diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md new file mode 100644 index 0000000..c43528d --- /dev/null +++ b/.github/pull_request_template.md @@ -0,0 +1,24 @@ +## TLDR of changes + + +## What kind of changes does this PR introduce? + +__Tick all that apply__ + +- [ ] fix: A bug fix. Correlates with PATCH in SemVer +- [ ] feat: A new feature. Correlates with MINOR in SemVer +- [ ] docs: Documentation only changes +- [ ] style: Changes that do not affect the meaning of the code (white-space, formatting, missing semi-colons, etc) +- [ ] refactor: A code change that neither fixes a bug nor adds a feature +- [ ] perf: A code change that improves performance +- [ ] test: Adding missing or correcting existing tests +- [ ] build: Changes that affect the build system or external dependencies (example scopes: pip, docker, npm) +- [ ] ci: Changes to CI configuration files and scripts (example scopes: GitLabCI) + + +## Please check if the PR fulfills these requirements + +- [ ] I have read and followed the [Contributing guidance](../CONTRIBUTE.md) +- [ ] Docs have been added / updated +- [ ] Tests and Linting in the CI are passing +- [ ] Changes have been reviewed and approved by a Project Maintainer diff --git a/CHANGELOG.md b/CHANGELOG.md index b81b644..e6682d5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,14 @@ +## v0.7.2 (2026-04-02) + +### Fix + +- amend messaging for missing CSV fields check in ddb reader (#83) +- ensure publish audit only captures information about the indivdual submission (#77) + +### Refactor + +- add extra clarification to the units presented in the file size row of the error report (#81) + ## v0.7.1 (2026-03-12) ### Fix diff --git a/CONTRIBUTE.md b/CONTRIBUTE.md index 2c95863..b5d1eed 100644 --- a/CONTRIBUTE.md +++ b/CONTRIBUTE.md @@ -1,30 +1,42 @@ # DVE Contributing guidelines -# Developer information +__If you're planning to contribute to the DVE, please follow all the guidance below. Failure to follow the guidance in this document may result in your contributions being automatically rejected.__ ## Getting started -To begin with I would recommend that users read all the documentation available within the [docs](./docs/). It gives an overview of how the DVE works and how to work with the dischema json document. +I would recommend that you read all the documentation available within the [docs](https://nhsdigital.github.io/data-validation-engine/). It gives an overview of how the DVE works and how to work with the dischema json document. ## General requirements -To start contributing to the DVE project you will need the following tooling available: + +To start contributing to the DVE project you will need the tooling listed within the `.tool-versions` or `mise.toml`. The following tools are required because... + | Tool | Version | Reason | | ---- | ------- | ------ | -| `Python` | 3.7.17 | Currently supported version of `Python` for the DVE. | -| `Poetry` | 1.4.2 | Build and venv tool used for the DVE. | +| `Python` | 3.11 | Latest version of Python supported by the DVE. | +| `Poetry` | 2.2.1 | Build and package manager tool used for the DVE. | | `Java` | java liberica-1.8.0 | `Java` version required for `PySpark`. | -| `pre-commit` | 2.21.0 | Currently installed as part of the `poetry` venv but seperate installation is fine. | -| `commitizen` | 3.9.1 | Like `pre-commit`, installed as part of the `poetry` venv but seperate installation is fine. This is used to manage commits and automated semantic versioning. | +| `pre-commit` | 4.3.0 | Currently installed as part of the `poetry` venv but seperate installation is fine. | +| `commitizen` | 4.9.1 | Like `pre-commit`, installed as part of the `poetry` venv but seperate installation is fine. This is used to manage commits and automated semantic versioning. | | `git-secrets` | Latest | Utilised as part of the `pre-commit` to ensure that no secrets are commited to the repository. There is a helper installation script within [scripts](/scripts/git-secrets/). | -Additionally, we have created a [asdf support](.tool-versions) and [mise-en-toml](.mise.toml) for those utilising `asdf` or `mise-en-toml` software. +You can install all the developer requirements with the