def test_build_params():
"""Test we build the right set of parameters."""
config = core.Config(molecule='nucleotide', verbose=False)
dl_id = 'TEST'
expected_params = {
'tool': 'ncbi-acc-download',
'retmode': 'text',
'rettype': 'gbwithparts',
'id': 'TEST',
'db': 'nucleotide'
}
params = core.build_params(dl_id, config)
assert params == expected_params
expected_params = {
'tool': 'ncbi-acc-download',
'retmode': 'text',
'rettype': 'fasta',
'id': 'TEST',
'db': 'protein'
}
config.molecule = 'protein'
params = core.build_params(dl_id, config)
assert params == expected_params
def test_generate_url():
"""Test URL generation."""
config = core.Config()
expected = "{}?{}".format(ENTREZ_URL, "retmode=text&id=FAKE&db=nucleotide&rettype=gbwithparts")
assert expected == core.generate_url("FAKE", config)
config.format = 'gff3'
expected = "{}?{}".format(SVIEWER_URL, "retmode=text&id=FAKE&db=nucleotide&report=gff3")
assert expected == core.generate_url("FAKE", config)
def test_validate_and_write_extended_validation(req):
"""Test extended validation before writing."""
handle = StringIO()
req.get('http://fake/', text=u'>foo\nMAGIC')
r = requests.get('http://fake/')
config = core.Config(extended_validation='loads', molecule='protein')
core._validate_and_write(r, handle, 'FAKE', config)
assert handle.getvalue() == u'>foo\nMAGIC'
def test_validate_and_write_error_pattern_raises(req):
"""Test scanning the download file for error patterns."""
handle = StringIO()
req.get('http://fake/', text=u'ID list is empty')
r = requests.get('http://fake/')
config = core.Config()
with pytest.raises(core.BadPatternError):
core._validate_and_write(r, handle, 'FAKE', config)
def test_download_to_file(req, tmpdir):
"""Test downloading things from NCBI."""
req.get(ENTREZ_URL, text='This works.')
outdir = tmpdir.mkdir('outdir')
filename = outdir.join('foo')
expected = outdir.join('foo.gbk')
config = core.Config(molecule='nucleotide', verbose=False)
core.download_to_file('FOO', config, filename=filename)
assert expected.check()
def test_validate_and_write_emit(req):
"""Test writing prints dots in verbose mode."""
handle = StringIO()
req.get('http://fake/', text=u'This is a sequence file, honest.')
r = requests.get('http://fake/')
output = StringIO()
config = core.Config()
config.emit = output.write
core._validate_and_write(r, handle, 'FAKE', config)
assert output.getvalue() == u'.\n'
assert handle.getvalue() == u'This is a sequence file, honest.'
def test_download_to_file_append(req, tmpdir):
"""Test appending multiple downloads into a single file."""
req.get(ENTREZ_URL, text='This works.\n')
outdir = tmpdir.mkdir('outdir')
filename = outdir.join('foo.txt')
expected = outdir.join('foo.txt')
config = core.Config(molecule='nucleotide', verbose=False, out='foo.txt')
core.download_to_file('FOO', config, filename=str(filename), append=False)
core.download_to_file('BAR', config, filename=str(filename), append=True)
core.download_to_file('BAZ', config, filename=str(filename), append=True)
assert expected.check()
assert len(expected.readlines()) == 3
def test_validate_and_write_error_pattern_raises(req):
"""Test scanning the download file for error patterns."""
handle = StringIO()
req.get('http://fake/', text=u'ID list is empty')
r = requests.get('http://fake/')
config = core.Config()
with pytest.raises(BadPatternError):
core._validate_and_write(r, handle, 'FAKE', config)
req.get('http://fake/', text=u'Error: CEFetchPApplication::proxy_stream(): Failed to retrieve sequence: NC_405534')
r = requests.get('http://fake/')
with pytest.raises(BadPatternError):
core._validate_and_write(r, handle, 'FAKE', config)
def test_generate_url_with_api_key():
"""Test URL generation for API key"""
config = core.Config(api_key='97ae64f04b7e33672d5591a575b5f0c4c908')
expected = "{}?{}".format(
ENTREZ_URL,
"retmode=text&id=FAKE&db=nucleotide&api_key=97ae64f04b7e33672d5591a575b5f0c4c908&rettype=gbwithparts"
)
assert expected == core.generate_url("FAKE", config)
config.format = 'gff3'
expected = "{}?{}".format(
SVIEWER_URL,
"retmode=text&id=FAKE&db=nucleotide&api_key=97ae64f04b7e33672d5591a575b5f0c4c908&report=gff3"
)
assert expected == core.generate_url("FAKE", config)
def test_download_to_file_retry(req, tmpdir):
"""Test downloading things from NCBI, retrying after a 429 status."""
req.get(ENTREZ_URL,
response_list=[
{
"text": u'Whoa, slow down',
"status_code": 429,
"headers": {
"Retry-After": "0"
}
},
{
"text": 'This works.'
},
])
outdir = tmpdir.mkdir('outdir')
filename = outdir.join('foo')
expected = outdir.join('foo.gbk')
config = core.Config(molecule='nucleotide', verbose=False)
core.download_to_file('FOO', config, filename=filename)
assert expected.check()
