def post(self, analysis_id):
analysis_id = int(analysis_id)
rarefaction_depth = self.get_argument('rarefaction-depth')
# convert to integer if rarefaction level given
if rarefaction_depth:
rarefaction_depth = int(rarefaction_depth)
else:
rarefaction_depth = None
analysis = Analysis(analysis_id)
check_analysis_access(self.current_user, analysis)
command_args = self.get_arguments("commands")
split = [x.split("#") for x in command_args]
moi_user_id = get_id_from_user(self.current_user.id)
moi_group = create_info(analysis_id, 'group', url='/analysis/',
parent=moi_user_id, store=True)
moi_name = 'Creating %s' % analysis.name
moi_result_url = '/analysis/results/%d' % analysis_id
submit(ctx_default, moi_group['id'], moi_name,
moi_result_url, run_analysis, analysis_id, split,
rarefaction_depth=rarefaction_depth)
r_client.hset('analyis-map', analysis_id, moi_group['id'])
self.render("analysis_waiting.html",
group_id=moi_group['id'], aname=analysis.name)
def post(self, analysis_id):
analysis_id = int(analysis_id)
rarefaction_depth = self.get_argument('rarefaction-depth')
mdsi = self.get_argument('merge-duplicated-sample-ids', default=False)
if mdsi == 'on':
mdsi = True
# convert to integer if rarefaction level given
if rarefaction_depth:
rarefaction_depth = int(rarefaction_depth)
else:
rarefaction_depth = None
analysis = Analysis(analysis_id)
check_analysis_access(self.current_user, analysis)
command_args = self.get_arguments("commands")
cmd_split = [x.split("#") for x in command_args]
moi_user_id = get_id_from_user(self.current_user.id)
moi_group = create_info(analysis_id, 'group', url='/analysis/',
parent=moi_user_id, store=True)
moi_name = ("Creating %s... When finished, please click the 'Success' "
"link to the right" % analysis.name)
moi_result_url = '/analysis/results/%d' % analysis_id
submit(ctx_default, moi_group['id'], moi_name,
moi_result_url, run_analysis, analysis_id, cmd_split,
rarefaction_depth=rarefaction_depth,
merge_duplicated_sample_ids=mdsi)
r_client.hset('analyis-map', analysis_id, moi_group['id'])
self.render("analysis_waiting.html",
group_id=moi_group['id'], aname=analysis.name)
def post(self, analysis_id):
analysis_id = int(analysis_id)
rarefaction_depth = self.get_argument('rarefaction-depth')
mdsi = self.get_argument('merge-duplicated-sample-ids', default=False)
if mdsi == 'on':
mdsi = True
# convert to integer if rarefaction level given
if rarefaction_depth:
rarefaction_depth = int(rarefaction_depth)
else:
rarefaction_depth = None
analysis = Analysis(analysis_id)
check_analysis_access(self.current_user, analysis)
command_args = self.get_arguments("commands")
cmd_split = [x.split("#") for x in command_args]
moi_user_id = get_id_from_user(self.current_user.id)
moi_group = create_info(analysis_id,
'group',
url='%s/analysis/' % qiita_config.portal_dir,
parent=moi_user_id,
store=True)
moi_name = ("Creating %s... When finished, please click the 'Success' "
"link to the right" % analysis.name)
moi_result_url = '%s/analysis/results/%d' % (qiita_config.portal_dir,
analysis_id)
submit(ctx_default,
moi_group['id'],
moi_name,
moi_result_url,
run_analysis,
analysis_id,
cmd_split,
rarefaction_depth=rarefaction_depth,
merge_duplicated_sample_ids=mdsi)
r_client.hset('analyis-map', analysis_id, moi_group['id'])
self.render("analysis_waiting.html",
group_id=moi_group['id'],
aname=analysis.name)
def post(self):
name = self.get_argument("jobname", None)
group_name = self.get_argument("jobgroup", None)
parent = get_id_from_user("no-user")
job_url = "/result"
if name is not None:
submit(ctx_default, parent, name, job_url, say_hello, name)
else:
group_url = "/group"
group = create_info(group_name, 'group', url=group_url,
parent=parent, store=True)
group_id = group['id']
for i in range(5):
name = group_name + '-%d' % i
submit(ctx_default, group_id, name, job_url, say_hello, name)
self.redirect('/')
def test_failure_callback(self):
"""Make sure failure at file creation step doesn't hang everything"""
# rename a needed file for creating the biom table
base = get_db_files_base_dir()
rename(join(base, "processed_data",
"1_study_1001_closed_reference_otu_table.biom"),
join(base, "processed_data", "1_study_1001.bak"))
analysis = Analysis(2)
group = get_id_from_user("*****@*****.**")
try:
app = RunAnalysis(moi_context=ctx_default,
moi_parent_id=group)
app(analysis, [], rarefaction_depth=100)
self.assertEqual(analysis.status, 'error')
for job_id in analysis.jobs:
self.assertEqual(Job(job_id).status, 'error')
finally:
rename(join(base, "processed_data", "1_study_1001.bak"),
join(base, "processed_data",
"1_study_1001_closed_reference_otu_table.biom"))
def post(self):
name = self.get_argument("jobname", None)
group_name = self.get_argument("jobgroup", None)
parent = get_id_from_user("no-user")
job_url = "/result"
if name is not None:
submit(ctx_default, parent, name, job_url, say_hello, name)
else:
group_url = "/group"
group = create_info(group_name,
'group',
url=group_url,
parent=parent,
store=True)
group_id = group['id']
for i in range(5):
name = group_name + '-%d' % i
submit(ctx_default, group_id, name, job_url, say_hello, name)
self.redirect('/')
def post(self, analysis_id):
analysis_id = int(analysis_id)
rarefaction_depth = self.get_argument('rarefaction-depth')
# convert to integer if rarefaction level given
if rarefaction_depth:
rarefaction_depth = int(rarefaction_depth)
else:
rarefaction_depth = None
analysis = Analysis(analysis_id)
check_analysis_access(self.current_user, analysis)
command_args = self.get_arguments("commands")
split = [x.split("#") for x in command_args]
moi_user_id = get_id_from_user(self.current_user.id)
moi_group = create_info(analysis_id,
'group',
url='/analysis/',
parent=moi_user_id,
store=True)
moi_name = ("Creating %s... When finished, please click the 'Success' "
"link to the right" % analysis.name)
moi_result_url = '/analysis/results/%d' % analysis_id
submit(ctx_default,
moi_group['id'],
moi_name,
moi_result_url,
run_analysis,
analysis_id,
split,
rarefaction_depth=rarefaction_depth)
r_client.hset('analyis-map', analysis_id, moi_group['id'])
self.render("analysis_waiting.html",
group_id=moi_group['id'],
aname=analysis.name)
def get_current_user(self):
user = self.get_secure_cookie("user")
if user is None:
raise ValueError("No user associated with the websocket!")
else:
return get_id_from_user(user.strip('" '))
def get(self):
self.set_current_user("no-user")
group_id = get_id_from_user("no-user")
self.render("moi_example.html", user=self.get_current_user(),
group_id=group_id)
def get(self):
self.set_current_user("no-user")
group_id = get_id_from_user("no-user")
self.render("moi_example.html",
user=self.get_current_user(),
group_id=group_id)
