def test_bool_filtered_query(self):
''' Test building and running a filtered boolean query. '''
query_bool = BoolQuery(must_not_arr=[Query.term("seqid", 2)],
should_arr=[RangeQuery("start", gte=10050)])
query_bool.must([Query.term("id", "rs768019142")]) \
.should(RangeQuery("start", gte=10054))
query = ElasticQuery.filtered_bool(Query.match_all(), query_bool, sources=["id", "seqid"])
elastic = Search(query, idx=ElasticSettings.idx('DEFAULT'))
self.assertTrue(elastic.search().hits_total == 1, "Elastic filtered query retrieved marker (rs768019142)")
def test_bool_filtered_query2(self):
''' Test building and running a filtered boolean query. '''
query_bool = BoolQuery()
query_bool.should(RangeQuery("start", lte=20000)) \
.should(Query.term("seqid", 2)) \
.must(Query.term("seqid", 1))
query_string = Query.query_string("rs768019142", fields=["id", "seqid"])
query = ElasticQuery.filtered_bool(query_string, query_bool, sources=["id", "seqid", "start"])
elastic = Search(query, idx=ElasticSettings.idx('DEFAULT'))
self.assertTrue(elastic.search().hits_total == 1, "Elastic filtered query retrieved marker (rs768019142)")
def get_elastic_query(cls, section=None, config=None):
''' function to build the elastic query object
@type section: string
@keyword section: The section in the criteria.ini file
@type config: string
@keyword config: The config object initialized from criteria.ini.
@return: L{Query}
'''
section_config = config[section]
source_fields = []
if 'source_fields' in section_config:
source_fields_str = section_config['source_fields']
source_fields = source_fields_str.split(',')
if 'mhc' in section:
seqid = '6'
start_range = 25000000
end_range = 35000000
seqid_param = section_config['seqid_param']
start_param = section_config['start_param']
end_param = section_config['end_param']
if section == 'is_gene_in_mhc':
# for region you should make a different query
# Defined MHC region as chr6:25,000,000..35,000,000
query = ElasticUtils.range_overlap_query(seqid, start_range, end_range,
source_fields,
seqid_param,
start_param,
end_param)
elif section == 'is_marker_in_mhc':
query_bool = BoolQuery()
query_bool.must(RangeQuery("start", lte=end_range)) \
.must(RangeQuery("start", gte=start_range)) \
.must(Query.term("seqid", seqid))
query = ElasticQuery.filtered_bool(Query.match_all(), query_bool, sources=["id", "seqid", "start"])
elif section == 'is_region_in_mhc':
query = ElasticQuery(Query.term("region_name", "MHC"))
elif section == 'marker_is_gwas_significant_in_ic':
# build a range query
gw_sig_p = 0.00000005
query = ElasticQuery(RangeQuery("p_value", lte=gw_sig_p))
else:
if len(source_fields) > 0:
query = ElasticQuery(Query.match_all(), sources=source_fields)
else:
# query = ElasticQuery(Query.match_all())
return None
return query
def test_bool_nested_filter(self):
''' Test combined Bool filter '''
query_bool_nest = BoolQuery()
query_bool_nest.must(Query.match("id", "rs768019142").query_wrap()) \
.must(Query.term("seqid", 1))
query_bool = BoolQuery()
query_bool.should(query_bool_nest) \
.should(Query.term("seqid", 2))
query = ElasticQuery.filtered_bool(Query.match_all(), query_bool, sources=["id", "seqid", "start"])
elastic = Search(query, idx=ElasticSettings.idx('DEFAULT'))
self.assertTrue(elastic.search().hits_total >= 1, "Nested bool filter query")
def test_bool_filtered_query4(self):
''' Test building and running a filtered boolean query.
