From 5d93389f9cb3536e4596d7d14814a83d5d321cb0 Mon Sep 17 00:00:00 2001 From: Jackson Antonio do Prado Lima Date: Fri, 16 Oct 2026 22:35:48 -0300 Subject: [PATCH 1/6] feat: add bounded controlled Java fault matrix --- README.md | 2 +- .../apache-cli51-junit3-arm64-v1.json | 1 + .../apache-codec65-junit3-arm64-v1.json | 1 + .../java-real-fault-matrix-arm64-v1.json | 1 + coleman/transports/junit_matrix.py | 319 +++++++++++ coleman/transports/junit_matrix_contracts.py | 173 ++++++ docs/benchmark-corpus.md | 5 + docs/index.md | 6 + docs/java-fault-matrix.md | 240 ++++++++ docs/junit-source-capture.md | 10 +- docs/releases/4.10.0.md | 59 ++ docs/roadmap.md | 8 + llms.txt | 342 +++++++++++- .../fixtures/junit-matrix-owned-v1.json | 1 + .../junit-matrix-receipt-owned-v1.json | 1 + tests/corpus/test_installed_junit_matrix.py | 124 +++++ tests/corpus/test_junit_matrix.py | 519 ++++++++++++++++++ zensical.toml | 2 + 18 files changed, 1808 insertions(+), 6 deletions(-) create mode 100644 coleman/corpus/resources/apache-cli51-junit3-arm64-v1.json create mode 100644 coleman/corpus/resources/apache-codec65-junit3-arm64-v1.json create mode 100644 coleman/corpus/resources/java-real-fault-matrix-arm64-v1.json create mode 100644 coleman/transports/junit_matrix.py create mode 100644 coleman/transports/junit_matrix_contracts.py create mode 100644 docs/java-fault-matrix.md create mode 100644 docs/releases/4.10.0.md create mode 100644 tests/corpus/fixtures/junit-matrix-owned-v1.json create mode 100644 tests/corpus/fixtures/junit-matrix-receipt-owned-v1.json create mode 100644 tests/corpus/test_installed_junit_matrix.py create mode 100644 tests/corpus/test_junit_matrix.py diff --git a/README.md b/README.md index b2819781..292c28f1 100644 --- a/README.md +++ b/README.md @@ -661,7 +661,7 @@ controlled reproductions and empirical benchmark corpora have different roles: | **Druid and Retrofit** | Bundled native/contextual Parquet examples, native runner and [descriptive profiles](docs/benchmark-corpus.md#local-profiles-and-the-first-diversity-matrix-44) | Runnable legacy experiments. Source terms, duration units and outcome availability still need corpus admission evidence. | | **Dune and its variants** | Bundled native Parquet, WTS/VTS workflows and [variant-aware inventory](docs/benchmark-corpus.md) | Runnable HCS examples. Variants/context files may share executions; broad HCS benchmark admission remains unfinished. | | **RTPTorrent / HikariCP** | [Verified ZIP64 → full analytical history → native-compatible Parquet → replay/recovery](docs/rtptorrent-parquet-etl.md) | Available in 4.8: 46,995 class executions / 1,662 jobs retained; eight declared jobs provide the bounded native preset. Explicit post-hoc assumptions; temporal admission remains blocked. | -| **Apache Commons CLI-13 buggy/fixed pair** | [Pinned source producer](docs/junit-source-capture.md), common 95-test fixture per revision and recoverable raw observations | One controlled Java pair; bundled recipe requires Docker/arm64. Independent of historical CI chronology; full Defects4J integration remains planned. | +| **Controlled Java real-fault sources** | Published [CLI-13 producer](docs/junit-source-capture.md); this revision adds a [three-fix CLI/Codec matrix](docs/java-fault-matrix.md) with typed indices and offline recovery | Two codebases, explicit common fixtures, 357 same-test pairs in the initial qualification. Docker/arm64; negative and inconclusive results remain visible. Controlled evidence, not historical CI or full Defects4J reconstruction. | | **Owned CI correctness fixtures** | Two tiny [serial/parallel corpus fixtures](docs/benchmark-corpus.md), validation and native integration examples | Available without network. One constructed family for contract/metric checks; no independent-project diversity. | | **Coverage and scenario-allocation microbenchmarks** | [Correctness and performance profiles](docs/decision-benchmarks.md), independent exhaustive references and JSON/Markdown reports | Runnable finite-model benchmarks with runtime/memory observations; separate from empirical CI-policy comparisons. | | **Pilot, resource and shadow examples** | [Operational accounting](docs/operational-pilot.md), [resource replay](docs/resource-replay.md) and [shadow recovery](docs/prospective-shadow.md) | Runnable synthetic demonstrations of accounting/recovery. Collected prospective evidence remains insufficient. | diff --git a/coleman/corpus/resources/apache-cli51-junit3-arm64-v1.json b/coleman/corpus/resources/apache-cli51-junit3-arm64-v1.json new file mode 100644 index 00000000..bc2a4594 --- /dev/null +++ b/coleman/corpus/resources/apache-cli51-junit3-arm64-v1.json @@ -0,0 +1 @@ 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curated direct-upstream focal fixes across two codebases; not a complete Defects4J reconstruction","CLI13 is Defects4J Cli1; CLI51 is Cli2; CODEC65 is Codec1. Framework metadata only identifies curated candidates","Both CLI fixes share project history; project and fault labels do not establish statistical independence","Multiple triggering tests and repeated trials never become additional faults or projects","Keep both-pass, both-fail, reversed, inconclusive and entirely missing pairs; test errors are not assertion-based expected detections","Same JVM and lexical test order; test-order independence is unverified","Constructed controlled functional evidence only; no CI chronology or policy evaluation/admission","Source producer process nanoseconds, case nanoseconds, runner work, peak memory and developer-visible latency remain distinct"],"matrix_id":"java-real-fault-matrix-arm64-v1","recipe":"junit3-controlled-matrix-v1","schema_version":1} diff --git a/coleman/transports/junit_matrix.py b/coleman/transports/junit_matrix.py new file mode 100644 index 00000000..cd953335 --- /dev/null +++ b/coleman/transports/junit_matrix.py @@ -0,0 +1,319 @@ +"""Optional bounded Java matrix transport, reusing existing source capture and controlled observations.""" + +from __future__ import annotations + +import argparse +import hashlib +import json +from collections import Counter +from importlib.metadata import version +from importlib.resources import files +from pathlib import Path +from typing import NamedTuple + +from coleman.artifacts import ArtifactWriter +from coleman.corpus.controlled import validate_controlled_dataset +from coleman.corpus.controlled_contracts import ControlledDataset, ControlledElapsed, ControlledObservation +from coleman.corpus.materialization import SourceCache, validate_cache_separation, validate_source_storage +from coleman.results.domain import canonical_json +from coleman.transports.junit_capture import capture_junit_source +from coleman.transports.junit_contracts import JunitRoleCapture +from coleman.transports.junit_matrix_contracts import ( + JunitMatrixCell, + JunitMatrixCellResult, + JunitMatrixReceipt, + JunitMatrixRecipe, + JunitMatrixRole, + JunitPairCounts, +) +from coleman.transports.junit_protocol import validate_role_bytes +from coleman.transports.junit_source import prepare_junit_inputs, validate_junit_report_budget + +_COMPLETION = "complete.json" +_DATASET_BYTES = 16 * 1024**2 +_PLAN_LIMIT_ERROR = "Java matrix plan exceeds its byte limit" + + +def _digest(payload: bytes) -> str: + """Return the explicit SHA-256 identity of exact bytes, with no filesystem access.""" + return "sha256:" + hashlib.sha256(payload).hexdigest() + + +def junit_matrix_producer() -> str: + """Bind matrix implementation/serialization bytes and package version; old capture provenance stays separate. + + A changed producer requires a new output generation. Unknown producers reject + on validation rather than silently relabeling existing observations. + """ + modules = ( + ("coleman.transports", "junit_matrix.py"), + ("coleman.transports", "junit_matrix_contracts.py"), + ("coleman.transports", "junit_capture.py"), + ("coleman.transports", "junit_contracts.py"), + ("coleman.transports", "junit_process.py"), + ("coleman.transports", "junit_protocol.py"), + ("coleman.transports", "junit_source.py"), + ("coleman.corpus", "controlled.py"), + ("coleman.corpus", "controlled_contracts.py"), + ("coleman.corpus", "source_views.py"), + ("coleman.corpus", "materialization.py"), + ("coleman.corpus", "materialization_contracts.py"), + ("coleman.corpus", "archives.py"), + ("coleman.results", "versioned.py"), + ("coleman.results", "domain.py"), + ("coleman.selection", "contracts.py"), + ("coleman", "artifacts.py"), + ) + pins = {package + "/" + name: _digest(files(package).joinpath(name).read_bytes()) for package, name in modules} + return _digest(canonical_json({"package_version": version("coleman"), "modules": pins}).encode()) + + +def _read(path: Path, maximum: int) -> bytes: + """Bound one metadata read; oversized input raises ValueError and I/O failures propagate.""" + with path.open("rb") as stream: + payload = stream.read(maximum + 1) + if len(payload) > maximum: + raise ValueError("Java matrix metadata exceeds its byte limit") + return payload + + +def _contained(root: Path, path: Path) -> Path: + """Reject escaped/symlink artifacts and nested Git storage before accessing source observations.""" + if path.is_symlink() or not path.resolve().is_relative_to(root.resolve()): + raise ValueError("Java matrix artifact must remain within its output tree") + validate_source_storage(path.parent) + return path + + +def _generation(plan: JunitMatrixRecipe, root: Path, producer: str) -> Path: + """Return a contained hash-only generation path; logical labels never become filesystem paths.""" + return _contained( + root, + root / "corpus-junit-matrix" / plan.fingerprint.removeprefix("sha256:") / producer.removeprefix("sha256:"), + ) + + +def _cell_result(cell: JunitMatrixCell, dataset: ControlledDataset, cache: SourceCache) -> JunitMatrixCellResult: + """Revalidate source/context and actual raw packets before deriving pair counts. + + This operates offline and starts no process. The existing source preparer may + republish identical owned cache metadata while rebuilding the exact context. + Normalized observations must correspond to every validated raw case, including + errors and zero-duration cases. Forged/missing/conflicting evidence rejects. + """ + validate_controlled_dataset(dataset, cache) + environments = [item for item in dataset.spec.context.inputs if item.name == "execution-environment"] + if len(environments) != 1: + raise ValueError("Java matrix dataset lacks its execution environment") + prepared = prepare_junit_inputs(cell.recipe, cache, environments[0].materialization) + if prepared.context != dataset.spec.context: + raise ValueError("Java matrix dataset context disagrees with its frozen source recipe") + packet = dataset.spec.report_materialization + roles = [] + observations = [] + for role in ("buggy", "fixed"): + name = role + "-capture.json" + members = [member for member in packet.spec.members if member.name == name] + if len(members) != 1: + raise ValueError("Java matrix dataset lacks a distinct raw role packet") + payload = _read(cache.member_path(packet, name), JunitRoleCapture.MAXIMUM_BYTES) + capture = JunitRoleCapture.from_json(payload) + validate_role_bytes(capture, cell.recipe) + if (capture.context_fingerprint, capture.trial_id, capture.role) != ( + prepared.context.fingerprint, + cell.trial_id, + role, + ): + raise ValueError("Java matrix raw role identity disagrees with its planned cell") + pin = _digest(payload) + if pin != members[0].sha256: + raise ValueError("Java matrix raw role bytes disagree with their source pin") + roles.append( + JunitMatrixRole( + role=capture.role, + packet_sha256=pin, + status=capture.status, + producer_elapsed=capture.producer_elapsed, + ) + ) + observations.extend( + ControlledObservation( + trial_id=capture.trial_id, + role=capture.role, + test_id=case.test_id, + outcome=case.outcome, + elapsed=ControlledElapsed(value=case.elapsed_ns, status="observed"), + capture_started_at=case.capture_started_at, + capture_finished_at=case.capture_finished_at, + diagnostics_sha256=pin, + ) + for case in capture.cases + ) + expected = tuple(sorted(observations, key=lambda item: item.logical_key)) + if dataset.observations != expected or dataset.input_rows != len(expected) or dataset.duplicates_excluded: + raise ValueError("Java matrix normalized observations disagree with actual raw cases") + counts = Counter(pair.classification for pair in dataset.pairs) + return JunitMatrixCellResult( + cell_id=cell.cell_id, + dataset_fingerprint=dataset.fingerprint, + context_fingerprint=prepared.context.fingerprint, + planned_pairs=len(cell.recipe.test_ids), + unobserved_pairs=len(cell.recipe.test_ids) - len(dataset.pairs), + pairs=JunitPairCounts(**counts), + roles=tuple(roles), + ) + + +def validate_junit_matrix(receipt: JunitMatrixReceipt, cache: SourceCache, output: Path) -> None: + """Verify an index against actual cached sources, raw packets and local controlled datasets offline. + + Unknown producer/schema, mutation or missing evidence raises ValueError or an + I/O error. No Docker, network, source execution or native experiment is used. + Identical source-view cache metadata may be republished by context validation. + This proves correspondence, never authentic execution or scientific admission. + """ + receipt = JunitMatrixReceipt.model_validate(receipt) + if receipt.producer_sha256 != junit_matrix_producer(): + raise ValueError("Unknown Java matrix producer; explicit generation/migration is required") + if len((receipt.plan.to_json() + "\n").encode()) > receipt.plan.MAXIMUM_BYTES: + raise ValueError(_PLAN_LIMIT_ERROR) + if len((receipt.to_json() + "\n").encode()) > receipt.MAXIMUM_BYTES: + raise ValueError("Java matrix receipt exceeds its byte limit") + validate_source_storage(output) + validate_cache_separation(cache.root, output) + actual = [] + references = {item.cell_id: item for item in receipt.cells} + for cell in receipt.plan.cells: + reference = references[cell.cell_id] + path = _contained( + output, + output / "corpus-controlled" / (reference.dataset_fingerprint.removeprefix("sha256:") + ".json"), + ) + dataset = ControlledDataset.from_json(_read(path, _DATASET_BYTES)) + if dataset.fingerprint != reference.dataset_fingerprint: + raise ValueError("Java matrix dataset identity disagrees with its index") + actual.append(_cell_result(cell, dataset, cache)) + if tuple(actual) != receipt.cells: + raise ValueError("Java matrix index disagrees with actual source evidence") + + +class JunitMatrixOutcome(NamedTuple): + """Typed local result; an incomplete receipt has no completion path or claimed benchmark success.""" + + receipt: JunitMatrixReceipt + receipt_path: Path + completion_path: Path | None + + +def capture_junit_matrix( + plan: JunitMatrixRecipe, cache: SourceCache, writer: ArtifactWriter, *, fetch: bool = False +) -> JunitMatrixOutcome: + """Collect predeclared source trials sequentially through the existing durable producer. + + Fetch is explicit/off by default; no image is pulled. Existing bounded Docker + collection retains started/raw role acknowledgments, negative outcomes and + same-trial interruption semantics. Concurrent ownership conflicts reject + without duplicate execution; retry after the owner finishes reuses captures. + A fresh collection needs a new trial ID. Infrastructure/preflight + exceptions propagate with earlier source artifacts retained; no completion is + written. Incomplete captures publish an honest index without a completion + marker. Immutable complete publication occurs last, after raw/source validation. + """ + plan = JunitMatrixRecipe.model_validate(plan) + if type(fetch) is not bool: + raise ValueError("Java matrix fetch flag must be boolean") + plan_payload = plan.to_json() + "\n" + if len(plan_payload.encode()) > plan.MAXIMUM_BYTES: + raise ValueError(_PLAN_LIMIT_ERROR) + validate_source_storage(writer.run_root) + validate_cache_separation(cache.root, writer.run_root) + producer = junit_matrix_producer() + generation = _generation(plan, writer.run_root, producer) + complete = _contained(writer.run_root, generation / _COMPLETION) + plan_path = _contained(writer.run_root, generation / "plan.json") + for cell in plan.cells: + validate_junit_report_budget(cell.recipe, cell.trial_id) + writer.write_immutable(plan_path, plan_payload) + if complete.exists(): + saved = JunitMatrixReceipt.from_json(_read(complete, JunitMatrixReceipt.MAXIMUM_BYTES)) + if saved.plan != plan or saved.status != "collected": + raise ValueError("Java matrix completion disagrees with the requested complete plan") + validate_junit_matrix(saved, cache, writer.run_root) + path = _contained(writer.run_root, generation / (saved.fingerprint.removeprefix("sha256:") + ".json")) + writer.write_immutable(path, saved.to_json() + "\n") + return JunitMatrixOutcome(saved, path, complete) + results = [] + for cell in plan.cells: + result = capture_junit_source(cell.recipe, cache, writer, cell.trial_id, fetch=fetch) + results.append(_cell_result(cell, result.dataset, cache)) + receipt = JunitMatrixReceipt( + schema_version=1, + plan=plan, + producer_sha256=producer, + cells=tuple(results), + status="collected" if all(item.collected for item in results) else "incomplete", + ) + payload = receipt.to_json() + "\n" + if len(payload.encode()) > receipt.MAXIMUM_BYTES: + raise ValueError("Java matrix receipt exceeds its byte limit") + validate_junit_matrix(receipt, cache, writer.run_root) + path = _contained(writer.run_root, generation / (receipt.fingerprint.removeprefix("sha256:") + ".json")) + writer.write_immutable(path, payload) + if receipt.status == "collected": + writer.write_immutable(complete, payload) + return JunitMatrixOutcome(receipt, path, complete) + return JunitMatrixOutcome(receipt, path, None) + + +def