def test_download_one(monkeypatch, mocker):
_download_mock = mocker.MagicMock()
monkeypatch.setattr(core, '_download', _download_mock)
fake_args = Namespace(section='refseq', domain='bacteria', uri=core.NCBI_URI,
output='/tmp/fake', file_format='genbank')
core.download(fake_args)
_download_mock.assert_called_with('refseq', 'bacteria', core.NCBI_URI, '/tmp/fake', 'genbank')
def test_download_all(monkeypatch, mocker):
_download_mock = mocker.MagicMock()
monkeypatch.setattr(core, '_download', _download_mock)
fake_args = Namespace(section='refseq', domain='all', uri=core.NCBI_URI,
output='/tmp/fake', file_format='genbank')
core.download(fake_args)
assert _download_mock.call_count == len(core.supported_domains)
def test_download_all(monkeypatch, mocker):
_download_mock = mocker.MagicMock()
monkeypatch.setattr(core, '_download', _download_mock)
fake_args = Namespace(section='refseq', domain='all', uri=core.NCBI_URI,
output='/tmp/fake', file_format='genbank', assembly_level='all',
genus='', species_taxid=None, taxid=None, parallel=1)
core.download(fake_args)
assert _download_mock.call_count == len(core.SUPPORTED_DOMAINS)
def test_download_one(monkeypatch, mocker):
_download_mock = mocker.MagicMock()
monkeypatch.setattr(core, '_download', _download_mock)
fake_args = Namespace(section='refseq', domain='bacteria', uri=core.NCBI_URI,
output='/tmp/fake', file_format='genbank', assembly_level='all',
genus='', species_taxid=None, taxid= None, parallel=1)
core.download(fake_args)
_download_mock.assert_called_with('refseq', 'bacteria', core.NCBI_URI, '/tmp/fake',
'genbank', 'all', '', None, None, 1)
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.create_downloadjob')
core.download(group='bacteria', output='/tmp/fake')
assert core.get_summary.call_count == 1
assert core.parse_summary.call_count == 1
assert core.create_downloadjob.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(group='bacteria', output='/tmp/fake')
assert core.get_summary.call_count == 1
assert core.parse_summary.call_count == 1
assert core.download_entry.call_count == 4
def test_download_type_material_no_match(monkeypatch, mocker, req):
summary_contents = open(_get_file('type_material.txt'), 'r').read()
req.get('https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
text=summary_contents)
print(summary_contents)
mocker.spy(core, 'get_summary')
mocker.spy(core, 'parse_summary')
mocker.patch('ncbi_genome_download.core.create_downloadjob')
core.download(group='bacteria', output='/tmp/fake', type_material=["neotype"])
assert core.get_summary.call_count == 1
assert core.parse_summary.call_count == 1
assert core.create_downloadjob.call_count == 0
def test_download_all(monkeypatch, mocker):
_download_mock = mocker.MagicMock()
monkeypatch.setattr(core, '_download', _download_mock)
fake_args = Namespace(section='refseq',
domain='all',
uri=core.NCBI_URI,
output='/tmp/fake',
file_format='genbank',
assembly_level='all',
genus='',
parallel=1)
core.download(fake_args)
assert _download_mock.call_count == len(core.supported_domains)
def test_download_contig(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.create_downloadjob')
core.download(group='bacteria', output='/tmp/fake', assembly_level='contig')
assert core.get_summary.call_count == 1
assert core.parse_summary.call_count == 1
assert core.create_downloadjob.call_count == 1
# Many nested tuples in call_args_list, no kidding.
assert core.create_downloadjob.call_args_list[0][0][0]['assembly_level'] == 'Contig'
def test_download_scaffold(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(group='bacteria', output='/tmp/fake', assembly_level='scaffold')
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'] == 'Scaffold'
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(group='bacteria', output='/tmp/fake', species_taxid='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'
def test_download_refseq_category(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.create_downloadjob')
core.download(group='bacteria', output='/tmp/fake', refseq_category='reference')
