Comments (1)
Ok great, after some time I also got this one on main, I will reopen #18:
=================================================================================== test session starts ====================================================================================
platform linux -- Python 3.10.12, pytest-7.4.2, pluggy-1.3.0
rootdir: /data/local/jfreige/geo-mining/easy-entrez
plugins: cov-4.1.0
collected 15 items
tests/test_api.py ..F [ 20%]
tests/test_parsing.py .... [ 46%]
tests/test_queries.py ........ [100%]
========================================================================================= FAILURES =========================================================================================
________________________________________________________________________________________ test_fetch ________________________________________________________________________________________
def test_fetch():
result = entrez_api.fetch(['4'], max_results=1, database='snp')
assert is_response_for(result, FetchQuery)
assert not is_response_for(result, SearchQuery)
snp = result.data[0]
namespaces = {'ns0': 'https://www.ncbi.nlm.nih.gov/SNP/docsum'}
> chromosome = snp.find('.//ns0:CHR', namespaces).text
E AttributeError: 'NoneType' object has no attribute 'text'
tests/test_api.py:38: AttributeError
===================================================================================== warnings summary =====================================================================================
tests/test_parsing.py:39
/data/local/jfreige/geo-mining/easy-entrez/tests/test_parsing.py:39: PytestUnknownMarkWarning: Unknown pytest.mark.optional - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
@pytest.mark.optional
tests/test_parsing.py:78
/data/local/jfreige/geo-mining/easy-entrez/tests/test_parsing.py:78: PytestUnknownMarkWarning: Unknown pytest.mark.optional - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
@pytest.mark.optional
tests/test_parsing.py:89
/data/local/jfreige/geo-mining/easy-entrez/tests/test_parsing.py:89: PytestUnknownMarkWarning: Unknown pytest.mark.optional - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
@pytest.mark.optional
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
================================================================================= short test summary info ==================================================================================
FAILED tests/test_api.py::test_fetch - AttributeError: 'NoneType' object has no attribute 'text'
======================================================================== 1 failed, 14 passed, 3 warnings in 13.46s =========================================================================
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Related Issues (14)
- problem of (ReadTimeout ) API time out with easy_entrez HOT 2
- Entrez search result limit HOT 20
- `fetch` method with JSON response raises exception HOT 1
- Examples fail to run HOT 2
- Request: officially supporting Python 3.12 HOT 1
- Docs request: possible tool names
- Docs request: significance of `email` HOT 2
- Request: `StrEnum` for all filters
- How to (1) search by title and (2) download abstract from matching paper HOT 1
- Suggestion: `pytest-vcr` for reliable testing HOT 2
- Request: `async` support
- Batch querying HOT 2
- How can I obrain the SNP rs ids using CHR:POS_A1_A2 format for > 3K SNPs? HOT 1
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