def ajax_range_overlap_search(request, src, start, stop, search_idx, ajax):
''' Return count or paginated range elastic result as a JSON '''
if ajax == 'count':
elastic = Search.range_overlap_query(src, start, stop, idx=search_idx)
return JsonResponse(elastic.get_count())
search_from = request.POST.get("from")
size = request.POST.get("size")
elastic = Search.range_overlap_query(src, start, stop, search_from=search_from,
size=size, idx=search_idx)
return JsonResponse(elastic.get_json_response())
def ajax_range_overlap_search(request, src, start, stop, search_idx, ajax):
''' Return count or paginated range elastic result as a JSON '''
if ajax == 'count':
elastic = Search.range_overlap_query(src, start, stop, idx=search_idx)
return JsonResponse(elastic.get_count())
search_from = request.POST.get("from")
size = request.POST.get("size")
elastic = Search.range_overlap_query(src,
start,
stop,
search_from=search_from,
size=size,
idx=search_idx)
return JsonResponse(elastic.get_json_response())
def gene_in_region(cls, hit, section=None, config=None, result_container={}):
try:
padded_region_doc = utils.Region.pad_region_doc(Document(hit))
except:
logger.warn('Region padding error ')
return result_container
# 'build_info': {'end': 22411939, 'seqid': '1', 'build': 38, 'start': 22326008}, 'region_id': '1p36.12_008'}
region_id = getattr(padded_region_doc, "region_id")
region_name = getattr(padded_region_doc, "region_name")
build_info = getattr(padded_region_doc, "build_info")
diseases = getattr(padded_region_doc, "tags")['disease']
seqid = build_info['seqid']
start = build_info['start']
end = build_info['end']
gene_index = ElasticSettings.idx('GENE', idx_type='GENE')
elastic = Search.range_overlap_query(seqid=seqid, start_range=start, end_range=end,
idx=gene_index, field_list=['start', 'stop', '_id'],
seqid_param="chromosome",
end_param="stop", size=10000)
result_docs = elastic.search().docs
genes = set()
for doc in result_docs:
genes.add(doc.doc_id())
result_container_populated = cls.populate_container(region_id,
region_name,
fnotes=None, features=genes,
diseases=diseases,
result_container=result_container)
return result_container_populated
def get_genes_for_region(seqid, start, end, must=None):
coding = []
non_coding = []
gene_index = ElasticSettings.idx('GENE', idx_type='GENE')
elastic = Search.range_overlap_query(seqid=seqid.lower(), start_range=start, end_range=end,
idx=gene_index, field_list=['start', 'stop', '_id', 'biotype', 'symbol'],
seqid_param="chromosome", end_param="stop", size=10000)
for doc in elastic.search().docs:
if getattr(doc, "biotype") == "protein_coding":
coding.append(doc)
else:
non_coding.append(doc)
return (coding, non_coding)
def _build_gene_query(chrom, segmin, segmax):
# get genes based on this segment
geneQuery = Search.range_overlap_query(seqid=chrom, start_range=segmin, end_range=segmax, search_from=0,
size=2000, idx=getattr(chicp_settings, 'CP_GENE_IDX')+'/genes/',
field_list=utils.geneFields)
geneResult = geneQuery.get_result()
genes = geneResult['data']
genes = utils.makeRelative(int(segmin), int(segmax), ['start', 'end'], genes)
genes = [utils.flattenAttr(o) for o in genes]
for o in genes:
o.update({"bumpLevel": 0})
o.update({"length": (o['end']-o['start'])})
genes.sort(key=operator.itemgetter('length'))
return genes
def range_overlap_search(request, src, start, stop, search_idx=ElasticSettings.indices_str()):
''' Renders a elastic result page based on the src, start and stop '''
elastic = Search.range_overlap_query(src, start, stop, idx=search_idx)
result = elastic.search()
context = {}
context['diseases'] = _add_diseases()
context['total'] = result.hits_total
context['db'] = result.idx
context['size'] = result.size
context['query'] = result.query