Note: ElasticQuery used to wrap match in a query object. '''
query_bool = BoolQuery()
query_bool.should(RangeQuery("start", lte=20000)) \
.should(Query.term("seqid", 2)) \
.must(Query.match("id", "rs768019142").query_wrap()) \
.must(Query.term("seqid", 1))
query = ElasticQuery.filtered_bool(Query.match_all(), query_bool, sources=["id", "seqid", "start"])
elastic = Search(query, idx=ElasticSettings.idx('DEFAULT'))
self.assertTrue(elastic.search().hits_total == 1, "Elastic filtered query retrieved marker (rs768019142)")
def _build_exon_query(chrom, segmin, segmax, genes):
# get exonic structure for genes in this section
geneExons = dict()
query_bool = BoolQuery()
query_bool.must([Query.term("seqid", chrom)])
if len(genes) > 0:
for g in genes:
query = ElasticQuery.filtered_bool(Query.query_string(g["gene_id"], fields=["name"]),
query_bool, sources=utils.snpFields)
elastic = Search(query, idx=getattr(chicp_settings, 'CP_GENE_IDX')+'/exons/', search_from=0, size=2000)
result = elastic.get_result()
exons = result['data']
exons = utils.makeRelative(int(segmin), int(segmax), ['start', 'end'], exons)
geneExons[g["gene_id"]] = sorted(exons, key=operator.itemgetter("start"))
return geneExons
def get_overlapping_hits(self, build, seqid, start, end):
query_bool = BoolQuery(must_arr=[RangeQuery("build_info.start", lte=start),
RangeQuery("build_info.end", gte=end)])
or_filter = OrFilter(RangeQuery("build_info.start", gte=start, lte=end))
or_filter.extend(RangeQuery("build_info.end", gte=start, lte=end)) \
.extend(query_bool)
range_query = FilteredQuery(BoolQuery(must_arr=[Query.term("build_info.seqid", seqid),
Query.term("build_info.build", build)]),
or_filter)
query = ElasticQuery.filtered_bool(
Query.nested("build_info", range_query),
BoolQuery(must_arr=[RangeQuery("tier", lte=2)]),
# sources=["disease", "marker", "chr_band", "tier", "build_info", "disease_locus"]
)
elastic = Search(search_query=query, idx=ElasticSettings.idx('REGION', 'STUDY_HITS'))
return elastic.search().docs
def test_elastic_group_name(self):
'''
Testing the workflow defined in: https://killin.cimr.cam.ac.uk/nextgensite/2015/08/05/region-authorization/
Testing various elastic queries
idx doc:
"_source":{"attr": {"region_id": "803", "group_name": "[\"DIL\"]", "Name": "4q27"},
"seqid": "chr4", "source": "immunobase", "type": "region",
"score": ".", "strand": ".", "phase": ".", "start": 122061159, "end": 122684373}
idx_query:
Private(in given group) OR Public
-d '{"query":{"filtered":{"filter":{"bool": {
"should": [
{"terms": {"group_name":["dil"]}},
{ "missing": { "field": "group_name" }}
]
}}}}}'
Private(in given group):
-d '{"query":{"filtered":{"filter":{"terms":{"group_name":["dil"]}}}}}'
Public:
-d {'query': {'filtered': {'filter': {'missing': {'field': 'group_name'}},
- 'query': {'term': {'match_all': '{}'}}}}}
'''
# get the groups for the given user
response = self.client.post('/accounts/login/', {
'username': '******',
'password': '******'
})
self.assertTrue(response.status_code, "200")
logged_in_user = User.objects.get(
id=self.client.session['_auth_user_id'])
if logged_in_user and logged_in_user.is_authenticated():
user_groups = get_user_groups(logged_in_user)
self.assertTrue('READ' in user_groups,
"user present in READ group")
# make sure the user is not yet in DIL group
self.assertFalse('DIL' in user_groups,
"user not present in DIL group")
group_names = get_user_groups(logged_in_user)
if 'READ' in group_names: group_names.remove('READ') # @IgnorePep8
group_names = [x.lower() for x in group_names]
self.assertTrue(len(group_names) == 0, "No group present")
# Match all query, as there is no group we do a match all
query = ElasticQuery(Query.match_all())
expected_query_string = {"query": {"match_all": {}}}
self.assertJSONEqual(json.dumps(query.query),
json.dumps(expected_query_string),
"Query string matched")
Search.index_refresh(self.index_name)
elastic = Search(query, idx=self.index_name)
docs = elastic.search().docs
self.assertTrue(
len(docs) == 12,
"Elastic string query retrieved all public regions")
# Filtered query for group names, add the user to DIL group and get the query string
self.dil_group = Group.objects.create(name='DIL')
logged_in_user.groups.add(self.dil_group)
group_names = get_user_groups(logged_in_user)
if 'READ' in group_names: group_names.remove('READ') # @IgnorePep8
group_names = [x.lower() for x in group_names]
self.assertTrue(len(group_names) > 0, "More than 1 group present")
