Merge branch 'v3'

requirements_web.txt

@@ -3,4 +3,4 @@ biothings[web_extra]==0.8.1
 elasticsearch==6.3.1
 elasticsearch-dsl==6.3.1
 #Optional
-raven
+raven

src/config_hub.py

@@ -214,7 +214,25 @@
 CACHE_FOLDER = None
 
 # when publishing releases, specify the targetted (ie. required) standalone version
-STANDALONE_VERSION = "standalone_v3"
+STANDALONE_VERSION = {"branch": "standalone_v3"}
+
+# Autohub configuration, either from a static definition...
+STANDALONE_CONFIG = {
+    "_default": {
+        "es_host": "localhost:9200",
+        "index": "mygene_test",
+        "doc_type": "gene"
+    },
+    "mygene.info": {
+        "es_host": "prodserver:9200",
+        "index": "mygene_prod",
+        "doc_type": "gene"
+    },
+}
+# ... or using a dynamic indexer factory and ES host (index names are then
+# taken from VERSION_URLS and all are managed on one given ES host)
+#AUTOHUB_INDEXER_FACTORY = "biothings.hub.dataindex.indexer.DynamicIndexerFactory"
+#AUTOHUB_ES_HOST = "localhost:9200"
 
 # Autohub configuration, either from a static definition...
 STANDALONE_CONFIG = {

src/config_web.py

@@ -145,7 +145,7 @@
 # Elasticsearch Query Pipeline
 # *****************************************************************************
 ES_QUERY_BUILDER = "web.pipeline.MygeneQueryBuilder"
-
+ES_RESULT_TRANSFORM = "web.pipeline.MygeneTransform"
 AVAILABLE_FIELDS_EXCLUDED = ['all', 'accession_agg', 'refseq_agg']
 
 # *****************************************************************************

src/web/pipeline/__init__.py

@@ -1 +1,2 @@
-from .build import MygeneQueryBuilder
+from .build import MygeneQueryBuilder
+from .transform import MygeneTransform

src/web/pipeline/transform.py

@@ -0,0 +1,14 @@
+from biothings.web.pipeline import ESResultTransform
+
+class MygeneTransform(ESResultTransform):
+
+    @staticmethod
+    def option_sorted(path, obj):
+        """
+        Sort a container in-place.
+        """
+        if path == 'homologene.genes':
+            return # do not sort this field
+
+        # delegate to super class for normal cases
+        ESResultTransform.option_sorted(path, obj)