def get(self, arguments):
study_id = int(self.get_argument('study_id'))
# this block is tricky because you can either pass the sample or the
# prep template and if none is passed then we will let an exception
# be raised because template will not be declared for the logic below
if self.get_argument('prep_template', None):
template = PrepTemplate(int(self.get_argument('prep_template')))
if self.get_argument('sample_template', None):
template = None
tid = int(self.get_argument('sample_template'))
try:
template = SampleTemplate(tid)
except QiitaDBUnknownIDError:
raise HTTPError(404, "SampleTemplate %d does not exist" % tid)
study = Study(template.study_id)
# check whether or not the user has access to the requested information
if not study.has_access(User(self.current_user)):
raise HTTPError(403, "You do not have access to access this "
"information.")
df = dataframe_from_template(template)
stats = stats_from_df(df)
self.render('metadata_summary.html', user=self.current_user,
study_title=study.title, stats=stats,
study_id=study_id)
def get(self, arguments):
study_id = int(self.get_argument('study_id'))
# Get the arguments
prep_template = self.get_argument('prep_template', None)
sample_template = self.get_argument('sample_template', None)
if prep_template and sample_template:
raise HTTPError(
500, "You should provide either a sample template "
"or a prep template, but not both")
elif prep_template:
# The prep template has been provided
template = self._get_template(PrepTemplate, prep_template)
back_button_path = (
"/study/description/%s?top_tab=raw_data_tab&sub_tab=%s"
"&prep_tab=%s" % (study_id, template.raw_data, template.id))
elif sample_template:
# The sample template has been provided
template = self._get_template(SampleTemplate, sample_template)
back_button_path = ("/study/description/%s" % study_id)
else:
# Neither a sample template or a prep template has been provided
# Fail nicely
raise HTTPError(
500, "You should provide either a sample template "
"or a prep template")
study = Study(template.study_id)
# check whether or not the user has access to the requested information
if not study.has_access(self.current_user):
raise HTTPError(
403, "You do not have access to access this "
"information.")
df = dataframe_from_template(template)
num_samples = df.shape[0]
stats = stats_from_df(df)
self.render('metadata_summary.html',
study_title=study.title,
stats=stats,
num_samples=num_samples,
back_button_path=back_button_path)
def get(self, arguments):
study_id = int(self.get_argument('study_id'))
# Get the arguments
prep_template = self.get_argument('prep_template', None)
sample_template = self.get_argument('sample_template', None)
if prep_template and sample_template:
raise HTTPError(500, "You should provide either a sample template "
"or a prep template, but not both")
elif prep_template:
# The prep template has been provided
template = self._get_template(PrepTemplate, prep_template)
back_button_path = (
"/study/description/%s?top_tab=prep_template_tab&sub_tab=%s"
% (study_id, template.id))
elif sample_template:
# The sample template has been provided
template = self._get_template(SampleTemplate, sample_template)
back_button_path = (
"/study/description/%s"
% study_id)
else:
# Neither a sample template or a prep template has been provided
# Fail nicely
raise HTTPError(500, "You should provide either a sample template "
"or a prep template")
study = Study(template.study_id)
# check whether or not the user has access to the requested information
if not study.has_access(self.current_user):
raise HTTPError(403, "You do not have access to access this "
"information.")
df = template.to_dataframe()
num_samples = df.shape[0]
stats = stats_from_df(df)
self.render('metadata_summary.html',
study_title=study.title, stats=stats,
num_samples=num_samples, back_button_path=back_button_path)
def test_stats_from_df(self):
obs = stats_from_df(SampleTemplate(1).to_dataframe())
for k in obs:
self.assertItemsEqual(obs[k], SUMMARY_STATS[k])
def test_stats_from_df(self):
obs = stats_from_df(SampleTemplate(1).to_dataframe())
for k in obs:
self.assertItemsEqual(obs[k], SUMMARY_STATS[k])
def test_stats_from_df(self):
obs = stats_from_df(dataframe_from_template(SampleTemplate(1)))
for k in obs:
self.assertEqual(obs[k], SUMMARY_STATS[k])
def test_stats_from_df(self):
obs = stats_from_df(dataframe_from_template(SampleTemplate(1)))
for k in obs:
self.assertEqual(obs[k], SUMMARY_STATS[k])