assert core.get_summary.call_count == 1
assert core.parse_summary.call_count == 1
assert core.create_downloadjob.call_count == 1
# Many nested tuples in call_args_list, no kidding.
assert core.create_downloadjob.call_args_list[0][0][0][
'organism_name'] == 'Streptomyces coelicolor A3(2)'
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.create_downloadjob')
core.download(group='bacteria', output='/tmp/fake', species_taxid='7')
assert core.get_summary.call_count == 1
assert core.parse_summary.call_count == 1
assert core.create_downloadjob.call_count == 1
# Many nested tuples in call_args_list, no kidding.
assert core.create_downloadjob.call_args_list[0][0][0][
'organism_name'] == 'Azorhizobium caulinodans ORS 571'
def test_download_metadata(monkeypatch, mocker, req, tmpdir):
"""Test creating the metadata file works."""
metadata_file = tmpdir.join('metadata.tsv')
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.create_downloadjob', return_value=[core.DownloadJob(None, None, None, None)])
core.download(group='bacteria', output='/tmp/fake', metadata_table=str(metadata_file))
assert core.get_summary.call_count == 1
assert core.parse_summary.call_count == 1
assert core.create_downloadjob.call_count == 4
assert metadata_file.check()
def test_download_refseq_category(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.create_downloadjob')
core.download(group='bacteria', output='/tmp/fake', refseq_category='reference')
assert core.get_summary.call_count == 1
assert core.parse_summary.call_count == 1
assert core.create_downloadjob.call_count == 1
# Many nested tuples in call_args_list, no kidding.
assert core.create_downloadjob.call_args_list[0][0][0][
'organism_name'] == 'Streptomyces coelicolor A3(2)'
def test_download_one(monkeypatch, mocker):
_download_mock = mocker.MagicMock()
monkeypatch.setattr(core, '_download', _download_mock)
fake_args = Namespace(section='refseq',
domain='bacteria',
uri=core.NCBI_URI,
output='/tmp/fake',
file_format='genbank',
assembly_level='all',
genus='',
parallel=1)
core.download(fake_args)
_download_mock.assert_called_with('refseq', 'bacteria', core.NCBI_URI,
'/tmp/fake', 'genbank', 'all', '', 1)
def test_download_metadata(monkeypatch, mocker, req, tmpdir):
"""Test creating the metadata file works."""
metadata_file = tmpdir.join('metadata.tsv')
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.create_downloadjob', return_value=[core.DownloadJob(None, None, None, None)])
core.download(group='bacteria', output='/tmp/fake', metadata_table=str(metadata_file))
assert core.get_summary.call_count == 1
assert core.parse_summary.call_count == 1
assert core.create_downloadjob.call_count == 4
assert metadata_file.check()
def test_download_type_material(monkeypatch, mocker, req):
summary_contents = open(_get_file('type_material.txt'), 'r').read()
req.get('https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
text=summary_contents)
print(summary_contents)
mocker.spy(core, 'get_summary')
mocker.spy(core, 'parse_summary')
mocker.patch('ncbi_genome_download.core.create_downloadjob')
core.download(group='bacteria', output='/tmp/fake', type_material=["all"])
assert core.get_summary.call_count == 1
assert core.parse_summary.call_count == 1
assert core.create_downloadjob.call_count == 1
# Many nested tuples in call_args_list, no kidding.
assert core.create_downloadjob.call_args_list[0][0][0][
'organism_name'] == 'Myxococcus fulvus'
def test_download_all(monkeypatch, mocker):
_download_mock = mocker.MagicMock()
monkeypatch.setattr(core, '_download', _download_mock)
fake_args = Namespace(section='refseq',
domain='all',
uri=core.NCBI_URI,
output='/tmp/fake',
file_format='genbank',
assembly_level='all',
genus='',
species_taxid=None,
taxid=None,
human_readable=False,
parallel=1)
core.download(fake_args)
assert _download_mock.call_count == len(core.SUPPORTED_DOMAINS)
def test_download_defaults(monkeypatch, mocker):
"""Test _download is called an appropriate number of times."""
