From 0a6a41d5cf5c2dda09a03cc833785bb79297c10c Mon Sep 17 00:00:00 2001 From: Michael Moen Allport Date: Thu, 7 Mar 2024 12:29:05 +0100 Subject: [PATCH] Write metadata to file (#351) * Initial commit * Add private/ to .gitignore for local files * Update poetry.lock * Properly write files * Make CI happy * Add Datadoc metadata README * Minor CI fixes --- .gitignore | 2 + README.md | 50 +- poetry.lock | 483 ++++++++++++------- pyproject.toml | 5 +- src/dapla_pseudo/v1/client.py | 2 +- src/dapla_pseudo/v1/result.py | 62 ++- src/dapla_pseudo/v1/supported_file_format.py | 32 +- tests/v1/test_result.py | 4 +- tests/v1/test_supported_file_format.py | 17 +- 9 files changed, 439 insertions(+), 218 deletions(-) diff --git a/.gitignore b/.gitignore index c5eb2245..918499e5 100644 --- a/.gitignore +++ b/.gitignore @@ -134,3 +134,5 @@ dmypy.json /.python-version /.pytype/ /docs/_build/ + +private/ diff --git a/README.md b/README.md index 38a35daf..e4e897ab 100644 --- a/README.md +++ b/README.md @@ -264,6 +264,9 @@ result_df = ( ) ``` + +_Note that depseudonymization requires elevated access privileges._ + ### Repseudonymize ```python @@ -271,8 +274,53 @@ result_df = ( ## TODO ``` +### Datadoc -_Note that depseudonymization requires elevated access privileges._ +Datadoc metadata is gathered while pseudonymizing, and can be seen like so: + +```python +result = ( + Pseudonymize.from_polars(df) + .on_fields("fornavn") + .with_default_encryption() + .run() +) + +print(result.datadoc) +``` + +Datadoc metadata is automatically written to the folder or bucket as the pseudonymized +data, when using the `to_file()` method on the result object. +The metadata file has the suffix `__DOC`, and is always a `.json` file. +The data and metadata is written to the file like so: + +```python +result = ( + Pseudonymize.from_polars(df) + .on_fields("fornavn") + .with_default_encryption() + .run() +) + +# The line of code below also writes the file "gs://bucket/test__DOC.json" +result.to_file("gs://bucket/test.parquet") +``` + +Note that if you choose to only use the DataFrame from the result, **the metadata will be lost forever**! +An example of how this can happen: + +```python +import dapla as dp +result = ( + Pseudonymize.from_polars(df) + .on_fields("fornavn") + .with_default_encryption() + .run() +) +df = result.to_pandas() + +dp.write_pandas(df, "gs://bucket/test.parquet", file_format="parquet") # The metadata is lost!! +``` ## Requirements diff --git a/poetry.lock b/poetry.lock index ee34abdf..fd982b47 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.0 and should not be changed by hand. [[package]] name = "aiohttp" @@ -662,6 +662,27 @@ files = [ [package.dependencies] colorama = {version = "*", markers = "platform_system == \"Windows\""} +[[package]] +name = "cloudpathlib" +version = "0.18.1" +description = "pathlib-style classes for cloud storage services." +optional = false +python-versions = ">=3.7" +files = [ + {file = "cloudpathlib-0.18.1-py3-none-any.whl", hash = "sha256:20efd5d772c75df91bb2ac52e053be53fd9000f5e9755fd92375a2a9fe6005e0"}, + {file = "cloudpathlib-0.18.1.tar.gz", hash = "sha256:ffd22f324bfbf9c3f2bc1bec6e8372cb372a0feef17c7f2b48030cd6810ea859"}, +] + +[package.dependencies] +google-cloud-storage = {version = "*", optional = true, markers = "extra == \"gs\""} +typing_extensions = {version = ">4", markers = "python_version < \"3.11\""} + +[package.extras] +all = ["cloudpathlib[azure]", "cloudpathlib[gs]", "cloudpathlib[s3]"] +azure = ["azure-storage-blob (>=12)"] +gs = ["google-cloud-storage"] +s3 = ["boto3"] + [[package]] name = "colorama" version = "0.4.6" @@ -813,34 +834,27 @@ test-randomorder = ["pytest-randomly"] [[package]] name = "dapla-toolbelt" -version = "2.0.6" +version = "2.0.8" description = "Dapla Toolbelt" optional = false python-versions = ">=3.10,<4.0" files = [ - 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+docs = ["sphinx"] +test = ["pytest", "pytest-cov"] + +[[package]] +name = "xlsxwriter" +version = "3.2.0" +description = "A Python module for creating Excel XLSX files." +optional = false +python-versions = ">=3.6" +files = [ + {file = "XlsxWriter-3.2.0-py3-none-any.whl", hash = "sha256:ecfd5405b3e0e228219bcaf24c2ca0915e012ca9464a14048021d21a995d490e"}, + {file = "XlsxWriter-3.2.0.tar.gz", hash = "sha256:9977d0c661a72866a61f9f7a809e25ebbb0fb7036baa3b9fe74afcfca6b3cb8c"}, +] + [[package]] name = "yarl" version = "1.9.4" @@ -4881,4 +4994,4 @@ multidict = ">=4.0" [metadata] lock-version = "2.0" python-versions = ">=3.10, <3.13" -content-hash = "8946c734356ab0b3b133b5e27c2ef6825b4e0fda4495b7a7fa3555eef165ec70" +content-hash = "cd0473c517e31c68b57a15d5fc75710ee526fee74580ac377216121a109a7740" diff --git a/pyproject.toml b/pyproject.toml index 3503ed0e..ac66e978 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "dapla-toolbelt-pseudo" -version = "1.2.2" +version = "1.3.0" description = "Pseudonymization extensions for Dapla" authors = ["Dapla Developers "] license = "MIT" @@ -29,7 +29,8 @@ polars = ">=0.18.2" pygments = ">2.15.0" click = ">=8.0.1" ssb-datadoc-model = ">=5.0.0" - +cloudpathlib = { extras = ["gs"], version = ">=0.17.0" } +pyarrow = ">=14.0.2, <15" [tool.poetry.group.test.dependencies] typeguard = ">=2.13.3" diff --git a/src/dapla_pseudo/v1/client.py b/src/dapla_pseudo/v1/client.py index 6e777992..c3e1b6dd 100644 --- a/src/dapla_pseudo/v1/client.py +++ b/src/dapla_pseudo/v1/client.py @@ -49,7 +49,7 @@ def __auth_token(self) -> str: auth_req = google.auth.transport.requests.Request() token = t.cast( str, - google.oauth2.id_token.fetch_id_token(auth_req, audience), # type: ignore[no-untyped-call] + google.oauth2.id_token.fetch_id_token(auth_req, audience), ) return token else: diff --git a/src/dapla_pseudo/v1/result.py b/src/dapla_pseudo/v1/result.py index 71972701..32c2fa68 100644 --- a/src/dapla_pseudo/v1/result.py +++ b/src/dapla_pseudo/v1/result.py @@ -1,22 +1,25 @@ """Common API models for builder packages.""" -import json import typing as t +from io import BufferedWriter from pathlib import Path from typing import Any import pandas as pd import polars as pl -from dapla import FileClient +from cloudpathlib import GSClient +from cloudpathlib import GSPath +from dapla import AuthClient from datadoc_model.model import MetadataContainer from datadoc_model.model import PseudonymizationMetadata from datadoc_model.model import PseudoVariable -from fsspec.spec import AbstractBufferedFile from dapla_pseudo.utils import get_file_format_from_file_name from dapla_pseudo.v1.pseudo_commons import PseudoFieldResponse from dapla_pseudo.v1.pseudo_commons import PseudoFileResponse +from dapla_pseudo.v1.supported_file_format import SupportedOutputFileFormat from dapla_pseudo.v1.supported_file_format import write_from_df +from dapla_pseudo.v1.supported_file_format import write_from_dicts class Result: @@ -120,11 +123,11 @@ def to_pandas(self, **kwargs: t.Any) -> pd.DataFrame: case _ as invalid_pseudo_data: raise ValueError(f"Invalid response type: {type(invalid_pseudo_data)}") - def to_file(self, file_path: str | Path, **kwargs: t.Any) -> None: - """Write pseudonymized data to a file. + def