load_junit_matrix(path: Path | None = None) -> JunitMatrixRecipe: + """Read a bounded plan or the bundled three-fix arm64 preset; never acquire or execute sources.""" + resource = path or files("coleman.corpus.resources").joinpath("java-real-fault-matrix-arm64-v1.json") + with resource.open("rb") as stream: + payload = stream.read(JunitMatrixRecipe.MAXIMUM_BYTES + 1) + if len(payload) > JunitMatrixRecipe.MAXIMUM_BYTES: + raise ValueError(_PLAN_LIMIT_ERROR) + return JunitMatrixRecipe.from_json(payload) + + +def main(argv: list[str] | None = None) -> int: + """Collect or offline-validate source evidence and emit JSON; incomplete collection returns 2. + + This optional transport does not run policies, alter admission, infer CI + chronology or interpret source errors as assertion-based fault detections. + """ + parser = argparse.ArgumentParser(description=__doc__) + choice = parser.add_mutually_exclusive_group() + choice.add_argument("--recipe", type=Path) + choice.add_argument("--validate", type=Path) + parser.add_argument("--cache", type=Path, required=True) + parser.add_argument("--output", type=Path, required=True) + parser.add_argument("--fetch", action="store_true") + args = parser.parse_args(argv) + if args.validate and args.fetch: + parser.error("Offline validation cannot fetch sources") + cache = SourceCache(args.cache) + if args.validate: + receipt = JunitMatrixReceipt.from_json(_read(args.validate, JunitMatrixReceipt.MAXIMUM_BYTES)) + validate_junit_matrix(receipt, cache, args.output) + print(json.dumps({"integrity": "verified", "receipt": receipt.fingerprint, "status": receipt.status})) + return 0 + outcome = capture_junit_matrix(load_junit_matrix(args.recipe), cache, ArtifactWriter(args.output), fetch=args.fetch) + print( + json.dumps( + { + "receipt": str(outcome.receipt_path), + "completion": str(outcome.completion_path) if outcome.completion_path else None, + "status": outcome.receipt.status, + "declared_projects": outcome.receipt.declared_projects, + "curated_focal_fixes": outcome.receipt.curated_focal_fixes, + "admission": outcome.receipt.admission, + "generalization": outcome.receipt.generalization, + }, + sort_keys=True, + ) + ) + return 0 if outcome.receipt.status == "collected" else 2 + + +if __name__ == "__main__": + raise SystemExit(main()) diff --git a/coleman/transports/junit_matrix_contracts.py b/coleman/transports/junit_matrix_contracts.py new file mode 100644 index 00000000..cb3afb6d --- /dev/null +++ b/coleman/transports/junit_matrix_contracts.py @@ -0,0 +1,173 @@ +"""Versioned optional Java matrix declarations; the controlled domain remains transport independent.""" + +from __future__ import annotations + +from typing import Annotated, ClassVar, Literal, Self + +from pydantic import Field, model_validator + +from coleman.corpus.controlled_contracts import Label +from coleman.results.domain import Fingerprint +from coleman.results.versioned import VersionedContract +from coleman.selection.contracts import Immutable +from coleman.transports.junit_contracts import JunitCaptureRecipe, ProducerElapsed + +Count = Annotated[int, Field(strict=True, ge=0, le=10000)] + + +class JunitMatrixCell(Immutable): + """Predeclare one trial of one focal fix, with passive curation and fixture-selection references. + + The recipe already pins both source views, common fixture, JARs, runtime and + harness. References are citations, never executable commands or acquisition + instructions. A curated label does not establish an independent unique fault. + """ + + cell_id: Label + trial_id: Label + source_reference: Label + fixture_selection: Label + reconstruction: Literal["direct-upstream-common-fixed-fixture-v1"] = "direct-upstream-common-fixed-fixture-v1" + recipe: JunitCaptureRecipe + + +class JunitMatrixRecipe(VersionedContract): + """Freeze at most sixteen bounded source trials before observing their outcomes. + + Cells sort by logical ID; physical declaration order does not affect identity. + Duplicate recipe/trial collections reject rather than inflating evidence. + Version 1 requires explicit schema version 1; legacy/missing/future versions + reject without implicit migration. This model performs no I/O or execution. + """ + + MAXIMUM_BYTES: ClassVar[int] = 4 * 1024**2 + recipe: Literal["junit3-controlled-matrix-v1"] = "junit3-controlled-matrix-v1" + matrix_id: Label + cells: Annotated[tuple[JunitMatrixCell, ...], Field(min_length=1, max_length=16)] + limitations: Annotated[tuple[Label, ...], Field(min_length=1, max_length=64)] + + @model_validator(mode="after") + def _identities(self) -> Self: + """Reject duplicate logical collections and canonicalize declaration order only.""" + if len({cell.cell_id for cell in self.cells}) != len(self.cells): + raise ValueError("Duplicate Java matrix cell identity") + keys = {(cell.recipe.fingerprint, cell.trial_id) for cell in self.cells} + if len(keys) != len(self.cells): + raise ValueError("Duplicate Java matrix recipe/trial collection") + object.__setattr__(self, "cells", tuple(sorted(self.cells, key=lambda cell: cell.cell_id))) + return self + + +class JunitPairCounts(Immutable): + """Numbers of same-test/trial pairs, not numbers of faults or independent observations.""" + + expected: Count = 0 + both_pass: Count = 0 + both_fail: Count = 0 + reversed: Count = 0 + inconclusive: Count = 0 + + @property + def total(self) -> int: + """Count observed pairs, including one-sided/inconclusive comparisons.""" + return self.expected + self.both_pass + self.both_fail + self.reversed + self.inconclusive + + +class JunitMatrixRole(Immutable): + """Bind a raw role packet and its process accounting; unavailable elapsed is null, never zero. + + Producer elapsed nanoseconds include container observation overhead. They are + distinct from harness case durations, peak memory, runner work and CI latency. + """ + + role: Literal["buggy", "fixed"] + packet_sha256: Fingerprint + status: Literal["collected", "process_error", "timeout", "output_limit", "protocol_error", "interrupted"] + producer_elapsed: ProducerElapsed + + @model_validator(mode="after") + def _elapsed(self) -> Self: + """Keep interrupted elapsed unavailable and measured process statuses observed; launch errors allow either.""" + if self.status == "interrupted" and self.producer_elapsed.status != "unavailable": + raise ValueError("Interrupted Java matrix role requires unavailable elapsed") + if self.status not in {"interrupted", "process_error"} and self.producer_elapsed.status != "observed": + raise ValueError("Observed Java matrix role requires observed elapsed") + return self + + +class JunitMatrixCellResult(Immutable): + """Reference a separately validated controlled dataset without copying its source/observation envelope. + + Entirely absent test pairs remain explicitly unobserved; one-sided pairs are + inconclusive. A complete collection can contain failures/errors and never + implies successful scientific admission or a wholly correct fixed revision. + """ + + cell_id: Label + dataset_fingerprint: Fingerprint + context_fingerprint: Fingerprint + planned_pairs: Count + unobserved_pairs: Count + pairs: JunitPairCounts + roles: Annotated[tuple[JunitMatrixRole, ...], Field(min_length=2, max_length=2)] + + @model_validator(mode="after") + def _accounting(self) -> Self: + """Conserve declared tests and require exactly one packet per role.""" + if {role.role for role in self.roles} != {"buggy", "fixed"}: + raise ValueError("Java matrix requires both distinct source roles") + if self.planned_pairs != self.pairs.total + self.unobserved_pairs: + raise ValueError("Java matrix pair conservation failed") + if self.collected and self.unobserved_pairs: + raise ValueError("Collected Java matrix cannot omit declared pairs") + object.__setattr__(self, "roles", tuple(sorted(self.roles, key=lambda role: role.role))) + return self + + @property + def collected(self) -> bool: + """Return process collection completeness, independently of assertion/test outcomes.""" + return all(role.status == "collected" for role in self.roles) + + +class JunitMatrixReceipt(VersionedContract): + """Deterministic bounded matrix index; actual datasets/raw packets must be independently revalidated. + + A receipt may describe incomplete evidence. Only fully collected receipts may + acquire a completion marker. Version 1 preserves all existing dataset/producer + contracts and grants no historical-CI or statistical-independence claim. + """ + + MAXIMUM_BYTES: ClassVar[int] = 8 * 1024**2 + plan: JunitMatrixRecipe + producer_sha256: Fingerprint + cells: Annotated[tuple[JunitMatrixCellResult, ...], Field(min_length=1, max_length=16)] + status: Literal["collected", "incomplete"] + history: Literal["constructed"] = "constructed" + admission: Literal["not_evaluated"] = "not_evaluated" + generalization: Literal["insufficient_evidence"] = "insufficient_evidence" + + @model_validator(mode="after") + def _bindings(self) -> Self: + """Require every planned cell exactly once and honest completion/coverage accounting.""" + expected = {cell.cell_id: len(cell.recipe.test_ids) for cell in self.plan.cells} + if len({cell.cell_id for cell in self.cells}) != len(self.cells): + raise ValueError("Duplicate Java matrix result cell") + if {cell.cell_id for cell in self.cells} != set(expected): + raise ValueError("Java matrix results do not cover planned cells") + if any(cell.planned_pairs != expected[cell.cell_id] for cell in self.cells): + raise ValueError("Java matrix planned test count disagrees with recipe") + status = "collected" if all(cell.collected for cell in self.cells) else "incomplete" + if self.status != status: + raise ValueError("Java matrix collection status disagrees with role evidence") + object.__setattr__(self, "cells", tuple(sorted(self.cells, key=lambda cell: cell.cell_id))) + return self + + @property + def declared_projects(self) -> int: + """Count distinct declared project labels, without asserting statistical independence.""" + return len({cell.recipe.project for cell in self.plan.cells}) + + @property + def curated_focal_fixes(self) -> int: + """Count distinct project/fault labels; tests and repeated trials never add focal fixes.""" + return len({(cell.recipe.project, cell.recipe.fault_id) for cell in self.plan.cells}) diff --git a/docs/benchmark-corpus.md b/docs/benchmark-corpus.md index e8a90744..c2e314c9 100644 --- a/docs/benchmark-corpus.md +++ b/docs/benchmark-corpus.md @@ -13,6 +13,11 @@ For the separate source-specific ETL workflows, see [Karaf](lrts-parquet-etl.md) views](lrts-stage-views.md). Those exports preserve their own provenance and admission blockers; they do not silently add admitted registrations to this registry. +For controlled Java sources, this revision adds a separate [CLI/Codec +matrix](java-fault-matrix.md) using the existing controlled/JUnit producer. +Its typed index preserves all selected outcomes and incomplete evidence. It does +not silently change this registry's admission or diversity coverage. + The registry contains two small repository-authored MIT-licensed CI fixtures and an inventory of ten existing public example Parquet artifacts. Historical sources remain **blocked for evaluation** until their data-specific terms, duration units, diff --git a/docs/index.md b/docs/index.md index 5101b3bc..b28e3877 100644 --- a/docs/index.md +++ b/docs/index.md @@ -35,6 +35,12 @@ remain explicit blockers. The workflow is a post-hoc serial simulation, and broader corpus admission and confirmation remain open. See the [4.9 release notes](releases/4.9.0.md). +This revision also adds a [controlled Java fault matrix](java-fault-matrix.md): +three curated upstream fixes across CLI and Codec, raw/source validation and +offline recovery. Its guide builds this revision's wheel. The initial 357 +same-test pairs retain both-fail and inconclusive results; this controlled layer +does not establish historical CI chronology, independence or policy efficacy. + ## Existing real-data workflows [Turn real RTPTorrent CI history into Parquet and native TCPCI replays](rtptorrent-parquet-etl.md). diff --git a/docs/java-fault-matrix.md b/docs/java-fault-matrix.md new file mode 100644 index 00000000..cb3c6de8 --- /dev/null +++ b/docs/java-fault-matrix.md @@ -0,0 +1,240 @@ +# Run a controlled Java fault matrix + +Collect three curated upstream fixes across Apache Commons CLI and Codec with +one frozen plan. Each cell runs buggy and fixed source against the same declared +fixed-tree fixture, retaining every observed pass, failure, test error and +incomplete collection. This is controlled functional evidence for TCPCI research; +it is separate from historical CI and policy comparisons. + +This revision adds the matrix transport. Build its wheel below; the published +4.9 wheel contains the existing single-pair producer, not the new matrix command. +The matrix reuses that producer and the generic [controlled-observation +domain](controlled-faults.md). It does not introduce a learning runner or change +existing source recipes, results, checkpoints or raw-capture semantics. + +## Install and collect outside checkout + +Use Python 3.14+, uv, POSIX and a native Linux arm64 Docker engine. These frozen +recipes pin Temurin `11.0.32.1`, the arm64 image digest and +`America/Los_Angeles`. A different architecture needs a separately reviewed +recipe; changing its label does not validate another runtime. + +Build from this revision, then install into a fresh external environment: + +```bash +uv build --wheel --out-dir /tmp/coleman-matrix-dist +uv venv /tmp/coleman-matrix-env --python 3.14 +uv pip install --python /tmp/coleman-matrix-env/bin/python /tmp/coleman-matrix-dist/*.whl + +# Explicit operator preparation; COLEMAN never pulls an image. +docker pull --platform linux/arm64 eclipse-temurin@sha256:e4b3ff0f1a427efb2deb02b092ff8316d58573480260720d767d6ecdd69999d8 + +mkdir -p /tmp/coleman-matrix-workspace +cd /tmp/coleman-matrix-workspace +/tmp/coleman-matrix-env/bin/python -m coleman.transports.junit_matrix \ + --cache /tmp/coleman-java-source-cache \ + --output /tmp/coleman-java-observations --fetch > matrix-summary.json + +# Same plan/trials: validate committed evidence rather than collect it again. +/tmp/coleman-matrix-env/bin/python -m coleman.transports.junit_matrix \ + --cache /tmp/coleman-java-source-cache \ + --output /tmp/coleman-java-observations +``` + +Only the first acquisition needs `--fetch`; it permits the existing individually +pinned HTTPS source/JAR downloads. Subject execution has no network. Both cache +and output must be outside Git and separate from each other. The system temporary +directory must also be outside Git. No third-party source or raw capture is bundled. + +The JSON summary reports the content-addressed receipt, optional completion path, +collection status, two declared project labels and three curated focal-fix labels. +Exit 0 means collection completed, including negative outcomes. Incomplete source +captures publish an index with `completion: null` and exit 2. Infrastructure, +preflight and publication errors exit nonzero and retain earlier durable evidence. +None of these statuses grants scientific admission. + +Validate a saved index without Docker or source execution: + +```bash +MATRIX_RECEIPT="$(/tmp/coleman-matrix-env/bin/python -c 'import json; print(json.load(open("matrix-summary.json"))["receipt"])')" +/tmp/coleman-matrix-env/bin/python -m coleman.transports.junit_matrix \ + --validate "$MATRIX_RECEIPT" \ + --cache /tmp/coleman-java-source-cache \ + --output /tmp/coleman-java-observations +``` + +Offline integrity validation can republish identical source-view cache metadata. +It verifies actual source members, context, raw protocol packets and normalized +observations; it starts no process and fetches nothing. Integrity is correspondence, +not authentication of execution truth or benchmark efficacy. + +## Frozen source selection + +| Curated fix | Direct upstream revisions | Common fixture | Relationship to framework metadata | +| --- | --- | --- | --- | +| CLI-13 | `8f46f467a33ace44ccd9f394910940b6c48a3827` → `b0e1b80b6d4a10a9c9f46539bc4c7a3cce55886e` | Existing published 95-test recipe, unchanged | Defects4J Cli **1**, not Cli13 | +| CLI-51 | `b0e1b80b6d4a10a9c9f46539bc4c7a3cce55886e` → `2ff9573ffb08dd52ec3a55a49f2d77a1e94efbdf` | Same fixed-tree policy, 96 tests | Defects4J Cli2 | +| CODEC-65 | `9c0cabead7cf075308b11362172ae1a48d41321c` → `52d82d1dfff8c2b2ded9d843e0b03017af6d747c` | Explicit partial fixed-tree fixture, 166 tests | Defects4J Codec1 | + +The [CLI-51 fix](https://github.com/apache/commons-cli/commit/2ff9573ffb08dd52ec3a55a49f2d77a1e94efbdf) +changes PosixParser and adds BugCLI51Test. The [CODEC-65 +fix](https://github.com/apache/commons-codec/commit/52d82d1dfff8c2b2ded9d843e0b03017af6d747c) +changes locale handling in several encoders. These are direct parent/fix source +reproductions with a common fixed fixture, not a full Defects4J reconstruction. +Framework subject labels do not replace source rights or reconstruction evidence. +Those labels were checked against the pinned Defects4J metadata revision +`8c16da8230843cdc918eaf4ddb449637f02b83c6` for +[Cli](https://github.com/rjust/defects4j/blob/8c16da8230843cdc918eaf4ddb449637f02b83c6/framework/projects/Cli/active-bugs.csv) +and [Codec](https://github.com/rjust/defects4j/blob/8c16da8230843cdc918eaf4ddb449637f02b83c6/framework/projects/Codec/active-bugs.csv). + +Codec retains all 25 production Java files per role, 15 fixed fixture Java files, +and original `LICENSE.txt`/`NOTICE.txt`. Fixture selection was recorded in +[#304](https://github.com/jacksonpradolima/coleman/issues/304) **before observing +new source outcomes**: + +- `DoubleMetaphoneTest.java` embeds separately noticed aspell data and non-UTF8 + bytes. It is outside the existing