def get(self, analysis_id):
analysis_id = int(analysis_id.split("/")[0])
analysis = Analysis(analysis_id)
check_analysis_access(self.current_user, analysis)
jobres = defaultdict(list)
for job in analysis.jobs:
jobject = Job(job)
jobres[jobject.datatype].append(
(jobject.command[0], jobject.results))
dropped = {}
dropped_samples = analysis.dropped_samples
if dropped_samples:
for proc_data_id, samples in viewitems(dropped_samples):
proc_data = ProcessedData(proc_data_id)
key = "Data type %s, Study: %s" % (proc_data.data_type(),
proc_data.study)
dropped[key] = samples
self.render("analysis_results.html",
jobres=jobres,
aname=analysis.name,
dropped=dropped,
basefolder=get_db_files_base_dir())
def get(self, analysis_id):
user = self.current_user
analysis_id = int(analysis_id)
check_analysis_access(User(user), analysis_id)
analysis = Analysis(analysis_id)
jobres = defaultdict(list)
for job in analysis.jobs:
jobject = Job(job)
jobres[jobject.datatype].append(
(jobject.command[0], jobject.results))
dropped = {}
for proc_data_id, samples in viewitems(analysis.dropped_samples):
proc_data = ProcessedData(proc_data_id)
key = "Data type %s, Study: %s" % (proc_data.data_type(),
proc_data.study)
dropped[key] = samples
self.render("analysis_results.html",
user=self.current_user,
jobres=jobres,
aname=analysis.name,
dropped=dropped,
basefolder=get_db_files_base_dir())
# wipe out cached messages for this analysis
r_server = Redis()
key = '%s:messages' % self.current_user
oldmessages = r_server.lrange(key, 0, -1)
if oldmessages is not None:
for message in oldmessages:
if '"analysis": %d' % analysis_id in message:
r_server.lrem(key, message, 1)
def render(self, study):
avail_pd = [(pd_id, ProcessedData(pd_id))
for pd_id in study.processed_data()]
return self.render_string(
"study_description_templates/processed_data_tab.html",
available_processed_data=avail_pd,
study_id=study.id)
def test_get_filepath(self):
"""Correctly returns the filepaths to the processed files"""
# check the test data
pd = ProcessedData(1)
obs = pd.get_filepaths()
exp = [(join(self.db_test_pd_dir,
'1_study_1001_closed_reference_otu_table.biom'), "biom")]
self.assertEqual(obs, exp)
def _selected_parser(self, analysis):
"""builds dictionaries of selected samples from analysis object"""
selsamples = {}
selproc_data = defaultdict(list)
for proc_data_id, samps in viewitems(analysis.samples):
study = ProcessedData(proc_data_id).study
selproc_data[study].append(proc_data_id)
selsamples[study] = set(samps)
return selproc_data, selsamples
def test_link_filepaths_status_setter(self):
pd = ProcessedData(1)
self.assertEqual(pd.link_filepaths_status, 'idle')
pd._set_link_filepaths_status('linking')
self.assertEqual(pd.link_filepaths_status, 'linking')
pd._set_link_filepaths_status('unlinking')
self.assertEqual(pd.link_filepaths_status, 'unlinking')
pd._set_link_filepaths_status('failed: error')
self.assertEqual(pd.link_filepaths_status, 'failed: error')
def test_data_type_id(self):
pd = ProcessedData(1)
self.assertEqual(pd.data_type(ret_id=True), 2)
def test_data_type(self):
pd = ProcessedData(1)
self.assertEqual(pd.data_type(), "18S")
def test_preprocessed_data(self):
"""Correctly returns the preprocessed_data"""
pd = ProcessedData(1)
self.assertEqual(pd.preprocessed_data, 1)
def test_get_filepath_ids(self):
pd = ProcessedData(1)
self.assertEqual(pd.get_filepath_ids(), [10])
def test_data_type_id(self):
"""Correctly returns the data_type of preprocessed_data"""
pd = ProcessedData(1)
self.assertEqual(pd.data_type(ret_id=True), 2)
def test_data_type(self):
"""Correctly returns the data_type of preprocessed_data"""
pd = ProcessedData(1)
self.assertEqual(pd.data_type(), "18S")
def test_processed_date(self):
pd = ProcessedData(1)
self.assertEqual(pd.processed_date, datetime(2012, 10, 1, 9, 30, 27))
def test_link_filepaths_status(self):
pd = ProcessedData(1)
self.assertEqual(pd.link_filepaths_status, 'idle')