diff --git a/datadoc/app.py b/datadoc/app.py index 446e0297..ba6ccbc4 100644 --- a/datadoc/app.py +++ b/datadoc/app.py @@ -95,7 +95,7 @@ def main(dataset_path: str = None): # Assume running in server mode is better (largely for development purposes) logger.debug("Starting in development mode") app = build_app(Dash) - app.run(debug=True) + app.run(debug=True, use_reloader=False) if __name__ == "__main__": diff --git a/datadoc/backend/DataDocMetadata.py b/datadoc/backend/DataDocMetadata.py index 16cf4e0a..8a77683a 100644 --- a/datadoc/backend/DataDocMetadata.py +++ b/datadoc/backend/DataDocMetadata.py @@ -5,12 +5,14 @@ import pathlib from typing import Dict, Optional +from datadoc_model import Model +from datadoc_model.Enums import DatasetState + import datadoc.frontend.fields.DisplayDataset as DisplayDataset import datadoc.frontend.fields.DisplayVariables as DisplayVariables -from datadoc.backend.DatasetReader import DatasetReader +from datadoc.backend.DatasetParser import DatasetParser +from datadoc.backend.StorageAdapter import StorageAdapter from datadoc.utils import calculate_percentage -from datadoc_model import Model -from datadoc_model.Enums import DatasetState logger = logging.getLogger(__name__) @@ -38,21 +40,20 @@ ] ) +METADATA_DOCUMENT_FILE_SUFFIX = "__DOC.json" + class DataDocMetadata: def __init__(self, dataset): - self.dataset = dataset - self.dataset_full_path = pathlib.Path(self.dataset) - self.dataset_directory = self.dataset_full_path.resolve().parent - self.dataset_stem = self.dataset_full_path.stem # filename without file ending - self.metadata_document_name = str(self.dataset_stem) + "__DOC.json" - self.metadata_document_full_path = self.dataset_directory.joinpath( - self.metadata_document_name - ) - self.dataset_state: DatasetState = self.get_dataset_state( - self.dataset_full_path + self.dataset: str = dataset + self.short_name: str = pathlib.Path( + self.dataset + ).stem # filename without file ending + self.metadata_document: StorageAdapter = StorageAdapter.for_path( + StorageAdapter.for_path(self.dataset).parent() ) - self.dataset_version = self.get_dataset_version(self.dataset_stem) + self.metadata_document.joinpath(self.short_name + METADATA_DOCUMENT_FILE_SUFFIX) + self.dataset_state: DatasetState = self.get_dataset_state(self.dataset) try: self.current_user = os.environ["JUPYTERHUB_USER"] except KeyError: @@ -73,20 +74,23 @@ def __init__(self, dataset): self.read_metadata_document() - def get_dataset_state( - self, dataset_path: pathlib.Path = None - ) -> Optional[DatasetState]: + def get_dataset_state(self, dataset: str) -> Optional[DatasetState]: """Use the path to attempt to guess the state of the dataset""" - - if dataset_path is None: - dataset_path = self.dataset_full_path - dataset_path_parts = list(dataset_path.parts) - if "kildedata" in dataset_path_parts: + if dataset is None: + return None + dataset_path_parts = list(pathlib.Path(dataset).parts) + if "utdata" in dataset_path_parts: + return DatasetState.OUTPUT_DATA + elif "statistikk" in dataset_path_parts: + return DatasetState.STATISTIC + elif "klargjorte-data" in dataset_path_parts: + return DatasetState.PROCESSED_DATA + elif "klargjorte_data" in dataset_path_parts: + return DatasetState.PROCESSED_DATA + elif "kildedata" in dataset_path_parts: return DatasetState.SOURCE_DATA elif "inndata" in dataset_path_parts: return DatasetState.INPUT_DATA - elif "klargjorte_data" in dataset_path_parts: - return DatasetState.PROCESSED_DATA else: return None @@ -106,32 +110,42 @@ def get_dataset_version(self, dataset_stem: str) -> Optional[str]: def read_metadata_document(self): fresh_metadata = {} - if self.metadata_document_full_path.exists(): - with open(self.metadata_document_full_path, encoding="utf-8") as file: - fresh_metadata = json.load(file) - logger.info( - f"Opened existing metadata file {self.metadata_document_full_path}" - ) - - variables_list = fresh_metadata.pop("variables", None) - - self.meta.variables = [Model.DataDocVariable(**v) for v in variables_list] - self.meta.dataset = Model.DataDocDataSet( - **fresh_metadata.pop("dataset", None) - ) + if self.metadata_document.exists(): + try: + with self.metadata_document.open(mode="r", encoding="utf-8") as file: + fresh_metadata = json.load(file) + logger.info( + f"Opened existing metadata file {self.metadata_document.location}" + ) + + variables_list = fresh_metadata.pop("variables", None) + + self.meta.variables = [ + Model.DataDocVariable(**v) for v in variables_list + ] + self.meta.dataset = Model.DataDocDataSet( + **fresh_metadata.pop("dataset", None) + ) + except json.JSONDecodeError: + logger.warning( + f"Could not open existing metadata file {self.metadata_document.location}. \ + Falling back to collecting data from the dataset", + exc_info=True, + ) + self.extract_metadata_from_dataset() else: - self.generate_new_metadata_document() + self.extract_metadata_from_dataset() self.variables_lookup = {v.short_name: v for v in self.meta.variables} - def generate_new_metadata_document(self): - self.ds_schema = DatasetReader.for_file(self.dataset) + def extract_metadata_from_dataset(self): + self.ds_schema = DatasetParser.for_file(self.dataset) self.meta.dataset = Model.DataDocDataSet( - short_name=self.dataset_stem, + short_name=self.short_name, dataset_state=self.dataset_state, - version=self.dataset_version, - data_source_path=str(self.dataset_full_path), + version=self.get_dataset_version(self.short_name), + data_source_path=self.dataset, created_date=self.current_datetime, created_by=self.current_user, ) @@ -140,10 +154,8 @@ def generate_new_metadata_document(self): def write_metadata_document(self) -> None: """Write all currently known metadata to file""" - self.metadata_document_full_path.write_text( - self.meta.json(indent=4, sort_keys=False), encoding="utf-8" - ) - logger.info(f"Saved metadata document {self.metadata_document_full_path}") + self.metadata_document.write_text(self.meta.json(indent=4, sort_keys=False)) + logger.info(f"Saved metadata document {self.metadata_document.location}") @property def percent_complete(self) -> int: diff --git a/datadoc/backend/DatasetReader.py b/datadoc/backend/DatasetParser.py similarity index 71% rename from datadoc/backend/DatasetReader.py rename to datadoc/backend/DatasetParser.py index 3b0b8e28..282755ed 100644 --- a/datadoc/backend/DatasetReader.py +++ b/datadoc/backend/DatasetParser.py @@ -4,11 +4,14 @@ import pandas as pd import pyarrow.parquet as pq -from datadoc import state from datadoc_model.Enums import Datatype +from datadoc_model.LanguageStrings import LanguageStrings from datadoc_model.Model import DataDocVariable -TDatasetReader = TypeVar("TDatasetReader", bound="DatasetReader") +from datadoc import state +from datadoc.backend.StorageAdapter import StorageAdapter + +TDatasetParser = TypeVar("TDatasetParser", bound="DatasetParser") KNOWN_INTEGER_TYPES = ( "int", @@ -65,19 +68,20 @@ KNOWN_BOOLEAN_TYPES = ("bool", "bool_", "boolean") -class DatasetReader(ABC): - def __init__(self, dataset): - self.dataset = dataset +class DatasetParser(ABC): + def __init__(self, dataset: str): + self.dataset: StorageAdapter = StorageAdapter.for_path(dataset) @staticmethod - def for_file(dataset: str) -> TDatasetReader: + def for_file(dataset: str) -> TDatasetParser: """Factory method to return the correct subclass based on the given dataset file""" supported_file_types = { - "parquet": DatasetReaderParquet, - "sas7bdat": DatasetReaderSas7bdat, + "parquet": DatasetParserParquet, + "sas7bdat": DatasetParserSas7Bdat, } + file_type = "Unknown" try: - file_type = str(pathlib.Path(dataset)).lower().split(".")[1] + file_type = str(pathlib.Path(dataset)).lower().split(".")[-1] # Extract the appropriate reader class from the SUPPORTED_FILE_TYPES dict and return an instance of it reader = supported_file_types[file_type](dataset) except IndexError as e: @@ -86,7 +90,7 @@ def for_file(dataset: str) -> TDatasetReader: f"Could not recognise file type for provided {dataset = }. Supported file types are: {', '.join(supported_file_types.keys())}" ) from e except KeyError as e: - # In this case the file type is not supported so we throw a helpful exception + # In this case the file type is not supported, so we throw a helpful exception raise NotImplementedError( f"{file_type = } is not supported. Please open one of the following supported files types: {', '.join(supported_file_types.keys())} or contact the maintainers to request support." ) from e @@ -116,34 +120,36 @@ def get_fields(self) -> List[DataDocVariable]: """Abstract method, must be implemented by subclasses""" -class DatasetReaderParquet(DatasetReader): - def __init__(self, dataset): +class DatasetParserParquet(DatasetParser): + def __init__(self, dataset: str): super().__init__(dataset) def get_fields(self) -> List[DataDocVariable]: fields = [] - data_table = pq.read_table(self.dataset) - for data_field in data_table.schema: - fields.append( - DataDocVariable( - short_name=data_field.name, - data_type=self.transform_data_type(str(data_field.type)), + with self.dataset.open(mode="rb") as f: + data_table = pq.read_table(f) + for data_field in data_table.schema: + fields.append( + DataDocVariable( + short_name=data_field.name, + data_type=self.transform_data_type(str(data_field.type)), + ) ) - ) return fields -class DatasetReaderSas7bdat(DatasetReader): - def __init__(self, dataset): +class DatasetParserSas7Bdat(DatasetParser): + def __init__(self, dataset: str): super().__init__(dataset) def get_fields(self) -> List[DataDocVariable]: fields = [] - # Use an iterator to avoid reading in the entire dataset - sas_reader = pd.read_sas(self.dataset, iterator=True) + with self.dataset.open(mode="rb") as f: + # Use an iterator to avoid reading in the entire dataset + sas_reader = pd.read_sas(f, format="sas7bdat", iterator=True) - # Get the first row from the iterator - row = next(sas_reader) + # Get the first row from the iterator + row = next(sas_reader) # Get all the values from the row and loop through them for i, v in enumerate(row.values.tolist()[0]): @@ -152,7 +158,9 @@ def get_fields(self) -> List[DataDocVariable]: short_name=sas_reader.columns[i].name, # Assume labels are defined in the default language (NORSK_BOKMÅL) # If this is not correct, the user may fix it via the UI - name={state.current_metadata_language: sas_reader.columns[i].label}, + name=LanguageStrings( + **{state.current_metadata_language: sas_reader.columns[i].label} + ), # Access the python type for the value and transform it to a DataDoc Data type data_type=self.transform_data_type(type(v).