self.assertTrue("dil" in group_names, "DIL group present")
# retrieves all docs with missing field group_name - 11 docs
terms_filter = TermsFilter.get_missing_terms_filter(
"field", "attr.group_name")
query = ElasticQuery.filtered(Query.match_all(), terms_filter)
elastic = Search(query, idx=self.index_name)
docs = elastic.search().docs
self.assertTrue(
len(docs) == 11,
"Elastic string query retrieved all public regions")
# build filtered boolean query to bring all public docs + private docs 11+1 = 12 docs
query_bool = BoolQuery()
query_bool.should(Query.missing_terms("field", "group_name")) \
.should(Query.terms("group_name", group_names).query_wrap())
query = ElasticQuery.filtered_bool(Query.match_all(), query_bool)
elastic = Search(query, idx=self.index_name)
docs = elastic.search().docs
self.assertTrue(
len(docs) == 12,
"Elastic string query retrieved both public + private regions")
terms_filter = TermsFilter.get_terms_filter("attr.group_name",
group_names)
query = ElasticQuery.filtered(Query.match_all(), terms_filter)
elastic = Search(query, idx=self.index_name)
docs = elastic.search().docs
self.assertTrue(
len(docs) == 1,
"Elastic string query retrieved one private regions")
self.assertEqual(docs[0].attr['Name'], "4q27", "type matched region")
self.assertEqual(docs[0].attr['region_id'], "803",
"type matched region")
self.assertEqual(docs[0].attr['group_name'], "[\"DIL\"]",
"type matched region")
def test_elastic_group_name(self):
'''
Testing the workflow defined in: https://killin.cimr.cam.ac.uk/nextgensite/2015/08/05/region-authorization/
Testing various elastic queries
idx doc:
"_source":{"attr": {"region_id": "803", "group_name": "[\"DIL\"]", "Name": "4q27"},
"seqid": "chr4", "source": "immunobase", "type": "region",
"score": ".", "strand": ".", "phase": ".", "start": 122061159, "end": 122684373}
idx_query:
Private(in given group) OR Public
-d '{"query":{"filtered":{"filter":{"bool": {
"should": [
{"terms": {"group_name":["dil"]}},
{ "missing": { "field": "group_name" }}
]
}}}}}'
Private(in given group):
-d '{"query":{"filtered":{"filter":{"terms":{"group_name":["dil"]}}}}}'
Public:
-d {'query': {'filtered': {'filter': {'missing': {'field': 'group_name'}},
- 'query': {'term': {'match_all': '{}'}}}}}
'''
# get the groups for the given user
response = self.client.post('/accounts/login/', {'username': '******', 'password': '******'})
self.assertTrue(response.status_code, "200")
logged_in_user = User.objects.get(id=self.client.session['_auth_user_id'])
if logged_in_user and logged_in_user.is_authenticated():
user_groups = get_user_groups(logged_in_user)
self.assertTrue('READ' in user_groups, "user present in READ group")
# make sure the user is not yet in DIL group
self.assertFalse('DIL' in user_groups, "user not present in DIL group")
group_names = get_user_groups(logged_in_user)
if 'READ' in group_names : group_names.remove('READ') # @IgnorePep8
group_names = [x.lower() for x in group_names]
self.assertTrue(len(group_names) == 0, "No group present")
# Match all query, as there is no group we do a match all
query = ElasticQuery(Query.match_all())
expected_query_string = {"query": {"match_all": {}}}
self.assertJSONEqual(json.dumps(query.query), json.dumps(expected_query_string), "Query string matched")
Search.index_refresh(self.index_name)
elastic = Search(query, idx=self.index_name)
docs = elastic.search().docs
self.assertTrue(len(docs) == 12, "Elastic string query retrieved all public regions")
# Filtered query for group names, add the user to DIL group and get the query string
self.dil_group = Group.objects.create(name='DIL')
logged_in_user.groups.add(self.dil_group)
group_names = get_user_groups(logged_in_user)
if 'READ' in group_names : group_names.remove('READ') # @IgnorePep8
group_names = [x.lower() for x in group_names]
self.assertTrue(len(group_names) > 0, "More than 1 group present")
self.assertTrue("dil" in group_names, "DIL group present")
# retrieves all docs with missing field group_name - 11 docs
terms_filter = TermsFilter.get_missing_terms_filter("field", "attr.group_name")
query = ElasticQuery.filtered(Query.match_all(), terms_filter)
elastic = Search(query, idx=self.index_name)
docs = elastic.search().docs
self.assertTrue(len(docs) == 11, "Elastic string query retrieved all public regions")
# build filtered boolean query to bring all public docs + private docs 11+1 = 12 docs
query_bool = BoolQuery()