following command: + +```bash +poetry install --with dev +``` ## Testing Requirements Testing requirements are given in [pyproject.toml](./poetry.toml#48) under `tool.poetry.group.test.dependencies`. These are always pinned versions for consistency, but should be updated regularly if new versions are released. The following core packages are used for testing: - [pytest](https://docs.pytest.org/en/stable/): Used for Python unit tests, and some small e2e tests which check coverage. - [behave](https://github.com/behave/behave): Used for full, business-driven end-to-end tests. - - [coverage](https://coverage.readthedocs.io/en/7.10.7/): Used to get coverage for `pytest` tests. + - [coverage](https://coverage.readthedocs.io/en/): Used to get coverage for `pytest` tests. + +You can install these requirements with the following command: + +```bash +poetry install --with test +``` ## Linting/Formatting/Type Checking Requirements @@ -38,6 +50,12 @@ This mostly breaks down to: We use these tools to ensure that code quality is not excessively compromised, even when working at pace. +You can install these requirements with the following command: + +```bash +poetry install --with lint +``` + ## Installation for Development We are utilising Poetry for build dependency management and packaging. If you're on a system that has `Make` available, you can simply run `make install` to setup a local virtual environment with all the dependencies installed (this won't install Poetry for you). @@ -50,6 +68,16 @@ Tests should be run after installing the package for development as outlined abo - To check the coverage run `poetry run coverage report -m` - To run the behave tests, run `poetry run behave tests/features` (these are not included in coverage calculations) +## Committing + +We use [commitizen](https://github.com/commitizen-tools/commitizen) to commit new changes. This ensures... + +1. A consistent standard for the commit messages +2. Generation of changelog from the commit messages +3. Allows for automatic bumping of the version based on the changes + +Please use `poetry run cz c` or `cz c` (if already in the venv). + ## Submitting a pull request If you want to contribute to the DVE then please follow the steps below: diff --git a/docs/user_guidance/install.md b/docs/user_guidance/install.md index 00d7a9c..4792a1f 100644 --- a/docs/user_guidance/install.md +++ b/docs/user_guidance/install.md @@ -83,6 +83,7 @@ Once you have installed the DVE you are almost ready to use it. To be able to ru | DVE Version | Python Version | DuckDB Version | Spark Version | Pydantic Version | | ------------ | -------------- | -------------- | ------------- | ---------------- | +| >=0.7.2 | >=3.10,<3.12 | 1.1.* | 3.4.* | 1.10.16 | | >=0.6 | >=3.10,<3.12 | 1.1.* | 3.4.* | 1.10.15 | | >=0.2,<0.6 | >=3.10,<3.12 | 1.1.0 | 3.4.4 | 1.10.15 | | 0.1 | >=3.7.2,<3.8 | 1.1.0 | 3.2.1 | 1.10.15 | diff --git a/poetry.lock b/poetry.lock index c7a90ed..56a4fc3 100644 --- a/poetry.lock +++ b/poetry.lock @@ -534,14 +534,14 @@ types-awscrt = "*" [[package]] name = "certifi" -version = "2026.1.4" +version = "2026.2.25" description = "Python package for providing Mozilla's CA Bundle." optional = false python-versions = ">=3.7" groups = ["dev", "test"] files = [ - {file = "certifi-2026.1.4-py3-none-any.whl", hash = "sha256:9943707519e4add1115f44c2bc244f782c0249876bf51b6599fee1ffbedd685c"}, - {file = "certifi-2026.1.4.tar.gz", hash = "sha256:ac726dd470482006e014ad384921ed6438c457018f4b3d204aea4281258b2120"}, + {file = "certifi-2026.2.25-py3-none-any.whl", hash = "sha256:027692e4402ad994f1c42e52a4997a9763c646b73e4096e4d5d6db8af1d6f0fa"}, + {file = "certifi-2026.2.25.tar.gz", hash = "sha256:e887ab5cee78ea814d3472169153c2d12cd43b14bd03329a39a9c6e2e80bfba7"}, ] [[package]] @@ -656,125 +656,141 @@ files = [ [[package]] name = "charset-normalizer" -version = "3.4.4" +version = "3.4.6" description = "The Real First Universal Charset Detector. 