def show_disease_bar(dis_list=None, expand_od=False, selected=None, href="/disease/"):
''' Template inclusion tag to render disease bar. '''
if type(dis_list) is str:
dis_list = [dis_list]
(main, other) = Disease.get_site_diseases(dis_list=dis_list)
return {'dis_main': main, 'dis_other': other, 'text': True, 'selected': selected, 'href': href,
'expand_od': expand_od}
def get_context_data(self, **kwargs):
context = super(StudiesEntryView, self).get_context_data(**kwargs)
studies = StudyDocument.get_studies(sources=['study_id', 'study_name', 'diseases',
'principal_paper', 'authors'])
for doc in studies:
setattr(doc, 'study_id', getattr(doc, 'study_id').replace('GDXHsS00', ''))
pmid = getattr(doc, 'principal_paper')
pubs = PublicationDocument.get_publications(pmid, sources=['date'])
if len(pubs) > 0:
setattr(doc, 'date', getattr(pubs[0], 'date'))
context['studies'] = studies
(core, other) = Disease.get_site_diseases()
diseases = list(core)
diseases.extend(other)
context['diseases'] = diseases
for dis in diseases:
docs = DiseaseLocusDocument.get_disease_loci_docs(getattr(dis, 'code'))
# get visible/authenticated hits id's
visible_hits = DiseaseLocusDocument.get_hits([h for r in docs for h in getattr(r, 'hits')],
sources=['seqid'])
visible_hits_ids = [h.doc_id() for h in visible_hits]
regions = 0
for r in docs:
hits = getattr(r, 'hits')
for h in hits:
if h in visible_hits_ids:
regions += 1
break
# number of visible regions
setattr(dis, 'count', regions)
return context
def get_disease_tags(cls, feature_id, idx=None, idx_type=None):
''' function to get the aggregated list of disease_tags for a given feature id, aggregated
from all criteria_types for a feature type
@type feature_id: string
@keyword feature_id: Id of the feature (gene => gene_id, region=>region_id)
@type idx: string
@param idx: name of the index
@type idx_type: string
@param idx_type: name of the idx type, each criteria is an index type
'''
query = ElasticQuery(Query.term("qid", feature_id))
agg = Agg("criteria_disease_tags", "terms", {"field": "disease_tags", "size": 0})
aggs = Aggs(agg)
if idx_type:
search = Search(query, aggs=aggs, idx=idx, idx_type=idx_type)
else:
search = Search(query, aggs=aggs, idx=idx)
disease_tags = []
try:
r_aggs = search.search().aggs
buckets = r_aggs['criteria_disease_tags'].get_buckets()
disease_tags = [dis_dict['key'].lower() for dis_dict in buckets]
except:
return []
# get disease docs
if (len(disease_tags) > 0):
(core, other) = Disease.get_site_diseases(dis_list=disease_tags)
diseases = list(core)
diseases.extend(other)
return diseases
else:
return None
def get_regions(cls, request, dis, context):
# is_authenticated = False
elastic_url = ElasticSettings.url()
(core, other) = Disease.get_site_diseases(dis_list=dis.upper().split(','))
if len(core) == 0 and len(other) == 0:
messages.error(request, 'Disease '+dis+' not found.')
raise Http404()
disease = core[0] if len(core) > 0 else other[0]
context['title'] = getattr(disease, "name")+" Regions"
docs = DiseaseLocusDocument.get_disease_loci_docs(dis)
if len(docs) == 0:
messages.error(request, 'No regions found for '+dis+'.')
raise Http404()
visible_hits = DiseaseLocusDocument.get_hits([h for r in docs for h in getattr(r, 'hits')])
meta_response = Search.elastic_request(elastic_url, ElasticSettings.idx("IC_STATS") + '/_mapping',
is_post=False)
regions = []
ens_all_cand_genes = []
all_markers = []
for r in docs:
region = r.get_disease_region(visible_hits)
if region is not None:
ens_all_cand_genes.extend(region['ens_cand_genes'])
all_markers.extend(region['markers'])
region['hits'] = StudyHitDocument.process_hits(r.hit_docs, region['all_diseases'])
(all_coding, all_non_coding) = get_genes_for_region(getattr(r, "seqid"),
region['rstart']-500000, region['rstop']+500000)
(region_coding, coding_up, coding_down) = _region_up_down(all_coding, region['rstart'], region['rstop'])
(region_non_coding, non_coding_up, non_coding_down) = \
_region_up_down(all_non_coding, region['rstart'], region['rstop'])
region['genes'] = {
'upstream': {'coding': coding_up, 'non_coding': non_coding_up},
'region': {'coding': region_coding, 'non_coding': region_non_coding},
'downstream': {'coding': coding_down, 'non_coding': non_coding_down},
}
regions.append(region)
# look for pleiotropy by looking for diseases for the markers in IC_STATS and other study hits
stats_query = ElasticQuery.filtered(Query.terms("marker", all_markers),
Filter(RangeQuery("p_value", lte=5E-08)))
stats_docs = Search(stats_query, idx=ElasticSettings.idx("IC_STATS"), size=len(all_markers)).search().docs
# get ensembl to gene symbol mapping for all candidate genes
all_cand_genes = gene.utils.get_gene_docs_by_ensembl_id(ens_all_cand_genes)
for region in regions:
region['cand_genes'] = {cg: all_cand_genes[cg] for cg in region.pop("ens_cand_genes", None)}
(study_ids, region['marker_stats']) = _process_stats(stats_docs, region['markers'], meta_response)
# add diseases from IC/GWAS stats
region['all_diseases'].extend([getattr(mstat, 'disease') for mstat in region['marker_stats']])
other_hits_query = ElasticQuery(
BoolQuery(must_arr=[RangeQuery("tier", lte=2), Query.terms("marker", region['markers'])],
must_not_arr=[Query.terms("dil_study_id", study_ids)]))
other_hits = Search(other_hits_query, idx=ElasticSettings.idx('REGION', 'STUDY_HITS'), size=100).search()
region['extra_markers'] = StudyHitDocument.process_hits(other_hits.docs, region['all_diseases'])
context['regions'] = regions
context['disease_code'] = [dis]
context['disease'] = getattr(disease, "name")
return context
def show_small_disease_bar(dis_list=None, href="/disease/"):
''' Template inclusion tag to render disease bar. '''
(main, other) = Disease.get_site_diseases(dis_list=dis_list)
if len(other) > 0:
main.append(Document({"_source": {"code": "OD", "colour": "grey", "name": "Other Diseases"}}))
return {'dis_main': main, 'text': False, 'href': href}
def show_disease_bar():
''' Template inclusion tag to render disease bar. '''
(main, other) = Disease.get_site_diseases()
return {'dis_main': main, 'dis_other': other}
def test_site_disease_codes(self):
''' Test getting all diseases on the site '''
from disease.utils import Disease
(main, other) = Disease.get_site_disease_codes()
self.assertEqual(12, len(main), "12 main diseases found ")
self.assertEqual(7, len(other), "7 other diseases found when searching for other diseases")
def test_main_diseases(self):
''' Test getting all diseases on the site '''
from disease.utils import Disease
(main, other) = Disease.get_site_diseases(tier=0)
self.assertEqual(12, len(main), "12 main diseases found when searching for main diseases")
self.assertEqual(0, len(other), "0 other diseases found when searching for main diseases")
