Tests for the data_handling Module

Tests for the data_handling submodule.

Tests for the data_handling.request Submodule

Tests for the scripts.data_handling.request submodule.

These unit tests are designed to test that genes are passed to the query correctly. They do not test the API, as tests of data returned by realworld API queries are best left to integrations tests.

tests.data_handling.test_request.test_no_no_output(tmp_path: pathlib.Path) → None

It doesn’t output a file when the gene is not found.

tests.data_handling.test_request.test_raises_http_error(tmp_path: pathlib.Path) → None

It raises an HTTPError.

tests.data_handling.test_request.test_return_none() → None

It returns gene when the gene is not found.

tests.data_handling.test_request.test_return_str() → None

It returns the id when the gene is found.

tests.data_handling.test_request.test_writes_file(tmp_path: pathlib.Path) → None

It writes the file.

Tests for the data_handling.biomart Submodule

Tests for the scripts.data_handling.biomart submodule.

tests.data_handling.test_biomart.test_raises_http_error(tmp_path: pathlib.Path) → None

It raises an HTTPError.

tests.data_handling.test_biomart.test_writes_file(tmp_path: pathlib.Path) → None

It writes the file.

Tests for the data_handling.process Submodule

Tests for the scripts.data_handling.process submodule.

These unit tests are designed to test that the results of the query are handled correctly. They assume the data returned by the API query is formatted correctly, as tests of data returned by realworld API queries are best left to integrations tests. As such, representative data is included in the tests.data module.

tests.data_handling.test_process.MANE

A minimal MANE dataset

Type

pd.DataFrame

tests.data_handling.test_process.test_results_columns(tmp_path: pathlib.Path) → None

Its columns are named correctly .

tests.data_handling.test_process.test_sorted_results(tmp_path: pathlib.Path) → None

The results are sorted by median.

As the merge_data function technically sorts on “MANE_status” as well, it would be ideal to test that sort, too. However, it it impossible to know in advance how many will have this status, so we cannot check count. Additionally, we cannot check the sort as most values are NaN, and knowing the correct order would require prior knowledge about the number of GTEx transcripts and the number with MANE status.

Parameters

tmp_path (Path) – pytest fixture for temporary path

tests.data_handling.test_process.test_writes_file(tmp_path: pathlib.Path) → None

It writes a file.