homogeneous-terms/UTF8 source-view profile. +- `SoundexTest.java` also contains non-UTF8 bytes and is excluded without transcoding. +- `AllTests.java` references those excluded classes and is excluded as their suite + aggregator. Per-TestCase discovery does not require it. + +All other fixed-tree Java fixture files remain. This includes +`RefinedSoundexTest.java`, a different file. Missing focal-class coverage stays +visible; this is not the complete upstream suite. No outcome-based filtering is +applied after collection. + +Source views preserve exact bytes and original notices. Apache-2.0 subject terms, +Commons Lang 2.1 terms and JUnit 3.8.1 CPL-1.0 terms remain separately reviewed and +pinned. The [Codec NOTICE](https://github.com/apache/commons-codec/blob/52d82d1dfff8c2b2ded9d843e0b03017af6d747c/NOTICE.txt) +identifies the omitted third-party test data; COLEMAN does not relabel it as +Apache-2.0. Codec needs only the pinned JUnit JAR; CLI retains its original two +dependencies. The recipe-only policy keeps foreign content in the external cache. + +## Observed results and their limits + +The initial installed-producer qualification collected **714 role observations**, +or **357 same-test/trial pairs**, under the frozen runtime: + +| Fix | Both pass | Both fail | Assertion failed → passed | Reversed | Inconclusive | +| --- | ---: | ---: | ---: | ---: | ---: | +| CLI-13 | 92 | 2 | 1 | 0 | 0 | +| CLI-51 | 93 | 2 | 0 | 0 | 1 | +| CODEC-65 | 163 | 0 | 3 | 0 | 0 | + +CLI-51's focal buggy test raises `UnrecognizedOptionException`; the fixed role +passes. The existing strict classifier calls this **inconclusive**, because a +test error is distinct from an assertion failure. The matrix preserves that +classification and raw diagnostic. Both CLI fixtures retain the two assertions +that fail in both revisions. A fixed revision is not presented as wholly correct. + +The three Codec assertions belong to Caverphone, Metaphone and RefinedSoundex +`testLocaleIndependence` methods. They concern **one** curated fix. The two CLI +fixes share project history. Tests, trials, seeds and JVM repetitions do not become +independent projects or new faults. These observations are runtime/fixture-specific, +not a guarantee about every future run. + +Each role uses the existing shared JVM and lexical test-ID order. Test-order +independence is unverified. Integer case nanoseconds include setup/teardown; parent +process nanoseconds also include startup/compilation. Observed zero remains zero; +unavailable elapsed values are null with `status: unavailable`. Negative counts, +negative elapsed counters, non-finite values and incompatible units reject. Neither +timer is CI queue time, parallel elapsed time, peak memory or removable runner work. +The existing guards bound each role to 60 seconds, 1 MiB combined output, two CPUs, +64 PIDs, 128 MiB tmpfs and 1 GiB memory in these presets. A resource limit is not +a measured peak. Captures are trusted-source reproductions within those guards. + +## Contract, artifacts and recovery + +```mermaid +flowchart LR + plan[Frozen typed Java matrix plan] --> preflight[Matrix storage and all-cell budget preflight] + preflight --> frozen[Immutable plan.json before source execution] + frozen --> source[Existing source cache and deterministic views] + source --> capture[Existing bounded JUnit producer] + capture --> raw[Durable role start markers and raw packets] + raw --> controlled[Existing generic ControlledDataset] + controlled --> verify[Offline context and raw observation validation] + verify --> index[Content-addressed typed matrix index] + index --> state{All roles collected?} + state -->|yes| complete[Atomic immutable complete.json last] + state -->|no| incomplete[Incomplete index; no completion marker] + complete --> replay[Offline verified replay; no runtime preflight] +``` + +Plans require schema version 1 and allow at most 16 cells / 4 MiB. Receipts require +schema version 1 and are bounded to 8 MiB. Canonical JSON and SHA-256 identities +include explicit source recipes, trial IDs, selection protocol and implementation +provenance. Reordering declared cells/roles does not change identity. Different +collected clocks or observations legitimately change a receipt; determinism means +identical captured evidence serializes identically, not that new executions have +identical elapsed time. + +Duplicate cell IDs and duplicate recipe/trial collections reject. Counts refer to +observed same-test pairs; `unobserved_pairs` preserves completely absent tests. +One-sided evidence remains inconclusive. The index references separately verified +controlled dataset fingerprints and actual raw packet digests, never arbitrary +transport dictionaries. It does not convert controlled observations into native +CI duration columns or historical builds. + +The original source producer owns role recovery. A start marker without a committed +packet recovers as interrupted, with no invented cases or elapsed time. It does +not silently rerun that role. Choose a new trial ID for a new collection; it stays +in the same declared dependence group. Concurrent ownership conflicts reject +without duplicate execution; retry after the owner finishes. A crash before matrix +completion leaves the frozen `plan.json` and committed role/data artifacts usable +for recovery. Unattempted cells remain visible in that plan without invented results. +An incomplete index is retained without `complete.json`; an all-role collected +index acquires that marker only after validation and immutable index publication. + +Idempotence uses the retained output/capture tree. A fresh output directory does +not restore another directory's acknowledgments; use new trial IDs for a fresh +physical collection. Copying an index alone is insufficient: offline validation +also needs its controlled datasets and the independently verified source cache. + +Existing completion is revalidated before any runtime preflight. Corrupt/unknown +schema or producer versions reject. Missing and older matrix schema versions are +unsupported; there is no implicit migration. A changed matrix implementation or +package version selects a new generation, preserving previous bytes. Explicit +offline validation requires the matching reviewed producer. Existing single-pair +JUnit recipes, source caches, controlled artifacts, native results and learning +checkpoints keep their previous contracts and require no migration. + +## Python and verification + +The optional producer API is also callable without its command-line parser: + +```python +from pathlib import Path +from coleman.artifacts import ArtifactWriter +from coleman.corpus.materialization import SourceCache +from coleman.transports.junit_matrix import ( + capture_junit_matrix, load_junit_matrix, validate_junit_matrix, +) + +cache = SourceCache("/tmp/coleman-java-source-cache") +writer = ArtifactWriter("/tmp/coleman-java-observations") +plan = load_junit_matrix() +outcome = capture_junit_matrix(plan, cache, writer) # Offline acquisition by default. +validate_junit_matrix(outcome.receipt, cache, Path(writer.run_root)) +assert outcome.receipt.admission == "not_evaluated" +``` + +Use `--recipe /absolute/path/matrix.json` for another reviewed typed plan. The +generic controlled domain stays independent of CLI, Docker transports and MCP. +Protected source admission and policy evaluation remain later #261 subtasks. + +Normal tests use owned small fixtures with no downloads. With the image prepared +and all three recipes acquired into an external cache, repeat installed real-source +capture, offline matrix validation, import-boundary checks and an independent owned +native CI/checkpoint workflow: + +```bash +COLEMAN_JUNIT_REAL_CACHE=/tmp/coleman-java-source-cache \ + uv run pytest tests/corpus/test_installed_junit_matrix.py --no-cov +``` + +The native CI fixture has its own exact-answer costs and outcomes; Java harness +elapsed counters are not substituted for CI costs. Actual historical-CI ETL/replay +remains available in the [Karaf](lrts-parquet-etl.md), +[ActiveMQ/Log4j](lrts-stage-views.md) and +[RTPTorrent](rtptorrent-parquet-etl.md) workflows. diff --git a/docs/junit-source-capture.md b/docs/junit-source-capture.md index 1a3d4a5d..9e5d3375 100644 --- a/docs/junit-source-capture.md +++ b/docs/junit-source-capture.md @@ -11,10 +11,16 @@ container images and raw captures remain outside the repository. It does not execute Defects4J or claim its complete reconstruction protocol. The generic [controlled domain](controlled-faults.md) imports no Docker, CLI or MCP adapter. +For a predeclared multi-fix workflow, this revision adds a separate +[controlled Java matrix](java-fault-matrix.md), reusing this producer unchanged. +It includes CLI-13, CLI-51 and an explicitly partial CODEC-65 fixture, with +negative/inconclusive results retained. + ## Prepare and run -Build and install this branch's wheel as shown in the controlled-observation guide. -The released 4.5 wheel predates this producer. The bundled preset requires POSIX, +The published 4.9 wheel includes this single-pair producer; use the verified +[setup command](setup.md#default-run-no-docker-required). Build this revision's +wheel for the new matrix command. The bundled preset requires POSIX, Docker, an arm64 host and arm64 Docker engine. It pins Temurin `11.0.32.1` and `America/Los_Angeles`. Other platforms require a separately reviewed recipe; changing a platform label does not validate a different image. diff --git a/docs/releases/4.10.0.md b/docs/releases/4.10.0.md new file mode 100644 index 00000000..096536af --- /dev/null +++ b/docs/releases/4.10.0.md @@ -0,0 +1,59 @@ +# COLEMAN 4.10 — Inspect controlled faults across Java codebases + +Reproduce a small, explicit matrix of real upstream fixes before making a +benchmark claim. COLEMAN now collects CLI-13, CLI-51 and CODEC-65 with frozen +sources, common test fixtures and the existing bounded JUnit producer. Every +selected result remains inspectable, including errors and failures that persist +in both revisions. + +## What you can do + +- **Collect a declared matrix.** One typed plan describes three focal fixes across + Apache Commons CLI and Codec. Pinned source views, original notices, JARs, + runtime image, architecture, timezone and harness make the protocol explicit. +- **Keep negative evidence.** The initial qualification retained 714 role + observations / 357 same-test pairs: 348 both-pass, four both-fail, four + assertion-failed-to-passed and one inconclusive comparison. CLI-51's test error + remains inconclusive under the existing classifier. Three Codec triggering + tests do not become three faults. +- **Resume without inventing observations.** Existing role acknowledgments and + raw packets retain interruption semantics. Typed indices distinguish observed + pairs from entirely unobserved tests; incomplete collection has no completion + marker. A verified completed matrix reopens offline without querying Docker. +- **Verify the evidence behind the index.** Offline validation checks actual + source/context bytes, raw protocols, normalized observations and diagnostic + references before accepting counts, identities or collection status. + +The [complete matrix guide](https://jacksonpradolima.github.io/coleman/java-fault-matrix/) +provides installation, explicit runtime preparation, source acquisition, typed +Python use, CLI collection/validation, recovery and the installed-package workflow. +Foreign sources, dependencies and captures stay in operator-owned external storage. + +## Compatibility and limits + +The new optional transport adds versioned matrix plans/indices while reusing the +existing generic controlled domain, source cache, JUnit producer and immutable +artifact writer. Old single-pair recipes, controlled artifacts, native results, +RunSpec identities and learning checkpoints retain their semantics and require +no migration. Unknown matrix schemas or producers reject; there is no implicit +reinterpretation of prior evidence. + +Codec's common fixture is explicitly partial. Before outcomes were observed, +three fixture files were excluded because of separately noticed third-party data, +non-UTF8 source bytes or dependencies on excluded classes. Remaining source bytes +and original LICENSE/NOTICE are preserved. This is direct-upstream reproduction, +not the complete original build or a full Defects4J reconstruction. + +The CLI fixes share project history. Multiple tests, seeds or trials do not +establish independent projects or unique faults. Collection clocks and harness +nanoseconds are not historical CI events, runner work or parallel wall-clock +savings. Shared-JVM test-order independence remains unverified. All outputs retain +`not_evaluated` and `insufficient_evidence`; diversified source admission, baseline +comparisons and confirmation in #261 remain open. + +Validation covers versioned goldens, old recipes, strict units/missingness, +non-finite rejection, deterministic identities, duplicate accounting, negative +results, source/raw/index correspondence, interrupted publication, concurrency, +offline continuation and domain import boundaries. Installed-package checks use +actual Java source collection and a separate native CI exact-answer/checkpoint +workflow. This validates the evidence pipeline, not algorithm effectiveness. diff --git a/docs/roadmap.md b/docs/roadmap.md index 6f649434..e66bd38d 100644 --- a/docs/roadmap.md +++ b/docs/roadmap.md @@ -87,6 +87,14 @@ confirmatory work continues through the public subtasks. #303's new profiles preserve all raw/processed stages and use exact context/node bindings, while retaining explicit missing temporal evidence. Remaining expansion begins with #304. +This revision implements #304's [bounded Java fault matrix](java-fault-matrix.md) +on the existing source producer: CLI-13, CLI-51 and an explicitly partial CODEC-65 +fixture. Typed plans, raw/context verification, honest incomplete indices and +offline recovery preserve all negative outcomes. Source qualification collected +714 role observations / 357 same-test pairs across two codebases. Controlled +source collection remains separate from admission and policy comparison in #309 +onward; the remaining source subtasks follow sequentially. + **4.9.0** publishes the stage-view contracts and three frozen presets: ActiveMQ, Log4j Ubuntu and Log4j Windows. All raw observations/processed stages remain analytical evidence; exact context/node bindings select one native view. The diff --git a/llms.txt b/llms.txt index 71fcba2f..260c1d83 100644 --- a/llms.txt +++ b/llms.txt @@ -43,6 +43,7 @@ parallel execution, and extensibility via hooks and namespaced custom config. - docs/finite-coverage.md - docs/getting-started.md - docs/index.md +- docs/java-fault-matrix.md - docs/junit-source-capture.md - docs/lrts-parquet-etl.md - docs/lrts-stage-views.md @@ -55,6 +56,7 @@ parallel execution, and extensibility via hooks and namespaced custom config. - docs/releases/3.6.1.md - docs/releases/4.0.0.md - docs/releases/4.1.0.md +- docs/releases/4.10.0.md - docs/releases/4.2.0.md - docs/releases/4.3.0.md - docs/releases/4.4.0.md @@ -742,7 +744,7 @@ controlled reproductions and empirical benchmark corpora have different roles: | **Druid and Retrofit** | Bundled native/contextual Parquet examples, native runner and [descriptive profiles](docs/benchmark-corpus.md#local-profiles-and-the-first-diversity-matrix-44) | Runnable legacy experiments. Source terms, duration units and outcome availability still need corpus admission evidence. | | **Dune and its variants** | Bundled native Parquet, WTS/VTS workflows and [variant-aware inventory](docs/benchmark-corpus.md) | Runnable HCS examples. Variants/context files may share executions; broad HCS benchmark admission remains unfinished. | | **RTPTorrent / HikariCP** | [Verified ZIP64 → full analytical history → native-compatible Parquet → replay/recovery](docs/rtptorrent-parquet-etl.md) | Available in 4.8: 46,995 class executions / 1,662 jobs retained; eight declared jobs provide the bounded native preset. Explicit post-hoc assumptions; temporal admission remains blocked. | -| **Apache Commons CLI-13 buggy/fixed pair** | [Pinned source producer](docs/junit-source-capture.md), common 95-test fixture per revision and recoverable raw observations | One controlled Java pair; bundled recipe requires Docker/arm64. Independent of historical CI chronology; full Defects4J integration remains planned. | +| **Controlled Java real-fault sources** | Published [CLI-13 producer](docs/junit-source-capture.md); this revision adds a [three-fix CLI/Codec matrix](docs/java-fault-matrix.md) with typed indices and offline recovery | Two codebases, explicit common fixtures, 357 same-test pairs in the initial qualification. Docker/arm64; negative and inconclusive results remain visible. Controlled evidence, not historical CI or full Defects4J reconstruction. | | **Owned CI correctness fixtures** | Two tiny [serial/parallel corpus fixtures](docs/benchmark-corpus.md), validation and native integration examples | Available without network. One constructed family for contract/metric checks; no independent-project diversity. | | **Coverage and scenario-allocation microbenchmarks** | [Correctness and performance profiles](docs/decision-benchmarks.md), independent exhaustive references and JSON/Markdown reports | Runnable finite-model benchmarks with runtime/memory observations; separate from empirical CI-policy comparisons. | | **Pilot, resource and shadow examples** | [Operational accounting](docs/operational-pilot.md), [resource replay](docs/resource-replay.md) and [shadow recovery](docs/prospective-shadow.md) | Runnable synthetic demonstrations of accounting/recovery. Collected prospective evidence remains