__name__.lower()), ) diff --git a/datadoc/backend/StorageAdapter.py b/datadoc/backend/StorageAdapter.py new file mode 100644 index 00000000..3952cc74 --- /dev/null +++ b/datadoc/backend/StorageAdapter.py @@ -0,0 +1,111 @@ +import logging +import os +import pathlib +from io import IOBase, TextIOWrapper +from typing import Protocol +from urllib.parse import urlsplit, urlunsplit + +from dapla import AuthClient, FileClient +from gcsfs import GCSFileSystem + +GCS_PROTOCOL_PREFIX = "gs://" + +logger = logging.getLogger(__name__) + + +class GCSObject: + def __init__(self, path: str): + self._url = urlsplit(path) + + if AuthClient.is_ready(): + # Running on Dapla, rely on dapla-toolbelt for auth + self.fs = FileClient.get_gcs_file_system() + else: + # All other environments, rely on Standard Google credential system + # If this doesn't work for you, try running the following commands: + # + # gcloud auth application-default revoke + # gcloud auth application-default login + self.fs = GCSFileSystem() + + def _rebuild_url(self, new_path: str) -> str: + return urlunsplit((self._url.scheme, self._url.netloc, new_path, None, None)) + + def open(self, **kwargs) -> IOBase: + return self.fs.open(self.location, **kwargs) + + def parent(self) -> str: + parent = os.path.dirname(self._url.path) + return self._rebuild_url(parent) + + def joinpath(self, part): + """Modify the path in place""" + self._url = urlsplit(self._rebuild_url(os.path.join(self._url.path, part))) + + def exists(self) -> bool: + return self.fs.exists(self.location) + + def write_text(self, text: str) -> None: + f: TextIOWrapper + with self.fs.open(self.location, mode="w") as f: + f.write(text) + + @property + def location(self) -> str: + return urlunsplit(self._url) + + +class LocalFile: + def __init__(self, path): + self._path_object: pathlib.Path = pathlib.Path(path) + + def open(self, **kwargs) -> IOBase: + return open(str(self._path_object), **kwargs) + + def parent(self) -> str: + return str(self._path_object.resolve().parent) + + def joinpath(self, part): + """Modify the path in place""" + self._path_object = self._path_object.joinpath(part) + + def exists(self) -> bool: + return self._path_object.exists() + + def write_text(self, text: str) -> None: + self._path_object.write_text(text, encoding="utf-8") + + @property + def location(self) -> str: + return str(self._path_object) + + +class StorageAdapter(Protocol): + @staticmethod + def for_path(path: str): + """ + Return a concrete class implementing this Protocol based on the structure of the path. + """ + if path.startswith(GCS_PROTOCOL_PREFIX): + return GCSObject(path) + else: + return LocalFile(path) + + def open(self, **kwargs) -> IOBase: + ... + + def parent(self) -> str: + ... + + def joinpath(self, part: str) -> None: + ... + + def exists(self) -> bool: + ... + + def write_text(self, text: str) -> None: + ... + + @property + def location(self) -> str: + ... diff --git a/datadoc/tests/storage_adapter_fixtures.py b/datadoc/tests/storage_adapter_fixtures.py new file mode 100644 index 00000000..8d357cfe --- /dev/null +++ b/datadoc/tests/storage_adapter_fixtures.py @@ -0,0 +1,34 @@ +import pytest + +from datadoc.tests.utils import TEST_BUCKET_PARQUET_FILEPATH, TEST_PARQUET_FILEPATH + +from ..backend.StorageAdapter import StorageAdapter + + +@pytest.fixture() +def mock_gcsfs_open(mocker): + mock = mocker.patch("gcsfs.GCSFileSystem.open") + return mock + + +@pytest.fixture() +def mock_gcsfs_exists(mocker): + mock = mocker.patch("gcsfs.GCSFileSystem.exists") + mock.return_value = True + return mock + + +@pytest.fixture() +def mock_pathlib_write_text(mocker): + mock = mocker.patch("pathlib.Path.write_text") + return mock + + +@pytest.fixture +def local_parquet_file(mock_pathlib_write_text): + return StorageAdapter.for_path(TEST_PARQUET_FILEPATH) + + +@pytest.fixture +def bucket_object_parquet_file(mock_gcsfs_open, mock_gcsfs_exists): + return StorageAdapter.for_path(TEST_BUCKET_PARQUET_FILEPATH) diff --git a/datadoc/tests/test_datadoc_metadata.py b/datadoc/tests/test_datadoc_metadata.py index b845bd16..a191693f 100644 --- a/datadoc/tests/test_datadoc_metadata.py +++ b/datadoc/tests/test_datadoc_metadata.py @@ -2,13 +2,15 @@ import shutil from copy import copy from pathlib import PurePath +from typing import List, Tuple import pytest -from datadoc.backend.DataDocMetadata import DataDocMetadata from datadoc_model import Enums from datadoc_model.Enums import DatasetState from datadoc_model.Model import DataDocDataSet, DataDocVariable, MetadataDocument +from datadoc.backend.DataDocMetadata import DataDocMetadata + from .utils import ( TEST_EXISTING_METADATA_FILE_NAME, TEST_EXISTING_METADATA_FILEPATH, @@ -22,13 +24,15 @@ def metadata(): yield DataDocMetadata(TEST_PARQUET_FILEPATH) -@pytest.fixture -def make_paths(): +def make_paths() -> List[Tuple[str, DatasetState]]: split_path = list(PurePath(TEST_PARQUET_FILEPATH).parts) initial_data = [ ("kildedata", DatasetState.SOURCE_DATA), ("inndata", DatasetState.INPUT_DATA), + ("roskildedata/klargjorte-data", DatasetState.PROCESSED_DATA), ("klargjorte_data", DatasetState.PROCESSED_DATA), + ("klargjorte-data", DatasetState.PROCESSED_DATA), + ("statistikk", DatasetState.STATISTIC), ("", None), ] test_data = [] @@ -38,7 +42,7 @@ def make_paths(): new_path = copy(split_path) new_path.insert(-2, to_insert) new_path = PurePath("").joinpath(*new_path) - test_data.append((new_path, state)) + test_data.append((str(new_path), state)) return test_data @@ -56,14 +60,16 @@ def existing_metadata_file(): yield None # Dummy value, No need to return anything in particular here -def test_get_dataset_state(metadata, make_paths): - for