def test_download_entry_missing(req, tmpdir):
name_map_copy = dict(core.FORMAT_NAME_MAP.items())
del name_map_copy['genbank']
entry, outdir, _ = prepare_download_entry(req, tmpdir, name_map_copy)
jobs = core.download_entry(entry, 'refseq', 'bacteria', str(outdir),
'genbank', None)
assert jobs == []
def test_download_entry_symlink_only(req, tmpdir):
entry, outdir, joblist = prepare_download_entry(req, tmpdir, human_readable=True,
create_local_file=True)
jobs = core.download_entry(entry, 'refseq', 'bacteria', str(outdir), 'genbank', True)
expected = [(core.DownloadJob(None, j[0].local_file, None, j[0].symlink_path), None)
for j in joblist if j[0].local_file.endswith('_genomic.gbff.gz')]
assert jobs == expected
def test_download_entry_missing(req, tmpdir):
name_map_copy = dict(core.format_name_map.items())
del name_map_copy['genbank']
entry, outdir, _ = prepare_download_entry(req, tmpdir, name_map_copy)
jobs = core.download_entry(entry, 'refseq', 'bacteria',
'http://fake/genomes', str(outdir), 'genbank')
assert jobs == []
def test_download_entry_genbank(req, tmpdir):
entry, outdir, joblist = prepare_download_entry(req, tmpdir)
jobs = core.download_entry(entry, 'refseq', 'bacteria', str(outdir),
'genbank', None)
expected = [
j for j in joblist if j.local_file.endswith('_genomic.gbff.gz')
]
assert jobs == expected
def test_download_entry_human_readable(req, tmpdir):
entry, outdir, joblist = prepare_download_entry(req, tmpdir, human_readable=True)
jobs = core.download_entry(entry, 'refseq', 'bacteria', str(outdir), 'genbank', True)
expected = [(j[0], None) for j in joblist if j[0].local_file.endswith('_genomic.gbff.gz')]
assert jobs == expected
def test_download_entry_all(req, tmpdir):
entry, outdir, expected = prepare_download_entry(req, tmpdir)
jobs = core.download_entry(entry, 'refseq', 'bacteria', str(outdir), 'all', None)
assert jobs == expected
def test_download_entry_missing(req, tmpdir):
name_map_copy = dict(core.format_name_map.items())
del name_map_copy['genbank']
entry, outdir, _ = prepare_download_entry(req, tmpdir, name_map_copy)
jobs = core.download_entry(entry, 'refseq', 'bacteria', 'http://fake/genomes', str(outdir), 'genbank')
assert jobs == []
def test_download_entry_all(req, tmpdir):
entry, outdir, expected = prepare_download_entry(req, tmpdir)
jobs = core.download_entry(entry, 'refseq', 'bacteria', 'http://fake/genomes', str(outdir), 'all')
assert jobs == expected
def test_download_entry_genbank(req, tmpdir):
entry, outdir, joblist = prepare_download_entry(req, tmpdir)
jobs = core.download_entry(entry, 'refseq', 'bacteria', 'http://fake/genomes', str(outdir), 'genbank')
expected = [j for j in joblist if j.local_file.endswith('_genomic.gbff.gz')]
assert jobs == expected
def test_download_entry_all(req, tmpdir):
entry, outdir = prepare_download_entry(req, tmpdir)
core.download_entry(entry, 'refseq', 'bacteria', 'http://fake/genomes', str(outdir), 'all')
for ending in core.format_name_map.values():
assert outdir.join('refseq', 'bacteria', 'FAKE0.1', 'fake{}'.format(ending)).check()
def test_download_entry_genbank(req, tmpdir):
entry, outdir = prepare_download_entry(req, tmpdir)
core.download_entry(entry, 'refseq', 'bacteria', 'http://fake/genomes', str(outdir), 'genbank')
assert outdir.join('refseq', 'bacteria', 'FAKE0.1', 'fake_genomic.gbff.gz').check()
def test_download_entry_missing(req, tmpdir):
name_map_copy = dict(core.format_name_map.items())
del name_map_copy['genbank']
entry, outdir = prepare_download_entry(req, tmpdir, name_map_copy)
core.download_entry(entry, 'refseq', 'bacteria', 'http://fake/genomes', str(outdir), 'genbank')
assert outdir.join('refseq', 'bacteria', 'FAKE0.1', 'fake_genomic.gbff.gz').check() == False
def test_download_entry_missing(req, tmpdir):
name_map_copy = dict(core.FORMAT_NAME_MAP.items())
del name_map_copy['genbank']
entry, outdir, _ = prepare_download_entry(req, tmpdir, name_map_copy)
jobs = core.download_entry(entry, 'refseq', 'bacteria', str(outdir), 'genbank')
assert jobs == []
