def test__download(monkeypatch, mocker, req): summary_contents = open(_get_file('partial_summary.txt'), 'r').read() req.get('http://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('refseq', 'bacteria', core.NCBI_URI, '/tmp/fake', 'genbank', 'all') assert core.get_summary.call_count == 1 assert core.parse_summary.call_count == 1 assert core.download_entry.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('refseq', 'bacteria', core.NCBI_URI, '/tmp/fake', 'genbank', 'all') assert core.get_summary.call_count == 1 assert core.parse_summary.call_count == 1 assert core.download_entry.call_count == 4
def test__download_contig(monkeypatch, mocker, req): summary_contents = open(_get_file('assembly_status.txt'), 'r').read() req.get('http://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('refseq', 'bacteria', core.NCBI_URI, '/tmp/fake', 'genbank', 'contig') 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'] == 'Contig'
def test__download_genus_lowercase(monkeypatch, mocker, req): summary_contents = open(_get_file('partial_summary.txt'), 'r').read() req.get('http://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('refseq', 'bacteria', core.NCBI_URI, '/tmp/fake', 'genbank', 'all', 'azorhizobium') 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_complete(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('refseq', 'bacteria', core.NCBI_URI, '/tmp/fake', 'genbank', 'complete') 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'] == 'Complete Genome'
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('refseq', 'bacteria', core.NCBI_URI, '/tmp/fake', 'genbank', 'all', '', '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'