query_bool.should(Query.missing_terms("field", "group_name")) \
.should(Query.terms("group_name", group_names).query_wrap())
query = ElasticQuery.filtered_bool(Query.match_all(), query_bool)
elastic = Search(query, idx=self.index_name)
docs = elastic.search().docs
self.assertTrue(len(docs) == 12, "Elastic string query retrieved both public + private regions")
terms_filter = TermsFilter.get_terms_filter("attr.group_name", group_names)
query = ElasticQuery.filtered(Query.match_all(), terms_filter)
elastic = Search(query, idx=self.index_name)
docs = elastic.search().docs
self.assertTrue(len(docs) == 1, "Elastic string query retrieved one private regions")
self.assertEqual(docs[0].attr['Name'], "4q27", "type matched region")
self.assertEqual(docs[0].attr['region_id'], "803", "type matched region")
self.assertEqual(docs[0].attr['group_name'], "[\"DIL\"]", "type matched region")
qnested = ElasticQuery(Query.nested('build_info', Query.term("build_info.build", build)))
elastic = Search(qnested, idx=idx, aggs=Aggs(build_info), search_type='count')
resultObj = elastic.search()
resultAggs = resultObj.aggs
seq_hits = getattr(resultAggs['build_info'], 'seq_hits')['buckets']
for chr_bucket in seq_hits:
seqid = chr_bucket['key'].upper()
for disease_bucket in chr_bucket['disease_hits']['diseases_by_seqid']['buckets']:
# print(disease_bucket)
disease_code = disease_bucket['key']
print("\n"+str(seqid)+" - "+disease_code)
query2 = ElasticQuery.filtered_bool(
Query.nested("build_info", BoolQuery(
must_arr=[Query.term("build_info.seqid", chr_bucket['key']), Query.term("build_info.build", build)])),
BoolQuery(must_arr=[Query.term("disease", disease_code), RangeQuery("tier", lte=tier_cutoff)]),
sources=["disease", "marker", "chr_band", "tier", "tags.weight", "species", "build_info"]
)
elastic2 = Search(search_query=query2, idx=idx, idx_type='hits',
size=int(disease_bucket['doc_count']+1), qsort=Sort(buildSort))
results = elastic2.search()
minPos = 0
maxPos = 0
tier = 4
weight = 0
regionCount = 1
regionName = ''
species = ''
doc_ids = []
if len(results.docs) > 0:
for doc in results.docs:
def chicpeaSearch(request, url):
queryDict = request.GET
user = request.user
targetIdx = queryDict.get("targetIdx")
blueprint = {}
hic = []
addList = []
searchType = 'gene'
searchTerm = queryDict.get("searchTerm").upper()
searchTerm = searchTerm.replace(",", "")
searchTerm = searchTerm.replace("..", "-")
searchTerm = searchTerm.replace(" ", "") # Chris suggestion to prevent issue with spaces in queries
snpTrack = queryDict.get("snp_track")
(idx_keys_auth, idx_type_keys_auth) = get_authenticated_idx_and_idx_types(
user=user, idx_keys=None, idx_type_keys=None)
if snpTrack:
mo = re.match(r"(.*)-(.*)", snpTrack)
(group, track) = mo.group(1, 2) # @UnusedVariable
if group != 'ud' and 'CP_STATS_'+group.upper()+'.'+snpTrack.upper() not in idx_type_keys_auth:
snpTrack = None
if targetIdx not in utils.tissues:
for target in getattr(chicp_settings, 'CP_TARGET'):
if 'CP_TARGET_'+target not in idx_keys_auth:
if targetIdx == target:
retJSON = {'error': 'Sorry, you do not have permission to view this dataset.'}
return JsonResponse(retJSON)
continue
elasticJSON = Search(idx=ElasticSettings.idx('CP_TARGET_'+target)).get_mapping(mapping_type="gene_target")
tissueList = list(elasticJSON[ElasticSettings.idx('CP_TARGET_'+target)]
['mappings']['gene_target']['_meta']['tissue_type'].keys())
utils.tissues['CP_TARGET_'+target] = tissueList
if queryDict.get("region") or re.match(r"(.*):(\d+)-(\d+)", searchTerm):
searchType = 'region'
region = searchTerm
if queryDict.get("region"):
region = queryDict.get("region")
else:
searchTerm = ""
mo = re.match(r"(.*):(\d+)-(\d+)", region)
(chrom, segmin, segmax) = mo.group(1, 2, 3)
chrom = chrom.replace('chr', "")
chrom = chrom.replace('CHR', "")
if re.search("^rs[0-9]+", searchTerm.lower()):
searchTerm = searchTerm.lower()
addList.append(_find_snp_position(snpTrack, searchTerm))
if addList[0].get("error"):
return JsonResponse({'error': addList[0]['error']})
position = addList[0]['end']
if searchType != 'region':
searchType = 'snp'
logger.warn("### "+searchType+" - "+searchTerm+' ###')
if searchType == 'region':
query_bool = BoolQuery()
filter_bool = BoolQuery()
if searchTerm and len(addList) == 0 and re.match(r"(.*):(\d+)-(\d+)",
queryDict.get("searchTerm").replace(",", "")) == None:
query_bool.must([Query.query_string(searchTerm, fields=["name", "ensg"]),
