js";
+import { STRUCTURE_PHASE_NAME } from "./structure.js";
+export const COVERAGE_PHASE_NAME = "coverage";
+/**
+ * Detection table, sorted by priority. Each entry names the on-disk probe
+ * path (relative to repoPath) plus its dispatch identifier.
+ */
+const CANDIDATES = [
+    { rel: "coverage/lcov.info", format: "lcov" },
+    { rel: "lcov.info", format: "lcov" },
+    { rel: "coverage.xml", format: "cobertura" },
+    { rel: "build/reports/jacoco/test/jacocoTestReport.xml", format: "jacoco" },
+    { rel: "coverage.json", format: "coverage-py" },
+];
+export const coveragePhase = {
+    name: COVERAGE_PHASE_NAME,
+    deps: [SCAN_PHASE_NAME, PROFILE_PHASE_NAME, STRUCTURE_PHASE_NAME],
+    async run(ctx) {
+        if (ctx.options.coverage !== true) {
+            return { ran: false, annotatedFileCount: 0, unmatchedFileCount: 0 };
+        }
+        return runCoverage(ctx);
+    },
+};
+async function runCoverage(ctx) {
+    const detected = await detectReport(ctx.repoPath);
+    if (detected === undefined) {
+        ctx.onProgress?.({
+            phase: COVERAGE_PHASE_NAME,
+            kind: "warn",
+            message: "coverage: enabled but no report found (looked for coverage/lcov.info, lcov.info, coverage.xml, build/reports/jacoco/test/jacocoTestReport.xml, coverage.json)",
+        });
+        return { ran: true, annotatedFileCount: 0, unmatchedFileCount: 0 };
+    }
+    let raw;
+    try {
+        raw = await fs.readFile(detected.absPath, "utf8");
+    }
+    catch (err) {
+        ctx.onProgress?.({
+            phase: COVERAGE_PHASE_NAME,
+            kind: "warn",
+            message: `coverage: failed to read ${detected.relPath}: ${err.message}`,
+        });
+        return {
+            ran: true,
+            format: detected.format,
+            reportPath: detected.relPath,
+            annotatedFileCount: 0,
+            unmatchedFileCount: 0,
+        };
+    }
+    const parsed = dispatchParser(detected.format, raw, ctx.repoPath);
+    // Apply parsed coverage to matching File nodes. Track both sides so
+    // operators can surface mismatches (e.g. path-root drift in jacoco reports).
+    const fileNodesByPath = new Map();
+    for (const n of ctx.graph.nodes()) {
+        if (n.kind === "File")
+            fileNodesByPath.set(n.filePath, n);
+    }
+    let annotated = 0;
+    let unmatched = 0;
+    // Sort by path so graph mutation order stays deterministic.
+    const sortedPaths = [...parsed.keys()].sort();
+    for (const filePath of sortedPaths) {
+        const cov = parsed.get(filePath);
+        if (cov === undefined)
+            continue;
+        const fileNode = fileNodesByPath.get(filePath);
+        if (fileNode === undefined) {
+            unmatched += 1;
+            continue;
+        }
+        const merged = {
+            ...fileNode,
+            coveragePercent: cov.coveragePercent,
+            coveredLines: cov.coveredLines,
+        };
+        ctx.graph.addNode(merged);
+        annotated += 1;
+    }
+    ctx.onProgress?.({
+        phase: COVERAGE_PHASE_NAME,
+        kind: "note",
+        message: `coverage: ${detected.format} report → ${annotated} files annotated, ${unmatched} unmatched`,
+    });
+    return {
+        ran: true,
+        format: detected.format,
+        reportPath: detected.relPath,
+        annotatedFileCount: annotated,
+        unmatchedFileCount: unmatched,
+    };
+}
+async function detectReport(repoRoot) {
+    for (const cand of CANDIDATES) {
+        const abs = path.join(repoRoot, cand.rel);
+        try {
+            const stat = await fs.stat(abs);
+            if (stat.isFile()) {
+                return { format: cand.format, absPath: abs, relPath: cand.rel };
+            }
+        }
+        catch {
+            // Missing file — try next candidate.
+        }
+    }
+    return undefined;
+}
+function dispatchParser(format, raw, repoRoot) {
+    switch (format) {
+        case "lcov":
+            return parseLcov(raw, repoRoot);
+        case "cobertura":
+            return parseCobertura(raw, repoRoot);
+        case "jacoco":
+            return parseJacoco(raw, repoRoot);
+        case "coverage-py":
+            return parseCoveragePy(raw, repoRoot);
+    }
+}
+//# sourceMappingURL=coverage.js.map

package/dist/pipeline/phases/coverage.js.map

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package/dist/pipeline/phases/cross-file.d.ts

@@ -0,0 +1,40 @@
+/**
+ * Cross-file phase — upgrade low-confidence CALLS edges after every file
+ * has contributed its exports.
+ *
+ * At parse time every call site is resolved through the three-tier
+ * {@link resolve} helper (same-file → import-scoped → global). A call that
+ * only matches at the global tier is emitted with confidence 0.5 because we
+ * cannot prove which declaration the call targets. Once the whole repo has
+ * been parsed we can do better: if the caller file imports a module that
+ * now exports a matching identifier, the call is *import-scoped* in
+ * hindsight and deserves confidence 0.9.
+ *
+ * Strategy:
+ *  1. Build a directed import graph of repository files (skip external npm
+ *     specifiers — they were already dropped at parse time).
+ *  2. Run Tarjan's SCC algorithm on that graph. Circular imports collapse
+ *     into a single component; we still visit every file in a component.
+ *  3. Topologically sort the condensation so dependencies of file F are
+ *     processed before F. Inside a component, order by filename for
+ *     determinism.
+ *  4. For each file, walk every low-confidence (0.5) CALLS edge. Re-run
+ *     the resolution strategy with the symbol index. If it now produces a
+ *     higher-tier candidate, re-add the edge with the better confidence;
+ *     the graph's dedupe keeps the stronger edge.
+ *
+ * Determinism: SCC discovery order is driven by sorted file iteration, and
+ * condensation order is produced by Kahn's algorithm with a lexical tie
+ * break. Two runs on the same repo produce identical edge upgrades.
+ */
+import type { PipelinePhase } from "../types.js";
+export declare const CROSS_FILE_PHASE_NAME = "crossFile";
+export interface CrossFileOutput {
+    readonly upgradedCallsCount: number;
+    readonly unresolvedRemaining: number;
+    readonly sccCount: number;
+    /** File SCCs with more than five members — typically cyclic import webs. */
+    readonly largeSccs: readonly string[];
+}
+export declare const crossFilePhase: PipelinePhase<CrossFileOutput>;
+//# sourceMappingURL=cross-file.d.ts.map

package/dist/pipeline/phases/cross-file.d.ts.map

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