path, expected_result in make_paths: - actual_state = metadata.get_dataset_state(path) - assert actual_state == expected_result +@pytest.mark.parametrize(("path", "expected_result"), make_paths()) +def test_get_dataset_state( + path: str, expected_result: DatasetState, metadata: DataDocMetadata +): + actual_state = metadata.get_dataset_state(path) + assert actual_state == expected_result -def test_get_dataset_state_no_parameter_supplied(metadata): - assert metadata.get_dataset_state() is None +def test_get_dataset_state_none(metadata): + assert metadata.get_dataset_state(None) is None def test_existing_metadata_file(existing_metadata_file, metadata, remove_document_file): @@ -85,11 +91,11 @@ def test_metadata_document_percent_complete(metadata): assert metadata.percent_complete == 11 -def test_get_dataset_version(metadata): - assert metadata.get_dataset_version(metadata.dataset_stem) == "1" +def test_get_dataset_version(metadata: DataDocMetadata): + assert metadata.get_dataset_version(metadata.short_name) == "1" -def test_get_dataset_version_unknown(metadata): +def test_get_dataset_version_unknown(metadata: DataDocMetadata): assert metadata.get_dataset_version("person_data.parquet") is None diff --git a/datadoc/tests/test_dataset_reader.py b/datadoc/tests/test_dataset_parser.py similarity index 79% rename from datadoc/tests/test_dataset_reader.py rename to datadoc/tests/test_dataset_parser.py index 6d4c7f38..f4467515 100644 --- a/datadoc/tests/test_dataset_reader.py +++ b/datadoc/tests/test_dataset_parser.py @@ -1,27 +1,34 @@ import random +import pytest +from datadoc_model.Enums import Datatype, SupportedLanguages +from datadoc_model.Model import DataDocVariable, LanguageStrings +from pytest import raises + from datadoc import state -from datadoc.backend.DatasetReader import ( +from datadoc.backend.DatasetParser import ( KNOWN_BOOLEAN_TYPES, KNOWN_DATETIME_TYPES, KNOWN_FLOAT_TYPES, KNOWN_INTEGER_TYPES, KNOWN_STRING_TYPES, - DatasetReader, + DatasetParser, ) -from datadoc_model.Enums import Datatype, SupportedLanguages -from datadoc_model.Model import DataDocVariable, LanguageStrings -from pytest import raises from .utils import TEST_PARQUET_FILEPATH, TEST_SAS7BDAT_FILEPATH +@pytest.fixture() +def local_parser(): + return DatasetParser.for_file(TEST_PARQUET_FILEPATH) + + def test_use_abstract_class_directly(): with raises(TypeError): - DatasetReader().get_fields() + DatasetParser().get_fields() -def test_get_fields_parquet(): +def test_get_fields_parquet(local_parser): expected_fields = [ DataDocVariable(short_name="pers_id", data_type=Datatype.STRING), DataDocVariable(short_name="tidspunkt", data_type=Datatype.DATETIME), @@ -32,9 +39,7 @@ def test_get_fields_parquet(): DataDocVariable(short_name="fullf_utdanning", data_type=Datatype.STRING), DataDocVariable(short_name="hoveddiagnose", data_type=Datatype.STRING), ] - - reader = DatasetReader.for_file(TEST_PARQUET_FILEPATH) - fields = reader.get_fields() + fields = local_parser.get_fields() assert fields == expected_fields @@ -57,7 +62,7 @@ def test_get_fields_sas7bdat(): ), ] - reader = DatasetReader.for_file(TEST_SAS7BDAT_FILEPATH) + reader = DatasetParser.for_file(TEST_SAS7BDAT_FILEPATH) fields = reader.get_fields() assert fields == expected_fields @@ -65,18 +70,18 @@ def test_get_fields_sas7bdat(): def test_get_fields_unknown_file_type(): with raises(NotImplementedError): - DatasetReader.for_file("my_dataset.csv").get_fields() + DatasetParser.for_file("my_dataset.csv").get_fields() def test_get_fields_no_extension_provided(): - with raises(FileNotFoundError): - DatasetReader.for_file("my_dataset").get_fields() + with raises(NotImplementedError): + DatasetParser.for_file("my_dataset").get_fields() def test_transform_datatype_unknown_type(): expected = None input_data = "definitely not a known data type" - actual = DatasetReader.transform_data_type(input_data) + actual = DatasetParser.transform_data_type(input_data) assert actual == expected @@ -89,5 +94,5 @@ def test_transform_datatype(): (Datatype.BOOLEAN, KNOWN_BOOLEAN_TYPES), ]: input_data = random.choice(input_options) - actual = DatasetReader.transform_data_type(input_data) + actual = DatasetParser.transform_data_type(input_data) assert actual == expected diff --git a/datadoc/tests/test_storage_adapter.py b/datadoc/tests/test_storage_adapter.py new file mode 100644 index 00000000..0f7788db --- /dev/null +++ b/datadoc/tests/test_storage_adapter.py @@ -0,0 +1,82 @@ +import pathlib + +import pytest + +from datadoc.tests.storage_adapter_fixtures import * # noqa pytest magic +from datadoc.tests.utils import TEST_BUCKET_PARQUET_FILEPATH, TEST_PARQUET_FILEPATH + +from ..backend.StorageAdapter import GCSObject, LocalFile, StorageAdapter + + +@pytest.mark.parametrize( + ("file", "expected_class"), + [("local_parquet_file", LocalFile), ("bucket_object_parquet_file", GCSObject)], +) +def test_factory(file: StorageAdapter, expected_class, request): + # Ugly pytest magic to get the actual fixture out + file = request.getfixturevalue(file) + assert isinstance(file, expected_class) + + +@pytest.mark.parametrize("file", ["local_parquet_file", "bucket_object_parquet_file"]) +def test_open(file: StorageAdapter, request): + # Ugly pytest magic to get the actual fixture out + file = request.getfixturevalue(file) + with file.open() as file_handle: + assert file_handle.readable() + + +@pytest.mark.parametrize( + ("file", "expected_parent"), + [ + ( + "local_parquet_file", + str(pathlib.Path(TEST_PARQUET_FILEPATH).parent.absolute()), + ), + ( + "bucket_object_parquet_file", + "/".join(TEST_BUCKET_PARQUET_FILEPATH.split("/")[:-1]), + ), + ], +) +def test_parent(file: StorageAdapter, expected_parent: str, request): + # Ugly pytest magic to get the actual fixture out + file = request.getfixturevalue(file) + assert file.parent() == expected_parent + + +@pytest.mark.parametrize( + ("file", "expected"), + [ + ( + "local_parquet_file", + "/".join([TEST_PARQUET_FILEPATH, "extra"]), + ), + ( + "bucket_object_parquet_file", + "/".join([TEST_BUCKET_PARQUET_FILEPATH, "extra"]), + ), + ], +) +def test_joinpath(file: StorageAdapter, expected: str, request): + # Ugly pytest magic to get the actual fixture out + file = request.getfixturevalue(file) + file.joinpath("extra") + assert file.location == expected + + +@pytest.mark.parametrize("file", ["local_parquet_file", "bucket_object_parquet_file"]) +def test_exists(file: StorageAdapter, request): + # Ugly pytest magic to get the actual fixture out + file = request.getfixturevalue(file) + assert file.exists() + + +def test_write_text_local_file(local_parquet_file: StorageAdapter, request): + local_parquet_file.write_text("12345") + mock = request.getfixturevalue("mock_pathlib_write_text") + mock.assert_called_once_with("12345", encoding="utf-8") + + +# Currently no test for writing to GCS +# Attempts to mock are failing with TypeError: cannot set 'write' attribute of immutable type '_io.BufferedWriter' diff --git a/datadoc/tests/utils.py b/datadoc/tests/utils.py index 23665480..b8814487 100644 --- a/datadoc/tests/utils.py +++ b/datadoc/tests/utils.py @@ -2,6 +2,7 @@ TEST_RESOURCES_DIRECTORY = "datadoc/tests/resources/" TEST_PARQUET_FILEPATH = os.path.join(TEST_RESOURCES_DIRECTORY, "person_data_v1.parquet") +TEST_BUCKET_PARQUET_FILEPATH = "gs://ssb-staging-dapla-felles-data-delt/datadoc/klargjorte_data/person_data_v1.parquet" TEST_SAS7BDAT_FILEPATH = os.path.join(TEST_RESOURCES_DIRECTORY, "sasdata.sas7bdat") TEST_EXISTING_METADATA_FILE_NAME = "person_data_v1__DOC.json" TEST_EXISTING_METADATA_FILEPATH = os.path.join( diff --git a/poetry.lock b/poetry.lock index badf2c28..71820abe 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,3 +1,51 @@ +[[package]] +name = "aiohttp" +version = "3.8.1" +description = "Async http client/server framework (asyncio)" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +aiosignal = ">=1.1.2" +async-timeout = ">=4.0.0a3,<5.0" +attrs = ">=17.3.0" +charset-normalizer = ">=2.0,<3.0" +frozenlist = ">=1.1.1" +multidict = ">=4.5,<7.0" +yarl = ">=1.0,<2.0" + +[package.extras] +speedups = ["aiodns", "brotli", "cchardet"] + +[[package]] +name = "aiosignal" +version = "1.2.0" +description = "aiosignal: a list of registered asynchronous callbacks" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +frozenlist = ">=1.1.0" + +[[package]] +name = "alembic" +version = "1.8.1" +description = "A database migration tool for SQLAlchemy." +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +importlib-metadata = {version = "*", markers = "python_version < \"3.9\""} +importlib-resources = {version = "*", markers = "python_version < \"3.9\""} +Mako = "*" +SQLAlchemy = ">=1.3.0" + +[package.extras] +tz = ["python-dateutil"] + [[package]] name = "ansi2html" version = "1.8.0" @@ -80,6 +128,22 @@ six = "*" [package.extras] test = ["pytest", "astroid (<=2.5.3)"] +[[package]] +name = "async-generator" +version = "1.10" +description = "Async generators and context managers for Python 3.5+" +category = "main" +optional = false +python-versions = ">=3.5" + +[[package]] +name = "async-timeout" +version = "4.0.2" +description = "Timeout context manager for asyncio programs" +category = "main" +optional = false +python-versions = ">=3.6" + [[package]] name = "atomicwrites" version = "1.4.1" @@ -92,7 +156,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" name = "attrs" version = "22.1.0" description = "Classes Without Boilerplate" -category = "dev" +category = "main" optional = false python-versions = ">=3.5" @@ -104,14 +168,15 @@ dev = ["cloudpickle", "pre-commit", "sphinx-notfound-page", "sphinx", "furo", "z [[package]] name = "autoflake" -version = "1.4" +version = "1.5.3" description = "Removes unused imports and unused variables" category = "dev" optional = false -python-versions = "*" +python-versions = ">=3.7" [package.dependencies] pyflakes = ">=1.1.0" +toml = ">=0.10.2" [[package]] name = "babel" @@ -149,7 +214,7 @@ lxml = ["lxml"] [[package]] name = "black" -version = "22.6.0" +version = "22.8.0" description = "The uncompromising code formatter." category = "dev" optional = false @@ -201,6 +266,14 @@ category = "dev" optional = false python-versions = ">=3.5" +[[package]] +name = "cachetools" +version = "5.2.0" +description = "Extensible memoizing collections and decorators" +category = "main" +optional = false +python-versions = "~=3.7" + [[package]] name = "certifi" version = "2022.6.15" @@ -209,6 +282,21 @@ category = "main" optional = false python-versions = ">=3.6" +[[package]] +name = "certipy" +version = "0.1.3" +description = "Utility to create and sign CAs and certificates" +category = "main" +optional = false +python-versions = "*" + +[package.dependencies] +pyopenssl = "*" + +[package.extras] +test = ["pytest"] +dev = ["pytest"] + [[package]] name = "cffi" version = "1.15.1" @@ -283,6 +371,41 @@ tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.1 [package.extras] toml = ["tomli"] +[[package]] +name = "cryptography" +version = "37.0.4" +description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers." +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +cffi = ">=1.12" + +[package.extras] +docs = ["sphinx (>=1.6.5,!