Query.term("baitChr", chrom),
Query.term("oeChr", chrom),
RangeQuery("dist", gte=-2e6, lte=2e6)])
else:
query_bool.must([Query.term("baitChr", chrom),
Query.term("oeChr", chrom),
RangeQuery("dist", gte=-2e6, lte=2e6)])
query_bool = _add_tissue_filter(query_bool, targetIdx)
if len(addList) > 0:
filter_bool.should([BoolQuery(must_arr=[RangeQuery("baitStart", lte=position),
RangeQuery("baitEnd", gte=position)]),
BoolQuery(must_arr=[RangeQuery("oeStart", lte=position),
RangeQuery("oeEnd", gte=position)])])
else:
filter_bool.should([BoolQuery(must_arr=[RangeQuery("baitStart", gte=segmin, lte=segmax),
RangeQuery("baitEnd", gte=segmin, lte=segmax)]),
BoolQuery(must_arr=[RangeQuery("oeStart", gte=segmin, lte=segmax),
RangeQuery("oeEnd", gte=segmin, lte=segmax)])])
query = ElasticQuery.filtered_bool(query_bool, filter_bool,
sources=utils.hicFields + utils.tissues['CP_TARGET_'+targetIdx])
(hic, v1, v2) = _build_hic_query(query, targetIdx, segmin, segmax) # @UnusedVariable
if "error" in hic:
return JsonResponse(hic)
if len(hic) == 0:
retJSON = {'error': queryDict.get("searchTerm")+' does not overlap any bait/target regions in this dataset.'}
return JsonResponse(retJSON)
elif searchType == 'snp':
if len(addList) > 0:
chrom = addList[0]['chr']
query_bool = BoolQuery()
query_bool.must([Query.term("baitChr", chrom),
Query.term("oeChr", chrom),
RangeQuery("dist", gte=-2e6, lte=2e6)])
query_bool = _add_tissue_filter(query_bool, targetIdx)
filter_bool = BoolQuery()
filter_bool.should([BoolQuery(must_arr=[RangeQuery("baitStart", lte=position),
RangeQuery("baitEnd", gte=position)]),
BoolQuery(must_arr=[RangeQuery("oeStart", lte=position),
RangeQuery("oeEnd", gte=position)])])
query = ElasticQuery.filtered_bool(query_bool, filter_bool,
sources=utils.hicFields + utils.tissues['CP_TARGET_'+targetIdx])
hic, segmin, segmax = _build_hic_query(query, targetIdx)
if "error" in hic:
return JsonResponse(hic)
if len(hic) == 0:
retJSON = {'error': 'Marker '+searchTerm+' does not overlap any bait/target regions in this dataset.'}
return JsonResponse(retJSON)
else:
# geneQuery = ElasticQuery.query_string(searchTerm, fields=["gene_name"])
geneQuery = ElasticQuery.filtered(Query.match_all(), Filter(Query.match("gene_name", searchTerm).query_wrap()))
resultObj = Search(idx=getattr(chicp_settings, 'CP_GENE_IDX') + '/genes/',
search_query=geneQuery, size=0, qsort=Sort('seqid:asc,start')).search()
if resultObj.hits_total > 1:
geneResults = []
resultObj2 = Search(idx=getattr(chicp_settings, 'CP_GENE_IDX') + '/genes/', search_query=geneQuery,
size=(resultObj.hits_total+1), qsort=Sort('seqid:asc,start')).search()
docs = resultObj2.docs
gene_ids = [getattr(doc, 'attr')['gene_id'][1:-1] for doc in docs]
query = ElasticQuery.filtered(Query.match_all(), TermsFilter.get_terms_filter('ensg', gene_ids))
agg = Agg('ensg_agg', "terms", {"field": "ensg", "size": 0})
res = Search(idx=ElasticSettings.idx('CP_TARGET_'+targetIdx), search_query=query, aggs=Aggs(agg),
size=0).search()
ensg_count = res.aggs['ensg_agg'].get_buckets()
gene_ids = [g['key'] for g in ensg_count]
for d in resultObj2.docs:
if getattr(d, "attr")["gene_id"].replace('\"', '') in gene_ids:
geneResults.append({
'gene_name': getattr(d, "attr")["gene_name"].replace('\"', ''),
'gene_id': getattr(d, "attr")["gene_id"].replace('\"', ''),
'location': "chr" + getattr(d, "seqid") + ":" +
locale.format_string("%d", getattr(d, "start"), grouping=True) + ".." +
locale.format_string("%d", getattr(d, "end"), grouping=True),
})
if len(geneResults) == 0:
retJSON = {'error': 'Gene name '+searchTerm+' not found in this dataset.'}
return JsonResponse(retJSON)
elif len(geneResults) > 1:
retJSON = {
'error': 'Gene name <strong>'+searchTerm+'</strong> returns too many hits, please select your prefered result from the list below.',
'results': geneResults,
'cols': ['HGNC Symbol', 'Ensembl Gene ID', 'Location']
}
return JsonResponse(retJSON)
query_bool = BoolQuery()
query_bool.must([RangeQuery("dist", gte=-2e6, lte=2e6)])
query_bool = _add_tissue_filter(query_bool, targetIdx)
query = ElasticQuery.filtered_bool(Query.query_string(searchTerm, fields=["name", "ensg", "oeName"]),
query_bool, sources=utils.hicFields + utils.tissues['CP_TARGET_'+targetIdx])
(hic, segmin, segmax) = _build_hic_query(query, targetIdx)
if "error" in hic:
return JsonResponse(hic)
if len(hic) == 0:
retJSON = {'error': 'Gene name '+searchTerm+' not found in this dataset.'}
