diff --git a/.github/workflows/build-and-test.yml b/.github/workflows/build-and-test.yml index 70c94b1..5ca4a73 100644 --- a/.github/workflows/build-and-test.yml +++ b/.github/workflows/build-and-test.yml @@ -34,6 +34,7 @@ jobs: python-version: ${{ matrix.python-version }} # Get the version from pyproject.toml + # This will be used to tag the release in the publishing workflow - name: Install toml package run: pip install toml - name: Get version from pyproject.toml @@ -43,22 +44,38 @@ jobs: echo Version: $VERSION echo "version=$VERSION" >> $GITHUB_OUTPUT + # Installation - name: Install dependencies run: | python -m pip install poetry poetry install - - name: Build the docs # just to see whether the build passes - run: | - poetry run make html --directory docs + + # Testing and checking - name: Test with pytest run: | poetry run pytest - # TODO: run pytype here? + - name: Type check + run: | + poetry run pytype . + + # Build the package - name: Build the package run: | poetry build - name: Archive build artifacts uses: actions/upload-artifact@v4 + if: github.ref == 'refs/heads/release' with: name: build-artifacts path: dist/ + + # Build the docs + - name: Build the docs + run: | + poetry run make html --directory docs + - name: Archive documentation + uses: actions/upload-artifact@v4 + if: github.ref == 'refs/heads/release' + with: + name: docs-html + path: docs/_build/html/ diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml new file mode 100644 index 0000000..789c242 --- /dev/null +++ b/.github/workflows/publish.yml @@ -0,0 +1,115 @@ +# Sources: +# https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/#workflow-definition +# https://github.com/marketplace/actions/pypi-publish + +name: Publish package and docs + +on: + push: + branches: [ release ] + +jobs: + build-and-test: + uses: ./.github/workflows/build-and-test.yml + + create-tag: + name: Create Git Tag + needs: build-and-test + runs-on: ubuntu-latest + steps: + - name: Checkout code + uses: actions/checkout@v4 + + - name: Create Git Tag + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + VERSION: ${{ needs.build-and-test.outputs.version }} + run: | + git config --global user.name 'github-actions' + git config --global user.email 'github-actions@github.com' + git tag "v${VERSION}" + git push origin "v${VERSION}" + + publish-to-pypi: + name: Publish to PyPI + needs: [build-and-test, create-tag] + runs-on: ubuntu-latest + environment: + name: pypi + url: https://pypi.org/p/tsdf + permissions: + id-token: write # mandatory for trusted publishing + + steps: + - name: Download all the dists + uses: actions/download-artifact@v4 + with: + name: build-artifacts + path: dist/ + - name: Publish distribution 📦 to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 + + + github-release: + name: Sign distribution and create GitHub release + needs: [build-and-test, create-tag] + runs-on: ubuntu-latest + + permissions: + contents: write # mandatory for making GitHub Releases + id-token: write # mandatory for sigstore + + steps: + - name: Download all the dists + uses: actions/download-artifact@v4 + with: + name: build-artifacts + path: dist/ + + - name: Sign the dists with Sigstore + uses: sigstore/gh-action-sigstore-python@v2.1.1 + with: + inputs: >- + ./dist/*.tar.gz + ./dist/*.whl + + - name: Create GitHub Release + env: + GITHUB_TOKEN: ${{ github.token }} + VERSION: ${{ needs.build-and-test.outputs.version }} + run: >- + gh release create + "v${VERSION}" + --repo '${{ github.repository }}' + --notes "" + + - name: Upload artifact signatures to GitHub Release + env: + GITHUB_TOKEN: ${{ github.token }} + VERSION: ${{ needs.build-and-test.outputs.version }} + # Upload to GitHub Release using the `gh` CLI. + # `dist/` contains the built packages, and the + # sigstore-produced signatures and certificates. + run: >- + gh release upload + "v${VERSION}" dist/** + --repo '${{ github.repository }}' + + + publish-docs: + name: Publish documentation + needs: build-and-test + runs-on: ubuntu-latest + permissions: + contents: write + steps: + - name: Download the documentation + uses: actions/download-artifact@v4 + with: + name: docs-html + path: docs/ + - name: Deploy + uses: peaceiris/actions-gh-pages@v3 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: docs/ diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml deleted file mode 100644 index 3232925..0000000 --- a/.github/workflows/python-package.yml +++ /dev/null @@ -1,54 +0,0 @@ -# This workflow will install Python dependencies, run tests and lint with a variety of Python versions -# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions - -name: Python package - -on: - push: - branches: [ main ] - pull_request: - branches: [ main ] - -jobs: - build: - - runs-on: ubuntu-latest - strategy: - matrix: - python-version: ['3.9'] - - steps: - - uses: actions/checkout@v2 - with: - fetch-depth: 0 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: | - python -m pip install poetry - poetry install - - name: Test with pytest - run: | - poetry run pytest - - name: Build the docs - run: | - poetry run mkdocs build - - name: Prepare for deploying - run: | - git config user.name 'github-actions[bot]' && git config user.email 'github-actions[bot]@users.noreply.github.com' - - name: Deploy the docs - run: | - poetry run mkdocs gh-deploy - - # poetry run coverage xml - # - name: Upload coverage - # if: matrix.python-version == 3.9 - # uses: codecov/codecov-action@v1 - # with: - # token: ${{ secrets.CODECOV_TOKEN }} #required - # file: ./coverage.xml #optional - # flags: unittests #optional - # name: codecov-umbrella #optional - # yml: ./codecov.yml #optional \ No newline at end of file diff --git a/.github/workflows/pytype-checking.yml b/.github/workflows/pytype-checking.yml deleted file mode 100644 index 9739dd8..0000000 --- a/.github/workflows/pytype-checking.yml +++ /dev/null @@ -1,27 +0,0 @@ -name: Pytype Type Check - -on: - push: - branches: [main] - pull_request: - branches: [main] - -jobs: - build: - runs-on: ubuntu-latest - - steps: - - uses: actions/checkout@v2 - - - name: Set up Python - uses: actions/setup-python@v2 - with: - python-version: '3.9' - - - name: Install dependencies - run: | - python -m pip install poetry - poetry install - - - name: Run pytype - run: poetry run pytype . diff --git a/docs/basic_reading_and_writing_pandas.ipynb b/docs/basic_reading_and_writing_pandas.ipynb index 914019a..8d95fad 100644 --- a/docs/basic_reading_and_writing_pandas.ipynb +++ b/docs/basic_reading_and_writing_pandas.ipynb @@ -154,7 +154,7 @@ "metadata_samples = metadata_dict[\"ppp_format_samples.bin\"]\n", "\n", "# Load the data\n", - "df = 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"sphinx (>=7.3)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinxext-opengraph"] fpx = ["olefile"] mic = ["olefile"] tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"] diff --git a/pyproject.toml b/pyproject.toml index 60bb3dd..c22f1d5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -40,6 +40,7 @@ sphinx-rtd-theme = "^2.0.0" [tool.poetry.scripts] validate-tsdf = "tsdf.validator:main" +#docs = "sphinx.cmd.build:main" [build-system] requires = ["poetry-core>=1.0.0"] diff --git a/src/tsdf/parse_metadata.py b/src/tsdf/parse_metadata.py index 