=1.8.0,!=3.1.0,!=3.1.1)", "sphinx-rtd-theme"] +docstest = ["pyenchant (>=1.6.11)", "twine (>=1.12.0)", "sphinxcontrib-spelling (>=4.0.1)"] +pep8test = ["black", "flake8", "flake8-import-order", "pep8-naming"] +sdist = ["setuptools_rust (>=0.11.4)"] +ssh = ["bcrypt (>=3.1.5)"] +test = ["pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-subtests", "pytest-xdist", "pretend", "iso8601", "pytz", "hypothesis (>=1.11.4,!=3.79.2)"] + +[[package]] +name = "dapla-toolbelt" +version = "1.3.1" +description = "Python module for use within Jupyterlab notebooks, specifically aimed for Statistics Norway's data platform called Dapla" +category = "main" +optional = false +python-versions = "*" + +[package.dependencies] +gcsfs = "*" +ipython = "*" +jupyterhub = "*" +lxml = "*" +pandas = "*" +pyarrow = "*" + [[package]] name = "dash" version = "2.6.1" @@ -370,7 +493,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [[package]] name = "distlib" -version = "0.3.5" +version = "0.3.6" description = "Distribution utilities" category = "dev" optional = false @@ -394,7 +517,7 @@ python-versions = "*" [[package]] name = "executing" -version = "0.10.0" +version = "1.0.0" description = "Get the currently executing AST node of a frame, and other information" category = "main" optional = false @@ -438,7 +561,7 @@ pyflakes = ">=2.5.0,<2.6.0" [[package]] name = "flake8-bugbear" -version = "22.8.22" +version = "22.8.23" description = "A plugin for flake8 finding likely bugs and design problems in your program. Contains warnings that don't belong in pyflakes and pycodestyle." category = "dev" optional = false @@ -544,6 +667,66 @@ python-versions = "*" brotli = "*" flask = "*" +[[package]] +name = "frozenlist" +version = "1.3.1" +description = "A list-like structure which implements collections.abc.MutableSequence" +category = "main" +optional = false +python-versions = ">=3.7" + +[[package]] +name = "fsspec" +version = "2022.8.2" +description = "File-system specification" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.extras] +abfs = ["adlfs"] +adl = ["adlfs"] +arrow = ["pyarrow (>=1)"] +dask = ["dask", "distributed"] +dropbox = ["dropboxdrivefs", "requests", "dropbox"] +entrypoints = ["importlib-metadata"] +fuse = ["fusepy"] +gcs = ["gcsfs"] +git = ["pygit2"] +github = ["requests"] +gs = ["gcsfs"] +gui = ["panel"] +hdfs = ["pyarrow (>=1)"] +http = ["requests", "aiohttp (!=4.0.0a0,!=4.0.0a1)"] +libarchive = ["libarchive-c"] +oci = ["ocifs"] +s3 = ["s3fs"] +sftp = ["paramiko"] +smb = ["smbprotocol"] +ssh = ["paramiko"] +tqdm = ["tqdm"] + +[[package]] +name = "gcsfs" +version = "2022.8.2" +description = "Convenient Filesystem interface over GCS" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +aiohttp = "<4.0.0a0 || >4.0.0a0,<4.0.0a1 || >4.0.0a1" +decorator = ">4.1.2" +fsspec = "2022.8.2" +google-auth = ">=1.2" +google-auth-oauthlib = "*" +google-cloud-storage = "*" +requests = "*" + +[package.extras] +crc = ["crcmod"] +gcsfuse = ["fusepy"] + [[package]] name = "gitdb" version = "4.0.9" @@ -566,6 +749,142 @@ python-versions = ">=3.7" [package.dependencies] gitdb = ">=4.0.1,<5" +[[package]] +name = "google-api-core" +version = "2.8.2" +description = "Google API client core library" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +google-auth = ">=1.25.0,<3.0dev" +googleapis-common-protos = ">=1.56.2,<2.0dev" +protobuf = ">=3.15.0,<5.0.0dev" +requests = ">=2.18.0,<3.0.0dev" + +[package.extras] +grpc = ["grpcio (>=1.33.2,<2.0dev)", "grpcio-status (>=1.33.2,<2.0dev)"] + +[[package]] +name = "google-auth" +version = "2.11.0" +description = "Google Authentication Library" +category = "main" +optional = false +python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*" + +[package.dependencies] +cachetools = ">=2.0.0,<6.0" +pyasn1-modules = ">=0.2.1" +rsa = {version = ">=3.1.4,<5", markers = "python_version >= \"3.6\""} +six = ">=1.9.0" + +[package.extras] +aiohttp = ["requests (>=2.20.0,<3.0.0dev)", "aiohttp (>=3.6.2,<4.0.0dev)"] +enterprise_cert = ["cryptography (==36.0.2)", "pyopenssl (==22.0.0)"] +pyopenssl = ["pyopenssl (>=20.0.0)"] +reauth = ["pyu2f (>=0.1.5)"] + +[[package]] +name = "google-auth-oauthlib" +version = "0.5.2" +description = "Google Authentication Library" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +google-auth = ">=1.0.0" +requests-oauthlib = ">=0.7.0" + +[package.extras] +tool = ["click (>=6.0.0)"] + +[[package]] +name = "google-cloud-core" +version = "2.3.2" +description = "Google Cloud API client core library" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +google-api-core = ">=1.31.6,<2.0.0 || >2.3.0,<3.0.0dev" +google-auth = ">=1.25.0,<3.0dev" + +[package.extras] +grpc = ["grpcio (>=1.38.0,<2.0dev)"] + +[[package]] +name = "google-cloud-storage" +version = "2.5.0" +description = "Google Cloud Storage API client library" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +google-api-core = ">=1.31.5,<2.0.0 || >2.3.0,<3.0.0dev" +google-auth = ">=1.25.0,<3.0dev" +google-cloud-core = ">=2.3.0,<3.0dev" +google-resumable-media = ">=2.3.2" +requests = ">=2.18.0,<3.0.0dev" + +[package.extras] +protobuf = ["protobuf (<5.0.0dev)"] + +[[package]] +name = "google-crc32c" +version = "1.3.0" +description = "A python wrapper of the C library 'Google CRC32C'" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.extras] +testing = ["pytest"] + +[[package]] +name = "google-resumable-media" +version = "2.3.3" +description = "Utilities for Google Media Downloads and Resumable Uploads" +category = "main" +optional = false +python-versions = ">= 3.6" + +[package.dependencies] +google-crc32c = ">=1.0,<2.0dev" + +[package.extras] +aiohttp = ["aiohttp (>=3.6.2,<4.0.0dev)"] +requests = ["requests (>=2.18.0,<3.0.0dev)"] + +[[package]] +name = "googleapis-common-protos" +version = "1.56.4" +description = "Common protobufs used in Google APIs" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +protobuf = ">=3.15.0,<5.0.0dev" + +[package.extras] +grpc = ["grpcio (>=1.0.0,<2.0.0dev)"] + +[[package]] +name = "greenlet" +version = "1.1.3" +description = "Lightweight in-process concurrent programming" +category = "main" +optional = false +python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*" + +[package.extras] +docs = ["sphinx"] + [[package]] name = "identify" version = "2.5.3" @@ -605,7 +924,7 @@ docs = ["rst.linker (>=1.9)", "jaraco.packaging (>=9)", "sphinx"] name = "importlib-resources" version = "5.9.0" description = "Read resources from Python packages" -category = "dev" +category = "main" optional = false python-versions = ">=3.7" @@ -626,7 +945,7 @@ python-versions = "*" [[package]] name = "ipykernel" -version = "6.15.1" +version = "6.15.2" description = "IPython Kernel for Jupyter" category = "main" optional = false @@ -755,9 +1074,9 @@ dev = ["hypothesis"] [[package]] name = "jsonschema" -version = "4.14.0" +version = "4.15.0" description = "An implementation of JSON Schema validation for Python" -category = "dev" +category = "main" optional = false python-versions = ">=3.7" @@ -773,7 +1092,7 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339- [[package]] name = "jupyter-client" -version = "7.3.4" +version = "7.3.5" description = "Jupyter protocol implementation and client libraries" category = "main" optional = false @@ -785,12 +1104,12 @@ jupyter-core = ">=4.9.2" nest-asyncio = ">=1.5.4" python-dateutil = ">=2.8.2" pyzmq = ">=23.0" -tornado = ">=6.0" +tornado = ">=6.2" traitlets = "*" [package.extras] -test = ["pytest-timeout", "pytest-cov", "pytest-asyncio (>=0.18)", "pytest", "pre-commit", "mypy", "ipython", "ipykernel (>=6.5)", "coverage", "codecov"] -doc = ["sphinxcontrib-github-alt", "sphinx (>=1.3.6)", "sphinx-rtd-theme", "myst-parser", "ipykernel"] +doc = ["ipykernel", "myst-parser", "sphinx-rtd-theme", "sphinx (>=1.3.6)", "sphinxcontrib-github-alt"] +test = ["codecov", "coverage", "ipykernel (>=6.5)", "ipython", "mypy", "pre-commit", "pytest", "pytest-asyncio (>=0.18)", "pytest-cov", "pytest-timeout"] [[package]] name = "jupyter-core" @@ -857,6 +1176,46 @@ websocket-client = "*" [package.extras] test = ["coverage", "ipykernel", "pre-commit", "pytest-console-scripts", "pytest-cov", "pytest-mock", "pytest-timeout", "pytest-tornasync", "pytest (>=6.0)", "requests"] +[[package]] +name = "jupyter-telemetry" +version = "0.1.0" +description = "Jupyter telemetry library" +category = "main" +optional = false +python-versions = ">=3.5" + +[package.dependencies] +jsonschema = "*" +python-json-logger = "*" +"ruamel.yaml" = "*" +traitlets = "*" + +[[package]] +name = "jupyterhub" +version = "2.3.1" +description = "JupyterHub: A multi-user server for Jupyter notebooks" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +alembic = ">=1.4" +async-generator = ">=1.9" +certipy = ">=0.1.2" +entrypoints = "*" +jinja2 = ">=2.11.0" +jupyter-telemetry = ">=0.1.0" +oauthlib = ">=3.0" +packaging = "*" +pamela = {version = "*", markers = "sys_platform != \"win32\""} +prometheus-client = ">=0.4.0" +psutil = {version = ">=5.6.5", markers = "sys_platform == \"win32\""} +python-dateutil = "*" +requests = "*" +SQLAlchemy = ">=1.1" +tornado = ">=5.1" +traitlets = ">=4.3.2" + [[package]] name = "jupyterlab" version = "3.4.5" @@ -890,7 +1249,7 @@ python-versions = ">=3.7" [[package]] name = "jupyterlab-server" -version = "2.15.0" +version = "2.15.1" description = "A set of server components for JupyterLab and JupyterLab like applications." category = "dev" optional = false @@ -907,14 +1266,14 @@ packaging = "*" requests = "*" [package.extras] -test = ["strict-rfc3339", "ruamel-yaml", "pytest (>=5.3.2)", "pytest-cov", "pytest-console-scripts", "openapi-spec-validator (<0.5)", "openapi-core (>=0.14.2)", "jupyter-server", "ipykernel", "codecov"] -openapi = ["ruamel-yaml", "openapi-core (>=0.14.2)"] +openapi = ["openapi-core (>=0.14.2)", "ruamel-yaml"] +test = ["codecov", "ipykernel", "jupyter-server", "openapi-core (>=0.14.2)", "openapi-spec-validator (<0.5)", "pytest-console-scripts", "pytest-cov", "pytest (>=5.3.2)", "ruamel-yaml", "strict-rfc3339"] [[package]] name = "lxml" version = "4.9.1" description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API." -category = "dev" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, != 3.4.