def execute_query(self, author, course, request):
return [p for p in Project.get_user_projects(author, course).filter(submitted=True)
if p.visible(request)]
def execute_query(self, author, course, request):
return [
p for p in Project.get_user_projects(author, course).filter(
submitted=True) if p.visible(request)
]
def cohort_detail(request, cohort_id=0, workbook_id=0, worksheet_id=0, create_workbook=False):
if debug: print >> sys.stderr,'Called '+sys._getframe().f_code.co_name
users = User.objects.filter(is_superuser=0).exclude(id=request.user.id)
cohort = None
shared_with_users = []
# service = build('meta', 'v1', discoveryServiceUrl=META_DISCOVERY_URL)
clin_attr = [
'Project',
'Study',
'vital_status',
# 'survival_time',
'gender',
'age_at_initial_pathologic_diagnosis',
'SampleTypeCode',
'tumor_tissue_site',
'histological_type',
'prior_dx',
'pathologic_stage',
'person_neoplasm_cancer_status',
'new_tumor_event_after_initial_treatment',
'neoplasm_histologic_grade',
# 'bmi',
'residual_tumor',
# 'targeted_molecular_therapy', TODO: Add to metadata_samples
'tobacco_smoking_history',
'icd_10',
'icd_o_3_site',
'icd_o_3_histology'
]
# data_attr = [
# 'has_Illumina_DNASeq',
# 'has_BCGSC_HiSeq_RNASeq',
# 'has_UNC_HiSeq_RNASeq',
# 'has_BCGSC_GA_RNASeq',
# 'has_UNC_GA_RNASeq',
# 'has_HiSeq_miRnaSeq',
# 'has_GA_miRNASeq',
# 'has_RPPA',
# 'has_SNP6',
# 'has_27k',
# 'has_450k'
# ]
data_attr = [
'DNA_sequencing',
'RNA_sequencing',
'miRNA_sequencing',
'Protein',
'SNP_CN',
'DNA_methylation'
]
molec_attr = [
'somatic_mutation_status',
'mRNA_expression',
'miRNA_expression',
'DNA_methylation',
'gene_copy_number',
'protein_quantification'
]
clin_attr_dsp = []
clin_attr_dsp += clin_attr
token = SocialToken.objects.filter(account__user=request.user, account__provider='Google')[0].token
data_url = METADATA_API + 'v2/metadata_counts'
payload = {
'token': token
}
results = urlfetch.fetch(data_url, method=urlfetch.POST, payload=json.dumps(payload), deadline=60, headers={'Content-Type': 'application/json'})
results = json.loads(results.content)
totals = results['total']
if USER_DATA_ON:
# Add in user data
user_attr = ['user_project','user_study']
projects = Project.get_user_projects(request.user, True)
studies = Study.get_user_studies(request.user, True)
features = User_Feature_Definitions.objects.filter(study__in=studies)
study_counts = {}
project_counts = {}
for count in results['count']:
if 'id' in count and count['id'].startswith('study:'):
split = count['id'].split(':')
study_id = split[1]
feature_name = split[2]
study_counts[study_id] = count['total']
user_studies = []
for study in studies:
count = study_counts[study.id] if study.id in study_counts else 0
if not study.project_id in project_counts:
project_counts[study.project_id] = 0
project_counts[study.project_id] += count
user_studies += ({
'count': str(count),
'value': study.name,
'id' : study.id
},)
user_projects = []
for project in projects:
user_projects += ({
'count': str(project_counts[project.id]) if project.id in project_counts else 0,
'value': project.name,
'id' : project.id
},)
results['count'].append({
'name': 'user_projects',
'values': user_projects
})
results['count'].append({
'name': 'user_studies',
'values': user_studies
})
# Get and sort counts
attr_details = {
'RNA_sequencing': [],
'miRNA_sequencing': [],
'DNA_methylation': []
}
keys = []
for item in results['count']:
#print item
key = item['name']
values = item['values']
if key.startswith('has_'):
data_availability_sort(key, values, data_attr, attr_details)
else:
keys.append(item['name'])
item['values'] = sorted(values, key=lambda k: int(k['count']), reverse=True)
if item['name'].startswith('user_'):
clin_attr_dsp += (item['name'],)
for key, value in attr_details.items():
results['count'].append({
'name': key,
'values': value,
'id': None
})
template_values = {
'request': request,
'users': users,
'attr_list': keys,
'attr_list_count': results['count'],
'total_samples': int(totals),
'clin_attr': clin_attr_dsp,
'data_attr': data_attr,
'molec_attr': molec_attr,
'base_url': settings.BASE_URL,
'base_api_url': settings.BASE_API_URL,
'token': token
}
if USER_DATA_ON:
template_values['user_attr'] = user_attr
if workbook_id and worksheet_id :
template_values['workbook'] = Workbook.objects.get(id=workbook_id)
template_values['worksheet'] = Worksheet.objects.get(id=worksheet_id)
elif create_workbook:
template_values['create_workbook'] = True
template = 'cohorts/new_cohort.html'
if cohort_id != 0:
try:
cohort = Cohort.objects.get(id=cohort_id, active=True)
cohort.perm = cohort.get_perm(request)
cohort.owner = cohort.get_owner()
if not cohort.perm:
messages.error(request, 'You do not have permission to view that cohort.')
return redirect('cohort_list')
cohort.mark_viewed(request)
shared_with_ids = Cohort_Perms.objects.filter(cohort=cohort, perm=Cohort_Perms.READER).values_list('user', flat=True)
shared_with_users = User.objects.filter(id__in=shared_with_ids)
template = 'cohorts/cohort_details.html'
template_values['cohort'] = cohort
template_values['total_samples'] = len(cohort.samples_set.all())
template_values['total_patients'] = len(cohort.patients_set.all())
template_values['shared_with_users'] = shared_with_users
except ObjectDoesNotExist:
# Cohort doesn't exist, return to user landing with error.
messages.error(request, 'The cohort you were looking for does not exist.')
return redirect('cohort_list')
return render(request, template, template_values)