0be023c..a75aaf1 100644 --- a/src/tsdf/parse_metadata.py +++ b/src/tsdf/parse_metadata.py @@ -6,6 +6,8 @@ import os from typing import Any, Dict, List +import re +from dateutil import parser from tsdf import constants from tsdf import tsdfmetadata @@ -82,7 +84,7 @@ def _read_struct( # levels of the TSDF structure. # Extend the mapping recursively with values provided at those levels. for key, value in remaining_data.items(): - if _is_a_list(value): + if isinstance(value, list): for each_value in value: all_streams = all_streams | _read_struct( each_value, defined_properties.copy(), source_path, version @@ -135,17 +137,6 @@ def _contains_file_name(data: Any) -> bool: return False -def _is_a_list(value) -> bool: - """ - Function returns True if the value is a list, otherwise it returns False. - - :param value: value to be checked. - - :return: True if the value is a list, otherwise False. - """ - return isinstance(value, list) - - def contains_tsdf_mandatory_fields(dictionary: Dict[str, Any]) -> bool: """ Verifies that all the mandatory properties for TSDF metadata are provided, @@ -242,4 +233,33 @@ def confirm_dir_of_metadata(metadatas: List["tsdfmetadata.TSDFMetadata"]) -> Non if init_metadata.file_name == curr_metadata.file_name: raise tsdfmetadata.TSDFMetadataFieldValueError( "Two metadata objects cannot reference the same binary file (file_name)." + #TODO: why not? ) + +def is_iso8601(date_string: str) -> bool: + """ + Checks if the given date string is in ISO8601 format. + + :param date_string: date string to be checked. + """ + # Note that we need both the regex and the parser to validate the date string + # The regex only still allows for invalid dates, e.g. 2021-02-29 + # The parser is too lenient in accepting different formats + iso8601_regex = r"^(-?(?:[1-9][0-9]*)?[0-9]{4})-(1[0-2]|0[1-9])-(3[01]|0[1-9]|[12][0-9])(T(2[0-3]|[01][0-9]):[0-5][0-9]:[0-5][0-9](?:\.[0-9]+)?(?:Z|[+-](?:2[0-3]|[01][0-9]):[0-5][0-9])?)?$" + if re.match(iso8601_regex, date_string): + try: + parser.parse(date_string) + return True + except tsdfmetadata.TSDFMetadataFieldValueError: + return False + return False + +def validate_datetimes(metadata: tsdfmetadata.TSDFMetadata) -> bool: + """ + Validates the start and end date format of the TSDFMetaData object. + """ + if not is_iso8601(metadata.start_iso8601): + raise tsdfmetadata.TSDFMetadataFieldValueError(f"Invalid start_iso8601: {metadata.start_iso8601}") + if not is_iso8601(metadata.end_iso8601): + raise tsdfmetadata.TSDFMetadataFieldValueError(f"Invalid end_iso8601: {metadata.end_iso8601}") + return True diff --git a/src/tsdf/tsdfmetadata.py b/src/tsdf/tsdfmetadata.py index 6da3811..15a23de 100644 --- a/src/tsdf/tsdfmetadata.py +++ b/src/tsdf/tsdfmetadata.py @@ -1,5 +1,7 @@ import copy from typing import Any, Dict, List +from datetime import datetime +from dateutil import parser from tsdf import parse_metadata @@ -48,11 +50,11 @@ class TSDFMetadata: file_dir_path: str """ A reference to the directory path, so we don't need it again when reading associated binary files. """ - metadata_file_name: str + metadata_file_name: str #TODO: do we need this?? / is it used? """ A reference to the source path, so we don't need it again when reading associated binary files. """ def __init__( - self, dictionary: Dict[str, Any], dir_path: str, metadata_file_name: str = "" + self, dictionary: Dict[str, Any], dir_path: str, metadata_file_name: str = "", do_validate: bool = True ) -> None: """ The default constructor takes a dictionary as an argument and creates each @@ -61,14 +63,34 @@ def __init__( :param dictionary: dictionary containing TSDF metadata. :param dir_path: path to the directory where the metadata file is stored. - :param file_name: (optional) name of the metadata file. + :param metadata_file_name: (optional) name of the metadata file. + :param do_validate: (optional) flag to validate the metadata. """ - parse_metadata.contains_tsdf_mandatory_fields(dictionary) #TODO: how to load a dict that is not complete yet? + + # Copy the attributes from the dictionary to the object for key, value in dictionary.items(): setattr(self, key, value) self.file_dir_path = dir_path self.metadata_file_name = metadata_file_name + # Validate the metadata + if do_validate: + if not self.validate(): + raise TSDFMetadataFieldValueError("The provided metadata is invalid.") + + + def validate(self) -> bool: + isValid: bool = True + + # Validate presence of mandatory fields + dict = self.get_plain_tsdf_dict_copy() + isValid = isValid and parse_metadata.contains_tsdf_mandatory_fields(dict) + + # Validate datetimes + isValid = isValid and parse_metadata.validate_datetimes(self) + + return isValid + def get_plain_tsdf_dict_copy(self) -> Dict[str, Any]: """ Method returns the a copy of the dict containing fields needed for the TSDF file. @@ -81,3 +103,31 @@ def get_plain_tsdf_dict_copy(self) -> Dict[str, Any]: if simple_dict.get("metadata_file_name") is not None: simple_dict.pop("metadata_file_name") return simple_dict + + def set_start_datetime(self, date_time: datetime) -> None: + """ + Sets the start date of the recording in ISO8601 format. + :param date_time: datetime object containing the start date. + """ + self.start_iso8601 = date_time.isoformat() + + def get_start_datetime(self) -> datetime: + """ + Returns the start date of the recording as a datetime object. + :return: datetime object containing the start date. + """ + return parser.parse(self.start_iso8601) + + def set_end_datetime(self, date_time: datetime) -> None: + """ + Sets the end date of the recording in ISO8601 format. + :param date_time: datetime object containing the end date. + """ + self.end_iso8601 = date_time.isoformat() + + def get_end_datetime(self) -> datetime: + """ + Returns the end date of the recording as a datetime object. + :return: datetime object containing the end date. + """ + return parser.parse(self.end_iso8601) diff --git a/src/tsdf/write_binary.py b/src/tsdf/write_binary.py index 117f4f1..397188c 100644 --- a/src/tsdf/write_binary.py +++ b/src/tsdf/write_binary.py @@ -19,12 +19,10 @@ def write_dataframe_to_binaries( """ Save binary file based on the provided pandas DataFrame. - :param file_dir: path to the directory where the file will be saved. - :param file_name: name of the file to be saved. - :param data: pandas DataFrame containing the data. - :param metadata: dictionary containing the metadata. - - :return: TSDFMetadata object. + :param file_dir: path to the directory where the file will be saved. + :param df: pandas DataFrame containing the data. + :param metadatas: list of metadata objects to be saved, also contains + channels to be retrieved from dataframe. """ for metadata in metadatas: file_name = metadata.file_name diff --git a/src/tsdf/write_tsdf.py b/src/tsdf/write_tsdf.py index d3251cd..ce14432 100644 --- a/src/tsdf/write_tsdf.py +++ b/src/tsdf/write_tsdf.py @@ -19,6 +19,9 @@ def write_metadata(metadatas: List[TSDFMetadata], file_name: str) -> None: :raises TSDFMetadataFieldValueError: if the metadata files cannot be combined (e.g. they have no common fields) or if the list of TSDFMetadata objects is empty. """ + for meta in metadatas: + meta.validate() + if len(metadatas) == 0: raise TSDFMetadataFieldValueError( "Metadata cannot be saved, as the list