return JsonResponse(retJSON)
chrom = hic[0]['baitChr']
try:
chrom
except NameError:
retJSON = {'error': 'No chromosome defined for search'}
return JsonResponse(retJSON)
# get genes based on this segment
genes = _build_gene_query(chrom, segmin, segmax)
(snps, snpMeta) = _build_snp_query(snpTrack, chrom, segmin, segmax)
frags = _build_frags_query(getattr(chicp_settings, 'DEFAULT_FRAG'), chrom, segmin, segmax)
addList = utils.makeRelative(int(segmin), int(segmax), ['start', 'end'], addList)
retJSON = {"hic": hic,
"frags": frags,
"meta": {"ostart": int(segmin),
"oend": int(segmax),
"rstart": 1,
"rend": int(segmax) - int(segmin),
"rchr": str(chrom),
"tissues": utils.tissues['CP_TARGET_'+targetIdx]},
"snps": snps,
"snp_meta": snpMeta,
"genes": genes,
"region": str(chrom) + ":" + str(segmin) + "-" + str(segmax),
"blueprint": blueprint,
"extra": addList
}
response = JsonResponse(retJSON)
return response
def chicpeaSearch(request, url):
queryDict = request.GET
targetIdx = queryDict.get("targetIdx")
blueprint = {}
hic = []
addList = []
searchType = 'gene'
searchTerm = queryDict.get("searchTerm").upper()
if targetIdx not in utils.tissues:
for idx in getattr(chicp_settings, 'TARGET_IDXS'):
elasticJSON = Search(idx=idx).get_mapping(mapping_type="gene_target")
tissueList = list(elasticJSON[idx]['mappings']['gene_target']['_meta']['tissue_type'].keys())
utils.tissues[idx] = tissueList
if queryDict.get("region") or re.match(r"(.*):(\d+)-(\d+)", queryDict.get("searchTerm")):
searchType = 'region'
region = queryDict.get("searchTerm")
if queryDict.get("region"):
region = queryDict.get("region")
else:
searchTerm = ""
mo = re.match(r"(.*):(\d+)-(\d+)", region)
(chrom, segmin, segmax) = mo.group(1, 2, 3)
chrom = chrom.replace('chr', "")
if re.search("^rs[0-9]+", queryDict.get("searchTerm").lower()):
searchTerm = queryDict.get("searchTerm").lower()
addList.append(_find_snp_position(queryDict.get("snp_track"), searchTerm))
if addList[0].get("error"):
return JsonResponse({'error': addList[0]['error']})
position = addList[0]['end']
if searchType != 'region':
searchType = 'snp'
logger.warn("### "+searchType+" - "+searchTerm+' ###')
if searchType == 'region':
query_bool = BoolQuery()
filter_bool = BoolQuery()
if searchTerm and len(addList) == 0 and re.match(r"(.*):(\d+)-(\d+)", queryDict.get("searchTerm")) == None:
query_bool.must([Query.query_string(searchTerm, fields=["name", "ensg"]),
Query.term("baitChr", chrom),
Query.term("oeChr", chrom),
RangeQuery("dist", gte=-2e6, lte=2e6)])
else:
query_bool.must([Query.term("baitChr", chrom),
Query.term("oeChr", chrom),
RangeQuery("dist", gte=-2e6, lte=2e6)])
query_bool = _add_tissue_filter(query_bool, targetIdx)
if len(addList) > 0:
filter_bool.should([BoolQuery(must_arr=[RangeQuery("baitStart", lte=position),
RangeQuery("baitEnd", gte=position)]),
BoolQuery(must_arr=[RangeQuery("oeStart", lte=position),
RangeQuery("oeEnd", gte=position)])])
else:
filter_bool.should([BoolQuery(must_arr=[RangeQuery("baitStart", gte=segmin, lte=segmax),
RangeQuery("baitEnd", gte=segmin, lte=segmax)]),
BoolQuery(must_arr=[RangeQuery("oeStart", gte=segmin, lte=segmax),
RangeQuery("oeEnd", gte=segmin, lte=segmax)])])
query = ElasticQuery.filtered_bool(query_bool, filter_bool, sources=utils.hicFields + utils.tissues[targetIdx])
(hic, v1, v2) = _build_hic_query(query, targetIdx, segmin, segmax)
# print(hic)
if len(hic) == 0:
retJSON = {'error': queryDict.get("searchTerm")+' does not overlap any bait/target regions in this dataset.'}
return JsonResponse(retJSON)
elif searchType == 'snp':
if len(addList) > 0:
chrom = addList[0]['chr']
query_bool = BoolQuery()
query_bool.must([Query.term("baitChr", chrom),
Query.term("oeChr", chrom),
RangeQuery("dist", gte=-2e6, lte=2e6)])
query_bool = _add_tissue_filter(query_bool, targetIdx)
filter_bool = BoolQuery()
filter_bool.should([BoolQuery(must_arr=[RangeQuery("baitStart", lte=position),
RangeQuery("baitEnd", gte=position)]),
BoolQuery(must_arr=[RangeQuery("oeStart", lte=position),
RangeQuery("oeEnd", gte=position)])])
query = ElasticQuery.filtered_bool(query_bool, filter_bool,
sources=utils.hicFields + utils.tissues[targetIdx])
hic, segmin, segmax = _build_hic_query(query, targetIdx)
if len(hic) == 0:
retJSON = {'error': 'Marker '+searchTerm+' does not overlap any bait/target regions in this dataset.'}
return JsonResponse(retJSON)
else:
query_bool = BoolQuery()
query_bool.must([RangeQuery("dist", gte=-2e6, lte=2e6)])
