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-rw-r--r--wqflask/wqflask/do_search.py58
1 files changed, 29 insertions, 29 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 04fd0688..48212877 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
@@ -15,6 +12,9 @@ import sys
from dbFunction import webqtlDatabaseFunction
+import logging
+from utility.logger import getLogger
+logger = getLogger(__name__ , level = logging.INFO)
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.debug("in do_search query is:", pf(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,
@@ -108,7 +108,7 @@ class QuickMrnaAssaySearch(DoSearch):
AGAINST ('%s' IN BOOLEAN MODE))
""" % (escape(self.search_term[0]))
- print("final query is:", pf(query))
+ logger.debug("final query is:", pf(query))
return self.execute(query)
@@ -176,14 +176,14 @@ class MrnaAssaySearch(DoSearch):
where_clause,
escape(str(self.dataset.id))))
- #print("query is:", pf(query))
+ #logger.debug("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)
@@ -198,18 +198,18 @@ class MrnaAssaySearch(DoSearch):
where_clause,
escape(str(self.dataset.id))))
- print("final query is:", pf(query))
+ logger.debug("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))
+ #logger.debug("final query is:", pf(query))
return self.execute(query)
@@ -290,14 +290,14 @@ class PhenotypeSearch(DoSearch):
escape(str(self.dataset.group.id)),
escape(str(self.dataset.id))))
- print("query is:", pf(query))
+ logger.debug("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)
@@ -313,7 +313,7 @@ class PhenotypeSearch(DoSearch):
escape(str(self.dataset.group.id)),
escape(str(self.dataset.id))))
- print("final query is:", pf(query))
+ logger.debug("final query is:", pf(query))
return self.execute(query)
@@ -364,7 +364,7 @@ class QuickPhenotypeSearch(PhenotypeSearch):
PublishXRef.InbredSetId = InbredSet.Id and
InbredSet.SpeciesId = Species.Id""" % where_clause)
- print("query is:", pf(query))
+ logger.debug("query is:", pf(query))
return query
@@ -408,7 +408,7 @@ 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
@@ -432,7 +432,7 @@ class GenotypeSearch(DoSearch):
and GenoFreeze.Id = %s"""% (where_clause,
escape(str(self.dataset.id))))
- print("query is:", pf(query))
+ logger.debug("query is:", pf(query))
return query
@@ -586,7 +586,7 @@ 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 +787,7 @@ 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 +795,7 @@ 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 +825,7 @@ 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
@@ -927,7 +927,7 @@ 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)
@@ -992,7 +992,7 @@ 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 +1004,4 @@ 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))
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-21 12:24:41 +0000