of TSDFMetadata objects is empty." @@ -42,7 +45,7 @@ def write_metadata(metadatas: List[TSDFMetadata], file_name: str) -> None: ) if len(plain_meta) > 0: - overlap["sensors"] = _calculate_ovelaps_rec(plain_meta) + overlap["sensors"] = _calculate_overlaps_rec(plain_meta) file_utils.write_to_file(overlap, metadatas[0].file_dir_path, file_name) @@ -76,7 +79,7 @@ def _extract_common_fields(metadatas: List[Dict[str, Any]]) -> Dict[str, Any]: return meta_overlap -def _calculate_ovelaps_rec(metadatas: List[Dict[str, Any]]) -> List[Dict[str, Any]]: +def _calculate_overlaps_rec(metadatas: List[Dict[str, Any]]) -> List[Dict[str, Any]]: """ A recursive call that optimises the structure of the TSDF metadata, by grouping common values. For the input the list of dictionaries corresponds to a list of "flat" metadata dictionaries. The output is a list of dictionaries (potentially of length 1) that contain @@ -107,11 +110,11 @@ def _calculate_ovelaps_rec(metadatas: List[Dict[str, Any]]) -> List[Dict[str, An # Handle the first group first_overlap = _extract_common_fields(first_group) if len(first_group) > 0: - first_overlap["sensors"] = _calculate_ovelaps_rec(first_group) + first_overlap["sensors"] = _calculate_overlaps_rec(first_group) final_metadata.append(first_overlap) # Handle the rest of the elements - second_overlap = _calculate_ovelaps_rec(second_grop) + second_overlap = _calculate_overlaps_rec(second_grop) final_metadata.extend(second_overlap) return final_metadata diff --git a/tests/data/date_format_fail.json b/tests/data/date_format_fail.json new file mode 100644 index 0000000..7b1ebe0 --- /dev/null +++ b/tests/data/date_format_fail.json @@ -0,0 +1,72 @@ +{ + "subject_id": "PD0234", + "study_id": "homestudy22", + "device_id": "XBT7456", + "endianness": "little", + "metadata_version": "0.1", + "data_type": "float", + "bits": 32, + "multi-day_session": [ + { + "start_iso8601": "2022-10-26 09:26:45.123+00:00", + "end_iso8601": "2022-10-26 09:36:52.266+00:00", + "bits": 32, + "sensors": [ + { + "rows": 60714, + "file_name": "accelerometer_t1.bin", + "channels": [ + "time,", + "magnitude" + ], + "units": [ + "ms", + "m/s/s" + ] + }, + { + "rows": 607, + "file_name": "temperature_t1.bin", + "channels": [ + "time", + "temperature" + ], + "units": [ + "s", + "deg_C" + ] + } + ] + }, + { + "start_iso8601": "2022-28-10T10:42:12Z", + "end_iso8601": "2019-02-29T13:54:36Z", + "sensors": [ + { + "rows": 1154411, + "file_name": "accelerometer_t2.bin", + "channels": [ + "time", + "magnitude" + ], + "units": [ + "ms", + "m/s/s" + ] + }, + { + "rows": 11544, + "file_name": "temperature_t2.bin", + "channels": [ + "time", + "temperature" + ], + "units": [ + "s", + "deg_C" + ] + } + ] + } + ] +} \ No newline at end of file diff --git a/tests/data/hierarchical_meta.json b/tests/data/hierarchical_meta.json index dcdf931..548fa88 100644 --- a/tests/data/hierarchical_meta.json +++ b/tests/data/hierarchical_meta.json @@ -8,8 +8,8 @@ "bits": 32, "multi-day_session": [ { - "start_iso8601": "2022-26-10T09:26:45.123+00:00", - "end_iso8601": "2022-26-10T09:36:52.266+00:00", + "start_iso8601": "2022-10-26T09:26:45.123+00:00", + "end_iso8601": "2022-10-26T09:36:52.266+00:00", "bits": 32, "sensors": [ { @@ -39,8 +39,8 @@ ] }, { - "start_iso8601": "2022-28-10T10:42:12.465+00:00", - "end_iso8601": "2019-28-10T13:54:36.578+00:00", + "start_iso8601": "2022-10-28T10:42:12.465+00:00", + "end_iso8601": "2019-10-28T13:54:36.578+00:00", "sensors": [ { "rows": 1154411, diff --git a/tests/data/missingkey_meta_fail.json b/tests/data/missingkey_meta_fail.json index 54c772c..3778e2a 100644 --- a/tests/data/missingkey_meta_fail.json +++ b/tests/data/missingkey_meta_fail.json @@ -7,8 +7,8 @@ "bits": 32, "multi-day_session": [ { - "start_iso8601": "2022-26-10T09:26:45.123+00:00", - "end_iso8601": "2022-26-10T09:36:52.266+00:00", + "start_iso8601": "2022-10-26T09:26:45.123+00:00", + "end_iso8601": "2022-10-26T09:36:52.266+00:00", "bits": 32, "sensors": [ { @@ -38,8 +38,8 @@ ] }, { - "start_iso8601": "2022-28-10T10:42:12.465+00:00", - "end_iso8601": "2019-28-10T13:54:36.578+00:00", + "start_iso8601": "2022-10-28T10:42:12.465+00:00", + "end_iso8601": "2019-10-28T13:54:36.578+00:00", "sensors": [ { "rows": 1154411, diff --git a/tests/test_parse_metadata.py b/tests/test_parse_metadata.py index 8c7c27d..ee38691 100644 --- a/tests/test_parse_metadata.py +++ b/tests/test_parse_metadata.py @@ -35,3 +35,12 @@ def test_load_flat_structure(shared_datadir): for key, value in data.items(): if parse_metadata.is_mandatory_type(key, version): assert(value == first_stream.__getattribute__(key)) + +def test_date_format_fail(shared_datadir): + """Test that a file with wrong date formats raises an exception.""" + + path = shared_datadir / "date_format_fail.json" + with open(path, "r") as file: + data = json.load(file) + with pytest.raises(TSDFMetadataFieldValueError): + parse_metadata.read_data(data, path) # This should trigger an exception diff --git a/tests/test_write_tsdf.py b/tests/test_write_tsdf.py index 06e1813..c8e85c9 100644 --- a/tests/test_write_tsdf.py +++ b/tests/test_write_tsdf.py @@ -1,6 +1,9 @@ +import os import numpy as np +import pytest import tsdf from tsdf import TSDFMetadata +from tsdf.tsdfmetadata import TSDFMetadataFieldValueError from utils import load_single_bin_file @@ -78,3 +81,53 @@ def test_bin_processing_and_writing_metadata(shared_datadir): final_data = load_single_bin_file(shared_datadir, new_name) assert final_data.shape == (10, 3) assert final_data.dtype == "float32" + + +def test_write_metadata_only(shared_datadir): + """ Construct simple metadata from scratch and write it to a file. """ + # Define the metadata + basic_metadata = { + "subject_id": "example", + "study_id": "example", + "device_id": "example", + "endianness": "little", + "metadata_version": "0.1", + "start_datetime_unix_ms": 1571135957025, + "start_iso8601": "2019-10-15T10:39:17.025000+00:00", # not iso8601 format + "end_datetime_unix_ms": 1571168851826, + "end_iso8601": "2019-10-15T19:47:31.826000+00:00", + "channels": ["x", "y", "z"], + "units": ["m/s/s", "m/s/s", "m/s/s"], + "data_type": "float", + "bits": 32, + "rows": 17, + "file_name": "example_17_1_float32.bin", + } + metadata = TSDFMetadata(basic_metadata, shared_datadir) + tsdf.write_metadata([metadata], "tmp_meta.json") + assert os.path.exists(os.path.join(shared_datadir, "tmp_meta.json")) + + +def test_write_metadata_validate_fail(shared_datadir): + """ Should fail on writing metadata with wrong date format. """ + # Define the metadata + basic_metadata = { + "subject_id": "example", + "study_id": "example", + "device_id": "example", + "endianness": "little", + "metadata_version": "0.1", + "start_datetime_unix_ms": 1571135957025, + "start_iso8601": "2019-10-15 10:39:17.025000+00:00", # not iso8601 format + "end_datetime_unix_ms": 1571168851826, + "end_iso8601": "2019-10-15T19:47:31.826000+00:00", + "channels": ["x", "y", "z"], + "units": ["m/s/s", "m/s/s", "m/s/s"], + "data_type": "float", + "bits": 32, + "rows": 17, + "file_name": "example_17_1_float32.bin", + } + metadata = TSDFMetadata(basic_metadata, shared_datadir, do_validate=False) # Should validate on write below + with pytest.raises(TSDFMetadataFieldValueError): + tsdf.write_metadata([metadata], "tmp_meta.json")