diff options
Diffstat (limited to 'wqflask/wqflask/do_search.py')
| -rw-r--r--[-rwxr-xr-x] | wqflask/wqflask/do_search.py | 67 |
1 files changed, 25 insertions, 42 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index d89facfe..ad3eab79 100755..100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -1,6 +1,3 @@ -#!/usr/bin/python - - from __future__ import print_function, division import string @@ -11,10 +8,13 @@ from MySQLdb import escape_string as escape from pprint import pformat as pf import sys -sys.path.append("..") +# sys.path.append("..") Never in a running webserver -from dbFunction import webqtlDatabaseFunction +from db import webqtlDatabaseFunction +import logging +from utility.logger import getLogger +logger = getLogger(__name__) class DoSearch(object): """Parent class containing parameters/functions used for all searches""" @@ -30,15 +30,15 @@ class DoSearch(object): self.dataset = dataset if self.dataset: - print("self.dataset is boo: ", type(self.dataset), pf(self.dataset)) - print("self.dataset.group is: ", pf(self.dataset.group)) + logger.debug("self.dataset is boo: ", type(self.dataset), pf(self.dataset)) + logger.debug("self.dataset.group is: ", pf(self.dataset.group)) #Get group information for dataset and the species id self.species_id = webqtlDatabaseFunction.retrieve_species_id(self.dataset.group.name) def execute(self, query): """Executes query and returns results""" query = self.normalize_spaces(query) - print("in do_search query is:", pf(query)) + logger.sql(query) results = g.db.execute(query, no_parameters=True).fetchall() return results @@ -56,7 +56,7 @@ class DoSearch(object): def mescape(self, *items): """Multiple escape""" escaped = [escape(str(item)) for item in items] - print("escaped is:", escaped) + logger.debug("escaped is:", escaped) return tuple(escaped) def normalize_spaces(self, stringy): @@ -66,13 +66,13 @@ class DoSearch(object): @classmethod def get_search(cls, search_type): - print("search_types are:", pf(cls.search_types)) + logger.debug("search_types are:", pf(cls.search_types)) search_type_string = search_type['dataset_type'] if 'key' in search_type: search_type_string += '_' + search_type['key'] - print("search_type_string is:", search_type_string) + logger.debug("search_type_string is:", search_type_string) if search_type_string in cls.search_types: return cls.search_types[search_type_string] @@ -100,7 +100,7 @@ class QuickMrnaAssaySearch(DoSearch): def run(self): """Generates and runs a search for assays across all mRNA expression datasets""" - print("Running ProbeSetSearch") + logger.debug("Running ProbeSetSearch") query = self.base_query + """WHERE (MATCH (ProbeSet.Name, ProbeSet.description, ProbeSet.symbol, @@ -108,8 +108,6 @@ class QuickMrnaAssaySearch(DoSearch): AGAINST ('%s' IN BOOLEAN MODE)) """ % (escape(self.search_term[0])) - print("final query is:", pf(query)) - return self.execute(query) @@ -175,15 +173,12 @@ class MrnaAssaySearch(DoSearch): """ % (escape(from_clause), where_clause, escape(str(self.dataset.id)))) - - #print("query is:", pf(query)) - return query def run_combined(self, from_clause = '', where_clause = ''): """Generates and runs a combined search of an mRNA expression dataset""" - print("Running ProbeSetSearch") + logger.debug("Running ProbeSetSearch") #query = self.base_query + from_clause + " WHERE " + where_clause from_clause = self.normalize_spaces(from_clause) @@ -198,19 +193,15 @@ class MrnaAssaySearch(DoSearch): where_clause, escape(str(self.dataset.id)))) - print("final query is:", pf(query)) - return self.execute(query) def run(self): """Generates and runs a simple search of an mRNA expression dataset""" - print("Running ProbeSetSearch") + logger.debug("Running ProbeSetSearch") where_clause = self.get_where_clause() query = self.base_query + "WHERE " + where_clause + "ORDER BY ProbeSet.symbol ASC" - #print("final query is:", pf(query)) - return self.execute(query) @@ -290,14 +281,12 @@ class PhenotypeSearch(DoSearch): escape(str(self.dataset.group.id)), escape(str(self.dataset.id)))) - print("query is:", pf(query)) - return query def run_combined(self, from_clause, where_clause): """Generates and runs a combined search of an phenotype dataset""" - print("Running PhenotypeSearch") + logger.debug("Running PhenotypeSearch") from_clause = self.normalize_spaces(from_clause) @@ -313,9 +302,6 @@ class PhenotypeSearch(DoSearch): escape(str(self.dataset.group.id)), escape(str(self.dataset.id)))) - print("final query is:", pf(query)) - - return self.execute(query) def run(self): @@ -364,8 +350,6 @@ class QuickPhenotypeSearch(PhenotypeSearch): PublishXRef.InbredSetId = InbredSet.Id and InbredSet.SpeciesId = Species.Id""" % where_clause) - print("query is:", pf(query)) - return query def run(self): @@ -408,7 +392,7 @@ class GenotypeSearch(DoSearch): where_clause.append('''%s REGEXP "%s"''' % ("%s.%s" % self.mescape(self.dataset.type, field), self.search_term)) - print("hello ;where_clause is:", pf(where_clause)) + logger.debug("hello ;where_clause is:", pf(where_clause)) where_clause = "(%s) " % ' OR '.join(where_clause) return where_clause @@ -432,8 +416,6 @@ class GenotypeSearch(DoSearch): and GenoFreeze.Id = %s"""% (where_clause, escape(str(self.dataset.id)))) - print("query is:", pf(query)) - return query def run(self): @@ -586,7 +568,7 @@ class LrsSearch(DoSearch): self.species_id) else: # Deal with >, <, >=, and <= - print("self.search_term is:", self.search_term) + logger.debug("self.search_term is:", self.search_term) where_clause = """ %sXRef.LRS %s %s """ % self.mescape(self.dataset.type, self.search_operator, self.search_term[0]) @@ -787,7 +769,7 @@ class MeanSearch(MrnaAssaySearch): def get_final_query(self): self.where_clause = self.get_where_clause() - print("where_clause is:", pf(self.where_clause)) + logger.debug("where_clause is:", pf(self.where_clause)) self.query = self.compile_final_query(where_clause = self.where_clause) @@ -795,7 +777,7 @@ class MeanSearch(MrnaAssaySearch): def run(self): self.where_clause = self.get_where_clause() - print("where_clause is:", pf(self.where_clause)) + logger.debug("where_clause is:", pf(self.where_clause)) self.query = self.compile_final_query(where_clause = self.where_clause) @@ -825,7 +807,7 @@ class RangeSearch(MrnaAssaySearch): WHERE ProbeSetData.Id = ProbeSetXRef.dataId) > %s """ % (escape(self.search_term[0])) - print("where_clause is:", pf(where_clause)) + logger.debug("where_clause is:", pf(where_clause)) return where_clause @@ -927,10 +909,11 @@ class PvalueSearch(MrnaAssaySearch): self.search_operator, self.search_term[0]) - print("where_clause is:", pf(self.where_clause)) + logger.debug("where_clause is:", pf(self.where_clause)) self.query = self.compile_final_query(where_clause = self.where_clause) + logger.sql(self.query) return self.execute(self.query) class AuthorSearch(PhenotypeSearch): @@ -966,7 +949,7 @@ if __name__ == "__main__": from base.data_set import create_dataset from base.templatePage import templatePage from utility import webqtlUtil - from dbFunction import webqtlDatabaseFunction + from db import webqtlDatabaseFunction db_conn = MySQLdb.Connect(db=webqtlConfig.DB_NAME, host=webqtlConfig.MYSQL_SERVER, @@ -992,7 +975,7 @@ if __name__ == "__main__": # ProbeSet.Id = ProbeSetXRef.ProbeSetId and # ProbeSetXRef.ProbeSetFreezeId = 112""") - #print(pf(cursor.fetchall())) + #logger.debug(pf(cursor.fetchall())) #results = ProbeSetSearch("shh", None, dataset, cursor, db_conn).run() results = PvalueSearch(['0.005'], '<', dataset, cursor, db_conn).run() #results = RifSearch("diabetes", dataset, cursor, db_conn).run() @@ -1004,4 +987,4 @@ if __name__ == "__main__": #results = GenotypeSearch("rs13475699", dataset, cursor, db_conn).run() #results = GoSearch("0045202", dataset, cursor, db_conn).run() - print("results are:", pf(results)) + logger.debug("results are:", pf(results)) |