to_file(self, file_path: str, **kwargs: t.Any) -> None: + """Write pseudonymized data to a file, with the metadata being written to the same folder. Args: - file_path (str | Path): The path to the file to be written. + file_path (str): The path to the file to be written. If writing to a bucket, use the "gs://" prefix. **kwargs: Additional keyword arguments to be passed the Polars writer function *if* the input data is a DataFrame. The specific writer function depends on the format of the output file, e.g. `write_csv()` for CSV files. @@ -135,29 +138,42 @@ def to_file(self, file_path: str | Path, **kwargs: t.Any) -> None: """ file_format = get_file_format_from_file_name(file_path) + datadoc_file_name = f"{Path(file_path).stem}__DOC.json" + + datadoc_file_path: Path | GSPath + if file_path.startswith(GSPath.cloud_prefix): + client = GSClient(credentials=AuthClient.fetch_google_credentials()) + gs_path = GSPath(file_path, client) + + file_handle = gs_path.open(mode="wb") + + datadoc_file_path = gs_path.parent.joinpath(Path(datadoc_file_name)) + datadoc_file_handle = datadoc_file_path.open(mode="w") + else: + file_handle = Path(file_path).open(mode="wb") + + datadoc_file_path = Path(file_path).parent.joinpath(Path(datadoc_file_name)) + datadoc_file_handle = datadoc_file_path.open(mode="w") + + file_handle = t.cast( + BufferedWriter, file_handle + ) # file handle is always BufferedWriter when opening with "wb" + match self._pseudo_data: case pl.DataFrame() as df: - if str(file_path).startswith("gs://"): - with FileClient().gcs_open( - str(file_path), mode="wb" - ) as file_handle: - # If we ask for a file to be opened in binary mode, we know that the type is AbstractBufferedFile - file_handle = t.cast(AbstractBufferedFile, file_handle) - write_from_df(df, file_format, file_handle, **kwargs) - else: - write_from_df(df, file_format, str(file_path), **kwargs) + write_from_df(df, file_format, file_handle, **kwargs) + datadoc_file_handle.write(self.datadoc) case list() as file_data: - if str(file_path).startswith("gs://"): - with FileClient().gcs_open(str(file_path), mode="w") as file_handle: - # If we ask for a file to be opened in binary mode, we know that the type is AbstractBufferedFile - file_handle.write(json.dumps(file_data)) - else: - with open(file_path, mode="w") as file_handle: - file_handle.write(json.dumps(file_data)) - + write_from_dicts( + file_data, SupportedOutputFileFormat(file_format), file_handle + ) + datadoc_file_handle.write(self.datadoc) case _ as invalid_pseudo_data: raise ValueError(f"Invalid response type: {type(invalid_pseudo_data)}") + file_handle.close() + datadoc_file_handle.close() + @property def metadata(self) -> dict[str, Any]: """Returns the pseudonymization metadata as a dictionary. diff --git a/src/dapla_pseudo/v1/supported_file_format.py b/src/dapla_pseudo/v1/supported_file_format.py index 18a773d6..5610eb2c 100644 --- a/src/dapla_pseudo/v1/supported_file_format.py +++ b/src/dapla_pseudo/v1/supported_file_format.py @@ -1,13 +1,15 @@ """Classes used to support reading of dataframes from file.""" +import json +import typing as t from enum import Enum +from io import BufferedWriter from io import BytesIO from pathlib import Path from typing import Any import pandas as pd import polars as pl -from fsspec.spec import AbstractBufferedFile from dapla_pseudo.exceptions import ExtensionNotValidError @@ -77,10 +79,33 @@ def read_to_polars_df( ) +def write_from_dicts( + data: list[dict[str, t.Any]], + supported_format: SupportedOutputFileFormat, + file_like: BufferedWriter, +) -> None: + """Writes data