diff options
Diffstat (limited to 'wqflask/base/trait.py')
| -rw-r--r-- | wqflask/base/trait.py | 99 |
1 files changed, 45 insertions, 54 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 7ebbc4bb..cfc02f8b 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -1,42 +1,30 @@ -from __future__ import absolute_import, division, print_function -from utility.logger import getLogger -from flask import Flask, g, request, url_for, redirect, make_response, render_template -from pprint import pformat as pf -from MySQLdb import escape_string as escape +import requests import simplejson as json from wqflask import app -import os -import string -import resource -import codecs -import requests -import random -import urllib - from base import webqtlConfig from base.webqtlCaseData import webqtlCaseData from base.data_set import create_dataset -from db import webqtlDatabaseFunction -from utility import webqtlUtil from utility import hmac from utility.authentication_tools import check_resource_availability -from utility.tools import GN2_BASE_URL, GN_VERSION -from utility.redis_tools import get_redis_conn -from utility.redis_tools import get_resource_id -from utility.redis_tools import get_resource_info +from utility.tools import GN2_BASE_URL +from utility.redis_tools import get_redis_conn, get_resource_id -Redis = get_redis_conn() +from utility.db_tools import escape + +from flask import g, request, url_for +from utility.logger import getLogger logger = getLogger(__name__) +Redis = get_redis_conn() + def create_trait(**kw): assert bool(kw.get('dataset')) != bool( kw.get('dataset_name')), "Needs dataset ob. or name" - permitted = True if kw.get('name'): if kw.get('dataset_name'): if kw.get('dataset_name') != "Temp": @@ -55,7 +43,9 @@ def create_trait(**kw): the_trait = GeneralTrait(**kw) if the_trait.dataset.type != "Temp": the_trait = retrieve_trait_info( - the_trait, the_trait.dataset, get_qtl_info=kw.get('get_qtl_info')) + the_trait, + the_trait.dataset, + get_qtl_info=kw.get('get_qtl_info')) return the_trait else: return None @@ -78,7 +68,9 @@ class GeneralTrait(object): if kw.get('dataset_name') == "Temp": temp_group = self.name.split("_")[2] self.dataset = create_dataset( - dataset_name="Temp", dataset_type="Temp", group_name=temp_group) + dataset_name="Temp", + dataset_type="Temp", + group_name=temp_group) else: self.dataset = create_dataset(kw.get('dataset_name')) else: @@ -113,9 +105,10 @@ class GeneralTrait(object): elif len(name2) == 3: self.dataset, self.name, self.cellid = name2 - # Todo: These two lines are necessary most of the time, but perhaps not all of the time - # So we could add a simple if statement to short-circuit this if necessary - if get_sample_info != False: + # Todo: These two lines are necessary most of the time, but + # perhaps not all of the time So we could add a simple if + # statement to short-circuit this if necessary + if get_sample_info is not False: self = retrieve_sample_data(self, self.dataset) def export_informative(self, include_variance=0): @@ -128,9 +121,9 @@ class GeneralTrait(object): vals = [] the_vars = [] sample_aliases = [] - for sample_name, sample_data in self.data.items(): - if sample_data.value != None: - if not include_variance or sample_data.variance != None: + for sample_name, sample_data in list(self.data.items()): + if sample_data.value is not None: + if not include_variance or sample_data.variance is not None: samples.append(sample_name) vals.append(sample_data.value) the_vars.append(sample_data.variance) @@ -154,7 +147,8 @@ class GeneralTrait(object): formatted = self.post_publication_description else: formatted = "Not available" - + if isinstance(formatted, bytes): + formatted = formatted.decode("utf-8") return formatted @property @@ -163,8 +157,8 @@ 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 @@ -183,7 +177,8 @@ class GeneralTrait(object): if human_response and mouse_response and other_response: alias_list = json.loads(human_response.content) + json.loads( - mouse_response.content) + json.loads(other_response.content) + mouse_response.content) + \ + json.loads(other_response.content) filtered_aliases = [] seen = set() @@ -201,7 +196,8 @@ class GeneralTrait(object): def location_fmt(self): """Return a text formatted location - While we're at it we set self.location in case we need it later (do we?) + While we're at it we set self.location in case we need it + later (do we?) """ @@ -223,7 +219,7 @@ class GeneralTrait(object): def retrieve_sample_data(trait, dataset, samplelist=None): - if samplelist == None: + if samplelist is None: samplelist = [] if dataset.type == "Temp": @@ -278,7 +274,9 @@ 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 @@ -289,7 +287,8 @@ def jsonable(trait): Actual turning into json doesn't happen here though""" dataset = create_dataset(dataset_name=trait.dataset.name, - dataset_type=trait.dataset.type, group_name=trait.dataset.group.name) + dataset_type=trait.dataset.type, + group_name=trait.dataset.group.name) if dataset.type == "ProbeSet": return dict(name=trait.name, @@ -471,8 +470,7 @@ 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 @@ -491,13 +489,15 @@ 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 for i, field in enumerate(dataset.display_fields): holder = trait_info[i] + if isinstance(holder, bytes): + holder = holder.decode("utf-8", errors="ignore") setattr(trait, field, holder) if dataset.type == 'Publish': @@ -523,13 +523,6 @@ 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: @@ -539,10 +532,8 @@ 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 str(description_string or "") != "" and description_string != 'None': description_display = description_string @@ -645,6 +636,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): if str(trait.lrs or "") != "": 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 |