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-rw-r--r--wqflask/base/data_set.py41
1 files changed, 11 insertions, 30 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 2f1549ae..0d4ac24b 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -18,13 +18,14 @@
#
# This module is used by GeneNetwork project (www.genenetwork.org)
-from __future__ import absolute_import, print_function, division
from db.call import fetchall, fetchone, fetch1
from utility.logger import getLogger
from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists, GN2_BASE_URL
from db.gn_server import menu_main
from pprint import pformat as pf
-from MySQLdb import escape_string as escape
+from utility.db_tools import escape
+from utility.db_tools import mescape
+from utility.db_tools import create_in_clause
from maintenance import get_group_samplelists
from utility.tools import locate, locate_ignore_error, flat_files
from utility import gen_geno_ob
@@ -34,7 +35,6 @@ from utility import webqtlUtil
from db import webqtlDatabaseFunction
from base import species
from base import webqtlConfig
-import reaper
from flask import Flask, g
import os
import math
@@ -45,7 +45,7 @@ import codecs
import json
import requests
import gzip
-import cPickle as pickle
+import pickle as pickle
import itertools
from redis import Redis
@@ -209,20 +209,6 @@ def create_datasets_list():
return datasets
-def create_in_clause(items):
- """Create an in clause for mysql"""
- in_clause = ', '.join("'{}'".format(x) for x in mescape(*items))
- in_clause = '( {} )'.format(in_clause)
- return in_clause
-
-
-def mescape(*items):
- """Multiple escape"""
- escaped = [escape(str(item)) for item in items]
- #logger.debug("escaped is:", escaped)
- return escaped
-
-
class Markers(object):
"""Todo: Build in cacheing so it saves us reading the same file more than once"""
@@ -257,12 +243,12 @@ class Markers(object):
logger.debug("length of self.markers:", len(self.markers))
logger.debug("length of p_values:", len(p_values))
- if type(p_values) is list:
+ if isinstance(p_values, list):
# THIS IS only needed for the case when we are limiting the number of p-values calculated
# if len(self.markers) > len(p_values):
# self.markers = self.markers[:len(p_values)]
- for marker, p_value in itertools.izip(self.markers, p_values):
+ for marker, p_value in zip(self.markers, p_values):
if not p_value:
continue
marker['p_value'] = float(p_value)
@@ -273,7 +259,7 @@ class Markers(object):
marker['lod_score'] = -math.log10(marker['p_value'])
# Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values
marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61
- elif type(p_values) is dict:
+ elif isinstance(p_values, dict):
filtered_markers = []
for marker in self.markers:
#logger.debug("marker[name]", marker['name'])
@@ -459,12 +445,7 @@ class DatasetGroup(object):
full_filename = str(locate(self.genofile, 'genotype'))
else:
full_filename = str(locate(self.name + '.geno', 'genotype'))
-
- if use_reaper:
- genotype_1 = reaper.Dataset()
- genotype_1.read(full_filename)
- else:
- genotype_1 = gen_geno_ob.genotype(full_filename)
+ genotype_1 = gen_geno_ob.genotype(full_filename)
if genotype_1.type == "group" and self.parlist:
genotype_2 = genotype_1.add(
@@ -707,7 +688,7 @@ class DataSet(object):
else:
query = "SELECT {}.Name,".format(escape(dataset_type))
data_start_pos = 1
- query += string.join(temp, ', ')
+ query += ', '.join(temp)
query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(dataset_type,
self.type,
self.type))
@@ -1053,9 +1034,9 @@ class MrnaAssayDataSet(DataSet):
# XZ, 12/08/2008: description
# XZ, 06/05/2009: Rob asked to add probe target description
- description_string = unicode(
+ description_string = str(
str(this_trait.description).strip(codecs.BOM_UTF8), 'utf-8')
- target_string = unicode(
+ target_string = str(
str(this_trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
if len(description_string) > 1 and description_string != 'None':