def test_download_wgs_parts_wgs_scafld(req):
cfg = Config(format="genbank")
wgs_contig = open(full_path('wgs_scafld.gbk'), 'rt')
with open(full_path('wgs_full.gbk'), 'rt') as handle:
full_file = handle.read()
req.get(ENTREZ_URL, text=full_file)
outhandle = wgs.download_wgs_parts(wgs_contig, cfg)
assert outhandle.getvalue() == full_file
wgs_contig.close()
def test_download_wgs_parts_wgs(req):
cfg = Config(format="genbank")
wgs_contig = open(full_path('wgs.gbk'), 'rt')
req.get(ENTREZ_URL, body=open(full_path('wgs_full.gbk'), 'rt'))
outhandle = wgs.download_wgs_parts(wgs_contig, cfg)
wgs_full = open(full_path('wgs_full.gbk'), 'rt')
assert outhandle.getvalue() == wgs_full.read()
wgs_full.close()
wgs_contig.close()
def test_download_wgs_no_parts(req):
cfg = Config(format="genbank")
supercontig = open(full_path('supercontig_full.gbk'), 'rt')
req.get(ENTREZ_URL, status_code=404)
outhandle = wgs.download_wgs_parts(supercontig, cfg)
supercontig_full = open(full_path('supercontig_full.gbk'), 'rt')
assert outhandle.getvalue() == supercontig_full.read()
supercontig_full.close()
supercontig.close()
def test_download_wgs_parts_no_biopython():
old_have_biopython = wgs.HAVE_BIOPYTHON
wgs.HAVE_BIOPYTHON = False
cfg = Config(format="genbank")
handle = StringIO()
new_handle = wgs.download_wgs_parts(handle, cfg)
wgs.HAVE_BIOPYTHON = old_have_biopython
assert handle == new_handle
def test_download_wgs_parts_wgs_retry(req):
cfg = Config(format="genbank")
wgs_contig = open(full_path('wgs.gbk'), 'rt')
req.get(ENTREZ_URL, response_list=[
{"text": u'Whoa, slow down', "status_code": 429, "headers": {"Retry-After": "0"}},
{"body": open(full_path('wgs_full.gbk'), 'rt')},
])
outhandle = wgs.download_wgs_parts(wgs_contig, cfg)
wgs_full = open(full_path('wgs_full.gbk'), 'rt')
assert outhandle.getvalue() == wgs_full.read()
wgs_full.close()
wgs_contig.close()
def _validate_and_write(request, orig_handle, dl_id, config):
if config.extended_validation != 'none' or config.recursive:
handle = StringIO()
else:
handle = orig_handle
write_stream(request, handle, dl_id, config)
if config.recursive:
downloaded = download_wgs_parts(handle, config)
handle = downloaded
if config.extended_validation != 'none':
if not run_extended_validation(handle, config.format, config.extended_validation):
raise ValidationError("Sequence(s) downloaded for {} failed to load.".format(dl_id))
if config.extended_validation != 'none' or config.recursive:
orig_handle.write(handle.getvalue())
