def efetch(req, id):
logger.info("Asked to fetch Id: %s", id)
session = entrez.EntrezSession(library_root())
abspath = session.fetch_id(id)
path = getrelpath(abspath)
try:
parsing.initial(abspath)
except:
messages.error(req,
"There was a problem loading file '%s', "
"please try again or try a different record."
% path)
return re_search(req)
path = getrelpath(abspath)
remaining_args = dict(req.REQUEST.items())
action = remaining_args.pop('action', 'run')
if action in ['run', 'config']:
return HttpResponseRedirect(
reverse(action, args=[path]) + dict_to_querystring(remaining_args))
else:
logger.error("Unknown action %r", action)
messages.error(req, "Unknown action.")
return re_search(req)
def mksavefile(prefix):
"""Wrapper around creating the file to save uploaded files in.
Returns the (fd, abspath, relpath)
"""
# we're using tempfile to ensure the file we get is unique and
# aren't overwriting another.
fd, abspath = tempfile.mkstemp(
dir=settings.MEDIA_ROOT, prefix=prefix)
relpath = getrelpath(abspath)
return (fd, abspath, relpath)
def clean_entrez_search_term(self):
cleaned_data = self.cleaned_data
if cleaned_data.get('entrez_search_term'):
self.active = 'entrez_search_term'
self.session = entrez.CachedEntrezSession(library_root())
self.session.search(cleaned_data['entrez_search_term'])
logger.debug(
"Search finished, found %d matches",
self.session.result_count)
if self.session.result_count == 1:
cleaned_data['path'] = getrelpath(self.session.fetch())
elif self.session.result_count > 1:
raise forms.ValidationError(
"Too many results (%d) found, need 1."
" Try refining the search or searching for a RefSeq id."
% (self.session.result_count))
else:
raise forms.ValidationError("No results found.")
def addgetrelpath(request):
return {'getrelpath': lambda p: p and getrelpath(p)}
def get_result_link(path):
if path.startswith('/'):
path = getrelpath(path)
return reverse('raw', args=[path])
def get_raw_url(request, path):
# return request.build_absolute_uri(reverse('raw', path))
# TODO: DEPRECATE in favor of get_result_link
if path.startswith('/'):
path = getrelpath(path)
return reverse('raw', args=[path])