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(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)
"input the taxon id. It will retrieve all the genomes desceding to the provided taxon; to separate multiple "
)
@click.option(
"-F",
"formats",
help='Which formats to download (default: %(default)s).'
'A comma-separated list of formats is also possible. For example: "fasta,assembly-report". '
'Choose from: {choices}'.format(
choices=NgdConfig.get_choices('file_formats')),
default='fasta')
@click.option(
"-o",
"odir",
help=
f"Create output hierarchy in specified folder (default: {NgdConfig.get_default('output')})",
default=NgdConfig.get_default('output'))
@click.option("-size",
"size_of_batch",
help=f"The size of each batch.",
default=20)
@click.option("-p",
"parallel",
help=f"Run N downloads in parallel (default: 10)",
default=5)
@click.option("-id",
"id_list",
help=f" ',' separated assembly ids or a single file ",
default='')
@click.option("-C",
"enable_check",
help=f"use summary file or use the id input directly",
@click.command(
help=
"It would split the list of assembly ids into batches. The size parameter would produce"
)
@click.option(
"-n",
"name",
help="input the phylum name or other. use ; to separate multiple ")
@click.option(
"-F",
"formats",
help='Which formats to download (default: %(default)s).'
'A comma-separated list of formats is also possible. For example: "fasta,assembly-report". '
'Choose from: {choices}'.format(
choices=NgdConfig.get_choices('file_formats')),
default=NgdConfig.get_default('file_formats'))
@click.option(
"-o",
"odir",
help=
f"Create output hierarchy in specified folder (default: {NgdConfig.get_default('output')})",
default=NgdConfig.get_default('output'))
@click.option("-size",
"size_of_batch",
help=f"The size of each batch.",
default=20)
@click.option("-p",
"parallel",
help=f"Run N downloads in parallel (default: 10)",
default=5)
def cli(name, odir, formats, size_of_batch, parallel):