Running pytest sometimes fails

krassowski / easy-entrez

Retrieve PubMed articles, text-mining annotations, or molecular data from >35 Entrez databases via easy to use Python package - built on top of Entrez E-utilities API.

GNU Lesser General Public License v3.0

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Running pytest (in a venv) on commit 6cd14fb sometimes fails with the following error:


(.venv) jfreige@sl-akali-p-cs1:easy-entrez (main)$ pytest
=================================================================== 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_search ________________________________________________________________________

    def test_search():
        result = entrez_api.search('cancer AND human[organism]', max_results=1)
        assert is_response_for(result, SearchQuery)
        assert not is_response_for(result, FetchQuery)
>       assert result.data['esearchresult']['count'] != 0

tests/test_api.py:29:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
easy_entrez/api.py:45: in data
    if self.content_type == 'json':
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <EntrezResponse status=502 for SearchQuery 'cancer AND human[organism]' in pubmed>

    @property
    def content_type(self) -> ReturnType:
        declared_type = self.response.headers['Content-Type']
        if declared_type.startswith('application/json'):
            return 'json'
        if declared_type.startswith('text/xml'):
            return 'xml'
>       raise ValueError(f'Unknown content type: {declared_type}')
E       ValueError: Unknown content type: text/plain

easy_entrez/api.py:41: ValueError
===================================================================== 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_search - ValueError: Unknown content type: text/plain
======================================================== 1 failed, 14 passed, 3 warnings in 13.15s =========================================================```

=================================================================================== 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 =========================================================================

krassowski / easy-entrez

Running pytest sometimes fails #19