From 783b04be1e3712ae4595cc6c73ebfb6328cc398f Mon Sep 17 00:00:00 2001
From: William Hayes <william.s.hayes@gmail.com>
Date: Fri, 13 Nov 2020 15:16:02 -0500
Subject: [PATCH] fixed naked nsarg species bug

---
 bel/resources/namespace.py | 16 +++++++++++-----
 bel/terms/terms.py         |  9 +++++----
 2 files changed, 16 insertions(+), 9 deletions(-)

diff --git a/bel/resources/namespace.py b/bel/resources/namespace.py
index aea237e..6dd74fc 100644
--- a/bel/resources/namespace.py
+++ b/bel/resources/namespace.py
@@ -218,9 +218,9 @@ def terms_iterator_for_arangodb(f: IO, version: str):
         term_key = term["key"]
         namespace = term["namespace"]
 
-        species_id = term.get("species_id", None)
-        # Skip if species not listed in species_list
-        if species_list and species_id and species_id not in species_list:
+        # Skip if species not listed in config species_list
+        species_key = term.get("species_key", None)
+        if species_list and species_key and species_key not in species_list:
             continue
 
         # Can't use original key formatted for Arangodb as some keys are longer than allowed (_key < 255 chars)
@@ -346,8 +346,8 @@ def terms_iterator_for_elasticsearch(f: IO, index_name: str, statistics: dict):
             ns, id_ = equivalence.split(":", 1)
             statistics["equivalenced_namespaces"][ns] += 1
 
-        # Filter species if enabled in config
-        species_key = term.get("species_key", "")
+        # Skip if species not listed in config species_list
+        species_key = term.get("species_key", None)
         if species_list and species_key and species_key not in species_list:
             continue
 
@@ -362,6 +362,12 @@ def terms_iterator_for_elasticsearch(f: IO, index_name: str, statistics: dict):
         term.pop("parent_keys", "")
         term.pop("equivalence_keys", "")
 
+        # Must not have species_key attribute to allow naked NSArg queries with filtered species
+        #    but allow non-species terms to be matched as well
+        if term.get("species_key", "") == "":
+            term.pop("species_key")
+            term.pop("species_label")
+
         record = {
             "_op_type": "index",
             "_index": index_name,
diff --git a/bel/terms/terms.py b/bel/terms/terms.py
index 407de18..9c00e8e 100644
--- a/bel/terms/terms.py
+++ b/bel/terms/terms.py
@@ -338,11 +338,12 @@ def get_term_completions(
     if entity_types:
         grp = [et for et in entity_types if et in settings.species_entity_types]
 
-    if grp and species_keys:
-        if isinstance(species_keys, str):
-            species_keys = [species_keys]
+    if isinstance(species_keys, str):
+        species_keys = [species_keys]
 
-        # Allow non-species specific terms to be found
+    # Allow non-species specific terms to be found along with species=[species_keys]
+    #   grp is set if inside a function and if not entity_types and annotation_types are None
+    if species_keys and (grp or (not entity_types and not annotation_types)):
         filters.append(
             {
                 "bool": {