from a list of dicts to a file of the given format.""" + match supported_format: + case SupportedOutputFileFormat.PARQUET: + df = pl.DataFrame(data) + # type hints lying + df.write_parquet(file_like) # type: ignore[arg-type] + case SupportedOutputFileFormat.CSV: + df = pl.DataFrame(data) + df.write_csv(file_like) + case SupportedOutputFileFormat.JSON: + file_like.write(bytes(json.dumps(data), encoding="utf-8")) + case SupportedOutputFileFormat.XML: + df_pandas = pd.DataFrame.from_records(data) + df_pandas.to_xml(file_like) + case _: + raise ValueError("Unsupported output file format") + + def write_from_df( df: pl.DataFrame, supported_format: SupportedOutputFileFormat, - file_like: AbstractBufferedFile | str, + file_like: BufferedWriter, **kwargs: Any, ) -> None: """Writes to a file with a supported file format from a Dataframe.""" @@ -92,4 +117,5 @@ def write_from_df( case SupportedOutputFileFormat.XML: df.to_pandas().to_xml(file_like, **kwargs) case SupportedOutputFileFormat.PARQUET: - df.write_parquet(file_like, **kwargs) + # type hints lying + df.write_parquet(file_like, **kwargs) # type: ignore[arg-type] diff --git a/tests/v1/test_result.py b/tests/v1/test_result.py index 0965388b..4aa2525a 100644 --- a/tests/v1/test_result.py +++ b/tests/v1/test_result.py @@ -70,7 +70,7 @@ def test_result_from_polars_to_pandas(df_personer: pl.DataFrame) -> None: def test_result_from_polars_to_file(tmp_path: Path, df_personer: pl.DataFrame) -> None: result = Result(PseudoFieldResponse(data=df_personer, raw_metadata=[])) - result.to_file(tmp_path / "polars_to_file.json") + result.to_file(str(tmp_path / "polars_to_file.json")) def test_result_from_file_to_polars(pseudo_file_response: PseudoFileResponse) -> None: @@ -88,4 +88,4 @@ def test_result_from_file_to_file( ) -> None: result = Result(pseudo_response=pseudo_file_response) file_extension = pseudo_file_response.content_type.name.lower() - result.to_file(tmp_path / f"file_to_file.{file_extension}") + result.to_file(str(tmp_path / f"file_to_file.{file_extension}")) diff --git a/tests/v1/test_supported_file_format.py b/tests/v1/test_supported_file_format.py index 219dd4c1..178fb06d 100644 --- a/tests/v1/test_supported_file_format.py +++ b/tests/v1/test_supported_file_format.py @@ -1,3 +1,4 @@ +import json from pathlib import Path import pandas as pd @@ -9,6 +10,7 @@ from dapla_pseudo.v1.supported_file_format import read_to_pandas_df from dapla_pseudo.v1.supported_file_format import read_to_polars_df from dapla_pseudo.v1.supported_file_format import write_from_df +from dapla_pseudo.v1.supported_file_format import write_from_dicts PKG = "dapla_pseudo.v1.supported_file_format" TEST_FILE_PATH = "tests/v1/test_files" @@ -51,5 +53,18 @@ def test_write_from_df( tmp_path: Path, df_personer: pl.DataFrame, file_format: str ) -> None: supported_format = SupportedOutputFileFormat(file_format) + file_handle = open(f"{tmp_path}/test.{file_format}", mode="wb") + write_from_df(df_personer, supported_format, file_handle) - write_from_df(df_personer, supported_format, f"{tmp_path}/test.{file_format}") + +@pytest.mark.parametrize("file_format", ["json", "csv", "parquet", "xml"]) +def test_write_from_dicts( + tmp_path: Path, personer_file_path: str, file_format: str +) -> None: + supported_format = SupportedOutputFileFormat(file_format) + print(open(personer_file_path).read()) + file_data = json.loads(open(personer_file_path).read()) + assert isinstance(file_data, list) + + dest_path = tmp_path / f"test.{file_format}" + write_from_dicts(file_data, supported_format, open(dest_path, mode="wb"))