def test_create_downloadjob_genbank(req, tmpdir):
entry, config, joblist = prepare_create_downloadjob(req, tmpdir)
jobs = core.create_downloadjob(entry, 'bacteria', config)
expected = [
j for j in joblist if j.local_file.endswith('_genomic.gbff.gz')
]
assert jobs == expected
def test_create_downloadjob_symlink_only(req, tmpdir):
entry, config, joblist = prepare_create_downloadjob(req, tmpdir, human_readable=True,
create_local_file=True)
jobs = core.create_downloadjob(entry, 'bacteria', config)
expected = [core.DownloadJob(None, j.local_file, None, j.symlink_path)
for j in joblist if j.local_file.endswith('_genomic.gbff.gz')]
assert jobs == expected
def test_create_downloadjob_missing(req, tmpdir):
name_map_copy = dict(core.EFormats.items())
del name_map_copy['genbank']
entry, outdir, _ = prepare_create_downloadjob(req, tmpdir, name_map_copy)
jobs = core.create_downloadjob(entry, 'refseq', 'bacteria', str(outdir),
['genbank'], None)
assert jobs == []
def test_create_downloadjob_symlink_only(req, tmpdir):
entry, config, joblist = prepare_create_downloadjob(req, tmpdir, human_readable=True,
create_local_file=True)
jobs = core.create_downloadjob(entry, 'bacteria', config)
expected = [core.DownloadJob(None, j.local_file, None, j.symlink_path)
for j in joblist if j.local_file.endswith('_genomic.gbff.gz')]
assert jobs == expected
def test_create_downloadjob_genbank(req, tmpdir):
entry, outdir, joblist = prepare_create_downloadjob(req, tmpdir)
jobs = core.create_downloadjob(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_metadata_fill(req, tmpdir):
entry, config, _ = prepare_create_downloadjob(req, tmpdir)
metadata.clear() #clear it, otherwise operations realized in other tests might impact it
mtable = metadata.get()
assert len(mtable.rows) == 0
jobs = core.create_downloadjob(entry, 'bacteria', config)
core.fill_metadata(jobs, entry, mtable)
assert len(mtable.rows) == 1
def test_create_downloadjob_missing(req, tmpdir):
name_map_copy = OrderedDict(NgdConfig._FORMATS)
del name_map_copy['genbank']
entry, config, _ = prepare_create_downloadjob(req, tmpdir, name_map_copy)
jobs = core.create_downloadjob(entry, 'bacteria', config)
assert jobs == []
def test_create_downloadjob_all(req, tmpdir):
entry, config, expected = prepare_create_downloadjob(req, tmpdir)
config.file_format = "all"
jobs = core.create_downloadjob(entry, 'bacteria', config)
assert jobs == expected
def test_create_downloadjob_all(req, tmpdir):
entry, outdir, expected = prepare_create_downloadjob(req, tmpdir)
jobs = core.create_downloadjob(entry, 'refseq', 'bacteria', str(outdir),
core.EFormats.keys(), None)
assert jobs == expected
def test_create_downloadjob_human_readable(req, tmpdir):
entry, config, joblist = prepare_create_downloadjob(req, tmpdir, human_readable=True)
jobs = core.create_downloadjob(entry, 'bacteria', config)
expected = [j for j in joblist if j.local_file.endswith('_genomic.gbff.gz')]
assert jobs == expected
def test_create_downloadjob_missing(req, tmpdir):
name_map_copy = OrderedDict(NgdConfig._FORMATS)
del name_map_copy['genbank']
entry, config, _ = prepare_create_downloadjob(req, tmpdir, name_map_copy)
jobs = core.create_downloadjob(entry, 'bacteria', config)
assert jobs == []
def test_create_downloadjob_all(req, tmpdir):
entry, config, expected = prepare_create_downloadjob(req, tmpdir)
config.file_format = "all"
jobs = core.create_downloadjob(entry, 'bacteria', config)
assert jobs == expected
