diff options
Diffstat (limited to 'wqflask/base')
| -rw-r--r-- | wqflask/base/GeneralObject.py | 11 | ||||
| -rw-r--r-- | wqflask/base/data_set.py | 41 | ||||
| -rw-r--r-- | wqflask/base/mrna_assay_tissue_data.py | 7 | ||||
| -rw-r--r-- | wqflask/base/species.py | 9 | ||||
| -rw-r--r-- | wqflask/base/trait.py | 33 |
5 files changed, 33 insertions, 68 deletions
diff --git a/wqflask/base/GeneralObject.py b/wqflask/base/GeneralObject.py index 0fccaab3..0122ee32 100644 --- a/wqflask/base/GeneralObject.py +++ b/wqflask/base/GeneralObject.py @@ -33,7 +33,7 @@ class GeneralObject: def __init__(self, *args, **kw): self.contents = list(args) - for name, value in kw.items(): + for name, value in list(kw.items()): setattr(self, name, value) def __setitem__(self, key, value): @@ -50,16 +50,17 @@ class GeneralObject: def __str__(self): s = '' - for key in self.__dict__.keys(): + for key in list(self.__dict__.keys()): if key != 'contents': s += '%s = %s\n' % (key, self.__dict__[key]) return s def __repr__(self): s = '' - for key in self.__dict__.keys(): + for key in list(self.__dict__.keys()): s += '%s = %s\n' % (key, self.__dict__[key]) return s - def __cmp__(self, other): - return len(self.__dict__.keys()).__cmp__(len(other.__dict__.keys())) + def __eq__(self, other): + return (len(list(self.__dict__.keys())) == + len(list(other.__dict__.keys()))) diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index afffe780..295f5c48 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 @@ -207,20 +207,6 @@ 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""" @@ -255,12 +241,12 @@ 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) @@ -271,7 +257,7 @@ 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']) @@ -457,12 +443,7 @@ 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( @@ -705,7 +686,7 @@ 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)) @@ -1051,9 +1032,9 @@ 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': diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py index 6fec5dcd..f1929518 100644 --- a/wqflask/base/mrna_assay_tissue_data.py +++ b/wqflask/base/mrna_assay_tissue_data.py @@ -1,5 +1,3 @@ -from __future__ import absolute_import, print_function, division - import collections from flask import g @@ -7,9 +5,8 @@ from flask import g from utility import db_tools from utility import Bunch -from MySQLdb import escape_string as escape +from utility.db_tools import escape -from pprint import pformat as pf from utility.logger import getLogger logger = getLogger(__name__ ) @@ -92,4 +89,4 @@ class MrnaAssayTissueData(object): else: symbol_values_dict[result.Symbol.lower()].append(result.value) - return symbol_values_dict
\ No newline at end of file + return symbol_values_dict diff --git a/wqflask/base/species.py b/wqflask/base/species.py index 6d99af65..2771d116 100644 --- a/wqflask/base/species.py +++ b/wqflask/base/species.py @@ -1,14 +1,7 @@ -from __future__ import absolute_import, print_function, division - import collections from flask import Flask, g -#from MySQLdb import escape_string as escape - -from utility import Bunch - -from pprint import pformat as pf from utility.logger import getLogger logger = getLogger(__name__ ) @@ -59,4 +52,4 @@ class Chromosomes(object): results = g.db.execute(query).fetchall() for item in results: - self.chromosomes[item.OrderId] = IndChromosome(item.Name, item.Length)
\ No newline at end of file + self.chromosomes[item.OrderId] = IndChromosome(item.Name, item.Length) diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 7666348e..6950cf11 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -1,12 +1,9 @@ -from __future__ import absolute_import, division, print_function - import os import string import resource import codecs import requests import random -import urllib from base import webqtlConfig from base.webqtlCaseData import webqtlCaseData @@ -22,7 +19,7 @@ Redis = get_redis_conn() from wqflask import app import simplejson as json -from MySQLdb import escape_string as escape +from utility.db_tools import escape from pprint import pformat as pf from flask import Flask, g, request, url_for, redirect, make_response, render_template @@ -118,7 +115,7 @@ class GeneralTrait(object): vals = [] the_vars = [] sample_aliases = [] - for sample_name, sample_data in self.data.items(): + for sample_name, sample_data in list(self.data.items()): if sample_data.value != None: if not include_variance or sample_data.variance != None: samples.append(sample_name) @@ -153,8 +150,8 @@ class GeneralTrait(object): alias = 'Not available' if getattr(self, "alias", None): - alias = string.replace(self.alias, ";", " ") - alias = string.join(string.split(alias), ", ") + alias = self.alias.replace(";", " ") + alias = ", ".join(alias.split()) return alias @@ -193,7 +190,7 @@ class GeneralTrait(object): ''' if self.chr and self.mb: - self.location = 'Chr %s @ %s Mb' % (self.chr,self.mb) + self.location = 'Chr %s @ %s Mb' % (self.chr, self.mb) elif self.chr: self.location = 'Chr %s @ Unknown position' % (self.chr) else: @@ -260,7 +257,7 @@ def get_sample_data(): trait_dict['pubmed_link'] = trait_ob.pubmed_link trait_dict['pubmed_text'] = trait_ob.pubmed_text - return json.dumps([trait_dict, {key: value.value for key, value in trait_ob.data.iteritems() }]) + return json.dumps([trait_dict, {key: value.value for key, value in list(trait_ob.data.items()) }]) else: return None @@ -440,7 +437,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): #XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name # to avoid the problem of same marker name from different species. elif dataset.type == 'Geno': - display_fields_string = string.join(dataset.display_fields,',Geno.') + display_fields_string = ',Geno.'.join(dataset.display_fields) display_fields_string = 'Geno.' + display_fields_string query = """ SELECT %s @@ -459,8 +456,8 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): query = """SELECT %s FROM %s WHERE Name = %s""" logger.sql(query) trait_info = g.db.execute(query, - (string.join(dataset.display_fields,','), - dataset.type, trait.name)).fetchone() + ','.join(dataset.display_fields), + dataset.type, trait.name).fetchone() if trait_info: trait.haveinfo = True @@ -491,10 +488,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): else: trait.description_display = "" - trait.abbreviation = unicode(str(trait.abbreviation).strip(codecs.BOM_UTF8), 'utf-8', errors="replace") - trait.description_display = unicode(str(trait.description_display).strip(codecs.BOM_UTF8), 'utf-8', errors="replace") - trait.authors = unicode(str(trait.authors).strip(codecs.BOM_UTF8), 'utf-8', errors="replace") - if not trait.year.isdigit(): trait.pubmed_text = "N/A" else: @@ -504,8 +497,8 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % trait.pubmed_id if dataset.type == 'ProbeSet' and dataset.group: - description_string = unicode(str(trait.description).strip(codecs.BOM_UTF8), 'utf-8') - target_string = unicode(str(trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8') + description_string = trait.description + target_string = trait.probe_target_description if len(description_string) > 1 and description_string != 'None': description_display = description_string @@ -605,6 +598,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): if trait.lrs != "": trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs else: - raise KeyError, `trait.name`+' information is not found in the database.' + raise KeyError(repr(trait.name)+' information is not found in the database.') - return trait
\ No newline at end of file + return trait |