query_bool = _add_tissue_filter(query_bool, targetIdx)
query = ElasticQuery.filtered_bool(Query.query_string(searchTerm, fields=["name", "ensg", "oeName"]),
query_bool, sources=utils.hicFields + utils.tissues[targetIdx])
hic, segmin, segmax = _build_hic_query(query, targetIdx)
if len(hic) == 0:
retJSON = {'error': 'Gene name '+searchTerm+' not found in this dataset.'}
return JsonResponse(retJSON)
chrom = hic[0]['baitChr']
try:
chrom
except NameError:
retJSON = {'error': 'No chromosome defined for search'}
return JsonResponse(retJSON)
# get genes based on this segment
genes = _build_gene_query(chrom, segmin, segmax)
(snps, snpMeta) = _build_snp_query(queryDict.get("snp_track"), chrom, segmin, segmax)
frags = _build_frags_query(getattr(chicp_settings, 'DEFAULT_FRAG'), chrom, segmin, segmax)
addList = utils.makeRelative(int(segmin), int(segmax), ['start', 'end'], addList)
retJSON = {"hic": hic,
"frags": frags,
"meta": {"ostart": int(segmin),
"oend": int(segmax),
"rstart": 1,
"rend": int(segmax) - int(segmin),
"rchr": str(chrom),
"tissues": utils.tissues[targetIdx]},
"snps": snps,
"snp_meta": snpMeta,
"genes": genes,
"region": str(chrom) + ":" + str(segmin) + "-" + str(segmax),
"blueprint": blueprint,
"extra": addList
}
response = JsonResponse(retJSON)
return response
def chicpeaSearch(request, url):
queryDict = request.GET
user = request.user
targetIdx = queryDict.get("targetIdx")
blueprint = {}
hic = []
addList = []
searchType = 'gene'
searchTerm = queryDict.get("searchTerm").upper()
searchTerm = searchTerm.replace(",", "")
searchTerm = searchTerm.replace("..", "-")
snpTrack = queryDict.get("snp_track")
(idx_keys_auth, idx_type_keys_auth) = get_authenticated_idx_and_idx_types(
user=user, idx_keys=None, idx_type_keys=None)
if snpTrack:
mo = re.match(r"(.*)-(.*)", snpTrack)
(group, track) = mo.group(1, 2) # @UnusedVariable
if group != 'ud' and 'CP_STATS_'+group.upper()+'.'+snpTrack.upper() not in idx_type_keys_auth:
snpTrack = None
if targetIdx not in utils.tissues:
for target in getattr(chicp_settings, 'CP_TARGET'):
if 'CP_TARGET_'+target not in idx_keys_auth:
if targetIdx == target:
retJSON = {'error': 'Sorry, you do not have permission to view this dataset.'}
return JsonResponse(retJSON)
continue
elasticJSON = Search(idx=ElasticSettings.idx('CP_TARGET_'+target)).get_mapping(mapping_type="gene_target")
tissueList = list(elasticJSON[ElasticSettings.idx('CP_TARGET_'+target)]
['mappings']['gene_target']['_meta']['tissue_type'].keys())
utils.tissues['CP_TARGET_'+target] = tissueList
if queryDict.get("region") or re.match(r"(.*):(\d+)-(\d+)", searchTerm):
searchType = 'region'
region = searchTerm
if queryDict.get("region"):
region = queryDict.get("region")
else:
searchTerm = ""
mo = re.match(r"(.*):(\d+)-(\d+)", region)
(chrom, segmin, segmax) = mo.group(1, 2, 3)
chrom = chrom.replace('chr', "")
chrom = chrom.replace('CHR', "")
if re.search("^rs[0-9]+", searchTerm.lower()):
searchTerm = searchTerm.lower()
addList.append(_find_snp_position(snpTrack, searchTerm))
if addList[0].get("error"):
return JsonResponse({'error': addList[0]['error']})
position = addList[0]['end']
if searchType != 'region':
searchType = 'snp'
logger.warn("### "+searchType+" - "+searchTerm+' ###')
if searchType == 'region':
query_bool = BoolQuery()
filter_bool = BoolQuery()
if searchTerm and len(addList) == 0 and re.match(r"(.*):(\d+)-(\d+)",
queryDict.get("searchTerm").replace(",", "")) == None:
query_bool.must([Query.query_string(searchTerm, fields=["name", "ensg"]),
Query.term("baitChr", chrom),
Query.term("oeChr", chrom),
RangeQuery("dist", gte=-2e6, lte=2e6)])
else:
query_bool.must([Query.term("baitChr", chrom),
Query.term("oeChr", chrom),
RangeQuery("dist", gte=-2e6, lte=2e6)])
query_bool = _add_tissue_filter(query_bool, targetIdx)
if len(addList) > 0:
filter_bool.should([BoolQuery(must_arr=[RangeQuery("baitStart", lte=position),
RangeQuery("baitEnd", gte=position)]),
BoolQuery(must_arr=[RangeQuery("oeStart", lte=position),
RangeQuery("oeEnd", gte=position)])])
else:
filter_bool.should([BoolQuery(must_arr=[RangeQuery("baitStart", gte=segmin, lte=segmax),
RangeQuery("baitEnd", gte=segmin, lte=segmax)]),
BoolQuery(must_arr=[RangeQuery("oeStart", gte=segmin, lte=segmax),
RangeQuery("oeEnd", gte=segmin, lte=segmax)])])
query = ElasticQuery.filtered_bool(query_bool, filter_bool,
sources=utils.hicFields + utils.tissues['CP_TARGET_'+targetIdx])