worker_mock = mocker.MagicMock()
_download_mock = mocker.MagicMock(
return_value=[core.DownloadJob(None, None, None, None)])
monkeypatch.setattr(core, '_download', _download_mock)
monkeypatch.setattr(core, 'worker', worker_mock)
assert core.download() == 0
assert _download_mock.call_count == len(core.SUPPORTED_TAXONOMIC_GROUPS)
def test_download_all_formats(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.create_downloadjob')
core.download(group='bacteria',
output='/tmp/fake',
assembly_level='complete',
file_format="all")
assert core.get_summary.call_count == 1
assert core.parse_summary.call_count == 1
assert core.create_downloadjob.call_count == 1
# Many nested tuples in call_args_list, no kidding.
assert core.create_downloadjob.call_args_list[0][0][0][
'assembly_level'] == 'Complete Genome'
print(core.create_downloadjob.call_args_list)
assert core.create_downloadjob.call_args_list[0][0][
4] == core.EFormats.keys()
def test_download_connection_err(monkeypatch, mocker):
_download_mock = mocker.MagicMock(side_effect=ConnectionError)
monkeypatch.setattr(core, '_download', _download_mock)
fake_args = Namespace(section='refseq',
domain='all',
uri=core.NCBI_URI,
output='/tmp/fake',
file_format='genbank',
assembly_level='all',
genus='',
species_taxid=None,
taxid=None,
human_readable=False,
parallel=1)
assert core.download(fake_args) == 75
def test_download_defaults(monkeypatch, mocker):
"""Test download does the right thing."""
entry = {
'assembly_accession': 'FAKE0.1',
'organism_name': 'Example species',
'infraspecific_name': 'strain=ABC 1234',
'ftp_path': 'https://fake/genomes/FAKE0.1'
}
worker_mock = mocker.MagicMock()
select_candidates_mock = mocker.MagicMock(return_value=[(entry, 'bacteria')])
create_downloadjob_mock = mocker.MagicMock(return_value=[core.DownloadJob(None, None, None, None)])
monkeypatch.setattr(core, 'select_candidates', select_candidates_mock)
monkeypatch.setattr(core, 'create_downloadjob', create_downloadjob_mock)
monkeypatch.setattr(core, 'worker', worker_mock)
assert core.download() == 0
assert select_candidates_mock.call_args_list[0][0][0].group == SUPPORTED_TAXONOMIC_GROUPS
assert create_downloadjob_mock.call_args_list[0][0][0] == entry
def test_download_defaults(monkeypatch, mocker):
"""Test download does the right thing."""
entry = {
'assembly_accession': 'FAKE0.1',
'organism_name': 'Example species',
'infraspecific_name': 'strain=ABC 1234',
'ftp_path': 'https://fake/genomes/FAKE0.1'
}
worker_mock = mocker.MagicMock()
select_candidates_mock = mocker.MagicMock(return_value=[(entry, 'bacteria')])
create_downloadjob_mock = mocker.MagicMock(return_value=[core.DownloadJob(None, None, None, None)])
monkeypatch.setattr(core, 'select_candidates', select_candidates_mock)
monkeypatch.setattr(core, 'create_downloadjob', create_downloadjob_mock)
monkeypatch.setattr(core, 'worker', worker_mock)
assert core.download() == 0
assert select_candidates_mock.call_args_list[0][0][0].group == SUPPORTED_TAXONOMIC_GROUPS
assert create_downloadjob_mock.call_args_list[0][0][0] == entry
def test_download_dry_run(monkeypatch, mocker):
"""Test _download is not called for a dry run."""
