diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/do_search.py | 25 | ||||
| -rw-r--r-- | wqflask/wqflask/search_results.py | 144 |
2 files changed, 76 insertions, 93 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 1e245d6a..fa18c10b 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -961,31 +961,6 @@ def is_number(s): return False -def get_aliases(symbol, species): - if species == "mouse": - symbol_string = symbol.capitalize() - elif species == "human": - symbol_string = symbol.upper() - else: - return [] - - filtered_aliases = [] - response = requests.get( - GN2_BASE_URL + "/gn3/gene/aliases/" + symbol_string) - if response: - alias_list = json.loads(response.content) - - 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 diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 858ca56d..52303c91 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -231,33 +231,6 @@ class SearchResultPage: # The same table can't be referenced twice in the from clause previous_from_clauses = [] - symbol_list = [] - if self.dataset.type == "ProbeSet": - for a_search in self.search_terms: - if a_search['key'] == None: - symbol_list.append(a_search['search_term'][0]) - - alias_terms = get_aliases(symbol_list, self.dataset.group.species) - - for i, a_search in enumerate(alias_terms): - the_search = self.get_search_ob(a_search) - if the_search != None: - get_from_clause = getattr( - the_search, "get_from_clause", None) - if callable(get_from_clause): - from_clause = the_search.get_from_clause() - if from_clause in previous_from_clauses: - pass - else: - previous_from_clauses.append(from_clause) - combined_from_clause += from_clause - where_clause = the_search.get_alias_where_clause() - combined_where_clause += "(" + where_clause + ")" - if self.and_or == "and": - combined_where_clause += "AND" - else: - combined_where_clause += "OR" - for i, a_search in enumerate(self.search_terms): if a_search['key'] == "GO": self.go_term = a_search['search_term'][0] @@ -267,28 +240,69 @@ class SearchResultPage: else: the_search = self.get_search_ob(a_search) if the_search != None: - get_from_clause = getattr( - the_search, "get_from_clause", None) - if callable(get_from_clause): - from_clause = the_search.get_from_clause() - if from_clause in previous_from_clauses: - pass - else: - previous_from_clauses.append(from_clause) - combined_from_clause += from_clause - where_clause = the_search.get_where_clause() - combined_where_clause += "(" + where_clause + ")" - if (i + 1) < len(self.search_terms): - if self.and_or == "and": - combined_where_clause += "AND" - else: - combined_where_clause += "OR" + if a_search['key'] == None and self.dataset.type == "ProbeSet": + alias_terms = get_alias_terms(a_search['search_term'][0], self.dataset.group.species) + alias_where_clauses = [] + for alias_search in alias_terms: + alias_search_ob = self.get_search_ob(alias_search) + if alias_search_ob != None: + get_from_clause = getattr( + alias_search_ob, "get_from_clause", None) + if callable(get_from_clause): + from_clause = alias_search_ob.get_from_clause() + if from_clause in previous_from_clauses: + pass + else: + previous_from_clauses.append(from_clause) + combined_from_clause += from_clause + where_clause = alias_search_ob.get_alias_where_clause() + alias_where_clauses.append(where_clause) + + get_from_clause = getattr( + the_search, "get_from_clause", None) + if callable(get_from_clause): + from_clause = the_search.get_from_clause() + if from_clause in previous_from_clauses: + pass + else: + previous_from_clauses.append(from_clause) + combined_from_clause += from_clause + + where_clause = the_search.get_where_clause() + alias_where_clauses.append(where_clause) + + combined_where_clause += "(" + " OR ".join(alias_where_clauses) + ")" + if (i + 1) < len(self.search_terms): + if self.and_or == "and": + combined_where_clause += "AND" + else: + combined_where_clause += "OR" + else: + get_from_clause = getattr( + the_search, "get_from_clause", None) + if callable(get_from_clause): + from_clause = the_search.get_from_clause() + if from_clause in previous_from_clauses: + pass + else: + previous_from_clauses.append(from_clause) + combined_from_clause += from_clause + + where_clause = the_search.get_where_clause() + combined_where_clause += "(" + where_clause + ")" + if (i + 1) < len(self.search_terms): + if self.and_or == "and": + combined_where_clause += "AND" + else: + combined_where_clause += "OR" else: self.search_term_exists = False + if self.search_term_exists: combined_where_clause = "(" + combined_where_clause + ")" final_query = the_search.compile_final_query( combined_from_clause, combined_where_clause) + results = the_search.execute(final_query) self.results.extend(results) @@ -345,39 +359,33 @@ def insert_newlines(string, every=64): return '\n'.join(lines) -def get_aliases(symbol_list, species): - - updated_symbols = [] - for symbol in symbol_list: - if species == "mouse": - updated_symbols.append(symbol.capitalize()) - elif species == "human": - updated_symbols.append(symbol.upper()) - else: - updated_symbols.append(symbol) - - symbols_string = ",".join(updated_symbols) +def get_alias_terms(symbol, species): + if species == "mouse": + symbol_string = symbol.capitalize() + elif species == "human": + symbol_string = symbol.upper() + else: + return [] filtered_aliases = [] response = requests.get( - GN2_BASE_URL + "gn3/gene/aliases/" + symbols_string) - + GN2_BASE_URL + "/gn3/gene/aliases/" + symbol_string) if response: - alias_lists = json.loads(response.content) + alias_list = json.loads(response.content) + seen = set() - for aliases in alias_lists: - for item in aliases[1]: - if item in seen: - continue - else: - filtered_aliases.append(item) - seen.add(item) + for item in alias_list: + if item in seen: + continue + else: + filtered_aliases.append(item) + seen.add(item) - search_terms = [] + alias_terms = [] for alias in filtered_aliases: the_search_term = {'key': None, 'search_term': [alias], 'separator': None} - search_terms.append(the_search_term) + alias_terms.append(the_search_term) - return search_terms + return alias_terms |