From f4a8789a5f28e1527d4c801b40176f47aa44146c Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 17 Sep 2020 17:16:28 +0300
Subject: Apply pep8
* wqflask/base/trait.py: Apply pep8.
* wqflask/utility/authentication_tools.py: Ditto.
---
wqflask/base/trait.py | 192 +++++++++++++++++++-------------
wqflask/utility/authentication_tools.py | 32 ++++--
2 files changed, 134 insertions(+), 90 deletions(-)
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 6950cf11..548ccc4c 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -1,36 +1,30 @@
-import os
-import string
-import resource
-import codecs
import requests
-import random
+import simplejson as json
+from wqflask import app
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, get_resource_id, get_resource_info
-Redis = get_redis_conn()
+from utility.tools import GN2_BASE_URL
+from utility.redis_tools import get_redis_conn, get_resource_id
-from wqflask import app
-
-import simplejson as json
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
+from flask import g, request, url_for
from utility.logger import getLogger
-logger = getLogger(__name__ )
+
+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";
+ 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":
@@ -40,18 +34,23 @@ def create_trait(**kw):
if kw.get('dataset_name') != "Temp":
if dataset.type == 'Publish':
- permissions = check_resource_availability(dataset, kw.get('name'))
+ permissions = check_resource_availability(
+ dataset, kw.get('name'))
else:
permissions = check_resource_availability(dataset)
if "view" in permissions['data']:
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 = retrieve_trait_info(
+ the_trait,
+ the_trait.dataset,
+ get_qtl_info=kw.get('get_qtl_info'))
return the_trait
else:
return None
+
class GeneralTrait(object):
"""
Trait class defines a trait in webqtl, can be either Microarray,
@@ -61,12 +60,17 @@ class GeneralTrait(object):
def __init__(self, get_qtl_info=False, get_sample_info=True, **kw):
# xor assertion
- assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. or name";
- self.name = kw.get('name') # Trait ID, ProbeSet ID, Published ID, etc.
+ assert bool(kw.get('dataset')) != bool(
+ kw.get('dataset_name')), "Needs dataset ob. or name"
+ # Trait ID, ProbeSet ID, Published ID, etc.
+ self.name = kw.get('name')
if kw.get('dataset_name'):
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)
+ self.dataset = create_dataset(
+ dataset_name="Temp",
+ dataset_type="Temp",
+ group_name=temp_group)
else:
self.dataset = create_dataset(kw.get('dataset_name'))
else:
@@ -74,7 +78,8 @@ class GeneralTrait(object):
self.cellid = kw.get('cellid')
self.identification = kw.get('identification', 'un-named trait')
self.haveinfo = kw.get('haveinfo', False)
- self.sequence = kw.get('sequence') # Blat sequence, available for ProbeSet
+ # Blat sequence, available for ProbeSet
+ self.sequence = kw.get('sequence')
self.data = kw.get('data', {})
self.view = True
@@ -100,9 +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):
@@ -116,13 +122,13 @@ class GeneralTrait(object):
the_vars = []
sample_aliases = []
for sample_name, sample_data in list(self.data.items()):
- if sample_data.value != None:
- if not include_variance or sample_data.variance != None:
+ 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)
sample_aliases.append(sample_data.name2)
- return samples, vals, the_vars, sample_aliases
+ return samples, vals, the_vars, sample_aliases
@property
def description_fmt(self):
@@ -161,12 +167,17 @@ class GeneralTrait(object):
alias = 'Not available'
if self.symbol:
- human_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.upper())
- mouse_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.capitalize())
- other_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.lower())
+ human_response = requests.get(
+ GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.upper())
+ mouse_response = requests.get(
+ GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.capitalize())
+ other_response = requests.get(
+ GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.lower())
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)
+ alias_list = json.loads(human_response.content) + json.loads(
+ mouse_response.content) + \
+ json.loads(other_response.content)
filtered_aliases = []
seen = set()
@@ -180,33 +191,34 @@ class GeneralTrait(object):
return alias
-
@property
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?)
