diff options
Diffstat (limited to 'wqflask/base/trait.py')
| -rw-r--r-- | wqflask/base/trait.py | 33 |
1 files changed, 13 insertions, 20 deletions
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 |