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=app.config['UPLOADS'], prefix=prefix)
relpath = getrelpath(abspath)
return (fd, abspath, relpath)
def save_track(path):
try:
pathconfig = build_config(path)
config = request.get_json()
track = config.get('track')
fn = track.get('filename')
path = _new_track_file_name(pathconfig, fn)
if not track:
raise ValueError('Must have a track to save')
# track = pyntrack.Track(**track)
_pretty_save_track_json(track, path)
return jsonify({'filename': getrelpath(path)})
except Exception as e:
logger.exception('Error While Saving Track')
return flask.make_response(repr(e), 500)
def efetch(id):
logger.info("Asked to fetch Id: %s", id)
searchsession = entrez.EntrezSession(app.config['UPLOADS'])
abspath = searchsession.fetch_id(id)
path = getrelpath(abspath)
try:
parsing.initial(abspath)
except:
flash("There was a problem loading file '%s', "
"please try again or try a different record."
% path)
return re_search()
args = dict(request.args.items())
return redirect(url_for('run_frame', path=path, **args))
def schedule_email(to, path, config):
config = main.process('allplots', config, executor=gexec)
try:
target_file = config.get('allplots_result')
assert target_file, \
"Configured for email but didn't get emailable file."
# The direct download link for the PS or PDF file.
result_link = url_for('raw',
path=getrelpath(target_file), _external=True)
# build path back to run screen.
run_link = url_for('run_frame', path=path, _external=True,
**dictforurl(config, exclude=['email']))
task = util.Task(send_email, to, path, config, result_link, run_link)
eid = gexec.enqueue(task, after=[target_file])
logger.info("Scheduled email to %r with jobid: %s", to, eid)
except:
logger.exception("Error scheduling email to send")
def search():
args = dict(request.values.items())
search = args.pop('search', None)
if not search:
flash('Accession Number Required')
return redirect(url_for('start', **args))
sess = entrez.CachedEntrezSession(app.config['UPLOADS'])
sess.search(search)
logger.debug(
"Search finished, found %d matches",
sess.result_count)
if sess.result_count == 1:
relpath = getrelpath(sess.fetch())
return redirect(url_for('run_frame', path=relpath, **args))
elif sess.result_count > 1:
flash(
"Too many results (%d) found, need 1."
" Try refining the search or searching for a RefSeq id."
% (sess.result_count))
return flask.render_template('start.html', sess=sess, search=search)
else:
flash("No results found.")
return redirect(url_for('start', **args))