(hic, v1, v2) = _build_hic_query(query, targetIdx, segmin, segmax) # @UnusedVariable
if "error" in hic:
return JsonResponse(hic)
if len(hic) == 0:
retJSON = {'error': queryDict.get("searchTerm")+' does not overlap any bait/target regions in this dataset.'}
return JsonResponse(retJSON)
elif searchType == 'snp':
if len(addList) > 0:
chrom = addList[0]['chr']
query_bool = BoolQuery()
query_bool.must([Query.term("baitChr", chrom),
Query.term("oeChr", chrom),
RangeQuery("dist", gte=-2e6, lte=2e6)])
query_bool = _add_tissue_filter(query_bool, targetIdx)
filter_bool = BoolQuery()
filter_bool.should([BoolQuery(must_arr=[RangeQuery("baitStart", lte=position),
RangeQuery("baitEnd", gte=position)]),
BoolQuery(must_arr=[RangeQuery("oeStart", lte=position),
RangeQuery("oeEnd", gte=position)])])
query = ElasticQuery.filtered_bool(query_bool, filter_bool,
sources=utils.hicFields + utils.tissues['CP_TARGET_'+targetIdx])
hic, segmin, segmax = _build_hic_query(query, targetIdx)
if "error" in hic:
return JsonResponse(hic)
if len(hic) == 0:
retJSON = {'error': 'Marker '+searchTerm+' does not overlap any bait/target regions in this dataset.'}
return JsonResponse(retJSON)
else:
# geneQuery = ElasticQuery.query_string(searchTerm, fields=["gene_name"])
geneQuery = ElasticQuery.filtered(Query.match_all(), Filter(Query.match("gene_name", searchTerm).query_wrap()))
resultObj = Search(idx=getattr(chicp_settings, 'CP_GENE_IDX') + '/genes/',
search_query=geneQuery, size=0, qsort=Sort('seqid:asc,start')).search()
if resultObj.hits_total > 1:
geneResults = []
resultObj2 = Search(idx=getattr(chicp_settings, 'CP_GENE_IDX') + '/genes/', search_query=geneQuery,
size=(resultObj.hits_total+1), qsort=Sort('seqid:asc,start')).search()
docs = resultObj2.docs
gene_ids = [getattr(doc, 'attr')['gene_id'][1:-1] for doc in docs]
query = ElasticQuery.filtered(Query.match_all(), TermsFilter.get_terms_filter('ensg', gene_ids))
agg = Agg('ensg_agg', "terms", {"field": "ensg", "size": 0})
res = Search(idx=ElasticSettings.idx('CP_TARGET_'+targetIdx), search_query=query, aggs=Aggs(agg),
size=0).search()
ensg_count = res.aggs['ensg_agg'].get_buckets()
gene_ids = [g['key'] for g in ensg_count]
for d in resultObj2.docs:
if getattr(d, "attr")["gene_id"].replace('\"', '') in gene_ids:
geneResults.append({
'gene_name': getattr(d, "attr")["gene_name"].replace('\"', ''),
'gene_id': getattr(d, "attr")["gene_id"].replace('\"', ''),
'location': "chr" + getattr(d, "seqid") + ":" +
locale.format_string("%d", getattr(d, "start"), grouping=True) + ".." +
locale.format_string("%d", getattr(d, "end"), grouping=True),
})
if len(geneResults) == 0:
retJSON = {'error': 'Gene name '+searchTerm+' not found in this dataset.'}
return JsonResponse(retJSON)
elif len(geneResults) > 1:
retJSON = {
'error': 'Gene name <strong>'+searchTerm+'</strong> returns too many hits, please select your prefered result from the list below.',
'results': geneResults,
'cols': ['HGNC Symbol', 'Ensembl Gene ID', 'Location']
}
return JsonResponse(retJSON)
query_bool = BoolQuery()
query_bool.must([RangeQuery("dist", gte=-2e6, lte=2e6)])
query_bool = _add_tissue_filter(query_bool, targetIdx)
query = ElasticQuery.filtered_bool(Query.query_string(searchTerm, fields=["name", "ensg", "oeName"]),
query_bool, sources=utils.hicFields + utils.tissues['CP_TARGET_'+targetIdx])
(hic, segmin, segmax) = _build_hic_query(query, targetIdx)
if "error" in hic:
return JsonResponse(hic)
if len(hic) == 0:
retJSON = {'error': 'Gene name '+searchTerm+' not found in this dataset.'}
return JsonResponse(retJSON)
chrom = hic[0]['baitChr']
try:
chrom
except NameError:
retJSON = {'error': 'No chromosome defined for search'}
return JsonResponse(retJSON)
# get genes based on this segment
genes = _build_gene_query(chrom, segmin, segmax)
(snps, snpMeta) = _build_snp_query(snpTrack, chrom, segmin, segmax)
frags = _build_frags_query(getattr(chicp_settings, 'DEFAULT_FRAG'), chrom, segmin, segmax)
addList = utils.makeRelative(int(segmin), int(segmax), ['start', 'end'], addList)
retJSON = {"hic": hic,
"frags": frags,
"meta": {"ostart": int(segmin),
"oend": int(segmax),
"rstart": 1,
"rend": int(segmax) - int(segmin),
"rchr": str(chrom),
"tissues": utils.tissues['CP_TARGET_'+targetIdx]},
"snps": snps,
"snp_meta": snpMeta,
"genes": genes,
"region": str(chrom) + ":" + str(segmin) + "-" + str(segmax),
"blueprint": blueprint,
"extra": addList
}
response = JsonResponse(retJSON)
return response