entry = {
'assembly_accession': 'FAKE0.1',
'organism_name': 'Example species',
'infraspecific_name': 'strain=ABC 1234',
'ftp_path': 'https://fake/genomes/FAKE0.1'
}
worker_mock = mocker.MagicMock()
select_candidates_mock = mocker.MagicMock(return_value=[(entry, 'bacteria')])
create_downloadjob_mock = mocker.MagicMock(return_value=[core.DownloadJob(None, None, None, None)])
monkeypatch.setattr(core, 'select_candidates', select_candidates_mock)
monkeypatch.setattr(core, 'create_downloadjob', create_downloadjob_mock)
monkeypatch.setattr(core, 'worker', worker_mock)
assert core.download(dry_run=True) == 0
assert select_candidates_mock.call_count == 1
assert create_downloadjob_mock.call_count == 0
assert worker_mock.call_count == 0
def test_download_dry_run(monkeypatch, mocker):
"""Test _download is not called for a dry run."""
entry = {
'assembly_accession': 'FAKE0.1',
'organism_name': 'Example species',
'infraspecific_name': 'strain=ABC 1234',
'ftp_path': 'https://fake/genomes/FAKE0.1'
}
worker_mock = mocker.MagicMock()
select_candidates_mock = mocker.MagicMock(return_value=[(entry, 'bacteria')])
create_downloadjob_mock = mocker.MagicMock(return_value=[core.DownloadJob(None, None, None, None)])
monkeypatch.setattr(core, 'select_candidates', select_candidates_mock)
monkeypatch.setattr(core, 'create_downloadjob', create_downloadjob_mock)
monkeypatch.setattr(core, 'worker', worker_mock)
assert core.download(dry_run=True) == 0
assert select_candidates_mock.call_count == 1
assert create_downloadjob_mock.call_count == 0
assert worker_mock.call_count == 0
def test_download_defaults_nomatch(monkeypatch, mocker):
"""Test download bails with a 1 return code if no entries match."""
select_candidates_mock = mocker.MagicMock(return_value=[])
monkeypatch.setattr(core, 'select_candidates', select_candidates_mock)
assert core.download() == 1
def test_download_connection_err(monkeypatch, mocker):
select_candidates_mock = mocker.MagicMock(side_effect=ConnectionError)
monkeypatch.setattr(core, 'select_candidates', select_candidates_mock)
assert core.download() == 75
def test_download_one(monkeypatch, mocker):
download_mock = mocker.MagicMock()
monkeypatch.setattr(core, 'download', download_mock)
kwargs = {'group': 'bacteria', 'output': '/tmp/fake'}
core.download(**kwargs)
download_mock.assert_called_with(**kwargs)
def test_download_connection_err(monkeypatch, mocker):
select_candidates_mock = mocker.MagicMock(side_effect=ConnectionError)
monkeypatch.setattr(core, 'select_candidates', select_candidates_mock)
assert core.download() == 75
def test_download_defaults_nomatch(monkeypatch, mocker):
"""Test download bails with a 1 return code if no entries match."""
select_candidates_mock = mocker.MagicMock(return_value=[])
monkeypatch.setattr(core, 'select_candidates', select_candidates_mock)
assert core.download() == 1
def test_download_connection_err(monkeypatch, mocker):
_download_mock = mocker.MagicMock(side_effect=ConnectionError)
monkeypatch.setattr(core, '_download', _download_mock)
assert core.download() == 75
def test_download_all(monkeypatch, mocker):
_download_mock = mocker.MagicMock()
monkeypatch.setattr(core, '_download', _download_mock)
core.download(group='all', output='/tmp/fake')
assert _download_mock.call_count == len(core.SUPPORTED_TAXONOMIC_GROUPS)
def test_download_defaults(monkeypatch, mocker):
_download_mock = mocker.MagicMock()
monkeypatch.setattr(core, '_download', _download_mock)
core.download()
assert _download_mock.call_count == len(core.SUPPORTED_TAXONOMIC_GROUPS)
def test_download_one(monkeypatch, mocker):
download_mock = mocker.MagicMock()
monkeypatch.setattr(core, 'download', download_mock)
kwargs = {'group': 'bacteria', 'output': '/tmp/fake'}
core.download(**kwargs)
download_mock.assert_called_with(**kwargs)