insufficient. | @@ -1922,6 +1924,11 @@ For the separate source-specific ETL workflows, see [Karaf](lrts-parquet-etl.md) views](lrts-stage-views.md). Those exports preserve their own provenance and admission blockers; they do not silently add admitted registrations to this registry. +For controlled Java sources, this revision adds a separate [CLI/Codec +matrix](java-fault-matrix.md) using the existing controlled/JUnit producer. +Its typed index preserves all selected outcomes and incomplete evidence. It does +not silently change this registry's admission or diversity coverage. + The registry contains two small repository-authored MIT-licensed CI fixtures and an inventory of ten existing public example Parquet artifacts. Historical sources remain **blocked for evaluation** until their data-specific terms, duration units, @@ -5730,6 +5737,12 @@ remain explicit blockers. The workflow is a post-hoc serial simulation, and broader corpus admission and confirmation remain open. See the [4.9 release notes](releases/4.9.0.md). +This revision also adds a [controlled Java fault matrix](java-fault-matrix.md): +three curated upstream fixes across CLI and Codec, raw/source validation and +offline recovery. Its guide builds this revision's wheel. The initial 357 +same-test pairs retain both-fail and inconclusive results; this controlled layer +does not establish historical CI chronology, independence or policy efficacy. + ## Existing real-data workflows [Turn real RTPTorrent CI history into Parquet and native TCPCI replays](rtptorrent-parquet-etl.md). @@ -5794,6 +5807,251 @@ For advanced customization and parallel extension contracts, see +### FILE: docs/java-fault-matrix.md + +# Run a controlled Java fault matrix + +Collect three curated upstream fixes across Apache Commons CLI and Codec with +one frozen plan. Each cell runs buggy and fixed source against the same declared +fixed-tree fixture, retaining every observed pass, failure, test error and +incomplete collection. This is controlled functional evidence for TCPCI research; +it is separate from historical CI and policy comparisons. + +This revision adds the matrix transport. Build its wheel below; the published +4.9 wheel contains the existing single-pair producer, not the new matrix command. +The matrix reuses that producer and the generic [controlled-observation +domain](controlled-faults.md). It does not introduce a learning runner or change +existing source recipes, results, checkpoints or raw-capture semantics. + +## Install and collect outside checkout + +Use Python 3.14+, uv, POSIX and a native Linux arm64 Docker engine. These frozen +recipes pin Temurin `11.0.32.1`, the arm64 image digest and +`America/Los_Angeles`. A different architecture needs a separately reviewed +recipe; changing its label does not validate another runtime. + +Build from this revision, then install into a fresh external environment: + +```bash +uv build --wheel --out-dir /tmp/coleman-matrix-dist +uv venv /tmp/coleman-matrix-env --python 3.14 +uv pip install --python /tmp/coleman-matrix-env/bin/python /tmp/coleman-matrix-dist/*.whl + +# Explicit operator preparation; COLEMAN never pulls an image. +docker pull --platform linux/arm64 eclipse-temurin@sha256:e4b3ff0f1a427efb2deb02b092ff8316d58573480260720d767d6ecdd69999d8 + +mkdir -p /tmp/coleman-matrix-workspace +cd /tmp/coleman-matrix-workspace +/tmp/coleman-matrix-env/bin/python -m coleman.transports.junit_matrix \ + --cache /tmp/coleman-java-source-cache \ + --output /tmp/coleman-java-observations --fetch > matrix-summary.json + +# Same plan/trials: validate committed evidence rather than collect it again. +/tmp/coleman-matrix-env/bin/python -m coleman.transports.junit_matrix \ + --cache /tmp/coleman-java-source-cache \ + --output /tmp/coleman-java-observations +``` + +Only the first acquisition needs `--fetch`; it permits the existing individually +pinned HTTPS source/JAR downloads. Subject execution has no network. Both cache +and output must be outside Git and separate from each other. The system temporary +directory must also be outside Git. No third-party source or raw capture is bundled. + +The JSON summary reports the content-addressed receipt, optional completion path, +collection status, two declared project labels and three curated focal-fix labels. +Exit 0 means collection completed, including negative outcomes. Incomplete source +captures publish an index with `completion: null` and exit 2. Infrastructure, +preflight and publication errors exit nonzero and retain earlier durable evidence. +None of these statuses grants scientific admission. + +Validate a saved index without Docker or source execution: + +```bash +MATRIX_RECEIPT="$(/tmp/coleman-matrix-env/bin/python -c 'import json; print(json.load(open("matrix-summary.json"))["receipt"])')" +/tmp/coleman-matrix-env/bin/python -m coleman.transports.junit_matrix \ + --validate "$MATRIX_RECEIPT" \ + --cache /tmp/coleman-java-source-cache \ + --output /tmp/coleman-java-observations +``` + +Offline integrity validation can republish identical source-view cache metadata. +It verifies actual source members, context, raw protocol packets and normalized +observations; it starts no process and fetches nothing. Integrity is correspondence, +not authentication of execution truth or benchmark efficacy. + +## Frozen source selection + +| Curated fix | Direct upstream revisions | Common fixture | Relationship to framework metadata | +| --- | --- | --- | --- | +| CLI-13 | `8f46f467a33ace44ccd9f394910940b6c48a3827` → `b0e1b80b6d4a10a9c9f46539bc4c7a3cce55886e` | Existing published 95-test recipe, unchanged | Defects4J Cli **1**, not Cli13 | +| CLI-51 | `b0e1b80b6d4a10a9c9f46539bc4c7a3cce55886e` → `2ff9573ffb08dd52ec3a55a49f2d77a1e94efbdf` | Same fixed-tree policy, 96 tests | Defects4J Cli2 | +| CODEC-65 | `9c0cabead7cf075308b11362172ae1a48d41321c` → `52d82d1dfff8c2b2ded9d843e0b03017af6d747c` | Explicit partial fixed-tree fixture, 166 tests | Defects4J Codec1 | + +The [CLI-51 fix](https://github.com/apache/commons-cli/commit/2ff9573ffb08dd52ec3a55a49f2d77a1e94efbdf) +changes PosixParser and adds BugCLI51Test. The [CODEC-65 +fix](https://github.com/apache/commons-codec/commit/52d82d1dfff8c2b2ded9d843e0b03017af6d747c) +changes locale handling in several encoders. These are direct parent/fix source +reproductions with a common fixed fixture, not a full Defects4J reconstruction. +Framework subject labels do not replace source rights or reconstruction evidence. +Those labels were checked against the pinned Defects4J metadata revision +`8c16da8230843cdc918eaf4ddb449637f02b83c6` for +[Cli](https://github.com/rjust/defects4j/blob/8c16da8230843cdc918eaf4ddb449637f02b83c6/framework/projects/Cli/active-bugs.csv) +and [Codec](https://github.com/rjust/defects4j/blob/8c16da8230843cdc918eaf4ddb449637f02b83c6/framework/projects/Codec/active-bugs.csv). + +Codec retains all 25 production Java files per role, 15 fixed fixture Java files, +and original `LICENSE.txt`/`NOTICE.txt`. Fixture selection was recorded in +[#304](https://github.com/jacksonpradolima/coleman/issues/304) **before observing +new source outcomes**: + +- `DoubleMetaphoneTest.java` embeds separately noticed aspell data and non-UTF8 + bytes. It is outside the existing homogeneous-terms/UTF8 source-view profile. +- `SoundexTest.java` also contains non-UTF8 bytes and is excluded without transcoding. +- `AllTests.java` references those excluded classes and is excluded as their suite + aggregator. Per-TestCase discovery does not require it. + +All other fixed-tree Java fixture files remain. This includes +`RefinedSoundexTest.java`, a different file. Missing focal-class coverage stays +visible; this is not the complete upstream suite. No outcome-based filtering is +applied after collection. + +Source views preserve exact bytes and original notices. Apache-2.0 subject terms, +Commons Lang 2.1 terms and JUnit 3.8.1 CPL-1.0 terms remain separately reviewed and +pinned. The [Codec NOTICE](https://github.com/apache/commons-codec/blob/52d82d1dfff8c2b2ded9d843e0b03017af6d747c/NOTICE.txt) +identifies the omitted third-party test data; COLEMAN does not relabel it as +Apache-2.0. Codec needs only the pinned JUnit JAR; CLI retains its original two +dependencies. The recipe-only policy keeps foreign content in the external cache. + +## Observed results and their limits + +The initial installed-producer qualification collected **714 role observations**, +or **357 same-test/trial pairs**, under the frozen runtime: + +| Fix | Both pass | Both fail | Assertion failed → passed | Reversed | Inconclusive | +| --- | ---: | ---: | ---: | ---: | ---: | +| CLI-13 | 92 | 2 | 1 | 0 | 0 | +| CLI-51 | 93 | 2 | 0 | 0 | 1 | +| CODEC-65 | 163 | 0 | 3 | 0 | 0 | + +CLI-51's focal buggy test raises `UnrecognizedOptionException`; the fixed role +passes. The existing strict classifier calls this **inconclusive**, because a +test error is distinct from an assertion failure. The matrix preserves that +classification and raw diagnostic. Both CLI fixtures retain the two assertions +that fail in both revisions. A fixed revision is not presented as wholly correct. + +The three Codec assertions belong to Caverphone, Metaphone and RefinedSoundex +`testLocaleIndependence` methods. They concern **one** curated fix. The two CLI +fixes share project history. Tests, trials, seeds and JVM repetitions do not become +independent projects or new faults. These observations are runtime/fixture-specific, +not a guarantee about every future run. + +Each role uses the existing shared JVM and lexical test-ID order. Test-order +independence is unverified. Integer case nanoseconds include setup/teardown; parent +process nanoseconds also include startup/compilation. Observed zero remains zero; +unavailable elapsed values are null with `status: unavailable`. Negative counts, +negative elapsed counters, non-finite values and incompatible units reject. Neither +timer is CI queue time, parallel elapsed time, peak memory or removable runner work. +The existing guards bound each role to 60 seconds, 1 MiB combined output, two CPUs, +64 PIDs, 128 MiB tmpfs and 1 GiB memory in these presets. A resource limit is not +a measured peak. Captures are trusted-source reproductions within those guards. + +## Contract, artifacts and recovery + +```mermaid +flowchart LR + plan[Frozen typed Java matrix plan] --> preflight[Matrix storage and all-cell budget preflight] + preflight --> frozen[Immutable plan.json before source execution] + frozen --> source[Existing source cache and deterministic views] + source --> capture[Existing bounded JUnit producer] + capture --> raw[Durable role start markers and raw packets] + raw --> controlled[Existing generic ControlledDataset] + controlled --> verify[Offline context and raw observation validation] + verify --> index[Content-addressed typed matrix index] + index --> state{All roles collected?} + state -->|yes| complete[Atomic immutable complete.json last] + state -->|no| incomplete[Incomplete index; no completion marker] + complete --> replay[Offline verified replay; no runtime preflight] +``` + +Plans require schema version 1 and allow at most 16 cells / 4 MiB. Receipts require +schema version 1 and are bounded to 8 MiB. Canonical JSON and SHA-256 identities +include explicit source recipes, trial IDs, selection protocol and implementation +provenance. Reordering declared cells/roles does not change identity. Different +collected clocks or observations legitimately change a receipt; determinism means +identical captured evidence serializes identically, not that new executions have +identical elapsed time. + +Duplicate cell IDs and duplicate recipe/trial collections reject. Counts refer to +observed same-test pairs; `unobserved_pairs` preserves completely absent tests. +One-sided evidence remains inconclusive. The index references separately verified +controlled dataset fingerprints and actual raw packet digests, never arbitrary +transport dictionaries. It does not convert controlled observations into native +CI duration columns or historical builds. + +The original source producer owns role recovery. A start marker without a committed +packet recovers as interrupted, with no invented cases or elapsed time. It does +not silently rerun that role. Choose a new trial ID for a new collection; it stays +in the same declared dependence group. Concurrent ownership conflicts reject +without duplicate execution; retry after the owner finishes. A crash before matrix +completion leaves the frozen `plan.json` and committed role/data artifacts usable +for recovery. Unattempted cells remain visible in that plan without invented results. +An incomplete index is retained without `complete.json`; an all-role collected +index acquires that marker only after validation and immutable index publication. + +Idempotence uses the retained output/capture tree. A fresh output directory does +not restore another directory's acknowledgments; use new trial IDs for a fresh +physical collection. Copying an index alone is insufficient: offline validation +also needs its controlled datasets and the independently verified source cache. + +Existing completion is revalidated before any runtime preflight. Corrupt/unknown +schema or producer versions reject. Missing and older matrix schema versions are +unsupported; there is no implicit migration. A changed matrix implementation or +package version selects a new generation, preserving previous bytes. Explicit +offline validation requires the matching reviewed producer. Existing single-pair +JUnit recipes, source caches, controlled artifacts, native results and learning +checkpoints keep their previous contracts and require no migration. + +## Python and verification + +The optional producer API is also callable without its command-line parser: + +```python +from pathlib import Path +from coleman.artifacts import ArtifactWriter +from coleman.corpus.materialization import SourceCache +from coleman.transports.junit_matrix import ( + capture_junit_matrix, load_junit_matrix, validate_junit_matrix, +) + +cache = SourceCache("/tmp/coleman-java-source-cache") +writer = ArtifactWriter("/tmp/coleman-java-observations") +plan = load_junit_matrix() +outcome = capture_junit_matrix(plan, cache, writer) # Offline acquisition by default. +validate_junit_matrix(outcome.receipt, cache, Path(writer.run_root)) +assert outcome.receipt.admission == "not_evaluated" +``` + +Use `--recipe /absolute/path/matrix.json` for another reviewed typed plan. The +generic controlled domain stays independent of CLI, Docker transports and MCP. +Protected source admission and policy evaluation remain later #261 subtasks. + +Normal tests use owned small fixtures with no downloads. With the image prepared +and all three recipes acquired into an external cache, repeat installed real-source +capture, offline matrix validation, import-boundary checks and an independent owned +native CI/checkpoint workflow: + +```bash +COLEMAN_JUNIT_REAL_CACHE=/tmp/coleman-java-source-cache \ + uv run pytest tests/corpus/test_installed_junit_matrix.py --no-cov +``` + +The native CI fixture has its own exact-answer costs and outcomes; Java harness +elapsed counters are not substituted for CI costs. Actual historical-CI ETL/replay +remains available in the [Karaf](lrts-parquet-etl.md), +[ActiveMQ/Log4j](lrts-stage-views.md) and +[RTPTorrent](rtptorrent-parquet-etl.md) workflows. + + + ### FILE: docs/junit-source-capture.md # Reproduce a pinned Java fault pair @@ -5809,10 +6067,16 @@ container images and raw captures remain outside the repository. It does not execute Defects4J or claim its complete reconstruction protocol. The generic [controlled domain](controlled-faults.md) imports no Docker, CLI or MCP adapter. +For a predeclared multi-fix workflow, this revision adds a separate +[controlled Java matrix](java-fault-matrix.md), reusing this producer unchanged. +It includes CLI-13, CLI-51 and an explicitly partial CODEC-65 fixture, with +negative/inconclusive results retained. + ## Prepare and run -Build and install this branch's wheel as shown in the controlled-observation guide. -The released 4.5 wheel predates this producer. The bundled preset requires POSIX, +The published 4.9 wheel includes this single-pair producer; use the verified +[setup command](setup.md#default-run-no-docker-required). Build this revision's +wheel for the new matrix command. The bundled preset requires POSIX, Docker, an arm64 host and arm64 Docker engine. It pins Temurin `11.0.32.1` and `America/Los_Angeles`. Other platforms require a separately reviewed recipe; changing a platform label does not validate a different image. @@ -8079,6 +8343,70 @@ remain work in the [public roadmap](https://jacksonpradolima.github.io/coleman/r +### FILE: docs/releases/4.10.0.md + +# COLEMAN 4.10 — Inspect controlled faults across Java codebases + +Reproduce a small, explicit matrix of real upstream fixes before making a +benchmark claim. COLEMAN now collects CLI-13, CLI-51 and CODEC-65 with frozen +sources, common test fixtures and the existing bounded JUnit producer. Every +selected result remains inspectable, including errors and failures that persist +in both revisions. + +## What you can do + +- **Collect a declared matrix.** One typed plan describes three focal fixes across + Apache Commons CLI and Codec. Pinned source views, original notices, JARs, + runtime image, architecture, timezone and harness make the protocol explicit. +- **Keep negative evidence.** The initial qualification retained 714 role + observations / 357 same-test pairs: 348 both-pass, four both-fail, four + assertion-failed-to-passed and one inconclusive comparison. CLI-51's test error + remains inconclusive under the existing classifier. Three Codec triggering + tests do not become three faults. +- **Resume without inventing observations.