From 8e22a5cc4ee6a3fc110d892065377dc2af6c3563 Mon Sep 17 00:00:00 2001
From: Pedro Assis <pedroh@stanford.edu>
Date: Fri, 25 Jun 2021 13:49:39 -1000
Subject: [PATCH] redirecting region search to data services

---
 src/encoded/genomic_data_service.py | 18 ++++++++++++++++++
 src/encoded/region_search.py        | 27 ++++++++++++---------------
 2 files changed, 30 insertions(+), 15 deletions(-)

diff --git a/src/encoded/genomic_data_service.py b/src/encoded/genomic_data_service.py
index 4f8c39b50b7..1f1b7bd25eb 100644
--- a/src/encoded/genomic_data_service.py
+++ b/src/encoded/genomic_data_service.py
@@ -14,6 +14,7 @@
 ]
 RNA_GET_EXPRESSIONS = '/expressions/bytes'
 RNA_GET_AUTOCOMPLETE = '/autocomplete'
+REGION_SEARCH = '/region-search'
 
 # react component orders columns by "the position" in the hash map
 RNA_GET_COLUMNS = {
@@ -262,3 +263,20 @@ def rna_get(self):
             }
 
         return response
+
+
+    def region_search(self, assembly, chromosome, start, end):
+        params = {
+            'assembly': assembly,
+            'chr': chromosome.replace('chr', ''),
+            'start': start,
+            'end': end
+        }
+
+        query_params = '&'.join([f'{k}={params[k]}' for k in params.keys()])
+
+        url = f'{self.path}{REGION_SEARCH}?{query_params}'
+
+        results = requests.get(url, timeout=3).json()
+
+        return results
diff --git a/src/encoded/region_search.py b/src/encoded/region_search.py
index 766fbd5a4c0..aabe3883174 100644
--- a/src/encoded/region_search.py
+++ b/src/encoded/region_search.py
@@ -8,6 +8,8 @@
 import requests
 from urllib.parse import urlencode
 
+from encoded.genomic_data_service import GenomicDataService
+
 import logging
 import re
 
@@ -253,6 +255,9 @@ def region_search(context, request):
     """
     Search files by region.
     """
+
+    data_service = GenomicDataService(context.registry, request)
+
     types = request.registry[TYPES]
     result = {
         '@id': '/region-search/' + ('?' + request.query_string.split('&referrer')[0] if request.query_string else ''),
@@ -314,25 +319,17 @@ def region_search(context, request):
             chr=chromosome, start=start, end=end
         )
 
-    # Search for peaks for the coordinates we got
     try:
-        # including inner hits is very slow
-        # figure out how to distinguish browser requests from .embed method requests
-        if 'peak_metadata' in request.query_string:
-            peak_query = get_peak_query(start, end, with_inner_hits=True, within_peaks=region_inside_peak_status)
-        else:
-            peak_query = get_peak_query(start, end, within_peaks=region_inside_peak_status)
-        peak_results = snp_es.search(body=peak_query,
-                                     index=chromosome.lower(),
-                                     doc_type=_GENOME_TO_ALIAS[assembly],
-                                     size=99999)
+        peak_results = data_service.region_search(_GENOME_TO_ALIAS[assembly], chromosome.lower(), start, end)
     except Exception:
         result['notification'] = 'Error during search'
         return result
+
     file_uuids = []
-    for hit in peak_results['hits']['hits']:
-        if hit['_id'] not in file_uuids:
-            file_uuids.append(hit['_id'])
+    for hit in peak_results['regions']:
+        region_uuid = hit['file_url'].split('/')[-1]
+        if region_uuid not in file_uuids:
+            file_uuids.append(region_uuid)
     file_uuids = list(set(file_uuids))
     result['notification'] = 'No results found'
 
@@ -363,7 +360,7 @@ def region_search(context, request):
         result['@graph'] = list(format_results(request, es_results['hits']['hits']))
         result['total'] = total = es_results['hits']['total']
         result['facets'] = format_facets(es_results, _FACETS, used_filters, schemas, total, principals)
-        result['peaks'] = list(peak_results['hits']['hits'])
+        result['peaks'] = list(peak_results['regions'])
         result['download_elements'] = get_peak_metadata_links(request)
         if result['total'] > 0:
             result['notification'] = 'Success'