def acgt_gamma(path):
config = build_config(path)
config = main.process('extract_json', config, executor=gexec)
config = main.process('extract', config, executor=gexec)
config = main.process('acgt_gamma', config, executor=gexec)
tid_output_directory = config['acgt_gamma_output']
gexec.result(tid_output_directory, timeout=None)
files = map(getrelpath, Path(tid_output_directory).listdir())
trackPaths = map(getrelpath, [
config.get('InputCDSFileJson'),
config['ModifiedOrfsFile'], config['NewOrfsFile'], config['HitsFile']])
return jsonify(trackPaths=trackPaths, files=files)
def default_tracks(path):
try:
config = build_config(path)
config = main.process('extract_json', config, executor=gexec)
config = main.process('extract', config, executor=gexec)
config = main.process('acgt_gamma', config, executor=gexec)
lst = [config.get('InputCDSFileJson'), config.get('ModifiedOrfsFile'),
config.get('NewOrfsFile'), config.get('HitsFile')]
return jsonify(filenames=map(getrelpath, lst))
except Exception as e:
logger.exception('Error While finding default tracks')
return flask.make_response(repr(e), 500)
def kickstart(request, path):
config = build_config(path, request)
verb = request.GET['verb']
verb = verb.split(',')
email = request.GET.get('email')
client.ensure_daemon()
executor = client.get_server()
for v in verb:
if email:
config = main.process('allplots', config, executor=executor)
build_email(request, path, config)
elif v == 'parse':
# we've already parsed in `build_config` above.
pass
else:
# main.process handles the rest of the verbs, or errors
config = main.process(v, config, executor=executor)
return HttpResponse(
json.dumps(sanitize_config_for_client(config)),
content_type="application/json")
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 kickstart(path):
config = build_config(path)
verb = request.args['verb']
verb = verb.split(',')
email = request.args.get('email')
for v in verb:
if email:
schedule_email(email, path, config)
elif v == 'parse':
# we've already parsed in `build_config` above.
pass
else:
# main.process handles the rest of the verbs, or errors
config = main.process(v, config, executor=gexec)
return flask.make_response(
json.dumps(sanitize_config_for_client(config)))
def getpdf(path):
config = build_config(path)
config = main.process('allplots', config, executor=gexec)
pdf = config['allplots_result']
gexec.result(pdf, timeout=None)
return send_file(pdf, as_attachment=True)
def test_process(mocker, gbkfile, executor, tmpdir):
mock = mocker.patch('pynpact.main.resolve_verb')
assert main.process(
'extract', gbkfile, executor=executor, outputdir=str(tmpdir))
assert mock.called