** Existing role acknowledgments and + raw packets retain interruption semantics. Typed indices distinguish observed + pairs from entirely unobserved tests; incomplete collection has no completion + marker. A verified completed matrix reopens offline without querying Docker. +- **Verify the evidence behind the index.** Offline validation checks actual + source/context bytes, raw protocols, normalized observations and diagnostic + references before accepting counts, identities or collection status. + +The [complete matrix guide](https://jacksonpradolima.github.io/coleman/java-fault-matrix/) +provides installation, explicit runtime preparation, source acquisition, typed +Python use, CLI collection/validation, recovery and the installed-package workflow. +Foreign sources, dependencies and captures stay in operator-owned external storage. + +## Compatibility and limits + +The new optional transport adds versioned matrix plans/indices while reusing the +existing generic controlled domain, source cache, JUnit producer and immutable +artifact writer. Old single-pair recipes, controlled artifacts, native results, +RunSpec identities and learning checkpoints retain their semantics and require +no migration. Unknown matrix schemas or producers reject; there is no implicit +reinterpretation of prior evidence. + +Codec's common fixture is explicitly partial. Before outcomes were observed, +three fixture files were excluded because of separately noticed third-party data, +non-UTF8 source bytes or dependencies on excluded classes. Remaining source bytes +and original LICENSE/NOTICE are preserved. This is direct-upstream reproduction, +not the complete original build or a full Defects4J reconstruction. + +The CLI fixes share project history. Multiple tests, seeds or trials do not +establish independent projects or unique faults. Collection clocks and harness +nanoseconds are not historical CI events, runner work or parallel wall-clock +savings. Shared-JVM test-order independence remains unverified. All outputs retain +`not_evaluated` and `insufficient_evidence`; diversified source admission, baseline +comparisons and confirmation in #261 remain open. + +Validation covers versioned goldens, old recipes, strict units/missingness, +non-finite rejection, deterministic identities, duplicate accounting, negative +results, source/raw/index correspondence, interrupted publication, concurrency, +offline continuation and domain import boundaries. Installed-package checks use +actual Java source collection and a separate native CI exact-answer/checkpoint +workflow. This validates the evidence pipeline, not algorithm effectiveness. + + + ### FILE: docs/releases/4.2.0.md # COLEMAN 4.2 — Reproduce what your CI decision knew @@ -9318,6 +9646,14 @@ confirmatory work continues through the public subtasks. #303's new profiles preserve all raw/processed stages and use exact context/node bindings, while retaining explicit missing temporal evidence. Remaining expansion begins with #304. +This revision implements #304's [bounded Java fault matrix](java-fault-matrix.md) +on the existing source producer: CLI-13, CLI-51 and an explicitly partial CODEC-65 +fixture. Typed plans, raw/context verification, honest incomplete indices and +offline recovery preserve all negative outcomes. Source qualification collected +714 role observations / 357 same-test pairs across two codebases. Controlled +source collection remains separate from admission and policy comparison in #309 +onward; the remaining source subtasks follow sequentially. + **4.9.0** publishes the stage-view contracts and three frozen presets: ActiveMQ, Log4j Ubuntu and Log4j Windows. All raw observations/processed stages remain analytical evidence; exact context/node bindings select one native view. The diff --git a/tests/corpus/fixtures/junit-matrix-owned-v1.json b/tests/corpus/fixtures/junit-matrix-owned-v1.json new file mode 100644 index 00000000..9a910403 --- /dev/null +++ b/tests/corpus/fixtures/junit-matrix-owned-v1.json @@ -0,0 +1 @@ +{"cells":[{"cell_id":"owned-0","fixture_selection":"Owned schema-only common fixture, not executable 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b/tests/corpus/test_installed_junit_matrix.py new file mode 100644 index 00000000..0c0c65e4 --- /dev/null +++ b/tests/corpus/test_installed_junit_matrix.py @@ -0,0 +1,124 @@ +"""Fresh base wheel: offline owned matrix, domain boundaries, native CI and optional actual Java sources.""" + +import json +import os +import shutil +import sys + +from coleman.transports import junit_matrix as matrix +from tests.corpus.test_installed_controlled import ROOT, command +from tests.corpus.test_junit_matrix import owned_capture + + +def test_installed_matrix_validation_native_ci_and_optional_real_sources(tmp_path, monkeypatch): + with monkeypatch.context() as external: + plan, cache, writer, _ = owned_capture(tmp_path, external) + owned = matrix.capture_junit_matrix(plan, cache, writer) + uv = shutil.which("uv") + assert uv is not None + env = {key: value for key, value in os.environ.items() if key not in {"PYTHONPATH", "PYTHONHOME"}} + env.update(UV_LINK_MODE="copy", UV_NO_PROGRESS="1") + dist = tmp_path / "dist" + command([uv, "build", "--wheel", "--out-dir", str(dist)], ROOT, env) + virtual = tmp_path / "installed" + command([uv, "venv", str(virtual), "--python", sys.executable], tmp_path, env) + python = virtual / "bin/python" + command([uv, "pip", "install", "--offline", "--python", str(python), str(next(dist.glob("*.whl")))], tmp_path, env) + outside = tmp_path / "outside" + outside.mkdir() + script = """ +import importlib.abc,json,sys +from pathlib import Path +class Boundary(importlib.abc.MetaPathFinder): + def find_spec(self,fullname,path=None,target=None): + if fullname=='coleman.cli' or fullname.startswith(('coleman.transports','mcp')): + raise AssertionError('Controlled domain imported a transport: '+fullname) +boundary=Boundary();sys.meta_path.insert(0,boundary) +from coleman.corpus.controlled import validate_controlled_dataset +from coleman.corpus.controlled_contracts import ControlledDataset +assert Path(sys.modules['coleman.corpus.controlled'].__file__).resolve().is_relative_to(Path(sys.prefix)) +sys.meta_path.remove(boundary) +from coleman.transports.junit_matrix import capture_junit_matrix,load_junit_matrix,validate_junit_matrix +from coleman.transports.junit_matrix_contracts import JunitMatrixRecipe,JunitMatrixReceipt +from coleman.transports.junit_source import digest,harness_bytes +from coleman.artifacts import ArtifactWriter +from coleman.corpus.materialization import SourceCache +assert Path(sys.modules['coleman.transports.junit_matrix'].__file__).resolve().is_relative_to(Path(sys.prefix)) +owned=JunitMatrixReceipt.from_json(Path(sys.argv[3]).read_bytes()) +cache=SourceCache(sys.argv[1]);output=Path(sys.argv[2]) +validate_junit_matrix(owned,cache,output) +# This must complete without querying Docker: the original owned image does not exist. +replay=capture_junit_matrix(owned.plan,cache,ArtifactWriter(output)) +assert replay.receipt==owned +assert replay.completion_path is not None +assert replay.completion_path.read_bytes()==Path(sys.argv[3]).read_bytes() +plan=load_junit_matrix() +assert sorted(len(cell.recipe.test_ids) for cell in plan.cells)==[95,96,166] +assert all(cell.recipe.harness_sha256==digest(harness_bytes()) for cell in plan.cells) +assert JunitMatrixRecipe.from_json(plan.to_json())==plan +future=json.loads(plan.to_json());future['schema_version']=99 +try:JunitMatrixRecipe.from_json(json.dumps(future)) +except ValueError:pass +else:raise AssertionError('Future matrix schema was accepted') +proof={'installed':True,'owned_offline_validation':True,'real_source_capture':False} +if sys.argv[4]!='-': + real_cache=SourceCache(sys.argv[4]);writer=ArtifactWriter('real-java-matrix') + first=capture_junit_matrix(plan,real_cache,writer) + second=capture_junit_matrix(plan,real_cache,writer) + assert first==second + validate_junit_matrix(first.receipt,real_cache,writer.run_root) + assert first.receipt.status=='collected' + assert first.receipt.declared_projects==2 + assert first.receipt.curated_focal_fixes==3 + expected={'cli-13':(1,92,2,0,0),'cli-51':(0,93,2,0,1),'codec-65':(3,163,0,0,0)} + for cell in first.receipt.cells: + counts=cell.pairs + values=(counts.expected,counts.both_pass,counts.both_fail,counts.reversed,counts.inconclusive) + assert values==expected[cell.cell_id] + assert cell.unobserved_pairs==0 + assert sum(cell.pairs.total for cell in first.receipt.cells)==357 + assert first.receipt.admission=='not_evaluated' + assert first.receipt.generalization=='insufficient_evidence' + proof.update(real_source_capture=True,real_receipt=str(first.receipt_path.resolve()), + actual_matrix=first.receipt.model_dump(mode='json')) +print(json.dumps(proof,sort_keys=True)) +""" + source_cache = env.get("COLEMAN_JUNIT_REAL_CACHE", "-") + result = command( + [str(python), "-c", script, str(cache.root), str(writer.run_root), str(owned.receipt_path), source_cache], + outside, + env, + ) + proof = json.loads(result.stdout) + assert proof["installed"] and proof["owned_offline_validation"] + assert proof["real_source_capture"] == (source_cache != "-") + cli = command( + [ + str(python), + "-m", + "coleman.transports.junit_matrix", + "--validate", + str(owned.receipt_path), + "--cache", + str(cache.root), + "--output", + str(writer.run_root), + ], + outside, + env, + ) + assert json.loads(cli.stdout)["integrity"] == "verified" + # Native CI uses its own owned exact-answer fixture, never Java elapsed counters as CI costs. + shutil.copyfile(ROOT / "examples/controlled_faults/ci.py", outside / "ci.py") + runs = [ + json.loads( + command([str(python), "ci.py", "native-owned", str(tmp_path / "native-cache")], outside, env) + .stdout.strip() + .splitlines()[-1] + ) + for _ in range(2) + ] + assert runs[0] == runs[1] + assert runs[0]["native_rows"] == 1 + proof["owned_native_ci_checkpoint"] = runs[0] + (tmp_path / "installed-junit-matrix-proof.json").write_text(json.dumps(proof, indent=2) + "\n") diff --git a/tests/corpus/test_junit_matrix.py b/tests/corpus/test_junit_matrix.py new file mode 100644 index 00000000..ef3fa5c2 --- /dev/null +++ b/tests/corpus/test_junit_matrix.py @@ -0,0 +1,519 @@ +"""Owned matrix contracts and real cache/capture publication; only external Docker is substituted.""" + +import io +import json +from concurrent.futures import ThreadPoolExecutor +from pathlib import Path +from types import SimpleNamespace + +import pytest + +from coleman.artifacts import ArtifactWriter +from coleman.corpus.archives import deterministic_zip_bytes +from coleman.corpus.controlled import convert_controlled_source, publish_controlled_dataset, validate_controlled_dataset +from coleman.corpus.controlled_contracts import ControlledDataset, ControlledReport +from coleman.corpus.materialization import materialize_source +from coleman.corpus.materialization_contracts import PackageMember +from coleman.transports import junit_capture as capture +from coleman.transports import junit_matrix as matrix +from coleman.transports.junit_contracts import ProducerElapsed +from coleman.transports.junit_matrix_contracts import ( + JunitMatrixCell, + JunitMatrixCellResult, + JunitMatrixReceipt, + JunitMatrixRecipe, + JunitMatrixRole, + JunitPairCounts, +) +from coleman.transports.junit_process import ProcessStreams +from tests.corpus.test_controlled import digest +from tests.corpus.test_junit_capture import prepared_inputs, substitute_docker +from tests.corpus.test_junit_protocol import changed, encoded, recipe, records + + +def owned_plan(spec=None, trials=("owned-trial",)): + """Declare schema-only owned inputs; no foreign Java code or image is present.""" + return JunitMatrixRecipe( + schema_version=1, + matrix_id="owned-java-matrix", + cells=tuple( + JunitMatrixCell( + cell_id="owned-" + str(index), + trial_id=trial, + source_reference="urn:coleman:owned:source-fix", + fixture_selection="Owned schema-only common fixture, not executable Java", + recipe=spec or recipe(), + ) + for index, trial in enumerate(trials) + ), + limitations=("Owned schema-only evidence; no real fault or independence claim",), + ) + + +def owned_capture(tmp_path, monkeypatch, trials=("owned-trial",)): + """Prepare actual source-cache contracts and substitute only external Docker process calls.""" + spec, cache, environment = prepared_inputs(tmp_path) + calls = [] + + def run(*args): + role = args[-2] + calls.append(role) + rows = records() + rows[1]["failures"] = int(role == "buggy") + return ProcessStreams(encoded(rows), b"owned diagnostic", 0, 0, "exited") + + substitute_docker(monkeypatch, environment, run) + return owned_plan(spec, trials), cache, ArtifactWriter(tmp_path / "results"), calls + + +def owned_receipt(): + """Construct stable schema-only index metadata; pins do not claim real datasets or execution.""" + plan = owned_plan() + roles = tuple( + JunitMatrixRole( + role=role, + packet_sha256="sha256:" + digit * 64, + status="collected", + producer_elapsed=ProducerElapsed(value=0, status="observed"), + ) + for role, digit in (("buggy", "2"), ("fixed", "3")) + ) + result = JunitMatrixCellResult( + cell_id=plan.cells[0].cell_id, + dataset_fingerprint="sha256:" + "0" * 64, + context_fingerprint="sha256:" + "1" * 64, + planned_pairs=1, + unobserved_pairs=0, + pairs=JunitPairCounts(expected=1), + roles=roles, + ) + return JunitMatrixReceipt( + schema_version=1, + plan=plan, + producer_sha256="sha256:" + "4" * 64, + cells=(result,), + status="collected", + ) + + +def test_plan_roundtrip_golden_and_declaration_order_metamorphism(): + plan = owned_plan(trials=("trial-a", "trial-b")) + assert JunitMatrixRecipe.from_json(plan.to_json()) == plan + assert changed(plan, cells=tuple(reversed(plan.cells))).fingerprint == plan.fingerprint + fixture = Path(__file__).with_name("fixtures") / "junit-matrix-owned-v1.json" + assert plan.to_json() + "\n" == fixture.read_text() + # Existing schema-1 JUnit recipes remain byte-identical, without a matrix wrapper. + old = Path(__file__).with_name("fixtures") / "junit-recipe-owned-v1.json" + assert recipe().to_json() + "\n" == old.read_text() + + +def test_receipt_roundtrip_versioned_golden_and_strict_accounting(): + receipt = owned_receipt() + fixture = Path(__file__).with_name("fixtures") / "junit-matrix-receipt-owned-v1.json" + assert receipt.to_json() + "\n" == fixture.read_text() + assert JunitMatrixReceipt.from_json(fixture.read_bytes()) == receipt + with pytest.raises(ValueError, match="collection status"): + changed(receipt, status="incomplete") + with pytest.raises(ValueError, match="conservation"): + changed(receipt.cells[0], unobserved_pairs=1) + with pytest.raises(ValueError, match="distinct source roles"): + changed(receipt.cells[0], roles=(receipt.cells[0].roles[0], receipt.cells[0].roles[0])) + unknown_cell = changed(receipt.cells[0], cell_id="unknown") + with pytest.raises(ValueError, match="cover planned"): + changed(receipt, cells=(unknown_cell,)) + with pytest.raises(ValueError, match="Duplicate Java matrix result"): + changed(receipt, cells=(receipt.cells[0], receipt.cells[0])) + + +@pytest.mark.parametrize("location", ["receipt", "plan", "source_recipe"]) +def test_unknown_versions_in_receipt_or_nested_contracts_reject(location): + data = json.loads(owned_receipt().to_json()) + target = data if location == "receipt" else data["plan"] + if location == "source_recipe": + target = target["cells"][0]["recipe"] + target["schema_version"] = 2 + payload = json.dumps(data) + with pytest.raises(ValueError): + JunitMatrixReceipt.from_json(payload) + + +@pytest.mark.parametrize( + "update", + [ + {"unit": "ms"}, + {"value": None}, + {"value": -1}, + {"value": float("inf")}, + {"value": float("nan")}, + {"status": "unavailable"}, + ], +) +def test_index_process_units_missingness_and_nonfinite_counters_reject(update): + data = owned_receipt().model_dump(mode="json") + data["cells"][0]["roles"][0]["producer_elapsed"].update(update) + with pytest.raises(ValueError): + JunitMatrixReceipt.model_validate(data) + + +@pytest.mark.parametrize("schema", [None, 0, 2, 99, True, 1.5]) +def test_plan_unknown_or_missing_schema_rejects(schema): + data = json.loads(owned_plan().to_json()) + if schema is None: + del data["schema_version"] + else: + data["schema_version"] = schema + payload = json.dumps(data) + with pytest.raises(ValueError): + JunitMatrixRecipe.from_json(payload) + + +def test_duplicate_ids_and_recipe_trial_collections_reject(): + plan = owned_plan(trials=("a", "b")) + duplicate_id = changed(plan.cells[1], cell_id=plan.cells[0].cell_id) + with pytest.raises(ValueError, match="cell identity"): + changed(plan, cells=(plan.cells[0], duplicate_id)) + duplicate_trial = changed(plan.cells[1], trial_id=plan.cells[0].trial_id) + with pytest.raises(ValueError, match="recipe/trial"): + changed(plan, cells=(plan.cells[0], duplicate_trial)) + + +@pytest.mark.parametrize("value", [-1, None, True, float("inf"), float("nan")]) +def test_pair_counts_reject_negative_missing_and_nonfinite_values(value): + with pytest.raises(ValueError): + JunitPairCounts(expected=value) + + +def test_capture_roundtrip_raw_correspondence_replay_and_cli(tmp_path, monkeypatch, capsys): + plan, cache, writer, calls = owned_capture(tmp_path, monkeypatch, ("a", "b")) + first = matrix.capture_junit_matrix(plan, cache, writer) + second = matrix.capture_junit_matrix(plan, cache, writer) + assert first == second + assert calls == ["buggy", "fixed", "buggy", "fixed"] + receipt = JunitMatrixReceipt.from_json(first.receipt_path.read_bytes()) + assert receipt == first.receipt + assert first.completion_path is not None + assert first.completion_path.read_bytes() == first.receipt_path.read_bytes() + assert receipt.status == "collected" + assert receipt.declared_projects == 1 + assert receipt.curated_focal_fixes == 1 + assert receipt.admission == "not_evaluated" + assert receipt.generalization == "insufficient_evidence" + assert all(cell.pairs.expected == 1 and cell.unobserved_pairs == 0 for cell in receipt.cells) + assert all(role.producer_elapsed.value == 0 for cell in receipt.cells for role in cell.roles) + matrix.validate_junit_matrix(receipt, cache, writer.run_root) + reversed_cells = tuple(changed(cell, roles=tuple(reversed(cell.roles))) for cell in reversed(receipt.cells)) + assert changed(receipt, cells=reversed_cells).fingerprint == receipt.fingerprint + path = tmp_path / "plan.json" + path.write_text(plan.to_json()) + assert matrix.main(["--recipe", str(path), "--cache", str(cache.root), "--output", str(writer.run_root)]) == 0 + summary = json.loads(capsys.readouterr().out) + assert summary["curated_focal_fixes"] == 1 + assert summary["declared_projects"] == 1 + assert ( + matrix.main( + ["--validate", str(first.receipt_path), "--cache", str(cache.root), "--output", str(writer.run_root)] + ) + == 0 + ) + assert json.loads(capsys.readouterr().out)["integrity"] == "verified" + assert len(calls) == 4 + + +def test_interrupted_roles_remain_unobserved_without_false_completion(tmp_path, monkeypatch): + plan, cache, writer, calls = owned_capture(tmp_path, monkeypatch) + + def interrupted(*args): + calls.append(args[-2]) + raise KeyboardInterrupt + + monkeypatch.setattr(capture, "_run_role", interrupted) + for _ in range(2): + with pytest.raises(KeyboardInterrupt): + matrix.capture_junit_matrix(plan, cache, writer) + assert not list(writer.run_root.rglob("complete.json")) + plans = list(writer.run_root.rglob("plan.json")) + assert len(plans) == 1 + assert plans[0].read_text() == plan.to_json() + "\n" + outcome = matrix.capture_junit_matrix(plan, cache, writer) + assert calls == ["buggy", "fixed"] + assert outcome.completion_path is None + assert outcome.receipt.status == "incomplete" + cell = outcome.receipt.cells[0] + assert cell.unobserved_pairs == 1 + assert cell.pairs.total == 0 + assert all(role.status == "interrupted" for role in cell.roles) + assert all(role.producer_elapsed.value is None for role in cell.roles) + assert all(role.producer_elapsed.status == "unavailable" for role in cell.roles) + assert matrix.capture_junit_matrix(plan, cache, writer) == outcome + assert not list(writer.run_root.rglob("complete.json")) + + +def test_completion_failure_recovers_existing_captures_without_rerun(tmp_path, monkeypatch): + plan, cache, writer, calls = owned_capture(tmp_path, monkeypatch) + original = writer.write_immutable + + def interrupted(path, content): + if path.name == "complete.json": + raise OSError("owned final publication interruption") + original(path, content) + + monkeypatch.setattr(writer, "write_immutable", interrupted) + with pytest.raises(OSError, match="publication interruption"): + matrix.capture_junit_matrix(plan, cache, writer) + assert not list(writer.run_root.rglob("complete.json")) + monkeypatch.setattr(writer, "write_immutable", original) + recovered = matrix.capture_junit_matrix(plan, cache, writer) + assert recovered.completion_path is not None + assert recovered.completion_path.exists() + assert calls == ["buggy", "fixed"] + + +def test_concurrent_contenders_preserve_existing_lock_rejection_and_replay(tmp_path, monkeypatch): + plan, cache, writer, calls = owned_capture(tmp_path, monkeypatch) + with ThreadPoolExecutor(max_workers=2) as pool: + futures = [pool.submit(matrix.capture_junit_matrix, plan, cache, writer) for _ in range(2)] + outcomes = [] + for future in futures: + try: + outcomes.append(future.result()) + except ValueError as error: + assert "Another producer owns this context/trial" in str(error) + assert outcomes + replay = matrix.capture_junit_matrix(plan, cache, writer) + assert all(outcome == replay for outcome in outcomes) + assert calls == ["buggy", "fixed"] + assert len(list(writer.run_root.rglob("complete.json"))) == 1 + + +def test_forged_index_counts_and_unknown_producer_reject(tmp_path, monkeypatch): + plan, cache, writer, _ = owned_capture(tmp_path, monkeypatch) + receipt = matrix.capture_junit_matrix(plan, cache, writer).receipt + altered_cell = changed(receipt.cells[0], pairs=JunitPairCounts(both_pass=1)) + forged = changed(receipt, cells=(altered_cell,)) + with pytest.raises(ValueError, match="actual source evidence"): + matrix.validate_junit_matrix(forged, cache, writer.run_root) + unknown = changed(receipt, producer_sha256="sha256:" + "f" * 64) + with pytest.raises(ValueError, match="Unknown Java matrix producer"): + matrix.validate_junit_matrix(unknown, cache, writer.run_root) + + +def test_nested_git_and_escaped_generation_reject_before_source_capture(tmp_path, monkeypatch): + plan, cache, writer, calls = owned_capture(tmp_path, monkeypatch) + base = writer.run_root / "corpus-junit-matrix" + base.mkdir(parents=True) + (base / ".git").mkdir() + with pytest.raises(ValueError, match="outside a repository"): + matrix.capture_junit_matrix(plan, cache, writer) + assert not calls + (base / ".git").rmdir() + base.rmdir() + elsewhere = tmp_path / "elsewhere" + elsewhere.mkdir() + base.symlink_to(elsewhere, target_is_directory=True) + with pytest.raises(ValueError, match="within its output tree"): + matrix.capture_junit_matrix(plan, cache, writer) + assert not calls + + +def test_metadata_bounds_fetch_type_and_validation_are_preflighted(tmp_path, monkeypatch): + plan, cache, writer, calls = owned_capture(tmp_path, monkeypatch) + invalid_fetch = json.loads("1") + with pytest.raises(ValueError, match="boolean"): + matrix.capture_junit_matrix(plan, cache, writer, fetch=invalid_fetch) + monkeypatch.setattr(JunitMatrixRecipe, "MAXIMUM_BYTES", 1) + with pytest.raises(ValueError, match="byte limit"): + matrix.capture_junit_matrix(plan, cache, writer) + oversized = tmp_path / "oversized.json" + oversized.write_bytes(b"{}") + with pytest.raises(ValueError, match="byte limit"): + matrix.load_junit_matrix(oversized) + assert not calls + + +def test_published_prior_recipe_and_new_frozen_presets_bind_actual_harness(): + plan = matrix.load_junit_matrix() + assert len(plan.cells) == 3 + assert {cell.recipe.project for cell in plan.cells} == {"Apache Commons CLI", "Apache Commons Codec"} + assert sorted(len(cell.recipe.test_ids) for cell in plan.cells) == [95, 96, 166] + codec = next(cell.recipe for cell in plan.cells if cell.recipe.fault_id == "CODEC-65") + assert len(codec.buggy.inputs) == len(codec.fixed.inputs) == 27 + assert len(codec.fixture.inputs) == 17 + names = {member.name for member in codec.fixture.output.members} + excluded = {"DoubleMetaphoneTest.java", "SoundexTest.java", "AllTests.java"} + assert not any(Path(name).name in excluded for name in names) + assert {"LICENSE.txt", "NOTICE.txt"}.issubset(names) + + +@pytest.mark.parametrize( + "status,elapsed", + [ + ("interrupted", ProducerElapsed(value=0, status="observed")), + ("collected", ProducerElapsed(value=None, status="unavailable")), + ("timeout", ProducerElapsed(value=None, status="unavailable")), + ("output_limit", ProducerElapsed(value=None, status="unavailable")), + ("protocol_error", ProducerElapsed(value=None, status="unavailable")), + ], +) +def test_role_status_cannot_invent_or_discard_elapsed_observations(status, elapsed): + with pytest.raises(ValueError, match="elapsed"): + JunitMatrixRole(role="buggy", packet_sha256="sha256:" + "a" * 64, status=status, producer_elapsed=elapsed) + + +def test_completed_matrix_replay_is_offline_without_runtime_preflight(tmp_path, monkeypatch): + plan, cache, writer, calls = owned_capture(tmp_path, monkeypatch) + first = matrix.capture_junit_matrix(plan, cache, writer) + + def unavailable(*args, **kwargs): + raise AssertionError("Completed matrix replay must not start runtime preflight or source capture") + + monkeypatch.setattr(matrix, "capture_junit_source", unavailable) + assert matrix.capture_junit_matrix(plan, cache, writer) == first + assert calls == ["buggy", "fixed"] + + +def test_corrupt_completion_rejects_before_source_capture(tmp_path, monkeypatch): + plan, cache, writer, calls = owned_capture(tmp_path, monkeypatch) + first = matrix.capture_junit_matrix(plan, cache, writer) + assert first.completion_path is not None + first.completion_path.write_text('{"schema_version":99}') + with pytest.raises(ValueError): + matrix.capture_junit_matrix(plan, cache, writer) + assert calls == ["buggy", "fixed"] + + +@pytest.mark.parametrize( + "buggy,fixed,classification", + [ + ((0, 0), (0, 0), "both_pass"), + ((1, 0), (1, 0), "both_fail"), + ((0, 0), (1, 0), "reversed"), + ((0, 1), (0, 0), "inconclusive"), + ], +) +def test_negative_reversed_and_error_results_remain_evidence(tmp_path, monkeypatch, buggy, fixed, classification): + plan, cache, writer, _ = owned_capture(tmp_path, monkeypatch) + + def observed(*args): + rows = records() + rows[1]["failures"], rows[1]["errors"] = buggy if args[-2] == "buggy" else fixed + return ProcessStreams(encoded(rows), b"owned compiler diagnostic", 0, 0, "exited") + + monkeypatch.setattr(capture, "_run_role", observed) + outcome = matrix.capture_junit_matrix(plan, cache, writer) + assert outcome.receipt.status == "collected" + assert getattr(outcome.receipt.cells[0].pairs, classification) == 1 + assert outcome.receipt.cells[0].pairs.total == 1 + assert outcome.receipt.admission == "not_evaluated" + + +def repinned_owned_forgery(dataset, cache, kind): + """Create coherent generic source envelopes that still violate the Java capture protocol. + + Recomputing all physical digests must not turn a rewritten normalized outcome, + context, missing packet or raw-case annotation into accepted Java evidence. + """ + package = dataset.spec.report_materialization + entries = {member.name: cache.member_path(package, member.name).read_bytes() for member in package.spec.members} + report = ControlledReport.from_json(entries["report.json"]) + context = dataset.spec.context + observations = list(report.observations) + if kind == "normalized_outcome": + observations = [changed(item, outcome="passed") if item.role == "buggy" else item for item in observations] + elif kind == "context": + context = changed(context, project="rewritten-owned-project") + elif kind == "missing_packet": + del entries["fixed-capture.json"] + observations = [item for item in observations if item.role != "fixed"] + else: + raw = json.loads(entries["buggy-capture.json"]) + if kind == "packet_identity": + raw["trial_id"] = "different-trial" + else: + raw["cases"][0]["elapsed_ns"] = 1 + entries["buggy-capture.json"] = json.dumps(raw, sort_keys=True).encode() + pin = digest(entries["buggy-capture.json"]) + observations = [ + changed(item, diagnostics_sha256=pin) if item.role == "buggy" else item for item in observations + ] + entries["report.json"] = ( + changed(report, context_fingerprint=context.fingerprint, observations=tuple(observations)).to_json().encode() + ) + payload = deterministic_zip_bytes( + tuple(sorted(entries.items())), maximum_member_bytes=16 * 1024**2, maximum_total_bytes=40 * 1024**2 + ) + spec = changed( + package.spec, + package_id="owned-repinned-forgery", + source=changed( + package.spec.source, + uri="urn:coleman:owned:repinned-forgery", + sha256=digest(payload), + size_bytes=len(payload), + ), + members=tuple( + PackageMember(name=name, sha256=digest(data), size_bytes=len(data)) + for name, data in sorted(entries.items()) + ), + ) + receipt = materialize_source(spec, cache, lambda: io.BytesIO(payload)) + return convert_controlled_source(changed(dataset.spec, context=context, report_materialization=receipt), cache) + + +@pytest.mark.parametrize( + "kind,problem", + [ + ("normalized_outcome", "normalized observations"), + ("context", "context disagrees"), + ("missing_packet", "raw role packet"), + ("packet_identity", "raw role identity"), + ("raw_annotation", "disagree with raw streams"), + ], +) +def test_repinning_all_digests_does_not_certify_forged_java_evidence(tmp_path, monkeypatch, kind, problem): + plan, cache, writer, _ = owned_capture(tmp_path, monkeypatch) + outcome = matrix.capture_junit_matrix(plan, cache, writer) + reference = outcome.receipt.cells[0] + path = writer.run_root / "corpus-controlled" / (reference.dataset_fingerprint.removeprefix("sha256:") + ".json") + dataset = ControlledDataset.from_json(path.read_bytes()) + forged = repinned_owned_forgery(dataset, cache, kind) + validate_controlled_dataset(forged, cache) + publish_controlled_dataset(forged, cache, writer) + index = changed(outcome.receipt, cells=(changed(reference, dataset_fingerprint=forged.fingerprint),)) + with pytest.raises(ValueError, match=problem): + matrix.validate_junit_matrix(index, cache, writer.run_root) + + +def test_validation_enforces_plan_receipt_and_dataset_budgets(tmp_path, monkeypatch): + plan, cache, writer, _ = owned_capture(tmp_path, monkeypatch) + receipt = matrix.capture_junit_matrix(plan, cache, writer).receipt + with monkeypatch.context() as limits: + limits.setattr(JunitMatrixRecipe, "MAXIMUM_BYTES", 1) + with pytest.raises(ValueError, match="plan exceeds"): + matrix.validate_junit_matrix(receipt, cache, writer.run_root) + with monkeypatch.context() as limits: + limits.setattr(JunitMatrixReceipt, "MAXIMUM_BYTES", 1) + with pytest.raises(ValueError, match="receipt exceeds"): + matrix.validate_junit_matrix(receipt, cache, writer.run_root) + monkeypatch.setattr(matrix, "_DATASET_BYTES", 1) + with pytest.raises(ValueError, match="metadata exceeds"): + matrix.validate_junit_matrix(receipt, cache, writer.run_root) + + +@pytest.mark.parametrize( + "package,module", [("coleman.transports", "junit_protocol.py"), ("coleman.corpus", "source_views.py")] +) +def test_changing_reused_producer_dependency_changes_matrix_generation(monkeypatch, package, module): + before = matrix.junit_matrix_producer() + original = matrix.files + + def altered_files(namespace): + def item(name): + payload = original(namespace).joinpath(name).read_bytes() + if (namespace, name) == (package, module): + payload += b"\n# Owned provenance metamorphism\n" + return SimpleNamespace(read_bytes=lambda: payload) + + return SimpleNamespace(joinpath=item) + + monkeypatch.setattr(matrix, "files", altered_files) + assert matrix.junit_matrix_producer() != before diff --git a/zensical.toml b/zensical.toml index c29e84af..5a7bbb68 100644 --- a/zensical.toml +++ b/zensical.toml @@ -32,6 +32,7 @@ nav = [ { "LRTS Stage Views & Larger Histories" = "lrts-stage-views.md" }, { "Controlled Fault Observations" = "controlled-faults.md" }, { "Pinned JUnit Source Capture" = "junit-source-capture.md" }, + { "Controlled Java Fault Matrix" = "java-fault-matrix.md" }, { "Point-in-time CI Observations" = "point-in-time-observations.md" }, { "ADR 001: Point-in-time Boundary" = "decisions/001-point-in-time-observations.md" }, { "Operational CI Pilot" = "operational-pilot.md" }, @@ -43,6 +44,7 @@ nav = [ { "Setup & Architecture" = "setup.md" }, { "Code Cost Evaluation" = "code-cost.md" }, { "Dependency Security" = "dependency-security.md" }, + { "COLEMAN 4.10" = "releases/4.10.0.md" }, { "COLEMAN 4.9" = "releases/4.9.0.md" }, { "COLEMAN 4.8" = "releases/4.8.0.md" }, { "COLEMAN 4.7" = "releases/4.7.0.md" }, From 9b62bb631dfd2a83cdaec8b10f79551ffff74fe1 Mon Sep 17 00:00:00 2001 From: Jackson Antonio do Prado Lima Date: Fri, 16 Oct 2026 22:57:01 -0300 Subject: [PATCH 2/6] fix: disclose uncaptured upstream fixture randomness --- .../apache-codec65-junit3-arm64-v1.json | 2 +- .../java-real-fault-matrix-arm64-v1.json | 2 +- docs/java-fault-matrix.md | 10 ++++++++++ docs/releases/4.10.0.md | 3 +++ llms.txt | 13 +++++++++++++ tests/corpus/test_junit_matrix.py | 16 ++++++++++++++++ 6 files changed, 44 insertions(+), 2 deletions(-) diff --git a/coleman/corpus/resources/apache-codec65-junit3-arm64-v1.json b/coleman/corpus/resources/apache-codec65-junit3-arm64-v1.json index 8a5bd1c7..346160ad 100644 --- a/coleman/corpus/resources/apache-codec65-junit3-arm64-v1.json +++ b/coleman/corpus/resources/apache-codec65-junit3-arm64-v1.json @@ 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curated direct-upstream focal fixes across two codebases; not a complete Defects4J reconstruction","CLI13 is Defects4J Cli1; CLI51 is Cli2; CODEC65 is Codec1. Framework metadata only identifies curated candidates","Both CLI fixes share project history; project and fault labels do not establish statistical independence","Multiple triggering tests and repeated trials never become additional faults or projects","Keep both-pass, both-fail, reversed, inconclusive and entirely missing pairs; test errors are not assertion-based expected detections","Same JVM and lexical test order; test-order independence is unverified","Constructed controlled functional evidence only; no CI chronology or policy evaluation/admission","Source producer process nanoseconds, case nanoseconds, runner work, peak memory and developer-visible latency remain distinct","Upstream Codec fixture randomness is uncontrolled and its generated inputs/seeds are unavailable; retain all selected tests and all observed outcomes"],"matrix_id":"java-real-fault-matrix-arm64-v1","recipe":"junit3-controlled-matrix-v1","schema_version":1} diff --git a/docs/java-fault-matrix.md b/docs/java-fault-matrix.md index cb3c6de8..2a0516d2 100644 --- a/docs/java-fault-matrix.md +++ b/docs/java-fault-matrix.md @@ -133,6 +133,16 @@ fixes share project history. Tests, trials, seeds and JVM repetitions do not bec independent projects or new faults. These observations are runtime/fixture-specific, not a guarantee about every future run. +Subsequent source inspection identified unseeded `java.util.Random` inputs in +[Base64Test](https://github.com/apache/commons-codec/blob/52d82d1dfff8c2b2ded9d843e0b03017af6d747c/src/test/org/apache/commons/codec/binary/Base64Test.java#L705), +[HexTest](https://github.com/apache/commons-codec/blob/52d82d1dfff8c2b2ded9d843e0b03017af6d747c/src/test/org/apache/commons/codec/binary/HexTest.java#L118) +and [DigestUtilsTest](https://github.com/apache/commons-codec/blob/52d82d1dfff8c2b2ded9d843e0b03017af6d747c/src/test/org/apache/commons/codec/digest/DigestUtilsTest.java#L40). +Generated bytes and seeds are unavailable in the capture protocol. All 166 +selected tests remain; only an explicit limitation was added to the recipes. +Source/dependency/runtime/harness pins and fixture selection are unchanged. +Saved observations replay deterministically, while fresh execution does not +reconstruct identical generated inputs. Source admission must assess that limit. + Each role uses the existing shared JVM and lexical test-ID order. Test-order independence is unverified. Integer case nanoseconds include setup/teardown; parent process nanoseconds also include startup/compilation. Observed zero remains zero; diff --git a/docs/releases/4.10.0.md b/docs/releases/4.10.0.md index 096536af..7522ea58 100644 --- a/docs/releases/4.10.0.md +++ b/docs/releases/4.10.0.md @@ -43,6 +43,9 @@ three fixture files were excluded because of separately noticed third-party data non-UTF8 source bytes or dependencies on excluded classes. Remaining source bytes and original LICENSE/NOTICE are preserved. This is direct-upstream reproduction, not the complete original build or a full Defects4J reconstruction. +Upstream Base64/Hex/Digest fixtures also generate unseeded random inputs whose +bytes/seeds are not captured. Those tests remain included with an explicit +limitation; deterministic saved-artifact replay does not reconstruct fresh inputs. The CLI fixes share project history. Multiple tests, seeds or trials do not establish independent projects or unique faults. Collection clocks and harness diff --git a/llms.txt b/llms.txt index 260c1d83..602c499c 100644 --- a/llms.txt +++ b/llms.txt @@ -5944,6 +5944,16 @@ fixes share project history. Tests, trials, seeds and JVM repetitions do not bec independent projects or new faults. These observations are runtime/fixture-specific, not a guarantee about every future run. +Subsequent source inspection identified unseeded `java.util.Random` inputs in +[Base64Test](https://github.com/apache/commons-codec/blob/52d82d1dfff8c2b2ded9d843e0b03017af6d747c/src/test/org/apache/commons/codec/binary/Base64Test.java#L705), +[HexTest](https://github.com/apache/commons-codec/blob/52d82d1dfff8c2b2ded9d843e0b03017af6d747c/src/test/org/apache/commons/codec/binary/HexTest.java#L118) +and [DigestUtilsTest](https://github.com/apache/commons-codec/blob/52d82d1dfff8c2b2ded9d843e0b03017af6d747c/src/test/org/apache/commons/codec/digest/DigestUtilsTest.java#L40). +Generated bytes and seeds are unavailable in the capture protocol. All 166 +selected tests remain; only an explicit limitation was added to the recipes. +Source/dependency/runtime/harness pins and fixture selection are unchanged. +Saved observations replay deterministically, while fresh execution does not +reconstruct identical generated inputs. Source admission must assess that limit. + Each role uses the existing shared JVM and lexical test-ID order. Test-order independence is unverified. Integer case nanoseconds include setup/teardown; parent process nanoseconds also include startup/compilation. Observed zero remains zero; @@ -8390,6 +8400,9 @@ three fixture files were excluded because of separately noticed third-party data non-UTF8 source bytes or dependencies on excluded classes. Remaining source bytes and original LICENSE/NOTICE are preserved. This is direct-upstream reproduction, not the complete original build or a full Defects4J reconstruction. +Upstream Base64/Hex/Digest fixtures also generate unseeded random inputs whose +bytes/seeds are not captured. Those tests remain included with an explicit +limitation; deterministic saved-artifact replay does not reconstruct fresh inputs. The CLI fixes share project history. Multiple tests, seeds or trials do not establish independent projects or unique faults. Collection clocks and harness diff --git a/tests/corpus/test_junit_matrix.py b/tests/corpus/test_junit_matrix.py index ef3fa5c2..2dd592bf 100644 --- a/tests/corpus/test_junit_matrix.py +++ b/tests/corpus/test_junit_matrix.py @@ -344,6 +344,22 @@ def test_published_prior_recipe_and_new_frozen_presets_bind_actual_harness(): assert {"LICENSE.txt", "NOTICE.txt"}.issubset(names) +def test_uncontrolled_upstream_fixture_inputs_are_disclosed_without_dropping_tests(): + plan = matrix.load_junit_matrix() + codec = next(cell.recipe for cell in plan.cells if cell.recipe.fault_id == "CODEC-65") + names = {Path(member.name).name for member in codec.fixture.output.members} + assert {"Base64Test.java", "HexTest.java", "DigestUtilsTest.java"}.issubset(names) + for classname in ( + "org.apache.commons.codec.binary.Base64Test", + "org.apache.commons.codec.binary.HexTest", + "org.apache.commons.codec.digest.DigestUtilsTest", + ): + assert any(test.startswith(classname + "::") for test in codec.test_ids) + assert len(codec.test_ids) == 166 + assert any("unseeded java.util.Random" in text and "not captured" in text for text in codec.limitations) + assert any("randomness is uncontrolled" in text for text in plan.limitations) + + @pytest.mark.parametrize( "status,elapsed", [ From 2c2fd9e4f133baf8c20795e8a7feb357df752696 Mon Sep 17 00:00:00 2001 From: Jackson Antonio do Prado Lima Date: Fri, 16 Oct 2026 23:44:06 -0300 Subject: [PATCH 3/6] fix: contain matrix validation reads and address review findings --- coleman/transports/junit_matrix.py | 46 ++++++++++++--------- docs/java-fault-matrix.md | 2 + llms.txt | 2 + tests/corpus/test_installed_junit_matrix.py | 3 +- tests/corpus/test_junit_matrix.py | 30 ++++++++++++++ 5 files changed, 63 insertions(+), 20 deletions(-) diff --git a/coleman/transports/junit_matrix.py b/coleman/transports/junit_matrix.py index cd953335..b37a0a75 100644 --- a/coleman/transports/junit_matrix.py +++ b/coleman/transports/junit_matrix.py @@ -31,12 +31,16 @@ _COMPLETION = "complete.json" _DATASET_BYTES = 16 * 1024**2 +_HASH_PREFIX = "sha256:" +_JSON_SUFFIX = ".json" +_TRANSPORT_PACKAGE = "coleman.transports" +_CORPUS_PACKAGE = "coleman.corpus" _PLAN_LIMIT_ERROR = "Java matrix plan exceeds its byte limit" def _digest(payload: bytes) -> str: """Return the explicit SHA-256 identity of exact bytes, with no filesystem access.""" - return "sha256:" + hashlib.sha256(payload).hexdigest() + return _HASH_PREFIX + hashlib.sha256(payload).hexdigest() def junit_matrix_producer() -> str: @@ -46,19 +50,19 @@ def junit_matrix_producer() -> str: on validation rather than silently relabeling existing observations. """ modules = ( - ("coleman.transports", "junit_matrix.py"), - ("coleman.transports", "junit_matrix_contracts.py"), - ("coleman.transports", "junit_capture.py"), - ("coleman.transports", "junit_contracts.py"), - ("coleman.transports", "junit_process.py"), - ("coleman.transports", "junit_protocol.py"), - ("coleman.transports", "junit_source.py"), - ("coleman.corpus", "controlled.py"), - ("coleman.corpus", "controlled_contracts.py"), - ("coleman.corpus", "source_views.py"), - ("coleman.corpus", "materialization.py"), - ("coleman.corpus", "materialization_contracts.py"), - ("coleman.corpus", "archives.py"), + (_TRANSPORT_PACKAGE, "junit_matrix.py"), + (_TRANSPORT_PACKAGE, "junit_matrix_contracts.py"), + (_TRANSPORT_PACKAGE, "junit_capture.py"), + (_TRANSPORT_PACKAGE, "junit_contracts.py"), + (_TRANSPORT_PACKAGE, "junit_process.py"), + (_TRANSPORT_PACKAGE, "junit_protocol.py"), + (_TRANSPORT_PACKAGE, "junit_source.py"), + (_CORPUS_PACKAGE, "controlled.py"), + (_CORPUS_PACKAGE, "controlled_contracts.py"), + (_CORPUS_PACKAGE, "source_views.py"), + (_CORPUS_PACKAGE, "materialization.py"), + (_CORPUS_PACKAGE, "materialization_contracts.py"), + (_CORPUS_PACKAGE, "archives.py"), ("coleman.results", "versioned.py"), ("coleman.results", "domain.py"), ("coleman.selection", "contracts.py"), @@ -89,7 +93,10 @@ def _generation(plan: JunitMatrixRecipe, root: Path, producer: str) -> Path: """Return a contained hash-only generation path; logical labels never become filesystem paths.""" return _contained( root, - root / "corpus-junit-matrix" / plan.fingerprint.removeprefix("sha256:") / producer.removeprefix("sha256:"), + root + / "corpus-junit-matrix" + / plan.fingerprint.removeprefix(_HASH_PREFIX) + / producer.removeprefix(_HASH_PREFIX), ) @@ -187,7 +194,7 @@ def validate_junit_matrix(receipt: JunitMatrixReceipt, cache: SourceCache, outpu reference = references[cell.cell_id] path = _contained( output, - output / "corpus-controlled" / (reference.dataset_fingerprint.removeprefix("sha256:") + ".json"), + output / "corpus-controlled" / (reference.dataset_fingerprint.removeprefix(_HASH_PREFIX) + _JSON_SUFFIX), ) dataset = ControlledDataset.from_json(_read(path, _DATASET_BYTES)) if dataset.fingerprint != reference.dataset_fingerprint: @@ -239,7 +246,7 @@ def capture_junit_matrix( if saved.plan != plan or saved.status != "collected": raise ValueError("Java matrix completion disagrees with the requested complete plan") validate_junit_matrix(saved, cache, writer.run_root) - path = _contained(writer.run_root, generation / (saved.fingerprint.removeprefix("sha256:") + ".json")) + path = _contained(writer.run_root, generation / (saved.fingerprint.removeprefix(_HASH_PREFIX) + _JSON_SUFFIX)) writer.write_immutable(path, saved.to_json() + "\n") return JunitMatrixOutcome(saved, path, complete) results = [] @@ -257,7 +264,7 @@ def capture_junit_matrix( if len(payload.encode()) > receipt.MAXIMUM_BYTES: raise ValueError("Java matrix receipt exceeds its byte limit") validate_junit_matrix(receipt, cache, writer.run_root) - path = _contained(writer.run_root, generation / (receipt.fingerprint.removeprefix("sha256:") + ".json")) + path = _contained(writer.run_root, generation / (receipt.fingerprint.removeprefix(_HASH_PREFIX) + _JSON_SUFFIX)) writer.write_immutable(path, payload) if receipt.status == "collected": writer.write_immutable(complete, payload) @@ -293,7 +300,8 @@ def main(argv: list[str] | None = None) -> int: parser.error("Offline validation cannot fetch sources") cache = SourceCache(args.cache) if args.validate: - receipt = JunitMatrixReceipt.from_json(_read(args.validate, JunitMatrixReceipt.MAXIMUM_BYTES)) + receipt_path = _contained(args.output, args.validate) + receipt = JunitMatrixReceipt.from_json(_read(receipt_path, JunitMatrixReceipt.MAXIMUM_BYTES)) validate_junit_matrix(receipt, cache, args.output) print(json.dumps({"integrity": "verified", "receipt": receipt.fingerprint, "status": receipt.status})) return 0 diff --git a/docs/java-fault-matrix.md b/docs/java-fault-matrix.md index 2a0516d2..631fdf73 100644 --- a/docs/java-fault-matrix.md +++ b/docs/java-fault-matrix.md @@ -67,6 +67,8 @@ Offline integrity validation can republish identical source-view cache metadata. It verifies actual source members, context, raw protocol packets and normalized observations; it starts no process and fetches nothing. Integrity is correspondence, not authentication of execution truth or benchmark efficacy. +The CLI accepts a validation receipt only inside the declared output tree; +parent traversal and escaping symlink aliases reject before that file is read. ## Frozen source selection diff --git a/llms.txt b/llms.txt index 602c499c..2a685ffe 100644 --- a/llms.txt +++ b/llms.txt @@ -5878,6 +5878,8 @@ Offline integrity validation can republish identical source-view cache metadata. It verifies actual source members, context, raw protocol packets and normalized observations; it starts no process and fetches nothing. Integrity is correspondence, not authentication of execution truth or benchmark efficacy. +The CLI accepts a validation receipt only inside the declared output tree; +parent traversal and escaping symlink aliases reject before that file is read. ## Frozen source selection diff --git a/tests/corpus/test_installed_junit_matrix.py b/tests/corpus/test_installed_junit_matrix.py index 0c0c65e4..1359f0cd 100644 --- a/tests/corpus/test_installed_junit_matrix.py +++ b/tests/corpus/test_installed_junit_matrix.py @@ -90,7 +90,8 @@ def find_spec(self,fullname,path=None,target=None): env, ) proof = json.loads(result.stdout) - assert proof["installed"] and proof["owned_offline_validation"] + assert proof["installed"] + assert proof["owned_offline_validation"] assert proof["real_source_capture"] == (source_cache != "-") cli = command( [ diff --git a/tests/corpus/test_junit_matrix.py b/tests/corpus/test_junit_matrix.py index 2dd592bf..313d8e6d 100644 --- a/tests/corpus/test_junit_matrix.py +++ b/tests/corpus/test_junit_matrix.py @@ -533,3 +533,33 @@ def item(name): monkeypatch.setattr(matrix, "files", altered_files) assert matrix.junit_matrix_producer() != before + + +@pytest.mark.parametrize("alias", ["parent", "symlink"]) +def test_cli_validation_cannot_read_a_receipt_outside_the_declared_output(tmp_path, monkeypatch, alias): + output = tmp_path / "output" + output.mkdir() + external = tmp_path / "external.json" + external.write_text(owned_receipt().to_json()) + candidate = output / ".." / external.name + if alias == "symlink": + candidate = output / "receipt.json" + candidate.symlink_to(external) + original = Path.open + + def guarded(path, *args, **kwargs): + if path.resolve() == external.resolve(): + raise AssertionError("Out-of-output artifact was read before containment validation") + return original(path, *args, **kwargs) + + monkeypatch.setattr(Path, "open", guarded) + arguments = [ + "--validate", + str(candidate), + "--cache", + str(tmp_path / "cache"), + "--output", + str(output), + ] + with pytest.raises(ValueError, match="within its output tree"): + matrix.main(arguments) From 87167b778a2361cb9153dde8292b3a632d3fc6e1 Mon Sep 17 00:00:00 2001 From: Jackson Antonio do Prado Lima Date: Sat, 17 Oct 2026 00:06:54 -0300 Subject: [PATCH 4/6] fix: validate matrix JSON through bounded stdin --- coleman/transports/junit_matrix.py | 11 ++++++++--- docs/java-fault-matrix.md | 10 ++++++---- llms.txt | 10 ++++++---- tests/corpus/test_installed_junit_matrix.py | 13 +++++++++---- tests/corpus/test_junit_matrix.py | 21 +++++++++++++-------- 5 files changed, 42 insertions(+), 23 deletions(-) diff --git a/coleman/transports/junit_matrix.py b/coleman/transports/junit_matrix.py index b37a0a75..19892320 100644 --- a/coleman/transports/junit_matrix.py +++ b/coleman/transports/junit_matrix.py @@ -5,6 +5,7 @@ import argparse import hashlib import json +import sys from collections import Counter from importlib.metadata import version from importlib.resources import files @@ -287,11 +288,13 @@ def main(argv: list[str] | None = None) -> int: This optional transport does not run policies, alter admission, infer CI chronology or interpret source errors as assertion-based fault detections. + Validation consumes bounded JSON bytes from stdin, never a receipt path; + malformed/oversized input fails before source/data correspondence checks. """ parser = argparse.ArgumentParser(description=__doc__) choice = parser.add_mutually_exclusive_group() choice.add_argument("--recipe", type=Path) - choice.add_argument("--validate", type=Path) + choice.add_argument("--validate", action="store_true", help="Validate bounded receipt JSON from stdin") parser.add_argument("--cache", type=Path, required=True) parser.add_argument("--output", type=Path, required=True) parser.add_argument("--fetch", action="store_true") @@ -300,8 +303,10 @@ def main(argv: list[str] | None = None) -> int: parser.error("Offline validation cannot fetch sources") cache = SourceCache(args.cache) if args.validate: - receipt_path = _contained(args.output, args.validate) - receipt = JunitMatrixReceipt.from_json(_read(receipt_path, JunitMatrixReceipt.MAXIMUM_BYTES)) + payload = sys.stdin.buffer.read(JunitMatrixReceipt.MAXIMUM_BYTES + 1) + if len(payload) > JunitMatrixReceipt.MAXIMUM_BYTES: + raise ValueError("Java matrix validation stdin exceeds its byte limit") + receipt = JunitMatrixReceipt.from_json(payload) validate_junit_matrix(receipt, cache, args.output) print(json.dumps({"integrity": "verified", "receipt": receipt.fingerprint, "status": receipt.status})) return 0 diff --git a/docs/java-fault-matrix.md b/docs/java-fault-matrix.md index 631fdf73..24cef7bd 100644 --- a/docs/java-fault-matrix.md +++ b/docs/java-fault-matrix.md @@ -58,17 +58,19 @@ Validate a saved index without Docker or source execution: ```bash MATRIX_RECEIPT="$(/tmp/coleman-matrix-env/bin/python -c 'import json; print(json.load(open("matrix-summary.json"))["receipt"])')" /tmp/coleman-matrix-env/bin/python -m coleman.transports.junit_matrix \ - --validate "$MATRIX_RECEIPT" \ + --validate \ --cache /tmp/coleman-java-source-cache \ - --output /tmp/coleman-java-observations + --output /tmp/coleman-java-observations < "$MATRIX_RECEIPT" ``` Offline integrity validation can republish identical source-view cache metadata. It verifies actual source members, context, raw protocol packets and normalized observations; it starts no process and fetches nothing. Integrity is correspondence, not authentication of execution truth or benchmark efficacy. -The CLI accepts a validation receipt only inside the declared output tree; -parent traversal and escaping symlink aliases reject before that file is read. +The CLI reads at most 8 MiB of receipt JSON from stdin; `--validate` accepts no +file path. The operator explicitly supplies the input descriptor. Referenced +controlled datasets remain confined to their declared output tree. The Python +API accepts the already parsed typed receipt. ## Frozen source selection diff --git a/llms.txt b/llms.txt index 2a685ffe..7f61d87b 100644 --- a/llms.txt +++ b/llms.txt @@ -5869,17 +5869,19 @@ Validate a saved index without Docker or source execution: ```bash MATRIX_RECEIPT="$(/tmp/coleman-matrix-env/bin/python -c 'import json; print(json.load(open("matrix-summary.json"))["receipt"])')" /tmp/coleman-matrix-env/bin/python -m coleman.transports.junit_matrix \ - --validate "$MATRIX_RECEIPT" \ + --validate \ --cache /tmp/coleman-java-source-cache \ - --output /tmp/coleman-java-observations + --output /tmp/coleman-java-observations < "$MATRIX_RECEIPT" ``` Offline integrity validation can republish identical source-view cache metadata. It verifies actual source members, context, raw protocol packets and normalized observations; it starts no process and fetches nothing. Integrity is correspondence, not authentication of execution truth or benchmark efficacy. -The CLI accepts a validation receipt only inside the declared output tree; -parent traversal and escaping symlink aliases reject before that file is read. +The CLI reads at most 8 MiB of receipt JSON from stdin; `--validate` accepts no +file path. The operator explicitly supplies the input descriptor. Referenced +controlled datasets remain confined to their declared output tree. The Python +API accepts the already parsed typed receipt. ## Frozen source selection diff --git a/tests/corpus/test_installed_junit_matrix.py b/tests/corpus/test_installed_junit_matrix.py index 1359f0cd..797e4108 100644 --- a/tests/corpus/test_installed_junit_matrix.py +++ b/tests/corpus/test_installed_junit_matrix.py @@ -3,6 +3,7 @@ import json import os import shutil +import subprocess import sys from coleman.transports import junit_matrix as matrix @@ -93,20 +94,24 @@ def find_spec(self,fullname,path=None,target=None): assert proof["installed"] assert proof["owned_offline_validation"] assert proof["real_source_capture"] == (source_cache != "-") - cli = command( + cli = subprocess.run( [ str(python), "-m", "coleman.transports.junit_matrix", "--validate", - str(owned.receipt_path), "--cache", str(cache.root), "--output", str(writer.run_root), ], - outside, - env, + cwd=outside, + env=env, + input=owned.receipt_path.read_text(), + capture_output=True, + text=True, + check=True, + timeout=240, ) assert json.loads(cli.stdout)["integrity"] == "verified" # Native CI uses its own owned exact-answer fixture, never Java elapsed counters as CI costs. diff --git a/tests/corpus/test_junit_matrix.py b/tests/corpus/test_junit_matrix.py index 313d8e6d..f640fe67 100644 --- a/tests/corpus/test_junit_matrix.py +++ b/tests/corpus/test_junit_matrix.py @@ -209,12 +209,8 @@ def test_capture_roundtrip_raw_correspondence_replay_and_cli(tmp_path, monkeypat summary = json.loads(capsys.readouterr().out) assert summary["curated_focal_fixes"] == 1 assert summary["declared_projects"] == 1 - assert ( - matrix.main( - ["--validate", str(first.receipt_path), "--cache", str(cache.root), "--output", str(writer.run_root)] - ) - == 0 - ) + monkeypatch.setattr("sys.stdin", SimpleNamespace(buffer=io.BytesIO(first.receipt_path.read_bytes()))) + assert matrix.main(["--validate", "--cache", str(cache.root), "--output", str(writer.run_root)]) == 0 assert json.loads(capsys.readouterr().out)["integrity"] == "verified" assert len(calls) == 4 @@ -536,7 +532,7 @@ def item(name): @pytest.mark.parametrize("alias", ["parent", "symlink"]) -def test_cli_validation_cannot_read_a_receipt_outside_the_declared_output(tmp_path, monkeypatch, alias): +def test_cli_validation_rejects_receipt_path_arguments_without_opening_files(tmp_path, monkeypatch, alias): output = tmp_path / "output" output.mkdir() external = tmp_path / "external.json" @@ -561,5 +557,14 @@ def guarded(path, *args, **kwargs): "--output", str(output), ] - with pytest.raises(ValueError, match="within its output tree"): + with pytest.raises(SystemExit) as error: + matrix.main(arguments) + assert error.value.code == 2 + + +def test_cli_validation_bounds_stdin_before_parsing(tmp_path, monkeypatch): + monkeypatch.setattr("sys.stdin", SimpleNamespace(buffer=io.BytesIO(b"{}"))) + monkeypatch.setattr(JunitMatrixReceipt, "MAXIMUM_BYTES", 1) + arguments = ["--validate", "--cache", str(tmp_path / "cache"), "--output", str(tmp_path / "output")] + with pytest.raises(ValueError, match="stdin exceeds"): matrix.main(arguments) From 30f180d97ae97d077e3ecc490d73a3353979bf58 Mon Sep 17 00:00:00 2001 From: Jackson Antonio do Prado Lima Date: Sat, 17 Oct 2026 00:28:13 -0300 Subject: [PATCH 5/6] fix: bind matrix generations to owned registry inputs --- coleman/transports/junit_matrix.py | 4 ++++ tests/corpus/test_junit_matrix.py | 15 ++++++++++++--- 2 files changed, 16 insertions(+), 3 deletions(-) diff --git a/coleman/transports/junit_matrix.py b/coleman/transports/junit_matrix.py index 19892320..65002360 100644 --- a/coleman/transports/junit_matrix.py +++ b/coleman/transports/junit_matrix.py @@ -47,6 +47,7 @@ def _digest(payload: bytes) -> str: def junit_matrix_producer() -> str: """Bind matrix implementation/serialization bytes and package version; old capture provenance stays separate. + Registry code, contracts and card bytes also bind producer-owned input terms. A changed producer requires a new output generation. Unknown producers reject on validation rather than silently relabeling existing observations. """ @@ -61,6 +62,9 @@ def junit_matrix_producer() -> str: (_CORPUS_PACKAGE, "controlled.py"), (_CORPUS_PACKAGE, "controlled_contracts.py"), (_CORPUS_PACKAGE, "source_views.py"), + (_CORPUS_PACKAGE, "registry.py"), + (_CORPUS_PACKAGE, "contracts.py"), + (_CORPUS_PACKAGE, "resources/registry-v1.json"), (_CORPUS_PACKAGE, "materialization.py"), (_CORPUS_PACKAGE, "materialization_contracts.py"), (_CORPUS_PACKAGE, "archives.py"), diff --git a/tests/corpus/test_junit_matrix.py b/tests/corpus/test_junit_matrix.py index f640fe67..2b967e54 100644 --- a/tests/corpus/test_junit_matrix.py +++ b/tests/corpus/test_junit_matrix.py @@ -512,9 +512,16 @@ def test_validation_enforces_plan_receipt_and_dataset_budgets(tmp_path, monkeypa @pytest.mark.parametrize( - "package,module", [("coleman.transports", "junit_protocol.py"), ("coleman.corpus", "source_views.py")] + "package,module", + [ + ("coleman.transports", "junit_protocol.py"), + ("coleman.corpus", "source_views.py"), + ("coleman.corpus", "registry.py"), + ("coleman.corpus", "contracts.py"), + ("coleman.corpus", "resources/registry-v1.json"), + ], ) -def test_changing_reused_producer_dependency_changes_matrix_generation(monkeypatch, package, module): +def test_changing_reused_producer_dependency_changes_matrix_generation(tmp_path, monkeypatch, package, module): before = matrix.junit_matrix_producer() original = matrix.files @@ -528,7 +535,9 @@ def item(name): return SimpleNamespace(joinpath=item) monkeypatch.setattr(matrix, "files", altered_files) - assert matrix.junit_matrix_producer() != before + after = matrix.junit_matrix_producer() + assert after != before + assert matrix._generation(owned_plan(), tmp_path, after) != matrix._generation(owned_plan(), tmp_path, before) @pytest.mark.parametrize("alias", ["parent", "symlink"]) From 8938121e70c677ff725a144ea27ccb32b6a8a661 Mon Sep 17 00:00:00 2001 From: Jackson Antonio do Prado Lima Date: Sat, 17 Oct 2026 00:50:15 -0300 Subject: [PATCH 6/6] fix: derive matrix producer identity from packaged resources --- coleman/transports/junit_matrix.py | 52 ++++++++++++++---------------- docs/java-fault-matrix.md | 10 ++++-- docs/releases/4.10.0.md | 3 ++ llms.txt | 13 ++++++-- tests/corpus/test_junit_matrix.py | 43 +++++++++++++++++++----- 5 files changed, 80 insertions(+), 41 deletions(-) diff --git a/coleman/transports/junit_matrix.py b/coleman/transports/junit_matrix.py index 65002360..9feffb34 100644 --- a/coleman/transports/junit_matrix.py +++ b/coleman/transports/junit_matrix.py @@ -9,6 +9,7 @@ from collections import Counter from importlib.metadata import version from importlib.resources import files +from importlib.resources.abc import Traversable from pathlib import Path from typing import NamedTuple @@ -34,8 +35,6 @@ _DATASET_BYTES = 16 * 1024**2 _HASH_PREFIX = "sha256:" _JSON_SUFFIX = ".json" -_TRANSPORT_PACKAGE = "coleman.transports" -_CORPUS_PACKAGE = "coleman.corpus" _PLAN_LIMIT_ERROR = "Java matrix plan exceeds its byte limit" @@ -44,36 +43,35 @@ def _digest(payload: bytes) -> str: return _HASH_PREFIX + hashlib.sha256(payload).hexdigest() +def _package_pins(root: Traversable, prefix: str = "coleman") -> dict[str, str]: + """Hash regular package resources recursively without importing their modules. + + Hidden files, bytecode and interpreter caches are incidental installation + state. All other packaged bytes participate, including new resource formats. + Reads propagate I/O errors; this never modifies a resource or executes it. + """ + pins = {} + for entry in sorted(root.iterdir(), key=lambda item: item.name): + if entry.name.startswith(".") or entry.name == "__pycache__" or entry.name.endswith((".pyc", ".pyo")): + continue + name = prefix + "/" + entry.name + if entry.is_dir(): + pins.update(_package_pins(entry, name)) + elif entry.is_file(): + pins[name] = _digest(entry.read_bytes()) + return pins + + def junit_matrix_producer() -> str: - """Bind matrix implementation/serialization bytes and package version; old capture provenance stays separate. + """Bind all COLEMAN package bytes and version; old capture provenance stays separate. - Registry code, contracts and card bytes also bind producer-owned input terms. + This conservatively includes unrelated packaged modules/resources so new + transitive dependencies cannot escape a manually maintained allowlist. + Hidden files, generated bytecode and interpreter caches are excluded. A changed producer requires a new output generation. Unknown producers reject on validation rather than silently relabeling existing observations. """ - modules = ( - (_TRANSPORT_PACKAGE, "junit_matrix.py"), - (_TRANSPORT_PACKAGE, "junit_matrix_contracts.py"), - (_TRANSPORT_PACKAGE, "junit_capture.py"), - (_TRANSPORT_PACKAGE, "junit_contracts.py"), - (_TRANSPORT_PACKAGE, "junit_process.py"), - (_TRANSPORT_PACKAGE, "junit_protocol.py"), - (_TRANSPORT_PACKAGE, "junit_source.py"), - (_CORPUS_PACKAGE, "controlled.py"), - (_CORPUS_PACKAGE, "controlled_contracts.py"), - (_CORPUS_PACKAGE, "source_views.py"), - (_CORPUS_PACKAGE, "registry.py"), - (_CORPUS_PACKAGE, "contracts.py"), - (_CORPUS_PACKAGE, "resources/registry-v1.json"), - (_CORPUS_PACKAGE, "materialization.py"), - (_CORPUS_PACKAGE, "materialization_contracts.py"), - (_CORPUS_PACKAGE, "archives.py"), - ("coleman.results", "versioned.py"), - ("coleman.results", "domain.py"), - ("coleman.selection", "contracts.py"), - ("coleman", "artifacts.py"), - ) - pins = {package + "/" + name: _digest(files(package).joinpath(name).read_bytes()) for package, name in modules} + pins = _package_pins(files("coleman")) return _digest(canonical_json({"package_version": version("coleman"), "modules": pins}).encode()) diff --git a/docs/java-fault-matrix.md b/docs/java-fault-matrix.md index 24cef7bd..1834f625 100644 --- a/docs/java-fault-matrix.md +++ b/docs/java-fault-matrix.md @@ -207,9 +207,13 @@ also needs its controlled datasets and the independently verified source cache. Existing completion is revalidated before any runtime preflight. Corrupt/unknown schema or producer versions reject. Missing and older matrix schema versions are -unsupported; there is no implicit migration. A changed matrix implementation or -package version selects a new generation, preserving previous bytes. Explicit -offline validation requires the matching reviewed producer. Existing single-pair +unsupported; there is no implicit migration. The producer identity hashes all +COLEMAN package code and resources without importing those modules. Hidden files, +generated bytecode and interpreter caches are excluded. Any other packaged-byte +change, including an unrelated module or a new resource format, conservatively +selects a new generation; the package version also participates. Previous bytes +remain intact. Explicit offline validation requires the matching reviewed producer. +Existing single-pair JUnit recipes, source caches, controlled artifacts, native results and learning checkpoints keep their previous contracts and require no migration. diff --git a/docs/releases/4.10.0.md b/docs/releases/4.10.0.md index 7522ea58..d7d590c2 100644 --- a/docs/releases/4.10.0.md +++ b/docs/releases/4.10.0.md @@ -37,6 +37,9 @@ artifact writer. Old single-pair recipes, controlled artifacts, native results, RunSpec identities and learning checkpoints retain their semantics and require no migration. Unknown matrix schemas or producers reject; there is no implicit reinterpretation of prior evidence. +The producer identity conservatively binds all COLEMAN packaged code/resources, +so even an unrelated packaged change selects a new generation. Incidental +bytecode, hidden files and interpreter caches do not affect that identity. Codec's common fixture is explicitly partial. Before outcomes were observed, three fixture files were excluded because of separately noticed third-party data, diff --git a/llms.txt b/llms.txt index 7f61d87b..75c929f3 100644 --- a/llms.txt +++ b/llms.txt @@ -6018,9 +6018,13 @@ also needs its controlled datasets and the independently verified source cache. Existing completion is revalidated before any runtime preflight. Corrupt/unknown schema or producer versions reject. Missing and older matrix schema versions are -unsupported; there is no implicit migration. A changed matrix implementation or -package version selects a new generation, preserving previous bytes. Explicit -offline validation requires the matching reviewed producer. Existing single-pair +unsupported; there is no implicit migration. The producer identity hashes all +COLEMAN package code and resources without importing those modules. Hidden files, +generated bytecode and interpreter caches are excluded. Any other packaged-byte +change, including an unrelated module or a new resource format, conservatively +selects a new generation; the package version also participates. Previous bytes +remain intact. Explicit offline validation requires the matching reviewed producer. +Existing single-pair JUnit recipes, source caches, controlled artifacts, native results and learning checkpoints keep their previous contracts and require no migration. @@ -8398,6 +8402,9 @@ artifact writer. Old single-pair recipes, controlled artifacts, native results, RunSpec identities and learning checkpoints retain their semantics and require no migration. Unknown matrix schemas or producers reject; there is no implicit reinterpretation of prior evidence. +The producer identity conservatively binds all COLEMAN packaged code/resources, +so even an unrelated packaged change selects a new generation. Incidental +bytecode, hidden files and interpreter caches do not affect that identity. Codec's common fixture is explicitly partial. Before outcomes were observed, three fixture files were excluded because of separately noticed third-party data, diff --git a/tests/corpus/test_junit_matrix.py b/tests/corpus/test_junit_matrix.py index 2b967e54..3db67ca2 100644 --- a/tests/corpus/test_junit_matrix.py +++ b/tests/corpus/test_junit_matrix.py @@ -519,27 +519,54 @@ def test_validation_enforces_plan_receipt_and_dataset_budgets(tmp_path, monkeypa ("coleman.corpus", "registry.py"), ("coleman.corpus", "contracts.py"), ("coleman.corpus", "resources/registry-v1.json"), + ("coleman.corpus", "zip_metadata.py"), + ("coleman.evaluation.protected", "temporal.py"), ], ) def test_changing_reused_producer_dependency_changes_matrix_generation(tmp_path, monkeypatch, package, module): before = matrix.junit_matrix_producer() original = matrix.files + target = package.replace(".", "/") + "/" + module - def altered_files(namespace): - def item(name): - payload = original(namespace).joinpath(name).read_bytes() - if (namespace, name) == (package, module): + def altered_resource(resource, path): + def read_bytes(): + payload = resource.read_bytes() + if path == target: payload += b"\n# Owned provenance metamorphism\n" - return SimpleNamespace(read_bytes=lambda: payload) - - return SimpleNamespace(joinpath=item) + return payload + + return SimpleNamespace( + name=resource.name, + is_dir=resource.is_dir, + is_file=resource.is_file, + read_bytes=read_bytes, + iterdir=lambda: (altered_resource(child, path + "/" + child.name) for child in resource.iterdir()), + ) - monkeypatch.setattr(matrix, "files", altered_files) + monkeypatch.setattr(matrix, "files", lambda namespace: altered_resource(original(namespace), namespace)) after = matrix.junit_matrix_producer() assert after != before assert matrix._generation(owned_plan(), tmp_path, after) != matrix._generation(owned_plan(), tmp_path, before) +def test_new_package_resources_change_identity_but_installation_caches_do_not(tmp_path, monkeypatch): + (tmp_path / "owned.py").write_bytes(b"# Owned package fixture\n") + monkeypatch.setattr(matrix, "files", lambda namespace: tmp_path) + before = matrix.junit_matrix_producer() + resources = tmp_path / "resources" + resources.mkdir() + (resources / "future-format.bin").write_bytes(b"owned future resource") + after = matrix.junit_matrix_producer() + assert after != before + (tmp_path / "owned.pyc").write_bytes(b"incidental bytecode") + (tmp_path / "owned.pyo").write_bytes(b"incidental optimized bytecode") + (tmp_path / ".installation-state").write_bytes(b"incidental hidden file") + cache = tmp_path / "__pycache__" + cache.mkdir() + (cache / "owned.cpython.pyc").write_bytes(b"incidental interpreter cache") + assert matrix.junit_matrix_producer() == after + + @pytest.mark.parametrize("alias", ["parent", "symlink"]) def test_cli_validation_rejects_receipt_path_arguments_without_opening_files(tmp_path, monkeypatch, alias): output = tmp_path / "output"