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"d83c9a1871a248d0bbad6811b26e87816863cb95600b8cd9ebc2bed33cd854d9" +content-hash = "19e9112d1197e3004d6fdb425fdd5917f9fdb54bd35a542df0baea15330734f3" diff --git a/pyproject.toml b/pyproject.toml index 7a0cda6..90f16cc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,12 +1,11 @@ -[tool.poetry] +[project] name = "data-validation-engine" -version = "0.7.1" +dynamic = [ "version" ] description = "`nhs data validation engine` is a framework used to validate data" -authors = ["NHS England "] -readme = "README.md" -packages = [ - { include = "dve", from = "src" }, +authors = [ + { name = "NHS England", email = "england.contactus@nhs.net" } ] +readme = "README.md" classifiers = [ "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.10", @@ -15,6 +14,20 @@ classifiers = [ "Topic :: Software Development :: Libraries", "Typing :: Typed", ] +license = "MIT" + +[project.urls] +Homepage = "https://github.com/NHSDigital/data-validation-engine" +Documentation = "https://nhsdigital.github.io/data-validation-engine/" +Repository = "https://github.com/NHSDigital/data-validation-engine.git" +Issues = "https://github.com/NHSDigital/data-validation-engine/issues" +Changelog = "https://github.com/NHSDigital/data-validation-engine/blob/main/CHANGELOG.md" + +[tool.poetry] +version = "0.7.2" +packages = [ + { include = "dve", from = "src" }, +] [tool.poetry.dependencies] python = ">=3.10,<3.12" @@ -28,7 +41,7 @@ openpyxl = "^3.1" pandas = "^2.2.2" polars = "0.20.*" pyarrow = "^17.0.0" -pydantic = "1.10.15" +pydantic = "1.10.16" pyspark = "3.4.*" typing_extensions = "^4.6.2" diff --git a/src/dve/core_engine/backends/implementations/duckdb/readers/csv.py b/src/dve/core_engine/backends/implementations/duckdb/readers/csv.py index 98b8cb8..5fb5bcc 100644 --- a/src/dve/core_engine/backends/implementations/duckdb/readers/csv.py +++ b/src/dve/core_engine/backends/implementations/duckdb/readers/csv.py @@ -82,11 +82,12 @@ def perform_field_check( messages=[ FeedbackMessage( entity=entity_name, - record=None, + record={"missing_fields": missing}, failure_type="submission", error_location="Whole File", + reporting_field="missing_fields", error_code=self.field_check_error_code, - error_message=f"{self.field_check_error_message} - missing fields: {missing}", # pylint: disable=line-too-long + error_message=f"{self.field_check_error_message}", # pylint: disable=line-too-long ) ], ) diff --git a/src/dve/pipeline/foundry_ddb_pipeline.py b/src/dve/pipeline/foundry_ddb_pipeline.py index 7a597cd..3b0e55f 100644 --- a/src/dve/pipeline/foundry_ddb_pipeline.py +++ b/src/dve/pipeline/foundry_ddb_pipeline.py @@ -42,11 +42,15 @@ def persist_audit_records(self, submission_info: SubmissionInfo) -> URI: write_to.parent.mkdir(parents=True, exist_ok=True) write_to = write_to.as_posix() self.write_parquet( # type: ignore # pylint: disable=E1101 - self._audit_tables._processing_status.get_relation(), # pylint: disable=W0212 + self._audit_tables._processing_status.get_relation().filter( # pylint: disable=W0212 + f"submission_id = '{submission_info.submission_id}'" + ), fh.joinuri(write_to, "processing_status.parquet"), ) self.write_parquet( # type: ignore # pylint: disable=E1101 - self._audit_tables._submission_statistics.get_relation(), # pylint: disable=W0212 + self._audit_tables._submission_statistics.get_relation().filter( # pylint: disable=W0212 + f"submission_id = '{submission_info.submission_id}'" + ), fh.joinuri(write_to, "submission_statistics.parquet"), ) return write_to diff --git a/src/dve/reporting/excel_report.py b/src/dve/reporting/excel_report.py index ce7c76a..82aa510 100644 --- a/src/dve/reporting/excel_report.py +++ b/src/dve/reporting/excel_report.py @@ -135,8 +135,11 @@ def _add_submission_info(self, status: str, summary: Worksheet): if "Status" not in self.summary_dict: summary.append(["", "Status", status]) + _key_renames = { + "File Size": "File Size (Bytes)", + } for key, value in self.summary_dict.items(): - summary.append(["", key, str(value)]) + summary.append(["", _key_renames.get(key, key), str(value)]) summary.append(["", ""]) diff --git a/tests/test_core_engine/test_backends/test_implementations/test_duckdb/test_audit_ddb.py b/tests/test_core_engine/test_backends/test_implementations/test_duckdb/test_audit_ddb.py index 6260965..5daa471 100644 --- a/tests/test_core_engine/test_backends/test_implementations/test_duckdb/test_audit_ddb.py +++ b/tests/test_core_engine/test_backends/test_implementations/test_duckdb/test_audit_ddb.py @@ -7,30 +7,32 @@ from uuid import uuid4 import pytest -from duckdb import ColumnExpression, ConstantExpression, DuckDBPyConnection +from duckdb import ColumnExpression, ConstantExpression, DuckDBPyConnection, connect from dve.core_engine.backends.implementations.duckdb.auditing import DDBAuditingManager from dve.core_engine.models import ProcessingStatusRecord, SubmissionInfo, SubmissionStatisticsRecord from dve.pipeline.utils import SubmissionStatus -from .....fixtures import temp_ddb_conn # pylint: disable=unused-import - @pytest.fixture(scope="function") -def ddb_audit_manager(temp_ddb_conn) -> Iterator[DDBAuditingManager]: - db_file: Path - conn: DuckDBPyConnection - db_file, conn = temp_ddb_conn - yield DDBAuditingManager(database_uri=db_file.as_uri(), connection=conn) +def ddb_audit_manager() -> Iterator[DDBAuditingManager]: + db = f"dve_{uuid4().hex}" + with tempfile.TemporaryDirectory(prefix="ddb_audit_testing") as tmp: + db_file = Path(tmp, db + ".duckdb") + conn = connect(database=db_file, read_only=False) + + yield DDBAuditingManager(database_uri=db_file.as_uri(), connection=conn) @pytest.fixture(scope="function") -def ddb_audit_manager_threaded(temp_ddb_conn) -> Iterator[DDBAuditingManager]: - db_file: Path - conn: DuckDBPyConnection - db_file, conn = temp_ddb_conn - with ThreadPoolExecutor(1) as pool: - yield DDBAuditingManager(database_uri=db_file.as_uri(), pool=pool, connection=conn) +def ddb_audit_manager_threaded() -> Iterator[DDBAuditingManager]: + db = f"dve_{uuid4().hex}" + with tempfile.TemporaryDirectory(prefix="ddb_audit_testing") as tmp: + db_file = Path(tmp, db + ".duckdb") + conn = connect(database=db_file, read_only=False) + + with ThreadPoolExecutor(1) as pool: + yield DDBAuditingManager(database_uri=db_file.as_uri(), pool=pool, connection=conn) @pytest.fixture @@ -421,25 +423,22 @@ def test_get_submission_status(ddb_audit_manager_threaded: DDBAuditingManager): SubmissionStatisticsRecord(submission_id=sub_1.submission_id, record_count=5, number_record_rejections=2, number_warnings=3), SubmissionStatisticsRecord(submission_id=sub_4.submission_id, record_count=20, number_record_rejections=0, number_warnings=1) ]) - - while not aud.queue.empty(): - time.sleep(0.05) - - sub_stats_1 = aud.get_submission_status(sub_1.submission_id) - assert sub_stats_1.submission_result == "validation_failed" - assert sub_stats_1.validation_failed - assert not sub_stats_1.processing_failed - assert sub_stats_1.number_of_records == 5 - sub_stats_2 = aud.get_submission_status(sub_2.submission_id) - assert sub_stats_2.submission_result == "processing_failed" - assert not sub_stats_2.validation_failed - assert sub_stats_2.processing_failed - sub_stats_3 = aud.get_submission_status(sub_3.submission_id) - assert not sub_stats_3.validation_failed - assert not sub_stats_3.processing_failed - sub_stats_4 = aud.get_submission_status(sub_4.submission_id) - assert sub_stats_4.submission_result == "success" - assert not sub_stats_4.validation_failed - assert not sub_stats_4.processing_failed - assert sub_stats_4.number_of_records == 20 - assert not aud.get_submission_status("5") \ No newline at end of file + + sub_stats_1 = ddb_audit_manager_threaded.get_submission_status(sub_1.submission_id) + assert sub_stats_1.submission_result == "validation_failed" + assert sub_stats_1.validation_failed + assert not sub_stats_1.processing_failed + assert sub_stats_1.number_of_records == 5 + sub_stats_2 = ddb_audit_manager_threaded.get_submission_status(sub_2.submission_id) + assert sub_stats_2.submission_result == "processing_failed" + assert not sub_stats_2.validation_failed + assert sub_stats_2.processing_failed + sub_stats_3 = ddb_audit_manager_threaded.get_submission_status(sub_3.submission_id) + assert not sub_stats_3.validation_failed + assert not sub_stats_3.processing_failed + sub_stats_4 = ddb_audit_manager_threaded.get_submission_status(sub_4.submission_id) + assert sub_stats_4.submission_result == "success" + assert not sub_stats_4.validation_failed + assert not sub_stats_4.processing_failed + assert sub_stats_4.number_of_records == 20 + assert not ddb_audit_manager_threaded.get_submission_status("5")