diff options
Diffstat (limited to 'gn2')
| -rw-r--r-- | gn2/wqflask/search_results.py | 207 |
1 files changed, 125 insertions, 82 deletions
diff --git a/gn2/wqflask/search_results.py b/gn2/wqflask/search_results.py index ad92d8c7..1add4fcd 100644 --- a/gn2/wqflask/search_results.py +++ b/gn2/wqflask/search_results.py @@ -2,6 +2,7 @@ import uuid from math import * import requests import unicodedata +from urllib.parse import urlencode, urljoin import re import json @@ -17,10 +18,9 @@ from gn2.wqflask.database import database_connection from gn2.utility import hmac from gn2.utility.authentication_tools import check_resource_availability -from gn2.utility.tools import get_setting, GN2_BASE_URL +from gn2.utility.tools import get_setting, GN2_BASE_URL, GN3_LOCAL_URL from gn2.utility.type_checking import is_str - class SearchResultPage: #maxReturn = 3000 @@ -36,7 +36,7 @@ class SearchResultPage: self.uc_id = uuid.uuid4() self.go_term = None - self.type = kw['search_type'] + self.search_type = kw['search_type'] if kw['search_terms_or']: self.and_or = "or" @@ -230,89 +230,92 @@ class SearchResultPage: """ self.search_terms = parser.parse(self.search_terms) - combined_from_clause = "" - combined_where_clause = "" - # The same table can't be referenced twice in the from clause - previous_from_clauses = [] - - for i, a_search in enumerate(self.search_terms): - if a_search['key'] == "GO": - self.go_term = a_search['search_term'][0] - gene_list = get_GO_symbols(a_search) - self.search_terms += gene_list - continue - else: - the_search = self.get_search_ob(a_search) - if the_search != None: - 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" + if self.search_type == "xapian": + self.results = requests.get(generate_xapian_request(self.dataset, self.search_terms, self.and_or)).json() + else: + combined_from_clause = "" + combined_where_clause = "" + # The same table can't be referenced twice in the from clause + previous_from_clauses = [] + + for i, a_search in enumerate(self.search_terms): + if a_search['key'] == "GO": + self.go_term = a_search['search_term'][0] + gene_list = get_GO_symbols(a_search) + self.search_terms += gene_list + continue else: - self.search_term_exists = False + the_search = self.get_search_ob(a_search) + if the_search != None: + 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) + 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) + results = the_search.execute(final_query) + self.results.extend(results) - if self.search_term_exists: - if the_search != None: - self.header_fields = the_search.header_fields + if self.search_term_exists: + if the_search != None: + self.header_fields = the_search.header_fields def get_search_ob(self, a_search): search_term = a_search['search_term'] @@ -432,3 +435,43 @@ def get_alias_terms(symbol, species): alias_terms.append(the_search_term) return alias_terms + +def generate_xapian_request(dataset, search_terms, and_or): + match dataset.type: + case "ProbeSet": + search_type = "gene" + case "Publish": + search_type = "phenotype" + case "Geno": + search_type = "genotype" + case _: # This should never happen, not sure if it's necessary + search_type = "gene" + + xapian_terms = and_or.join([create_xapian_term(dataset, term) for term in search_terms]) + + return urljoin(GN3_LOCAL_URL, "/api/search?" + urlencode({"query": xapian_terms, + "type": search_type})) + +def create_xapian_term(dataset, term): + search_term = term['search_term'] + xapian_term = f"species:{dataset.group.species} AND group:{dataset.group.name} AND dataset:{dataset.name} AND " + match term['key']: + case 'MEAN': + return xapian_term + f"mean:{search_term[0]}..{search_term[1]}" + case 'POSITION': + return xapian_term + f"chr:{search_term[0].lower().replace('chr', '')} AND position:{search_term[1]}..{search_term[2]}" + case 'AUTHOR': + return xapian_term + f"author:{search_term[0]}" + case 'LRS': + xapian_term += f"peak:{search_term[0]}..{search_term[1]}" + if len(term) == 5: + xapian_term += f"peakchr:{search_term[2].lower().replace('chr', '')} AND peakmb:{search_term[3]}..{search_term[4]}" + return xapian_term + case 'LOD': # Basically just LRS search but all values are multiplied by 4.61 + xapian_term += f"peak:{float(search_term[0]) * 4.61}..{float(search_term[1]) * 4.61}" + if len(term) == 5: + xapian_term += f"peakchr:{search_term[2].lower().replace('chr', '')} AND " + xapian_term += f"peakmb:{float(search_term[3]) * 4.61}..{float(search_term[4]) * 4.61}" + return xapian_term + case None: + return xapian_term + f"{search_term[0]}"
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