def test__download(monkeypatch, mocker, req):
summary_contents = open(_get_file('partial_summary.txt'), 'r').read()
req.get('http://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
text=summary_contents)
mocker.spy(core, 'get_summary')
mocker.spy(core, 'parse_summary')
mocker.patch('ncbi_genome_download.core.download_entry')
core._download('refseq', 'bacteria', core.NCBI_URI, '/tmp/fake', 'genbank', 'all')
assert core.get_summary.call_count == 1
assert core.parse_summary.call_count == 1
assert core.download_entry.call_count == 4
def test__download(monkeypatch, mocker, req):
summary_contents = open(_get_file('partial_summary.txt'), 'r').read()
req.get(
'https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
text=summary_contents)
mocker.spy(core, 'get_summary')
mocker.spy(core, 'parse_summary')
mocker.patch('ncbi_genome_download.core.download_entry')
core._download('refseq', 'bacteria', core.NCBI_URI, '/tmp/fake', 'genbank',
'all')
assert core.get_summary.call_count == 1
assert core.parse_summary.call_count == 1
assert core.download_entry.call_count == 4
def test__download_contig(monkeypatch, mocker, req):
summary_contents = open(_get_file('assembly_status.txt'), 'r').read()
req.get('http://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
text=summary_contents)
mocker.spy(core, 'get_summary')
mocker.spy(core, 'parse_summary')
mocker.patch('ncbi_genome_download.core.download_entry')
core._download('refseq', 'bacteria', core.NCBI_URI, '/tmp/fake', 'genbank', 'contig')
assert core.get_summary.call_count == 1
assert core.parse_summary.call_count == 1
assert core.download_entry.call_count == 1
# Many nested tuples in call_args_list, no kidding.
assert core.download_entry.call_args_list[0][0][0]['assembly_level'] == 'Contig'
def test__download_genus_lowercase(monkeypatch, mocker, req):
summary_contents = open(_get_file('partial_summary.txt'), 'r').read()
req.get('http://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
text=summary_contents)
mocker.spy(core, 'get_summary')
mocker.spy(core, 'parse_summary')
mocker.patch('ncbi_genome_download.core.download_entry')
core._download('refseq', 'bacteria', core.NCBI_URI, '/tmp/fake', 'genbank', 'all', 'azorhizobium')
assert core.get_summary.call_count == 1
assert core.parse_summary.call_count == 1
assert core.download_entry.call_count == 1
# Many nested tuples in call_args_list, no kidding.
assert core.download_entry.call_args_list[0][0][0]['organism_name'] == 'Azorhizobium caulinodans ORS 571'
def test__download_complete(monkeypatch, mocker, req):
summary_contents = open(_get_file('assembly_status.txt'), 'r').read()
req.get(
'https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
text=summary_contents)
mocker.spy(core, 'get_summary')
mocker.spy(core, 'parse_summary')
mocker.patch('ncbi_genome_download.core.download_entry')
core._download('refseq', 'bacteria', core.NCBI_URI, '/tmp/fake', 'genbank',
'complete')
assert core.get_summary.call_count == 1
assert core.parse_summary.call_count == 1
assert core.download_entry.call_count == 1
# Many nested tuples in call_args_list, no kidding.
assert core.download_entry.call_args_list[0][0][0][
'assembly_level'] == 'Complete Genome'
def test__download_species_taxid(monkeypatch, mocker, req):
summary_contents = open(_get_file('partial_summary.txt'), 'r').read()
req.get(
'https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
text=summary_contents)
mocker.spy(core, 'get_summary')
mocker.spy(core, 'parse_summary')
mocker.patch('ncbi_genome_download.core.download_entry')
core._download('refseq', 'bacteria', core.NCBI_URI, '/tmp/fake', 'genbank',
'all', '', '7')
assert core.get_summary.call_count == 1
assert core.parse_summary.call_count == 1
assert core.download_entry.call_count == 1
# Many nested tuples in call_args_list, no kidding.
assert core.download_entry.call_args_list[0][0][0][
'organism_name'] == 'Azorhizobium caulinodans ORS 571'