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'
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)
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)
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'
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'
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'