diff options
Diffstat (limited to 'wqflask/wqflask/do_search.py')
| -rw-r--r-- | wqflask/wqflask/do_search.py | 30 |
1 files changed, 29 insertions, 1 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 8476649f..e0f4eb17 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -1,6 +1,8 @@ from __future__ import print_function, division import string +import requests +import json from flask import Flask, g @@ -108,6 +110,12 @@ class MrnaAssaySearch(DoSearch): def get_where_clause(self): + aliases = get_aliases(escape(self.search_term[0]), self.dataset.group.species) + if len(aliases) > 0: + search_string = " ".join(aliases) + else: + search_string = escape(self.search_term[0]) + if self.search_term[0] != "*": match_clause = """(MATCH (ProbeSet.Name, ProbeSet.description, @@ -117,7 +125,7 @@ class MrnaAssaySearch(DoSearch): UniGeneId, Probe_Target_Description) AGAINST ('%s' IN BOOLEAN MODE)) and - """ % (escape(self.search_term[0])) + """ % (search_string) else: match_clause = "" @@ -868,6 +876,26 @@ def is_number(s): except ValueError: return False +def get_aliases(symbol, species): + if species == "mouse": + symbol_string = symbol.capitalize() + elif species == "human": + symbol_string = symbol.upper() + + response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + symbol_string) + alias_list = json.loads(response.content) + + filtered_aliases = [] + seen = set() + for item in alias_list: + if item in seen: + continue + else: + filtered_aliases.append(item) + seen.add(item) + + return filtered_aliases + if __name__ == "__main__": ### Usually this will be used as a library, but call it from the command line for testing ### And it runs the code below |