'''
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:
self.location = 'Not available'
fmt = self.location
- ##XZ: deal with direction
+ # XZ: deal with direction
if self.strand_probe == '+':
fmt += (' on the plus strand ')
elif self.strand_probe == '-':
fmt += (' on the minus strand ')
return fmt
-
+
+
def retrieve_sample_data(trait, dataset, samplelist=None):
- if samplelist == None:
+ if samplelist is None:
samplelist = []
if dataset.type == "Temp":
@@ -222,16 +234,19 @@ def retrieve_sample_data(trait, dataset, samplelist=None):
all_samples_ordered = dataset.group.all_samples_ordered()
for i, item in enumerate(results):
try:
- trait.data[all_samples_ordered[i]] = webqtlCaseData(all_samples_ordered[i], float(item))
+ trait.data[all_samples_ordered[i]] = webqtlCaseData(
+ all_samples_ordered[i], float(item))
except:
pass
else:
for item in results:
name, value, variance, num_cases, name2 = item
if not samplelist or (samplelist and name in samplelist):
- trait.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases)
+ # name, value, variance, num_cases)
+ trait.data[name] = webqtlCaseData(*item)
return trait
+
@app.route("/trait/get_sample_data")
def get_sample_data():
params = request.args
@@ -247,7 +262,8 @@ def get_sample_data():
trait_dict['group'] = trait_ob.dataset.group.name
trait_dict['tissue'] = trait_ob.dataset.tissue
trait_dict['species'] = trait_ob.dataset.group.species
- trait_dict['url'] = url_for('show_trait_page', trait_id = trait, dataset = dataset)
+ trait_dict['url'] = url_for(
+ 'show_trait_page', trait_id=trait, dataset=dataset)
trait_dict['description'] = trait_ob.description_display
if trait_ob.dataset.type == "ProbeSet":
trait_dict['symbol'] = trait_ob.symbol
@@ -257,22 +273,27 @@ 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 list(trait_ob.data.items()) }])
+ return json.dumps([trait_dict, {key: value.value for
+ key, value in list(
+ trait_ob.data.items())}])
else:
return None
-
+
+
def jsonable(trait):
"""Return a dict suitable for using as json
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 = create_dataset(dataset_name=trait.dataset.name,
+ dataset_type=trait.dataset.type,
+ group_name=trait.dataset.group.name)
+
if dataset.type == "ProbeSet":
return dict(name=trait.name,
symbol=trait.symbol,
dataset=dataset.name,
- dataset_name = dataset.shortname,
+ dataset_name=dataset.shortname,
description=trait.description_display,
mean=trait.mean,
location=trait.location_repr,
@@ -284,7 +305,7 @@ def jsonable(trait):
if trait.pubmed_id:
return dict(name=trait.name,
dataset=dataset.name,
- dataset_name = dataset.shortname,
+ dataset_name=dataset.shortname,
description=trait.description_display,
abbreviation=trait.abbreviation,
authors=trait.authors,
@@ -297,7 +318,7 @@ def jsonable(trait):
else:
return dict(name=trait.name,
dataset=dataset.name,
- dataset_name = dataset.shortname,
+ dataset_name=dataset.shortname,
description=trait.description_display,
abbreviation=trait.abbreviation,
authors=trait.authors,
@@ -309,19 +330,20 @@ def jsonable(trait):
elif dataset.type == "Geno":
return dict(name=trait.name,
dataset=dataset.name,
- dataset_name = dataset.shortname,
+ dataset_name=dataset.shortname,
location=trait.location_repr
)
else:
return dict()
+
def jsonable_table_row(trait, dataset_name, index):
"""Return a list suitable for json and intended to be displayed in a table
Actual turning into json doesn't happen here though"""
dataset = create_dataset(dataset_name)
-
+
if dataset.type == "ProbeSet":
if trait.mean == "":
mean = "N/A"
@@ -333,11 +355,13 @@ def jsonable_table_row(trait, dataset_name, index):
additive = "%.3f" % round(float(trait.additive), 2)
return ['',
index,
- ''+str(trait.name)+'',
+ ''+str(trait.name)+'',
trait.symbol,
trait.description_display,
trait.location_repr,
- mean,
+ mean,
trait.LRS_score_repr,
trait.LRS_location_repr,
additive]
@@ -349,7 +373,9 @@ def jsonable_table_row(trait, dataset_name, index):
if trait.pubmed_id:
return ['',
index,
- ''+str(trait.name)+'',
+ ''+str(trait.name)+'',
trait.description_display,
trait.authors,
'' + trait.pubmed_text + '',
@@ -359,7 +385,9 @@ def jsonable_table_row(trait, dataset_name, index):
else:
return ['',
index,
- ''+str(trait.name)+'',
+ ''+str(trait.name)+'',
trait.description_display,
trait.authors,
trait.pubmed_text,
@@ -369,7 +397,9 @@ def jsonable_table_row(trait, dataset_name, index):
elif dataset.type == "Geno":
return ['',
index,
- ''+str(trait.name)+'',
+ ''+str(trait.name)+'',
trait.location_repr]
else:
return dict()
@@ -380,14 +410,16 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
resource_id = get_resource_id(dataset, trait.name)
if dataset.type == 'Publish':
- the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id)
+ the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view".format(
+ resource_id, g.user_session.user_id)
else:
- the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name)
+ the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(
+ resource_id, g.user_session.user_id, trait.name)
try:
response = requests.get(the_url).content
trait_info = json.loads(response)
- except: #ZS: I'm assuming the trait is viewable if the try fails for some reason; it should never reach this point unless the user has privileges, since that's dealt with in create_trait
+ except: # ZS: I'm assuming the trait is viewable if the try fails for some reason; it should never reach this point unless the user has privileges, since that's dealt with in create_trait
if dataset.type == 'Publish':
query = """
SELECT
@@ -416,8 +448,8 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
logger.sql(query)
trait_info = g.db.execute(query).fetchone()
- #XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name
- #XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms.
+ # XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name
+ # XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms.
elif dataset.type == 'ProbeSet':
display_fields_string = ', ProbeSet.'.join(dataset.display_fields)
display_fields_string = 'ProbeSet.' + display_fields_string
@@ -430,11 +462,11 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
ProbeSetFreeze.Name = '%s' AND
ProbeSet.Name = '%s'
""" % (escape(display_fields_string),
- escape(dataset.name),
- escape(str(trait.name)))
+ escape(dataset.name),
+ escape(str(trait.name)))
logger.sql(query)
trait_info = g.db.execute(query).fetchone()
- #XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name
+ # 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 = ',Geno.'.join(dataset.display_fields)
@@ -448,11 +480,11 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
GenoFreeze.Name = '%s' AND
Geno.Name = '%s'
""" % (escape(display_fields_string),
- escape(dataset.name),
- escape(trait.name))
+ escape(dataset.name),
+ escape(trait.name))
logger.sql(query)
trait_info = g.db.execute(query).fetchone()
- else: #Temp type
+ else: # Temp type
query = """SELECT %s FROM %s WHERE Name = %s"""
logger.sql(query)
trait_info = g.db.execute(query,
@@ -462,7 +494,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
if trait_info:
trait.haveinfo = True
for i, field in enumerate(dataset.display_fields):
- holder = trait_info[i]
+ holder = trait_info[i]
setattr(trait, field, holder)
if dataset.type == 'Publish':
@@ -475,9 +507,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
description = trait.post_publication_description
- #If the dataset is confidential and the user has access to confidential
- #phenotype traits, then display the pre-publication description instead
- #of the post-publication description
+ # If the dataset is confidential and the user has access to confidential
+ # phenotype traits, then display the pre-publication description instead
+ # of the post-publication description
if trait.confidential:
trait.abbreviation = trait.pre_publication_abbreviation
trait.description_display = trait.pre_publication_description
@@ -514,15 +546,17 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
trait.location_repr = 'N/A'
if trait.chr and trait.mb:
- trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb))
+ trait.location_repr = 'Chr%s: %.6f' % (
+ trait.chr, float(trait.mb))
elif dataset.type == "Geno":
trait.location_repr = 'N/A'
if trait.chr and trait.mb:
- trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb))
+ trait.location_repr = 'Chr%s: %.6f' % (
+ trait.chr, float(trait.mb))
if get_qtl_info:
- #LRS and its location
+ # LRS and its location
trait.LRS_score_repr = "N/A"
trait.LRS_location_repr = "N/A"
trait.locus = trait.locus_chr = trait.locus_mb = trait.lrs = trait.pvalue = trait.additive = ""
@@ -594,10 +628,12 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
trait.locus = trait.lrs = trait.additive = ""
if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and trait.locus_chr != "" and trait.locus_mb != "":
- trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (trait.locus_chr, float(trait.locus_mb))
+ trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (
+ trait.locus_chr, float(trait.locus_mb))
if trait.lrs != "":
trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs
else:
- raise KeyError(repr(trait.name)+' information is not found in the database.')
-
+ raise KeyError(repr(trait.name) +
+ ' information is not found in the database.')
+
return trait
diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 390ad75a..ce0c0749 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -1,30 +1,37 @@
import json
import requests
-from base import data_set, webqtlConfig
-
-from utility import hmac
-from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id, add_resource
-Redis = get_redis_conn()
+from flask import g
+from base import webqtlConfig
-logger = logging.getLogger(__name__)
+from utility.redis_tools import (get_redis_conn,
+ get_resource_info,
+ get_resource_id,
+ add_resource)
+Redis = get_redis_conn()
def check_resource_availability(dataset, trait_id=None):
-
# At least for now assume temporary entered traits are accessible
if type(dataset) == str or dataset.type == "Temp":
return webqtlConfig.DEFAULT_PRIVILEGES
resource_id = get_resource_id(dataset, trait_id)
- if resource_id: # ZS: This should never be false, but it's technically possible if a non-Temp dataset somehow had a type other than Publish/ProbeSet/Geno
+ # ZS: This should never be false, but it's technically possible if
+ # a non-Temp dataset somehow had a type other than
+ # Publish/ProbeSet/Geno
+ if resource_id:
resource_info = get_resource_info(resource_id)
- if not resource_info: # ZS: If resource isn't already in redis, add it with default privileges
+
+ # ZS: If resource isn't already in redis, add it with default
+ # privileges
+ if not resource_info:
resource_info = add_new_resource(dataset, trait_id)
- # ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy
+ # ZS: Check if super-user - we should probably come up with some
+ # way to integrate this into the proxy
if g.user_session.user_id in Redis.smembers("super_users"):
return webqtlConfig.SUPER_PRIVILEGES
@@ -76,8 +83,9 @@ def add_new_resource(dataset, trait_id=None):
def get_group_code(dataset):
- results = g.db.execute("SELECT InbredSetCode from InbredSet where Name='{}'".format(
- dataset.group.name)).fetchone()
+ results = g.db.execute(
+ "SELECT InbredSetCode from InbredSet where Name='{}'".format(
+ dataset.group.name)).fetchone()
if results[0]:
return results[0]
else:
--
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