context["idxs"] = _categories(result.idx)
context["chromosome"] = src
context["start"] = start
context["stop"] = stop
return render(request, 'search/searchresults.html', context,
content_type='text/html')
def range_overlap_search(request,
src,
start,
stop,
search_idx=ElasticSettings.indices_str()):
''' Renders a elastic result page based on the src, start and stop '''
elastic = Search.range_overlap_query(src, start, stop, idx=search_idx)
result = elastic.search()
context = {}
context['diseases'] = _add_diseases()
context['total'] = result.hits_total
context['db'] = result.idx
context['size'] = result.size
context['query'] = result.query
context["idxs"] = _categories(result.idx)
context["chromosome"] = src
context["start"] = start
context["stop"] = stop
return render(request,
'search/searchresults.html',
context,
content_type='text/html')
def filter_queryset(self, request, queryset, view):
''' Override this method to request feature locations. '''
try:
filterable = getattr(view, 'filter_fields', [])
filters = dict([(k, v) for k, v in request.GET.items() if k in filterable])
ftype = filters.get('ftype').upper()
build = self._get_build(filters.get('build', settings.DEFAULT_BUILD))
if ftype is None or ftype == '':
return [ElasticObject(initial={'error': 'No feature type provided.'})]
idx = 'REGION' if ftype == 'ASSOC_SNP' else ftype
idx_type = 'STUDY_HITS' if idx == 'REGION' else ftype
print(idx_type)
doc_class_str = ElasticSettings.get_label(idx, idx_type, label='class')
doc_class = import_string(doc_class_str) if doc_class_str is not None else None
if ftype == 'REGION':
features = doc_class.get_overlapping_features(build, filters.get('chr').replace('chr', ''),
filters.get('start'), filters.get('end'))
return features
if ftype == 'ASSOC_SNP':
hits = doc_class.get_overlapping_hits(build, filters.get('chr').replace('chr', ''),
filters.get('start'), filters.get('end'))
features = Region.get_immune_snps(hits)
return features
sources = ['start', 'stop', 'seqid', 'chromosome', 'strand',
'biotype', 'giestain', 'name', 'symbol', 'id', 'ref', 'alt']
seqid_param = 'seqid'
end_param = 'stop'
start_param = 'start'
if ftype == 'GENE':
seqid_param = 'chromosome'
elastic = Search.range_overlap_query(filters.get('chr').replace('chr', ''), filters.get('start'),
filters.get('end'), idx=ElasticSettings.idx(idx, idx_type), size=10000,
seqid_param=seqid_param, end_param=end_param, start_param=start_param,
field_list=sources)
docs = elastic.search().docs
features = []
for doc in docs:
if isinstance(doc, RegionDocument):
doc = Region.pad_region_doc(doc)
loc = doc.get_position(build=build).split(':')
pos = loc[1].replace(',', '').split('-')
attributes = {}
feature = {
'name': doc.get_name(),
'id': doc.doc_id(),
'chr': loc[0],
'start': int(pos[0]),
'end': int(pos[1]) if len(pos) > 1 else int(pos[0]),
'strand': doc.get_strand_as_int()
}
if hasattr(doc, "biotype") and getattr(doc, "biotype") is not None:
attributes["biotype"] = getattr(doc, "biotype")
if hasattr(doc, "giestain") and getattr(doc, "giestain") is not None:
attributes["stain"] = getattr(doc, "giestain")
if hasattr(doc, "ref") and hasattr(doc, "alt") and getattr(doc, "ref") is not None and getattr(doc, "alt") is not None:
attributes["alleles"] = getattr(doc, "ref")+"/"+getattr(doc, "alt")
feature['attributes'] = attributes
features.append(ElasticObject(feature))
return features
except (ConnectionError) as err:
logger.error(err)
raise Http404
def test_range_query(self):
''' Test range overlap django-elastic function. '''
elastic = Search.range_overlap_query(seqid='chr1', start_range=1, end_range=206770620,
idx=IDX['GFF_GENERIC']['indexName'], field_list=['start', 'end'])
self.assertEquals(len(elastic.search().docs), 4)
