Exemplos de get_summary em Python

Exemplo n.º 1

Arquivo: test_core.py Projeto: promexjm/ncbi-genome-download

def test_get_summary(monkeypatch, req, tmpdir):
    """Test getting the assembly summary file."""
    cache_dir = tmpdir.mkdir('cache')
    monkeypatch.setattr(core, 'CACHE_DIR', str(cache_dir))
    cache_file = cache_dir.join('refseq_bacteria_assembly_summary.txt')
    req.get(
        'https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
        text='test')

    ret = core.get_summary('refseq', 'bacteria', NgdConfig.get_default('uri'),
                           False)
    assert ret.read() == 'test'
    assert not cache_file.check()

    ret = core.get_summary('refseq', 'bacteria', NgdConfig.get_default('uri'),
                           True)
    assert ret.read() == 'test'
    assert cache_file.check()

    req.get(
        'https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
        text='never read')
    ret = core.get_summary('refseq', 'bacteria', NgdConfig.get_default('uri'),
                           True)
    assert ret.read() == 'test'

Exemplo n.º 2

def test_get_summary_error_handling(monkeypatch, mocker, req, tmpdir):
    """Test get_summary error handling."""
    cache_dir = tmpdir.join('cache')
    monkeypatch.setattr(core, 'CACHE_DIR', str(cache_dir))
    req.get('https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt', text='test')

    fake_makedirs = mocker.MagicMock(side_effect=OSError(13, "Permission denied"))
    monkeypatch.setattr(os, 'makedirs', fake_makedirs)
    with pytest.raises(OSError):
        core.get_summary('refseq', 'bacteria', NgdConfig.get_default('uri'), True)

Exemplo n.º 3

Arquivo: test_core.py Projeto: kblin/ncbi-genome-download

def test_get_summary_error_handling(monkeypatch, mocker, req, tmpdir):
    """Test get_summary error handling."""
    cache_dir = tmpdir.join('cache')
    monkeypatch.setattr(core, 'CACHE_DIR', str(cache_dir))
    req.get('https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt', text='test')

    fake_makedirs = mocker.MagicMock(side_effect=OSError(13, "Permission denied"))
    monkeypatch.setattr(os, 'makedirs', fake_makedirs)
    with pytest.raises(OSError):
        core.get_summary('refseq', 'bacteria', NgdConfig.get_default('uri'), True)

Exemplo n.º 4

Arquivo: test_core.py Projeto: kblin/ncbi-genome-download

def test_get_summary(monkeypatch, req, tmpdir):
    """Test getting the assembly summary file."""
    cache_dir = tmpdir.mkdir('cache')
    monkeypatch.setattr(core, 'CACHE_DIR', str(cache_dir))
    cache_file = cache_dir.join('refseq_bacteria_assembly_summary.txt')
    req.get('https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt', text='test')

    ret = core.get_summary('refseq', 'bacteria', NgdConfig.get_default('uri'), False)
    assert ret.read() == 'test'
    assert not cache_file.check()

    ret = core.get_summary('refseq', 'bacteria', NgdConfig.get_default('uri'), True)
    assert ret.read() == 'test'
    assert cache_file.check()

    req.get('https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt', text='never read')
    ret = core.get_summary('refseq', 'bacteria', NgdConfig.get_default('uri'), True)
    assert ret.read() == 'test'

Exemplo n.º 5

Arquivo: test_core.py Projeto: mbourqui/ncbi-genome-download

def test_get_summary(req):
    req.get('https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt', text='test')
    ret = core.get_summary('refseq', 'bacteria', dflt.URI.default)
    assert ret.read() == 'test'

Exemplo n.º 6

Arquivo: test_core.py Projeto: metagenomics/ncbi-genome-download

def test_get_summary(req):
    req.get('http://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt', text='test')
    ret = core.get_summary('refseq', 'bacteria', core.NCBI_URI)
    assert ret.read() == 'test'