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_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