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authorBonfaceKilz2020-10-27 01:18:38 +0300
committerGitHub2020-10-27 01:18:38 +0300
commit37c391bc62e9080effcf83c6ff0056ab8841b7fb (patch)
tree1e794c5616c25e82869314a2f4e91f64c4d40ea9 /wqflask/base
parent85896707ef1f9e214b45298f6b5b1a9dc37bc839 (diff)
parentb369489e6c075eee3f58bb33e493c901b052b0a1 (diff)
downloadgenenetwork2-37c391bc62e9080effcf83c6ff0056ab8841b7fb.tar.gz
Merge pull request #422 from BonfaceKilz/build/python3-migration
Build/python3 migration
Diffstat (limited to 'wqflask/base')
-rw-r--r--wqflask/base/GeneralObject.py11
-rw-r--r--wqflask/base/data_set.py41
-rw-r--r--wqflask/base/mrna_assay_tissue_data.py7
-rw-r--r--wqflask/base/species.py9
-rw-r--r--wqflask/base/trait.py99
5 files changed, 65 insertions, 102 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 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':
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 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