Upgrade to biothings 0.9.1

biothings · Mar 26, 2021 · cb9c113 · cb9c113
1 parent 29125c2
commit cb9c113
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Showing 3 changed files with 5 additions and 5 deletions.
diff --git a/requirements_web.txt b/requirements_web.txt
@@ -1,5 +1,5 @@
 # biothings
-biothings[web_extra]==0.8.5
+biothings[web_extra]==0.9.1
 elasticsearch==6.3.1
 elasticsearch-dsl==6.3.1
 

diff --git a/src/config_web.py b/src/config_web.py
@@ -22,7 +22,7 @@
 API_VERSION = 'v1'
 APP_LIST = [
     (r'/v1/variant/(chr.{1,2}):(?!g\.)[g\.]{0,2}(\d+.*)', 'tornado.web.RedirectHandler', {'url': '/v1/variant/{0}:g.{1}'}),
-] + APP_LIST + [
+    *APP_LIST,
     (r"/{pre}/metadata/fields/?", 'web.handlers.MVMetadataFieldHandler'),
     (r"/{pre}/metadata/?", 'web.handlers.MVMetadataSourceHandler'),
     (r"/{pre}/{ver}/metadata/fields/?", 'web.handlers.MVMetadataFieldHandler'),

diff --git a/src/web/pipeline.py b/src/web/pipeline.py
@@ -4,7 +4,8 @@
 from biothings.web.pipeline import ESQueryBuilder, ESQueryBackend
 
 
-INTERVAL_PATTERN = re.compile(r'(?P<pre_query>.+(?P<pre_and>[Aa][Nn][Dd]))*(?P<interval>\s*chr(?P<chr>[1-9xXyYmM][0-9tT]?):(?P<gstart>[0-9,]+)-(?P<gend>[0-9,]+)\s*)(?P<post_query>(?P<post_and>[Aa][Nn][Dd]).+)*')
+INTERVAL_PATTERN = re.compile(
+    r'(?P<pre_query>.+(?P<pre_and>[Aa][Nn][Dd]))*(?P<interval>\s*chr(?P<chr>[1-9xXyYmM][0-9tT]?):(?P<gstart>[0-9,]+)-(?P<gend>[0-9,]+)\s*)(?P<post_query>(?P<post_and>[Aa][Nn][Dd]).+)*')
 SNP_PATTERN = re.compile(r'(?P<pre_query>.+(?P<pre_and>[Aa][Nn][Dd]))*(?P<interval>\s*chr(?P<chr>[1-9xXyYmM][0-9tT]?):(?P<gend>(?P<gstart>[0-9,]+))\s*)(?P<post_query>(?P<post_and>[Aa][Nn][Dd]).+)*')
 PATTERNS = [INTERVAL_PATTERN, SNP_PATTERN]
 
@@ -41,7 +42,7 @@ def default_string_query(self, q, options):
             search = search.filter('range', **{assembly + ".end": {"gte": match['gstart']}})
 
         else:  # default query
-            search = AsyncSearch().query("query_string", query=q)
+            search = super().default_string_query(q, options)
 
         return search
 
@@ -55,4 +56,3 @@ def execute(self, query, options):
             options.biothing_type = 'hg38'
 
         return super().execute(query, options)
-