*" @@ -924,6 +1283,22 @@ htmlsoup = ["beautifulsoup4"] html5 = ["html5lib"] cssselect = ["cssselect (>=0.7)"] +[[package]] +name = "mako" +version = "1.2.2" +description = "A super-fast templating language that borrows the best ideas from the existing templating languages." +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +MarkupSafe = ">=0.9.2" + +[package.extras] +babel = ["babel"] +lingua = ["lingua"] +testing = ["pytest"] + [[package]] name = "markupsafe" version = "2.1.1" @@ -959,6 +1334,14 @@ category = "dev" optional = false python-versions = "*" +[[package]] +name = "multidict" +version = "6.0.2" +description = "multidict implementation" +category = "main" +optional = false +python-versions = ">=3.7" + [[package]] name = "mypy" version = "0.950" @@ -1167,6 +1550,19 @@ category = "main" optional = false python-versions = ">=3.8" +[[package]] +name = "oauthlib" +version = "3.2.0" +description = "A generic, spec-compliant, thorough implementation of the OAuth request-signing logic" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.extras] +rsa = ["cryptography (>=3.0.0)"] +signals = ["blinker (>=1.4.0)"] +signedtoken = ["cryptography (>=3.0.0)", "pyjwt (>=2.0.0,<3)"] + [[package]] name = "packaging" version = "21.3" @@ -1178,9 +1574,17 @@ python-versions = ">=3.6" [package.dependencies] pyparsing = ">=2.0.2,<3.0.5 || >3.0.5" +[[package]] +name = "pamela" +version = "1.0.0" +description = "PAM interface using ctypes" +category = "main" +optional = false +python-versions = "*" + [[package]] name = "pandas" -version = "1.4.3" +version = "1.4.4" description = "Powerful data structures for data analysis, time series, and statistics" category = "main" optional = false @@ -1188,16 +1592,16 @@ python-versions = ">=3.8" [package.dependencies] numpy = [ - {version = ">=1.21.0", markers = "python_version >= \"3.10\""}, - {version = ">=1.20.0", markers = "platform_machine == \"arm64\" and python_version < \"3.10\""}, - {version = ">=1.19.2", markers = "platform_machine == \"aarch64\" and python_version < \"3.10\""}, {version = ">=1.18.5", markers = "platform_machine != \"aarch64\" and platform_machine != \"arm64\" and python_version < \"3.10\""}, + {version = ">=1.19.2", markers = "platform_machine == \"aarch64\" and python_version < \"3.10\""}, + {version = ">=1.20.0", markers = "platform_machine == \"arm64\" and python_version < \"3.10\""}, + {version = ">=1.21.0", markers = "python_version >= \"3.10\""}, ] python-dateutil = ">=2.8.1" pytz = ">=2020.1" [package.extras] -test = ["pytest-xdist (>=1.31)", "pytest (>=6.0)", "hypothesis (>=5.5.3)"] +test = ["hypothesis (>=5.5.3)", "pytest (>=6.0)", "pytest-xdist (>=1.31)"] [[package]] name = "pandocfilters" @@ -1221,11 +1625,11 @@ testing = ["docopt", "pytest (<6.0.0)"] [[package]] name = "pathspec" -version = "0.9.0" +version = "0.10.0" description = "Utility library for gitignore style pattern matching of file paths." category = "dev" optional = false -python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" +python-versions = ">=3.7" [[package]] name = "pep8-naming" @@ -1261,7 +1665,7 @@ python-versions = "*" name = "pkgutil-resolve-name" version = "1.3.10" description = "Resolve a name to an object." -category = "dev" +category = "main" optional = false python-versions = ">=3.6" @@ -1320,7 +1724,7 @@ virtualenv = ">=20.0.8" name = "prometheus-client" version = "0.14.1" description = "Python client for the Prometheus monitoring system." -category = "dev" +category = "main" optional = false python-versions = ">=3.6" @@ -1338,6 +1742,14 @@ python-versions = ">=3.6.2" [package.dependencies] wcwidth = "*" +[[package]] +name = "protobuf" +version = "4.21.5" +description = "" +category = "main" +optional = false +python-versions = ">=3.7" + [[package]] name = "psutil" version = "5.9.1" @@ -1387,6 +1799,25 @@ python-versions = ">=3.7" [package.dependencies] numpy = ">=1.16.6" +[[package]] +name = "pyasn1" +version = "0.4.8" +description = "ASN.1 types and codecs" +category = "main" +optional = false +python-versions = "*" + +[[package]] +name = "pyasn1-modules" +version = "0.2.8" +description = "A collection of ASN.1-based protocols modules." +category = "main" +optional = false +python-versions = "*" + +[package.dependencies] +pyasn1 = ">=0.4.6,<0.5.0" + [[package]] name = "pychalk" version = "2.0.1" @@ -1416,14 +1847,14 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "pydantic" -version = "1.9.2" +version = "1.10.1" description = "Data validation and settings management using python type hints" category = "main" optional = false -python-versions = ">=3.6.1" +python-versions = ">=3.7" [package.dependencies] -typing-extensions = ">=3.7.4.3" +typing-extensions = ">=4.1.0" [package.extras] dotenv = ["python-dotenv (>=0.10.4)"] @@ -1448,6 +1879,21 @@ python-versions = ">=3.6" [package.extras] plugins = ["importlib-metadata"] +[[package]] +name = "pyopenssl" +version = "22.0.0" +description = "Python wrapper module around the OpenSSL library" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +cryptography = ">=35.0" + +[package.extras] +docs = ["sphinx", "sphinx-rtd-theme"] +test = ["flaky", "pretend", "pytest (>=3.0.1)"] + [[package]] name = "pyparsing" version = "3.0.9" @@ -1463,7 +1909,7 @@ diagrams = ["jinja2", "railroad-diagrams"] name = "pyrsistent" version = "0.18.1" description = "Persistent/Functional/Immutable data structures" -category = "dev" +category = "main" optional = false python-versions = ">=3.7" @@ -1503,6 +1949,20 @@ pytest = ">=4.6" [package.extras] testing = ["virtualenv", "pytest-xdist", "six", 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