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[package.dependencies] -greenlet = {version = "!=0.4.17", markers = "python_version < \"3.13\" and (platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\")"} +greenlet = {version = "!=0.4.17", markers = "python_version < \"3.14\" and (platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\")"} typing-extensions = ">=4.6.0" [package.extras] @@ -4735,4 +4760,4 @@ type = ["pytest-mypy"] [metadata] lock-version = "2.0" python-versions = ">=3.10,<3.13" -content-hash = "9a4ec2b0a7509c70a540b2aa317423ef706ff1bcd3b90c9a40b82b95a2df364d" +content-hash = "cba513c73d76ca48eace6b62b94bee6547ccaefea369d24efd10a9394c2b48e5" diff --git a/pyproject.toml b/pyproject.toml index e2d5dee34..e0596d4e4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -44,6 +44,7 @@ tomli = {version = "^2.0.1", python = "<3.11"} tomli-w = "^1.0.0" tqdm = "^4.66.2" xarray = ">=2024.6,<2026.0" +openpyxl = "^3.1.5" [tool.poetry.group.types.dependencies] types-dataclasses = "^0.6.6" diff --git a/tests/core/data/garbage.csv b/tests/core/data/garbage.csv new file mode 100644 index 000000000..c55856dbd --- /dev/null +++ b/tests/core/data/garbage.csv @@ -0,0 +1,2 @@ +a,b,c +1,2,"3 \ No newline at end of file diff --git a/tests/core/data/garbage.xlsx b/tests/core/data/garbage.xlsx new file mode 100644 index 000000000..bd39652b1 Binary files /dev/null and b/tests/core/data/garbage.xlsx differ diff --git a/tests/core/data/reader_test.csv b/tests/core/data/reader_test.csv new file mode 100644 index 000000000..7b3295bed --- /dev/null +++ b/tests/core/data/reader_test.csv @@ -0,0 +1,4 @@ +var1,var2 +1,4 +2,5 +3,6 \ No newline at end of file diff --git a/tests/core/data/reader_test.xlsx b/tests/core/data/reader_test.xlsx new file mode 100644 index 000000000..d017787dc Binary files /dev/null and b/tests/core/data/reader_test.xlsx differ diff --git a/tests/core/test_readers.py b/tests/core/test_readers.py index 5c3bbdba7..b4bc9364e 100644 --- a/tests/core/test_readers.py +++ b/tests/core/test_readers.py @@ -2,8 +2,10 @@ from contextlib import nullcontext as does_not_raise from logging import CRITICAL, DEBUG, INFO +from zipfile import BadZipFile import pytest +from pandas.errors import ParserError from xarray import DataArray from tests.conftest import log_check @@ -93,7 +95,11 @@ def test_func(): ], ) def test_load_netcdf(shared_datadir, caplog, file, file_var, exp_err, expected_log): - """Test the netdcf variable loader.""" + """Test the netdcf variable loader. + + The tests here are dependent on the test_file_format_loader, so cannot be run + individually. + """ from virtual_ecosystem.core.readers import load_netcdf @@ -105,6 +111,98 @@ def test_load_netcdf(shared_datadir, caplog, file, file_var, exp_err, expected_l log_check(caplog, expected_log) +@pytest.mark.parametrize( + argnames=["file", "file_var", "exp_err", "expected_log"], + argvalues=[ + ( + "not_there.csv", + "irrelevant", + pytest.raises(FileNotFoundError), + ((CRITICAL, "Data file not found"),), + ), + ( + "garbage.csv", + "irrelevant", + pytest.raises(ParserError), + ((CRITICAL, "Could not load data from"),), + ), + ( + "reader_test.csv", + "missing", + pytest.raises(KeyError), + ((CRITICAL, "Variable missing not found in"),), + ), + ( + "reader_test.csv", + "var1", + does_not_raise(), + (), + ), + ], +) +def test_load_csv(shared_datadir, caplog, file, file_var, exp_err, expected_log): + """Test the netdcf variable loader. + + The tests here are dependent on the test_file_format_loader, so cannot be run + individually. + """ + + from virtual_ecosystem.core.readers import load_csv + + with exp_err: + darray = load_csv(shared_datadir / file, file_var) + assert isinstance(darray, DataArray) + + # Check the error reports + log_check(caplog, expected_log) + + +@pytest.mark.parametrize( + argnames=["file", "file_var", "exp_err", "expected_log"], + argvalues=[ + ( + "not_there.xlsx", + "irrelevant", + pytest.raises(FileNotFoundError), + ((CRITICAL, "Data file not found"),), + ), + ( + "garbage.xlsx", + "irrelevant", + pytest.raises(BadZipFile), + ((CRITICAL, "Could not load data from"),), + ), + ( + "reader_test.xlsx", + "missing", + pytest.raises(KeyError), + ((CRITICAL, "Variable missing not found in"),), + ), + ( + "reader_test.xlsx", + "var1", + does_not_raise(), + (), + ), + ], +) +def test_load_excel(shared_datadir, caplog, file, file_var, exp_err, expected_log): + """Test the netdcf variable loader. + + The tests here are dependent on the test_file_format_loader, so cannot be run + individually. + """ + + from virtual_ecosystem.core.readers import load_excel + + with exp_err: + darray = load_excel(shared_datadir / file, file_var) + assert isinstance(darray, DataArray) + + # Check the error reports + log_check(caplog, expected_log) + + @pytest.mark.parametrize( argnames=[ "filename", diff --git a/virtual_ecosystem/core/readers.py b/virtual_ecosystem/core/readers.py index ee0dce21f..ff057efbb 100644 --- a/virtual_ecosystem/core/readers.py +++ b/virtual_ecosystem/core/readers.py @@ -33,7 +33,10 @@ def new_function_to_load_tif_data(...): from collections.abc import Callable from pathlib import Path +from zipfile import BadZipFile +from pandas import read_csv, read_excel +from pandas.errors import ParserError from xarray import DataArray, load_dataset from virtual_ecosystem.core.logger import LOGGER @@ -55,7 +58,7 @@ def new_function_to_load_tif_data(...): """ -def register_file_format_loader(file_types: tuple[str]) -> Callable: +def register_file_format_loader(file_types: tuple[str, ...]) -> Callable: """Adds a data loader function to the data loader registry. This decorator is used to register a function that loads data from a given file type @@ -134,6 +137,88 @@ def load_netcdf(file: Path, var_name: str) -> DataArray: return dataset[var_name] +@register_file_format_loader(file_types=(".csv",)) +def load_csv(file: Path, var_name: str) -> DataArray: + """Loads a DataArray from a csv file. + + Args: + file: A Path for a csv or excel file containing the variable to load. + var_name: A string providing the name of the variables in this file. + + Raises: + FileNotFoundError: with bad file path names. + ParserError: if the csv data is not readable. + """ + + to_raise: Exception + + # Try to load file + try: + dataset = read_csv(file) + except FileNotFoundError: + to_raise = FileNotFoundError(f"Data file not found: {file}") + LOGGER.critical(to_raise) + raise to_raise + except ParserError as err: + to_raise = ParserError(f"Could not load data from {file}: {err}.") + LOGGER.critical(to_raise) + raise to_raise + + # Check if file var is in the dataset + if var_name not in dataset.columns: + to_raise = KeyError(f"Variable {var_name} not found in {file}") + LOGGER.critical(to_raise) + raise to_raise + + return dataset[var_name].to_xarray() + + +@register_file_format_loader(file_types=(".xlsx",)) +def load_excel(file: Path, var_name: str) -> DataArray: + """Loads a DataArray from an excel file. + + Args: + file: A Path for a csv or excel file containing the variable to load. + var_name: A string providing the name of the variables in this file. + + Raises: + FileNotFoundError: with bad file path names. + BadZipFile: if the excel file is corrupted. + Exception: catches other exceptions from openpyxl. + + Note: BadZipFile is the most common error thrown by openpyxl for corrupted excel + files, which is based on their internal processing files as zips. The general + exception is included to cover other possible issues from openpyxl, as it has + various other potential failure modes. + """ + + to_raise: Exception + + # Determine dataframe file type & load file + try: + dataset = read_excel(file, engine="openpyxl") + except FileNotFoundError: + to_raise = FileNotFoundError(f"Data file not found: {file}") + LOGGER.critical(to_raise) + raise to_raise + except BadZipFile as err: + to_raise = BadZipFile(f"Could not load data from {file}: {err}.") + LOGGER.critical(to_raise) + raise to_raise + except Exception as err: + to_raise = Exception(f"Unidentified exception opening {file}: {err}") + LOGGER.critical(to_raise) + raise to_raise + + # Check if file var is in the dataset + if var_name not in dataset.columns: + to_raise = KeyError(f"Variable {var_name} not found in {file}") + LOGGER.critical(to_raise) + raise to_raise + + return dataset[var_name].to_xarray() + + def load_to_dataarray( file: Path, var_name: str,